Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold145
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: 2608604
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28749 characters in sequence are not A, C, G, or T
File 6 of 15
Found at i:1093237 original size:392 final size:394
Alignment explanation
Indices: 1092507--1093866 Score: 2485
Period size: 392 Copynumber: 3.4 Consensus size: 394
1092497 GGATGTCAAC
* *
1092507 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1092572 AGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
66 AGCGATATTGGACTT--A-A-GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
*
1092637 AAGATGAAGATGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAA
127 AAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAA
1092702 TGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAA
192 TGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAA
1092767 GGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
257 GGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
*
1092832 CTTAAAGATGGAAAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAG
322 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAG
1092897 GTGCCAAT
387 GTGCCAAT
1092905 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1092970 AGCGATATTGGACTT-A-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
66 AGCGATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
1093033 TGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
131 TGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
1093098 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCC
196 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCC
1093163 AGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
261 AGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
1093228 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGC
326 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGC
1093293 CAAT
391 CAAT
1093297 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1093362 AGCGATATTGGACTT-A-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
66 AGCGATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
1093425 TGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
131 TGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
1093490 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCC
196 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCC
1093555 AGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
261 AGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
1093620 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGC
326 AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGC
1093685 CAAT
391 CAAT
*
1093689 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAG
* *
1093754 GCCAGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
63 GCCAGCGATATTGGACTT--A-A-GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
* *
1093819 TTAAAGATGGAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATT
124 TTAAAGAT-G-AAGA-TGCCAATATGCTGATTCAAGGCCAGCGATATT
1093867 TGGCTTAGAG
Statistics
Matches: 941, Mismatches: 9, Indels: 18
0.97 0.01 0.02
Matches are distributed among these distances:
392 738 0.78
393 1 0.00
394 1 0.00
395 39 0.04
398 78 0.08
399 1 0.00
401 48 0.05
402 1 0.00
403 3 0.00
404 31 0.03
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (394 bp):
GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGA
TGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCC
AGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
AAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGC
CAAT
Found at i:1093974 original size:32 final size:33
Alignment explanation
Indices: 1093878--1093970 Score: 163
Period size: 33 Copynumber: 2.8 Consensus size: 33
1093868 GGCTTAGAGG
1093878 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1093911 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG-A
1 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1093944 -GTTGCCACCGACTTGTGTGGGCTTTGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGG
1093971 GAAGGAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.03
32 25 0.42
33 27 0.46
34 5 0.08
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.29
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
Found at i:1094043 original size:36 final size:35
Alignment explanation
Indices: 1093972--1094543 Score: 361
Period size: 36 Copynumber: 15.9 Consensus size: 35
1093962 GGGCTTTGGG
* *
1093972 AAGGAAAAAAAGATGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAGAG-TGCCACGGAGTTGTGGGCTTTAA
1094007 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1094043 AA-GAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
1094077 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* **
1094112 ACGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAA
1 AAGG-AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
* * ** * ***
1094149 AAGGGAAAGAGAGTACCACAAAGTCGTAGGTGCCACAGA
1 AA-GGAAAAAGAGTGCCACGGAGTTGT-GG-GCTTTA-A
** * ** * * **** **
1094188 GTTGTGGGCTTTAAAAGA---AAAAGGTGCCACGGAG-TTGTGGGC
1 ----AAGG---AAAAAGAGTGCCACGGAGTTGTGG-GCTT-T--AA
*** * * *
1094230 TTTGAAGAAG-GTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AAGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTTTA--A
* * *
1094269 AGGGAGAAAGA-TGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1094302 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1094338 AA-GAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
1094372 AAGGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GG-AAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1094409 ACA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAA
1 A-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
*
1094444 AA-GAAGAAAGAGTGCCACGAAGTTGTGGGCTTTAA
1 AAGGAA-AAAGAGTGCCACGGAGTTGTGGGCTTTAA
* *
1094479 AA-GAAGAAG-GTGCCACAGAGTTGTGGGCTTTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * *
1094512 AAAGAAGAAG-GTGCCACGGAGTTGTGGACTTT
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1094544 GAGACAAAAT
Statistics
Matches: 429, Mismatches: 64, Indels: 89
0.74 0.11 0.15
Matches are distributed among these distances:
33 72 0.17
34 84 0.20
35 74 0.17
36 100 0.23
37 31 0.07
38 41 0.10
39 10 0.02
40 4 0.01
41 3 0.01
42 5 0.01
45 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (35 bp):
AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
Found at i:1094213 original size:33 final size:33
Alignment explanation
Indices: 1094176--1094543 Score: 404
Period size: 34 Copynumber: 10.7 Consensus size: 33
1094166 ACAAAGTCGT
*
1094176 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
*
1094209 AGGTGCCACGGAGTTGTGGGCTTT----GAAGA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
* * * *
1094238 AGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAA
1 AGG-TGCCACGGA-GT-TGTGGGCTTTA--AA-AGAAAA
* *
1094277 AGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAA
1094311 AGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
*
1094345 AAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAA--G-AAAA
1094382 AGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAA-AGAAAA
1094417 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAAGAA-AA
* *
1094452 AGAGTGCCACGAAGTTGTGGGCTTTAAAAGAAGA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
* *
1094486 AGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAGA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAA
*
1094520 AGGTGCCACGGAGTTGTGGACTTT
1 AGGTGCCACGGAGTTGTGGGCTTT
1094544 GAGACAAAAT
Statistics
Matches: 289, Mismatches: 22, Indels: 47
0.81 0.06 0.13
Matches are distributed among these distances:
29 7 0.02
30 8 0.03
31 1 0.00
32 10 0.03
33 67 0.23
34 76 0.26
35 40 0.14
36 35 0.12
37 9 0.03
38 31 0.11
39 5 0.02
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.21
Consensus pattern (33 bp):
AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
Found at i:1094510 original size:103 final size:102
Alignment explanation
Indices: 1094176--1094545 Score: 418
Period size: 103 Copynumber: 3.6 Consensus size: 102
1094166 ACAAAGTCGT
1094176 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTG--AAGAA
1 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
* ** * *
1094239 G---G-TTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAA
66 GAAAGAGTGCCA-CGAAGT-TGTGGGCTTTA--AAAGAAG-A
* * *
1094277 AGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA
1 AGGTGCCACAGAGTTGTGGGCTTTAAAA--GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAA
* *
1094340 GAA-AAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAA
63 GAAGAAAGAGTGCCACGAAGTTGTGGGCTTT-AAAA--G-AAGA
*
1094382 AGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AG-GTGCCACAGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1094447 AAGAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAGAAGA
64 AAGAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAGAAGA
* *
1094486 AGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGACTTTGA
1 AGGTGCCACAGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
1094546 GACAAAATGC
Statistics
Matches: 232, Mismatches: 17, Indels: 38
0.81 0.06 0.13
Matches are distributed among these distances:
100 6 0.03
101 18 0.08
102 7 0.03
103 75 0.32
104 23 0.10
105 31 0.13
106 37 0.16
107 12 0.05
108 23 0.10
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.21
Consensus pattern (102 bp):
AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
GAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAGAAGA
Found at i:1094603 original size:62 final size:63
Alignment explanation
Indices: 1094489--1094667 Score: 199
Period size: 62 Copynumber: 2.8 Consensus size: 63
1094479 AAGAAGAAGG
* * * * *
1094489 TGCCACAGAGTTGTGGGCTTTAAAAAGAAGAAGG-TGCCACGGAGTTGTGGACTTTGAGACA-A-
1 TGCCACTGAGTCGTGGACTTT--AAAG-AGAAGGATGCCACTGAGTCGTGGACTTTGAG-CAGAG
1094551 AA
62 AA
* *
1094553 TGCCACTGAGTCGTGGACTTTAAAGAGAAGGATGCCACTGCGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAAGAGAAGGATGCCACTGAGTCGTGGACTTTGAGCAGAGAA
1094616 TGCCACTGAGTCGTGGACTTT---GAGAAGAGATTGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTTAAAGAGAAG-GA-TGCCACTGAGTCGTGGACTTT
1094668 TTTTTTTGAC
Statistics
Matches: 102, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
60 6 0.06
61 10 0.10
62 46 0.45
63 22 0.22
64 18 0.18
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (63 bp):
TGCCACTGAGTCGTGGACTTTAAAGAGAAGGATGCCACTGAGTCGTGGACTTTGAGCAGAGAA
Found at i:1094623 original size:31 final size:31
Alignment explanation
Indices: 1094523--1094667 Score: 172
Period size: 31 Copynumber: 4.7 Consensus size: 31
1094513 AAGAAGAAGG
* * *
1094523 TGCCACGGAGTTGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
*
1094553 TGCCACTGAGTCGTGGACTTTAAAG-AGAAGGA-
1 TGCCACTGAGTCGTGGACTTT-GAGCAG-A-GAT
*
1094585 TGCCACTGCGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
*
1094616 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
1094647 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
1094668 TTTTTTTGAC
Statistics
Matches: 101, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.01
30 21 0.21
31 56 0.55
32 22 0.22
33 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.26
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
Found at i:1094680 original size:13 final size:13
Alignment explanation
Indices: 1094662--1094697 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1094652 CTGAGTCGTG
1094662 GACTTTTTTTTTT
1 GACTTTTTTTTTT
1094675 GACTTTTTTTTTT
1 GACTTTTTTTTTT
*
1094688 TA-TTTTTTTT
1 GACTTTTTTTT
1094698 ATTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.08, C:0.06, G:0.06, T:0.81
Consensus pattern (13 bp):
GACTTTTTTTTTT
Found at i:1094693 original size:9 final size:9
Alignment explanation
Indices: 1094681--1094706 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1094671 TTTTGACTTT
1094681 TTTTTTTTA
1 TTTTTTTTA
1094690 TTTTTTTTA
1 TTTTTTTTA
1094699 TTTTTTTT
1 TTTTTTTT
1094707 TTAAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1094706 original size:13 final size:13
Alignment explanation
Indices: 1094665--1094708 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
1094655 AGTCGTGGAC
* *
1094665 TTTTTTTTTTGAC
1 TTTTTTTTTTTAT
1094678 TTTTTTTTTTTAT
1 TTTTTTTTTTTAT
1094691 TTTTTTTATTTT-T
1 TTTTTTT-TTTTAT
1094704 TTTTT
1 TTTTT
1094709 AAAAAAAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 24 0.86
14 4 0.14
ACGTcount: A:0.07, C:0.02, G:0.02, T:0.89
Consensus pattern (13 bp):
TTTTTTTTTTTAT
Found at i:1095672 original size:15 final size:15
Alignment explanation
Indices: 1095652--1095686 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1095642 TGAAAAGGGG
1095652 TTTTTTC-TTCTTTTT
1 TTTTTTCGTT-TTTTT
1095667 TTTTTTCGTTTTTTT
1 TTTTTTCGTTTTTTT
1095682 TTTTT
1 TTTTT
1095687 GAAGAGTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.89
Consensus pattern (15 bp):
TTTTTTCGTTTTTTT
Found at i:1103001 original size:52 final size:52
Alignment explanation
Indices: 1102931--1103051 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1102921 GAAAATTTAT
*
1102931 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1102983 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1103035 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1103052 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1103064 original size:52 final size:51
Alignment explanation
Indices: 1102931--1103071 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1102921 GAAAATTTAT
1102931 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1102983 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1103035 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1103072 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1103078 original size:13 final size:13
Alignment explanation
Indices: 1103060--1103084 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1103050 CAAAGATCAG
1103060 TGTATCGATACAA
1 TGTATCGATACAA
1103073 TGTATCGATACA
1 TGTATCGATACA
1103085 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1103169 original size:13 final size:13
Alignment explanation
Indices: 1103151--1103175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1103141 CAAAAAAATA
1103151 TGTATCGATACAT
1 TGTATCGATACAT
1103164 TGTATCGATACA
1 TGTATCGATACA
1103176 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1103171 original size:33 final size:33
Alignment explanation
Indices: 1103129--1103195 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1103119 AGTAGCTTAA
1103129 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1103162 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1103195 A
1 A
1103196 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1106255 original size:19 final size:19
Alignment explanation
Indices: 1106226--1106269 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1106216 AAGAAAATTT
* *
1106226 ATATGATTTCACATCCCTA
1 ATATAATTTCACATACCTA
*
1106245 TTATAATTTCACATACCTA
1 ATATAATTTCACATACCTA
1106264 ATATAA
1 ATATAA
1106270 ATTTTATAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (19 bp):
ATATAATTTCACATACCTA
Found at i:1111803 original size:29 final size:31
Alignment explanation
Indices: 1111766--1111833 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 31
1111756 AAATTATATA
*
1111766 TAAATATTTATAATATAAAT-TATTAA-AATTT
1 TAAA-ATTTATAAGATAAATATA-TAATAATTT
1111797 T-AAA-TT-TAAGATAAATATATAATAATTT
1 TAAAATTTATAAGATAAATATATAATAATTT
1111825 TAAAATTTA
1 TAAAATTTA
1111834 ATCATAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
27 12 0.39
28 10 0.32
29 4 0.13
30 4 0.13
31 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
TAAAATTTATAAGATAAATATATAATAATTT
Found at i:1111825 original size:28 final size:28
Alignment explanation
Indices: 1111780--1111834 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
1111770 TATTTATAAT
1111780 ATAAATTATTAAAATTTT-AAATTTAAG
1 ATAAATTATTAAAATTTTAAAATTTAAG
1111807 ATAAA-TATATAATAATTTTAAAATTTAA
1 ATAAATTAT-TAA-AATTTTAAAATTTAA
1111835 TCATAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 3 0.12
27 8 0.32
28 6 0.24
29 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
ATAAATTATTAAAATTTTAAAATTTAAG
Found at i:1111845 original size:28 final size:26
Alignment explanation
Indices: 1111780--1111846 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 26
1111770 TATTTATAAT
*
1111780 ATAAATTATTAAAATTTTAAATTTAAG
1 ATAAATTA-TAAAATTTTAAATTTAAC
1111807 ATAAATATATAATAATTTTAAAATTTAATC
1 ATAAAT-TATAA-AATTTT-AAATTTAA-C
1111837 AT-AATTATAA
1 ATAAATTATAA
1111847 CTTAATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
27 9 0.26
28 13 0.37
29 11 0.31
30 2 0.06
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (26 bp):
ATAAATTATAAAATTTTAAATTTAAC
Found at i:1111881 original size:19 final size:19
Alignment explanation
Indices: 1111849--1111886 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1111839 AATTATAACT
*
1111849 TAATTAAATAATATTAATA
1 TAATTAAATAATATAAATA
1111868 TAATATAAAT-ATATAAATA
1 TAAT-TAAATAATATAAATA
1111887 AAAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATTAAATAATATAAATA
Found at i:1113303 original size:13 final size:15
Alignment explanation
Indices: 1113274--1113315 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
1113264 ATAAAAAAAT
1113274 ATTTATAAATATTAA
1 ATTTATAAATATTAA
1113289 ATTT-TAAAT-TTAA
1 ATTTATAAATATTAA
*
1113302 ATTTATTAATATTA
1 ATTTATAAATATTA
1113316 TTTTTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 8 0.33
14 9 0.38
15 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTATAAATATTAA
Found at i:1115634 original size:10 final size:10
Alignment explanation
Indices: 1115604--1115647 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
1115594 TTATTATAAT
1115604 TATATTTAAA
1 TATATTTAAA
1115614 -ATA-TT--A
1 TATATTTAAA
1115620 TATATTTAAA
1 TATATTTAAA
1115630 TATATTTAAA
1 TATATTTAAA
1115640 TAT-TTTAA
1 TATATTTAA
1115648 TAATTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
6 1 0.03
7 3 0.10
8 4 0.13
9 8 0.27
10 14 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TATATTTAAA
Found at i:1117976 original size:14 final size:13
Alignment explanation
Indices: 1117956--1117990 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1117946 ATAATTATTT
1117956 TTAAAAATAAAAA
1 TTAAAAATAAAAA
*
1117969 TTACAAAATTAAAA
1 TTA-AAAATAAAAA
1117983 TTAAAAAT
1 TTAAAAAT
1117991 CTCAACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (13 bp):
TTAAAAATAAAAA
Found at i:1118826 original size:14 final size:13
Alignment explanation
Indices: 1118807--1118837 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1118797 ATAGATATAT
1118807 TAAAAAATAATAAA
1 TAAAAAATAAT-AA
1118821 TAAAAAATAATAA
1 TAAAAAATAATAA
1118834 TAAA
1 TAAA
1118838 CTGAATTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAAATAATAA
Found at i:1120198 original size:19 final size:19
Alignment explanation
Indices: 1120176--1120212 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1120166 TATTAAATAA
1120176 ATAAAAATCATATA-AAATT
1 ATAAAAAT-ATATATAAATT
1120195 ATAAAAATATATATAAAT
1 ATAAAAATATATATAAAT
1120213 AATTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAAAATATATATAAATT
Found at i:1120214 original size:16 final size:17
Alignment explanation
Indices: 1120172--1120214 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
1120162 ATCGTATTAA
1120172 ATAAATAAAAATCATAT
1 ATAAATAAAAATCATAT
*
1120189 AAAATTATAAAAAT-ATAT
1 ATAA--ATAAAAATCATAT
1120207 ATAAATAA
1 ATAAATAA
1120215 TTTAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 4 0.18
17 3 0.14
18 7 0.32
19 8 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAATAAAAATCATAT
Found at i:1120258 original size:25 final size:25
Alignment explanation
Indices: 1120201--1120259 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1120191 AATTATAAAA
1120201 ATATATATAAATAATTTAATTTTAC
1 ATATATATAAATAATTTAATTTTAC
* *
1120226 AT-TAATATAAATGAATTT-CTTTTAT
1 ATAT-ATATAAAT-AATTTAATTTTAC
1120251 ATATATATA
1 ATATATATA
1120260 TATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 1 0.03
25 22 0.76
26 6 0.21
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (25 bp):
ATATATATAAATAATTTAATTTTAC
Found at i:1120498 original size:13 final size:13
Alignment explanation
Indices: 1120466--1120511 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
1120456 TTATTAATTA
* *
1120466 TAAAAATTATACT
1 TAAAAATAATAAT
*
1120479 TACAAATAATAAT
1 TAAAAATAATAAT
1120492 TAAAAAT-ATAA-
1 TAAAAATAATAAT
1120503 TAAAAATAA
1 TAAAAATAA
1120512 CTTGGATCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 7 0.25
12 5 0.18
13 16 0.57
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAAAATAATAAT
Found at i:1128506 original size:13 final size:14
Alignment explanation
Indices: 1128481--1128514 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1128471 AGTTTAAATA
1128481 AAAATATTAAATTT
1 AAAATATTAAATTT
1128495 AAAATA-TAAATTT
1 AAAATATTAAATTT
1128508 -AAATATT
1 AAAATATT
1128515 TGATCTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.26
13 8 0.42
14 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATATTAAATTT
Found at i:1128860 original size:2 final size:2
Alignment explanation
Indices: 1128847--1128885 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1128837 ACCCTCAAAT
* *
1128847 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1128886 GTGTGTGTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1131497 original size:26 final size:24
Alignment explanation
Indices: 1131451--1131499 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
1131441 AAATTTTTTT
*
1131451 AAATTTTATATTTATTTATTAATA
1 AAATATTATATTTATTTATTAATA
1131475 AAATATTATTATTTAATTTATTAAT
1 AAATATTA-TATTT-ATTTATTAAT
1131500 GATATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 5 0.23
26 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
AAATATTATATTTATTTATTAATA
Found at i:1135051 original size:35 final size:35
Alignment explanation
Indices: 1135005--1135074 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1134995 CTCTTATATT
1135005 CCATCAAATTACCATTCAATCTTTGCTCCAATTTA
1 CCATCAAATTACCATTCAATCTTTGCTCCAATTTA
1135040 CCATCAAATTACCATTCAATCTTTGCTCCAATTTA
1 CCATCAAATTACCATTCAATCTTTGCTCCAATTTA
1135075 AGAAAACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.37
Consensus pattern (35 bp):
CCATCAAATTACCATTCAATCTTTGCTCCAATTTA
Found at i:1136273 original size:2 final size:2
Alignment explanation
Indices: 1136266--1136297 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1136256 TGTAGTAGTA
1136266 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1136298 GCTAGTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1136730 original size:27 final size:23
Alignment explanation
Indices: 1136700--1136751 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 23
1136690 ATTATTTATT
1136700 AATATATAAAATAATTATTTATTTTAA
1 AATAT-TAAAAT--TTA-TTATTTTAA
1136727 AATATTAAAATTTATTATTTTAA
1 AATATTAAAATTTATTATTTTAA
1136750 AA
1 AA
1136752 AAATAGGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 11 0.44
24 3 0.12
26 6 0.24
27 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATTAAAATTTATTATTTTAA
Found at i:1138296 original size:20 final size:20
Alignment explanation
Indices: 1138245--1138297 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1138235 TTCTTATTTT
* *
1138245 ATATATAAAAATATTAATTA
1 ATATATAATAATATCAATTA
*
1138265 ATATTTAATAATATCAATTA
1 ATATATAATAATATCAATTA
1138285 AT-TATAATTAATA
1 ATATATAA-TAATA
1138298 AAAGTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATAATAATATCAATTA
Found at i:1144137 original size:95 final size:94
Alignment explanation
Indices: 1143975--1144161 Score: 302
Period size: 95 Copynumber: 2.0 Consensus size: 94
1143965 TCCCCAGGGC
* * *
1143975 ACATAGCTGCTTGTACAATAGGTAAATGATCTTAGATTGTCTTTTTACAAACTTTATCTGTAAAA
1 ACATAGCTGCATGTACAATAGGTAAATGATCTTAGATAGACTTTTTACAAACTTTATCTGTAAAA
* *
1144040 TAACAACCACCCCAATAGGGAATCTTTTT
66 TAACAACCACCCCAACAAGGAATCTTTTT
*
1144069 ACATAGCTGCATGTACAATAGGTAAATGATCTTTAGATAGACTTTTTACAAGCTTTATCTGTAAA
1 ACATAGCTGCATGTACAATAGGTAAATGATC-TTAGATAGACTTTTTACAAACTTTATCTGTAAA
*
1144134 ATAACAACCATCCCAACAAGGAATCTTT
65 ATAACAACCACCCCAACAAGGAATCTTT
1144162 GAATCCTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 30 0.35
95 55 0.65
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (94 bp):
ACATAGCTGCATGTACAATAGGTAAATGATCTTAGATAGACTTTTTACAAACTTTATCTGTAAAA
TAACAACCACCCCAACAAGGAATCTTTTT
Found at i:1145379 original size:16 final size:15
Alignment explanation
Indices: 1145358--1145400 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1145348 ATACACATTT
1145358 AAAAATAAATAAAATA
1 AAAAATAAA-AAAATA
*
1145374 AAAAATTTAAAAAATA
1 AAAAA-TAAAAAAATA
*
1145390 AATAATAAAAA
1 AAAAATAAAAA
1145401 TAAAATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 15 0.65
17 3 0.13
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:1146289 original size:16 final size:16
Alignment explanation
Indices: 1146244--1146292 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1146234 AGTGTGCCAT
* * *
1146244 AAAAAAATTATAATTT
1 AAAAAAATTAAAAATA
*
1146260 AAAAAAATAAAAAAATA
1 AAAAAAAT-TAAAAATA
1146277 AAAAAAATTAAAAATA
1 AAAAAAATTAAAAATA
1146293 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAAATTAAAAATA
Found at i:1146295 original size:9 final size:9
Alignment explanation
Indices: 1146258--1146298 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
1146248 AAATTATAAT
1146258 TTAAAAAAA
1 TTAAAAAAA
1146267 -TAAAAAAA
1 TTAAAAAAA
*
1146275 TAAAAAAAA
1 TTAAAAAAA
*
1146284 TTAAAAATA
1 TTAAAAAAA
1146293 TTAAAA
1 TTAAAA
1146299 TTTAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:1153256 original size:2 final size:2
Alignment explanation
Indices: 1153249--1153283 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1153239 TACCTATCTA
1153249 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
1153284 AATTTGGGTT
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:1153425 original size:3 final size:3
Alignment explanation
Indices: 1153417--1153451 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1153407 TCACACACAA
1153417 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1153452 CGACAACAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1153653 original size:5 final size:5
Alignment explanation
Indices: 1153643--1153809 Score: 54
Period size: 5 Copynumber: 34.4 Consensus size: 5
1153633 AACTATGTAT
* * *
1153643 TTATA TTATA TT-TA -TATA TTTTA TTAAA TTATAA TTATA TT-TA ATATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA
* * *
1153691 TTTATA TTAATA TGA-A TTTTAA TT-TA TTA-A TAAT- TTATA TTATA
1 -TTATA TT-ATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTATA
* ** * * *
1153735 -TAAA GTT-TA AAATA TT-TA -AAAA TTTATA TTAATA TTTTA TTTATA
1 TTATA -TTATA TTATA TTATA TTATA T-TATA TT-ATA TTATA -TTATA
*
1153780 TTATA TTATA TTATA TT-T- TTTTA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TT
1153810 TTAATTATTT
Statistics
Matches: 117, Mismatches: 24, Indels: 42
0.64 0.13 0.23
Matches are distributed among these distances:
3 3 0.03
4 26 0.22
5 59 0.50
6 29 0.25
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:1153775 original size:25 final size:26
Alignment explanation
Indices: 1153747--1153803 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
1153737 AAGTTTAAAA
1153747 TATTTA-AAAAT-TTATATTAATATTT
1 TATTTATAAAATATTATATT-ATATTT
**
1153772 TATTTATATTATATTATATTATATTT
1 TATTTATAAAATATTATATTATATTT
1153798 T-TTTAT
1 TATTTAT
1153804 TATATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 11 0.39
26 10 0.36
27 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TATTTATAAAATATTATATTATATTT
Found at i:1155695 original size:49 final size:47
Alignment explanation
Indices: 1155607--1155702 Score: 124
Period size: 49 Copynumber: 2.0 Consensus size: 47
1155597 GTATAGACAA
1155607 TTTCAGTTTCAACTTGTAATAGATCAACTAGAGATTGGTTTTTCCAGGG
1 TTTCAGTTTCAACTTGTAATAGATCAACTA-AGA-TGGTTTTTCCAGGG
1155656 TTTCAGTTTCAACTTGTTTGCAATAGATCAACT-AG-TGGTTTTTCCAG
1 TTTCAGTTTCAACTTG--T--AATAGATCAACTAAGATGGTTTTTCCAG
1155703 ATTTGACTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
49 28 0.65
51 3 0.07
53 12 0.28
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (47 bp):
TTTCAGTTTCAACTTGTAATAGATCAACTAAGATGGTTTTTCCAGGG
Found at i:1156397 original size:12 final size:12
Alignment explanation
Indices: 1156380--1156412 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1156370 GGTGACTACT
*
1156380 CTTTGCAGCCCA
1 CTTTGCAACCCA
1156392 CTTTGCAACCCA
1 CTTTGCAACCCA
1156404 CTTTGCAAC
1 CTTTGCAAC
1156413 AGCCCGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.39, G:0.12, T:0.27
Consensus pattern (12 bp):
CTTTGCAACCCA
Found at i:1161036 original size:6 final size:6
Alignment explanation
Indices: 1161025--1161084 Score: 52
Period size: 6 Copynumber: 9.7 Consensus size: 6
1161015 TAAATTTTTT
* *
1161025 ATTTAA ATTTAA ATTT-G ATTTAA TTTTAA ATTTAA A-TTAA TATTATAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA -ATT-T-AA
1161074 ATATTAA ATTT
1 AT-TTAA ATTT
1161085 TTTATTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
5 8 0.18
6 24 0.55
7 5 0.11
8 4 0.09
9 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:1161045 original size:17 final size:17
Alignment explanation
Indices: 1161025--1161057 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1161015 TAAATTTTTT
1161025 ATTTAAATTTAAATTTG
1 ATTTAAATTTAAATTTG
*
1161042 ATTTAATTTTAAATTT
1 ATTTAAATTTAAATTT
1161058 AAATTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTAAATTTAAATTTG
Found at i:1161064 original size:17 final size:17
Alignment explanation
Indices: 1161027--1161065 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1161017 AATTTTTTAT
* * *
1161027 TTAAATTTAAATTTGAT
1 TTAATTTTAAATTTAAA
1161044 TTAATTTTAAATTTAAA
1 TTAATTTTAAATTTAAA
1161061 TTAAT
1 TTAAT
1161066 ATTATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAATTTTAAATTTAAA
Found at i:1161113 original size:21 final size:20
Alignment explanation
Indices: 1161074--1161126 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
1161064 ATATTATAAA
*
1161074 ATATTAAATTT-TTTATTTT
1 ATATTAAATTTATATATTTT
1161093 ATATTAATATTTATATATTTT
1 ATATTAA-ATTTATATATTTT
1161114 ATAATTAAATTTA
1 AT-ATTAAATTTA
1161127 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 14 0.47
22 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTAAATTTATATATTTT
Found at i:1161137 original size:18 final size:20
Alignment explanation
Indices: 1161116--1161163 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
1161106 TATATTTTAT
1161116 AATTAAATTTAAAT-AA-AA
1 AATTAAATTTAAATCAATAA
1161134 AATTAAATTTAAATCAATAA
1 AATTAAATTTAAATCAATAA
1161154 AATATAAATT
1 AAT-TAAATT
1161164 CACCTAACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.52
19 2 0.07
20 5 0.19
21 6 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTAAATTTAAATCAATAA
Found at i:1161845 original size:12 final size:11
Alignment explanation
Indices: 1161822--1161928 Score: 56
Period size: 11 Copynumber: 10.5 Consensus size: 11
1161812 GTGCCGAATT
1161822 ATATAAATATA
1 ATATAAATATA
1161833 ATATAACATATA
1 ATATAA-ATATA
*
1161845 ATATTAAT-TA
1 ATATAAATATA
1161855 AT-TAAATAT-
1 ATATAAATATA
1161864 -T-TAAA-AT-
1 ATATAAATATA
* * *
1161871 TTTTATAT-TA
1 ATATAAATATA
1161881 ATATAAA-ATA
1 ATATAAATATA
* *
1161891 TTTTAAATATA
1 ATATAAATATA
1161902 AT-TATAATATA
1 ATATA-AATATA
1161913 ATA-AAATATAA
1 ATATAAATAT-A
1161924 ATATA
1 ATATA
1161929 TAATTATTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
7 2 0.03
8 6 0.08
9 8 0.11
10 23 0.31
11 25 0.33
12 11 0.15
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATAAATATA
Found at i:1161903 original size:21 final size:20
Alignment explanation
Indices: 1161865--1161908 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1161855 ATTAAATATT
*
1161865 TAAAATTTTTATATTAA-TA
1 TAAAATTTTTAAATTAATTA
1161884 TAAAATATTTTAAATATAATTA
1 TAAAAT-TTTTAAAT-TAATTA
1161906 TAA
1 TAA
1161909 TATAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
21 3 0.14
22 5 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAATTTTTAAATTAATTA
Found at i:1167079 original size:48 final size:47
Alignment explanation
Indices: 1166990--1167083 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 47
1166980 TAATTAGATA
*
1166990 AAAAAATATTATGTTTTAAAATATAATTAGTGAGTATTTTTTAAAAT
1 AAAAAATATTATGTTTTAAAATATAATTAGTGAATATTTTTTAAAAT
*
1167037 AAAAAATAATTAT-TTTTAAATTTATATAATTA-TTAATATTTTTTAAA
1 AAAAAAT-ATTATGTTTTAAA---ATATAATTAGTGAATATTTTTTAAA
1167084 TTTTTTAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
47 14 0.34
48 5 0.12
49 13 0.32
50 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (47 bp):
AAAAAATATTATGTTTTAAAATATAATTAGTGAATATTTTTTAAAAT
Found at i:1167410 original size:17 final size:17
Alignment explanation
Indices: 1167390--1167422 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1167380 AATTAAAAGT
1167390 TTAAAAT-TATATTTAAA
1 TTAAAATAT-TATTTAAA
1167407 TTAAAATATTATTTAA
1 TTAAAATATTATTTAA
1167423 TAAATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAAATATTATTTAAA
Found at i:1168120 original size:21 final size:22
Alignment explanation
Indices: 1168089--1168129 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1168079 CAATTTATAT
1168089 AAATATATTATAATTATATTTA
1 AAATATATTATAATTATATTTA
*
1168111 AAATAT-TTATATTTATATT
1 AAATATATTATAATTATATT
1168130 ATTTTATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AAATATATTATAATTATATTTA
Found at i:1169818 original size:15 final size:16
Alignment explanation
Indices: 1169800--1169834 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1169790 AGATTATTAA
1169800 TTTATTTAT-AATTTT
1 TTTATTTATAAATTTT
1169815 TTTATTTATGAAATTTT
1 TTTATTTAT-AAATTTT
1169832 TTT
1 TTT
1169835 GATGATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTATTTATAAATTTT
Found at i:1170068 original size:31 final size:30
Alignment explanation
Indices: 1170035--1170123 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 30
1170025 CAAGAATTAT
1170035 TTTTAAAATATTATAA-TATATTGATATAAA
1 TTTTAAAATATTATAATTATATT-ATATAAA
*
1170065 TTTTAATATATTTATAATTTATATT-TATAAA
1 TTTTAAAATA-TTATAA-TTATATTATATAAA
*
1170096 TTTTAAAATATTTTAATTATATTATATA
1 TTTTAAAATATTATAATTATATTATATA
1170124 TTTTTCATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
29 7 0.13
30 18 0.35
31 21 0.40
33 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
TTTTAAAATATTATAATTATATTATATAAA
Found at i:1170109 original size:41 final size:46
Alignment explanation
Indices: 1170064--1170146 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
1170054 ATTGATATAA
1170064 ATTTTAA-TATATT-TATA-ATTT-ATATTT-ATAAATTTTAAAAT
1 ATTTTAATTATATTATATATATTTCATATTTAATAAATTTTAAAAT
* *
1170105 ATTTTAATTATATTATATATTTTTCATATTTAATTAATTTTA
1 ATTTTAATTATATTATATATATTTCATATTTAATAAATTTTA
1170147 TATTAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 7 0.20
42 6 0.17
43 4 0.11
44 3 0.09
45 6 0.17
46 9 0.26
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (46 bp):
ATTTTAATTATATTATATATATTTCATATTTAATAAATTTTAAAAT
Found at i:1170147 original size:61 final size:61
Alignment explanation
Indices: 1170035--1170150 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
1170025 CAAGAATTAT
*
1170035 TTTTAAAATATTATAATATATTGATATAAATTTTAATATATTTATAATTTATATTTATAAA
1 TTTTAAAATATTATAATATATTGATATAAATTTTAATATATTAATAATTTATATTTATAAA
* * *
1170096 TTTTAAAATATTTTAATTATATT-ATAT-ATTTTTCATAT-TTAATTAATTTTATATT
1 TTTTAAAATATTATAA-TATATTGATATAAATTTTAATATATTAA-TAA-TTTATATT
1170151 AAATTTAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 3 0.06
60 12 0.25
61 27 0.56
62 6 0.12
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (61 bp):
TTTTAAAATATTATAATATATTGATATAAATTTTAATATATTAATAATTTATATTTATAAA
Found at i:1170387 original size:27 final size:27
Alignment explanation
Indices: 1170328--1170388 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
1170318 AATTTTTTTT
*
1170328 TTCAAA-TCAAAAAAATAAAAATCAAT
1 TTCAAACTCAAAAAAATAAAAATCAAC
*
1170354 TTCAAACTCAACAAAA-AAAAATGCAAC
1 TTCAAACTCAAAAAAATAAAAAT-CAAC
*
1170381 TTGAAACT
1 TTCAAACT
1170389 TAGTTTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.59, C:0.16, G:0.03, T:0.21
Consensus pattern (27 bp):
TTCAAACTCAAAAAAATAAAAATCAAC
Found at i:1170427 original size:9 final size:9
Alignment explanation
Indices: 1170413--1170438 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1170403 TAGTTAATTA
1170413 AAATTTAAT
1 AAATTTAAT
1170422 AAATTTAAT
1 AAATTTAAT
1170431 AAATTTAA
1 AAATTTAA
1170439 AATTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAATTTAAT
Found at i:1170908 original size:21 final size:20
Alignment explanation
Indices: 1170860--1170909 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1170850 TAATTAAATT
*
1170860 TAAATAAA-AATAATTTTTA
1 TAAATAAATAATAATTTATA
*
1170879 TTAATTAAATAATAATTTATA
1 -TAAATAAATAATAATTTATA
1170900 TAAACTAAAT
1 TAAA-TAAAT
1170910 TAAAACCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATAAATAATAATTTATA
Found at i:1171787 original size:18 final size:18
Alignment explanation
Indices: 1171750--1171796 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1171740 TATGTTTTAT
* *
1171750 AAAAATTT-AATTAATTA
1 AAAAATTTAAAATAATAA
*
1171767 AAATATTTAAAATAATAA
1 AAAAATTTAAAATAATAA
1171785 AAAAATTTAAAA
1 AAAAATTTAAAA
1171797 ATTTAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTTAAAATAATAA
Found at i:1175744 original size:8 final size:8
Alignment explanation
Indices: 1175731--1175755 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1175721 TTTACTTGAT
1175731 ACACATGC
1 ACACATGC
1175739 ACACATGC
1 ACACATGC
1175747 ACACATGC
1 ACACATGC
1175755 A
1 A
1175756 TATCTAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.36, G:0.12, T:0.12
Consensus pattern (8 bp):
ACACATGC
Found at i:1179244 original size:1 final size:1
Alignment explanation
Indices: 1179240--1179272 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
1179230 TCTTTTTGTT
*
1179240 CCCCCCCTCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1179273 TCTCCTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:1183738 original size:18 final size:18
Alignment explanation
Indices: 1183693--1183750 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
1183683 TTTTCAAAAC
*
1183693 AAATAAATATATTAATTAA
1 AAATAATTATA-TAATTAA
*
1183712 ATAAT-ATTATATATTTAA
1 A-AATAATTATATAATTAA
1183730 AAATAATTATATAAATTAA
1 AAATAATTATAT-AATTAA
1183749 AA
1 AA
1183751 TTTTATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.09
18 14 0.42
19 13 0.39
20 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATAATTATATAATTAA
Found at i:1183751 original size:18 final size:18
Alignment explanation
Indices: 1183693--1183764 Score: 51
Period size: 17 Copynumber: 4.0 Consensus size: 18
1183683 TTTTCAAAAC
* *
1183693 AAATAAATATATTAATT-
1 AAATAATTATATAAATTA
*
1183710 AAATAA-TATTATATATTTAA
1 AAATAATTA-TATA-AATT-A
1183730 AAATAATTATATAAATTA
1 AAATAATTATATAAATTA
* *
1183748 AAAT-TTTATAAAAATTA
1 AAATAATTATATAAATTA
1183765 CGGTAAATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 2 0.04
17 20 0.44
18 8 0.18
19 3 0.07
20 10 0.22
21 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATAATTATATAAATTA
Found at i:1184092 original size:2 final size:2
Alignment explanation
Indices: 1184087--1184116 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1184077 GTATAAGGAA
*
1184087 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1184117 GTTGCTCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1186656 original size:32 final size:33
Alignment explanation
Indices: 1186615--1186678 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1186605 TATATTTTTA
*
1186615 ATATAAATTTTAAAATATTAAT-TATTTATATT
1 ATATAAATTTTAAAAGATTAATATATTTATATT
*
1186647 ATATAAATTTTAAAAGATTTATATATTTATAT
1 ATATAAATTTTAAAAGATTAATATATTTATAT
1186679 CGTATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (33 bp):
ATATAAATTTTAAAAGATTAATATATTTATATT
Found at i:1187005 original size:10 final size:10
Alignment explanation
Indices: 1186990--1187043 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
1186980 GAACATTATC
*
1186990 TAAATCTATA
1 TAAATATATA
** *
1187000 TAAATCCATC
1 TAAATATATA
1187010 TAAATATATA
1 TAAATATATA
*
1187020 TATATATATA
1 TAAATATATA
*
1187030 TATATATATA
1 TAAATATATA
1187040 TAAA
1 TAAA
1187044 ATCTTTCTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 37 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAATATATA
Found at i:1187018 original size:2 final size:2
Alignment explanation
Indices: 1187013--1187041 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1187003 ATCCATCTAA
1187013 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 A
1187042 AAATCTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1188629 original size:39 final size:41
Alignment explanation
Indices: 1188578--1188681 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 41
1188568 ATTTTTTTTA
1188578 TTATTTGA-TTATAATATAATTAATATTATT-AT-TTGTGTT
1 TTATTT-ATTTATAATATAATTAATATTATTAATATTGTGTT
* *
1188617 TTATTTATTTATAATATAATTAATAATATTAATATTTTGTT
1 TTATTTATTTATAATATAATTAATATTATTAATATTGTGTT
* * *
1188658 AT-TTTATTTAAAAT-TAATAAATAT
1 TTATTTATTTATAATATAATTAATAT
1188682 ATTTGTTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
38 1 0.02
39 35 0.62
40 13 0.23
41 7 0.12
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (41 bp):
TTATTTATTTATAATATAATTAATATTATTAATATTGTGTT
Found at i:1188763 original size:20 final size:20
Alignment explanation
Indices: 1188717--1188768 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
1188707 TAAATTTATT
1188717 TATTT-ATTATTCATAAATA
1 TATTTAATTATTCATAAATA
* *
1188736 TATTTTTAATTGTTCATGAATA
1 TA--TTTAATTATTCATAAATA
1188758 TATTTAATTAT
1 TATTTAATTAT
1188769 ATATTCATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.07
20 8 0.30
21 3 0.11
22 14 0.52
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTAATTATTCATAAATA
Found at i:1188864 original size:29 final size:29
Alignment explanation
Indices: 1188794--1188884 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 29
1188784 GTATTTATAA
*
1188794 ATAAATTTATTT-AA-TTTAAATAAACAA-
1 ATAAATATATTTAAATTTTAAATAAA-AAC
*
1188821 ATATAA-ATACCTTAAATTTTAAATAAAAAC
1 ATA-AATATA-TTTAAATTTTAAATAAAAAC
*
1188851 ATAAATATATTTAAAATTTTTAAT--AAAC
1 ATAAATATATTT-AAATTTTAAATAAAAAC
1188879 ATAAAT
1 ATAAAT
1188885 TAAATATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
27 5 0.09
28 14 0.26
29 8 0.15
30 26 0.49
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (29 bp):
ATAAATATATTTAAATTTTAAATAAAAAC
Found at i:1188895 original size:28 final size:28
Alignment explanation
Indices: 1188808--1188895 Score: 65
Period size: 30 Copynumber: 3.0 Consensus size: 28
1188798 ATTTATTTAA
1188808 TTTAAAT-AAACA-AATATAAATACCTTAAAT
1 TTTAAATAAAACATAA-ATAAATA---TAAAT
* *
1188838 TTTAAATAAAAACATAAATATATTTAAAAT
1 TTTAAAT-AAAACATAAATAAATAT-AAAT
*
1188868 TTTTAAT-AAACATAAATTAAATATAAAT
1 TTTAAATAAAACATAAA-TAAATATAAAT
1188896 AAATTTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
28 13 0.27
29 6 0.12
30 17 0.35
32 10 0.21
33 2 0.04
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (28 bp):
TTTAAATAAAACATAAATAAATATAAAT
Found at i:1189050 original size:42 final size:43
Alignment explanation
Indices: 1188998--1189091 Score: 163
Period size: 42 Copynumber: 2.2 Consensus size: 43
1188988 GTTAAGATAA
1188998 GAAAAAAAGAAAAAGAAAAATTCTAATGTGAAAATTTA-AGGG
1 GAAAAAAAGAAAAAGAAAAATTCTAATGTGAAAATTTAGAGGG
*
1189040 GAAAAAAAGAAAAAGAAAAATTCTAATGTGAAAATTTAGGGGGG
1 GAAAAAAAGAAAAAGAAAAATTCTAATGTGAAAATTTA-GAGGG
1189084 GAAAAAAA
1 GAAAAAAA
1189092 ACAAGATGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 38 0.78
44 11 0.22
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.17
Consensus pattern (43 bp):
GAAAAAAAGAAAAAGAAAAATTCTAATGTGAAAATTTAGAGGG
Found at i:1196822 original size:14 final size:14
Alignment explanation
Indices: 1196800--1196842 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1196790 TAGAAAAAGT
*
1196800 AATTATAAATATTA
1 AATTTTAAATATTA
*
1196814 AATTTTAAATTTTA
1 AATTTTAAATATTA
1196828 AATTTATTAAATATT
1 AA-TT-TTAAATATT
1196843 TTTTAAGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 14 0.58
15 2 0.08
16 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTTAAATATTA
Found at i:1198298 original size:4 final size:4
Alignment explanation
Indices: 1198289--1198325 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
1198279 GTCTTAGGCT
*
1198289 TGTC TGTC TGTT TGTC TGTC TGTC TGTC TGTC TGTC T
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC T
1198326 TTCTTTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.22, G:0.24, T:0.54
Consensus pattern (4 bp):
TGTC
Found at i:1199015 original size:15 final size:15
Alignment explanation
Indices: 1198991--1199091 Score: 59
Period size: 15 Copynumber: 6.7 Consensus size: 15
1198981 AAATAAGATA
*
1198991 TAATAGATAAATAAT
1 TAATATATAAATAAT
1199006 TAATATATAAATAAT
1 TAATATATAAATAAT
* *
1199021 ATGCATATATTAA-AAT
1 -T-AATATATAAATAAT
* *
1199037 TATCTAATATAAATTAT
1 TA-AT-ATATAAATAAT
*
1199054 TAATTTAT-AATAAT
1 TAATATATAAATAAT
1199068 T--TATATAAAT-AT
1 TAATATATAAATAAT
*
1199080 ATAATATTTAAA
1 -TAATATATAAA
1199092 ATATAATTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
12 6 0.09
13 4 0.06
14 6 0.09
15 26 0.40
16 11 0.17
17 12 0.18
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TAATATATAAATAAT
Found at i:1199102 original size:20 final size:18
Alignment explanation
Indices: 1199058--1199105 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
1199048 AATTATTAAT
*
1199058 TTATAATAATTTATATAAA
1 TTATAAT-ATTTAAATAAA
1199077 TATATAATATTTAAAATATAA
1 T-TATAATATTT-AAATA-AA
1199098 TTATAATA
1 TTATAATA
1199106 AAAAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.20
20 17 0.68
21 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATAATATTTAAATAAA
Found at i:1199380 original size:2 final size:2
Alignment explanation
Indices: 1199373--1199398 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1199363 ATTGCACTTT
1199373 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1199399 ATTTATTTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1203175 original size:2 final size:2
Alignment explanation
Indices: 1203168--1203212 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1203158 TGCGTTCATT
*
1203168 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1203210 TA T
1 TA T
1203213 TCATGAGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1204081 original size:21 final size:21
Alignment explanation
Indices: 1204057--1204105 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1204047 CATCTTCCAG
1204057 CTTTTGCACATCAGCTCTCAA
1 CTTTTGCACATCAGCTCTCAA
** * *
1204078 CTTTTGCATTTTAGCTTTCAA
1 CTTTTGCACATCAGCTCTCAA
1204099 CTTTTGC
1 CTTTTGC
1204106 CCCAACTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.27, G:0.10, T:0.45
Consensus pattern (21 bp):
CTTTTGCACATCAGCTCTCAA
Found at i:1209628 original size:14 final size:14
Alignment explanation
Indices: 1209609--1209636 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1209599 CTTTACTCCC
1209609 GGTTTCAATTTTGG
1 GGTTTCAATTTTGG
1209623 GGTTTCAATTTTGG
1 GGTTTCAATTTTGG
1209637 CTGATGCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.29, T:0.50
Consensus pattern (14 bp):
GGTTTCAATTTTGG
Found at i:1211888 original size:356 final size:356
Alignment explanation
Indices: 1211235--1211930 Score: 1374
Period size: 356 Copynumber: 2.0 Consensus size: 356
1211225 TAACTAAAGG
1211235 TAGGAGGTGGTTTCCAGTAATAGGAACACTTATTAGTAAAATTTATGCATTTGAACTATTTCAGC
1 TAGGAGGTGGTTTCCAGTAATAGGAACACTTATTAGTAAAATTTATGCATTTGAACTATTTCAGC
1211300 AATGCACAAAACAAGATATTTCAATATCCAACAGCCAGAATAATGAGGCTATTATTCTGAATCTG
66 AATGCACAAAACAAGATATTTCAATATCCAACAGCCAGAATAATGAGGCTATTATTCTGAATCTG
1211365 ATACATTTTATCCGGTTTATTCCATAAGGAAGGCTAAAATGTTAAAAAGATAATGAGAATGGCTT
131 ATACATTTTATCCGGTTTATTCCATAAGGAAGGCTAAAATGTTAAAAAGATAATGAGAATGGCTT
1211430 TGTTATCTCTCTTAGAATAAATCTGATACATTAAGGCCCATTTAAAGCATGTTTCAAGAAATGTT
196 TGTTATCTCTCTTAGAATAAATCTGATACATTAAGGCCCATTTAAAGCATGTTTCAAGAAATGTT
1211495 ATACTACCAATGCTTTTGCCTCAATCCTGATATAGAACAGTATCAGCAAAGACAGACTATTCGGG
261 ATACTACCAATGCTTTTGCCTCAATCCTGATATAGAACAGTATCAGCAAAGACAGACTATTCGGG
1211560 TTCAGTCAAAAGATTTGCCTCAATCCTGAAA
326 TTCAGTCAAAAGATTTGCCTCAATCCTGAAA
*
1211591 TAGGAGGTGGTTTGCAGTAATAGGAACACTTATTAGTAAAATTTATGCATTTGAACTATTTCAGC
1 TAGGAGGTGGTTTCCAGTAATAGGAACACTTATTAGTAAAATTTATGCATTTGAACTATTTCAGC
1211656 AATGCACAAAACAAGATATTTCAATATCCAACAGCCAGAATAATGAGGCTATTATTCTGAATCTG
66 AATGCACAAAACAAGATATTTCAATATCCAACAGCCAGAATAATGAGGCTATTATTCTGAATCTG
1211721 ATACATTTTATCCGGTTTATTCCATAAGGAAGGCTAAAATGTTAAAAAGATAATGAGAATGGCTT
131 ATACATTTTATCCGGTTTATTCCATAAGGAAGGCTAAAATGTTAAAAAGATAATGAGAATGGCTT
1211786 TGTTATCTCTCTTAGAATAAATCTGATACATTAAGGCCCATTTAAAGCATGTTTCAAGAAATGTT
196 TGTTATCTCTCTTAGAATAAATCTGATACATTAAGGCCCATTTAAAGCATGTTTCAAGAAATGTT
1211851 ATACTACCAATGCTTTTGCCTCAATCCTGATATAGAACAGTATCAGCAAAGACAGACTATTCGGG
261 ATACTACCAATGCTTTTGCCTCAATCCTGATATAGAACAGTATCAGCAAAGACAGACTATTCGGG
*
1211916 TTCAGTCAGAAGATT
326 TTCAGTCAAAAGATT
1211931 CACAATGCAA
Statistics
Matches: 338, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
356 338 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (356 bp):
TAGGAGGTGGTTTCCAGTAATAGGAACACTTATTAGTAAAATTTATGCATTTGAACTATTTCAGC
AATGCACAAAACAAGATATTTCAATATCCAACAGCCAGAATAATGAGGCTATTATTCTGAATCTG
ATACATTTTATCCGGTTTATTCCATAAGGAAGGCTAAAATGTTAAAAAGATAATGAGAATGGCTT
TGTTATCTCTCTTAGAATAAATCTGATACATTAAGGCCCATTTAAAGCATGTTTCAAGAAATGTT
ATACTACCAATGCTTTTGCCTCAATCCTGATATAGAACAGTATCAGCAAAGACAGACTATTCGGG
TTCAGTCAAAAGATTTGCCTCAATCCTGAAA
Found at i:1212537 original size:16 final size:17
Alignment explanation
Indices: 1212513--1212545 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1212503 AAATATTTAC
1212513 AATAATCATTG-AAGAA
1 AATAATCATTGCAAGAA
*
1212529 AATAGTCATTGCAAGAA
1 AATAATCATTGCAAGAA
1212546 CCATGAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (17 bp):
AATAATCATTGCAAGAA
Found at i:1213700 original size:174 final size:174
Alignment explanation
Indices: 1213407--1213756 Score: 524
Period size: 174 Copynumber: 2.0 Consensus size: 174
1213397 TTTCTTGTTC
* *
1213407 TGCTAACAATCAAGTTTACTTATCTGATTGTTCACAGCTATTTCTGAATATAGAAAACAACCAAA
1 TGCTAACAATCAAGTTAACTTATCTGATAGTTCACAGCTATTTCTGAATATAGAAAACAACCAAA
** *
1213472 TATATGCTTCAAGAATTTCACAATTGAACCAAAGATCAAATCCGACGTTAACTAGCATTTAAGGT
66 TATATGCTTCAAGAATTTCACAATTGAACCAAAGATCAAATCCGACCCTAACTAGCATTAAAGGT
* * *
1213537 -AAAAATCTATGACATCAAATATCAGAATCTACAATGTGATTCTT
131 CAAAAA-CTATAACATCAAATATCAGAATCCACAATATGATTCTT
* * * *
1213581 TGCTAACTATCAAGTTAACTTATCTGATAGTTCACAGCTATTTCTGAATGTAGAAAATAATCAAA
1 TGCTAACAATCAAGTTAACTTATCTGATAGTTCACAGCTATTTCTGAATATAGAAAACAACCAAA
* * *
1213646 TATATGTTTCAAGAATTTTACAATTGAACCGAAGATCAAAT-CGTACCCTAACTAGCATTAAAGG
66 TATATGCTTCAAGAATTTCACAATTGAACCAAAGATCAAATCCG-ACCCTAACTAGCATTAAAGG
*
1213710 TCAAAAACTATAACATCAAATATCAGAATCCACAATATGGTTCTT
130 TCAAAAACTATAACATCAAATATCAGAATCCACAATATGATTCTT
1213755 TG
1 TG
1213757 TTAGTTTCCC
Statistics
Matches: 158, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
173 2 0.01
174 151 0.96
175 5 0.03
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (174 bp):
TGCTAACAATCAAGTTAACTTATCTGATAGTTCACAGCTATTTCTGAATATAGAAAACAACCAAA
TATATGCTTCAAGAATTTCACAATTGAACCAAAGATCAAATCCGACCCTAACTAGCATTAAAGGT
CAAAAACTATAACATCAAATATCAGAATCCACAATATGATTCTT
Found at i:1225924 original size:3 final size:3
Alignment explanation
Indices: 1225918--1225968 Score: 50
Period size: 3 Copynumber: 16.0 Consensus size: 3
1225908 CATCATCCAA
*
1225918 ATC ATC ATC ATC ATC ATC ATC TTC ATTC AATGGC -TC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC A-TC -AT--C ATC ATC ATC ATC ATC
1225966 ATC
1 ATC
1225969 TCCTGTATCG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
2 1 0.02
3 34 0.83
4 4 0.10
5 1 0.02
6 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.04, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:1226712 original size:21 final size:20
Alignment explanation
Indices: 1226687--1226726 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1226677 ATTAAGATAA
1226687 AAGGTAAGCAAAAAAGAAAAG
1 AAGGTAAG-AAAAAAGAAAAG
* *
1226708 AAGGTTAGGAAAAAGAAAA
1 AAGGTAAGAAAAAAGAAAA
1226727 ACAGCTTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (20 bp):
AAGGTAAGAAAAAAGAAAAG
Found at i:1236423 original size:2 final size:2
Alignment explanation
Indices: 1236416--1236464 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1236406 AGACCTAAAA
1236416 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1236458 AG AG AG A
1 AG AG AG A
1236465 CGTGGTCAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1236733 original size:20 final size:19
Alignment explanation
Indices: 1236687--1236743 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
1236677 ACTTCAGTAT
*
1236687 TAATTTAATTTATAA-ATTT
1 TAATTTAATTT-TAATATTG
1236706 TAATTTTAATTTTAATATGTG
1 TAA-TTTAATTTTAATAT-TG
* *
1236727 TAATTTATTTTTTATAT
1 TAATTTAATTTTAATAT
1236744 CTTAAAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.19
20 22 0.69
21 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
TAATTTAATTTTAATATTG
Found at i:1237105 original size:2 final size:2
Alignment explanation
Indices: 1237058--1237089 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1237048 GAATTGGAAT
1237058 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1237090 TAGAGTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1237191 original size:2 final size:2
Alignment explanation
Indices: 1237184--1237217 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1237174 AAATCTTGTT
1237184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1237218 ACAGGGAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1237854 original size:6 final size:6
Alignment explanation
Indices: 1237845--1237878 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1237835 TTTTTAATAT
*
1237845 TTTTTA TTTTTA TTTTTA TTTTTA ATTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1237879 CAATTATTCA
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:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:1237883 original size:12 final size:12
Alignment explanation
Indices: 1237846--1237883 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1237836 TTTTAATATT
*
1237846 TTTTATTTTTAT
1 TTTTATTTTTAA
1237858 TTTTATTTTTAA
1 TTTTATTTTTAA
*
1237870 TTTTATTTTCAA
1 TTTTATTTTTAA
1237882 TT
1 TT
1237884 ATTCAAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:1241958 original size:2 final size:2
Alignment explanation
Indices: 1241953--1241988 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1241943 ACACACACAC
1241953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1241989 GGCCTCGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1242212 original size:2 final size:2
Alignment explanation
Indices: 1242205--1242241 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1242195 AGTAATTGGA
*
1242205 TG TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1242242 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:1242406 original size:18 final size:18
Alignment explanation
Indices: 1242383--1242418 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1242373 ATTATGAAAG
1242383 TTTATTAAATTTTCAATT
1 TTTATTAAATTTTCAATT
1242401 TTTATTAAATTTTCAATT
1 TTTATTAAATTTTCAATT
1242419 AATTTTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTATTAAATTTTCAATT
Found at i:1246161 original size:22 final size:22
Alignment explanation
Indices: 1246117--1246157 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1246107 AAATTTTATT
1246117 TAAATTTAATTATTAAAATATA
1 TAAATTTAATTATTAAAATATA
1246139 TAAATATTAA-TA-TAAAATA
1 TAAAT-TTAATTATTAAAATA
1246158 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATTTAATTATTAAAATATA
Found at i:1246168 original size:24 final size:24
Alignment explanation
Indices: 1246141--1246188 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1246131 AAAATATATA
* *
1246141 AATATTAATA-TAAAATAATATTTT
1 AATAATAATACTAAAACAA-ATTTT
1246165 AATAATAATACTAAAACAAATTTT
1 AATAATAATACTAAAACAAATTTT
1246189 TAAATCAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
AATAATAATACTAAAACAAATTTT
Found at i:1247613 original size:17 final size:17
Alignment explanation
Indices: 1247591--1247624 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1247581 ATAATTAAAA
*
1247591 TATATTAAAATTAAATT
1 TATATTAAAAATAAATT
1247608 TATATTAAAAATAAATT
1 TATATTAAAAATAAATT
1247625 AATAAAATAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATTAAAAATAAATT
Found at i:1250844 original size:24 final size:23
Alignment explanation
Indices: 1250787--1250850 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
1250777 AATGTAAATA
1250787 TAATCTATATTAAATATATGCTAT
1 TAAT-TATATTAAATATATGCTAT
*
1250811 TAATTATATTTAAATATAT-CATGT
1 TAATTATA-TTAAATATATGC-TAT
1250835 TATATT-TATTAAATAT
1 TA-ATTATATTAAATAT
1250851 TATATATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 13 0.36
24 20 0.56
25 3 0.08
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (23 bp):
TAATTATATTAAATATATGCTAT
Found at i:1251132 original size:3 final size:3
Alignment explanation
Indices: 1251109--1251151 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
1251099 AAATCATCAA
*
1251109 TAT TA- TAT TAAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1251152 GTAAATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1251527 original size:16 final size:13
Alignment explanation
Indices: 1251496--1251520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1251486 GAAAATTGAT
1251496 TTAATAATATATA
1 TTAATAATATATA
1251509 TTAATAATATAT
1 TTAATAATATAT
1251521 TTTATTATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAATAATATATA
Found at i:1251553 original size:30 final size:31
Alignment explanation
Indices: 1251499--1251569 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
1251489 AATTGATTTA
*
1251499 ATAATATATATTAATAATATATTTTAT-TATATT
1 ATAAT-TATATT-ATAAAATATTTTATATATA-T
*
1251532 ATAATTATATT-TAAAATATTTTATATTTAT
1 ATAATTATATTATAAAATATTTTATATATAT
1251562 ATAATTAT
1 ATAATTAT
1251570 TATATCTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 21 0.60
31 3 0.09
32 6 0.17
33 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
ATAATTATATTATAAAATATTTTATATATAT
Found at i:1262585 original size:2 final size:2
Alignment explanation
Indices: 1262572--1262606 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1262562 TCTGCTGTTT
*
1262572 TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1262607 TTGTTTTGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1263476 original size:13 final size:13
Alignment explanation
Indices: 1263450--1263483 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1263440 AAAAAATATA
*
1263450 AGAGAGGATGCTTG
1 AGAG-GGATACTTG
1263464 AGAGGGATACTTG
1 AGAGGGATACTTG
1263477 AGAGGGA
1 AGAGGGA
1263484 GGAGGAAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.32, C:0.06, G:0.44, T:0.18
Consensus pattern (13 bp):
AGAGGGATACTTG
Found at i:1263624 original size:27 final size:27
Alignment explanation
Indices: 1263562--1263625 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
1263552 AAATAACATG
*
1263562 CCACCATTTTTGACAAATAAAAAGAAA
1 CCACCATTTTTAACAAATAAAAAGAAA
* * *
1263589 TCACCATTTTTAACAAATACAAAGTAA
1 CCACCATTTTTAACAAATAAAAAGAAA
*
1263616 CCACAATTTT
1 CCACCATTTT
1263626 GACAAACAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (27 bp):
CCACCATTTTTAACAAATAAAAAGAAA
Found at i:1265557 original size:21 final size:22
Alignment explanation
Indices: 1265531--1265576 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1265521 ATCTGTTGAA
* *
1265531 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
1265552 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
1265574 ACT
1 ACT
1265577 TATCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:1268188 original size:27 final size:27
Alignment explanation
Indices: 1268151--1268216 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1268141 ACATGTCAAC
* *
1268151 ATTTTTAACAAATAAAAAAAAACTATA
1 ATTTTTGACAAATAAAAAAAAACCATA
* **
1268178 ATTTTTGACAAATACAAAGTAACCATA
1 ATTTTTGACAAATAAAAAAAAACCATA
1268205 ATTTTTGACAAA
1 ATTTTTGACAAA
1268217 CAATGGGTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (27 bp):
ATTTTTGACAAATAAAAAAAAACCATA
Found at i:1273190 original size:13 final size:14
Alignment explanation
Indices: 1273160--1273196 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
1273150 ATCAATAATT
1273160 TTAAATTTTATTTTA
1 TTAAATTTTA-TTTA
1273175 TTAAATTTTA-TTA
1 TTAAATTTTATTTA
1273188 TTAAATTTT
1 TTAAATTTT
1273197 TACCATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTAAATTTTATTTA
Found at i:1273207 original size:3 final size:3
Alignment explanation
Indices: 1273201--1273230 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1273191 AATTTTTACC
1273201 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1273231 TGTGGTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1277820 original size:3 final size:3
Alignment explanation
Indices: 1277812--1277844 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1277802 ACCTATGTCA
1277812 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1277845 TTCCTAGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1277992 original size:24 final size:24
Alignment explanation
Indices: 1277965--1278010 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1277955 CATAAACTGA
1277965 TTAGATTAAAGTTTAAACTCGGAG
1 TTAGATTAAAGTTTAAACTCGGAG
1277989 TTAGATTAAAGTTTAAACTCGG
1 TTAGATTAAAGTTTAAACTCGG
1278011 GGTTGGAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (24 bp):
TTAGATTAAAGTTTAAACTCGGAG
Found at i:1279374 original size:18 final size:19
Alignment explanation
Indices: 1279337--1279374 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1279327 TTTAATTTAT
*
1279337 AATATTAAACTTAATTAAA
1 AATATTAAACTTAATAAAA
*
1279356 AATATTATA-TTAATAAAA
1 AATATTAAACTTAATAAAA
1279374 A
1 A
1279375 TTAGAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATTAAACTTAATAAAA
Found at i:1279791 original size:2 final size:2
Alignment explanation
Indices: 1279786--1279811 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1279776 TGATTAATAA
1279786 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
1279812 CCACAAAATT
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:1281522 original size:10 final size:10
Alignment explanation
Indices: 1281507--1281540 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1281497 TAATCCATTT
*
1281507 TATACATACA
1 TATACATATA
1281517 TATACATATA
1 TATACATATA
*
1281527 TATATATATA
1 TATACATATA
1281537 TATA
1 TATA
1281541 TATGATGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (10 bp):
TATACATATA
Found at i:1286798 original size:19 final size:19
Alignment explanation
Indices: 1286774--1286813 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1286764 GAATATTAAC
*
1286774 AATAAATATCCGAAATGTT
1 AATAAATATCCAAAATGTT
1286793 AATAAATATCCAAAATGTT
1 AATAAATATCCAAAATGTT
1286812 AA
1 AA
1286814 CAATATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (19 bp):
AATAAATATCCAAAATGTT
Found at i:1288231 original size:2 final size:2
Alignment explanation
Indices: 1288224--1288260 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1288214 ATTTAAGAAG
1288224 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1288261 GTTACAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.