Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 166 of 202
Found at i:51917410 original size:44 final size:44
Alignment explanation
Indices: 51917362--51917552 Score: 140
Period size: 44 Copynumber: 4.3 Consensus size: 44
51917352 CCAGTAATTC
51917362 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
** * ** * * * *
51917406 TATCTCCCTAAGCAGTAGTGGAGCAGA-TCAAGGATGACGGATTT
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAA-GATTACAGATCT
* * * * * *
51917450 TACCTCCCTGAGGTTA-CAGTGGAGTACATTGAAG---CCAGTAACT
1 TATCTCCCTG-GG-CAGCAGTGGAATAGATTGAAGATTACAG-ATCT
* *
51917493 CTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGGTCT
1 -TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
*
51917538 TATCTCCCTAGGCAG
1 TATCTCCCTGGGCAG
51917553 TGAAGTAGAT
Statistics
Matches: 107, Mismatches: 30, Indels: 20
0.68 0.19 0.13
Matches are distributed among these distances:
42 3 0.03
43 23 0.21
44 61 0.57
45 13 0.12
46 7 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
Found at i:51917431 original size:132 final size:132
Alignment explanation
Indices: 51917261--51917553 Score: 518
Period size: 132 Copynumber: 2.2 Consensus size: 132
51917251 AAGTAGATCA
*
51917261 AAGA-TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA-GATGGCGGATTTTACCTC
1 AAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-AAGGATGACGGATTTTACCTC
* *
51917324 CCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGA
65 CCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCTATCTCCCTGGGCAACAGTGGAATAGA
51917389 TTG
130 TTG
51917392 AAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGATGACGGATTTTACCTCC
1 AAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGATGACGGATTTTACCTCC
51917457 CTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCTATCTCCCTGGGCAACAGTGGAATAGAT
66 CTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCTATCTCCCTGGGCAACAGTGGAATAGAT
51917522 TG
131 TG
* *
51917524 AAGATTACAGGTCTTATCTCCCTAGGCAGT
1 AAGATTACAGATCTTATCTCCCTAAGCAGT
51917554 GAAGTAGATC
Statistics
Matches: 155, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
131 6 0.04
132 149 0.96
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (132 bp):
AAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGATGACGGATTTTACCTCC
CTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCTATCTCCCTGGGCAACAGTGGAATAGAT
TG
Found at i:51917660 original size:45 final size:44
Alignment explanation
Indices: 51917565--51917670 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 44
51917555 AAGTAGATCA
* * *
51917565 AAGTTGCAATGGGGCAGACTAAGGAAGCAAGTTTTATCCTCTTG
1 AAGTTGCAGTGGGGCAGACTAAGGAAGCAAGTCTTATCCTCCTG
**
51917609 AAGTTGCAGTGGGGCAGACTGAAGGTGGCCAA-TCTTAT-CTCCCTG
1 AAGTTGCAGTGGGGCAGACT-AAGGAAG-CAAGTCTTATCCT-CCTG
*
51917654 AAGTTGCAGTGGAGCAG
1 AAGTTGCAGTGGGGCAG
51917671 GTTAAAGCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
44 21 0.40
45 29 0.55
46 3 0.06
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (44 bp):
AAGTTGCAGTGGGGCAGACTAAGGAAGCAAGTCTTATCCTCCTG
Found at i:51917743 original size:44 final size:43
Alignment explanation
Indices: 51917640--51917874 Score: 156
Period size: 44 Copynumber: 5.7 Consensus size: 43
51917630 AAGGTGGCCA
*
51917640 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGG-TTA-AAGCCAATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC-GGATTAGAA-CCAA-G
* * *
51917684 ATCCTATTTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAGAACCA-AG
* * * * * *
51917728 ATCTTATCTCTCTGAAGTTGCAG-AGAGCGGA-TCGCATCTAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAGAACCAAG
*
51917769 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TAGAA-C-A-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAGAACCAAG
* ** *
51917807 A----A-CTCCTTGAAGTTGCAACGGAGTGGATTAGAACCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAGAACCA-AG
* ** *
51917846 ATCTCATCTTTCTGAAGTTGCAGTAGAGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC
51917875 AGATCGCATT
Statistics
Matches: 147, Mismatches: 29, Indels: 30
0.71 0.14 0.15
Matches are distributed among these distances:
34 20 0.14
35 6 0.04
36 1 0.01
38 1 0.01
39 2 0.01
40 22 0.15
41 11 0.07
42 3 0.02
43 10 0.07
44 68 0.46
45 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAGAACCAAG
Found at i:51922354 original size:20 final size:20
Alignment explanation
Indices: 51922329--51922394 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
51922319 AATATAAAAG
51922329 TTTAAAATATTTTTAAAATT
1 TTTAAAATATTTTTAAAATT
***
51922349 TTTAAAA-AAAATTAAAATCT
1 TTTAAAATATTTTTAAAAT-T
51922369 TTTAAAAT-TCATTTT-AAATT
1 TTTAAAATAT--TTTTAAAATT
51922389 TTTAAA
1 TTTAAA
51922395 TCACGAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.22
20 22 0.61
21 4 0.11
22 2 0.06
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAAAATATTTTTAAAATT
Found at i:51922944 original size:14 final size:14
Alignment explanation
Indices: 51922925--51923122 Score: 55
Period size: 14 Copynumber: 13.9 Consensus size: 14
51922915 CTAGTTAATC
51922925 TAAACCCTAAACCA
1 TAAACCCTAAACCA
* *
51922939 TAAA-CCTGAACCC
1 TAAACCCTAAACCA
*
51922952 TAAAACCTTAAAACCA
1 T-AAACCCT-AAACCA
* * *
51922968 TAAATCTTTAACACA
1 TAAACCCTAAAC-CA
*
51922983 T-AACCTCTAAACCT
1 TAAACC-CTAAACCA
* * *
51922997 TAAACCC-CAGCCTT
1 TAAACCCTAAACC-A
**
51923011 TAAACCAAAAACCA
1 TAAACCCTAAACCA
* * * *
51923025 TAAATCATAACCCC
1 TAAACCCTAAACCA
*
51923039 TAAACCCATAATCCA
1 TAAACCC-TAAACCA
*
51923054 TAAACCTTAAA--A
1 TAAACCCTAAACCA
* * *
51923066 TGGTAACACCTAAATCT
1 T--AAAC-CCTAAACCA
* *
51923083 TAAACTCAAAACCA
1 TAAACCCTAAACCA
*
51923097 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
51923111 AAAACCCTAAAC
1 TAAACCCTAAAC
51923123 TATAGTGATA
Statistics
Matches: 130, Mismatches: 40, Indels: 28
0.66 0.20 0.14
Matches are distributed among these distances:
12 2 0.02
13 11 0.08
14 70 0.54
15 41 0.32
16 5 0.04
17 1 0.01
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:51923064 original size:22 final size:22
Alignment explanation
Indices: 51923022--51923064 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
51923012 AAACCAAAAA
*
51923022 CCATAAATCATAACCCCTAAAC
1 CCATAAATCATAAACCCTAAAC
*
51923044 CCAT-AATCCATAAACCTTAAA
1 CCATAAAT-CATAAACCCTAAA
51923065 ATGGTAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (22 bp):
CCATAAATCATAAACCCTAAAC
Found at i:51923406 original size:41 final size:41
Alignment explanation
Indices: 51923319--51923467 Score: 178
Period size: 41 Copynumber: 3.7 Consensus size: 41
51923309 CATTAGCGGT
** * *
51923319 GCTTTCT-AGAAAACGCCGCTAAA-AATAGAGCATTCACAGC
1 GCTTTCTCA-AAAACGCCGCTAAAGCCTTGAGCATTCGCAGC
* *
51923359 GTTTTCTCAAAAACGTCGCTAAAGCCTTGAGCATTCGCAGC
1 GCTTTCTCAAAAACGCCGCTAAAGCCTTGAGCATTCGCAGC
* *
51923400 GCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGC-GAC
1 GCTTTCTCAAAAACGCCGCTAAAGCCTTGAGCATTCGCAG-C
*
51923441 GCTTTCTTAAAAACGCCGCTAAAGCCT
1 GCTTTCTCAAAAACGCCGCTAAAGCCT
51923468 CGAAAGCTCA
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
40 20 0.21
41 74 0.79
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (41 bp):
GCTTTCTCAAAAACGCCGCTAAAGCCTTGAGCATTCGCAGC
Found at i:51923551 original size:39 final size:39
Alignment explanation
Indices: 51923502--51923597 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 39
51923492 TGGGCTTACG
* *
51923502 TTTTTTGCGGCGCTTT-ATGGAAAACGCCGCTAATGCTT-A
1 TTTTTAGCGGCGCTTTCAT--AAAACACCGCTAATGCTTGA
* *
51923541 TTTTTAGCGGCGTTTTCCATAAAGCACCGCTAATGCTTGA
1 TTTTTAGCGGCGCTTT-CATAAAACACCGCTAATGCTTGA
* *
51923581 TCTTTAGCGGCGTTTTC
1 TTTTTAGCGGCGCTTTC
51923598 CAAAAAGCGC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 31 0.63
40 16 0.33
41 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGCTTTCATAAAACACCGCTAATGCTTGA
Found at i:51923594 original size:40 final size:39
Alignment explanation
Indices: 51923528--51923613 Score: 136
Period size: 40 Copynumber: 2.2 Consensus size: 39
51923518 ATGGAAAACG
* *
51923528 CCGCTAATGCTTATTTTTAGCGGCGTTTTCCATAAAGCA
1 CCGCTAATGCTTATCTTTAGCGGCGTTTTCCAAAAAGCA
*
51923567 CCGCTAATGCTTGATCTTTAGCGGCGTTTTCCAAAAAGCG
1 CCGCTAATGCTT-ATCTTTAGCGGCGTTTTCCAAAAAGCA
51923607 CCGCTAA
1 CCGCTAA
51923614 AACGCCGCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
39 12 0.28
40 31 0.72
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (39 bp):
CCGCTAATGCTTATCTTTAGCGGCGTTTTCCAAAAAGCA
Found at i:51924694 original size:84 final size:84
Alignment explanation
Indices: 51924513--51924768 Score: 238
Period size: 84 Copynumber: 3.1 Consensus size: 84
51924503 TAATATAATT
* * * * *
51924513 AAATCAAAATAAAAT-TTGTTAAACGACA-TGAATAAATCTCAAAATAGA-ATTATTTGA-TT-A
1 AAATC-AAATAAAATATTGTTAAACGA-AGAGAATAAATCTCGAAACAGATTTTATTTAATTTAA
** *
51924573 CGTCTTTATTTGGAAACAAAACA
64 C-TC-CAATTTGGAAACAAAATA
* * **
51924596 ATATCGAATAAAATATTGTTAAACGGCTG-GAATAAAT-TCCGAAACAGATTTTATTTAATTTAA
1 AAATCAAATAAAATATTGTTAAAC-GAAGAGAATAAATCT-CGAAACAGATTTTATTTAATTTAA
* * *
51924659 TTCTAATTTAGAAACAAAATA
64 CTCCAATTTGGAAACAAAATA
* * *
51924680 AAATCAAATCAAATATTGTTAAACGAAGAGAATAAATCTTGAAATAGATTTTATTTAATTTAACT
1 AAATCAAATAAAATATTGTTAAACGAAGAGAATAAATCTCGAAACAGATTTTATTTAATTTAACT
*
51924745 CCAATTTGGAAATAAAATA
66 CCAATTTGGAAACAAAATA
51924764 AAATC
1 AAATC
51924769 TTGTTAAACA
Statistics
Matches: 141, Mismatches: 23, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
82 9 0.06
83 30 0.21
84 96 0.68
85 5 0.04
86 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (84 bp):
AAATCAAATAAAATATTGTTAAACGAAGAGAATAAATCTCGAAACAGATTTTATTTAATTTAACT
CCAATTTGGAAACAAAATA
Found at i:51925053 original size:87 final size:87
Alignment explanation
Indices: 51924914--51925083 Score: 207
Period size: 87 Copynumber: 2.0 Consensus size: 87
51924904 ATACTCGTTC
* * * * * *
51924914 TTTGGAAATAAAATCAAAATTAGAATAAAATTCATTGAACGGCAGGAGTAAATCCCAAAATAGAT
1 TTTGGAAATAAAATAAAAAATAGAATAAAATCCATTAAACAGCAGGAATAAATCCCAAAATAGAT
51924979 TTTAGTTAAATTTAATTTCCCG
66 TTTAGTTAAATTTAATTTCCCG
* ** *
51925001 TTTGGAAATAAAATAAAAAATGGAATAAAATCCATTAAACAGC-GAGAATAAATCCTGAAATGGA
1 TTTGGAAATAAAATAAAAAATAGAATAAAATCCATTAAACAGCAG-GAATAAATCCCAAAATAGA
* **
51925065 TTTTATTTACTTTTAATTT
65 TTTTAGTTAAATTTAATTT
51925084 GAAAACAAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
86 1 0.01
87 68 0.99
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (87 bp):
TTTGGAAATAAAATAAAAAATAGAATAAAATCCATTAAACAGCAGGAATAAATCCCAAAATAGAT
TTTAGTTAAATTTAATTTCCCG
Found at i:51925141 original size:73 final size:73
Alignment explanation
Indices: 51925017--51925154 Score: 188
Period size: 73 Copynumber: 1.9 Consensus size: 73
51925007 AATAAAATAA
* * ***
51925017 AAAATGGAATAAAATCCATTAAACAGCGAGAATAAATCCTGAAATGGATTTTATTTACTTTTAAT
1 AAAATCGAATAAAATCCATTAAACAGCGAGAATAAATCCCGAAACAAATTTTATTTACTTTTAAT
51925082 TTGAAAAC
66 TTGAAAAC
* * *
51925090 AAAATCGAATAAAATCTATTAAAC-GACGGGAATAAATCCCGAAACAAATTTTATTTAGTTTTAA
1 AAAATCGAATAAAATCCATTAAACAG-CGAGAATAAATCCCGAAACAAATTTTATTTACTTTTAA
51925154 T
65 T
51925155 ATTCTTTTGG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 1 0.02
73 55 0.98
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (73 bp):
AAAATCGAATAAAATCCATTAAACAGCGAGAATAAATCCCGAAACAAATTTTATTTACTTTTAAT
TTGAAAAC
Found at i:51928561 original size:21 final size:21
Alignment explanation
Indices: 51928499--51928563 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
51928489 CAGCGGTGGC
* * *
51928499 GGTGAGATTAGTTACTGTAGC
1 GGTGAGATTGGATACTGTAGT
*
51928520 AGTGAGATTGGATACTGTAGT
1 GGTGAGATTGGATACTGTAGT
51928541 GGTGAGATTGGATACTGTAGT
1 GGTGAGATTGGATACTGTAGT
51928562 GG
1 GG
51928564 AGTGTGTGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.25, C:0.06, G:0.37, T:0.32
Consensus pattern (21 bp):
GGTGAGATTGGATACTGTAGT
Found at i:51936030 original size:20 final size:22
Alignment explanation
Indices: 51936005--51936050 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
51935995 GGCGAGACAT
51936005 TTGAGTA-AAGAAACAAG-CGG
1 TTGAGTACAAGAAACAAGTCGG
**
51936025 TTGAGTACGGGAAACAAGTCGG
1 TTGAGTACAAGAAACAAGTCGG
51936047 TTGA
1 TTGA
51936051 TTTCAACTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 7 0.32
ACGTcount: A:0.37, C:0.11, G:0.33, T:0.20
Consensus pattern (22 bp):
TTGAGTACAAGAAACAAGTCGG
Found at i:51946355 original size:12 final size:11
Alignment explanation
Indices: 51946338--51946371 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
51946328 CAATAGTAAC
51946338 ACAACAGAAGAA
1 ACAACAGAA-AA
51946350 ACAACAGATAAA
1 ACAACAGA-AAA
51946362 ACAACAGAAA
1 ACAACAGAAA
51946372 TAATGAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 18 0.86
13 1 0.05
ACGTcount: A:0.68, C:0.18, G:0.12, T:0.03
Consensus pattern (11 bp):
ACAACAGAAAA
Found at i:51946599 original size:41 final size:35
Alignment explanation
Indices: 51946554--51946637 Score: 87
Period size: 36 Copynumber: 2.2 Consensus size: 35
51946544 AAGAAGAGAG
51946554 ATAAAATTTATTAACATGCAAGAAAATAAAGAAAATAAAA
1 ATAAAATTTA-TAACA-G-AAGAAAA-AAA-AAAATAAAA
* * *
51946594 TATAAAATATATAACAGAATAAAAATAAAAATAAAA
1 -ATAAAATTTATAACAGAAGAAAAAAAAAAATAAAA
51946630 ATAAAATT
1 ATAAAATT
51946638 AGTTTGCCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 7 0.18
36 9 0.23
37 2 0.05
38 6 0.15
39 1 0.03
40 5 0.13
41 9 0.23
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.24
Consensus pattern (35 bp):
ATAAAATTTATAACAGAAGAAAAAAAAAAATAAAA
Found at i:51946602 original size:12 final size:11
Alignment explanation
Indices: 51946585--51946636 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
51946575 GAAAATAAAG
51946585 AAAATAAAATAT
1 AAAATAAAA-AT
* *
51946597 AAAATATATAAC
1 AAAATA-AAAAT
*
51946609 AGAATAAAAAT
1 AAAATAAAAAT
51946620 AAAAATAAAAAT
1 -AAAATAAAAAT
51946632 AAAAT
1 AAAAT
51946637 TAGTTTGCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
11 8 0.25
12 22 0.69
13 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:51946607 original size:25 final size:24
Alignment explanation
Indices: 51946579--51946626 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
51946569 ATGCAAGAAA
51946579 ATAA-AGAAAATAAAATATAAAATAT
1 ATAACAGAAAA-AAAATA-AAAATAT
*
51946604 ATAACAGAATAAAAATAAAAATA
1 ATAACAGAAAAAAAATAAAAATA
51946627 AAAATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 10 0.48
26 5 0.24
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (24 bp):
ATAACAGAAAAAAAATAAAAATAT
Found at i:51946622 original size:6 final size:6
Alignment explanation
Indices: 51946611--51946635 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
51946601 TATATAACAG
51946611 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
51946636 TTAGTTTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:51948240 original size:24 final size:24
Alignment explanation
Indices: 51948208--51948255 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
51948198 AACAATCGAA
51948208 AACATCATCCAAATTTCGTACTAT
1 AACATCATCCAAATTTCGTACTAT
51948232 AACATCATCCAAATTTCGTACTAT
1 AACATCATCCAAATTTCGTACTAT
51948256 GAGATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (24 bp):
AACATCATCCAAATTTCGTACTAT
Found at i:51953529 original size:12 final size:13
Alignment explanation
Indices: 51953503--51953568 Score: 60
Period size: 13 Copynumber: 5.0 Consensus size: 13
51953493 CTAGTTTAGC
51953503 AATGCTTTTAAAA
1 AATGCTTTTAAAA
*
51953516 AATGCTTTTGAAA
1 AATGCTTTTAAAA
* * *
51953529 ACTGCTGTGAAAA
1 AATGCTTTTAAAA
* *
51953542 AATGATTTTAAGA
1 AATGCTTTTAAAA
*
51953555 AGTGCTTTTGAAAA
1 AATGCTTTT-AAAA
51953569 GTTTGGTTTA
Statistics
Matches: 39, Mismatches: 13, Indels: 1
0.74 0.25 0.02
Matches are distributed among these distances:
13 36 0.92
14 3 0.08
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.35
Consensus pattern (13 bp):
AATGCTTTTAAAA
Found at i:51961537 original size:6 final size:6
Alignment explanation
Indices: 51961526--51961560 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
51961516 TAATAATTAC
51961526 ATATTT ATATTT ATATTT ATATTT ATATTT ATATT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATT
51961561 AAATCACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATATTT
Found at i:51961747 original size:39 final size:39
Alignment explanation
Indices: 51961662--51961749 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
51961652 AAAATTTATA
* * *
51961662 TTTAATACAATAAAATATTTATTATATTTATTTGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTATTGGTGTTT
*
51961701 TTTAATATAATGAAACATTTATTATATTTA-TGGTAGTTT
1 TTTAATATAATAAAACATTTATTATATTTATTGGT-GTTT
51961740 TTTAATATAA
1 TTTAATATAA
51961750 ATATTTTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 3 0.07
39 41 0.93
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (39 bp):
TTTAATATAATAAAACATTTATTATATTTATTGGTGTTT
Found at i:51964837 original size:19 final size:21
Alignment explanation
Indices: 51964810--51964858 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
51964800 GCGTTTAGCT
*
51964810 TATT-TTTTATCTCA-CGCTA
1 TATTATTTAATCTCATCGCTA
51964829 TATTATTTAATCTCATCGCTA
1 TATTATTTAATCTCATCGCTA
*
51964850 CCATTATTT
1 -TATTATTT
51964859 TTACACTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 9 0.36
21 5 0.20
22 7 0.28
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (21 bp):
TATTATTTAATCTCATCGCTA
Found at i:51964855 original size:22 final size:20
Alignment explanation
Indices: 51964818--51964858 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
51964808 CTTATTTTTT
*
51964818 ATCTCACGCTATATTATTTA
1 ATCTCACGCTACATTATTTA
51964838 ATCTCATCGCTACCATTATTT
1 ATCTCA-CGCTA-CATTATTT
51964859 TTACACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (20 bp):
ATCTCACGCTACATTATTTA
Found at i:51971202 original size:38 final size:40
Alignment explanation
Indices: 51971160--51971239 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 40
51971150 CAATTTGATT
51971160 CTAATATCTAATCAGG-TT-TACACAATTCAAAATCCATC
1 CTAATATCTAATCAGGTTTCTACACAATTCAAAATCCATC
* *
51971198 CTAATATCTTATCAGGTTTCCTACACAATTCGAAATCCATC
1 CTAATATCTAATCAGGTTT-CTACACAATTCAAAATCCATC
51971239 C
1 C
51971240 AAACTCTACC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 15 0.41
39 2 0.05
41 20 0.54
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.33
Consensus pattern (40 bp):
CTAATATCTAATCAGGTTTCTACACAATTCAAAATCCATC
Found at i:51986371 original size:31 final size:31
Alignment explanation
Indices: 51986333--51986397 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
51986323 GCTTGTGGCC
51986333 ATGGCAGCTTGAGCCTCCTTTGGGTGAGCCA
1 ATGGCAGCTTGAGCCTCCTTTGGGTGAGCCA
51986364 ATGGCAGCTTGAGCCTCCTTTGGGTGAGCCA
1 ATGGCAGCTTGAGCCTCCTTTGGGTGAGCCA
51986395 ATG
1 ATG
51986398 TGAAGAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.17, C:0.25, G:0.32, T:0.26
Consensus pattern (31 bp):
ATGGCAGCTTGAGCCTCCTTTGGGTGAGCCA
Found at i:51993591 original size:142 final size:142
Alignment explanation
Indices: 51993335--51993713 Score: 695
Period size: 142 Copynumber: 2.7 Consensus size: 142
51993325 GAACCAACAA
* *
51993335 GACAAAGAAGGGCAAAGCCAAAGCCGGCAGTAAAGGAACAACCCTGCATACAGAGACATACTTAT
1 GACAAAGAAGGGCAAAGCCAAAGCCGACAGTAAAGGAACAACCCTGCATACAGAGACATCCTTAT
51993400 GGCGTAAGATGAAAGATGTTGAGAAAATGGTTACTTCCATCAACAATAGGCAAATCAAACTTGTC
66 GGCGTAAGATGAAAGATGTTGAGAAAATGGTTACTTCCATCAACAATAGGCAAATCAAACTTGTC
51993465 GCTACTATTGAG
131 GCTACTATTGAG
51993477 GACAAAGAAGGGCAAAGCCAAAGCCGACAGTAAAGGAACAACCCTGCATACAGAGACATCCTTAT
1 GACAAAGAAGGGCAAAGCCAAAGCCGACAGTAAAGGAACAACCCTGCATACAGAGACATCCTTAT
* *
51993542 GGCGTAAGATGAAAGATGTTGGGAAAATGGTTACTTCTATCAACAATAGGCAAATCAAACTTGTC
66 GGCGTAAGATGAAAGATGTTGAGAAAATGGTTACTTCCATCAACAATAGGCAAATCAAACTTGTC
51993607 GCTACTATTGAG
131 GCTACTATTGAG
* *
51993619 GACAAAGAAGGGCGAAGCCAAAGCCGACAGTAAAGGAACAACCCTGGATACAGAGACATCCTTAT
1 GACAAAGAAGGGCAAAGCCAAAGCCGACAGTAAAGGAACAACCCTGCATACAGAGACATCCTTAT
*
51993684 GGCGTAAGATGAAAGATGTTGATAAAATGG
66 GGCGTAAGATGAAAGATGTTGAGAAAATGG
51993714 CAAATCAAAC
Statistics
Matches: 229, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 229 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (142 bp):
GACAAAGAAGGGCAAAGCCAAAGCCGACAGTAAAGGAACAACCCTGCATACAGAGACATCCTTAT
GGCGTAAGATGAAAGATGTTGAGAAAATGGTTACTTCCATCAACAATAGGCAAATCAAACTTGTC
GCTACTATTGAG
Found at i:51994600 original size:17 final size:17
Alignment explanation
Indices: 51994578--51994614 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
51994568 CATAGGTATA
* *
51994578 CATTGTCATTGCATTTT
1 CATTGTCATTACATATT
51994595 CATTGTCATTACATATT
1 CATTGTCATTACATATT
51994612 CAT
1 CAT
51994615 GTTAGTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (17 bp):
CATTGTCATTACATATT
Found at i:51995695 original size:66 final size:66
Alignment explanation
Indices: 51995571--51995700 Score: 170
Period size: 66 Copynumber: 2.0 Consensus size: 66
51995561 CTTATTGCAT
* *** * *
51995571 TAATGTCACTGCATGAGTTAATTCCAAATTGCGTCCAGAATTGTTGTCGCAGTTGACAGATGTCC
1 TAATGTCACTGCATGAGTTAATTCCAAATTGCGTCCAGAATTATCACCACAGTAGACAGATGTCC
51995636 G
66 G
* * * *
51995637 TAATGTCATTGCATGAGTTAATTCCAGATTGCGTCCAGAATTATCACCATAGTAGACAGCTGTC
1 TAATGTCACTGCATGAGTTAATTCCAAATTGCGTCCAGAATTATCACCACAGTAGACAGATGTC
51995701 TAATAAAAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (66 bp):
TAATGTCACTGCATGAGTTAATTCCAAATTGCGTCCAGAATTATCACCACAGTAGACAGATGTCC
G
Found at i:52017581 original size:25 final size:24
Alignment explanation
Indices: 52017536--52017582 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
52017526 TTATGAATTA
*
52017536 GAAAAATATCTTTAGAAATTTTCT
1 GAAAAATATCTTCAGAAATTTTCT
* *
52017560 GAAATAATCTCTTCAGAGATTTT
1 GAAA-AATATCTTCAGAAATTTT
52017583 TCCCCCTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (24 bp):
GAAAAATATCTTCAGAAATTTTCT
Found at i:52017837 original size:20 final size:19
Alignment explanation
Indices: 52017787--52017839 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
52017777 CTACAAGATA
52017787 AATATTAAATT--TAATTT
1 AATATTAAATTAATAATTT
52017804 AATATTAAGA-TAATAACTTT
1 AATATTAA-ATTAATAA-TTT
52017824 AATATTAAATTAATAA
1 AATATTAAATTAATAA
52017840 AATATTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.29
18 1 0.03
19 4 0.13
20 17 0.55
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AATATTAAATTAATAATTT
Found at i:52017843 original size:25 final size:25
Alignment explanation
Indices: 52017796--52017843 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
52017786 AAATATTAAA
*
52017796 TTTAATTTAATATTAAGATAATAAC
1 TTTAATTTAATATTAAGAAAATAAC
*
52017821 TTTAATATTAA-ATTAATAAAATA
1 TTTAAT-TTAATATTAAGAAAATA
52017844 TTATTAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATAAC
Found at i:52017896 original size:68 final size:71
Alignment explanation
Indices: 52017754--52017898 Score: 172
Period size: 68 Copynumber: 2.1 Consensus size: 71
52017744 TATTAAATCT
*
52017754 TATTAAAATAATAAAATGTTTATCTACAAGATAAATATTAAATTTAATTTAATATTAAGATAATA
1 TATTAAAATAATAAAATGATTATCTA-AAGATAAATATTAAATTTAATTTAATATTAAGATAATA
****
52017819 ACTTTAA
65 AAAACAA
* * *
52017826 TATTAAATTAATAAAAT-ATTAT-T-AAGATAAGTATTAAATTTAATTTAATATTTAA-ATATTA
1 TATTAAAATAATAAAATGATTATCTAAAGATAAATATTAAATTTAATTTAATA-TTAAGATAATA
52017887 AAAACAA
65 AAAACAA
52017894 TATTA
1 TATTA
52017899 TTTTTGGAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
68 39 0.61
69 4 0.06
70 1 0.02
71 4 0.06
72 16 0.25
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (71 bp):
TATTAAAATAATAAAATGATTATCTAAAGATAAATATTAAATTTAATTTAATATTAAGATAATAA
AAACAA
Found at i:52021333 original size:3 final size:3
Alignment explanation
Indices: 52021327--52021427 Score: 148
Period size: 3 Copynumber: 33.3 Consensus size: 3
52021317 TTTTTTTTTG
* *
52021327 TTA TTA TTA TTA TTA TTA TTA TCA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
52021375 TTA TCA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TATA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
52021421 TTA TTA T
1 TTA TTA T
52021428 ACTTACATAT
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
3 85 0.98
4 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:52021507 original size:2 final size:2
Alignment explanation
Indices: 52021491--52021536 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
52021481 TTCAAACACC
*
52021491 TA TA CA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52021532 TA TA T
1 TA TA T
52021537 TATTNNNNNN
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52027769 original size:133 final size:132
Alignment explanation
Indices: 52027553--52028190 Score: 756
Period size: 133 Copynumber: 4.8 Consensus size: 132
52027543 GAGCAGGTTG
* * * * *
52027553 AAGATTTCAGATCTTGCCTCC-C-TAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCT
1 AAGATTTCAGATCTTGCCTCCGCATAA--A-CAGCGGAGCAGATCAAAGATGGTGAATTTTACCT
* ** *
52027616 CTCTGACATTGCAGTCGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAG
63 CCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAG
52027681 ATT-A
128 ATTAA
*
52027685 ACGATTTCAGATCTTGCCTTCCTGCATAAACAGCGGAGCAGATCAAAGATGGTGAATTTTACCTC
1 AAGATTTCAGATCTTGCC-TCC-GCATAAACAGCGGAGCAGATCAAAGATGGTGAATTTTACCTC
*
52027750 CCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGTAGTGGAATAGA
64 CCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAGA
52027815 TT-A
129 TTAA
* *
52027818 AAGATTTCAGATCTTGCCTTCCTGCATAGACAGCGGAGCAGGTCAAAGATGGTGAATTTTACCTC
1 AAGATTTCAGATCTTGCC-TCC-GCATAAACAGCGGAGCAGATCAAAGATGGTGAATTTTACCTC
52027883 CCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAGA
64 CCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAGA
52027948 TTAA
129 TTAA
* * * ** * *
52027952 AAGATTTTAGATCTTGTCTCCCCA-AGCAGTAGTGGAGCAGATCAAAGATGATGAATTTTACCTC
1 AAGATTTCAGATCTTGCCTCCGCATA--AACAGCGGAGCAGATCAAAGATGGTGAATTTTACCTC
* * * * * * *
52028016 CCTGTGGTTACAGTGGAGTACATTGAAGTCGGTAATTCTACTTCCCTGGGCAGCAG-CGAATAGA
64 CCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAGA
*
52028080 TT-G
129 TTAA
* * * * * * *
52028083 AAGATTTCAGGTCTTGTCTCC-C-TAAGCTGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCT
1 AAGATTTCAGATCTTGCCTCCGCATAAAC---AGCGGAGCAGATCAAAGATGGTGAATTTTACCT
* * *
52028146 CCCTGAAGTTGCA-TGGAGTACATTGAAGCCAGTAATTTTACTTCC
63 CCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCC
52028191 TTAGCAGTGC
Statistics
Matches: 450, Mismatches: 45, Indels: 24
0.87 0.09 0.05
Matches are distributed among these distances:
128 2 0.00
130 31 0.07
131 59 0.13
132 28 0.06
133 308 0.68
134 18 0.04
135 1 0.00
136 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (132 bp):
AAGATTTCAGATCTTGCCTCCGCATAAACAGCGGAGCAGATCAAAGATGGTGAATTTTACCTCCC
TGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAGATT
AA
Found at i:52028060 original size:266 final size:265
Alignment explanation
Indices: 52027553--52028190 Score: 839
Period size: 266 Copynumber: 2.4 Consensus size: 265
52027543 GAGCAGGTTG
52027553 AAGATTTCAGATCTTGCCTCCCT--A-AGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
1 AAGATTTCAGATCTTGCCTCCCTGCATAG-A-TAGTGGAGCAGATCGAAGATGGCGGATTTTACC
* *
52027615 TCTCTGACA-TTGCAGTCGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAAT
64 TCCCTGA-AGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAAT
* * *
52027679 AGATTAACGATTTCAGATCTTGCCTTCCTGCATAAACAGCGGAGCAGATCAAAGATGGTGAATTT
128 AGATTAAAGATTTCAGATCTTGCCTTCCTCCATAAACAGCGGAGCAGATCAAAGATGATGAATTT
* * * *
52027744 TACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGTAGTGG
193 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGGCAGCAG-CG
52027809 AATAGATTA
257 AATAGATTA
* * * * * * *
52027818 AAGATTTCAGATCTTGCCTTCCTGCATAGACAGCGGAGCAGGTCAAAGATGGTGAATTTTACCTC
1 AAGATTTCAGATCTTGCCTCCCTGCATAGATAGTGGAGCAGATCGAAGATGGCGGATTTTACCTC
*
52027883 CCTGAGGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAGA
66 CCTGAAGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAGA
* * ** *
52027948 TTAAAAGATTTTAGATCTTGTC-TCC-CCA-AGCAGTAGTGGAGCAGATCAAAGATGATGAATTT
131 TT-AAAGATTTCAGATCTTGCCTTCCTCCATA--AACAGCGGAGCAGATCAAAGATGATGAATTT
* * * *
52028010 TACCTCCCTGTGGTTACAGTGGAGTACATTGAAGTCGGTAATTCTACTTCCCTGGGCAGCAGCGA
193 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGGCAGCAGCGA
*
52028075 ATAGATTG
258 ATAGATTA
* *
52028083 AAGATTTCAGGTCTTGTCTCCCTAAGC-T-G-TAGTGGAGCAGATCGAAGATGGCGGATTTTACC
1 AAGATTTCAGATCTTGCCTCCCT--GCATAGATAGTGGAGCAGATCGAAGATGGCGGATTTTACC
* *
52028145 TCCCTGAAGTTGCA-TGGAGTACATTGAAGCCAGTAATTTTACTTCC
64 TCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCC
52028191 TTAGCAGTGC
Statistics
Matches: 325, Mismatches: 39, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
263 30 0.09
264 41 0.13
265 54 0.17
266 178 0.55
267 20 0.06
268 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (265 bp):
AAGATTTCAGATCTTGCCTCCCTGCATAGATAGTGGAGCAGATCGAAGATGGCGGATTTTACCTC
CCTGAAGTTGCAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGTCAGCAGTGGAATAGA
TTAAAGATTTCAGATCTTGCCTTCCTCCATAAACAGCGGAGCAGATCAAAGATGATGAATTTTAC
CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGAAATTCTACTTCCCTGGGCAGCAGCGAATA
GATTA
Found at i:52028313 original size:50 final size:49
Alignment explanation
Indices: 52028194--52028668 Score: 364
Period size: 50 Copynumber: 9.5 Consensus size: 49
52028184 TACTTCCTTA
*
52028194 GCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCT
1 GCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCT
* * * ** * * * * **
52028243 GATATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTATTTCGTT
1 G-CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCT
*
52028293 AGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGGTTTCCCT
1 -GCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCT-GATTTCCCT
* ** * * * * * *
52028344 G-ATGTTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTT
1 GCA-G-TGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCT
*
52028394 AGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCT
1 -GCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCT
* * * ** * * * * *
52028444 GATATTGCAATTAAAAAGATTGAAGCCACGACGGCGGATCTTACTTCCTT
1 G-CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCT
*
52028494 AGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCT
1 -GCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCT
* * * ** * * * *
52028544 GATATTGCAATTAAAAAGATTGAAG-TCACAACGGCGGATCTTACTTCCCT
1 G-CAGTGCAGTGGAACAGATTGAAGCT-ACGACGGCGGATCTGATTTCCCT
* * *
52028594 GACGGTGCGGTGGAACAGATTGAAGCTACGACGGCGGATCT-AGTTTCCCC
1 G-CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGA-TTTCCCT
* *
52028644 GACA-TAGCAGTGGAATAGACTGAAG
1 G-CAGT-GCAGTGGAACAGATTGAAG
52028669 ATTTCAGATC
Statistics
Matches: 321, Mismatches: 91, Indels: 27
0.73 0.21 0.06
Matches are distributed among these distances:
49 7 0.02
50 273 0.85
51 40 0.12
52 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (49 bp):
GCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGATTTCCCT
Found at i:52028528 original size:201 final size:200
Alignment explanation
Indices: 52028183--52028642 Score: 814
Period size: 201 Copynumber: 2.3 Consensus size: 200
52028173 GCCAGTAATT
52028183 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
* *
52028248 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTATTTCGTTAGCAGTGCAGTGGAACAGAT
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGAT
*
52028313 TGAAGCTACGACGGCGGATCTGGGTTTCCCTGATGTTGCAATTAAAAAGATTGAAGCCACAACGG
131 TGAAGCTACGACGGCGGATCT-GGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAACGG
52028378 CGGATC
195 CGGATC
52028384 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
52028449 TGCAATTAAAAAGATTGAAGCCACGACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGAT
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGAT
*
52028514 TGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGTCACAACGGC
131 TGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAACGGC
52028579 GGATC
196 GGATC
* * * *
52028584 TTACTTCCCT-GACGGTGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTAGTTTCCC
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCC
52028643 CGACATAGCA
Statistics
Matches: 249, Mismatches: 9, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
199 1 0.00
200 100 0.40
201 148 0.59
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (200 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGGAACAGAT
TGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATTGAAGCCACAACGGC
GGATC
Found at i:52028668 original size:100 final size:100
Alignment explanation
Indices: 52028183--52028642 Score: 814
Period size: 100 Copynumber: 4.6 Consensus size: 100
52028173 GCCAGTAATT
52028183 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
52028248 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * *
52028283 TTATTTCGTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGGTTTCCCTGATG
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCT-GGTTTCCCTGATA
52028348 TTGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
65 TTGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
52028384 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
52028449 TGCAATTAAAAAGATTGAAGCCACGACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
52028484 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
52028549 TGCAATTAAAAAGATTGAAGTCACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * * *
52028584 TTACTTCCCT-GACGGTGCGGTGGAACAGATTGAAGCTACGACGGCGGATCTAGTTTCCC
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCC
52028643 CGACATAGCA
Statistics
Matches: 345, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
99 1 0.00
100 247 0.72
101 97 0.28
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (100 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
Found at i:52028833 original size:132 final size:132
Alignment explanation
Indices: 52028649--52028889 Score: 392
Period size: 132 Copynumber: 1.8 Consensus size: 132
52028639 TCCCCGACAT
* * *
52028649 AGCAGTGGAATAGACTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
1 AGCAGCGGAATAGACTAAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA
* *
52028714 TGGCAGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGG
66 TGACAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGG
52028779 GC
131 GC
* **
52028781 AGCAGCGGAATAGATTAAAGATTTCAGATCTTGTTTCCCTAAGCAGTAGTGGAGCAGATCAAAGA
1 AGCAGCGGAATAGACTAAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA
**
52028846 TGACAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG
66 TGACAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAG
52028890 TCAATATTCT
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 99 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (132 bp):
AGCAGCGGAATAGACTAAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGA
TGACAGATTTTACCTCCCTGAAGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGG
GC
Found at i:52035262 original size:7 final size:7
Alignment explanation
Indices: 52035252--52035281 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
52035242 TTAAAATACT
52035252 TTTTAAA
1 TTTTAAA
52035259 TTTTAAA
1 TTTTAAA
52035266 TTTTAAA
1 TTTTAAA
52035273 TTTTTAAA
1 -TTTTAAA
52035281 T
1 T
52035282 ACTTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTTAAA
Found at i:52035269 original size:33 final size:33
Alignment explanation
Indices: 52035232--52035332 Score: 121
Period size: 33 Copynumber: 2.9 Consensus size: 33
52035222 TATTTATTTT
*
52035232 ATTTTTTATTTTAAAATACTTTTTAAATTTTAA
1 ATTTTATATTTTAAAATACTTTTTAAATTTTAA
* * * *
52035265 ATTTTAAATTTTTAAATACTTTTTAATTTTTGA
1 ATTTTATATTTTAAAATACTTTTTAAATTTTAA
52035298 ATTTTAAAATATTTTAAAATACTTTTTTAAATTTT
1 ATTTT---ATATTTTAAAATAC-TTTTTAAATTTT
52035333 GTTTTAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
33 33 0.59
36 12 0.21
37 11 0.20
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (33 bp):
ATTTTATATTTTAAAATACTTTTTAAATTTTAA
Found at i:52035271 original size:14 final size:15
Alignment explanation
Indices: 52035252--52035315 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 15
52035242 TTAAAATACT
52035252 TTTTAAA-TTTTAAA
1 TTTTAAATTTTTAAA
52035266 TTTTAAATTTTTAAATA
1 TTTTAAATTTTT-AA-A
* *
52035283 CTTTTTAATTTTTGAA
1 -TTTTAAATTTTTAAA
52035299 TTTTAAAATATTTTAAA
1 TTTT-AAAT-TTTTAAA
52035316 ATACTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 7 0.17
15 8 0.20
16 6 0.15
17 8 0.20
18 11 0.28
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTTAAATTTTTAAA
Found at i:52035288 original size:26 final size:25
Alignment explanation
Indices: 52035259--52035317 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
52035249 ACTTTTTAAA
*
52035259 TTTTAAATTTTAAATTTTTAAATACT
1 TTTTAAATTTTAAATTTTAAAATA-T
* *
52035285 TTTTAATTTTTGAATTTTAAAATAT
1 TTTTAAATTTTAAATTTTAAAATAT
*
52035310 TTTAAAAT
1 TTTTAAAT
52035318 ACTTTTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTAAATTTTAAATTTTAAAATAT
Found at i:52035294 original size:7 final size:8
Alignment explanation
Indices: 52035251--52035315 Score: 62
Period size: 8 Copynumber: 8.0 Consensus size: 8
52035241 TTTAAAATAC
52035251 TTTTTAAA
1 TTTTTAAA
52035259 -TTTTAAA
1 TTTTTAAA
52035266 -TTTTAAA
1 TTTTTAAA
52035273 TTTTTAAA
1 TTTTTAAA
*
52035281 TACTTTTTAA
1 T--TTTTAAA
*
52035291 TTTTTGAA
1 TTTTTAAA
*
52035299 TTTTAAAA
1 TTTTTAAA
52035307 TATTTTAAA
1 T-TTTTAAA
52035316 ATACTTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
7 14 0.29
8 21 0.44
9 6 0.12
10 7 0.15
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (8 bp):
TTTTTAAA
Found at i:52037000 original size:7 final size:7
Alignment explanation
Indices: 52036980--52037025 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
52036970 CCAGAATCTC
52036980 GAACCTT
1 GAACCTT
52036987 GAA-CTT
1 GAACCTT
52036993 GAACCTT
1 GAACCTT
52037000 GAACCTT
1 GAACCTT
52037007 GAACCTT
1 GAACCTT
* *
52037014 AAACTTT
1 GAACCTT
52037021 GAACC
1 GAACC
52037026 CCAAATCCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (7 bp):
GAACCTT
Found at i:52037457 original size:23 final size:23
Alignment explanation
Indices: 52037430--52037475 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
52037420 TTGTTTTTAA
52037430 ATTTTGATGATGTGGTAAAATTT
1 ATTTTGATGATGTGGTAAAATTT
52037453 ATTTTGATGATGTGGTAAAATTT
1 ATTTTGATGATGTGGTAAAATTT
52037476 TATTGGTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (23 bp):
ATTTTGATGATGTGGTAAAATTT
Found at i:52040903 original size:29 final size:30
Alignment explanation
Indices: 52040817--52040927 Score: 82
Period size: 31 Copynumber: 3.7 Consensus size: 30
52040807 AATTAAATCA
* * * *
52040817 AAATTAAAGTTTCAAGTATGCATTTGAACC
1 AAATTAAAGTTTCATGTATACAATTGCACC
* * * * *
52040847 ACAATTAGACTTTCATGTGTATAGTTGCACC
1 A-AATTAAAGTTTCATGTATACAATTGCACC
*
52040878 AAATTAAAGTTT-ATGTATACAATTGCACATT
1 AAATTAAAGTTTCATGTATACAATTGCAC--C
*
52040909 AAATCAAAG-TTCATGTATA
1 AAATTAAAGTTTCATGTATA
52040928 ATTTTGAGAT
Statistics
Matches: 62, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
29 13 0.21
30 12 0.19
31 37 0.60
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTTCATGTATACAATTGCACC
Found at i:52042713 original size:31 final size:31
Alignment explanation
Indices: 52042662--52042736 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
52042652 ATAAAGCAAG
* * * * *
52042662 AATTTTAA-TTTAATTGAATTGTATTTATGA
1 AATTTTAATTTTAACTCAATTGAATATATAA
52042692 AATTTTAATTTTAACTCAATTGAATATATAA
1 AATTTTAATTTTAACTCAATTGAATATATAA
*
52042723 AAATTTATATTTTA
1 AATTTTA-ATTTTA
52042737 TTAAATAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 8 0.22
31 23 0.62
32 6 0.16
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (31 bp):
AATTTTAATTTTAACTCAATTGAATATATAA
Found at i:52055489 original size:16 final size:16
Alignment explanation
Indices: 52055457--52055503 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
52055447 GTTATGTATG
*
52055457 AATTTTAA-TAATTTA
1 AATTTTAATTAATATA
52055472 AATTTTAATTAATATA
1 AATTTTAATTAATATA
* *
52055488 AAATGTAATTCAATAT
1 AATTTTAATT-AATAT
52055504 TTCTCAGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 8 0.30
16 14 0.52
17 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
AATTTTAATTAATATA
Found at i:52059463 original size:18 final size:18
Alignment explanation
Indices: 52059428--52059465 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
52059418 TAAATGATGA
52059428 ATTTTAAGTATTAGTTGTT
1 ATTTTAAGTATTA-TTGTT
52059447 ATTTATAAGTATT-TTGTT
1 ATTT-TAAGTATTATTGTT
52059465 A
1 A
52059466 AGTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (18 bp):
ATTTTAAGTATTATTGTT
Found at i:52060262 original size:20 final size:19
Alignment explanation
Indices: 52060186--52060262 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 19
52060176 TGTACGAGAT
52060186 TTGCACTTCGGTG-CCTCTG
1 TTGCACTTCGGTGCCCT-TG
* *
52060205 TATACACTTCTGTGTCCC-TG
1 T-TGCACTTCGGTG-CCCTTG
*
52060225 TTCGCACTACGGTGGCCCTTG
1 TT-GCACTTCGGT-GCCCTTG
52060246 TCTGCACTTCGGTGCCC
1 T-TGCACTTCGGTGCCC
52060263 CTATTATGCA
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
19 2 0.04
20 27 0.60
21 13 0.29
22 3 0.07
ACGTcount: A:0.09, C:0.34, G:0.23, T:0.34
Consensus pattern (19 bp):
TTGCACTTCGGTGCCCTTG
Found at i:52060272 original size:21 final size:20
Alignment explanation
Indices: 52060187--52060272 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
52060177 GTACGAGATT
* *
52060187 TGCACTTCGGTGCCTCTGTA
1 TGCACTTCGGTGCCCCTTTA
* * *
52060207 TACACTTCTGTGTCCCTGTT-
1 TGCACTTCGGTGCCCCT-TTA
* * * *
52060227 CGCACTACGGTGGCCCTTGTC
1 TGCACTTCGGTGCCCCTT-TA
52060248 TGCACTTCGGTGCCCCTATTA
1 TGCACTTCGGTGCCCCT-TTA
52060269 TGCA
1 TGCA
52060273 TCTATGATGC
Statistics
Matches: 48, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
19 1 0.02
20 26 0.54
21 20 0.42
22 1 0.02
ACGTcount: A:0.12, C:0.33, G:0.22, T:0.34
Consensus pattern (20 bp):
TGCACTTCGGTGCCCCTTTA
Found at i:52062977 original size:28 final size:28
Alignment explanation
Indices: 52062888--52063052 Score: 156
Period size: 29 Copynumber: 5.8 Consensus size: 28
52062878 CACTTAACTA
* * *
52062888 AGATAGCCACAAATGCATCTTTTTAATAG
1 AGATAGCCACAAAGGC-TCCTTTTAACAG
* *
52062917 AGATAGCCATAAAGGTTTCCTTTTAAC-G
1 AGATAGCCACAAAGG-CTCCTTTTAACAG
52062945 AAGATAGCCACAAAGGCTCCTTTTAACAG
1 -AGATAGCCACAAAGGCTCCTTTTAACAG
* *
52062974 AGATATCCACAAAGGCTCC-TTTAACAT
1 AGATAGCCACAAAGGCTCCTTTTAACAG
* *
52063001 AGATTAGCCACAAAGGATTTCTTTTAACAG
1 AGA-TAGCCACAAAGG-CTCCTTTTAACAG
* *
52063031 AGATCA-CCATAAAGGCTTCTTT
1 AGAT-AGCCACAAAGGCTCCTTT
52063053 ATAATAGATA
Statistics
Matches: 114, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
27 10 0.09
28 46 0.40
29 47 0.41
30 11 0.10
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (28 bp):
AGATAGCCACAAAGGCTCCTTTTAACAG
Found at i:52063025 original size:57 final size:56
Alignment explanation
Indices: 52062891--52063088 Score: 165
Period size: 57 Copynumber: 3.4 Consensus size: 56
52062881 TTAACTAAGA
* * * *
52062891 TAGCCACAAATGCATCT-TTTTAATAGAGATAGCCATAAAGGTTTCCTTTTAACGA-AGA-
1 TAGCCACAAA-GGATTTCTTTTAACAGAGATA-CCATAAAGG-CTCC-TTTAAC-ATAGAT
* * *
52062949 TAGCCACAAAGG-CTCCTTTTAACAGAGATATCCACAAAGGCTCCTTTAACATAGAT
1 TAGCCACAAAGGATTTCTTTTAACAGAGATA-CCATAAAGGCTCCTTTAACATAGAT
*
52063005 TAGCCACAAAGGATTTCTTTTAACAGAGATCACCATAAAGGCTTCTTTATA-ATAGAT
1 TAGCCACAAAGGATTTCTTTTAACAGAGAT-ACCATAAAGGCTCCTTTA-ACATAGAT
* *
52063062 ATCA-CTACAAAGGCTTTCATTTTAACA
1 -T-AGCCACAAAGGATTTC-TTTTAACA
52063089 TATTTTTCTA
Statistics
Matches: 117, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
54 1 0.01
55 9 0.08
56 15 0.13
57 58 0.50
58 25 0.21
59 9 0.08
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (56 bp):
TAGCCACAAAGGATTTCTTTTAACAGAGATACCATAAAGGCTCCTTTAACATAGAT
Found at i:52063065 original size:29 final size:28
Alignment explanation
Indices: 52062894--52063088 Score: 130
Period size: 29 Copynumber: 6.8 Consensus size: 28
52062884 ACTAAGATAG
* * *
52062894 CCACAAATGCATCTTTTTAATAGAGAT-A
1 CCACAAAGGCTTC-TTTTAACAGAGATCA
* *
52062922 GCCATAAAGGTTTCCTTTTAAC-GAAGAT-A
1 -CCACAAAGGCTT-CTTTTAACAG-AGATCA
*
52062951 GCCACAAAGGCTCCTTTTAACAGAGAT-A
1 -CCACAAAGGCTTCTTTTAACAGAGATCA
* * *
52062979 TCCACAAAGGC-TCCTTTAACATAGATTA
1 -CCACAAAGGCTTCTTTTAACAGAGATCA
*
52063007 GCCACAAAGGATTTCTTTTAACAGAGATCA
1 -CCACAAAGG-CTTCTTTTAACAGAGATCA
* * *
52063037 CCATAAAGGCTTCTTTATAATAGATATCA
1 CCACAAAGGCTTCTTT-TAACAGAGATCA
*
52063066 CTACAAAGGCTTTCATTTTAACA
1 CCACAAAGGC-TTC-TTTTAACA
52063089 TATTTTTCTA
Statistics
Matches: 133, Mismatches: 24, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
27 12 0.09
28 40 0.30
29 56 0.42
30 22 0.17
31 3 0.02
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (28 bp):
CCACAAAGGCTTCTTTTAACAGAGATCA
Found at i:52066594 original size:2 final size:2
Alignment explanation
Indices: 52066587--52066626 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
52066577 TTATAGGGAG
52066587 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52066627 GTGTGTTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52077094 original size:26 final size:26
Alignment explanation
Indices: 52077065--52077126 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
52077055 TACCTACAAT
52077065 AGTTTCAGAATATCATAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* * *
52077091 AGTTTCAGAATATTATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
52077117 AGTTTCAGAA
1 AGTTTCAGAA
52077127 CACTAACAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:52077569 original size:4 final size:4
Alignment explanation
Indices: 52077560--52077590 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
52077550 CCATAAAGTA
*
52077560 AAAT AAAT AAAT AAAT AAAT AAAT AACT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
52077591 ATTTAAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:52083949 original size:21 final size:22
Alignment explanation
Indices: 52083925--52083967 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
52083915 AATAGGTATG
52083925 ATTTTATTTA-AATTTTTGTAA
1 ATTTTATTTAGAATTTTTGTAA
52083946 ATTTTATTTATGAATTTTTGTA
1 ATTTTATTTA-GAATTTTTGTA
52083968 TGTTTAGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.50
23 10 0.50
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
ATTTTATTTAGAATTTTTGTAA
Found at i:52090585 original size:19 final size:19
Alignment explanation
Indices: 52090561--52090597 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
52090551 TAGGATGCAC
*
52090561 ATATAATTGGAGCCAATAT
1 ATATAATTGAAGCCAATAT
52090580 ATATAATTGAAGCCAATA
1 ATATAATTGAAGCCAATA
52090598 CAAGAGAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (19 bp):
ATATAATTGAAGCCAATAT
Found at i:52092703 original size:9 final size:9
Alignment explanation
Indices: 52092689--52092717 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
52092679 GTTGAGAAAA
52092689 TAATTTAAT
1 TAATTTAAT
52092698 TAATTTAAT
1 TAATTTAAT
52092707 TAA-TTAAT
1 TAATTTAAT
52092715 TAA
1 TAA
52092718 GTAATATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TAATTTAAT
Found at i:52101393 original size:35 final size:35
Alignment explanation
Indices: 52101347--52101417 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
52101337 TGTTATATGC
52101347 AATTTTGAAAAAGAAAGTCCATTAATGTTGGGAAA
1 AATTTTGAAAAAGAAAGTCCATTAATGTTGGGAAA
52101382 AATTTTGAAAAAGAAAGTCCATTAATGTTGGGAAA
1 AATTTTGAAAAAGAAAGTCCATTAATGTTGGGAAA
52101417 A
1 A
52101418 GTATCCTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (35 bp):
AATTTTGAAAAAGAAAGTCCATTAATGTTGGGAAA
Found at i:52110341 original size:24 final size:24
Alignment explanation
Indices: 52110293--52110339 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
52110283 ATTGGTCACA
*
52110293 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAGGAGGAATATTTG
*
52110317 GAGATATTTGAGGAGAGAATATT
1 GAGAGATTTGAGGAG-GAATATT
52110340 GGGGATTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.36, T:0.30
Consensus pattern (24 bp):
GAGAGATTTGAGGAGGAATATTTG
Found at i:52110550 original size:55 final size:55
Alignment explanation
Indices: 52110466--52110582 Score: 191
Period size: 55 Copynumber: 2.1 Consensus size: 55
52110456 CACATTGCCT
*
52110466 GGGAATCAAGGGTGCGATGATCATCGATTTG-TGGCATAAGAGTGTTCGGATCGAA
1 GGGAATCAAGGGTGCGATGATCATCGATTTGCT-GAATAAGAGTGTTCGGATCGAA
* *
52110521 GGGAATCAAGGGTGCGATGATCATTGATTTGCTGAATAAGAGTGTTTGGATCGAA
1 GGGAATCAAGGGTGCGATGATCATCGATTTGCTGAATAAGAGTGTTCGGATCGAA
52110576 GGGAATC
1 GGGAATC
52110583 TGCAAATCGC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 57 0.98
56 1 0.02
ACGTcount: A:0.28, C:0.11, G:0.34, T:0.26
Consensus pattern (55 bp):
GGGAATCAAGGGTGCGATGATCATCGATTTGCTGAATAAGAGTGTTCGGATCGAA
Found at i:52111061 original size:27 final size:27
Alignment explanation
Indices: 52111031--52111181 Score: 130
Period size: 27 Copynumber: 5.6 Consensus size: 27
52111021 CCTTGAAGGT
52111031 TAAAATGACCGAAATAACCTCGATGGG
1 TAAAATGACCGAAATAACCTCGATGGG
*
52111058 TAAAATGACCGAAAT-ACTCTTGATGGG
1 TAAAATGACCGAAATAAC-CTCGATGGG
* *
52111085 TAAAATGATCGAAATACCCTCGATGGG
1 TAAAATGACCGAAATAACCTCGATGGG
* * * * *
52111112 TACAATGACTGACAT--GCTCCCATAGGG
1 TAAAATGACCGAAATAACCT-CGAT-GGG
* * *
52111139 TAAAATGACCGAAATACCCCCG-TAAGG
1 TAAAATGACCGAAATAACCTCGAT-GGG
*
52111166 TAAAATGACCGTAATA
1 TAAAATGACCGAAATA
52111182 CCCCTGTAGG
Statistics
Matches: 100, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.02
26 5 0.05
27 90 0.90
28 2 0.02
29 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (27 bp):
TAAAATGACCGAAATAACCTCGATGGG
Found at i:52111080 original size:54 final size:55
Alignment explanation
Indices: 52111014--52111346 Score: 233
Period size: 54 Copynumber: 6.2 Consensus size: 55
52111004 TATCTGGACT
* * *
52111014 GAAATACCCTTGAAGGTTAAAATGACCGAAATAACCTCGAT-GGGTAAAATGACC
1 GAAATACCCTTGAAGGGTAAAATGACCGAAATACCCCCGATAGGGTAAAATGACC
* * * * * *
52111068 GAAATACTCTTGATGGGTAAAATGATCGAAATACCCTCGAT-GGGTACAATGACT
1 GAAATACCCTTGAAGGGTAAAATGACCGAAATACCCCCGATAGGGTAAAATGACC
* * * *
52111122 GACATGCTCC--CATAGGGTAAAATGACCGAAATACCCCCG-TAAGGTAAAATGACC
1 GAAATAC-CCTTGA-AGGGTAAAATGACCGAAATACCCCCGATAGGGTAAAATGACC
* * * * * * *
52111176 GTAATACCCCTGTAGGGTAAAATGACTGTAAT-GCCCCTATAGGGTAAAATGACC
1 GAAATACCCTTGAAGGGTAAAATGACCGAAATACCCCCGATAGGGTAAAATGACC
* * * * * *
52111230 GTAATGCCCTTGTAGGGTAAAATGACAG-TAT-CGCCCTTG-TAGGGTAAAATGACC
1 GAAATACCCTTGAAGGGTAAAATGACCGAAATAC-CCC-CGATAGGGTAAAATGACC
** * * *
52111284 GTCATACCCCTT--AGGGTAAAATGACCGTAATGCCCCTC--TAGGGTAAAATAACC
1 GAAATA-CCCTTGAAGGGTAAAATGACCGAAATACCCC-CGATAGGGTAAAATGACC
*
52111337 GTAATACCCT
1 GAAATACCCT
52111347 GGTGGGTAAA
Statistics
Matches: 227, Mismatches: 41, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
52 4 0.02
53 43 0.19
54 173 0.76
55 7 0.03
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (55 bp):
GAAATACCCTTGAAGGGTAAAATGACCGAAATACCCCCGATAGGGTAAAATGACC
Found at i:52111149 original size:81 final size:81
Alignment explanation
Indices: 52111055--52111345 Score: 283
Period size: 81 Copynumber: 3.6 Consensus size: 81
52111045 TAACCTCGAT
* * *
52111055 GGGTAAAATGACCGAAATACTCTTG-ATGGGTAAAATGATCGAAATA-CCCTCG-ATGGGTACAA
1 GGGTAAAATGACCGAAATACCCTTGTA-GGGTAAAATGACCGAAATACCCCT-GTA-GGGTAAAA
52111117 TGACTG-ACATGCTCCC-ATA
63 TGACTGTA-ATGC-CCCTATA
** * *
52111136 GGGTAAAATGACCGAAATACCCCCGTAAGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGA
1 GGGTAAAATGACCGAAATACCCTTGTAGGGTAAAATGACCGAAATACCCCTGTAGGGTAAAATGA
52111201 CTGTAATGCCCCTATA
66 CTGTAATGCCCCTATA
* * * *
52111217 GGGTAAAATGACCGTAATGCCCTTGTAGGGTAAAATGACAG-TAT-CGCCCTTGTAGGGTAAAAT
1 GGGTAAAATGACCGAAATACCCTTGTAGGGTAAAATGACCGAAATAC-CCC-TGTAGGGTAAAAT
* * *
52111280 GACCGTCATACCCCT-TA
64 GACTGTAATGCCCCTATA
* * * * * *
52111297 GGGTAAAATGACCGTAATGCCCCTCTAGGGTAAAATAACCGTAATACCC
1 GGGTAAAATGACCGAAATACCCTTGTAGGGTAAAATGACCGAAATACCC
52111346 TGGTGGGTAA
Statistics
Matches: 179, Mismatches: 22, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
79 1 0.01
80 47 0.26
81 123 0.69
82 8 0.04
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (81 bp):
GGGTAAAATGACCGAAATACCCTTGTAGGGTAAAATGACCGAAATACCCCTGTAGGGTAAAATGA
CTGTAATGCCCCTATA
Found at i:52111182 original size:27 final size:27
Alignment explanation
Indices: 52111134--52111345 Score: 268
Period size: 27 Copynumber: 7.9 Consensus size: 27
52111124 CATGCTCCCA
* *
52111134 TAGGGTAAAATGACCGAAATACCCCCG
1 TAGGGTAAAATGACCGTAATACCCCTG
*
52111161 TAAGGTAAAATGACCGTAATACCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* * *
52111188 TAGGGTAAAATGACTGTAATGCCCCTA
1 TAGGGTAAAATGACCGTAATACCCCTG
* *
52111215 TAGGGTAAAATGACCGTAATGCCCTTG
1 TAGGGTAAAATGACCGTAATACCCCTG
*
52111242 TAGGGTAAAATGACAGT-AT-CGCCCTTG
1 TAGGGTAAAATGACCGTAATAC-CCC-TG
*
52111269 TAGGGTAAAATGACCGTCATACCCCT-
1 TAGGGTAAAATGACCGTAATACCCCTG
* *
52111295 TAGGGTAAAATGACCGTAATGCCCCTC
1 TAGGGTAAAATGACCGTAATACCCCTG
*
52111322 TAGGGTAAAATAACCGTAATACCC
1 TAGGGTAAAATGACCGTAATACCC
52111346 TGGTGGGTAA
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
25 1 0.01
26 28 0.17
27 128 0.79
28 5 0.03
29 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (27 bp):
TAGGGTAAAATGACCGTAATACCCCTG
Found at i:52111433 original size:24 final size:25
Alignment explanation
Indices: 52111406--52111452 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
52111396 ATGTGGTTAA
*
52111406 ATGACTAATTTTTCTGTG-TTTGGT
1 ATGACTAATTTGTCTGTGATTTGGT
*
52111430 ATGACTGATTTGTCTGTGATTTG
1 ATGACTAATTTGTCTGTGATTTG
52111453 AATACTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.17, C:0.09, G:0.23, T:0.51
Consensus pattern (25 bp):
ATGACTAATTTGTCTGTGATTTGGT
Found at i:52111688 original size:32 final size:32
Alignment explanation
Indices: 52111634--52111902 Score: 251
Period size: 32 Copynumber: 8.5 Consensus size: 32
52111624 ACTACGATGC
* * *
52111634 TACTGATAGCTTTGTGCTGATCATAGTACCGT
1 TACTGATGGCTTTGTACCGATCATAGTACCGT
*
52111666 TACTAATGGCTTTGTACCGATCATAGTACCGT
1 TACTGATGGCTTTGTACCGATCATAGTACCGT
*
52111698 TACTGATGGCTTTGTACCGATCATATTACCGT
1 TACTGATGGCTTTGTACCGATCATAGTACCGT
* * *
52111730 TACTGATGGCTTTGTGCCAATCATATTACCGT
1 TACTGATGGCTTTGTACCGATCATAGTACCGT
* * * ** *
52111762 TACCGATGGCTGTGTACCAAT-ATTTTACTGT
1 TACTGATGGCTTTGTACCGATCATAGTACCGT
* * * *
52111793 TATTGATGGCTATGTACCGATCATA-TCACTGC
1 TACTGATGGCTTTGTACCGATCATAGT-ACCGT
* *
52111825 CACTGATGGCTTTGTGCCGATCAT-GTTACCGT
1 TACTGATGGCTTTGTACCGATCATAG-TACCGT
* ** * *
52111857 TACTGATGGCTATGTGTCGATCATA-TCACTGC
1 TACTGATGGCTTTGTACCGATCATAGT-ACCGT
52111889 TAC-GATGGCTTTGT
1 TACTGATGGCTTTGT
52111903 GCCAATCACA
Statistics
Matches: 200, Mismatches: 31, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
31 37 0.19
32 162 0.81
33 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTACCGATCATAGTACCGT
Found at i:52111739 original size:64 final size:64
Alignment explanation
Indices: 52111632--52111930 Score: 300
Period size: 64 Copynumber: 4.7 Consensus size: 64
52111622 TTACTACGAT
* * * *
52111632 GCTACTGATAGCTTTGTGCTGATCATAGTACCGTTACTAATGGCTTTGTACCGATCATAGT-ACC
1 GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTACCGATCATA-TCACC
* * * * *
52111696 GTTACTGATGGCTTTGTACCGATCATATTACCGTTACTGATGGCTTTGTGCCAATCATATTACC
1 GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTACCGATCATATCACC
* * * * * * * * * *
52111760 GTTACCGATGGCTGTGTACCAAT-ATTTTACTGTTATTGATGGCTATGTACCGATCATATCACT
1 GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTACCGATCATATCACC
* * * ** *
52111823 GCCACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTATGTGTCGATCATATCACT
1 GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTACCGATCATATCACC
* * * *
52111887 GCTAC-GATGGCTTTGTGCCAATCACATTACTG-TACTTATGGCTT
1 GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTT
52111931 GTAGCCATTC
Statistics
Matches: 196, Mismatches: 37, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
62 10 0.05
63 73 0.37
64 113 0.58
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (64 bp):
GCTACTGATGGCTTTGTGCCGATCATATTACCGTTACTGATGGCTTTGTACCGATCATATCACC
Found at i:52111917 original size:127 final size:127
Alignment explanation
Indices: 52111671--52111919 Score: 322
Period size: 127 Copynumber: 2.0 Consensus size: 127
52111661 ACCGTTACTA
* **
52111671 ATGGCTTTGTACCGATCATAGTACCGTTACTGATGGCTTTGTACCGATCATATTACCGTTACTGA
1 ATGGCTATGTACCGATCATAGTACCGCCACTGATGGCTTTGTACCGATCATATTACCGTTACTGA
* * * **
52111736 TGGCTTTGTGCCAATCATATTACCGTTACCGATGGCTGTGTACCAATATTTTACTGTTATTG
66 TGGCTATGTGCCAATCATATCACCGCTACCGATGGCTGTGTACCAATACATTACTGTTATTG
* * *
52111798 ATGGCTATGTACCGATCATA-TCACTGCCACTGATGGCTTTGTGCCGATCATGTTACCGTTACTG
1 ATGGCTATGTACCGATCATAGT-ACCGCCACTGATGGCTTTGTACCGATCATATTACCGTTACTG
* * * * *
52111862 ATGGCTATGTGTCGATCATATCACTGCTA-CGATGGCTTTGTGCCAATCACATTACTGT
65 ATGGCTATGTGCCAATCATATCACCGCTACCGATGGCTGTGTACCAAT-ACATTACTGT
52111920 ACTTATGGCT
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
126 17 0.16
127 87 0.84
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (127 bp):
ATGGCTATGTACCGATCATAGTACCGCCACTGATGGCTTTGTACCGATCATATTACCGTTACTGA
TGGCTATGTGCCAATCATATCACCGCTACCGATGGCTGTGTACCAATACATTACTGTTATTG
Found at i:52115349 original size:42 final size:42
Alignment explanation
Indices: 52115290--52115376 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
52115280 AATTGATGAA
52115290 GATACGGTGGTTCTCATGATCCAAATTCGGAACATCGTGTTC
1 GATACGGTGGTTCTCATGATCCAAATTCGGAACATCGTGTTC
52115332 GATACGGTGGTTCTCATGATCCAAATTCGGAACATCGTGTTC
1 GATACGGTGGTTCTCATGATCCAAATTCGGAACATCGTGTTC
52115374 GAT
1 GAT
52115377 CTCTTCCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (42 bp):
GATACGGTGGTTCTCATGATCCAAATTCGGAACATCGTGTTC
Found at i:52124637 original size:28 final size:28
Alignment explanation
Indices: 52124547--52124637 Score: 130
Period size: 28 Copynumber: 3.2 Consensus size: 28
52124537 ATACAGCATG
* * *
52124547 CAGTAACAGTCTGGGCCTTAGCCCGATA
1 CAGTAACTGTGTGGGCCTTAGCCCAATA
*
52124575 TAGTAA-TAGTGTGGGCCTTAGCCCAATA
1 CAGTAACT-GTGTGGGCCTTAGCCCAATA
52124603 CAGTAACTGTGTGGGCCTTAGCCCAATA
1 CAGTAACTGTGTGGGCCTTAGCCCAATA
52124631 CAGTAAC
1 CAGTAAC
52124638 CAGTACAGTG
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 55 0.98
29 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (28 bp):
CAGTAACTGTGTGGGCCTTAGCCCAATA
Found at i:52124791 original size:26 final size:25
Alignment explanation
Indices: 52124762--52124850 Score: 110
Period size: 26 Copynumber: 3.4 Consensus size: 25
52124752 CAAAGCTACA
52124762 AGTAATAGTATCATAGCAAGGTTGCC
1 AGTAATAGTATCATAGCAA-GTTGCC
*
52124788 AGTAACAGTATCGCGATA--AAGTTGCC
1 AGTAATAGTAT--C-ATAGCAAGTTGCC
52124814 AGTAATAGTATCATAGCAAAGTTGCC
1 AGTAATAGTATCATAGC-AAGTTGCC
52124840 AGTAATAGTAT
1 AGTAATAGTAT
52124851 ACTTCCTCCA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
23 3 0.05
24 1 0.02
26 45 0.82
27 2 0.04
28 1 0.02
29 3 0.05
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (25 bp):
AGTAATAGTATCATAGCAAGTTGCC
Found at i:52125071 original size:27 final size:27
Alignment explanation
Indices: 52125029--52125361 Score: 224
Period size: 27 Copynumber: 12.6 Consensus size: 27
52125019 TTCACCCTTT
* * *
52125029 AGGGCATTTTGGTCATTTTACCCTACG
1 AGGGTATTTCGGTCATTTTACCCTTCG
* *
52125056 GGGGTATTTCAGTCATTTTA-CCTTACG
1 AGGGTATTTCGGTCATTTTACCCTT-CG
* *
52125083 AGGGTATTTCGGTTATTTCACCCTTCG
1 AGGGTATTTCGGTCATTTTACCCTTCG
* * *
52125110 AGGGTA-TTCTGGTTATTTCACCCTTTG
1 AGGGTATTTC-GGTCATTTTACCCTTCG
* *
52125137 GGGGTA-TTCCG--A--TT-CCCTTCG
1 AGGGTATTTCGGTCATTTTACCCTTCG
* * *
52125158 GGGGTATTTCGATCATTTTACCCTTCA
1 AGGGTATTTCGGTCATTTTACCCTTCG
* * *
52125185 AGAGTATTTCGGTCATTTTATCCTT-T
1 AGGGTATTTCGGTCATTTTACCCTTCG
* *
52125211 AAGGTATTTCGGTCATTTTACCTTTCG
1 AGGGTATTTCGGTCATTTTACCCTTCG
* ** *
52125238 -GAGGTATTTCAGTCATTTTACAATTTG
1 AG-GGTATTTCGGTCATTTTACCCTTCG
* ** *
52125265 GGGGTATTTTAGACATTTTACCCTAT-G
1 AGGGTATTTCGGTCATTTTACCCT-TCG
* *
52125292 AGGTTATTTCGATCATTTTACCCTAT-G
1 AGGGTATTTCGGTCATTTTACCCT-TCG
* *
52125319 GGGGTATTTCGATCATTTTACCCTAT-G
1 AGGGTATTTCGGTCATTTTACCCT-TCG
*
52125346 AGGGTATTTTGGTCAT
1 AGGGTATTTCGGTCAT
52125362 AACAGTGTAA
Statistics
Matches: 246, Mismatches: 47, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
21 12 0.05
22 4 0.02
24 2 0.01
26 30 0.12
27 192 0.78
28 6 0.02
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
AGGGTATTTCGGTCATTTTACCCTTCG
Found at i:52125154 original size:21 final size:21
Alignment explanation
Indices: 52125130--52125170 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52125120 GGTTATTTCA
*
52125130 CCCTTTGGGGGTATTCCGATT
1 CCCTTCGGGGGTATTCCGATT
*
52125151 CCCTTCGGGGGTATTTCGAT
1 CCCTTCGGGGGTATTCCGAT
52125171 CATTTTACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.24, G:0.29, T:0.37
Consensus pattern (21 bp):
CCCTTCGGGGGTATTCCGATT
Found at i:52126723 original size:22 final size:21
Alignment explanation
Indices: 52126688--52126731 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
52126678 CCACTATACC
* *
52126688 ACAAGCTCTTTTATGTCATAAA
1 ACAAGCACTATTAT-TCATAAA
*
52126710 ACAAGCACTATTATTTATAAA
1 ACAAGCACTATTATTCATAAA
52126731 A
1 A
52126732 TCTATATGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (21 bp):
ACAAGCACTATTATTCATAAA
Found at i:52128844 original size:3 final size:3
Alignment explanation
Indices: 52128836--52128900 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
52128826 AGGGTAGATG
52128836 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
52128884 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
52128901 GCATTTAGTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:52130383 original size:6 final size:6
Alignment explanation
Indices: 52130353--52130394 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
52130343 AGTACCTGAT
* *
52130353 CAGTAAA CAGTAA CGGTAG CAGTAA CAGTAA CAGTAA CAGTA
1 CAGT-AA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
52130395 TTCAACACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (6 bp):
CAGTAA
Found at i:52130442 original size:45 final size:45
Alignment explanation
Indices: 52130372--52130481 Score: 168
Period size: 45 Copynumber: 2.4 Consensus size: 45
52130362 GTAACGGTAG
* *
52130372 CAGTAACAGTAACAGTAACAGTATTCAACACACAAAGT-GCTGAAT
1 CAGTAACAGTAACAGTAACAATATTCAACACACAAAGTATC-GAAT
* *
52130417 CTGTAACAGTAACAGTAACAATATTCGACACACAAAGTATCGAAT
1 CAGTAACAGTAACAGTAACAATATTCAACACACAAAGTATCGAAT
52130462 CAGTAACAGTAACAGTAACA
1 CAGTAACAGTAACAGTAACA
52130482 GTAGTCGGCA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 58 0.98
46 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAATATTCAACACACAAAGTATCGAAT
Found at i:52131976 original size:5 final size:5
Alignment explanation
Indices: 52131956--52132005 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
52131946 CTTTCTTTTG
52131956 ATAT- ATATA TATATA ATATA ATATA ATAT- AT-TA ATAATA ATATA ATATA
1 ATATA ATATA -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA
52132005 A
1 A
52132006 AAACATAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 23 0.56
6 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:52131986 original size:19 final size:19
Alignment explanation
Indices: 52131956--52132004 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
52131946 CTTTCTTTTG
52131956 ATATATATATATATAAT-ATA
1 ATATA-ATATAT-TAATAATA
52131976 ATATAATATATTAATAATA
1 ATATAATATATTAATAATA
52131995 ATATAATATA
1 ATATAATATA
52132005 AAAACATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.14
19 19 0.68
20 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAATATATTAATAATA
Found at i:52132014 original size:24 final size:24
Alignment explanation
Indices: 52131968--52132014 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
52131958 ATATATATAT
* *
52131968 ATAATATAATATAATATATTAATA
1 ATAATATAATATAATAAAATAATA
52131992 ATAATATAATATAA-AAACATAAT
1 ATAATATAATATAATAAA-ATAAT
52132015 CATTACTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATA
Found at i:52137831 original size:49 final size:48
Alignment explanation
Indices: 52137765--52137897 Score: 142
Period size: 49 Copynumber: 2.7 Consensus size: 48
52137755 AGCACTCACA
* *
52137765 CCAACTGGTTAGTAACTAAGATACCCTACCAGTGG-CTCATCATACATG
1 CCAACTGGTTAGCAACTAACATACCCTACCAGTGGCCT-ATCATACATG
* * *
52137813 CCAATCTGGTTAGCAACTAACATGCCCTACCAGTGGCCTATCATATAATC
1 CCAA-CTGGTTAGCAACTAACATACCCTACCAGTGGCCTATCATA-CATG
* * * * *
52137863 CCACCTAGTTAGCAACTAGCATGCCTTACCAGTGG
1 CCAACTGGTTAGCAACTAACATACCCTACCAGTGG
52137898 TCTAGCACAT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
48 4 0.05
49 62 0.85
50 7 0.10
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (48 bp):
CCAACTGGTTAGCAACTAACATACCCTACCAGTGGCCTATCATACATG
Found at i:52137920 original size:49 final size:49
Alignment explanation
Indices: 52137821--52137947 Score: 148
Period size: 49 Copynumber: 2.6 Consensus size: 49
52137811 TGCCAATCTG
* *
52137821 GTTAGCAACTAACATGCCCTACCAGTGGCCTATCATATAATCCCACCTA
1 GTTAGCAACTAACATGCCCTACCAGTGGCCTAGCACATAATCCCACCTA
* * * * **
52137870 GTTAGCAACTAGCATGCCTTACCAGTGGTCTAGCACAT-GTACCCTTCTA
1 GTTAGCAACTAACATGCCCTACCAGTGGCCTAGCACATAAT-CCCACCTA
* *
52137919 GTTTGCAACTACCATGCCCTACCAGTGGC
1 GTTAGCAACTAACATGCCCTACCAGTGGC
52137948 TCATGATAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 1 0.02
49 64 0.98
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (49 bp):
GTTAGCAACTAACATGCCCTACCAGTGGCCTAGCACATAATCCCACCTA
Found at i:52140494 original size:16 final size:17
Alignment explanation
Indices: 52140475--52140513 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
52140465 ACGGTTGGCT
52140475 AACTCTAAGATTGGA-A
1 AACTCTAAGATTGGACA
* *
52140491 AACTCTAAGGTTTGACA
1 AACTCTAAGATTGGACA
52140508 AACTCT
1 AACTCT
52140514 TTTATAAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (17 bp):
AACTCTAAGATTGGACA
Found at i:52142595 original size:20 final size:20
Alignment explanation
Indices: 52142562--52142601 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52142552 GGTCTCGATA
* *
52142562 CTAAGGGAAGGTATCAATAC
1 CTAAGAGAAAGTATCAATAC
*
52142582 CTAAGAGAAAGTATCGATAC
1 CTAAGAGAAAGTATCAATAC
52142602 TTCAAGCATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (20 bp):
CTAAGAGAAAGTATCAATAC
Found at i:52149002 original size:25 final size:25
Alignment explanation
Indices: 52148969--52149032 Score: 101
Period size: 25 Copynumber: 2.5 Consensus size: 25
52148959 AAATAATTCA
*
52148969 GCAACTTAAACAAAAGGCTTAATCAG
1 GCAA-TTAACCAAAAGGCTTAATCAG
*
52148995 GCAATTAACCAAAAGGCTTAATTAG
1 GCAATTAACCAAAAGGCTTAATCAG
52149020 GCAATTAACCAAA
1 GCAATTAACCAAA
52149033 TCAAATCTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 32 0.89
26 4 0.11
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.20
Consensus pattern (25 bp):
GCAATTAACCAAAAGGCTTAATCAG
Found at i:52149918 original size:26 final size:26
Alignment explanation
Indices: 52149888--52149954 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
52149878 AGGGACAACC
* * *
52149888 ATAAAAATAAAAATATAGTTTAA-CAT
1 ATAAAAATAAAAATA-AGTCTAAGAAA
*
52149914 ATAAAAAT-GAAATAAGTCTAAGAAA
1 ATAAAAATAAAAATAAGTCTAAGAAA
52149939 ATAAAAATAAAAATAA
1 ATAAAAATAAAAATAA
52149955 AAATAAAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 6 0.18
25 14 0.41
26 14 0.41
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (26 bp):
ATAAAAATAAAAATAAGTCTAAGAAA
Found at i:52149945 original size:6 final size:6
Alignment explanation
Indices: 52149936--52149962 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52149926 TAAGTCTAAG
52149936 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
52149963 CAAATAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:52151389 original size:16 final size:16
Alignment explanation
Indices: 52151356--52151398 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
52151346 TAAGAATCAT
*
52151356 AAAAAATAACAAGTAA
1 AAAAAATAAAAAGTAA
*
52151372 AAAAAATAAAACAGAAA
1 AAAAAATAAAA-AGTAA
52151389 ACAAAAATAA
1 A-AAAAATAA
52151399 TAATAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 10 0.43
17 5 0.22
18 8 0.35
ACGTcount: A:0.79, C:0.07, G:0.05, T:0.09
Consensus pattern (16 bp):
AAAAAATAAAAAGTAA
Found at i:52151403 original size:6 final size:6
Alignment explanation
Indices: 52151373--52151442 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
52151363 AACAAGTAAA
* * * * *
52151373 AAAAAT AAAACA- GAAAAC AAAAAT AATAAT AAGAAT AATAAT GAAAAAT
1 AAAAAT AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT
*
52151422 AACAAAT AAAAAT AAGAAT AA
1 AA-AAAT AAAAAT AAAAAT AA
52151443 TAACTAAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
5 1 0.02
6 39 0.75
7 12 0.23
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:52151444 original size:22 final size:24
Alignment explanation
Indices: 52151409--52151455 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
52151399 TAATAAGAAT
52151409 AATAATGAAAAATAAC-AAATAAA
1 AATAATGAAAAATAACTAAATAAA
*
52151432 AATAA-GAATAATAACTAAATAAA
1 AATAATGAAAAATAACTAAATAAA
52151455 A
1 A
52151456 GATAGGGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.19
Consensus pattern (24 bp):
AATAATGAAAAATAACTAAATAAA
Found at i:52158277 original size:46 final size:46
Alignment explanation
Indices: 52158225--52158455 Score: 367
Period size: 46 Copynumber: 5.0 Consensus size: 46
52158215 ACATTGCTAT
* *
52158225 AACTCAGTATGGTTTTCTTCCTTGAAATACTATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCCTTGAAACACCATACCTACTTTTCAC
* *
52158271 AACTCAGTATGGTTTTCTTCATTTAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCCTTGAAACACCATACCTACTTTTCAC
*
52158317 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCCTTGAAACACCATACCTACTTTTCAC
* *
52158363 AACTCAGTATGGTTTTCTTCAC-CGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTC-CTTGAAACACCATACCTACTTTTCAC
52158409 AACTCAGTATGGTTTTCTTCAC-TGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTC-CTTGAAACACCATACCTACTTTTCAC
52158455 A
1 A
52158456 CTTTTCCATG
Statistics
Matches: 174, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
46 174 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCCTTGAAACACCATACCTACTTTTCAC
Found at i:52167750 original size:51 final size:51
Alignment explanation
Indices: 52167663--52167775 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 51
52167653 AAGACCATAA
* *
52167663 ATGAAAGATGTTATAGTAGTCTAGTATGTGGCACGTAGCGTAAGGTCATGG
1 ATGAAAGATGTTATAGTAGTCTAGTATATGGCACGTAGCGTAAGGCCATGG
* *
52167714 ATGAAAGATGTTATAGTAGTCTGGTATATGGTACGTAGCGTAAGGCCATGG
1 ATGAAAGATGTTATAGTAGTCTAGTATATGGCACGTAGCGTAAGGCCATGG
52167765 ATGAAAGATGT
1 ATGAAAGATGT
52167776 CATGGCAGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (51 bp):
ATGAAAGATGTTATAGTAGTCTAGTATATGGCACGTAGCGTAAGGCCATGG
Found at i:52168002 original size:33 final size:33
Alignment explanation
Indices: 52167965--52168058 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
52167955 TAGTCCTCCG
* *
52167965 GGACAGTAAACACGAAACAGAGTAAGTTCGTCA
1 GGACAGTAAACACGAAAAAGAGTAAGTCCGTCA
* * * *
52167998 GGACAGTAAACATGGAATAGAGTAAGTCCGTCG
1 GGACAGTAAACACGAAAAAGAGTAAGTCCGTCA
* *
52168031 GGATAGTAAATACGAAAAAGAGTAAGTC
1 GGACAGTAAACACGAAAAAGAGTAAGTC
52168059 TATTGAGACA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.17
Consensus pattern (33 bp):
GGACAGTAAACACGAAAAAGAGTAAGTCCGTCA
Found at i:52188086 original size:21 final size:21
Alignment explanation
Indices: 52188054--52188094 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
52188044 GAACATTTGG
52188054 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
52188075 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
52188095 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:52206569 original size:7 final size:7
Alignment explanation
Indices: 52206551--52206614 Score: 74
Period size: 7 Copynumber: 9.1 Consensus size: 7
52206541 TTTCTTAAGC
52206551 GATGTGG
1 GATGTGG
* *
52206558 AATGTGT
1 GATGTGG
52206565 GATGTGG
1 GATGTGG
52206572 GATGTGG
1 GATGTGG
52206579 GATGTGG
1 GATGTGG
*
52206586 GATATGG
1 GATGTGG
*
52206593 GATATGG
1 GATGTGG
*
52206600 GATATGG
1 GATGTGG
*
52206607 GATATGG
1 GATGTGG
52206614 G
1 G
52206615 TATATATAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.22, C:0.00, G:0.48, T:0.30
Consensus pattern (7 bp):
GATGTGG
Found at i:52207111 original size:58 final size:58
Alignment explanation
Indices: 52207014--52207191 Score: 293
Period size: 58 Copynumber: 3.0 Consensus size: 58
52207004 CAAAATCTTA
52207014 ATATTTATATATAAAATATTATGTGTTACTATATGTGTAAGTTTGTCTTTCTTTTTTT
1 ATATTTATATATAAAATATTATGTGTTACTATATGTGTAAGTTTGTCTTTCTTTTTTT
* * *
52207072 ATATCTATATATAAAATATTATGTGTTACTATATATGTAAGTTTGTCTCTTTTTTTTTAT
1 ATATTTATATATAAAATATTATGTGTTACTATATGTGTAAGTTTGTCT-TTCTTTTTT-T
* *
52207132 ATATTTATATATAAAATATTCTGTGTTACTATATGTGCAAGTTTGTCTTTCTTTTTTT
1 ATATTTATATATAAAATATTATGTGTTACTATATGTGTAAGTTTGTCTTTCTTTTTTT
52207190 AT
1 AT
52207192 TGGACTTTTT
Statistics
Matches: 110, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
58 49 0.45
59 16 0.15
60 45 0.41
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.56
Consensus pattern (58 bp):
ATATTTATATATAAAATATTATGTGTTACTATATGTGTAAGTTTGTCTTTCTTTTTTT
Found at i:52207190 original size:60 final size:60
Alignment explanation
Indices: 52207014--52207191 Score: 290
Period size: 60 Copynumber: 3.0 Consensus size: 60
52207004 CAAAATCTTA
52207014 ATATTTATATATAAAATATTATGTGTTACTATATGTGTAAGTTTGTCTTTC-TTTTTT-T
1 ATATTTATATATAAAATATTATGTGTTACTATATGTGTAAGTTTGTCTTTCTTTTTTTAT
* *
52207072 ATATCTATATATAAAATATTATGTGTTACTATATATGTAAGTTTGTCTCTT-TTTTTTTAT
1 ATATTTATATATAAAATATTATGTGTTACTATATGTGTAAGTTTGTCT-TTCTTTTTTTAT
* *
52207132 ATATTTATATATAAAATATTCTGTGTTACTATATGTGCAAGTTTGTCTTTCTTTTTTTAT
1 ATATTTATATATAAAATATTATGTGTTACTATATGTGTAAGTTTGTCTTTCTTTTTTTAT
52207192 TGGACTTTTT
Statistics
Matches: 110, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
58 46 0.42
59 10 0.09
60 54 0.49
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.56
Consensus pattern (60 bp):
ATATTTATATATAAAATATTATGTGTTACTATATGTGTAAGTTTGTCTTTCTTTTTTTAT
Found at i:52211183 original size:13 final size:13
Alignment explanation
Indices: 52211165--52211189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52211155 AAAATATATT
52211165 ATTAATTAAAAAC
1 ATTAATTAAAAAC
52211178 ATTAATTAAAAA
1 ATTAATTAAAAA
52211190 AATTTGAAAC
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:52214092 original size:61 final size:59
Alignment explanation
Indices: 52214022--52214199 Score: 155
Period size: 61 Copynumber: 2.9 Consensus size: 59
52214012 TTGTTAAATT
52214022 ATATTTAATAATAATTATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGA
1 ATATTTAATAATAA-TATTTTATA-TATTATATATTATGATTTTAGTAAATTCATATAAGA
* * * * ** * * * *
52214083 ATATTTAATACTAAGAATTTTATTAAATTATATATTTTTG-TTAAATTATATTTA-ATAATA
1 ATATTTAATAATAA-TATTTTA-TATATTATATA-TTATGATTTTAGTAAATTCATATAAGA
* * *
52214143 ATTATTTTA-AATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCATATA
1 A-TATTTAATAATAATATTTTAT-ATATTATATATTATGATTTTAGTAAATTCATATA
52214200 TTTTATCAAA
Statistics
Matches: 88, Mismatches: 23, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
58 4 0.05
59 24 0.27
60 12 0.14
61 42 0.48
62 6 0.07
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (59 bp):
ATATTTAATAATAATATTTTATATATTATATATTATGATTTTAGTAAATTCATATAAGA
Found at i:52214152 original size:26 final size:25
Alignment explanation
Indices: 52214114--52214172 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
52214104 ATTAAATTAT
*
52214114 ATATTTTTGTTAAATTATATTTAATA
1 ATATTATT-TTAAATTATATTTAATA
*
52214140 ATAATTATTTTAAATTATATTTTATA
1 AT-ATTATTTTAAATTATATTTAATA
52214166 ATATTAT
1 ATATTAT
52214173 ATATTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 20 0.67
27 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATTATTTTAAATTATATTTAATA
Found at i:52214171 original size:15 final size:15
Alignment explanation
Indices: 52214127--52214182 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
52214117 TTTTTGTTAA
*
52214127 ATTATATTTAATAAT
1 ATTATATTTTATAAT
*
52214142 AAT-TA-TTT-TAA-
1 ATTATATTTTATAAT
52214153 ATTATATTTTATAAT
1 ATTATATTTTATAAT
*
52214168 ATTATATATTATAAT
1 ATTATATTTTATAAT
52214183 TTTAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 5 0.15
14 5 0.15
15 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTATAAT
Found at i:52214200 original size:41 final size:40
Alignment explanation
Indices: 52214037--52214222 Score: 122
Period size: 41 Copynumber: 4.6 Consensus size: 40
52214027 TAATAATAAT
* *
52214037 TATTTTATAGTATTATATATTATGATTTTAGTAAATTCATA
1 TATTTTATAATATTATATATTATAATTTTAGTAAATT-ATA
* * * *
52214078 TA----AGAATATT-TAATACTAAGAATTTTATTAAATTATA
1 TATTTTATAATATTAT-ATA-TTATAATTTTAGTAAATTATA
* **
52214115 TATTTTTGTTAA-ATTATAT-TTAATAATAATTATTTTAAA-T-TA
1 TA-TTTT-ATAATATTATATATT-ATAAT--TT-TAGTAAATTATA
52214157 TATTTTATAATATTATATATTATAATTTTAGTAAATTCATA
1 TATTTTATAATATTATATATTATAATTTTAGTAAATT-ATA
52214198 TATTTTATCAA-ATTATATATTATAA
1 TATTTTAT-AATATTATATATTATAA
52214223 AAAAATATAT
Statistics
Matches: 112, Mismatches: 14, Indels: 38
0.68 0.09 0.23
Matches are distributed among these distances:
36 1 0.01
37 14 0.12
38 19 0.17
39 3 0.03
40 4 0.04
41 46 0.41
42 13 0.12
43 6 0.05
44 6 0.05
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (40 bp):
TATTTTATAATATTATATATTATAATTTTAGTAAATTATA
Found at i:52214217 original size:17 final size:17
Alignment explanation
Indices: 52214175--52214218 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
52214165 AATATTATAT
52214175 ATTATA-ATTTTAGTAA
1 ATTATATATTTTAGTAA
52214191 ATTCATATATTTTA-TCAA
1 ATT-ATATATTTTAGT-AA
52214209 ATTATATATT
1 ATTATATATT
52214219 ATAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.12
17 11 0.44
18 11 0.44
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTATATATTTTAGTAA
Found at i:52214446 original size:44 final size:45
Alignment explanation
Indices: 52214396--52214486 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
52214386 ACCTCTATTC
**
52214396 CATTCAACCAAACACAAGA-TTACTATTATGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTTACTATTACACCTCTATTCCATTA
*** *
52214440 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTTACTATTACACCTCTATTCCATTA
52214485 CA
1 CA
52214487 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.33
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTTACTATTACACCTCTATTCCATTA
Found at i:52214486 original size:16 final size:16
Alignment explanation
Indices: 52214467--52214518 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
52214457 GATTTGCTAT
* *
52214467 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
52214483 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52214499 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52214515 TACA
1 TACA
52214519 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:52217202 original size:24 final size:24
Alignment explanation
Indices: 52217174--52217219 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
52217164 TCTTTCTAGA
**
52217174 ATATTTAGTATTTATTAGTATAAT
1 ATATTTAACATTTATTAGTATAAT
52217198 ATATTTAACATTTATTAGTATA
1 ATATTTAACATTTATTAGTATA
52217220 GTTTATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (24 bp):
ATATTTAACATTTATTAGTATAAT
Found at i:52219030 original size:26 final size:26
Alignment explanation
Indices: 52218991--52219045 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
52218981 TGCATAGTTC
*
52218991 AAGATAGGCTCGTGGTGGGCTTTGGA
1 AAGATAGGCCCGTGGTGGGCTTTGGA
*
52219017 AAGATAGGCCCGTGGTGTGCTTTGGA
1 AAGATAGGCCCGTGGTGGGCTTTGGA
52219043 AAG
1 AAG
52219046 GATGGCGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.22, C:0.13, G:0.40, T:0.25
Consensus pattern (26 bp):
AAGATAGGCCCGTGGTGGGCTTTGGA
Found at i:52221320 original size:43 final size:43
Alignment explanation
Indices: 52221247--52221386 Score: 126
Period size: 43 Copynumber: 3.3 Consensus size: 43
52221237 ATATCCCGGA
* * * *
52221247 TATGGTCTTACATGTAACCTCGTATCGATGCCAATAGCCCAGC
1 TATGGTCTTACACGAAATCTCATATCGATGCCAATAGCCCAGC
* *
52221290 TATGGTCTTACACGAAAT-TACATATTGATGCCAAT-GTCCCAAAC
1 TATGGTCTTACACGAAATCT-CATATCGATGCCAATAG-CCC-AGC
* * * * *
52221334 -ATGGTCTCACACGAAGTCTCATATCGATGCC-ATATCTCAGA
1 TATGGTCTTACACGAAATCTCATATCGATGCCAATAGCCCAGC
52221375 TATGGTCTTACA
1 TATGGTCTTACA
52221387 TGTAATCTAA
Statistics
Matches: 77, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
41 1 0.01
42 16 0.21
43 57 0.74
44 3 0.04
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (43 bp):
TATGGTCTTACACGAAATCTCATATCGATGCCAATAGCCCAGC
Found at i:52236582 original size:61 final size:63
Alignment explanation
Indices: 52236486--52236604 Score: 188
Period size: 61 Copynumber: 1.9 Consensus size: 63
52236476 CTGGGCTTGG
* *
52236486 CACTTTATTTTTTCTAATTTGGTATCTATATTTTTTTGGCTCA-ATTTGGTACTTGAATTTAA
1 CACTTTATTTTTTCTAATTTGGTATCTAAACTTTTTTGGCTCATATTTGGTACTTGAATTTAA
* *
52236548 CACTTT-TTTTTTTTAATTTGGTATCTAAACTTTTTTGGGTCATATTTGGTACTTGAA
1 CACTTTATTTTTTCTAATTTGGTATCTAAACTTTTTTGGCTCATATTTGGTACTTGAA
52236605 CTTGACTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 32 0.62
62 20 0.38
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.55
Consensus pattern (63 bp):
CACTTTATTTTTTCTAATTTGGTATCTAAACTTTTTTGGCTCATATTTGGTACTTGAATTTAA
Found at i:52236616 original size:61 final size:60
Alignment explanation
Indices: 52236487--52236616 Score: 172
Period size: 62 Copynumber: 2.1 Consensus size: 60
52236477 TGGGCTTGGC
* * * *
52236487 ACTTTATTTTTTCTAATTTGGTATCTATATTTTTTTGGCTCAATTTGGTACTTGAATTTAA
1 ACTTTTTTTTTTCTAATTTGGTATCTAAACTTTTTTGGCTCAATTTGGTACTTGAACTT-A
* *
52236548 CACTTTTTTTTTT-TAATTTGGTATCTAAACTTTTTTGGGTCATATTTGGTACTTGAACTTG
1 -ACTTTTTTTTTTCTAATTTGGTATCTAAACTTTTTTGGCTCA-ATTTGGTACTTGAACTTA
52236609 ACTTTTTT
1 ACTTTTTT
52236617 CCTAATTTGG
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
60 8 0.13
61 26 0.43
62 27 0.44
ACGTcount: A:0.21, C:0.11, G:0.12, T:0.56
Consensus pattern (60 bp):
ACTTTTTTTTTTCTAATTTGGTATCTAAACTTTTTTGGCTCAATTTGGTACTTGAACTTA
Found at i:52237725 original size:16 final size:15
Alignment explanation
Indices: 52237704--52237747 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
52237694 TTTAAAAATT
52237704 ATAAAAATATTTAAAA
1 ATAAAAA-ATTTAAAA
*
52237720 ATAAAAAATTCAAAA
1 ATAAAAAATTTAAAA
*
52237735 TTCAAAAAATTTA
1 AT-AAAAAATTTA
52237748 TAAGAGTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAAAAATTTAAAA
Found at i:52238848 original size:29 final size:29
Alignment explanation
Indices: 52238801--52238936 Score: 148
Period size: 30 Copynumber: 4.7 Consensus size: 29
52238791 TGTTTTACAG
* ** * *
52238801 ATTTTATAGTTTTTTCACTGTTTTTCTAG
1 ATTTTACAGTTTTGCCACTGTTTTTCCAA
*
52238830 ATTTTACAGTTTTGCCACT-TGTTTCCAA
1 ATTTTACAGTTTTGCCACTGTTTTTCCAA
* * * *
52238858 AATTTACAGTTCTGCCACTATTTTTTCTAA
1 ATTTTACAGTTTTGCCACT-GTTTTTCCAA
*
52238888 ATTTTACAATTTTGCCACTGGTTTTTCCAA
1 ATTTTACAGTTTTGCCACT-GTTTTTCCAA
52238918 ATTTTACAGTTTTGCCACT
1 ATTTTACAGTTTTGCCACT
52238937 ATTCTTGAAA
Statistics
Matches: 88, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
28 23 0.26
29 16 0.18
30 49 0.56
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.50
Consensus pattern (29 bp):
ATTTTACAGTTTTGCCACTGTTTTTCCAA
Done.