Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 147 of 171
Found at i:44505392 original size:59 final size:58
Alignment explanation
Indices: 44505286--44505451 Score: 174
Period size: 59 Copynumber: 2.8 Consensus size: 58
44505276 GGATGCTTCG
* * * * * * *
44505286 AGGGTAGAATGGTAATTTTTGGACACTCGGGGGCAAAAATGTGATTTTTGGGCATTC-
1 AGGGTAAAATGGTAATTTTTGAAAACTCAGGGGCAAAAATGTAATTTTTGGACATCCA
* *
44505343 AGTGGTAAAATGGTAATTTTTGAAAAGTTCAGGGTCAAAAATGTAATTTTTGGACATCCA
1 AG-GGTAAAATGGTAATTTTTGAAAA-CTCAGGGGCAAAAATGTAATTTTTGGACATCCA
* * * *
44505403 AGGGTAAAATGGTAATTTTTGGATATTCAGGGG-TAAAATGGTAATTTTT
1 AGGGTAAAATGGTAATTTTTGAAAACTCAGGGGCAAAAAT-GTAATTTTT
44505452 CAAAGTTTTA
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
57 7 0.08
58 36 0.39
59 47 0.51
60 2 0.02
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (58 bp):
AGGGTAAAATGGTAATTTTTGAAAACTCAGGGGCAAAAATGTAATTTTTGGACATCCA
Found at i:44505397 original size:88 final size:88
Alignment explanation
Indices: 44505297--44505487 Score: 226
Period size: 88 Copynumber: 2.2 Consensus size: 88
44505287 GGGTAGAATG
** * * *
44505297 GTAATTTTTGGACA-CTCGGGGGCAAAAAT-GTGATTTTTGGGCATTCAGTGGTAAAATGGTAAT
1 GTAATTTTTGGACATC-CAAGGG-AAAAATGGTAATTTTTGGACATTCAGGGGTAAAATGGTAAT
44505360 TTTTGAAAAG-TTCAGGGTCAAAAAT
64 TTTT-AAAAGTTTCAGGGTCAAAAAT
* *
44505385 GTAATTTTTGGACATCCAAGGGTAAAATGGTAATTTTTGGATATTCAGGGGTAAAATGGTAATTT
1 GTAATTTTTGGACATCCAAGGGAAAAATGGTAATTTTTGGACATTCAGGGGTAAAATGGTAATTT
* * *
44505450 TTCAAAGTTTTAGGGTTAAAAAT
66 TTAAAAGTTTCAGGGTCAAAAAT
* *
44505473 GGAATTTTTGCACAT
1 GTAATTTTTGGACAT
44505488 TTTGGGGCTA
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
87 9 0.10
88 78 0.89
89 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (88 bp):
GTAATTTTTGGACATCCAAGGGAAAAATGGTAATTTTTGGACATTCAGGGGTAAAATGGTAATTT
TTAAAAGTTTCAGGGTCAAAAAT
Found at i:44505502 original size:60 final size:59
Alignment explanation
Indices: 44505408--44505542 Score: 173
Period size: 60 Copynumber: 2.3 Consensus size: 59
44505398 ATCCAAGGGT
* * *
44505408 AAAATGGTAATTTTTGGATATTCAGGGGTAAAATGGTAATTTTTCAAAGTTTTAGG-GTTA
1 AAAATGG-AATTTTTGCACATTCAGGGGTAAAATGGTAATTTTTCAAAGTTTT-GGAGTCA
** *
44505468 AAAATGGAATTTTTGCACATTTTGGGGCTAAAATGGTAATTTTTGAAAGTTTTGGAGTCA
1 AAAATGGAATTTTTGCACATTCAGGGG-TAAAATGGTAATTTTTCAAAGTTTTGGAGTCA
*
44505528 AAAATGAAATTTTTG
1 AAAATGGAATTTTTG
44505543 AAAACTTCAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 18 0.27
60 48 0.73
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.39
Consensus pattern (59 bp):
AAAATGGAATTTTTGCACATTCAGGGGTAAAATGGTAATTTTTCAAAGTTTTGGAGTCA
Found at i:44507521 original size:6 final size:6
Alignment explanation
Indices: 44507497--44507562 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
44507487 GTTTAAAACC
** *
44507497 ATTTCAA ATTT-A A-TTAA ATTTAA ATTTAA AAATAG ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
**
44507544 ATTTAA AAATAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
44507563 ACCAATTTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
4 2 0.04
5 4 0.09
6 37 0.79
7 4 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:44507537 original size:24 final size:24
Alignment explanation
Indices: 44507510--44507562 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
44507500 TCAAATTTAA
*
44507510 TTAAATTTAAATTTAAAAATAGAT
1 TTAAATTTAAATTTAAAAATAAAT
44507534 TTAAATTTAAATTTAAAAATAAAT
1 TTAAATTTAAATTTAAAAATAAAT
44507558 TTAAA
1 TTAAA
44507563 ACCAATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TTAAATTTAAATTTAAAAATAAAT
Found at i:44508262 original size:39 final size:39
Alignment explanation
Indices: 44508219--44508306 Score: 140
Period size: 39 Copynumber: 2.3 Consensus size: 39
44508209 AACGGTTGCA
* *
44508219 ATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGTTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATG
*
44508258 ATCTGACCCAAGCTCGGGGTAAGAGATTTGCTGATGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATG
*
44508297 ATCCGCCCCA
1 ATCTGCCCCA
44508307 CTAGAATGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTTGCTGATGATG
Found at i:44508693 original size:98 final size:98
Alignment explanation
Indices: 44508518--44509011 Score: 661
Period size: 98 Copynumber: 5.0 Consensus size: 98
44508508 CTTCAATCCG
* * * * *
44508518 CATGGTGCTAAATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-TCTCTAAGGTATAAAGTTC
1 CATGGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGGTTC
* * * *** *
44508582 GTCATTGCAACTTAAACCTTTCCCTTTGTGTCTT
65 GCCGTTGCGACTTAAACCTTTCCCTCCATATCTT
* * *
44508616 TATGGTACTGGATTTACCGTTGCGGCTTAAATCTTTCCCTTCATG-TCTCTGAGGTATAAGGTTC
1 CATGGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGGTTC
* * *
44508680 GCCATTACGACTTAAACCTTTCCCTTCATATCTT
65 GCCGTTGCGACTTAAACCTTTCCCTCCATATCTT
* * *
44508714 CGTGGTACTAGATT-AGCTGTTGCGGCTTAAATATTTCCCTTCATGCTTCTGAGGTATAAGGTTC
1 CATGGTACTAGATTCA-CCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTC
44508778 GCCGTTGCGACTTAAACCTTTCCCTCCATATCTT
65 GCCGTTGCGACTTAAACCTTTCCCTCCATATCTT
* * * * *
44508812 CGTGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTCG
1 CATGGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCG
*
44508877 CCGTTGCGACTTAAACCTTTCCCTCTATATCTT
66 CCGTTGCGACTTAAACCTTTCCCTCCATATCTT
* * *
44508910 CATAGTACTAGATTCACCGTTGTGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCG
1 CATGGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCG
*
44508975 CCGTTACGACTTAAACCTTTCCCTCCATATCTT
66 CCGTTGCGACTTAAACCTTTCCCTCCATATCTT
44509008 CATG
1 CATG
44509012 TTTTTCTCAG
Statistics
Matches: 355, Mismatches: 38, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
97 1 0.00
98 353 0.99
99 1 0.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (98 bp):
CATGGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCG
CCGTTGCGACTTAAACCTTTCCCTCCATATCTT
Found at i:44508930 original size:49 final size:50
Alignment explanation
Indices: 44508529--44509008 Score: 387
Period size: 49 Copynumber: 9.8 Consensus size: 50
44508519 ATGGTGCTAA
* * * * *
44508529 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTAAGGTA-TAA
1 ATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTCTGAGGTACTAG
* * * ** * *
44508577 AGTTCGTCATTGCAACTTAAACCTTTCCCTTTGTGTCTT-T-ATGGTACTGG
1 A-TTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTCTGA-GGTACTAG
** * * *
44508627 ATTTACCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTA-TAAG
1 ATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTCTGAGGTACT-AG
* * * *
44508676 GTTCGCCATTACGACTTAAACCTTTCCCTTCATATCTTC-GTGGTACTAG
1 ATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTCTGAGGTACTAG
* * * ** *
44508725 ATTAGCTGTTGCGGCTTAAATATTTCCCTTCAT-GCTTCTGAGGTA-TAAG
1 ATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTCTGAGGTACT-AG
* * *
44508774 GTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTC-GTGGTACTAG
1 ATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTCTGAGGTACTAG
* * * * * *
44508823 ATTCGCCATTGCGGCTTAAATCTTTCCCTTCAT-GCTTTTGAGGTACAAG
1 ATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTCTGAGGTACTAG
*
44508872 GTTCGCCGTTGCGACTTAAACCTTTCCC-TCTATATCTTCAT-A-GTACTAG
1 ATTCGCCGTTGCGACTTAAACCTTTCCCTTC-ATATCTTC-TGAGGTACTAG
* * * * * *
44508921 ATTCACCGTTGTGGCTTAAATCTTTCCCTTCAT-GCTTCTGAGGTACAAG
1 ATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTCTGAGGTACTAG
* * *
44508970 GTTCGCCGTTACGACTTAAACCTTTCCCTCCATATCTTC
1 ATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTC
44509009 ATGTTTTTCT
Statistics
Matches: 333, Mismatches: 78, Indels: 40
0.74 0.17 0.09
Matches are distributed among these distances:
47 1 0.00
48 19 0.06
49 290 0.87
50 22 0.07
51 1 0.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.38
Consensus pattern (50 bp):
ATTCGCCGTTGCGACTTAAACCTTTCCCTTCATATCTTCTGAGGTACTAG
Found at i:44516586 original size:16 final size:17
Alignment explanation
Indices: 44516560--44516593 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
44516550 GTTTAAAACC
44516560 ATTTCAAATTTAATTTA
1 ATTTCAAATTTAATTTA
44516577 ATTT-AAATTTAATTTA
1 ATTTCAAATTTAATTTA
44516593 A
1 A
44516594 AATCAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTCAAATTTAATTTA
Found at i:44516587 original size:11 final size:11
Alignment explanation
Indices: 44516566--44516594 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
44516556 AACCATTTCA
44516566 AATTT-AATTT
1 AATTTAAATTT
44516576 AATTTAAATTT
1 AATTTAAATTT
44516587 AATTTAAA
1 AATTTAAA
44516595 ATCAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:44517407 original size:17 final size:17
Alignment explanation
Indices: 44517387--44517449 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 17
44517377 CCCTTGACTT
44517387 TTAACCTTTCATCTTCC
1 TTAACCTTTCATCTTCC
44517404 TTAACC--TC-TCTTAACC
1 TTAACCTTTCATCTT--CC
* *
44517420 TTTAACTTTTTATCTTCC
1 -TTAACCTTTCATCTTCC
*
44517438 TTAATCTTTCAT
1 TTAACCTTTCAT
44517450 ATTTTTGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
14 4 0.11
15 2 0.06
16 2 0.06
17 20 0.57
18 2 0.06
19 1 0.03
20 4 0.11
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAACCTTTCATCTTCC
Found at i:44524330 original size:26 final size:26
Alignment explanation
Indices: 44524301--44524362 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
44524291 TGTGGAGCTT
**
44524301 GCTGACGTGGACATGATGATGTGGCA
1 GCTGACGTGGACATGATGACATGGCA
* * *
44524327 GCTGACGTGGACGTGCTGACATGGTA
1 GCTGACGTGGACATGATGACATGGCA
44524353 GCTGACGTGG
1 GCTGACGTGG
44524363 CGGCTTAGGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.19, C:0.18, G:0.40, T:0.23
Consensus pattern (26 bp):
GCTGACGTGGACATGATGACATGGCA
Found at i:44524506 original size:17 final size:17
Alignment explanation
Indices: 44524493--44524584 Score: 96
Period size: 17 Copynumber: 5.4 Consensus size: 17
44524483 TTAAATTTTT
*
44524493 ATTTTAAATAAATTTAA
1 ATTTAAAATAAATTTAA
44524510 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
* ** *
44524527 ACTCCAAATAAGTTTAA
1 ATTTAAAATAAATTTAA
*
44524544 ATTTATAATAAATTTAA
1 ATTTAAAATAAATTTAA
* *
44524561 AATTAAAATGAA-TTAA
1 ATTTAAAATAAATTTAA
44524577 GATTTAAA
1 -ATTTAAA
44524585 TTTTAAAGTT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
16 4 0.07
17 56 0.93
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:44524993 original size:23 final size:23
Alignment explanation
Indices: 44524965--44525021 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
44524955 TCACACAACA
* *
44524965 ATATAATTTTTTTATCAAAATAT
1 ATATAATTTTTGTATAAAAATAT
44524988 ATATAATTTTTGTATAAAAATAT
1 ATATAATTTTTGTATAAAAATAT
*
44525011 ATATTATTTTT
1 ATATAATTTTT
44525022 ATTAATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
ATATAATTTTTGTATAAAAATAT
Found at i:44525394 original size:14 final size:16
Alignment explanation
Indices: 44525373--44525412 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
44525363 TAATGTGTTG
44525373 AAATATTTTT-ATA-A
1 AAATATTTTTAATATA
*
44525387 ATATATTTTTAATATA
1 AAATATTTTTAATATA
44525403 AAATATTTTT
1 AAATATTTTT
44525413 GTTTGTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 3 0.14
16 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAATATTTTTAATATA
Found at i:44527926 original size:30 final size:29
Alignment explanation
Indices: 44527870--44527944 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 29
44527860 TTCCTTCGCC
44527870 AATGACCCCAATGCCTTTTTCTTTTTGACAA
1 AATGACCCC-ATG-CTTTTTCTTTTTGACAA
*
44527901 AATGGCCCCATGCTTTTTCCTTTTTGACAA
1 AATGACCCCATGCTTTTT-CTTTTTGACAA
*
44527931 AATGCCTCCCATGC
1 AATGAC-CCCATGC
44527945 ATTTGTTTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 6 0.15
30 19 0.47
31 15 0.38
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.36
Consensus pattern (29 bp):
AATGACCCCATGCTTTTTCTTTTTGACAA
Found at i:44533155 original size:24 final size:24
Alignment explanation
Indices: 44533128--44533219 Score: 166
Period size: 24 Copynumber: 3.8 Consensus size: 24
44533118 CTCAAGCAAC
44533128 TAAATAGAGTTTAATTGAAACAAA
1 TAAATAGAGTTTAATTGAAACAAA
44533152 TAAATAGAGTTTAATTGAAACAAA
1 TAAATAGAGTTTAATTGAAACAAA
44533176 TAAATAGAGTTTAATTGAAACAAA
1 TAAATAGAGTTTAATTGAAACAAA
* *
44533200 TAAACAGAGTTTAACTGAAA
1 TAAATAGAGTTTAATTGAAA
44533220 GATTATTTCT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.53, C:0.05, G:0.13, T:0.28
Consensus pattern (24 bp):
TAAATAGAGTTTAATTGAAACAAA
Found at i:44535176 original size:24 final size:24
Alignment explanation
Indices: 44535149--44535199 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
44535139 AATTTGACTC
* *
44535149 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
44535173 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
44535197 AAA
1 AAA
44535200 GATTGTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:44538912 original size:17 final size:17
Alignment explanation
Indices: 44538890--44538928 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
44538880 CTCCACCTTG
* *
44538890 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
44538907 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
44538924 ACAAG
1 ACAAG
44538929 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:44541144 original size:35 final size:34
Alignment explanation
Indices: 44541105--44541220 Score: 160
Period size: 35 Copynumber: 3.4 Consensus size: 34
44541095 CCAAACTCAT
* *
44541105 TTTAAATTTATTTTAAGGTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGTTTAAATTTATTTT-AAA
* *
44541140 TTTAAATTTATTTTAAATTTAAATTTATTCTAAA
1 TTTAAATTTATTTTAAGTTTAAATTTATTTTAAA
*
44541174 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAGTTTAAATTTATTTT-AAA
*
44541209 TTTAAAATTATT
1 TTTAAATTTATT
44541221 ATAAATCTAA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 31 0.44
35 40 0.56
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAGTTTAAATTTATTTTAAA
Found at i:44541148 original size:6 final size:6
Alignment explanation
Indices: 44541137--44541214 Score: 76
Period size: 6 Copynumber: 13.5 Consensus size: 6
44541127 ATTTGTTTTA
*
44541137 AAATTT AAATTT -ATTTT AAATTT AAATTT --ATTCT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T AAATTT AAATTT
* *
44541183 -AATTT AAGTTT AAATTT -ATTTT CAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
44541215 ATTATTATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
4 3 0.05
5 14 0.24
6 35 0.59
7 7 0.12
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:44541154 original size:11 final size:11
Alignment explanation
Indices: 44541140--44541212 Score: 50
Period size: 11 Copynumber: 6.9 Consensus size: 11
44541130 TGTTTTAAAA
44541140 TTTAAATTTAT
1 TTTAAATTTAT
44541151 TTT-AA---AT
1 TTTAAATTTAT
44541158 -TTAAATTTAT
1 TTTAAATTTAT
* *
44541168 TCTAAATTTAAA
1 TTTAAATTT-AT
*
44541180 TTT-AATTTAAG
1 TTTAAATTT-AT
44541191 TTTAAATTTAT
1 TTTAAATTTAT
44541202 TTTCAAATTTA
1 TTT-AAATTTA
44541213 AAATTATTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
6 2 0.04
7 4 0.08
10 4 0.08
11 24 0.49
12 15 0.31
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:44541167 original size:52 final size:52
Alignment explanation
Indices: 44541105--44541225 Score: 154
Period size: 52 Copynumber: 2.3 Consensus size: 52
44541095 CCAAACTCAT
* * **
44541105 TTTAAATTTATTTTAAGGTTAAATTTGTTTTAAAATTTAAATTTATTTT-AAA
1 TTTAAATTTATTCTAAAGTTAAATTTAATTT-AAATTTAAATTTATTTTCAAA
* *
44541157 TTTAAATTTATTCTAAATTTAAATTTAATTTAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTATTCTAAAGTTAAATTTAATTTAAATTTAAATTTATTTTCAAA
* *
44541209 TTTAAAATTATTATAAA
1 TTTAAATTTATTCTAAA
44541226 TCTAAAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 16 0.27
52 44 0.73
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (52 bp):
TTTAAATTTATTCTAAAGTTAAATTTAATTTAAATTTAAATTTATTTTCAAA
Found at i:44541233 original size:17 final size:17
Alignment explanation
Indices: 44541105--44541231 Score: 155
Period size: 17 Copynumber: 7.4 Consensus size: 17
44541095 CCAAACTCAT
*
44541105 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
* *
44541122 GTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
44541140 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
44541157 TTTAAATTTATTCTAAA
1 TTTAAATTTATTTTAAA
* *
44541174 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
44541191 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
* *
44541209 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
*
44541226 TCTAAA
1 TTTAAA
44541232 ATAAATAAGT
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
17 66 0.70
18 28 0.30
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:44542817 original size:29 final size:27
Alignment explanation
Indices: 44542779--44542999 Score: 122
Period size: 29 Copynumber: 7.6 Consensus size: 27
44542769 GAAGGTCCCT
* *
44542779 AAACTGTCCAAAAATTATCTTTTGGCCCTA
1 AAACT-TCCAAAAATTAT-TTTTGACCC-C
*
44542809 AAACTTCCAAAAATTATATTTTTACCCCC
1 AAACTTCCAAAAATTAT-TTTTGA-CCCC
*
44542838 GAACTTCCAAAAATTCCATTTTTGACCCC
1 AAACTTCCAAAAATT--ATTTTTGACCCC
* *
44542867 GAAACTTCAAAAAATTACCATTTT-ACCCCC
1 -AAACTTCCAAAAATTA--TTTTTGA-CCCC
* * *
44542897 AAATTTCCAAAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATT--ATTTTTGACC-CC
** * *
44542927 AAACTTCCAAAAATTACAATTTAACCCT
1 AAACTTCCAAAAATTA-TTTTTGACCCC
* *
44542955 AAATTTAC-AAAATTCCATTTTTGACCCC
1 AAACTTCCAAAAATT--ATTTTTGACCCC
*
44542983 AAAGCTTTCAAAAATTA
1 AAA-CTTCCAAAAATTA
44543000 CCATTTTACC
Statistics
Matches: 150, Mismatches: 25, Indels: 34
0.72 0.12 0.16
Matches are distributed among these distances:
27 6 0.04
28 20 0.13
29 65 0.43
30 56 0.37
31 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.32
Consensus pattern (27 bp):
AAACTTCCAAAAATTATTTTTGACCCC
Found at i:44542880 original size:59 final size:59
Alignment explanation
Indices: 44542809--44543095 Score: 309
Period size: 59 Copynumber: 4.9 Consensus size: 59
44542799 TTTGGCCCTA
* * * *
44542809 AAACTTCCAAAAATTA-TATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCG
1 AAACTTCAAAAAATTACCA-TTTTACCCCCAAATTTCCAAAAATTCCATTTTTGACCCCG
* *
44542868 AAACTTCAAAAAATTACCATTTTACCCCCAAATTTCCAAAAATTCCATTTTTAACCTCG
1 AAACTTCAAAAAATTACCATTTTACCCCCAAATTTCCAAAAATTCCATTTTTGACCCCG
* * * * *
44542927 AAACTTCCAAAAATTA-CAATTTAACCCTAAATTTAC-AAAATTCCATTTTTGACCCC-
1 AAACTTCAAAAAATTACCATTTTACCCCCAAATTTCCAAAAATTCCATTTTTGACCCCG
* * * *
44542983 AAAGCTTTC-AAAAATTACCATTTTACCCCCGAATGTCCAAAAACTCCATTTTT-ACCCCA
1 AAA-C-TTCAAAAAATTACCATTTTACCCCCAAATTTCCAAAAATTCCATTTTTGACCCCG
* * * * *
44543042 AAACCTTC-AAAAATTACCATTTTACCTCTAGATGTCCAAAAATTCTATTTTTGA
1 AAA-CTTCAAAAAATTACCATTTTACCCCCAAATTTCCAAAAATTCCATTTTTGA
44543096 TCTCGATTTT
Statistics
Matches: 194, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
56 3 0.02
57 27 0.14
58 79 0.41
59 84 0.43
60 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.32
Consensus pattern (59 bp):
AAACTTCAAAAAATTACCATTTTACCCCCAAATTTCCAAAAATTCCATTTTTGACCCCG
Found at i:44543010 original size:29 final size:27
Alignment explanation
Indices: 44542845--44543067 Score: 141
Period size: 29 Copynumber: 7.7 Consensus size: 27
44542835 CCCGAACTTC
*
44542845 CAAAAATT-CCATTTTTGACCCCGAAACTT
1 CAAAAATTACCA-TTTT-ACCCC-AAATTT
44542874 CAAAAAATTACCATTTTACCCCCAAATTT
1 C-AAAAATTACCATTTTA-CCCCAAATTT
* *
44542903 CCAAAAATT-CCATTTTTAACCTCGAAACTTC
1 -CAAAAATTACCA-TTTT-ACC-CCAAA-TTT
* * *
44542934 CAAAAATTACAATTTAACCCTAAATTT
1 CAAAAATTACCATTTTACCCCAAATTT
44542961 -ACAAAATT-CCATTTTTGACCCCAAAGCTTT
1 CA-AAAATTACCA-TTTT-ACCCCAAA--TTT
* *
44542991 CAAAAATTACCATTTTACCCCCGAATGTC
1 CAAAAATTACCATTTTA-CCCCAAAT-TT
* *
44543020 CAAAAACT-CCATTTTTACCCCAAAACCTT
1 CAAAAATTACCA-TTTTACCCC-AAA-TTT
44543049 CAAAAATTACCATTTTACC
1 CAAAAATTACCATTTTACC
44543068 TCTAGATGTC
Statistics
Matches: 155, Mismatches: 17, Indels: 44
0.72 0.08 0.20
Matches are distributed among these distances:
26 3 0.02
27 11 0.07
28 22 0.14
29 54 0.35
30 54 0.35
31 11 0.07
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (27 bp):
CAAAAATTACCATTTTACCCCAAATTT
Found at i:44543058 original size:58 final size:58
Alignment explanation
Indices: 44542783--44543095 Score: 316
Period size: 58 Copynumber: 5.4 Consensus size: 58
44542773 GTCCCTAAAC
* * * *
44542783 TGTCCAAAAATT--ATCTTTTGGCCCTAAAACTTCCAAAAATTA-TATTTTTACCCCCGAAC
1 TGTCCAAAAATTCCAT-TTTTGACCCCAAAACTT-CAAAAATTACCA-TTTTACCCCC-AAA
*
44542842 T-TCCAAAAATTCCATTTTTGACCCCGAAACTTCAAAAAATTACCATTTTACCCCCAAA
1 TGTCCAAAAATTCCATTTTTGACCCCAAAACTTC-AAAAATTACCATTTTACCCCCAAA
* * * * * * *
44542900 TTTCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTA-CAATTTAACCCTAAA
1 TGTCCAAAAATTCCATTTTTGACCCCAAAACTT-CAAAAATTACCATTTTACCCCCAAA
* * * *
44542958 TTTAC-AAAATTCCATTTTTGACCCCAAAGCTTTCAAAAATTACCATTTTACCCCCGAA
1 TGTCCAAAAATTCCATTTTTGACCCCAAAAC-TTCAAAAATTACCATTTTACCCCCAAA
* * * *
44543016 TGTCCAAAAACTCCATTTTT-ACCCCAAAACCTTCAAAAATTACCATTTTACCTCTAGA
1 TGTCCAAAAATTCCATTTTTGACCCCAAAA-CTTCAAAAATTACCATTTTACCCCCAAA
*
44543074 TGTCCAAAAATTCTATTTTTGA
1 TGTCCAAAAATTCCATTTTTGA
44543096 TCTCGATTTT
Statistics
Matches: 214, Mismatches: 29, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
57 30 0.14
58 95 0.44
59 85 0.40
60 4 0.02
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.33
Consensus pattern (58 bp):
TGTCCAAAAATTCCATTTTTGACCCCAAAACTTCAAAAATTACCATTTTACCCCCAAA
Found at i:44555692 original size:202 final size:199
Alignment explanation
Indices: 44555283--44555907 Score: 710
Period size: 201 Copynumber: 3.1 Consensus size: 199
44555273 ACCAAATTCG
* * * * *
44555283 TCTTCCTGATGAGATATAGAAAAGTATACCAACTCGAGGCTCAAAGGCGAGCAAATTTTCGAACC
1 TCTTCCTGATGAGATACAGAGAAGTATACCAAATCAAGGCTCAAAGGCGAGCAAATCTTC-AACC
* * *
44555348 CCAGCTTCTTAATGAGATACTGAGAAACAGGTCGAAGTAATAAATGGTTAGCTTCC-ACATGAGA
65 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAATGGTTAGCTTCCTA-ATGAGA
*
44555412 TACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACTAGTGAG
129 TACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTGAG
*
44555477 ACGGTCG
194 -CGGTCA
*
44555484 TCTTCCTGATGAGATACAGAGAAGTATACCAATTCAAGGCTCAAAGGCGAGCAAATCTTCTAACC
1 TCTTCCTGATGAGATACAGAGAAGTATACCAAATCAAGGCTCAAAGGCGAGCAAATCTTC-AACC
* ** *
44555549 CCAGCTTCCTGATGAGATATTGAGAAGCAGGTTAAAGCAATAAAATGGTTAGCTTCCTAATGAGA
65 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAAT-AAATGGTTAGCTTCCTAATGAGA
** * * * **
44555614 TACTGAGAAGCCGACCAAATTTGTCTTCTTAATGAGATACAAAGAAGC-AGATTGAAACAAACGA
129 TACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGA-ATTGAAACAAGTGA
*
44555678 TGCAGTCA
193 -GCGGTCA
* * * *
44555686 TCTTCCTGAT-AG-T---GAGAAGAAGACCAAATCAAACCCGCGCTCGATA--TGAGCAAATCTT
1 TCTTCCTGATGAGATACAGAGAAGTATACCAAATC-AA---G-GCTC-AAAGGCGAGCAAATCTT
** * * * * *
44555744 CATACTTCAGCTTCCTGATGAGACACTGAGAAGCAGATCGAAGTAATAACTAGTTAGCTTCCTGA
60 CA-ACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAATGGTTAGCTTCCTAA
* *
44555809 TGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAATTGAAACAA
124 TGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAA
44555874 GTGACGCGGTCA
189 GTGA-GCGGTCA
* *
44555886 TCTTCCTGATAAGATACTGAGA
1 TCTTCCTGATGAGATACAGAGA
44555908 CAAAGGCCAA
Statistics
Matches: 357, Mismatches: 50, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
197 14 0.04
198 2 0.01
200 91 0.25
201 148 0.41
202 94 0.26
203 4 0.01
205 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (199 bp):
TCTTCCTGATGAGATACAGAGAAGTATACCAAATCAAGGCTCAAAGGCGAGCAAATCTTCAACCC
CAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAATGGTTAGCTTCCTAATGAGATA
CTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAGTGAGCG
GTCA
Found at i:44556259 original size:17 final size:17
Alignment explanation
Indices: 44556236--44556345 Score: 130
Period size: 17 Copynumber: 6.4 Consensus size: 17
44556226 CCAAACTCAT
*
44556236 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
* *
44556253 GTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
44556271 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
44556288 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
44556305 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
44556323 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
*
44556340 TCTAAA
1 TTTAAA
44556346 ATAAATAAGT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
17 51 0.65
18 28 0.35
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:44556275 original size:35 final size:34
Alignment explanation
Indices: 44556236--44556345 Score: 114
Period size: 35 Copynumber: 3.2 Consensus size: 34
44556226 CCAAACTCAT
* **
44556236 TTTAAATTTATTTTAAGGTTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAGTTAAATTTAATTT-AAA
* *
44556271 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAAGTTAAATTTAATTTAAA
* *
44556305 TTTAAATTTATTTTTAAATTTAAAATT-ATTATAAA
1 TTTAAATTTA-TTTTAAAGTTAAATTTAATT-TAAA
*
44556340 TCTAAA
1 TTTAAA
44556346 ATAAATAAGT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
34 15 0.23
35 50 0.77
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAAGTTAAATTTAATTTAAA
Found at i:44556279 original size:6 final size:6
Alignment explanation
Indices: 44556268--44556328 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
44556258 ATTTGTTTTA
* *
44556268 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
**
44556314 ATTTTT AAATTT AAA
1 AAATTT AAATTT AAA
44556329 ATTATTATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
5 9 0.20
6 36 0.80
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:44556285 original size:11 final size:11
Alignment explanation
Indices: 44556271--44556326 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
44556261 TGTTTTAAAA
44556271 TTTAAATTTAT
1 TTTAAATTTAT
*
44556282 TTTAAATTTAAA
1 TTTAAATTT-AT
*
44556294 TTT-AATTTAAG
1 TTTAAATTT-AT
44556305 TTTAAATTTATT
1 TTTAAATTTA-T
44556317 TTTAAATTTA
1 TTTAAATTTA
44556327 AAATTATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 20 0.51
12 19 0.49
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:44556297 original size:52 final size:52
Alignment explanation
Indices: 44556236--44556345 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
44556226 CCAAACTCAT
* * * *
44556236 TTTAAATTTATTTTAAGGTTAAATTTGTTTTAAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAGGTTAAATTTATTTTAAAATTTAAAATTATTATAAA
* *
44556288 TTTAAATTTAATTTAAGTTTAAATTTATTTTTAAATTTAAAATTATTATAAA
1 TTTAAATTTAATTTAAGGTTAAATTTATTTTAAAATTTAAAATTATTATAAA
*
44556340 TCTAAA
1 TTTAAA
44556346 ATAAATAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (52 bp):
TTTAAATTTAATTTAAGGTTAAATTTATTTTAAAATTTAAAATTATTATAAA
Found at i:44558253 original size:28 final size:27
Alignment explanation
Indices: 44558205--44558312 Score: 99
Period size: 29 Copynumber: 3.8 Consensus size: 27
44558195 TTGGCTCCAA
* *
44558205 AACTTCCAAAAAATACAATTTTGCCCTTG
1 AACTTCC-AAAAATTCCATTTTGCCC-TG
**
44558234 AACTTCCAAAAATTCCATTTTTGACCCAA
1 AACTTCCAAAAATTCCA-TTTTG-CCCTG
* * *
44558263 AATTTCCAACAATTACCATTTTACCCCTG
1 AACTTCCAAAAATT-CCATTTT-GCCCTG
44558292 AACTTCCAAAAATTCCATTTT
1 AACTTCCAAAAATTCCATTTT
44558313 TGACCCCAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
28 15 0.23
29 43 0.67
30 6 0.09
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (27 bp):
AACTTCCAAAAATTCCATTTTGCCCTG
Found at i:44558284 original size:30 final size:30
Alignment explanation
Indices: 44558237--44558330 Score: 113
Period size: 29 Copynumber: 3.2 Consensus size: 30
44558227 GCCCTTGAAC
44558237 TTCCAAAAATTCCATTTTTGA-CCCAAAAT
1 TTCCAAAAATTCCATTTTTGACCCCAAAAT
* ** *
44558266 TTCCAACAATTACCA-TTTT-ACCCCTGAAC
1 TTCCAAAAATT-CCATTTTTGACCCCAAAAT
44558295 TTCCAAAAATTCCATTTTTGACCCCAAAAT
1 TTCCAAAAATTCCATTTTTGACCCCAAAAT
*
44558325 TACCAA
1 TTCCAA
44558331 TTTACCCTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
28 4 0.08
29 33 0.63
30 15 0.29
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (30 bp):
TTCCAAAAATTCCATTTTTGACCCCAAAAT
Found at i:44558326 original size:49 final size:49
Alignment explanation
Indices: 44558268--44558372 Score: 165
Period size: 49 Copynumber: 2.1 Consensus size: 49
44558258 CCCAAAATTT
* * *
44558268 CCAACAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACC
1 CCAA-AATTACCAATTTACCCCTAAACTTCCAAAAATTCCATTTTTAACC
*
44558318 CCAAAATTACCAATTTACCCTTAAACTTCCAAAAATTCCATTTTTAACC
1 CCAAAATTACCAATTTACCCCTAAACTTCCAAAAATTCCATTTTTAACC
44558367 CCAAAA
1 CCAAAA
44558373 CTTCCAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
49 47 0.92
50 4 0.08
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.30
Consensus pattern (49 bp):
CCAAAATTACCAATTTACCCCTAAACTTCCAAAAATTCCATTTTTAACC
Found at i:44558354 original size:29 final size:31
Alignment explanation
Indices: 44558320--44558386 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
44558310 TTTTGACCCC
**
44558320 AAAATTACCA-ATTT-ACCCTTAAACTTCCA
1 AAAATTACCATATTTAACCCCAAAACTTCCA
*
44558349 AAAATT-CCATTTTTAACCCCAAAACTTCCA
1 AAAATTACCATATTTAACCCCAAAACTTCCA
44558379 AAAATTAC
1 AAAATTAC
44558387 ATTTTTATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 3 0.09
29 9 0.28
30 19 0.59
31 1 0.03
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (31 bp):
AAAATTACCATATTTAACCCCAAAACTTCCA
Found at i:44558376 original size:30 final size:30
Alignment explanation
Indices: 44558340--44558451 Score: 102
Period size: 30 Copynumber: 3.7 Consensus size: 30
44558330 ATTTACCCTT
44558340 AAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
* * *
44558370 AAACTTCCAAAAATTACATTTTTATCCAC-
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
* * * * *
44558399 GAACTT-TACAAGATTCCATTTTTTACCCTA
1 AAACTTCCA-AAAATTCCATTTTTAACCCCA
* *
44558429 AAATTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
44558452 ACCCTCAAAT
Statistics
Matches: 63, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
28 1 0.02
29 19 0.30
30 35 0.56
31 8 0.13
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCCCA
Found at i:44558383 original size:59 final size:58
Alignment explanation
Indices: 44558320--44558539 Score: 176
Period size: 59 Copynumber: 3.7 Consensus size: 58
44558310 TTTTGACCCC
* *
44558320 AAAATTACCAATTTACCCTTAAACT-TCCAAAAATTCCATTTTTAACCCCAAAACTTCCA
1 AAAATTACCATTTTACCCTCAAA-TATCCAAAAATTCCATTTTTAACCCCAAAACTT-CA
* * * * * * * * *
44558379 AAAATTA-CATTTTTATCCACGAACTTTAC-AAGATTCCATTTTTTACCCTAAAATTTTCA
1 AAAATTACCA-TTTTACCCTC-AAATATCCAAAAATTCCATTTTTAACCCCAAAA-CTTCA
* * * * * * **
44558438 AAAATTACCATTTTACCCTCAAATATCTAAAAACTCAATTTTTGACCTCGAAACCTTTT
1 AAAATTACCATTTTACCCTCAAATATCCAAAAATTCCATTTTTAACC-CCAAAACTTCA
* *
44558497 AAAATTACCATTTTACCCTCGAATATCCAAAAATTCTATTTTT
1 AAAATTACCATTTTACCCTCAAATATCCAAAAATTCCATTTTT
44558540 GATCCTGATT
Statistics
Matches: 125, Mismatches: 29, Indels: 14
0.74 0.17 0.08
Matches are distributed among these distances:
58 6 0.05
59 107 0.86
60 12 0.10
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCAAATATCCAAAAATTCCATTTTTAACCCCAAAACTTCA
Found at i:44558559 original size:59 final size:60
Alignment explanation
Indices: 44558432--44558573 Score: 173
Period size: 59 Copynumber: 2.4 Consensus size: 60
44558422 TACCCTAAAA
* *
44558432 TTTTCAAAAATTACCATTTTACCCTCAAATATCTAAAAACTCAATTTTTGACCTCGAAAC
1 TTTTCTAAAATTACCATTTTACCCTCAAATATCCAAAAACTCAATTTTTGACCTCGAAAC
* * * * **
44558492 CTTT-TAAAATTACCATTTTACCCTCGAATATCCAAAAATTCTATTTTTGATCCT-G-ATT
1 TTTTCTAAAATTACCATTTTACCCTCAAATATCCAAAAACTCAATTTTTGA-CCTCGAAAC
44558550 TTTTCTAAAAATTACCATTTTACC
1 TTTTCT-AAAATTACCATTTTACC
44558574 TCAGGTTTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
58 4 0.06
59 43 0.61
60 23 0.33
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.40
Consensus pattern (60 bp):
TTTTCTAAAATTACCATTTTACCCTCAAATATCCAAAAACTCAATTTTTGACCTCGAAAC
Found at i:44570221 original size:29 final size:31
Alignment explanation
Indices: 44570188--44570245 Score: 93
Period size: 29 Copynumber: 1.9 Consensus size: 31
44570178 TAACATAGGT
*
44570188 ACTTATTTAACTAAAA-A-AATAATTTAAGA
1 ACTTATTTAAATAAAATATAATAATTTAAGA
44570217 ACTTATTTAAATAAAATATAATAATTTAA
1 ACTTATTTAAATAAAATATAATAATTTAA
44570246 AGGCTTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 15 0.58
30 1 0.04
31 10 0.38
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (31 bp):
ACTTATTTAAATAAAATATAATAATTTAAGA
Found at i:44574736 original size:21 final size:21
Alignment explanation
Indices: 44574712--44574757 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
44574702 TAATCACAAC
*
44574712 TTTATCAAACGAATTCAGTTT
1 TTTATCAAACAAATTCAGTTT
*
44574733 TTTATCAACCAAATTCAGTTT
1 TTTATCAAACAAATTCAGTTT
44574754 TTTA
1 TTTA
44574758 GCTAGACTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (21 bp):
TTTATCAAACAAATTCAGTTT
Found at i:44575962 original size:23 final size:23
Alignment explanation
Indices: 44575934--44575996 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
44575924 TAAAACTTAC
*
44575934 ATATATGATTTTTTTATCAAAAT
1 ATATATGATTTTTTTATAAAAAT
*
44575957 ATATATGATTTTTGTATAAAAAT
1 ATATATGATTTTTTTATAAAAAT
44575980 ATATAT-ATTATTTTTAT
1 ATATATGATT-TTTTTAT
44575997 TAATTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 3 0.08
23 33 0.92
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (23 bp):
ATATATGATTTTTTTATAAAAAT
Found at i:44576624 original size:2 final size:2
Alignment explanation
Indices: 44576619--44576656 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
44576609 ATAAAAAAAC
*
44576619 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44576657 AACAGAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44576643 original size:17 final size:17
Alignment explanation
Indices: 44576621--44576654 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44576611 AAAAAAACAT
44576621 ATATATATATATATATA
1 ATATATATATATATATA
*
44576638 ATATATATATGTATATA
1 ATATATATATATATATA
44576655 TAAACAGAAA
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:44576643 original size:19 final size:19
Alignment explanation
Indices: 44576619--44576657 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
44576609 ATAAAAAAAC
44576619 ATATATATATATATATATA
1 ATATATATATATATATATA
*
44576638 ATATATATATGTATATATA
1 ATATATATATATATATATA
44576657 A
1 A
44576658 ACAGAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATATATATATATATATA
Found at i:44576795 original size:184 final size:184
Alignment explanation
Indices: 44576479--44576810 Score: 574
Period size: 184 Copynumber: 1.8 Consensus size: 184
44576469 TGGAGAAAGT
* * *
44576479 AATAAACATATCCACTTACCACTTTCAGAGCGAAGAAGTAACTCCAAGAATTTGATTGTGAGAGT
1 AATAAACATATCCACTTACCACTTTCAGAACGAAAAAGTAACTCCAAGAATTTGATTGTGAAAGT
*
44576544 AAATAATCCAAACAGTCTTTTAGCTCTGATTTGCTTCAACAACAACCTAAAAAAGATATGTTCAG
66 AAATAATCCAAACACTCTTTTAGCTCTGATTTGCTTCAACAACAACCTAAAAAAGATATGTTCAG
44576609 ATAAAAAAACATATATATATATATATATAATATATATATGTATATATAAACAGA
131 ATAAAAAAACATATATATATATATATATAATATATATATGTATATATAAACAGA
* * *
44576663 AATAAAGATATCCACTTACCACTTTCAGAATGAAAAAGTAACTCTAAGAATTTGATTGTGAAAGT
1 AATAAACATATCCACTTACCACTTTCAGAACGAAAAAGTAACTCCAAGAATTTGATTGTGAAAGT
*
44576728 AAATAATCCAAACACTCTTTTAGCTCTGATTTGCTTCAACAACAACCTAAAAACGATATGTTCAG
66 AAATAATCCAAACACTCTTTTAGCTCTGATTTGCTTCAACAACAACCTAAAAAAGATATGTTCAG
**
44576793 ATAAAAAAATGTATATAT
131 ATAAAAAAACATATATAT
44576811 TATGAGTTAA
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
184 138 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (184 bp):
AATAAACATATCCACTTACCACTTTCAGAACGAAAAAGTAACTCCAAGAATTTGATTGTGAAAGT
AAATAATCCAAACACTCTTTTAGCTCTGATTTGCTTCAACAACAACCTAAAAAAGATATGTTCAG
ATAAAAAAACATATATATATATATATATAATATATATATGTATATATAAACAGA
Found at i:44577441 original size:15 final size:15
Alignment explanation
Indices: 44577421--44577453 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
44577411 ATAACACATC
*
44577421 AAATTTTATATAAAT
1 AAATTTTAAATAAAT
44577436 AAATTTTAAATAAAT
1 AAATTTTAAATAAAT
44577451 AAA
1 AAA
44577454 ATTATGTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATTTTAAATAAAT
Found at i:44580679 original size:30 final size:30
Alignment explanation
Indices: 44580617--44580681 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
44580607 ACTTATTTTA
* * *
44580617 TTGTTAATTTTGTTATTGTTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAAAGGCAT
44580647 TTGTTAATTTTGTTACTATTTTAAAGAG-AT
1 TTGTTAATTTTGTTACTATTTTAAAG-GCAT
44580677 TTGTT
1 TTGTT
44580682 TGTTAAGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAAGGCAT
Found at i:44581492 original size:28 final size:27
Alignment explanation
Indices: 44581432--44581588 Score: 101
Period size: 28 Copynumber: 5.6 Consensus size: 27
44581422 GTCAAGATAA
44581432 TAAAAATTGAAAAAAAAATTAGGT-CTCC-
1 TAAAAATTGAAAAAAAAATT--GTAC-CCT
*
44581460 TAAAAGTTGAAAAAAAAATTGTACCCT
1 TAAAAATTGAAAAAAAAATTGTACCCT
** * *
44581487 TAAAAACTAAAAAAAAAAATTTGCAGCTCT
1 TAAAAA-TTGAAAAAAAAA-TTGTA-CCCT
* * *
44581517 TAAAAGTTAGTAAAAAAAA-TGTTAACCT
1 TAAAAATT-GAAAAAAAAATTG-TACCCT
44581545 ATAAAAATT-AAAAAAAAATTG-AGCCCAT
1 -TAAAAATTGAAAAAAAAATTGTA-CCC-T
44581573 TAAAAATT-AAAAAAAA
1 TAAAAATTGAAAAAAAA
44581589 TTAAACTCTT
Statistics
Matches: 102, Mismatches: 16, Indels: 23
0.72 0.11 0.16
Matches are distributed among these distances:
26 5 0.05
27 32 0.31
28 36 0.35
29 13 0.13
30 16 0.16
ACGTcount: A:0.58, C:0.10, G:0.08, T:0.24
Consensus pattern (27 bp):
TAAAAATTGAAAAAAAAATTGTACCCT
Found at i:44581563 original size:57 final size:55
Alignment explanation
Indices: 44581431--44581564 Score: 139
Period size: 57 Copynumber: 2.4 Consensus size: 55
44581421 AGTCAAGATA
*
44581431 ATAAAAATTGAAAAAAAAATTAGGTCTCCTAAAAGTTGAAAAAAAAATTGTACCCT
1 ATAAAAATT-AAAAAAAAATTAGGTCTCCTAAAAGTTGAAAAAAAAATTGTAACCT
* * * *
44581487 -TAAAAACTAAAAAAAAAAATTTGCAG-CTCTTAAAAGTTAGTAAAAAAAA-TGTTAACCT
1 ATAAAAA-T-TAAAAAAAAATTAG--GTCTCCTAAAAGTT-GAAAAAAAAATTG-TAACCT
44581545 ATAAAAATTAAAAAAAAATT
1 ATAAAAATTAAAAAAAAATT
44581565 GAGCCCATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
55 6 0.09
56 13 0.20
57 24 0.37
58 16 0.25
59 6 0.09
ACGTcount: A:0.57, C:0.09, G:0.08, T:0.25
Consensus pattern (55 bp):
ATAAAAATTAAAAAAAAATTAGGTCTCCTAAAAGTTGAAAAAAAAATTGTAACCT
Found at i:44581602 original size:27 final size:27
Alignment explanation
Indices: 44581528--44581594 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
44581518 AAAAGTTAGT
* *
44581528 AAAAAAAATGTTAACCTA-TAAAAATTA
1 AAAAAAAAT-TAAACCCATTAAAAATTA
* *
44581555 AAAAAAAATTGAGCCCATTAAAAATT-
1 AAAAAAAATTAAACCCATTAAAAATTA
44581581 AAAAAAAATTAAAC
1 AAAAAAAATTAAAC
44581595 TCTTTTAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 17 0.50
27 17 0.50
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.22
Consensus pattern (27 bp):
AAAAAAAATTAAACCCATTAAAAATTA
Found at i:44587624 original size:22 final size:22
Alignment explanation
Indices: 44587586--44587663 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
44587576 GAACGTTAGC
44587586 GTGCTTACTGTTCAGCACTGTGT
1 GTGCTT-CTGTTCAGCACTGTGT
* *
44587609 GTGCTTCTGATCAGCACTATGT
1 GTGCTTCTGTTCAGCACTGTGT
44587631 GTGCTTCTGTTCAGCACTGTGT
1 GTGCTTCTGTTCAGCACTGTGT
44587653 GTGCTTCTGTT
1 GTGCTTCTGTT
44587664 TCCCCAGCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 45 0.88
23 6 0.12
ACGTcount: A:0.12, C:0.22, G:0.26, T:0.41
Consensus pattern (22 bp):
GTGCTTCTGTTCAGCACTGTGT
Found at i:44588326 original size:23 final size:22
Alignment explanation
Indices: 44588291--44588357 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
44588281 AGTGCTGGGG
*
44588291 AATTAGTAAGCACACATAGTGC
1 AATTAGTAAGCACACACAGTGC
*
44588313 AATTCAGTAGGCACACACAGTGC
1 AATT-AGTAAGCACACACAGTGC
*
44588336 TGAA-CAG-AAGCACACACAGTGC
1 --AATTAGTAAGCACACACAGTGC
44588358 TGAACAGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 18 0.47
23 18 0.47
25 2 0.05
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (22 bp):
AATTAGTAAGCACACACAGTGC
Found at i:44588351 original size:22 final size:23
Alignment explanation
Indices: 44588295--44588369 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
44588285 CTGGGGAATT
*
44588295 AGTAAGCACACATAGTGC--AATTC
1 AGTAAGCACACACAGTGCTGAA--C
*
44588318 AGTAGGCACACACAGTGCTGAAC
1 AGTAAGCACACACAGTGCTGAAC
44588341 AG-AAGCACACACAGTGCTGAAC
1 AGTAAGCACACACAGTGCTGAAC
44588363 AGTAAGC
1 AGTAAGC
44588370 GCGCTAGCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
22 21 0.46
23 23 0.50
25 2 0.04
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.15
Consensus pattern (23 bp):
AGTAAGCACACACAGTGCTGAAC
Found at i:44592934 original size:23 final size:23
Alignment explanation
Indices: 44592904--44592980 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
44592894 ACGCTAGCGC
* *
44592904 GCTTACTGTTTCTCACTTCATGT
1 GCTTACTGTTTCGCACTTCGTGT
*
44592927 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
44592950 GCTTATTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
44592973 GCCTACTG
1 GCTTACTG
44592981 ATTTGCGCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.10, C:0.25, G:0.19, T:0.45
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:44593033 original size:23 final size:22
Alignment explanation
Indices: 44592924--44593047 Score: 97
Period size: 23 Copynumber: 5.5 Consensus size: 22
44592914 TCTCACTTCA
* * *
44592924 TGTGCTTACTGTTTCGCACTTTG
1 TGTGCCTACTGATT-GCACTGTG
* * *
44592947 TGTGCTTATTGTTTCGCACT-TCG
1 TGTGCCTACTGATT-GCACTGT-G
* *
44592970 TGTGCCTACTGATTTGCGCTATG
1 TGTGCCTACTGA-TTGCACTGTG
* *
44592993 TGCGCCAACTGATTGCACTGTG
1 TGTGCCTACTGATTGCACTGTG
44593015 TGTGCCTACTGGATTGCACTGTG
1 TGTGCCTACT-GATTGCACTGTG
*
44593038 TGTGCTTACT
1 TGTGCCTACT
44593048 ATTTCCCCAG
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
22 17 0.20
23 65 0.76
24 3 0.04
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (22 bp):
TGTGCCTACTGATTGCACTGTG
Found at i:44595458 original size:18 final size:19
Alignment explanation
Indices: 44595435--44595504 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 19
44595425 AAACACATAA
*
44595435 AAAATT-ATTAAAATCATT
1 AAAATTAATTAAAAACATT
* *
44595453 AAAATT-ATAAAAAAAATT
1 AAAATTAATTAAAAACATT
*
44595471 AAAATTCA-TAAAAACATTT
1 AAAATTAATTAAAAACA-TT
*
44595490 GAAATTAATTAAAAA
1 AAAATTAATTAAAAA
44595505 TAATCAGATT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 27 0.64
19 9 0.21
20 6 0.14
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAATTAATTAAAAACATT
Found at i:44595465 original size:28 final size:28
Alignment explanation
Indices: 44595431--44595484 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
44595421 TACAAAACAC
* *
44595431 ATAAAAAATTATTAAAA-TCATTAAAATT
1 ATAAAAAA-AATTAAAATTCATAAAAATT
44595459 ATAAAAAAAATTAAAATTCATAAAAA
1 ATAAAAAAAATTAAAATTCATAAAAA
44595485 CATTTGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (28 bp):
ATAAAAAAAATTAAAATTCATAAAAATT
Found at i:44595795 original size:19 final size:18
Alignment explanation
Indices: 44595754--44595797 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
44595744 ATATTTATAA
* *
44595754 ATTATTTTTTTCTAATTT
1 ATTATTTTTTTATAAATT
*
44595772 TTTATTTTTTTAATAAATT
1 ATTATTTTTTT-ATAAATT
44595791 ATTATTT
1 ATTATTT
44595798 ATAAATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTATTTTTTTATAAATT
Found at i:44595850 original size:9 final size:9
Alignment explanation
Indices: 44595822--44595864 Score: 59
Period size: 10 Copynumber: 4.4 Consensus size: 9
44595812 ATTTCTTGAT
44595822 TTTTAATTAA
1 TTTTAA-TAA
44595832 TTTCTAATAA
1 TTT-TAATAA
44595842 TTTTAATAA
1 TTTTAATAA
44595851 TTTTAATAAA
1 TTTTAAT-AA
44595861 TTTT
1 TTTT
44595865 TATGGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 13 0.42
10 15 0.48
11 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTTAATAA
Found at i:44595851 original size:19 final size:20
Alignment explanation
Indices: 44595822--44595864 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
44595812 ATTTCTTGAT
44595822 TTTTAATTAATTTCTAAT-AA
1 TTTTAATTAATTT-TAATAAA
44595842 TTTTAA-TAATTTTAATAAA
1 TTTTAATTAATTTTAATAAA
44595861 TTTT
1 TTTT
44595865 TATGGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.18
19 12 0.55
20 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTAATTAATTTTAATAAA
Found at i:44600887 original size:27 final size:27
Alignment explanation
Indices: 44600857--44600909 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
44600847 TTTATCTTAT
*
44600857 TTTATTTTTTCAAAATTAAACTAAATA
1 TTTATTTTTACAAAATTAAACTAAATA
44600884 TTTATTTTTACAAAATTAAACTAAAT
1 TTTATTTTTACAAAATTAAACTAAAT
44600910 TTATACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTATTTTTACAAAATTAAACTAAATA
Found at i:44600921 original size:27 final size:27
Alignment explanation
Indices: 44600867--44600921 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
44600857 TTTATTTTTT
* *
44600867 CAAAATTAAACTAAATATTTATTTTTA
1 CAAAATTAAACTAAATATTTACTATTA
44600894 CAAAATTAAACTAAAT-TTATACTATTA
1 CAAAATTAAACTAAATATT-TACTATTA
44600921 C
1 C
44600922 TTAAGCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (27 bp):
CAAAATTAAACTAAATATTTACTATTA
Found at i:44601888 original size:19 final size:20
Alignment explanation
Indices: 44601864--44601917 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
44601854 TTTAAAATAA
44601864 AAAATAAAATATTTTTAA-T
1 AAAATAAAATATTTTTAATT
**
44601883 AAAATAATTTA-TTTTAATT
1 AAAATAAAATATTTTTAATT
*
44601902 ATAA-AAAATATTTTTA
1 AAAATAAAATATTTTTA
44601918 TAATTTTACT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATAAAATATTTTTAATT
Found at i:44610074 original size:30 final size:31
Alignment explanation
Indices: 44610040--44610102 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
44610030 CATTTAACAC
44610040 AACAGTCACTCAAC-TT-T-GAAAATGTGACAA
1 AACAGTCACT-AACGTTATCGAAAA-GTGACAA
44610070 AACAGTCACTAACGTTATCGAAAAGTGACAA
1 AACAGTCACTAACGTTATCGAAAAGTGACAA
44610101 AA
1 AA
44610103 ATCAACTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 3 0.10
30 12 0.40
31 10 0.33
32 5 0.17
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (31 bp):
AACAGTCACTAACGTTATCGAAAAGTGACAA
Found at i:44610182 original size:13 final size:13
Alignment explanation
Indices: 44610164--44610189 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44610154 TCACTCAACT
44610164 TTGAAAATGTGGC
1 TTGAAAATGTGGC
44610177 TTGAAAATGTGGC
1 TTGAAAATGTGGC
44610190 AAAACAGTTA
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:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
TTGAAAATGTGGC
Found at i:44620336 original size:29 final size:32
Alignment explanation
Indices: 44620272--44620331 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
44620262 AATAAATGTT
* *
44620272 AATTCAATATGTTTCCTTTTTTTTATAGTAGA
1 AATTCAATATGTTTCCTTTTTTGTAAAGTAGA
44620304 AATTCAATATGTTT-C-TTTTTGTAGAAGT
1 AATTCAATATGTTTCCTTTTTTGTA-AAGT
44620332 GAATTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 4 0.16
32 14 0.56
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (32 bp):
AATTCAATATGTTTCCTTTTTTGTAAAGTAGA
Found at i:44626432 original size:22 final size:22
Alignment explanation
Indices: 44626399--44626447 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
44626389 GCCACGCCTA
*
44626399 CTGTTCAGCACTGTGTGTGCTT
1 CTGTTCAGCACTATGTGTGCTT
44626421 CTGTTCTA-CACTATGTGTGCTT
1 CTGTTC-AGCACTATGTGTGCTT
44626443 CTGTT
1 CTGTT
44626448 TCCCTAGCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (22 bp):
CTGTTCAGCACTATGTGTGCTT
Found at i:44630149 original size:13 final size:13
Alignment explanation
Indices: 44630131--44630155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44630121 AAAAACTTAC
44630131 AATTAATTAATTA
1 AATTAATTAATTA
44630144 AATTAATTAATT
1 AATTAATTAATT
44630156 TTATTTTCCA
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):
AATTAATTAATTA
Found at i:44631648 original size:15 final size:15
Alignment explanation
Indices: 44631628--44631661 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
44631618 TTGGTTTAGG
44631628 TTTCATCTTCCTCTT
1 TTTCATCTTCCTCTT
* *
44631643 TTTCATGTTCCTTTT
1 TTTCATCTTCCTCTT
44631658 TTTC
1 TTTC
44631662 TTGTCTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.26, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTCATCTTCCTCTT
Found at i:44634243 original size:25 final size:24
Alignment explanation
Indices: 44634194--44634244 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
44634184 GTTATGTATT
*
44634194 ATTTTTTTAATTTTATATATTATA
1 ATTTTTTTAATTTCATATATTATA
*
44634218 ATTTTTATTAA-TTCATATTTTAATA
1 ATTTTT-TTAATTTCATATATT-ATA
44634243 AT
1 AT
44634245 AATTATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTTTTTTAATTTCATATATTATA
Found at i:44634307 original size:58 final size:59
Alignment explanation
Indices: 44634206--44634372 Score: 205
Period size: 58 Copynumber: 2.8 Consensus size: 59
44634196 TTTTTTAATT
* * * *
44634206 TTATATATTATAATTTTTATTAATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAA
1 TTATATATTATTATTATTA--AATT-ATA-TTTAATAATAATTATATTAAAAATATAATTAAA
* *
44634269 TTATATATTATT-TTATTAAATTGTATTTAATAATAATTATGTT-AAAATATAATTAAA
1 TTATATATTATTATTATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAAA
*
44634326 TTATTTATTATTATTATTAAATTATATTTAATAATAATCT-TATTAAA
1 TTATATATTATTATTATTAAATTATATTTAATAATAAT-TATATTAAA
44634373 TTTTAATAAC
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
57 23 0.25
58 44 0.48
59 5 0.05
60 4 0.04
62 5 0.05
63 11 0.12
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (59 bp):
TTATATATTATTATTATTAAATTATATTTAATAATAATTATATTAAAAATATAATTAAA
Found at i:44636479 original size:30 final size:30
Alignment explanation
Indices: 44636443--44636502 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
44636433 AAAAGATAGT
44636443 TTTTGAATGGTGGAAAATTTGAGTTTATCA
1 TTTTGAATGGTGGAAAATTTGAGTTTATCA
44636473 TTTTGAATGGTGGAAAATTTGAGTTTATCA
1 TTTTGAATGGTGGAAAATTTGAGTTTATCA
44636503 AAGAAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.43
Consensus pattern (30 bp):
TTTTGAATGGTGGAAAATTTGAGTTTATCA
Found at i:44640295 original size:15 final size:15
Alignment explanation
Indices: 44640275--44640304 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44640265 TATATACGAG
*
44640275 TTAGCTTCTTTGCAT
1 TTAGCTTATTTGCAT
44640290 TTAGCTTATTTGCAT
1 TTAGCTTATTTGCAT
44640305 GCTTAGTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (15 bp):
TTAGCTTATTTGCAT
Found at i:44641147 original size:59 final size:58
Alignment explanation
Indices: 44641026--44641554 Score: 390
Period size: 58 Copynumber: 8.9 Consensus size: 58
44641016 CGACACAACT
* * * * * *
44641026 TTTTTTATCT-ACAAAAAAATTAATTTTTTTGTGTTGGTCATTGCATGGCCCAACATCTCC
1 TTTTTTATCTGA-TAAAAAATTAATTTTTTTGTGTTGGCCATTGCTTGG-TCGACA-CCCC
* * * * *
44641086 TTTTTTATTTGATAAAAAATCAATTTTTTTTATATTGACCATTGCTTGG-CTGACACCCC
1 TTTTTTATCTGATAAAAAATTAA-TTTTTTTGTGTTGGCCATTGCTTGGTC-GACACCCC
* * * * * * *
44641145 -TTTTTGTCAGATAAAAAA-TATTTTTTTTTGGTGTTAGCCA-TGCTTTGGCCGACATCGCT
1 TTTTTTATCTGATAAAAAATTA-ATTTTTTT-GTGTTGGCCATTGC-TTGGTCGACA-CCCC
* * *
44641204 TTTTTTATCTGGA-AAAAAATTAA-TTTTTT-TGTTGGTCATTGCATAGTCGACA-CCC
1 TTTTTTATCT-GATAAAAAATTAATTTTTTTGTGTTGGCCATTGCTTGGTCGACACCCC
* * *
44641259 TCTTTTTATCTGGTAAAAAATTAATTTTTTTGTGTTGGCCATTGCATGGTCGACACTCTC
1 T-TTTTTATCTGATAAAAAATTAATTTTTTTGTGTTGGCCATTGCTTGGTCGACAC-CCC
* * *
44641319 TTTTTTATCT-AGTAAAAAATCAATTTTTTTGTGTTGGCCATT-ATATGGTCGACACCCT
1 TTTTTTATCTGA-TAAAAAATTAATTTTTTTGTGTTGGCCATTGCT-TGGTCGACACCCC
* *
44641377 TTTTTTATCTGATAAAAAATTTAATTTTTTTTTCGTATTGGCCA-TGCATTGGCCGACACCAACA
1 TTTTTTATCTGATAAAAAA-TTAA--TTTTTTT-GTGTTGGCCATTGC-TTGGTCGACACC--C-
*
44641441 T
58 C
* * *
44641442 TTTTTTATCAGAT--AACATT--TTTTTATGGTGTTGGCCATTGCTTGGTCGACACCACC
1 TTTTTTATCTGATAAAAAATTAATTTTT-TTGTGTTGGCCATTGCTTGGTCGACACC-CC
*
44641498 TTTTTTATCTGATAAAAAATTTAATTTTTTTTGTGTTGGCCA-TGCACTGGTCGACAC
1 TTTTTTATCTGATAAAAAA-TTAA-TTTTTTTGTGTTGGCCATTGC-TTGGTCGACAC
44641555 TAACTTTCCA
Statistics
Matches: 375, Mismatches: 55, Indels: 77
0.74 0.11 0.15
Matches are distributed among these distances:
55 3 0.01
56 31 0.08
57 33 0.09
58 99 0.26
59 71 0.19
60 40 0.11
61 54 0.14
62 26 0.07
63 4 0.01
64 1 0.00
65 13 0.03
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (58 bp):
TTTTTTATCTGATAAAAAATTAATTTTTTTGTGTTGGCCATTGCTTGGTCGACACCCC
Found at i:44641382 original size:117 final size:117
Alignment explanation
Indices: 44640988--44641555 Score: 452
Period size: 120 Copynumber: 4.8 Consensus size: 117
44640978 TTTTTGATGT
** * *
44640988 TTTTTTTGTGTATTGGCCA-TGCCTTGACCGACACAACTTTTTTTATCT-ACAAAAAAATTAATT
1 TTTTTTTGTG--TTGGCCATTG-CTTGGTCGACAC-CCTTTTTTTATCTGA-TAAAAAATTAATT
* * * *
44641051 TTTTTGTGTTGGTCATTGCATGGCCCA-ACATCTCCTTTTTTAT-TTGATAAAAAATCAA
61 TTTTTGTGTTGGCCA-TGCATGGCCGACAC-TCTCTTTTTTTATCTAG-TAAAAAATCAA
* * * * * * *
44641109 TTTTTTTTATATTGACCATTGCTTGG-CTGACACCC-CTTTTTGTCAGATAAAAAA-TATTTTTT
1 -TTTTTTTGTGTTGGCCATTGCTTGGTC-GACACCCTTTTTTTATCTGATAAAAAATTA-ATTTT
* * * * * *
44641171 TTTGGTGTTAGCCATGCTTTGGCCGACA-TCGCTTTTTTTATCTGGAAAAAAATTAA
63 TTT-GTGTTGGCCATGC-ATGGCCGACACTCTCTTTTTTTATCTAGTAAAAAATCAA
* * * * *
44641227 -TTTTTT-TGTTGGTCATTGCATAGTCGACACCCTCTTTTTATCTGGTAAAAAATTAATTTTTTT
1 TTTTTTTGTGTTGGCCATTGCTTGGTCGACACCCTTTTTTTATCTGATAAAAAATTAATTTTTTT
*
44641290 GTGTTGGCCATTGCATGGTCGACACTCTC-TTTTTTATCTAGTAAAAAATCAA
66 GTGTTGGCCA-TGCATGGCCGACACTCTCTTTTTTTATCTAGTAAAAAATCAA
*
44641342 TTTTTTTGTGTTGGCCATT-ATATGGTCGACACCCTTTTTTTATCTGATAAAAAATTTAATTTTT
1 TTTTTTTGTGTTGGCCATTGCT-TGGTCGACACCCTTTTTTTATCTGATAAAAAA-TTAA--TTT
* * * *
44641406 TTTTCGTATTGGCCATGCATTGGCCGACAC-CAACATTTTTTTATC-AG---ATAA-CAT
62 TTTT-GTGTTGGCCATGCA-TGGCCGACACTC-TC-TTTTTTTATCTAGTAAAAAATCAA
*
44641460 TTTTTTATGGTGTTGGCCATTGCTTGGTCGACACCACCTTTTTTATCTGATAAAAAATTTAATTT
1 TTTTTT-T-GTGTTGGCCATTGCTTGGTCGACACC-CTTTTTTTATCTGATAAAAAA-TTAA-TT
*
44641525 TTTTTGTGTTGGCCATGCACTGGTCGACACT
61 TTTTTGTGTTGGCCATGCA-TGGCCGACACT
44641556 AACTTTCCAT
Statistics
Matches: 366, Mismatches: 51, Indels: 60
0.77 0.11 0.13
Matches are distributed among these distances:
115 56 0.15
116 42 0.11
117 43 0.12
118 55 0.15
119 45 0.12
120 59 0.16
121 47 0.13
122 10 0.03
123 9 0.02
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (117 bp):
TTTTTTTGTGTTGGCCATTGCTTGGTCGACACCCTTTTTTTATCTGATAAAAAATTAATTTTTTT
GTGTTGGCCATGCATGGCCGACACTCTCTTTTTTTATCTAGTAAAAAATCAA
Found at i:44643479 original size:25 final size:23
Alignment explanation
Indices: 44643421--44643471 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
44643411 ATTCATTTGT
*
44643421 AAAAA-AAG-TTTCGAAAATGTA
1 AAAAATAAGATTTCAAAAATGTA
*
44643442 AAAAATAATATTTCAAAAATGTA
1 AAAAATAAGATTTCAAAAATGTA
44643465 AAAAATA
1 AAAAATA
44643472 TAAGATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 5 0.19
22 2 0.08
23 19 0.73
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.25
Consensus pattern (23 bp):
AAAAATAAGATTTCAAAAATGTA
Found at i:44643619 original size:51 final size:52
Alignment explanation
Indices: 44643545--44643681 Score: 143
Period size: 54 Copynumber: 2.6 Consensus size: 52
44643535 AAAAATATAT
* * *
44643545 TAAAAAATTTATTTTGAAGATATAAAAAT-TTAT-TTAACAAAAATTTGAAAAGC
1 TAAAAAA--TATTTCGAAAATATAAAAATATTATCTTAA-AAAAATTTGAAAAGA
* * **
44643598 TAATAAATATTTCGAAAATATAAAAAAATATTATCTTTAAAAAATTTGAAACTA
1 TAAAAAATATTTCGAAAATAT--AAAAATATTATCTTAAAAAAATTTGAAAAGA
*
44643652 TAAAAAATATTTCGAAAATAGAAAAATATT
1 TAAAAAATATTTCGAAAATATAAAAATATT
44643682 GTAAAAAATT
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
51 12 0.17
52 9 0.13
53 12 0.17
54 35 0.49
55 3 0.04
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (52 bp):
TAAAAAATATTTCGAAAATATAAAAATATTATCTTAAAAAAATTTGAAAAGA
Found at i:44643676 original size:20 final size:18
Alignment explanation
Indices: 44643636--44643681 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
44643626 TATTATCTTT
44643636 AAAAA-ATTTGAAACTATA-
1 AAAAATATTTGAAA--ATAG
44643654 AAAAATATTTCGAAAATAG
1 AAAAATATTT-GAAAATAG
44643673 AAAAATATT
1 AAAAATATT
44643682 GTAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.32
19 13 0.52
20 4 0.16
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (18 bp):
AAAAATATTTGAAAATAG
Found at i:44643842 original size:18 final size:17
Alignment explanation
Indices: 44643793--44643842 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
44643783 GACCATCTGA
*
44643793 AAAATTAAAAAATAATT
1 AAAATTAAAAAATAAAT
* *
44643810 AGAATAAAAATAATAAAT
1 AAAATTAAAA-AATAAAT
44643828 AAAATTTAAAAAATA
1 AAAA-TTAAAAAATA
44643843 TAAAATCGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 8 0.31
18 13 0.50
19 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAATTAAAAAATAAAT
Found at i:44644998 original size:94 final size:93
Alignment explanation
Indices: 44644894--44645431 Score: 806
Period size: 94 Copynumber: 5.8 Consensus size: 93
44644884 ATAATTTTTT
* *
44644894 ATTTAGATATTAAAATTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
1 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
*
44644959 AAAATAATAATAGTTTTTTTATTTAATAA
66 AATATAATAATAG-TTTTTTATTTAATAA
* * *
44644988 ATTTAAATATTAAAATTTGATAAATAATGTATTATCAAATCAACACATTATTTTATAAAAATTGT
1 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
44645053 AATATAATAATAGTTTTTTATTTAAATAA
66 AATATAATAATAGTTTTTTATTT-AATAA
* * *
44645082 ATTTAAATATTAAAATTTGGTAAATAATTTATTGTCAAATCAACACAATATTTGATAAAAATTAT
1 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
*
44645147 AATATAATAATA----ATT-TTT--T--
66 AATATAATAATAGTTTTTTATTTAATAA
*
44645166 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACAAATTATTTGATAAAAATTAT
1 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
44645231 AATATAATAATAGTTTTTTATTTAAATAA
66 AATATAATAATAGTTTTTTATTT-AATAA
*
44645260 ATTTAAATATTAAAATTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
1 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
* *
44645325 AATATAATAATAGTCTTTTTATTCAAAAAA
66 AATATAATAATAGT-TTTTTATT-TAATAA
* * * *
44645355 ATTTAAATATTAAAATTTAATAAATAATGTATTGTCAAATCAATATATTATTTGATAAAAATTAA
1 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
44645420 AATATAATAATA
66 AATATAATAATA
44645432 ATAATTTTTT
Statistics
Matches: 404, Mismatches: 27, Indels: 25
0.89 0.06 0.05
Matches are distributed among these distances:
84 73 0.18
86 1 0.00
88 2 0.00
89 6 0.01
90 2 0.00
92 1 0.00
93 10 0.02
94 225 0.56
95 84 0.21
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (93 bp):
ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
AATATAATAATAGTTTTTTATTTAATAA
Found at i:44645174 original size:178 final size:181
Alignment explanation
Indices: 44644894--44645459 Score: 780
Period size: 178 Copynumber: 3.0 Consensus size: 181
44644884 ATAATTTTTT
* *
44644894 ATTTAGATATTAAAATTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
1 ATTTAAATATTAAAATTTGGTAAATAATGTATTGTCAAATCAACACAATATTTGATAAAAATTAT
* ** *
44644959 AAAATAATAATAGTTTTTTTATTTAATAAATTTAAATATTAAAATTTGATAAATAATGTATTATC
66 AATATAATAATA--CATTTTA--T--T-AATTTAAATATTAAAATTTGATAAATAATGTATTGTC
* * *
44645024 AAATCAACACATTATTTTATAAAAATTGTAATATAATAATAGTTTTTTATTTAAATAA
124 AAATCAACAAATTATTTGATAAAAATTATAATATAATAATAGTTTTTTATTTAAATAA
*
44645082 ATTTAAATATTAAAATTTGGTAAATAATTTATTGTCAAATCAACACAATATTTGATAAAAATTAT
1 ATTTAAATATTAAAATTTGGTAAATAATGTATTGTCAAATCAACACAATATTTGATAAAAATTAT
44645147 AATATAATAATA-ATTTT-TT-ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAA
66 AATATAATAATACATTTTATTAATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAA
44645209 CAAATTATTTGATAAAAATTATAATATAATAATAGTTTTTTATTTAAATAA
131 CAAATTATTTGATAAAAATTATAATATAATAATAGTTTTTTATTTAAATAA
*
44645260 ATTTAAATATTAAAATTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
1 ATTTAAATATTAAAATTTGGTAAATAATGTATTGTCAAATCAACACAATATTTGATAAAAATTAT
* *
44645325 AATATAATAATAGTCTTTTTATTCAAAAAAATTTAAATATTAAAATTTAATAAATAATGTATTGT
66 AATATAATAATA--CATTTTATT------AATTTAAATATTAAAATTTGATAAATAATGTATTGT
* * * *
44645390 CAAATCAATATATTATTTGATAAAAATTAAAATATAATAATAATAATTTTTTATTTAAAT-A
123 CAAATCAACAAATTATTTGATAAAAATT-ATA-AT-ATAATAATAGTTTTTTATTTAAATAA
44645451 ATGTTAAAT
1 AT-TTAAAT
44645460 TAATTTTAAA
Statistics
Matches: 346, Mismatches: 17, Indels: 26
0.89 0.04 0.07
Matches are distributed among these distances:
178 165 0.48
180 1 0.00
181 4 0.01
182 3 0.01
185 4 0.01
188 73 0.21
189 60 0.17
190 2 0.01
191 5 0.01
192 29 0.08
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (181 bp):
ATTTAAATATTAAAATTTGGTAAATAATGTATTGTCAAATCAACACAATATTTGATAAAAATTAT
AATATAATAATACATTTTATTAATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAA
CAAATTATTTGATAAAAATTATAATATAATAATAGTTTTTTATTTAAATAA
Found at i:44645405 original size:95 final size:94
Alignment explanation
Indices: 44645166--44645431 Score: 451
Period size: 95 Copynumber: 2.8 Consensus size: 94
44645156 ATAATTTTTT
44645166 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACAAATTATTTGATAAAAATTAT
1 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACAAATTATTTGATAAAAATTAT
* *
44645231 AATATAATAATAGTTTTTTATTTAAATAA
66 AATATAATAATAGTTTTTTATTCAAAAAA
* *
44645260 ATTTAAATATTAAAATTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTAT
1 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACAAATTATTTGATAAAAATTAT
44645325 AATATAATAATAGTCTTTTTATTCAAAAAA
66 AATATAATAATAGT-TTTTTATTCAAAAAA
* * * *
44645355 ATTTAAATATTAAAATTTAATAAATAATGTATTGTCAAATCAATATATTATTTGATAAAAATTAA
1 ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACAAATTATTTGATAAAAATTAT
44645420 AATATAATAATA
66 AATATAATAATA
44645432 ATAATTTTTT
Statistics
Matches: 162, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
94 77 0.48
95 85 0.52
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (94 bp):
ATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACAAATTATTTGATAAAAATTAT
AATATAATAATAGTTTTTTATTCAAAAAA
Found at i:44645420 original size:52 final size:49
Alignment explanation
Indices: 44645282--44645433 Score: 136
Period size: 52 Copynumber: 3.1 Consensus size: 49
44645272 AAATTTGGTA
*
44645282 AATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTATAATATAAT
1 AATAATGTATTGTCAAATCAA-A-ATTATTTGATAAAAATTAAAATATAAT
* ** * * * * *
44645333 AAT-A-GTCTT-TTTATTCAAAA-AAATT--TAAATATTAAAATTTAAT
1 AATAATGTATTGTCAAATCAAAATTATTTGATAAAAATTAAAATATAAT
44645376 AAATAATGTATTGTCAAATCAATATATTATTTGATAAAAATTAAAATATAAT
1 -AATAATGTATTGTCAAATCAA-A-ATTATTTGATAAAAATTAAAATATAAT
44645428 AATAAT
1 AATAAT
44645434 AATTTTTTAT
Statistics
Matches: 75, Mismatches: 17, Indels: 18
0.68 0.15 0.16
Matches are distributed among these distances:
43 15 0.20
44 3 0.04
45 4 0.05
46 5 0.07
47 7 0.09
48 7 0.09
49 5 0.07
50 4 0.05
51 9 0.12
52 16 0.21
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (49 bp):
AATAATGTATTGTCAAATCAAAATTATTTGATAAAAATTAAAATATAAT
Found at i:44645477 original size:12 final size:11
Alignment explanation
Indices: 44645443--44645480 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
44645433 TAATTTTTTA
44645443 TTTAAA-TAAT
1 TTTAAATTAAT
*
44645453 GTTAAATTAAT
1 TTTAAATTAAT
44645464 TTTAAATGTAAT
1 TTTAAAT-TAAT
44645476 TTTAA
1 TTTAA
44645481 TTTCAACTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 5 0.21
11 10 0.42
12 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (11 bp):
TTTAAATTAAT
Found at i:44645608 original size:17 final size:16
Alignment explanation
Indices: 44645572--44645611 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
44645562 ACATTAATTT
* *
44645572 TTAAATTAATTTCAAC
1 TTAATTTAATTTCAAA
44645588 TTAATTTAATATTCAAA
1 TTAATTTAAT-TTCAAA
44645605 TTAATTT
1 TTAATTT
44645612 TTATACAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATTTAATTTCAAA
Found at i:44648803 original size:29 final size:31
Alignment explanation
Indices: 44648748--44648806 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
44648738 CAGATAAAAT
* *
44648748 AAATTATAAATAATTGTTAATATTAATACACG
1 AAATTATAAAT-ATTGTGAATAATAATACACG
44648780 AAATTATAAAT-TT-TGAATAATAATACA
1 AAATTATAAATATTGTGAATAATAATACA
44648807 AAATAACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 2 0.08
32 11 0.44
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (31 bp):
AAATTATAAATATTGTGAATAATAATACACG
Found at i:44649511 original size:61 final size:58
Alignment explanation
Indices: 44649428--44649664 Score: 246
Period size: 59 Copynumber: 4.0 Consensus size: 58
44649418 TGAAAAATTG
* *
44649428 GTGTCGGCCAGTGC-ATGGCCAACACCAAAAAATTGATTTTTTACCAAATAAAAAAAAGGGA
1 GTGTTGGCCA-TGCAATGGCCAACACAAAAAAATTGATTTTTTACCAAAT--AAAAAA-GGA
* *
44649489 GTGTTGGCCAT-TACATGGCCAACACAAAAAAAAATTGATTTTTTACCAGATAAAAAAGGA
1 GTGTTGGCCATGCA-ATGGCCAACAC--AAAAAAATTGATTTTTTACCAAATAAAAAAGGA
* ** ** * * *
44649549 GATGCTGATCATGCAATGATCAACACCAAAAAATTGATTTTTTACCAGATAAGAAAGGA
1 G-TGTTGGCCATGCAATGGCCAACACAAAAAAATTGATTTTTTACCAAATAAAAAAGGA
* *
44649608 GGTGTCGGCCATGCAATGGCCAACACAAAAAAATTGATTTTTT-CCTAATAAAAAAGG
1 -GTGTTGGCCATGCAATGGCCAACACAAAAAAATTGATTTTTTACCAAATAAAAAAGG
44649665 TGGTGTCGAT
Statistics
Matches: 147, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
58 11 0.07
59 65 0.44
60 6 0.04
61 42 0.29
62 1 0.01
63 22 0.15
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (58 bp):
GTGTTGGCCATGCAATGGCCAACACAAAAAAATTGATTTTTTACCAAATAAAAAAGGA
Found at i:44649582 original size:122 final size:117
Alignment explanation
Indices: 44649447--44649664 Score: 307
Period size: 122 Copynumber: 1.8 Consensus size: 117
44649437 AGTGCATGGC
*
44649447 CAACACCAAAAAATTGATTTTTTACCAAATAAAAAAAAGG-GAGTGTTGGCCATTAC-ATGGCCA
1 CAACACCAAAAAATTGATTTTTTACCAAAT--AAAAAAGGAG-GTGTCGGCCA-TACAATGGCCA
44649510 ACACAAAAAAAAATTGATTTTTTACC-AGATAAAAAAGGAGATGCTGATCATGCAATGAT
62 ACAC--AAAAAAATTGATTTTTT-CCTA-ATAAAAAAGGAGATGCTGATCATGCAATGAT
* * *
44649569 CAACACCAAAAAATTGATTTTTTACCAGATAAGAAAGGAGGTGTCGGCCATGCAATGGCCAACAC
1 CAACACCAAAAAATTGATTTTTTACCAAATAAAAAAGGAGGTGTCGGCCATACAATGGCCAACAC
44649634 AAAAAAATTGATTTTTTCCTAATAAAAAAGG
66 AAAAAAATTGATTTTTTCCTAATAAAAAAGG
44649665 TGGTGTCGAT
Statistics
Matches: 89, Mismatches: 4, Indels: 11
0.86 0.04 0.11
Matches are distributed among these distances:
117 12 0.13
118 18 0.20
119 2 0.02
120 27 0.30
121 1 0.01
122 29 0.33
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (117 bp):
CAACACCAAAAAATTGATTTTTTACCAAATAAAAAAGGAGGTGTCGGCCATACAATGGCCAACAC
AAAAAAATTGATTTTTTCCTAATAAAAAAGGAGATGCTGATCATGCAATGAT
Found at i:44649685 original size:58 final size:59
Alignment explanation
Indices: 44649439--44649691 Score: 225
Period size: 59 Copynumber: 4.2 Consensus size: 59
44649429 TGTCGGCCAG
* * * *
44649439 TGCATGGCCAACACCAAAAAATTGATTTTTTACCAAATAAAAAAAAGGGAGTGTTGGCCATT-A
1 TGCATGGCCAACACAAAAAAATTGATTTTTTACCAGAT--AAAAAA-GGAG-G-TGTCGATTCA
*
44649502 --CATGGCCAACACAAAAAAAAATTGATTTTTTACCAGATAAAAAAGGAGATG-CTGA-TCA
1 TGCATGGCCAACAC--AAAAAAATTGATTTTTTACCAGATAAAAAAGGAGGTGTC-GATTCA
** * * **
44649560 TGCAATGATCAACACCAAAAAATTGATTTTTTACCAGATAAGAAAGGAGGTGTCG-GCCA
1 TGC-ATGGCCAACACAAAAAAATTGATTTTTTACCAGATAAAAAAGGAGGTGTCGATTCA
* *
44649619 TGCAATGGCCAACACAAAAAAATTGATTTTTT-CCTA-ATAAAAAAGGTGGTGTCGATTAA
1 TGC-ATGGCCAACACAAAAAAATTGATTTTTTACC-AGATAAAAAAGGAGGTGTCGATTCA
*
44649678 GGCATGGCCAACAC
1 TGCATGGCCAACAC
44649692 CAAATTTTTT
Statistics
Matches: 160, Mismatches: 19, Indels: 27
0.78 0.09 0.13
Matches are distributed among these distances:
57 2 0.01
58 33 0.21
59 70 0.44
60 6 0.04
61 27 0.17
63 22 0.14
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (59 bp):
TGCATGGCCAACACAAAAAAATTGATTTTTTACCAGATAAAAAAGGAGGTGTCGATTCA
Found at i:44649826 original size:93 final size:94
Alignment explanation
Indices: 44649698--44649868 Score: 222
Period size: 93 Copynumber: 1.8 Consensus size: 94
44649688 ACACCAAATT
* ** * * *
44649698 TTTTTTTATTTGACAAAAAGGGGTGTCAATTATGCAAGGGTTAATACCAAAAAAAA-TGA-TTTT
1 TTTTTTTATATGACAAAAAGGGGTGTCAACCATGCAAGGGTCAACA-CAAAAAAAATTAATTTTT
44649761 TT-CAGATAAAAAAAGATCTAACATCAAAA
65 TTCCAGATAAAAAAAGATCTAACATCAAAA
** *
44649790 TTTTTTTATATGACAAAAAAGGGGTGTCGGCCATGCAATGGTCAACACAAAAAAAATTAATTTTT
1 TTTTTTTATATGAC-AAAAAGGGGTGTCAACCATGCAAGGGTCAACACAAAAAAAATTAATTTTT
44649855 TTCCAGATAAAAAA
65 TTCCAGATAAAAAA
44649869 GGTGGTGTCG
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
92 22 0.33
93 27 0.41
94 6 0.09
95 11 0.17
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (94 bp):
TTTTTTTATATGACAAAAAGGGGTGTCAACCATGCAAGGGTCAACACAAAAAAAATTAATTTTTT
TCCAGATAAAAAAAGATCTAACATCAAAA
Found at i:44649903 original size:60 final size:57
Alignment explanation
Indices: 44649804--44649935 Score: 142
Period size: 60 Copynumber: 2.3 Consensus size: 57
44649794 TTTATATGAC
* *
44649804 AAAAAAGGGGTGTCGGCCATGCAATGGTCAACACAAAAAAAATTAATTTTTTTCCAGAT
1 AAAAAAGGGGTGTCGGCCAGGCAATGATCAACACAAAAAAAA-T-ATTTTTTTCCAGAT
* * * *
44649863 AAAAAAGGTGGTGTCGGCCAAGGC-ATGATCTACACCAAAAAAATATTTTTTAT-CTGAC
1 AAAAAAGG-GGTGTCGGCC-AGGCAATGATCAACACAAAAAAAATATTTTTT-TCCAGAT
*
44649921 AAAAAGGGGGTGTCG
1 AAAAAAGGGGTGTCG
44649936 ATCATGCAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
57 7 0.11
58 17 0.27
59 10 0.16
60 26 0.41
61 3 0.05
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (57 bp):
AAAAAAGGGGTGTCGGCCAGGCAATGATCAACACAAAAAAAATATTTTTTTCCAGAT
Found at i:44650533 original size:21 final size:22
Alignment explanation
Indices: 44650492--44650533 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
44650482 AAAAATTCAA
*
44650492 GTTTAATTGAATAACTCAATTC
1 GTTTAATTCAATAACTCAATTC
*
44650514 GTTTAATTCAA-AATTCAATT
1 GTTTAATTCAATAACTCAATT
44650534 TTTTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
GTTTAATTCAATAACTCAATTC
Found at i:44652124 original size:133 final size:135
Alignment explanation
Indices: 44651885--44652272 Score: 354
Period size: 141 Copynumber: 2.8 Consensus size: 135
44651875 CAACATATTT
* * * * **
44651885 ATTAATTAAAAATTAAAAAAAAAACTTGAAACAACATG-AATAAAAATTACAAATGTATTTA-GA
1 ATTAATTAAAAA-T-AATAAAAAGCTTAAAACAACATGAAATAAAAAATACAAATGTAAGTAGGA
** * * *
44651948 AGAGGAGGAATTGAACCTGGGACTCAAGAATAAAATCATTATTATTTAACCA-T-GAGAGTTGAT
64 A-A--A-GAATCAAACCCGGGACTCAAGAATAAAATCATTATTATTTAACCATTAGAGAGCTAAT
*
44652011 ATATTAAAAAT
125 ATATTAAAAAC
* * * * *
44652022 ATTAATTAAAAATAATAAAAAGCTTAAAATAACATGAAATAAAAAATATAAATGTGAGTGGGAGA
1 ATTAATTAAAAATAATAAAAAGCTTAAAACAACATGAAATAAAAAATACAAATGTAAGTAGGAAA
* * *
44652087 AGCATCAAACTCGGGACTCAATG-ATATAATCATTATTATTTAACCATTTAACCAAGAGAGCTAA
66 AGAATCAAACCCGGGACTCAA-GAATAAAATCATTATTATTTAACCA-TT-----AGAGAGCTAA
* *
44652151 TATGTTAAAAGC
124 TATATTAAAAAC
* *
44652163 ATTAATTAAAAATAATAAACAGCTTAAAACAACATGAAATAAATAATACAAATGTAAGTAGGAAA
1 ATTAATTAAAAATAATAAAAAGCTTAAAACAACATGAAATAAAAAATACAAATGTAAGTAGGAAA
* * * **
44652228 ATAATCAAACCCGGGACTCAAAGAACAAAACCATTAAAATTTAAC
66 AGAATCAAACCCGGGACTC-AAGAATAAAATCATTATTATTTAAC
44652273 TATCTAACTA
Statistics
Matches: 201, Mismatches: 37, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
133 37 0.18
134 2 0.01
135 20 0.10
136 19 0.09
137 14 0.07
141 91 0.45
142 18 0.09
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.26
Consensus pattern (135 bp):
ATTAATTAAAAATAATAAAAAGCTTAAAACAACATGAAATAAAAAATACAAATGTAAGTAGGAAA
AGAATCAAACCCGGGACTCAAGAATAAAATCATTATTATTTAACCATTAGAGAGCTAATATATTA
AAAAC
Found at i:44652159 original size:141 final size:141
Alignment explanation
Indices: 44651991--44652248 Score: 372
Period size: 141 Copynumber: 1.8 Consensus size: 141
44651981 AATCATTATT
* * * * *
44651991 ATTTAACCATGAGAGTTGATATATTAAAAATATTAATTAAAAATAATAAAAAGCTTAAAATAACA
1 ATTTAACCAAGAGAGCTAATATATTAAAAACATTAATTAAAAATAATAAAAAGCTTAAAACAACA
* * * * * *
44652056 TGAAATAAAAAATATAAATGTGAGTGGGAGAAGCATCAAACTCGGGACTCAATGATATAATCATT
66 TGAAATAAAAAATACAAATGTAAGTAGGAAAAGAATCAAACCCGGGACTCAATGATATAATCATT
44652121 ATTATTTAACC
131 ATTATTTAACC
* * *
44652132 ATTTAACCAAGAGAGCTAATATGTTAAAAGCATTAATTAAAAATAATAAACAGCTTAAAACAACA
1 ATTTAACCAAGAGAGCTAATATATTAAAAACATTAATTAAAAATAATAAAAAGCTTAAAACAACA
* *
44652197 TGAAATAAATAATACAAATGTAAGTAGGAAAATAATCAAACCCGGGACTCAA
66 TGAAATAAAAAATACAAATGTAAGTAGGAAAAGAATCAAACCCGGGACTCAA
44652249 AGAACAAAAC
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
141 101 1.00
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (141 bp):
ATTTAACCAAGAGAGCTAATATATTAAAAACATTAATTAAAAATAATAAAAAGCTTAAAACAACA
TGAAATAAAAAATACAAATGTAAGTAGGAAAAGAATCAAACCCGGGACTCAATGATATAATCATT
ATTATTTAACC
Found at i:44652315 original size:141 final size:140
Alignment explanation
Indices: 44652009--44652319 Score: 306
Period size: 141 Copynumber: 2.2 Consensus size: 140
44651999 ATGAGAGTTG
* * *
44652009 ATATATTAAAA-ATATTAATTAAAAATAATAAAAAGCTTAAAATAACATGAAATAAAAAATATAA
1 ATATATTAAAACATA--AATAAAAAATAATAAAAAGCTTAAAACAACATGAAATAAAAAATACAA
* * * * * * * * * ** *
44652073 ATGTGAGTGGGAGAAGCATCAAACTCGGGACTCAATGATATAATCATTATTATTTAACCATTTAA
64 ATGTAAGTAGGAAAAGAATCAAACCCGGGACTCAAAGACAAAACCATTAAAATTTAACCATCTAA
* * *
44652138 CCAAGAGAGCTA
129 CCAAAAAAACTA
* * * * *
44652150 ATATGTTAAAAGCATTAATTAAAAATAATAAACAGCTTAAAACAACATGAAATAAATAATACAAA
1 ATATATTAAAA-CATAAATAAAAAATAATAAAAAGCTTAAAACAACATGAAATAAAAAATACAAA
* *
44652215 TGTAAGTAGGAAAATAATCAAACCCGGGACTCAAAGAACAAAACCATTAAAATTTAACTATCTAA
65 TGTAAGTAGGAAAAGAATCAAACCCGGGACTCAAAG-ACAAAACCATTAAAATTTAACCATCTAA
*
44652280 CTAAAAAAACTA
129 CCAAAAAAACTA
44652292 ATTATATTAAAA-A-AAAGTAAAAAA-AATA
1 A-TATATTAAAACATAAA-TAAAAAATAATA
44652320 TGTAACTTAA
Statistics
Matches: 138, Mismatches: 27, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
140 6 0.04
141 91 0.66
142 30 0.22
143 11 0.08
ACGTcount: A:0.55, C:0.11, G:0.10, T:0.25
Consensus pattern (140 bp):
ATATATTAAAACATAAATAAAAAATAATAAAAAGCTTAAAACAACATGAAATAAAAAATACAAAT
GTAAGTAGGAAAAGAATCAAACCCGGGACTCAAAGACAAAACCATTAAAATTTAACCATCTAACC
AAAAAAACTA
Found at i:44653087 original size:25 final size:26
Alignment explanation
Indices: 44653059--44653116 Score: 100
Period size: 25 Copynumber: 2.3 Consensus size: 26
44653049 AGTAAAAGAC
*
44653059 ATATAAATTTACCAAAA-TTATATAA
1 ATATAAATTTACCAAAATTTACATAA
44653084 ATATAAATTTACCAAAATTTACATAA
1 ATATAAATTTACCAAAATTTACATAA
44653110 ATATAAA
1 ATATAAA
44653117 ACAATTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (26 bp):
ATATAAATTTACCAAAATTTACATAA
Found at i:44656030 original size:23 final size:23
Alignment explanation
Indices: 44656004--44656124 Score: 165
Period size: 23 Copynumber: 5.2 Consensus size: 23
44655994 ACACTAGCGC
44656004 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
44656027 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
44656050 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
44656075 GCTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
44656098 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
44656121 GCTC
1 GCTC
44656125 AGTACTTTGT
Statistics
Matches: 88, Mismatches: 4, Indels: 12
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.05
23 63 0.72
24 1 0.01
25 17 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:44656073 original size:48 final size:46
Alignment explanation
Indices: 44656004--44656124 Score: 181
Period size: 48 Copynumber: 2.6 Consensus size: 46
44655994 ACACTAGCGC
*
44656004 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGT-GT
*
44656050 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGTGT
*
44656098 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
44656125 AGTACTTTGT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
46 26 0.38
48 42 0.61
49 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGTGT
Found at i:44656153 original size:39 final size:39
Alignment explanation
Indices: 44656089--44656163 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
44656079 TCTGATTAGC
*
44656089 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
44656128 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
44656164 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:44656158 original size:23 final size:23
Alignment explanation
Indices: 44656123--44656216 Score: 95
Period size: 23 Copynumber: 4.0 Consensus size: 23
44656113 CTTTGTGTGC
*
44656123 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
44656146 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
44656169 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
*
44656194 TCAGCACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
44656216 T
1 T
44656217 TGTTCCGTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 17 0.28
23 21 0.35
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.27, G:0.19, T:0.43
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:44671027 original size:58 final size:58
Alignment explanation
Indices: 44670942--44671087 Score: 183
Period size: 58 Copynumber: 2.5 Consensus size: 58
44670932 TATTATTATA
* *
44670942 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-ATT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
* *
44670999 ATTATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
44671059 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
44671088 CATTAAAATT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 1 0.01
58 48 0.62
59 11 0.14
60 10 0.13
61 8 0.10
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:44671226 original size:39 final size:44
Alignment explanation
Indices: 44671171--44671275 Score: 114
Period size: 46 Copynumber: 2.5 Consensus size: 44
44671161 TTTCTTATGC
*
44671171 TATTACAGCATC-ATTCCATT-CAACCAA-ACACAA-GAA-TA-T
1 TATTACAGC-TCTATTCCATTCCAACCAACAAACAATGAATTACT
*
44671210 TATTACAGCTCTATTCCATTCCAATCAACCAAACAATTGAATTACT
1 TATTACAGCTCTATTCCATTCCAACCAA-CAAACAA-TGAATTACT
*
44671256 GATTACAGCTCTATTCCATT
1 TATTACAGCTCTATTCCATT
44671276 ACAGCTCTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
38 2 0.04
39 17 0.31
40 6 0.11
42 5 0.09
44 3 0.05
45 2 0.04
46 20 0.36
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (44 bp):
TATTACAGCTCTATTCCATTCCAACCAACAAACAATGAATTACT
Found at i:44671274 original size:46 final size:44
Alignment explanation
Indices: 44671182--44671275 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
44671172 ATTACAGCAT
* *
44671182 CATTCCATTCAACCAAACACAAGAATATTATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
*
44671226 CATTCCAATCAACCAAACA-ATTGAATTACTGATTACAGCTCTATTC
1 CATTCCAATCAACCAAACACA-AGAA-TA-TGATTACAGCTCTATTC
44671272 CATT
1 CATT
44671276 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 2 0.05
46 20 0.45
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCCAATCAACCAAACACAAGAATATGATTACAGCTCTATTC
Found at i:44671278 original size:16 final size:16
Alignment explanation
Indices: 44671257--44671312 Score: 96
Period size: 16 Copynumber: 3.5 Consensus size: 16
44671247 TGAATTACTG
44671257 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
44671273 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
44671289 ATTACA-CTTCTATTCC
1 ATTACAGC-TCTATTCC
44671305 ATTACAGC
1 ATTACAGC
44671313 GAACCAAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
15 1 0.03
16 36 0.95
17 1 0.03
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:44675425 original size:105 final size:105
Alignment explanation
Indices: 44675245--44675463 Score: 237
Period size: 105 Copynumber: 2.1 Consensus size: 105
44675235 ACTATAGGTA
* *
44675245 ACAACATTAGGCTCAATGCCTTGCTTTCTCATCGAGTCAACAATATCCTCGACTTCAGAGACCAT
1 ACAACATCAGGCTCAATGCCTTGCTTTCTCATCGAGTCAACAATATCCTCGACTTCAGAAACCAT
* * *
44675310 CCCTTGCTTGCAATGCACATCAACCAATGTATTATACGTG
66 CCCTTCCTTGCAAAGCACATCAACCAATATATTATACGTG
** * * *
44675350 ACAACATCAGGCTCAATGCCTTGCTTTCTCATC-ATGTCAACGGTCT-CTAC-AGCTTTAGAAAT
1 ACAACATCAGGCTCAATGCCTTGCTTTCTCATCGA-GTCAACAATATCCT-CGA-CTTCAGAAAC
* * ** * *
44675412 CATGCTTTCCTTGCAAAGTGCATCGATCAATATATTATACGTG
63 CATCCCTTCCTTGCAAAGCACATCAACCAATATATTATACGTG
*
44675455 ACAATATCA
1 ACAACATCA
44675464 AGTGAAATAT
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
104 4 0.04
105 90 0.96
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (105 bp):
ACAACATCAGGCTCAATGCCTTGCTTTCTCATCGAGTCAACAATATCCTCGACTTCAGAAACCAT
CCCTTCCTTGCAAAGCACATCAACCAATATATTATACGTG
Found at i:44677812 original size:5 final size:5
Alignment explanation
Indices: 44677802--44677832 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
44677792 ATGCACCATC
44677802 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
44677833 CTTTGTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:44678251 original size:37 final size:37
Alignment explanation
Indices: 44678146--44678251 Score: 115
Period size: 37 Copynumber: 2.9 Consensus size: 37
44678136 GTGTCGGTGA
* * * *
44678146 ATTCGACCTATGTGCCTAGCAGGTTTCGTGCCGGTGT
1 ATTCGGCCTATGTGCCTAGAAGGCTTCGTGCCAGTGT
* * * *
44678183 ATTCAAG-CTATTTGCCTAGTAGGCTTTGTGCCAGTGT
1 ATTC-GGCCTATGTGCCTAGAAGGCTTCGTGCCAGTGT
*
44678220 ATTCGGCCTATGTGCCTAGAAAGCTTCGTGCC
1 ATTCGGCCTATGTGCCTAGAAGGCTTCGTGCC
44678252 GATGTAATTG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
36 1 0.02
37 54 0.98
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (37 bp):
ATTCGGCCTATGTGCCTAGAAGGCTTCGTGCCAGTGT
Found at i:44678267 original size:74 final size:75
Alignment explanation
Indices: 44678131--44678294 Score: 179
Period size: 74 Copynumber: 2.2 Consensus size: 75
44678121 AAGTATTCAA
* * * * * * **
44678131 GCTTTGTGTCGGTGAATTCGACCTATGTGCCTAGCAGGTTTCGTGCCGGTGTATTCAAGCTATTT
1 GCTTTGTGCCAGTGAATTCGACCTATGTGCCTAGAAAGCTTCGTGCCGATGTATTCAAGCTATAA
*
44678196 GCCTAG-TAG
66 GCCTAGCAAG
* * **
44678205 GCTTTGTGCCAGTGTATTCGGCCTATGTGCCTAGAAAGCTTCGTGCCGATGTAATT-GGGCTATA
1 GCTTTGTGCCAGTGAATTCGACCTATGTGCCTAGAAAGCTTCGTGCCGATGT-ATTCAAGCTATA
44678269 AGCCTAGCAAG
65 AGCCTAGCAAG
*
44678280 CCTTTGTGCCAGTGA
1 GCTTTGTGCCAGTGA
44678295 TTAAAGACTA
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
74 55 0.75
75 18 0.25
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.32
Consensus pattern (75 bp):
GCTTTGTGCCAGTGAATTCGACCTATGTGCCTAGAAAGCTTCGTGCCGATGTATTCAAGCTATAA
GCCTAGCAAG
Found at i:44680733 original size:12 final size:14
Alignment explanation
Indices: 44680716--44680747 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44680706 AATTACTCAG
44680716 AAATTA-TTATT-T
1 AAATTATTTATTGT
44680728 AAATTATTTATTGT
1 AAATTATTTATTGT
44680742 AAATTA
1 AAATTA
44680748 GTTCACATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 5 0.28
14 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
AAATTATTTATTGT
Found at i:44681511 original size:3 final size:3
Alignment explanation
Indices: 44681503--44681541 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
44681493 GGAATTTGGT
44681503 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
44681542 GTGAAGTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:44683860 original size:19 final size:19
Alignment explanation
Indices: 44683828--44683869 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
44683818 TGATGTTTCA
* *
44683828 TTTTCTATTTTTTTTTTAGT
1 TTTTCTATTGTTTTGTTA-T
44683848 TTTTCT-TTGTTTTGTTAT
1 TTTTCTATTGTTTTGTTAT
44683866 TTTT
1 TTTT
44683870 ATGCTACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 9 0.45
20 6 0.30
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.81
Consensus pattern (19 bp):
TTTTCTATTGTTTTGTTAT
Found at i:44696841 original size:21 final size:21
Alignment explanation
Indices: 44696815--44696861 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
44696805 TTAGGGTCCA
*
44696815 ATTGCCCCGGAGGAGTAGAGT
1 ATTGCCCCGGAGGAGTAAAGT
*
44696836 ATTGCCCGGGAGGAGTAAAGT
1 ATTGCCCCGGAGGAGTAAAGT
44696857 ATTGC
1 ATTGC
44696862 GGTGGCTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (21 bp):
ATTGCCCCGGAGGAGTAAAGT
Found at i:44696993 original size:12 final size:12
Alignment explanation
Indices: 44696962--44696997 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
44696952 TCATCCAATG
* *
44696962 CCTCCTCCTCCT
1 CCTCCTCTTCTT
44696974 CCTCCTCTTCTT
1 CCTCCTCTTCTT
44696986 CCTCCTCTTCTT
1 CCTCCTCTTCTT
44696998 GTTGCTCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (12 bp):
CCTCCTCTTCTT
Found at i:44698893 original size:16 final size:16
Alignment explanation
Indices: 44698872--44698921 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
44698862 TGATGGGAAT
44698872 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
44698888 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
44698903 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
44698918 ATTA
1 ATTA
44698922 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:44699318 original size:95 final size:95
Alignment explanation
Indices: 44699114--44699387 Score: 385
Period size: 95 Copynumber: 2.9 Consensus size: 95
44699104 TATATTATTT
44699114 TTTTAAATCAATAAATATGAACAATATTTTTTACTTATTACTACTACTACTATTAACAACAAAAA
1 TTTTAAATCAATAAATATGAACAATATTTTTTAC---TTACTACTACTAC---TAACAAC-AAAA
* ***
44699179 TAAAATTACTAACTAAT-TTTTTTAAACATTATTAAA
59 TAAAATTACTAACTAGTAAAATTTAAACATTATTAAA
*
44699215 TTTTAAATCAATAAATATAAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
*
44699280 ATTAACTAGTAAAATTTAAACATTATTAAA
66 ACTAACTAGTAAAATTTAAACATTATTAAA
*
44699310 TTTTAAATCAATAAATATGAACAATATGTTTTAC-T--TACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
*
44699372 ACTAACTAGCAAAATT
66 ACTAACTAGTAAAATT
44699388 AAATTAAAGT
Statistics
Matches: 162, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
92 41 0.25
94 20 0.12
95 55 0.34
98 13 0.08
101 33 0.20
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (95 bp):
TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
ACTAACTAGTAAAATTTAAACATTATTAAA
Found at i:44699376 original size:20 final size:21
Alignment explanation
Indices: 44699351--44699393 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
44699341 TACTTACTAC
44699351 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
44699371 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
44699392 TA
1 TA
44699394 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:44699570 original size:26 final size:27
Alignment explanation
Indices: 44699510--44699576 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
44699500 AAGAAAACAA
*
44699510 AAAACTTAAAATA--ATCAAATTAACT
1 AAAACTTAAAATATTATAAAATTAACT
* *
44699535 AACAAATTAAAATATTTTAAAATTAAC-
1 AA-AACTTAAAATATTATAAAATTAACT
44699562 AAAACTTAAAATATT
1 AAAACTTAAAATATT
44699577 CATTAAACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 2 0.06
26 22 0.63
27 2 0.06
28 9 0.26
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAACTTAAAATATTATAAAATTAACT
Done.