Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold344
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: 1758742
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 8 of 11
Found at i:1255271 original size:13 final size:13
Alignment explanation
Indices: 1255253--1255278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1255243 CCCCTTCAAA
1255253 AAAAATTCATACT
1 AAAAATTCATACT
1255266 AAAAATTCATACT
1 AAAAATTCATACT
1255279 TCTCCCCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTCATACT
Found at i:1255507 original size:19 final size:18
Alignment explanation
Indices: 1255470--1255519 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
1255460 AATAGCAAGA
1255470 CAAACAAATGTCATTCAT
1 CAAACAAATGTCATTCAT
* *
1255488 CAAACATAATTTCGTTCAT
1 CAAACA-AATGTCATTCAT
*
1255507 CAAAAAAAT-TCAT
1 CAAACAAATGTCAT
1255520 GTACAAGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.11
18 9 0.33
19 15 0.56
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (18 bp):
CAAACAAATGTCATTCAT
Found at i:1255583 original size:12 final size:12
Alignment explanation
Indices: 1255566--1255600 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1255556 TCAACTAGCA
*
1255566 TATGACTACTCC
1 TATGACTAATCC
1255578 TATGACTAATCC
1 TATGACTAATCC
*
1255590 TACGACTAATC
1 TATGACTAATC
1255601 GTCACTCAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.31
Consensus pattern (12 bp):
TATGACTAATCC
Found at i:1256821 original size:13 final size:13
Alignment explanation
Indices: 1256803--1256827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1256793 AACGGTGCCC
1256803 ATGTATCGATACA
1 ATGTATCGATACA
1256816 ATGTATCGATAC
1 ATGTATCGATAC
1256828 TAAGAACATT
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):
ATGTATCGATACA
Found at i:1260327 original size:3 final size:3
Alignment explanation
Indices: 1260319--1260358 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
1260309 CGAGTCAACT
* *
1260319 TCA TCA TCA TCA TTA TCA TCA TCA TCA TCT TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1260359 TGATGGTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (3 bp):
TCA
Found at i:1261902 original size:20 final size:20
Alignment explanation
Indices: 1261877--1261994 Score: 69
Period size: 20 Copynumber: 5.8 Consensus size: 20
1261867 ATACGCTCCT
1261877 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
*
1261897 ATGTATCGATAC-ATACAT-
1 ATGTATCGATACAATTCATA
* * ** * *
1261915 TTGAAATTTATAGCCATTGGCCTTA
1 ATG-TATCGATA-CAATT--CAT-A
* * **
1261940 ATGTATCGATATATTTCACC
1 ATGTATCGATACAATTCATA
*
1261960 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATA
1261980 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1261995 GTATCCATAC
Statistics
Matches: 71, Mismatches: 20, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
18 2 0.03
19 10 0.14
20 45 0.63
21 3 0.04
23 4 0.06
24 5 0.07
25 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:1262078 original size:19 final size:20
Alignment explanation
Indices: 1262054--1262103 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
1262044 CAATTCAATG
*
1262054 TGTATCAATACTAAG-AACA
1 TGTATCGATACTAAGCAACA
*
1262073 TGTATCGATACTAAGCAATA
1 TGTATCGATACTAAGCAACA
1262093 TGTATCGATAC
1 TGTATCGATAC
1262104 ATCTAGGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
TGTATCGATACTAAGCAACA
Found at i:1262097 original size:20 final size:20
Alignment explanation
Indices: 1262032--1262103 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
1262022 TTGCCAGTTT
*
1262032 TATGTATCGATAC-AATTCAA
1 TATGTATCGATACTAA-GCAA
* *
1262052 TGTGTATCAATACTAAG-AA
1 TATGTATCGATACTAAGCAA
*
1262071 CATGTATCGATACTAAGCAA
1 TATGTATCGATACTAAGCAA
1262091 TATGTATCGATAC
1 TATGTATCGATAC
1262104 ATCTAGGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.37
20 25 0.58
21 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (20 bp):
TATGTATCGATACTAAGCAA
Found at i:1269254 original size:15 final size:14
Alignment explanation
Indices: 1269234--1269263 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1269224 TTAACAGTAA
1269234 TTTTTAGAAAATTAT
1 TTTTTA-AAAATTAT
1269249 TTTTTAAAAATTAT
1 TTTTTAAAAATTAT
1269263 T
1 T
1269264 GATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TTTTTAAAAATTAT
Found at i:1270507 original size:14 final size:13
Alignment explanation
Indices: 1270453--1270499 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
1270443 TATTATTTTT
1270453 AAATAAATTATCATA
1 AAATAAATTAT--TA
1270468 ATAAT-AATTATTTA
1 A-AATAAATTA-TTA
1270482 AAATAAATTATTA
1 AAATAAATTATTA
1270495 AAATA
1 AAATA
1270500 TTATTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.38
14 8 0.28
15 6 0.21
16 4 0.14
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATAAATTATTA
Found at i:1270510 original size:29 final size:30
Alignment explanation
Indices: 1270443--1270510 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
1270433 TAATGGGTGC
* *
1270443 TATTATTTTTAAATAAATTATCATAATAAT
1 TATTATTTTAAAATAAATTATCAAAATAAT
* *
1270473 AATTA-TTTAAAATAAATTATTAAAAT-AT
1 TATTATTTTAAAATAAATTATCAAAATAAT
1270501 TATTATTTTA
1 TATTATTTTA
1270511 GTTTATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 6 0.19
29 22 0.69
30 4 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (30 bp):
TATTATTTTAAAATAAATTATCAAAATAAT
Found at i:1270726 original size:18 final size:18
Alignment explanation
Indices: 1270696--1270740 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1270686 ATTTTTTAAA
*
1270696 ATTAATAAAAAATTATATT
1 ATTAAT-AAAAATAATATT
1270715 ATTAATAAAAATAATATT
1 ATTAATAAAAATAATATT
1270733 ATT-ATAAA
1 ATTAATAAA
1270741 TACAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 5 0.20
18 14 0.56
19 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAATAAAAATAATATT
Found at i:1270737 original size:21 final size:21
Alignment explanation
Indices: 1270696--1270768 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 21
1270686 ATTTTTTAAA
*
1270696 ATTAATAAAAA-ATTA-TATT
1 ATTAATAAAAATAATATTATT
1270715 ATTAATAAAAATAATATTATT
1 ATTAATAAAAATAATATTATT
* * *
1270736 ATAAATACAATAATAGCTTTTATT
1 ATTAATA-AA-AATA-ATATTATT
1270760 ATTAA-AAAA
1 ATTAATAAAA
1270769 TTATTTCATT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.25
20 3 0.07
21 11 0.25
22 4 0.09
23 5 0.11
24 10 0.23
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (21 bp):
ATTAATAAAAATAATATTATT
Found at i:1270976 original size:30 final size:32
Alignment explanation
Indices: 1270923--1270985 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
1270913 TCATATAATT
1270923 ATTAAGGGTAGTAAATCATCTAATT-TTTTAA
1 ATTAAGGGTAGTAAATCATCTAATTATTTTAA
*
1270954 ATTAAGGGT--TATAATTATCTAATTATTTTAA
1 ATTAAGGGTAGTA-AATCATCTAATTATTTTAA
1270985 A
1 A
1270986 ATTTTAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 2 0.07
30 11 0.38
31 16 0.55
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (32 bp):
ATTAAGGGTAGTAAATCATCTAATTATTTTAA
Found at i:1271519 original size:13 final size:13
Alignment explanation
Indices: 1271501--1271547 Score: 67
Period size: 13 Copynumber: 3.4 Consensus size: 13
1271491 AAAATAATAA
1271501 TATTTTAATAATT
1 TATTTTAATAATT
1271514 TATTTTAAATTAATAT
1 TATTTT-AA-TAAT-T
1271530 TATTTTAATAATT
1 TATTTTAATAATT
1271543 TATTT
1 TATTT
1271548 AAAAGTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 12 0.39
14 6 0.19
15 6 0.19
16 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTAATAATT
Found at i:1271533 original size:29 final size:30
Alignment explanation
Indices: 1271495--1271556 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
1271485 TAGATCAAAA
*
1271495 TAATAATATTTTAATAATTTATTTTAAA-T
1 TAATAATATTTTAATAATTTATTTAAAAGT
*
1271524 TAATATTATTTTAATAATTTATTTAAAAGT
1 TAATAATATTTTAATAATTTATTTAAAAGT
1271554 TAA
1 TAA
1271557 AAGATACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTAATAATTTATTTAAAAGT
Found at i:1272693 original size:2 final size:2
Alignment explanation
Indices: 1272686--1272716 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1272676 TATGACGGTG
1272686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1272717 GTACGGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1274279 original size:18 final size:19
Alignment explanation
Indices: 1274256--1274291 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1274246 TAATTGATGT
*
1274256 ATTAATTT-TTTAAAATTA
1 ATTAATTTAATTAAAATTA
1274274 ATTAATTTAATTAAAATT
1 ATTAATTTAATTAAAATT
1274292 TTCCAACTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTAATTTAATTAAAATTA
Found at i:1277444 original size:12 final size:12
Alignment explanation
Indices: 1277405--1277487 Score: 64
Period size: 12 Copynumber: 7.1 Consensus size: 12
1277395 TGCCATTGGT
*
1277405 TGCTGTGGCTGC
1 TGCTGTTGCTGC
* *
1277417 TGTTGTTGGGTGC
1 TGCTGTT-GCTGC
1277430 TGCTGTTGCTGC
1 TGCTGTTGCTGC
* *
1277442 TGCCGTTGCAGC
1 TGCTGTTGCTGC
* *
1277454 TACTGTTGCTAC
1 TGCTGTTGCTGC
*
1277466 TGTTGTTGCTG-
1 TGCTGTTGCTGC
1277477 T--TGTTGCTGC
1 TGCTGTTGCTGC
1277487 T
1 T
1277488 ATTTTTGGTG
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
9 8 0.15
10 1 0.02
11 1 0.02
12 35 0.64
13 10 0.18
ACGTcount: A:0.04, C:0.20, G:0.34, T:0.42
Consensus pattern (12 bp):
TGCTGTTGCTGC
Found at i:1277487 original size:24 final size:24
Alignment explanation
Indices: 1277460--1277508 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1277450 CAGCTACTGT
*
1277460 TGCTACTGTTGTTGCTGTTGTTGC
1 TGCTACTGTTGGTGCTGTTGTTGC
* * *
1277484 TGCTATTTTTGGTGCTGTTTTTGC
1 TGCTACTGTTGGTGCTGTTGTTGC
1277508 T
1 T
1277509 TGTTGTTGGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.04, C:0.14, G:0.27, T:0.55
Consensus pattern (24 bp):
TGCTACTGTTGGTGCTGTTGTTGC
Found at i:1277595 original size:28 final size:27
Alignment explanation
Indices: 1277556--1277609 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1277546 TTGGTTGCTT
* * *
1277556 TCTTTTTTTTGTTTCGGTTTTGTTTTA
1 TCTTTTTGTTGTTTCGATTCTGTTTTA
1277583 TCTTTTTGGTTGTTTCGATTCTGTTTT
1 TCTTTTT-GTTGTTTCGATTCTGTTTT
1277610 TCTATTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.04, C:0.09, G:0.17, T:0.70
Consensus pattern (27 bp):
TCTTTTTGTTGTTTCGATTCTGTTTTA
Found at i:1277833 original size:25 final size:26
Alignment explanation
Indices: 1277793--1277845 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
1277783 CATTTCAGCC
*
1277793 GCTGTCGATTTTTTCTCTTCATTGCA
1 GCTGTCGATTTCTTCTCTTCATTGCA
* *
1277819 GCTGTC-ATTTCTTCTCTTTATTTCA
1 GCTGTCGATTTCTTCTCTTCATTGCA
1277844 GC
1 GC
1277846 AGCTATTTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.11, C:0.25, G:0.13, T:0.51
Consensus pattern (26 bp):
GCTGTCGATTTCTTCTCTTCATTGCA
Found at i:1277927 original size:61 final size:61
Alignment explanation
Indices: 1277859--1278001 Score: 189
Period size: 61 Copynumber: 2.3 Consensus size: 61
1277849 TATTTCGTTT
** *
1277859 GCATTTCATGCATGAATTGTTGCTACCATTTCTATTTTGGTTTTCAGTAGCTGATTCATTTA
1 GCATTTCATGCATGAATTGTTGCTACCATTTCTATTTTGGTTTTCAACAGCTGATTCA-TCA
** * * *
1277921 -CATTTCATGCATGAATCATTGCTGCCATTTTTGTTTTGGTTTTCAACAGCTGATTCATCA
1 GCATTTCATGCATGAATTGTTGCTACCATTTCTATTTTGGTTTTCAACAGCTGATTCATCA
*
1277981 GCATTTCATGAATGAATTGTT
1 GCATTTCATGCATGAATTGTT
1278002 TAATTGCTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 2 0.03
61 67 0.97
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (61 bp):
GCATTTCATGCATGAATTGTTGCTACCATTTCTATTTTGGTTTTCAACAGCTGATTCATCA
Found at i:1278178 original size:12 final size:12
Alignment explanation
Indices: 1278158--1278192 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1278148 TTGTCAAGTT
* *
1278158 CATGTATGAAAG
1 CATGCATGAAAA
1278170 CATGCATGAAAA
1 CATGCATGAAAA
1278182 CATGCATGAAA
1 CATGCATGAAA
1278193 TGAATGCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (12 bp):
CATGCATGAAAA
Found at i:1278346 original size:43 final size:41
Alignment explanation
Indices: 1278280--1278362 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 41
1278270 TCGTTTTCAT
* * *
1278280 GCATGCAAGCATGAATTGCCACCTAATTGATTTAGGTGGCA
1 GCATGCAAGCATGAATTGCCACCTAAATAAATTAGGTGGCA
1278321 GCATGCAATGCAATGCAA-TGCCACCTAAATAAATTAGGTGGC
1 GCATGCAA-GC-ATG-AATTGCCACCTAAATAAATTAGGTGGC
1278363 TAAAATGCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 8 0.22
42 2 0.06
43 24 0.67
44 2 0.06
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (41 bp):
GCATGCAAGCATGAATTGCCACCTAAATAAATTAGGTGGCA
Found at i:1278417 original size:16 final size:17
Alignment explanation
Indices: 1278391--1278428 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
1278381 AATGAATCAT
1278391 TTTTTTAATTAT-TATTA
1 TTTTTTAATTATATA-TA
1278408 TTTTTT-ATTATATATA
1 TTTTTTAATTATATATA
1278424 TTTTT
1 TTTTT
1278429 ATTTAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTAATTATATATA
Found at i:1278435 original size:36 final size:38
Alignment explanation
Indices: 1278390--1278467 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
1278380 GAATGAATCA
*
1278390 TTTT-TTTAATTATTATTAT-TT-TTT-ATTATATATAT
1 TTTTATTTAATTATGATTATATTATTTCATT-TATATAT
* *
1278425 TTTTATTTAATTGTGATTATATTATTTCATTTATTTAT
1 TTTTATTTAATTATGATTATATTATTTCATTTATATAT
1278463 TTTTA
1 TTTTA
1278468 CCTTTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 4 0.11
36 13 0.36
37 2 0.06
38 14 0.39
39 3 0.08
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (38 bp):
TTTTATTTAATTATGATTATATTATTTCATTTATATAT
Found at i:1279270 original size:83 final size:84
Alignment explanation
Indices: 1279119--1279281 Score: 238
Period size: 83 Copynumber: 2.0 Consensus size: 84
1279109 CTACAGGCAG
* ** * * * *
1279119 ACTAAAGGTAAATAAGTCTCTAGTGTCAAAGCTGACAAGTAGACTAAAGGTTAGGAAGTCTCCAA
1 ACTAAAGGTAAAGAAGTCTCTAGTGTCAAAGCCAACAAGTACACTAAAAGTAAAGAAGTCTCCAA
1279184 GGTCAAAGCCGACAAACAA
66 GGTCAAAGCCGACAAACAA
* *
1279203 ACTAAAGGTAAAGAAGTCTCTAG-GTCAAAGCCAACAGGTACACTAAAAGTAAAGAAGTCTCTAA
1 ACTAAAGGTAAAGAAGTCTCTAGTGTCAAAGCCAACAAGTACACTAAAAGTAAAGAAGTCTCCAA
1279267 GGTCAAAGCCGACAA
66 GGTCAAAGCCGACAA
1279282 GCTGACTGAA
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
83 48 0.69
84 22 0.31
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (84 bp):
ACTAAAGGTAAAGAAGTCTCTAGTGTCAAAGCCAACAAGTACACTAAAAGTAAAGAAGTCTCCAA
GGTCAAAGCCGACAAACAA
Found at i:1279281 original size:125 final size:125
Alignment explanation
Indices: 1279048--1279439 Score: 421
Period size: 125 Copynumber: 3.1 Consensus size: 125
1279038 AATGGAAAAA
* * * * * ** *
1279048 AAGTCTCCAAGGTCAAAGCCTATAGGTAAACTAAAGATAAGGAAGTATCTAGAGTCAAAATCTAC
1 AAGTCTCCAAGGTCAAAGCCGACAGGCAAACTAAAGGTAAGGAAGTCTCTAG-GTCAAAGCCAAC
* * *
1279113 AGGCAGACTAAAGGTAAATAAGTCTCT-AGTGTCAAAGCTGACAAGTAGACTAAAGGTTAGG
65 AGGCAGACTAAAGGTAAAGAAGTCTCTAAG-GTCAAAGCCGACAAGTAGACTAAAGGTAAGG
** *
1279174 AAGTCTCCAAGGTCAAAGCCGACAAACAAACTAAAGGTAAAGAAGTCTCTAGGTCAAAGCCAACA
1 AAGTCTCCAAGGTCAAAGCCGACAGGCAAACTAAAGGTAAGGAAGTCTCTAGGTCAAAGCCAACA
* * * * *
1279239 GGTACACTAAAAGTAAAGAAGTCTCTAAGGTCAAAGCCGACAAGCT-GACTGAAGGCAAGG
66 GGCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAAG-TAGACTAAAGGTAAGG
* * * * * *
1279299 AAGTCTCCAAGGTCAAAACTGACAGGCAGA-TTAAGGTAAGGAAGTCTCCAGGGTCAAAGCTAAC
1 AAGTCTCCAAGGTCAAAGCCGACAGGCAAACTAAAGGTAAGGAAGTCTCTA-GGTCAAAGCCAAC
* * * * * * * *
1279363 AAGCAGACTAAAGGTTAGGAAGTGTCCAAGGTCAAAGTCGACAAGCAGACTAAAAGTAAGG
65 AGGCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAAGTAGACTAAAGGTAAGG
*
1279424 AAGTGTCCAAGGTCAA
1 AAGTCTCCAAGGTCAA
1279440 CTGATATGTA
Statistics
Matches: 220, Mismatches: 42, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
124 17 0.08
125 156 0.71
126 47 0.21
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (125 bp):
AAGTCTCCAAGGTCAAAGCCGACAGGCAAACTAAAGGTAAGGAAGTCTCTAGGTCAAAGCCAACA
GGCAGACTAAAGGTAAAGAAGTCTCTAAGGTCAAAGCCGACAAGTAGACTAAAGGTAAGG
Found at i:1279302 original size:83 final size:83
Alignment explanation
Indices: 1279119--1279439 Score: 230
Period size: 83 Copynumber: 3.8 Consensus size: 83
1279109 CTACAGGCAG
* * ** * * * *
1279119 ACTAAAGGTAAATAAGTCTCTAGTGTCAAAGCTGACAAGTAGACTAAAGGTTAGGAAGTCTCCAA
1 ACTAAAGGCAAAGAAGTCTCTAG-GTCAAAGCCAACAAGTACACTAAAAGTAAAGAAGTCTCCAA
1279184 GGTCAAAGCCGACAAACAA
65 GGTCAAAGCCGACAAACAA
* * *
1279203 ACTAAAGGTAAAGAAGTCTCTAGGTCAAAGCCAACAGGTACACTAAAAGTAAAGAAGTCTCTAAG
1 ACTAAAGGCAAAGAAGTCTCTAGGTCAAAGCCAACAAGTACACTAAAAGTAAAGAAGTCTCCAAG
* **
1279268 GTCAAAGCCGACAAGCTG
66 GTCAAAGCCGACAAACAA
* * * * ** * * * * * * *
1279286 ACTGAAGGCAAGGAAGTCTCCAAGGTCAAAACTGACAGGCAGA-TTAAGGTAAGGAAGTCTCCAG
1 ACTAAAGGCAAAGAAGTCT-CTAGGTCAAAGCCAACAAGTACACTAAAAGTAAAGAAGTCTCCAA
** * *
1279350 GGTCAAAGCTAACAAGCAG
65 GGTCAAAGCCGACAAACAA
** * * * * * * * * *
1279369 ACTAAAGGTTAGGAAGTGTCCAAGGTCAAAGTCGACAAGCAGACTAAAAGTAAGGAAGTGTCCAA
1 ACTAAAGGCAAAGAAGTCT-CTAGGTCAAAGCCAACAAGTACACTAAAAGTAAAGAAGTCTCCAA
1279434 GGTCAA
65 GGTCAA
1279440 CTGATATGTA
Statistics
Matches: 194, Mismatches: 41, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
83 132 0.68
84 62 0.32
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (83 bp):
ACTAAAGGCAAAGAAGTCTCTAGGTCAAAGCCAACAAGTACACTAAAAGTAAAGAAGTCTCCAAG
GTCAAAGCCGACAAACAA
Found at i:1279428 original size:42 final size:42
Alignment explanation
Indices: 1279048--1279439 Score: 342
Period size: 42 Copynumber: 9.4 Consensus size: 42
1279038 AATGGAAAAA
* * * * * *
1279048 AAGTCTCCAAGGTCAAAGCCTATAGGTAAACTAAAGATAAGG
1 AAGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAAGGTAAGG
* * ** * * **
1279090 AAGTAT-CTAGAGTCAAAATCTACAGGCAGACTAAAGGTAAAT
1 AAGTCTCCAAG-GTCAAAGCCGACAAGCAGACTAAAGGTAAGG
* * * *
1279132 AAGTCT-CTAGTGTCAAAGCTGACAAGTAGACTAAAGGTTAGG
1 AAGTCTCCAAG-GTCAAAGCCGACAAGCAGACTAAAGGTAAGG
* * *
1279174 AAGTCTCCAAGGTCAAAGCCGACAAACAAACTAAAGGTAAAG
1 AAGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAAGGTAAGG
* * * * * * *
1279216 AAGTCT-CTAGGTCAAAGCCAACAGGTACACTAAAAGTAAAG
1 AAGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAAGGTAAGG
* * * *
1279257 AAGTCTCTAAGGTCAAAGCCGACAAGCTGACTGAAGGCAAGG
1 AAGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAAGGTAAGG
* * * *
1279299 AAGTCTCCAAGGTCAAAACTGACAGGCAGA-TTAAGGTAAGG
1 AAGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAAGGTAAGG
* ** *
1279340 AAGTCTCCAGGGTCAAAGCTAACAAGCAGACTAAAGGTTAGG
1 AAGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAAGGTAAGG
* * *
1279382 AAGTGTCCAAGGTCAAAGTCGACAAGCAGACTAAAAGTAAGG
1 AAGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAAGGTAAGG
*
1279424 AAGTGTCCAAGGTCAA
1 AAGTCTCCAAGGTCAA
1279440 CTGATATGTA
Statistics
Matches: 280, Mismatches: 66, Indels: 8
0.79 0.19 0.02
Matches are distributed among these distances:
41 72 0.26
42 205 0.73
43 3 0.01
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (42 bp):
AAGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAAGGTAAGG
Found at i:1279555 original size:43 final size:42
Alignment explanation
Indices: 1279476--1279612 Score: 157
Period size: 43 Copynumber: 3.2 Consensus size: 42
1279466 CTATTTAGTC
* * *
1279476 TAAGGAAGTCTCCAAGGTGAAAGCCGACAGGCAGACTAAAGT
1 TAAGGAAGTCTCCAAGGTCAAAGCCGACAGGAAGACTAAAGG
*
1279518 TTAGGAAGTCTCCAAGGTCAAAAGCCGACAGGAAGACTAAAGG
1 TAAGGAAGTCTCCAAGGTC-AAAGCCGACAGGAAGACTAAAGG
* * * * * *
1279561 TAAGAAAGTCTCTAGGGTCAAAGCCAACAGGACAAACTAAAAG
1 TAAGGAAGTCTCCAAGGTCAAAGCCGACAGGA-AGACTAAAGG
*
1279604 TAAAGAAGT
1 TAAGGAAGT
1279613 TAAAAGTGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 29 0.36
43 51 0.64
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.15
Consensus pattern (42 bp):
TAAGGAAGTCTCCAAGGTCAAAGCCGACAGGAAGACTAAAGG
Found at i:1279964 original size:44 final size:42
Alignment explanation
Indices: 1279863--1280070 Score: 154
Period size: 44 Copynumber: 4.8 Consensus size: 42
1279853 AAAAAAAACC
* * *
1279863 TGACTAGGGTGGTAACC--ACGTCAAA-CAGAAAGGAATGGGATT
1 TGACCAGGGTGGTAACCATACGTCAAATCA-AAATG-A-GAGATT
* * *
1279905 TAACTAGGGTGGTAACCATACGTTAAATCAAAATGAGACGATTT
1 TGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGA-GA-TT
* * * * *
1279949 TGACCAGGGTGGTAACCATACATCAAACCGAAATGAAAAAAGTT
1 TGACCAGGGTGGTAACCATACGTCAAATCAAAATG-AGAGA-TT
* *
1279993 TGACCAGGGTGGTAACCATATGTCAAA-CATAAAGGAAAGAGATT
1 TGACCAGGGTGGTAACCATACGTCAAATCA-AAATG--AGAGATT
* * *
1280037 TAACTAGGGTGGTAACCATAAGTCAAATCAAAAT
1 TGACCAGGGTGGTAACCATACGTCAAATCAAAAT
1280071 AAGAAGAATC
Statistics
Matches: 134, Mismatches: 23, Indels: 16
0.77 0.13 0.09
Matches are distributed among these distances:
42 17 0.13
43 4 0.03
44 103 0.77
45 10 0.07
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (42 bp):
TGACCAGGGTGGTAACCATACGTCAAATCAAAATGAGAGATT
Found at i:1280092 original size:44 final size:44
Alignment explanation
Indices: 1279902--1280095 Score: 164
Period size: 44 Copynumber: 4.4 Consensus size: 44
1279892 AAGGAATGGG
* * * * *
1279902 ATTTAACTAGGGTGGTAACCATACGTTAAATCAAAATGAGACGA
1 ATTTAACCAGGGTGGTAACCATAAGTCAAATCAAAATAAGAAGA
* * * *
1279946 TTTTGACCAGGGTGGTAACCATACA-TCAAACCGAAATGAA-AA-A
1 ATTTAACCAGGGTGGTAACCATA-AGTCAAATCAAAAT-AAGAAGA
* * * *
1279989 AGTTTGACCAGGGTGGTAACCATATGTCAAA-CATAA-AGGAAAGA
1 A-TTTAACCAGGGTGGTAACCATAAGTCAAATCAAAATAAG-AAGA
*
1280033 GATTTAACTAGGGTGGTAACCATAAGTCAAATCAAAATAAGAAGA
1 -ATTTAACCAGGGTGGTAACCATAAGTCAAATCAAAATAAGAAGA
* *
1280078 ATCTAACCAAGGTGGTAA
1 ATTTAACCAGGGTGGTAA
1280096 TACGTCATAC
Statistics
Matches: 118, Mismatches: 22, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
41 1 0.01
43 6 0.05
44 99 0.84
45 10 0.08
46 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.22
Consensus pattern (44 bp):
ATTTAACCAGGGTGGTAACCATAAGTCAAATCAAAATAAGAAGA
Found at i:1281583 original size:13 final size:13
Alignment explanation
Indices: 1281553--1281582 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1281543 CTTGTTTAGG
1281553 TTTTTATTTGATT
1 TTTTTATTTGATT
1281566 TTTTTATTTG-TT
1 TTTTTATTTGATT
1281578 TTTTT
1 TTTTT
1281583 TTGGGACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTTATTTGATT
Found at i:1282977 original size:15 final size:16
Alignment explanation
Indices: 1282949--1282978 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1282939 TAGGGGACTT
1282949 ATAGGTGCTCATCTCG
1 ATAGGTGCTCATCTCG
1282965 ATAGGTG-TCATCTC
1 ATAGGTGCTCATCTC
1282979 TTGTCCCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (16 bp):
ATAGGTGCTCATCTCG
Found at i:1294818 original size:27 final size:25
Alignment explanation
Indices: 1294787--1294855 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 25
1294777 TCTTTTTTTT
1294787 TGTTTCGATTTTGTTTTCTCTTCTTGC
1 TGTTTCGATTTTGTTTTCTC-TCTT-C
*
1294814 TGTTTCGATTCTGTTTT-TCTCTTC
1 TGTTTCGATTTTGTTTTCTCTCTTC
*
1294838 TG-TTCTATTTTGTTTTCT
1 TGTTTCGATTTTGTTTTCT
1294856 TTTGTTCGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 12 0.32
24 4 0.11
25 4 0.11
26 2 0.05
27 16 0.42
ACGTcount: A:0.04, C:0.17, G:0.13, T:0.65
Consensus pattern (25 bp):
TGTTTCGATTTTGTTTTCTCTCTTC
Found at i:1295583 original size:16 final size:16
Alignment explanation
Indices: 1295558--1295654 Score: 63
Period size: 16 Copynumber: 5.6 Consensus size: 16
1295548 ATAAATTGTG
1295558 TTTTTT-TTATTATTA
1 TTTTTTATTATTATTA
1295573 TTTTTTATTATATATATA
1 TTTTTTATTAT-TAT-TA
*
1295591 TGTTTTATTTAATAATGATTA
1 TTTTTTA-TT-AT--T-ATTA
1295612 TATTTTTATT-TTATTTTA
1 T-TTTTTATTATTA--TTA
* *
1295630 TTTTTCATTATTTTTA
1 TTTTTTATTATTATTA
1295646 TTTTTTATT
1 TTTTTTATT
1295655 TTTTAAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
15 6 0.09
16 16 0.24
17 11 0.17
18 14 0.21
19 3 0.05
20 2 0.03
21 7 0.11
22 7 0.11
ACGTcount: A:0.25, C:0.01, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTTTATTATTATTA
Found at i:1299784 original size:2 final size:2
Alignment explanation
Indices: 1299777--1299820 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
1299767 GTCAAGTTGT
*
1299777 TA TA TA TA TA TA TA TA TA TA TA TA TA TG T- 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
1299818 TA T
1 TA T
1299821 TTAATGACGT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1300011 original size:20 final size:20
Alignment explanation
Indices: 1299986--1300062 Score: 54
Period size: 20 Copynumber: 3.9 Consensus size: 20
1299976 ACAATTCAAT
1299986 TAAAATTATTATTTAATTTA
1 TAAAATTATTATTTAATTTA
1300006 TAAAA-TATTTAAGTTTAA-TTA
1 TAAAATTA-TT-A-TTTAATTTA
* * *
1300027 TAAAAATATAATATTAATATA
1 TAAAATTATTAT-TTAATTTA
*
1300048 -AAAATAATT-TTTAAT
1 TAAAATTATTATTTAAT
1300063 ATATTTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
18 5 0.11
19 4 0.09
20 18 0.39
21 12 0.26
22 7 0.15
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (20 bp):
TAAAATTATTATTTAATTTA
Found at i:1300297 original size:2 final size:2
Alignment explanation
Indices: 1300292--1300332 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1300282 AAAAAACAAA
1300292 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1300333 ATACTTCGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1305258 original size:50 final size:51
Alignment explanation
Indices: 1305184--1305326 Score: 180
Period size: 50 Copynumber: 2.8 Consensus size: 51
1305174 AAAAGTCATA
* * * * * *
1305184 TTTTTACCCCGATGTATCGATACATTTTTTAATATATCGATATATTTTGT-
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
** *
1305234 TTTTTACTTAGATGTATCAATACATTTTTCAATGTATCGATACATTCTATC
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
* *
1305285 TTTTTACCCAGGTATATCGATACATTTTTCAATGTATCGATA
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATA
1305327 GATCTAGTTA
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 41 0.53
51 37 0.47
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (51 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
Found at i:1307700 original size:121 final size:121
Alignment explanation
Indices: 1307476--1307703 Score: 352
Period size: 121 Copynumber: 1.9 Consensus size: 121
1307466 TATTTATCGA
* * *
1307476 GGATACTCCAATCCTGTTTTTAAAACATGTCAAGATTTGCATCTTATCTTTGCCTAAATTGTCAT
1 GGATACTCCAATCCTGTTTTTAAAACATGTCAAGATTTGAATCTTATCCTTGCCTAAATTATCAT
* * **
1307541 CATTGGGGACACTTCAACCTTATTTTTCCGAGAGGATACTCCTTATTCCTTTGAGG
66 CATTGGGGACACTCCAACCTCATTCCTCCGAGAGGATACTCCTTATTCCTTTGAGG
1307597 GGATACTCCAA-CCTCGTTTTTAAAACATGTCAAGATTTGAATCTTATCCTTGCCTAAATTATCA
1 GGATACTCCAATCCT-GTTTTTAAAACATGTCAAGATTTGAATCTTATCCTTGCCTAAATTATCA
*
1307661 TCATTGGGGACACTCCAACCTCATTCCTCTGAG-GAGATACTCC
65 TCATTGGGGACACTCCAACCTCATTCCTCCGAGAG-GATACTCC
1307704 AACCCTGTTT
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
120 4 0.04
121 93 0.96
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (121 bp):
GGATACTCCAATCCTGTTTTTAAAACATGTCAAGATTTGAATCTTATCCTTGCCTAAATTATCAT
CATTGGGGACACTCCAACCTCATTCCTCCGAGAGGATACTCCTTATTCCTTTGAGG
Found at i:1308887 original size:28 final size:28
Alignment explanation
Indices: 1308805--1308987 Score: 162
Period size: 28 Copynumber: 6.6 Consensus size: 28
1308795 TGCTACCTAG
*
1308805 TGTGAGCTTTGACTTATG-TG-CAACTAA
1 TGTGGGCTTTGACTTA-GATGCCAACTAA
* * *
1308832 TGTGGGCTTTAACAT-GAATGCCAGCTAA
1 TGTGGGCTTTGACTTAG-ATGCCAACTAA
*
1308860 TGTGGGCTTTGACTTAGATACCAACTAA
1 TGTGGGCTTTGACTTAGATGCCAACTAA
* * *
1308888 TGTGGCCTTTGACCTAGGTGCCAA-TAA
1 TGTGGGCTTTGACTTAGATGCCAACTAA
* **
1308915 GTATGGGCTTTGACTCGGATGCCAACTAA
1 -TGTGGGCTTTGACTTAGATGCCAACTAA
* *
1308944 TGTGGGCTTTGACTTA-AGTG-CTAGTAA
1 TGTGGGCTTTGACTTAGA-TGCCAACTAA
1308971 GTGTGGGCTTTGACTTA
1 -TGTGGGCTTTGACTTA
1308988 AGTGCAACTA
Statistics
Matches: 125, Mismatches: 23, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
25 1 0.01
27 23 0.18
28 97 0.78
29 4 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (28 bp):
TGTGGGCTTTGACTTAGATGCCAACTAA
Found at i:1308910 original size:56 final size:56
Alignment explanation
Indices: 1308803--1308987 Score: 189
Period size: 56 Copynumber: 3.3 Consensus size: 56
1308793 GGTGCTACCT
* * * * *
1308803 AGTGTGAGCTTTGACTTATG-T-GCAACTAATGTGGGCTTTAACATGAA-TGCCAGCTA
1 AGTGTGGGCTTTGACTTA-GATACCAACTAATGTGGCCTTTGACCT-AAGTGCCAG-TA
* *
1308859 A-TGTGGGCTTTGACTTAGATACCAACTAATGTGGCCTTTGACCTAGGTGCCAATA
1 AGTGTGGGCTTTGACTTAGATACCAACTAATGTGGCCTTTGACCTAAGTGCCAGTA
* ** * * * *
1308914 AGTATGGGCTTTGACTCGGATGCCAACTAATGTGGGCTTTGACTTAAGTGCTAGTA
1 AGTGTGGGCTTTGACTTAGATACCAACTAATGTGGCCTTTGACCTAAGTGCCAGTA
1308970 AGTGTGGGCTTTGACTTA
1 AGTGTGGGCTTTGACTTA
1308988 AGTGCAACTA
Statistics
Matches: 106, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
54 1 0.01
55 20 0.19
56 85 0.80
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (56 bp):
AGTGTGGGCTTTGACTTAGATACCAACTAATGTGGCCTTTGACCTAAGTGCCAGTA
Found at i:1309186 original size:28 final size:28
Alignment explanation
Indices: 1309067--1309197 Score: 86
Period size: 28 Copynumber: 4.7 Consensus size: 28
1309057 TTAACTTAAG
* *
1309067 TGCCAGCAAGTATGGGCCTT-GACTC-GAA
1 TGCCAGCTAGTGTGGG-CTTAGACTCAG-A
* * * * **
1309095 TGCTAGCTAATTTGGGCTTCGACTCATT
1 TGCCAGCTAGTGTGGGCTTAGACTCAGA
* * *
1309123 TGCCAACTAGTGTGGGCTTTGACTCAGG
1 TGCCAGCTAGTGTGGGCTTAGACTCAGA
**
1309151 TGCCAGCTAGTGTGGGCTTAGACTTTGA
1 TGCCAGCTAGTGTGGGCTTAGACTCAGA
* * *
1309179 TGCTAGCTAATGTAGGCTT
1 TGCCAGCTAGTGTGGGCTT
1309198 TGATTCATGT
Statistics
Matches: 80, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
27 3 0.04
28 77 0.96
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (28 bp):
TGCCAGCTAGTGTGGGCTTAGACTCAGA
Found at i:1309197 original size:84 final size:84
Alignment explanation
Indices: 1309051--1309215 Score: 199
Period size: 84 Copynumber: 2.0 Consensus size: 84
1309041 CTAGGCAGTA
* * *
1309051 TGGGCTTTAACTTAAGTGCCAGCAAGTATGGGCCTTGACTCGAATGCTAGCTAATTTGGGCTTCG
1 TGGGCTTTAACTCAAGTGCCAGCAAGTATGGGCCTTGACTCGAATGCTAGCTAATGTAGGCTTCG
*
1309116 ACTCATTTGCCAACTAGTG
66 ACTCATGTGCCAACTAGTG
* * * * *
1309135 TGGGCTTTGACTCAGGTGCCAGCTAGTGTGGG-CTTAGACTTTG-ATGCTAGCTAATGTAGGCTT
1 TGGGCTTTAACTCAAGTGCCAGCAAGTATGGGCCTT-GAC-TCGAATGCTAGCTAATGTAGGCTT
* *
1309198 TGATTCATGTGCCAACTA
64 CGACTCATGTGCCAACTA
1309216 ATATAAGCTT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
83 3 0.04
84 63 0.93
85 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (84 bp):
TGGGCTTTAACTCAAGTGCCAGCAAGTATGGGCCTTGACTCGAATGCTAGCTAATGTAGGCTTCG
ACTCATGTGCCAACTAGTG
Found at i:1309216 original size:28 final size:28
Alignment explanation
Indices: 1309109--1309266 Score: 129
Period size: 28 Copynumber: 5.6 Consensus size: 28
1309099 AGCTAATTTG
* * * *
1309109 GGCTTCGACTCATTTGCCAACTAGTGTG
1 GGCTTTGACTCATGTGCCAACTAATGTA
* * * *
1309137 GGCTTTGACTCAGGTGCCAGCTAGTGTG
1 GGCTTTGACTCATGTGCCAACTAATGTA
* * * *
1309165 GGCTTAGACT-TTGATGCTAGCTAATGTA
1 GGCTTTGACTCATG-TGCCAACTAATGTA
* *
1309193 GGCTTTGATTCATGTGCCAACTAATATA
1 GGCTTTGACTCATGTGCCAACTAATGTA
* * * *
1309221 AGCTTTTATTCAAGTGCCAACTAATGTA
1 GGCTTTGACTCATGTGCCAACTAATGTA
*
1309249 GGCTTTAACTCATGTGCC
1 GGCTTTGACTCATGTGCC
1309267 CGCTACAATG
Statistics
Matches: 104, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
27 1 0.01
28 101 0.97
29 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (28 bp):
GGCTTTGACTCATGTGCCAACTAATGTA
Found at i:1309226 original size:84 final size:84
Alignment explanation
Indices: 1309094--1309253 Score: 185
Period size: 84 Copynumber: 1.9 Consensus size: 84
1309084 CTTGACTCGA
* * * * * ** * *
1309094 ATGCTAGCTAATTTGGGCTTCGACTCATTTGCCAACTAGTGTGGGCTTTGACTCAGGTGCCAGCT
1 ATGCTAGCTAATGTAGGCTTCGACTCATGTGCCAACTAATATAAGCTTTGACTCAAGTGCCAACT
* *
1309159 AGTGTGGGCTTAGACTTTG
66 AATGTAGGCTTAGACTTTG
* * * *
1309178 ATGCTAGCTAATGTAGGCTTTGATTCATGTGCCAACTAATATAAGCTTTTATTCAAGTGCCAACT
1 ATGCTAGCTAATGTAGGCTTCGACTCATGTGCCAACTAATATAAGCTTTGACTCAAGTGCCAACT
1309243 AATGTAGGCTT
66 AATGTAGGCTT
1309254 TAACTCATGT
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
84 61 1.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (84 bp):
ATGCTAGCTAATGTAGGCTTCGACTCATGTGCCAACTAATATAAGCTTTGACTCAAGTGCCAACT
AATGTAGGCTTAGACTTTG
Found at i:1309374 original size:82 final size:82
Alignment explanation
Indices: 1309123--1309379 Score: 205
Period size: 82 Copynumber: 3.1 Consensus size: 82
1309113 TCGACTCATT
* * * * * * *
1309123 TGCCAACTAGTGTGGGCTTTGACTCAGGTGCCAGCTAGTGTGGGCTTAGACT-TTGATGCTAGCT
1 TGCCAACTAGTGTAGGCTTTAATTCAAGTGCCAACTAATGTGGGCTTAGACTCATG-TGCTAGCT
* * *
1309187 AATGTAGGCTTTGATTCATG
65 AATGTGGGC-TT-ATTTAAG
* * * * * **
1309207 TGCCAACTAATATAAGCTTTTATTCAAGTGCCAACTAATGTAGGCTTTA-ACTCATGTGCCCGCT
1 TGCCAACTAGTGTAGGCTTTAATTCAAGTGCCAACTAATGTGGGC-TTAGACTCATGTGCTAGCT
* * * * **
1309271 ACA-ATGAGTTTACTTGGG
65 A-ATGTGGGCTTATTTAAG
* * *
1309289 TGCCAGCTAGTGTAGGCTTCAATTCAAGTGCCAACTAATGTGGGCTTAGACTCGTGTGCTAGCTA
1 TGCCAACTAGTGTAGGCTTTAATTCAAGTGCCAACTAATGTGGGCTTAGACTCATGTGCTAGCTA
*
1309354 GTGTGGGCTTATTTAAG
66 ATGTGGGCTTATTTAAG
1309371 TGCCAACTA
1 TGCCAACTA
1309380 CTATGGGCTT
Statistics
Matches: 129, Mismatches: 39, Indels: 12
0.72 0.22 0.07
Matches are distributed among these distances:
81 3 0.02
82 71 0.55
83 2 0.02
84 47 0.36
85 6 0.05
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (82 bp):
TGCCAACTAGTGTAGGCTTTAATTCAAGTGCCAACTAATGTGGGCTTAGACTCATGTGCTAGCTA
ATGTGGGCTTATTTAAG
Found at i:1309387 original size:54 final size:55
Alignment explanation
Indices: 1309288--1309392 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 55
1309278 GTTTACTTGG
*
1309288 GTGCCAGCTAGTGTAGGCTTCAATTCAAGTGCCAACTAATGTGGGCTTAGACTCGT
1 GTGCCAGCTAGTGTAGGCTT-AATTCAAGTGCCAACTAATATGGGCTTAGACTCGT
* * * *
1309344 GTGCTAGCTAGTGTGGGCTT-ATTTAAGTGCCAACTACTATGGGCTTAGA
1 GTGCCAGCTAGTGTAGGCTTAATTCAAGTGCCAACTAATATGGGCTTAGA
1309393 TTTAGATGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 26 0.59
56 18 0.41
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (55 bp):
GTGCCAGCTAGTGTAGGCTTAATTCAAGTGCCAACTAATATGGGCTTAGACTCGT
Found at i:1309389 original size:82 final size:82
Alignment explanation
Indices: 1309123--1309431 Score: 198
Period size: 82 Copynumber: 3.7 Consensus size: 82
1309113 TCGACTCATT
* * * * * * * *
1309123 TGCCAACTAGTGTGGGCTTTGACTCAGGTGCCAGCTAGTGTGGGCTTAGACT-TTGATGCTAGCT
1 TGCCAACTAGTATAGGCTTTAATTCAAGTGCCAACTAATGTGGGCTTAGACTCATG-TGCTAGCT
* * *
1309187 AATGTAGGCTTTGATTCATG
65 AATGTGGGC-TT-ATTTAAG
* * * * **
1309207 TGCCAACTAATATAAGCTTTTATTCAAGTGCCAACTAATGTAGGCTTTA-ACTCATGTGCCCGCT
1 TGCCAACTAGTATAGGCTTTAATTCAAGTGCCAACTAATGTGGGC-TTAGACTCATGTGCTAGCT
* * * * **
1309271 ACA-ATGAGTTTACTTGGG
65 A-ATGTGGGCTTATTTAAG
* * * *
1309289 TGCCAGCTAGTGTAGGCTTCAATTCAAGTGCCAACTAATGTGGGCTTAGACTCGTGTGCTAGCTA
1 TGCCAACTAGTATAGGCTTTAATTCAAGTGCCAACTAATGTGGGCTTAGACTCATGTGCTAGCTA
*
1309354 GTGTGGGCTTATTTAAG
66 ATGTGGGCTTATTTAAG
* * * * * *
1309371 TGCCAACTACTATGGGC-TTAGATT-TAGATGCCATCTAAAGTGGGCTTCA-ATTCATGTGCTA
1 TGCCAACTAGTATAGGCTTTA-ATTCAAG-TGCCAACTAATGTGGGCTT-AGACTCATGTGCTA
1309432 ATTGATATGG
Statistics
Matches: 169, Mismatches: 48, Indels: 18
0.72 0.20 0.08
Matches are distributed among these distances:
81 7 0.04
82 106 0.63
83 3 0.02
84 47 0.28
85 6 0.04
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (82 bp):
TGCCAACTAGTATAGGCTTTAATTCAAGTGCCAACTAATGTGGGCTTAGACTCATGTGCTAGCTA
ATGTGGGCTTATTTAAG
Found at i:1309442 original size:28 final size:28
Alignment explanation
Indices: 1309303--1309483 Score: 86
Period size: 28 Copynumber: 6.5 Consensus size: 28
1309293 AGCTAGTGTA
* * *
1309303 GGCTTCAATTCAAGTGCCAACTAATGTG
1 GGCTTCAATTCATGTGCTAACTAATATG
* * * * *
1309331 GGCTT-AGACTCGTGTGCTAGCTAGTGTG
1 GGCTTCA-ATTCATGTGCTAACTAATATG
* * * *
1309359 GGCTT--ATTTAAGTGCCAACTACTATG
1 GGCTTCAATTCATGTGCTAACTAATATG
* * *
1309385 GGCTT-AGATTTA-GATGCCATCTAA-AGTG
1 GGCTTCA-ATTCATG-TGCTAACTAATA-TG
* *
1309413 GGCTTCAATTCATGTGCTAATTGATATG
1 GGCTTCAATTCATGTGCTAACTAATATG
* * *
1309441 GGCCTCAATTCAAGTGCTAACTAATGTG
1 GGCTTCAATTCATGTGCTAACTAATATG
**
1309469 GGCTTTGATTCATGT
1 GGCTTCAATTCATGT
1309484 TCCAACTAGT
Statistics
Matches: 115, Mismatches: 30, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
26 18 0.16
27 3 0.03
28 91 0.79
29 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (28 bp):
GGCTTCAATTCATGTGCTAACTAATATG
Found at i:1310768 original size:15 final size:15
Alignment explanation
Indices: 1310748--1310785 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1310738 ACAGCTCTTT
1310748 AACACCTCTCAAGGA
1 AACACCTCTCAAGGA
1310763 AACACCTCTCAAGGA
1 AACACCTCTCAAGGA
1310778 AACACCTC
1 AACACCTC
1310786 ACCTCCTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.37, G:0.11, T:0.13
Consensus pattern (15 bp):
AACACCTCTCAAGGA
Found at i:1324123 original size:14 final size:15
Alignment explanation
Indices: 1324099--1324134 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
1324089 CTATGTCCAA
1324099 AAAAAATTAAAAATC
1 AAAAAATTAAAAATC
1324114 AAAAAA-TAAAAATC
1 AAAAAATTAAAAATC
1324128 AACAAAA
1 AA-AAAA
1324135 CAAGTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAAATTAAAAATC
Found at i:1326217 original size:80 final size:80
Alignment explanation
Indices: 1326063--1326287 Score: 231
Period size: 80 Copynumber: 2.8 Consensus size: 80
1326053 AATCTTCTTT
* * * * * *
1326063 CCAAGCTTAATGTTGCTAGCCTTGAA-CTAGCACATTGGCACCCCGTCTATGTCAAAAGGCACTT
1 CCAAGCCTAATGTTGTTGGCCTTGAATC-AGCACATTGGCACCTCATCTATGTCAAAAGGCATTT
*
1326127 GTCATATAGTTCTAGC
65 CTCATATAGTTCTAGC
* * *
1326143 CCAAGCCTAATGTTGTTGGCCTTGAATCAGCACATTGGTACCTCACCTATGCCAAAAGGCATTTC
1 CCAAGCCTAATGTTGTTGGCCTTGAATCAGCACATTGGCACCTCATCTATGTCAAAAGGCATTTC
** * *
1326208 TTGTGTAGTTCTAGT
66 TCATATAGTTCTAGC
* ** * *
1326223 CAAAG-CTCAAAATCGTTGGCCTTGAATCAACACATTGGCACCTCATC-ATTGTCAAAAGGCATT
1 CCAAGCCT-AATGTTGTTGGCCTTGAATCAGCACATTGGCACCTCATCTA-TGTCAAAAGGCATT
1326286 TC
64 TC
1326288 GCCAAAAAAT
Statistics
Matches: 120, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
79 3 0.03
80 116 0.97
81 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (80 bp):
CCAAGCCTAATGTTGTTGGCCTTGAATCAGCACATTGGCACCTCATCTATGTCAAAAGGCATTTC
TCATATAGTTCTAGC
Found at i:1326890 original size:15 final size:15
Alignment explanation
Indices: 1326870--1326898 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1326860 AAGTGTTTGG
1326870 GAGGTAAAAGGTATA
1 GAGGTAAAAGGTATA
1326885 GAGGTAAAAGGTAT
1 GAGGTAAAAGGTAT
1326899 GAAAAAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (15 bp):
GAGGTAAAAGGTATA
Found at i:1327038 original size:20 final size:21
Alignment explanation
Indices: 1326988--1327039 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1326978 TTCTATAATT
1326988 TGTATCGATACAACAAGTCAA
1 TGTATCGATACAACAAGTCAA
* * * *
1327009 TATATTGATAC-ATAAGTGAA
1 TGTATCGATACAACAAGTCAA
1327029 TGTATCGATAC
1 TGTATCGATAC
1327040 TAAAGCTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAACAAGTCAA
Found at i:1327143 original size:21 final size:20
Alignment explanation
Indices: 1327099--1327156 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1327089 CTAAAAAATT
* **
1327099 TGTATCGATACATAAGTGAA
1 TGTATCGATACACACTTGAA
1327119 TGTATCGATACACACTTGCAA
1 TGTATCGATACACACTTG-AA
*
1327140 TGTATCAATACATCACT
1 TGTATCGATACA-CACT
1327157 CATTGCAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 15 0.47
21 13 0.41
22 4 0.12
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (20 bp):
TGTATCGATACACACTTGAA
Found at i:1331802 original size:19 final size:19
Alignment explanation
Indices: 1331778--1331838 Score: 113
Period size: 19 Copynumber: 3.2 Consensus size: 19
1331768 AGTAAGTTAA
1331778 TAATTTTAGTTCTATATAT
1 TAATTTTAGTTCTATATAT
*
1331797 TAATTTTAGTTTTATATAT
1 TAATTTTAGTTCTATATAT
1331816 TAATTTTAGTTCTATATAT
1 TAATTTTAGTTCTATATAT
1331835 TAAT
1 TAAT
1331839 GATATTCTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TAATTTTAGTTCTATATAT
Found at i:1333691 original size:13 final size:13
Alignment explanation
Indices: 1333673--1333698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1333663 CAATTTTTTA
1333673 TGTATCGATACAT
1 TGTATCGATACAT
1333686 TGTATCGATACAT
1 TGTATCGATACAT
1333699 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1333714 original size:32 final size:33
Alignment explanation
Indices: 1333653--1333716 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1333643 TGCAAGCCAA
**
1333653 TGTATCGATACAATTTTTTATGTATCGATACAT
1 TGTATCGATACAATACTTTATGTATCGATACAT
*
1333686 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTATGTATCGATACA
1333717 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTATGTATCGATACAT
Found at i:1334458 original size:12 final size:12
Alignment explanation
Indices: 1334443--1334468 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1334433 TTATAAGATA
1334443 ATTTACACACAT
1 ATTTACACACAT
1334455 ATTTACACACAT
1 ATTTACACACAT
1334467 AT
1 AT
1334469 CAAAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (12 bp):
ATTTACACACAT
Found at i:1336292 original size:13 final size:13
Alignment explanation
Indices: 1336274--1336298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1336264 ATAATCCCCC
1336274 TGTATCGATACAT
1 TGTATCGATACAT
1336287 TGTATCGATACA
1 TGTATCGATACA
1336299 AAGAAAAATG
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:1342495 original size:13 final size:13
Alignment explanation
Indices: 1342477--1342502 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1342467 CAATTTTTTG
1342477 TGTATCGATACAT
1 TGTATCGATACAT
1342490 TGTATCGATACAT
1 TGTATCGATACAT
1342503 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1342514 original size:32 final size:33
Alignment explanation
Indices: 1342457--1342520 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1342447 TGCAAGCCAA
**
1342457 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1342490 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1342521 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1344419 original size:22 final size:21
Alignment explanation
Indices: 1344370--1344421 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1344360 GTACAAATTA
* * *
1344370 ATAACAATTAAAATGATCAAT
1 ATAAAAATCAAAATAATCAAT
1344391 ATAAAAATCAAAATAATACAAT
1 ATAAAAATCAAAATAAT-CAAT
*
1344413 ATTAAAATC
1 ATAAAAATC
1344422 TATATCTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAAAAATCAAAATAATCAAT
Found at i:1351835 original size:18 final size:18
Alignment explanation
Indices: 1351800--1351835 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1351790 ATGATGATTT
*
1351800 TTTTTAAACAAAATAAAA
1 TTTTTAAACAAAAAAAAA
*
1351818 TTTTTAAAGAAAAAAAAA
1 TTTTTAAACAAAAAAAAA
1351836 CAGATCATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TTTTTAAACAAAAAAAAA
Found at i:1352836 original size:14 final size:14
Alignment explanation
Indices: 1352807--1352844 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1352797 TTATTAATTA
1352807 TATTTTAAAT-TTT
1 TATTTTAAATATTT
1352820 TATTTTAAATATTT
1 TATTTTAAATATTT
*
1352834 TATATTAAATA
1 TATTTTAAATA
1352845 ATAAATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTTAAATATTT
Found at i:1354077 original size:27 final size:26
Alignment explanation
Indices: 1354047--1354097 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1354037 CAATTCCGTG
*
1354047 CAAAATTAATGATAAAAGGAATAACTA
1 CAAAA-TAATGATAAAAAGAATAACTA
* *
1354074 CAAAATACTGGTAAAAAGAATAAC
1 CAAAATAATGATAAAAAGAATAAC
1354098 CGAATTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.20
Consensus pattern (26 bp):
CAAAATAATGATAAAAAGAATAACTA
Found at i:1368363 original size:19 final size:20
Alignment explanation
Indices: 1368339--1368391 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1368329 CTACCACTGT
*
1368339 TTGTATCGATACAT-ATTCA
1 TTGTATCGATACATGATTAA
*
1368358 TTGTATCGATACATGGTTAA
1 TTGTATCGATACATGATTAA
1368378 TTGTATCGATACAT
1 TTGTATCGATACAT
1368392 TGAGCCCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATGATTAA
Found at i:1369959 original size:96 final size:97
Alignment explanation
Indices: 1369711--1369945 Score: 375
Period size: 97 Copynumber: 2.4 Consensus size: 97
1369701 TGAAAAACGA
* *
1369711 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCAATGATGACAATTTAAGTGAGAA
1 GGTTGGAGTATCCCCTCGGAGGAATGGGATTGAAGTGTCCCCAATGATGACAATTTAAGTGAGAA
* *
1369776 TAAAATTTAAACTTTGATGCGTTTAAAAGCAG
66 AAAAAATTAAACTTTGATGCGTTTAAAAGCAG
* *
1369808 GGTTGGAGTATCCCCTCGGAGGAAT-AGAGTTGAAGTGTCCCCAATGATGACAATTTAAGTGGGA
1 GGTTGGAGTATCCCCTCGGAGGAATGGGA-TTGAAGTGTCCCCAATGATGACAATTTAAGTGAGA
*
1369872 AAAAAAATTAAACTTT-ATGCGTTTAAAAGCGG
65 AAAAAAATTAAACTTTGATGCGTTTAAAAGCAG
*
1369904 GGTTGGAGTATCCCTTCGGAGGAATGGGATTGAAGTGTCCCC
1 GGTTGGAGTATCCCCTCGGAGGAATGGGATTGAAGTGTCCCC
1369946 GATAAATAAA
Statistics
Matches: 127, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
96 53 0.42
97 74 0.58
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (97 bp):
GGTTGGAGTATCCCCTCGGAGGAATGGGATTGAAGTGTCCCCAATGATGACAATTTAAGTGAGAA
AAAAAATTAAACTTTGATGCGTTTAAAAGCAG
Found at i:1372150 original size:51 final size:48
Alignment explanation
Indices: 1372093--1372268 Score: 154
Period size: 51 Copynumber: 3.7 Consensus size: 48
1372083 TTTTAACTAG
*
1372093 ATGTATCGATACATTGAAAAATGTATTGATACATCCGAGTAAAAAGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACAT-CG-GT-AAAAGATAGA
* *
1372144 ATGTATCGATACATT-AAAGAATGTATCGATACAT---T----CATA-C
1 ATGTATCGATACATTGAAA-AATGTATCGATACATCGGTAAAAGATAGA
* * *
1372184 ATGTATCGATATATTGAAGAATGTATTGATACATCTGGGTAAAAGGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATC--GGTAAAA-GATAGA
* *
1372235 ATGTATCGATTCATTGAAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACAT
1372269 TCATACATGT
Statistics
Matches: 101, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
40 28 0.28
41 5 0.05
45 1 0.01
46 1 0.01
50 6 0.06
51 60 0.59
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (48 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCGGTAAAAGATAGA
Found at i:1372166 original size:20 final size:20
Alignment explanation
Indices: 1372141--1372217 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
1372131 GTAAAAAGAT
1372141 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
*
1372161 AGAATGTATCGATACATTCAT
1 AGAATGTATCGATACATT-AA
* * *
1372182 A-CATGTATCGATATATTGA
1 AGAATGTATCGATACATTAA
*
1372201 AGAATGTATTGATACAT
1 AGAATGTATCGATACAT
1372218 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.94
21 2 0.04
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Found at i:1372236 original size:71 final size:71
Alignment explanation
Indices: 1372161--1372295 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 71
1372151 GATACATTAA
* * * *
1372161 AGAATGTATCGATACATTCATA-CATGTATCGATATATTGA-AGAATGTATTGATACATCTGGGT
1 AGAATGTATCGATACATTCA-AGAATGTATCGATACATTCATA-AATGTATCGATACATCTGGGT
1372224 AAAAGGAT
64 AAAAGGAT
* * *
1372232 AGAATGTATCGATTCATTGAAGAATGTATCGATACATTCATACATGTATCGATACATCTGGGTA
1 AGAATGTATCGATACATTCAAGAATGTATCGATACATTCATAAATGTATCGATACATCTGGGTA
1372296 CTTTTTCATA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
70 1 0.02
71 53 0.96
72 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (71 bp):
AGAATGTATCGATACATTCAAGAATGTATCGATACATTCATAAATGTATCGATACATCTGGGTAA
AAGGAT
Found at i:1372255 original size:91 final size:91
Alignment explanation
Indices: 1372093--1372288 Score: 329
Period size: 91 Copynumber: 2.2 Consensus size: 91
1372083 TTTTAACTAG
1372093 ATGTATCGATACATTGAAAAATGTATTGATACATCCGAGTAAAAAGATAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATTGATACATCCGAGTAAAAAGATAGAATGTATCGATACAT
1372158 TAAAGAATGTATCGATACATTCATAC
66 TAAAGAATGTATCGATACATTCATAC
* * * * * *
1372184 ATGTATCGATATATTGAAGAATGTATTGATACATCTGGGTAAAAGGATAGAATGTATCGATTCAT
1 ATGTATCGATACATTGAAAAATGTATTGATACATCCGAGTAAAAAGATAGAATGTATCGATACAT
*
1372249 TGAAGAATGTATCGATACATTCATAC
66 TAAAGAATGTATCGATACATTCATAC
1372275 ATGTATCGATACAT
1 ATGTATCGATACAT
1372289 CTGGGTACTT
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 97 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (91 bp):
ATGTATCGATACATTGAAAAATGTATTGATACATCCGAGTAAAAAGATAGAATGTATCGATACAT
TAAAGAATGTATCGATACATTCATAC
Found at i:1372257 original size:20 final size:20
Alignment explanation
Indices: 1372232--1372288 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1372222 GTAAAAGGAT
*
1372232 AGAATGTATCGATTCATTGA
1 AGAATGTATCGATACATTGA
*
1372252 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
1372272 TA-CATGTATCGATACAT
1 -AGAATGTATCGATACAT
1372289 CTGGGTACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1373301 original size:28 final size:28
Alignment explanation
Indices: 1373214--1373824 Score: 819
Period size: 28 Copynumber: 21.5 Consensus size: 28
1373204 TACCGACTCG
* *
1373214 TGTGGGCTTTGAAAAGAGTTACCACT-AGCT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGA-CT
** *
1373244 TGTGGGCTTTGAAAATAGTGCCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1373273 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1373301 TATGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1373329 TATGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1373357 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1373385 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
1373414 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1373442 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1373470 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1373498 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1373527 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
1373555 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1373584 CGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
1373613 CGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
1373641 TGTGGGCTTTGAAAAAAGTGCCACTAACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
1373670 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1373698 CGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* **
1373726 TGTGGGCTTTGAAAAGAGTTGCCACCAACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * * *
1373756 CGTGGGCTCTGAGAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1373784 TGTGGGCTTTCAAAGGGTGTCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
1373812 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
1373825 GAGATGAACG
Statistics
Matches: 523, Mismatches: 51, Indels: 16
0.89 0.09 0.03
Matches are distributed among these distances:
28 331 0.63
29 156 0.30
30 36 0.07
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:1373311 original size:57 final size:57
Alignment explanation
Indices: 1373182--1373824 Score: 798
Period size: 57 Copynumber: 11.2 Consensus size: 57
1373172 CACTAACTTG
* * * * *
1373182 TGTGGGCTTTCAAAAGAGTTGCTACCGACTCGTGTGGGCTTTGAAAAGAGTTACCACT-AGCT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTG-AAAG-GGTGCCACTGA-CT
* *
1373244 TGTGGGCTTTGAAAATAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
1373301 TATGGGCTTTG-AAAGGGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
1373357 TGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACT
* * *
1373414 TGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1373470 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1373527 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
1373584 CGTGGGCTTTGAAAAGAGTGCCACTGACTCGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* *
1373641 TGTGGGCTTTGAAAAAAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * **
1373698 CGTGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACCAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * * * * *
1373756 CGTGGGCTCTGAGAGGA-TGCCACTGACTTGTGGGCTTTCAAAGGGTGTCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
1373812 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
1373825 GAGATGAACG
Statistics
Matches: 521, Mismatches: 52, Indels: 22
0.88 0.09 0.04
Matches are distributed among these distances:
56 167 0.32
57 243 0.47
58 76 0.15
59 11 0.02
61 8 0.02
62 16 0.03
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (57 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:1373337 original size:85 final size:86
Alignment explanation
Indices: 1373214--1373824 Score: 876
Period size: 85 Copynumber: 7.2 Consensus size: 86
1373204 TACCGACTCG
* * *
1373214 TGTGGGCTTTGAAAAGAGTTACCACT-AGCTTGTGGGCTTTGAAAATAGTGCCATTGACTTGTGG
1 TGTGGGCTTTGAAAAGAG-TGCCACTGA-CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
1373278 GCTTTGAAAGGGTGCCACTGACT
64 GCTTTGAAAGGGTGCCACTGACT
* * * *
1373301 TATGGGCTTTG-AAAGGGTGCCACTGACTTATGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
1373364 TTTGAAAGGATGCCACTAACT
66 TTTGAAAGGGTGCCACTGACT
* * *
1373385 TGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
*
1373449 TTTGAAAGGGTGCCACTAACT
66 TTTGAAAGGGTGCCACTGACT
*
1373470 TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1373534 TTTGAAAGGGTGCCACTGACT
66 TTTGAAAGGGTGCCACTGACT
* *
1373555 TGTGGGCTTTGAAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACTGACTCGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
1373620 TTTGAAAGGGTGCCACTGACT
66 TTTGAAAGGGTGCCACTGACT
* * * *
1373641 TGTGGGCTTTGAAAAAAGTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGACTCGTGGGC
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
* *
1373705 TTTGAAAGGATGCCACTAACT
66 TTTGAAAGGGTGCCACTGACT
** * * * *
1373726 TGTGGGCTTTGAAAAGAGTTGCCACCAACTCGTGGGCTCTGAGAGGA-TGCCACTGACTTGTGGG
1 TGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGG
* *
1373790 CTTTCAAAGGGTGTCACTGACT
65 CTTTGAAAGGGTGCCACTGACT
1373812 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
1373825 GAGATGAACG
Statistics
Matches: 477, Mismatches: 41, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
84 76 0.16
85 209 0.44
86 180 0.38
87 12 0.03
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (86 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC
TTTGAAAGGGTGCCACTGACT
Found at i:1375062 original size:10 final size:8
Alignment explanation
Indices: 1375041--1375118 Score: 79
Period size: 8 Copynumber: 9.8 Consensus size: 8
1375031 ATCTAGACCC
1375041 TTTTTTGT
1 TTTTTTGT
1375049 TTTTTTG-
1 TTTTTTGT
* *
1375056 CTATTT-T
1 TTTTTTGT
* *
1375063 TTCTTGGT
1 TTTTTTGT
1375071 TTTTTTGTT
1 TTTTTTG-T
1375080 TTTTTTGT
1 TTTTTTGT
*
1375088 TTTCTTGT
1 TTTTTTGT
1375096 TTTTTTGTT
1 TTTTTTG-T
1375105 TTTTTTGT
1 TTTTTTGT
1375113 TTTTTT
1 TTTTTT
1375119 TGGTGTAAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
7 7 0.12
8 34 0.60
9 16 0.28
ACGTcount: A:0.01, C:0.04, G:0.12, T:0.83
Consensus pattern (8 bp):
TTTTTTGT
Found at i:1375062 original size:17 final size:16
Alignment explanation
Indices: 1375041--1375118 Score: 79
Period size: 17 Copynumber: 4.9 Consensus size: 16
1375031 ATCTAGACCC
1375041 TTTTTTGTTTTTTTG-
1 TTTTTTGTTTTTTTGT
* * * *
1375056 CTATTT-TTTCTTGGT
1 TTTTTTGTTTTTTTGT
1375071 TTTTTTGTTTTTTTTGT
1 TTTTTTG-TTTTTTTGT
*
1375088 TTTCTTGTTTTTTTGTT
1 TTTTTTGTTTTTTTG-T
1375105 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
1375119 TGGTGTAAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
14 6 0.12
15 8 0.16
16 8 0.16
17 27 0.55
ACGTcount: A:0.01, C:0.04, G:0.12, T:0.83
Consensus pattern (16 bp):
TTTTTTGTTTTTTTGT
Found at i:1375073 original size:9 final size:9
Alignment explanation
Indices: 1375060--1375122 Score: 67
Period size: 9 Copynumber: 7.1 Consensus size: 9
1375050 TTTTTGCTAT
1375060 TTTTTCTTGG
1 TTTTT-TTGG
1375070 TTTTTTT-G
1 TTTTTTTGG
*
1375078 TTTTTTTTG
1 TTTTTTTGG
*
1375087 TTTTCTT-G
1 TTTTTTTGG
*
1375095 TTTTTTTGT
1 TTTTTTTGG
*
1375104 TTTTTTTGT
1 TTTTTTTGG
1375113 TTTTTTTGG
1 TTTTTTTGG
1375122 T
1 T
1375123 GTAAAGGACG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
8 15 0.32
9 27 0.57
10 5 0.11
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (9 bp):
TTTTTTTGG
Found at i:1375103 original size:25 final size:26
Alignment explanation
Indices: 1375061--1375115 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 26
1375051 TTTTGCTATT
1375061 TTTTCTTGGTTTTTTTGTTTTTTTTG
1 TTTTCTTGGTTTTTTTGTTTTTTTTG
1375087 TTTTCTT-GTTTTTTTGTTTTTTTTG
1 TTTTCTTGGTTTTTTTGTTTTTTTTG
1375112 TTTT
1 TTTT
1375116 TTTTGGTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 22 0.76
26 7 0.24
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.84
Consensus pattern (26 bp):
TTTTCTTGGTTTTTTTGTTTTTTTTG
Found at i:1379525 original size:165 final size:165
Alignment explanation
Indices: 1379244--1379581 Score: 595
Period size: 165 Copynumber: 2.0 Consensus size: 165
1379234 TCATTTTTAA
* * * *
1379244 ACCCAAATGGGTGCTTTCTGAAAGAAAAGTTTAATTATTGGCAATCCTTCTCCCATAAATGTCAC
1 ACCCCAATGGGTGCTTTCTGAAAGAAAAGTTCAATTATTGGCAACCCTTCTCCCACAAATGTCAC
*
1379309 ATTAATGAATTCAAAGGATTGGAAAGACAACTCCAGTGCTTTTTTAGTTGGCTCTATGTAGACAT
66 ATTAATGAATTCAAAGGATTGGAAAGACAACTCCAGTGCTTTTTCAGTTGGCTCTATGTAGACAT
1379374 CATCAGTGAAAGCAGTGGCAATCATTTCTTCTTCT
131 CATCAGTGAAAGCAGTGGCAATCATTTCTTCTTCT
*
1379409 ACCCCAATGGGTGCTTTCTGAAAGAAAAGTTCAATTATTGGCAACCCTTCTCCCACAAATGTCGC
1 ACCCCAATGGGTGCTTTCTGAAAGAAAAGTTCAATTATTGGCAACCCTTCTCCCACAAATGTCAC
* * *
1379474 ATTAATGAATTTAAAGGATTGGAAAGATAGCTCCAGTGCTTTTTCAGTTGGCTCTATGTAGACAT
66 ATTAATGAATTCAAAGGATTGGAAAGACAACTCCAGTGCTTTTTCAGTTGGCTCTATGTAGACAT
1379539 CATCAGTGAAAGCAGTGGCAATCATTTCTTCTTCT
131 CATCAGTGAAAGCAGTGGCAATCATTTCTTCTTCT
1379574 ACCCCAAT
1 ACCCCAAT
1379582 AGTGACTACC
Statistics
Matches: 164, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
165 164 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (165 bp):
ACCCCAATGGGTGCTTTCTGAAAGAAAAGTTCAATTATTGGCAACCCTTCTCCCACAAATGTCAC
ATTAATGAATTCAAAGGATTGGAAAGACAACTCCAGTGCTTTTTCAGTTGGCTCTATGTAGACAT
CATCAGTGAAAGCAGTGGCAATCATTTCTTCTTCT
Found at i:1386814 original size:97 final size:97
Alignment explanation
Indices: 1386576--1386819 Score: 362
Period size: 97 Copynumber: 2.5 Consensus size: 97
1386566 TTTTTGAGTG
* * **
1386576 AAAAACGGGATTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTAACCCCAATGATGACAATTTA
1 AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCAATGATGACAATTTA
* ***
1386641 AGTGAGAATAAAATTTAAACTTTGATGTGTTT
66 AGTGAGAAAAAAATTTAAACTTTGATACATTT
* *
1386673 AAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCAATGATTACAATTTA
1 AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCAATGATGACAATTTA
1386738 AGTGAGAAAAAAATTTAAACTTTGATACATTT
66 AGTGAGAAAAAAATTTAAACTTTGATACATTT
* * * *
1386770 AAAAACGGGGTTGGAGTATCCCTTCGAAGAAATGGGATTGAAGTGTCCCC
1 AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCC
1386820 GATAAATAAT
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 132 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (97 bp):
AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCAATGATGACAATTTA
AGTGAGAAAAAAATTTAAACTTTGATACATTT
Found at i:1388986 original size:20 final size:20
Alignment explanation
Indices: 1388961--1389105 Score: 101
Period size: 20 Copynumber: 6.7 Consensus size: 20
1388951 TTTTAACTAG
1388961 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
1388981 ATGTATCGATACATCTGGGTAAAAAGAAAGA
1 ATGTATCGATACAT-T--G-------AAA-A
*
1389012 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
1389032 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
* * * *
1389052 ATGTATCAATACATTCATAC
1 ATGTATCGATACATTGAAAA
* *
1389072 ATGTATCAATACATTGAAGA
1 ATGTATCGATACATTGAAAA
1389092 ATGTATCGATACAT
1 ATGTATCGATACAT
1389106 CTGGGTACTT
Statistics
Matches: 103, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
20 79 0.77
21 3 0.03
23 1 0.01
28 1 0.01
30 4 0.04
31 15 0.15
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:1404900 original size:20 final size:20
Alignment explanation
Indices: 1404871--1404908 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1404861 TATTGCCAGT
*
1404871 TTCATGTATCGATACAATTC
1 TTCATATATCGATACAATTC
1404891 TTCATATATCGATACAAT
1 TTCATATATCGATACAAT
1404909 GAACATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (20 bp):
TTCATATATCGATACAATTC
Found at i:1408214 original size:53 final size:53
Alignment explanation
Indices: 1408156--1408262 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
1408146 CACCTCAATG
1408156 TGGTGCAATCCAAAGTATTATTAAGAAGTTTTACCCATGGTTGAAAAGACTGA
1 TGGTGCAATCCAAAGTATTATTAAGAAGTTTTACCCATGGTTGAAAAGACTGA
1408209 TGGTGCAATCCAAAGTATTATTAAGAAGTTTTACCCATGGTTGAAAAGACTGA
1 TGGTGCAATCCAAAGTATTATTAAGAAGTTTTACCCATGGTTGAAAAGACTGA
1408262 T
1 T
1408263 TGAACTGGCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (53 bp):
TGGTGCAATCCAAAGTATTATTAAGAAGTTTTACCCATGGTTGAAAAGACTGA
Found at i:1408581 original size:23 final size:23
Alignment explanation
Indices: 1408530--1408574 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1408520 ATAATTTAAT
* *
1408530 ATATTTTATATTTATTTAATATA
1 ATATTTTATATATATTTAAAATA
*
1408553 ATATTTTTTATATATTTAAAAT
1 ATATTTTATATATATTTAAAAT
1408575 CCTATTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATATTTTATATATATTTAAAATA
Found at i:1408930 original size:30 final size:29
Alignment explanation
Indices: 1408874--1408950 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
1408864 TTAAATTATT
* *
1408874 TATTTAATATATATAATTAGTCAATTAAAA
1 TATTTAATAAATAT-ATTAATCAATTAAAA
* *
1408904 TATTTGAATAAATATATTAATTAATTAATA
1 TATTT-AATAAATATATTAATCAATTAAAA
1408934 TATTTAAATAAATATAT
1 TATTT-AATAAATATAT
1408951 AAAATCATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 33 0.80
31 8 0.20
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (29 bp):
TATTTAATAAATATATTAATCAATTAAAA
Found at i:1408947 original size:14 final size:14
Alignment explanation
Indices: 1408899--1408950 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1408889 ATTAGTCAAT
*
1408899 TAAA-ATATTTGAA
1 TAAATATATTTAAA
*
1408912 TAAATATATTAATTAA
1 TAAATATATT--TAAA
*
1408928 TTAATATATTTAAA
1 TAAATATATTTAAA
1408942 TAAATATAT
1 TAAATATAT
1408951 AAAATCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 4 0.12
14 16 0.50
16 12 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TAAATATATTTAAA
Found at i:1409435 original size:31 final size:34
Alignment explanation
Indices: 1409362--1409435 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 34
1409352 AGATATAATG
*
1409362 AATAATTAAAAATTATTAAAATTATATTTATATTA
1 AATAA-TAAAAATTATTAAAATAATATTTATATTA
* * *
1409397 AACAATAAAAA-TA-T-AAATAATATTTATTTTT
1 AATAATAAAAATTATTAAAATAATATTTATATTA
1409428 AATAATAA
1 AATAATAA
1409436 TTAATAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
31 21 0.62
32 1 0.03
33 2 0.06
34 6 0.18
35 4 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (34 bp):
AATAATAAAAATTATTAAAATAATATTTATATTA
Found at i:1409464 original size:24 final size:24
Alignment explanation
Indices: 1409431--1409481 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1409421 TATTTTTAAT
*
1409431 AATAATTAA-TAAAATTTTATGAAA
1 AATAAATAATTAAAA-TTTATGAAA
*
1409455 AATAAATAATTAAAATTTATTAAA
1 AATAAATAATTAAAATTTATGAAA
1409479 AAT
1 AAT
1409482 TCTATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
AATAAATAATTAAAATTTATGAAA
Found at i:1409480 original size:25 final size:24
Alignment explanation
Indices: 1409401--1409481 Score: 60
Period size: 24 Copynumber: 3.4 Consensus size: 24
1409391 ATATTAAACA
**
1409401 ATAAAAATATAAATAATATTTATTTT
1 ATAAAAA-ATAAATAATA-AAATTTT
* *
1409427 -T-AATAATAATTAATAAAATTTT
1 ATAAAAAATAAATAATAAAATTTT
*
1409449 ATGAAAAATAAATAATTAAAA-TTT
1 ATAAAAAATAAATAA-TAAAATTTT
*
1409473 ATTAAAAAT
1 ATAAAAAAT
1409482 TCTATTAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
22 5 0.11
23 10 0.22
24 24 0.53
25 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
ATAAAAAATAAATAATAAAATTTT
Found at i:1409504 original size:16 final size:17
Alignment explanation
Indices: 1409473--1409505 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1409463 ATTAAAATTT
*
1409473 ATTAAAAATTCTATTAA
1 ATTAAAAATACTATTAA
1409490 ATTAAAAATAC-ATTAA
1 ATTAAAAATACTATTAA
1409506 TAAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTAAAAATACTATTAA
Found at i:1410283 original size:13 final size:13
Alignment explanation
Indices: 1410248--1410286 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1410238 TCGTTGGGCT
*
1410248 CAATGTATCAATA
1 CAATGTATCGATA
1410261 CAATGTATCGATA
1 CAATGTATCGATA
*
1410274 CACTGTATCGATA
1 CAATGTATCGATA
1410287 TTGAGTAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1410377 original size:32 final size:33
Alignment explanation
Indices: 1410336--1410399 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1410326 CAATTTACTG
*
1410336 TGTATCGATACCAA-AAACATTTATCGATACAA
1 TGTATCGATACCAAGAAACATGTATCGATACAA
* *
1410368 TGTATCGATACCAAGTAATATGTATCGATACA
1 TGTATCGATACCAAGAAACATGTATCGATACA
1410400 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (33 bp):
TGTATCGATACCAAGAAACATGTATCGATACAA
Found at i:1412100 original size:20 final size:20
Alignment explanation
Indices: 1412075--1412130 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
1412065 GTATCAATAC
1412075 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
1412095 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
1412115 ATTGTATCGATACATG
1 ATTGTATCGATACATG
1412131 AAATTGGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:1412196 original size:13 final size:13
Alignment explanation
Indices: 1412175--1412204 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1412165 CGATACATGG
1412175 TACAATGTATCGA
1 TACAATGTATCGA
*
1412188 TACATTGTATCGA
1 TACAATGTATCGA
1412201 TACA
1 TACA
1412205 GGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:1420803 original size:20 final size:19
Alignment explanation
Indices: 1420760--1420813 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1420750 ACACATCCAG
**
1420760 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGGACA
*
1420779 TTGTATCGATATATGGACAA
1 TTGTATCGATACATGGAC-A
1420799 TTGTATCGATACATG
1 TTGTATCGATACATG
1420814 AAATTAGTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:1421971 original size:33 final size:33
Alignment explanation
Indices: 1421929--1421995 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1421919 TCATGGAAAG
1421929 AGTAAGGGTCAAATCATGACCCATAAGATAGGA
1 AGTAAGGGTCAAATCATGACCCATAAGATAGGA
1421962 AGTAAGGGTCAAATCATGACCCATAAGATAGGA
1 AGTAAGGGTCAAATCATGACCCATAAGATAGGA
1421995 A
1 A
1421996 TGGATAGCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.18
Consensus pattern (33 bp):
AGTAAGGGTCAAATCATGACCCATAAGATAGGA
Found at i:1422911 original size:33 final size:33
Alignment explanation
Indices: 1422873--1422938 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1422863 AAGAGTACCT
*
1422873 ATGTATCGATACAAAGAATGCAGTATCGATACA
1 ATGTATCGATACAAAGAATGCAATATCGATACA
* *
1422906 ATGTATCGATGCTAAGAATGCAATATCGATACA
1 ATGTATCGATACAAAGAATGCAATATCGATACA
1422939 TCTAGGTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATGCAATATCGATACA
Found at i:1423132 original size:20 final size:21
Alignment explanation
Indices: 1423094--1423133 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1423084 AAAACAACAT
* *
1423094 AATTGAACACCAATTATCAAC
1 AATTAAACACCAATCATCAAC
1423115 AATTAAACA-CAATCATCAA
1 AATTAAACACCAATCATCAA
1423134 AAATCATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.53, C:0.23, G:0.03, T:0.23
Consensus pattern (21 bp):
AATTAAACACCAATCATCAAC
Found at i:1424693 original size:28 final size:28
Alignment explanation
Indices: 1424653--1424729 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
1424643 AAAAAAAAAT
* * *
1424653 CGGGATTGGAGTATCCCC-TTGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAT-GAAATAA
1424681 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
1424709 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1424730 TGTGAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 42 0.98
29 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1424775 original size:52 final size:49
Alignment explanation
Indices: 1424712--1424841 Score: 145
Period size: 52 Copynumber: 2.5 Consensus size: 49
1424702 GAAATAACGA
* * *
1424712 GGTTGGAGTATCCTCGATTGTGAAAATTTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCTCGATTGTGAAAA-TTGG-AGTTTTGAAAATAAAACCG
*
1424763 GAGTTGGAGTATCCTCGATTAAAG-GAAAATTGGCGTTTTGAAAATAAAACCG
1 G-GTTGGAGTATCCTCGATT---GTGAAAATTGGAGTTTTGAAAATAAAACCG
*
1424815 GGATTGGAGTATCCCCGATTGTGAAAA
1 GG-TTGGAGTATCCTCGATTGTGAAAA
1424842 AATTAGTGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
49 1 0.01
50 5 0.07
51 2 0.03
52 50 0.74
53 4 0.06
54 5 0.07
55 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (49 bp):
GGTTGGAGTATCCTCGATTGTGAAAATTGGAGTTTTGAAAATAAAACCG
Found at i:1424844 original size:52 final size:52
Alignment explanation
Indices: 1424714--1424879 Score: 144
Period size: 52 Copynumber: 3.2 Consensus size: 52
1424704 AATAACGAGG
* * * *
1424714 TTGGAGTATCCTCGATTGTG-AAAATTTGGTATTTTTGGAAATAAAATC-GGA
1 TTGGAGTATCCTCGATTGTGAAAAAATTGG-AGTTTTGAAAATAAAACCGGGA
* *
1424765 GTTGGAGTATCCTCGA-T-TAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGA
1 -TTGGAGTATCCTCGATTGTGAA--AAAATTGGAGTTTTGAAAATAAAACCGGGA
* * * ** *
1424818 TTGGAGTATCCCCGATTGTGAAAAAATTAGTGTTTT-AGCGATAAAACCGGGG
1 TTGGAGTATCCTCGATTGTGAAAAAATTGGAGTTTTGA-AAATAAAACCGGGA
1424870 TTGGAGTATC
1 TTGGAGTATC
1424880 TCCTCGGAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 14
0.78 0.11 0.12
Matches are distributed among these distances:
50 1 0.01
51 3 0.03
52 76 0.81
53 11 0.12
54 3 0.03
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (52 bp):
TTGGAGTATCCTCGATTGTGAAAAAATTGGAGTTTTGAAAATAAAACCGGGA
Found at i:1424902 original size:184 final size:184
Alignment explanation
Indices: 1424681--1425022 Score: 503
Period size: 185 Copynumber: 1.9 Consensus size: 184
1424671 TTGGAAGTAA
* * *
1424681 CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAA-AATTTGGTA
1 CGGGGTTGGAGTATCCCCGA-GAAATAACGAGGTTGGAGTATCCCCGATAGTGAAGAAATTGGTA
* * *
1424745 -TTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTAAAGGAAAATTGGCGTTTTGAAAATA
65 TTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAA-GAAAATTAGCGTTTTGAAAATA
*
1424809 AAACCGG-GATTGGAGTATCCCCGATTGTGAAAAAATTAGTGTTTTAGCGATAAAAC
129 AAACCGGAG-TTGGAATATCCCCGATTGTGAAAAAATTAGTGTTTTAGCGATAAAAC
*
1424865 CGGGGTTGGAGTATCTCCTCG-GAAATAACGGGGTTGGAGTATCCCCGATAGTGAAGAAATTGGT
1 CGGGGTTGGAGTATC-CC-CGAGAAATAACGAGGTTGGAGTATCCCCGATAGTGAAGAAATTGGT
* *
1424929 ATTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATA
64 ATTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAGAAAATTAGCGTTTTGAAAATA
* *
1424994 AAATCGGAGTTGGAATATCCCTGATTGTG
129 AAACCGGAGTTGGAATATCCCCGATTGTG
1425023 GAGAATTGAG
Statistics
Matches: 141, Mismatches: 12, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
184 46 0.33
185 54 0.38
186 41 0.29
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (184 bp):
CGGGGTTGGAGTATCCCCGAGAAATAACGAGGTTGGAGTATCCCCGATAGTGAAGAAATTGGTAT
TTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAA
ACCGGAGTTGGAATATCCCCGATTGTGAAAAAATTAGTGTTTTAGCGATAAAAC
Found at i:1427404 original size:33 final size:33
Alignment explanation
Indices: 1427362--1427424 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1427352 TTTCCAAATG
***
1427362 TATCGATACAAAGATCCATGTATCGATACAATA
1 TATCGATACAAAGAAAAATGTATCGATACAATA
*
1427395 TATCGATACACAGAAAAATGTATCGATACA
1 TATCGATACAAAGAAAAATGTATCGATACA
1427425 TTTTCTTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (33 bp):
TATCGATACAAAGAAAAATGTATCGATACAATA
Found at i:1427468 original size:19 final size:19
Alignment explanation
Indices: 1427444--1427510 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
1427434 CAGTAGCTAA
1427444 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
1427463 TTATGTATCGAT---ATA-
1 TTATGTATCGATACAATAC
*
1427478 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAATAC
1427495 TTATGTATCGATACAA
1 TTATGTATCGATACAA
1427511 ATTGTTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 9 0.22
14 1 0.02
16 5 0.12
18 1 0.02
19 25 0.61
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (19 bp):
TTATGTATCGATACAATAC
Found at i:1427488 original size:32 final size:32
Alignment explanation
Indices: 1427447--1427507 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1427437 TAGCTAATTA
*
1427447 TGTATCGATACAATACTTATGTATCGATATAT
1 TGTATCGATACAAAACTTATGTATCGATATAT
1427479 TGTATCGATACAAAACTTATGTATCGATA
1 TGTATCGATACAAAACTTATGTATCGATA
1427508 CAAATTGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATATAT
Found at i:1427591 original size:21 final size:21
Alignment explanation
Indices: 1427567--1427623 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1427557 CATTTGTAGG
1427567 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1427588 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1427609 ATGTATCGATACATT
1 ATGTATCGATACATT
1427624 TGGATAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1430264 original size:3 final size:3
Alignment explanation
Indices: 1430256--1430293 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1430246 CGAGTCAACT
**
1430256 TCA TCA TCA TCA TCA TCA TCA TCA TTT TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1430294 TTTGATGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:1432080 original size:21 final size:20
Alignment explanation
Indices: 1432029--1432067 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1432019 ATATGTATTG
*
1432029 TTACATCTGGGTGTGTATCA
1 TTACATCTAGGTGTGTATCA
1432049 TTACATCTAGGTGTGTATC
1 TTACATCTAGGTGTGTATC
1432068 GATACTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (20 bp):
TTACATCTAGGTGTGTATCA
Found at i:1433771 original size:21 final size:21
Alignment explanation
Indices: 1433747--1433793 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1433737 TTTGAAGCTG
1433747 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
1433767 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
1433788 ATTTTG
1 ATTTTG
1433794 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:1433932 original size:13 final size:13
Alignment explanation
Indices: 1433914--1433952 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1433904 ATAATCCCCC
*
1433914 TGTATCGATACAG
1 TGTATCGATACAA
1433927 TGTATCGATACAA
1 TGTATCGATACAA
1433940 TGTATCGATACAA
1 TGTATCGATACAA
1433953 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1437909 original size:22 final size:20
Alignment explanation
Indices: 1437860--1437911 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1437850 ATCATGCAAG
1437860 TTTTTATTTTTCTTAGCTAAT
1 TTTTTA-TTTTCTTAGCTAAT
**
1437881 TCATTATTTTCATTAGCTAAAT
1 TTTTTATTTTC-TTAGCT-AAT
1437903 TTTTTATTT
1 TTTTTATTT
1437912 CAACTTGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 5 0.20
21 10 0.40
22 10 0.40
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTATTTTCTTAGCTAAT
Found at i:1440159 original size:13 final size:13
Alignment explanation
Indices: 1440141--1440166 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1440131 AATTTTTTGG
1440141 TGTATCGATACAT
1 TGTATCGATACAT
1440154 TGTATCGATACAT
1 TGTATCGATACAT
1440167 ACATGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1440170 original size:17 final size:18
Alignment explanation
Indices: 1440148--1440184 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1440138 TGGTGTATCG
1440148 ATACAT-TGTATCGATAC
1 ATACATGTGTATCGATAC
1440165 ATACATGGTGTATCGATAC
1 ATACAT-GTGTATCGATAC
1440184 A
1 A
1440185 AGTTTGGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (18 bp):
ATACATGTGTATCGATAC
Found at i:1441756 original size:25 final size:23
Alignment explanation
Indices: 1441715--1441764 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
1441705 CATTTTGATA
1441715 ATTTCCAAAAAAATGAC-AAGAAT
1 ATTTCCAAAAAAATGACGAA-AAT
1441738 ATTTCCCAAAAAAATTGACGAAAAT
1 ATTT-CCAAAAAAA-TGACGAAAAT
1441763 AT
1 AT
1441765 GACGAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 4 0.17
24 9 0.38
25 9 0.38
26 2 0.08
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (23 bp):
ATTTCCAAAAAAATGACGAAAAT
Done.