Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold115
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: 1475684
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 9 of 10
Found at i:1293958 original size:52 final size:51
Alignment explanation
Indices: 1293823--1293967 Score: 186
Period size: 52 Copynumber: 2.8 Consensus size: 51
1293813 ATATGAAAAC
* *
1293823 TTGCCTGCATGTATCGATACATTTCAT-GGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGCAAAT
* *
1293875 TTGCCTGTATGTATCGATACATTTCAT-AGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGCAAAT
*
1293927 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATAC-AACATCAGTGTATCGATACA
1293968 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.97
53 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACAACATCAGTGTATCGATACATCTGGGCAAAT
Found at i:1293974 original size:13 final size:13
Alignment explanation
Indices: 1293956--1293980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1293946 CAAAGATCAG
1293956 TGTATCGATACAA
1 TGTATCGATACAA
1293969 TGTATCGATACA
1 TGTATCGATACA
1293981 TTTGAGTAAT
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:1294041 original size:13 final size:13
Alignment explanation
Indices: 1294019--1294108 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
1294009 GGCAGTAGCT
*
1294019 TTGTAGCGATACA
1 TTGTATCGATACA
1294032 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
1294048 CTTATGTATCGATACA
1 --T-TGTATCGATACA
1294064 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
1294080 CTTATGTATCGATACA
1 --T-TGTATCGATACA
1294096 TTGTATCGATACA
1 TTGTATCGATACA
1294109 ACACTTATGT
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 32 0.50
14 2 0.03
16 8 0.12
18 2 0.03
19 20 0.31
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1294057 original size:19 final size:18
Alignment explanation
Indices: 1294033--1294129 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
1294023 AGCGATACAT
1294033 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1294052 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1294065 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1294084 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1294097 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1294116 TGTATCGATACAAA
1 TGTATCGATACAAA
1294130 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 3 0.05
19 35 0.53
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1294066 original size:32 final size:32
Alignment explanation
Indices: 1294020--1294127 Score: 198
Period size: 32 Copynumber: 3.4 Consensus size: 32
1294010 GCAGTAGCTT
* *
1294020 TGTAGCGATACATTGTATCGATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1294052 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1294084 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1294116 TGTATCGATACA
1 TGTATCGATACA
1294128 AATCGTTGAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:1294967 original size:49 final size:49
Alignment explanation
Indices: 1294747--1295128 Score: 382
Period size: 49 Copynumber: 7.8 Consensus size: 49
1294737 AAAAGGATGT
* * * * * *
1294747 CAATGTGCTGATTTACGGTCAGCG-TCATTAGACTTGAAGAAGAA--TGC
1 CAATGTGCTGATTCAAGGCCAGCGAT-ATTGGACTTAAAGATGAAGGTGC
* **
1294794 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA--AAAATGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * ** *
1294841 CAATGTGTTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGACAAAGGCGC
1 CAATGTGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGATG---AAGGTGC
* *
1294894 CAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * * *
1294943 CAATGTGCTGAGTCAACGCCAGCGACATTGGACTTAAAGAAGAA--TGT
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * *
1294990 CAATGTGTTGATTCAAGGCCAACGATATTGGACTTAAAGGTAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * *
1295039 CAATATGTTGATTCAAGGTCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* *
1295088 CAATATGCTGATTCAAAGCCAGCGATATTGGACTTAGAAGA
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
1295129 AGATGCCACC
Statistics
Matches: 278, Mismatches: 45, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
45 2 0.01
47 101 0.36
48 9 0.03
49 123 0.44
50 4 0.01
52 11 0.04
53 28 0.10
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
Found at i:1294967 original size:149 final size:148
Alignment explanation
Indices: 1294692--1295129 Score: 557
Period size: 149 Copynumber: 3.0 Consensus size: 148
1294682 ATAAAAGGAT
* * * *
1294692 CAATATGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTG
1 CAATGTGTTGATTCAAGGCCAACGATATTGGGTTTAAAGAT--GAAAAAGG-TGCCAATATGCTG
* * * * * *
1294757 ATTTACGGTCAGCG-TCATTAGACTTGAAGAAGAA--TGCCAATGTGCTGATTCAAGGCCAGCGA
63 ATTCAAGGTCAGCGAT-ATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAAGCCAGCGA
1294819 CATTGGACTTAAAGAAAAATGC
127 CATTGGACTTAAAGAAAAATGC
* * *
1294841 CAATGTGTTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGACAAAGGCGCCAATATGCTGAT
1 CAATGTGTTGATTCAAGGCCAACGATATTGGG-TTTAAAGATGAAAAAGGTGCCAATATGCTGAT
* *
1294906 TCAAGG-CTAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAACGCCAGCGACA
65 TCAAGGTC-AGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAAGCCAGCGACA
* *
1294970 TTGGACTTAAAGAAGAATGT
129 TTGGACTTAAAGAAAAATGC
** * *
1294990 CAATGTGTTGATTCAAGGCCAACGATATTGGACTTAAAG--G-TAAAGGTGCCAATATGTTGATT
1 CAATGTGTTGATTCAAGGCCAACGATATTGGGTTTAAAGATGAAAAAGGTGCCAATATGCTGATT
* *
1295052 CAAGGTCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAAGCCAGCGATATT
66 CAAGGTCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAAGCCAGCGACATT
1295117 GGACTTAGAAGAA
131 GGACTTA-AAGAA
1295130 GATGCCACCA
Statistics
Matches: 256, Mismatches: 26, Indels: 17
0.86 0.09 0.06
Matches are distributed among these distances:
145 85 0.33
146 8 0.03
147 35 0.14
148 14 0.05
149 105 0.41
150 9 0.04
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (148 bp):
CAATGTGTTGATTCAAGGCCAACGATATTGGGTTTAAAGATGAAAAAGGTGCCAATATGCTGATT
CAAGGTCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAAGCCAGCGACATT
GGACTTAAAGAAAAATGC
Found at i:1295109 original size:145 final size:148
Alignment explanation
Indices: 1294791--1295136 Score: 513
Period size: 145 Copynumber: 2.4 Consensus size: 148
1294781 TGAAGAAGAA
* *
1294791 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAAATGCCAATGTGTTGATTCA
1 TGCCAATGTGCTGATTCAAAGCCAGCGACATTGGACTTAAAGAAGAATGCCAATGTGTTGATTCA
**
1294856 AGGCCAACGACATTGGGTTTTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCTAGCGATA
66 AGGCCAACGACATTGGGACTTAAAGA-GACAAAGGCGCCAATATGCTGATTCAAGGCTAGCGATA
1294921 TTGGACTTAAAGATGAAGG
130 TTGGACTTAAAGATGAAGG
* * *
1294940 TGCCAATGTGCTGAGTCAACGCCAGCGACATTGGACTTAAAGAAGAATGTCAATGTGTTGATTCA
1 TGCCAATGTGCTGATTCAAAGCCAGCGACATTGGACTTAAAGAAGAATGCCAATGTGTTGATTCA
* * * *
1295005 AGGCCAACGATATT-GGACTTAAAG-G-TAAAGGTGCCAATATGTTGATTCAAGG-TCAGCGATA
66 AGGCCAACGACATTGGGACTTAAAGAGACAAAGGCGCCAATATGCTGATTCAAGGCT-AGCGATA
1295066 TTGGACTTAAAGATGAAGG
130 TTGGACTTAAAGATGAAGG
* *
1295085 TGCCAATATGCTGATTCAAAGCCAGCGATATTGGACTTAGAAGAAG-ATGCCA
1 TGCCAATGTGCTGATTCAAAGCCAGCGACATTGGACTTA-AAGAAGAATGCCA
1295137 CCAACTTGTG
Statistics
Matches: 180, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
144 1 0.01
145 90 0.50
146 7 0.04
148 8 0.04
149 74 0.41
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (148 bp):
TGCCAATGTGCTGATTCAAAGCCAGCGACATTGGACTTAAAGAAGAATGCCAATGTGTTGATTCA
AGGCCAACGACATTGGGACTTAAAGAGACAAAGGCGCCAATATGCTGATTCAAGGCTAGCGATAT
TGGACTTAAAGATGAAGG
Found at i:1295136 original size:96 final size:96
Alignment explanation
Indices: 1294742--1295136 Score: 395
Period size: 96 Copynumber: 4.1 Consensus size: 96
1294732 TGAGAAAAAG
* * * * * * * * * *
1294742 GATGTCAATGTGCTGATTTACGGTCAGCGTCATTAGACTTGAAGAAGAA--TGCCAATGTGCTGA
1 GATGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATATGCTGA
*
1294805 TTCAAGGCCAGCGACATTGGACTTAAAGAAA
66 TTCAAGGCCAGCGATATTGGACTTAAAGAAA
* * ** *
1294836 AATGCCAATGTGTTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGACAAAGGCGCCAATATG
1 GATGCCAATGTGTTGATTCAAGGCCAGCGACATT-GGACTTAAAGATG---AAGGTGCCAATATG
*
1294901 CTGATTCAAGGCTAGCGATATTGGACTTAAAGATGAA
62 CTGATTCAAGGCCAGCGATATTGGACTTAAAGA--AA
* * * * * * * *
1294938 GGTGCCAATGTGCTGAGTCAACGCCAGCGACATTGGACTTAAAGAAGAA--TGTCAATGTGTTGA
1 GATGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATATGCTGA
*
1295001 TTCAAGGCCAACGATATTGGACTTAAAGGTAAA
66 TTCAAGGCCAGCGATATTGGACTTAAA-G-AAA
* * * *
1295034 GGTGCCAATATGTTGATTCAAGGTCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGA
1 GATGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATATGCTGA
*
1295099 TTCAAAGCCAGCGATATTGGACTTAGAAG-AA
66 TTCAAGGCCAGCGATATTGGACTTA-AAGAAA
1295130 GATGCCA
1 GATGCCA
1295137 CCAACTTGTG
Statistics
Matches: 243, Mismatches: 45, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
94 26 0.11
95 8 0.03
96 87 0.36
97 1 0.00
98 40 0.16
99 2 0.01
100 39 0.16
101 10 0.04
102 30 0.12
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (96 bp):
GATGCCAATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATATGCTGA
TTCAAGGCCAGCGATATTGGACTTAAAGAAA
Found at i:1295166 original size:30 final size:30
Alignment explanation
Indices: 1295132--1295205 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
1295122 TAGAAGAAGA
*
1295132 TGCCACCAACTTGTGTGGGCTTTTGAA-GGT
1 TGCCACCAACTTGTGTGGGC-TTTGAAGGGG
**
1295162 TGCCACTGAC-T-TGTGGGCTTTGAATGGGG
1 TGCCACCAACTTGTGTGGGCTTTGAA-GGGG
*
1295191 TGCTACCAACTTGTG
1 TGCCACCAACTTGTG
1295206 GGCTTAAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
27 6 0.18
28 7 0.21
29 10 0.29
30 9 0.26
31 2 0.06
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.32
Consensus pattern (30 bp):
TGCCACCAACTTGTGTGGGCTTTGAAGGGG
Found at i:1295319 original size:36 final size:36
Alignment explanation
Indices: 1295211--1295378 Score: 231
Period size: 34 Copynumber: 4.8 Consensus size: 36
1295201 TTGTGGGCTT
* *
1295211 AAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGA
*
1295245 AAAAGAGTGCCACAGAGTTGTGAGC-TT-AAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGA
1295279 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGA
*
1295315 AAAAGAGTGCCGCAGAGTTGTGGGCTTTAAAAA-GA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGA
* *
1295350 AGAAAG-GTGCCACGGAGTTGTGGACTTTA
1 A-AAAGAGTGCCACAGAGTTGTGGGCTTTA
1295379 GAAGGTTGCC
Statistics
Matches: 123, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
34 55 0.45
35 25 0.20
36 43 0.35
ACGTcount: A:0.37, C:0.12, G:0.32, T:0.20
Consensus pattern (36 bp):
AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGA
Found at i:1295331 original size:70 final size:70
Alignment explanation
Indices: 1295211--1295378 Score: 243
Period size: 70 Copynumber: 2.4 Consensus size: 70
1295201 TTGTGGGCTT
*
1295211 AAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGGAAAAAGAGTGCCACAGAGTTGTGAGC-TTA
1 AAAAAGGTGCCACAGAGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGAGCTTTA
*
1295273 AAAGG
66 AAAAG
* * *
1295278 AAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAAAGAGTGCCGCAGAGTTGTGGGCTTT
1 AAAAAG-GTGCCACAGAGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGAGCTTT
1295343 AAAAAG
65 AAAAAG
*
1295349 AAGAAAGGTGCCACGGAGTTGTGGACTTTA
1 AA-AAAGGTGCCACAGAGTTGTGGACTTTA
1295379 GAAGGTTGCC
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
67 5 0.06
68 18 0.20
69 2 0.02
70 30 0.34
71 30 0.34
72 4 0.04
ACGTcount: A:0.37, C:0.12, G:0.32, T:0.20
Consensus pattern (70 bp):
AAAAAGGTGCCACAGAGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGAGCTTTA
AAAAG
Found at i:1295723 original size:57 final size:57
Alignment explanation
Indices: 1295355--1295719 Score: 561
Period size: 57 Copynumber: 6.4 Consensus size: 57
1295345 AAAGAAGAAA
* * * ** ** *
1295355 GGTGCCACGGAGTTGTGGACTTTAGAAGGTTGCCGTTGGCTTGTGGGCTTTGGAAAAT
1 GGTGCCACTGATTTGTGGGCTTT-GAAGGTTGCCACTGATTTGTGGGCTTTGGAAAAG
* *
1295413 GGTGCCACTGATTTGTGGGCTTTAAAGGTTGCCACTAATTTGTGGGCTTTGGAAAAG
1 GGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTTGTGGGCTTTGGAAAAG
* *
1295470 GGTGCCACTGATTTGTGGGCTTTAAAGGTTGCCACTGATTTGTGGGCTTCGGAAAAG
1 GGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTTGTGGGCTTTGGAAAAG
* *
1295527 GGTGACACTGATTTGTAGGCTTTGAAGGTTGCCACTGATTTGTGGGCTTTGGAAAAG
1 GGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTTGTGGGCTTTGGAAAAG
*
1295584 GGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTAGTGGGCTTTGGAAAAG
1 GGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTTGTGGGCTTTGGAAAAG
*
1295641 GGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTTGTGGGCTTT-GAAAAT
1 GGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTTGTGGGCTTTGGAAAAG
*
1295697 GGTGCCACTGACTTGTGGGCTTT
1 GGTGCCACTGATTTGTGGGCTTT
1295720 TGAAAAGGGT
Statistics
Matches: 285, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
56 27 0.09
57 238 0.84
58 20 0.07
ACGTcount: A:0.19, C:0.15, G:0.34, T:0.33
Consensus pattern (57 bp):
GGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGATTTGTGGGCTTTGGAAAAG
Found at i:1297175 original size:12 final size:12
Alignment explanation
Indices: 1297155--1297254 Score: 78
Period size: 12 Copynumber: 8.2 Consensus size: 12
1297145 ATCTGGACCC
1297155 TTTTTGTTGTTG
1 TTTTTGTTGTTG
* *
1297167 TTGTTGTTGTTT
1 TTTTTGTTGTTG
*
1297179 TTTTTGTT-TTT
1 TTTTTGTTGTTG
*
1297190 TTCTTTGTTTTTTG
1 TT-TTTG-TTGTTG
* *
1297204 TTTTTGTTTTTT
1 TTTTTGTTGTTG
1297216 TTTTTGTTGTTG
1 TTTTTGTTGTTG
* * *
1297228 TTTTTTTTCTTC
1 TTTTTGTTGTTG
1297240 TTTTT-TTGTTTG
1 TTTTTGTTG-TTG
1297252 TTT
1 TTT
1297255 GTTTTTGTGG
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
11 7 0.10
12 55 0.76
13 6 0.08
14 4 0.06
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (12 bp):
TTTTTGTTGTTG
Found at i:1297182 original size:1 final size:1
Alignment explanation
Indices: 1297176--1297260 Score: 53
Period size: 1 Copynumber: 85.0 Consensus size: 1
1297166 GTTGTTGTTG
* * * * * * * * * *
1297176 TTTTTTTTGTTTTTTTCTTTGTTTTTTGTTTTTGTTTTTTTTTTTGTTGTTGTTTTTTTTCTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
1297241 TTTTTTGTTTGTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTT
1297261 GTGGAGGACG
Statistics
Matches: 58, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.85
Consensus pattern (1 bp):
T
Found at i:1314222 original size:52 final size:52
Alignment explanation
Indices: 1314144--1314272 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
1314134 CAAAATATGA
*
1314144 AAATTTGCCTGCATGTATCGATACATTTCATGGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1314196 AAATTTTCCT-CTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGC-ATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1314248 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1314273 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
51 1 0.01
52 70 0.97
53 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1314283 original size:52 final size:51
Alignment explanation
Indices: 1314144--1314292 Score: 178
Period size: 52 Copynumber: 2.9 Consensus size: 51
1314134 CAAAATATGA
* *
1314144 AAATTTGCCTGCATGTATCGATACATTTCAT-GGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGC
* *
1314196 AAATTTTCCT-CTATGTATCGATACATTTCAT-AGTGTATCGATACATCTGGGC
1 AAATTTGCCTGC-ATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGC
*
1314248 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATAC-AACATCAGTGTATCGATACA
1314293 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
51 3 0.03
52 83 0.94
53 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACAACATCAGTGTATCGATACATCTGGGC
Found at i:1314286 original size:20 final size:20
Alignment explanation
Indices: 1314261--1314326 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1314251 TTTGCCTGCA
1314261 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
1314281 TGTATCGATAC----A--A-
1 TGTATCGATACAAAGATCAG
1314294 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
1314314 TGTATCGATACAA
1 TGTATCGATACAA
1314327 TGTATCGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 24 0.62
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGATCAG
Found at i:1314299 original size:13 final size:13
Alignment explanation
Indices: 1314281--1314338 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
1314271 CAAAGATCAG
1314281 TGTATCGATACAA
1 TGTATCGATACAA
1314294 TGTATCGATACAA
1 TGTATCGATACAA
*
1314307 ---A--GAT-CAG
1 TGTATCGATACAA
1314314 TGTATCGATACAA
1 TGTATCGATACAA
1314327 TGTATCGATACA
1 TGTATCGATACA
1314339 TTTGAGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
10 2 0.05
12 3 0.08
13 27 0.73
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1314302 original size:33 final size:33
Alignment explanation
Indices: 1314260--1314338 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
1314250 ATTTGCCTGC
1314260 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
1314293 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
1314326 ATGTATCGATACA
1 ATGTATCGATACA
1314339 TTTGAGTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAGTGTATCGATACA
Found at i:1314401 original size:13 final size:13
Alignment explanation
Indices: 1314383--1314466 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
1314373 AGCTTCGTAG
1314383 CGATACATTGTAT
1 CGATACATTGTAT
1314396 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1314415 CGATACATTGTAT
1 CGATACATTGTAT
1314428 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
1314447 CGATACATTGTAT
1 CGATACATTGTAT
1314460 CGATACA
1 CGATACA
1314467 ACACTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1314415 original size:19 final size:18
Alignment explanation
Indices: 1314391--1314487 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
1314381 AGCGATACAT
1314391 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1314410 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1314423 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1314442 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1314455 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1314474 TGTATCGATACAAA
1 TGTATCGATACAAA
1314488 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 3 0.05
19 35 0.53
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1314424 original size:32 final size:32
Alignment explanation
Indices: 1314261--1314485 Score: 192
Period size: 32 Copynumber: 7.0 Consensus size: 32
1314251 TTTGCCTGCA
* *
1314261 TGTATCGATACAAAGA-TCAGTGTATCGATACAA
1 TGTATCGATACAAA-ACTTA-TGTATCGATACAT
* *
1314294 TGTATCGATACAAAGA-TCAGTGTATCGATACAA
1 TGTATCGATACAAA-ACTTA-TGTATCGATACAT
** * *
1314327 TGTATCGATACATTTGAGTAATGTATCGATACAT
1 TGTATCGATACA--AAACTTATGTATCGATACAT
* * * * * *
1314361 T-T-TC-TTGGCAGTAGCTT-CGTAGCGATACAT
1 TGTATCGAT-ACA-AAACTTATGTATCGATACAT
1314391 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
1314423 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
1314455 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1314486 AATCGTTGAA
Statistics
Matches: 164, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
30 12 0.07
31 8 0.05
32 81 0.49
33 47 0.29
34 14 0.09
35 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1316105 original size:55 final size:55
Alignment explanation
Indices: 1315960--1317142 Score: 1443
Period size: 55 Copynumber: 20.9 Consensus size: 55
1315950 CATTTTTCTT
* * * * *
1315960 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTTAAAGAGCAGGATGCTTTTTCTTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----ACCTC
1316021 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1316076 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
*
1316131 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1316186 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * *
1316241 TTAAAGCCCACACAAGTTGGTGGCACCTTTT--AGTCCCCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAGGACACCTC
* *
1316296 TCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1316351 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * * *
1316406 TCAAAGCCCACACAAGTTGGTGGCACCTTT-C-GTCCCCAAAGAGCAAGACGCCTTC
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACC-TC
* * *
1316461 TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTC
1 T-C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC-TC
** *
1316522 TCCTTTTAAAGCCCACACAAGTTGGTGGCATCCTCCAGTCCTCAAAGAGCAGGACACCTT
1 T-C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
*
1316582 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* *
1316637 TCAAAGCCCACACAAGTTGGTGGCACCTTTT---GTCCCCAAAGAGCAGGACGCCTTC
1 TCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAGGACACC-TC
* * *
1316692 TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAAAGCAGGACGCCTTCACCT
1 T-C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA------CACCT
*
1316757 T
55 C
*
1316758 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * * * *
1316813 TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCTTTTTCTTT
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA--C----ACCTC
* *
1316874 TCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACACCTT
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTC
*
1316929 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * *
1316984 TTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACACCTC
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * * * *
1317039 TTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGTAGGACGCCTT
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
* * * *
1317094 TCAAAGCCCACACGAGTTGGTGGCACTTTT-TACTCCTCAATGAGCAGGA
1 TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
1317143 TACACTTTAT
Statistics
Matches: 1008, Mismatches: 73, Indels: 88
0.86 0.06 0.08
Matches are distributed among these distances:
53 4 0.00
54 42 0.04
55 645 0.64
56 15 0.01
57 9 0.01
58 2 0.00
59 6 0.01
60 49 0.05
61 230 0.23
65 1 0.00
66 2 0.00
67 3 0.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (55 bp):
TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTC
Found at i:1316352 original size:27 final size:27
Alignment explanation
Indices: 1316322--1316404 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
1316312 TTGGTGGCAT
1316322 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
1316349 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
1316377 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
1316404 T
1 T
1316405 CTCAAAGCCC
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 11 0.30
28 10 0.27
29 5 0.14
30 3 0.08
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:1316610 original size:231 final size:227
Alignment explanation
Indices: 1315957--1317142 Score: 1576
Period size: 231 Copynumber: 5.2 Consensus size: 227
1315947 ACGCATTTTT
* * * * *
1315957 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTTAAAGAGCAGGATGCTTTTTCTTT
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTCTCTTT
* *
1316021 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC-TCTC-AAAGCC
65 T-AAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTTCTCTAAAGCC
*
1316084 CACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTT
129 CACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTT
1316149 GGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
194 GGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* *
1316183 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGAC-AC--CTC--T
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTCTCTTT
** *
1316242 TAAAGCCCACACAAGTTGGTGGCACCTT-TTAGTCCCCAAAGAGCAGGACACCTT-TC-AAAGCC
65 TAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACACCTTCTCTAAAGCC
*
1316304 CACATAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTT
129 CACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTT
1316369 GGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
194 GGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * *
1316403 CTCTCAAAGCCCACACAAGTTGGTGGCACCTTTC-GTCCCCAAAGAGCAAGACGCCTTCTCCTTT
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCT-CTTT
*
1316467 TAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAA
65 TAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTTCT-C---TAAA
**
1316532 GCCCACACAAGTTGGTGGCATCCTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAA
126 GCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAA
*
1316597 GTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACAC
191 GTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * *
1316634 CTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-TGTCCCCAAAGAGCAGGACGCCTTCTCCTTT
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCT-CTTT
* * *
1316698 TAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAAAGCAGGACGCCTTCACCTTTCAAA
65 TAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTT---CTCT-AAA
*
1316763 GCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACA
126 GCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACA
* *
1316827 AGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCTTTTTC
190 AGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA--C----AC
* *
1316871 TTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTT-TC----
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCTTTT
* * *
1316931 AAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACACC-TCT-TAAAGCCCA
66 AAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTTCTCTAAAGCCCA
* *
1316994 CACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTT
131 CACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTT
* * *
1317057 GGTGGCATTTTTCAGTCCTCAAAGAGTAGGACGC
194 GGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * * * *
1317091 CTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGA
1 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
1317143 TACACTTTAT
Statistics
Matches: 872, Mismatches: 55, Indels: 72
0.87 0.06 0.07
Matches are distributed among these distances:
219 16 0.02
220 225 0.26
221 8 0.01
222 2 0.00
223 3 0.00
224 4 0.00
225 50 0.06
226 139 0.16
227 6 0.01
228 2 0.00
230 1 0.00
231 307 0.35
232 51 0.06
233 1 0.00
234 2 0.00
236 1 0.00
237 33 0.04
238 21 0.02
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (227 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCTTTT
AAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACACCTTCTCTAAAGCCCA
CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGG
TGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
Found at i:1318096 original size:19 final size:19
Alignment explanation
Indices: 1318072--1318126 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
1318062 AATTCAACAA
1318072 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1318091 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1318110 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1318127 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1318097 original size:123 final size:123
Alignment explanation
Indices: 1317878--1318107 Score: 451
Period size: 123 Copynumber: 1.9 Consensus size: 123
1317868 ATTTTTGTCC
1317878 AAATGTATCGATACATTGTTTGAATGTATCGATACAAGGTCCCAACGGTCAAAAATTTTGAAATT
1 AAATGTATCGATACATTGTTTGAATGTATCGATACAAGGTCCCAACGGTCAAAAATTTTGAAATT
1317943 CAACAATTTGTATCGATACATAAGTATTGTATCGATACATAATTAGCTACTGCCAACG
66 CAACAATTTGTATCGATACATAAGTATTGTATCGATACATAATTAGCTACTGCCAACG
1318001 AAATGTATCGATACATTGTTTGAATGTATCGATACAAGGTCCCAACGGTCAAAAATTTTGAAATT
1 AAATGTATCGATACATTGTTTGAATGTATCGATACAAGGTCCCAACGGTCAAAAATTTTGAAATT
*
1318066 CAACAATTTGTATCGATACATAAGTTTTGTATCGATACATAA
66 CAACAATTTGTATCGATACATAAGTATTGTATCGATACATAA
1318108 GTATTGTATC
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 106 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (123 bp):
AAATGTATCGATACATTGTTTGAATGTATCGATACAAGGTCCCAACGGTCAAAAATTTTGAAATT
CAACAATTTGTATCGATACATAAGTATTGTATCGATACATAATTAGCTACTGCCAACG
Found at i:1318184 original size:13 final size:13
Alignment explanation
Indices: 1318166--1318191 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1318156 CATTTTTCTG
1318166 TGTATCGATACAT
1 TGTATCGATACAT
1318179 TGTATCGATACAT
1 TGTATCGATACAT
1318192 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1318188 original size:33 final size:33
Alignment explanation
Indices: 1318146--1318212 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1318136 GCCAAGGAAA
***
1318146 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1318179 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1318212 T
1 T
1318213 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1318685 original size:65 final size:65
Alignment explanation
Indices: 1318581--1318710 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
1318571 AGGGAAAATA
1318581 CCATAATACCCTTGGTTTGTCCCCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTG
1 CCATAATACCCTTGGTTTGTCCCCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTG
1318646 CCATAATACCCTTGGTTTGTCCCCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTG
1 CCATAATACCCTTGGTTTGTCCCCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTG
1318711 GCTCAGCAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (65 bp):
CCATAATACCCTTGGTTTGTCCCCTAATCCTATTGGCCAAGCTTGATTATAAGTAGTGGCTGTTG
Found at i:1319666 original size:28 final size:28
Alignment explanation
Indices: 1319630--1319706 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
1319620 ATTTTTCACA
* * *
1319630 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
1319658 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
1319686 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1319707 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:1321915 original size:20 final size:20
Alignment explanation
Indices: 1321890--1321966 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 20
1321880 TTTTCACAAT
*
1321890 TTGTATTGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
1321910 TTGTATCGATACATT-TTGTA
1 TTGTATCGATACATTGTT-CA
* * * **
1321930 TCGTATCGGTGCATTACTCA
1 TTGTATCGATACATTGTTCA
*
1321950 TTGTATTGATACATTGT
1 TTGTATCGATACATTGT
1321967 ATCAATACAT
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
19 2 0.05
20 39 0.93
21 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1324511 original size:28 final size:27
Alignment explanation
Indices: 1324453--1324521 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 27
1324443 TCATAATTGA
*
1324453 GGATACTCAAACCCCGTTATTTCATCAG
1 GGATACTCCAACCCCGTTATTT-ATCAG
1324481 GGATACTCCAACCCCGTTATTT-TCGAGG
1 GGATACTCCAACCCCGTTATTTATC-A-G
1324509 GGATACTCCAACC
1 GGATACTCCAACC
1324522 TCGGCTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
26 2 0.05
27 1 0.03
28 35 0.92
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (27 bp):
GGATACTCCAACCCCGTTATTTATCAG
Found at i:1324595 original size:28 final size:28
Alignment explanation
Indices: 1324555--1324629 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
1324545 ATTTTTCATA
*
1324555 ATCGGGGGTACTCCAACCCCGTTATGTC
1 ATCGGGGATACTCCAACCCCGTTATGTC
* * *
1324583 ATCGGGGATACTCTAATCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATGTC
1324611 -T-GAGGAGATACTCCAACCC
1 ATCG-GG-GATACTCCAACCC
1324630 TGATTTTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.03
27 3 0.08
28 35 0.90
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATGTC
Found at i:1324638 original size:107 final size:107
Alignment explanation
Indices: 1324403--1324678 Score: 342
Period size: 107 Copynumber: 2.6 Consensus size: 107
1324393 CGCAATCGAG
* * * * *
1324403 GATACTCCAACTCC-GATTTTATTTCCAAAACACCAATTTTTCATAATTGAGGATACTCAAACCC
1 GATACTCCAAC-CCTGATTTTATTTCTAAAATACCAATTTTTCATAATCGGGGATACTCCAACCC
* *
1324467 CGTTATTTCATCAGGGATACTCCAACCCCGTTATTTTCGAGGG
65 CGTTATGTCATCAGGGATACTCCAACCCCGTTATTTTCGAGGA
** * *** *
1324510 GATACTCCAA-CCTCGGCTTTATATCTAAAATATTGATTTTTCATAATCGGGGGTACTCCAACCC
1 GATACTCCAACCCT-GATTTTATTTCTAAAATACCAATTTTTCATAATCGGGGATACTCCAACCC
* * *
1324574 CGTTATGTCATCGGGGATACTCTAATCCCGTTA-TTTCTGAGGA
65 CGTTATGTCATCAGGGATACTCCAACCCCGTTATTTTC-GAGGA
*
1324617 GATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1 GATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCATAATCGGGGATACTCCAAC
1324679 TCCGATTTTA
Statistics
Matches: 140, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
105 2 0.01
106 4 0.03
107 131 0.94
108 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (107 bp):
GATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCATAATCGGGGATACTCCAACCCC
GTTATGTCATCAGGGATACTCCAACCCCGTTATTTTCGAGGA
Found at i:1324678 original size:51 final size:51
Alignment explanation
Indices: 1324617--1324733 Score: 168
Period size: 51 Copynumber: 2.3 Consensus size: 51
1324607 TTTCTGAGGA
1324617 GATACTCCAACCCTGATTTTA-TTTCTAAAATACCAATTTT-TCACAATCGGG
1 GATACTCCAACCCTGATTTTATTTTC-AAAATACCAATTTTCT-ACAATCGGG
* *
1324668 GATACTCCAACTCC-GATTTTATTTTCAAAATACCAATTTTCTATAATCTGG
1 GATACTCCAAC-CCTGATTTTATTTTCAAAATACCAATTTTCTACAATCGGG
1324719 GATACTCCAACCCTG
1 GATACTCCAACCCTG
1324734 TTATTTCCGA
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
50 2 0.03
51 51 0.85
52 7 0.12
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.35
Consensus pattern (51 bp):
GATACTCCAACCCTGATTTTATTTTCAAAATACCAATTTTCTACAATCGGG
Found at i:1324800 original size:79 final size:79
Alignment explanation
Indices: 1324667--1324896 Score: 264
Period size: 79 Copynumber: 2.9 Consensus size: 79
1324657 TCACAATCGG
* * *
1324667 GGATACTCCAACTCCGATTTTATTTTCAAAATACCAATTTTCTATAATCTGGGATACTCCAACCC
1 GGATACTCCAACCCCGATTTTAGTTTCAAAATACCAATTTTCTATAATCAGGGATACTCCAACCC
1324732 TGTTATTTCCGAGA
66 TGTTATTTCCGAGA
*** *
1324746 GGATACTCCAACCCCGATTTTAGTTTCAAAATATTGATTTTCTATAATCAGGGATATTCCAACCC
1 GGATACTCCAACCCCGATTTTAGTTTCAAAATACCAATTTTCTATAATCAGGGATACTCCAACCC
*** *
1324811 TGTTATTTTTTAGG
66 TGTTATTTCCGAGA
* * * * * * * *
1324825 GGACACTCCAACCTCAATTTTACTTCCAAAACACCAATTTT-TCATAATCGGGGATACTCCAGCC
1 GGATACTCCAACCCCGATTTTAGTTTCAAAATACCAATTTTCT-ATAATCAGGGATACTCCAACC
*
1324889 CCGTTATT
65 CTGTTATT
1324897 ATCTCCAAAA
Statistics
Matches: 126, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
78 1 0.01
79 125 0.99
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (79 bp):
GGATACTCCAACCCCGATTTTAGTTTCAAAATACCAATTTTCTATAATCAGGGATACTCCAACCC
TGTTATTTCCGAGA
Found at i:1325892 original size:20 final size:19
Alignment explanation
Indices: 1325850--1325919 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
1325840 GTTGTGACAA
*
1325850 TATCGATACAACAAGTTAATG
1 TATCGATAC-A-AAGTGAATG
1325871 TATCGATACAAGAGTGAATG
1 TATCGATACAA-AGTGAATG
*
1325891 TATAGATACATAAGTGAATG
1 TATCGATACA-AAGTGAATG
1325911 TATCGATAC
1 TATCGATAC
1325920 TAGGCCATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
19 1 0.02
20 33 0.75
21 10 0.23
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (19 bp):
TATCGATACAAAGTGAATG
Found at i:1326080 original size:52 final size:48
Alignment explanation
Indices: 1325957--1326144 Score: 207
Period size: 52 Copynumber: 3.7 Consensus size: 48
1325947 TCTAAAAAGA
* *
1325957 AAATGTATCGATGCATGTTT-ATTGTATCGATACATTCTGGGTTTGATCC
1 AAATGTATCGATACAT-TTTCATTGTATCGATACATTCTGGTTTTGA-CC
*
1326006 AAATATATCGATACATTTTTCATTGTATCGATACATTCTAGGTTTTTGACC
1 AAATGTATCGATACA-TTTTCATTGTATCGATACATTCT-GG-TTTTGACC
*
1326057 TAAATGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTGGCCC
1 -AAATGTATCGATACATT-TTCATTGTATCGATACATTCT-GGTTTT-GACC
* * * *
1326109 AAATTTATCGATAAATTCTTCAATGTATTGATACAT
1 AAATGTATCGATACATT-TTCATTGTATCGATACAT
1326145 CCAGTTAATT
Statistics
Matches: 121, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
49 16 0.13
50 19 0.16
51 41 0.34
52 45 0.37
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (48 bp):
AAATGTATCGATACATTTTCATTGTATCGATACATTCTGGTTTTGACC
Found at i:1326136 original size:51 final size:51
Alignment explanation
Indices: 1325977--1326144 Score: 221
Period size: 52 Copynumber: 3.3 Consensus size: 51
1325967 ATGCATGTTT
* *
1325977 ATTGTATCGATACATTCTGGG-TTTGATCCAAATATATCGATACATTTTTC
1 ATTGTATCGATACATTCTGGGTTTTGACCCAAATATATCGATACATTATTC
* * *
1326027 ATTGTATCGATACATTCTAGGTTTTTGACCTAAATGTATCGATACATTATTC
1 ATTGTATCGATACATTCT-GGGTTTTGACCCAAATATATCGATACATTATTC
* * * *
1326079 ATTGTATCGATACATTCTGGGTTTTGGCCCAAATTTATCGATAAATTCTTC
1 ATTGTATCGATACATTCTGGGTTTTGACCCAAATATATCGATACATTATTC
* *
1326130 AATGTATTGATACAT
1 ATTGTATCGATACAT
1326145 CCAGTTAATT
Statistics
Matches: 103, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
50 18 0.17
51 42 0.41
52 43 0.42
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (51 bp):
ATTGTATCGATACATTCTGGGTTTTGACCCAAATATATCGATACATTATTC
Found at i:1327793 original size:21 final size:21
Alignment explanation
Indices: 1327769--1327819 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1327759 AATCTTAAAC
1327769 GATTTTTCTCAAATTTTATAG
1 GATTTTTCTCAAATTTTATAG
1327790 GATTTTTCTCAAATTTTATAG
1 GATTTTTCTCAAATTTTATAG
*
1327811 CATTTTTCT
1 GATTTTTCT
1327820 TTGAAAATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (21 bp):
GATTTTTCTCAAATTTTATAG
Found at i:1332877 original size:20 final size:20
Alignment explanation
Indices: 1332852--1332976 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1332842 TTTTAACTAG
1332852 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTAAAAA
1332872 ATGTATCGATACATCTAGGTAAAAAGACAAA
1 ATGTATCGATACA--T---T---AA-A-A-A
* *
1332903 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTAAAAA
* * *
1332923 ATGTATCGATACATTTATAC
1 ATGTATCGATACATTAAAAA
1332943 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTAAAAA
1332963 ATGTATCGATACAT
1 ATGTATCGATACAT
1332977 CTAGGTAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
20 61 0.72
22 2 0.02
23 1 0.01
25 1 0.01
26 1 0.01
28 2 0.02
29 2 0.02
30 1 0.01
31 14 0.16
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTAAAAA
Found at i:1333024 original size:90 final size:91
Alignment explanation
Indices: 1332852--1333026 Score: 298
Period size: 91 Copynumber: 1.9 Consensus size: 91
1332842 TTTTAACTAG
1332852 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACAAAATGTATCGATACAT
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACAAAATGTATCGATACAT
* *
1332917 TGAAGAATGTATCGATACATTTATAC
66 TGAAAAATATATCGATACATTTATAC
* *
1332943 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGT-AAAAGACAGAATGTATTGATACAT
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACAAAATGTATCGATACAT
*
1333007 TGAAAAATATATTGATACAT
66 TGAAAAATATATCGATACAT
1333027 CTAGGTAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 39 0.49
91 40 0.51
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (91 bp):
ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACAAAATGTATCGATACAT
TGAAAAATATATCGATACATTTATAC
Found at i:1336948 original size:18 final size:20
Alignment explanation
Indices: 1336915--1336951 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
1336905 AGATTTTTTC
1336915 AATTTATATGTAAAAATTTG
1 AATTTATATGTAAAAATTTG
1336935 AATTT-TAT-TAAAAATTT
1 AATTTATATGTAAAAATTT
1336952 TAGAGCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AATTTATATGTAAAAATTTG
Found at i:1340428 original size:194 final size:194
Alignment explanation
Indices: 1340099--1340448 Score: 691
Period size: 194 Copynumber: 1.8 Consensus size: 194
1340089 ATTAATAGTA
1340099 AGATATGTGTTTGGATCTAGTATAGCAAGGTGAGTACGGTAAATTATAGTGTGAAAAAAATTATT
1 AGATATGTGTTTGGATCTAGTATAGCAAGGTGAGTACGGTAAATTATAGTGTGAAAAAAATTATT
1340164 ATTTGGAATATTAGATTGAAATATAAGTGTGTGTATATATATATATACAAAGAAAATTAAAAGTT
66 ATTTGGAATATTAGATTGAAATATAAGTGTGTGTATATATATATATACAAAGAAAATTAAAAGTT
1340229 ATTTGATATTTATAAAAGTAATAAATTATAATAATTTTTTTCACACTAGTGTGAAAAAGTGATG
131 ATTTGATATTTATAAAAGTAATAAATTATAATAATTTTTTTCACACTAGTGTGAAAAAGTGATG
1340293 AGATATGTGTTTGGATCTAGTATAGCAAGGTGAGTACGGTAAATTATAGTGTGAAAAAAATTATT
1 AGATATGTGTTTGGATCTAGTATAGCAAGGTGAGTACGGTAAATTATAGTGTGAAAAAAATTATT
*
1340358 ATTTGGAATATTAGATTGAAATATAAGTGTGTGTATATATATATCTACAAAGAAAATTAAAAGTT
66 ATTTGGAATATTAGATTGAAATATAAGTGTGTGTATATATATATATACAAAGAAAATTAAAAGTT
1340423 ATTTGATATTTATAAAAGTAATAAAT
131 ATTTGATATTTATAAAAGTAATAAAT
1340449 AATTAAAATT
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
194 155 1.00
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (194 bp):
AGATATGTGTTTGGATCTAGTATAGCAAGGTGAGTACGGTAAATTATAGTGTGAAAAAAATTATT
ATTTGGAATATTAGATTGAAATATAAGTGTGTGTATATATATATATACAAAGAAAATTAAAAGTT
ATTTGATATTTATAAAAGTAATAAATTATAATAATTTTTTTCACACTAGTGTGAAAAAGTGATG
Found at i:1341767 original size:20 final size:20
Alignment explanation
Indices: 1341738--1341790 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1341728 TTAAATAATA
1341738 TTAT-ATTATAATTATTATT
1 TTATAATTATAATTATTATT
*
1341757 TTATAATTATATTTATTATT
1 TTATAATTATAATTATTATT
*
1341777 TTATAATTTTAATT
1 TTATAATTATAATT
1341791 TTTTATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATAATTATAATTATTATT
Found at i:1341773 original size:17 final size:16
Alignment explanation
Indices: 1341725--1341769 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
1341715 GGCTCCAATA
*
1341725 ATTTTA-AATAATATT
1 ATTTTATAATTATATT
*
1341740 ATATTATAA-T-TATT
1 ATTTTATAATTATATT
1341754 ATTTTATAATTATATT
1 ATTTTATAATTATATT
1341770 TATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
14 12 0.50
15 6 0.25
16 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTATAATTATATT
Found at i:1342283 original size:30 final size:30
Alignment explanation
Indices: 1342241--1342356 Score: 87
Period size: 31 Copynumber: 3.8 Consensus size: 30
1342231 ATAATAGATA
1342241 ATATTT-AAATATTTTATTATATTATAATT
1 ATATTTAAAATATTTTATTATATTATAATT
*
1342270 ATATTTAAAATATTTT-TATAAATTAATAATT
1 ATATTTAAAATATTTTAT-TATATT-ATAATT
** *
1342301 -TATATTATAAA-ATTTTAAAATATTTATATTT
1 ATAT-TTA-AAATATTTTATTATA-TTATAATT
* * *
1342332 ATTTTTAATTATTTTTTATTATATT
1 ATATTTAA-AATATTTTATTATATT
1342357 TATTTATCAG
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
29 7 0.10
30 18 0.27
31 27 0.40
32 15 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
ATATTTAAAATATTTTATTATATTATAATT
Found at i:1342377 original size:26 final size:26
Alignment explanation
Indices: 1342319--1342378 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
1342309 AAAATTTTAA
* *
1342319 AATATTTATATTTATTTTTAATTATTT
1 AATA-TTATATTTATTTATAAGTATTT
** *
1342346 TTTATTATATTTATTTATCAGTATTT
1 AATATTATATTTATTTATAAGTATTT
1342372 AATATTA
1 AATATTA
1342379 CTAGTTACAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
AATATTATATTTATTTATAAGTATTT
Found at i:1342682 original size:22 final size:21
Alignment explanation
Indices: 1342634--1342683 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
1342624 AATTAAGCAT
1342634 TATCATATCAATTTAAACAAA
1 TATCATATCAATTTAAACAAA
* *
1342655 TCTCAT-TCACTTTAAATTCAAA
1 TATCATATCAATTTAAA--CAAA
1342677 TATCATA
1 TATCATA
1342684 ACATACCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 9 0.39
21 5 0.22
22 9 0.39
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (21 bp):
TATCATATCAATTTAAACAAA
Found at i:1344990 original size:27 final size:28
Alignment explanation
Indices: 1344958--1345023 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
1344948 ATTTTTATAT
1344958 TAATATTTATATATTTA-AATTAAAATAA
1 TAATATTTATATATTTATAATT-AAATAA
* *
1344986 -AATATTT-TATTTTTATTATTAAATAA
1 TAATATTTATATATTTATAATTAAATAA
*
1345012 TAATTTTTATAT
1 TAATATTTATAT
1345024 TAATTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 13 0.41
27 16 0.50
28 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TAATATTTATATATTTATAATTAAATAA
Found at i:1345035 original size:18 final size:19
Alignment explanation
Indices: 1344989--1345040 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
1344979 AAAATAAAAT
1344989 ATTTT-ATTTTTATTATTAA
1 ATTTTAATTTTTA-TATTAA
**
1345008 ATAATAATTTTTATATT-A
1 ATTTTAATTTTTATATTAA
1345026 ATTTTAATTTTTATA
1 ATTTTAATTTTTATA
1345041 AAATTTATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.50
19 7 0.25
20 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTAATTTTTATATTAA
Found at i:1345157 original size:61 final size:61
Alignment explanation
Indices: 1345062--1345177 Score: 205
Period size: 61 Copynumber: 1.9 Consensus size: 61
1345052 AACGTAAATC
*
1345062 TGTACGGACTAAACCATCTTGATAATCATATCCTTAAGTAGGTCTACTTAACAATCAGCTA
1 TGTACCGACTAAACCATCTTGATAATCATATCCTTAAGTAGGTCTACTTAACAATCAGCTA
* *
1345123 TGTACCGACTAAACCCTGTTGATAATCATATCCTTAAGTAGGTCTACTTAACAAT
1 TGTACCGACTAAACCATCTTGATAATCATATCCTTAAGTAGGTCTACTTAACAAT
1345178 TAGCAATTGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (61 bp):
TGTACCGACTAAACCATCTTGATAATCATATCCTTAAGTAGGTCTACTTAACAATCAGCTA
Found at i:1345290 original size:29 final size:29
Alignment explanation
Indices: 1345256--1345317 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1345246 ACATAATTTA
* * *
1345256 ATTATAAATT-TATTTATATTATTTTATAT
1 ATTAT-AATTATATTTAAAATATTATATAT
1345285 ATTATAATTATATTTAAAATATTATATAT
1 ATTATAATTATATTTAAAATATTATATAT
1345314 -TTAT
1 ATTAT
1345318 TTAAATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTATAATTATATTTAAAATATTATATAT
Found at i:1345306 original size:20 final size:19
Alignment explanation
Indices: 1345260--1345334 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 19
1345250 AATTTAATTA
*
1345260 TAAAT-TTATTTATATTATTT
1 TAAATATTATATAT-TTA-TT
*
1345280 TATATATTATA-ATTATATT
1 TAAATATTATATATT-TATT
1345299 TAAAATATTATATATTTATT
1 T-AAATATTATATATTTATT
1345319 TAAATATTAATATATT
1 TAAATATT-ATATATT
1345335 AATAATTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 11 0.23
20 29 0.62
21 7 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAAATATTATATATTTATT
Found at i:1345326 original size:39 final size:40
Alignment explanation
Indices: 1345248--1345327 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
1345238 TTGAATAGAC
* *
1345248 ATAATTTAATTATAAATTTATTTATATTATTTTATATATT
1 ATAATTTAATTATAAATTTATATATATTATTTTAAATATT
*
1345288 ATAATTATATTTA-AAATATTATATAT-TTA-TTTAAATATT
1 ATAATT-TAATTATAAAT-TTATATATATTATTTTAAATATT
1345327 A
1 A
1345328 ATATATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
39 10 0.29
40 13 0.37
41 12 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (40 bp):
ATAATTTAATTATAAATTTATATATATTATTTTAAATATT
Found at i:1345328 original size:27 final size:26
Alignment explanation
Indices: 1345279--1345344 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
1345269 TTATATTATT
* *
1345279 TTATATATTATAATTATATTTAAAATA
1 TTATATATT-TATTTAAATTTAAAATA
*
1345306 TTATATATTTATTTAAATATTAATATA
1 TTATATATTTATTTAAAT-TTAAAATA
1345333 TTA-ATAATTTAT
1 TTATAT-ATTTAT
1345345 ATCAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTATATATTTATTTAAATTTAAAATA
Found at i:1348959 original size:17 final size:17
Alignment explanation
Indices: 1348914--1348960 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1348904 TTTTATTAAA
1348914 ATGAAATTTAT-TTTTT
1 ATGAAATTTATATTTTT
*
1348930 ATCAAATTT-TATTTTT
1 ATGAAATTTATATTTTT
1348946 -TGAAATTTAATATTT
1 ATGAAATTT-ATATTT
1348961 ATGTCCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 8 0.31
16 13 0.50
17 5 0.19
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
ATGAAATTTATATTTTT
Found at i:1349263 original size:15 final size:16
Alignment explanation
Indices: 1349243--1349275 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1349233 TTTGAGTTAA
*
1349243 TTATATAA-ATGATTT
1 TTATATAATATCATTT
1349258 TTATATAATATCATTT
1 TTATATAATATCATTT
1349274 TT
1 TT
1349276 CTAAATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATATAATATCATTT
Found at i:1350420 original size:21 final size:20
Alignment explanation
Indices: 1350395--1350439 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1350385 TTGTTACGTT
*
1350395 TTATTCTGTCTTTTAAAATTA
1 TTATTCTATCTTTTAAAA-TA
* *
1350416 TTATTTTATTTTTTAAAATA
1 TTATTCTATCTTTTAAAATA
1350436 TTAT
1 TTAT
1350440 ATATATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATTCTATCTTTTAAAATA
Found at i:1350450 original size:21 final size:21
Alignment explanation
Indices: 1350405--1350469 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1350395 TTATTCTGTC
* *
1350405 TTTTAAAATTATTATTTTATT
1 TTTTAAAATTATTATTATATA
1350426 TTTTAAAA-TATTATATATATA
1 TTTTAAAATTATTAT-TATATA
* * * *
1350447 TTTTTATATTTTTAATATATA
1 TTTTAAAATTATTATTATATA
1350468 TT
1 TT
1350470 AAATATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 6 0.17
21 26 0.72
22 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAAAATTATTATTATATA
Found at i:1350461 original size:30 final size:31
Alignment explanation
Indices: 1350419--1350479 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
1350409 AAAATTATTA
*
1350419 TTTTATTTTTTAA-A-ATATTATATATATAT
1 TTTTATTTTTTAATATATATTAAATATATAT
1350448 TTTTATATTTTTAATATATATTAAATATATAT
1 TTTTAT-TTTTTAATATATATTAAATATATAT
1350480 ATTAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 6 0.21
30 7 0.25
31 1 0.04
32 14 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTATTTTTTAATATATATTAAATATATAT
Found at i:1350481 original size:15 final size:15
Alignment explanation
Indices: 1350461--1350495 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
1350451 TATATTTTTA
1350461 ATATATATT-AAAT-
1 ATATATATTAAAATC
1350474 ATATATATTAAAATC
1 ATATATATTAAAATC
1350489 ATATATA
1 ATATATA
1350496 CAAATATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 4 0.20
15 7 0.35
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATATATTAAAATC
Found at i:1350905 original size:2 final size:2
Alignment explanation
Indices: 1350898--1350923 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1350888 CCTTTTCATC
1350898 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1350924 TATGTATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1356045 original size:32 final size:32
Alignment explanation
Indices: 1356008--1356072 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1355998 AATTTTTACT
* **
1356008 AGTCAAAATAGATTAGTGGTAATTTTAAATTA
1 AGTCAAAATAGATTAATAATAATTTTAAATTA
1356040 AGTCAAAATAGATTAATAATAATTTTAAATTA
1 AGTCAAAATAGATTAATAATAATTTTAAATTA
1356072 A
1 A
1356073 ATGAGTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.37
Consensus pattern (32 bp):
AGTCAAAATAGATTAATAATAATTTTAAATTA
Found at i:1358872 original size:16 final size:16
Alignment explanation
Indices: 1358841--1358883 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1358831 TATAAAATGA
*
1358841 AATAAATTTATAATTTT
1 AATAAATTAAT-ATTTT
1358858 -ATAAAATTAATATTTT
1 AAT-AAATTAATATTTT
1358874 AATAAATTAA
1 AATAAATTAA
1358884 CTATCAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATAAATTAATATTTT
Found at i:1359655 original size:26 final size:24
Alignment explanation
Indices: 1359620--1359680 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 24
1359610 GTATTAATCT
1359620 CATATAAAAAATTAATAAATCACATCA
1 CATATAAAAAATT-AT--ATCACATCA
* *
1359647 CTTATAAAAAATTGTATCACATCA
1 CATATAAAAAATTATATCACATCA
1359671 CATATAAAAA
1 CATATAAAAA
1359681 GAATTAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.58
26 1 0.03
27 12 0.39
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.28
Consensus pattern (24 bp):
CATATAAAAAATTATATCACATCA
Found at i:1359794 original size:13 final size:14
Alignment explanation
Indices: 1359772--1359812 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1359762 ATCAATTGAT
1359772 TTTAAG-TTAAATA
1 TTTAAGCTTAAATA
*
1359785 TTT-ATCTTAAA-A
1 TTTAAGCTTAAATA
1359797 TTTAAGCTTAAATA
1 TTTAAGCTTAAATA
1359811 TT
1 TT
1359813 GATTTAGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
12 5 0.22
13 15 0.65
14 3 0.13
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (14 bp):
TTTAAGCTTAAATA
Found at i:1365780 original size:15 final size:15
Alignment explanation
Indices: 1365760--1365791 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1365750 TTGATAAATT
1365760 AAAAATTAAATATTA
1 AAAAATTAAATATTA
*
1365775 AAAAATTAAGTATTA
1 AAAAATTAAATATTA
1365790 AA
1 AA
1365792 TTTTTAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAAATTAAATATTA
Found at i:1366121 original size:134 final size:133
Alignment explanation
Indices: 1365964--1366217 Score: 397
Period size: 134 Copynumber: 1.9 Consensus size: 133
1365954 AAGTTATTTT
* *
1365964 TCAATTATTTCGGACTCAAATCAATTAGATTT-ACGCTTGAGATAATCAGATTCAGGTTATTT-T
1 TCAATTATTTCGGACTCAAATCAATTAGATTTAACGC-TGAGATAATCAGATCCAGGTTATTTGG
* *
1366027 GACTTAGATCATTTTTAAGTTAAGTCAATCGAGTTTAACATTTTTAAATTAATTAATTTATGGTT
65 GACTTAGATCA-TTTAAAGTCAAGTCAATCGAGTTTAACA-TTTTAAA-TAATTAATTTATGGTT
1366092 GAGCTAA
127 GAGCTAA
*
1366099 TCAATTATTTC-GACTCAAATCAATTAGATTTAACGCTGAGCTAATCAGATCCAGGTTATTTGGG
1 TCAATTATTTCGGACTCAAATCAATTAGATTTAACGCTGAGATAATCAGATCCAGGTTATTTGGG
*
1366163 ACTTAGATCATTTAAAGTCAAGTCAATCGGGTTTAACATTTTAAATAATTAATTT
66 ACTTAGATCATTTAAAGTCAAGTCAATCGAGTTTAACATTTTAAATAATTAATTT
1366218 TAGATTTATA
Statistics
Matches: 111, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
132 10 0.09
133 7 0.06
134 68 0.61
135 26 0.23
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (133 bp):
TCAATTATTTCGGACTCAAATCAATTAGATTTAACGCTGAGATAATCAGATCCAGGTTATTTGGG
ACTTAGATCATTTAAAGTCAAGTCAATCGAGTTTAACATTTTAAATAATTAATTTATGGTTGAGC
TAA
Found at i:1373819 original size:20 final size:20
Alignment explanation
Indices: 1373791--1373865 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1373781 TTTTACCCTG
1373791 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1373811 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * * *
1373831 ATGTATTGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
1373851 ATGTATCGATACATT
1 ATGTATCGATACATT
1373866 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1373858 original size:40 final size:39
Alignment explanation
Indices: 1373791--1373868 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1373781 TTTTACCCTG
* *
1373791 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTGCAATATATCGATACAT-TATGA
* * *
1373831 ATGTATTGATATATTCTGCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTGCAATATATCGATACATTATG
1373869 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTGCAATATATCGATACATTATGA
Found at i:1374811 original size:23 final size:23
Alignment explanation
Indices: 1374775--1374826 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1374765 AGCCTTTGAC
1374775 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1374797 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1374820 CATGCAT
1 CATGCAT
1374827 CTTTAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1378836 original size:11 final size:11
Alignment explanation
Indices: 1378820--1378844 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1378810 TGTAATAGGG
1378820 TAACCTTGTGA
1 TAACCTTGTGA
1378831 TAACCTTGTGA
1 TAACCTTGTGA
1378842 TAA
1 TAA
1378845 ACAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (11 bp):
TAACCTTGTGA
Found at i:1379554 original size:14 final size:13
Alignment explanation
Indices: 1379530--1379559 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1379520 CTAAAAACAT
1379530 TAAAAATAAATAA
1 TAAAAATAAATAA
1379543 TAAAAGATAAATAA
1 TAAAA-ATAAATAA
1379557 TAA
1 TAA
1379560 TAAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
TAAAAATAAATAA
Found at i:1379560 original size:17 final size:18
Alignment explanation
Indices: 1379533--1379566 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1379523 AAAACATTAA
1379533 AAATAAATAATAAAAGAT
1 AAATAAATAATAAAAGAT
1379551 AAAT-AATAATAAAAGA
1 AAATAAATAATAAAAGA
1379567 AAAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (18 bp):
AAATAAATAATAAAAGAT
Found at i:1379670 original size:2 final size:2
Alignment explanation
Indices: 1379665--1379704 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1379655 AAAAACTATT
1379665 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1379705 ACACTCGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1380438 original size:20 final size:20
Alignment explanation
Indices: 1380409--1380454 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1380399 ATTTATATCT
1380409 TTAA-TTTTTATTTTTTATAA
1 TTAATTTTTTATTTTTT-TAA
1380429 -TAATTTTTTATTTTTTTAA
1 TTAATTTTTTATTTTTTTAA
1380448 TTAATTT
1 TTAATTT
1380455 CTAACTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTAATTTTTTATTTTTTTAA
Found at i:1381817 original size:15 final size:15
Alignment explanation
Indices: 1381787--1381837 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
1381777 GAATTTAAAT
*
1381787 AAAAGATAATGATTTA
1 AAAAAATAAT-ATTTA
*
1381803 AAAAAAT-TTATTTTA
1 AAAAAATAATA-TTTA
1381818 AAAAAATAATATTTA
1 AAAAAATAATATTTA
1381833 AAAAA
1 AAAAA
1381838 GTGGTTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 1 0.03
15 21 0.70
16 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (15 bp):
AAAAAATAATATTTA
Found at i:1381964 original size:22 final size:22
Alignment explanation
Indices: 1381934--1381982 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1381924 TAATATTTTT
*
1381934 ATTTTATT-ATTTTATATTATAA
1 ATTTAATTAATTTT-TATTATAA
*
1381956 ATTTAATTAATTTTTTTTATAA
1 ATTTAATTAATTTTTATTATAA
1381978 ATTTA
1 ATTTA
1381983 TAAACTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTAATTAATTTTTATTATAA
Found at i:1382264 original size:26 final size:26
Alignment explanation
Indices: 1382235--1382297 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
1382225 TTATATTGAT
1382235 TTAAAAATTTTATATA-AA-AATTAAAA
1 TTAAAAATTTTAT-TACAAGAA-TAAAA
* *
1382261 TT-AAAATTATATTACAAGAATGAAA
1 TTAAAAATTTTATTACAAGAATAAAA
1382286 TTAAAAATTTTA
1 TTAAAAATTTTA
1382298 AGTTTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 2 0.06
25 17 0.55
26 12 0.39
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (26 bp):
TTAAAAATTTTATTACAAGAATAAAA
Found at i:1382440 original size:17 final size:17
Alignment explanation
Indices: 1382409--1382446 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1382399 TTTATATGCT
*
1382409 TTTTAAAATATAATA-A
1 TTTTAAAAAATAATATA
1382425 TTTTAAAAAATAAATATA
1 TTTTAAAAAAT-AATATA
1382443 TTTT
1 TTTT
1382447 CACTCACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 4 0.21
18 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTAAAAAATAATATA
Found at i:1383239 original size:41 final size:39
Alignment explanation
Indices: 1383146--1383244 Score: 92
Period size: 41 Copynumber: 2.4 Consensus size: 39
1383136 GAAACAATAA
*
1383146 AAATTTATAAATATCAAATATTAAAATAAAAATAAAAAATTT
1 AAATTT-TAAATA--AAATATTAAAAGAAAAATAAAAAATTT
** *
1383188 ATGTTATTTAAATAAAATATTAAAAGAAAAATATAAATATTT
1 A-AAT-TTTAAATAAAATATTAAAAGAAAAATA-AAAAATTT
1383230 GAAATTTT-AATAAAA
1 -AAATTTTAAATAAAA
1383245 ATTTATACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
40 7 0.15
41 21 0.45
42 9 0.19
43 8 0.17
44 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (39 bp):
AAATTTTAAATAAAATATTAAAAGAAAAATAAAAAATTT
Found at i:1383246 original size:41 final size:41
Alignment explanation
Indices: 1383161--1383244 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
1383151 TATAAATATC
* **
1383161 AAATATTAAAATAAAAATAAAAAATTTATGTTATTTAAATA
1 AAATATTAAAAGAAAAATAAAAAATTTATGAAATTTAAATA
* *
1383202 AAATATTAAAAGAAAAAT-ATAAATATT-TGAAATTTTAATA
1 AAATATTAAAAGAAAAATAAAAAAT-TTATGAAATTTAAATA
1383242 AAA
1 AAA
1383245 ATTTATACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 18 0.49
41 19 0.51
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (41 bp):
AAATATTAAAAGAAAAATAAAAAATTTATGAAATTTAAATA
Found at i:1384337 original size:16 final size:17
Alignment explanation
Indices: 1384316--1384350 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1384306 ATTATAACTA
1384316 AAAATAATTCGAA-ATT
1 AAAATAATTCGAATATT
1384332 AAAATAATTCGAATATT
1 AAAATAATTCGAATATT
1384349 AA
1 AA
1384351 CTTAAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAATAATTCGAATATT
Found at i:1384492 original size:16 final size:16
Alignment explanation
Indices: 1384467--1384532 Score: 105
Period size: 16 Copynumber: 4.1 Consensus size: 16
1384457 TGATATAAAC
* *
1384467 TTAAATTTAAAAAAAT
1 TTAAAATTAAAATAAT
1384483 TTAAAATTAAAATAAT
1 TTAAAATTAAAATAAT
*
1384499 TTAAATTTAAAATAAT
1 TTAAAATTAAAATAAT
1384515 TTAAAATTAAAATAAT
1 TTAAAATTAAAATAAT
1384531 TT
1 TT
1384533 TTAAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAATTAAAATAAT
Found at i:1384503 original size:32 final size:32
Alignment explanation
Indices: 1384467--1384532 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1384457 TGATATAAAC
1384467 TTAAATTTAAAAAAATTTAAAATTAAAATAAT
1 TTAAATTTAAAAAAATTTAAAATTAAAATAAT
*
1384499 TTAAATTTAAAATAATTTAAAATTAAAATAAT
1 TTAAATTTAAAAAAATTTAAAATTAAAATAAT
1384531 TT
1 TT
1384533 TTAAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TTAAATTTAAAAAAATTTAAAATTAAAATAAT
Found at i:1384543 original size:32 final size:31
Alignment explanation
Indices: 1384474--1384545 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 31
1384464 AACTTAAATT
1384474 TAAAAA-AATTTAAAATTAAAATAATTTAAA
1 TAAAAATAATTTAAAATTAAAATAATTTAAA
*
1384504 TTTAAAATAATTTAAAATTAAAATAATTTTTAAA
1 -TAAAAATAATTTAAAATTAAAATAA--TTTAAA
1384538 -AAAAATAA
1 TAAAAATAA
1384546 CTCTTTGCGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 5 0.14
32 25 0.69
34 6 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
TAAAAATAATTTAAAATTAAAATAATTTAAA
Found at i:1386622 original size:2 final size:2
Alignment explanation
Indices: 1386615--1386643 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1386605 TTTATTTGAT
1386615 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
1386644 CTTTTGGAAA
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:1390616 original size:21 final size:21
Alignment explanation
Indices: 1390579--1390620 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1390569 GTCATAAACT
*
1390579 AACAAAAAAAATCAAAAAGGG
1 AACAAAAAAAATAAAAAAGGG
1390600 AACAAAAAAGAA-AAAAAAGGG
1 AACAAAAAA-AATAAAAAAGGG
1390621 TGAGAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.74, C:0.07, G:0.17, T:0.02
Consensus pattern (21 bp):
AACAAAAAAAATAAAAAAGGG
Found at i:1391259 original size:20 final size:20
Alignment explanation
Indices: 1391234--1391290 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
1391224 TTTTACCTAG
* * *
1391234 ATGTATTGATATATTTTTCA
1 ATGTATCGATACATTCTTCA
1391254 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
1391274 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1391291 GTCTTTTTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1395561 original size:21 final size:21
Alignment explanation
Indices: 1395532--1395578 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1395522 AAGGAAGGGC
* *
1395532 CATTTTTTTTTTATTGA-TGTT
1 CATTCTTTTATTATT-ACTGTT
*
1395553 CATTCTTTTATTCTTACTGTT
1 CATTCTTTTATTATTACTGTT
1395574 CATTC
1 CATTC
1395579 CCATTGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.64
Consensus pattern (21 bp):
CATTCTTTTATTATTACTGTT
Found at i:1402621 original size:962 final size:961
Alignment explanation
Indices: 1399567--1404356 Score: 8032
Period size: 962 Copynumber: 5.0 Consensus size: 961
1399557 GCAGCGGGGC
* * * * * * *
1399567 ATGACATCAAAAATTGTAATGCCCTTAAGAGAAAAGTGTAAAGTCTCATCAAATCGAAGGTGCTG
1 ATGACATCAAAAGTTGCATTGCCCTTAAAAGAAAAGTGCAAAGTCTCATCGACTCGAAGGTGCTG
* * *
1399632 TAGTTCGGGACTAATCAAGGACCTAATGTTGCCGCGAATCCTTTACCAAACCATACAGAACCAAA
66 CAGTTCGGGACAAATCAAGGACCTAATGTTGCCGCGAATCCTTTACCAAACCATACAGAACCAGA
* *
1399697 TGCAAACATGATTGGCATCGAGAATAAATATAAAGTTAAGATAAGCATAGAAGAGGTAAGGATGC
131 TGCAAACATGATTGGCATCGAGAATAAATATAAAGTTAAGATAAGCATAGAGGAAGTAAGGATGC
* *
1399762 CGATGTTCTTAGTTTGGGAAGCATTGAGTCAAGTCGGATTGCTTAATGCAGCAAAAAAGTTGAAA
196 CAATGTTCTTAGTTTGGGAAGCATTGAGTCAAGTCGGATTGCTTAATGCAGCGAAAAAGTTGAAA
*
1399827 GATAAGCTCGATAACTTCTATGACTTCCACACTGTTGTAGGTCATACCTTACAAACATGCAA-AG
261 GATAAGCTCGACAACTTCTATGACTTCCACACTGTTGTAGGTCATACCTTACAAACATGCAAGA-
*
1399891 AGTTTAGGGCCATGGTTCAGAGAATGATGGATGAAGGCCAGATAGAATTCTATCATGAAGCCACA
325 AGTTTAGGGCCATGGTTTAGAGAATGATGGATGAAGGCCAGATAGAATTCTATCATGAAGCCACA
* *
1399956 CCTGCTGTCGAATCCATCAACATGATAGGAGACAAAGCAATGCAGCCATCTTAC-GAGAGGAATT
390 CCTGCTGTCGAATCCATCAACATGATAGGAGACAAAGCAATGCAGCCACCTTACAG-GAGGAATC
1400020 GACCCTTAATTCTTTTTGGCAAGTCAAGTTTTGAGGCTAGTTCTTCGACACCTACACCAATATTA
454 GACCCTTAATTCTTTTTGGCAAGTCAAGTTTTGAGGCTAGTTCTTCGACACCTACACCAATATTA
*
1400085 GTTGTGGAGGTACCTAAACCGTTCTCATATAAGAGCAACAAAGCAGTCCCTTGGAGGTACGAGAA
519 GTCGTGGAGGTACCTAAACCGTTCTCATATAAGAGCAACAAAGCAGTCCCTTGGAGGTACGAGAA
* * * *
1400150 TCAGGTAGTGATAATTGGAGAACAAACTCCCTTGACTGCTGTGATGGAACTGTTAGGGGTTAGTC
584 TCAGGTAGTGATAATTGGAGAACAAACTCCCTCGGCTGCTGTGATGGAACTGTCAAGGGTTAGTC
*
1400215 ACCTAACCCGTAGTGGTAGGTGTTATGCTCCCCCAATTCATGAAAAATAGAAGGTTGATGCATTT
649 ACCTAACCCGTAGTGGTAGGTGTTATGCTCCCCCAATTCAAGAAAAATAGAAGGTTGATGCATTT
*
1400280 CCAAGCACTAGTACCTTTCAAAAACAAGCGAAGAACCCAAAGCTAGAAAAAGTCAAAGAAACGGT
714 CCAAGCACTAGTACCTTTCAAAAACAAGCGAAGAACCCAGAGCTAGAAAAAGTCAAAGAAACGGT
* * *
1400345 GAATAAAGATGAAGCTACAAAGTTTCTTAAGTTCATCAAGCACAGCGAATATAGTATTGTGGATC
779 GAATGAAGATGAAGCTACAGAGTTTCTCAAGTTCATCAAGCACAGCGAATATAGTATTGTGGATC
**
1400410 AACTAAGCAAACAACCTGCAAAGATTTCTGTGCTCTCTTTGCTTCTTAATTCGGAGGTTCACTTA
844 AACTAAGCAAACAACCTGCAAAGATTTCTGTGCTCTCTTTGCTTCTTAATTCGGAGGTTCACCGA
*** * *
1400475 AATGCATTGCTGAAGGTGTTAAACGAAGCATATGTACCATTGAACGTCTTTGT
909 AATGCATTGCTGAAGGTGTTAAACGAAGCATATGTACCACCCAACATCTCTGT
*
1400528 ATGACATCGAAAGTTGCATTGCCCTTAAAAGAAAAGTGCAAAGTCTCATCGACTCGAAGGTGCTG
1 ATGACATCAAAAGTTGCATTGCCCTTAAAAGAAAAGTGCAAAGTCTCATCGACTCGAAGGTGCTG
*
1400593 CAGTTCGGGACAAA-CTAAGGACCTAATGTTGCCGTGAATCCTTTACCAAACCATACAGAACCAG
66 CAGTTCGGGACAAATC-AAGGACCTAATGTTGCCGCGAATCCTTTACCAAACCATACAGAACCAG
* *
1400657 ATGCAAACATGATTGGCATCGAGAATAAATATAAAGTTAAGATAACCATAGAAGAAGTAAGGATG
130 ATGCAAACATGATTGGCATCGAGAATAAATATAAAGTTAAGATAAGCATAGAGGAAGTAAGGATG
1400722 CCAATGTTCTTAGTTTGGGAAGCATTGAGTCAAGTCGGATTGCTTAATGCAGCGAAAAAGTTGAA
195 CCAATGTTCTTAGTTTGGGAAGCATTGAGTCAAGTCGGATTGCTTAATGCAGCGAAAAAGTTGAA
* *
1400787 AGATAAGCTCGACAACTTCTATGACTTCCACACTGTTGTAAGTCATACCTTACAAACATGCAAGG
260 AGATAAGCTCGACAACTTCTATGACTTCCACACTGTTGTAGGTCATACCTTACAAACATGCAAGA
* * *
1400852 AGTTTAGGGCCATAGTTCAAAGAATGATGGATGAAGGCCAGATAGAATTCTATCATGAAGCCACA
325 AGTTTAGGGCCATGGTTTAGAGAATGATGGATGAAGGCCAGATAGAATTCTATCATGAAGCCACA
* * *
1400917 CCTGCTGTCGAATCCATCAACATGATAGAAGACAAAGCAATGTAGCCACCTTACGGGAGGAATCG
390 CCTGCTGTCGAATCCATCAACATGATAGGAGACAAAGCAATGCAGCCACCTTACAGGAGGAATCG
1400982 A-CCTTAATTCTTTTTGGCAAGTCAAGTTTTGAGGCTAGTTCTTCGACACCTACACCAATATTAG
455 ACCCTTAATTCTTTTTGGCAAGTCAAGTTTTGAGGCTAGTTCTTCGACACCTACACCAATATTAG
* *
1401046 TCATGGAGGTACCTAAACCGTTCTCATATAAGAGCAACAAAGCAGTCCCTTGGAGCTACGAGAAT
520 TCGTGGAGGTACCTAAACCGTTCTCATATAAGAGCAACAAAGCAGTCCCTTGGAGGTACGAGAAT
* * * *
1401111 CAGGTAATGATAATTGGAGAACAAACTCCCTTGGCTGCTGTGATGGAATTGTCAGGGGTTAGTCA
585 CAGGTAGTGATAATTGGAGAACAAACTCCCTCGGCTGCTGTGATGGAACTGTCAAGGGTTAGTCA
* *
1401176 CCTAACCCGTAGTGGTAGGTGTTATGCTCCACCAATTCAAGAAAAATAGAAGGTTGATGCTTTTC
650 CCTAACCCGTAGTGGTAGGTGTTATGCTCCCCCAATTCAAGAAAAATAGAAGGTTGATGCATTTC
* * *
1401241 CAAGCACTAGTACCTTTCAAAAACAAGCGAAGAACTCAGAGCTAGAAAAAGTCAAGGAAATGGTG
715 CAAGCACTAGTACCTTTCAAAAACAAGCGAAGAACCCAGAGCTAGAAAAAGTCAAAGAAACGGTG
* *
1401306 AATGAAGATAAAGCTACAGAGTTTCTCAAGTTCATCAAGCACAGCGAAGATAGTATTGTGGATCA
780 AATGAAGATGAAGCTACAGAGTTTCTCAAGTTCATCAAGCACAGCGAATATAGTATTGTGGATCA
*
1401371 ACTAAGCAAACAACCTGCAAAGATTTTTGTGCTCTCTTTGCTTCTTAATTCGGAGGTTCACCGAA
845 ACTAAGCAAACAACCTGCAAAGATTTCTGTGCTCTCTTTGCTTCTTAATTCGGAGGTTCACCGAA
* * * * * * *
1401436 ATGCATTACTAAATGTATTAAACGAAGCATATGTATCACCCGACGTCTCTGT
910 ATGCATTGCTGAAGGTGTTAAACGAAGCATATGTACCACCCAACATCTCTGT
*
1401488 ATGACATCGAAAGTTGCATTGCCCTTAAAAGAAAAGTGCAAAGTCTCATCGACTCGAAGGTGCTG
1 ATGACATCAAAAGTTGCATTGCCCTTAAAAGAAAAGTGCAAAGTCTCATCGACTCGAAGGTGCTG
* * * **
1401553 CAGTTTGGGACAAATCTAA-GACCTAATGTTGCTGCAAATCCTTTATGAAACCATACAGAACCAG
66 CAGTTCGGGACAAATC-AAGGACCTAATGTTGCCGCGAATCCTTTACCAAACCATACAGAACCAG
1401617 ATGCAAACATGATTGGCATCGAGAATAAATATAAAGTTAAGATAAGCATAGAGGAAGTAAGGATG
130 ATGCAAACATGATTGGCATCGAGAATAAATATAAAGTTAAGATAAGCATAGAGGAAGTAAGGATG
* *
1401682 CCAATGTTCTTAGTTTGGGAAGCATTGAGTCAAGTCGGTTTGCTTAATACAGCGAAAAAGTTGAA
195 CCAATGTTCTTAGTTTGGGAAGCATTGAGTCAAGTCGGATTGCTTAATGCAGCGAAAAAGTTGAA
1401747 AGATAAGCTCGACAACTTCTATGACTTCCACACTGTTGTAGGTCATACCTTACAAACATGCAAGA
260 AGATAAGCTCGACAACTTCTATGACTTCCACACTGTTGTAGGTCATACCTTACAAACATGCAAGA
* *
1401812 AGTTTAGGGCCATGGTTTAGAGAATGATGGATGAAGGTCAGATAGAATTTTATCATGAAGCCACA
325 AGTTTAGGGCCATGGTTTAGAGAATGATGGATGAAGGCCAGATAGAATTCTATCATGAAGCCACA
* * *
1401877 CCTGCTGTCGAATCCATCAACATGATAGGCGAGAAAGCAACGCAGCCACCTTACAGGAGGAATCG
390 CCTGCTGTCGAATCCATCAACATGATAGGAGACAAAGCAATGCAGCCACCTTACAGGAGGAATCG
*
1401942 ACCCTTAATTCTTTTTGGCAAGACAAGTTTTGAGGCTAGTTCTTCGACACCTACACCAATATTAG
455 ACCCTTAATTCTTTTTGGCAAGTCAAGTTTTGAGGCTAGTTCTTCGACACCTACACCAATATTAG
* ** *
1402007 TCGTGGAGGTACCTAAACCGTTCTCATATAAGAGCAACAAAGCAGTCCTTTAAAGGTATGAGAAT
520 TCGTGGAGGTACCTAAACCGTTCTCATATAAGAGCAACAAAGCAGTCCCTTGGAGGTACGAGAAT
* *
1402072 CACGTAGTGATAATTGGAGAACAAACTCCCTCGGCTGCTGCGATGGAACTGTCAAGGGTTAGTCA
585 CAGGTAGTGATAATTGGAGAACAAACTCCCTCGGCTGCTGTGATGGAACTGTCAAGGGTTAGTCA
1402137 CCTAACCCGTAGTGGTAGGTGTTATGCTCCCCCAATTCAAGAAAAATAGAAGGTTGATGCATTTC
650 CCTAACCCGTAGTGGTAGGTGTTATGCTCCCCCAATTCAAGAAAAATAGAAGGTTGATGCATTTC
* *
1402202 CAAGCACCAATACCTTTCAAAAACAAGCGAAGAACCCAGAGCTTAGAAAAAGTCAAAGAAACGGT
715 CAAGCACTAGTACCTTTCAAAAACAAGCGAAGAACCCAGAGC-TAGAAAAAGTCAAAGAAACGGT
* *
1402267 GAATGAAGATGAAGCTACAAAGTTTCTCAAGTTCATCAAGCACAGTGAATATAGTATTGTGGATC
779 GAATGAAGATGAAGCTACAGAGTTTCTCAAGTTCATCAAGCACAGCGAATATAGTATTGTGGATC
*
1402332 AACTACGCAAACAACCTGCAAAGATTTCTGTGCTCTCTTTGCTTCTTAATTCGGAGGTTCACCGA
844 AACTAAGCAAACAACCTGCAAAGATTTCTGTGCTCTCTTTGCTTCTTAATTCGGAGGTTCACCGA
* *
1402397 AATGCATTGCTGAAGGTGTTAAACGAAGCATATATACCACCCAACATCTTTGT
909 AATGCATTGCTGAAGGTGTTAAACGAAGCATATGTACCACCCAACATCTCTGT
*
1402450 AAGACATCAAAAGTTGCATTGCCCTTAAAAGAAAAGTGCAAAGTCTCATCGACTCGAAGGTGCTG
1 ATGACATCAAAAGTTGCATTGCCCTTAAAAGAAAAGTGCAAAGTCTCATCGACTCGAAGGTGCTG
** *
1402515 CAGTTCAAGACAAATCAAGGACCTAATGTTGCCGCGAATCCTTTATCAAACCATACAGAACCAGA
66 CAGTTCGGGACAAATCAAGGACCTAATGTTGCCGCGAATCCTTTACCAAACCATACAGAACCAGA
*
1402580 TGCAAACATGATTGGCATTGAGAATAAATATAAAGTTAAGATAAGCATAGAGGAAGTAAGGATGC
131 TGCAAACATGATTGGCATCGAGAATAAATATAAAGTTAAGATAAGCATAGAGGAAGTAAGGATGC
* * *
1402645 CAATGTTCTTAGTTTGGGAAGCATTGAGTCAAGTCGGTTTGCTTAA-GATAGTGAAAAAGTTGAA
196 CAATGTTCTTAGTTTGGGAAGCATTGAGTCAAGTCGGATTGCTTAATG-CAGCGAAAAAGTTGAA
1402709 AGATAAGCTCGACAACTTCTATGACTTCCACACTGTTGTAGGTCATACCTTACAAACATGCAAGA
260 AGATAAGCTCGACAACTTCTATGACTTCCACACTGTTGTAGGTCATACCTTACAAACATGCAAGA
* *
1402774 AGTTTAGGGCCATGGTTTAGAGAATGATGGATGAAGGTCAGATAGAATTTTATCATGAAGCCACA
325 AGTTTAGGGCCATGGTTTAGAGAATGATGGATGAAGGCCAGATAGAATTCTATCATGAAGCCACA
* * *
1402839 CCTGCTGTCGAATCCATCAACATGATAGGCGAGAAAGCAACGCAGCCACCTTACAGGAGGAATCG
390 CCTGCTGTCGAATCCATCAACATGATAGGAGACAAAGCAATGCAGCCACCTTACAGGAGGAATCG
1402904 ACCCTTAATTCTTTTTGGCAAGTCAAGTTTTGAGGCTAGTTCTTCGACACCTACACCAATATTAG
455 ACCCTTAATTCTTTTTGGCAAGTCAAGTTTTGAGGCTAGTTCTTCGACACCTACACCAATATTAG
* *
1402969 TCGTGGAGGTACCTAAACCGTTCTCATATAAGAGCAACAAAGCAGTCCTTTAGAGGTACGAGAAT
520 TCGTGGAGGTACCTAAACCGTTCTCATATAAGAGCAACAAAGCAGTCCCTTGGAGGTACGAGAAT
* *
1403034 CACGTAGTGATAATTGGAGAACAAACTCCCTCGGCTGCTGCGATGGAACTGTCAAGGGTTAGTCA
585 CAGGTAGTGATAATTGGAGAACAAACTCCCTCGGCTGCTGTGATGGAACTGTCAAGGGTTAGTCA
1403099 CCTAACCCGTAGTGGTAGGTGTTATGCTCCCCCAATTCAAGAAAAATAGAAGGTTGATGCATTTC
650 CCTAACCCGTAGTGGTAGGTGTTATGCTCCCCCAATTCAAGAAAAATAGAAGGTTGATGCATTTC
* * *
1403164 CAAGCACCAATACCTTTCAAAAACAAGCGAAGAACCCAGAGCTTAGAAAAAGTCAAAGAAACAGT
715 CAAGCACTAGTACCTTTCAAAAACAAGCGAAGAACCCAGAGC-TAGAAAAAGTCAAAGAAACGGT
* *
1403229 GAATGAAGATGAAGCTACAGAGTTTCTCAAGTTCATCAAGCATAGTGAATATAGTATTGTGGATC
779 GAATGAAGATGAAGCTACAGAGTTTCTCAAGTTCATCAAGCACAGCGAATATAGTATTGTGGATC
* *
1403294 AACTATGCAAACAACCTGGAAAGATTTCTGTGCTCTCTTTGCTTCTTAATTCGGAGGTTCACCGA
844 AACTAAGCAAACAACCTGCAAAGATTTCTGTGCTCTCTTTGCTTCTTAATTCGGAGGTTCACCGA
*
1403359 AATGCATTGCTGAAGGTGTTAAACGAAGCATATGTACCACCCAACATCTCTAT
909 AATGCATTGCTGAAGGTGTTAAACGAAGCATATGTACCACCCAACATCTCTGT
1403412 ATGACATCAAAAGTTGCATTGCCCTTAAAAGAAAAGTGCAAAGTCTCATCGACTCGAAGGTGCTG
1 ATGACATCAAAAGTTGCATTGCCCTTAAAAGAAAAGTGCAAAGTCTCATCGACTCGAAGGTGCTG
* *
1403477 CAGTTCGAGACAAATCAAGGACCTAATGTTGCCGCGAATCCTTTACCAAACCATACAGAACTAGA
66 CAGTTCGGGACAAATCAAGGACCTAATGTTGCCGCGAATCCTTTACCAAACCATACAGAACCAGA
1403542 TGCAAACATGATTGGCATCGAGAATAAATATAAAGTTAAGATAAGCATAGAGGAAGTAAGGATGC
131 TGCAAACATGATTGGCATCGAGAATAAATATAAAGTTAAGATAAGCATAGAGGAAGTAAGGATGC
* *
1403607 CAATGTTCTTAGTTTGGGAAGCATTGAGTTAAGTCAGATTGCTTAATGCAGCGAAAAAGTTGAAA
196 CAATGTTCTTAGTTTGGGAAGCATTGAGTCAAGTCGGATTGCTTAATGCAGCGAAAAAGTTGAAA
* * ** *
1403672 GATAAGCTTGACAACTTCTGTGACTTCCACACTGTTGTAGGTCATACCTTACAAACATGTGAGGA
261 GATAAGCTCGACAACTTCTATGACTTCCACACTGTTGTAGGTCATACCTTACAAACATGCAAGAA
* *
1403737 TTTTAGGGCCATGGTTTAGAGAATGGTGGATGAAGGCCAGATAGAATTCTATCATGAAGCCACAC
326 GTTTAGGGCCATGGTTTAGAGAATGATGGATGAAGGCCAGATAGAATTCTATCATGAAGCCACAC
* *
1403802 CTGCTGTCGAATCCATCAACATGATAGGAGACAAAGCAATGTAGCCACCTTACGGGAGGAATCGA
391 CTGCTGTCGAATCCATCAACATGATAGGAGACAAAGCAATGCAGCCACCTTACAGGAGGAATCGA
* *
1403867 CCCTTAATTCTTTTTGGCAAGTCAAGTTTCGAGGCTAGTTTTTCGACACCTACACCAATATTAGT
456 CCCTTAATTCTTTTTGGCAAGTCAAGTTTTGAGGCTAGTTCTTCGACACCTACACCAATATTAGT
* * ** *
1403932 CATGGTGGTACCTAAATAGTTCTCATATAAGAGCAACAAAGTAGTCCCTTGGAGGTACGAGAATC
521 CGTGGAGGTACCTAAACCGTTCTCATATAAGAGCAACAAAGCAGTCCCTTGGAGGTACGAGAATC
* * *
1403997 AGGTAGTGATAATTGGAGAACAAGCTCCCTCGTCTGCTTTGATGGAACTGTCAAGGGTTAGTCAC
586 AGGTAGTGATAATTGGAGAACAAACTCCCTCGGCTGCTGTGATGGAACTGTCAAGGGTTAGTCAC
* * * * *
1404062 CTAACCTGTAGTTGCAGGTGTTATGC-CCCCCAATTCAAAAAAAATAGAAGGTTGATGCATCTCC
651 CTAACCCGTAGTGGTAGGTGTTATGCTCCCCCAATTCAAGAAAAATAGAAGGTTGATGCATTTCC
* * *
1404126 AAGCACTAGTACCTTTCAAAAACAAGCGAAGAACCTAGAGCTAGAAAAAGTCAGAGAAACAGTGA
716 AAGCACTAGTACCTTTCAAAAACAAGCGAAGAACCCAGAGCTAGAAAAAGTCAAAGAAACGGTGA
*
1404191 ATGAAGATGAGGCTACAGAGTTTCTCAAGTTCATCAAGCACAGCGAATATAGTATTGTGGATCAA
781 ATGAAGATGAAGCTACAGAGTTTCTCAAGTTCATCAAGCACAGCGAATATAGTATTGTGGATCAA
* * * * *
1404256 CTAAGCAAAGAACCTACAAAGATTTCTGTG--CTCTTTGCTTTTTAATTCAGAGGTTCATCGAAA
846 CTAAGCAAACAACCTGCAAAGATTTCTGTGCTCTCTTTGCTTCTTAATTCGGAGGTTCACCGAAA
*
1404319 TGCATTGCTAAAGGTGTTAAACGAAGCATATGTACCAC
911 TGCATTGCTGAAGGTGTTAAACGAAGCATATGTACCAC
1404357 TTGACGTCTC
Statistics
Matches: 3624, Mismatches: 196, Indels: 21
0.94 0.05 0.01
Matches are distributed among these distances:
958 67 0.02
960 1012 0.28
961 787 0.22
962 1757 0.48
963 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (961 bp):
ATGACATCAAAAGTTGCATTGCCCTTAAAAGAAAAGTGCAAAGTCTCATCGACTCGAAGGTGCTG
CAGTTCGGGACAAATCAAGGACCTAATGTTGCCGCGAATCCTTTACCAAACCATACAGAACCAGA
TGCAAACATGATTGGCATCGAGAATAAATATAAAGTTAAGATAAGCATAGAGGAAGTAAGGATGC
CAATGTTCTTAGTTTGGGAAGCATTGAGTCAAGTCGGATTGCTTAATGCAGCGAAAAAGTTGAAA
GATAAGCTCGACAACTTCTATGACTTCCACACTGTTGTAGGTCATACCTTACAAACATGCAAGAA
GTTTAGGGCCATGGTTTAGAGAATGATGGATGAAGGCCAGATAGAATTCTATCATGAAGCCACAC
CTGCTGTCGAATCCATCAACATGATAGGAGACAAAGCAATGCAGCCACCTTACAGGAGGAATCGA
CCCTTAATTCTTTTTGGCAAGTCAAGTTTTGAGGCTAGTTCTTCGACACCTACACCAATATTAGT
CGTGGAGGTACCTAAACCGTTCTCATATAAGAGCAACAAAGCAGTCCCTTGGAGGTACGAGAATC
AGGTAGTGATAATTGGAGAACAAACTCCCTCGGCTGCTGTGATGGAACTGTCAAGGGTTAGTCAC
CTAACCCGTAGTGGTAGGTGTTATGCTCCCCCAATTCAAGAAAAATAGAAGGTTGATGCATTTCC
AAGCACTAGTACCTTTCAAAAACAAGCGAAGAACCCAGAGCTAGAAAAAGTCAAAGAAACGGTGA
ATGAAGATGAAGCTACAGAGTTTCTCAAGTTCATCAAGCACAGCGAATATAGTATTGTGGATCAA
CTAAGCAAACAACCTGCAAAGATTTCTGTGCTCTCTTTGCTTCTTAATTCGGAGGTTCACCGAAA
TGCATTGCTGAAGGTGTTAAACGAAGCATATGTACCACCCAACATCTCTGT
Found at i:1408674 original size:20 final size:20
Alignment explanation
Indices: 1408649--1408695 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1408639 GAGTCTTGAC
*
1408649 ACATTCTTCAATGTATCGAT
1 ACATTCTTCAATATATCGAT
*
1408669 ACATTCTTTAATATATCGAT
1 ACATTCTTCAATATATCGAT
1408689 ACATTCT
1 ACATTCT
1408696 GTCTTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (20 bp):
ACATTCTTCAATATATCGAT
Found at i:1408735 original size:20 final size:20
Alignment explanation
Indices: 1408710--1408762 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1408700 TTTTTCCTAG
*
1408710 ATGTATTAATACATTTTTCA
1 ATGTATCAATACATTTTTCA
1408730 ATGTATCAATACATTTTTCA
1 ATGTATCAATACATTTTTCA
*
1408750 ATGTATCGATACA
1 ATGTATCAATACA
1408763 ACTAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (20 bp):
ATGTATCAATACATTTTTCA
Found at i:1409661 original size:20 final size:22
Alignment explanation
Indices: 1409621--1409661 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1409611 TAGCCTTTGA
*
1409621 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
1409643 CCATGCA-TTTTTAAC-ATGT
1 CCATGCATTTTTTAACTATGT
1409662 CTAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:1417163 original size:20 final size:20
Alignment explanation
Indices: 1417138--1417188 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1417128 ACCCTTAAAA
1417138 GTATCGATACACAATT-CAAT
1 GTATCGATACA-AATTGCAAT
**
1417158 GTATCGATACATGTTGCAAT
1 GTATCGATACAAATTGCAAT
1417178 GTATCGATACA
1 GTATCGATACA
1417189 TGAAAAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
GTATCGATACAAATTGCAAT
Found at i:1417278 original size:13 final size:13
Alignment explanation
Indices: 1417260--1417285 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1417250 TACACAAAGT
1417260 ATGTATCGATACA
1 ATGTATCGATACA
1417273 ATGTATCGATACA
1 ATGTATCGATACA
1417286 CAAAAATATT
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:1417283 original size:32 final size:34
Alignment explanation
Indices: 1417242--1417306 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
1417232 TAGCCAAACT
*
1417242 TGTATCGATACAC-AAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAATATTGTATCGATACAA
1417274 TGTATCGATACACAAAAATATTGTATCGATACA
1 TGTATCGATACACAAAAATATTGTATCGATACA
1417307 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 5 0.17
34 12 0.40
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (34 bp):
TGTATCGATACACAAAAATATTGTATCGATACAA
Found at i:1421373 original size:15 final size:15
Alignment explanation
Indices: 1421353--1421383 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1421343 TAAAAATATC
*
1421353 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1421368 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1421383 C
1 C
1421384 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1423482 original size:13 final size:13
Alignment explanation
Indices: 1423464--1423501 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1423454 CATTTTTCTT
1423464 TGTATCGATACAA
1 TGTATCGATACAA
*
1423477 TGTATCGATACAC
1 TGTATCGATACAA
1423490 TGTATCGATACA
1 TGTATCGATACA
1423502 GGGGGATTAT
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:1425919 original size:20 final size:20
Alignment explanation
Indices: 1425894--1425944 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1425884 ACCCTTAAAA
1425894 GTATCGATACACAATT-CAAT
1 GTATCGATACA-AATTGCAAT
**
1425914 GTATCGATACATGTTGCAAT
1 GTATCGATACAAATTGCAAT
1425934 GTATCGATACA
1 GTATCGATACA
1425945 TGAAAAAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
GTATCGATACAAATTGCAAT
Found at i:1426034 original size:13 final size:13
Alignment explanation
Indices: 1426016--1426041 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1426006 TACACAAAGT
1426016 ATGTATCGATACA
1 ATGTATCGATACA
1426029 ATGTATCGATACA
1 ATGTATCGATACA
1426042 CAAAAACATT
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:1426060 original size:34 final size:32
Alignment explanation
Indices: 1425998--1426062 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1425988 TAGCCAAACT
**
1425998 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAACATGTATCGATACAA
1426030 TGTATCGATACACAAAAACATTGTATCGATACA
1 TGTATCGATACAC-AAAACA-TGTATCGATACA
1426063 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAACATGTATCGATACAA
Found at i:1430102 original size:23 final size:23
Alignment explanation
Indices: 1430053--1430102 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1430043 CACTAAATTT
* *
1430053 TTAAATAATAATAATTAATTAAT
1 TTAAATAAAAATAATTAATTAAA
*
1430076 TTAAATAAAAATATTTTAA-TAAA
1 TTAAATAAAAATA-ATTAATTAAA
1430099 TTAA
1 TTAA
1430103 TTTCAAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAAATAAAAATAATTAATTAAA
Found at i:1431641 original size:2 final size:2
Alignment explanation
Indices: 1431629--1431662 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1431619 AACCTATACT
*
1431629 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1431663 CACATTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1431764 original size:3 final size:3
Alignment explanation
Indices: 1431753--1431806 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
1431743 TTCAAGACCC
* * * *
1431753 TCT TTT TCT TCT TCT TCC TCT TCT TCT TCG TCT TCT TCT TC- CCT TGCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT
1431801 TCT TCT
1 TCT TCT
1431807 CAGCAAGCCT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 1 0.02
3 37 0.90
4 3 0.07
ACGTcount: A:0.00, C:0.35, G:0.04, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:1431768 original size:12 final size:12
Alignment explanation
Indices: 1431759--1431805 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
1431749 ACCCTCTTTT
1431759 TCTTCTTCTTCC
1 TCTTCTTCTTCC
*
1431771 TCTTCTTCTTCG
1 TCTTCTTCTTCC
1431783 TCTTCTTCTTCC
1 TCTTCTTCTTCC
1431795 -CTTGCTTCTTC
1 TCTT-CTTCTTC
1431806 TCAGCAAGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 3 0.09
12 29 0.91
ACGTcount: A:0.00, C:0.38, G:0.04, T:0.57
Consensus pattern (12 bp):
TCTTCTTCTTCC
Found at i:1432802 original size:24 final size:24
Alignment explanation
Indices: 1432774--1432826 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1432764 ACGTTTATTC
1432774 ATATATATT-TATAATATAAAAATA
1 ATATATATTATATAAT-TAAAAATA
*
1432798 ATATATATTATATAATTAAAAATT
1 ATATATATTATATAATTAAAAATA
1432822 ATATA
1 ATATA
1432827 GGATTAAGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATATATTATATAATTAAAAATA
Found at i:1432832 original size:25 final size:25
Alignment explanation
Indices: 1432774--1432832 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
1432764 ACGTTTATTC
*
1432774 ATATATATT-TATAATATAAAAATA
1 ATATAGATTATATAATATAAAAATA
* *
1432798 ATATATATTATATAAT-TAAAAATT
1 ATATAGATTATATAATATAAAAATA
1432822 ATATAGGATTA
1 ATATA-GATTA
1432833 AGTCAAGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 21 0.68
25 10 0.32
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
ATATAGATTATATAATATAAAAATA
Found at i:1433306 original size:112 final size:110
Alignment explanation
Indices: 1433152--1433402 Score: 276
Period size: 112 Copynumber: 2.3 Consensus size: 110
1433142 ACACTAATGC
* * * *
1433152 ATATAATGAGTTTGTTTTAGATACACTAACGCTTGAGTTTTTTAATTTTA-AATGTAGGATTAAT
1 ATATAATGAGTTTGTTTTTGATACACTGACGCTTGAGGTTTTTAATTTTACAA-CTAGGATTAAT
* * * * *
1433216 ACTGTC-A-CATGTGTTTTTTGAATTAGTTTTTTAAAATTTTTTTTAGAT
65 A--GACAACCACGAGTTTTTTGAATTAGTTTTTTAAAA--ATTTTTAAAT
* * **
1433264 GTATAATGAGTTTGTTTTTGACACACTGTTG-TTGGAGGTTTTTAATTTTACAACTAGGATTAAT
1 ATATAATGAGTTTGTTTTTGATACACTGACGCTT-GAGGTTTTTAATTTTACAACTAGGATTAAT
*
1433328 AGACAACCACGAGTTTTTTTAATTAGTTTTTTAAAAATTTTTAAAT
65 AGACAACCACGAGTTTTTTGAATTAGTTTTTTAAAAATTTTTAAAT
* *
1433374 AAATAATGGGTTTGTTTTTGATACACTGA
1 ATATAATGAGTTTGTTTTTGATACACTGA
1433403 AGATGGAATT
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
110 34 0.29
111 3 0.03
112 77 0.66
113 2 0.02
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (110 bp):
ATATAATGAGTTTGTTTTTGATACACTGACGCTTGAGGTTTTTAATTTTACAACTAGGATTAATA
GACAACCACGAGTTTTTTGAATTAGTTTTTTAAAAATTTTTAAAT
Found at i:1435339 original size:2 final size:2
Alignment explanation
Indices: 1435334--1435365 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1435324 ATTTTTTTTT
1435334 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1435366 AATATATGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1438738 original size:2 final size:2
Alignment explanation
Indices: 1438731--1438768 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1438721 TTCCTCAAAA
1438731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1438769 TCTTCTTTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1439621 original size:2 final size:2
Alignment explanation
Indices: 1439614--1439643 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1439604 GTTGGTGCAA
1439614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1439644 TAGTTGAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1440333 original size:17 final size:17
Alignment explanation
Indices: 1440311--1440343 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1440301 TTCAATAAAC
1440311 ATATTAATTT-CAAAATA
1 ATATT-ATTTACAAAATA
1440328 ATATTATTTACAAAAT
1 ATATTATTTACAAAAT
1440344 CAGGTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTATTTACAAAATA
Found at i:1440491 original size:38 final size:37
Alignment explanation
Indices: 1440449--1440520 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
1440439 CATAAGTTAG
*
1440449 AACAAAAACTACTATTCTAATCCGGTGGCACGGTTCAA
1 AACAAAAACTACTATTCTAA-CCGATGGCACGGTTCAA
* * *
1440487 AACAAAAATTACTATTTTTACCGATGGCACGGTT
1 AACAAAAACTACTATTCTAACCGATGGCACGGTT
1440521 GGAACAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 13 0.43
38 17 0.57
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (37 bp):
AACAAAAACTACTATTCTAACCGATGGCACGGTTCAA
Found at i:1440552 original size:37 final size:38
Alignment explanation
Indices: 1440447--1440552 Score: 119
Period size: 37 Copynumber: 2.8 Consensus size: 38
1440437 GGCATAAGTT
* *
1440447 AGAACAAAAA-CTACTATTCTAATCCGGTGGCACGGTTC
1 AGAACAAAAATC-ACTATTTTTATCCGGTGGCACGGTTC
* * *
1440485 AAAACAAAAATTACTATTTTTA-CCGATGGCACGGTT-
1 AGAACAAAAATCACTATTTTTATCCGGTGGCACGGTTC
* *
1440521 GGAACAAAAATCACTATTTTTATTCGGTGGCA
1 AGAACAAAAATCACTATTTTTATCCGGTGGCA
1440553 TAGTAAAACT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
36 19 0.34
37 20 0.36
38 17 0.30
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (38 bp):
AGAACAAAAATCACTATTTTTATCCGGTGGCACGGTTC
Found at i:1441446 original size:14 final size:15
Alignment explanation
Indices: 1441427--1441455 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1441417 TTATGACTAG
1441427 AAAATA-ATTTATTA
1 AAAATATATTTATTA
1441441 AAAATATATTTATTA
1 AAAATATATTTATTA
1441456 TGTCATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATATATTTATTA
Found at i:1446322 original size:37 final size:37
Alignment explanation
Indices: 1446281--1446392 Score: 129
Period size: 37 Copynumber: 3.1 Consensus size: 37
1446271 CTGTAGCATA
*
1446281 GGTTAGAACAAAAACCACTATTCTAATCCGGTGGCAC
1 GGTTAGAACAAAAACCACTATTCTTATCCGGTGGCAC
* * * *
1446318 GGTTA-AAAAAAAACTACTATTCTTA-CCGATGGCATA
1 GGTTAGAACAAAAACCACTATTCTTATCCGGTGGCA-C
* * *
1446354 GGTTGGAACAAAAATCACTATTCTTATCCAGTGGCAC
1 GGTTAGAACAAAAACCACTATTCTTATCCGGTGGCAC
1446391 GG
1 GG
1446393 CAAAAACTAC
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
35 8 0.13
36 21 0.35
37 24 0.40
38 7 0.12
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (37 bp):
GGTTAGAACAAAAACCACTATTCTTATCCGGTGGCAC
Done.