Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 87 of 344
Found at i:29036912 original size:10 final size:10
Alignment explanation
Indices: 29036883--29036943 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
29036873 TTTATATTTT
*
29036883 TAAAAAATATA
1 TAAAAAAT-TC
29036894 TATAAAAATTC
1 TA-AAAAATTC
29036905 TAAAAAATTC
1 TAAAAAATTC
29036915 TAAAAAAATTC
1 T-AAAAAATTC
* *
29036926 TAAAATA-TA
1 TAAAAAATTC
29036935 TAAAAAATT
1 TAAAAAATT
29036944 AAAATTTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
9 7 0.16
10 15 0.35
11 15 0.35
12 6 0.14
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (10 bp):
TAAAAAATTC
Found at i:29036921 original size:21 final size:22
Alignment explanation
Indices: 29036883--29036941 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
29036873 TTTATATTTT
*
29036883 TAAAAAATATATATAAAAATTC
1 TAAAAAATATATAAAAAAATTC
*
29036905 TAAAAAAT-TCTAAAAAAATTC
1 TAAAAAATATATAAAAAAATTC
29036926 T--AAAATATATAAAAAA
1 TAAAAAATATATAAAAAA
29036942 TTAAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 5 0.15
20 8 0.24
21 12 0.36
22 8 0.24
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAATATATAAAAAAATTC
Found at i:29038706 original size:63 final size:63
Alignment explanation
Indices: 29038638--29038792 Score: 222
Period size: 63 Copynumber: 2.5 Consensus size: 63
29038628 TTTTAAGCAT
* * *
29038638 AAACAGTGAGTTACATGGCCTGGGCACACACCCGTGTCCCTGGTCGTATGGA-TTTTATACTAC
1 AAACAGTGAGTTACACGGCCTGGGCACACACCCGTGCCCCTGGCCGTAT-GATTTTTATACTAC
** *
29038701 AAACAGTGAGTTACACGGCCTGGGCACACACCTTTGCCCCTGGCCGTGTGATTTTTATACTAC
1 AAACAGTGAGTTACACGGCCTGGGCACACACCCGTGCCCCTGGCCGTATGATTTTTATACTAC
* *
29038764 AAACAGTGAGTTACACGACCTAGGCACAC
1 AAACAGTGAGTTACACGGCCTGGGCACAC
29038793 GTTCGTGTGA
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
62 2 0.02
63 81 0.98
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (63 bp):
AAACAGTGAGTTACACGGCCTGGGCACACACCCGTGCCCCTGGCCGTATGATTTTTATACTAC
Found at i:29039454 original size:27 final size:26
Alignment explanation
Indices: 29039423--29039477 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
29039413 GATTAATTGT
*
29039423 AAAAGAAGAAAGAAGAAAAAGAAATTA
1 AAAAGAAGAAAGAACAAAAA-AAATTA
* *
29039450 AAAAGAAGGAAGAACAACAAAAATTA
1 AAAAGAAGAAAGAACAAAAAAAATTA
29039476 AA
1 AA
29039478 GAATCAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (26 bp):
AAAAGAAGAAAGAACAAAAAAAATTA
Found at i:29039455 original size:24 final size:26
Alignment explanation
Indices: 29039428--29039477 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
29039418 ATTGTAAAAG
*
29039428 AAGAAAGAAGAA-AA-AGAAATTAAA
1 AAGAAAGAAGAACAACAAAAATTAAA
*
29039452 AAGAAGGAAGAACAACAAAAATTAAA
1 AAGAAAGAAGAACAACAAAAATTAAA
29039478 GAATCAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 2 0.09
26 9 0.41
ACGTcount: A:0.72, C:0.04, G:0.16, T:0.08
Consensus pattern (26 bp):
AAGAAAGAAGAACAACAAAAATTAAA
Found at i:29041147 original size:46 final size:46
Alignment explanation
Indices: 29040995--29041195 Score: 183
Period size: 46 Copynumber: 4.3 Consensus size: 46
29040985 ATTTGTTTGT
* * * * * *
29040995 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGA-GACGA
* * * * *
29041041 GAGCCAGCGTAAGACCATGTCTAGGACATGGCATCGGCATTGAAACGA
1 GAGCCAGTGTAAGA-CATGTCTAGGACAT-GCATCAGCCTCGAGACGA
*
29041089 GAGCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGACG-A
* * *
29041136 -AGCCAGTGTAAGACATGTTTGGGACATGCATCAG-CTACGAGATGA
1 GAGCCAGTGTAAGACATGTCTAGGACATGCATCAGCCT-CGAGACGA
* *
29041181 TAGTCAGTGTAAGAC
1 GAGCCAGTGTAAGAC
29041196 CGTATCTGGG
Statistics
Matches: 130, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
45 3 0.02
46 75 0.58
47 28 0.22
48 23 0.18
49 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.21
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGACGA
Found at i:29042904 original size:23 final size:23
Alignment explanation
Indices: 29042871--29042918 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
29042861 GGTGTTTTAA
*
29042871 CAAAAACGCCGCTAAAAACTGAG
1 CAAAAACGCCGCTAAAAACAGAG
*
29042894 CAAAAATGCCGCTAAAAACAGAG
1 CAAAAACGCCGCTAAAAACAGAG
29042917 CA
1 CA
29042919 TTAGCGGCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.50, C:0.25, G:0.17, T:0.08
Consensus pattern (23 bp):
CAAAAACGCCGCTAAAAACAGAG
Found at i:29042965 original size:41 final size:41
Alignment explanation
Indices: 29042896--29043031 Score: 202
Period size: 41 Copynumber: 3.3 Consensus size: 41
29042886 AAACTGAGCA
*
29042896 AAAATGCCGCTAAA-AACAGAGCATTAGCGGCGCTTTTGGT
1 AAAATGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
*
29042936 AAAATGCTGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAATGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
** *
29042977 AAAGCGCCGCTAAAGACTAGAGCATTAGCGGCGCTTTTGGT
1 AAAATGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
* *
29043018 AAAACGCCACTAAA
1 AAAATGCCGCTAAA
29043032 AGTTATATAA
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 13 0.15
41 74 0.85
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21
Consensus pattern (41 bp):
AAAATGCCGCTAAAGACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:29043671 original size:24 final size:24
Alignment explanation
Indices: 29043644--29043692 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29043634 CATATATTTA
29043644 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
29043668 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
29043692 T
1 T
29043693 GTTATTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAAAGTTTATATAAAAATTAAT
Found at i:29044180 original size:8 final size:8
Alignment explanation
Indices: 29044161--29044204 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
29044151 AATCTTCAAA
29044161 AAAAATTT
1 AAAAATTT
29044169 -AAAATTT
1 AAAAATTT
*
29044176 AAAAA-TA
1 AAAAATTT
29044183 AAAAATTT
1 AAAAATTT
29044191 AAAAATTT
1 AAAAATTT
29044199 AAAAAT
1 AAAAAT
29044205 AAAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 13 0.41
8 19 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
AAAAATTT
Found at i:29044181 original size:15 final size:15
Alignment explanation
Indices: 29044161--29044251 Score: 69
Period size: 15 Copynumber: 6.1 Consensus size: 15
29044151 AATCTTCAAA
*
29044161 AAAAATTTAAAATTT
1 AAAAATTAAAAATTT
*
29044176 AAAAATAAAAAATTT
1 AAAAATTAAAAATTT
29044191 AAAAATTTAAAAA--T
1 AAAAA-TTAAAAATTT
* * *
29044205 AAAAAATAAAAAATA
1 AAAAATTAAAAATTT
* *
29044220 AAAAATAAAAAACTT
1 AAAAATTAAAAATTT
* * *
29044235 AAATATTTAATATTT
1 AAAAATTAAAAATTT
29044250 AA
1 AA
29044252 TATTTAATAT
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
13 6 0.10
14 6 0.10
15 41 0.69
16 6 0.10
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATTAAAAATTT
Found at i:29044185 original size:23 final size:22
Alignment explanation
Indices: 29044160--29044244 Score: 109
Period size: 23 Copynumber: 3.8 Consensus size: 22
29044150 AAATCTTCAA
29044160 AAAAAATTTAAAATTTAAAAAT
1 AAAAAATTTAAAATTTAAAAAT
29044182 AAAAAATTTAAAAATTTAAAAAT
1 AAAAAATTT-AAAATTTAAAAAT
* * *
29044205 AAAAAA-TAAAAAATAAAAAAT
1 AAAAAATTTAAAATTTAAAAAT
*
29044226 AAAAAACTTAAATATTTAA
1 AAAAAATTTAAA-ATTTAA
29044245 TATTTAATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
21 17 0.31
22 14 0.26
23 23 0.43
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAAATTTAAAATTTAAAAAT
Found at i:29044195 original size:30 final size:30
Alignment explanation
Indices: 29044161--29044218 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
29044151 AATCTTCAAA
* *
29044161 AAAAATTTAAAATTTAAAAATAAAAAATTT
1 AAAAATTTAAAAATAAAAAATAAAAAATTT
29044191 AAAAATTTAAAAATAAAAAATAAAAAAT
1 AAAAATTTAAAAATAAAAAATAAAAAAT
29044219 AAAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (30 bp):
AAAAATTTAAAAATAAAAAATAAAAAATTT
Found at i:29044207 original size:14 final size:14
Alignment explanation
Indices: 29044169--29044230 Score: 63
Period size: 14 Copynumber: 4.3 Consensus size: 14
29044159 AAAAAAATTT
*
29044169 AAAATTTAAAAATAA
1 AAAATTAAAAAAT-A
*
29044184 AAAATTTAAAAATTTA
1 AAAA-TTAAAAA-ATA
29044200 AAAA-TAAAAAATA
1 AAAATTAAAAAATA
*
29044213 AAAAATAAAAAATA
1 AAAATTAAAAAATA
29044227 AAAA
1 AAAA
29044231 ACTTAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 6 0.15
14 19 0.46
15 4 0.10
16 11 0.27
17 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATTAAAAAATA
Found at i:29044210 original size:8 final size:7
Alignment explanation
Indices: 29044176--29044231 Score: 76
Period size: 7 Copynumber: 7.7 Consensus size: 7
29044166 TTTAAAATTT
29044176 AAAAATA
1 AAAAATA
29044183 AAAAATTTA
1 AAAAA--TA
* *
29044192 AAAATTT
1 AAAAATA
29044199 AAAAATA
1 AAAAATA
29044206 AAAAATA
1 AAAAATA
29044213 AAAAATA
1 AAAAATA
29044220 AAAAATA
1 AAAAATA
29044227 AAAAA
1 AAAAA
29044232 CTTAAATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 37 0.86
9 6 0.14
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAAAATA
Found at i:29044246 original size:7 final size:7
Alignment explanation
Indices: 29044236--29044263 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
29044226 AAAAAACTTA
29044236 AATATTT
1 AATATTT
29044243 AATATTT
1 AATATTT
29044250 AATATTT
1 AATATTT
29044257 AATATTT
1 AATATTT
29044264 TAATCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATATTT
Found at i:29044320 original size:12 final size:13
Alignment explanation
Indices: 29044297--29044321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29044287 TTTAATATTC
29044297 AAAATTTAAAAAA
1 AAAATTTAAAAAA
29044310 AAAATTTAAAAA
1 AAAATTTAAAAA
29044322 TGATAATCTC
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATTTAAAAAA
Found at i:29044364 original size:8 final size:8
Alignment explanation
Indices: 29044351--29044388 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
29044341 AATTTGAAAG
29044351 AAAAAATA
1 AAAAAATA
29044359 AAAAAATA
1 AAAAAATA
29044367 AAAAAA-A
1 AAAAAATA
*
29044374 ATAAAATA
1 AAAAAATA
*
29044382 ATAAAAT
1 AAAAAAT
29044389 TAAACAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAAAATA
Found at i:29044369 original size:15 final size:16
Alignment explanation
Indices: 29044351--29044388 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
29044341 AATTTGAAAG
29044351 AAAAAATAAA-AAAAT
1 AAAAAATAAATAAAAT
29044366 AAAAAA-AAATAAAAT
1 AAAAAATAAATAAAAT
29044381 AATAAAAT
1 AA-AAAAT
29044389 TAAACAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.15
15 13 0.65
16 4 0.20
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAATAAATAAAAT
Found at i:29044374 original size:18 final size:18
Alignment explanation
Indices: 29044351--29044387 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
29044341 AATTTGAAAG
29044351 AAAAAATAAAAAAATAAA
1 AAAAAATAAAAAAATAAA
*
29044369 AAAAAATAAAATAATAAA
1 AAAAAATAAAAAAATAAA
29044387 A
1 A
29044388 TTAAACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAAATAAAAAAATAAA
Found at i:29047615 original size:20 final size:20
Alignment explanation
Indices: 29047555--29047616 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
29047545 AAATTTCAAA
*
29047555 AATTAAACATAATATAATATTT
1 AATTAAA-ATAAAAT-ATATTT
*
29047577 AA-CATAAA-AAAATATTATTT
1 AATTA-AAATAAAATA-TATTT
29047597 AATTAAAATAAAATATATTT
1 AATTAAAATAAAATATATTT
29047617 TTTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
19 1 0.03
20 19 0.58
21 9 0.27
22 4 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAAAATAAAATATATTT
Found at i:29047774 original size:43 final size:43
Alignment explanation
Indices: 29047633--29047774 Score: 176
Period size: 43 Copynumber: 3.3 Consensus size: 43
29047623 ATTCATGATT
* * * * ** *
29047633 TTTAGCGGCGTTTTTGAGAAAAGCGCTTCTAAAGGTCATAGTC
1 TTTAGTGGCGTTTGTAAAAAAAGCGCCGCTAAAGGTCATGGTC
* * *
29047676 TTTAGCGGCATTTGTAAAAAAAGCGTCGCTAAAGGTCATGGTC
1 TTTAGTGGCGTTTGTAAAAAAAGCGCCGCTAAAGGTCATGGTC
*
29047719 TTTAGTGGCGTTTGTAAAAAAAGCGCCGCTAAAAGTCATGGTC
1 TTTAGTGGCGTTTGTAAAAAAAGCGCCGCTAAAGGTCATGGTC
*
29047762 TTTAGTGACGTTT
1 TTTAGTGGCGTTT
29047775 TTTTAAATAA
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
TTTAGTGGCGTTTGTAAAAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:29049744 original size:19 final size:19
Alignment explanation
Indices: 29049704--29049755 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 19
29049694 TCAACCTTTA
29049704 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-GTTTC
29049724 AATCAAGTTAGAAAT-TTTC
1 AATCAAGTTA-AAATGTTTC
29049743 AATCAAAGTTAAA
1 AATC-AAGTTAAA
29049756 CTATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.33
20 16 0.53
21 4 0.13
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.33
Consensus pattern (19 bp):
AATCAAGTTAAAATGTTTC
Found at i:29051960 original size:20 final size:20
Alignment explanation
Indices: 29051935--29052005 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
29051925 CGTGATTTGG
29051935 TATCGATACCATTTTAAAAT
1 TATCGATACCATTTTAAAAT
*
29051955 TATCGATA-TATTTATAAAAT
1 TATCGATACCATTT-TAAAAT
* * *
29051975 TATCGATACCCTCTTAAAGAA
1 TATCGATACCATTTTAAA-AT
29051996 TATCGATACC
1 TATCGATACC
29052006 TATCGGGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.09
20 26 0.60
21 13 0.30
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (20 bp):
TATCGATACCATTTTAAAAT
Found at i:29055873 original size:24 final size:24
Alignment explanation
Indices: 29055841--29055888 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29055831 CATGTTCTCC
29055841 ATCTTATCATTACTTAGAATTTTT
1 ATCTTATCATTACTTAGAATTTTT
29055865 ATCTTATCATTACTTAGAATTTTT
1 ATCTTATCATTACTTAGAATTTTT
29055889 GTCCTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (24 bp):
ATCTTATCATTACTTAGAATTTTT
Found at i:29057172 original size:19 final size:20
Alignment explanation
Indices: 29057132--29057183 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
29057122 TCAGCATTTA
29057132 AATCAAGTT-AAAATGGTTTC
1 AATCAAGTTAAAAAT-GTTTC
29057152 AATCAAGTTAAAAAT-TTTC
1 AATCAAGTTAAAAATGTTTC
29057171 AATCAAAGTTAAA
1 AATC-AAGTTAAA
29057184 TTATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.27
20 17 0.57
21 5 0.17
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
AATCAAGTTAAAAATGTTTC
Found at i:29061322 original size:63 final size:62
Alignment explanation
Indices: 29061197--29061327 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 62
29061187 CATGTTCGAA
29061197 TGTTATTGTTTTGAGTAGCATATTTTGTAGTACTAATTATGGAAAAGTCATTATAAACGGAT
1 TGTTATTGTTTTGAGTAGCATATTTTGTAGTACTAATTATGGAAAAGTCATTATAAACGGAT
29061259 TGTTATTGTTTTGAGTAGCATATTTTGTAGTAACTAATTATGGAAAAGTCATTATAAACGGAT
1 TGTTATTGTTTTGAGTAGCATATTTTGTAGT-ACTAATTATGGAAAAGTCATTATAAACGGAT
29061322 TGTTAT
1 TGTTAT
29061328 CTTTGTTTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
62 31 0.46
63 37 0.54
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (62 bp):
TGTTATTGTTTTGAGTAGCATATTTTGTAGTACTAATTATGGAAAAGTCATTATAAACGGAT
Found at i:29061381 original size:52 final size:52
Alignment explanation
Indices: 29061320--29061422 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
29061310 TTATAAACGG
29061320 ATTGTTATCTTTGTTTTTCCCTTTTAAATGTGGTGTTGGGTATCTAGACTGT
1 ATTGTTATCTTTGTTTTTCCCTTTTAAATGTGGTGTTGGGTATCTAGACTGT
29061372 ATTGTTATCTTTGTTTTTCCCTTTTAAATGTGGTGTTGGGTATCTAGACTG
1 ATTGTTATCTTTGTTTTTCCCTTTTAAATGTGGTGTTGGGTATCTAGACTG
29061423 ATCGTCTTCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.16, C:0.12, G:0.21, T:0.51
Consensus pattern (52 bp):
ATTGTTATCTTTGTTTTTCCCTTTTAAATGTGGTGTTGGGTATCTAGACTGT
Found at i:29063964 original size:25 final size:25
Alignment explanation
Indices: 29063932--29063984 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
29063922 AAGATATAAT
29063932 AGGAGGCGAAGTATGTTTTTCATTG
1 AGGAGGCGAAGTATGTTTTTCATTG
29063957 AGGAGGCGAAGTATGTTTTTCATTG
1 AGGAGGCGAAGTATGTTTTTCATTG
29063982 AGG
1 AGG
29063985 TTATTCTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.34, T:0.34
Consensus pattern (25 bp):
AGGAGGCGAAGTATGTTTTTCATTG
Found at i:29065120 original size:10 final size:10
Alignment explanation
Indices: 29065082--29065140 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 10
29065072 TAAAAATTAC
*
29065082 AAAATAATTC
1 AAAATAATTT
29065092 AAAATAATTTT
1 AAAATAA-TTT
*
29065103 CAAA-AATTT
1 AAAATAATTT
29065112 AAAATAATTT
1 AAAATAATTT
**
29065122 TTAA-AATTT
1 AAAATAATTT
29065131 AAAAT-ATTT
1 AAAATAATTT
29065140 A
1 A
29065141 TAAAGATTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
9 18 0.46
10 16 0.41
11 5 0.13
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
AAAATAATTT
Found at i:29065129 original size:19 final size:20
Alignment explanation
Indices: 29065087--29065136 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
29065077 ATTACAAAAT
*
29065087 AATTCAAAATAATTTTCAAA
1 AATTTAAAATAATTTTCAAA
*
29065107 AATTTAAAATAATTTT-TAA
1 AATTTAAAATAATTTTCAAA
29065126 AATTTAAAATA
1 AATTTAAAATA
29065137 TTTATAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTTAAAATAATTTTCAAA
Found at i:29065144 original size:18 final size:19
Alignment explanation
Indices: 29065087--29065144 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
29065077 ATTACAAAAT
*
29065087 AATTCAAAATAATTT-TCAAA
1 AATTTAAAATAATTTAT--AA
*
29065107 AATTTAAAATAATTTTTAA
1 AATTTAAAATAATTTATAA
29065126 AATTTAAAAT-ATTTATAA
1 AATTTAAAATAATTTATAA
29065144 A
1 A
29065145 GATTCCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.23
19 12 0.34
20 14 0.40
21 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTTAAAATAATTTATAA
Found at i:29077412 original size:35 final size:35
Alignment explanation
Indices: 29077348--29077435 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
29077338 ATATACTCAG
* * *
29077348 TCAGACACAGATGCAGATTCGGGCTTAAGCCCAT-
1 TCAGATACAGATACAGATTCGGGCCTAAGCCCATC
* *
29077382 TACGGATATAGATACAGATTCGGGCCTAAGCCCATC
1 T-CAGATACAGATACAGATTCGGGCCTAAGCCCATC
29077418 TCAGATACAGATACAGAT
1 TCAGATACAGATACAGAT
29077436 GTACAAATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 1 0.02
35 43 0.96
36 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (35 bp):
TCAGATACAGATACAGATTCGGGCCTAAGCCCATC
Found at i:29079031 original size:19 final size:19
Alignment explanation
Indices: 29079007--29079043 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29078997 ACAATGCCCG
29079007 ATAAATGATAATACCTGAA
1 ATAAATGATAATACCTGAA
*
29079026 ATAAATGATAATGCCTGA
1 ATAAATGATAATACCTGA
29079044 TAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (19 bp):
ATAAATGATAATACCTGAA
Found at i:29079048 original size:17 final size:17
Alignment explanation
Indices: 29078999--29079053 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
29078989 CATATTCGAC
*
29078999 AATGCCCGATAAATGAT
1 AATGCCTGATAAATGAT
*
29079016 AATACCTGAAATAAATGAT
1 AATGCCTG--ATAAATGAT
*
29079035 AATGCCTGATAAATAAT
1 AATGCCTGATAAATGAT
29079052 AA
1 AA
29079054 ATGATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 16 0.50
19 16 0.50
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (17 bp):
AATGCCTGATAAATGAT
Found at i:29087313 original size:22 final size:22
Alignment explanation
Indices: 29087277--29087325 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
29087267 TAATCGTAGA
29087277 TTTATTATTCTATTTTAATTAT
1 TTTATTATTCTATTTTAATTAT
29087299 TTTAGTTATTC-ATTTTAATTAT
1 TTTA-TTATTCTATTTTAATTAT
29087321 TTTAT
1 TTTAT
29087326 CTGATTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.73
23 6 0.23
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTATTATTCTATTTTAATTAT
Found at i:29090379 original size:21 final size:22
Alignment explanation
Indices: 29090340--29090380 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
29090330 GTTGAAATGT
29090340 CACACGGGCGTGTTGCCCCTCC
1 CACACGGGCGTGTTGCCCCTCC
29090362 CACACGGGCGTG-TGCCCCT
1 CACACGGGCGTGTTGCCCCT
29090381 ATGTTAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.10, C:0.44, G:0.29, T:0.17
Consensus pattern (22 bp):
CACACGGGCGTGTTGCCCCTCC
Found at i:29093957 original size:18 final size:19
Alignment explanation
Indices: 29093917--29093958 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
29093907 TCTTGTTGAC
29093917 ATAAAATTAGTAAATAACT
1 ATAAAATTAGTAAATAACT
* *
29093936 -TAAAA-TAGTTAATAATT
1 ATAAAATTAGTAAATAACT
29093953 ATAAAA
1 ATAAAA
29093959 AAATTTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAAAATTAGTAAATAACT
Found at i:29094929 original size:19 final size:19
Alignment explanation
Indices: 29094905--29094942 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29094895 AGATAAAATA
29094905 ATCAAAAAATTAAAGCTAT
1 ATCAAAAAATTAAAGCTAT
29094924 ATCAAAAAATTAAAGCTAT
1 ATCAAAAAATTAAAGCTAT
29094943 CATCTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (19 bp):
ATCAAAAAATTAAAGCTAT
Found at i:29095826 original size:25 final size:24
Alignment explanation
Indices: 29095798--29095857 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
29095788 CGATACTCAA
*
29095798 CTCATATGAGCTTACCGTTATGTAG
1 CTCATATGAGCTTACC-TTATATAG
* * * *
29095823 CTCAGAGGACCTTACCTTTTATAG
1 CTCATATGAGCTTACCTTATATAG
29095847 CTCATATGAGC
1 CTCATATGAGC
29095858 ATACATGTAC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (24 bp):
CTCATATGAGCTTACCTTATATAG
Found at i:29103363 original size:25 final size:25
Alignment explanation
Indices: 29103301--29103379 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
29103291 GTCATTAGGG
* *
29103301 TTACCAATTC-CAGCTCTTATGAGC
1 TTACCAATACTCAGCTCGTATGAGC
*
29103325 TTATCAATACTCAGCTCGTATGAGC
1 TTACCAATACTCAGCTCGTATGAGC
** * * *
29103350 TTACCGTTATTCAGCTCGGAGGAGC
1 TTACCAATACTCAGCTCGTATGAGC
29103375 TTACC
1 TTACC
29103380 TTTTATAGCC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 8 0.18
25 37 0.82
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (25 bp):
TTACCAATACTCAGCTCGTATGAGC
Found at i:29109484 original size:37 final size:37
Alignment explanation
Indices: 29109433--29109506 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
29109423 TAATCACTAA
29109433 GCCTCAAACATAGGGTACGATGCCGATGCCATGTTCC
1 GCCTCAAACATAGGGTACGATGCCGATGCCATGTTCC
* *
29109470 GCCTCAAACGTAGGGTACGATGTCGATGCCATGTTCC
1 GCCTCAAACATAGGGTACGATGCCGATGCCATGTTCC
29109507 AAACATGGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (37 bp):
GCCTCAAACATAGGGTACGATGCCGATGCCATGTTCC
Found at i:29109610 original size:49 final size:49
Alignment explanation
Indices: 29109495--29109671 Score: 187
Period size: 49 Copynumber: 3.6 Consensus size: 49
29109485 TACGATGTCG
* * * * * * *
29109495 ATGCCATGTTCCAAACATGGTCTTACACT-A-GCTCACATATCTAAGTCG
1 ATGCCATGTCCCAAACA-GGTCTTACACTGACTCTCATATATCGATGCCA
* * *
29109543 ATGCCATGTCCTAGACAGGTCTTACACTGACTTTCATATATCGATGCCA
1 ATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATATCGATGCCA
* * * * * *
29109592 ATGCCATATCCCAAACAGGTCTTACACTGGCTCTCATCTATCGGTGTCG
1 ATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATATCGATGCCA
29109641 ATGCCATGTCCCAAACAGGTCTTACACTGAC
1 ATGCCATGTCCCAAACAGGTCTTACACTGAC
29109672 ACATGTCAAG
Statistics
Matches: 106, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
47 11 0.10
48 15 0.14
49 80 0.75
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (49 bp):
ATGCCATGTCCCAAACAGGTCTTACACTGACTCTCATATATCGATGCCA
Found at i:29109659 original size:98 final size:97
Alignment explanation
Indices: 29109495--29109671 Score: 248
Period size: 98 Copynumber: 1.8 Consensus size: 97
29109485 TACGATGTCG
* * * * *
29109495 ATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATATCTAAGTCGATGCCATGTCCTAGACA
1 ATGCCATATCCCAAACATGGTCTTACACTAGCTCACATATCGAAGTCGATGCCATGTCCCAAACA
29109560 GGTCTTACACTGACTTTCATATATCGATGCCA
66 GGTCTTACACTGACTTTCATATATCGATGCCA
* * **
29109592 ATGCCATATCCCAAACA-GGTCTTACACTGGCTCTCATCTATCGGTGTCGATGCCATGTCCCAAA
1 ATGCCATATCCCAAACATGGTCTTACACTAGCTCACA--TATCGAAGTCGATGCCATGTCCCAAA
29109656 CAGGTCTTACACTGAC
64 CAGGTCTTACACTGAC
29109672 ACATGTCAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
96 17 0.25
97 15 0.22
98 37 0.54
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (97 bp):
ATGCCATATCCCAAACATGGTCTTACACTAGCTCACATATCGAAGTCGATGCCATGTCCCAAACA
GGTCTTACACTGACTTTCATATATCGATGCCA
Found at i:29117791 original size:22 final size:21
Alignment explanation
Indices: 29117755--29117799 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
29117745 GTGTCTTCAA
*
29117755 GCCTGTGTTGCGACACCCTCTG
1 GCCTGTGTCGCGACACCCT-TG
* *
29117777 GCCTGTGTCGTGACATCCTTG
1 GCCTGTGTCGCGACACCCTTG
29117798 GC
1 GC
29117800 AGATTGTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.09, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
GCCTGTGTCGCGACACCCTTG
Found at i:29122400 original size:14 final size:14
Alignment explanation
Indices: 29122381--29122420 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29122371 TTGATTGGCA
29122381 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
29122395 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
29122409 GAAAAATGTTTT
1 GTAAAATGTTTT
29122421 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:29122433 original size:34 final size:35
Alignment explanation
Indices: 29122389--29122455 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
29122379 CAGTAAAATG
* *
29122389 TTTTCCGTAAAATGA-TTTCTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGAAAAATATTTTAC
* *
29122423 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGAAAAATATTTT
29122456 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGAAAAATATTTTAC
Found at i:29122442 original size:20 final size:20
Alignment explanation
Indices: 29122404--29122443 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29122394 CGTAAAATGA
**
29122404 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGACTTACT
*
29122424 TTTCTGTAAAATGACTTACT
1 TTTCTGAAAAATGACTTACT
29122444 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTCTGAAAAATGACTTACT
Found at i:29127515 original size:24 final size:24
Alignment explanation
Indices: 29127479--29127525 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
29127469 ATAGCCTGAT
*
29127479 TAGTAGTGATATATGATCTTTGAA
1 TAGTAGTGATATATGATCCTTGAA
*
29127503 TAGTAGTGCTATATGATCCTTGA
1 TAGTAGTGATATATGATCCTTGA
29127526 CTATATAGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (24 bp):
TAGTAGTGATATATGATCCTTGAA
Found at i:29128966 original size:30 final size:32
Alignment explanation
Indices: 29128905--29128969 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
29128895 TGAATCTGTC
* *
29128905 AATACTATTAACAGTGTTATCAGTCAGCAGTT
1 AATACTATTAACACTGTTAACAGTCAGCAGTT
*
29128937 AATACTATTAACACTG-TAACGGT-AGCAGTT
1 AATACTATTAACACTGTTAACAGTCAGCAGTT
29128967 AAT
1 AAT
29128970 GTTATTAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 10 0.33
31 5 0.17
32 15 0.50
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (32 bp):
AATACTATTAACACTGTTAACAGTCAGCAGTT
Found at i:29131118 original size:3 final size:3
Alignment explanation
Indices: 29131110--29131141 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29131100 GCAAGAGGTG
29131110 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT GT
29131142 AAATACATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
GTT
Found at i:29133748 original size:22 final size:20
Alignment explanation
Indices: 29133723--29133764 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
29133713 AATAAAAGAG
29133723 TTAAAAATAAAAAATACATTAA
1 TTAAAAAT-AAAAATA-ATTAA
*
29133745 TTAAAAATGAAAATAATTAA
1 TTAAAAATAAAAATAATTAA
29133765 AAAATATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
TTAAAAATAAAAATAATTAA
Found at i:29134547 original size:38 final size:39
Alignment explanation
Indices: 29134504--29134589 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 39
29134494 AACCAGTCCA
* *
29134504 ACACACCA-TGTGGGGATAGAATCGACCCACCCAACCCT
1 ACACACCAGTATGGGGATAGAATCAACCCACCCAACCCT
* *
29134542 ACACACCAAGTATGGGGATATAATCAACCCATCCAACCCT
1 ACACACC-AGTATGGGGATAGAATCAACCCACCCAACCCT
29134582 ACACACCA
1 ACACACCA
29134590 AAAGGTACTG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 7 0.17
39 2 0.05
40 33 0.79
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (39 bp):
ACACACCAGTATGGGGATAGAATCAACCCACCCAACCCT
Found at i:29134561 original size:40 final size:40
Alignment explanation
Indices: 29134514--29134590 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
29134504 ACACACCATG
*
29134514 TGGGGATAGAATCGACCCACCCAACCCTACACACCAAGTA
1 TGGGGATAGAATCAACCCACCCAACCCTACACACCAAGTA
* *
29134554 TGGGGATATAATCAACCCATCCAACCCTACACACCAA
1 TGGGGATAGAATCAACCCACCCAACCCTACACACCAA
29134591 AAGGTACTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.35, G:0.14, T:0.14
Consensus pattern (40 bp):
TGGGGATAGAATCAACCCACCCAACCCTACACACCAAGTA
Found at i:29142290 original size:18 final size:18
Alignment explanation
Indices: 29142267--29142309 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
29142257 GCTCATCGAA
29142267 CACACGGTCGTGTATCAC
1 CACACGGTCGTGTATCAC
29142285 CACACGGTCGTGTATCAC
1 CACACGGTCGTGTATCAC
29142303 CACACGG
1 CACACGG
29142310 CCTCTATACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (18 bp):
CACACGGTCGTGTATCAC
Found at i:29143608 original size:138 final size:139
Alignment explanation
Indices: 29143256--29143721 Score: 686
Period size: 140 Copynumber: 3.3 Consensus size: 139
29143246 GTTACAAAAT
* * *
29143256 AATTAAAAAATCTTGAAGCAACATGAAACGAAAAATACAAATGTGAGTAGTAGAGGAATCCAACT
1 AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGTAGA-GAATCCAACT
* *
29143321 CGAGACTCAAGGATGTAATTACAACTATGTAATCACCTAACGAAAAAACTAATATGTTAAAAAAC
65 CGAGACTCAAGGATGTAATTACAACTATCTAATCATCTAACGAAAAAACTAATATGTTAAAAAAC
29143386 ATTAATTAAA
130 ATTAATTAAA
* * * * *
29143396 AATTTAAAAAGCTTCAAGCAACATGAAATAAAAAATACAAATTTGAGTAGGAGAGAAATCAAACT
1 AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGTAGAG-AATCCAACT
* ** * *
29143461 CGAGACTCAAAGATGTAACAACAACTATCTAATCATCTAACCAAAGAACTAATATGTTAAAAAA-
65 CGAGACTCAAGGATGTAATTACAACTATCTAATCATCTAACGAAAAAACTAATATGTTAAAAAAC
29143525 ATTAATT-AA
130 ATTAATTAAA
*
29143534 AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGTAGATGAATCCAGCT
1 AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGTAGA-GAATCCAACT
* *
29143599 TGAGACTCAAGGATGTAATTACAACTATCTAA-CAATGTAACGAAAAAACTAATATGTTAAAAAA
65 CGAGACTCAAGGATGTAATTACAACTATCTAATC-ATCTAACGAAAAAACTAATATGTTAAAAAA
29143663 CATTAATTAAA
129 CATTAATTAAA
* * *
29143674 AAATTAAAAAGCTTAAAGCAACATGAAATAAAAAATACAAATGTGAGT
1 AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGT
29143722 GGGAGAGCAA
Statistics
Matches: 290, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
137 1 0.00
138 114 0.39
139 16 0.06
140 159 0.55
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (139 bp):
AATTTAAAAAGCTTGAAGCAACATGAAACAAAAAATACAAATGTGAGTAGTAGAGAATCCAACTC
GAGACTCAAGGATGTAATTACAACTATCTAATCATCTAACGAAAAAACTAATATGTTAAAAAACA
TTAATTAAA
Found at i:29156545 original size:39 final size:39
Alignment explanation
Indices: 29156502--29156583 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
29156492 GTAGAGATCC
29156502 CTAAGTTATGTTATTATCCCTATTCAAGACTAATAACGT
1 CTAAGTTATGTTATTATCCCTATTCAAGACTAATAACGT
29156541 CTAAGTTATGTTATTATCCCTATTCAAGACTAATAACGT
1 CTAAGTTATGTTATTATCCCTATTCAAGACTAATAACGT
29156580 CTAA
1 CTAA
29156584 TCCTTAGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (39 bp):
CTAAGTTATGTTATTATCCCTATTCAAGACTAATAACGT
Found at i:29163387 original size:3 final size:3
Alignment explanation
Indices: 29163379--29163406 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29163369 ATTGAATTCC
29163379 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29163407 AGAAATGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29163651 original size:6 final size:6
Alignment explanation
Indices: 29163640--29163667 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29163630 TATTTTTATG
29163640 AATTAA AATTAA AATTAA AATTAA AATT
1 AATTAA AATTAA AATTAA AATTAA AATT
29163668 TTTAACTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
AATTAA
Found at i:29166164 original size:12 final size:12
Alignment explanation
Indices: 29166129--29166158 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
29166119 AACTATTTGT
29166129 TAAAAATACTAA
1 TAAAAATACTAA
29166141 T-AAAATACTAA
1 TAAAAATACTAA
29166152 TAAAAAT
1 TAAAAAT
29166159 TATAATTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAAATACTAA
Found at i:29166174 original size:18 final size:19
Alignment explanation
Indices: 29166151--29166195 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
29166141 TAAAATACTA
*
29166151 ATAAAAATTATAATTTA-G
1 ATAAAAATTAGAATTTAGG
29166169 ATAAAAA-TAGAATTTAGG
1 ATAAAAATTAGAATTTAGG
*
29166187 AAAAAAATT
1 ATAAAAATT
29166196 TAAGAGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 14 0.61
19 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (19 bp):
ATAAAAATTAGAATTTAGG
Found at i:29169617 original size:49 final size:49
Alignment explanation
Indices: 29169544--29169650 Score: 178
Period size: 49 Copynumber: 2.2 Consensus size: 49
29169534 AGAATTTTGG
* *
29169544 GCCCACATACCCGTTTGGCCCACATGCCCAAATTGGCTTCACCCGTGTA
1 GCCCACATGCCCATTTGGCCCACATGCCCAAATTGGCTTCACCCGTGTA
* *
29169593 GCCCACATGCCCATTTGGCTCACATGCCCAAATTGGCTTCACCCGTGTG
1 GCCCACATGCCCATTTGGCCCACATGCCCAAATTGGCTTCACCCGTGTA
29169642 GCCCACATG
1 GCCCACATG
29169651 ACCTGGCCCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.20, C:0.38, G:0.20, T:0.22
Consensus pattern (49 bp):
GCCCACATGCCCATTTGGCCCACATGCCCAAATTGGCTTCACCCGTGTA
Found at i:29169630 original size:18 final size:17
Alignment explanation
Indices: 29169596--29169630 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
29169586 CCGTGTAGCC
*
29169596 CACATGCCCATTTGGCT
1 CACATGCCCAATTGGCT
29169613 CACATGCCCAAATTGGCT
1 CACATGCCC-AATTGGCT
29169631 TCACCCGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (17 bp):
CACATGCCCAATTGGCT
Found at i:29171392 original size:29 final size:31
Alignment explanation
Indices: 29171328--29171392 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
29171318 ATTTGGTCTT
* *
29171328 ATTTGATTCATTTTAATAGTACAATGATCAA
1 ATTTGATCCATTTTAAGAGTACAATGATCAA
* *
29171359 A-TTGATCCA-TTTAAGAGTAGAGTGA-CAA
1 ATTTGATCCATTTTAAGAGTACAATGATCAA
29171387 ATTTGA
1 ATTTGA
29171393 CCAGATCCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 4 0.14
29 17 0.59
30 7 0.24
31 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (31 bp):
ATTTGATCCATTTTAAGAGTACAATGATCAA
Found at i:29171903 original size:26 final size:26
Alignment explanation
Indices: 29171874--29171928 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
29171864 CATCAACCTC
29171874 TTTCCAAAAGTATAAAGCCCCAAAAA
1 TTTCCAAAAGTATAAAGCCCCAAAAA
29171900 TTTCCAAAAGTATAAAGCCCCAAAAA
1 TTTCCAAAAGTATAAAGCCCCAAAAA
29171926 TTT
1 TTT
29171929 GAACTTCTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24
Consensus pattern (26 bp):
TTTCCAAAAGTATAAAGCCCCAAAAA
Found at i:29172961 original size:63 final size:63
Alignment explanation
Indices: 29172873--29173039 Score: 201
Period size: 63 Copynumber: 2.7 Consensus size: 63
29172863 TGGTAGGCCA
* * * *
29172873 TGTAACTCGCTGTTTTGGAATTAGAGTCACATAGGCTAGAGACACG-GACGTGTGTCTAAGCCG
1 TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACACGAG-CGTGTATCTAAGCAG
* ** * * * *
29172936 TGTAACTCACTATTTTAAAATTAGAGTCACACGGGCCAGAGACACGAGCGTGTATTTAGGCAG
1 TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACACGAGCGTGTATCTAAGCAG
* *
29172999 TGTAACTCACTGTTTCGGAATTAGAGTCACACAAGCTAGAG
1 TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAG
29173040 GCATAGACGT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 84 0.99
64 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (63 bp):
TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACACGAGCGTGTATCTAAGCAG
Found at i:29173057 original size:63 final size:62
Alignment explanation
Indices: 29172873--29173058 Score: 192
Period size: 63 Copynumber: 3.0 Consensus size: 62
29172863 TGGTAGGCCA
* * * * * *
29172873 TGTAACTCGCTGTTTTGGAATTAGAGTCACATAGGCTAGAGACACGGACGTGTGTCTAAGCCG
1 TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACA-AGACGTGTGTTTAGGCAG
* ** * * * *
29172936 TGTAACTCACTATTTTAAAATTAGAGTCACACGGGCCAGAGACACGAGCGTGTATTTAGGCAG
1 TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACAAGA-CGTGTGTTTAGGCAG
* * * *
29172999 TGTAACTCACTGTTTCGGAATTAGAGTCACACAAGCTAGAGGCATAGACGTATGTTTAGG
1 TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACA-AGACGTGTGTTTAGG
29173059 TCGTGTGAGA
Statistics
Matches: 98, Mismatches: 23, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
62 2 0.02
63 94 0.96
64 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (62 bp):
TGTAACTCACTGTTTTGGAATTAGAGTCACACAGGCTAGAGACAAGACGTGTGTTTAGGCAG
Found at i:29173475 original size:42 final size:42
Alignment explanation
Indices: 29173428--29173512 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
29173418 TCGAATAAGT
29173428 AAGTGTGTTTTGTATTTTATGA-ACATAATCTGAATTCGTATC
1 AAGTGTGTTTTGTATTTTATGAGA-ATAATCTGAATTCGTATC
29173470 AAGTGTGTTTTGTATTTTATGAGAATAATCTGAATTCGTATC
1 AAGTGTGTTTTGTATTTTATGAGAATAATCTGAATTCGTATC
29173512 A
1 A
29173513 CTATATATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (42 bp):
AAGTGTGTTTTGTATTTTATGAGAATAATCTGAATTCGTATC
Found at i:29176414 original size:37 final size:37
Alignment explanation
Indices: 29176362--29176435 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
29176352 AGCCATGTTT
* *
29176362 TCTAGTGACTGAAATTTGCAAAAAATGGGGTTTTTGG
1 TCTAGCGACTAAAATTTGCAAAAAATGGGGTTTTTGG
29176399 TCTAGCGACTAAAATTTGCAAAAAATGGGGTTTTTGG
1 TCTAGCGACTAAAATTTGCAAAAAATGGGGTTTTTGG
29176436 CATACACCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (37 bp):
TCTAGCGACTAAAATTTGCAAAAAATGGGGTTTTTGG
Found at i:29178364 original size:25 final size:25
Alignment explanation
Indices: 29178330--29178383 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
29178320 TGATTATTAC
29178330 TTTTAAGATTGAACTCTATGAAATG
1 TTTTAAGATTGAACTCTATGAAATG
29178355 TTTTAAGATTGAACTCTATGAAATG
1 TTTTAAGATTGAACTCTATGAAATG
29178380 TTTT
1 TTTT
29178384 GAGAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (25 bp):
TTTTAAGATTGAACTCTATGAAATG
Found at i:29180109 original size:32 final size:32
Alignment explanation
Indices: 29180053--29180126 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
29180043 AAATTTTTAT
* * *
29180053 TATTTTAAATTAAGTACTATTAATAATATAAA
1 TATTTTAAAATAAATACTAATAATAATATAAA
* *
29180085 TATTTTAAAATAAATATTAATAATAATATACA
1 TATTTTAAAATAAATACTAATAATAATATAAA
29180117 TATTTTAAAA
1 TATTTTAAAA
29180127 ATGTTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (32 bp):
TATTTTAAAATAAATACTAATAATAATATAAA
Found at i:29183894 original size:87 final size:87
Alignment explanation
Indices: 29183790--29183987 Score: 243
Period size: 87 Copynumber: 2.3 Consensus size: 87
29183780 ATAATTTGTG
* * ** * * * * *
29183790 ACACTAATGGTTTATCCACGAATTTACTGGTAGCTCTTATCTGCAAGCATGTTGTGTACTCATAA
1 ACACTAATGGTTCATCCACAAATTTACTGACAACTCTTATCTACAAACACGTTGTGTACTCACAA
*
29183855 TCTACTGGCAGTTTATATGCAA
66 CCTACTGGCAGTTTATATGCAA
* * * *
29183877 ACACTAATGGTTCATCCAAAAACTTACTGACAACTTTTATCTACAAACACGTTGTGTATTCACAA
1 ACACTAATGGTTCATCCACAAATTTACTGACAACTCTTATCTACAAACACGTTGTGTACTCACAA
* *
29183942 CCTACTGGTAGTTTATCTGCAA
66 CCTACTGGCAGTTTATATGCAA
*
29183964 ACACTGATGGTTCATCCACAAATT
1 ACACTAATGGTTCATCCACAAATT
29183988 GAAGTGTCCG
Statistics
Matches: 92, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
87 92 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (87 bp):
ACACTAATGGTTCATCCACAAATTTACTGACAACTCTTATCTACAAACACGTTGTGTACTCACAA
CCTACTGGCAGTTTATATGCAA
Found at i:29186393 original size:5 final size:5
Alignment explanation
Indices: 29186378--29186448 Score: 52
Period size: 5 Copynumber: 13.8 Consensus size: 5
29186368 TATATCGGAA
* * * * * *
29186378 CATAT CTTAT CATAT CAAAG CATAT TATAAAT CATAC CATAC CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CAT--AT CATAT CATAT CATAT CATAT
* *
29186430 TATAT CATAT TATAT CATA
1 CATAT CATAT CATAT CATA
29186449 CCATGCAATG
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
5 46 0.92
7 4 0.08
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.38
Consensus pattern (5 bp):
CATAT
Found at i:29189823 original size:47 final size:46
Alignment explanation
Indices: 29189755--29190053 Score: 232
Period size: 47 Copynumber: 6.4 Consensus size: 46
29189745 GATGTGAACT
* *
29189755 AGTGTATGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-GATGAGAGTC
* * *
29189801 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CATTGAGACGAGAG-C
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCA-CGAGATGAGAGTC
* ** * * *
29189848 TAGTGTAAGACATGTCTAGGACATGCATTAGCCTCGAGACGTA-AGCC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATG-AGAGTC
* * * *
29189895 AGTGTAAGACATGTCTAGGACATGCATCGACTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAGAGTC
* * * *
29189941 AGTGTAAGACCATGTCTGAGACATACATCGGCTACGAGATGATAGTC
1 AGTGTAAGA-CATGTCTGGGACATGCATCGGCCACGAGATGAGAGTC
* * * ** *
29189988 AATGTAAGACCATGTTTGGGACATGGCATC-GACTTGAGAT-ATGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACGAGATGA-GAGTC
29190035 AGTGTAAGACCATGTCTGG
1 AGTGTAAGA-CATGTCTGG
29190054 AATATGACAT
Statistics
Matches: 209, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
45 1 0.00
46 69 0.33
47 113 0.54
48 25 0.12
49 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAGAGTC
Found at i:29190010 original size:140 final size:140
Alignment explanation
Indices: 29189755--29190012 Score: 317
Period size: 140 Copynumber: 1.8 Consensus size: 140
29189745 GATGTGAACT
* * * * *
29189755 AGTGTATGACATGTCTGGGACATGCATCGGCCACATTATGAGAGTCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTAGGACATGCATCGACCACATGATGAGAGTCAGTGTAAGACCATGTCTGA
* * *
29189820 GACATGGCATCAGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACATGCATTAGCCTCGA
66 GACATGACATCAGCATCGAGACGAGAGCTAATGTAAGACATGTCTAGGACATGCATTAGCCTCGA
29189885 GACGTAAGCC
131 GACGTAAGCC
* *
29189895 AGTGTAAGACATGTCTAGGACATGCATCGACTACGA-GATGATAGTCAGTGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTAGGACATGCATCGACCAC-ATGATGAGAGTCAGTGTAAGACCATGTCTG
* * * * *
29189959 AGACAT-ACATCGGC-TACGAGATGATAG-TCAATGTAAGACCATGTTTGGGACATG
65 AGACATGACATCAGCAT-CGAGACGAGAGCT-AATGTAAGA-CATGTCTAGGACATG
29190013 GCATCGACTT
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
138 2 0.02
139 22 0.22
140 74 0.75
141 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTAGGACATGCATCGACCACATGATGAGAGTCAGTGTAAGACCATGTCTGA
GACATGACATCAGCATCGAGACGAGAGCTAATGTAAGACATGTCTAGGACATGCATTAGCCTCGA
GACGTAAGCC
Found at i:29190035 original size:140 final size:140
Alignment explanation
Indices: 29189755--29190051 Score: 316
Period size: 140 Copynumber: 2.1 Consensus size: 140
29189745 GATGTGAACT
* * * * *
29189755 AGTGTATGACATGTCTGGGACATGCATCGGCCACATTATGAGAGTCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTAGGACATGCATCGACCACATGATGAGAGTCAGTGTAAGACCATGTCTGA
* * * *
29189820 GACATGGCATCAGCATTGAGACGAGAGCTAGTGTAAGACATGTCTAGGACATGCATTAGCCTCGA
66 GACATGACATCAGCATCGAGACGAGAGCTAATGTAAGACATGTCTAGGACATGCATTAGACTCGA
*
29189885 GACGTAAGCC
131 GACATAAGCC
* *
29189895 AGTGTAAGACATGTCTAGGACATGCATCGACTACGA-GATGATAGTCAGTGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTAGGACATGCATCGACCAC-ATGATGAGAGTCAGTGTAAGACCATGTCTG
* * * * * *
29189959 AGACAT-ACATCGGC-TACGAGATGATAG-TCAATGTAAGACCATGTTTGGGACATGGCA-TCGA
65 AGACATGACATCAGCAT-CGAGACGAGAGCT-AATGTAAGA-CATGTCTAGGACAT-GCATTAGA
* * *
29190020 CTTGAGATATGAGCC
126 CTCGAGACATAAGCC
29190035 AGTGTAAGACCATGTCT
1 AGTGTAAGA-CATGTCT
29190052 GGAATATGAC
Statistics
Matches: 130, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
138 2 0.02
139 22 0.17
140 95 0.73
141 11 0.08
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (140 bp):
AGTGTAAGACATGTCTAGGACATGCATCGACCACATGATGAGAGTCAGTGTAAGACCATGTCTGA
GACATGACATCAGCATCGAGACGAGAGCTAATGTAAGACATGTCTAGGACATGCATTAGACTCGA
GACATAAGCC
Found at i:29190041 original size:94 final size:93
Alignment explanation
Indices: 29189755--29190052 Score: 281
Period size: 94 Copynumber: 3.2 Consensus size: 93
29189745 GATGTGAACT
* * * * *
29189755 AGTGTATGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGTCAGTGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTGAGACATGCATCGGCTACGA-GATGATAGTCAGTGTAAGACCATGTCTG
* *
29189819 GGACATGGCATC-AGCATTGAGACGA-GAGCT
65 GGACATGGCATCGA-C-TTGAGA-TATGAGCC
* * * *
29189849 AGTGTAAGACATGTCT-AGGACATGCATTAGCCT-CGAGACG-TAAGCCAGTGTAAGA-CATGTC
1 AGTGTAAGACATGTCTGA-GACATGCA-TCGGCTACGAGATGAT-AGTCAGTGTAAGACCATGTC
* * *
29189910 TAGGACAT-GCATCGACTACGAGATGAT-AGTC
63 TGGGACATGGCATCGACT-TGAGAT-ATGAGCC
* * *
29189941 AGTGTAAGACCATGTCTGAGACATACATCGGCTACGAGATGATAGTCAATGTAAGACCATGTTTG
1 AGTGTAAGA-CATGTCTGAGACATGCATCGGCTACGAGATGATAGTCAGTGTAAGACCATGTCTG
29190006 GGACATGGCATCGACTTGAGATATGAGCC
65 GGACATGGCATCGACTTGAGATATGAGCC
29190035 AGTGTAAGACCATGTCTG
1 AGTGTAAGA-CATGTCTG
29190053 GAATATGACA
Statistics
Matches: 165, Mismatches: 24, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
91 1 0.01
92 26 0.16
93 47 0.28
94 78 0.47
95 13 0.08
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (93 bp):
AGTGTAAGACATGTCTGAGACATGCATCGGCTACGAGATGATAGTCAGTGTAAGACCATGTCTGG
GACATGGCATCGACTTGAGATATGAGCC
Found at i:29194110 original size:34 final size:34
Alignment explanation
Indices: 29194072--29194139 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
29194062 TCATATCTGA
* *
29194072 TACTGAAACCGAAATGGGCTAAGGCTCAAACTGC
1 TACTGAAACCAAAATGGGCTAAGGCCCAAACTGC
* *
29194106 TACTGAAACTAAAATGGGCTTAGGCCCAAACTGC
1 TACTGAAACCAAAATGGGCTAAGGCCCAAACTGC
29194140 ATTTGACTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (34 bp):
TACTGAAACCAAAATGGGCTAAGGCCCAAACTGC
Found at i:29198891 original size:17 final size:17
Alignment explanation
Indices: 29198869--29198902 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29198859 GTTCATTCAG
*
29198869 AATTAAATCAGCCACCC
1 AATTAAAACAGCCACCC
29198886 AATTAAAACAGCCACCC
1 AATTAAAACAGCCACCC
29198903 TTTCAGTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.35, G:0.06, T:0.15
Consensus pattern (17 bp):
AATTAAAACAGCCACCC
Found at i:29202997 original size:23 final size:23
Alignment explanation
Indices: 29202970--29203024 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
29202960 CTATGCCAGA
*
29202970 AGAAAGAGCGTGTCAAAAGACAG
1 AGAAAGAGCGTGCCAAAAGACAG
29202993 AGAAAGAGCGTGCCAAAAGACAG
1 AGAAAGAGCGTGCCAAAAGACAG
*
29203016 AAAAAGAGC
1 AGAAAGAGC
29203025 TATTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.51, C:0.15, G:0.29, T:0.05
Consensus pattern (23 bp):
AGAAAGAGCGTGCCAAAAGACAG
Found at i:29203747 original size:16 final size:17
Alignment explanation
Indices: 29203712--29203744 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29203702 AAAACATGGT
29203712 TTTTTTTCTTTATAAAA
1 TTTTTTTCTTTATAAAA
29203729 TTTTTTTCTTTATAAA
1 TTTTTTTCTTTATAAA
29203745 TTTGGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTTCTTTATAAAA
Found at i:29211438 original size:6 final size:6
Alignment explanation
Indices: 29211427--29211460 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
29211417 GTGATGTGGT
*
29211427 AATGGG AATGGG AATGGG AATAGG AATGGG AATG
1 AATGGG AATGGG AATGGG AATGGG AATGGG AATG
29211461 AACATGTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.44, T:0.18
Consensus pattern (6 bp):
AATGGG
Found at i:29214062 original size:27 final size:27
Alignment explanation
Indices: 29214023--29214154 Score: 133
Period size: 27 Copynumber: 5.0 Consensus size: 27
29214013 AAAGATACAT
* * *
29214023 CACATATGGGCAAAACAGCCATCTTAA
1 CACATAAGGGCAAAACAGTCATTTTAA
* * *
29214050 CATATAAGGGCAAAATAGTAATTTT-A
1 CACATAAGGGCAAAACAGTCATTTTAA
* * *
29214076 C-CACAAGGGCAAAACGGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAA
* * *
29214102 CATATAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAA
*
29214129 CACATAAGGGCAAAACAATCATTTTA
1 CACATAAGGGCAAAACAGTCATTTTA
29214155 TCAATTTGGG
Statistics
Matches: 84, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
25 18 0.21
26 3 0.04
27 63 0.75
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAA
Found at i:29214106 original size:52 final size:53
Alignment explanation
Indices: 29214030--29214154 Score: 180
Period size: 52 Copynumber: 2.4 Consensus size: 53
29214020 CATCACATAT
* *
29214030 GGGCAAAACAGCCATCTTAACATATAAGGGCAAAATAGTAATTTTACCAC-AA
1 GGGCAAAACAGTCATTTTAACATATAAGGGCAAAATAGTAATTTTACCACAAA
* * *
29214082 GGGCAAAACGGTCATTTTACCATATAAGGGCAAAATAGTCATTTTACCACATAA
1 GGGCAAAACAGTCATTTTAACATATAAGGGCAAAATAGTAATTTTACCACA-AA
*
29214136 GGGCAAAACAATCATTTTA
1 GGGCAAAACAGTCATTTTA
29214155 TCAATTTGGG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
52 45 0.70
54 19 0.30
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (53 bp):
GGGCAAAACAGTCATTTTAACATATAAGGGCAAAATAGTAATTTTACCACAAA
Found at i:29217485 original size:18 final size:18
Alignment explanation
Indices: 29217462--29217496 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29217452 TGACCCATTA
29217462 CAGTAACAATAAACAGTG
1 CAGTAACAATAAACAGTG
*
29217480 CAGTAACAGTAAACAGT
1 CAGTAACAATAAACAGT
29217497 ATGCAAGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (18 bp):
CAGTAACAATAAACAGTG
Found at i:29217906 original size:30 final size:29
Alignment explanation
Indices: 29217813--29217951 Score: 130
Period size: 27 Copynumber: 5.0 Consensus size: 29
29217803 AAATATACAT
* * *
29217813 CACATAGGGGCAAAACAGTCATCTTAT--
1 CACATAAGGGCAAAATAGTCATTTTATAC
* *
29217840 CATATAAGGGAAAAATAGTCA-TTT-TAC
1 CACATAAGGGCAAAATAGTCATTTTATAC
*
29217867 TACATAAGGGCAAAAT-GATCATTTTATCAC
1 CACATAAGGGCAAAATAG-TCATTTTAT-AC
* * *
29217897 CATATAAGGGTAGAATAGTCA-TTT-TAC
1 CACATAAGGGCAAAATAGTCATTTTATAC
29217924 CACATAAGGGCAAAATAGTCATTTTATA
1 CACATAAGGGCAAAATAGTCATTTTATA
29217952 AATTTTGGGG
Statistics
Matches: 88, Mismatches: 15, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
25 1 0.01
26 3 0.03
27 53 0.60
28 7 0.08
29 6 0.07
30 17 0.19
31 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (29 bp):
CACATAAGGGCAAAATAGTCATTTTATAC
Found at i:29217918 original size:57 final size:57
Alignment explanation
Indices: 29217813--29217950 Score: 185
Period size: 57 Copynumber: 2.5 Consensus size: 57
29217803 AAATATACAT
* * *
29217813 CACATAGGGGCAAAACAGTCATCTTAT---CATATAAGGGAAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTATCACCATATAAGGGAAAAATAGTCATTTTAC
* * *
29217867 TACATAAGGGCAAAAT-GATCATTTTATCACCATATAAGGGTAGAATAGTCATTTTAC
1 CACATAAGGGCAAAATAG-TCATTTTATCACCATATAAGGGAAAAATAGTCATTTTAC
29217924 CACATAAGGGCAAAATAGTCATTTTAT
1 CACATAAGGGCAAAATAGTCATTTTAT
29217951 AAATTTTGGG
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
53 1 0.01
54 21 0.29
57 49 0.68
58 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (57 bp):
CACATAAGGGCAAAATAGTCATTTTATCACCATATAAGGGAAAAATAGTCATTTTAC
Found at i:29220640 original size:36 final size:36
Alignment explanation
Indices: 29220579--29220649 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
29220569 GGAGCACATC
*
29220579 AGTCAAAATAGATCTGAAAAACTGTTGGAA-TGAATT
1 AGTCAAAATAGATCCGAAAAACTGTT-GAATTGAATT
* **
29220615 AGTCAGAATAGATCCGAAAGGCTGTTGAATTGAAT
1 AGTCAAAATAGATCCGAAAAACTGTTGAATTGAAT
29220650 AGAGTTTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 3 0.10
36 27 0.90
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.27
Consensus pattern (36 bp):
AGTCAAAATAGATCCGAAAAACTGTTGAATTGAATT
Found at i:29222670 original size:18 final size:20
Alignment explanation
Indices: 29222647--29222691 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
29222637 ATAGTTTAAC
29222647 ATTTAATTAAA-CCTAATT-
1 ATTTAATTAAATCCTAATTA
* *
29222665 ATTTAACTAAATCTTAATTA
1 ATTTAATTAAATCCTAATTA
29222685 ATTTAAT
1 ATTTAAT
29222692 ATTAAGCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 10 0.45
19 6 0.27
20 6 0.27
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAATTAAATCCTAATTA
Found at i:29224646 original size:19 final size:19
Alignment explanation
Indices: 29224622--29224683 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
29224612 ATTTTGAAAA
* *
29224622 TTTTATAAATATTTTGATT
1 TTTTATAAATATATTGAAT
29224641 TTTTATAAATATATTGAAT
1 TTTTATAAATATATTGAAT
*
29224660 TTTTA-AAATTTATTTCGAAT
1 TTTTATAAATATA-TT-GAAT
29224680 TTTT
1 TTTT
29224684 TTTGTATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.16
19 24 0.63
20 8 0.21
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTATAAATATATTGAAT
Found at i:29224672 original size:45 final size:45
Alignment explanation
Indices: 29224583--29224670 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 45
29224573 TTATTCTATA
29224583 AAATTTTTAATTTTTTAAAAAATATATAAATTTTGAAAATTTTAT
1 AAATTTTTAATTTTTTAAAAAATATATAAATTTTGAAAATTTTAT
* * * *
29224628 AAATATTTTGATTTTTT-ATAAATATATTGAATTTTTAAAATTT
1 AAAT-TTTTAATTTTTTAAAAAATATA-TAAATTTTGAAAATTT
29224671 ATTTCGAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 12 0.32
46 25 0.68
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (45 bp):
AAATTTTTAATTTTTTAAAAAATATATAAATTTTGAAAATTTTAT
Found at i:29228648 original size:38 final size:38
Alignment explanation
Indices: 29228606--29228683 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
29228596 AACTACAGGG
29228606 AATTACAAGCTGAACAGTAAGGTACTAACTATAAAACT
1 AATTACAAGCTGAACAGTAAGGTACTAACTATAAAACT
*
29228644 AATTACAAGCTGAACAGTAAGTTACTAACTATAAAACT
1 AATTACAAGCTGAACAGTAAGGTACTAACTATAAAACT
29228682 AA
1 AA
29228684 CTGCAAAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (38 bp):
AATTACAAGCTGAACAGTAAGGTACTAACTATAAAACT
Found at i:29230825 original size:12 final size:12
Alignment explanation
Indices: 29230808--29230844 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29230798 TTGATACAAT
*
29230808 TTATTAAATAAA
1 TTATTAAAAAAA
29230820 TTATTAAAAAAA
1 TTATTAAAAAAA
29230832 -T-TTAAAAAAA
1 TTATTAAAAAAA
29230842 TTA
1 TTA
29230845 ATTCAACCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 9 0.41
11 2 0.09
12 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTATTAAAAAAA
Found at i:29232379 original size:26 final size:26
Alignment explanation
Indices: 29232320--29232372 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
29232310 TGAATTTTCA
* * *
29232320 TCAAATAAAGAAAGTGAGAATTATAT
1 TCAAAAAAAGAAAGTGAGAATCAAAT
*
29232346 TCAAAAAAAGAAAGTGATAATCAAAT
1 TCAAAAAAAGAAAGTGAGAATCAAAT
29232372 T
1 T
29232373 AACAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.57, C:0.06, G:0.13, T:0.25
Consensus pattern (26 bp):
TCAAAAAAAGAAAGTGAGAATCAAAT
Found at i:29233319 original size:27 final size:28
Alignment explanation
Indices: 29233281--29233812 Score: 229
Period size: 28 Copynumber: 19.2 Consensus size: 28
29233271 TCAGTAGAAA
* * *
29233281 GGTACCTTTAGGAGTTGTGCTGT-GATG
1 GGTACCATTAGGAGTTGTACCGTGGATG
*
29233308 GGTACCATTAGGAGTAGTACCGTGGATG
1 GGTACCATTAGGAGTTGTACCGTGGATG
* * *
29233336 GGTACCATTAGGAGTTATACCAT-GAAG
1 GGTACCATTAGGAGTTGTACCGTGGATG
* * * * * * **
29233363 GATACTAGTAAGAGTTATACCGTAGAAA
1 GGTACCATTAGGAGTTGTACCGTGGATG
* * * *
29233391 GATACCTTTAAGAGTTGTATCGTGGATG
1 GGTACCATTAGGAGTTGTACCGTGGATG
* * * *
29233419 AGTACCA-TAGGAGTCGTACCATGGAGG
1 GGTACCATTAGGAGTTGTACCGTGGATG
*** *
29233446 GGTACCATTAGGAGCCATACCATGGAT-
1 GGTACCATTAGGAGTTGTACCGTGGATG
* * * ****
29233473 GATACCTTTAAGAGTTGTGTAATGGATG
1 GGTACCATTAGGAGTTGTACCGTGGATG
* * *
29233501 GGTGCCATTAGGAGTTGTACGGTAGATG
1 GGTACCATTAGGAGTTGTACCGTGGATG
** * **
29233529 CATACCTTTAGGAGTCATACCGTGGATG
1 GGTACCATTAGGAGTTGTACCGTGGATG
* ** * *
29233557 GGTACC-TATAGGAATCATGCCATGGATG
1 GGTACCAT-TAGGAGTTGTACCGTGGATG
* ** * * *
29233585 GATACCATTATGG-GTCATACCATAGATA
1 GGTACCATTA-GGAGTTGTACCGTGGATG
* * ** * *
29233613 GGTACCTTTAGGAGTCGTGTCGTAGACG
1 GGTACCATTAGGAGTTGTACCGTGGATG
* * * * *
29233641 GATACAACTAGGAGTTGTACCATGGAGG
1 GGTACCATTAGGAGTTGTACCGTGGATG
* * **
29233669 GGAACCATTAGGAGTTTTATTGTGGATG
1 GGTACCATTAGGAGTTGTACCGTGGATG
* * *
29233697 GCTACTATTAGGAGTCATGT--TGTGGAT-
1 GGTACCATTAGGAGT--TGTACCGTGGATG
* * * *
29233724 GGTACCGTTAGGAGTCGTACCATGGATA
1 GGTACCATTAGGAGTTGTACCGTGGATG
* *
29233752 GGTACCTTTCA-GAGTTGTATCGTGGATG
1 GGTACCATT-AGGAGTTGTACCGTGGATG
** *
29233780 GACACCATTAGGAGTTGTATCGTGGATG
1 GGTACCATTAGGAGTTGTACCGTGGATG
29233808 GGTAC
1 GGTAC
29233813 TATAACACCC
Statistics
Matches: 373, Mismatches: 117, Indels: 29
0.72 0.23 0.06
Matches are distributed among these distances:
25 2 0.01
27 100 0.27
28 265 0.71
29 4 0.01
30 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (28 bp):
GGTACCATTAGGAGTTGTACCGTGGATG
Found at i:29233805 original size:83 final size:82
Alignment explanation
Indices: 29233649--29233808 Score: 182
Period size: 83 Copynumber: 1.9 Consensus size: 82
29233639 CGGATACAAC
* * * * *
29233649 TAGGAGTTGTACCATGGAGGGGAACCATTAGGAGTTTTATTGTGGATGGCTACTATTAGGAGTCA
1 TAGGAGTCGTACCATGGAGAGGAACCATTAGGAGTTGTATCGTGGATGGCTACCATTAGGAGT-A
29233714 TGTTGTGGATGGTACCGT
65 TGTTGTGGATGGTACCGT
* * *
29233732 TAGGAGTCGTACCATGGATAGGTACCTTTCA-GAGTTGTATCGTGGATGGAC-ACCATTAGGAGT
1 TAGGAGTCGTACCATGGAGAGGAACCATT-AGGAGTTGTATCGTGGATGG-CTACCATTAGGAGT
29233795 -TGTATCGTGGATGG
64 ATGT-T-GTGGATGG
29233809 GTACTATAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
81 3 0.05
82 1 0.02
83 59 0.91
84 2 0.03
ACGTcount: A:0.23, C:0.12, G:0.33, T:0.31
Consensus pattern (82 bp):
TAGGAGTCGTACCATGGAGAGGAACCATTAGGAGTTGTATCGTGGATGGCTACCATTAGGAGTAT
GTTGTGGATGGTACCGT
Found at i:29234121 original size:80 final size:81
Alignment explanation
Indices: 29234018--29234234 Score: 312
Period size: 81 Copynumber: 2.7 Consensus size: 81
29234008 GCACGAATTA
* * * **
29234018 TGACCAAATTGAAAAGTTCTAAAAATTCAGGATCAA-ATCGTGACATCATCTCTCTCTGGTTGGA
1 TGACCAAATTGCAAAGTTTTAAAAATTCAGGATCAATATCGTGACGTCATCTCTCTCTCATTGGA
* *
29234082 TGA-CGCACCCCTCATT
66 T-ATCACACCCCTCACT
*
29234098 TGACCAAATTGCAAAGTTTTAAAAATTCAGGATCAATATCATGACGTCATCTCTCTCTCATTGGA
1 TGACCAAATTGCAAAGTTTTAAAAATTCAGGATCAATATCGTGACGTCATCTCTCTCTCATTGGA
*
29234163 TATCACACTCCTCACT
66 TATCACACCCCTCACT
* *
29234179 TAACCAAATTGCAAATTTTTAAAAATTCAGGATCAATATCGTGACGTCATCTCTCT
1 TGACCAAATTGCAAAGTTTTAAAAATTCAGGATCAATATCGTGACGTCATCTCTCT
29234235 TTCGTTGTCG
Statistics
Matches: 123, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
80 35 0.28
81 88 0.72
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (81 bp):
TGACCAAATTGCAAAGTTTTAAAAATTCAGGATCAATATCGTGACGTCATCTCTCTCTCATTGGA
TATCACACCCCTCACT
Found at i:29236125 original size:29 final size:29
Alignment explanation
Indices: 29236083--29236139 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
29236073 AACACCAAAC
29236083 AAGTTGATTCTTCAGGGACTAATTGACAT
1 AAGTTGATTCTTCAGGGACTAATTGACAT
29236112 AAGTTGATTCTTCAGGGACTAATTGACA
1 AAGTTGATTCTTCAGGGACTAATTGACA
29236140 ATTTTAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (29 bp):
AAGTTGATTCTTCAGGGACTAATTGACAT
Found at i:29236261 original size:150 final size:149
Alignment explanation
Indices: 29236029--29236475 Score: 720
Period size: 150 Copynumber: 3.0 Consensus size: 149
29236019 ATCAAATACA
29236029 TAACAACCTAAATAAATAAATACCATATGAACTTACCTGATCAAAACACCAAACAAGTTGATTCT
1 TAACAA-CTAAATAAATAAATACCATATGAACTTACCTGATCAAAACACCAAACAAGTTGATTCT
*
29236094 TCAGGGACTAATTGACATAAGTTGATTCTTCAGGGACTAATTGACAATTTTAGCTTTTCTTCAAT
65 TCAGGGACTAATCGACATAAGTTGATTCTTCAGGGACTAATTGACAATTTTAGCTTTTCTTCAAT
29236159 TACCTCCGTTTTGATCCAAT
130 TACCTCCGTTTTGATCCAAT
* *
29236179 TAACAATCTAAATAAATAAATACCATATGAACTTACTTGATCAAAAAACCAAACAAGTTGATTCT
1 TAACAA-CTAAATAAATAAATACCATATGAACTTACCTGATCAAAACACCAAACAAGTTGATTCT
* * *
29236244 TCAGGGACTAATCGACATAAGTTGATTATTAAGGGACTAATTGACAATTTTAGCTTTTCTTCAGT
65 TCAGGGACTAATCGACATAAGTTGATTCTTCAGGGACTAATTGACAATTTTAGCTTTTCTTCAAT
29236309 TACCTCCGTTTTGATCCAAT
130 TACCTCCGTTTTGATCCAAT
**
29236329 TAAC-AC--CCTAAATAAATACCATATGAACTTACCTGATCAAAACACCAAACAAGTTGATTCTT
1 TAACAACTAAATAAATAAATACCATATGAACTTACCTGATCAAAACACCAAACAAGTTGATTCTT
* * * * * *
29236391 CGGGGACTAATCGGCACAAGTTAATTCTTCAGGGGCTAATTGACAATTTTAGCTTTTCTTTAATT
66 CAGGGACTAATCGACATAAGTTGATTCTTCAGGGACTAATTGACAATTTTAGCTTTTCTTCAATT
*
29236456 ACCTCCATTTTGATCCAAT
131 ACCTCCGTTTTGATCCAAT
29236475 T
1 T
29236476 TTTGATCTAT
Statistics
Matches: 276, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
146 127 0.46
148 1 0.00
149 1 0.00
150 147 0.53
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (149 bp):
TAACAACTAAATAAATAAATACCATATGAACTTACCTGATCAAAACACCAAACAAGTTGATTCTT
CAGGGACTAATCGACATAAGTTGATTCTTCAGGGACTAATTGACAATTTTAGCTTTTCTTCAATT
ACCTCCGTTTTGATCCAAT
Found at i:29236278 original size:29 final size:29
Alignment explanation
Indices: 29236233--29236289 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
29236223 AAAACCAAAC
* *
29236233 AAGTTGATTCTTCAGGGACTAATCGACAT
1 AAGTTGATTATTAAGGGACTAATCGACAT
*
29236262 AAGTTGATTATTAAGGGACTAATTGACA
1 AAGTTGATTATTAAGGGACTAATCGACA
29236290 ATTTTAGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (29 bp):
AAGTTGATTATTAAGGGACTAATCGACAT
Found at i:29246155 original size:12 final size:13
Alignment explanation
Indices: 29246136--29246175 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
29246126 TTGTTATATA
29246136 TATATATAATTTTT
1 TATATATAA-TTTT
29246150 TATATATAATTTT
1 TATATATAATTTT
*
29246163 T-TTTATAATTTT
1 TATATATAATTTT
29246175 T
1 T
29246176 GAGATGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.44
13 5 0.20
14 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATATAATTTT
Found at i:29246155 original size:16 final size:14
Alignment explanation
Indices: 29246136--29246175 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
29246126 TTGTTATATA
29246136 TATATATAATTTTT
1 TATATATAATTTTT
29246150 TATATATAATTTTT
1 TATATATAATTTTT
29246164 T-T-TATAATTTTT
1 TATATATAATTTTT
29246176 GAGATGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 10 0.38
13 1 0.04
14 15 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATATATAATTTTT
Found at i:29256140 original size:3 final size:3
Alignment explanation
Indices: 29256132--29256157 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29256122 TCCTTTGTTG
29256132 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
29256158 GAGGTAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:29256593 original size:31 final size:31
Alignment explanation
Indices: 29256558--29256624 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
29256548 TAATAGTTTG
*
29256558 GTGACATGAATAAAAATTTTCAAATAATTCA
1 GTGACATAAATAAAAATTTTCAAATAATTCA
* *
29256589 GTGACTTAAATGAAAATTTTCAAATAATTCA
1 GTGACATAAATAAAAATTTTCAAATAATTCA
*
29256620 CTGAC
1 GTGAC
29256625 TATTTTGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (31 bp):
GTGACATAAATAAAAATTTTCAAATAATTCA
Found at i:29257298 original size:18 final size:20
Alignment explanation
Indices: 29257255--29257299 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
29257245 TTTATTCAAT
*
29257255 AATA-ATATTTTAATTTTTG
1 AATATATATTTTAATTTGTG
*
29257274 AATATATATTTTAATTTGTA
1 AATATATATTTTAATTTGTG
29257294 AATATA
1 AATATA
29257300 ATTATTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
AATATATATTTTAATTTGTG
Found at i:29266161 original size:11 final size:11
Alignment explanation
Indices: 29266145--29266169 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29266135 GTGTATAAAG
29266145 CTTGTGAAGTA
1 CTTGTGAAGTA
29266156 CTTGTGAAGTA
1 CTTGTGAAGTA
29266167 CTT
1 CTT
29266170 TGTGTTCAGC
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:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (11 bp):
CTTGTGAAGTA
Found at i:29266404 original size:42 final size:42
Alignment explanation
Indices: 29266345--29266430 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
29266335 ACACATTGGG
29266345 ATTTAGATTTATATAAGCATTTGGGTTAATGATAAAGGACAT
1 ATTTAGATTTATATAAGCATTTGGGTTAATGATAAAGGACAT
29266387 ATTTAGATTTATATAAGCATTTGGGTTAATGATAAAGGACAT
1 ATTTAGATTTATATAAGCATTTGGGTTAATGATAAAGGACAT
29266429 AT
1 AT
29266431 GTGTACTTGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (42 bp):
ATTTAGATTTATATAAGCATTTGGGTTAATGATAAAGGACAT
Found at i:29267125 original size:7 final size:7
Alignment explanation
Indices: 29267113--29267141 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
29267103 CGGGCTAAGA
29267113 GTTTAGG
1 GTTTAGG
29267120 GTTTAGG
1 GTTTAGG
29267127 GTTTAGG
1 GTTTAGG
29267134 GTTTAGG
1 GTTTAGG
29267141 G
1 G
29267142 GTGTGATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (7 bp):
GTTTAGG
Found at i:29268316 original size:68 final size:69
Alignment explanation
Indices: 29268238--29268369 Score: 221
Period size: 68 Copynumber: 1.9 Consensus size: 69
29268228 TAATATTATT
* *
29268238 TTAATATTAAATTTAATTTAATATTTATCTTAAT-AGTATTTTATTAATTTAATATTAAAGTGAC
1 TTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGAC
29268302 CATC
66 CATC
* *
29268306 TTAATATTAAATTTAATTTAATGTTTATCTTGATAAATATTATATTAATTTAATATTAAAGTGA
1 TTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGA
29268370 TTAAGTTTAA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
68 32 0.54
69 27 0.46
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (69 bp):
TTAATATTAAATTTAATTTAATATTTATCTTAATAAATATTATATTAATTTAATATTAAAGTGAC
CATC
Found at i:29273604 original size:40 final size:40
Alignment explanation
Indices: 29273549--29273770 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
29273539 TATTCGGATG
* * **
29273549 ATATCCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTCCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
29273589 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
29273629 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
29273669 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
29273709 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
29273749 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
29273771 TACTTGGGTT
Statistics
Matches: 173, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 14 0.08
40 157 0.91
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:29278041 original size:30 final size:30
Alignment explanation
Indices: 29278004--29278119 Score: 187
Period size: 30 Copynumber: 3.9 Consensus size: 30
29277994 CTAGCCTTTG
29278004 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
29278034 TCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
29278064 CCACCACCAACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
29278094 CCACTACCTACTCCACCAGCCACACT
1 CCACCACCAACTCCACTAGCCACACT
29278120 CCACCACCAC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.27, C:0.49, G:0.06, T:0.18
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:29278067 original size:18 final size:18
Alignment explanation
Indices: 29278044--29278099 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
29278034 TCACCACCAA
29278044 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
29278062 CTCCACCA-CCA-A----
1 CTCCACTAGCCACACTTG
*
29278074 CTCCATTAGCCACACTTG
1 CTCCACTAGCCACACTTG
29278092 CTCCACTA
1 CTCCACTA
29278100 CCTACTCCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
12 6 0.21
13 3 0.11
14 1 0.04
16 1 0.04
17 3 0.11
18 14 0.50
ACGTcount: A:0.25, C:0.46, G:0.07, T:0.21
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:29278722 original size:27 final size:27
Alignment explanation
Indices: 29278692--29278829 Score: 90
Period size: 25 Copynumber: 5.3 Consensus size: 27
29278682 ATATTACGTA
*
29278692 TATATATATATTTTATACTATTTTATG
1 TATATATATATTTTATACTATATTATG
* * * *
29278719 --TATATATCTTTAATATTATATTATT
1 TATATATATATTTTATACTATATTATG
* * *
29278744 TATATATATATTTTTTTAC-ATGTTATCT
1 TATATATATA-TTTTATACTATATTAT-G
* *
29278772 TATGTATATATCTTA-ACTATATTATG
1 TATATATATATTTTATACTATATTATG
* * *
29278798 TATGTAT-T-TTTAACACTATATTATG
1 TATATATATATTTTATACTATATTATG
*
29278823 TACATAT
1 TATATAT
29278830 TTTTAATATT
Statistics
Matches: 86, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
24 3 0.03
25 37 0.43
26 9 0.10
27 22 0.26
28 15 0.17
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (27 bp):
TATATATATATTTTATACTATATTATG
Found at i:29278744 original size:30 final size:30
Alignment explanation
Indices: 29278704--29278785 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 30
29278694 TATATATATT
*
29278704 TTATACTATTTTATGTATATATCTTTAATA
1 TTATATTATTTTATGTATATATCTTTAATA
* **
29278734 TTATATTA-TTTATATATATAT-TTTTTTA
1 TTATATTATTTTATGTATATATCTTTAATA
* * *
29278762 -CATGTTATCTTATGTATATATCTT
1 TTATATTATTTTATGTATATATCTT
29278786 AACTATATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 5 0.12
28 16 0.38
29 14 0.33
30 7 0.17
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (30 bp):
TTATATTATTTTATGTATATATCTTTAATA
Found at i:29279015 original size:16 final size:15
Alignment explanation
Indices: 29278991--29279038 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
29278981 TAATTATTAT
*
29278991 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
29279007 TATTTTAATATTTTA
1 TATTTTAATATTTTA
29279022 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
29279038 T
1 T
29279039 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:29279026 original size:7 final size:8
Alignment explanation
Indices: 29278991--29279042 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
29278981 TAATTATTAT
*
29278991 TATTCTAA
1 TATTTTAA
*
29278999 TATTTTGA
1 TATTTTAA
29279007 TATTTTAA
1 TATTTTAA
29279015 TATTTT-A
1 TATTTTAA
29279022 TATTTTATA
1 TATTTTA-A
*
29279031 TATTTTAT
1 TATTTTAA
29279039 TATT
1 TATT
29279043 CACATCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:29283454 original size:12 final size:12
Alignment explanation
Indices: 29283437--29283461 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29283427 CACCTTACTC
29283437 CTGTTGGATACA
1 CTGTTGGATACA
29283449 CTGTTGGATACA
1 CTGTTGGATACA
29283461 C
1 C
29283462 AGACTCAGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (12 bp):
CTGTTGGATACA
Found at i:29284069 original size:16 final size:16
Alignment explanation
Indices: 29284048--29284078 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29284038 TTCACTATTA
*
29284048 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
29284064 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
29284079 GCATGTATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:29287713 original size:46 final size:46
Alignment explanation
Indices: 29287593--29287813 Score: 241
Period size: 46 Copynumber: 4.8 Consensus size: 46
29287583 TAACATTCTA
*
29287593 TATTCTCCAGTCCACAACATATGCAGAAGCTGAGAACTAAAATCTG
1 TATTCTCCAGTCCACAACATATGCAGAAGCTGAGAACCAAAATCTG
* *
29287639 TATT-TCCAGCCCACAACATATGCAGAAGCTGAGAACCGAAATCTG
1 TATTCTCCAGTCCACAACATATGCAGAAGCTGAGAACCAAAATCTG
* * *
29287684 TATTCTCCAGTCCGCAACATATG-ATGAAGCTGGGAACCTAAATCTG
1 TATTCTCCAGTCCACAACATATGCA-GAAGCTGAGAACCAAAATCTG
* * ** * *
29287730 TATTCTCCAATCCACAACATATGCAGGATATGAGAATCTAAATC-G
1 TATTCTCCAGTCCACAACATATGCAGAAGCTGAGAACCAAAATCTG
* * * * * *
29287775 ATATTCTCTAATTCGCAACATATGCAGGAGCTGGGAACC
1 -TATTCTCCAGTCCACAACATATGCAGAAGCTGAGAACC
29287814 TAGGCAAGAA
Statistics
Matches: 150, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
45 44 0.29
46 105 0.70
47 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (46 bp):
TATTCTCCAGTCCACAACATATGCAGAAGCTGAGAACCAAAATCTG
Found at i:29288683 original size:20 final size:19
Alignment explanation
Indices: 29288632--29288686 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
29288622 TTAACTTATT
*
29288632 AATTAATCTTAATTAGTTT
1 AATTAATCTTAATTAGTTA
*
29288651 AATAAATCATTAATTCA-TTAA
1 AATTAATC-TTAATT-AGTT-A
29288672 AATTAATCTTAATTA
1 AATTAATCTTAATTA
29288687 ACACTTTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.27
20 14 0.47
21 8 0.27
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTAATCTTAATTAGTTA
Done.