Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold61
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: 1437555
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 9 of 10
Found at i:1262938 original size:21 final size:21
Alignment explanation
Indices: 1262912--1262964 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1262902 GTGGCATTTT
*
1262912 TTTCATCCAAAAAATGCATTC-
1 TTTCATCCAAAAAATACA-TCA
**
1262933 TTTCATCCAATCAATACATCA
1 TTTCATCCAAAAAATACATCA
1262954 TTTCATCCAAA
1 TTTCATCCAAA
1262965 TATACCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (21 bp):
TTTCATCCAAAAAATACATCA
Found at i:1267554 original size:29 final size:29
Alignment explanation
Indices: 1267500--1267555 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
1267490 TGAAAGAGTT
* * *
1267500 AAAAATAATTAATTTAAAATATTTTAAGA
1 AAAAATAATAAAATTAAAATAGTTTAAGA
1267529 AAAAATGAATAAAATTAAAAT-GTTTAA
1 AAAAAT-AATAAAATTAAAATAGTTTAA
1267556 AGGTTGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 11 0.48
30 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAAATAATAAAATTAAAATAGTTTAAGA
Found at i:1269196 original size:16 final size:16
Alignment explanation
Indices: 1269175--1269206 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1269165 AATTAAAATA
*
1269175 TAATTTAATAATAATT
1 TAATTTAAAAATAATT
1269191 TAATTTAAAAATAATT
1 TAATTTAAAAATAATT
1269207 AAAGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTTAAAAATAATT
Found at i:1271051 original size:5 final size:5
Alignment explanation
Indices: 1271043--1271080 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
1271033 GTACAAAACA
* *
1271043 AAATG AAATG AAATG AAATG AAACG AAATG AAACG AAA
1 AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAA
1271081 CAAAACAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.63, C:0.05, G:0.18, T:0.13
Consensus pattern (5 bp):
AAATG
Found at i:1271991 original size:19 final size:19
Alignment explanation
Indices: 1271955--1271994 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1271945 AAAGGGGTGG
**
1271955 TTGCCCAAACCTTTCATTA
1 TTGCCCAAACCTAGCATTA
*
1271974 TTGCCCAAAGCTAGCATTA
1 TTGCCCAAACCTAGCATTA
1271993 TT
1 TT
1271995 TTCCACATCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.35
Consensus pattern (19 bp):
TTGCCCAAACCTAGCATTA
Found at i:1282305 original size:24 final size:24
Alignment explanation
Indices: 1282272--1282318 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1282262 GTATGGAACA
*
1282272 ATTATGGTATTTGCTTATTCCACG
1 ATTATAGTATTTGCTTATTCCACG
1282296 ATTATAGTATTTGCTTATTCCAC
1 ATTATAGTATTTGCTTATTCCAC
1282319 CCCAGCTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (24 bp):
ATTATAGTATTTGCTTATTCCACG
Found at i:1288149 original size:52 final size:52
Alignment explanation
Indices: 1288000--1288128 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1287990 CGAAATTTGA
*
1288000 AAATTTGACTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
1288052 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1288104 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1288129 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:1288195 original size:19 final size:20
Alignment explanation
Indices: 1288171--1288223 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
1288161 TAGCTTAAAT
*
1288171 TGTATCGATACAAAAC-TTC
1 TGTATCGATACAAAACTTTA
*
1288190 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAACTTTA
1288210 TGTATCGATACAAA
1 TGTATCGATACAAA
1288224 TCGTTGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (20 bp):
TGTATCGATACAAAACTTTA
Found at i:1289029 original size:48 final size:48
Alignment explanation
Indices: 1288965--1289302 Score: 390
Period size: 48 Copynumber: 6.9 Consensus size: 48
1288955 GTTAGACTTG
* * * *
1288965 AAGGTGACAATGTGCTGATTCAAGGCCAGCGACACTGGTCTTAAAGAC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAC
* * * * **
1289013 AAGGTGCCAATTTGCTGATTCAAGGCCAGCGATATTGGGCTTGAAGGT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAC
* * * * *
1289061 GAGGTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-C
* * *
1289110 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA---GAC
* *
1289161 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-C
* *
1289211 AA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAC
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAC
* * *
1289258 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA
1289303 AGAAGACGCC
Statistics
Matches: 248, Mismatches: 35, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
47 2 0.01
48 159 0.64
49 42 0.17
52 45 0.18
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (48 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAC
Found at i:1289229 original size:149 final size:145
Alignment explanation
Indices: 1288963--1289302 Score: 493
Period size: 149 Copynumber: 2.3 Consensus size: 145
1288953 CAGTTAGACT
* * * * * *
1288963 TGAAGGTGACAATGTGCTGATTCAAGGCCAGCGACACTGGTCTTAAAGACAAGGTGCCAATTTGC
1 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAGGTGCCAATATGC
* * * *
1289028 TGATTCAAGGCCAGCGATATTGGGCTTGAAGGTGAGGTACCAATGTGCTGATTCAAGGCCAGCTA
66 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTACCAATGTGCTGATTCAAGGCCAGCTA
1289093 CATTGGACTTAAAGA
131 CATTGGACTTAAAGA
* *
1289108 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAAAGGTGCCAAT
1 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA---GAC-AAGGTGCCAAT
*
1289173 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTGCCAATGTGCTGATTCAAGGCCA
62 ATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTACCAATGTGCTGATTCAAGGCCA
1289238 GCTACATTGGACTTAAAGA
127 GCTACATTGGACTTAAAGA
* * *
1289257 -CAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1289303 AGAAGACGCC
Statistics
Matches: 174, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
145 41 0.24
148 44 0.25
149 89 0.51
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (145 bp):
TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGACAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGTACCAATGTGCTGATTCAAGGCCAGCTA
CATTGGACTTAAAGA
Found at i:1289379 original size:28 final size:28
Alignment explanation
Indices: 1289322--1289469 Score: 174
Period size: 28 Copynumber: 5.2 Consensus size: 28
1289312 CACCAACTTG
*
1289322 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTT-AAAGG-TTGCCACT-GACT
* *
1289351 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
1289379 TGTGGGCTTTTAAAGATTGCTACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
1289407 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
1289435 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1289465 TGTGG
1 TGTGG
1289470 TCTTAAAAGG
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
27 3 0.03
28 70 0.67
29 11 0.11
30 20 0.19
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.36
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:1289476 original size:84 final size:85
Alignment explanation
Indices: 1289322--1289476 Score: 194
Period size: 84 Copynumber: 1.8 Consensus size: 85
1289312 CACCAACTTG
* * *
1289322 TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGGGCTTTTGAAGGGTGCCACTAACTTGTGGGCT
*
1289387 TTTAAAGATTGCTACTGACT
66 CTTAAAGATTGCTACTGACT
*
1289407 TGTGGGCTTTT-AAAGG-TTGCCA-CTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGT-
1 TGTGGGCTTTTGAAAGGTTTG-CATC-AACTTGTGGGCTTTTG--AAGGGTGCCACTAACTTGTG
1289468 GG-TCTTAAA
62 GGCTCTTAAA
1289477 AGGAAAAAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
83 4 0.07
84 27 0.44
85 13 0.21
86 17 0.28
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.37
Consensus pattern (85 bp):
TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGGGCTTTTGAAGGGTGCCACTAACTTGTGGGCT
CTTAAAGATTGCTACTGACT
Found at i:1289502 original size:34 final size:34
Alignment explanation
Indices: 1289464--1289538 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 34
1289454 TGCCACTAAC
* *
1289464 TTGTGGTCTTA-AAAGGAAAAAGAGTGCTACGGAG
1 TTGTGG-CTTACAAAAGAAAAAGAGTGCCACGGAG
1289498 TTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAG
1 TTGTG-GCTTACAAAAGAAAAAGAGTGCCACGGAG
1289533 TTGTGG
1 TTGTGG
1289539 ACTTTGGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 10 0.27
35 27 0.73
ACGTcount: A:0.35, C:0.11, G:0.32, T:0.23
Consensus pattern (34 bp):
TTGTGGCTTACAAAAGAAAAAGAGTGCCACGGAG
Found at i:1289651 original size:29 final size:29
Alignment explanation
Indices: 1289368--1289687 Score: 191
Period size: 29 Copynumber: 10.7 Consensus size: 29
1289358 TTTTGAAGGT
*
1289368 TGCCACTGACTTGTGGGCTTT--TAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAAAGA
* * * *
1289395 TTGCTACTGACTTGTGGGCTTT-TAAAGGT
1 -TGCCACTGACTTGTGGGCTTTGAAAAAGA
* *
1289424 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGC-TTTGAAAAAGA
* * *
1289454 TGCCACTAACTTGTGGTCTTAAAAGGAAAAAGA
1 TGCCACTGACTTGTGGGCTT----TGAAAAAGA
* * * * *
1289487 GTGCTACGGAGTTGTGAGCTTACAAAAGAAAAAGA
1 -TGCCACTGACTTGTGGGCTT-----TGAAAAAGA
* * * * *
1289522 GTGCCACGGAGTTGTGGACTTTGGAAAATA
1 -TGCCACTGACTTGTGGGCTTTGAAAAAGA
* * * * *
1289552 TACCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTT-TGAAAAAGA
* * * *
1289582 TGCCATTGATTTGTGGGCTTTG--AAGGT
1 TGCCACTGACTTGTGGGCTTTGAAAAAGA
* *
1289609 TGCCACTGATTTGTGGACTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAAAGA
1289638 TGCCACTGACTTGTGGGCTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAAAGA
*
1289667 TGCCACTAACTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTT
1289688 TGAAGGGTGA
Statistics
Matches: 232, Mismatches: 48, Indels: 23
0.77 0.16 0.08
Matches are distributed among these distances:
27 24 0.10
28 37 0.16
29 75 0.32
30 47 0.20
33 6 0.03
34 14 0.06
35 29 0.12
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGAAAAAGA
Found at i:1289690 original size:86 final size:86
Alignment explanation
Indices: 1289523--1289693 Score: 218
Period size: 86 Copynumber: 2.0 Consensus size: 86
1289513 AGAAAAAGAG
* * * * *
1289523 TGCCACGGAGTTGTGGACTTTGGAAAATATACCACCGACTTGTGGGCTTCGGAAAAGGGTGCCAT
1 TGCCACGGAGTTGTGGACTTTGAAAAAGATACCACCGACTTGTGGGCTTCGGAAAAAGATGCCAC
* *
1289588 TGATTTGTGGGCTTTGAAGGT
66 TAACTTGTGGGCTTTGAAGGT
* * * * *
1289609 TGCCACTGATTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTT-TGAAAAAGATGCCAC
1 TGCCACGGAGTTGTGGACTTTGAAAAAGATACCACCGACTTGTGGGCTTCGGAAAAAGATGCCAC
1289673 TAACTTGTGGGCTTTTGAAGG
66 TAACTTGTGGGC-TTTGAAGG
1289694 GTGAGGAATG
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
85 21 0.29
86 51 0.71
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (86 bp):
TGCCACGGAGTTGTGGACTTTGAAAAAGATACCACCGACTTGTGGGCTTCGGAAAAAGATGCCAC
TAACTTGTGGGCTTTGAAGGT
Found at i:1291161 original size:15 final size:15
Alignment explanation
Indices: 1291141--1291189 Score: 73
Period size: 14 Copynumber: 3.3 Consensus size: 15
1291131 TGTTGTTTTG
1291141 TTTTTTTTTTTG-TT
1 TTTTTTTTTTTGTTT
*
1291155 TTTTTTTGTTTGTTT
1 TTTTTTTTTTTGTTT
1291170 TTTTTTTGTTTTGTTT
1 TTTTTTT-TTTTGTTT
1291186 TTTT
1 TTTT
1291190 CTATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 11 0.35
15 9 0.29
16 11 0.35
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (15 bp):
TTTTTTTTTTTGTTT
Found at i:1291173 original size:26 final size:26
Alignment explanation
Indices: 1291125--1291187 Score: 92
Period size: 25 Copynumber: 2.4 Consensus size: 26
1291115 TCTGGACCCT
*
1291125 TTTTGTTGTTGTTTTGTTTTTTTTTTTG
1 TTTTGTTTTTG-TTTG-TTTTTTTTTTG
1291153 TTTT-TTTTTGTTTGTTTTTTTTTTG
1 TTTTGTTTTTGTTTGTTTTTTTTTTG
1291178 TTTTGTTTTT
1 TTTTGTTTTT
1291188 TTCTATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 15 0.45
26 9 0.27
27 5 0.15
28 4 0.12
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (26 bp):
TTTTGTTTTTGTTTGTTTTTTTTTTG
Found at i:1291177 original size:37 final size:38
Alignment explanation
Indices: 1291126--1291199 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 38
1291116 CTGGACCCTT
* *
1291126 TTTGTTGTTGTTTTGTTTT-TTTTTTTGTTTTTTTTTG
1 TTTGTTGTTGTTTTGTTTTGTTTTTTTCTATTTTTTTG
* *
1291163 TTTGTTTTTTTTTTGTTTTGTTTTTTTCTATTTTTTT
1 TTTGTTGTTGTTTTGTTTTGTTTTTTTCTATTTTTTT
1291200 ATTATTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 17 0.53
38 15 0.47
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.85
Consensus pattern (38 bp):
TTTGTTGTTGTTTTGTTTTGTTTTTTTCTATTTTTTTG
Found at i:1291186 original size:11 final size:11
Alignment explanation
Indices: 1291125--1291187 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
1291115 TCTGGACCCT
*
1291125 TTTTGTTGTTG
1 TTTTGTTTTTG
*
1291136 TTTTGTTTTTTT
1 TTTTG-TTTTTG
1291148 TTTTGTTTTT-
1 TTTTGTTTTTG
1291158 TTTTG--TTTG
1 TTTTGTTTTTG
*
1291167 TTTTTTTTTTG
1 TTTTGTTTTTG
1291178 TTTTGTTTTT
1 TTTTGTTTTT
1291188 TTCTATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 3 0.07
9 4 0.09
10 5 0.11
11 23 0.52
12 9 0.20
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:1291189 original size:30 final size:30
Alignment explanation
Indices: 1291124--1291189 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1291114 ATCTGGACCC
* *
1291124 TTTTTGTTGTTGTTTTGTTTTTTTTTTTGT
1 TTTTTTTTGTTGTTTTGTTTTTTGTTTTGT
1291154 TTTTTTTTGTTTGTTTT-TTTTTTGTTTTGT
1 TTTTTTTTG-TTGTTTTGTTTTTTGTTTTGT
1291184 TTTTTT
1 TTTTTT
1291190 CTATTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (30 bp):
TTTTTTTTGTTGTTTTGTTTTTTGTTTTGT
Found at i:1291196 original size:15 final size:13
Alignment explanation
Indices: 1291136--1291199 Score: 71
Period size: 14 Copynumber: 4.9 Consensus size: 13
1291126 TTTGTTGTTG
1291136 TTTTG-TTTTTTT
1 TTTTGTTTTTTTT
1291148 TTTTGTTTTTTTT
1 TTTTGTTTTTTTT
1291161 TGTTTG--TTTTTT
1 T-TTTGTTTTTTTT
1291173 TTTTGTTTTGTTTT
1 TTTTGTTTT-TTTT
*
1291187 TTTCTATTTTTTT
1 TTT-TGTTTTTTT
1291200 ATTATTATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
11 4 0.09
12 12 0.27
13 10 0.22
14 14 0.31
15 5 0.11
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (13 bp):
TTTTGTTTTTTTT
Found at i:1291196 original size:25 final size:25
Alignment explanation
Indices: 1291124--1291199 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
1291114 ATCTGGACCC
1291124 TTTTTGTTGTTGTTTTG--T-TTTTT
1 TTTTTGTT-TTGTTTTGTTTCTTTTT
* *
1291147 TTTTTGTTTTTTTTTGTTTGTTTTT
1 TTTTTGTTTTGTTTTGTTTCTTTTT
*
1291172 TTTTTGTTTTGTTTT-TTTCTATTT
1 TTTTTGTTTTGTTTTGTTTCTTTTT
1291196 TTTT
1 TTTT
1291200 ATTATTATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 7 0.15
23 8 0.17
24 12 0.26
25 19 0.41
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.86
Consensus pattern (25 bp):
TTTTTGTTTTGTTTTGTTTCTTTTT
Found at i:1291219 original size:1 final size:1
Alignment explanation
Indices: 1291136--1291199 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
1291126 TTTGTTGTTG
* * * * * * * *
1291136 TTTTGTTTTTTTTTTTGTTTTTTTTTGTTTGTTTTTTTTTTGTTTTGTTTTTTTCTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1291200 ATTATTATTA
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:1305087 original size:52 final size:52
Alignment explanation
Indices: 1305009--1305141 Score: 230
Period size: 52 Copynumber: 2.6 Consensus size: 52
1304999 CGAAATTTGA
* * *
1305009 AAATTTGACTGCATGTATCAATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1305061 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
*
1305113 AAATTTGCCTGCATGTATCGAAACATTTT
1 AAATTTGCCTGCATGTATCGATACATTTT
1305142 TTTTGGCAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 77 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
Found at i:1305200 original size:32 final size:33
Alignment explanation
Indices: 1305161--1305225 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
1305151 TAGCTTAAAT
*
1305161 TGTATCGATACAAAAC-TTATGTATTGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
*
1305193 TGTATCGATACAATACTTTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
1305226 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCGATACAA
Found at i:1310848 original size:23 final size:23
Alignment explanation
Indices: 1310809--1310853 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1310799 GATTTATAAA
* *
1310809 ATTAAAAAAATTATTATTAATAT
1 ATTAAAAAAAATATTATAAATAT
1310832 ATTAAAAATAAAT-TTATAAATA
1 ATTAAAAA-AAATATTATAAATA
1310854 AAAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTAAAAAAAATATTATAAATAT
Found at i:1310866 original size:16 final size:18
Alignment explanation
Indices: 1310834--1310869 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
1310824 ATTAATATAT
1310834 TAAAAATAAATTTATAAA
1 TAAAAATAAATTTATAAA
1310852 TAAAAAT-AA-TTATAAA
1 TAAAAATAAATTTATAAA
1310868 TA
1 TA
1310870 TATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATAAATTTATAAA
Found at i:1310890 original size:39 final size:39
Alignment explanation
Indices: 1310814--1310890 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 39
1310804 ATAAAATTAA
* * **
1310814 AAAAATTATTATTAATATATTAAAAATAAATTTATAAAT
1 AAAAATAATTATAAATATATTAAAAATAAATAAATAAAT
* * *
1310853 AAAAATAATTATAAATATATTTAAATTGAATAAATAAA
1 AAAAATAATTATAAATATATTAAAAATAAATAAATAAA
1310891 ATTATATTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (39 bp):
AAAAATAATTATAAATATATTAAAAATAAATAAATAAAT
Found at i:1310977 original size:22 final size:21
Alignment explanation
Indices: 1310952--1311010 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1310942 AATATATTAA
*
1310952 AATATTAAAATTTAATTTTTAT
1 AATATTAAAA-TAAATTTTTAT
*
1310974 AATATTTAAATAAATTTTTAT
1 AATATTAAAATAAATTTTTAT
1310995 -AT-TT-AAATAATATTTT
1 AATATTAAAATAA-ATTTT
1311011 AAAATAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 6 0.18
19 7 0.21
20 2 0.06
21 10 0.29
22 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATTAAAATAAATTTTTAT
Found at i:1310991 original size:21 final size:19
Alignment explanation
Indices: 1310965--1311010 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 19
1310955 ATTAAAATTT
1310965 AATTTTTATAATATTTAAATA
1 AATTTTT-T-ATATTTAAATA
1310986 AA-TTTTTATATTTAAATA
1 AATTTTTTATATTTAAATA
1311004 ATATTTT
1 A-ATTTT
1311011 AAAATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 12 0.52
19 2 0.09
20 7 0.30
21 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTTTTATATTTAAATA
Found at i:1310998 original size:18 final size:19
Alignment explanation
Indices: 1310975--1311010 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1310965 AATTTTTATA
1310975 ATATTTAAATAA-ATTTTT
1 ATATTTAAATAATATTTTT
1310993 ATATTTAAATAATATTTT
1 ATATTTAAATAATATTTT
1311011 AAAATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTAAATAATATTTTT
Found at i:1311368 original size:4 final size:4
Alignment explanation
Indices: 1311361--1311386 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1311351 ACACACACAA
1311361 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1311387 GTTTTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1311647 original size:26 final size:27
Alignment explanation
Indices: 1311617--1311670 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1311607 TTACCATTAG
* *
1311617 AATTTTAAATATTAAAAA-TAAAAATA
1 AATTTAAAATAATAAAAATTAAAAATA
1311643 AATTTAAAATAATAAAAATTTAAAAATA
1 AATTTAAAATAATAAAAA-TTAAAAATA
1311671 TAAAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
28 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AATTTAAAATAATAAAAATTAAAAATA
Found at i:1311668 original size:17 final size:17
Alignment explanation
Indices: 1311623--1311677 Score: 69
Period size: 16 Copynumber: 3.2 Consensus size: 17
1311613 TTAGAATTTT
*
1311623 AAATATTAAAAATAAAAA
1 AAAT-TTAAAAATAATAA
1311641 TAAATTT-AAAATAATAA
1 -AAATTTAAAAATAATAA
1311658 AAATTTAAAAAT-ATAA
1 AAATTTAAAAATAATAA
1311674 AAAT
1 AAAT
1311678 AATAAAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.41
17 14 0.41
18 2 0.06
19 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATTTAAAAATAATAA
Found at i:1311683 original size:17 final size:17
Alignment explanation
Indices: 1311623--1311684 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
1311613 TTAGAATTTT
*
1311623 AAATATTAAAAATAAAAA
1 AAATA-TAAAAATAATAA
*
1311641 TAAAT-TTAAAATAATAA
1 -AAATATAAAAATAATAA
*
1311658 AAATTTAAAAAT-ATAA
1 AAATATAAAAATAATAA
1311674 AAATAATAAAA
1 AAAT-ATAAAA
1311685 TTATTTTATC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
16 12 0.32
17 21 0.57
19 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATATAAAAATAATAA
Found at i:1312514 original size:18 final size:21
Alignment explanation
Indices: 1312491--1312549 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
1312481 TATGAATATC
*
1312491 ATATGA-AAAAT-TATTAA-A
1 ATATGACAAAATATATAAATA
1312509 ATATGACAAAATATATAAATA
1 ATATGACAAAATATATAAATA
1312530 ATATGATC--AATATATAAATA
1 ATATGA-CAAAATATATAAATA
1312550 CATGAACGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 6 0.17
19 5 0.14
20 17 0.47
21 7 0.19
22 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (21 bp):
ATATGACAAAATATATAAATA
Found at i:1312993 original size:21 final size:21
Alignment explanation
Indices: 1312967--1313021 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1312957 AAATATTTTA
1312967 AATATAATTATAATATAAAAT
1 AATATAATTATAATATAAAAT
* **
1312988 AATATAAATATAATATATGAT
1 AATATAATTATAATATAAAAT
1313009 AAT-TATATTATAA
1 AATATA-ATTATAA
1313022 ATTTTTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AATATAATTATAATATAAAAT
Found at i:1312997 original size:16 final size:17
Alignment explanation
Indices: 1312965--1313004 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1312955 AAAAATATTT
1312965 TAAATATAATTATAATA
1 TAAATATAATTATAATA
1312982 TAAA-ATAA-TATAA-A
1 TAAATATAATTATAATA
1312996 TATAATATA
1 TA-AATATA
1313005 TGATAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.14
15 7 0.33
16 7 0.33
17 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATATAATTATAATA
Found at i:1313914 original size:15 final size:15
Alignment explanation
Indices: 1313894--1313935 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1313884 TTTTTAAATT
1313894 ATTTTTAAATTTTAA
1 ATTTTTAAATTTTAA
*
1313909 ATTTTTATA-TTTAA
1 ATTTTTAAATTTTAA
1313923 ATTATTTTAAATT
1 A-T-TTTTAAATT
1313936 CAAGTCATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.27
15 9 0.41
16 6 0.27
17 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTTAAATTTTAA
Found at i:1321515 original size:44 final size:43
Alignment explanation
Indices: 1321440--1321610 Score: 225
Period size: 44 Copynumber: 3.9 Consensus size: 43
1321430 ATAACAACCT
* *** * *
1321440 TAATTCACCATCTAAAAACTAATAGTTAACAAAGTTGCTGACTC
1 TAATTCACCATCAAAAAACTAA-AACCAACAAACTTGCTTACTC
1321484 TAATTCACCATCTAAAAAACTAAAACCAACAAACTTGCTTACTC
1 TAATTCACCATC-AAAAAACTAAAACCAACAAACTTGCTTACTC
* * *
1321528 TAATTCACCATCCAAAAACTAATACTTAACAAACTTGCTTACTC
1 TAATTCACCATCAAAAAACTAAAAC-CAACAAACTTGCTTACTC
*
1321572 TAATTCACCATCAAAAAACTAATACCAACAAACTTGCTT
1 TAATTCACCATCAAAAAACTAAAACCAACAAACTTGCTT
1321611 TATCTATCCT
Statistics
Matches: 114, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
43 24 0.21
44 81 0.71
45 9 0.08
ACGTcount: A:0.43, C:0.25, G:0.04, T:0.27
Consensus pattern (43 bp):
TAATTCACCATCAAAAAACTAAAACCAACAAACTTGCTTACTC
Found at i:1321589 original size:88 final size:87
Alignment explanation
Indices: 1321440--1321610 Score: 288
Period size: 88 Copynumber: 2.0 Consensus size: 87
1321430 ATAACAACCT
* * *
1321440 TAATTCACCATCTAAAAACTAATAGTTAACAAAGTTGCTGACTCTAATTCACCATCTAAAAAACT
1 TAATTCACCATCCAAAAACTAATACTTAACAAACTTGCTGACTCTAATTCACCATC-AAAAAACT
1321505 AAAACCAACAAACTTGCTTACTC
65 AAAACCAACAAACTTGCTTACTC
*
1321528 TAATTCACCATCCAAAAACTAATACTTAACAAACTTGCTTACTCTAATTCACCATCAAAAAACTA
1 TAATTCACCATCCAAAAACTAATACTTAACAAACTTGCTGACTCTAATTCACCATCAAAAAACTA
*
1321593 ATACCAACAAACTTGCTT
66 AAACCAACAAACTTGCTT
1321611 TATCTATCCT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 26 0.33
88 52 0.67
ACGTcount: A:0.43, C:0.25, G:0.04, T:0.27
Consensus pattern (87 bp):
TAATTCACCATCCAAAAACTAATACTTAACAAACTTGCTGACTCTAATTCACCATCAAAAAACTA
AAACCAACAAACTTGCTTACTC
Found at i:1322610 original size:21 final size:21
Alignment explanation
Indices: 1322586--1322625 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1322576 TATTTTTATT
1322586 TAAAT-TTAATTATAAAAATTA
1 TAAATATTAA-TATAAAAATTA
1322607 TAAATATTAATATAAAAAT
1 TAAATATTAATATAAAAAT
1322626 ATTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATATAAAAATTA
Found at i:1324730 original size:16 final size:16
Alignment explanation
Indices: 1324693--1324807 Score: 85
Period size: 16 Copynumber: 7.3 Consensus size: 16
1324683 AAAAAATTTA
* *
1324693 TAAAATTAATTCAAATT
1 TAAAA-TAATTTAAACT
*
1324710 TAAAATAGTTTAAACT
1 TAAAATAATTTAAACT
* *
1324726 TAAAAGAATTTAAAACA
1 TAAAATAATTT-AAACT
* *
1324743 AAAAAT-ATTTAAATT
1 TAAAATAATTTAAACT
*
1324758 TAAAATAATTTAAAAT
1 TAAAATAATTTAAACT
* *
1324774 T--TATAATTTAAATT
1 TAAAATAATTTAAACT
*
1324788 TAAAATAATCTAAA-T
1 TAAAATAATTTAAACT
1324803 TAAAA
1 TAAAA
1324808 AAAAAATTGA
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
14 12 0.15
15 14 0.18
16 39 0.50
17 13 0.17
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.37
Consensus pattern (16 bp):
TAAAATAATTTAAACT
Found at i:1324761 original size:32 final size:33
Alignment explanation
Indices: 1324711--1324772 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
1324701 ATTCAAATTT
1324711 AAAATAGTTTAAACTTAAAAGAATTTAAAACAA
1 AAAATAGTTTAAACTTAAAAGAATTTAAAACAA
* *
1324744 AAAATA-TTTAAATTTAAAATAATTTAAAA
1 AAAATAGTTTAAACTTAAAAGAATTTAAAA
1324773 TTTATAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (33 bp):
AAAATAGTTTAAACTTAAAAGAATTTAAAACAA
Found at i:1326390 original size:2 final size:2
Alignment explanation
Indices: 1326377--1326413 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1326367 ATTTGTACCA
* *
1326377 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1326414 CATCTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1329943 original size:97 final size:96
Alignment explanation
Indices: 1329842--1330026 Score: 248
Period size: 97 Copynumber: 1.9 Consensus size: 96
1329832 ATCTTCTATA
*
1329842 ATGATAA-TTAAGGCAAAAACAAGATTTAAATCATGACAAGTTTAAAAAC-AAGTTTGGAGTATC
1 ATGATAATTTAA-GCAAAAACAAGATTTAAATCATGACAAGTTTAAAAACGAAGTTT-GAATATC
*
1329905 TCCTTGGAAAAATAGGGTTAGAGTATCCCCGATG
64 -CCTTCGAAAAATAGGGTTAGAGTATCCCCGATG
* * * **
1329939 ATGATAATTTAAGCAAAAATAAGATTTAAATCTTGATAAGTTTAAAAACGGGGTTTGAATATCCC
1 ATGATAATTTAAGCAAAAACAAGATTTAAATCATGACAAGTTTAAAAACGAAGTTTGAATATCCC
* *
1330004 TTCGAAAGATGGGGTTAGAGTAT
66 TTCGAAAAATAGGGTTAGAGTAT
1330027 TCCCATGGGT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
96 22 0.29
97 47 0.61
98 8 0.10
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (96 bp):
ATGATAATTTAAGCAAAAACAAGATTTAAATCATGACAAGTTTAAAAACGAAGTTTGAATATCCC
TTCGAAAAATAGGGTTAGAGTATCCCCGATG
Found at i:1331526 original size:52 final size:51
Alignment explanation
Indices: 1331469--1331658 Score: 192
Period size: 52 Copynumber: 3.7 Consensus size: 51
1331459 ATTTAACTAG
* *
1331469 ATGTATCGATA-AATTGAAGAATATATCGATATATTTGGGTCAAAAACTCATA
1 ATGTATCGATACAA-T-AAGAATATATCGATACATTTGGATCAAAAACTCATA
* * * * *
1331521 ATGTATCGATACAATGAAAAATGTATTGATACATTTGGAT-TAAAACT-AGA
1 ATGTATCGATACAAT-AAGAATATATCGATACATTTGGATCAAAAACTCATA
* *
1331571 ATGCATCGATACAATAAGAA-ATGCATCAATACATTTGGATCAAAAAC-CTATA
1 ATGTATCGATACAATAAGAATAT--ATCGATACATTTGGATCAAAAACTC-ATA
*
1331623 ATGTATCGATACAATAAGAAATGTATCGATACATTT
1 ATGTATCGATACAATAAG-AATATATCGATACATTT
1331659 TCTTTCCAAA
Statistics
Matches: 113, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
48 1 0.01
49 4 0.04
50 30 0.27
51 11 0.10
52 62 0.55
53 4 0.04
54 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (51 bp):
ATGTATCGATACAATAAGAATATATCGATACATTTGGATCAAAAACTCATA
Found at i:1331875 original size:2 final size:2
Alignment explanation
Indices: 1331868--1331893 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1331858 TCGTTTACTC
1331868 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
1331894 TCAATCTTAC
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:1332305 original size:3 final size:3
Alignment explanation
Indices: 1332297--1332330 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1332287 ATTCTTATAG
1332297 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1332331 TATGTAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1332707 original size:15 final size:16
Alignment explanation
Indices: 1332681--1332710 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1332671 AATAAAAGAT
1332681 AATATATAATTAAATA
1 AATATATAATTAAATA
1332697 AATATAT-ATTAAAT
1 AATATATAATTAAAT
1332711 CATAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATATAATTAAATA
Found at i:1339144 original size:20 final size:20
Alignment explanation
Indices: 1339121--1339159 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1339111 ATATCAATAC
*
1339121 ATTCACTTATGTATCGATAA
1 ATTCACCTATGTATCGATAA
1339141 ATTCACCTATGTATCGATA
1 ATTCACCTATGTATCGATA
1339160 CATCAACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
ATTCACCTATGTATCGATAA
Found at i:1339659 original size:13 final size:13
Alignment explanation
Indices: 1339624--1339668 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1339614 AAGTTTTATT
*
1339624 TTTTTACTTAA-A
1 TTTTTATTTAATA
*
1339636 TTTATTTTTTAATA
1 TTT-TTATTTAATA
1339650 TTTTTATTTAATA
1 TTTTTATTTAATA
1339663 TTTTTA
1 TTTTTA
1339669 AATATCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 3 0.11
13 21 0.75
14 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTATTTAATA
Found at i:1341486 original size:17 final size:19
Alignment explanation
Indices: 1341447--1341489 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
1341437 GGGCGTAATA
*
1341447 AAATATTTTATTTCATTTTT
1 AAATA-TTTATTTCATTTAT
1341467 AAATATTT-TTT-ATTTAT
1 AAATATTTATTTCATTTAT
1341484 AAATAT
1 AAATAT
1341490 CTTTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
18 3 0.14
19 3 0.14
20 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATATTTATTTCATTTAT
Found at i:1342144 original size:16 final size:16
Alignment explanation
Indices: 1342123--1342156 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1342113 AAATCTGAAT
*
1342123 TCAAAATAGTTCAAAC
1 TCAAAATAATTCAAAC
*
1342139 TCAAAATAATTCGAAC
1 TCAAAATAATTCAAAC
1342155 TC
1 TC
1342157 GAAAGAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (16 bp):
TCAAAATAATTCAAAC
Found at i:1343919 original size:20 final size:20
Alignment explanation
Indices: 1343896--1343933 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1343886 ATTTGTATCG
1343896 ATATACATA-AAAATGTATTA
1 ATATA-ATATAAAATGTATTA
*
1343916 ATATAATATAGAATGTAT
1 ATATAATATAAAATGTAT
1343934 CGATACATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (20 bp):
ATATAATATAAAATGTATTA
Found at i:1350096 original size:20 final size:20
Alignment explanation
Indices: 1350067--1350105 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1350057 GTTTCCAAAT
* *
1350067 TATATTGATACATTCACTAA
1 TATATCGATACATACACTAA
1350087 TATATCGATACATACACTA
1 TATATCGATACATACACTA
1350106 TATTAGGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
TATATCGATACATACACTAA
Found at i:1354899 original size:2 final size:2
Alignment explanation
Indices: 1354844--1354879 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1354834 ACAATAACTT
1354844 TA TA -A TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1354880 ACATACACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1355125 original size:21 final size:20
Alignment explanation
Indices: 1355100--1355147 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1355090 ATCATATCTC
*
1355100 ATTTATAAGTAAATAAATAAA
1 ATTTATAAAT-AATAAATAAA
* *
1355121 ATTTAAAAATAATTAATAAA
1 ATTTATAAATAATAAATAAA
*
1355141 AATTATA
1 ATTTATA
1355148 TCTTTTGTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTTATAAATAATAAATAAA
Found at i:1355227 original size:16 final size:18
Alignment explanation
Indices: 1355195--1355227 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1355185 TTTTAAAATC
1355195 ATATTTCAAATTATTTAT
1 ATATTTCAAATTATTTAT
1355213 ATATTT-AAATT-TTTA
1 ATATTTCAAATTATTTA
1355228 AAAAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTCAAATTATTTAT
Found at i:1355826 original size:64 final size:63
Alignment explanation
Indices: 1355717--1355853 Score: 195
Period size: 64 Copynumber: 2.2 Consensus size: 63
1355707 TCAAAGCAAA
*
1355717 TTTGGGTTTTTATTAATGGTAAACAAAATAAGAATCTCAGCTACCAAAAGAAAAAAAATTAGGT
1 TTTGGGTTTTTATTAATGCTAAACAAAATAAGAATCTCAGCTACCAAAAG-AAAAAAATTAGGT
* * **
1355781 TTTGGGTTTTTATTCATGCTAAAGAAAATAAGAAT-TACATTTACCAAAAGAAAAAAATTAGGT
1 TTTGGGTTTTTATTAATGCTAAACAAAATAAGAATCT-CAGCTACCAAAAGAAAAAAATTAGGT
*
1355844 TTTAGGTTTT
1 TTTGGGTTTT
1355854 AAGTGCGTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 23 0.35
64 43 0.65
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.34
Consensus pattern (63 bp):
TTTGGGTTTTTATTAATGCTAAACAAAATAAGAATCTCAGCTACCAAAAGAAAAAAATTAGGT
Found at i:1356366 original size:16 final size:16
Alignment explanation
Indices: 1356347--1356389 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1356337 CTCGAACCCG
1356347 AACTTGAAAAA-ACCTA
1 AACTT-AAAAAGACCTA
*
1356363 AACTTAAAAAGACCTG
1 AACTTAAAAAGACCTA
*
1356379 AACATAAAAAG
1 AACTTAAAAAG
1356390 GTCAAAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.58, C:0.16, G:0.09, T:0.16
Consensus pattern (16 bp):
AACTTAAAAAGACCTA
Found at i:1357173 original size:16 final size:16
Alignment explanation
Indices: 1357149--1357183 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1357139 ATAATATACA
1357149 TTTCCTTTTATTCCTT
1 TTTCCTTTTATTCCTT
* *
1357165 TTTCTTTTTATTTCTT
1 TTTCCTTTTATTCCTT
1357181 TTT
1 TTT
1357184 TTATTCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCCTTTTATTCCTT
Found at i:1358074 original size:42 final size:43
Alignment explanation
Indices: 1358027--1358111 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 43
1358017 CCCTAGGCCA
* *
1358027 AGTTTAAGAGTTTTAGTAAATCATATT-TATTTTTTTTAATTT
1 AGTTTAAGAGTTTTAGTAAATCATATTCAAATTTTTTTAATTT
* *
1358069 AGTTTAAGAGTTTTATTATATCATATTCAAATTTTTTTAATTT
1 AGTTTAAGAGTTTTAGTAAATCATATTCAAATTTTTTTAATTT
1358112 TCATTTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 25 0.66
43 13 0.34
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (43 bp):
AGTTTAAGAGTTTTAGTAAATCATATTCAAATTTTTTTAATTT
Found at i:1358696 original size:22 final size:22
Alignment explanation
Indices: 1358671--1358712 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1358661 ATTTTAAAAT
1358671 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
1358693 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
1358713 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:1361033 original size:2 final size:2
Alignment explanation
Indices: 1361026--1361060 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1361016 TGTATGAATA
1361026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1361061 ATCATGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1362148 original size:51 final size:50
Alignment explanation
Indices: 1362059--1362277 Score: 210
Period size: 52 Copynumber: 4.3 Consensus size: 50
1362049 TAGTTGGATA
*
1362059 TAAATAATAAAAAAATATTTTATATTAAATCATAAATTATTATTTAAAAAGT
1 TAAA-AATTAAAAAATATTTTATATTAAATCATAAATTATTATTTAAAAA-T
* ** *
1362111 TAAAAATTAAAAAATATTTTATATTAATTTTTGAATTATTATTTAAAAA-
1 TAAAAATTAAAAAATATTTTATATTAAATCATAAATTATTATTTAAAAAT
* * * * *
1362160 TAATAA-TAAAAAACTATTTTACATTAAATCCTAAATAACTATTTAAAAAT
1 TAAAAATTAAAAAA-TATTTTATATTAAATCATAAATTATTATTTAAAAAT
* * * *
1362210 AATAAAACTTAAAAAATATTTTATATTAAATC-TCTAGTTACTATTTAAAAATT
1 --TAAAAATTAAAAAATATTTTATATTAAATCAT-AAATTATTATTTAAAAA-T
*
1362263 TATAAAATAAAAAAA
1 TA-AAAATTAAAAAA
1362278 ATTATACTAA
Statistics
Matches: 138, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
48 7 0.05
49 33 0.24
51 43 0.31
52 47 0.34
53 8 0.06
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (50 bp):
TAAAAATTAAAAAATATTTTATATTAAATCATAAATTATTATTTAAAAAT
Found at i:1362180 original size:25 final size:24
Alignment explanation
Indices: 1362150--1362214 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 24
1362140 TTTGAATTAT
1362150 TATTTAAAAATAATAATAAAAAAC
1 TATTTAAAAATAATAATAAAAAAC
* * * ** *
1362174 TATTTTACATTAAATCCTAAATAAC
1 TATTTAAAAAT-AATAATAAAAAAC
1362199 TATTTAAAAATAATAA
1 TATTTAAAAATAATAA
1362215 AACTTAAAAA
Statistics
Matches: 29, Mismatches: 11, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
TATTTAAAAATAATAATAAAAAAC
Found at i:1362238 original size:52 final size:51
Alignment explanation
Indices: 1362068--1362277 Score: 223
Period size: 51 Copynumber: 4.1 Consensus size: 51
1362058 ATAAATAATA
* * *
1362068 AAAAAATATTTTATATTAAATCATAAATTATTATTTAAAAAGTTA-AAAATT
1 AAAAAATATTTTATATTAAATCCTAAATTACTATTTAAAAA-TAATAAAATT
* ** * *
1362119 AAAAAATATTTTATATTAATTTTTGAATTATTATTTAAAAATAAT--AA-T
1 AAAAAATATTTTATATTAAATCCTAAATTACTATTTAAAAATAATAAAATT
* *
1362167 AAAAAACTATTTTACATTAAATCCTAAATAACTATTTAAAAATAATAAAACTT
1 AAAAAA-TATTTTATATTAAATCCTAAATTACTATTTAAAAATAATAAAA-TT
* * *
1362220 AAAAAATATTTTATATTAAATCTCT-AGTTACTATTTAAAAATTTATAAAATA
1 AAAAAATATTTTATATTAAATC-CTAAATTACTATTTAAAAA-TAATAAAATT
1362272 AAAAAA
1 AAAAAA
1362278 ATTATACTAA
Statistics
Matches: 134, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
48 7 0.05
49 34 0.25
50 2 0.01
51 39 0.29
52 36 0.27
53 16 0.12
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (51 bp):
AAAAAATATTTTATATTAAATCCTAAATTACTATTTAAAAATAATAAAATT
Found at i:1362258 original size:101 final size:100
Alignment explanation
Indices: 1362061--1362261 Score: 271
Period size: 100 Copynumber: 2.0 Consensus size: 100
1362051 GTTGGATATA
* * *
1362061 AATAATAAAAAAATATTTTATATTAAATCATAAATTATTATTTAAAAAGTTAAAAATTAAAAAAT
1 AATAATAAAAAAATATTTTACATTAAATCATAAATAACTATTTAAAAAGTTAAAAATTAAAAAAT
* * *
1362126 ATTTTATATTAATTTTTGAATTATTATTTAAAAAT
66 ATTTTATATTAATCTCTGAATTACTATTTAAAAAT
* * *
1362161 AATAATAAAAAACTATTTTACATTAAATCCTAAATAACTATTTAAAAA-TAATAAAACTTAAAAA
1 AATAATAAAAAAATATTTTACATTAAATCATAAATAACTATTTAAAAAGT--TAAAAATTAAAAA
*
1362225 ATATTTTATATTAAATCTCT-AGTTACTATTTAAAAAT
64 ATATTTTATATT-AATCTCTGAATTACTATTTAAAAAT
1362262 TTATAAAATA
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
99 1 0.01
100 43 0.49
101 39 0.44
102 5 0.06
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (100 bp):
AATAATAAAAAAATATTTTACATTAAATCATAAATAACTATTTAAAAAGTTAAAAATTAAAAAAT
ATTTTATATTAATCTCTGAATTACTATTTAAAAAT
Found at i:1362277 original size:53 final size:52
Alignment explanation
Indices: 1362067--1362279 Score: 170
Period size: 49 Copynumber: 4.2 Consensus size: 52
1362057 TATAAATAAT
* * * * *
1362067 AAAAAAATATTTTATATTAAATCATAAATTATTATTTAAAAAGTTA-AAAAT-
1 AAAAAAATATTTTACATTAAATCCTAAATAACTATTTAAAAA-TAATAAAATA
* * * ** * * *
1362118 TAAAAAATATTTTATATTAATTTTTGAATTATTATTTAAAAATAAT--AAT-
1 AAAAAAATATTTTACATTAAATCCTAAATAACTATTTAAAAATAATAAAATA
*
1362167 AAAAAACTATTTTACATTAAATCCTAAATAACTATTTAAAAATAATAAAACT-
1 AAAAAAATATTTTACATTAAATCCTAAATAACTATTTAAAAATAATAAAA-TA
* * * * *
1362219 TAAAAAATATTTTATATTAAATCTCT-AGTTACTATTTAAAAATTTATAAAATA
1 AAAAAAATATTTTACATTAAATC-CTAAATAACTATTTAAAAA-TAATAAAATA
1362272 AAAAAAAT
1 AAAAAAAT
1362280 TATACTAAAT
Statistics
Matches: 133, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
49 40 0.30
50 2 0.02
51 39 0.29
52 36 0.27
53 16 0.12
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (52 bp):
AAAAAAATATTTTACATTAAATCCTAAATAACTATTTAAAAATAATAAAATA
Found at i:1362289 original size:101 final size:97
Alignment explanation
Indices: 1362058--1362290 Score: 227
Period size: 101 Copynumber: 2.3 Consensus size: 97
1362048 TTAGTTGGAT
* * *
1362058 ATAAATAATAAAAAAATATTTTATATTAAATCATAAATTATTATTTAAAAAGTTAAAAATTAAAA
1 ATAAA-AATAAAAAAA-A--TTATACTAAATCATAAATAACTATTTAAAAAGTTAAAAATTAAAA
* * *
1362123 AATATTTTATATTAATTTTTGAATTATTATTTAAAA
62 AATATTTTATATTAATCTCTGAATTACTATTTAAAA
* * * * *
1362159 ATAATAATAAAAAACTATTTTACATTAAATCCTAAATAACTATTTAAAAA-TAATAAAACTTAAA
1 ATAAAAATAAAAAA-AATTATAC--TAAATCATAAATAACTATTTAAAAAGT--TAAAAATTAAA
*
1362223 AAATATTTTATATTAAATCTCT-AGTTACTATTTAAAA
61 AAATATTTTATATT-AATCTCTGAATTACTATTTAAAA
1362260 ATTTATAAAATAAAAAAAATTATACTAAATC
1 A--TA-AAAATAAAAAAAATTATACTAAATC
1362291 TCAAATTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 18
0.77 0.11 0.13
Matches are distributed among these distances:
98 4 0.04
99 1 0.01
100 32 0.30
101 48 0.44
102 5 0.05
103 8 0.07
104 10 0.09
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.39
Consensus pattern (97 bp):
ATAAAAATAAAAAAAATTATACTAAATCATAAATAACTATTTAAAAAGTTAAAAATTAAAAAATA
TTTTATATTAATCTCTGAATTACTATTTAAAA
Found at i:1363161 original size:20 final size:19
Alignment explanation
Indices: 1363136--1363190 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1363126 CTGCCAGTTT
*
1363136 TATGTATCAATACAATTAA
1 TATGTATCAATACAATGAA
*
1363155 GTATGTATCGATACTAA-GAA
1 -TATGTATCAATAC-AATGAA
*
1363175 CATGTATCAATACAAT
1 TATGTATCAATACAAT
1363191 ATATCAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.07
19 11 0.38
20 14 0.48
21 2 0.07
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.33
Consensus pattern (19 bp):
TATGTATCAATACAATGAA
Found at i:1363221 original size:33 final size:32
Alignment explanation
Indices: 1363160--1363221 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
1363150 ATTAAGTATG
*
1363160 TATCGATACTAAGAACATGTATCAATACAATA
1 TATCAATACTAAGAACATGTATCAATACAATA
* *
1363192 TATCAATACTAAGCAATATGTATCGATACA
1 TATCAATACTAAG-AACATGTATCAATACA
1363222 TCTAGGTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.46
33 14 0.54
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (32 bp):
TATCAATACTAAGAACATGTATCAATACAATA
Found at i:1363837 original size:26 final size:26
Alignment explanation
Indices: 1363807--1363870 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
1363797 TTATTTTATA
*
1363807 CAAATTTTTAATAAGAGGTTTTAAGG
1 CAAATTTTCAATAAGAGGTTTTAAGG
1363833 CAAATTTTCAATAAGAGGTTTTAAGG
1 CAAATTTTCAATAAGAGGTTTTAAGG
*
1363859 TAAATTTTCAAT
1 CAAATTTTCAAT
1363871 TTAGTACTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (26 bp):
CAAATTTTCAATAAGAGGTTTTAAGG
Found at i:1364165 original size:30 final size:31
Alignment explanation
Indices: 1364129--1364186 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1364119 ACTTTTCTCA
* *
1364129 TGCATTCAT-AATAACAAGGTAAACATTAAT
1 TGCATTCATGAATAACAAAGCAAACATTAAT
*
1364159 TGCATTCATGAATAGCAAAGCAAACATT
1 TGCATTCATGAATAACAAAGCAAACATT
1364187 CATAATAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.28
Consensus pattern (31 bp):
TGCATTCATGAATAACAAAGCAAACATTAAT
Found at i:1370412 original size:3 final size:3
Alignment explanation
Indices: 1370404--1370428 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1370394 TGAGTCAACT
1370404 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
1370429 TGATGGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:1372515 original size:18 final size:18
Alignment explanation
Indices: 1372489--1372523 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1372479 TTACATTTAA
*
1372489 AAATGATAAATATATATC
1 AAATAATAAATATATATC
*
1372507 AAATAATAAATTTATAT
1 AAATAATAAATATATAT
1372524 ATATTAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
AAATAATAAATATATATC
Found at i:1372541 original size:22 final size:23
Alignment explanation
Indices: 1372498--1372546 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1372488 AAAATGATAA
1372498 ATATATATCAAATAATAAATTT-
1 ATATATATCAAATAATAAATTTG
* *
1372520 ATATATATTAAA-ACATATATTTG
1 ATATATATCAAATA-ATAAATTTG
1372543 ATAT
1 ATAT
1372547 TTGTTTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 18 0.78
23 4 0.17
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATATATCAAATAATAAATTTG
Found at i:1374488 original size:18 final size:18
Alignment explanation
Indices: 1374465--1374502 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1374455 AACAATGTTA
1374465 AAGAAATATTCACATCTC
1 AAGAAATATTCACATCTC
* *
1374483 AAGAAATTTTCACTTCTC
1 AAGAAATATTCACATCTC
1374501 AA
1 AA
1374503 TCATTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (18 bp):
AAGAAATATTCACATCTC
Found at i:1374586 original size:26 final size:26
Alignment explanation
Indices: 1374550--1374600 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1374540 TTTTGTAAAT
*
1374550 ATATATATATATATATATGTAATTTG
1 ATATATATATATATATATATAATTTG
* *
1374576 ATATATTTATATATGTATATAATTT
1 ATATATATATATATATATATAATTT
1374601 ACATTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (26 bp):
ATATATATATATATATATATAATTTG
Found at i:1374922 original size:6 final size:7
Alignment explanation
Indices: 1374906--1374931 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1374896 GATATTACTG
1374906 AAAATTA
1 AAAATTA
1374913 AAAATTA
1 AAAATTA
1374920 AAAATTA
1 AAAATTA
1374927 AAAAT
1 AAAAT
1374932 AATTATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:1375900 original size:24 final size:24
Alignment explanation
Indices: 1375873--1375934 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
1375863 AACTAAAATG
1375873 TAAAACAATAATAATTTTAAATTA
1 TAAAACAATAATAATTTTAAATTA
1375897 TAAAACAATAATAATTTTAAATTA
1 TAAAACAATAATAATTTTAAATTA
* *
1375921 -AAAATAAAAATAAT
1 TAAAACAATAATAAT
1375935 AAATTAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 12 0.33
24 24 0.67
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAAACAATAATAATTTTAAATTA
Found at i:1377411 original size:157 final size:155
Alignment explanation
Indices: 1377241--1377567 Score: 379
Period size: 157 Copynumber: 2.1 Consensus size: 155
1377231 TCCGGTGATT
* * *
1377241 CTAAAGGATTTAAAAAGGATTATAGATAGGATGAACCTATCTTAAATACCCACATTC-GACATAA
1 CTAAAAGACTTAAAAAGGATTATAGATAGGATAAACCTATCTTAAATACCCACATTCAG-CATAA
* * * * * ** *
1377305 AAGC-AAAGTAGTGGCAACTTAGGACTCGATTTTGAAAAAATTATGAAAATACCCCTAGGTTTGA
65 AAGCGAAACTAGTGACAACTTAGGAATCAATTCT-AAAAAATTACAAAAATACCCCTAGG--AGA
* **
1377369 TATCTTCGACTTAAAAGTGTTCGATATCC
127 TACCTTCGACTTAAAAGTGCCCGATATCC
* * *
1377398 CTAAAAGACTTAAAAAGGATTATAGATGGGATAAACCTATCTTAAATACCTACCTTCAGCATAAA
1 CTAAAAGACTTAAAAAGGATTATAGATAGGATAAACCTATCTTAAATACCCACATTCAGCATAAA
* * * * * *
1377463 AGCGGACCTAGTGATAACTTAGGAATCAATTCTAAAAAATTACAAAAATGCTCTTAGGAGATACC
66 AGCGAAACTAGTGACAACTTAGGAATCAATTCTAAAAAATTACAAAAATACCCCTAGGAGATACC
* *
1377528 TTTGACTTAAAAGTGCCCGATATCT
131 TTCGACTTAAAAGTGCCCGATATCC
1377553 CTAAAAGACTTAAAA
1 CTAAAAGACTTAAAA
1377568 TGGTAAAAGG
Statistics
Matches: 143, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
155 41 0.29
157 80 0.56
158 22 0.15
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (155 bp):
CTAAAAGACTTAAAAAGGATTATAGATAGGATAAACCTATCTTAAATACCCACATTCAGCATAAA
AGCGAAACTAGTGACAACTTAGGAATCAATTCTAAAAAATTACAAAAATACCCCTAGGAGATACC
TTCGACTTAAAAGTGCCCGATATCC
Found at i:1378193 original size:16 final size:17
Alignment explanation
Indices: 1378172--1378228 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
1378162 GATAAAATAA
*
1378172 TATTTA-TTTATTATTT
1 TATTTATTTTATAATTT
1378188 TATTTATTTTATAATTT
1 TATTTATTTTATAATTT
*
1378205 T-TTTAATTTTTGAAAATTT
1 TATTT-A-TTTT-ATAATTT
1378224 TATTT
1 TATTT
1378229 CATGCCTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 9 0.26
17 11 0.32
18 4 0.12
19 7 0.21
20 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTTATTTTATAATTT
Found at i:1378193 original size:184 final size:182
Alignment explanation
Indices: 1377838--1378302 Score: 619
Period size: 184 Copynumber: 2.5 Consensus size: 182
1377828 TTTTATTTAA
* * *
1377838 TTTTTAATTTTCAAAAA-TTCATTTCGTACCTTAAT-AGAGAACTAAAAAGATACGAAAAGTTTT
1 TTTTTAATTTTTAAAAATTTCATTTCGTACCTTAATGA-AAAACTAAAAAGATACGAAAAATTTT
* * * * * * *
1377901 AAAGATTTCTATACCCCTACGAAAAACCATAGGAATATTAGAAATCTCAAAAACTAAGATAATAA
65 AAATATTTCTATACCCTTACGAACAA-CATAAGAAAACTAAAAATCTCAAAAACTAAGATAATAA
* *
1377966 TTTTTGTTTAGTGATAAAATAATATTTATTTATTATGTTATTTATTTTATTATT
129 TTTTTATTTAGTGATAAAATAATATTTATTTATTATGTTATTTATTTTATAATT
* ** *
1378020 TTTTTAATTTTTAAAAATTTCATTTCGTACCTTATTGAAAAACCGAAAACATACGAAAAATTTTA
1 TTTTTAATTTTTAAAAATTTCATTTCGTACCTTAATGAAAAACTAAAAAGATACGAAAAATTTTA
* * *
1378085 AATATTTCTATACCCTTACGAACAACAATAAGAAAACTAAAAATCTTGAAAAATTAAGATAATGA
66 AATATTTCTATACCCTTACGAACAAC-ATAAGAAAACTAAAAATC-TCAAAAACTAAGATAATAA
*
1378150 TTTTTATTTAGTGATAAAATAATATTTATTTATTATTTTATTTATTTTATAATT
129 TTTTTATTTAGTGATAAAATAATATTTATTTATTATGTTATTTATTTTATAATT
* * * * * *
1378204 TTTTTAATTTTTGAAAATTTTATTTCATGCCTTAATGGAAAACTAAAAAGATACAAAAAATTTTA
1 TTTTTAATTTTTAAAAATTTCATTTCGTACCTTAATGAAAAACTAAAAAGATACGAAAAATTTTA
* *
1378269 AATATTTCTATACCTTTACGGACAATCATAAGAA
66 AATATTTCTATACCCTTACGAACAA-CATAAGAA
1378303 TAATAGAAAT
Statistics
Matches: 246, Mismatches: 32, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
182 17 0.07
183 75 0.30
184 153 0.62
185 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (182 bp):
TTTTTAATTTTTAAAAATTTCATTTCGTACCTTAATGAAAAACTAAAAAGATACGAAAAATTTTA
AATATTTCTATACCCTTACGAACAACATAAGAAAACTAAAAATCTCAAAAACTAAGATAATAATT
TTTATTTAGTGATAAAATAATATTTATTTATTATGTTATTTATTTTATAATT
Found at i:1378766 original size:3 final size:3
Alignment explanation
Indices: 1378753--1378791 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1378743 ACATAAAATC
*
1378753 CAT CTT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1378792 TTTAGATTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (3 bp):
CAT
Found at i:1379077 original size:11 final size:10
Alignment explanation
Indices: 1379059--1379092 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1379049 TTTAGCTAGG
1379059 TTTTTCTTTT
1 TTTTTCTTTT
1379069 TTCTTTCTTTT
1 TT-TTTCTTTT
*
1379080 TTTCTCTTTT
1 TTTTTCTTTT
1379090 TTT
1 TTT
1379093 ATCTCCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:1379931 original size:164 final size:163
Alignment explanation
Indices: 1379731--1380138 Score: 483
Period size: 164 Copynumber: 2.5 Consensus size: 163
1379721 AGAGAATTTC
* *
1379731 AGAAAAAATGAAAAACTTATGAAAATAAATGAATTTTTTAAAACTAATTTAATGTAAATTAAATG
1 AGAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTAAAAACTAATTTAATGT-AATTAAATG
1379796 ATAATATTTAAAGAATTTCAAAAATTTTAAACTAAGAAAAACTCCAT-TGAAAA-CATTTATGAA
65 ATAATATTTAAAGAATTTCAAAAATTTTAAACTAAGAAAAA-TCC-TCT-AAAAGCATTTATGAA
* *
1379859 GTAGCAAAC-CTATATTTCGAAAATAGGTAGA-TTTTA
127 GTAGCAAACTCCATATTTCGAAAATAGG-AAATTTTTA
* * *
1379895 AGAAAAAATAAAAAACTCATG-AAATAAAAGGAATTTTGAAAAACTAATTTACTATG-AATTAAA
1 AGAAAAAATGAAAAACTCATGAAAAT-AAATGAATTTTTAAAAACTAATTTA--ATGTAATTAAA
* * * * * * *
1379958 TGATGATATTTGATGAATTTTAAAAATTTTAAACTGAGCAAAATCCTCCTAAAAGCATTTATGGA
63 TGATAATATTTAAAGAATTTCAAAAATTTTAAACTAAGAAAAATCCT-CTAAAAGCATTTATGAA
* * *
1380023 GTATCAAACTCCGTATTTTGAAAATAGGAAATTTTTA
127 GTAGCAAACTCCATATTTCGAAAATAGGAAATTTTTA
* * * *
1380060 AGAAAAAATGAAAAACTCATAAAAATAAATGAA-ATTTCAAAACTAATATAATG--ATTAAATGA
1 AGAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTAAAAACTAATTTAATGTAATTAAATGA
1380122 TAATATTTAAAGAATTT
66 TAATATTTAAAGAATTT
1380139 TGAAGTTAAA
Statistics
Matches: 208, Mismatches: 27, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
161 23 0.11
162 4 0.02
163 11 0.05
164 118 0.57
165 45 0.22
166 7 0.03
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (163 bp):
AGAAAAAATGAAAAACTCATGAAAATAAATGAATTTTTAAAAACTAATTTAATGTAATTAAATGA
TAATATTTAAAGAATTTCAAAAATTTTAAACTAAGAAAAATCCTCTAAAAGCATTTATGAAGTAG
CAAACTCCATATTTCGAAAATAGGAAATTTTTA
Found at i:1381263 original size:84 final size:84
Alignment explanation
Indices: 1381058--1381340 Score: 309
Period size: 85 Copynumber: 3.3 Consensus size: 84
1381048 GTCAAGAAGT
* * ** * * * *
1381058 CAAGTCAACAAAGTATCAAAGGGGTTAC-CCAGGACTAAGCCATCATGTAAATAAAGGATAAAAA
1 CAAGTCAACAAAGGATAAAAGGATTTACTCGA-GACTAAGCCAACAAGTAAACAAAGGAT-AAAA
*
1381122 AGTTGATCGGGGTTGAACCAA
64 AGTTGATCGGGATTGAACCAA
* *
1381143 CAAGTCAACAAAGGATAAAAGGATTTACTTGGGACTAAGCCAACAAGTAAACAAAGGATACAAAA
1 CAAGTCAACAAAGGATAAAAGGATTTACTCGAGACTAAGCCAACAAGTAAACAAAGGATA-AAAA
* * *
1381208 GCTGATC-GGATTGAATCGA
65 GTTGATCGGGATTGAACCAA
* * * * **
1381227 CAAGTCAACAAATGATAAGAGGATTTACTCGAGACTAAGCCGACAAGCAAACAAAGCCTAAAATA
1 CAAGTCAACAAAGGATAAAAGGATTTACTCGAGACTAAGCCAACAAGTAAACAAAGGATAAAA-A
*
1381292 GTTGGTCGGGATTGAACCAA
65 GTTGATCGGGATTGAACCAA
* *
1381312 CAAGTTAATAAAGGATAAAAGGATTTACT
1 CAAGTCAACAAAGGATAAAAGGATTTACT
1381341 TGATAAGGTT
Statistics
Matches: 164, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
83 3 0.02
84 68 0.41
85 93 0.57
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (84 bp):
CAAGTCAACAAAGGATAAAAGGATTTACTCGAGACTAAGCCAACAAGTAAACAAAGGATAAAAAG
TTGATCGGGATTGAACCAA
Found at i:1381272 original size:43 final size:42
Alignment explanation
Indices: 1381142--1381282 Score: 119
Period size: 43 Copynumber: 3.3 Consensus size: 42
1381132 GGTTGAACCA
* *
1381142 ACAAGTCAACAAAGGATAAAAGGATTTACTTGGGACTAAGCCA
1 ACAAGTCAACAAAGGATAAAAGGATTTAC-TCGGACTAAGCCG
* * * * * *
1381185 ACAAGTAAACAAAGGATACAAAAG-CTGA-TCGGATTGAA-TCG
1 ACAAGTCAACAAAGGATA-AAAGGATTTACTCGGACT-AAGCCG
* *
1381226 ACAAGTCAACAAATGATAAGAGGATTTACTCGAGACTAAGCCG
1 ACAAGTCAACAAAGGATAAAAGGATTTACTCG-GACTAAGCCG
1381269 ACAAG-CAAACAAAG
1 ACAAGTC-AACAAAG
1381283 CCTAAAATAG
Statistics
Matches: 74, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
40 3 0.04
41 24 0.32
42 8 0.11
43 35 0.47
44 4 0.05
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (42 bp):
ACAAGTCAACAAAGGATAAAAGGATTTACTCGGACTAAGCCG
Found at i:1381529 original size:41 final size:41
Alignment explanation
Indices: 1381484--1381652 Score: 132
Period size: 41 Copynumber: 4.2 Consensus size: 41
1381474 GTCAAATGAA
*
1381484 TAAAAGGGTTGACTAGGGTGAAACCAATGAAGTCAACCAAT
1 TAAAAGGGTTGACTAGGGTGAAACCAATAAAGTCAACCAAT
* * ** *** *
1381525 TAAAAGGGTTGACCAAGGCAAAATTGATGAAA-TTAA-CAAGT
1 TAAAAGGGTTGACTAGGGTGAAACCAAT-AAAGTCAACCAA-T
* * * *
1381566 TAAAAGGGTTGACTAAGGCT-TAACCGATAAAGTGAACC-AT
1 TAAAAGGGTTGACT-AGGGTGAAACCAATAAAGTCAACCAAT
* * *
1381606 TAAAA-GGTTGGCTAGGATGAAATCAATAAAGTCAACCAAT
1 TAAAAGGGTTGACTAGGGTGAAACCAATAAAGTCAACCAAT
1381646 TAAAAGG
1 TAAAAGG
1381653 ATTGGCCAGG
Statistics
Matches: 97, Mismatches: 23, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
38 4 0.04
39 21 0.22
40 19 0.20
41 48 0.49
42 5 0.05
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.21
Consensus pattern (41 bp):
TAAAAGGGTTGACTAGGGTGAAACCAATAAAGTCAACCAAT
Found at i:1381675 original size:40 final size:39
Alignment explanation
Indices: 1381590--1381676 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
1381580 AAGGCTTAAC
* * *
1381590 CGATAAAGTGAACCATTAAAAGGTTGGCTAGGATGAAAT
1 CGATAAAGTCAACCATTAAAAGGTTGGCCAGGACGAAAT
* *
1381629 CAATAAAGTCAACCAATTAAAAGGATTGGCCAGGGCGAAA-
1 CGATAAAGTCAACC-ATTAAAAGG-TTGGCCAGGACGAAAT
1381669 CGATAAAG
1 CGATAAAG
1381677 CTAACGGGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 12 0.30
40 16 0.40
41 12 0.30
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (39 bp):
CGATAAAGTCAACCATTAAAAGGTTGGCCAGGACGAAAT
Found at i:1381702 original size:121 final size:122
Alignment explanation
Indices: 1381484--1381702 Score: 255
Period size: 121 Copynumber: 1.8 Consensus size: 122
1381474 GTCAAATGAA
* * *
1381484 TAAAAGGGTTGACTAGGGTGAAACCAATGAAGTCAACCAATTAAAAGGGTTGACCAAGGCAAAAT
1 TAAAAGGGTTGACTAGGATGAAACCAATAAAGTCAACCAATTAAAAGGATTGACCAAGGCAAAAT
* * ***
1381549 TGATGAAATTAACAAGTTAAAAGGGTTGACTAAGGCTTAACCGATAAAGTGAACCAT
66 CGATGAAACTAACAAGTTAAAAGGGAAAACTAAGGCTTAACCGATAAAGTGAACCAT
* * * * *
1381606 TAAAA-GGTTGGCTAGGATGAAATCAATAAAGTCAACCAATTAAAAGGATTGGCCAGGGCGAAA-
1 TAAAAGGGTTGACTAGGATGAAACCAATAAAGTCAACCAATTAAAAGGATTGACCAAGGCAAAAT
** *
1381669 CGAT-AAAGCTAACGGGTTAGAAGGGAAAAACTAA
66 CGATGAAA-CTAACAAGTTAAAAGGG-AAAACTAA
1381703 TAAAGTTAAC
Statistics
Matches: 79, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
119 3 0.04
120 16 0.20
121 55 0.70
122 5 0.06
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (122 bp):
TAAAAGGGTTGACTAGGATGAAACCAATAAAGTCAACCAATTAAAAGGATTGACCAAGGCAAAAT
CGATGAAACTAACAAGTTAAAAGGGAAAACTAAGGCTTAACCGATAAAGTGAACCAT
Found at i:1381746 original size:71 final size:71
Alignment explanation
Indices: 1381630--1381764 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 71
1381620 GGATGAAATC
* * *
1381630 AATAAAGTCAACCAATTAAAAGGATTGGCCAGGGCGAAACGATAAAGCTAACGGGTTAGAAGGGA
1 AATAAAGTCAACCAATTAAAAGGATTAGCCAAGGCGAAACGATAAAGCCAACGGGTTAGAAGGGA
1381695 AAAACT
66 AAAACT
* * *
1381701 AATAAAGTTAACCAATTAAAAGG-TTAGCCAAGGCGAAACCGATAAAGCCAATGGGTTGGAAGGG
1 AATAAAGTCAACCAATTAAAAGGATTAGCCAAGGCGAAA-CGATAAAGCCAACGGGTTAGAAGGG
1381765 TTAACTAGGG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 13 0.23
71 44 0.77
ACGTcount: A:0.44, C:0.14, G:0.26, T:0.16
Consensus pattern (71 bp):
AATAAAGTCAACCAATTAAAAGGATTAGCCAAGGCGAAACGATAAAGCCAACGGGTTAGAAGGGA
AAAACT
Found at i:1381805 original size:61 final size:61
Alignment explanation
Indices: 1381718--1381833 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 61
1381708 TTAACCAATT
* * * *
1381718 AAAAGGTTAGCCAAGGCGAAACCGATAAAGCCAATGGGTTGGAAGGGTTAACTAGGGCGAA
1 AAAAAGTTAGCCAAGGCAAAACCGATAAAGCCAATGGGTTAGAAAGGTTAACTAGGGCGAA
* * *
1381779 AAAAAGTTGGCCAAGGCAAAAGCGATAAAGCCAATGGGTTAGAAAGGTTGACTAG
1 AAAAAGTTAGCCAAGGCAAAACCGATAAAGCCAATGGGTTAGAAAGGTTAACTAG
1381834 TGTAGACACC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.40, C:0.14, G:0.31, T:0.16
Consensus pattern (61 bp):
AAAAAGTTAGCCAAGGCAAAACCGATAAAGCCAATGGGTTAGAAAGGTTAACTAGGGCGAA
Found at i:1382148 original size:13 final size:13
Alignment explanation
Indices: 1382130--1382156 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1382120 CATTTTTCTA
1382130 TGTATCGATACAT
1 TGTATCGATACAT
1382143 TGTATCGATACAT
1 TGTATCGATACAT
1382156 T
1 T
1382157 CAGGCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1384504 original size:51 final size:51
Alignment explanation
Indices: 1384444--1384560 Score: 138
Period size: 51 Copynumber: 2.4 Consensus size: 51
1384434 AATTCTCCGC
1384444 AATCGGGGATA-TCCCAACTCCGATTTCATTT-TCAAAACA-CTAATTTTCTAT
1 AATCGGGGATACT-CCAACTCCGATTTCATTTCT-AAAACATC-AATTTTCTAT
* *
1384495 AATCGGGGATACTTCAACTCCGATTTTATTTCTAAAACATCAA-TTT-T-T
1 AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTAT
*
1384543 CATCGGGGATACTCCAAC
1 AATCGGGGATACTCCAAC
1384561 CCCGTTATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
48 17 0.29
49 1 0.02
50 3 0.05
51 35 0.59
52 3 0.05
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (51 bp):
AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTCTAT
Found at i:1384641 original size:80 final size:77
Alignment explanation
Indices: 1384501--1384720 Score: 255
Period size: 80 Copynumber: 2.8 Consensus size: 77
1384491 CTATAATCGG
* * *
1384501 GGATACTTCAACTCC-GATTTTATTTCTAAAACATCAATTTT-TCATCGGGGATACTCCAACCCC
1 GGATACTCCAACCCCGGA-TTTATTTCTAAAACATCAATTTTCTAATCGGGGATACTCCAACCCC
* * *
1384564 GTTATTTTCGAGG
65 GTTATCTCCGAGA
* *
1384577 GGATACTCCAACCCCCGGATTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAACC
1 GGATACTCCAA-CCCCGGATTTATTTCTAAAACATCAATTT-TC-TAATCGGGGATACTCCAACC
1384642 CCGTTATCTCCGAGA
63 CCGTTATCTCCGAGA
* * * *
1384657 GGATACTCCAACCCTGGTTTTATTTCCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAAC
1 GGATACTCCAACCCCGGATTTATTTCTAAAACATCAATTTT-C--TAATCGGGGATACTCCAAC
1384721 TCCGATTTTA
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
76 10 0.08
77 23 0.19
78 4 0.03
79 24 0.20
80 61 0.50
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (77 bp):
GGATACTCCAACCCCGGATTTATTTCTAAAACATCAATTTTCTAATCGGGGATACTCCAACCCCG
TTATCTCCGAGA
Found at i:1384765 original size:52 final size:52
Alignment explanation
Indices: 1384656--1384773 Score: 141
Period size: 52 Copynumber: 2.3 Consensus size: 52
1384646 TATCTCCGAG
* ** *
1384656 AGGATACTCCAACCCTGGTTTTATTTCCAAAACACCAATTTTCCTTTAATCG
1 AGGATACTCCAACCCTGATTTTATTTCCAAAACACCAATTTTCCTACAATCA
* * *
1384708 GGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAATTTTTC-ACAATTA
1 AGGATACTCCAAC-CCTGATTTTATTTCC-AAAACACCAATTTTCCTACAATCA
1384760 AGGATACTCCAACC
1 AGGATACTCCAACC
1384774 TCGTTATTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
51 1 0.02
52 38 0.68
53 17 0.30
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.31
Consensus pattern (52 bp):
AGGATACTCCAACCCTGATTTTATTTCCAAAACACCAATTTTCCTACAATCA
Found at i:1385574 original size:1 final size:1
Alignment explanation
Indices: 1385568--1385609 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
1385558 AAAGTGTTTG
***
1385568 AAAAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1385610 TTTAAATGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:1385595 original size:23 final size:23
Alignment explanation
Indices: 1385565--1385609 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1385555 GATAAAGTGT
1385565 TTGAAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAAA
1385588 TTGAAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAAA
1385610 TTTAAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.87, C:0.00, G:0.04, T:0.09
Consensus pattern (23 bp):
TTGAAAAAAAAAAAAAAAAAAAA
Found at i:1385597 original size:22 final size:22
Alignment explanation
Indices: 1385569--1385611 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1385559 AAGTGTTTGA
1385569 AAAAAAAAAAAAAAAAAAATTG
1 AAAAAAAAAAAAAAAAAAATTG
1385591 AAAAAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAAAAATT
1385612 TAAATGTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.09
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAAAATTG
Found at i:1385638 original size:21 final size:21
Alignment explanation
Indices: 1385614--1385670 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1385604 AAAAAATTTA
1385614 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1385635 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1385656 AATGTATCGATACAT
1 AATGTATCGATACAT
1385671 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1385750 original size:19 final size:19
Alignment explanation
Indices: 1385726--1385793 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1385716 AATTCAACAA
1385726 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1385745 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1385760 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1385777 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1385794 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1385765 original size:13 final size:13
Alignment explanation
Indices: 1385747--1385771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1385737 ACATAAGTTT
1385747 TGTATCGATACAA
1 TGTATCGATACAA
1385760 TGTATCGATACA
1 TGTATCGATACA
1385772 TAAGTATTGT
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:1385769 original size:32 final size:32
Alignment explanation
Indices: 1385728--1385790 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1385718 TTCAACAATT
*
1385728 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1385760 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1385791 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1385851 original size:13 final size:13
Alignment explanation
Indices: 1385833--1385858 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1385823 CATTTTTCTG
1385833 TGTATCGATACAT
1 TGTATCGATACAT
1385846 TGTATCGATACAT
1 TGTATCGATACAT
1385859 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:1385855 original size:33 final size:33
Alignment explanation
Indices: 1385813--1385879 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1385803 GCCAAGGAAA
***
1385813 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1385846 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1385879 T
1 T
1385880 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:1388446 original size:51 final size:51
Alignment explanation
Indices: 1388387--1388557 Score: 207
Period size: 51 Copynumber: 3.3 Consensus size: 51
1388377 TTATTTCTGA
* * *
1388387 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
1388438 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** *
1388491 GGGGATACTCCAATTCCGATTTTATTTTCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1388543 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1388558 TCGTTATTTC
Statistics
Matches: 98, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.18
53 33 0.34
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1388572 original size:28 final size:28
Alignment explanation
Indices: 1388540--1388621 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 28
1388530 ATTTTTCACA
1388540 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCTCGTTATTTC
* *
1388568 ATCGAGGATACTCCAACCCCGTTACTTC
1 ATCGAGGATACTCCAACCTCGTTATTTC
*
1388596 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCGA-GG-ATACTCCAACCTCGTTATT
1388622 ATCTCCAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.06
27 2 0.04
28 42 0.89
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCTCGTTATTTC
Found at i:1390080 original size:507 final size:507
Alignment explanation
Indices: 1389079--1390094 Score: 1761
Period size: 507 Copynumber: 2.0 Consensus size: 507
1389069 ATTCATCGTG
1389079 TCCCTCACTTCTCCGAGGTGCATAGGTGATATAAGTTTTCATCTTAAACCCGGATTTGTAGTTTT
1 TCCCTCACTTCTCCGAGGTGCATAGGTGATATAAGTTTTCATCTTAAACCCGGATTTGTAGTTTT
* *
1389144 CACAAAACTTCATGCATTAGAGGGAATCACATCTAAGTAATGATGAAAATGGAACCGAGAAAATC
66 CACAAAACTTCACGCATTAGAGGGAATCACATCTAAGTAATGATGAAAATGGAACCGAAAAAATC
* * * *
1389209 AAGATTTTAGTAAGACGTAGTTAGAAGGTACCGATTTCGGGCGTCGTGGGGGTGCTAATCCTTCC
131 AAGATTTCAGTAAGACATAGTTAGAAGGTACCGATTTCGAGCATCGTGGGGGTGCTAATCCTTCC
1389274 CCACGCGTAACCAACTCCCGAGCCCAAACACGAATCTCTGAATTACGTAGACCGCGAAATCGATG
196 CCACGCGTAACCAACTCCCGAGCCCAAACACGAATCTCTGAATTACGTAGACCGCGAAATCGATG
1389339 TTTTGAGTTTCGTGACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGA
261 TTTTGAGTTTCGTGACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGA
*
1389404 TCGGTGGCGACTCCAAGTTCATGGTCATTTCGTAATGACCACCCGAGACTTATAGGACGAACGAC
326 TCGGTGGCGACTCCAAGTTCATGGTCATTTCGTAATGACCACCCGAGACTTATAGGACGAACAAC
* * * *
1389469 TCGTCCGATAGTCTTTCATCCCCGCACATTGACTATCCCCTTTTATTTAAGTCGAGTGAGCTTTG
391 TCATCCGATAGTCCTTCATCCCCGCACATCGACTATCCCCTTTTATTTAAGTCGAGCGAGCTTTG
*
1389534 GCTCTTCGGATTGTCCGAAGTACTCGTAAAAAAGGCCGAGCGCACGTTGCGACA
456 GCTCTTCGGA-T-TCCGAAGTACCCGTAAAAAAGGCCGAGCGCACGTTGCGACA
* *
1389588 TCCCTCATTTCTCGGAGGTGCATAGGTGATATAAGTTTTCATCTTAAACCCGGATTTGTAGTTTT
1 TCCCTCACTTCTCCGAGGTGCATAGGTGATATAAGTTTTCATCTTAAACCCGGATTTGTAGTTTT
* *
1389653 CAC-AAATTTCACGCATTAGAGGGAATTACATCTAAGTAATGAT-AAAATGGAACCGAAAAAATC
66 CACAAAACTTCACGCATTAGAGGGAATCACATCTAAGTAATGATGAAAATGGAACCGAAAAAATC
1389716 AAGATTTCAGTAAGACATAGTTAGAAGGTACCGATTTCGAGCATCGTGGGGGTGCTAATCCTTCC
131 AAGATTTCAGTAAGACATAGTTAGAAGGTACCGATTTCGAGCATCGTGGGGGTGCTAATCCTTCC
1389781 CCACGCGTAACCAACTCCCGAGCCCAAACACGAATCTCTGAATTACGTAGACCGCGAAATCGATG
196 CCACGCGTAACCAACTCCCGAGCCCAAACACGAATCTCTGAATTACGTAGACCGCGAAATCGATG
*
1389846 TTTTGAGTTTTGTGACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGA
261 TTTTGAGTTTCGTGACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGA
* *
1389911 TCGGTGGCGACTCCAAGTTCATGGTCATTTCGTAATGACCACCCGAGACTTATAGGACGAGCAAT
326 TCGGTGGCGACTCCAAGTTCATGGTCATTTCGTAATGACCACCCGAGACTTATAGGACGAACAAC
* *
1389976 TCATCCGATAGTCCTTCATCCCTGCATATCGACTATCCCCTTTTATTTTAAGTCGAGCGAGCTTT
391 TCATCCGATAGTCCTTCATCCCCGCACATCGACTATCCCCTTTTA-TTTAAGTCGAGCGAGCTTT
1390041 GGCTCTTCGGA-T-CGAAGTACCCGTAAAAAAGGGGGCCGAGCGCACGTTGCGACA
455 GGCTCTTCGGATTCCGAAGTACCCGTAAAAAA---GGCCGAGCGCACGTTGCGACA
1390095 ACTAGGATGA
Statistics
Matches: 482, Mismatches: 21, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
504 17 0.04
505 1 0.00
507 332 0.69
508 66 0.14
509 66 0.14
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (507 bp):
TCCCTCACTTCTCCGAGGTGCATAGGTGATATAAGTTTTCATCTTAAACCCGGATTTGTAGTTTT
CACAAAACTTCACGCATTAGAGGGAATCACATCTAAGTAATGATGAAAATGGAACCGAAAAAATC
AAGATTTCAGTAAGACATAGTTAGAAGGTACCGATTTCGAGCATCGTGGGGGTGCTAATCCTTCC
CCACGCGTAACCAACTCCCGAGCCCAAACACGAATCTCTGAATTACGTAGACCGCGAAATCGATG
TTTTGAGTTTCGTGACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCCTAGCCCGAAATGA
TCGGTGGCGACTCCAAGTTCATGGTCATTTCGTAATGACCACCCGAGACTTATAGGACGAACAAC
TCATCCGATAGTCCTTCATCCCCGCACATCGACTATCCCCTTTTATTTAAGTCGAGCGAGCTTTG
GCTCTTCGGATTCCGAAGTACCCGTAAAAAAGGCCGAGCGCACGTTGCGACA
Found at i:1390291 original size:41 final size:41
Alignment explanation
Indices: 1390108--1390546 Score: 239
Period size: 41 Copynumber: 10.4 Consensus size: 41
1390098 AGGATGAAAG
* * * * **
1390108 CGATAAAATCAACCAATTAAAAGGGTTCACCAAGGTGAAAT
1 CGATAAAGTCAACCAATTAAAAAGGTTGACCAGGGCAAAAT
* *** * * *
1390149 CGATAAAGCCAACGTGTTAGAAAGGTTGACTAAGGCAAAAT
1 CGATAAAGTCAACCAATTAAAAAGGTTGACCAGGGCAAAAT
*
1390190 CGATAAAGTCAACCAATTCAAAAA--TTGATCAGGGCAAAAT
1 CGATAAAGTCAACCAATT-AAAAAGGTTGACCAGGGCAAAAT
* ** * ***
1390230 CAATAAAACCGACGGGTTAAAAAGGTTGACCAGGGCAAAAAT
1 CGATAAAGTCAACCAATTAAAAAGGTTGACCAGGGC-AAAAT
* *
1390272 -GATAAAGTCAACCAATTAAAGGTTGGAAGAGTAGACCAGGGCAAAAC
1 CGATAAAGTCAACCAATTAAA------AAG-GTTGACCAGGGCAAAAT
* ** *
1390319 CGATAAAGTCAATCAATT-GCAAGGTTGGCCAGGGCAAAAT
1 CGATAAAGTCAACCAATTAAAAAGGTTGACCAGGGCAAAAT
* * * * *
1390359 CGATAAAGCCAA-CAGGTTAGAAGGGTTGACCAGGGCAAAAC
1 CGATAAAGTCAACCA-ATTAAAAAGGTTGACCAGGGCAAAAT
* * * *
1390400 CTATAAAGTCAACTAATTAAAAGGTTGGAAGGTTGACTAGGGCGAAA-
1 CGATAAAGTCAACCAATT-AAA------AAGGTTGACCAGGGCAAAAT
* * *
1390447 CTGATAAAGTCAACCAATTTAAAAGTTTG-CCAGGGTAAAAT
1 C-GATAAAGTCAACCAATTAAAAAGGTTGACCAGGGCAAAAT
* * *
1390488 CGATAAAG-CTAA-CAGGTTAGAAAGGTTGACCAAGGCAAAAT
1 CGATAAAGTC-AACCA-ATTAAAAAGGTTGACCAGGGCAAAAT
* *
1390529 CAATAGAGTCAACCAATT
1 CGATAAAGTCAACCAATT
1390547 GAAAGTTTGG
Statistics
Matches: 297, Mismatches: 72, Indels: 58
0.70 0.17 0.14
Matches are distributed among these distances:
39 10 0.03
40 77 0.26
41 127 0.43
42 15 0.05
47 10 0.03
48 58 0.20
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (41 bp):
CGATAAAGTCAACCAATTAAAAAGGTTGACCAGGGCAAAAT
Found at i:1390328 original size:48 final size:48
Alignment explanation
Indices: 1390251--1390471 Score: 170
Period size: 48 Copynumber: 4.9 Consensus size: 48
1390241 ACGGGTTAAA
**
1390251 AAGGTTGACCAGGGCAAAAATGATAAAGTCAACCAATT-AAAGGTTGG
1 AAGGTTGACCAGGGCAAAACCGATAAAGTCAACCAATTAAAAGGTTGG
* * *
1390298 AAGAGTAGACCAGGGCAAAACCGATAAAGT----CAA-T-CAA--TTGC
1 AAG-GTTGACCAGGGCAAAACCGATAAAGTCAACCAATTAAAAGGTTGG
* * * *
1390339 AAGGTTGGCCAGGGCAAAATCGATAAAG----CC----AACAGGTTAG
1 AAGGTTGACCAGGGCAAAACCGATAAAGTCAACCAATTAAAAGGTTGG
* *
1390379 AAGGGTTGACCAGGGCAAAACCTATAAAGTCAACTAATTAAAAGGTTGG
1 AA-GGTTGACCAGGGCAAAACCGATAAAGTCAACCAATTAAAAGGTTGG
* * *
1390428 AAGGTTGACTAGGGCGAAACTGATAAAGTCAACCAATTTAAAAG
1 AAGGTTGACCAGGGCAAAACCGATAAAGTCAACCAA-TTAAAAG
1390472 TTTGCCAGGG
Statistics
Matches: 136, Mismatches: 23, Indels: 28
0.73 0.12 0.15
Matches are distributed among these distances:
38 1 0.01
40 27 0.20
41 29 0.21
43 3 0.02
44 3 0.02
45 1 0.01
47 3 0.02
48 52 0.38
49 17 0.12
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (48 bp):
AAGGTTGACCAGGGCAAAACCGATAAAGTCAACCAATTAAAAGGTTGG
Found at i:1390352 original size:129 final size:127
Alignment explanation
Indices: 1390182--1390556 Score: 430
Period size: 129 Copynumber: 2.9 Consensus size: 127
1390172 GGTTGACTAA
* * ** * * * *
1390182 GGCAAAATCGATAAAGTCAACCAATTCAAAAATTGATCAGGGCAAAATCAATAAAACCGACGGGT
1 GGCAAAACCGATAAAGTCAACCAATTC-AAAGTTGGCCAGGGCAAAATCGATAAAGCCAACAGGT
*
1390247 TAAAAAGGTTGACCAGGGCAAAAATGATAAAGTCAACCAATT-AAAGGTTGGAAGAGTAGACCAG
65 TAGAAAGGTTGACCAGGGCAAAAAT-ATAAAGTCAACCAATTAAAAGGTTGGAAG-GTAGACCAG
* *
1390311 GGCAAAACCGATAAAGTCAATCAATTGCAAGGTTGGCCAGGGCAAAATCGATAAAGCCAACAGGT
1 GGCAAAACCGATAAAGTCAACCAATT-CAAAGTTGGCCAGGGCAAAATCGATAAAGCCAACAGGT
* * * * *
1390376 TAGAAGGGTTGACCAGGGCAAAACCTATAAAGTCAACTAATTAAAAGGTTGGAAGGTTGACTAG
65 TAGAAAGGTTGACCAGGGCAAAA-ATATAAAGTCAACCAATTAAAAGGTTGGAAGGTAGACCAG
* * * * * *
1390440 GGCGAAACTGATAAAGTCAACCAATTTAAAAGTTTGCCAGGGTAAAATCGATAAAGCTAACAGGT
1 GGCAAAACCGATAAAGTCAACCAA-TTCAAAGTTGGCCAGGGCAAAATCGATAAAGCCAACAGGT
* * * *
1390505 TAGAAAGGTTGACCAAGGC-AAAATCAATAGAGTCAACCAATTGAAAGTTTGG
65 TAGAAAGGTTGACCAGGGCAAAAAT--ATAAAGTCAACCAATTAAAAGGTTGG
1390557 CAAAGGTGAA
Statistics
Matches: 209, Mismatches: 31, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
127 1 0.00
128 3 0.01
129 189 0.90
130 16 0.08
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (127 bp):
GGCAAAACCGATAAAGTCAACCAATTCAAAGTTGGCCAGGGCAAAATCGATAAAGCCAACAGGTT
AGAAAGGTTGACCAGGGCAAAAATATAAAGTCAACCAATTAAAAGGTTGGAAGGTAGACCAG
Found at i:1391292 original size:87 final size:89
Alignment explanation
Indices: 1391036--1391292 Score: 342
Period size: 87 Copynumber: 2.9 Consensus size: 89
1391026 GTTGGGATAT
* *
1391036 CCTTGCCCCAAGGAAATCAGGCTTTATGATGCATCAA-ACCATCTAGTAGTTGGGTGAAGGGGAT
1 CCTTGCCCCAAGGAAATCAGGCTTTATGATGCATCAATACCATCTAGTGGTTGAGTGAAGGGGAT
*
1391100 ATGATT-GGAATGTGTAGGCTACA
66 ATGATTGGGAATGTGTGGGCTACA
* * * * * ** * * * * *
1391123 CCTTACACCAAGGAAATCAAGCTTTGTGATGCATCAATACCAGCTAAAGGCTAAATGAAAGGGAC
1 CCTTGCCCCAAGGAAATCAGGCTTTATGATGCATCAATACCATCTAGTGGTTGAGTGAAGGGGAT
1391188 ATGATTGGGAATGTGTGGGCTACA
66 ATGATTGGGAATGTGTGGGCTACA
*
1391212 CCTTGCCCCAAGGAAATTAGGC-TT-TGATGCATCAATACCATCTAGTGGTTGAGTGAAGGGGAT
1 CCTTGCCCCAAGGAAATCAGGCTTTATGATGCATCAATACCATCTAGTGGTTGAGTGAAGGGGAT
1391275 ATGATTGGGAATGTGTGG
66 ATGATTGGGAATGTGTGG
1391293 TTTTTACAAT
Statistics
Matches: 141, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
87 82 0.58
88 25 0.18
89 34 0.24
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (89 bp):
CCTTGCCCCAAGGAAATCAGGCTTTATGATGCATCAATACCATCTAGTGGTTGAGTGAAGGGGAT
ATGATTGGGAATGTGTGGGCTACA
Found at i:1393671 original size:28 final size:27
Alignment explanation
Indices: 1393638--1393710 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
1393628 AATAAAGCCA
* **
1393638 GGGTTGGAGTGTCCCCTCGGAAATAACG
1 GGGTTGGAGTATCCCCGAGG-AATAACG
* *
1393666 GGGTTGGAGTATCCCCGATGATTAACG
1 GGGTTGGAGTATCCCCGAGGAATAACG
1393693 GGGTTGGAGTATCCCCGA
1 GGGTTGGAGTATCCCCGA
1393711 TTGTGAAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 24 0.60
28 16 0.40
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCGAGGAATAACG
Found at i:1393795 original size:51 final size:53
Alignment explanation
Indices: 1393699--1393825 Score: 152
Period size: 51 Copynumber: 2.4 Consensus size: 53
1393689 AACGGGGTTG
* * *
1393699 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCAGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCAGAGTTA
* *
1393753 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTT
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCAGAGTTA
* *
1393804 GAATATCCCCGATTATGGAGAA
1 GAGTATCCCCGATTATGAAGAA
1393826 TTGAGAAACT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
51 35 0.55
52 4 0.06
53 10 0.16
54 15 0.23
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCAGAGTTA
Found at i:1396139 original size:13 final size:13
Alignment explanation
Indices: 1396121--1396146 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1396111 ACAAAGATCC
1396121 ATGTATCGATACA
1 ATGTATCGATACA
1396134 ATGTATCGATACA
1 ATGTATCGATACA
1396147 CAGAAAAATG
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:1396142 original size:33 final size:33
Alignment explanation
Indices: 1396100--1396166 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1396090 AAAATTTCCA
***
1396100 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1396133 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1396166 A
1 A
1396167 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1396230 original size:32 final size:32
Alignment explanation
Indices: 1396189--1396251 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1396179 TAGCTAATTA
** *
1396189 TGTATCGATACAATGCTTATGTATTGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1396221 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1396252 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Done.