Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold128
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: 1835488
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 499 characters in sequence are not A, C, G, or T
File 3 of 11
Found at i:470945 original size:21 final size:21
Alignment explanation
Indices: 470921--470979 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
470911 TAATATTCTT
* *
470921 GAAAAGAAATGAAGTGAATTA
1 GAAAAGAAAAGAAATGAATTA
470942 GAAAAGAAAAGAAATGAATTA
1 GAAAAGAAAAGAAATGAATTA
470963 -AAAGAGAAAAGAAATGA
1 GAAA-AGAAAAGAAATGA
470980 GTGGCAAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 3 0.09
21 32 0.91
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.14
Consensus pattern (21 bp):
GAAAAGAAAAGAAATGAATTA
Found at i:470970 original size:26 final size:26
Alignment explanation
Indices: 470921--470976 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
470911 TAATATTCTT
* **
470921 GAAAAGAAATGAAGTGAATTAGAAAA
1 GAAAAGAAATGAAGTAAAAGAGAAAA
*
470947 GAAAAGAAATGAATTAAAAGAGAAAA
1 GAAAAGAAATGAAGTAAAAGAGAAAA
470973 GAAA
1 GAAA
470977 TGAGTGGCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.12
Consensus pattern (26 bp):
GAAAAGAAATGAAGTAAAAGAGAAAA
Found at i:474347 original size:10 final size:10
Alignment explanation
Indices: 474332--474384 Score: 52
Period size: 10 Copynumber: 4.9 Consensus size: 10
474322 TCGATATACC
474332 ACTGTTCATA
1 ACTGTTCATA
474342 ACTGTTCATGTA
1 ACTGTTCA--TA
*
474354 TCACTATTCATA
1 --ACTGTTCATA
*
474366 ACTGTTCATC
1 ACTGTTCATA
474376 ACTGTTCAT
1 ACTGTTCAT
474385 GTATAGTGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 25 0.69
12 4 0.11
14 7 0.19
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (10 bp):
ACTGTTCATA
Found at i:475180 original size:21 final size:19
Alignment explanation
Indices: 475154--475207 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
475144 CTGCCAGTTT
**
475154 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
*
475175 CATGTATCGTTACAATGAA
1 CATGTATCGATACAATGAA
475194 CATGTATCGATACA
1 CATGTATCGATACA
475208 TCTGGCTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.52
21 14 0.48
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:479561 original size:52 final size:51
Alignment explanation
Indices: 479483--479621 Score: 179
Period size: 51 Copynumber: 2.7 Consensus size: 51
479473 ATTTGCCTGC
* * **
479483 ATGTATCGATACATTAAAGAATGTATCTCTACATTTGGGTAAAAAACCCAGA
1 ATGTATCGATACAATGAAGAATGTATCAATACATTTGGGT-AAAAACCCAGA
* * * *
479535 ATGTATCGATACAGTGAAGAATGTATCAATACATTTGGGTTAAAACCTATA
1 ATGTATCGATACAATGAAGAATGTATCAATACATTTGGGTAAAAACCCAGA
* *
479586 ATGTATCGATACAATGAAAAATGTATCGATACATTT
1 ATGTATCGATACAATGAAGAATGTATCAATACATTT
479622 TCATTATAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 41 0.53
52 36 0.47
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (51 bp):
ATGTATCGATACAATGAAGAATGTATCAATACATTTGGGTAAAAACCCAGA
Found at i:486342 original size:28 final size:28
Alignment explanation
Indices: 486302--486916 Score: 586
Period size: 28 Copynumber: 21.7 Consensus size: 28
486292 AAAAAATGCT
486302 ACTGACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
486330 ACTGACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
*
486358 ACTGACTTGTGGGCTTTGAAAGGATGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
* *
486386 ACTGAATTGTGGGCTTTGAAAGGATGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
* * *
486414 ACTGATTTGTGGGCTTTAAAAAGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
* * *
486442 CCTGACTTATGGGCTTTG-AAGAGATG--
1 ACTGACTTGTGGGCTTTGAAAG-GGTGCC
* * * * * ** *
486468 AATG--TTCTAGAC--AG-AAGTTCTTGACG
1 ACTGACTTGTGGGCTTTGAAAG--GGTG-CC
* * * * * * *
486494 A-TAATTTCTTGACAAATGGAAAAAGGGTCTTGGCC
1 ACTGACTTGTGGGC--TTTG--AAAGGG---T-GCC
* *
486529 GACT--CGTGTGGGCTTTGAAAAGAGTGCC
1 -ACTGACTTGTGGGCTTTG-AAAGGGTGCC
*
486557 ACTAACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
*
486585 ACTGACTTGTGGGCTTTGAAAGGATGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
**
486613 ACTGACTTGTGGGCTTTGAAAAGACTGCC
1 ACTGACTTGTGGGCTTTG-AAAGGGTGCC
* *
486642 ACTGACTTGTGGGCTTCGAAAGGATGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
* *
486670 ACTAACTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTG-AAAGGGTGCC
486699 ACTGACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
** **
486727 ACTGACTTGTCAGCTTTGAAAAAAGTGCC
1 ACTGACTTGTGGGCTTTG-AAAGGGTGCC
* *
486756 ACTGACTTGTGTGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTG-AAAGGGTGCC
486785 ACTGACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
*
486813 ACTGACTTGTGGGCTTTGAATGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
* *
486841 ACTAACTTGTGGGCTTTGAAAGGATGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
*
486869 ACTGACTTGTGGCCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGGTGCC
*
486897 ACTAACTTGTGGGCTTTGAA
1 ACTGACTTGTGGGCTTTGAA
486917 GAGATGAACG
Statistics
Matches: 494, Mismatches: 68, Indels: 50
0.81 0.11 0.08
Matches are distributed among these distances:
22 4 0.01
23 2 0.00
24 5 0.01
25 1 0.00
26 3 0.01
27 12 0.02
28 332 0.67
29 114 0.23
31 1 0.00
32 6 0.01
33 2 0.00
34 3 0.01
35 6 0.01
36 2 0.00
37 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
ACTGACTTGTGGGCTTTGAAAGGGTGCC
Found at i:487837 original size:1 final size:1
Alignment explanation
Indices: 487831--487896 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
487821 CCCCTTTCTG
* * * * * * * *
487831 TTTTTTTGTTATTTTTTCTTTTTTTTGTTTTTTTTTGTTTTTTGTTGTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
487896 T
1 T
487897 GGGTATAAAG
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:487847 original size:10 final size:9
Alignment explanation
Indices: 487831--487897 Score: 80
Period size: 9 Copynumber: 6.9 Consensus size: 9
487821 CCCCTTTCTG
487831 TTTTTTTGT
1 TTTTTTTGT
*
487840 TATTTTTTCT
1 T-TTTTTTGT
487850 TTTTTTTGTT
1 TTTTTTTG-T
487860 TTTTTTTGT
1 TTTTTTTGT
487869 TTTTTGTTGTTT
1 TTTTT-TTG--T
487881 TTTTTTTGT
1 TTTTTTTGT
487890 TTTTTTTG
1 TTTTTTTG
487898 GGTATAAAGG
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
9 22 0.43
10 20 0.39
11 3 0.06
12 6 0.12
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.87
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:487847 original size:11 final size:10
Alignment explanation
Indices: 487831--487896 Score: 89
Period size: 10 Copynumber: 6.6 Consensus size: 10
487821 CCCCTTTCTG
487831 TTTTTTTGTT
1 TTTTTTTGTT
* *
487841 ATTTTTT-CT
1 TTTTTTTGTT
487850 TTTTTTTGTT
1 TTTTTTTGTT
487860 TTTTTTTGTT
1 TTTTTTTGTT
*
487870 TTTTGTTGTTT
1 TTTTTTTG-TT
487881 TTTTTTTGTT
1 TTTTTTTGTT
487891 TTTTTT
1 TTTTTT
487897 GGGTATAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
9 7 0.15
10 32 0.67
11 9 0.19
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.88
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:501966 original size:20 final size:20
Alignment explanation
Indices: 501895--501969 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
501885 AAAAGGATAG
*
501895 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
* * * *
501915 AGTGTCTCGATACATTCATA
1 AATGTATCGATACATTGAAA
* * *
501935 AATGTGTTGATACGTTGAAA
1 AATGTATCGATACATTGAAA
501955 AATGTATCGATACAT
1 AATGTATCGATACAT
501970 CTAGGTACTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:502509 original size:27 final size:27
Alignment explanation
Indices: 502471--502544 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
502461 GGTGTCTACA
*
502471 CAACCTTTTAAGTCCACAACTTCGTGG
1 CAACCTTTTAAGTCCACAACTCCGTGG
*
502498 CAACCTCTTAAGTCCACAACTCCGTGG
1 CAACCTTTTAAGTCCACAACTCCGTGG
* *
502525 CATCCTTTTAAAGCCCACAA
1 CAACCTTTT-AAGTCCACAA
502545 GTCATTGGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 32 0.78
28 9 0.22
ACGTcount: A:0.28, C:0.34, G:0.12, T:0.26
Consensus pattern (27 bp):
CAACCTTTTAAGTCCACAACTCCGTGG
Found at i:502553 original size:28 final size:29
Alignment explanation
Indices: 502511--502795 Score: 302
Period size: 28 Copynumber: 10.2 Consensus size: 29
502501 CCTCTTAAGT
* *
502511 CCACAACTCCGTGGCATCCTTTT-AAAGC
1 CCACAAGTCAGTGGCATCCTTTTCAAAGC
* * *
502539 CCACAAGTCATTGGCAT-CTTTTCCAGGC
1 CCACAAGTCAGTGGCATCCTTTTCAAAGC
* *
502567 CCACAAATCAGTGACA-CCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTTCAAAGC
* *
502595 CCACAAGTTAGTGGCA-CCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTTCAAAGC
* **
502623 CCACAATTCAGTGGCATCC-TTTCAAAAT
1 CCACAAGTCAGTGGCATCCTTTTCAAAGC
*
502651 CCACAAGTTAGTGGCATCCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTTCAAAGC
*
502680 CCACAAGTTAGTGGCAT-CTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTTCAAAGC
* *
502708 CCACAAGTCAGTGGCA-CCTTTTGAAATC
1 CCACAAGTCAGTGGCATCCTTTTCAAAGC
** * *
502736 CCATGAGTCAATGGCA-CCTTTTGAAAGC
1 CCACAAGTCAGTGGCATCCTTTTCAAAGC
**
502764 CCATGAGTCAGTGGCATCC-TTT-AAAGC
1 CCACAAGTCAGTGGCATCCTTTTCAAAGC
502791 CCACA
1 CCACA
502796 TAAGTTAGTG
Statistics
Matches: 219, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
27 13 0.06
28 178 0.81
29 28 0.13
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.25
Consensus pattern (29 bp):
CCACAAGTCAGTGGCATCCTTTTCAAAGC
Found at i:502751 original size:113 final size:112
Alignment explanation
Indices: 502522--502813 Score: 322
Period size: 113 Copynumber: 2.6 Consensus size: 112
502512 CACAACTCCG
* * * * * *
502522 TGGCATCCTTTTAAAGCCCACAAGTCATTGGCAT-CTTTTCCAGGCCCACAAATCAGTGACACCT
1 TGGCATCCTTTTAAAACCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTTAGTGACA-CT
* * *
502586 TTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAATTCAG
65 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAA
* * * *
502634 TGGCATCCTTTCAAAATCCACAAGTTAGTGGCATCCTTTTCAAAGCCCACAAGTTAGTGGCATCT
1 TGGCATCCTTTTAAAACCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTTAGTGACA-CT
* * * **
502699 TTTCAAAGCCCACAAGTCAGTGGCACCTTTTGAAATCCCATGAGTCAA
65 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAA
* **
502747 TGGCA-CCTTTTGAAAGCCCATGAGTCAGTGGCATCC-TTT-AAAGCCCACATAAGTTAGTGACA
1 TGGCATCCTTTT-AAAACCCACAAGTCAGTGGCATCCTTTTCAAAGCCCAC--AAGTTAGTGACA
502809 CTTTT
63 CTTTT
502814 TTTTAAAAGC
Statistics
Matches: 150, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
111 9 0.06
112 42 0.28
113 99 0.66
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (112 bp):
TGGCATCCTTTTAAAACCCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAGTTAGTGACACTT
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAA
Found at i:502763 original size:141 final size:140
Alignment explanation
Indices: 502521--502785 Score: 368
Period size: 141 Copynumber: 1.9 Consensus size: 140
502511 CCACAACTCC
* * *
502521 GTGGCATCCTTTTAAAGCCCACAAGTCATTGGCATCTTTTCCAGGCCCACAAATCAGTGACACCT
1 GTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAATCAGTGACACCT
* * *
502586 TTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAATTCAGTGGCATCCTTTCAAAAT
66 TTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAT
502651 CCACAAGTTA
131 CCACAAGTTA
* * *
502661 GTGGCATCCTTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACC
1 GTGGCATCCTTTT-AAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAATCAGTGACACC
* * ** * * **
502726 TTTTGAAATCCCATGAGTCAATGGCACCTTTTGAAAGCCCATGAGTCAGTGGCATCCTTT
65 TTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTT
502786 AAAGCCCACA
Statistics
Matches: 107, Mismatches: 17, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
140 13 0.12
141 94 0.88
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (140 bp):
GTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAATCAGTGACACCT
TTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAT
CCACAAGTTA
Found at i:503038 original size:48 final size:48
Alignment explanation
Indices: 502918--503133 Score: 292
Period size: 48 Copynumber: 4.5 Consensus size: 48
502908 GGCACCTTTA
* * **
502918 TTAGCTCAATGTCGCTAGCCTTGAATCAGCACATTGTCCAC-CTT-GA
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* * * * *
502964 TTTGCTCAATTTTGCTGGCCTTGAATCAGCATATTATCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
*
503012 TTAGCTCAATGTCGATGGCCTTGAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
*
503060 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCT
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
* * *
503108 TTAACTCGATGTCGTTGGCCTTGAAT
1 TTAGCTCAATGTCGCTGGCCTTGAAT
503134 TGGCACGTTG
Statistics
Matches: 148, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
46 35 0.24
47 2 0.01
48 111 0.75
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCC
Found at i:506681 original size:62 final size:62
Alignment explanation
Indices: 506615--506735 Score: 224
Period size: 62 Copynumber: 2.0 Consensus size: 62
506605 GCTTGACACG
506615 GAATACACAGTTTTCAAAGTAAAATCCAAAGGTCATTTTATGTCTCTATGTTCTCCATCACA
1 GAATACACAGTTTTCAAAGTAAAATCCAAAGGTCATTTTATGTCTCTATGTTCTCCATCACA
* *
506677 GAATACCCAGTTTTCAAAGTAAAATCCAGAGGTCATTTTATGTCTCTATGTTCTCCATC
1 GAATACACAGTTTTCAAAGTAAAATCCAAAGGTCATTTTATGTCTCTATGTTCTCCATC
506736 TCTTTGGGGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (62 bp):
GAATACACAGTTTTCAAAGTAAAATCCAAAGGTCATTTTATGTCTCTATGTTCTCCATCACA
Found at i:507704 original size:84 final size:82
Alignment explanation
Indices: 507616--507800 Score: 183
Period size: 83 Copynumber: 2.2 Consensus size: 82
507606 TAAAATCAAC
* * * **
507616 AAGTCAATAAAGGATAAAGAAATTTATCTA-AGACTAAGCCGACAGGTAAACAAGGGATGAAAGG
1 AAGTCAATAAAGG-TAAAGAAATTTA-CTAGAGACTAAGCCAACAAGTAAA-AAGAGATGAAACA
* **
507680 TTGACCAGGGCTGATTCGAT
63 TTGACCAGGGCTAAACCGAT
* * * * * * *
507700 AAGTCAACAAAGTGTAAGGGAGTTTACTAGGGATTAAGCCAACAAGTAAATAGAGATGAAACATT
1 AAGTCAATAAAG-GTAAAGAAATTTACTAGAGACTAAGCCAACAAGTAAAAAGAGATGAAACATT
507765 GACCAGGGCTAAACCGAT
65 GACCAGGGCTAAACCGAT
507783 AAGTCAATAAAGGGTAAA
1 AAGTCAATAAA-GGTAAA
507801 AGAGTTTACC
Statistics
Matches: 81, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
83 43 0.53
84 37 0.46
85 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.19
Consensus pattern (82 bp):
AAGTCAATAAAGGTAAAGAAATTTACTAGAGACTAAGCCAACAAGTAAAAAGAGATGAAACATTG
ACCAGGGCTAAACCGAT
Found at i:507818 original size:83 final size:83
Alignment explanation
Indices: 507671--507834 Score: 195
Period size: 83 Copynumber: 2.0 Consensus size: 83
507661 GTAAACAAGG
** * ** * ** * *
507671 GATGAAAGGTTGACCAGGGCTGATTCGATAAGTCAACAAAGTGTAAGGGAGTTTACTAGGGATTA
1 GATGAAACATTGACCAGGGCTAAACCGATAAGTCAACAAAGGGTAAAAGAGTTTACCAAGGATTA
*
507736 AGCCA-ACAAGTAAATAGA
66 AG-CAGACAAATAAATAGA
* *
507754 GATGAAACATTGACCAGGGCTAAACCGATAAGTCAATAAAGGGTAAAAGAGTTTACCAATGATTA
1 GATGAAACATTGACCAGGGCTAAACCGATAAGTCAACAAAGGGTAAAAGAGTTTACCAAGGATTA
507819 AGCAGACAAATAAATA
66 AGCAGACAAATAAATA
507835 AGGAATCGAG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
82 2 0.03
83 65 0.97
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.21
Consensus pattern (83 bp):
GATGAAACATTGACCAGGGCTAAACCGATAAGTCAACAAAGGGTAAAAGAGTTTACCAAGGATTA
AGCAGACAAATAAATAGA
Found at i:508218 original size:44 final size:43
Alignment explanation
Indices: 508170--508511 Score: 212
Period size: 44 Copynumber: 7.8 Consensus size: 43
508160 TGTCAACCAG
* *
508170 GAATGAAGCAGATTTGACCAGGGTGGTAACCATGCATCAAATCA
1 GAATGAAGAAGATTTGACCAGGGTGGTAACCATACATCAAA-CA
* ** * * *
508214 GAATGAA-AAGAATCTGATTAGGGTGGTAACCATACATTAGACC
1 GAATGAAGAAG-ATTTGACCAGGGTGGTAACCATACATCAAACA
* * *
508257 GAAAT-AAGAAAAGTTTGACCAAGGTAGTAACCATACATCAAACA
1 G-AATGAAGAAGA-TTTGACCAGGGTGGTAACCATACATCAAACA
* *
508301 GGAA--AATGGCAGATTTGACCAGTGTGGTAACCATACATCAAATCA
1 -GAATGAA--GAAGATTTGACCAGGGTGGTAACCATACATCAAA-CA
* * * * * * * *
508346 AAAT-AAAAAGAATCTGACGAGGGTGGTAACCATACTTTAGACC
1 GAATGAAGAAG-ATTTGACCAGGGTGGTAACCATACATCAAACA
* *
508389 GAAATGAA-AAGAGTTTGACTAGGGTGGTAACCATACGTCAAACAA
1 G-AATGAAGAAGA-TTTGACCAGGGTGGTAACCATACATCAAAC-A
* * * * ** *
508434 GAATGAGGCAGATTTGACTAGGGTGGTAACCACATGTCAAATTA
1 GAATGAAGAAGATTTGACCAGGGTGGTAACCATACATCAAA-CA
* * *
508478 AAATGAA-AAGAATCTGACTAGGGTGGTAACCATA
1 GAATGAAGAAG-ATTTGACCAGGGTGGTAACCATA
508512 TGTTGTAGAC
Statistics
Matches: 232, Mismatches: 49, Indels: 34
0.74 0.16 0.11
Matches are distributed among these distances:
43 15 0.06
44 203 0.88
45 14 0.06
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (43 bp):
GAATGAAGAAGATTTGACCAGGGTGGTAACCATACATCAAACA
Found at i:508303 original size:132 final size:131
Alignment explanation
Indices: 508162--508511 Score: 465
Period size: 132 Copynumber: 2.6 Consensus size: 131
508152 TAACGACATG
* *
508162 TCAACCAGGAATGAAGCAGATTTGACCAGGGTGGTAACCATGCATCAAATCAGAATGAAAAGAAT
1 TCAAACAGGAATGAAGCAGATTTGACCAGGGTGGTAACCAT-CATCAAATCAAAATGAAAAGAAT
*
508227 CTGATTAGGGTGGTAACCATACATTAGACCGAAAT-AAGAAAAGTTTGACCAAGGTAGTAACCAT
65 CTGACTAGGGTGGTAACCATACATTAGACCGAAATGAA-AAAAGTTTGACCAAGGTAGTAACCAT
508291 ACA
129 ACA
* *
508294 TCAAACAGGAA--AATGGCAGATTTGACCAGTGTGGTAACCATACATCAAATCAAAATAAAAAGA
1 TCAAACAGGAATGAA--GCAGATTTGACCAGGGTGGTAACCAT-CATCAAATCAAAATGAAAAGA
* * * * * *
508357 ATCTGACGAGGGTGGTAACCATACTTTAGACCGAAATGAAAAGAGTTTGACTAGGGTGGTAACCA
63 ATCTGACTAGGGTGGTAACCATACATTAGACCGAAATGAAAAAAGTTTGACCAAGGTAGTAACCA
*
508422 TACG
128 TACA
* * * *
508426 TCAAACAAGAATGAGGCAGATTTGACTAGGGTGGTAACCA-CATGTCAAATTAAAATGAAAAGAA
1 TCAAACAGGAATGAAGCAGATTTGACCAGGGTGGTAACCATCA--TCAAATCAAAATGAAAAGAA
508490 TCTGACTAGGGTGGTAACCATA
64 TCTGACTAGGGTGGTAACCATA
508512 TGTTGTAGAC
Statistics
Matches: 191, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
130 4 0.02
132 184 0.96
133 2 0.01
134 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.21
Consensus pattern (131 bp):
TCAAACAGGAATGAAGCAGATTTGACCAGGGTGGTAACCATCATCAAATCAAAATGAAAAGAATC
TGACTAGGGTGGTAACCATACATTAGACCGAAATGAAAAAAGTTTGACCAAGGTAGTAACCATAC
A
Found at i:508912 original size:13 final size:13
Alignment explanation
Indices: 508894--508921 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
508884 ATTACTCAAA
508894 TGTATCGATACAT
1 TGTATCGATACAT
508907 TGTATCGATACAT
1 TGTATCGATACAT
508920 TG
1 TG
508922 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:522308 original size:1 final size:1
Alignment explanation
Indices: 522302--522382 Score: 63
Period size: 1 Copynumber: 81.0 Consensus size: 1
522292 CGTCCTCCAC
* * * * * * * * * *
522302 AAAAAAAAAACAAACAAACAAACAAAACAAAAAAAAAAGAGAAAAAAAACAAAACAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
522367 AAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAA
522383 TGAAAACAAA
Statistics
Matches: 58, Mismatches: 22, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:522333 original size:27 final size:25
Alignment explanation
Indices: 522303--522420 Score: 114
Period size: 27 Copynumber: 4.4 Consensus size: 25
522293 GTCCTCCACA
522303 AAAAAAAAACAAACAAACAAACAAAAC
1 AAAAAAAAACAAA-AAACAAA-AAAAC
*
522330 AAAAAAAAA-AGAGAAAAAAAACAAAAC
1 AAAAAAAAACA-A-AAAACAAA-AAAAC
522357 AAAAAAAAACAAAAAACAAAAAAA-
1 AAAAAAAAACAAAAAACAAAAAAAC
522381 AATGAAAACAAACAAACAAACAAAAAAAC
1 AA--AAAA-AAACAAA-AAACAAAAAAAC
522410 AACAACAAAAA
1 AA-AA-AAAAA
522421 AGGTCCGGAT
Statistics
Matches: 79, Mismatches: 3, Indels: 17
0.80 0.03 0.17
Matches are distributed among these distances:
24 2 0.03
25 4 0.05
26 12 0.15
27 39 0.49
28 18 0.23
29 4 0.05
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.01
Consensus pattern (25 bp):
AAAAAAAAACAAAAAACAAAAAAAC
Found at i:522350 original size:15 final size:15
Alignment explanation
Indices: 522300--522421 Score: 93
Period size: 15 Copynumber: 7.5 Consensus size: 15
522290 GGCGTCCTCC
*
522300 ACAAAAAAAAAACAA
1 ACAAAAAAAAAAAAA
522315 ACAAACAAACAAAACAAA
1 ACAAA-AAA-AAAA-AAA
*
522333 AAAAAAAGAGAAAAAAA
1 ACAAAAA-A-AAAAAAA
*
522350 ACAAAACAAAAAAAA
1 ACAAAAAAAAAAAAA
522365 ACAAAAAACAAAAAAA
1 ACAAAAAA-AAAAAAA
* * *
522381 A-ATGAAAACAAACAA
1 ACA-AAAAAAAAAAAA
522396 ACAAACAAAAAAACAACA
1 ACAAA-AAAAAAA-AA-A
522414 ACAAAAAA
1 ACAAAAAA
522422 GGTCCGGATG
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
15 27 0.32
16 23 0.27
17 18 0.21
18 17 0.20
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (15 bp):
ACAAAAAAAAAAAAA
Found at i:522367 original size:42 final size:43
Alignment explanation
Indices: 522302--522421 Score: 135
Period size: 42 Copynumber: 2.8 Consensus size: 43
522292 CGTCCTCCAC
*
522302 AAAAAAA-AAACAAACAAACAAACAA-AACAAAAAAAAAAGA-GA
1 AAAAAAACAAACAAACAAAAAAACAACAA-AAAAAAAAAA-ATGA
522344 AAAAAAACAAA-ACAA-AAAAAAACAA-AAAACAAAAAAAAATGA
1 AAAAAAACAAACA-AACAAAAAAACAACAAAA-AAAAAAAAATGA
* *
522386 AAACAAACAAACAAACAAAAAAACAACAACAAAAAA
1 AAAAAAACAAACAAACAAAAAAACAACAAAAAAAAA
522422 GGTCCGGATG
Statistics
Matches: 68, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
41 3 0.04
42 41 0.60
43 21 0.31
44 3 0.04
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.01
Consensus pattern (43 bp):
AAAAAAACAAACAAACAAAAAAACAACAAAAAAAAAAAAATGA
Found at i:522393 original size:4 final size:4
Alignment explanation
Indices: 522300--522411 Score: 71
Period size: 4 Copynumber: 29.0 Consensus size: 4
522290 GGCGTCCTCC
* * *
522300 ACAA A-AA AAAA ACAA ACAA ACAA ACAAA ACAA A-AA AAAA AGAGA A-AA
1 ACAA ACAA ACAA ACAA ACAA ACAA AC-AA ACAA ACAA ACAA ACA-A ACAA
*
522347 A-AA ACAAA ACAA A-AA A-AA ACAA A-AA ACAA A-AA A-AA ATGAAA ACAA
1 ACAA AC-AA ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA A--CAA ACAA
*
522392 ACAA ACAA ACAA AAAA ACAA
1 ACAA ACAA ACAA ACAA ACAA
522412 CAACAAAAAA
Statistics
Matches: 92, Mismatches: 5, Indels: 22
0.77 0.04 0.18
Matches are distributed among these distances:
3 26 0.28
4 53 0.58
5 10 0.11
6 3 0.03
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.01
Consensus pattern (4 bp):
ACAA
Found at i:522419 original size:12 final size:11
Alignment explanation
Indices: 522300--522420 Score: 81
Period size: 11 Copynumber: 10.6 Consensus size: 11
522290 GGCGTCCTCC
*
522300 ACAAAAAAAAA
1 ACAAAAACAAA
522311 ACAAACAA-ACAA
1 ACAAA-AACA-AA
522323 AC-AAAACAAA
1 ACAAAAACAAA
* *
522333 AAAAAAAGAGAA
1 ACAAAAACA-AA
522345 A-AAAAACAAA
1 ACAAAAACAAA
522355 ACAAAAA-AAA
1 ACAAAAACAAA
522365 ACAAAAAACAAA
1 AC-AAAAACAAA
*
522377 A-AAAAATGAAA
1 ACAAAAA-CAAA
522388 ACAAACAAACAAA
1 AC-AA-AAACAAA
*
522401 CAAAAAAACAACA
1 -ACAAAAACAA-A
522414 ACAAAAA
1 ACAAAAA
522421 AGGTCCGGAT
Statistics
Matches: 89, Mismatches: 7, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
10 18 0.20
11 34 0.38
12 25 0.28
13 8 0.09
14 4 0.04
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (11 bp):
ACAAAAACAAA
Found at i:524366 original size:15 final size:15
Alignment explanation
Indices: 524346--524380 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
524336 AATCATCAAA
524346 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
524361 GATGATGATGATAAT
1 GATGATGAAGATAAT
524376 GATGA
1 GATGA
524381 AGTTGACTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:535173 original size:63 final size:63
Alignment explanation
Indices: 535074--535198 Score: 250
Period size: 63 Copynumber: 2.0 Consensus size: 63
535064 TTCCACAACC
535074 TGGTATTCGAATCACTTTTTATGGGTATACAAATCCCTCTTTGTAATTTATGACAAAAGCTTT
1 TGGTATTCGAATCACTTTTTATGGGTATACAAATCCCTCTTTGTAATTTATGACAAAAGCTTT
535137 TGGTATTCGAATCACTTTTTATGGGTATACAAATCCCTCTTTGTAATTTATGACAAAAGCTT
1 TGGTATTCGAATCACTTTTTATGGGTATACAAATCCCTCTTTGTAATTTATGACAAAAGCTT
535199 ATTTTTCATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (63 bp):
TGGTATTCGAATCACTTTTTATGGGTATACAAATCCCTCTTTGTAATTTATGACAAAAGCTTT
Found at i:536069 original size:3 final size:3
Alignment explanation
Indices: 536063--536105 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
536053 AACACAACTG
*
536063 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
536106 CTAGACTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:537372 original size:32 final size:30
Alignment explanation
Indices: 537279--537381 Score: 106
Period size: 32 Copynumber: 3.4 Consensus size: 30
537269 TAGAGTTGCC
*
537279 AATTT-TA-AATATAAATTAAAATATATAA
1 AATTTATATAATATAAATTATAATATATAA
537307 AATTTATGATATATTATAAA-TAT-ATAGTATAA
1 AATTTAT-ATA-A-TATAAATTATAATA-TATAA
537339 AATTTATATAATATAAATTATTAATATATTAA
1 AATTTATATAATATAAATTA-TAATATA-TAA
*
537371 AATTAATATAA
1 AATTTATATAA
537382 ATATCAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
28 5 0.08
29 7 0.11
30 4 0.06
31 10 0.16
32 31 0.49
33 6 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
AATTTATATAATATAAATTATAATATATAA
Found at i:537375 original size:14 final size:15
Alignment explanation
Indices: 537287--537380 Score: 70
Period size: 16 Copynumber: 6.1 Consensus size: 15
537277 CCAATTTTAA
*
537287 ATAT-AAATTAAAAT
1 ATATAAAATTAATAT
*
537301 ATATAAAATTTATGAT
1 ATATAAAATTAAT-AT
537317 ATATTATAAA-T-ATAT
1 ATA-TA-AAATTAATAT
*
537332 AGTATAAAATTTATAT
1 A-TATAAAATTAATAT
537348 AATATAAATTATTAATAT
1 -ATATAAA--ATTAATAT
537366 AT-TAAAATTAATAT
1 ATATAAAATTAATAT
537380 A
1 A
537381 AATATCAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
14 16 0.24
15 12 0.18
16 23 0.34
17 6 0.09
18 10 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATATAAAATTAATAT
Found at i:537385 original size:18 final size:17
Alignment explanation
Indices: 537334--537416 Score: 59
Period size: 18 Copynumber: 4.9 Consensus size: 17
537324 AAATATATAG
*
537334 TATAAAATTTATAT-AA
1 TATAAAATTAATATAAA
537350 TAT-AAATT-AT-TAATA
1 TATAAAATTAATATAA-A
537365 TATTAAAATTAATATAAA
1 TA-TAAAATTAATATAAA
* * *
537383 TATCAAAAATATTTTAAA
1 TAT-AAAATTAATATAAA
537401 TATAATAA-TAATATAA
1 TATAA-AATTAATATAA
537417 TAAAATATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 1 0.02
14 3 0.06
15 8 0.15
16 4 0.07
17 14 0.26
18 21 0.39
19 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAAAATTAATATAAA
Found at i:537394 original size:29 final size:30
Alignment explanation
Indices: 537344--537442 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 30
537334 TATAAAATTT
**
537344 ATATAATATAAAT-T-ATTAATATATTAAA
1 ATATAATATAAATATCAAAAATATATTAAA
*
537372 AT-TAATATAAATATCAAAAATAT-TTTAA
1 ATATAATATAAATATCAAAAATATATTAAA
*
537400 ATATAATA-ATAATATAATAAAATATA-T-AA
1 ATATAATATA-AATATCA-AAAATATATTAAA
*
537429 TTATAATATAAATA
1 ATATAATATAAATA
537443 CATAAATTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
27 10 0.17
28 10 0.17
29 30 0.51
30 9 0.15
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (30 bp):
ATATAATATAAATATCAAAAATATATTAAA
Found at i:537420 original size:20 final size:21
Alignment explanation
Indices: 537400--537442 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
537390 AATATTTTAA
*
537400 ATATAATAATAATATAATAAAAT
1 ATATAATAATAATAT-A-AATAT
*
537423 ATATAATTATAATATAAATA
1 ATATAATAATAATATAAATA
537443 CATAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 1 0.06
23 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATAATAATAATATAAATAT
Found at i:537450 original size:20 final size:18
Alignment explanation
Indices: 537399--537452 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 18
537389 AAATATTTTA
*
537399 AATATAATA-ATAA-TAT
1 AATAAAATACATAATTAT
*
537415 AATAAAATATATAATTAT
1 AATAAAATACATAATTAT
537433 AATATAAATACATAAATTAT
1 AATA-AAATACAT-AATTAT
537453 CAAATTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 8 0.25
17 4 0.12
18 7 0.22
19 7 0.22
20 6 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAAATACATAATTAT
Found at i:538412 original size:18 final size:17
Alignment explanation
Indices: 538389--538438 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
538379 TTCTTCTTTC
538389 AAATTCTAAGAATTTTAA
1 AAATTCTAA-AATTTTAA
*
538407 AAATTCTAAAATTTTATT
1 AAATTCTAAAATTTTA-A
*
538425 AAATTTTAAAATTT
1 AAATTCTAAAATTT
538439 CATTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (17 bp):
AAATTCTAAAATTTTAA
Found at i:538445 original size:13 final size:13
Alignment explanation
Indices: 538427--538451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
538417 ATTTTATTAA
538427 ATTTTAAAATTTC
1 ATTTTAAAATTTC
538440 ATTTTAAAATTT
1 ATTTTAAAATTT
538452 TGAAAATATC
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTAAAATTTC
Found at i:539013 original size:25 final size:25
Alignment explanation
Indices: 538968--539032 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
538958 TTAATTTAAA
538968 TATT-CATAATAT-TATAATAATAC
1 TATTACATAATATATATAATAATAC
*
538991 -ATTACATAATATAATATATTAATAC
1 TATTACATAATAT-ATATAATAATAC
539016 TATTA-ATAATATTATAT
1 TATTACATAATA-TATAT
539033 TATGAAAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 3 0.08
23 8 0.22
25 20 0.56
26 5 0.14
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTACATAATATATATAATAATAC
Found at i:542349 original size:19 final size:19
Alignment explanation
Indices: 542325--542374 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
542315 AGCGATACAT
542325 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
542344 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
542363 TGTATCGATACA
1 TGTATCGATACA
542375 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:542381 original size:13 final size:13
Alignment explanation
Indices: 542363--542387 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
542353 ACAACACTTA
542363 TGTATCGATACAT
1 TGTATCGATACAT
542376 TGTATCGATACA
1 TGTATCGATACA
542388 AATTGTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:543408 original size:15 final size:16
Alignment explanation
Indices: 543388--543420 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
543378 TTACATAATT
543388 TTAAA-TTAAAAAAAC
1 TTAAATTTAAAAAAAC
543403 TTAAATTTTAAAAAAAC
1 TTAAA-TTTAAAAAAAC
543420 T
1 T
543421 ACTCATTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAATTTAAAAAAAC
Found at i:545437 original size:23 final size:23
Alignment explanation
Indices: 545390--545436 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
545380 TATCATTTAA
545390 TTATAATAATATAATAATATATT
1 TTATAATAATATAATAATATATT
545413 TTATAATAATA-AA-AATATAATT
1 TTATAATAATATAATAATAT-ATT
545435 TT
1 TT
545437 TTTTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.22
22 7 0.30
23 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATAATAATATAATAATATATT
Found at i:546016 original size:22 final size:22
Alignment explanation
Indices: 545974--546018 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
545964 TGAATCATAT
* *
545974 AATTTTATTAATTTATAAATTA
1 AATTTAATTAATTAATAAATTA
545996 AATTTAATTAA-TAATAGAATTA
1 AATTTAATTAATTAATA-AATTA
546018 A
1 A
546019 TAAATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AATTTAATTAATTAATAAATTA
Found at i:546974 original size:15 final size:16
Alignment explanation
Indices: 546954--546984 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
546944 TGTCATAACA
546954 ATATTATTT-TAAAAT
1 ATATTATTTCTAAAAT
546969 ATATTATTTCTAAAAT
1 ATATTATTTCTAAAAT
546985 TTCATATAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTATTTCTAAAAT
Found at i:549392 original size:33 final size:32
Alignment explanation
Indices: 549345--549412 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
549335 CGTTACAAGC
* **
549345 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCAATACATACTAT-GTGTATCGATA
*
549378 CAATGTATCAATACATACTGTGTGTATCGATA
1 CAATGTATCAATACATACTATGTGTATCGATA
549410 CAA
1 CAA
549413 GTTTAGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCAATACATACTATGTGTATCGATA
Found at i:549470 original size:20 final size:20
Alignment explanation
Indices: 549445--549495 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
549435 CCAATGACTT
*
549445 GTATCGATACACTTT-TTCAA
1 GTATCGATACA-TTTAGTCAA
*
549465 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
549485 GTATCGATACA
1 GTATCGATACA
549496 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:549501 original size:13 final size:13
Alignment explanation
Indices: 549483--549508 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
549473 ACATTTAGTC
549483 ATGTATCGATACA
1 ATGTATCGATACA
549496 ATGTATCGATACA
1 ATGTATCGATACA
549509 GTGCAACATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:550101 original size:21 final size:21
Alignment explanation
Indices: 550063--550102 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
550053 TTTTCTTTTC
* *
550063 TCTCCTCCTTAATCAAATATT
1 TCTCCCCCTTAATAAAATATT
*
550084 TCTCCCCCTTAGTAAAATA
1 TCTCCCCCTTAATAAAATA
550103 ATTTAACACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.38
Consensus pattern (21 bp):
TCTCCCCCTTAATAAAATATT
Found at i:550166 original size:19 final size:19
Alignment explanation
Indices: 550142--550189 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
550132 TTTTTTTTTT
550142 CTTAATCATATTTCTCCCC
1 CTTAATCATATTTCTCCCC
*
550161 CTTAATCATATTTCTCCCT
1 CTTAATCATATTTCTCCCC
550180 CTTAATCATA
1 CTTAATCATA
550190 AAAATTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (19 bp):
CTTAATCATATTTCTCCCC
Found at i:551851 original size:20 final size:21
Alignment explanation
Indices: 551821--551861 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
551811 TGTTTTTGAT
551821 GATGTTTTTG-A-TGAAAAAC
1 GATGTTTTTGAAGTGAAAAAC
551840 GATGTATTTTGAAGTGAAAAAC
1 GATGT-TTTTGAAGTGAAAAAC
551862 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 5 0.26
21 1 0.05
22 8 0.42
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (21 bp):
GATGTTTTTGAAGTGAAAAAC
Found at i:552219 original size:8 final size:8
Alignment explanation
Indices: 552206--552231 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
552196 AACAACATTC
552206 ATCACAAA
1 ATCACAAA
552214 ATCACAAA
1 ATCACAAA
552222 ATCACAAA
1 ATCACAAA
552230 AT
1 AT
552232 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:556564 original size:3 final size:3
Alignment explanation
Indices: 556556--556589 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
556546 TCTGAGTCAC
* *
556556 CAT CAT CAT CAT CAT CTT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
556590 CTTGATGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.38
Consensus pattern (3 bp):
CAT
Found at i:556570 original size:9 final size:9
Alignment explanation
Indices: 556556--556589 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
556546 TCTGAGTCAC
*
556556 CATCATCAT
1 CATCATCTT
556565 CATCATCTT
1 CATCATCTT
556574 CATCATCTT
1 CATCATCTT
556583 CATCATC
1 CATCATC
556590 CTTGATGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.38
Consensus pattern (9 bp):
CATCATCTT
Found at i:558195 original size:13 final size:13
Alignment explanation
Indices: 558177--558201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
558167 CATTTTATGG
558177 TGTATCGATACAA
1 TGTATCGATACAA
558190 TGTATCGATACA
1 TGTATCGATACA
558202 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:558217 original size:32 final size:33
Alignment explanation
Indices: 558154--558221 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
558144 CGTTACAAGC
**
558154 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
558187 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
558219 CAA
1 CAA
558222 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:558279 original size:20 final size:20
Alignment explanation
Indices: 558254--558304 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
558244 CCAATGACTT
**
558254 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
558274 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
558294 GTATCGATACA
1 GTATCGATACA
558305 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:558310 original size:13 final size:13
Alignment explanation
Indices: 558292--558316 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
558282 ACATTTAGTC
558292 ATGTATCGATACA
1 ATGTATCGATACA
558305 ATGTATCGATAC
1 ATGTATCGATAC
558317 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:559618 original size:21 final size:21
Alignment explanation
Indices: 559594--559633 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
559584 GTAATATTTA
*
559594 TCATATCATATTTTTGTTGAT
1 TCATATCATATTTATGTTGAT
* *
559615 TCATGTTATATTTATGTTG
1 TCATATCATATTTATGTTG
559634 TTTTATGTGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.57
Consensus pattern (21 bp):
TCATATCATATTTATGTTGAT
Found at i:560892 original size:158 final size:157
Alignment explanation
Indices: 560380--561161 Score: 701
Period size: 156 Copynumber: 5.0 Consensus size: 157
560370 AAAAATCATC
* * * *
560380 ATTATTTATCATTTTAATGTCCACTAGGGTTACTGGA-ATACTTTCATATCGAAGGTATACTTAT
1 ATTACTTATCATTTTAATGTCCACTAGGGTTA-TCGAGATACTTTCATGTCGAAGGTATACCTAT
* * * * *
560444 AGAGGTATTTTCGTAATTTTTCTATAACCAACTCCTAGGTTGTCACTGAGTCCGTTTTTATGCCG
65 AG-GGCATTTTCGTAATTTTTCTAGAACCAAGTCCTAGGTTGTCACTGGGTCCGCTTTTATGCCG
* *
560509 AAGGTAGG-TATTTAGGATAAGTTCATCTT
129 AAGGT-GGATATTTAGGATAGGTTCATCCT
* * * * *
560538 ATTACTTATCATTTTAGTGTCCACTAAGGTTACCGAGATACTTTCACGTCGAAGATATACCTATA
1 ATTACTTATCATTTTAATGTCCACTAGGGTTATCGAGATACTTTCATGTCGAAGGTATACCTATA
** * * ** * *
560603 GGGGCATTTTTTTAATTTTT-TGGAA-TAGAGTTTTAGGTTGTCACCGGGTCTGC-TTTATGCCG
66 -GGGCATTTTCGTAATTTTTCTAGAACCA-AGTCCTAGGTTGTCACTGGGTCCGCTTTTATGCCG
* * *
560665 AAGGTGGGTATTTAGGATAGGTTCACCCC
129 AAGGTGGATATTTAGGATAGGTTCATCCT
* * * * * * * * *
560694 AGCTA-TAACCTTTTTAATGTCCACTAGGGTTACCGGGATATTTTCATGTTGAAGGTATACCCAT
1 A-TTACTTATCATTTTAATGTCCACTAGGGTTATCGAGATACTTTCATGTCGAAGGTATACCTAT
* * * * **
560758 AGGGACATTTTCGTAATTTTTCTATAACCAACTCCTAGGCTGTCACTGAGTCCGCTTTTATGCTA
65 AGGG-CATTTTCGTAATTTTTCTAGAACCAAGTCCTAGGTTGTCACTGGGTCCGCTTTTATGCCG
* *
560823 AATGTGGATATTTAGGATAGGTTTATCCT
129 AAGGTGGATATTTAGGATAGGTTCATCCT
* * * * * *
560852 ATTACTTATCATTTTAGTGTCTACTAGGGTTATCGAGATATTTTCACGTCAAAGGTATACCTAGA
1 ATTACTTATCATTTTAATGTCCACTAGGGTTATCGAGATACTTTCATGTCGAAGGTATACCTATA
* * * * * *
560917 GAGGCATTCTCGTAATTTTTCTAAAATCAAGTCCTA-G-TATCACTGGGTCTGCTTTTATGTCGA
66 G-GGCATTTTCGTAATTTTTCTAGAACCAAGTCCTAGGTTGTCACTGGGTCCGCTTTTATGCCGA
* *
560980 AAGT-GAGTATTTAGGATATGTTCA-CC-
130 AGGTGGA-TATTTAGGATAGGTTCATCCT
* * *** * *
561006 -TTAGCTATAACCTTTTTAA-GTCTTTTAGGATTATCGAGATACTTTCATGTCGAAGGTATACCC
1 ATTA-CT-T-ATCATTTTAATGTCCACTAGGGTTATCGAGATACTTTCATGTCGAAGGTATACCT
* * * * *
561069 ATAGGGGCATTTTCGTAA-TTTTCTAGAACAAAGTCTTAGGTTATCATTGGGTTCGCTTTTATGC
63 ATA-GGGCATTTTCGTAATTTTTCTAGAACCAAGTCCTAGGTTGTCACTGGGTCCGCTTTTATGC
**
561133 CGAAGGTGGGCATTTAGGATAGGTTCATC
127 CGAAGGTGGATATTTAGGATAGGTTCATC
561162 TTTTTTATAA
Statistics
Matches: 497, Mismatches: 107, Indels: 41
0.77 0.17 0.06
Matches are distributed among these distances:
153 3 0.01
154 18 0.04
155 62 0.12
156 182 0.37
157 51 0.10
158 178 0.36
159 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (157 bp):
ATTACTTATCATTTTAATGTCCACTAGGGTTATCGAGATACTTTCATGTCGAAGGTATACCTATA
GGGCATTTTCGTAATTTTTCTAGAACCAAGTCCTAGGTTGTCACTGGGTCCGCTTTTATGCCGAA
GGTGGATATTTAGGATAGGTTCATCCT
Found at i:560992 original size:314 final size:312
Alignment explanation
Indices: 560391--561161 Score: 940
Period size: 314 Copynumber: 2.5 Consensus size: 312
560381 TTATTTATCA
* * * ** *
560391 TTTTAATGTCCACTAGGGTTACTGGAATACTTTCATATCGAAGGTATACTTATAGAGGTATTTTC
1 TTTTAATGTCCACTAGGGTTACCGGGATACTTTCATGTCGAAGGTATACCCATAG-GGCATTTTC
*
560456 GTAATTTTTCTATAACCAACTCCTAGGTTGTCACTGAGTCCGTTTTTATGCCGAAGGTAGGTATT
65 GTAATTTTTCTATAACCAACTCCTAGGTTGTCACTGAGTCCGCTTTTATGCCGAAGGT-GGTATT
* *
560521 TAGGATAAGTTCATCTTATTACTTATCATTTTAGTGTCCACTAAGGTTACCGAGATACTTTCACG
129 TAGGATAGGTTCATCCTATTACTTATCATTTTAGTGTCCACTAAGGTTACCGAGATACTTTCACG
* * * * ** ** ** *
560586 TCGAAGATATACCTATAGGGGCATTTTTTTAATTTTTTGGAATAGAGTTTTAGGTTGTCACCGGG
194 TCAAAGATATACCTAGAGAGGCATTCTCGTAATTTTTTAAAATAGAGTCCTAGGTTATCACCGGG
* *
560651 TCTGCTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCACCCCAGCTATAACCT
259 TCTGCTTTATGCCGAAAGTGAGTATTTAGGATAGGTTCACCCCAGCTATAACCT
* *
560705 TTTTAATGTCCACTAGGGTTACCGGGATATTTTCATGTTGAAGGTATACCCATAGGGACATTTTC
1 TTTTAATGTCCACTAGGGTTACCGGGATACTTTCATGTCGAAGGTATACCCATAGGG-CATTTTC
* ** *
560770 GTAATTTTTCTATAACCAACTCCTAGGCTGTCACTGAGTCCGCTTTTATGCTAAATGTGGATATT
65 GTAATTTTTCTATAACCAACTCCTAGGTTGTCACTGAGTCCGCTTTTATGCCGAAGGTGG-TATT
* * * * *
560835 TAGGATAGGTTTATCCTATTACTTATCATTTTAGTGTCTACTAGGGTTATCGAGATATTTTCACG
129 TAGGATAGGTTCATCCTATTACTTATCATTTTAGTGTCCACTAAGGTTACCGAGATACTTTCACG
* *
560900 TCAAAGGTATACCTAGAGAGGCATTCTCGTAATTTTTCTAAAATCA-AGTCCTA-G-TATCACTG
194 TCAAAGATATACCTAGAGAGGCATTCTCGTAATTTTT-TAAAAT-AGAGTCCTAGGTTATCACCG
* * **
560962 GGTCTGCTTTTATGTCGAAAGTGAGTATTTAGGATATGTTCACCTTAGCTATAACCT
257 GGTCTGC-TTTATGCCGAAAGTGAGTATTTAGGATAGGTTCACCCCAGCTATAACCT
*** * * *
561019 TTTTAA-GTCTTTTAGGATTATCGAGATACTTTCATGTCGAAGGTATACCCATAGGGGCATTTTC
1 TTTTAATGTCCACTAGGGTTACCGGGATACTTTCATGTCGAAGGTATACCCATA-GGGCATTTTC
* * * * * * * * *
561083 GTAA-TTTTCTAGAACAAAGTCTTAGGTTATCATTGGGTTCGCTTTTATGCCGAAGGTGGGCATT
65 GTAATTTTTCTATAACCAACTCCTAGGTTGTCACTGAGTCCGCTTTTATGCCGAAGGT-GGTATT
561147 TAGGATAGGTTCATC
129 TAGGATAGGTTCATC
561162 TTTTTTATAA
Statistics
Matches: 389, Mismatches: 61, Indels: 16
0.83 0.13 0.03
Matches are distributed among these distances:
312 58 0.15
313 69 0.18
314 252 0.65
315 9 0.02
316 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (312 bp):
TTTTAATGTCCACTAGGGTTACCGGGATACTTTCATGTCGAAGGTATACCCATAGGGCATTTTCG
TAATTTTTCTATAACCAACTCCTAGGTTGTCACTGAGTCCGCTTTTATGCCGAAGGTGGTATTTA
GGATAGGTTCATCCTATTACTTATCATTTTAGTGTCCACTAAGGTTACCGAGATACTTTCACGTC
AAAGATATACCTAGAGAGGCATTCTCGTAATTTTTTAAAATAGAGTCCTAGGTTATCACCGGGTC
TGCTTTATGCCGAAAGTGAGTATTTAGGATAGGTTCACCCCAGCTATAACCT
Found at i:561171 original size:156 final size:156
Alignment explanation
Indices: 560375--561252 Score: 668
Period size: 156 Copynumber: 5.6 Consensus size: 156
560365 AGGGTAAAAA
* * * *
560375 TCATCATTATT-T-ATCATTTTAATGTCCACTAGGGTTACTG-GAATACTTTCATATCGAAGGTA
1 TCATC-TTATTATAATCTTTTTAA-GTCCATTAGGGTTACCGAG-ATACTTTCATGTCGAAGGTA
* * * * * * * * *
560437 TACTTATAGAGGTATTTTCGTAATTTTTCTATAACCAACTCCTAGGTTGTCACTGAGTCCGTTTT
63 TACCTATAGGGGCATTTTCGTAATTTTTCTAGAACAAAGTCCTAGGTTGTCACTGGGTTCGCTTT
* *
560502 TATGCCGAAGGTAGGTATTTAGGATAAGT
128 TATGCCGAAGGTGGGTATTTAGGATAGGT
* * * * * * *
560531 TCATCTTATTACTTATCATTTTAGTGTCCACTAAGGTTACCGAGATACTTTCACGTCGAAGATAT
1 TCATCTTATTA-TAATCTTTTTA-AGTCCATTAGGGTTACCGAGATACTTTCATGTCGAAGGTAT
** * * * ** *
560596 ACCTATAGGGGCATTTTTTTAATTTTT-TGGAATAGAGTTTTAGGTTGTCACCGGG-TCTGC-TT
64 ACCTATAGGGGCATTTTCGTAATTTTTCTAGAACAAAGTCCTAGGTTGTCACTGGGTTC-GCTTT
560658 TATGCCGAAGGTGGGTATTTAGGATAGGT
128 TATGCCGAAGGTGGGTATTTAGGATAGGT
* ** * * * * * *
560687 TCACCCCAGCTATAACCTTTTTAATGTCCACTAGGGTTACCGGGATATTTTCATGTTGAAGGTAT
1 TCATCTTA-TTATAATCTTTTTAA-GTCCATTAGGGTTACCGAGATACTTTCATGTCGAAGGTAT
* * * * * * * *
560752 ACCCATAGGGACATTTTCGTAATTTTTCTATAACCAACTCCTAGGCTGTCACTGAGTCCGCTTTT
64 ACCTATAGGGGCATTTTCGTAATTTTTCTAGAACAAAGTCCTAGGTTGTCACTGGGTTCGCTTTT
** * *
560817 ATGCTAAATGTGGATATTTAGGATAGGT
129 ATGCCGAAGGTGGGTATTTAGGATAGGT
* * * * * * * * * * *
560845 TTATCCTATTACTTATCATTTTAGTGTCTACTAGGGTTATCGAGATATTTTCACGTCAAAGGTAT
1 TCATCTTATTA-TAATCTTTTTA-AGTCCATTAGGGTTACCGAGATACTTTCATGTCGAAGGTAT
* * * * *
560910 ACCTAGAGAGGCATTCTCGTAATTTTTCTAAAATC-AAGTCCTA-G-TATCACTGGG-TCTGCTT
64 ACCTATAGGGGCATTTTCGTAATTTTTCTAGAA-CAAAGTCCTAGGTTGTCACTGGGTTC-GCTT
* * * *
560971 TTATGTCGAAAGTGAGTATTTAGGATATGT
127 TTATGCCGAAGGTGGGTATTTAGGATAGGT
* * * ** * *
561001 TCACCTTAGCTATAACCTTTTTAAGTCTTTTAGGATTATCGAGATACTTTCATGTCGAAGGTATA
1 TCATCTTA-TTATAATCTTTTTAAGTCCATTAGGGTTACCGAGATACTTTCATGTCGAAGGTATA
* * * *
561066 CCCATAGGGGCATTTTCGTAA-TTTTCTAGAACAAAGTCTTAGGTTATCATTGGGTTCGCTTTTA
65 CCTATAGGGGCATTTTCGTAATTTTTCTAGAACAAAGTCCTAGGTTGTCACTGGGTTCGCTTTTA
*
561130 TGCCGAAGGTGGGCATTTAGGATAGGT
130 TGCCGAAGGTGGGTATTTAGGATAGGT
* * * ** *
561157 TCATCTTTTTTATAATCTTTTTAAGTCCTTTAGGGGTA-TAAGGTAC-TTCTATGTCGAAGGTAT
1 TCATC-TTATTATAATCTTTTTAAGTCCATTAGGGTTACCGAGATACTTTC-ATGTCGAAGGTAT
* ** * * *
561220 CCCT-TAAAGGTATTTTCATAATTTTTCTTGAAC
64 ACCTATAGGGGCATTTTCGTAATTTTTCTAGAAC
561253 TTAGCTCTTT
Statistics
Matches: 566, Mismatches: 133, Indels: 47
0.76 0.18 0.06
Matches are distributed among these distances:
153 1 0.00
154 32 0.06
155 89 0.16
156 219 0.39
157 50 0.09
158 173 0.31
159 2 0.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (156 bp):
TCATCTTATTATAATCTTTTTAAGTCCATTAGGGTTACCGAGATACTTTCATGTCGAAGGTATAC
CTATAGGGGCATTTTCGTAATTTTTCTAGAACAAAGTCCTAGGTTGTCACTGGGTTCGCTTTTAT
GCCGAAGGTGGGTATTTAGGATAGGT
Found at i:565247 original size:13 final size:13
Alignment explanation
Indices: 565229--565254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
565219 CAATTTTTTG
565229 TGTATCGATACAT
1 TGTATCGATACAT
565242 TGTATCGATACAT
1 TGTATCGATACAT
565255 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:565339 original size:20 final size:20
Alignment explanation
Indices: 565314--565385 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
565304 CATCCTTTTT
565314 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*****
565334 ATGTATCGATACATTTTTTT
1 ATGTATCGATACATTGCAAC
565354 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
565374 ATGTATCGATAC
1 ATGTATCGATAC
565386 TTTGAATTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:565362 original size:40 final size:41
Alignment explanation
Indices: 565293--565385 Score: 170
Period size: 40 Copynumber: 2.3 Consensus size: 41
565283 CTGCCAAGAA
565293 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
565334 ATGTATCGATACAT-TTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
565374 ATGTATCGATAC
1 ATGTATCGATAC
565386 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 37 0.73
41 14 0.27
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:565399 original size:40 final size:40
Alignment explanation
Indices: 565293--565405 Score: 149
Period size: 40 Copynumber: 2.8 Consensus size: 40
565283 CTGCCAAGAA
*
565293 ATGTATCGATACATCCTT-TTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAT--TTAATTATGTATCGATACATTGCAAC
**
565334 ATGTATCGATACATTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTAATTATGTATCGATACATTGCAAC
*
565374 ATGTATCGATAC-TTTGAATTGTGTATCGATAC
1 ATGTATCGATACATTT-AATTATGTATCGATAC
565406 TTTTAGGGGT
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
39 5 0.07
40 48 0.72
41 14 0.21
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (40 bp):
ATGTATCGATACATTTAATTATGTATCGATACATTGCAAC
Found at i:565990 original size:48 final size:48
Alignment explanation
Indices: 565935--566030 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
565925 AAATTTTACG
565935 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
565983 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
566031 TTATCTCCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.29, G:0.08, T:0.38
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:567886 original size:13 final size:13
Alignment explanation
Indices: 567868--567906 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
567858 ATAATCACCC
*
567868 TGTATCGATACAG
1 TGTATCGATACAA
567881 TGTATCGATACAA
1 TGTATCGATACAA
567894 TGTATCGATACAA
1 TGTATCGATACAA
567907 GGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:570005 original size:15 final size:15
Alignment explanation
Indices: 569985--570015 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
569975 ATTTCGTTTG
*
569985 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
570000 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
570015 G
1 G
570016 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:574099 original size:13 final size:13
Alignment explanation
Indices: 574081--574106 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
574071 CAATTTTTTG
574081 TGTATCGATACAT
1 TGTATCGATACAT
574094 TGTATCGATACAT
1 TGTATCGATACAT
574107 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:574171 original size:21 final size:19
Alignment explanation
Indices: 574145--574221 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 19
574135 CTGCCAAGAA
574145 ATGTATCGATACATCCTTTTT
1 ATGTATCGATACAT--TTTTT
****
574166 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATT-TTTT
574186 ATGTATCGATACATTTTTTTT
1 ATGTATCGATACA--TTTTTT
574207 ATGTATCGATACATT
1 ATGTATCGATACATT
574222 GCAACATGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
19 3 0.07
20 13 0.29
21 27 0.60
22 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (19 bp):
ATGTATCGATACATTTTTT
Found at i:574191 original size:20 final size:20
Alignment explanation
Indices: 574166--574238 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
574156 CATCCTTTTT
574166 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*****
574186 ATGTATCGATACATTTTTTTT
1 ATGTATCGATACA-TTGCAAC
574207 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
574227 ATGTATCGATAC
1 ATGTATCGATAC
574239 TTTGAATTGT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:574206 original size:41 final size:41
Alignment explanation
Indices: 574145--574238 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
574135 CTGCCAAGAA
574145 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
**
574186 ATGTATCGATACATTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
574227 ATGTATCGATAC
1 ATGTATCGATAC
574239 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:583118 original size:21 final size:18
Alignment explanation
Indices: 583067--583124 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
583057 TGGCAGTAGC
*
583067 CAAACTTGTATCGATACA
1 CAAAGTTGTATCGATACA
*
583085 CCAAGTATGTATCGATACA
1 CAAAGT-TGTATCGATACA
583104 CAAAAAAGTTGTATCGATACA
1 C---AAAGTTGTATCGATACA
583125 TTGGCTTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 4 0.12
19 13 0.39
21 12 0.36
22 4 0.12
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (18 bp):
CAAAGTTGTATCGATACA
Found at i:585355 original size:21 final size:21
Alignment explanation
Indices: 585322--585366 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
585312 TTGCAAGTTG
*
585322 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
585344 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
585364 AAA
1 AAA
585367 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:587189 original size:15 final size:15
Alignment explanation
Indices: 587169--587199 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
587159 TAAAAATGTC
*
587169 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
587184 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
587199 C
1 C
587200 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:589296 original size:13 final size:13
Alignment explanation
Indices: 589278--589303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
589268 ACATTTTTCT
589278 TTGTATCGATACA
1 TTGTATCGATACA
589291 TTGTATCGATACA
1 TTGTATCGATACA
589304 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:589467 original size:20 final size:20
Alignment explanation
Indices: 589424--589469 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
589414 AAATCTTTTG
589424 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
589445 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
589465 CAAAA
1 CAAAA
589470 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:591866 original size:13 final size:13
Alignment explanation
Indices: 591848--591873 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
591838 TACACCAAGT
591848 ATGTATCGATACA
1 ATGTATCGATACA
591861 ATGTATCGATACA
1 ATGTATCGATACA
591874 CAAAAAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:593246 original size:3 final size:3
Alignment explanation
Indices: 593232--593268 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
593222 CGAGTCAACC
* *
593232 TCA TCA TTA TCA TCA TCA TCA TCA TCA TCT TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
593269 ATTTGATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (3 bp):
TCA
Found at i:594355 original size:19 final size:19
Alignment explanation
Indices: 594331--594398 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
594321 AATTCAACAA
594331 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
594350 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
594365 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
594382 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
594399 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:594370 original size:13 final size:13
Alignment explanation
Indices: 594352--594376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
594342 ACATAAGTTT
594352 TGTATCGATACAA
1 TGTATCGATACAA
594365 TGTATCGATACA
1 TGTATCGATACA
594377 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:594374 original size:32 final size:32
Alignment explanation
Indices: 594333--594395 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
594323 TTCAACAATT
*
594333 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
594365 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
594396 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:594456 original size:13 final size:13
Alignment explanation
Indices: 594438--594463 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
594428 CATTTTTCTG
594438 TGTATCGATACAT
1 TGTATCGATACAT
594451 TGTATCGATACAT
1 TGTATCGATACAT
594464 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:594460 original size:33 final size:33
Alignment explanation
Indices: 594418--594484 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
594408 GCCAAGGAAA
***
594418 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
594451 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
594484 T
1 T
594485 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:596755 original size:13 final size:13
Alignment explanation
Indices: 596737--596766 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
596727 ACAATTCTTC
596737 ATGTATCGATACA
1 ATGTATCGATACA
596750 ATGTATCGATACA
1 ATGTATCGATACA
596763 ATGT
1 ATGT
596767 GCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:596856 original size:19 final size:19
Alignment explanation
Indices: 596811--596884 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
596801 ACTGCCAGTT
*
596811 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAA-AGA
596830 TGCATGTATCGATACAAAGA
1 T-CATGTATCGATACAAAGA
596850 TCATGTATCGATACAAAGCA
1 TCATGTATCGATACAAAG-A
*
596870 TAATGTATCGATACA
1 TCATGTATCGATACA
596885 TCTGGATATG
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 19 0.38
20 31 0.62
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (19 bp):
TCATGTATCGATACAAAGA
Found at i:597250 original size:28 final size:28
Alignment explanation
Indices: 597210--597309 Score: 119
Period size: 28 Copynumber: 3.4 Consensus size: 28
597200 GCATCTTTCT
*
597210 TTTTTTCCAAGTCCACGACTTAGTGGCA
1 TTTTTTCAAAGTCCACGACTTAGTGGCA
*
597238 TTTTTTGAAAGTCCACGACTTAGTGGCA
1 TTTTTTCAAAGTCCACGACTTAGTGGCA
* *
597266 TCTTTTTCTTCCAAGTCCACGACTCAGTGGCA
1 ---TTTT-TTCAAAGTCCACGACTTAGTGGCA
*
597298 TTTCTTCAAAGT
1 TTTTTTCAAAGT
597310 TCACAGCCCA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
28 33 0.54
29 3 0.05
31 4 0.07
32 21 0.34
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (28 bp):
TTTTTTCAAAGTCCACGACTTAGTGGCA
Found at i:597335 original size:60 final size:60
Alignment explanation
Indices: 597207--597331 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
597197 ATGGCATCTT
* * * **
597207 TCTTTTT-TTCCAAGTCCACGACTTAGTGGCATTTTTTGAAAGTCCACGACTTAGTGGCA
1 TCTTTTTCTTCCAAGTCCACGACTCAGTGGCATTTCTTCAAAGTCCACGACCCAGTGGCA
*
597266 TCTTTTTCTTCCAAGTCCACGACTCAGTGGCATTTCTTCAAAGTTCAC-AGCCCAGTGGCA
1 TCTTTTTCTTCCAAGTCCACGACTCAGTGGCATTTCTTCAAAGTCCACGA-CCCAGTGGCA
597326 -CTTTTT
1 TCTTTTT
597332 TCTTTTCAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
59 14 0.24
60 44 0.76
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.37
Consensus pattern (60 bp):
TCTTTTTCTTCCAAGTCCACGACTCAGTGGCATTTCTTCAAAGTCCACGACCCAGTGGCA
Found at i:597358 original size:34 final size:31
Alignment explanation
Indices: 597320--597643 Score: 209
Period size: 27 Copynumber: 10.5 Consensus size: 31
597310 TCACAGCCCA
*
597320 GTGGCACTTTTTTCTTTTCAAAGTCCACAACTTC
1 GTGGCAC-TTTTCCTTTT--AAGTCCACAACTTC
597354 GTGGCACCTTGTTCCTTTTAAGTCCACAAC-TC
1 GTGGCA-CTT-TTCCTTTTAAGTCCACAACTTC
* *
597386 TATGGCAC----CCTTTTAAGTCCAAAACTTC
1 -GTGGCACTTTTCCTTTTAAGTCCACAACTTC
* * *
597414 ATGGCACTATTTTCTTTTCAAAGTCCACAACTCC
1 GTGGCACT-TTTCCTTTT--AAGTCCACAACTTC
597448 GTGGCAC----CCTTTTAAGTCCACAACTTC
1 GTGGCACTTTTCCTTTTAAGTCCACAACTTC
* *
597475 GTGGCACCTTTTCTTTTTCAAAG-CCAACAACTCC
1 GTGGCA-CTTTTCCTTTT--AAGTCC-ACAACTTC
* * * *
597509 ATGGAACCTTTTCCTTTTAAGTTCACAACTCC
1 GTGGCA-CTTTTCCTTTTAAGTCCACAACTTC
*
597541 GTGGCAC----CCTTTTAAGTCCACAACTCC
1 GTGGCACTTTTCCTTTTAAGTCCACAACTTC
** *
597568 AAGGCACCTTTTCCTTTTAAGTCCATAAC-TC
1 GTGGCA-CTTTTCCTTTTAAGTCCACAACTTC
*
597599 TGTGGCA----TCCTTTTAAGTCCACAACTTT
1 -GTGGCACTTTTCCTTTTAAGTCCACAACTTC
*
597627 GTGGCACCTTTCCTTTT
1 GTGGCACTTTTCCTTTT
597644 TAAATCCATA
Statistics
Matches: 233, Mismatches: 26, Indels: 65
0.72 0.08 0.20
Matches are distributed among these distances:
27 88 0.38
28 5 0.02
29 5 0.02
31 9 0.04
32 48 0.21
33 19 0.08
34 51 0.22
35 8 0.03
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (31 bp):
GTGGCACTTTTCCTTTTAAGTCCACAACTTC
Found at i:597412 original size:60 final size:60
Alignment explanation
Indices: 597340--597579 Score: 230
Period size: 61 Copynumber: 4.0 Consensus size: 60
597330 TTTCTTTTCA
*
597340 AAGTCCACAACTTCGTGGCACCTTGTTCCTTTT-AAGTCCACAACTCTATGGCACCCTTTT
1 AAGTCCACAACTTCGTGGCACCTT-TTCCTTTTAAAGTCCACAACTCCATGGCACCCTTTT
* * * *
597400 AAGTCCAAAACTTCATGGCA-CTATTTTCTTTTCAAAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTTCGTGGCACCT-TTTCCTTTT-AAAGTCCACAACTCCATGGCACCCTTTT
* *
597461 AAGTCCACAACTTCGTGGCACCTTTTCTTTTTCAAAG-CCAACAACTCCATGGAACCTTTTCCTT
1 AAGTCCACAACTTCGTGGCACCTTTTCCTTTT-AAAGTCC-ACAACTCCATGGCA-C----CCTT
597525 TT
59 TT
* * *
597527 AAGTTCACAACTCCGTGGCA-C----CCTTTT-AAGTCCACAACTCCAAGGCA-CCTTTT
1 AAGTCCACAACTTCGTGGCACCTTTTCCTTTTAAAGTCCACAACTCCATGGCACCCTTTT
597580 CCTTTTAAGT
Statistics
Matches: 153, Mismatches: 16, Indels: 29
0.77 0.08 0.15
Matches are distributed among these distances:
53 6 0.04
59 24 0.16
60 23 0.15
61 72 0.47
62 3 0.02
65 1 0.01
66 24 0.16
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (60 bp):
AAGTCCACAACTTCGTGGCACCTTTTCCTTTTAAAGTCCACAACTCCATGGCACCCTTTT
Found at i:597567 original size:59 final size:59
Alignment explanation
Indices: 597455--597624 Score: 198
Period size: 59 Copynumber: 2.8 Consensus size: 59
597445 TCCGTGGCAC
* *
597455 CCTTTTAAGTCCACAACTTCGTGGCACCTTTTCTTTTTCAAAG-CCAACAACTCCATGGAACCTT
1 CCTTTTAAGTCCACAACTCCGTGGCACC----C-TTTT--AAGTCC-ACAACTCCAAGGAACCTT
597519 TT
58 TT
* *
597521 CCTTTTAAGTTCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCAAGGCACCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCAAGGAACCTTTT
* * *
597580 CCTTTTAAGTCCATAACTCTGTGGCATCCTTTTAAGTCCACAACT
1 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACT
597625 TTGTGGCACC
Statistics
Matches: 95, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
59 62 0.65
60 2 0.02
61 4 0.04
62 1 0.01
66 26 0.27
ACGTcount: A:0.24, C:0.31, G:0.11, T:0.34
Consensus pattern (59 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCAAGGAACCTTTT
Found at i:597697 original size:31 final size:31
Alignment explanation
Indices: 597662--597740 Score: 104
Period size: 33 Copynumber: 2.5 Consensus size: 31
597652 TACAAGCCAG
597662 TGGCACCCCTTCTAAAGCCCACACAAGTCGA
1 TGGCACCCCTTCTAAAGCCCACACAAGTCGA
* * *
597693 TGGCAACCCTTTCCTAAAGCCCACACAAGTTGG
1 TGGC-ACCCCTT-CTAAAGCCCACACAAGTCGA
*
597726 TGGCAACCCTTCTAA
1 TGGCACCCCTTCTAA
597741 GCCTAATGGC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 8 0.20
32 11 0.27
33 22 0.54
ACGTcount: A:0.28, C:0.35, G:0.16, T:0.20
Consensus pattern (31 bp):
TGGCACCCCTTCTAAAGCCCACACAAGTCGA
Found at i:597715 original size:33 final size:33
Alignment explanation
Indices: 597673--597736 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
597663 GGCACCCCTT
597673 CTAAAGCCCACACAAGTCGATGGCAACCCTTTC
1 CTAAAGCCCACACAAGTCGATGGCAACCCTTTC
* *
597706 CTAAAGCCCACACAAGTTGGTGGCAACCCTT
1 CTAAAGCCCACACAAGTCGATGGCAACCCTT
597737 CTAAGCCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (33 bp):
CTAAAGCCCACACAAGTCGATGGCAACCCTTTC
Found at i:597807 original size:39 final size:39
Alignment explanation
Indices: 597752--597843 Score: 130
Period size: 39 Copynumber: 2.4 Consensus size: 39
597742 CCTAATGGCG
* *
597752 CTGGCCTTGAATCAGCACATTAACACAAATCCAATATCG
1 CTGGCCTTGAATCAGCACATTAACACAAACCCAATATCA
* ** *
597791 TTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCA
1 CTGGCCTTGAATCAGCACATTAACACAAACCCAATATCA
597830 CTGGCCTTGAATCA
1 CTGGCCTTGAATCA
597844 TTATATTGGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (39 bp):
CTGGCCTTGAATCAGCACATTAACACAAACCCAATATCA
Found at i:597943 original size:52 final size:51
Alignment explanation
Indices: 597821--598526 Score: 422
Period size: 52 Copynumber: 14.8 Consensus size: 51
597811 TGGCACAAGC
* ** *
597821 CCAATATCACTGGCCTTGAATCATTATATTGGCACCTTGAC--CTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACATCTTTAAGT
* * * *
597870 CCAATATTGCTAGCCTGGAATCAGCATATTGGCATCTTTACCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA-CATCTTTAAGT
** * * *
597922 CCAACGTCGCTGGCCTTGAATCAGCACATTGGCACCTTT--ATCTTCAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACATCTTTAAGT
* *
597971 CCAATATCGCTAGCCTTGAATCAGCATATTTGGCACC-TT-CATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATA-TTGGCACCTTTACATCTTTAAGT
* * *
598021 CCAATGTCACTGGCCTTGAATCAGCACATTGG---C---AC-T-TTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACATCTTTAAGT
* *
598064 CCAATATCGCTGGCCTTGAATCAACATATTGGTACCTTTACCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA-CATCTTTAAGT
* * * * *
598116 CTAATGTCGCTGGCCTTAAATCAGCACATTGG--------CA-C---AAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACATCTTTAAGT
* *
598155 CCAATATCGCTGGCCTTGAATCAGCACATTGG--------CA-C---AAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACATCTTTAAGT
* *
598194 CCAATATCGCTGGCCTTGAATCAGCATATTGACACC-TT-CATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACATCTTTAAGT
* *
598243 CCAATGTCGCTGGCCTTGAATCAGCATAGTGG---C---ACA-----AA-T
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACATCTTTAAGT
* * *
598282 CCAATATCGCTAGCCTTGAATCAGGATATTGGCACCTTTACCACCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA-CATCTTTAAGT
* * * * * *
598334 CAAATATCGCTGGCCTTAAATCAGTATATTGGCATCATTATCATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTA-CATCTTTAAGT
* * * * * * *
598386 CCAATGTCACTGGCCTTGAATCAACACATTGGCA-TTTTCTCATCTTCAAGT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-ACATCTTTAAGT
* * * * * * * * ** * *
598437 CTAATGTTGCTGGTCGTGAATTAGCACATTGGTATTTTTGTCATCTTTAAGC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-ACATCTTTAAGT
* *
598489 CCCATATCGTTGGCCTTGAATCAGCATATTGGC-CCTTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
598527 TATCATTCTT
Statistics
Matches: 520, Mismatches: 96, Indels: 80
0.75 0.14 0.11
Matches are distributed among these distances:
39 97 0.19
40 2 0.00
42 2 0.00
43 36 0.07
44 1 0.00
45 6 0.01
46 6 0.01
49 103 0.20
50 42 0.08
51 43 0.08
52 182 0.35
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (51 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACATCTTTAAGT
Found at i:598177 original size:39 final size:39
Alignment explanation
Indices: 598122--598316 Score: 201
Period size: 39 Copynumber: 4.7 Consensus size: 39
598112 AAGTCTAATG
* *
598122 TCGCTGGCCTTAAATCAGCACATTGGCACAAGCCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACAAGCCCAATA
*
598161 TCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACAAGCCCAATA
* * *
598200 TCGCTGGCCTTGAATCAGCATATTGACACCTTCATCTTTAAGACCAATG
1 TCGCTGGCCTTGAATCAGCATATTG------GCA-C---AAGCCCAATA
* **
598249 TCGCTGGCCTTGAATCAGCATAGTGGCACAAATCCAATA
1 TCGCTGGCCTTGAATCAGCATATTGGCACAAGCCCAATA
* *
598288 TCGCTAGCCTTGAATCAGGATATTGGCAC
1 TCGCTGGCCTTGAATCAGCATATTGGCAC
598317 CTTTACCACC
Statistics
Matches: 133, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
39 95 0.71
42 1 0.01
43 2 0.02
45 2 0.02
46 1 0.01
49 32 0.24
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (39 bp):
TCGCTGGCCTTGAATCAGCATATTGGCACAAGCCCAATA
Found at i:598276 original size:127 final size:130
Alignment explanation
Indices: 598021--598316 Score: 391
Period size: 127 Copynumber: 2.3 Consensus size: 130
598011 ATCTTTAAGA
* * *
598021 CCAATGTCACTGGCCTTGAATCAGCACATTGGCACTTTTAAGTCCAATATCGCTGGCCTTGAATC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCAC---TAAGCCCAATATCGCTGGCCTTGAATC
** * * *
598086 AACATATTGGTACCTTTACCATCTTTAAGTCTAATGTCGCTGGCCTTAAATCAGCACATTGGCAC
63 AACATATTGACACCTTTA-CATCTTTAAGACCAATGTCGCTGGCCTTAAATCAGCACAGTGGCAC
*
598151 AAGC
127 AAAC
*
598155 CCAATATCGCTGGCCTTGAATCAGCACATTGGCAC-AAGCCCAATATCGCTGGCCTTGAATCAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACTAAGCCCAATATCGCTGGCCTTGAATCAAC
* * *
598219 ATATTGACACC-TT-CATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATAGTGGCACAAAT
66 ATATTGACACCTTTACATCTTTAAGACCAATGTCGCTGGCCTTAAATCAGCACAGTGGCACAAAC
* * *
598282 CCAATATCGCTAGCCTTGAATCAGGATATTGGCAC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
598317 CTTTACCACC
Statistics
Matches: 146, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
127 75 0.51
129 2 0.01
130 36 0.25
134 33 0.23
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (130 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACTAAGCCCAATATCGCTGGCCTTGAATCAAC
ATATTGACACCTTTACATCTTTAAGACCAATGTCGCTGGCCTTAAATCAGCACAGTGGCACAAAC
Found at i:598304 original size:88 final size:90
Alignment explanation
Indices: 598155--598367 Score: 286
Period size: 88 Copynumber: 2.4 Consensus size: 90
598145 TGGCACAAGC
* * *
598155 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAACCCAATATCGCTAGCCTTGAATCAGCA
*
598220 TATTGACACC-TT-CATCTTTAAGA
66 TATTGACACCTTTACACCTTTAAGA
* * * *
598243 CCAATGTCGCTGGCCTTGAATCAGCATAGTGGCACAAATCCAATATCGCTAGCCTTGAATCAGGA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAACCCAATATCGCTAGCCTTGAATCAGCA
* *
598308 TATTGGCACCTTTACCACCTTTAAGT
66 TATTGACACCTTTA-CACCTTTAAGA
* * *
598334 CAAATATCGCTGGCCTTAAATCAGTATATTGGCA
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCA
598368 TCATTATCAT
Statistics
Matches: 107, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
88 67 0.63
89 2 0.02
91 38 0.36
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (90 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACAAACCCAATATCGCTAGCCTTGAATCAGCA
TATTGACACCTTTACACCTTTAAGA
Found at i:598349 original size:218 final size:220
Alignment explanation
Indices: 597966--598367 Score: 628
Period size: 218 Copynumber: 1.8 Consensus size: 220
597956 CCTTTATCTT
*
597966 CAAGCCCAATATCGCTAGCCTTGAATCAGCATATTTGGCACCTTCATCTTTAAGACCAATGTCAC
1 CAAGCCCAATATCGCTAGCCTTGAATCAGCATATTTGACACCTTCATCTTTAAGACCAATGTCAC
* * *
598031 TGGCCTTGAATCAGCACATTGGCACTTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGG
66 TGGCCTTGAATCAGCACAGTGGCAC---TAAATCCAATATCGCTAGCCTTGAATCAACATATTGG
* * * *
598096 TACCTTTACCATCTTTAAGTCTAATGTCGCTGGCCTTAAATCAGCACATTGGCACAAGCCCAATA
128 CACCTTTACCACCTTTAAGTCAAATATCGCTGGCCTTAAATCAGCACATTGGCACAAGCCCAATA
598161 TCGCTGGCCTTGAATCAGCACATTGGCA
193 TCGCTGGCCTTGAATCAGCACATTGGCA
* *
598189 CAAGCCCAATATCGCTGGCCTTGAATCAGCATA-TTGACACCTTCATCTTTAAGACCAATGTCGC
1 CAAGCCCAATATCGCTAGCCTTGAATCAGCATATTTGACACCTTCATCTTTAAGACCAATGTCAC
* **
598253 TGGCCTTGAATCAGCATAGTGGCAC-AAATCCAATATCGCTAGCCTTGAATCAGGATATTGGCAC
66 TGGCCTTGAATCAGCACAGTGGCACTAAATCCAATATCGCTAGCCTTGAATCAACATATTGGCAC
* *
598317 CTTTACCACCTTTAAGTCAAATATCGCTGGCCTTAAATCAGTATATTGGCA
131 CTTTACCACCTTTAAGTCAAATATCGCTGGCCTTAAATCAGCACATTGGCA
598368 TCATTATCAT
Statistics
Matches: 164, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
218 80 0.49
222 52 0.32
223 32 0.20
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (220 bp):
CAAGCCCAATATCGCTAGCCTTGAATCAGCATATTTGACACCTTCATCTTTAAGACCAATGTCAC
TGGCCTTGAATCAGCACAGTGGCACTAAATCCAATATCGCTAGCCTTGAATCAACATATTGGCAC
CTTTACCACCTTTAAGTCAAATATCGCTGGCCTTAAATCAGCACATTGGCACAAGCCCAATATCG
CTGGCCTTGAATCAGCACATTGGCA
Found at i:598487 original size:373 final size:365
Alignment explanation
Indices: 597738--598423 Score: 873
Period size: 373 Copynumber: 1.9 Consensus size: 365
597728 GCAACCCTTC
* ** * *
597738 TAAGCCTAATGGCGCTGGCCTTGAATCAGCACATTAACACAAATCCAATATCGTTGGCCTTGAAT
1 TAAGCCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAACCCAATATCGCTGGCCTTGAAT
** * *
597803 CAGCACATTGGCACAAGCCCAATATCACTGGCCTTGAATCATTATATTGGCACCTTGACCTTTAA
66 CAGCACATTGGCACAAGCCCAATATCACTGGCCTTGAATCAGCATATTGACACCTTCACCTTTAA
* * * *
597868 GTCCAATATTGCTAGCCTGGAATCAGCATATTGGCATCTTTACCATCTTTAAGTCCAACGTCGCT
131 GACCAATATCGCTAGCCTGGAATCAGCATAGTGG-A-C--TACCA----TAAGTCCAACATCGCT
* * * *
597933 GGCCTTGAATCAGCACATTGGCACCTTTATCTTCAAGCCCAATATCGCTAGCCTTGAATCAGCAT
188 AGCCTTGAATCAGCACATTGGCACCTTTACCTTCAAGCCAAATATCGCTAGCCTTAAATCAGCAT
*
597998 ATTTGGCACCTTCATCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACTTTTAAG
253 ATTTGGCACCTTCATCTTTAAGACCAATGTCACTGGCCTTGAATCAACACATTGGCACTTTTAAG
* *
598063 TCCAATATCGCTGGCCTTGAATCAACATATTGGTACCTTTACCATCTT
318 TCCAATATCGCTGGCCGTGAATCAACACATTGGTACCTTTACCATCTT
* * *
598111 TAAGTCTAATGTCGCTGGCCTTAAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAAT
1 TAAGCCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAACCCAATATCGCTGGCCTTGAAT
* *
598176 CAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTCATCTTTAA
66 CAGCACATTGGCACAAGCCCAATATCACTGGCCTTGAATCAGCATATTGACACCTTCACCTTTAA
* * * *
598241 GACCAATGTCGCTGGCCTTGAATCAGCATAGTGG-C-A-CA-AA-TCCAATATCGCTAGCCTTGA
131 GACCAATATCGCTAGCCTGGAATCAGCATAGTGGACTACCATAAGTCCAACATCGCTAGCCTTGA
* * * * * *
598301 ATCAGGATATTGGCACCTTTACCACCTTTAAGTCAAATATCGCTGGCCTTAAATCAGTATA-TTG
196 ATCAGCACATTGGCACCTTT---ACCTTCAAGCCAAATATCGCTAGCCTTAAATCAGCATATTTG
*
598365 GCATCATTATCATCTTTAAGACCAATGTCACTGGCCTTGAATCAACACATTGGCA-TTTT
258 GCA-C-CT-TCATCTTTAAGACCAATGTCACTGGCCTTGAATCAACACATTGGCACTTTT
598424 CTCATCTTCA
Statistics
Matches: 273, Mismatches: 34, Indels: 21
0.83 0.10 0.06
Matches are distributed among these distances:
360 35 0.13
361 2 0.01
362 6 0.02
363 32 0.12
364 5 0.02
365 45 0.16
366 2 0.01
367 1 0.00
370 1 0.00
373 144 0.53
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (365 bp):
TAAGCCTAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAACCCAATATCGCTGGCCTTGAAT
CAGCACATTGGCACAAGCCCAATATCACTGGCCTTGAATCAGCATATTGACACCTTCACCTTTAA
GACCAATATCGCTAGCCTGGAATCAGCATAGTGGACTACCATAAGTCCAACATCGCTAGCCTTGA
ATCAGCACATTGGCACCTTTACCTTCAAGCCAAATATCGCTAGCCTTAAATCAGCATATTTGGCA
CCTTCATCTTTAAGACCAATGTCACTGGCCTTGAATCAACACATTGGCACTTTTAAGTCCAATAT
CGCTGGCCGTGAATCAACACATTGGTACCTTTACCATCTT
Found at i:598505 original size:373 final size:365
Alignment explanation
Indices: 597750--598521 Score: 854
Period size: 373 Copynumber: 2.1 Consensus size: 365
597740 AGCCTAATGG
** * *
597750 CGCTGGCCTTGAATCAGCACATTAACACAAATCCAATATCGTTGGCCTTGAATCAGCACATTGGC
1 CGCTGGCCTTGAATCAGCACATTGGCACAAACCCAATATCGCTGGCCTTGAATCAGCACATTGGC
** * * * *
597815 ACAAGCCCAATATCACTGGCCTTGAATCATTATATTGGCACCTTGACCTTTAAGTCCAATATTGC
66 ACAAGCCCAATATCACTGGCCTTGAATCAGCATATTGACACCTTCACCTTTAAGACCAATATCGC
* * *
597880 TAGCCTGGAATCAGCATATTGGCATCTTTACCATCTTTAAGTCCAACGTCGCTGGCCTTGAATCA
131 TAGCCTGGAATCAGCATAGTGG-A-C--TACCA----TAAGTCCAACATCGCTAGCCTTGAATCA
* * *
597945 GCACATTGGCACCTTTATCTTCAAGCCCAATATCGCTAGCCTTGAATCAGCATATTTGGCACCTT
188 GCACATTGGCACCTTTACCTTCAAGCCAAATATCGCTAGCCTTAAATCAGCATATTTGGCACCTT
*
598010 CATCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACTTTTAAGTCCAATATCGCT
253 CATCTTTAAGACCAATGTCACTGGCCTTGAATCAACACATTGGCACTTTTAAGTCCAATATCGCT
* * * * *
598075 GGCCTTGAATCAACATATTGGTACCTTTACCATCTTTAAGTCTAATGT
318 GGCCGTGAATCAACACATTGGTACCTTTACCATCTTTAAGCCCAATAT
* *
598123 CGCTGGCCTTAAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGC
1 CGCTGGCCTTGAATCAGCACATTGGCACAAACCCAATATCGCTGGCCTTGAATCAGCACATTGGC
* * *
598188 ACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGACACCTTCATCTTTAAGACCAATGTCGC
66 ACAAGCCCAATATCACTGGCCTTGAATCAGCATATTGACACCTTCACCTTTAAGACCAATATCGC
* * * * *
598253 TGGCCTTGAATCAGCATAGTGG-C-A-CA-AA-TCCAATATCGCTAGCCTTGAATCAGGATATTG
131 TAGCCTGGAATCAGCATAGTGGACTACCATAAGTCCAACATCGCTAGCCTTGAATCAGCACATTG
* * * * *
598313 GCACCTTTACCACCTTTAAGTCAAATATCGCTGGCCTTAAATCAGTATA-TTGGCATCATTATCA
196 GCACCTTT---ACCTTCAAGCCAAATATCGCTAGCCTTAAATCAGCATATTTGGCA-C-CT-TCA
*
598377 TCTTTAAGACCAATGTCACTGGCCTTGAATCAACACATTGGCATTTTCTCATCTTCAAGTCTAAT
255 TCTTTAAGACCAATGTCACTGGCCTTGAATCAACACATTGGCA----CT--T-TT-AAGTCCAAT
* * * * * ** ** *
598442 GTTGCTGGTCGTGAATTAGCACATTGGTATTTTTGTCATCTTTAAGCCCCATAT
312 ATCGCTGGCCGTGAATCAACACATTGGTACCTTTACCATCTTTAAGCCCAATAT
* *
598496 CGTTGGCCTTGAATCAGCATATTGGC
1 CGCTGGCCTTGAATCAGCACATTGGC
598522 CCTTTTATCA
Statistics
Matches: 334, Mismatches: 51, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
360 35 0.10
361 2 0.01
362 6 0.02
363 32 0.10
364 1 0.00
365 45 0.13
366 2 0.01
367 1 0.00
369 2 0.01
370 1 0.00
371 1 0.00
372 2 0.01
373 204 0.61
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (365 bp):
CGCTGGCCTTGAATCAGCACATTGGCACAAACCCAATATCGCTGGCCTTGAATCAGCACATTGGC
ACAAGCCCAATATCACTGGCCTTGAATCAGCATATTGACACCTTCACCTTTAAGACCAATATCGC
TAGCCTGGAATCAGCATAGTGGACTACCATAAGTCCAACATCGCTAGCCTTGAATCAGCACATTG
GCACCTTTACCTTCAAGCCAAATATCGCTAGCCTTAAATCAGCATATTTGGCACCTTCATCTTTA
AGACCAATGTCACTGGCCTTGAATCAACACATTGGCACTTTTAAGTCCAATATCGCTGGCCGTGA
ATCAACACATTGGTACCTTTACCATCTTTAAGCCCAATAT
Found at i:604242 original size:20 final size:20
Alignment explanation
Indices: 604217--604275 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
604207 ATAAAAAAAT
*
604217 ACAAAAAAAGAAAAAGAAAG
1 ACAAAAAAAGAAAAAGAAAC
604237 ACAAAAAAAGAGAAAAGAAAC
1 ACAAAAAAAGA-AAAAGAAAC
604258 A-AAAAAAATG-AAAAGAAA
1 ACAAAAAAA-GAAAAAGAAA
604276 AAGAAAGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 8 0.22
20 18 0.50
21 10 0.28
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.02
Consensus pattern (20 bp):
ACAAAAAAAGAAAAAGAAAC
Found at i:604270 original size:19 final size:18
Alignment explanation
Indices: 604219--604275 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 18
604209 AAAAAAATAC
604219 AAAAAAAGAAAAAGAAAGACA
1 AAAAAAAG-AAAAG-AA-ACA
604240 AAAAAAGAGAAAAGAAACA
1 AAAAAA-AGAAAAGAAACA
604259 AAAAAAATGAAAAGAAA
1 AAAAAAA-GAAAAGAAA
604276 AAGAAAGTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 2 0.06
21 11 0.32
22 2 0.06
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAAAAGAAAAGAAACA
Found at i:604276 original size:11 final size:10
Alignment explanation
Indices: 604209--604281 Score: 65
Period size: 10 Copynumber: 7.1 Consensus size: 10
604199 TTCTCAAAAT
* *
604209 AAAAAAATAC
1 AAAAAAAGAA
604219 AAAAAAAGAA
1 AAAAAAAGAA
* *
604229 AAAGAAAGAC
1 AAAAAAAGAA
604239 AAAAAAAGAGA
1 AAAAAAAGA-A
* *
604250 AAAGAAACAA
1 AAAAAAAGAA
*
604260 AAAAAATGAA
1 AAAAAAAGAA
604270 AAGAAAAAGAA
1 AA-AAAAAGAA
604281 A
1 A
604282 GTACAGATAG
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
10 34 0.69
11 15 0.31
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:608129 original size:34 final size:35
Alignment explanation
Indices: 608091--608157 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
608081 CCTTACAACA
608091 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
608125 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
608158 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:608646 original size:13 final size:13
Alignment explanation
Indices: 608627--608665 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
608617 ACTATTTATG
608627 ATGTATCGATACA
1 ATGTATCGATACA
*
608640 CTGTATCGATACA
1 ATGTATCGATACA
*
608653 ATGTAGCGATACA
1 ATGTATCGATACA
608666 TAAATAGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:608763 original size:22 final size:22
Alignment explanation
Indices: 608737--608792 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 22
608727 ACAGTGATCT
608737 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
*
608759 ATGAA-GGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
608780 ATGAACAGTGATG
1 ATGAACAGTGATG
608793 AATAGTGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 20 0.65
22 11 0.35
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:608799 original size:10 final size:10
Alignment explanation
Indices: 608780--608810 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
608770 GTATCGATAC
608780 ATGAACAGTG
1 ATGAACAGTG
*
608790 ATGAATAGTG
1 ATGAACAGTG
608800 ATGAACAGTG
1 ATGAACAGTG
608810 A
1 A
608811 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:608898 original size:53 final size:53
Alignment explanation
Indices: 608834--608970 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
608824 CTACTACCAA
608834 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
608887 TGTATCGATACATATTGTGTGTAGCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
608940 TCTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
608971 TATGCAATCT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 65 0.84
54 12 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:609003 original size:20 final size:20
Alignment explanation
Indices: 608958--609011 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
608948 TACATATTTG
*
608958 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATGAAA
* *
608978 TCTGTATCGATAC-ATTTAAA
1 TGTGTATCGATACTA-TGAAA
608998 TGTGTATCGATACT
1 TGTGTATCGATACT
609012 TTTCAGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTGTATCGATACTATGAAA
Found at i:609076 original size:21 final size:21
Alignment explanation
Indices: 609050--609090 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
609040 GTCAACCTTG
609050 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
609071 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
609091 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:610751 original size:13 final size:13
Alignment explanation
Indices: 610733--610757 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
610723 ACTGAAGCAA
610733 TGTATCGATACAT
1 TGTATCGATACAT
610746 TGTATCGATACA
1 TGTATCGATACA
610758 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:613770 original size:433 final size:433
Alignment explanation
Indices: 612964--613834 Score: 1715
Period size: 433 Copynumber: 2.0 Consensus size: 433
612954 AGGAGACTCG
612964 GTTGTACTCGCTTGGGCCGAGAGCACAAAACAACGTGTGCATTGCCTTCGCATTGAGTTGTGCCA
1 GTTGTACTCGCTTGGGCCGAGAGCACAAAACAACGTGTGCATTGCCTTCGCATTGAGTTGTGCCA
613029 TCTTCATGTCTTGCTCGTTCCATTCTTCTTCTTCTTTTGGCACAACAACATCACCAACTCTCTTT
66 TCTTCATGTCTTGCTCGTTCCATTCTTCTTCTTCTTTTGGCACAACAACATCACCAACTCTCTTT
613094 GAGGGGATTCGAGGTCCATTGACAATGATCTTCCAAACTTCATAATCATTGGCTTGTATGAACAA
131 GAGGGGATTCGAGGTCCATTGACAATGATCTTCCAAACTTCATAATCATTGGCTTGTATGAACAA
613159 TCTCATTCTTGTTCTCCAATATGAATAATTTTCACCATTGAAGAGTGGAGGTCTCAAGGTGGAGT
196 TCTCATTCTTGTTCTCCAATATGAATAATTTTCACCATTGAAGAGTGGAGGTCTCAAGGTGGAGT
613224 GGCCCTCTACACCAATGGCATTTGAATGAGTCTCGAAGGCCATGAGACATACTTCTTCTTGGCTC
261 GGCCCTCTACACCAATGGCATTTGAATGAGTCTCGAAGGCCATGAGACATACTTCTTCTTGGCTC
613289 GCCATTTGTTGTGAAGCTTTAACCATTGCTACATTTTCCATTTTTGAGCTGAGAAAGATCGTCTC
326 GCCATTTGTTGTGAAGCTTTAACCATTGCTACATTTTCCATTTTTGAGCTGAGAAAGATCGTCTC
613354 TTCCGGGTGTTAATCCGATGAAGGAGGTTAGGCTCTGATACCA
391 TTCCGGGTGTTAATCCGATGAAGGAGGTTAGGCTCTGATACCA
*
613397 GTTGTACTCGCTTGGGCCGAGAGCACAAAACAACGTGTGCATTGCCTTCGCGTTGAGTTGTGCCA
1 GTTGTACTCGCTTGGGCCGAGAGCACAAAACAACGTGTGCATTGCCTTCGCATTGAGTTGTGCCA
613462 TCTTCATGTCTTGCTCGTTCCATTCTTCTTCTTCTTTTGGCACAACAACATCACCAACTCTCTTT
66 TCTTCATGTCTTGCTCGTTCCATTCTTCTTCTTCTTTTGGCACAACAACATCACCAACTCTCTTT
613527 GAGGGGATTCGAGGTCCATTGACAATGATCTTCCAAACTTCATAATCATTGGCTTGTATGAACAA
131 GAGGGGATTCGAGGTCCATTGACAATGATCTTCCAAACTTCATAATCATTGGCTTGTATGAACAA
613592 TCTCATTCTTGTTCTCCAATATGAATAATTTTCACCATTGAAGAGTGGAGGTCTCAAGGTGGAGT
196 TCTCATTCTTGTTCTCCAATATGAATAATTTTCACCATTGAAGAGTGGAGGTCTCAAGGTGGAGT
613657 GGCCCTCTACACCAATGGCATTTGAATGAGTCTCGAAGGCCATGAGACATACTTCTTCTTGGCTC
261 GGCCCTCTACACCAATGGCATTTGAATGAGTCTCGAAGGCCATGAGACATACTTCTTCTTGGCTC
*
613722 GCCATTTGTTGTGAAGCTTTAACCATTGCTACGTTTTCCATTTTTGAGCTGAGAAAGATCGTCTC
326 GCCATTTGTTGTGAAGCTTTAACCATTGCTACATTTTCCATTTTTGAGCTGAGAAAGATCGTCTC
613787 TTCCGGGTGTTAATCCGATGAAGGAGGTTAGGCTCTGATACCA
391 TTCCGGGTGTTAATCCGATGAAGGAGGTTAGGCTCTGATACCA
*
613830 ATTGT
1 GTTGT
613835 GAGCTCAAAA
Statistics
Matches: 435, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
433 435 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (433 bp):
GTTGTACTCGCTTGGGCCGAGAGCACAAAACAACGTGTGCATTGCCTTCGCATTGAGTTGTGCCA
TCTTCATGTCTTGCTCGTTCCATTCTTCTTCTTCTTTTGGCACAACAACATCACCAACTCTCTTT
GAGGGGATTCGAGGTCCATTGACAATGATCTTCCAAACTTCATAATCATTGGCTTGTATGAACAA
TCTCATTCTTGTTCTCCAATATGAATAATTTTCACCATTGAAGAGTGGAGGTCTCAAGGTGGAGT
GGCCCTCTACACCAATGGCATTTGAATGAGTCTCGAAGGCCATGAGACATACTTCTTCTTGGCTC
GCCATTTGTTGTGAAGCTTTAACCATTGCTACATTTTCCATTTTTGAGCTGAGAAAGATCGTCTC
TTCCGGGTGTTAATCCGATGAAGGAGGTTAGGCTCTGATACCA
Found at i:614119 original size:34 final size:35
Alignment explanation
Indices: 614081--614147 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
614071 CCTTACAACA
614081 CTATC-TTTC-AAGGCTAAGATAGAAGCCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAGAA-CCTCTCTCT
614115 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
614148 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 10 0.33
37 15 0.50
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:614636 original size:13 final size:13
Alignment explanation
Indices: 614617--614655 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
614607 ACTATTTATG
614617 ATGTATCGATACA
1 ATGTATCGATACA
*
614630 CTGTATCGATACA
1 ATGTATCGATACA
*
614643 ATGTAGCGATACA
1 ATGTATCGATACA
614656 TAAATAGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:614745 original size:21 final size:21
Alignment explanation
Indices: 614719--614759 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
614709 AGTGTGAACA
614719 GTGATGTAACGATACATGAAG
1 GTGATGTAACGATACATGAAG
*
614740 GTGATGTATCGATACATGAA
1 GTGATGTAACGATACATGAA
614760 CAGTGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (21 bp):
GTGATGTAACGATACATGAAG
Found at i:614774 original size:10 final size:10
Alignment explanation
Indices: 614755--614785 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
614745 GTATCGATAC
*
614755 ATGAACAGTG
1 ATGAATAGTG
614765 ATGAATAGTG
1 ATGAATAGTG
614775 ATGAATAGTG
1 ATGAATAGTG
614785 A
1 A
614786 AAATGAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:614873 original size:53 final size:53
Alignment explanation
Indices: 614809--614945 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
614799 CTACTACCAA
614809 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
614862 TGTATCGATACATATTGTGTGTAGCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
614915 TCTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
614946 TATGCAATCT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 65 0.84
54 12 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:614978 original size:20 final size:20
Alignment explanation
Indices: 614933--614986 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
614923 TACATATTTG
*
614933 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATGAAA
* *
614953 TCTGTATCGATAC-ATTTAAA
1 TGTGTATCGATACTA-TGAAA
614973 TGTGTATCGATACT
1 TGTGTATCGATACT
614987 TTTCAGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTGTATCGATACTATGAAA
Done.