Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 54 of 199
Found at i:21195378 original size:71 final size:72
Alignment explanation
Indices: 21195262--21195408 Score: 287
Period size: 71 Copynumber: 2.1 Consensus size: 72
21195252 TTATTATTTT
21195262 ATTATTTAGTATATATATGTGGAAAGAAAGATGAAAAACCACCATTACAGCATCTTTCCCATGCA
1 ATTATTTAGTATATATATGTGGAAAGAAAGATGAAAAACCACCATTACAGCATCTTTCCCATGCA
21195327 TTTCA-C
66 TTTCACC
21195333 ATTATTTAGTATATATATGTGGAAAGAAAGATGAAAAACCACCATTACAGCATCTTTCCCATGCA
1 ATTATTTAGTATATATATGTGGAAAGAAAGATGAAAAACCACCATTACAGCATCTTTCCCATGCA
21195398 TTTCACC
66 TTTCACC
21195405 ATTA
1 ATTA
21195409 CAGCATCTTT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 70 0.93
72 5 0.07
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (72 bp):
ATTATTTAGTATATATATGTGGAAAGAAAGATGAAAAACCACCATTACAGCATCTTTCCCATGCA
TTTCACC
Found at i:21195414 original size:29 final size:29
Alignment explanation
Indices: 21195372--21195432 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
21195362 GATGAAAAAC
21195372 CACCATTACAGCATCTTTCCCATGCATTT
1 CACCATTACAGCATCTTTCCCATGCATTT
21195401 CACCATTACAGCATCTTTCCCATGCATTT
1 CACCATTACAGCATCTTTCCCATGCATTT
21195430 CAC
1 CAC
21195433 GTTAGTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.25, C:0.36, G:0.07, T:0.33
Consensus pattern (29 bp):
CACCATTACAGCATCTTTCCCATGCATTT
Found at i:21199728 original size:320 final size:319
Alignment explanation
Indices: 21199146--21199786 Score: 946
Period size: 320 Copynumber: 2.0 Consensus size: 319
21199136 AACCGAAGGT
* * *
21199146 CAAGATTACAATACATCGATAGACGAGATTCATCCTATCTTTTAAATCATGGGATTTACAAGATA
1 CAAGATTACAATACATCGAGAGACGAGATTCATCCTATCTTTTAAATCATGAGATTTACAAGACA
*
21199211 TGCCATATCAAATCAAATCAAATCTTTACAAGATATGATTCTATCAATCTTCTAATATTAGTTAC
66 TGCCATATCAAATCAAATCAAATCTTTACAAGATATGATTCTATCAATCTTCTAAGATTAGTTAC
21199276 CAAAATAGCCTAAATTGCCATATCTTCATTATCGGGCCAACCAAGCTTCAATCTAATGGGCTTCT
131 CAAAATAGCCTAAATTGCCATATCTTCATTATCGGGCCAACCAAGCTTCAATCTAAT-GGCTTCT
* * * *
21199341 CCAATAAGTTACCGAATCAGGCCAGTTCTTACGGGCCAAATGATCCTTATCTACATAATAGACCT
195 CCAACAAGTTACCAAATCAGGCCAGTTCTTACGGGCCAAATGATCCTCATCTACACAATAGACCT
* * * *
21199406 TCATTGGATGCATTTGGTGCGATGCTCACAGGCTTTGAACTCTGGCCCGTGACATTCTCC
260 TCATCGGATGCATTTGGTGAGATGCTCACAGACTTTGAACTCCGGCCCGTGACATTCTCC
*
21199466 CAAGATTACAATACATCGACGA-ACGAGATTCATCCTATCTTTTAAATCATGAGATTTACGAGAC
1 CAAGATTACAATACATCGA-GAGACGAGATTCATCCTATCTTTTAAATCATGAGATTTACAAGAC
* * *
21199530 ATGTCATATGAAATCTAAT-ATAATCTTTACAAGATATGATTCTATCAATCTTCTAAGATTAGTT
65 ATGCCATATCAAATCAAATCA-AATCTTTACAAGATATGATTCTATCAATCTTCTAAGATTAGTT
* * * * * * * * *
21199594 ACCGAAATAGCCTAAGTTGTCATATTTTTATTATCGGGCTAACCAGGCTTTAATCTGGCAT-GCT
129 ACCAAAATAGCCTAAATTGCCATATCTTCATTATCGGGCCAACCAAGCTTCAATCT--AATGGCT
* *
21199658 TCTCTAACAAGTTACCAAATCAGGCCAGTTTTTACGGGCCAAATGATCCTCATCTACACAATAGA
192 TCTCCAACAAGTTACCAAATCAGGCCAGTTCTTACGGGCCAAATGATCCTCATCTACACAATAGA
* * *
21199723 CCTTCATCGGATGCATTTGGTGAGATGGTCATAGACTTTGAACTCCGGCCCTTGACATTCTCC
257 CCTTCATCGGATGCATTTGGTGAGATGCTCACAGACTTTGAACTCCGGCCCGTGACATTCTCC
21199786 C
1 C
21199787 CCACCCATTC
Statistics
Matches: 287, Mismatches: 30, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
319 1 0.00
320 283 0.99
321 1 0.00
322 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (319 bp):
CAAGATTACAATACATCGAGAGACGAGATTCATCCTATCTTTTAAATCATGAGATTTACAAGACA
TGCCATATCAAATCAAATCAAATCTTTACAAGATATGATTCTATCAATCTTCTAAGATTAGTTAC
CAAAATAGCCTAAATTGCCATATCTTCATTATCGGGCCAACCAAGCTTCAATCTAATGGCTTCTC
CAACAAGTTACCAAATCAGGCCAGTTCTTACGGGCCAAATGATCCTCATCTACACAATAGACCTT
CATCGGATGCATTTGGTGAGATGCTCACAGACTTTGAACTCCGGCCCGTGACATTCTCC
Found at i:21202598 original size:50 final size:50
Alignment explanation
Indices: 21202480--21202756 Score: 428
Period size: 50 Copynumber: 5.5 Consensus size: 50
21202470 GATAATAACA
** * *
21202480 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTACTAATGTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* * * **
21202531 TGCCCATGCCATATCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
21202581 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
21202631 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
21202681 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
21202731 TGCCAACGCCATGTCCCAGACATGGT
1 TGCCAAAGCCATGTCCCAGACATGGT
21202757 GTAACACCCC
Statistics
Matches: 207, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
50 174 0.84
51 33 0.16
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:21204023 original size:27 final size:27
Alignment explanation
Indices: 21203991--21204042 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
21203981 ACCCTGAATC
*
21203991 GGGGAATCAGCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
21204018 GGGGAATCAGCACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
21204043 TTTCATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.25, T:0.13
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:21204117 original size:70 final size:71
Alignment explanation
Indices: 21204000--21204151 Score: 243
Period size: 70 Copynumber: 2.1 Consensus size: 71
21203990 CGGGGAATCA
* *
21204000 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAA-CCCCTTTTCATTTCAAATATACAATG
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATG
21204064 GATATC
66 GATATC
***
21204070 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATACAAT
21204135 GGATATC
65 GGATATC
21204142 GCACTTAGCA
1 GCACTTAGCA
21204152 CCACCAATGA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 38 0.51
71 7 0.09
72 30 0.40
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (71 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATG
GATATC
Found at i:21204187 original size:77 final size:71
Alignment explanation
Indices: 21204000--21204188 Score: 229
Period size: 70 Copynumber: 2.6 Consensus size: 71
21203990 CGGGGAATCA
* * *
21204000 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAA-CCCCTTTTCATTTCAAATATACAATG
1 GCACTTAGCAACCCCTCCGGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATG
21204064 GATATC
66 GATATC
* ***
21204070 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCCGGGGAATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATACAAT
21204135 GGATATC
65 GGATATC
*
21204142 GCACTTAGC-ACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCC
1 GCACTTAGCAACC-CC--T---CCGGGGAATCAGCACATAGCAACCCC
21204189 TCGGGGGAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
70 38 0.37
71 10 0.10
72 31 0.30
74 1 0.01
77 24 0.23
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (71 bp):
GCACTTAGCAACCCCTCCGGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATG
GATATC
Found at i:21204197 original size:104 final size:103
Alignment explanation
Indices: 21204070--21204292 Score: 376
Period size: 104 Copynumber: 2.2 Consensus size: 103
21204060 AATGGATATC
21204070 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
21204135 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACC-ATAAACCGGGGAATCA
21204174 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
*
21204239 GGATCACGCACATAGCACCACCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCATAAACCGGGGAATCA
**
21204277 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
21204293 TTATATACAA
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
103 28 0.25
104 84 0.74
105 1 0.01
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCATAAACCGGGGAATCA
Found at i:21204647 original size:29 final size:29
Alignment explanation
Indices: 21204614--21204677 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
21204604 TAATCCACCA
21204614 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
21204643 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
21204673 CCCAA
1 CCCAA
21204678 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:21204651 original size:30 final size:30
Alignment explanation
Indices: 21204621--21204677 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
21204611 CCACCCAACT
21204621 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
21204650 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
21204678 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:21211524 original size:25 final size:25
Alignment explanation
Indices: 21211496--21211543 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
21211486 CGCTGAATCG
*
21211496 GGGAATCAGCACTTAGCAACCCCTC
1 GGGAATCAGCACATAGCAACCCCTC
21211521 GGGAATCAGCACATAGCAACCCC
1 GGGAATCAGCACATAGCAACCCC
21211544 CTTTTCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.35, G:0.21, T:0.12
Consensus pattern (25 bp):
GGGAATCAGCACATAGCAACCCCTC
Found at i:21211618 original size:71 final size:70
Alignment explanation
Indices: 21211504--21211654 Score: 232
Period size: 72 Copynumber: 2.1 Consensus size: 70
21211494 CGGGGAATCA
*
21211504 GCACTTAGCAACCCCTCGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATACAATGG
1 GCACTTAGCAACCCCTCGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
*
21211568 ATATT
66 ATATC
***
21211573 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTC--GGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAAT
21211638 GGATATC
64 GGATATC
21211645 GCACTTAGCA
1 GCACTTAGCA
21211655 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 17 0.23
71 27 0.36
72 30 0.41
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (70 bp):
GCACTTAGCAACCCCTCGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATGG
ATATC
Found at i:21211690 original size:77 final size:71
Alignment explanation
Indices: 21211504--21211691 Score: 229
Period size: 72 Copynumber: 2.6 Consensus size: 71
21211494 CGGGGAATCA
*
21211504 GCACTTAGCAACCCCT-C-GGGAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATACAATG
1 GCACTTAGCAACCCCTCCGGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATG
*
21211567 GATATT
66 GATATC
* ***
21211573 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCCGGGGAATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATACAAT
21211638 GGATATC
65 GGATATC
*
21211645 GCACTTAGC-ACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCC
1 GCACTTAGCAACC-CC--T---CCGGGGAATCAGCACATAGCAACCCC
21211692 TCGGGGGAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
69 16 0.16
71 30 0.29
72 31 0.30
74 1 0.01
77 24 0.24
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (71 bp):
GCACTTAGCAACCCCTCCGGGGAATCAGCACATAGCAACCCCCTTTACATTTCAAAGATACAATG
GATATC
Found at i:21211707 original size:104 final size:105
Alignment explanation
Indices: 21211573--21211785 Score: 376
Period size: 105 Copynumber: 2.0 Consensus size: 105
21211563 AATGGATATT
21211573 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATATGG
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATGG
* *
21211637 TGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 TGGATCA-CGCACATAGAACCACCAATGAACCGGGGAATCA
21211677 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATGG
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATGG
*
21211742 TGGATCACGCACATAGAACCACCAATGAATCGGGGAATCA
66 TGGATCACGCACATAGAACCACCAATGAACCGGGGAATCA
21211782 GCAC
1 GCAC
21211786 ACAACAACCC
Statistics
Matches: 104, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
104 43 0.41
105 60 0.58
106 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (105 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATATGG
TGGATCACGCACATAGAACCACCAATGAACCGGGGAATCA
Found at i:21213136 original size:13 final size:13
Alignment explanation
Indices: 21213115--21213144 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21213105 GCTTGGATAA
21213115 TCATCAAATAAAT
1 TCATCAAATAAAT
*
21213128 TCATGAAATAAAT
1 TCATCAAATAAAT
21213141 TCAT
1 TCAT
21213145 AGTTGCTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:21213393 original size:30 final size:28
Alignment explanation
Indices: 21213358--21213413 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
21213348 CCTCGACTCT
*
21213358 AACTTTTTCAAAATTACGATTTTGCCCCTA
1 AACTTTTACAAAATTAC-ATTTT-CCCCTA
*
21213388 AACTTTTACATAATTACATTTTCCCC
1 AACTTTTACAAAATTACATTTTCCCC
21213414 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 5 0.21
30 15 0.62
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (28 bp):
AACTTTTACAAAATTACATTTTCCCCTA
Found at i:21216029 original size:4 final size:4
Alignment explanation
Indices: 21216020--21216064 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
21216010 CCAGATATAT
21216020 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
21216065 TATGAAACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:21224709 original size:252 final size:252
Alignment explanation
Indices: 21224264--21224769 Score: 976
Period size: 252 Copynumber: 2.0 Consensus size: 252
21224254 TCAATCACCA
21224264 ATCTAGTTCTAAAAACTTTGGTTTTGATCTAGATCTCTTCCGTCTTTGGCTTTTAGAGGAGATAA
1 ATCTAGTTCTAAAAACTTTGGTTTTGATCTAGATCTCTTCCGTCTTTGGCTTTTAGAGGAGATAA
*
21224329 TTCAGAAGATCGTTGGGATACCTCCACCTCATTCAGCAACCGGGGTTGACAAGATTATTTGGAGA
66 TTCAGAAGATCGTCGGGATACCTCCACCTCATTCAGCAACCGGGGTTGACAAGATTATTTGGAGA
21224394 GGTACTTCGACTTGTGGTTTCTCCCTTAAAAATGCTTATATGAAGCTTCAGGAGGGATCGTGGAA
131 GGTACTTCGACTTGTGGTTTCTCCCTTAAAAATGCTTATATGAAGCTTCAGGAGGGATCGTGGAA
* *
21224459 TCTGAAAGAGCCTATGTGAAGAATTTCATGGAAATTTCAAGGACCTCAATAGATTAG
196 TCCGAAAGAGCCTATGTGAAGAATTTCATGGAAATTTCAAGGACCCCAATAGATTAG
21224516 ATCTAGTTCTAAAAACTTTGGTTTTGATCTAGATCTCTTCCGTCTTTGGCTTTTAGAGGAGATAA
1 ATCTAGTTCTAAAAACTTTGGTTTTGATCTAGATCTCTTCCGTCTTTGGCTTTTAGAGGAGATAA
*
21224581 TTCAGAAGATCGTCGGGATACCTCCACCTCATTCGGCAACCGGGGTTGACAAGATTATTTGGAGA
66 TTCAGAAGATCGTCGGGATACCTCCACCTCATTCAGCAACCGGGGTTGACAAGATTATTTGGAGA
21224646 GGTACTTCGACTTGTGGTTTCTCCCTTAAAAATGCTTATATGAAGCTTCAGGAGGGATCGTGGAA
131 GGTACTTCGACTTGTGGTTTCTCCCTTAAAAATGCTTATATGAAGCTTCAGGAGGGATCGTGGAA
21224711 TCCGAAAGAGCCTATGTGAAGAATTTCATGGAAATTTCAAGGACCCCAATAGATTAG
196 TCCGAAAGAGCCTATGTGAAGAATTTCATGGAAATTTCAAGGACCCCAATAGATTAG
21224768 AT
1 AT
21224770 TATTTATTTG
Statistics
Matches: 250, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
252 250 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (252 bp):
ATCTAGTTCTAAAAACTTTGGTTTTGATCTAGATCTCTTCCGTCTTTGGCTTTTAGAGGAGATAA
TTCAGAAGATCGTCGGGATACCTCCACCTCATTCAGCAACCGGGGTTGACAAGATTATTTGGAGA
GGTACTTCGACTTGTGGTTTCTCCCTTAAAAATGCTTATATGAAGCTTCAGGAGGGATCGTGGAA
TCCGAAAGAGCCTATGTGAAGAATTTCATGGAAATTTCAAGGACCCCAATAGATTAG
Found at i:21229805 original size:12 final size:13
Alignment explanation
Indices: 21229780--21229811 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
21229770 AATAAAGAAT
21229780 AAATAGATAAAAG
1 AAATAGATAAAAG
21229793 AAATAGA-AAAAG
1 AAATAGATAAAAG
21229805 AAATAGA
1 AAATAGA
21229812 GATAGAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
AAATAGATAAAAG
Found at i:21230147 original size:18 final size:19
Alignment explanation
Indices: 21230114--21230151 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
21230104 GTGAAAATTT
21230114 TGAAATTTAGGAATTTAAA
1 TGAAATTTAGGAATTTAAA
*
21230133 TGAAA-TTAGGGATTTAAA
1 TGAAATTTAGGAATTTAAA
21230151 T
1 T
21230152 TTAGTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (19 bp):
TGAAATTTAGGAATTTAAA
Found at i:21230837 original size:40 final size:40
Alignment explanation
Indices: 21230710--21230838 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 40
21230700 TTCGAGTCAG
* * *
21230710 TGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTCGA
1 TGAGACACTGGGTGTCAATTTATTACTTCGGATT-ATCCGA
* * * * * * *
21230751 TAAGGCATTGGGTGCCAA--T-TTACTTCGGTTTAGCTGA
1 TGAGACACTGGGTGTCAATTTATTACTTCGGATTATCCGA
* *
21230788 TGAAACACTGGGTGTCAATTTATTACTTCGAATTATCCGA
1 TGAGACACTGGGTGTCAATTTATTACTTCGGATTATCCGA
*
21230828 TGAGGCACTGG
1 TGAGACACTGG
21230839 ATGCCAAACT
Statistics
Matches: 64, Mismatches: 21, Indels: 7
0.70 0.23 0.08
Matches are distributed among these distances:
37 16 0.25
38 9 0.14
39 2 0.03
40 23 0.36
41 14 0.22
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (40 bp):
TGAGACACTGGGTGTCAATTTATTACTTCGGATTATCCGA
Found at i:21233533 original size:20 final size:20
Alignment explanation
Indices: 21233508--21233547 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21233498 AATATTTTTC
*
21233508 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
21233528 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
21233548 TTATTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:21233554 original size:34 final size:35
Alignment explanation
Indices: 21233496--21233562 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
21233486 CAAACACCAG
* *
21233496 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
21233531 AAAACATTTTCCAG-AAATTATTTTACAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
21233563 TATTTTACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:21233559 original size:14 final size:14
Alignment explanation
Indices: 21233531--21233573 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
21233521 ACAGAAAAGT
* *
21233531 AAAACATTTTCCAG
1 AAAATATTTTACAG
*
21233545 AAATTATTTTACAG
1 AAAATATTTTACAG
21233559 AAAATATTTTACAG
1 AAAATATTTTACAG
21233573 A
1 A
21233574 TTCAATCGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35
Consensus pattern (14 bp):
AAAATATTTTACAG
Found at i:21235185 original size:20 final size:20
Alignment explanation
Indices: 21235134--21235187 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
21235124 AGGATGGTTA
21235134 ATTATTATTTCTATTTAAACT
1 ATTATTATTT-TATTTAAACT
*
21235155 -TGT-TTATTTTTATTTAAGCT
1 AT-TATTA-TTTTATTTAAACT
21235175 ATTATTATTTTAT
1 ATTATTATTTTAT
21235188 GTTTAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.63
Consensus pattern (20 bp):
ATTATTATTTTATTTAAACT
Found at i:21238722 original size:11 final size:11
Alignment explanation
Indices: 21238706--21238737 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
21238696 AGAGAGAAAG
21238706 AAAAGGAAAAT
1 AAAAGGAAAAT
21238717 AAAAGGAAAAT
1 AAAAGGAAAAT
*
21238728 AAAAAGAAAA
1 AAAAGGAAAA
21238738 GGGAGAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (11 bp):
AAAAGGAAAAT
Found at i:21251430 original size:65 final size:65
Alignment explanation
Indices: 21251361--21251487 Score: 209
Period size: 65 Copynumber: 2.0 Consensus size: 65
21251351 AATAGTAAAT
* *
21251361 ATATATTTATAACCCTAAACCTCGGATTATAAAGAGGTGCTAATGTAATAAACTTAGTTAAAAAA
1 ATATATTTATAACCCTAAACCTCGAATCATAAAGAGGTGCTAATGTAATAAACTTAGTTAAAAAA
* * *
21251426 ATATATTTATAATCCTAAACCTCGAATCATAAAGAGGTGTTGATGTAATAAACTTAGTTAAA
1 ATATATTTATAACCCTAAACCTCGAATCATAAAGAGGTGCTAATGTAATAAACTTAGTTAAA
21251488 CTAAGATGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (65 bp):
ATATATTTATAACCCTAAACCTCGAATCATAAAGAGGTGCTAATGTAATAAACTTAGTTAAAAAA
Found at i:21258344 original size:16 final size:17
Alignment explanation
Indices: 21258320--21258353 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21258310 AGATGAAATC
*
21258320 TTTATTTAAT-TTAATT
1 TTTACTTAATGTTAATT
21258336 TTTACTTAATGTTAATT
1 TTTACTTAATGTTAATT
21258353 T
1 T
21258354 AAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTACTTAATGTTAATT
Found at i:21285396 original size:14 final size:14
Alignment explanation
Indices: 21285377--21285403 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21285367 ATAATCTGTC
21285377 GTTGTTGCCTTACT
1 GTTGTTGCCTTACT
21285391 GTTGTTGCCTTAC
1 GTTGTTGCCTTAC
21285404 AGTTCCATTT
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:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
GTTGTTGCCTTACT
Found at i:21285604 original size:12 final size:12
Alignment explanation
Indices: 21285587--21285616 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
21285577 TATTTGAAAT
*
21285587 TTTATATTCTGG
1 TTTATAATCTGG
21285599 TTTATAATCTGG
1 TTTATAATCTGG
21285611 TTTATA
1 TTTATA
21285617 CCTTGTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (12 bp):
TTTATAATCTGG
Found at i:21287195 original size:13 final size:13
Alignment explanation
Indices: 21287177--21287201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21287167 GGCCGGGTCT
21287177 GGACAAAATTTCA
1 GGACAAAATTTCA
21287190 GGACAAAATTTC
1 GGACAAAATTTC
21287202 GGGCCGGGCC
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
GGACAAAATTTCA
Found at i:21288862 original size:23 final size:23
Alignment explanation
Indices: 21288835--21288956 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
21288825 AGTGTTATTG
*
21288835 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
21288858 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
21288881 AACAGTGCTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
21288904 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
21288927 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
21288950 ATCAGTG
1 ATCAGTG
21288957 TTGCACTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 86 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:21288907 original size:46 final size:46
Alignment explanation
Indices: 21288837--21288956 Score: 204
Period size: 46 Copynumber: 2.6 Consensus size: 46
21288827 TGTTATTGAT
*
21288837 CAGTGGTAGCTTCGGCTACGTTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
* *
21288883 CAGTGCTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
*
21288929 CAGTGGTAGCTTCGGCTACATATCAGTG
1 CAGTGGTAGCTTCGGCTACATTTCAGTG
21288957 TTGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.31
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
Found at i:21291988 original size:46 final size:46
Alignment explanation
Indices: 21291918--21292056 Score: 190
Period size: 46 Copynumber: 3.0 Consensus size: 46
21291908 ACAATGCTAT
21291918 AACTCAGTATGGTTTT-ATTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCATT-ACTGAAATACCATACCTACTTTTCAC
* * *
21291964 AACTCAGTATGGTTTTCCTTACTGAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCATTACTGAAATACCATACCTACTTTTCAC
* * * * *
21292010 AACTCAGTATAGTTTTCTTTTCTGAACTATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCATTACTGAAATACCATACCTACTTTTCAC
21292056 A
1 A
21292057 CTTTGCCATG
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 80 0.98
47 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCATTACTGAAATACCATACCTACTTTTCAC
Found at i:21294215 original size:25 final size:25
Alignment explanation
Indices: 21294187--21294249 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
21294177 TACGAGCACT
*
21294187 TAACGGGAAGCTC-TTTCAAGCCATA
1 TAACGGGAAGCTCATGT-AAGCCATA
* *
21294212 TAACGGGAAGCTCATGTGAGCCATG
1 TAACGGGAAGCTCATGTAAGCCATA
21294237 TAACGGGAAGCTC
1 TAACGGGAAGCTC
21294250 CGGAGAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 32 0.94
26 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (25 bp):
TAACGGGAAGCTCATGTAAGCCATA
Found at i:21303501 original size:24 final size:24
Alignment explanation
Indices: 21303452--21303518 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 24
21303442 ACTATATGTT
* *
21303452 AAATATATTTTTTTATTTTTTGATC
1 AAATATATTTATTTA-TTTTTAATC
21303477 AAATATATTTATTTATTTTTAATC
1 AAATATATTTATTTATTTTTAATC
*
21303501 AAATATATATTATATATT
1 AAATATAT-TTATTTATT
21303519 AAATATATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 16 0.42
25 22 0.58
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (24 bp):
AAATATATTTATTTATTTTTAATC
Found at i:21303522 original size:18 final size:17
Alignment explanation
Indices: 21303501--21303534 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
21303491 ATTTTTAATC
21303501 AAATATATATTATATATT
1 AAATATATATTA-ATATT
21303519 AAATATATATTAATAT
1 AAATATATATTAATAT
21303535 GGGCCGGGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATATATATTAATATT
Found at i:21305304 original size:15 final size:15
Alignment explanation
Indices: 21305279--21305311 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
21305269 TATTATTTAA
21305279 ATTTTAAAA-TTATT
1 ATTTTAAAATTTATT
21305293 ATTTTCAAAATTTATT
1 ATTTT-AAAATTTATT
21305309 ATT
1 ATT
21305312 AAAATAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 4 0.24
16 8 0.47
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTAAAATTTATT
Found at i:21306501 original size:20 final size:20
Alignment explanation
Indices: 21306347--21306520 Score: 119
Period size: 21 Copynumber: 8.7 Consensus size: 20
21306337 GCGCCAATGG
* *
21306347 GTAA-TTTTGTATGTATATT
1 GTAATTTTTTTATGAATATT
*
21306366 GTAACTTTTTGTATGAATATT
1 GTAA-TTTTTTTATGAATATT
* *
21306387 ATAA-TTTTGTATGAATATT
1 GTAATTTTTTTATGAATATT
* *
21306406 GTAATTATTTTATAATTAATTTT
1 GTAATT-TTTT-T-ATGAATATT
* *
21306429 GT-ATTTATAGTTT-TGGAT-TA
1 GTAATTT-T--TTTATGAATATT
* *
21306449 GT-A-TTTTGTATGAATAGT
1 GTAATTTTTTTATGAATATT
21306467 GTAATTTTTTGTATGAATATT
1 GTAATTTTTT-TATGAATATT
21306488 GTAATTTTTTTATGAATATT
1 GTAATTTTTTTATGAATATT
*
21306508 GTAATTATTTTAT
1 GTAATTTTTTTAT
21306521 AATTAATTTT
Statistics
Matches: 125, Mismatches: 16, Indels: 27
0.74 0.10 0.16
Matches are distributed among these distances:
16 2 0.02
17 4 0.03
18 3 0.02
19 25 0.20
20 31 0.25
21 43 0.34
22 5 0.04
23 10 0.08
24 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (20 bp):
GTAATTTTTTTATGAATATT
Found at i:21306532 original size:23 final size:21
Alignment explanation
Indices: 21306450--21306816 Score: 107
Period size: 23 Copynumber: 17.3 Consensus size: 21
21306440 TTTGGATTAG
*
21306450 TATTTTGTATGAATAGTGTAAT
1 TATTTT-TATGAATATTGTAAT
21306472 T-TTTTGTATGAATATTGTAAT
1 TATTTT-TATGAATATTGTAAT
21306493 T-TTTTTATGAATATTGTAAT
1 TATTTTTATGAATATTGTAAT
* * *
21306513 TATTTTATAATTAATTTTGTATT
1 TATTTT-T-ATGAATATTGTAAT
*
21306536 TATAGTTTT-TG-AT-TAGT-A-
1 TAT--TTTTATGAATATTGTAAT
*
21306554 T-TTTGTATGAATATTGTAATTTT
1 TATTTTTATGAATATTGTAA---T
21306577 ATAATTTTGTATGAATATTGTAAT
1 -T-ATTTT-TATGAATATTGTAAT
* * *
21306601 TATTTTATAATTAATTTTGTATT
1 TATTTT-T-ATGAATATTGTAAT
* *
21306624 TATAGTTTT-TG-GT-TAGT-A-
1 TAT--TTTTATGAATATTGTAAT
* * *
21306642 T-TTTGTATGAACATTATAA-
1 TATTTTTATGAATATTGTAAT
* *
21306661 T-GTTGTATGAATATTGTAAT
1 TATTTTTATGAATATTGTAAT
* * *
21306681 TATTTTATAATTAATTTTGTATT
1 TATTTT-T-ATGAATATTGTAAT
*
21306704 TATAGTTTTA-G-AT-TAGT-A-
1 TAT--TTTTATGAATATTGTAAT
*
21306722 T-TTTGTATGAATATTGTAATTTT
1 TATTTTTATGAATATTGTAA---T
21306745 GTAATTTTGTATGAATATTGTAATAT
1 -T-ATTTT-TATGAATATTGT-A-AT
*
21306771 TATTTGTATGAATATTGTAA-
1 TATTTTTATGAATATTGTAAT
*
21306791 T-TTTGTATGAATATTGTAAT
1 TATTTTTATGAATATTGTAAT
21306811 TATTTT
1 TATTTT
21306817 ATAATTAATT
Statistics
Matches: 260, Mismatches: 39, Indels: 93
0.66 0.10 0.24
Matches are distributed among these distances:
15 10 0.04
16 5 0.02
17 7 0.03
18 11 0.04
19 37 0.14
20 28 0.11
21 39 0.15
22 12 0.05
23 56 0.22
24 10 0.04
25 10 0.04
26 7 0.03
27 26 0.10
28 1 0.00
29 1 0.00
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (21 bp):
TATTTTTATGAATATTGTAAT
Found at i:21306535 original size:102 final size:102
Alignment explanation
Indices: 21306350--21306608 Score: 394
Period size: 102 Copynumber: 2.5 Consensus size: 102
21306340 CCAATGGGTA
* * * *
21306350 ATTTTGTATGTATATTGTAACTTTTTGTATGAATATTATAA-TTTTGTATGAATATTGTAATTAT
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTTTTATGAATATTGTAATTAT
21306414 TTTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
66 TTTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
*
21306451 ATTTTGTATGAATAGTGTAATTTTTTGTATGAATATTGTAATTTTTTTATGAATATTGTAATTAT
1 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTTTTATGAATATTGTAATTAT
*
21306516 TTTATAATTAATTTTGTATTTATAGTTTTTGATTAGT
66 TTTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
*
21306553 ATTTTGTATGAATATTGTAATTTTATAATTTTGTATGAATATTGTAATTATTTTAT
1 ATTTTGTATGAATATTGTAA---T-T--TTTTGTATGAATATTGTAATTTTTTTAT
21306609 AATTAATTTT
Statistics
Matches: 143, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
101 37 0.26
102 77 0.54
105 1 0.01
106 1 0.01
108 27 0.19
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (102 bp):
ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTTTTATGAATATTGTAATTAT
TTTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
Found at i:21306545 original size:27 final size:27
Alignment explanation
Indices: 21306513--21306633 Score: 70
Period size: 27 Copynumber: 4.2 Consensus size: 27
21306503 ATATTGTAAT
21306513 TATTTTATAATTAATTTTGTATTTATAG
1 TATTTTATAATT-ATTTTGTATTTATAG
* * * *
21306541 T-TTTTGATTAGTATTTTGTATGAATATTG
1 TATTTT-ATAATTATTTTGTAT--TTATAG
*
21306570 TAATTTTATAATT-TTGTATGAATATTGTA-AT
1 T-ATTTTATAATTATT-T-TG--TATT-TATAG
21306601 TATTTTATAATTAATTTTGTATTTATAG
1 TATTTTATAATT-ATTTTGTATTTATAG
21306629 T-TTTT
1 TATTTT
21306634 GGTTAGTATT
Statistics
Matches: 70, Mismatches: 10, Indels: 27
0.65 0.09 0.25
Matches are distributed among these distances:
27 19 0.27
28 11 0.16
29 7 0.10
30 18 0.26
31 8 0.11
32 4 0.06
33 3 0.04
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (27 bp):
TATTTTATAATTATTTTGTATTTATAG
Found at i:21306590 original size:88 final size:88
Alignment explanation
Indices: 21306493--21306768 Score: 442
Period size: 88 Copynumber: 3.2 Consensus size: 88
21306483 ATATTGTAAT
*
21306493 TTTTTTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTT
1 TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTT
21306558 GTATGAATATTGTAATTTTATAA
66 GTATGAATATTGTAATTTTATAA
*
21306581 TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGGTTAGTATTTT
1 TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTT
*
21306646 GTATG-A-A----CA--TTATAA
66 GTATGAATATTGTAATTTTATAA
* *
21306661 TGTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTAGATTAGTATTTT
1 TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTT
*
21306726 GTATGAATATTGTAATTTTGTAA
66 GTATGAATATTGTAATTTTATAA
21306749 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
21306769 ATTATTTGTA
Statistics
Matches: 171, Mismatches: 9, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
80 73 0.43
81 1 0.01
82 2 0.01
86 2 0.01
87 1 0.01
88 92 0.54
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (88 bp):
TTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTT
GTATGAATATTGTAATTTTATAA
Found at i:21306667 original size:80 final size:80
Alignment explanation
Indices: 21306575--21306747 Score: 301
Period size: 80 Copynumber: 2.2 Consensus size: 80
21306565 TATTGTAATT
* *
21306575 TTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGGTTAG
1 TTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTAGATTAG
21306640 TATTTTGTATGAACA
66 TATTTTGTATGAACA
*
21306655 TTATAATGTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTAGATTAG
1 TTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTAGATTAG
*
21306720 TATTTTGTATGAATA
66 TATTTTGTATGAACA
*
21306735 TTGTAATTTTGTA
1 TTATAATTTTGTA
21306748 ATTTTGTATG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 87 1.00
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.56
Consensus pattern (80 bp):
TTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTAGATTAG
TATTTTGTATGAACA
Found at i:21306742 original size:50 final size:46
Alignment explanation
Indices: 21306688--21306810 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 46
21306678 AATTATTTTA
** *
21306688 TAATTAATTTTGTATTTATAGTTTTAGATTAGTATTTTGTATGAATATTG
1 TAATTAATTTTGTATGAATA-TTGTA-A-TAGTA-TTTGTATGAATATTG
*
21306738 TAATTTTGTAATTTTGTATGAATATTGTAATATTATTTGTATGAATATTG
1 TAA---T-TAATTTTGTATGAATATTGTAATAGTATTTGTATGAATATTG
21306788 ----TAATTTTGTATGAATATTGTAAT
1 TAATTAATTTTGTATGAATATTGTAAT
21306811 TATTTTATAA
Statistics
Matches: 65, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
42 23 0.35
50 18 0.28
51 4 0.06
52 1 0.02
53 5 0.08
54 14 0.22
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (46 bp):
TAATTAATTTTGTATGAATATTGTAATAGTATTTGTATGAATATTG
Found at i:21306745 original size:19 final size:19
Alignment explanation
Indices: 21306743--21306811 Score: 102
Period size: 19 Copynumber: 3.4 Consensus size: 19
21306733 TATTGTAATT
21306743 TTGTAATTTTGTATGAATA
1 TTGTAATTTTGTATGAATA
21306762 TTGTAATATTATTTGTATGAATA
1 TTGT-A-A-T-TTTGTATGAATA
21306785 TTGTAATTTTGTATGAATA
1 TTGTAATTTTGTATGAATA
21306804 TTGTAATT
1 TTGTAATT
21306812 ATTTTATAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
19 24 0.52
20 2 0.04
21 2 0.04
22 2 0.04
23 16 0.35
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (19 bp):
TTGTAATTTTGTATGAATA
Found at i:21306751 original size:27 final size:27
Alignment explanation
Indices: 21306721--21306797 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
21306711 TTAGATTAGT
21306721 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
21306748 ATTTTGTATGAATATTGTAA-TAT-T-
1 ATTTTGTATGAATATTGTAATTTTGTA
21306772 A-TTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
21306798 TGAATATTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 18 0.40
24 3 0.07
25 2 0.04
26 2 0.04
27 20 0.44
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATTTTGTA
Found at i:21307192 original size:7 final size:7
Alignment explanation
Indices: 21307180--21307204 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21307170 ATGGAACAGG
21307180 AAAATGA
1 AAAATGA
21307187 AAAATGA
1 AAAATGA
21307194 AAAATGA
1 AAAATGA
21307201 AAAA
1 AAAA
21307205 AAAAAGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAATGA
Found at i:21309118 original size:2 final size:2
Alignment explanation
Indices: 21309113--21309140 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21309103 GTGTGTGTGT
21309113 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
21309141 AACATAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21309725 original size:4 final size:4
Alignment explanation
Indices: 21309709--21309745 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
21309699 CAAAAAAGGC
*
21309709 TACA TACA GACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
21309746 TCAGATTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:21313319 original size:15 final size:16
Alignment explanation
Indices: 21313288--21313321 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21313278 TAGTATGCCA
*
21313288 AAATAAAAAACACTTT
1 AAATAAAAAACAATTT
21313304 AAATAAAAAA-AATTT
1 AAATAAAAAACAATTT
21313319 AAA
1 AAA
21313322 CAATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAAAAACAATTT
Found at i:21313331 original size:17 final size:18
Alignment explanation
Indices: 21313311--21313352 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
21313301 TTTAAATAAA
21313311 AAAAATTTAAACAATTT-
1 AAAAATTTAAACAATTTC
* * *
21313328 AAAAATATAAATATTTTC
1 AAAAATTTAAACAATTTC
21313346 AAAAATT
1 AAAAATT
21313353 CAAAACATGT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAAATTTAAACAATTTC
Found at i:21314318 original size:21 final size:20
Alignment explanation
Indices: 21314292--21314338 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
21314282 AATTTTAGAA
*
21314292 TTTTTTAAAATTTTA-AAGAT
1 TTTTTTTAAATTTTACAA-AT
*
21314312 TTTTTTTGAATTTTACAAAT
1 TTTTTTTAAATTTTACAAAT
21314332 TTTTTTT
1 TTTTTTT
21314339 TCATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTTTTAAATTTTACAAAT
Found at i:21314338 original size:20 final size:20
Alignment explanation
Indices: 21314300--21314338 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
21314290 AATTTTTTAA
21314300 AATTTTAAAGATTTTTTTTG
1 AATTTTAAAGATTTTTTTTG
21314320 AATTTTACAA-ATTTTTTTT
1 AATTTTA-AAGATTTTTTTT
21314339 TCATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
AATTTTAAAGATTTTTTTTG
Found at i:21315973 original size:105 final size:101
Alignment explanation
Indices: 21315802--21316031 Score: 273
Period size: 105 Copynumber: 2.2 Consensus size: 101
21315792 ACACATGCAT
* * ** * *
21315802 TGCCATGGCCCTACCATGGTCTTACATTTGTAGTGCCATAACCCAATTATGGTCTTATCATCAAA
1 TGCCATGGTCCAACCATGGTCTTACATTTCAAGTGCCATAACCCAATTACGGTATTATCATCAAA
* * *
21315867 ATGCCATAGCCCAGCTATGGTCTTACACATATATATATAC
66 ATGCCATAGCCCAACTATGGTCTT--ACAT-T-TAAACAC
* * * *
21315907 TGCCATGGTCCAACCATGGTCTTAC-TTTCAAGGTGTCATAACCCAGTTACGGTATTTTCATTAA
1 TGCCATGGTCCAACCATGGTCTTACATTTCAA-GTGCCATAACCCAATTACGGTATTATCATCAA
*
21315971 AATGTCATAGCCCAACTATGGTCTTACATTTAAACAC
65 AATGCCATAGCCCAACTATGGTCTTACATTTAAACAC
*
21316008 TGTCATGGTCCAACCATGGTCTTA
1 TGCCATGGTCCAACCATGGTCTTA
21316032 TCCATCAATT
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
101 28 0.26
102 1 0.01
103 4 0.04
104 4 0.04
105 72 0.66
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (101 bp):
TGCCATGGTCCAACCATGGTCTTACATTTCAAGTGCCATAACCCAATTACGGTATTATCATCAAA
ATGCCATAGCCCAACTATGGTCTTACATTTAAACAC
Found at i:21316004 original size:33 final size:33
Alignment explanation
Indices: 21315769--21316031 Score: 91
Period size: 33 Copynumber: 7.7 Consensus size: 33
21315759 GTTTTCTTTG
* * ** ** *
21315769 TGCCGTAGTCCAACTATGGTCTTACACATGCAT
1 TGCCATAGCCCAACTATGGTCTTACATTTAAAA
* * * ** *
21315802 TGCCATGGCCCTACCATGGTCTTACATTTGTAG
1 TGCCATAGCCCAACTATGGTCTTACATTTAAAA
* * *
21315835 TGCCATAACCCAATTATGGTCTTATCA-TCAAAA
1 TGCCATAGCCCAACTATGGTCTTA-CATTTAAAA
* *
21315868 TGCCATAGCCCAGCTATGGTCTTACACATATATATATAC
1 TGCCATAGCCCAACTATGGTCTT--ACAT-T-TA-A-AA
* * * **
21315907 TGCCATGGTCCAACCATGGTCTTAC-TTTCAAGG
1 TGCCATAGCCCAACTATGGTCTTACATTT-AAAA
* * ** * * *
21315940 TGTCATAACCCAGTTACGGTATTTTCA-TTAAAA
1 TGCCATAGCCCAACTATGGT-CTTACATTTAAAA
*
21315973 TGTCATAGCCCAACTATGGTCTTACATTTAAACA
1 TGCCATAGCCCAACTATGGTCTTACATTTAAA-A
* * * *
21316007 CTGTCATGGTCCAACCATGGTCTTA
1 -TGCCATAGCCCAACTATGGTCTTA
21316032 TCCATCAATT
Statistics
Matches: 166, Mismatches: 50, Indels: 26
0.69 0.21 0.11
Matches are distributed among these distances:
32 4 0.02
33 100 0.60
34 12 0.07
35 24 0.14
36 2 0.01
37 3 0.02
38 1 0.01
39 20 0.12
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (33 bp):
TGCCATAGCCCAACTATGGTCTTACATTTAAAA
Found at i:21317775 original size:41 final size:43
Alignment explanation
Indices: 21317689--21317776 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 43
21317679 TCAAATTTAA
* *
21317689 TTTAATTATTTTATTTTTTATTTTGAAGTAAATAAGATTACATT
1 TTTAATTATTTTA-TTTTTATTTTGAAGCAAATAAGATTAAATT
* *
21317733 TTTAATTGTTTTA-TTTT-TTTTGAAGCAAATAATATTAAATT
1 TTTAATTATTTTATTTTTATTTTGAAGCAAATAAGATTAAATT
21317774 TTT
1 TTT
21317777 CAAGTTTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 24 0.60
42 4 0.10
44 12 0.30
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (43 bp):
TTTAATTATTTTATTTTTATTTTGAAGCAAATAAGATTAAATT
Found at i:21336351 original size:4 final size:4
Alignment explanation
Indices: 21336342--21336370 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
21336332 AACCACTTGC
21336342 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
21336371 ATTGTTGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:21345280 original size:14 final size:14
Alignment explanation
Indices: 21345261--21345289 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21345251 ATTTCATTCT
21345261 TGTACTTTTTAAAC
1 TGTACTTTTTAAAC
21345275 TGTACTTTTTAAAC
1 TGTACTTTTTAAAC
21345289 T
1 T
21345290 TTGAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TGTACTTTTTAAAC
Found at i:21345591 original size:21 final size:19
Alignment explanation
Indices: 21345549--21345595 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
21345539 AATAAAATAA
*
21345549 AATAAAATATTAATTAGTT
1 AATAAAATAGTAATTAGTT
*
21345568 AATAATAATAGTAATTGGGTT
1 AATAA-AATAGTAATT-AGTT
21345589 AATAAAA
1 AATAAAA
21345596 ATATATTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 11 0.46
21 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
AATAAAATAGTAATTAGTT
Found at i:21345598 original size:21 final size:20
Alignment explanation
Indices: 21345552--21345598 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
21345542 AAAATAAAAT
*
21345552 AAAATATTAATTAGTTAATA
1 AAAATAGTAATTAGTTAATA
* *
21345572 ATAATAGTAATTGGGTTAATA
1 AAAATAGTAATT-AGTTAATA
21345593 AAAATA
1 AAAATA
21345599 TATTAGTGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (20 bp):
AAAATAGTAATTAGTTAATA
Found at i:21347083 original size:15 final size:16
Alignment explanation
Indices: 21347051--21347084 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21347041 CATTATGTTG
21347051 TGTTATGCGAACCCTA
1 TGTTATGCGAACCCTA
*
21347067 TGTTATGTGAA-CCTA
1 TGTTATGCGAACCCTA
21347082 TGT
1 TGT
21347085 GTATTGCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.38
Consensus pattern (16 bp):
TGTTATGCGAACCCTA
Found at i:21348988 original size:15 final size:14
Alignment explanation
Indices: 21348967--21349002 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
21348957 ATGATCCTTA
*
21348967 ATAATTATCTTAAT
1 ATAATTATCCTAAT
21348981 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
21348996 ATAATTA
1 ATAATTA
21349003 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:21350094 original size:18 final size:18
Alignment explanation
Indices: 21350071--21350105 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
21350061 AGTACATAGG
21350071 TTTGCCGAAATGGGGAGT
1 TTTGCCGAAATGGGGAGT
21350089 TTTGCCGAAATGGGGAG
1 TTTGCCGAAATGGGGAG
21350106 GGCTCGCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.40, T:0.26
Consensus pattern (18 bp):
TTTGCCGAAATGGGGAGT
Found at i:21352160 original size:18 final size:16
Alignment explanation
Indices: 21352138--21352187 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
21352128 GAAACTTAGA
21352138 TTACTATTATTATTAT
1 TTACTATTATTATTAT
*
21352154 TACTACTCTTATTTATCTAT
1 T--TACTATTA-TTAT-TAT
21352174 TTACTATTATTATT
1 TTACTATTATTATT
21352188 TGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 2 0.07
17 4 0.14
18 14 0.50
19 4 0.14
20 4 0.14
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (16 bp):
TTACTATTATTATTAT
Found at i:21352195 original size:21 final size:21
Alignment explanation
Indices: 21352139--21352188 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
21352129 AAACTTAGAT
21352139 TACTATTA-TTAT-TA-TTAC
1 TACTATTATTTATCTATTTAC
*
21352157 TACTCTTATTTATCTATTTAC
1 TACTATTATTTATCTATTTAC
*
21352178 TATTATTATTT
1 TACTATTATTT
21352189 GTTTATTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 7 0.27
19 4 0.15
20 2 0.08
21 13 0.50
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (21 bp):
TACTATTATTTATCTATTTAC
Found at i:21376324 original size:3 final size:3
Alignment explanation
Indices: 21376318--21376369 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
21376308 TTGGGCTTCA
* * * * *
21376318 CTT CTT CTT CTT CTT CCT CTT CTT CTC CTT CAT CAT CAT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
21376366 CTT C
1 CTT C
21376370 ATCTCCCTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (3 bp):
CTT
Found at i:21391027 original size:17 final size:17
Alignment explanation
Indices: 21391005--21391039 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21390995 CAATTACTTA
21391005 GCTTAACAGAATAGTTT
1 GCTTAACAGAATAGTTT
21391022 GCTTAACAGAATAGTTT
1 GCTTAACAGAATAGTTT
21391039 G
1 G
21391040 TGAAGCACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (17 bp):
GCTTAACAGAATAGTTT
Found at i:21394616 original size:34 final size:32
Alignment explanation
Indices: 21394578--21394680 Score: 95
Period size: 34 Copynumber: 3.1 Consensus size: 32
21394568 TAATTTATAT
*
21394578 TTTATGATCATTATATCAAACTATTTAAATATTA
1 TTTATG-TCATTATATTAAA-TATTTAAATATTA
*
21394612 TTTAT-T-ATTATACTTAAATTTTTAAAATATT-
1 TTTATGTCATTATA-TTAAATATTT-AAATATTA
* *
21394643 TTTTTGTCTAATATATTAAATTATTTAAATATTA
1 TTTATGTC-ATTATATTAAA-TATTTAAATATTA
21394677 TTTA
1 TTTA
21394681 AATTATTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
31 14 0.25
32 13 0.23
33 12 0.21
34 17 0.30
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (32 bp):
TTTATGTCATTATATTAAATATTTAAATATTA
Found at i:21394693 original size:33 final size:31
Alignment explanation
Indices: 21394530--21394680 Score: 100
Period size: 33 Copynumber: 4.9 Consensus size: 31
21394520 ATATTCATAT
*
21394530 TTATATT-AATTATTTAAA-ATATATTTA-AA
1 TTATATTAAATTATTTAAATAT-TATTTATTA
* * * * *
21394559 TT-T-TTAGATTAATTTATATTTTA-TGATCA
1 TTATATTAAATT-ATTTAAATATTATTTATTA
* *
21394588 TTATATCAAACTATTTAAATATTATTTATTA
1 TTATATTAAATTATTTAAATATTATTTATTA
* *
21394619 TTATACTTAAATT-TTTAAAATATTTTTTTGTCTA
1 TTATA-TTAAATTATTT-AAATA-TTATTTAT-TA
*
21394653 ATATATTAAATTATTTAAATATTATTTA
1 TTATATTAAATTATTTAAATATTATTTA
21394681 AATTATTTTA
Statistics
Matches: 91, Mismatches: 19, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
27 2 0.02
28 6 0.07
29 13 0.14
30 12 0.13
31 16 0.18
32 15 0.16
33 18 0.20
34 9 0.10
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (31 bp):
TTATATTAAATTATTTAAATATTATTTATTA
Found at i:21395582 original size:25 final size:24
Alignment explanation
Indices: 21395550--21395603 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
21395540 ATTGAACATC
*
21395550 AAATTAATTGAGAATT-TATAAAAA
1 AAATTAATTG-GAATTCAATAAAAA
*
21395574 AAATGTAATTGGACTTCAATAAAAA
1 AAAT-TAATTGGAATTCAATAAAAA
21395599 AAATT
1 AAATT
21395604 TAACATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (24 bp):
AAATTAATTGGAATTCAATAAAAA
Found at i:21395787 original size:16 final size:16
Alignment explanation
Indices: 21395752--21395797 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
21395742 TAAAAAAGTT
*
21395752 ATATTATTTTAATTTA-
1 ATATTA-TTTATTTTAG
21395768 ATATTATTTATTTTAG
1 ATATTATTTATTTTAG
21395784 ATA-T-TTTATTTTAG
1 ATATTATTTATTTTAG
21395798 TAAAATTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.36
15 9 0.32
16 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (16 bp):
ATATTATTTATTTTAG
Found at i:21400046 original size:57 final size:57
Alignment explanation
Indices: 21399955--21400082 Score: 202
Period size: 57 Copynumber: 2.2 Consensus size: 57
21399945 TTAACATGAG
* *
21399955 CCTAAAGTCACCAAAATAGAAACAGGGCCTACCTAAATTGACTCTAAAGGACCCAAA
1 CCTAAAGTCACCAAAACAGAAACAGGGCCCACCTAAATTGACTCTAAAGGACCCAAA
* * * *
21400012 CCTAAAGTTACCAAAACGGAAACAGGTCCCACCTAAATTGATTCTAAAGGACCCAAA
1 CCTAAAGTCACCAAAACAGAAACAGGGCCCACCTAAATTGACTCTAAAGGACCCAAA
21400069 CCTAAAGTCACCAA
1 CCTAAAGTCACCAA
21400083 GGAACCCAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.43, C:0.27, G:0.13, T:0.16
Consensus pattern (57 bp):
CCTAAAGTCACCAAAACAGAAACAGGGCCCACCTAAATTGACTCTAAAGGACCCAAA
Found at i:21403540 original size:26 final size:26
Alignment explanation
Indices: 21403511--21403560 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
21403501 CTATATTTTC
*
21403511 AAATTAAACTATGATTTAAATTAATA
1 AAATTAAACCATGATTTAAATTAATA
*
21403537 AAATTAAACCATGATTTGAATTAA
1 AAATTAAACCATGATTTAAATTAA
21403561 CACTTCATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (26 bp):
AAATTAAACCATGATTTAAATTAATA
Found at i:21403624 original size:16 final size:16
Alignment explanation
Indices: 21403567--21403626 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
21403557 TTAACACTTC
21403567 ATTCAAATTTA-AATA
1 ATTCAAATTTATAATA
*
21403582 AGTCATAATTTAAATCAATA
1 ATTCA-AATTT--AT-AATA
21403602 TATTCAAATTTATAATA
1 -ATTCAAATTTATAATA
21403619 ATTCAAAT
1 ATTCAAAT
21403627 CAACGTAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
15 4 0.11
16 13 0.35
17 4 0.11
18 3 0.08
20 9 0.24
21 4 0.11
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTCAAATTTATAATA
Found at i:21418319 original size:2 final size:2
Alignment explanation
Indices: 21418312--21418336 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21418302 TGTACTACTT
21418312 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21418337 TAATATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21421536 original size:20 final size:20
Alignment explanation
Indices: 21421511--21421557 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
21421501 GATATTTGCT
21421511 TTTATATTGATATT-ACTA-TA
1 TTTATATT-ATATTGA-TATTA
21421531 TTTATATTATATTGATATTA
1 TTTATATTATATTGATATTA
21421551 TTTATAT
1 TTTATAT
21421558 CTTTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATATTATATTGATATTA
Found at i:21434019 original size:44 final size:44
Alignment explanation
Indices: 21433871--21434308 Score: 211
Period size: 44 Copynumber: 10.0 Consensus size: 44
21433861 TAGGTTTATT
* **
21433871 ATACAGG-TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-A
* ** * *
21433916 ATTTCA-GATCTTATCTCCCTGAGATTACAACGGAGTAGATT-GA
1 A-TACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * * *
21433959 A-GCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
1 ATAC-AG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* * ** * ***
21434004 ATAAAGGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGA-TCGC
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA
* * * **
21434047 AT-CAGGATCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA--TTA-AA
* ** * *
21434093 TTTTA-GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-GA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
** * **
21434135 AGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCGA
1 ATACAG-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* ** * *
21434179 AGACACTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAA
1 ATACAGGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAA
* * * ** * ***
21434223 ATAAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGA-TCGC
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
* *
21434266 AT-CAGG-TCTTATCTCCCTGATATTACAGTGGAGTAGACTTAAA
1 ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAAA
21434309 CCTAAAACCT
Statistics
Matches: 289, Mismatches: 82, Indels: 46
0.69 0.20 0.11
Matches are distributed among these distances:
41 27 0.09
42 36 0.12
43 38 0.13
44 119 0.41
45 6 0.02
46 62 0.21
47 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
ATACAGGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA
Found at i:21434146 original size:132 final size:133
Alignment explanation
Indices: 21433971--21434213 Score: 303
Period size: 132 Copynumber: 1.8 Consensus size: 133
21433961 CTAGTAATCC
* * *
21433971 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGA-AGTTACAGC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGA-TTACAGC
* * * * * * *
21434035 AGAGTAGATCGCA-TCAGGATCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTTAG
65 AGAGCAGATCGAAGACACGATCCTATCTCCCTGAAGTTACAGTGGAGTAGACCGGAGAATTTTAG
21434099 ATCT
130 ATCT
* * * *
21434103 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATTACAGC
* *
21434167 GGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAG
65 AGAGCAGATCGAAGACACGATCCTATCTCCCTGAAGTTACAGTGGAG
21434214 CGGATTAAAA
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
131 2 0.02
132 62 0.67
133 28 0.30
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (133 bp):
TATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
GAGCAGATCGAAGACACGATCCTATCTCCCTGAAGTTACAGTGGAGTAGACCGGAGAATTTTAGA
TCT
Found at i:21434212 original size:87 final size:87
Alignment explanation
Indices: 21434103--21434264 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
21434093 TTTTAGATCT
* * * *
21434103 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATTACAGC
*
21434167 GGAGCAGATCGAAGACACTATCC
65 AGAGCAGATCGAAGACACTATCC
* * * *
21434190 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
*
21434255 GAGTAGATCG
66 GAGCAGATCG
21434265 CATCAGGTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 62 0.97
88 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
GAGCAGATCGAAGACACTATCC
Found at i:21435818 original size:25 final size:25
Alignment explanation
Indices: 21435790--21435837 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
21435780 AATATCAAAG
* *
21435790 ATATTTGTTTTATATTGATATTACT
1 ATATTTATATTATATTGATATTACT
21435815 ATATTTATATTATATTGATATTA
1 ATATTTATATTATATTGATATTA
21435838 TTTATATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.58
Consensus pattern (25 bp):
ATATTTATATTATATTGATATTACT
Found at i:21435821 original size:20 final size:20
Alignment explanation
Indices: 21435798--21435844 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
21435788 AGATATTTGT
21435798 TTTATATTGATATT-ACTA-TA
1 TTTATATT-ATATTGA-TATTA
21435818 TTTATATTATATTGATATTA
1 TTTATATTATATTGATATTA
21435838 TTTATAT
1 TTTATAT
21435845 CTTTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATATTATATTGATATTA
Found at i:21442110 original size:14 final size:14
Alignment explanation
Indices: 21442093--21442129 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
21442083 ATAAATTTGA
21442093 AATAATAAT-TATT
1 AATAATAATATATT
21442106 GAATAATAATATATT
1 -AATAATAATATATT
21442121 AA-AATAATA
1 AATAATAATA
21442130 AATTTGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 11 0.50
15 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
AATAATAATATATT
Found at i:21444345 original size:46 final size:45
Alignment explanation
Indices: 21444278--21444587 Score: 244
Period size: 38 Copynumber: 7.6 Consensus size: 45
21444268 TTTGAGTACT
* *
21444278 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
21444324 TCTGATCAAGTGAAAAAGTGATAA---GT-G-TTA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
21444360 TCTGATCAAGTG-AAAA---A-AAGTGATAAG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGT-AGCTTAGCTACACTTA
* *
21444398 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
21444444 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
21444480 TCTGATCAAGTGAAAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTG--AAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
21444518 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
21444563 TCTGATC-AGGGACAAA-TGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
21444588 ATCATACATA
Statistics
Matches: 225, Mismatches: 10, Indels: 61
0.76 0.03 0.21
Matches are distributed among these distances:
31 2 0.01
32 1 0.00
34 1 0.00
35 5 0.02
36 47 0.21
38 54 0.24
39 5 0.02
40 7 0.03
41 2 0.01
42 6 0.03
43 20 0.09
44 8 0.04
45 13 0.06
46 54 0.24
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:21444360 original size:36 final size:36
Alignment explanation
Indices: 21444314--21444544 Score: 282
Period size: 38 Copynumber: 6.0 Consensus size: 36
21444304 GGTAGCTTTA
*
21444314 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
21444350 GTTATACTTATCTGATCAAGTGAAAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTG--AAAAAGTGATAAGT
* * *
21444388 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAA---GT
21444427 AGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GC--TA--T--ACTTATCTGATCAAGTGAAAAAGTGATAAGT
21444470 GCTATACTTATCTGATCAAGTGAAAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTG--AAAAAGTGATAAGT
*
21444508 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
21444544 G
1 G
21444545 GTAGCTTAGC
Statistics
Matches: 171, Mismatches: 10, Indels: 28
0.82 0.05 0.13
Matches are distributed among these distances:
36 62 0.36
38 70 0.41
39 2 0.01
40 4 0.02
42 4 0.02
43 2 0.01
46 27 0.16
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:21444416 original size:74 final size:72
Alignment explanation
Indices: 21444314--21444544 Score: 282
Period size: 74 Copynumber: 3.0 Consensus size: 72
21444304 GGTAGCTTTA
*
21444314 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGTGAAAAAAA
1 GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGTG--AAAAA
21444379 GTGATAAGT
64 GTGATAAGT
*
21444388 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGAGAAAAAGTGATAA---GT-G--TTA--T--ACTTATCTGATCAA
21444453 GTGAAAAAGTGATAAGT
56 GTGAAAAAGTGATAAGT
* * * *
21444470 GCTATACTTATCTGATCAAGTGAAAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGACAAA
1 GCTACACTTATCTGATCAA--GAGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGTGAAAAA
21444535 GTGATAAGT
64 GTGATAAGT
21444544 G
1 G
21444545 GTAGCTTAGC
Statistics
Matches: 138, Mismatches: 7, Indels: 24
0.82 0.04 0.14
Matches are distributed among these distances:
74 63 0.46
76 1 0.01
77 2 0.01
78 3 0.02
80 4 0.03
81 2 0.01
82 33 0.24
84 30 0.22
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (72 bp):
GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGTGAAAAAGT
GATAAGT
Found at i:21444491 original size:120 final size:120
Alignment explanation
Indices: 21444278--21444587 Score: 545
Period size: 120 Copynumber: 2.6 Consensus size: 120
21444268 TTTGAGTACT
*
21444278 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
21444343 GATAAGTGTTATACTTATCTGATCAAGTGAAAAAAAGTGATAAGTGCTACACTTA
66 GATAAGTGCTATACTTATCTGATCAAGTGAAAAAAAGTGATAAGTGCTACACTTA
21444398 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
21444463 GATAAGTGCTATACTTATCTGATCAAGTGAAAAAAAGTGATAAGTGCTATACTTA
66 GATAAGTGCTATACTTATCTGATCAAGTGAAAAAAAGTGATAAGTGCTACACTTA
* * *
21444518 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATC-AGGGACAAA-T
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
21444580 GATAAGTG
66 GATAAGTG
21444588 ATCATACATA
Statistics
Matches: 184, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
117 9 0.05
118 7 0.04
119 20 0.11
120 148 0.80
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (120 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTATACTTATCTGATCAAGTGAAAAAAAGTGATAAGTGCTACACTTA
Found at i:21451840 original size:42 final size:42
Alignment explanation
Indices: 21451778--21451884 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 42
21451768 AGTTAACTCA
* * *
21451778 TATGAGTTTCCGTCTAACCC-TAACGAGTTTCAGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTAACGAGTTTC-GTTCAGCTCT
* ** *
21451820 TTTGAGCTTCAGTTTAACCCTTATGGATTTTCGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTAACGAGTTTCGTTCAGCTCT
*
21451862 TATGAGCTTCCA-TTCAACCCTTA
1 TATGAGCTT-CAGTTTAACCCTTA
21451885 TGGGTTTCCG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 44 0.81
43 10 0.19
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTAACGAGTTTCGTTCAGCTCT
Found at i:21451877 original size:21 final size:21
Alignment explanation
Indices: 21451853--21451913 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 21
21451843 TGGATTTTCG
*
21451853 TTCAGCTCTTATGAGCTTCCA
1 TTCAGCACTTATGAGCTTCCA
* * * * *
21451874 TTCAACCCTTATGGGTTTCCG
1 TTCAGCACTTATGAGCTTCCA
* *
21451895 TTTAGCACTTATGTGCTTC
1 TTCAGCACTTATGAGCTTC
21451914 TATGCAGCCT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.41
Consensus pattern (21 bp):
TTCAGCACTTATGAGCTTCCA
Found at i:21451885 original size:42 final size:43
Alignment explanation
Indices: 21451805--21451913 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 43
21451795 CCCTAACGAG
* *
21451805 TTTCAGTTCAGCTCTTTTGAGCTT-CAGTTTAACCCTTATGGAT
1 TTTC-GTTCAGCTCTTATGAGCTTCCAGTTCAACCCTTATGGAT
*
21451848 TTTCGTTCAGCTCTTATGAGCTTCCA-TTCAACCCTTATGGGT
1 TTTCGTTCAGCTCTTATGAGCTTCCAGTTCAACCCTTATGGAT
* * * *
21451890 TTCCGTTTAGCACTTATGTGCTTC
1 TTTCGTTCAGCTCTTATGAGCTTC
21451914 TATGCAGCCT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
42 52 0.90
43 6 0.10
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (43 bp):
TTTCGTTCAGCTCTTATGAGCTTCCAGTTCAACCCTTATGGAT
Found at i:21455027 original size:42 final size:42
Alignment explanation
Indices: 21454963--21455071 Score: 137
Period size: 42 Copynumber: 2.6 Consensus size: 42
21454953 TCTTAACGAG
* *
21454963 TTTCAGTTCAGCTCTTTTGAGCTTCAGTTTAACCCTCATGGGT
1 TTTC-GTTCAGCTCTTATGAGCTTCAGTTCAACCCTCATGGGT
* *
21455006 TTTCGTTCAGCTCTTATGAGCTTCCGTTCAACCCTTATGGGT
1 TTTCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTCATGGGT
* * * *
21455048 TTCCGTTTAGCACTTATGTGCTTC
1 TTTCGTTCAGCTCTTATGAGCTTC
21455072 TGTGCAGCCT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 54 0.93
43 4 0.07
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (42 bp):
TTTCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTCATGGGT
Found at i:21455035 original size:21 final size:21
Alignment explanation
Indices: 21454968--21455080 Score: 64
Period size: 21 Copynumber: 5.4 Consensus size: 21
21454958 ACGAGTTTCA
* * *
21454968 GTTCAGCTCTTTTGAGCTTCA
1 GTTCAGCCCTTATGAGCTTCC
* * * * * *
21454989 GTTTAACCCTCATGGGTTTTC
1 GTTCAGCCCTTATGAGCTTCC
*
21455010 GTTCAGCTCTTATGAGCTTCC
1 GTTCAGCCCTTATGAGCTTCC
* * *
21455031 GTTCAACCCTTATGGGTTTCC
1 GTTCAGCCCTTATGAGCTTCC
* * * *
21455052 GTTTAGCACTTATGTGCTTCT
1 GTTCAGCCCTTATGAGCTTCC
*
21455073 GTGCAGCC
1 GTTCAGCC
21455081 TTCGAGCTTC
Statistics
Matches: 63, Mismatches: 29, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (21 bp):
GTTCAGCCCTTATGAGCTTCC
Found at i:21462565 original size:18 final size:19
Alignment explanation
Indices: 21462530--21462567 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
21462520 ATTAATATAA
*
21462530 ATTAATAAAATTACATTTT
1 ATTAATAAAATAACATTTT
*
21462549 ATTAAT-AAATAATATTTT
1 ATTAATAAAATAACATTTT
21462567 A
1 A
21462568 GACCAAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAATAAAATAACATTTT
Found at i:21462920 original size:23 final size:23
Alignment explanation
Indices: 21462894--21462950 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
21462884 TTTCTATGCA
* *
21462894 TTTTTATTATTGTTTCGCTGTCG
1 TTTTTAATATTGTTTCACTGTCG
** *
21462917 TTTTTAAGGTTGTTTCACTGTTG
1 TTTTTAATATTGTTTCACTGTCG
21462940 TTTTTAATATT
1 TTTTTAATATT
21462951 ATTTGGATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.61
Consensus pattern (23 bp):
TTTTTAATATTGTTTCACTGTCG
Found at i:21463896 original size:2 final size:2
Alignment explanation
Indices: 21463885--21463919 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
21463875 ACGTAGCGCC
21463885 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21463920 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:21464075 original size:12 final size:12
Alignment explanation
Indices: 21464058--21464090 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
21464048 CGGCCTGCCC
21464058 ATATTAATTTTT
1 ATATTAATTTTT
21464070 ATATT-ATTTTT
1 ATATTAATTTTT
21464081 ATA-TAATTTT
1 ATATTAATTTT
21464091 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:21464248 original size:30 final size:30
Alignment explanation
Indices: 21464212--21464276 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
21464202 CAACTTAACA
*
21464212 AACAAATGCCTCTAAAATATTAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
* *
21464242 AACAAATGTCTTTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
21464272 AACAA
1 AACAA
21464277 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.26
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:21464331 original size:22 final size:22
Alignment explanation
Indices: 21464306--21464348 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
21464296 TATACAAACA
21464306 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
21464328 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
21464349 AATAGAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:21464352 original size:11 final size:11
Alignment explanation
Indices: 21464313--21464353 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
21464303 ACAATAACAA
21464313 CAAAATAGTAG
1 CAAAATAGTAG
* *
21464324 CAACATAATAG
1 CAAAATAGTAG
*
21464335 TAAAATAGTAG
1 CAAAATAGTAG
21464346 CAAAATAG
1 CAAAATAG
21464354 AGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:21464361 original size:22 final size:22
Alignment explanation
Indices: 21464314--21464363 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
21464304 CAATAACAAC
* *
21464314 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
21464336 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
21464358 AAAATA
1 AAAATA
21464364 ATAAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.60, C:0.06, G:0.16, T:0.18
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:21465051 original size:18 final size:18
Alignment explanation
Indices: 21465015--21465050 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
21465005 TTTAGAGCAC
*
21465015 TATAAAAAAATTCTAAAA
1 TATAAAAAAATCCTAAAA
21465033 TATAAGAAAAATCCTAAA
1 TATAA-AAAAATCCTAAA
21465051 TCTAATAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.25
Consensus pattern (18 bp):
TATAAAAAAATCCTAAAA
Found at i:21465404 original size:32 final size:32
Alignment explanation
Indices: 21465362--21465423 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
21465352 AAAATGATTA
* * * *
21465362 AAAATTAGAAAAAAATATTTTAAAAAATAAGC
1 AAAATGAGAAAAAAAAACTATAAAAAATAAGC
21465394 AAAATGAGAAAAAAAAACTATAAAAAATAA
1 AAAATGAGAAAAAAAAACTATAAAAAATAA
21465424 AATATTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (32 bp):
AAAATGAGAAAAAAAAACTATAAAAAATAAGC
Found at i:21465591 original size:20 final size:22
Alignment explanation
Indices: 21465568--21465620 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
21465558 AATGTATTAG
*
21465568 AATTCTTAAAAAA-TA-ATAAA
1 AATTCTAAAAAAATTATATAAA
*
21465588 AATTGTAAAAAAATTATATAAA
1 AATTCTAAAAAAATTATATAAA
*
21465610 AAATCATAAAA
1 AATTC-TAAAA
21465621 GCTTGATCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.42
21 2 0.08
22 8 0.31
23 5 0.19
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (22 bp):
AATTCTAAAAAAATTATATAAA
Found at i:21466305 original size:25 final size:27
Alignment explanation
Indices: 21466244--21466305 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 27
21466234 AAACATTTTT
* *
21466244 TTATAAATTTAAATCAATTTTCATATTT
1 TTATAAA-TTAAATCAATTTTAATATTC
21466272 TTA-ATAATT-AAT-AATTTTAATATTC
1 TTATA-AATTAAATCAATTTTAATATTC
21466297 TTATAAATT
1 TTATAAATT
21466306 TTCTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 18 0.60
26 4 0.13
27 3 0.10
28 5 0.17
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATAAATTAAATCAATTTTAATATTC
Found at i:21474576 original size:7 final size:7
Alignment explanation
Indices: 21474561--21474598 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
21474551 CCAAAGCATC
*
21474561 AAAGAGA
1 AAAGGGA
21474568 AAAGGGA
1 AAAGGGA
21474575 AAAGGGA
1 AAAGGGA
21474582 AAAGGGA
1 AAAGGGA
21474589 AAAGGGA
1 AAAGGGA
21474596 AAA
1 AAA
21474599 AATGGGGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (7 bp):
AAAGGGA
Found at i:21486209 original size:40 final size:40
Alignment explanation
Indices: 21486154--21486233 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
21486144 TGACCTTTTG
21486154 CATTATGCATCCTTTTTCATAAACAATTTGCATTTTTCCC
1 CATTATGCATCCTTTTTCATAAACAATTTGCATTTTTCCC
21486194 CATTATGCATCCTTTTTCATAAACAATTTGCATTTTTCCC
1 CATTATGCATCCTTTTTCATAAACAATTTGCATTTTTCCC
21486234 TCAAAAATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.45
Consensus pattern (40 bp):
CATTATGCATCCTTTTTCATAAACAATTTGCATTTTTCCC
Found at i:21492416 original size:13 final size:12
Alignment explanation
Indices: 21492379--21492417 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
21492369 ACACATATTG
21492379 AATATTTAATTA
1 AATATTTAATTA
21492391 AATATTTTAAATTA
1 AATA-TTT-AATTA
21492405 AATATTATAATTA
1 AATATT-TAATTA
21492418 TTTTGAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.17
13 10 0.42
14 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATATTTAATTA
Found at i:21496916 original size:6 final size:6
Alignment explanation
Indices: 21496905--21496974 Score: 140
Period size: 6 Copynumber: 11.7 Consensus size: 6
21496895 ACACGTGTAC
21496905 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
21496953 ATATGT ATATGT ATATGT ATAT
1 ATATGT ATATGT ATATGT ATAT
21496975 ATACACGTAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:21498262 original size:23 final size:24
Alignment explanation
Indices: 21498236--21498288 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
21498226 TATTATAATT
21498236 TATTATTT-TTAGT-TTAATTTAAA
1 TATTATTTCTTAGTATTAATTT-AA
21498259 TATT-TTTCTTAGTAAGTTAATTTAA
1 TATTATTTCTTAGT-A-TTAATTTAA
21498284 TATTA
1 TATTA
21498289 ATTGTTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
22 3 0.12
23 9 0.36
25 6 0.24
26 7 0.28
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
TATTATTTCTTAGTATTAATTTAA
Found at i:21501606 original size:18 final size:18
Alignment explanation
Indices: 21501579--21501615 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21501569 TTGATTTTCA
*
21501579 AATTCAAATAACTCGAAT
1 AATTCAAATAAATCGAAT
*
21501597 AATTCGAATAAATCGAAT
1 AATTCAAATAAATCGAAT
21501615 A
1 A
21501616 TCAGACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTCAAATAAATCGAAT
Found at i:21501772 original size:21 final size:21
Alignment explanation
Indices: 21501748--21501790 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21501738 ACTCTCCCCA
21501748 TTTACTTTCCCCCCAAAATTT
1 TTTACTTTCCCCCCAAAATTT
* * *
21501769 TTTATTTTCCCCCTAAACTTT
1 TTTACTTTCCCCCCAAAATTT
21501790 T
1 T
21501791 ACTTCTCACC
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:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTACTTTCCCCCCAAAATTT
Found at i:21504268 original size:15 final size:16
Alignment explanation
Indices: 21504248--21504277 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21504238 TCTAAAATTA
21504248 TTTTTG-AGAAATAAG
1 TTTTTGAAGAAATAAG
21504263 TTTTTGAAGAAATAA
1 TTTTTGAAGAAATAA
21504278 TTAAGAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (16 bp):
TTTTTGAAGAAATAAG
Found at i:21505677 original size:15 final size:15
Alignment explanation
Indices: 21505628--21505677 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
21505618 TGTTTGATAA
*
21505628 ATTGAAAAATTAAAT
1 ATTGAAAAAATAAAT
* **
21505643 ATTAAAAAAATATCT
1 ATTGAAAAAATAAAT
*
21505658 GTTGAAAAAATAAAT
1 ATTGAAAAAATAAAT
21505673 ATTGA
1 ATTGA
21505678 GAGTGTGAAT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (15 bp):
ATTGAAAAAATAAAT
Found at i:21508938 original size:19 final size:19
Alignment explanation
Indices: 21508906--21508944 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
21508896 CAAAAATTAC
21508906 AAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAAT-TTTAT
*
21508926 AAAAATTTC-AAATTTTAT
1 AAAAAATTCAAAATTTTAT
21508944 A
1 A
21508945 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAAATTCAAAATTTTAT
Found at i:21510131 original size:22 final size:19
Alignment explanation
Indices: 21510086--21510133 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
21510076 ATTAATTAAA
21510086 TTTTTATAATTAAAATATT
1 TTTTTATAATTAAAATATT
* *
21510105 GTTTTATAATATAAAGGTTATT
1 TTTTTATAAT-TAAA--ATATT
21510127 TTTTTAT
1 TTTTTAT
21510134 TTATTAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 4 0.17
22 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTTTATAATTAAAATATT
Found at i:21517892 original size:99 final size:98
Alignment explanation
Indices: 21517738--21517926 Score: 265
Period size: 99 Copynumber: 1.9 Consensus size: 98
21517728 CCTTTGAGTC
* * *
21517738 AGTTTGTTGATATAACCTTGTGTGATTATTGCATTTCCTTTTTCTCTTGATAGTATGCTGTTTGT
1 AGTTTGTTGATATAACATTGTGTGATTATTGCAATTCCTTTTTCTCTTGAAAGTATGCTGTTTGT
21517803 GCATTAAACAAACAAAGTTAAAATTTGAAGTGTG
66 GCATTAAACAAAC-AAGTTAAAATTTGAAGTGTG
* * *
21517837 AGTTTGTTGATGTAACATCTG-GTGATTATTGCAATT-CTTTGTTGTCTTTAAAGTATGCTGTTT
1 AGTTTGTTGATATAACAT-TGTGTGATTATTGCAATTCCTTT-TTCTCTTGAAAGTATGCTGTTT
* *
21517900 GTGCATTAAAGAAACAAGTTGAAATTT
64 GTGCATTAAACAAACAAGTTAAAATTT
21517927 AAATTTTTGT
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
98 15 0.19
99 63 0.79
100 2 0.03
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (98 bp):
AGTTTGTTGATATAACATTGTGTGATTATTGCAATTCCTTTTTCTCTTGAAAGTATGCTGTTTGT
GCATTAAACAAACAAGTTAAAATTTGAAGTGTG
Found at i:21529288 original size:18 final size:18
Alignment explanation
Indices: 21529256--21529303 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
21529246 TTATAACTAT
*
21529256 TTATATATATCTTTATATC
1 TTAT-TATATATTTATATC
21529275 TTATTATATATTTATATC
1 TTATTATATATTTATATC
21529293 TTATTATATAT
1 TTATTATATAT
21529304 ATCTATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATATATTTATATC
Found at i:21529322 original size:18 final size:18
Alignment explanation
Indices: 21529261--21529322 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
21529251 ACTATTTATA
*
21529261 TATATCTTTATATCTTAT
1 TATATCTTTATATCTTTT
*
21529279 TATATATTTATATCTTATTAT
1 TATATCTTTATATC-T-TT-T
*
21529300 ATATATCTATATATCTTTT
1 -TATATCTTTATATCTTTT
21529319 TATA
1 TATA
21529323 AACATATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.47
19 2 0.06
20 3 0.08
21 2 0.06
22 12 0.33
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATCTTTATATCTTTT
Found at i:21529557 original size:27 final size:30
Alignment explanation
Indices: 21529526--21529604 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 30
21529516 GTACCCATTT
21529526 TATATATATACATATTTATAC-T-TTTATA
1 TATATATATACATATTTATACGTGTTTATA
*
21529554 -ATATATATACATAGTATATACGTGTTTATA
1 TATATATATACATA-TTTATACGTGTTTATA
* *
21529584 TATATATACACATACTTATAC
1 TATATATATACATATTTATAC
21529605 ATATTATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
27 13 0.30
28 6 0.14
29 1 0.02
30 11 0.26
31 12 0.28
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.46
Consensus pattern (30 bp):
TATATATATACATATTTATACGTGTTTATA
Found at i:21538540 original size:10 final size:9
Alignment explanation
Indices: 21538516--21538549 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
21538506 ATCTCAGAAT
21538516 TCAAAAAAA
1 TCAAAAAAA
*
21538525 TCAAAAACA
1 TCAAAAAAA
21538534 TCTAAAAAAA
1 TC-AAAAAAA
21538544 TCAAAA
1 TCAAAA
21538550 GTCAAATAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.71, C:0.15, G:0.00, T:0.15
Consensus pattern (9 bp):
TCAAAAAAA
Done.