Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold100
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: 904619
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 4 of 8
Found at i:446368 original size:33 final size:33
Alignment explanation
Indices: 446324--446395 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
446314 GCTGCTACCA
*
446324 TGGAAGCTGGAAATTGCTCAAGCTGCTGGTTCG
1 TGGATGCTGGAAATTGCTCAAGCTGCTGGTTCG
* *
446357 TGGATGCTGGAAGTTGCTCGAGCTGCTGGTTCG
1 TGGATGCTGGAAATTGCTCAAGCTGCTGGTTCG
446390 TGGATG
1 TGGATG
446396 TTGCTGCTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.29
Consensus pattern (33 bp):
TGGATGCTGGAAATTGCTCAAGCTGCTGGTTCG
Found at i:446374 original size:84 final size:84
Alignment explanation
Indices: 446262--446453 Score: 285
Period size: 84 Copynumber: 2.3 Consensus size: 84
446252 TCATGGAAGT
* * * *
446262 TGCTGCGTCCGTGGAAGTTGGAATTTGCTCGAGCTGCTGGTTCGTGGATGCTGCTGCTACCATGG
1 TGCTG-GTTCGTGGATGCTGGAAGTTGCTCGAGCTGCTGGTTCGTGGATGCTGCTGCTACCATGG
446327 AAGCTGGAAATTGCTCAAGC
65 AAGCTGGAAATTGCTCAAGC
* ** *
446347 TGCTGGTTCGTGGATGCTGGAAGTTGCTCGAGCTGCTGGTTCGTGGATGTTGCTGCTGTCGTGGA
1 TGCTGGTTCGTGGATGCTGGAAGTTGCTCGAGCTGCTGGTTCGTGGATGCTGCTGCTACCATGGA
*
446412 AGCTGGAAGTTGCTCAAGC
66 AGCTGGAAATTGCTCAAGC
*
446431 TACTGGTTCGTGGATGCTGGAAG
1 TGCTGGTTCGTGGATGCTGGAAG
446454 AAACTCGAAC
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
84 92 0.95
85 5 0.05
ACGTcount: A:0.16, C:0.19, G:0.36, T:0.30
Consensus pattern (84 bp):
TGCTGGTTCGTGGATGCTGGAAGTTGCTCGAGCTGCTGGTTCGTGGATGCTGCTGCTACCATGGA
AGCTGGAAATTGCTCAAGC
Found at i:446409 original size:51 final size:53
Alignment explanation
Indices: 446345--446446 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 53
446335 AATTGCTCAA
* * *
446345 GCTGCTGGTTCGTGGATGCTGGAAGTTGCTCGAGCTGCTGGTTCGTGGATGTT
1 GCTGCTGGTTCGTGGAAGCTGGAAGTTGCTCAAGCTACTGGTTCGTGGATGTT
446398 GCTGCT-G-TCGTGGAAGCTGGAAGTTGCTCAAGCTACTGGTTCGTGGATG
1 GCTGCTGGTTCGTGGAAGCTGGAAGTTGCTCAAGCTACTGGTTCGTGGATG
446447 CTGGAAGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 39 0.85
52 1 0.02
53 6 0.13
ACGTcount: A:0.13, C:0.18, G:0.38, T:0.31
Consensus pattern (53 bp):
GCTGCTGGTTCGTGGAAGCTGGAAGTTGCTCAAGCTACTGGTTCGTGGATGTT
Found at i:446937 original size:26 final size:25
Alignment explanation
Indices: 446908--446989 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 25
446898 CAGCCTTTCC
446908 ACATTTTTTATTCATTCCATCATGCT
1 ACATTTTTTATTCATTCCAT-ATGCT
* **
446934 ACA-TTTTTAGTC--TCCATACTTTT
1 ACATTTTTTATTCATTCCATA-TGCT
* *
446957 TCCTTTTTTATTCATTCCATAATGCT
1 ACATTTTTTATTCATTCCAT-ATGCT
446983 ACATTTT
1 ACATTTT
446990 CAGTCTCTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
22 1 0.02
23 8 0.20
24 8 0.20
25 8 0.20
26 15 0.37
27 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.52
Consensus pattern (25 bp):
ACATTTTTTATTCATTCCATATGCT
Found at i:447024 original size:49 final size:49
Alignment explanation
Indices: 446916--447017 Score: 123
Period size: 49 Copynumber: 2.1 Consensus size: 49
446906 CCACATTTTT
* * ****
446916 TATTCATTCCATCATGCTACATTTTTAGTCTCCATACTTTTTCCTTTTT
1 TATTCATTCCATAATGCTACATTTTCAGTCTCCATACTTTTTCCTCCCA
** *
446965 TATTCATTCCATAATGCTACATTTTCAGTCTCTTTGCTTTTTCCTCCCA
1 TATTCATTCCATAATGCTACATTTTCAGTCTCCATACTTTTTCCTCCCA
447014 TATT
1 TATT
447018 GCTTCCACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.19, C:0.25, G:0.05, T:0.51
Consensus pattern (49 bp):
TATTCATTCCATAATGCTACATTTTCAGTCTCCATACTTTTTCCTCCCA
Found at i:447186 original size:9 final size:9
Alignment explanation
Indices: 447172--447200 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
447162 TCAATTTGTG
447172 TTTATTTTA
1 TTTATTTTA
447181 TTTATTTTA
1 TTTATTTTA
447190 TTT-TTTTA
1 TTTATTTTA
447198 TTT
1 TTT
447201 TTGATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTATTTTA
Found at i:447191 original size:14 final size:13
Alignment explanation
Indices: 447172--447219 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 13
447162 TCAATTTGTG
447172 TTTATTTTATTTAT
1 TTTATTTT-TTTAT
447186 TTTATTTTTTTATT
1 TTTATTTTTTTA-T
447200 TTTGATTTTTTTAAT
1 TTT-ATTTTTTT-AT
447215 TTTAT
1 TTTAT
447220 ATCAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.13
14 14 0.45
15 12 0.39
16 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTATTTTTTTAT
Found at i:447198 original size:8 final size:8
Alignment explanation
Indices: 447176--447217 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
447166 TTTGTGTTTA
447176 TTTTATTT
1 TTTTATTT
447184 ATTTTATTT
1 -TTTTATTT
447193 TTTTA-TT
1 TTTTATTT
*
447200 TTTGATTT
1 TTTTATTT
447208 TTTTAATTT
1 TTTT-ATTT
447217 T
1 T
447218 ATATCAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 6 0.21
8 10 0.34
9 13 0.45
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (8 bp):
TTTTATTT
Found at i:447562 original size:15 final size:17
Alignment explanation
Indices: 447531--447562 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
447521 GTCCAAGAAT
447531 AAAACAAGAATGCAGGA
1 AAAACAAGAATGCAGGA
447548 AAAACAA-AA-GCAGGA
1 AAAACAAGAATGCAGGA
447563 CCACACAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.62, C:0.12, G:0.22, T:0.03
Consensus pattern (17 bp):
AAAACAAGAATGCAGGA
Found at i:447726 original size:54 final size:53
Alignment explanation
Indices: 447662--447771 Score: 130
Period size: 53 Copynumber: 2.1 Consensus size: 53
447652 ACCAACGGGC
* * *
447662 AGACTTAGGGAAAAAAAAGTCTCCAGAGACAAAGCCGACAGGCAAACTGAGGGA
1 AGACTGAGGG-AAAAAAAGTCTCCAGAGACAAAGCCGACAAGCAAACTAAGGGA
** * * * *
447716 AGACTGAGGGAAGGAAAGTCTTCAGGGTCAAAGCCGACAAGCAGACTAAGGGA
1 AGACTGAGGGAAAAAAAGTCTCCAGAGACAAAGCCGACAAGCAAACTAAGGGA
447769 AGA
1 AGA
447772 AAAGTTTTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
53 38 0.81
54 9 0.19
ACGTcount: A:0.42, C:0.17, G:0.31, T:0.10
Consensus pattern (53 bp):
AGACTGAGGGAAAAAAAGTCTCCAGAGACAAAGCCGACAAGCAAACTAAGGGA
Found at i:447776 original size:42 final size:42
Alignment explanation
Indices: 447716--448901 Score: 1131
Period size: 42 Copynumber: 28.3 Consensus size: 42
447706 AACTGAGGGA
* * * *
447716 AGACTGAGGGAAGGAAAGTCTTCAGGGTCAAAGCCGACAAGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* *
447758 AGACTAAGGGAAGAAAAGTTTTCAGGGTCAAAGCCGACAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * *
447800 AGACTGAGGGAAGGAAAGTCTCCAGGGTCAAAGTCGACAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
** * *
447842 AGACTAAGGGTTGAAAAGTCTCCAGGGTTAAA-CCGATAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * *
447883 AGACTGAGGGATGAAAAGTCTCCAGGGTCAAAACCGATAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * ** * *
447925 AGACGAAGGGATGAAAAGTTTTTAGGGTCAAAACCGATAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * *
447967 AGACTAAGGGAA-AAAAGTTTCCAGGGCCAAAGCCTACAAGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * *
448008 AGATTGAGGGAA-AGAAAGTCTCCAAGGTCAAAGCTGACAGGC
1 AGACTAAGGGAAGA-AAAGTCTCCAGGGTCAAAGCCGACAGGC
* * *
448050 AGACTGAA-GGAAGGAAAGTCTCCAAGGTCAAAGCCGATAGGC
1 AGACT-AAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* ** *
448092 AGACTAAGGGATGAAAAGTCTTTAGGGTCAAAACCGACAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * * *
448134 AGACTAAGAGATGAAAAGTCTCCAAGTTCAAAACCGACAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
*
448176 AGACTAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGACAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * * * *
448218 AAATTGAA-GGAAGGAAAGTCTCTAAGGTCAAAGCCGACAGAC
1 AGACT-AAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * *
448260 AGACTGAA-GAAAGGAAAGTCTCCAAGGTCAAAGCCGACAGGC
1 AGACT-AAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* *
448302 AAACTAAGGGACA-AGAAAGTCTCTAGGGTCAAAGCCGACAGGC
1 AGACTAAGGGA-AGA-AAAGTCTCCAGGGTCAAAGCCGACAGGC
* ** * *
448345 AGACTGAGGGTTGAAAAGTCTCCAGGGTTAAA-CTGACAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * *
448386 AGACTAAGGGAAAGGAAAGTCTTCAGGGTCAAAACCCGACAGGT
1 AGACTAAGGG-AAGAAAAGTCTCCAGGGTC-AAAGCCGACAGGC
** * * * ** *
448430 AGACTAAGGGTTGAAAAGTCTTCAGGGTTAAA-TCGATGGGG
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * *
448471 AGACTAAGGGATGAAAAGTCTCCA-AGTCAAAACCGACAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * **
448512 AGACCAAGGGATGAAAAGTCTCTAGGGTCAAAATCGACAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * * *
448554 ATACCAAGGGATGAACAGTCTCCAGGGTCAAAACCGACAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * *
448596 ACACTGAGGGAAGAAAAGTCTCTAGGGTCAAAGCCGACAGGC
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * *
448638 AGACTGAGGGAA-AGAAAGTCTCCAGGGTTAAAGCCAACAAGC
1 AGACTAAGGGAAGA-AAAGTCTCCAGGGTCAAAGCCGACAGGC
* * *
448680 AAACTGAA-GAAAGGAAAGTCTCCAGGGTCAAAGCCGACAGGC
1 AGACT-AAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * * * *
448722 AGACAAAGGGAAAGGAAAGTCTCCTGGGTCATAGCCGACTGGC
1 AGACTAAGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * ** * * * **
448765 AAACTGAGGGTTGAAAAGTTTCCAGGGTTAAA-CCAACAGAA
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* * *
448806 AGACTAAGGGATGAAAAGTCTTCAGGGTCAAAGCCGACAGGT
1 AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
* *
448848 AGACTAAGGGTATG-AAAGTCTCTAGGGTCAAAGCCGACAGGC
1 AGACTAAGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
448890 AGACTAAGGGAA
1 AGACTAAGGGAA
448902 AACAAAAAAG
Statistics
Matches: 952, Mismatches: 170, Indels: 45
0.82 0.15 0.04
Matches are distributed among these distances:
40 5 0.01
41 179 0.19
42 654 0.69
43 97 0.10
44 17 0.02
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.14
Consensus pattern (42 bp):
AGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGACAGGC
Found at i:453105 original size:13 final size:13
Alignment explanation
Indices: 453087--453111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
453077 CATAAAGTGT
453087 TGTATCGATACAA
1 TGTATCGATACAA
453100 TGTATCGATACA
1 TGTATCGATACA
453112 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:453109 original size:33 final size:33
Alignment explanation
Indices: 453067--453133 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
453057 TTCAACGATT
453067 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
453100 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
453133 T
1 T
453134 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:453236 original size:52 final size:52
Alignment explanation
Indices: 453194--453318 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
453184 CATTGATCTT
453194 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
* * *
453246 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
*
453298 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
453319 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:460269 original size:23 final size:23
Alignment explanation
Indices: 460212--460283 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
460202 AAAAATGATG
*
460212 AAAAAGTCAAAAGTAAACACAAA
1 AAAAAGTCAAAAGAAAACACAAA
**
460235 AAACAAAACAAAA-AAAACACAAA
1 AAA-AAGTCAAAAGAAAACACAAA
* *
460258 AAAAAGTGCAAAGGAAAA-ATAAA
1 AAAAAGT-CAAAAGAAAACACAAA
460281 AAA
1 AAA
460284 GGGAGCACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
22 2 0.05
23 26 0.67
24 11 0.28
ACGTcount: A:0.75, C:0.11, G:0.08, T:0.06
Consensus pattern (23 bp):
AAAAAGTCAAAAGAAAACACAAA
Found at i:460552 original size:28 final size:29
Alignment explanation
Indices: 460506--460561 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
460496 TTTCTAAAAA
*
460506 AAGAAACAAAAC-AAAAAAAGAAACAAAC
1 AAGAAACAAAACAAAAAAAAAAAACAAAC
460534 AAGAAAC-AAACAAACAAAAAAAAACAAA
1 AAGAAACAAAACAAA-AAAAAAAAACAAA
460562 AGAAGAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 4 0.16
28 9 0.36
29 12 0.48
ACGTcount: A:0.80, C:0.14, G:0.05, T:0.00
Consensus pattern (29 bp):
AAGAAACAAAACAAAAAAAAAAAACAAAC
Found at i:461418 original size:16 final size:17
Alignment explanation
Indices: 461393--461430 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
461383 TTGTGCTATA
* *
461393 ATCATGACATC-ATGAC
1 ATCATAACATCAATAAC
461409 ATCATAACATCAATAAC
1 ATCATAACATCAATAAC
461426 ATCAT
1 ATCAT
461431 TATTTGCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (17 bp):
ATCATAACATCAATAAC
Found at i:461559 original size:31 final size:31
Alignment explanation
Indices: 461519--461640 Score: 124
Period size: 31 Copynumber: 4.0 Consensus size: 31
461509 AATTCTTCAC
461519 ATCTCCTTCTTAAAGTCCACGACTCAGTGGCA
1 ATCT-CTTCTTAAAGTCCACGACTCAGTGGCA
* *
461551 ATCTCTTCTCAAAGCCCACGACTCAGTGGCA
1 ATCTCTTCTTAAAGTCCACGACTCAGTGGCA
* * * * * * *
461582 TTTTGTCCTAAAAGTCCACAATTCAGTGGC-
1 ATCTCTTCTTAAAGTCCACGACTCAGTGGCA
*
461612 ATCCCTT-TT-AAGTCCACGACTCAGTGGCA
1 ATCTCTTCTTAAAGTCCACGACTCAGTGGCA
461641 TCAAAGTCCA
Statistics
Matches: 71, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
28 17 0.24
29 1 0.01
30 2 0.03
31 47 0.66
32 4 0.06
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.28
Consensus pattern (31 bp):
ATCTCTTCTTAAAGTCCACGACTCAGTGGCA
Found at i:461788 original size:28 final size:27
Alignment explanation
Indices: 461740--461800 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
461730 GCACCTTGTT
* *
461740 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAA
*
461767 CCTTTTAAAGCCCACAATTCCGTGGCAA
1 CCTTTT-AAGCCCACAACTCCGTGGCAA
461795 CCTTTT
1 CCTTTT
461801 TCTTCTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAA
Found at i:461800 original size:96 final size:95
Alignment explanation
Indices: 461673--461973 Score: 338
Period size: 96 Copynumber: 3.0 Consensus size: 95
461663 ACCTTTTTCT
* * *
461673 TTTTAAAGCCCACAACTCCGTGTCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCACCTTG
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAGCCCACAACTCCGTGGCACCTTT
* *
461738 TTCCTTTT-AAGTCCACAACTCCGTGGCACCC
64 TTCTTTTTAAAGCCCACAACTCCGTGGCACCC
* * * *
461769 TTTTAAAGCCCACAATTCCGTGGCAACCTTTTT-CTTCTCAAAGCCCACCACTCTGTGGCA-CTT
1 TTTTAAAGCCCACAACTCCGTGGC-ACCTTTTTCCTT-T-TAAGCCCACAACTCCGTGGCACCTT
*
461832 TTTCTTTTTAAACCCCACAACTCCGTGGCACTCTTTTTCCC
63 TTTCTTTTTAAAGCCCACAACTCCGTGGCA--------CCC
*
461873 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTT
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGCCCACAACTCCGTGGCACCTTT
*
461938 TTCTTTTTAAAGCCCACAACTCCGTGGCACTC
64 TTCTTTTTAAAGCCCACAACTCCGTGGCACCC
461970 TTTT
1 TTTT
461974 TCCCTTTTAA
Statistics
Matches: 172, Mismatches: 17, Indels: 31
0.78 0.08 0.14
Matches are distributed among these distances:
94 3 0.02
95 11 0.06
96 63 0.37
97 8 0.05
104 34 0.20
105 53 0.31
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (95 bp):
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACCTTTTT
CTTTTTAAAGCCCACAACTCCGTGGCACCC
Found at i:461916 original size:34 final size:34
Alignment explanation
Indices: 461653--462006 Score: 422
Period size: 34 Copynumber: 10.5 Consensus size: 34
461643 AAAGTCCATG
461653 ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
1 ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
* * *
461687 ACTCCGTGTCACTCTTTTTCCCTTTT-AAGTCCACA
1 ACTCCGTGGCAC-CTTTTT-CTTTTTAAAGCCCACA
* * *
461722 ACTCCGTGGCACCTTGTTCCTTTT-AAGTCCACA
1 ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
461755 ACTCCGTGGCACC-----C-TTTTAAAGCCCACA
1 ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
* * * *
461783 ATTCCGTGGCAACCTTTTTCTTCTCAAAGCCCACC
1 ACTCCGTGGC-ACCTTTTTCTTTTTAAAGCCCACA
* *
461818 ACTCTGTGGCA-CTTTTTCTTTTTAAACCCCACA
1 ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
*
461851 ACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACA
1 ACTCCGTGGCAC-CTTTTT--CTTTTTAAAGCCCACA
461888 ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
1 ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
461922 ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
1 ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
* *
461956 ACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCCACA
1 ACTCCGTGGCAC-CTTTTT-CTTTTTAAAGCCCACA
*
461991 ACTCCGTGGCATCTTT
1 ACTCCGTGGCACCTTT
462007 CACCCCCTCA
Statistics
Matches: 281, Mismatches: 23, Indels: 32
0.84 0.07 0.10
Matches are distributed among these distances:
27 4 0.01
28 18 0.06
29 3 0.01
33 56 0.20
34 83 0.30
35 75 0.27
36 16 0.06
37 26 0.09
ACGTcount: A:0.19, C:0.34, G:0.12, T:0.34
Consensus pattern (34 bp):
ACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACA
Found at i:461947 original size:105 final size:103
Alignment explanation
Indices: 461766--462006 Score: 376
Period size: 105 Copynumber: 2.3 Consensus size: 103
461756 CTCCGTGGCA
* * *
461766 CCCTTTTAAAGCCCACAATTCCGTGGCAACCTTTTTCTTCTCAAAGCCCACCACTCTGTGGCACT
1 CCCTTTTAAAGCCCACAACTCCGTGGC-ACCTTTTTCTTCTCAAAGCCCACAACTCCGTGGCACT
461831 TTTTCTTTTTAAACCCCACAACTCCGTGGCACTCTTTTT
65 TTTTCTTTTTAAACCCCACAACTCCGTGGCACTCTTTTT
* *
461870 CCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACC
1 CCCTTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTTCTCAAAGCCCACAACTCCGTGGCA-C
*
461935 TTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
64 TTTTTCTTTTTAAACCCCACAACTCCGTGGCACTCTTTTT
* *
461975 CCCTTTT-AAGTCCACAACTCCGTGGCATCTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACCTTT
462007 CACCCCCTCA
Statistics
Matches: 127, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
103 23 0.18
104 38 0.30
105 66 0.52
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.34
Consensus pattern (103 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTTCTCAAAGCCCACAACTCCGTGGCACTT
TTTCTTTTTAAACCCCACAACTCCGTGGCACTCTTTTT
Found at i:462122 original size:33 final size:34
Alignment explanation
Indices: 462016--462209 Score: 269
Period size: 33 Copynumber: 5.9 Consensus size: 34
462006 TCACCCCCTC
*
462016 AAAGCCCACACAAGTTGGTGGCAATCCC--C-TCT
1 AAAGCCCACACAAGTCGGTGGCAA-CCCTTCTTCT
*
462048 AAAGCCCACACAAGTCGGTGGCAACCCTT-ATC-
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCT
*
462080 AAAGCCCACATAAGTCGGTGGCAA-CCTTCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCT
462113 AAAGCCCACACAAGTCGGTGGCAACCCTT-TTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCT
* * *
462146 AAAGCCCACACAGGTTGGTGGCAACCATTC-TCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCT
462179 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
462210 AAGTCCAATG
Statistics
Matches: 144, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
31 7 0.05
32 48 0.33
33 85 0.59
34 4 0.03
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (34 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTTCT
Found at i:462186 original size:66 final size:64
Alignment explanation
Indices: 462014--462207 Score: 300
Period size: 66 Copynumber: 3.0 Consensus size: 64
462004 TTTCACCCCC
*
462014 TCAAAGCCCACACAAGTTGGTGGCAATCC-CCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTA
1 TCAAAGCCCACACAAGTTGGTGGCAA-CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTA
* * *
462078 TCAAAGCCCACATAAGTCGGTGGCAACCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTT
1 TCAAAGCCCACACAAGTTGGTGGCAACCTTC-TCTAAAGCCCACACAAGTCGGTGGCAACCCTTA
*
462143 TCTAAAGCCCACACAGGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
1 TC-AAAGCCCACACAAGTTGGTGGCAACC-TTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
462208 CTAAGTCCAA
Statistics
Matches: 119, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
63 2 0.02
64 25 0.21
65 34 0.29
66 55 0.46
67 3 0.03
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (64 bp):
TCAAAGCCCACACAAGTTGGTGGCAACCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTA
Found at i:462321 original size:49 final size:49
Alignment explanation
Indices: 462209--462638 Score: 439
Period size: 49 Copynumber: 9.0 Consensus size: 49
462199 GCAACCCTTC
* *
462209 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
*
462252 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
462301 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
462344 TAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
462393 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
462436 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCT-TCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-TATCTT
*
462485 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC-CTTT--ATCTT
* * * *
462537 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * * * * *
462592 TAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
462639 ACTTTTCTCA
Statistics
Matches: 325, Mismatches: 35, Indels: 48
0.80 0.09 0.12
Matches are distributed among these distances:
43 113 0.35
44 3 0.01
48 2 0.01
49 122 0.38
50 3 0.01
51 2 0.01
52 39 0.12
53 1 0.00
54 1 0.00
55 38 0.12
56 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:462366 original size:92 final size:92
Alignment explanation
Indices: 462209--462524 Score: 580
Period size: 92 Copynumber: 3.4 Consensus size: 92
462199 GCAACCCTTC
462209 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
462274 GAATCAGCATATTGGCACCTTTATCTT
66 GAATCAGCATATTGGCACCTTTATCTT
462301 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
*
462366 GAATCAACATATTGGCACCTTTATCTT
66 GAATCAGCATATTGGCACCTTTATCTT
462393 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
*
462458 GAATCAGCATATTGGCATCTTCT-TCTT
66 GAATCAGCATATTGGCACCTT-TATCTT
* *
462485 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
462525 ATTTTCCATC
Statistics
Matches: 218, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
92 217 1.00
93 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (92 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
GAATCAGCATATTGGCACCTTTATCTT
Found at i:462618 original size:107 final size:101
Alignment explanation
Indices: 462433--462630 Score: 252
Period size: 101 Copynumber: 1.9 Consensus size: 101
462423 ACATTGGCAC
* * * *
462433 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCTTCTTTAAGTCCAATATA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCTTCTTCTTTAAGCCCAATATA
* *
462498 GCTGGCCTTGAATCAGCATATTGGCACATTTTCCAT
66 GCTGGCCGTGAATCAACATATTGGCACATTTTCCAT
* *
462534 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACAT-C---TTCT--TCTTTAAGCCC
* *
462599 AATATCGTTGGCCGTGAATCAACATATTGGCA
60 AATATAGCTGGCCGTGAATCAACATATTGGCA
462631 TCTTTATCAC
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
101 38 0.47
102 1 0.01
105 4 0.05
107 38 0.47
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (101 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCTTCTTCTTTAAGCCCAATATA
GCTGGCCGTGAATCAACATATTGGCACATTTTCCAT
Found at i:463464 original size:13 final size:13
Alignment explanation
Indices: 463446--463470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
463436 CATAAAGTGT
463446 TGTATCGATACAA
1 TGTATCGATACAA
463459 TGTATCGATACA
1 TGTATCGATACA
463471 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:463468 original size:33 final size:33
Alignment explanation
Indices: 463426--463492 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
463416 TTCAACGATT
463426 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
463459 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
463492 T
1 T
463493 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:463551 original size:13 final size:13
Alignment explanation
Indices: 463533--463557 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
463523 ATTACTCAAA
463533 TGTATCGATACAT
1 TGTATCGATACAT
463546 TGTATCGATACA
1 TGTATCGATACA
463558 CTATTAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:463572 original size:33 final size:34
Alignment explanation
Indices: 463512--463578 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
463502 TGCCAAAAAA
*
463512 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACACTACTCAAATGTATCGATACAT
*
463546 TGTATCGATACACTA-TTAAATGTATCGATACAT
1 TGTATCGATACACTACTCAAATGTATCGATACAT
463579 GCAAGCAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (34 bp):
TGTATCGATACACTACTCAAATGTATCGATACAT
Found at i:470268 original size:18 final size:20
Alignment explanation
Indices: 470231--470270 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
470221 CATAATTCTC
*
470231 ATAAAAAAATTTATTATGCA
1 ATAAAAAAAATTATTATGCA
470251 ATAAAAAAAATT-TT-TGCA
1 ATAAAAAAAATTATTATGCA
470269 AT
1 AT
470271 TTTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
ATAAAAAAAATTATTATGCA
Found at i:472688 original size:51 final size:51
Alignment explanation
Indices: 472628--472744 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
472618 AGCGACTGGG
* * * *
472628 AGTTCGTGGAAGTTGCTGCTATCGTGGAAGTTGAAAGTTGCTCGAGCTGCT
1 AGTTCGTGGATGTTGCTGCTACCGTGGAAGCTGAAAGTTGCTCAAGCTGCT
* * * *
472679 AGTTCGTGGATGCTGCTGCTGCCGTGGAAGCTGGAAGTTGCTCAAGGTGCT
1 AGTTCGTGGATGTTGCTGCTACCGTGGAAGCTGAAAGTTGCTCAAGCTGCT
472730 AGTTCGTGGATGTTG
1 AGTTCGTGGATGTTG
472745 GAAGTTGCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.17, C:0.16, G:0.36, T:0.31
Consensus pattern (51 bp):
AGTTCGTGGATGTTGCTGCTACCGTGGAAGCTGAAAGTTGCTCAAGCTGCT
Found at i:472738 original size:33 final size:33
Alignment explanation
Indices: 472701--472769 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
472691 CTGCTGCTGC
*
472701 CGTGGAAGCTGGAAGTTGCTCAAGGTGCTAGTT
1 CGTGGAAGCTGGAAGTTGCTCAAGCTGCTAGTT
* * * *
472734 CGTGGATGTTGGAAGTTGCTCGAGCTGCTGGTT
1 CGTGGAAGCTGGAAGTTGCTCAAGCTGCTAGTT
472767 CGT
1 CGT
472770 AGATGCTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.38, T:0.30
Consensus pattern (33 bp):
CGTGGAAGCTGGAAGTTGCTCAAGCTGCTAGTT
Found at i:472750 original size:84 final size:84
Alignment explanation
Indices: 472642--472832 Score: 287
Period size: 84 Copynumber: 2.3 Consensus size: 84
472632 CGTGGAAGTT
* * * *
472642 GCTGCTA--TCGTGGAAGTTGAAAGTTGCTCGAGCTGCTAGTTCGTGGATGCTGCTGCTGCCGTG
1 GCTGCTAGTTCGTGGATGTTGGAAGTTGCTCGAGCTGCTAGTTCGTAGATGCTGCTGCTGCCGCG
472705 GAAGCTGGAAGTTGCTCAA
66 GAAGCTGGAAGTTGCTCAA
* * *
472724 GGTGCTAGTTCGTGGATGTTGGAAGTTGCTCGAGCTGCTGGTTCGTAGATGCTGTTGCTGCCGCG
1 GCTGCTAGTTCGTGGATGTTGGAAGTTGCTCGAGCTGCTAGTTCGTAGATGCTGCTGCTGCCGCG
472789 GAAGCTGGAAGTTGCTCAA
66 GAAGCTGGAAGTTGCTCAA
* *
472808 GCTGCTGGTTCGTGGATGCTGGAAG
1 GCTGCTAGTTCGTGGATGTTGGAAG
472833 AAACTCGAAC
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
82 6 0.06
84 91 0.94
ACGTcount: A:0.16, C:0.18, G:0.37, T:0.29
Consensus pattern (84 bp):
GCTGCTAGTTCGTGGATGTTGGAAGTTGCTCGAGCTGCTAGTTCGTAGATGCTGCTGCTGCCGCG
GAAGCTGGAAGTTGCTCAA
Found at i:473355 original size:49 final size:49
Alignment explanation
Indices: 473301--473399 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
473291 CTTTTCCACA
473301 TTTTTTATTAATTCCATCATGCTACATTTTTAGTCTCCATGCTTTTTCC
1 TTTTTTATTAATTCCATCATGCTACATTTTTAGTCTCCATGCTTTTTCC
* *
473350 TTTTTTATTCATTCCATCATGCTATATTTTTAGTCTCCATGCTTTTTCC
1 TTTTTTATTAATTCCATCATGCTACATTTTTAGTCTCCATGCTTTTTCC
473399 T
1 T
473400 CCCATATTGC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.17, C:0.22, G:0.06, T:0.55
Consensus pattern (49 bp):
TTTTTTATTAATTCCATCATGCTACATTTTTAGTCTCCATGCTTTTTCC
Found at i:473414 original size:49 final size:49
Alignment explanation
Indices: 473306--473415 Score: 150
Period size: 49 Copynumber: 2.2 Consensus size: 49
473296 CCACATTTTT
* ****
473306 TATTAATTCCATCATGCTACATTTTTAGTCTCCATGCTTTTTCCTTTTT
1 TATTCATTCCATCATGCTACATTTTTAGTCTCCATGCTTTTTCCTCCCA
*
473355 TATTCATTCCATCATGCTATATTTTTAGTCTCCATGCTTTTTCCTCCCA
1 TATTCATTCCATCATGCTACATTTTTAGTCTCCATGCTTTTTCCTCCCA
473404 TATTGC-TTCCAT
1 TATT-CATTCCAT
473416 TTTTCCCTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
49 53 0.98
50 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.06, T:0.50
Consensus pattern (49 bp):
TATTCATTCCATCATGCTACATTTTTAGTCTCCATGCTTTTTCCTCCCA
Found at i:473581 original size:17 final size:16
Alignment explanation
Indices: 473561--473603 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
473551 TTTCTGTTTA
473561 TTTTATTAATTTAGATT
1 TTTTATT-ATTTAGATT
*
473578 TTTTATTTTTTAGATT
1 TTTTATTATTTAGATT
473594 TTTT-TTATTT
1 TTTTATTATTT
473604 TTGATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (16 bp):
TTTTATTATTTAGATT
Found at i:473589 original size:16 final size:16
Alignment explanation
Indices: 473570--473621 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
473560 ATTTTATTAA
473570 TTTAGATTTTTTATTT
1 TTTAGATTTTTTATTT
473586 TTTAGATTTTTT-TTAT
1 TTTAGATTTTTTATT-T
* *
473602 TTTTGATATTTTGATTT
1 TTTAGAT-TTTTTATTT
473619 TTT
1 TTT
473622 TAAATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 2 0.06
16 19 0.61
17 8 0.26
18 2 0.06
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (16 bp):
TTTAGATTTTTTATTT
Found at i:473612 original size:18 final size:18
Alignment explanation
Indices: 473576--473613 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
473566 TTAATTTAGA
*
473576 TTTTTTATTTTTTAGATT
1 TTTTTTATTTTTGAGATT
*
473594 TTTTTTATTTTTGATATT
1 TTTTTTATTTTTGAGATT
473612 TT
1 TT
473614 GATTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTTTATTTTTGAGATT
Found at i:473628 original size:25 final size:26
Alignment explanation
Indices: 473570--473629 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
473560 ATTTTATTAA
* * *
473570 TTTAGATTTTTTATTTTTTAGATTTT
1 TTTAAATTTTTGATATTTTAGATTTT
*
473596 TTT-TATTTTTGATATTTT-GATTTT
1 TTTAAATTTTTGATATTTTAGATTTT
473620 TTTAAATTTT
1 TTTAAATTTT
473630 ATATAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 9 0.31
25 17 0.59
26 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (26 bp):
TTTAAATTTTTGATATTTTAGATTTT
Found at i:475719 original size:124 final size:124
Alignment explanation
Indices: 475499--475747 Score: 453
Period size: 124 Copynumber: 2.0 Consensus size: 124
475489 ATATGACACC
*
475499 TACGATTGAGGAGATCTCAGCTATCCTCGGGTTTGGGTCACTAGAGACGAGGCCAATATATTGTA
1 TACGATTAAGGAGATCTCAGCTATCCTCGGGTTTGGGTCACTAGAGACGAGGCCAATATATTGTA
* *
475564 AGGAGAGATGTCCAGCCACATTCCAAAAGAAGTTAAATTAGGTTCTAGAGCTTGGTCCA
66 AGGAGAGATGTCCAACCACATTCCAAAAGAAGTTAAATCAGGTTCTAGAGCTTGGTCCA
475623 TACGATTAAGGAGATCTCAGCTATCCTCGGGTTTGGGTCACTAGAGACGAGGCCAATATATTGTA
1 TACGATTAAGGAGATCTCAGCTATCCTCGGGTTTGGGTCACTAGAGACGAGGCCAATATATTGTA
* *
475688 AGGAGAGATGTCCAACCACATTCCGAAAGAAGTTAAGTCAGGTTCTAGAGCTTGGTCCA
66 AGGAGAGATGTCCAACCACATTCCAAAAGAAGTTAAATCAGGTTCTAGAGCTTGGTCCA
475747 T
1 T
475748 GTATGGAGTA
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 120 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (124 bp):
TACGATTAAGGAGATCTCAGCTATCCTCGGGTTTGGGTCACTAGAGACGAGGCCAATATATTGTA
AGGAGAGATGTCCAACCACATTCCAAAAGAAGTTAAATCAGGTTCTAGAGCTTGGTCCA
Found at i:477509 original size:22 final size:19
Alignment explanation
Indices: 477479--477527 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
477469 TTAATGGCAT
477479 TCATATTCATGACATTCATTCA
1 TCATATTCAT-A-A-TCATTCA
*
477501 TCATTTTCATAATCATTCA
1 TCATATTCATAATCATTCA
477520 TCAGTATT
1 TCA-TATT
477528 TGCTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
21 1 0.04
22 9 0.38
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (19 bp):
TCATATTCATAATCATTCA
Found at i:485246 original size:42 final size:41
Alignment explanation
Indices: 485185--486227 Score: 979
Period size: 42 Copynumber: 24.9 Consensus size: 41
485175 CTTTTTTGTT
* *
485185 TTCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAAACTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTC
*
485226 TTACCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTC
1 TT-CCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
* * *
485269 ATCCCTTAGTCTACCTGTCGG-TTTAACCCTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
** * * *
485310 AACCCTCAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-C
* * *
485352 TGTCCCTTAATCTGCCTGTTGGCTTTGACCTTGGAGACTTTAC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-C
* * *
485395 TT-CCTTCAGTATGCCTGTCAGCTTTGACCTTGGAGACTTTCC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-C
*
485437 TT-CCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
* * * * *
485479 ATCCCTTAGTCTGCTTGTCAGCTTTAACCCTGGAGATTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGA-CTTTC
* * ** *
485521 TTCTCTTAGTCTGCCTGTCGGATTTGACGTTCGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
* * * * *
485563 ATCCCTTAATCTGCCTATCGG-TTTGACCTTGGAGACTTTT
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTC
* *
485603 TATCCCTTAGTCTGCCTGTCAGTTTTGACCCTGGAGACTTTC
1 T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTC
*
485645 ATGTCCCTTAGTCTGCCTGTCGGCTTTGACTCTGGAGACTTTTC
1 -T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
*
485689 TT-CCTTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-C
* * * *
485731 TTCCCTCAGTCTGCCTGTCAGCTTTTAACCTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-C
* * *
485773 TTCCCTCAGTCTGTCTGTCGGCTTTGACCCTGCAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
* * *
485815 TTCCCTTAGTCTACCTGTCGGTTTTGACCCTAGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
* * * *
485857 ATCCCTTAGTTTGCCTGTCGGTTTTGACCCTGGAAACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
* ** * *
485899 ATCCCTTAGTCTGCCTGTTAGTTTTGACCTTGGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
* * ** * *
485941 ATCCCTTAGTCTGCCTATC-AATTTAACCCTAGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
** * * *
485982 AACCCTCAGTTTGCCTGTCGGCTTTGACCTTGGAGACTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTC
486023 TTGTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
1 -T-TCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
* *
486067 TT-CCTTCAGTCTGCTTGTC-GATTTGACCCTGGAGACTTTTC
1 TTCCCTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
* ** *
486108 ATCCCTTAGTCTGCCTGTC-AATTTAACCCTGGAGACTTTCC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTT-C
* ** * *
486149 TTCCCTCAGTCTGTTTGTCGGCTTTGTCCCTAGAGACTTTTC
1 TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTTC
* * * * * *
486191 TTTCCCTAAGTTTGCCCGTTGGTTTTGACCCGGGAGA
1 -TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGA
486228 ATATTTTCTT
Statistics
Matches: 842, Mismatches: 132, Indels: 54
0.82 0.13 0.05
Matches are distributed among these distances:
40 6 0.01
41 185 0.22
42 492 0.58
43 151 0.18
44 8 0.01
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.38
Consensus pattern (41 bp):
TTCCCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTC
Found at i:485715 original size:294 final size:291
Alignment explanation
Indices: 485186--486190 Score: 1209
Period size: 294 Copynumber: 3.4 Consensus size: 291
485176 TTTTTTGTTT
* * * *
485186 TCCCTTAGTCTGCCTGTCGGCTTTGACCTTGGAAAC-TTTCTTACCCTTAGTCTGCCTGTCGGCT
1 TCCCTTAGTCTGCTTGTCGGCTTTGACCCTGGAGACTTTTCTT-CCCTTAGTCTGCCTGTCGGAT
* * * *
485250 TTGACCTTGGAGACTTTTCATCCCTTAGTCTACCTGTCGGTTTAACCCTGGAGACTTTTCAACCC
65 TTGACCTTAGAGACTTTTCATCCCTTAGTCTGCCTGTCGGTTTGACCCTGGAGACTTTTCATCCC
* * * * *
485315 TCAGTCTGCCTGTC-GACTTTGACCTTGGAGACTTTCCTGTCCCTTAATCTGCCTGTTGGCTTTG
130 TTAGTCTGCCTGTCAG-TTTTGACCTTGGAGACTTTCATGTCCCTTAGTCTGCCTGTCGGCTTTG
* *
485379 ACCTTGGAGACTTTACTTCCTTCAGTATGCCTGTCAGCTTTGACCTTGGAGACTTTCCTTCCTTC
194 ACC-TGGAGACTTTTCTTCCTTCAGTATGCCTGTCGGCTTTGACCTTGGAGACTTTCCTTCCTTC
485444 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTC
258 AGTCTGCCTGTCGGCTTTGACC-TGGAGACTTTTC
* * * *
485479 ATCCCTTAGTCTGCTTGTCAGCTTTAACCCTGGAGATTTTTCTTCTCTTAGTCTGCCTGTCGGAT
1 -TCCCTTAGTCTGCTTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGAT
* * * * * *
485544 TTGACGTTCGAGACTTTTCATCCCTTAATCTGCCTATCGGTTTGACCTTGGAGACTTTTTATCCC
65 TTGACCTTAGAGACTTTTCATCCCTTAGTCTGCCTGTCGGTTTGACCCTGGAGACTTTTCATCCC
*
485609 TTAGTCTGCCTGTCAGTTTTGACCCTGGAGACTTTCATGTCCCTTAGTCTGCCTGTCGGCTTTGA
130 TTAGTCTGCCTGTCAGTTTTGACCTTGGAGACTTTCATGTCCCTTAGTCTGCCTGTCGGCTTTGA
* * * *
485674 CTCTGGAGACTTTTCTTCCTTCAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCTTCCCTCA
195 C-CTGGAGACTTTTCTTCCTTCAGTATGCCTGTCGGCTTTGACCTTGGAGACTTTCCTTCCTTCA
* * *
485739 GTCTGCCTGTCAGCTTTTAACCTGGAGACTTTCC
259 GTCTGCCTGTCGGC-TTTGACCTGGAGACTTTTC
* * * *
485773 TTCCCTCAGTCTG-TCTGTCGGCTTTGACCCTGCAGACTTTTCTTCCCTTAGTCTACCTGTCGGT
1 -TCCCTTAGTCTGCT-TGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGA
* * *
485837 TTTGACCCTAGAGACTTTTCATCCCTTAGTTTGCCTGTCGGTTTTGACCCTGGAAACTTTTCATC
64 TTTGACCTTAGAGACTTTTCATCCCTTAGTCTGCCTGTCGG-TTTGACCCTGGAGACTTTTCATC
* * **
485902 CCTTAGTCTGCCTGTTAGTTTTGACCTTGGAGACTTTTCA--TCCCTTAGTCTGCCTATC-AATT
128 CCTTAGTCTGCCTGTCAGTTTTGACCTTGGAGAC-TTTCATGTCCCTTAGTCTGCCTGTCGGCTT
* * ** * * *
485964 TAACCCTAGAGACTTTTCAACCCTCAGTTTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTGTCC
192 TGA-CCTGGAGACTTTTCTTCCTTCAGTATGCCTGTCGGCTTTGACCTTGGAGACTTTCCT-T-C
486029 CTT-AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC
254 CTTCAGTCTGCCTGTCGGCTTTGA-CCTGGAGACTTTTC
* * * *
486067 TTCCTTCAGTCTGCTTGTC-GATTTGACCCTGGAGACTTTTCATCCCTTAGTCTGCCTGTC-AAT
1 TCCCTT-AGTCTGCTTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGAT
* * * * * * ** * *
486130 TTAACCCTGGAGACTTTCCTTCCCTCAGTCTGTTTGTCGGCTTTGTCCCTAGAGACTTTTC
65 TTGACCTTAGAGACTTTTCATCCCTTAGTCTGCCTGTCGG-TTTGACCCTGGAGACTTTTC
486191 TTTCCCTAAG
Statistics
Matches: 610, Mismatches: 88, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
292 50 0.08
293 98 0.16
294 387 0.63
295 70 0.11
296 5 0.01
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.39
Consensus pattern (291 bp):
TCCCTTAGTCTGCTTGTCGGCTTTGACCCTGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGATT
TGACCTTAGAGACTTTTCATCCCTTAGTCTGCCTGTCGGTTTGACCCTGGAGACTTTTCATCCCT
TAGTCTGCCTGTCAGTTTTGACCTTGGAGACTTTCATGTCCCTTAGTCTGCCTGTCGGCTTTGAC
CTGGAGACTTTTCTTCCTTCAGTATGCCTGTCGGCTTTGACCTTGGAGACTTTCCTTCCTTCAGT
CTGCCTGTCGGCTTTGACCTGGAGACTTTTC
Found at i:486683 original size:8 final size:8
Alignment explanation
Indices: 486670--486720 Score: 70
Period size: 8 Copynumber: 6.5 Consensus size: 8
486660 AAAATTAAGA
486670 AAAAAATC
1 AAAAAATC
486678 AAAAAATC
1 AAAAAATC
*
486686 -AAAAATA
1 AAAAAATC
486693 AAAAAATC
1 AAAAAATC
486701 TAAAAAATC
1 -AAAAAATC
486710 -AAAAATC
1 AAAAAATC
486717 AAAA
1 AAAA
486721 TTAATAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
7 13 0.34
8 17 0.45
9 8 0.21
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAAATC
Found at i:486697 original size:16 final size:14
Alignment explanation
Indices: 486678--486720 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
486668 GAAAAAAATC
486678 AAAAAATCAAAAATA
1 AAAAAATCAAAAA-A
486693 AAAAAATCTAAAAAA
1 AAAAAATC-AAAAAA
*
486708 TCAAAAATCAAAA
1 -AAAAAATCAAAA
486721 TTAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAATCAAAAAA
Found at i:486705 original size:24 final size:23
Alignment explanation
Indices: 486669--486720 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
486659 TAAAATTAAG
486669 AAAAAAATCAAAAAATCAAAAAT
1 AAAAAAATCAAAAAATCAAAAAT
486692 AAAAAAATCTAAAAAATCAAAAAT
1 AAAAAAATC-AAAAAATCAAAAAT
*
486716 CAAAA
1 AAAAA
486721 TTAATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (23 bp):
AAAAAAATCAAAAAATCAAAAAT
Found at i:486714 original size:31 final size:32
Alignment explanation
Indices: 486670--486730 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
486660 AAAATTAAGA
486670 AAAAAATCAAAAAATCAAAAATAAAAAAATCT
1 AAAAAATCAAAAAATCAAAAATAAAAAAATCT
* *
486702 AAAAAATC-AAAAATCAAAATTAATAAAAT
1 AAAAAATCAAAAAATCAAAAATAAAAAAAT
486731 AAACACAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (32 bp):
AAAAAATCAAAAAATCAAAAATAAAAAAATCT
Found at i:486721 original size:6 final size:7
Alignment explanation
Indices: 486671--486720 Score: 55
Period size: 7 Copynumber: 6.6 Consensus size: 7
486661 AAATTAAGAA
486671 AAAAATC
1 AAAAATC
486678 AAAAAATC
1 -AAAAATC
*
486686 AAAAATAA
1 AAAAAT-C
486694 AAAAATC
1 AAAAATC
486701 TAAAAAATC
1 --AAAAATC
486710 AAAAATC
1 AAAAATC
486717 AAAA
1 AAAA
486721 TTAATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
7 17 0.46
8 13 0.35
9 7 0.19
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATC
Found at i:486946 original size:25 final size:25
Alignment explanation
Indices: 486917--486996 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
486907 GCATGGAGAC
486917 TAAAAATGTAGCATGATGGAATGAA
1 TAAAAATGTAGCATGATGGAATGAA
* * ** * *
486942 TAAAAAAGGAAAAAGCATGG-A-GAC
1 TAAAAATGTAGCATG-ATGGAATGAA
486966 TAAAAATGTAGCATGATGGAATGAA
1 TAAAAATGTAGCATGATGGAATGAA
486991 TAAAAA
1 TAAAAA
486997 ATGTGGAAAG
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
23 4 0.10
24 13 0.32
25 19 0.47
26 4 0.10
ACGTcount: A:0.54, C:0.05, G:0.23, T:0.19
Consensus pattern (25 bp):
TAAAAATGTAGCATGATGGAATGAA
Found at i:486952 original size:49 final size:49
Alignment explanation
Indices: 486899--486997 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
486889 GCAATATCGG
486899 AGGAAAAAGCATGGAGACTAAAAATGTAGCATGATGGAATGAATAAAAA
1 AGGAAAAAGCATGGAGACTAAAAATGTAGCATGATGGAATGAATAAAAA
486948 AGGAAAAAGCATGGAGACTAAAAATGTAGCATGATGGAATGAATAAAAA
1 AGGAAAAAGCATGGAGACTAAAAATGTAGCATGATGGAATGAATAAAAA
486997 A
1 A
486998 TGTGGAAAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.54, C:0.06, G:0.24, T:0.16
Consensus pattern (49 bp):
AGGAAAAAGCATGGAGACTAAAAATGTAGCATGATGGAATGAATAAAAA
Found at i:486984 original size:23 final size:23
Alignment explanation
Indices: 486909--486985 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
486899 AGGAAAAAGC
486909 ATGGAGACTAAAAATGTAGCATG
1 ATGGAGACTAAAAATGTAGCATG
* * * ** *
486932 ATGGAATGAATAAAAAAGGAAAAAG
1 ATGG-A-GACTAAAAATGTAGCATG
486957 CATGGAGACTAAAAATGTAGCATG
1 -ATGGAGACTAAAAATGTAGCATG
486981 ATGGA
1 ATGGA
486986 ATGAATAAAA
Statistics
Matches: 39, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
23 9 0.23
24 13 0.33
25 13 0.33
26 4 0.10
ACGTcount: A:0.49, C:0.06, G:0.26, T:0.18
Consensus pattern (23 bp):
ATGGAGACTAAAAATGTAGCATG
Found at i:486998 original size:26 final size:26
Alignment explanation
Indices: 486918--487000 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 26
486908 CATGGAGACT
486918 AAAAATGTAGCATGATGGAATGAATA
1 AAAAATGTAGCATGATGGAATGAATA
* ** * *
486944 AAAAA-GGAAAAAGCATGG-A-GACT-
1 AAAAATGTAGCATG-ATGGAATGAATA
486967 AAAAATGTAGCATGATGGAATGAATA
1 AAAAATGTAGCATGATGGAATGAATA
486993 AAAAATGT
1 AAAAATGT
487001 GGAAAGGCTG
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
23 9 0.21
24 8 0.19
25 8 0.19
26 17 0.40
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.19
Consensus pattern (26 bp):
AAAAATGTAGCATGATGGAATGAATA
Found at i:487558 original size:33 final size:33
Alignment explanation
Indices: 487520--487656 Score: 165
Period size: 33 Copynumber: 4.3 Consensus size: 33
487510 ACGGCAGCAA
487520 CAGCATCCATGAACCAGCAGCTCGAGCAACTTC
1 CAGCATCCATGAACCAGCAGCTCGAGCAACTTC
* *
487553 CAGCATCCATGAACCAGTAGCTTGAGCAACTT-
1 CAGCATCCATGAACCAGCAGCTCGAGCAACTTC
*
487585 ---CATCCATGAACCAGCAACTCGAGCAACTTC
1 CAGCATCCATGAACCAGCAGCTCGAGCAACTTC
* * * *
487615 CAGCATCCACGAACCAACAGATTGAGCAACTTC
1 CAGCATCCATGAACCAGCAGCTCGAGCAACTTC
* *
487648 TAGCTTCCA
1 CAGCATCCA
487657 CGGCAGCAGC
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
29 26 0.30
33 62 0.70
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (33 bp):
CAGCATCCATGAACCAGCAGCTCGAGCAACTTC
Found at i:487592 original size:62 final size:62
Alignment explanation
Indices: 487523--487647 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
487513 GCAGCAACAG
* * ** *
487523 CATCCATGAACCAGCAGCTCGAGCAACTTCCAGCATCCATGAACCAGTAGCTTGAGCAACTT
1 CATCCATGAACCAGCAACTCGAGCAACTTCCAGCATCCACGAACCAACAGATTGAGCAACTT
487585 CATCCATGAACCAGCAACTCGAGCAACTTCCAGCATCCACGAACCAACAGATTGAGCAACTT
1 CATCCATGAACCAGCAACTCGAGCAACTTCCAGCATCCACGAACCAACAGATTGAGCAACTT
487647 C
1 C
487648 TAGCTTCCAC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.33, C:0.34, G:0.16, T:0.18
Consensus pattern (62 bp):
CATCCATGAACCAGCAACTCGAGCAACTTCCAGCATCCACGAACCAACAGATTGAGCAACTT
Found at i:487612 original size:29 final size:29
Alignment explanation
Indices: 487523--487614 Score: 121
Period size: 29 Copynumber: 3.0 Consensus size: 29
487513 GCAGCAACAG
487523 CATCCATGAACCAGCAGCTCGAGCAACTT
1 CATCCATGAACCAGCAGCTCGAGCAACTT
* *
487552 CCAGCATCCATGAACCAGTAGCTTGAGCAACTT
1 ----CATCCATGAACCAGCAGCTCGAGCAACTT
*
487585 CATCCATGAACCAGCAACTCGAGCAACTT
1 CATCCATGAACCAGCAGCTCGAGCAACTT
487614 C
1 C
487615 CAGCATCCAC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
29 27 0.50
33 27 0.50
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (29 bp):
CATCCATGAACCAGCAGCTCGAGCAACTT
Found at i:487693 original size:51 final size:51
Alignment explanation
Indices: 487615--487730 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
487605 GAGCAACTTC
* *
487615 CAGCATCCACGAACCAACAGATTGAGCAACTTCTAGCTTCCACGGCAGCAG
1 CAGCATCCACGAACCAACAGATCGAGCAACTTCCAGCTTCCACGGCAGCAG
* *
487666 CAGCATCCACGAACCAGCAGCTCGAGCAACTTCCAGCTTCCACGGCAGCAG
1 CAGCATCCACGAACCAACAGATCGAGCAACTTCCAGCTTCCACGGCAGCAG
* *
487717 CAACTTCCACGAAC
1 CAGCATCCACGAAC
487731 TCCCAGTCGT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.37, G:0.19, T:0.14
Consensus pattern (51 bp):
CAGCATCCACGAACCAACAGATCGAGCAACTTCCAGCTTCCACGGCAGCAG
Found at i:487719 original size:25 final size:25
Alignment explanation
Indices: 487639--487725 Score: 72
Period size: 25 Copynumber: 3.4 Consensus size: 25
487629 CAACAGATTG
*
487639 AGCAACTTCTAGCTTCCACGGCAGC
1 AGCAACTTCCAGCTTCCACGGCAGC
* * **
487664 AGCAGCATCCA-CGAACCA--GCAGCTC
1 AGCAACTTCCAGC-TTCCACGGCAG--C
487689 GAGCAACTTCCAGCTTCCACGGCAGC
1 -AGCAACTTCCAGCTTCCACGGCAGC
487715 AGCAACTTCCA
1 AGCAACTTCCA
487726 CGAACTCCCA
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
23 4 0.09
24 1 0.02
25 23 0.50
26 13 0.28
27 1 0.02
28 4 0.09
ACGTcount: A:0.28, C:0.38, G:0.20, T:0.15
Consensus pattern (25 bp):
AGCAACTTCCAGCTTCCACGGCAGC
Found at i:489162 original size:8 final size:8
Alignment explanation
Indices: 489146--489193 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
489136 GTACGAAAGT
*
489146 AAAATTAA
1 AAAAATAA
489154 AAAAATAAA
1 AAAAAT-AA
489163 AAATAATAA
1 AAA-AATAA
*
489172 CAAAATAA
1 AAAAATAA
*
489180 AATAATAA
1 AAAAATAA
489188 AAAAAT
1 AAAAAT
489194 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
8 21 0.64
9 9 0.27
10 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (8 bp):
AAAAATAA
Found at i:489181 original size:16 final size:16
Alignment explanation
Indices: 489151--489193 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
489141 AAAGTAAAAT
489151 TAAAAAAATAAAAAATAA
1 TAAAAAAAT--AAAATAA
*
489169 TAACAAAATAAAATAA
1 TAAAAAAATAAAATAA
489185 TAAAAAAAT
1 TAAAAAAAT
489194 TTTATCTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
18 8 0.35
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAAAAATAAAATAA
Found at i:490706 original size:11 final size:11
Alignment explanation
Indices: 490689--490737 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
490679 TAAAATTAAA
490689 TATATTTA-AT
1 TATATTTATAT
490699 TAATATTTATAT
1 T-ATATTTATAT
490711 TATATTTATAT
1 TATATTTATAT
* *
490722 TTTAATTA-AT
1 TATATTTATAT
490732 TATATT
1 TATATT
490738 ATCGTCACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 7 0.21
11 23 0.70
12 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATATTTATAT
Found at i:496047 original size:21 final size:21
Alignment explanation
Indices: 495975--496047 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
495965 ATCTTTTTTC
*
495975 AATTATA-TAAGTATATAATAT
1 AATTATAGTAAATATAT-ATAT
*
495996 ATATTAT-GTAATTTATATTATAT
1 A-ATTATAGTAA-ATATA-TATAT
*
496019 AA--AGAGTAAATATATATAT
1 AATTATAGTAAATATATATAT
496038 AATTATAGTA
1 AATTATAGTA
496048 TAGATATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
19 7 0.17
20 5 0.12
21 10 0.24
22 9 0.22
23 9 0.22
24 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
AATTATAGTAAATATATATAT
Found at i:497796 original size:19 final size:19
Alignment explanation
Indices: 497774--497820 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
497764 ATATAATTAA
497774 ATTTAAATAAAAAAATATT
1 ATTTAAATAAAAAAATATT
* **
497793 ATTTTAATTTAAAAATATT
1 ATTTAAATAAAAAAATATT
497812 ATTTTAAAT
1 A-TTTAAAT
497821 TGAATAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAATAAAAAAATATT
Found at i:502461 original size:37 final size:38
Alignment explanation
Indices: 502409--502491 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 38
502399 ATTATTTATG
* *
502409 AAATAAAATTTATTATTATTTTAATTTAAAAATATTAATATA
1 AAAT-AAA-TTATTATTATTAT-ATTT-AAAATACTAATATA
*
502451 AAATAAATTATTATTATTATTATTTTAAATACTAATATA
1 AAATAAATTATTATTATTA-TATTTAAAATACTAATATA
502490 AA
1 AA
502492 TTTTTAGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
39 14 0.38
40 15 0.41
41 4 0.11
42 4 0.11
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (38 bp):
AAATAAATTATTATTATTATATTTAAAATACTAATATA
Found at i:510783 original size:66 final size:66
Alignment explanation
Indices: 510657--510783 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 66
510647 TTCTTGTTGC
* * ** * * * **
510657 AGGTAGTCCATCCAAGTAAAATCATCTGCACCAGCATCATTTTCCTGGAGTGTATTCTCCATTAC
1 AGGTAATCCATCCAAGCAAAATCATCTGCACCAGCAGAATTGTCCTGCACTGTACACTCCATTAC
510722 G
66 G
*
510723 AGGTAATCCATCCAAGCAAAATCATCTGTC-CCAGCAGAATTGTCCTTCACTGTACACTCCA
1 AGGTAATCCATCCAAGCAAAATCATCTG-CACCAGCAGAATTGTCCTGCACTGTACACTCCA
510784 CAACTTGCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 49 0.98
67 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (66 bp):
AGGTAATCCATCCAAGCAAAATCATCTGCACCAGCAGAATTGTCCTGCACTGTACACTCCATTAC
G
Found at i:512682 original size:174 final size:172
Alignment explanation
Indices: 512386--512736 Score: 517
Period size: 174 Copynumber: 2.0 Consensus size: 172
512376 AGAAAAACAA
* *
512386 TCCAAACCATATACTTTCACGTACATATCTGATGAGGATTAGCATCTATGAAAATACCCAAAATA
1 TCCAAACCATACACTTTCACGTACATAGCTGATGAGGATTAGCATCTATGAAAATACCCAAAATA
**
512451 ACTATCAAGTAAGCAGAATCAGAGATTGAAACAAAAAAACTATAAAAGCATGCAAATTTAGAAGA
66 ACTATCAAGTAAGCAGAATCAGAGATTGAAACAAAAAAAAAATAAAAGCATGCAAATTTAGAAGA
* *
512516 AGACCCAGATTATGATTTGGATTCATAAATGCAAAACAGAAGCT
131 AGAACCAGATT-TGATTTGGATTCATAAATGC-AAACAGAAACT
* ** * **
512560 TCCAAACTATACACTTTCGTGTTCATAGCTGATGAGGATTAGTGTCTATGAAAATACCCAAAATA
1 TCCAAACCATACACTTTCACGTACATAGCTGATGAGGATTAGCATCTATGAAAATACCCAAAATA
512625 ACTATCAAGTAAGCAGAATCAGAGATTGAAACAAATAAAAAAATAAAGAG-A-GCAAATTTAGAA
66 ACTATCAAGTAAGCAGAATCAGAGATTGAAACAAA-AAAAAAATAAA-AGCATGCAAATTTAGAA
* * *
512688 GATGAACCAGGTTTTATTTGGATTCATAAATGCAAACAGAAACT
129 GAAGAACCAGATTTGATTTGGATTCATAAATGCAAACAGAAACT
512732 TCCAA
1 TCCAA
512737 TCTGCTGAGG
Statistics
Matches: 160, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
172 15 0.09
173 19 0.12
174 114 0.71
175 10 0.06
176 2 0.01
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.25
Consensus pattern (172 bp):
TCCAAACCATACACTTTCACGTACATAGCTGATGAGGATTAGCATCTATGAAAATACCCAAAATA
ACTATCAAGTAAGCAGAATCAGAGATTGAAACAAAAAAAAAATAAAAGCATGCAAATTTAGAAGA
AGAACCAGATTTGATTTGGATTCATAAATGCAAACAGAAACT
Found at i:514275 original size:25 final size:26
Alignment explanation
Indices: 514246--514297 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
514236 TCTATTTTAT
514246 TCGA-TTTTTTAATTTTTTTACCAAA
1 TCGATTTTTTTAATTTTTTTACCAAA
*
514271 TCGATTTTTTTATTTTTTTTACCAAA
1 TCGATTTTTTTAATTTTTTTACCAAA
514297 T
1 T
514298 AAACCGATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.60
Consensus pattern (26 bp):
TCGATTTTTTTAATTTTTTTACCAAA
Found at i:515386 original size:20 final size:19
Alignment explanation
Indices: 515349--515429 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 19
515339 TACCAGAAGA
515349 TAAATATTATTAAT-TTAAAT
1 TAAATA-TATT-ATCTTAAAT
*
515369 TACATATTATTATCTTAAA-
1 TAAATA-TATTATCTTAAAT
515388 TAAATAT-TTA-CTTAAAT
1 TAAATATATTATCTTAAAT
*
515405 TAAATATATGTATCCTAAA-
1 TAAATATAT-TATCTTAAAT
515424 TAAATA
1 TAAATA
515430 ATACAAAAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
16 6 0.11
17 10 0.19
18 2 0.04
19 15 0.28
20 20 0.38
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.44
Consensus pattern (19 bp):
TAAATATATTATCTTAAAT
Found at i:517242 original size:21 final size:22
Alignment explanation
Indices: 517218--517260 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
517208 AAAACACAAC
517218 ATAACATGAAAAATAAT-TAAA
1 ATAACATGAAAAATAATATAAA
517239 ATAACATGAAAAATAATATAAA
1 ATAACATGAAAAATAATATAAA
517261 TATGATATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (22 bp):
ATAACATGAAAAATAATATAAA
Found at i:517528 original size:23 final size:22
Alignment explanation
Indices: 517496--517548 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
517486 TACTATTTTA
* *
517496 CCTTTTAAAATATTTTATATAT
1 CCTTTTAAAATAATTAATATAT
*
517518 CCTTTATAAAATAATTAATATAA
1 CCTTT-TAAAATAATTAATATAT
517541 CTCTTTTA
1 C-CTTTTA
517549 TATTTTAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 17 0.65
24 4 0.15
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (22 bp):
CCTTTTAAAATAATTAATATAT
Found at i:518338 original size:18 final size:17
Alignment explanation
Indices: 518315--518356 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
518305 AATGATTTGA
518315 ATTAAAAC-AATTTTAGAT
1 ATTAAAACTAA-TTTA-AT
518333 ATTAAAAACTAATTTAAT
1 ATT-AAAACTAATTTAAT
518351 ATTAAA
1 ATTAAA
518357 TAAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.14
18 8 0.36
19 9 0.41
20 2 0.09
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTAAAACTAATTTAAT
Found at i:518939 original size:21 final size:22
Alignment explanation
Indices: 518900--518944 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
518890 AAAAAAAATA
* * *
518900 TTAAATTAAAAACATTTAT-TT
1 TTAAACTAAAAAAAATTATGTT
518921 TTAAACTAAAAAAAATTATGTT
1 TTAAACTAAAAAAAATTATGTT
518943 TT
1 TT
518945 TATTATATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (22 bp):
TTAAACTAAAAAAAATTATGTT
Found at i:520149 original size:7 final size:7
Alignment explanation
Indices: 520137--520171 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
520127 AAATATATTT
520137 TTATATA
1 TTATATA
520144 TTATATA
1 TTATATA
520151 TTATATA
1 TTATATA
*
520158 TTTTATA
1 TTATATA
*
520165 TCATATA
1 TTATATA
520172 AAAATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATATA
Found at i:520150 original size:23 final size:23
Alignment explanation
Indices: 520113--520204 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
520103 GACTTAACTC
520113 TTTTT-TA-ATTATATAAATATA
1 TTTTTATATATTATATAAATATA
*
520134 TTTTTATATATTATAT-ATTATA
1 TTTTTATATATTATATAAATATA
*
520156 TATTTTATATCA-TATAAAAATAAATA
1 T-TTTTATAT-ATTATATAAAT--ATA
* *
520182 TTTATAATATATAATATAAATAT
1 TTT-TTATATATTATATAAATAT
520205 TTAAAATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
21 5 0.09
22 8 0.14
23 19 0.34
24 5 0.09
25 3 0.05
26 16 0.29
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTATATATTATATAAATATA
Found at i:520213 original size:20 final size:22
Alignment explanation
Indices: 520122--520220 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
520112 CTTTTTTAAT
* *
520122 TATATAA-ATATATTTTTATATA
1 TATATAATATAAATATTTATA-A
* *
520144 TTATATATTATATAT-TTTAT-A
1 -TATATAATATAAATATTTATAA
*
520165 TCATATAAAAATAAATATTTATAA
1 T-ATAT-AATATAAATATTTATAA
*
520189 TATATAATATAAATATTTAAAA
1 TATATAATATAAATATTTATAA
*
520211 TATATTATAT
1 TATATAATAT
520221 TATTTTATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
20 1 0.02
21 5 0.08
22 30 0.47
23 20 0.31
24 8 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (22 bp):
TATATAATATAAATATTTATAA
Found at i:520278 original size:16 final size:16
Alignment explanation
Indices: 520241--520284 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
520231 TAAAATTTAA
*
520241 TAAAAATATTAGATTAT
1 TAAAAA-ATTAAATTAT
*
520258 T-AAAAATTAAATTTT
1 TAAAAAATTAAATTAT
520273 TAAAAAATTAAA
1 TAAAAAATTAAA
520285 AAAATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 9 0.38
16 14 0.58
17 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
TAAAAAATTAAATTAT
Found at i:520954 original size:39 final size:39
Alignment explanation
Indices: 520890--520973 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
520880 CCTAAGAAAA
*
520890 CAAAAGCTTCTATTGATGGTGAGATTAAACTTGGATAAC
1 CAAAAGCTTCTATTGATGGTAAGATTAAACTTGGATAAC
* * *
520929 CAAAAGCTTTTATTGGTGGTAAGATTAAACTTTGATAAC
1 CAAAAGCTTCTATTGATGGTAAGATTAAACTTGGATAAC
*
520968 TAAAAG
1 CAAAAG
520974 AGTTAATATC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (39 bp):
CAAAAGCTTCTATTGATGGTAAGATTAAACTTGGATAAC
Found at i:524927 original size:102 final size:102
Alignment explanation
Indices: 524747--525251 Score: 454
Period size: 113 Copynumber: 4.6 Consensus size: 102
524737 CCTTAAGCCT
* *
524747 TCCATAGTTTTCGAATGAGCAGATAAGCATAATAGAACTAAAATCATGGCATGGAATAAAATGAA
1 TCCATAGTTTTCGAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATCGAATAAAATGAA
* * * *
524812 TGTACAATGTTTTCTATAACAAAAACCAAAGAATTTG
66 TGTACACTGTTTTCTACAGCCAAAACCAAAGAATTTG
* * *
524849 TCCATGGTTTTCGAATGAGCAGATAAGCATAATACTACTAAAATCATGACATCGAATAAAATGAA
1 TCCATAGTTTTCGAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATCGAATAAAATGAA
* *
524914 TGTACACTCTTTTCTACAGCCAAAACCAGAGAATGTGTCGATAAACCG
66 TGTACACTGTTTTCTACAGCCAAAACCAAAGAA--T-T---T-----G
** * * *
524962 TCCATAGTTTTCGAATGAGTGGATAAGCATTATACAACTAAAATCATGGCATCGAGTAAACTGAA
1 TCCATAGTTTTCGAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATCGAATAAAATGAA
* **
525027 TGTACACTGTGTTCTACAGCCAAAACCAAAGAATGCG
66 TGTACACTGTTTTCTACAGCCAAAACCAAAGAATTTG
* *
525064 TCACTAAACCTTCTGTAGTTTCTGAATGAGCAGATAAGCATAATTCAACTAAAATCATGGCATCG
1 TC-C---A---T-AGT--TTTC-GAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATCG
* * *
525129 TATAAAATGAATGTACACTGTTTTCTACATCCAAAACCGAAGAATGTGTTG
55 AATAAAATGAATGTACACTGTTTTCTACAGCCAAAACCAAAGAA--T-TTG
* * *
525180 ACAAACCATCCATAGTTTTCCAATAAGCGGATAAGCATAATACAACTAAAATCATGGCA-CTGAA
1 --------TCCATAGTTTTCGAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATC-GAA
525244 TAAAATGA
57 TAAAATGA
525252 TCAGTCAAGG
Statistics
Matches: 326, Mismatches: 43, Indels: 57
0.77 0.10 0.13
Matches are distributed among these distances:
102 90 0.28
103 1 0.00
104 1 0.00
105 1 0.00
106 1 0.00
108 1 0.00
109 1 0.00
110 2 0.01
111 1 0.00
112 5 0.02
113 209 0.64
114 4 0.01
115 1 0.00
116 3 0.01
117 1 0.00
120 1 0.00
123 1 0.00
124 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (102 bp):
TCCATAGTTTTCGAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATCGAATAAAATGAA
TGTACACTGTTTTCTACAGCCAAAACCAAAGAATTTG
Found at i:525265 original size:113 final size:112
Alignment explanation
Indices: 524849--525251 Score: 515
Period size: 113 Copynumber: 3.6 Consensus size: 112
524839 AAAGAATTTG
* * *
524849 TCCATGGTTTTCGAATGAGCAGATAAGCATAATACTACTAAAATCATGACATCGAATAAAATGAA
1 TCCATAGTTTTCGAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATCGAATAAAATGAA
* * * *
524914 TGTACACTCTTTTCTACAGCCAAAACCAGAGAATGTGTCGATAAACCG
66 TGTACACTGTTTTCTACAGCCAAAACCA-AGAATGTGTTGACAAACCA
** * * *
524962 TCCATAGTTTTCGAATGAGTGGATAAGCATTATACAACTAAAATCATGGCATCGAGTAAACTGAA
1 TCCATAGTTTTCGAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATCGAATAAAATGAA
* * * *
525027 TGTACACTGTGTTCTACAGCCAAAACCAAAGAATGCG-TCACTAAACCT
66 TGTACACTGTTTTCTACAGCCAAAACC-AAGAATGTGTTGAC-AAACCA
** * *
525075 TCTGTAG-TTTCTGAATGAGCAGATAAGCATAATTCAACTAAAATCATGGCATCGTATAAAATGA
1 TCCATAGTTTTC-GAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATCGAATAAAATGA
*
525139 ATGTACACTGTTTTCTACATCCAAAACCGAAGAATGTGTTGACAAACCA
65 ATGTACACTGTTTTCTACAGCCAAAACC-AAGAATGTGTTGACAAACCA
* * *
525188 TCCATAGTTTTCCAATAAGCGGATAAGCATAATACAACTAAAATCATGGCA-CTGAATAAAATGA
1 TCCATAGTTTTCGAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATC-GAATAAAATGA
525252 TCAGTCAAGG
Statistics
Matches: 247, Mismatches: 37, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
112 6 0.02
113 233 0.94
114 8 0.03
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (112 bp):
TCCATAGTTTTCGAATGAGCAGATAAGCATAATACAACTAAAATCATGGCATCGAATAAAATGAA
TGTACACTGTTTTCTACAGCCAAAACCAAGAATGTGTTGACAAACCA
Found at i:525968 original size:2 final size:2
Alignment explanation
Indices: 525963--526003 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
525953 AGGATCATAG
*
525963 TA TA TA TA TA TA TA TA GTA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
526004 ATGTTGTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:527427 original size:2 final size:2
Alignment explanation
Indices: 527414--527449 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
527404 CAAATGTATC
*
527414 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
527450 AATGCATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:527899 original size:17 final size:17
Alignment explanation
Indices: 527869--527902 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
527859 TAAAAAATAT
*
527869 AAAGAAATCCCAGATGA
1 AAAGAAATACCAGATGA
*
527886 AAAGAAATATCAGATGA
1 AAAGAAATACCAGATGA
527903 CAGTTTACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.18, T:0.15
Consensus pattern (17 bp):
AAAGAAATACCAGATGA
Found at i:528027 original size:14 final size:14
Alignment explanation
Indices: 528008--528034 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
527998 AGAAGCTTAA
528008 ATATTATAACCCTT
1 ATATTATAACCCTT
528022 ATATTATAACCCT
1 ATATTATAACCCT
528035 AAAATAAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATTATAACCCTT
Found at i:528383 original size:16 final size:16
Alignment explanation
Indices: 528362--528412 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
528352 ATTAATATTT
528362 TAAATTTTATATAATA
1 TAAATTTTATATAATA
*
528378 TAAATTATTA-AT-TTA
1 TAAATT-TTATATAATA
528393 TAATATTTTATA-AATA
1 TAA-ATTTTATATAATA
528409 TAAA
1 TAAA
528413 ATATCTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
15 9 0.31
16 17 0.59
17 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATTTTATATAATA
Found at i:528401 original size:32 final size:33
Alignment explanation
Indices: 528337--528454 Score: 106
Period size: 32 Copynumber: 3.7 Consensus size: 33
528327 ATAAATATAA
* * *
528337 ATATTATAAAAATATATTAATATTTTAAATTTT
1 ATATAATATAAATATATTAATATTATAAATTTT
528370 ATATAATATAAAT-TATTAAT-TTATAATATTTT
1 ATATAATATAAATATATTAATATTATAA-ATTTT
* *
528402 ATA-AATATAAAATATCTTAA-A-TAT-AATTATA
1 ATATAATAT-AAATATATTAATATTATAAATT-TT
*
528433 ATATAATA-AAATATATAAATAT
1 ATATAATATAAATATATTAATAT
528455 AATTTATCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
30 12 0.17
31 16 0.23
32 26 0.37
33 16 0.23
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATAATATAAATATATTAATATTATAAATTTT
Found at i:528456 original size:29 final size:28
Alignment explanation
Indices: 528400--528458 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
528390 TTATAATATT
*
528400 TTATAAATATAAAATATCTTAAATATAA
1 TTATAAATATAAAATATCATAAATATAA
528428 TTATAATATAATAAAATAT-ATAAATATAA
1 TTATAA-AT-ATAAAATATCATAAATATAA
528457 TT
1 TT
528459 TATCTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.21
29 13 0.46
30 9 0.32
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TTATAAATATAAAATATCATAAATATAA
Found at i:531180 original size:21 final size:21
Alignment explanation
Indices: 531150--531192 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
531140 AGTCAGTTTG
*
531150 ATTTATTTAAATTAAAAATTA
1 ATTTAATTAAATTAAAAATTA
* *
531171 ATTTAATTAAATTTAATATTA
1 ATTTAATTAAATTAAAAATTA
531192 A
1 A
531193 AATCGATCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTAATTAAATTAAAAATTA
Found at i:531320 original size:95 final size:91
Alignment explanation
Indices: 531192--531370 Score: 220
Period size: 95 Copynumber: 1.9 Consensus size: 91
531182 TTTAATATTA
* *
531192 AAATCGATCGATATTAAATTCAAAATCGAATTAA-TTGAACATACG-AAGATTGATCGATTTTTT
1 AAATCGATCGATATTAAATTCAAAATCGAATTAACTT-AACAAACGAAAG-TCGATCG-TTTTTT
531255 TTAGGTTCAAAGTTAATATTTTTTTCAAAATC
63 TT---TTCAAAGTTAATATTTTTTTCAAAATC
* *
531287 AAATCGATCGATATTAAGTTCAAAA-CTGTATTAACTTAACAAACGAAAGTCGATCGTTTTTTTT
1 AAATCGATCGATATTAAATTCAAAATC-GAATTAACTTAACAAACGAAAGTCGATCGTTTTTTTT
* *
531351 TTCAGAGTTAGTATTTTTTT
65 TTCAAAGTTAATATTTTTTT
531371 TGTTTTGTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
91 18 0.24
94 9 0.12
95 43 0.57
96 5 0.07
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (91 bp):
AAATCGATCGATATTAAATTCAAAATCGAATTAACTTAACAAACGAAAGTCGATCGTTTTTTTTT
TCAAAGTTAATATTTTTTTCAAAATC
Found at i:531419 original size:23 final size:22
Alignment explanation
Indices: 531392--531443 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
531382 CATAGATTTG
*
531392 AGTTTAAGTTTAGATAAGCTTTT
1 AGTTTAAGTTTAGATAAG-TTTA
*
531415 AGTTTAGGTTTAGATAAGTTTA
1 AGTTTAAGTTTAGATAAGTTTA
531437 AGTTTAA
1 AGTTTAA
531444 AATTATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (22 bp):
AGTTTAAGTTTAGATAAGTTTA
Found at i:532752 original size:20 final size:19
Alignment explanation
Indices: 532727--532784 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
532717 AGTAATTAAG
532727 AAAAATTATAAAAAATAAAT
1 AAAAATTA-AAAAAATAAAT
*
532747 AAAAA-TAAGAAAAA-AATCTT
1 AAAAATTAA-AAAAATAA--AT
532767 AAAAATTAAAAAAATAAA
1 AAAAATTAAAAAAATAAA
532785 AGTAAACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
18 3 0.10
19 7 0.23
20 16 0.52
21 5 0.16
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAATTAAAAAAATAAAT
Found at i:537408 original size:2 final size:2
Alignment explanation
Indices: 537401--537426 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
537391 ATATGTTCAC
537401 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
537427 TCATCCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:538466 original size:28 final size:29
Alignment explanation
Indices: 538435--538489 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
538425 ATAAATTTGA
* *
538435 ATTTGAAAATATTTGAA-TTTTAATTTAG
1 ATTTCAAAATATTTGAACGTTTAATTTAG
* *
538463 ATTTCATAATTTTTGAACGTTTAATTT
1 ATTTCAAAATATTTGAACGTTTAATTT
538490 TTATCAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 14 0.64
29 8 0.36
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (29 bp):
ATTTCAAAATATTTGAACGTTTAATTTAG
Found at i:538597 original size:14 final size:14
Alignment explanation
Indices: 538578--538624 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
538568 ATATAAAATG
538578 TATTATTTTTATTA
1 TATTATTTTTATTA
538592 TATTATTTTTATTTA
1 TATTATTTTTA-TTA
538607 TATCATATTTTATATTA
1 TAT--TATTTT-TATTA
538624 T
1 T
538625 GTTTAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.38
15 6 0.21
17 10 0.34
18 2 0.07
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATTTTTATTA
Found at i:538624 original size:17 final size:17
Alignment explanation
Indices: 538581--538624 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
538571 TAAAATGTAT
*
538581 TATTTT-TATTATATTA
1 TATTTTATATTATATCA
538597 T-TTTTAT-TTATATCA
1 TATTTTATATTATATCA
538612 TATTTTATATTAT
1 TATTTTATATTAT
538625 GTTTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 12 0.50
16 8 0.33
17 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTATATTATATCA
Found at i:538683 original size:94 final size:95
Alignment explanation
Indices: 538580--538779 Score: 246
Period size: 94 Copynumber: 2.1 Consensus size: 95
538570 ATAAAATGTA
* * * *
538580 TTATTTTTATTATAT-TATTTTTATTTATATCATA-TTTTATATTATGT-TTAAATTTATTAATT
1 TTATTTTTATTAAATATA-TTATATTTATATCATATTTTTATATCATATCTTAAATTTA--AATT
*
538642 TAATTAAAATAATTTAAATATAAA-TTATTATT
63 CAATTAAAATAATTTAAATATAAACTTATTATT
* * * *
538674 TTATATTTATTAAATATATTATATTTATATTATATTTTTTTATCATATCTTAAATTTAAATTCCA
1 TTATTTTTATTAAATATATTATATTTATATCATATTTTTATATCATATCTTAAATTTAAATTCAA
* *
538739 TTAAAATAATTTATATATAAACTTATTTTT
66 TTAAAATAATTTAAATATAAACTTATTATT
538769 TTATTTTTATT
1 TTATTTTTATT
538780 TTCATTATGC
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
94 52 0.58
95 29 0.32
96 9 0.10
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.59
Consensus pattern (95 bp):
TTATTTTTATTAAATATATTATATTTATATCATATTTTTATATCATATCTTAAATTTAAATTCAA
TTAAAATAATTTAAATATAAACTTATTATT
Found at i:539122 original size:21 final size:21
Alignment explanation
Indices: 539098--539171 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 21
539088 ATTATATACA
539098 ATAATTTTTAAAAAATAAGTG
1 ATAATTTTTAAAAAATAAGTG
539119 ATAATTTTTTTAAAAAATTAA---
1 ATAA--TTTTTAAAAAA-TAAGTG
* *
539140 AT-TTTTTTAAAAAATATGTAG
1 ATAATTTTTAAAAAATAAGT-G
539161 ATAATTTTTAA
1 ATAATTTTTAA
539172 GATTTAATGA
Statistics
Matches: 42, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
17 2 0.05
18 11 0.26
21 8 0.19
22 7 0.17
23 11 0.26
24 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
ATAATTTTTAAAAAATAAGTG
Found at i:539563 original size:16 final size:16
Alignment explanation
Indices: 539542--539588 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
539532 ATATATTAAA
539542 ATAAAAATAATTTTTT
1 ATAAAAATAATTTTTT
*
539558 ATAAAAATTATTAATTTT
1 ATAAAAATAATT--TTTT
539576 -TAAATAATAATTT
1 ATAAA-AATAATTT
539589 GAGCTTTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 12 0.46
17 4 0.15
18 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAAAATAATTTTTT
Found at i:539810 original size:27 final size:28
Alignment explanation
Indices: 539748--539823 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
539738 ATGTCAAATT
*
539748 TATATAATAAAAAT-TATTAAGATATTAAAA
1 TATATAA-AAAAATATATT-ATA-ATTAAAA
* * *
539778 TTTAT-ATAAAATATATTATAATTATAA
1 TATATAAAAAAATATATTATAATTAAAA
539805 TATATAAAAAAATATATTA
1 TATATAAAAAAATATATTA
539824 CCAAATCTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 10 0.26
28 19 0.50
29 5 0.13
30 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
TATATAAAAAAATATATTATAATTAAAA
Found at i:540578 original size:16 final size:17
Alignment explanation
Indices: 540559--540592 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
540549 TTATCTTATA
540559 TATATTTTAATA-CATT
1 TATATTTTAATATCATT
*
540575 TATATTTTTATATCATT
1 TATATTTTAATATCATT
540592 T
1 T
540593 TCAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTTTAATATCATT
Found at i:541770 original size:19 final size:21
Alignment explanation
Indices: 541719--541771 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
541709 TATTTTAATT
541719 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
541740 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
*
541760 -ATATTTTAATAT
1 TAAATTTTAATAT
541772 TTTTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 11 0.39
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:544824 original size:16 final size:17
Alignment explanation
Indices: 544798--544830 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
544788 AAAAAGACTT
544798 TTACACAAATCAATTAA
1 TTACACAAATCAATTAA
544815 TTAC-CAAATCAATTAA
1 TTACACAAATCAATTAA
544831 GTTATGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (17 bp):
TTACACAAATCAATTAA
Found at i:547415 original size:42 final size:42
Alignment explanation
Indices: 547364--547511 Score: 210
Period size: 42 Copynumber: 3.6 Consensus size: 42
547354 GGATTGTACT
*
547364 CTTGTTAAACTTCATTTTGATTTGCAAGTTGGATTTTTAGTG
1 CTTGTTAAACTTCATTTTCATTTGCAAGTTGGATTTTTAGTG
* ** * *
547406 CTTGTTAAACTTTATTTTCATTTTTAAGTTGGA-TTGTACT-
1 CTTGTTAAACTTCATTTTCATTTGCAAGTTGGATTTTTAGTG
*
547446 CTTGTTAAACTTCATTTTGATTTGCAAGTTGGATTTTTAGTG
1 CTTGTTAAACTTCATTTTCATTTGCAAGTTGGATTTTTAGTG
*
547488 CTTGTTAAACTTTATTTTCATTTG
1 CTTGTTAAACTTCATTTTCATTTG
547512 TAGAGTAATT
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 29 0.32
41 10 0.11
42 51 0.57
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.53
Consensus pattern (42 bp):
CTTGTTAAACTTCATTTTCATTTGCAAGTTGGATTTTTAGTG
Found at i:547431 original size:82 final size:82
Alignment explanation
Indices: 547344--547510 Score: 334
Period size: 82 Copynumber: 2.0 Consensus size: 82
547334 TTTAATTTAC
547344 TTTTTAAGTTGGATTGTACTCTTGTTAAACTTCATTTTGATTTGCAAGTTGGATTTTTAGTGCTT
1 TTTTTAAGTTGGATTGTACTCTTGTTAAACTTCATTTTGATTTGCAAGTTGGATTTTTAGTGCTT
547409 GTTAAACTTTATTTTCA
66 GTTAAACTTTATTTTCA
547426 TTTTTAAGTTGGATTGTACTCTTGTTAAACTTCATTTTGATTTGCAAGTTGGATTTTTAGTGCTT
1 TTTTTAAGTTGGATTGTACTCTTGTTAAACTTCATTTTGATTTGCAAGTTGGATTTTTAGTGCTT
547491 GTTAAACTTTATTTTCA
66 GTTAAACTTTATTTTCA
547508 TTT
1 TTT
547511 GTAGAGTAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.22, C:0.10, G:0.16, T:0.53
Consensus pattern (82 bp):
TTTTTAAGTTGGATTGTACTCTTGTTAAACTTCATTTTGATTTGCAAGTTGGATTTTTAGTGCTT
GTTAAACTTTATTTTCA
Found at i:550116 original size:2 final size:2
Alignment explanation
Indices: 550109--550135 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
550099 AGATGCATTC
550109 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
550136 GTAGTGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:551673 original size:2 final size:2
Alignment explanation
Indices: 551666--551705 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
551656 TAACTTAGCA
*
551666 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
551706 TTATTTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:552261 original size:18 final size:18
Alignment explanation
Indices: 552240--552282 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
552230 CCAATGATTT
*
552240 TAAATA-AATTATTTAAAA
1 TAAATATAATTA-ATAAAA
*
552258 TAAAAATAATTAATAAAA
1 TAAATATAATTAATAAAA
552276 TAAATAT
1 TAAATAT
552283 TTTATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATATAATTAATAAAA
Found at i:553900 original size:20 final size:20
Alignment explanation
Indices: 553875--553928 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
553865 CTATCACTAT
* *
553875 TTGTATCGATACATGGTACA
1 TTGTATCGATACATAGTAAA
553895 TTGTATCGATACATAGTAAA
1 TTGTATCGATACATAGTAAA
**
553915 AAGTATCGATACAT
1 TTGTATCGATACAT
553929 TGTGCCCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATAGTAAA
Found at i:559969 original size:20 final size:20
Alignment explanation
Indices: 559944--560007 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
559934 AAACTCATAT
559944 GTATCGATACAAGGAACTTA
1 GTATCGATACAAGGAACTTA
559964 GTATCGATAC-----A-TT-
1 GTATCGATACAAGGAACTTA
559977 GTATCGATACAAGGAACTTA
1 GTATCGATACAAGGAACTTA
559997 GTATCGATACA
1 GTATCGATACA
560008 TTGTATCGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.27
14 2 0.05
15 1 0.03
18 1 0.03
19 2 0.05
20 21 0.57
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (20 bp):
GTATCGATACAAGGAACTTA
Found at i:559982 original size:13 final size:13
Alignment explanation
Indices: 559964--560020 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 13
559954 AAGGAACTTA
559964 GTATCGATACATT
1 GTATCGATACATT
559977 GTATCGATACAAGGAACTT
1 GTATCGATAC-----A-TT
559996 AGTATCGATACATT
1 -GTATCGATACATT
560010 GTATCGATACA
1 GTATCGATACA
560021 AGGGCACTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.57
14 2 0.05
15 1 0.03
18 1 0.03
19 2 0.05
20 10 0.27
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:559985 original size:33 final size:33
Alignment explanation
Indices: 559943--560023 Score: 162
Period size: 33 Copynumber: 2.5 Consensus size: 33
559933 AAAACTCATA
559943 TGTATCGATACAAGGAACTTAGTATCGATACAT
1 TGTATCGATACAAGGAACTTAGTATCGATACAT
559976 TGTATCGATACAAGGAACTTAGTATCGATACAT
1 TGTATCGATACAAGGAACTTAGTATCGATACAT
560009 TGTATCGATACAAGG
1 TGTATCGATACAAGG
560024 GCACTATTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.30
Consensus pattern (33 bp):
TGTATCGATACAAGGAACTTAGTATCGATACAT
Found at i:562660 original size:32 final size:33
Alignment explanation
Indices: 562600--562661 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
562590 CCCTAGAAAG
562600 TATCGATACATAGTGCATTGTATCGATACACTA
1 TATCGATACATAGTGCATTGTATCGATACACTA
*
562633 TATCGATACATGGT-C-TTGGTATCGATACA
1 TATCGATACATAGTGCATT-GTATCGATACA
562662 TAGTGAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 2 0.07
32 12 0.44
33 13 0.48
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (33 bp):
TATCGATACATAGTGCATTGTATCGATACACTA
Found at i:562748 original size:26 final size:25
Alignment explanation
Indices: 562712--562773 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 25
562702 TTACCTCTGT
562712 TTGTATCGATATCAATAGATGGTACA
1 TTGTATCGATA-CAATAGATGGTACA
562738 TTGTATCG-----ATAGATGGTACA
1 TTGTATCGATACAATAGATGGTACA
562758 TTGTATCGATACAATA
1 TTGTATCGATACAATA
562774 CATAGTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
20 20 0.65
25 3 0.10
26 8 0.26
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (25 bp):
TTGTATCGATACAATAGATGGTACA
Found at i:562749 original size:20 final size:20
Alignment explanation
Indices: 562721--562768 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
562711 TTTGTATCGA
*
562721 TATCAATAGATGGTACATTG
1 TATCGATAGATGGTACATTG
562741 TATCGATAGATGGTACATTG
1 TATCGATAGATGGTACATTG
562761 TATCGATA
1 TATCGATA
562769 CAATACATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.35
Consensus pattern (20 bp):
TATCGATAGATGGTACATTG
Found at i:562994 original size:2 final size:2
Alignment explanation
Indices: 562987--563040 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
562977 TAACTTAGCA
*
562987 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
563029 AT AT AT AT AT AT
1 AT AT AT AT AT AT
563041 TCATGGGAGC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:566603 original size:20 final size:20
Alignment explanation
Indices: 566578--566654 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
566568 GTAAAAAGAT
566578 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
566598 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
566618 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
566638 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
566655 CTGGGTACTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 49 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:570217 original size:27 final size:27
Alignment explanation
Indices: 570151--570220 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
570141 AAGTATCTGC
*
570151 CATAGGTATTTTGGCATAGGTACCTGG
1 CATAGGTATTTTGGCATAGGTACCTAG
* ** *
570178 TATAAATACTTTGGCATAGGTACCTAG
1 CATAGGTATTTTGGCATAGGTACCTAG
*
570205 CATAGGCATTTTGGCA
1 CATAGGTATTTTGGCA
570221 CAGATACTTG
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (27 bp):
CATAGGTATTTTGGCATAGGTACCTAG
Found at i:570297 original size:14 final size:15
Alignment explanation
Indices: 570241--570300 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 15
570231 GCACAAACAC
* * *
570241 TTTGGCACAAGTATT
1 TTTGGCATAGGTACT
* *
570256 TTTAGCATAGGTACC
1 TTTGGCATAGGTACT
**
570271 TTTGGCACGGGTA-T
1 TTTGGCATAGGTACT
570285 TTTGGCATAGGTACT
1 TTTGGCATAGGTACT
570300 T
1 T
570301 GGCATAGCAG
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
14 11 0.33
15 22 0.67
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (15 bp):
TTTGGCATAGGTACT
Found at i:570297 original size:29 final size:30
Alignment explanation
Indices: 570240--570298 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
570230 GGCACAAACA
570240 CTTTGGCACAAGTATTTTTAGCATAGGTAC
1 CTTTGGCACAAGTATTTTTAGCATAGGTAC
** *
570270 CTTTGGCACGGGTA-TTTTGGCATAGGTAC
1 CTTTGGCACAAGTATTTTTAGCATAGGTAC
570299 TTGGCATAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (30 bp):
CTTTGGCACAAGTATTTTTAGCATAGGTAC
Found at i:575973 original size:79 final size:78
Alignment explanation
Indices: 575797--575978 Score: 244
Period size: 79 Copynumber: 2.3 Consensus size: 78
575787 TATTTTGGAG
575797 ATAAAGACGGA-GTTGGAGTATCCCCTCAAAAATAACGGGGCTGGAGTATCCCGATTGTGAAAAA
1 ATAAA-ACGGAGGTTGGAGTATCCCCTCAAAAATAACGGGGCTGGAGTATCCCGATTGTGAAAAA
***
575861 TTGGTGTTCTAAAA
65 TCAATGTTCTAAAA
* * *
575875 ATAAAACGGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGT-AGAAA
1 ATAAAACGGAGGTTGGAGTATCCCCTCAAAAATAACGGGGCTGGAGTAT-CCCGATTGTGA-AAA
*
575939 ATCAATGTTCTGAAA
64 ATCAATGTTCTAAAA
575954 ATAAAATC-GAGGTTGGAGTATCCCC
1 ATAAAA-CGGAGGTTGGAGTATCCCC
575979 GATGGTGGAA
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
77 4 0.04
78 42 0.46
79 45 0.49
80 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (78 bp):
ATAAAACGGAGGTTGGAGTATCCCCTCAAAAATAACGGGGCTGGAGTATCCCGATTGTGAAAAAT
CAATGTTCTAAAA
Done.