Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold198
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: 3915534
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 240068 characters in sequence are not A, C, G, or T
File 11 of 13
Found at i:3081703 original size:43 final size:43
Alignment explanation
Indices: 3081656--3081918 Score: 306
Period size: 43 Copynumber: 6.3 Consensus size: 43
3081646 GATATGTTTT
**
3081656 TAGCGGCGTTTGTGTAAAAAGCGTTGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * *
3081699 TAGCGGCGTTTGTAG-AGAAAGTGCCGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGT-GTAAAAAGCGCCGCTAAAGGTCTTGATCTA
** * *
3081742 TAGCGGCGTTTGTGTGGAAAGCGCCGCTAAAGATATTGATCTA
1 TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * *
3081785 TAGCGGCGTTTGTGTGAAAAGCACCGCTAAAGGTATTG----A
1 TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * *
3081824 T--CGGCGTTTGTGGAAAAATCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
* * *
3081865 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGATCTA
1 TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
3081908 TAGCGGCGTTT
1 TAGCGGCGTTT
3081919 ATATAAATAA
Statistics
Matches: 190, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
37 29 0.15
39 2 0.01
41 2 0.01
42 1 0.01
43 155 0.82
44 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTGTGTAAAAAGCGCCGCTAAAGGTCTTGATCTA
Found at i:3082521 original size:34 final size:34
Alignment explanation
Indices: 3082469--3082547 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
3082459 TTTTGTATAA
*
3082469 ATAAGTTAGAACACCATATGAAGTCTGTACAATGAT
1 ATAA-TTA-AACACCATATGAAGTATGTACAATGAT
3082505 ATAATTAAACACCATATGAAGTATGTACAATGAT
1 ATAATTAAACACCATATGAAGTATGTACAATGAT
3082539 ATAATTAAA
1 ATAATTAAA
3082548 TTTTTGTGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
34 35 0.83
35 3 0.07
36 4 0.10
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (34 bp):
ATAATTAAACACCATATGAAGTATGTACAATGAT
Found at i:3085430 original size:12 final size:12
Alignment explanation
Indices: 3085415--3085452 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
3085405 TGCAGTGAAA
3085415 TAGACCATTGGT
1 TAGACCATTGGT
3085427 TAGACCATTGGT
1 TAGACCATTGGT
3085439 TAGACCATTGGT
1 TAGACCATTGGT
3085451 TA
1 TA
3085453 ATTAGACCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (12 bp):
TAGACCATTGGT
Found at i:3085459 original size:16 final size:16
Alignment explanation
Indices: 3085438--3085469 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3085428 AGACCATTGG
3085438 TTAGACCATTGGTTAA
1 TTAGACCATTGGTTAA
3085454 TTAGACCATTGGTTAA
1 TTAGACCATTGGTTAA
3085470 GTTGGTAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (16 bp):
TTAGACCATTGGTTAA
Found at i:3086479 original size:50 final size:50
Alignment explanation
Indices: 3086404--3086575 Score: 290
Period size: 50 Copynumber: 3.4 Consensus size: 50
3086394 CATTTGGGTA
3086404 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* *
3086454 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* ** *
3086504 GAGAGGTCCCCCGTAACACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
3086554 AAGAGGTCCCATGTAAGACCAT
1 AAGAGGTCCCATGTAAGACCAT
3086576 ATCTAGGATA
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 110 1.00
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:3090805 original size:495 final size:495
Alignment explanation
Indices: 3089875--3090865 Score: 1982
Period size: 495 Copynumber: 2.0 Consensus size: 495
3089865 GTCCATAAAT
3089875 GCGGCAGGTGCATTCGTCAACCCAAATGGCATGACAAGAAACTTGAAATGCCCTTAACGAGTCCT
1 GCGGCAGGTGCATTCGTCAACCCAAATGGCATGACAAGAAACTTGAAATGCCCTTAACGAGTCCT
3089940 AAAAGTCGTCTTCATAACATCGACATCCTTCACCTTCAACTGATAGTACCCAGACCTAAATCTAT
66 AAAAGTCGTCTTCATAACATCGACATCCTTCACCTTCAACTGATAGTACCCAGACCTAAATCTAT
3090005 CTTCGAGAAAATTAAATCTCTCCGAAACTAGTCAAACAAATCATCGATCCTTGGAAGTGGATACT
131 CTTCGAGAAAATTAAATCTCTCCGAAACTAGTCAAACAAATCATCGATCCTTGGAAGTGGATACT
3090070 TATTCTTAATGGTCAACTTATTCAGCTAGCGATAATCAATGCACAGCCTCAAAGTCCCATCCTTC
196 TATTCTTAATGGTCAACTTATTCAGCTAGCGATAATCAATGCACAGCCTCAAAGTCCCATCCTTC
3090135 TTCTTCACAAATAGAATTGGCACTTGCTACGATGACAGACTCGGTCGAATAAACCCTAGTCAGCA
261 TTCTTCACAAATAGAATTGGCACTTGCTACGATGACAGACTCGGTCGAATAAACCCTAGTCAGCA
3090200 ACTCTTGCAACTGAAGCTTCAAATCTTTCAATTCCTTAGGTTCCATACGATAGAGCGCAATTGAC
326 ACTCTTGCAACTGAAGCTTCAAATCTTTCAATTCCTTAGGTTCCATACGATAGAGCGCAATTGAC
3090265 ACCGGACTGTATCGGGATAGAGCTCAATACCGAACTCAACTTTTCTATCCAGTGGTAAACCAGAA
391 ACCGGACTGTATCGGGATAGAGCTCAATACCGAACTCAACTTTTCTATCCAGTGGTAAACCAGAA
3090330 AACTCCTCAGGAAACACATCTGGAAAGTCACAAACAGCTC
456 AACTCCTCAGGAAACACATCTGGAAAGTCACAAACAGCTC
3090370 GCGGCAGGTGCATTCGTCAACCCAAATGGCATGACAAGAAACTTGAAATGCCCTTAACGAGTCCT
1 GCGGCAGGTGCATTCGTCAACCCAAATGGCATGACAAGAAACTTGAAATGCCCTTAACGAGTCCT
3090435 AAAAGTCGTCTTCATAACATCGACATCCTTCACCTTCAACTGATAGTACCCAGACCTAAATCTAT
66 AAAAGTCGTCTTCATAACATCGACATCCTTCACCTTCAACTGATAGTACCCAGACCTAAATCTAT
3090500 CTTCGAGAAAATTAAATCTCTCCGAAACTAGTCAAACAAATCATCGATCCTTGGAAGTGGATACT
131 CTTCGAGAAAATTAAATCTCTCCGAAACTAGTCAAACAAATCATCGATCCTTGGAAGTGGATACT
3090565 TATTCTTAATGGTCAACTTATTCAGCTAGCGATAATCAATGCACAGCCTCAAAGTCCCATCCTTC
196 TATTCTTAATGGTCAACTTATTCAGCTAGCGATAATCAATGCACAGCCTCAAAGTCCCATCCTTC
3090630 TTCTTCACAAATAGAATTGGCACTTGCTACGATGACAGACTCGGTCGAATAAACCCTAGTCAGCA
261 TTCTTCACAAATAGAATTGGCACTTGCTACGATGACAGACTCGGTCGAATAAACCCTAGTCAGCA
3090695 ACTCTTGCAACTGAAGCTTCAAATCTTTCAATTCCTTAGGTTCCATACGATAGAGCGCAATTGAC
326 ACTCTTGCAACTGAAGCTTCAAATCTTTCAATTCCTTAGGTTCCATACGATAGAGCGCAATTGAC
3090760 ACCGGACTGTATCGGGATAGAGCTCAATACCGAACTCAACTTTTCTATCCAGTGGTAAACCAGAA
391 ACCGGACTGTATCGGGATAGAGCTCAATACCGAACTCAACTTTTCTATCCAGTGGTAAACCAGAA
3090825 AACTCCTCAGGAAACACATCTGGAAAGTCACAAACAGCTC
456 AACTCCTCAGGAAACACATCTGGAAAGTCACAAACAGCTC
3090865 G
1 G
3090866 AATCTCATCC
Statistics
Matches: 496, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
495 496 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (495 bp):
GCGGCAGGTGCATTCGTCAACCCAAATGGCATGACAAGAAACTTGAAATGCCCTTAACGAGTCCT
AAAAGTCGTCTTCATAACATCGACATCCTTCACCTTCAACTGATAGTACCCAGACCTAAATCTAT
CTTCGAGAAAATTAAATCTCTCCGAAACTAGTCAAACAAATCATCGATCCTTGGAAGTGGATACT
TATTCTTAATGGTCAACTTATTCAGCTAGCGATAATCAATGCACAGCCTCAAAGTCCCATCCTTC
TTCTTCACAAATAGAATTGGCACTTGCTACGATGACAGACTCGGTCGAATAAACCCTAGTCAGCA
ACTCTTGCAACTGAAGCTTCAAATCTTTCAATTCCTTAGGTTCCATACGATAGAGCGCAATTGAC
ACCGGACTGTATCGGGATAGAGCTCAATACCGAACTCAACTTTTCTATCCAGTGGTAAACCAGAA
AACTCCTCAGGAAACACATCTGGAAAGTCACAAACAGCTC
Found at i:3095611 original size:44 final size:45
Alignment explanation
Indices: 3095554--3095643 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 45
3095544 AATAATAACA
3095554 GATACACGATGGAATCAGCACATAGCAACCACC-TTATAATCAAT
1 GATACACGATGGAATCAGCACATAGCAACCACCTTTATAATCAAT
* * *
3095598 GATACTCGGTGGAATCAGCACATAGCAACCACCTTTATAGTCAAT
1 GATACACGATGGAATCAGCACATAGCAACCACCTTTATAATCAAT
3095643 G
1 G
3095644 GTACCCAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 31 0.74
45 11 0.26
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (45 bp):
GATACACGATGGAATCAGCACATAGCAACCACCTTTATAATCAAT
Found at i:3095716 original size:51 final size:51
Alignment explanation
Indices: 3095658--3095842 Score: 203
Period size: 51 Copynumber: 3.6 Consensus size: 51
3095648 CCAGTTCACA
* * *
3095658 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATTTTCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCCATTAT-ATCCGGTACACG
* * *** * * *
3095709 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCCATTATATCCGGTACACG
* * *
3095760 TAGTAGCTTGCACATAGTACTACACATGCGACCCATTAT-TCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCCATTATATCCGGTACACG
* *
3095810 TAGTAGCCTACACATAGTACTACACACATGACC
1 TAGTAGCCTGCACATAGTACTACACACGTGACC
3095843 ATCACTTTCA
Statistics
Matches: 108, Mismatches: 25, Indels: 3
0.79 0.18 0.02
Matches are distributed among these distances:
50 36 0.33
51 69 0.64
52 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCCATTATATCCGGTACACG
Found at i:3095864 original size:101 final size:99
Alignment explanation
Indices: 3095655--3095840 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 99
3095645 TACCCAGTTC
* * *
3095655 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTTTCATCCGATACACGTAGTAGCCTGC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACCATTAT-ATCCGATACACGTAGTAGCCTAC
* *
3095720 ACATAGTACTACACACGTGATCGAAGCTATCTGGT
65 ACATAGTACTACACACATGATCCAAGCTATCTGGT
* *
3095755 ACGCATAGTAGCTTGCACATAGTACTACACATGCGACCCATTAT-TCCGGTACACGTAGTAGCCT
1 A--CATAGTAGCCTGCACATAGTACTACACATGCGA-CCATTATATCCGATACACGTAGTAGCCT
3095819 ACACATAGTACTACACACATGA
63 ACACATAGTACTACACACATGA
3095841 CCATCACTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
100 1 0.01
101 39 0.51
102 31 0.40
103 6 0.08
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (99 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCGACCATTATATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACATGATCCAAGCTATCTGGT
Found at i:3100731 original size:50 final size:48
Alignment explanation
Indices: 3100692--3100829 Score: 141
Period size: 50 Copynumber: 2.8 Consensus size: 48
3100682 TATTGAGCTT
*
3100692 ATGAGAGGTCCCATGTAAGACCATGCCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGCCTGGGACATGGCATT-G-ACCGAG
* * * *
3100742 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGCCTGGGACATGGCAT-TG-ACCGAG
** * * * *
3100792 ATGAGAACTCCCATGTAAGACTATGTCTAGGACATGGC
1 ATGAGAGGTCCCACGTAAGACCATGCCTGGGACATGGC
3100830 TTTGGCATGT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.20
Consensus pattern (48 bp):
ATGAGAGGTCCCACGTAAGACCATGCCTGGGACATGGCATTGACCGAG
Found at i:3101088 original size:12 final size:12
Alignment explanation
Indices: 3101071--3101103 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3101061 GCAAGAGAGT
3101071 AAGTAAAGAAGA
1 AAGTAAAGAAGA
3101083 AAGTAAAGAAGA
1 AAGTAAAGAAGA
3101095 AAGTAAAGA
1 AAGTAAAGA
3101104 TCATGATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (12 bp):
AAGTAAAGAAGA
Found at i:3107904 original size:54 final size:54
Alignment explanation
Indices: 3107840--3107946 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
3107830 ATAAGAAACA
3107840 TGAAATTTGATAAAGAACACGAATCTAAATCATTGCTCTAAGCTACCTTACCGG
1 TGAAATTTGATAAAGAACACGAATCTAAATCATTGCTCTAAGCTACCTTACCGG
3107894 TGAAATTTGATAAAGAACACGAATCTAAATCATTGCTCTAAGCTACCTTACCG
1 TGAAATTTGATAAAGAACACGAATCTAAATCATTGCTCTAAGCTACCTTACCG
3107947 ATGTTCCACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (54 bp):
TGAAATTTGATAAAGAACACGAATCTAAATCATTGCTCTAAGCTACCTTACCGG
Found at i:3118382 original size:29 final size:29
Alignment explanation
Indices: 3118357--3118477 Score: 147
Period size: 29 Copynumber: 4.2 Consensus size: 29
3118347 ACCATCCCAA
3118357 TTCATATTCGATAGTCAAAGCTATCCCTT
1 TTCATATTCGATAGTCAAAGCTATCCCTT
* ** * *
3118386 TTCATAGTT-GATGGTCGTCA-CCATCCTTT
1 TTCATA-TTCGATAGTC-AAAGCTATCCCTT
* *
3118415 TTCATAATCGATAGCCAAAGCTATCCCTT
1 TTCATATTCGATAGTCAAAGCTATCCCTT
3118444 TTCATATTCGATAGTCAAAGCTATCCCTT
1 TTCATATTCGATAGTCAAAGCTATCCCTT
3118473 TTCAT
1 TTCAT
3118478 TATCTGAGGA
Statistics
Matches: 74, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
28 2 0.03
29 69 0.93
30 3 0.04
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.38
Consensus pattern (29 bp):
TTCATATTCGATAGTCAAAGCTATCCCTT
Found at i:3121401 original size:51 final size:48
Alignment explanation
Indices: 3121325--3121424 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 48
3121315 ACCTTGATAT
*
3121325 ACATTATGTTTAGAACTAATGACCAATTTTGGTTGTTGTTTATGTAATTTA
1 ACATTATGCTTAGAACTAATGACCAATTTT-G--GTTGTTTATGTAATTTA
*
3121376 ACATTATGCTTGGAACTAATGACCAATTTTGGTTGTTTATGTAATTTA
1 ACATTATGCTTAGAACTAATGACCAATTTTGGTTGTTTATGTAATTTA
3121424 A
1 A
3121425 TTTAACTTAG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 18 0.38
50 1 0.02
51 28 0.60
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (48 bp):
ACATTATGCTTAGAACTAATGACCAATTTTGGTTGTTTATGTAATTTA
Found at i:3124599 original size:39 final size:39
Alignment explanation
Indices: 3124540--3124616 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
3124530 ATTCTAAATG
* *
3124540 AAAATGAAATAAATGAAATAGAAATAGATAAATAATATA
1 AAAAGGAAATAAATAAAATAGAAATAGATAAATAATATA
* *
3124579 AAAAGGAAATAAATAAAATAGAAATATATCAATAATAT
1 AAAAGGAAATAAATAAAATAGAAATAGATAAATAATAT
3124617 TAATATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.23
Consensus pattern (39 bp):
AAAAGGAAATAAATAAAATAGAAATAGATAAATAATATA
Found at i:3124602 original size:15 final size:15
Alignment explanation
Indices: 3124534--3124604 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
3124524 ATCAAAATTC
3124534 TAAATGAAAAT-GAAA
1 TAAAT-AAAATAGAAA
*
3124549 TAAATGAAATAGAAA
1 TAAATAAAATAGAAA
*
3124564 TAGAT-AAAT---AA
1 TAAATAAAATAGAAA
3124575 T--ATAAAA-AGGAAA
1 TAAATAAAATA-GAAA
3124588 TAAATAAAATAGAAA
1 TAAATAAAATAGAAA
3124603 TA
1 TA
3124605 TATCAATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 18
0.69 0.03 0.28
Matches are distributed among these distances:
9 2 0.04
10 3 0.07
11 3 0.07
13 3 0.07
14 8 0.18
15 25 0.56
16 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (15 bp):
TAAATAAAATAGAAA
Found at i:3124624 original size:11 final size:11
Alignment explanation
Indices: 3124610--3124679 Score: 62
Period size: 11 Copynumber: 6.7 Consensus size: 11
3124600 AAATATATCA
3124610 ATAATATTAAT
1 ATAATATTAAT
3124621 ATAATATTAAT
1 ATAATATTAAT
3124632 ATAATAATCTAAT
1 ATAAT-AT-TAAT
*
3124645 ATATTA-TAA-
1 ATAATATTAAT
*
3124654 ATAA-AAT-AT
1 ATAATATTAAT
3124663 ATAA-ATTAAT
1 ATAATATTAAT
3124673 -TAATATT
1 ATAATATT
3124680 CTAACATCTA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
8 2 0.04
9 13 0.26
10 8 0.16
11 16 0.32
12 3 0.06
13 8 0.16
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (11 bp):
ATAATATTAAT
Found at i:3124656 original size:24 final size:23
Alignment explanation
Indices: 3124610--3124661 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
3124600 AAATATATCA
*
3124610 ATAAT-ATTAATATAATATTAAT
1 ATAATAATTAATATAATATAAAT
*
3124632 ATAATAATCTAATATATTATAAAT
1 ATAATAAT-TAATATAATATAAAT
*
3124656 AAAATA
1 ATAATA
3124662 TATAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.20
23 2 0.08
24 18 0.72
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAATAATTAATATAATATAAAT
Found at i:3125697 original size:23 final size:23
Alignment explanation
Indices: 3125671--3125716 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3125661 ATTTTGTGAG
3125671 GCATTTGTTTCCAAAATTAATTT
1 GCATTTGTTTCCAAAATTAATTT
3125694 GCATTTGTTTCCAAAATTAATTT
1 GCATTTGTTTCCAAAATTAATTT
3125717 ATCTCCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (23 bp):
GCATTTGTTTCCAAAATTAATTT
Found at i:3126659 original size:41 final size:41
Alignment explanation
Indices: 3126614--3126695 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
3126604 TATTGAAAAA
* *
3126614 TTTTCAATTTAATATTACAATATCTAAAGCTATTTTGCCAT
1 TTTTCAATTTAATACTACAATATCTAAAGCTATTTTACCAT
* *
3126655 TTTTCAATTTAATACTACAATATTTAAGGCTATTTTACCAT
1 TTTTCAATTTAATACTACAATATCTAAAGCTATTTTACCAT
3126696 AATTTTAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (41 bp):
TTTTCAATTTAATACTACAATATCTAAAGCTATTTTACCAT
Found at i:3127460 original size:100 final size:100
Alignment explanation
Indices: 3127338--3127538 Score: 368
Period size: 100 Copynumber: 2.0 Consensus size: 100
3127328 CAAAAATTAC
*
3127338 AGTTTAGCGCCTCTGAATAAGGAAATCTGAGTTCTACTCAAAACCC-ATTATTGCCATAAGAACC
1 AGTTTAGCACCTCTGAATAAGGAAATCTGAGTTCTACTCAAAACCCGA-TATTGCCATAAGAACC
3127402 ACTATAACCGATACACAATGAACAACATATCTGAAT
65 ACTATAACCGATACACAATGAACAACATATCTGAAT
*
3127438 AGTTTAGCACCTCTGAATAAGGAAATCTGAGTTCTACTCAAAACCCGATATTGCCATAATAACCA
1 AGTTTAGCACCTCTGAATAAGGAAATCTGAGTTCTACTCAAAACCCGATATTGCCATAAGAACCA
3127503 CTATAACCGATACACAATGAACAACATATCTGAAT
66 CTATAACCGATACACAATGAACAACATATCTGAAT
3127538 A
1 A
3127539 CTTTCATCTT
Statistics
Matches: 98, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
100 97 0.99
101 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (100 bp):
AGTTTAGCACCTCTGAATAAGGAAATCTGAGTTCTACTCAAAACCCGATATTGCCATAAGAACCA
CTATAACCGATACACAATGAACAACATATCTGAAT
Found at i:3132798 original size:35 final size:35
Alignment explanation
Indices: 3132752--3132852 Score: 157
Period size: 35 Copynumber: 2.9 Consensus size: 35
3132742 CTGTTTGGCT
3132752 TGTTTCGGTTGGACTAGCTCTTATGAGCATTGACC
1 TGTTTCGGTTGGACTAGCTCTTATGAGCATTGACC
* * *
3132787 TGTTTCTGTTGGACTAGCTCTTATGAGCATTGGCG
1 TGTTTCGGTTGGACTAGCTCTTATGAGCATTGACC
* *
3132822 TGTTTCGGTTAGACTAGCTCTTGTGAGCATT
1 TGTTTCGGTTGGACTAGCTCTTATGAGCATT
3132853 TGATGTGTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.16, C:0.18, G:0.27, T:0.40
Consensus pattern (35 bp):
TGTTTCGGTTGGACTAGCTCTTATGAGCATTGACC
Found at i:3136520 original size:33 final size:34
Alignment explanation
Indices: 3136472--3136540 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
3136462 AGTAGTCATG
* *
3136472 CAGTATCAGTCTGGGCCTGAGCCCTATACAGTAA
1 CAGTATCAGTCTGGGCCTGAGCCCAAAACAGTAA
* *
3136506 CAGTA-CAGTGTGGGCCTTAGCCCAAAACAGTAA
1 CAGTATCAGTCTGGGCCTGAGCCCAAAACAGTAA
3136539 CA
1 CA
3136541 ATGTGGCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.20
Consensus pattern (34 bp):
CAGTATCAGTCTGGGCCTGAGCCCAAAACAGTAA
Found at i:3136584 original size:28 final size:28
Alignment explanation
Indices: 3136512--3136635 Score: 178
Period size: 28 Copynumber: 4.5 Consensus size: 28
3136502 GTAACAGTAC
* *
3136512 AGTGTGGGCCTTAGCCCAAAACAGTAAC
1 AGTGTGGGCCTTAGCCCAATACAGTAAT
* * *
3136540 AATGT-GGCCTTAACCCAATACAATAAT
1 AGTGTGGGCCTTAGCCCAATACAGTAAT
*
3136567 AGTGTGGGCCTTAGCCCAATGCAGTAAT
1 AGTGTGGGCCTTAGCCCAATACAGTAAT
*
3136595 AGTGTGGGCCTTAGCCCACTACAGTAAT
1 AGTGTGGGCCTTAGCCCAATACAGTAAT
3136623 AGTGTGGGCCTTA
1 AGTGTGGGCCTTA
3136636 TATACCAATG
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 22 0.26
28 62 0.74
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (28 bp):
AGTGTGGGCCTTAGCCCAATACAGTAAT
Found at i:3137630 original size:40 final size:40
Alignment explanation
Indices: 3137459--3137657 Score: 249
Period size: 40 Copynumber: 5.0 Consensus size: 40
3137449 AATTATTGAA
* ** *
3137459 TGTTTGCACATTCGTGCCCCTATTCGTACTTCAATACACC
1 TGTTTGCACATTCGTGCCCCTGTTCGTACTTCGGTACCCC
*
3137499 TGTTTACACATTCGTGCCCCTGTTCGTACTTCGGTACCCC
1 TGTTTGCACATTCGTGCCCCTGTTCGTACTTCGGTACCCC
* * *
3137539 TGTTTGCACATTTGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGTTTGCACATTCGTGCCCCTGTTCGTACTTCGGTACCCC
* * * *
3137579 TATTTGTACATACATGCCCCTGTTCGTACTTCGGTACCCC
1 TGTTTGCACATTCGTGCCCCTGTTCGTACTTCGGTACCCC
* * *
3137619 TGTTTGCACATACGT--ACCTGTTTGTACTTCGGTACCCC
1 TGTTTGCACATTCGTGCCCCTGTTCGTACTTCGGTACCCC
3137657 T
1 T
3137658 AAAATCTAAT
Statistics
Matches: 138, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
38 22 0.16
40 116 0.84
ACGTcount: A:0.15, C:0.31, G:0.17, T:0.37
Consensus pattern (40 bp):
TGTTTGCACATTCGTGCCCCTGTTCGTACTTCGGTACCCC
Found at i:3137635 original size:20 final size:20
Alignment explanation
Indices: 3137459--3137657 Score: 122
Period size: 20 Copynumber: 10.1 Consensus size: 20
3137449 AATTATTGAA
* *
3137459 TGTTTGCACATTCGTGCCCC
1 TGTTTGTACATTCGTACCCC
* * * *
3137479 TATTCGTAC-TTCAATACACC
1 TGTTTGTACATTC-GTACCCC
** *
3137499 TGTTTACACATTCGTGCCCC
1 TGTTTGTACATTCGTACCCC
*
3137519 TGTTCGTAC-TTCGGTACCCC
1 TGTTTGTACATTC-GTACCCC
* * *
3137539 TGTTTGCACATTTGTGCCCC
1 TGTTTGTACATTCGTACCCC
* *
3137559 TGTTTGTACTTTGGTACCCC
1 TGTTTGTACATTCGTACCCC
* * * *
3137579 TATTTGTACATACATGCCCC
1 TGTTTGTACATTCGTACCCC
*
3137599 TGTTCGTAC-TTCGGTACCCC
1 TGTTTGTACATTC-GTACCCC
* *
3137619 TGTTTGCACATACGTA--CC
1 TGTTTGTACATTCGTACCCC
3137637 TGTTTGTAC-TTCGGTACCCC
1 TGTTTGTACATTC-GTACCCC
3137657 T
1 T
3137658 AAAATCTAAT
Statistics
Matches: 129, Mismatches: 41, Indels: 18
0.69 0.22 0.10
Matches are distributed among these distances:
17 2 0.02
18 13 0.10
19 8 0.06
20 99 0.77
21 7 0.05
ACGTcount: A:0.15, C:0.31, G:0.17, T:0.37
Consensus pattern (20 bp):
TGTTTGTACATTCGTACCCC
Found at i:3137653 original size:18 final size:18
Alignment explanation
Indices: 3137597--3137654 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
3137587 CATACATGCC
*
3137597 CCTGTTCGTACTTCGGTA
1 CCTGTTTGTACTTCGGTA
* *
3137615 CCCCTGTTTGCACATAC-GTA
1 --CCTGTTTGTAC-TTCGGTA
3137635 CCTGTTTGTACTTCGGTA
1 CCTGTTTGTACTTCGGTA
3137653 CC
1 CC
3137655 CCTAAAATCT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 2 0.06
18 15 0.48
20 12 0.39
21 2 0.06
ACGTcount: A:0.14, C:0.31, G:0.19, T:0.36
Consensus pattern (18 bp):
CCTGTTTGTACTTCGGTA
Found at i:3145440 original size:11 final size:11
Alignment explanation
Indices: 3145403--3145440 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
3145393 TCCTTCATTC
3145403 ATCATCCCTCA
1 ATCATCCCTCA
*
3145414 AGCATCCCTCA
1 ATCATCCCTCA
3145425 ATCATCCCTCA
1 ATCATCCCTCA
*
3145436 TTCAT
1 ATCAT
3145441 TCTCATCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.26, C:0.42, G:0.03, T:0.29
Consensus pattern (11 bp):
ATCATCCCTCA
Found at i:3157684 original size:27 final size:27
Alignment explanation
Indices: 3157639--3157691 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3157629 GTAACAGAAC
* *
3157639 AGAACAATGTGGGATTTAGCCCAATAT
1 AGAACAAGGTGGGACTTAGCCCAATAT
* *
3157666 AGAACAAGGTGGGCCTTAGCCGAATA
1 AGAACAAGGTGGGACTTAGCCCAATA
3157692 CCATATCAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (27 bp):
AGAACAAGGTGGGACTTAGCCCAATAT
Found at i:3159021 original size:38 final size:42
Alignment explanation
Indices: 3158940--3159036 Score: 121
Period size: 43 Copynumber: 2.4 Consensus size: 42
3158930 ACAACCCAAG
* * *
3158940 TTTAAATTCTTTTTTCAATAAGCCAAGAGTATCTTCTCATCTT
1 TTTAAATTCTTTTTTCAACAACCCAAGAGTATCATCT-ATCTT
3158983 TTTAAATTCTTTTTTCAACAACCCAAGA-T-T-ATCT-TCTT
1 TTTAAATTCTTTTTTCAACAACCCAAGAGTATCATCTATCTT
*
3159021 TTTAAATTATTTTTTC
1 TTTAAATTCTTTTTTC
3159037 TAGGATAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
38 19 0.38
40 3 0.06
41 1 0.02
42 1 0.02
43 26 0.52
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.51
Consensus pattern (42 bp):
TTTAAATTCTTTTTTCAACAACCCAAGAGTATCATCTATCTT
Found at i:3164511 original size:21 final size:21
Alignment explanation
Indices: 3164486--3164539 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
3164476 CTTGTTGAGA
*
3164486 AGGAAGTTGCTACTGCAGAAG
1 AGGAAGTTGCTACTGAAGAAG
* *
3164507 AGGAAGTTGTTGCTGAAGAAG
1 AGGAAGTTGCTACTGAAGAAG
*
3164528 AAGAAGTTGCTA
1 AGGAAGTTGCTA
3164540 AAAATGAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.33, T:0.22
Consensus pattern (21 bp):
AGGAAGTTGCTACTGAAGAAG
Found at i:3164848 original size:17 final size:15
Alignment explanation
Indices: 3164826--3164859 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
3164816 ATAAAAAATG
3164826 AAAGAAGGAAGAGAAGA
1 AAAGAAGG-AG-GAAGA
3164843 AAAGAAGGAGGAAGA
1 AAAGAAGGAGGAAGA
3164858 AA
1 AA
3164860 CATCATGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 2 0.12
17 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AAAGAAGGAGGAAGA
Found at i:3168414 original size:10 final size:10
Alignment explanation
Indices: 3168399--3168436 Score: 58
Period size: 10 Copynumber: 3.6 Consensus size: 10
3168389 GAACATGATG
3168399 AATTTTAATT
1 AATTTTAATT
3168409 AATTTTATAGTT
1 AATTTTA-A-TT
3168421 AATTTTAATT
1 AATTTTAATT
3168431 AATTTT
1 AATTTT
3168437 GACTATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 2 0.08
12 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (10 bp):
AATTTTAATT
Found at i:3179893 original size:13 final size:13
Alignment explanation
Indices: 3179875--3179927 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
3179865 AGTTTAACAA
*
3179875 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
3179888 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
3179901 TGCTTTGGAGAAG
1 TGCTTTTGAAAAG
3179914 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
3179927 T
1 T
3179928 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:3179911 original size:26 final size:26
Alignment explanation
Indices: 3179875--3179927 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3179865 AGTTTAACAA
*
3179875 TGCTTTTGAGAAGTGCTTTTGAAAAG
1 TGCTTTGGAGAAGTGCTTTTGAAAAG
3179901 TGCTTTGGAGAAGTGCTTTTGAAAAG
1 TGCTTTGGAGAAGTGCTTTTGAAAAG
3179927 T
1 T
3179928 TTTGTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (26 bp):
TGCTTTGGAGAAGTGCTTTTGAAAAG
Found at i:3180107 original size:15 final size:15
Alignment explanation
Indices: 3180078--3180106 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3180068 TAAGAATATA
3180078 AAAAAATATTATTTT
1 AAAAAATATTATTTT
3180093 AAAAAATATT-TTTT
1 AAAAAATATTATTTT
3180107 TTACTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAAATATTATTTT
Found at i:3186769 original size:29 final size:29
Alignment explanation
Indices: 3186695--3186933 Score: 307
Period size: 29 Copynumber: 8.2 Consensus size: 29
3186685 GTGTGCTAAA
* * * *
3186695 CGATGGTCAAAACCATACCTTTTCTTTAAT
1 CGATGGTCGAAACCATCCCTTTTC-ATATT
*
3186725 CAATGGTCGAAACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
*
3186754 CGATGGTCGAAGCCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
**
3186783 CGATGGTCGTTACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* *
3186812 CGATGGTTGAAACCATCCCTTTTAATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
*
3186841 CGATGGTCAAAACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * *
3186870 CGATGGTCAAAATCATTCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
* * **
3186899 TGATGGTTGTCACCATCCCTTTTCATATT
1 CGATGGTCGAAACCATCCCTTTTCATATT
3186928 CGATGG
1 CGATGG
3186934 ACGTCGATAC
Statistics
Matches: 182, Mismatches: 27, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
29 161 0.88
30 21 0.12
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (29 bp):
CGATGGTCGAAACCATCCCTTTTCATATT
Found at i:3201604 original size:16 final size:17
Alignment explanation
Indices: 3201572--3201604 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3201562 ATTCAATTTA
3201572 TTACAAAATTCATACTT
1 TTACAAAATTCATACTT
3201589 TTACAAAATT-ATACTT
1 TTACAAAATTCATACTT
3201605 GTTCCCCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (17 bp):
TTACAAAATTCATACTT
Found at i:3212290 original size:25 final size:24
Alignment explanation
Indices: 3212256--3212305 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
3212246 TTAAGACGTC
*
3212256 ATCATTTCTTTTCTATTCTTAATTT
1 ATCATTTCTTTTCTACT-TTAATTT
*
3212281 ATCATTTCTTTTTTACTTTAATTT
1 ATCATTTCTTTTCTACTTTAATTT
3212305 A
1 A
3212306 GTTATTGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.64
Consensus pattern (24 bp):
ATCATTTCTTTTCTACTTTAATTT
Found at i:3229558 original size:137 final size:138
Alignment explanation
Indices: 3229311--3229578 Score: 319
Period size: 137 Copynumber: 1.9 Consensus size: 138
3229301 AATGGGCCTA
* * * * *
3229311 CTCACATAAGCTGTCGGTCAAAATGTAAGCTACACGATACTACTCACATAAGCTGTTGAGTATCC
1 CTCACACAAGCTGTCGGTCAAAACGTAAGCTACACGATACTACTCACACAAGCTGTCGAGTATAC
* * * *
3229376 ACAACTAATGCCGAACCTCATCCATCAGTAGGAAATTCTAGACCAGCACCCAAAACATGGTAACC
66 ACAACTAATGCCGAAACTCAGCCATCAGTAGGAAATTCAAGACCAGCACCCAAAACACGGTAACC
3229441 TGGGTCTT
131 TGGGTCTT
* * * * *
3229449 CTCACACAAGCTGTCGGTCGAAACGT-AGCTACACGGTGCTGCTCACACAAGCTGTCGAGTATAT
1 CTCACACAAGCTGTCGGTCAAAACGTAAGCTACACGATACTACTCACACAAGCTGTCGAGTATAC
* * **
3229513 GCAAC-ACATGTCGAAACTCAGCCATC-GCTAGGATGTT-AAGGACCAGCACCCAAAACACGGTA
66 ACAACTA-ATGCCGAAACTCAGCCATCAG-TAGGAAATTCAA-GACCAGCACCCAAAACACGGTA
3229575 ACCT
128 ACCT
3229579 TAATGACATG
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
136 3 0.03
137 83 0.76
138 23 0.21
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (138 bp):
CTCACACAAGCTGTCGGTCAAAACGTAAGCTACACGATACTACTCACACAAGCTGTCGAGTATAC
ACAACTAATGCCGAAACTCAGCCATCAGTAGGAAATTCAAGACCAGCACCCAAAACACGGTAACC
TGGGTCTT
Found at i:3232088 original size:75 final size:75
Alignment explanation
Indices: 3232004--3232229 Score: 452
Period size: 75 Copynumber: 3.0 Consensus size: 75
3231994 TTATTCTCAT
3232004 ACTTGCCATTGCATTTCCAAGTATTCATTAGCTTCATGTATTGTATACATCGCTATTCCTATTAC
1 ACTTGCCATTGCATTTCCAAGTATTCATTAGCTTCATGTATTGTATACATCGCTATTCCTATTAC
3232069 TTGCCACTGC
66 TTGCCACTGC
3232079 ACTTGCCATTGCATTTCCAAGTATTCATTAGCTTCATGTATTGTATACATCGCTATTCCTATTAC
1 ACTTGCCATTGCATTTCCAAGTATTCATTAGCTTCATGTATTGTATACATCGCTATTCCTATTAC
3232144 TTGCCACTGC
66 TTGCCACTGC
3232154 ACTTGCCATTGCATTTCCAAGTATTCATTAGCTTCATGTATTGTATACATCGCTATTCCTATTAC
1 ACTTGCCATTGCATTTCCAAGTATTCATTAGCTTCATGTATTGTATACATCGCTATTCCTATTAC
3232219 TTGCCACTGC
66 TTGCCACTGC
3232229 A
1 A
3232230 TACTTATCAT
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 151 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (75 bp):
ACTTGCCATTGCATTTCCAAGTATTCATTAGCTTCATGTATTGTATACATCGCTATTCCTATTAC
TTGCCACTGC
Found at i:3242403 original size:14 final size:15
Alignment explanation
Indices: 3242370--3242408 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
3242360 CAACACCTTT
*
3242370 TTTTTTTAGTTCACGA
1 TTTTTTTAATTCAC-A
3242386 TTTTTTTAATTCAC-
1 TTTTTTTAATTCACA
3242400 TTTTTTTAA
1 TTTTTTTAA
3242409 AATTTCGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
16 13 0.59
ACGTcount: A:0.21, C:0.10, G:0.05, T:0.64
Consensus pattern (15 bp):
TTTTTTTAATTCACA
Found at i:3242774 original size:23 final size:23
Alignment explanation
Indices: 3242748--3242915 Score: 191
Period size: 23 Copynumber: 7.3 Consensus size: 23
3242738 ATAAGTGCCA
**
3242748 CACTGATATGTAGCTAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3242771 CACTGATATGTAGCC-ATAGCTAC
1 CACTGATATGTAGCCGA-AGCTAC
* * *
3242794 CACTGAAATGCAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
3242817 TACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3242840 CACTGA-ATTGTAGCCGAAGCCAC
1 CACTGATA-TGTAGCCGAAGCTAC
3242863 CACTGACT-TGTAGCCGAAGCTAC
1 CACTGA-TATGTAGCCGAAGCTAC
*
3242886 CACCGA-ATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
3242909 CACTGAT
1 CACTGAT
3242916 CAATAACACT
Statistics
Matches: 122, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.02
23 119 0.98
24 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3243828 original size:23 final size:23
Alignment explanation
Indices: 3243763--3243836 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
3243753 GTTTAATTAG
** *
3243763 GAAATGGTTTTGGTTTTTGGTAA
1 GAAATGGAATTGGATTTTGGTAA
*
3243786 GAAATGGAATTGGATGTTGGTAA
1 GAAATGGAATTGGATTTTGGTAA
* *
3243809 GAAATGGTA-TGAGATTTTGGTAT
1 GAAATGGAATTG-GATTTTGGTAA
3243832 GAAAT
1 GAAAT
3243837 AAACCAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 2 0.05
23 41 0.95
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (23 bp):
GAAATGGAATTGGATTTTGGTAA
Found at i:3248142 original size:24 final size:23
Alignment explanation
Indices: 3248098--3248148 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
3248088 TTTTTTCAAA
*
3248098 TTTTCTTTCTTTTTCTCATTTTTC
1 TTTTCTTTCTTTTACTCA-TTTTC
*
3248122 TTTTCTTTGTTTTCACT-ATTTTC
1 TTTTCTTTCTTTT-ACTCATTTTC
3248145 TTTT
1 TTTT
3248149 TCTCTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 13 0.54
25 2 0.08
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTCTTTCTTTTACTCATTTTC
Found at i:3248143 original size:23 final size:21
Alignment explanation
Indices: 3248086--3248148 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 21
3248076 CTTTTCACTC
*
3248086 TCTTTTT-TCAAATTTTC-TT
1 TCTTTTTCTCATATTTTCTTT
3248105 TCTTTTTCTCAT-TTTTCTTT
1 TCTTTTTCTCATATTTTCTTT
*
3248125 TCTTTGTTTTCACTATTTTCTTT
1 TCTTT-TTCTCA-TATTTTCTTT
3248148 T
1 T
3248149 TCTCTCATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 12 0.32
20 10 0.27
21 5 0.14
22 1 0.03
23 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCATATTTTCTTT
Found at i:3249708 original size:16 final size:15
Alignment explanation
Indices: 3249664--3249705 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
3249654 ATCACAACAC
3249664 CTTTTTTTTAATTCA
1 CTTTTTTTTAATTCA
*
3249679 CGATTTTTTTAATTCA
1 C-TTTTTTTTAATTCA
3249695 CTTTTTTTTAA
1 CTTTTTTTTAA
3249706 ATTTCGTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.64
Consensus pattern (15 bp):
CTTTTTTTTAATTCA
Found at i:3250076 original size:23 final size:22
Alignment explanation
Indices: 3250050--3250171 Score: 147
Period size: 23 Copynumber: 5.3 Consensus size: 22
3250040 ATAAGTGCGA
*
3250050 CACTGATATGTAGCTGAAACTAC
1 CACTGATATGTAGC-GAAGCTAC
*
3250073 CACTGATATGTAGCCATAGCTAC
1 CACTGATATGTAGCGA-AGCTAC
*
3250096 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGC-GAAGCTAC
*
3250119 CACTGATATGTAGCCATAGCTAC
1 CACTGATATGTAGCGA-AGCTAC
3250142 CACTGA-ATTGTAGCCGAAGCTAC
1 CACTGATA-TGTAG-CGAAGCTAC
3250165 CACTGAT
1 CACTGAT
3250172 CAATAACACT
Statistics
Matches: 86, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
22 3 0.03
23 80 0.93
24 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (22 bp):
CACTGATATGTAGCGAAGCTAC
Found at i:3250119 original size:46 final size:46
Alignment explanation
Indices: 3250050--3250171 Score: 208
Period size: 46 Copynumber: 2.7 Consensus size: 46
3250040 ATAAGTGCGA
* *
3250050 CACTGATATGTAGCTGAAACTACCACTGATATGTAGCCATAGCTAC
1 CACTGAAATGTAGCTGAAGCTACCACTGATATGTAGCCATAGCTAC
3250096 CACTGAAATGTAGCTGAAGCTACCACTGATATGTAGCCATAGCTAC
1 CACTGAAATGTAGCTGAAGCTACCACTGATATGTAGCCATAGCTAC
* *
3250142 CACTGAATTGTAGCCGAAGCTACCACTGAT
1 CACTGAAATGTAGCTGAAGCTACCACTGAT
3250172 CAATAACACT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (46 bp):
CACTGAAATGTAGCTGAAGCTACCACTGATATGTAGCCATAGCTAC
Found at i:3251072 original size:23 final size:23
Alignment explanation
Indices: 3251007--3251080 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
3250997 GTTTAATTAG
** *
3251007 GAAATGGTTTTGGTTTTTGGTAA
1 GAAATGGAATTGGATTTTGGTAA
*
3251030 GAAATGGAATTGGATGTTGGTAA
1 GAAATGGAATTGGATTTTGGTAA
* *
3251053 GAAATGGTA-TGAGATTTTGGTAC
1 GAAATGGAATTG-GATTTTGGTAA
3251076 GAAAT
1 GAAAT
3251081 AAGCCAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 2 0.05
23 41 0.95
ACGTcount: A:0.31, C:0.01, G:0.31, T:0.36
Consensus pattern (23 bp):
GAAATGGAATTGGATTTTGGTAA
Found at i:3254781 original size:14 final size:13
Alignment explanation
Indices: 3254755--3254793 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
3254745 AACTTGAGCC
*
3254755 TTTATTTATTTTT
1 TTTATTTATTTTA
3254768 TTTCATTTCATTTTA
1 TTT-ATTT-ATTTTA
3254783 TTTATTTATTT
1 TTTATTTATTT
3254794 ACAAGCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.30
14 8 0.35
15 8 0.35
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:3256168 original size:49 final size:49
Alignment explanation
Indices: 3256107--3256227 Score: 147
Period size: 49 Copynumber: 2.5 Consensus size: 49
3256097 GGGCCATTTA
3256107 TAGGGCATGTTAGTTGCTAACCAGATGGGCGAATAAG-G-TGGGCCACTGG
1 TAGGGCATGTTAGTTGCTAACCAGATGGGC--ATAAGTGTTGGGCCACTGG
* * * * *
3256156 TAGGGCATGTTAGTTGCTAACTAGATTGGCATGAGTGTTGGGTCTCTGG
1 TAGGGCATGTTAGTTGCTAACCAGATGGGCATAAGTGTTGGGCCACTGG
* *
3256205 TGGGGCACGTTAGTTGCTAACCA
1 TAGGGCATGTTAGTTGCTAACCA
3256228 ACCTGGCATT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
47 4 0.06
48 1 0.02
49 57 0.92
ACGTcount: A:0.21, C:0.16, G:0.35, T:0.28
Consensus pattern (49 bp):
TAGGGCATGTTAGTTGCTAACCAGATGGGCATAAGTGTTGGGCCACTGG
Found at i:3261172 original size:50 final size:50
Alignment explanation
Indices: 3261117--3261286 Score: 187
Period size: 50 Copynumber: 3.3 Consensus size: 50
3261107 TCCTAAATAC
* * *
3261117 GGTCTTACATGAGAGTTCTCATATCGGTGCCAATGCCATGACCCAGACAT
1 GGTCTTACATGGGACTTCTCATATCGGTGCCAATGCCATGTCCCAGACAT
* * * * *
3261167 GGTCTTATAGGGGACTTCTCATCTCGGTACCAACGCCATGTCCCAGACAT
1 GGTCTTACATGGGACTTCTCATATCGGTGCCAATGCCATGTCCCAGACAT
* *
3261217 GGTCTTACATGGGACCTCTCATAACCTCAATAGTGCCAATGCCATGTCCCAGACAT
1 GGTCTTACATGGGACTTCTCAT-A--TC---GGTGCCAATGCCATGTCCCAGACAT
*
3261273 GGTATTACATGGGA
1 GGTCTTACATGGGA
3261287 TCTCATTCCC
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
50 61 0.62
53 2 0.02
56 35 0.36
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (50 bp):
GGTCTTACATGGGACTTCTCATATCGGTGCCAATGCCATGTCCCAGACAT
Found at i:3274455 original size:56 final size:51
Alignment explanation
Indices: 3274339--3274473 Score: 157
Period size: 50 Copynumber: 2.6 Consensus size: 51
3274329 AGTGCCCATG
** *
3274339 CCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGATAGCAATGT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAATAGCAATGT
*
3274390 -CATGTCCCAGACATGGTCTTGCATGGGACCTCTCATAACCTCAATAATGCCAAT-T
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CTCAAT-A-G-CAATGT
*
3274445 CCATGTCCCAGACATGATCTTACATGGGA
1 CCATGTCCCAGACATGGTCTTACATGGGA
3274474 TCTCATTCCC
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
50 33 0.46
53 5 0.07
54 1 0.01
55 2 0.03
56 30 0.42
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (51 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAATAGCAATGT
Found at i:3277358 original size:22 final size:22
Alignment explanation
Indices: 3277333--3277387 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
3277323 TCCTTCATTC
*
3277333 ATCATCCCTCAAGCACCCCTTA
1 ATCATCCCTCAAGCACCCCTCA
*
3277355 ATCATCCCTCAAGCATCCCTCA
1 ATCATCCCTCAAGCACCCCTCA
*
3277377 ATCATTCCTCA
1 ATCATCCCTCA
3277388 TACATACTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.27, C:0.44, G:0.04, T:0.25
Consensus pattern (22 bp):
ATCATCCCTCAAGCACCCCTCA
Found at i:3277363 original size:11 final size:11
Alignment explanation
Indices: 3277333--3277387 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
3277323 TCCTTCATTC
3277333 ATCATCCCTCA
1 ATCATCCCTCA
* * *
3277344 AGCACCCCTTA
1 ATCATCCCTCA
3277355 ATCATCCCTCA
1 ATCATCCCTCA
*
3277366 AGCATCCCTCA
1 ATCATCCCTCA
*
3277377 ATCATTCCTCA
1 ATCATCCCTCA
3277388 TACATACTCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.27, C:0.44, G:0.04, T:0.25
Consensus pattern (11 bp):
ATCATCCCTCA
Found at i:3304674 original size:21 final size:21
Alignment explanation
Indices: 3304645--3304684 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3304635 AGTTAGTTCC
*
3304645 AATCTAACTAAACAGAATTGA
1 AATCCAACTAAACAGAATTGA
*
3304666 AATCCAACTAATCAGAATT
1 AATCCAACTAAACAGAATT
3304685 CAACCAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.25
Consensus pattern (21 bp):
AATCCAACTAAACAGAATTGA
Found at i:3306358 original size:16 final size:16
Alignment explanation
Indices: 3306337--3306367 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3306327 CAAAATAAGT
3306337 TTTATATATCCATTAC
1 TTTATATATCCATTAC
*
3306353 TTTATATATGCATTA
1 TTTATATATCCATTA
3306368 TTATATTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTATATATCCATTAC
Found at i:3316199 original size:47 final size:47
Alignment explanation
Indices: 3316147--3316258 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
3316137 CACAGTAATG
* * *
3316147 CAGATAAACTGCCAATAATCAAAATTGTGGACAAGCT-ACTAAAATCA
1 CAGATAAACTGCCAATAATAAAAATCGTGGACAAG-TAACCAAAATCA
* **
3316194 TAGATATTCTGCCAATAATAAAAATCGTGGACAAGTAACCAAAATCA
1 CAGATAAACTGCCAATAATAAAAATCGTGGACAAGTAACCAAAATCA
* *
3316241 CATATAAATTGCCAATAA
1 CAGATAAACTGCCAATAA
3316259 CTTCCACCTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
46 1 0.02
47 52 0.98
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (47 bp):
CAGATAAACTGCCAATAATAAAAATCGTGGACAAGTAACCAAAATCA
Found at i:3316930 original size:13 final size:13
Alignment explanation
Indices: 3316912--3316936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3316902 TGATTGCAGA
3316912 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
3316925 TTTTTCTTCTTT
1 TTTTTCTTCTTT
3316937 GGATTTTTTT
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:3317168 original size:17 final size:17
Alignment explanation
Indices: 3317136--3317167 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3317126 AGATTTTAAG
3317136 TTTTTTTTAAGGTTTTA
1 TTTTTTTTAAGGTTTTA
3317153 TTTTTTTTAA-GTTTT
1 TTTTTTTTAAGGTTTT
3317168 TTTAAAGCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTTTTTAAGGTTTTA
Found at i:3317826 original size:24 final size:24
Alignment explanation
Indices: 3317791--3317859 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
3317781 ATATTTTTTG
3317791 AAGTTATTGTGTATTATTATTCTAA
1 AAGTTATTGTGTATTATTATT-TAA
*
3317816 AA-TTATTGTGTATTATTACTTAA
1 AAGTTATTGTGTATTATTATTTAA
3317839 AAGTTA-TGCTGTATTATTATT
1 AAGTTATTG-TGTATTATTATT
3317860 ATTTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.17
24 31 0.77
25 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (24 bp):
AAGTTATTGTGTATTATTATTTAA
Found at i:3321915 original size:44 final size:44
Alignment explanation
Indices: 3321446--3321885 Score: 619
Period size: 44 Copynumber: 10.0 Consensus size: 44
3321436 CAGCGAAACC
3321446 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
1 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
* *
3321490 ACAATTCCTATTTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
1 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
3321534 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
1 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
*
3321578 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTAAAGATT
1 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
* * *
3321622 ACAAGTCCTATCTCCCTGAATAGCAATGGAATAGGTTAAAGATT
1 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
*
3321666 ACAATTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
1 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
** * * * *
3321710 GTAAGTCCTATCTCCCTGAATAGAAGTGGAATAGGTGGAAGGTT
1 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
** *
3321754 GTAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTGGAAGATT
1 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
** * * ** * * *
3321798 GTAAGGCATATCTATCTAAACAACAGTGGAATAGGTGGAAGATT
1 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
* * * *
3321842 ATAAGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATT
1 ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
3321886 GTAGATCATG
Statistics
Matches: 358, Mismatches: 38, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 358 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
ACAAGTCCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATT
Found at i:3322103 original size:88 final size:88
Alignment explanation
Indices: 3321987--3322939 Score: 1483
Period size: 88 Copynumber: 10.8 Consensus size: 88
3321977 AGTCCTATCT
* ** * *
3321987 CCTGAGCAGCAGTGGAGTAGGTTAAAAATAATAGATCTTGTCTTCCTATATTGGCAGTGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
*
3322052 ATCGAAGACCCCAGCCTTATCTC
66 ATCGAAGACCCCAGCCTTGTCTC
* *
3322075 CCTGAGCAGCAGTAGAGTAGGTTGAAAATAGCAGATCTTGTCTTTCTGTATTGGCAGCGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
3322140 ATCGAAGACCCCAGCCTTGTCTC
66 ATCGAAGACCCCAGCCTTGTCTC
*
3322163 CCTGAGCAACAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
* *
3322228 ATCGAAGACCCTAGCCTTGCCTC
66 ATCGAAGACCCCAGCCTTGTCTC
** ** * *
3322251 CCTGAATAGCAGTAAAGTAGCTTGAAAATAACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
* * ** *
3322316 ATCAAAAACCAAAGCCTTGTCCC
66 ATCGAAGACCCCAGCCTTGTCTC
*
3322339 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTAGCAGCGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
3322404 ATCGAAGACCCCAGCCTTGTCTC
66 ATCGAAGACCCCAGCCTTGTCTC
*
3322427 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
* * *
3322492 ATCAAAGATCCCAGCTTTGTCTC
66 ATCGAAGACCCCAGCCTTGTCTC
** * * * *
3322515 CCTGAGCAATAGCGGAGTATGTTGAAAATAGTAGATCTTATCTTCCTGTATTGGCAGCGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
*
3322580 ATCGAAGACCCTAGCCTTGTCTC
66 ATCGAAGACCCCAGCCTTGTCTC
* * *
3322603 CCTGAGTAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTTCTGTATTAGCAGCGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
* *
3322668 ATCGAAGACCCCAACATTGTCTC
66 ATCGAAGACCCCAGCCTTGTCTC
* * *
3322691 CCTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTAGCAGCGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
3322756 ATCGAAGACCCCAGCCTTGTCTC
66 ATCGAAGACCCCAGCCTTGTCTC
* * *
3322779 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGTAGATCTTGTTTTCCTGTATTGGAAGCGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
**
3322844 ATCGAAGATACCAGCCTTGTCTC
66 ATCGAAGACCCCAGCCTTGTCTC
3322867 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
3322932 ATCGAAGA
66 ATCGAAGA
3322940 AACTAATCCT
Statistics
Matches: 782, Mismatches: 83, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 782 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (88 bp):
CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAG
ATCGAAGACCCCAGCCTTGTCTC
Found at i:3322159 original size:44 final size:44
Alignment explanation
Indices: 3322023--3322937 Score: 272
Period size: 44 Copynumber: 20.8 Consensus size: 44
3322013 AATAATAGAT
* * * *
3322023 CTTGTCTTCCTATATTGGCAGTGAAGTAGATCGAAGACCCCAGC
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAGC
* * ** * * * *** *
3322067 CTTATCTCCCTG-AGCAGCAG-TAGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTTCCTGTATTAGCAGCGA-AGTAGATCGAAAACCCCAG-C
* * *
3322111 CTTGTCTTTCTGTATTGGCAGCGAAGTAGATCGAAGACCCCAGC
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAGC
* ** * * * * * *** *
3322155 CTTGTCTCCCTG-AGCAACAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAG-C
* * *
3322199 CTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACCCTAGC
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAGC
* * * ** * * *** *
3322243 CTTGCCTCCCTG-AATAGCAGTAAAGTAGCTTGAAAATAACAGAT
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAG-C
* * **
3322287 CTTGTCTTCCTGTATTGGCAGCGAAGTAGATCAAAAACCAAAGC
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAGC
** ** * * * * *** *
3322331 CTTGTCCCCCTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAG-C
*
3322375 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAGACCCCAGC
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAGC
* ** * * * * ** * **
3322419 CTTGTCTCCCTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAAAT
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAA-CCCCAGC
* *
3322463 CTTGTCTTCCTGTATTGGCAGCGAAGTAGATC-AAAGATCCCAGC
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAA-ACCCCAGC
* * ** ** * * **** *
3322507 TTTGTCTCCCTG-AGCAATAGCGGAGTATG-TTGAAAATAGTAGAT
1 CTTGTCTTCCTGTATTAGCAGCGAAGTA-GATCGAAAACCCCAG-C
* * * *
3322551 CTTATCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACCCTAGC
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAGC
* * * * * * *** *
3322595 CTTGTCTCCCTG-AGTAGCAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAG-C
* * *
3322639 CTTGTCTTTCTGTATTAGCAGCGAAGTAGATCGAAGACCCCAAC
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAGC
* * ** * * * * * *** *
3322683 ATTGTCTCCCTG-AGCAGTAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAG-C
* *
3322727 CTTGTCTTCCTATATTAGCAGCGAAGTAGATCGAAGACCCCAGC
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAGC
* ** * * * * **** *
3322771 CTTGTCTCCCTG-AGCAGCAGTGGAGTAGGTTGAAAATAGTAGAT
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAG-C
* * * * **
3322815 CTTGTTTTCCTGTATTGGAAGCGAAGTAGATCGAAGATACCAGC
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAGC
* ** * * * * *** *
3322859 CTTGTCTCCCTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAG-C
*
3322903 CTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAA
1 CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAA
3322938 GAAACTAATC
Statistics
Matches: 571, Mismatches: 274, Indels: 51
0.64 0.31 0.06
Matches are distributed among these distances:
42 1 0.00
43 180 0.32
44 211 0.37
45 178 0.31
46 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.27
Consensus pattern (44 bp):
CTTGTCTTCCTGTATTAGCAGCGAAGTAGATCGAAAACCCCAGC
Found at i:3323012 original size:44 final size:43
Alignment explanation
Indices: 3322949--3323239 Score: 211
Period size: 44 Copynumber: 6.8 Consensus size: 43
3322939 AAACTAATCC
3322949 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACC-CAGATCT
* * * ** *
3322993 TATCTCTCTGAATTTGCAGTAGAGCGGATT-GCATCCAG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCCAGATCT
* * * ** * *
3323034 TATCTCCCTAAAGTTGTAGTGG-GCAGACAGAAGAAACCA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCGGA-TTAA-AACCCAGATCT
*
3323077 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACC-CAGATCT
* * * * ** * *
3323121 TATCTCTCTGAAGTTGTAGTAGAGCAGATT-GCATCCA-ATAT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCCAGATCT
* * * * *
3323162 TATCTCCCTAAAGTTGTAGTGGAGCAGA-TAGAAGAGACCAG-TCC
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTA-AA-A-CCCAGATCT
*
3323206 TATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
3323240 TGATGGATCT
Statistics
Matches: 189, Mismatches: 45, Indels: 27
0.72 0.17 0.10
Matches are distributed among these distances:
40 5 0.03
41 48 0.25
42 8 0.04
43 37 0.20
44 90 0.48
45 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCCAGATCT
Found at i:3323110 original size:128 final size:129
Alignment explanation
Indices: 3322935--3323294 Score: 535
Period size: 128 Copynumber: 2.8 Consensus size: 129
3322925 GAAGTAGATC
*
3322935 GAAGAAACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
1 GAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
* *
3323000 CTGAATTTGCAGTAGAGCGGATTGCATCCAGTCTTATCTCCCTAAAGTTGTAGTGG-GCAGACA
66 CTGAAGTTGCAGTAGAGCAGATTGCATCCAGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACA
*
3323063 GAAGAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
1 GAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
* * * *
3323128 CTGAAGTTGTAGTAGAGCAGATTGCATCCAATATTATCTCCCTAAAGTTGTAGTGGAGCAGATA
66 CTGAAGTTGCAGTAGAGCAGATTGCATCCAGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACA
* * * ** ** * *
3323192 GAAGAGACCAGTCCTATCTCCCTGAAGTTGCAGTGGAGCGGATCAAAATGATGGATCTCATCCCT
1 GAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
* *
3323257 CTGAAGTTGCAGTAGAGCAGATCGCAT-CAGACTTATCT
66 CTGAAGTTGCAGTAGAGCAGATTGCATCCAGTCTTATCT
3323295 TTAAAGTTGC
Statistics
Matches: 208, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
128 122 0.59
129 86 0.41
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (129 bp):
GAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCT
CTGAAGTTGCAGTAGAGCAGATTGCATCCAGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACA
Found at i:3324110 original size:13 final size:13
Alignment explanation
Indices: 3324092--3324116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3324082 TGATTGCACA
3324092 TTTTTCTTCTTTC
1 TTTTTCTTCTTTC
3324105 TTTTTCTTCTTT
1 TTTTTCTTCTTT
3324117 GGATTCTTTT
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:3325013 original size:24 final size:24
Alignment explanation
Indices: 3324977--3325045 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
3324967 CATATTTTTG
*
3324977 AAGTTATTGTGTATTATTATTCTAA
1 AAGTTATTATGTATTATTATT-TAA
*
3325002 AA-TTATTATGTATTATTACTTAA
1 AAGTTATTATGTATTATTATTTAA
**
3325025 AAGTTATGCTGTATTATTATT
1 AAGTTATTATGTATTATTATT
3325046 ATTTTATTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
23 5 0.13
24 31 0.82
25 2 0.05
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.52
Consensus pattern (24 bp):
AAGTTATTATGTATTATTATTTAA
Found at i:3332132 original size:374 final size:371
Alignment explanation
Indices: 3331447--3332565 Score: 1633
Period size: 374 Copynumber: 3.0 Consensus size: 371
3331437 GATAGCTCCA
* * * *
3331447 CCACTACTCAACCACTGTAATTGATATTTATTAACATTAAAAGATAATCT--A-AAATAAATAAA
1 CCACTACTCAACCACTATACTTGATATCTATTAACATAAAAAGATAATCTAAATAAATAAATAAA
* * * *
3331509 TAATAAATAAAATTTGGACAACCACTCTCTT-GGTTCATTAACCTAATTTCTACTAACCCAATTT
66 TAATAAATAAAATTTGGGCGACCACTCT-TTCGGTTCATTAACCCAATTTCTACTAATCCAATTT
* * **
3331573 TTGGGATGTAACAACTCTCCCCTCATTGAAAAGAGTTTTGTCCTCAAAATTCCTATTGTCAAGCC
130 TTGGGATGTGACAACTCTCCCCTCATTGAAAAGAATTTTGTCCTTGAAATTCCTATTGTCAAGCC
* *
3331638 AATTCACTTATCCATAAAATTCATAACTCTTCTTTCTAAACCATCCACCACGCTCTCGCTGCGCA
195 AATTCACTTATCCAT-AAATTCATAACTCTTCTTTCTAAACCATCCACCACGCTTTCGTTGC-CA
* **
3331703 ACTCTGATTTCAGCGTAGTTCCAATACTTCACCTTAAATCTCTAATGGATTTCTTATCTACTTAC
258 ACTCTGATTCCAATGTAGTTCCAATACTTCACCTTAAATCTCTAATGGATTTCTTATCTACTTAC
*
3331768 ACGTATTGTCTCAAGGGACTATCTATAGAAATATCACTAACAATTTTCT
323 ACGTATTGTCTCAAGGGACTATCTATAGAAATATCACTAACAATTTCCT
*
3331817 CCACTACTCAACCACTATACTTGATATCTATTAACATCAAAAGATAATCTAGAATAAATAAATAA
1 CCACTACTCAACCACTATACTTGATATCTATTAACATAAAAAGATAATCTA-AATAAATAAATAA
* * **
3331882 ATAATAAATAAAATTTGGGTGACCACTCTTTCGGTTTATTAACCCAATTTCTACTAATCTGATTT
65 ATAATAAATAAAATTTGGGCGACCACTCTTTCGGTTCATTAACCCAATTTCTACTAATCCAATTT
** *
3331947 TTGGGATGTGACAACTCTCCCCTCATTGAGAAA-AATTTCATCCTTGAAATTCCTATTGCCAAGC
130 TTGGGATGTGACAACTCTCCCCTCATTGA-AAAGAATTTTGTCCTTGAAATTCCTATTGTCAAGC
* * *
3332011 CAATTCACTTATCCATACATTTCATAACTCTTATTTCTAAACCATCCACCATGCTTTCGTTGCAC
194 CAATTCACTTATCCATA-AATTCATAACTCTTCTTTCTAAACCATCCACCACGCTTTCGTTGC-C
* * * *
3332076 AACTTTGATTCCAATGTAGTTCCAATACTTCACCTTAAATCTCAAATGGATTTCTTATCTATTTG
257 AACTCTGATTCCAATGTAGTTCCAATACTTCACCTTAAATCTCTAATGGATTTCTTATCTACTTA
* * *
3332141 CACGTATTATCTCAAGGGACTATCTATTGAAATATCACTAACGATTTCCT
322 CACGTATTGTCTCAAGGGACTATCTATAGAAATATCACTAACAATTTCCT
* *
3332191 CCACTACTCAACCACTATACTTGATATCGATTAAAATAAAAAGATAATCTAAAATAAATAAATAA
1 CCACTACTCAACCACTATACTTGATATCTATTAACATAAAAAGATAATCT-AAATAAATAAATAA
*
3332256 ATAA-ATAATAAAATTTGGGCGACCACTCTCTCGGTTCATTAACCCAATTTCTACTAATCCAATT
65 ATAATA-AATAAAATTTGGGCGACCACTCTTTCGGTTCATTAACCCAATTTCTACTAATCCAATT
3332320 TTTGGGATGTGACAACTCTCCCCTCATTGAAAAGAATTTTGTCCTTGAAATTCCTATTGTCAAGC
129 TTTGGGATGTGACAACTCTCCCCTCATTGAAAAGAATTTTGTCCTTGAAATTCCTATTGTCAAGC
* * * *
3332385 CAATTCACTTACCCATAACGTTCATAGCTCTTCTTTCTAAACCATCCACCACACTTTCGCTATG-
194 CAATTCACTTATCCATAA-ATTCATAACTCTTCTTTCTAAACCATCCACCACGCTTTCG-T-TGC
* * *
3332449 CAACTCTAATTCCAATGTAATTCCAATACTTCACCTTAAATCTCTAATGGATTTCTTATCTCCTT
256 CAACTCTGATTCCAATGTAGTTCCAATACTTCACCTTAAATCTCTAATGGATTTCTTATCTACTT
* *
3332514 ACA-GATATCGTCTCAAGGGACTATCTATAGAAATATCACTAATAATTTCCT
321 ACACG-TATTGTCTCAAGGGACTATCTATAGAAATATCACTAACAATTTCCT
3332565 C
1 C
3332566 ATTCACAAAT
Statistics
Matches: 670, Mismatches: 65, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
370 46 0.07
373 10 0.01
374 607 0.91
375 5 0.01
376 2 0.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (371 bp):
CCACTACTCAACCACTATACTTGATATCTATTAACATAAAAAGATAATCTAAATAAATAAATAAA
TAATAAATAAAATTTGGGCGACCACTCTTTCGGTTCATTAACCCAATTTCTACTAATCCAATTTT
TGGGATGTGACAACTCTCCCCTCATTGAAAAGAATTTTGTCCTTGAAATTCCTATTGTCAAGCCA
ATTCACTTATCCATAAATTCATAACTCTTCTTTCTAAACCATCCACCACGCTTTCGTTGCCAACT
CTGATTCCAATGTAGTTCCAATACTTCACCTTAAATCTCTAATGGATTTCTTATCTACTTACACG
TATTGTCTCAAGGGACTATCTATAGAAATATCACTAACAATTTCCT
Found at i:3335032 original size:15 final size:16
Alignment explanation
Indices: 3335001--3335035 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3334991 TTGTTTGTCA
3335001 AAAAGGAGAGAAAATG
1 AAAAGGAGAGAAAATG
*
3335017 AAAATGAGAG-AAATG
1 AAAAGGAGAGAAAATG
3335032 AAAA
1 AAAA
3335036 AAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.09
Consensus pattern (16 bp):
AAAAGGAGAGAAAATG
Found at i:3335036 original size:16 final size:17
Alignment explanation
Indices: 3335000--3335036 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3334990 GTTGTTTGTC
3335000 AAAAAGGAGAGAAAATG
1 AAAAAGGAGAGAAAATG
*
3335017 -AAAATGAGAG-AAATG
1 AAAAAGGAGAGAAAATG
3335032 AAAAA
1 AAAAA
3335037 AAAAGAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (17 bp):
AAAAAGGAGAGAAAATG
Found at i:3335533 original size:17 final size:16
Alignment explanation
Indices: 3335489--3335534 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3335479 TATTTGAGTG
*
3335489 ATTAAATGGATTAATGA
1 ATTAAATGG-TAAATGA
3335506 A-TAAA-GGTAAATGAA
1 ATTAAATGGTAAATG-A
3335521 ATTAAATGGTAAAT
1 ATTAAATGGTAAAT
3335535 AAACCATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 5 0.20
15 4 0.16
16 8 0.32
17 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.30
Consensus pattern (16 bp):
ATTAAATGGTAAATGA
Found at i:3336622 original size:6 final size:6
Alignment explanation
Indices: 3336611--3336635 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3336601 GCAACGATAT
3336611 AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA A
3336636 TGGTTTTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:3337381 original size:20 final size:20
Alignment explanation
Indices: 3337356--3337403 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3337346 AAGTTTAAGC
3337356 TAAGTAAACAG-AATGGAAAG
1 TAAGTAAA-AGAAATGGAAAG
* *
3337376 TAAGTAAATGAAATGGTAAG
1 TAAGTAAAAGAAATGGAAAG
3337396 TAAGTAAA
1 TAAGTAAA
3337404 TGAAGTGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.21
Consensus pattern (20 bp):
TAAGTAAAAGAAATGGAAAG
Found at i:3337404 original size:20 final size:20
Alignment explanation
Indices: 3337367--3337412 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3337357 AAGTAAACAG
*
3337367 AATGGAAAGTAAGTAAATGA
1 AATGGTAAGTAAGTAAATGA
3337387 AATGGTAAGTAAGTAAATGA
1 AATGGTAAGTAAGTAAATGA
*
3337407 AGTGGT
1 AATGGT
3337413 TCATAGTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (20 bp):
AATGGTAAGTAAGTAAATGA
Found at i:3343912 original size:94 final size:94
Alignment explanation
Indices: 3343738--3343913 Score: 248
Period size: 94 Copynumber: 1.9 Consensus size: 94
3343728 TCTTCTCTTA
* *
3343738 TTGGATATTTAATTGGACATTGGAAACCTTATGATCTTTTGAACTACACCAATAACATTACACAA
1 TTGGATATTTAATTGGACATTGAAAACATTATGATCTTTTGAAC-ACACCAATAACATTACACAA
* *
3343803 ACGGTGATAGCTCAATCTTATTTTGTCTGT
65 ACGGTGAAAGATCAATCTTATTTTGTCTGT
* * *
3343833 TTGGATATTTAATTGGACATTGAAAATATTCATGATCTTTTGAA-ACACTAATAACATTTCACAA
1 TTGGATATTTAATTGGACATTGAAAACATT-ATGATCTTTTGAACACACCAATAACATTACACAA
3343897 TA-GGTGAAAGATCAATC
65 -ACGGTGAAAGATCAATC
3343914 GTACTCCTGT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
94 31 0.43
95 28 0.39
96 13 0.18
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (94 bp):
TTGGATATTTAATTGGACATTGAAAACATTATGATCTTTTGAACACACCAATAACATTACACAAA
CGGTGAAAGATCAATCTTATTTTGTCTGT
Found at i:3344496 original size:18 final size:17
Alignment explanation
Indices: 3344454--3344496 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
3344444 CCATAGAATA
*
3344454 TTTTTTTTCTTTTTTCT
1 TTTTTTTTCTATTTTCT
*
3344471 TTTCTTTTCGTATTTTCT
1 TTTTTTTTC-TATTTTCT
3344489 TTTTTTTT
1 TTTTTTTT
3344497 GTACTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (17 bp):
TTTTTTTTCTATTTTCT
Found at i:3348561 original size:44 final size:44
Alignment explanation
Indices: 3348499--3348601 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 44
3348489 ACCTGGTGTG
* ** * *
3348499 ATCTACTCTACTACAACTTTAGAGAGATAAGATCTACT-ATTTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGAT-TACTGACTTCA
* * *
3348543 ATCTACTCCACTGTAACTTCAGGGAGATAGGATTACTGGCTTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATTACTGACTTCA
*
3348587 ATGTACTCCACTGTA
1 ATCTACTCCACTGTA
3348602 TCCTCAGGGA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 4 0.08
44 45 0.92
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (44 bp):
ATCTACTCCACTGTAACTTCAGAGAGATAAGATTACTGACTTCA
Found at i:3348860 original size:218 final size:217
Alignment explanation
Indices: 3348455--3349019 Score: 860
Period size: 218 Copynumber: 2.6 Consensus size: 217
3348445 TTCACTATTC
* * * * * * *
3348455 TCAGTCTGCCCCACTGTAACTTCAGGGGGATAAGACCTGGTGTGATCTACTCTACTACAACTTTA
1 TCAGTCTGCTCCACTGCAACCTCAGGGGGATAAGACCTGATGCGATCTACTCTACTGCAACTTCA
* ** * *
3348520 GAGAGATAAGATCTACTATTTCAATCTACTCCACTGTAACTTCAGGGAGATAGGATTACTGGCTT
66 GAGAGATAAGACCTTTTATTTCAATCCACTCCACTGCAACTTCAGGGAGATAGGATTACTGGCTT
*
3348585 CAATGTACTCCACTGTATCCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTAATTCT
131 CAATGTACTCCACTGTATCCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTAATGCT
*
3348650 TAGGGAGATAATATCTGTTTCT
196 TAGGGAGATAAGATCTGTTTCT
* * * *
3348672 TCGGTCTGCTCCATTGCAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCA
1 TCAGTCTGCTCCACTGCAACCTCAGGGGGATAAGACCTGATGCGATCTACTCTACTGCAACTTCA
*
3348737 GAGAGATAATACCTTTTTATTTCAATCCACTCCACTGCAACTTCAGGGAGATAGGATTACTGGCT
66 GAGAGATAAGACC-TTTTATTTCAATCCACTCCACTGCAACTTCAGGGAGATAGGATTACTGGCT
* *
3348802 TCAATGTACTCCACTGTATCCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
130 TCAATGTACTCCACTGTATCCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTAATGC
3348867 TTAGGGAGATAAGATCTGTTTCT
195 TTAGGGAGATAAGATCTGTTTCT
** * *
3348890 TCAGTCTGCTCTGCTGCAACCTCAGGGGGATAAGACTTGATACGATCTACTCTACTGCAACTTCA
1 TCAGTCTGCTCCACTGCAACCTCAGGGGGATAAGACCTGATGCGATCTACTCTACTGCAACTTCA
* * * *
3348955 GAGAGATAAGACCTTTTATTTTAATCCACTCCGCTGCGACTTCAGGGAGATAGGATTAGTGGCTT
66 GAGAGATAAGACCTTTTATTTCAATCCACTCCACTGCAACTTCAGGGAGATAGGATTACTGGCTT
3349020 AAATCTGCTT
Statistics
Matches: 313, Mismatches: 34, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
217 113 0.36
218 200 0.64
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (217 bp):
TCAGTCTGCTCCACTGCAACCTCAGGGGGATAAGACCTGATGCGATCTACTCTACTGCAACTTCA
GAGAGATAAGACCTTTTATTTCAATCCACTCCACTGCAACTTCAGGGAGATAGGATTACTGGCTT
CAATGTACTCCACTGTATCCTCAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTAATGCT
TAGGGAGATAAGATCTGTTTCT
Found at i:3350407 original size:20 final size:19
Alignment explanation
Indices: 3350378--3350415 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
3350368 AGCTAATAAC
3350378 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
3350397 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
3350416 CAAAAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:3368109 original size:20 final size:20
Alignment explanation
Indices: 3368084--3368123 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3368074 TACTTTCTTC
3368084 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
3368104 TTTACTTACTTGCTTACTTG
1 TTTACTTACTTGCTTACTTG
3368124 AATAACTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.15, C:0.23, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:3368461 original size:50 final size:50
Alignment explanation
Indices: 3368407--3368519 Score: 145
Period size: 50 Copynumber: 2.3 Consensus size: 50
3368397 GGTCTTACAT
* * *
3368407 GGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAAACATGATCTTACGG
1 GGGAGCTCTCATATCGGTGCCAACGCCATGTCCCAAACATGATCTTACGG
* * * **
3368457 GGGAGCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACAT
1 GGGAGCTCTCATATCGGTGCCAACGCCATGTCCCAAACATGATCTTACGG
*
3368507 GGGACCTCTCATA
1 GGGAGCTCTCATA
3368520 ACCTCAATAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.25
Consensus pattern (50 bp):
GGGAGCTCTCATATCGGTGCCAACGCCATGTCCCAAACATGATCTTACGG
Found at i:3373292 original size:23 final size:23
Alignment explanation
Indices: 3373264--3373307 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3373254 CTTTCTTACT
*
3373264 GTAGTAATTTTCGGGGTATTATA
1 GTAGTAATTTTCGGGATATTATA
3373287 GTAGTAATTTTCGGGATATTA
1 GTAGTAATTTTCGGGATATTA
3373308 CAGTTTGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.43
Consensus pattern (23 bp):
GTAGTAATTTTCGGGATATTATA
Found at i:3378198 original size:14 final size:15
Alignment explanation
Indices: 3378165--3378203 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
3378155 CACCCAAAAC
3378165 ACACCTCAACTTTATA
1 ACACCTCAAC-TTATA
*
3378181 ACACCTCAA-TTCTA
1 ACACCTCAACTTATA
3378195 ACACCTCAA
1 ACACCTCAA
3378204 GACCACCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
16 9 0.41
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (15 bp):
ACACCTCAACTTATA
Found at i:3380260 original size:21 final size:19
Alignment explanation
Indices: 3380217--3380261 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3380207 GAGCTCAAAT
* *
3380217 GAGCTGAAATGAGTTCATG
1 GAGCTGAAATGAGCTAATG
3380236 GAGCTGGAAATGAGCTAATTG
1 GAGCT-GAAATGAGCTAA-TG
3380257 GAGCT
1 GAGCT
3380262 CAATGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24
Consensus pattern (19 bp):
GAGCTGAAATGAGCTAATG
Found at i:3385305 original size:25 final size:25
Alignment explanation
Indices: 3385257--3385306 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3385247 GAACTGGTCA
* *
3385257 TAGAGAGAATTGAGGAGGGGATATT
1 TAGAGAGAATTGAGGAGAGAATATT
*
3385282 TAGAGAGATTTGAGGAGAGAATATT
1 TAGAGAGAATTGAGGAGAGAATATT
3385307 GGGATTTGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.26
Consensus pattern (25 bp):
TAGAGAGAATTGAGGAGAGAATATT
Found at i:3386189 original size:27 final size:27
Alignment explanation
Indices: 3385971--3386382 Score: 386
Period size: 27 Copynumber: 15.3 Consensus size: 27
3385961 TCGATATCTG
* *
3385971 GACCGAAATA-CCCTCAAAGGGTAAAAT
1 GACCGTAATACCCCT-ATAGGGTAAAAT
* * * *
3385998 GACTGAAATACCCTCGAT-GAGTAAAAT
1 GACCGTAATACCC-CTATAGGGTAAAAT
* * *
3386025 GACTGAAATACCCTCGAT-GGGTAAAAT
1 GACCGTAATACCC-CTATAGGGTAAAAT
* * *
3386052 GACCGAAATTCCCCCATAGGGTAAAAT
1 GACCGTAATACCCCTATAGGGTAAAAT
** * * *
3386079 GATTGAAATACCCCTGTAGGGTAGAAT
1 GACCGTAATACCCCTATAGGGTAAAAT
* * * *
3386106 -ACCGAAATACCCCCATAGGATAACAT
1 GACCGTAATACCCCTATAGGGTAAAAT
*
3386132 GACCGTAATACCCCTGTAGGGTAAAAT
1 GACCGTAATACCCCTATAGGGTAAAAT
*
3386159 GACCGTAATACCCTTATAGGGTAAAAT
1 GACCGTAATACCCCTATAGGGTAAAAT
* *
3386186 GACCGT-ATGCCCCTGTAGGGTAAAAT
1 GACCGTAATACCCCTATAGGGTAAAAT
3386212 GACTC-TAATACCCCTATAGGGTAAAAT
1 GAC-CGTAATACCCCTATAGGGTAAAAT
* * *
3386239 GACCATAATGCCCCTGTAGGGTAAAAT
1 GACCGTAATACCCCTATAGGGTAAAAT
* * *
3386266 GATCGTAATGCCCCTGTAGGGTAAAAT
1 GACCGTAATACCCCTATAGGGTAAAAT
* * * *
3386293 GGCCGTAATGCCCTTGTAGGGTAAAAT
1 GACCGTAATACCCCTATAGGGTAAAAT
* *
3386320 GACTGTAATGCCCCTATAGGGTAAAAT
1 GACCGTAATACCCCTATAGGGTAAAAT
* * *
3386347 GACCGTAATGCCCTTGTAGGGTAAAAT
1 GACCGTAATACCCCTATAGGGTAAAAT
3386374 GACCGTAAT
1 GACCGTAAT
3386383 GCCCTGGTGG
Statistics
Matches: 331, Mismatches: 47, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
26 44 0.13
27 283 0.85
28 3 0.01
29 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.23
Consensus pattern (27 bp):
GACCGTAATACCCCTATAGGGTAAAAT
Found at i:3386315 original size:81 final size:81
Alignment explanation
Indices: 3386043--3386382 Score: 407
Period size: 80 Copynumber: 4.2 Consensus size: 81
3386033 TACCCTCGAT
* * ** ** * * * *
3386043 GGGTAAAATGACCGAAATTCCCCCATAGGGTAAAATGATTGAAATACCCCTGTAGGGTAGAAT-A
1 GGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGA
* * **
3386107 CCGAAATACCCCCATA
66 CCGTAATGCCCCTGTA
* * * *
3386123 GGATAACATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGGTAAAATGA
1 GGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGA
3386188 CCGT-ATGCCCCTGTA
66 CCGTAATGCCCCTGTA
* * *
3386203 GGGTAAAATGACTC-TAATACCCCTATAGGGTAAAATGACCATAATGCCCCTGTAGGGTAAAATG
1 GGGTAAAATGAC-CGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATG
*
3386267 ATCGTAATGCCCCTGTA
65 ACCGTAATGCCCCTGTA
* * * *
3386284 GGGTAAAATGGCCGTAATGCCCTTGTAGGGTAAAATGACTGTAATGCCCCTATAGGGTAAAATGA
1 GGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGA
*
3386349 CCGTAATGCCCTTGTA
66 CCGTAATGCCCCTGTA
3386365 GGGTAAAATGACCGTAAT
1 GGGTAAAATGACCGTAAT
3386383 GCCCTGGTGG
Statistics
Matches: 222, Mismatches: 34, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
80 119 0.54
81 103 0.46
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (81 bp):
GGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGA
CCGTAATGCCCCTGTA
Found at i:3386383 original size:27 final size:27
Alignment explanation
Indices: 3386043--3386401 Score: 406
Period size: 27 Copynumber: 13.4 Consensus size: 27
3386033 TACCCTCGAT
* * **
3386043 GGGTAAAATGACCGAAATTCCCCCATA
1 GGGTAAAATGACCGTAATGCCCCTGTA
** * *
3386070 GGGTAAAATGATTGAAATACCCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* * * **
3386097 GGGTAGAAT-ACCGAAATACCCCCATA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* * *
3386123 GGATAACATGACCGTAATACCCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* * *
3386150 GGGTAAAATGACCGTAATACCCTTATA
1 GGGTAAAATGACCGTAATGCCCCTGTA
3386177 GGGTAAAATGACCGT-ATGCCCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* *
3386203 GGGTAAAATGACTC-TAATACCCCTATA
1 GGGTAAAATGAC-CGTAATGCCCCTGTA
*
3386230 GGGTAAAATGACCATAATGCCCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTGTA
*
3386257 GGGTAAAATGATCGTAATGCCCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* *
3386284 GGGTAAAATGGCCGTAATGCCCTTGTA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* *
3386311 GGGTAAAATGACTGTAATGCCCCTATA
1 GGGTAAAATGACCGTAATGCCCCTGTA
*
3386338 GGGTAAAATGACCGTAATGCCCTTGTA
1 GGGTAAAATGACCGTAATGCCCCTGTA
3386365 GGGTAAAATGACCGTAATG-CCCTGGT-
1 GGGTAAAATGACCGTAATGCCCCT-GTA
3386391 GGGT-AAATGAC
1 GGGTAAAATGAC
3386402 TATTTTTGCC
Statistics
Matches: 287, Mismatches: 40, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
25 7 0.02
26 48 0.17
27 232 0.81
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (27 bp):
GGGTAAAATGACCGTAATGCCCCTGTA
Found at i:3386449 original size:23 final size:23
Alignment explanation
Indices: 3386422--3386506 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 23
3386412 CCTCGAGGTC
*
3386422 AAATGATTG-TTTTGTCTGTGGTT
1 AAATGACTGATTTT-TCTGTGGTT
3386445 AAATGACTGATTTTTCTGTGGTT
1 AAATGACTGATTTTTCTGTGGTT
** * * *
3386468 GGTATAACTGATTTGTCTGTGATTT
1 -AAATGACTGATTTTTCTGTG-GTT
*
3386493 GAATGACTGATTTT
1 AAATGACTGATTTT
3386507 GAGCATGACA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
23 17 0.34
24 31 0.62
25 2 0.04
ACGTcount: A:0.21, C:0.07, G:0.24, T:0.48
Consensus pattern (23 bp):
AAATGACTGATTTTTCTGTGGTT
Found at i:3386629 original size:27 final size:27
Alignment explanation
Indices: 3386573--3386632 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
3386563 GGAAGTACTG
*
3386573 TACTGGTGGCTCTGCCACAATCACTGT
1 TACTGGTGGCTCTGCCACAATCACTAT
*
3386600 TACTGGTGGCT-TGGCCA-AATATACTAT
1 TACTGGTGGCTCT-GCCACAAT-CACTAT
3386627 TACTGG
1 TACTGG
3386633 CAGCTTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (27 bp):
TACTGGTGGCTCTGCCACAATCACTAT
Found at i:3386678 original size:26 final size:26
Alignment explanation
Indices: 3386620--3386685 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
3386610 TTGGCCAAAT
* * *
3386620 ATACTATTACTGGCAGCTTTGGTGCG
1 ATACTATTGCTGGCAGCTTTGCTACG
*
3386646 ATACTATTGCTGGCAGCTTTGCTATG
1 ATACTATTGCTGGCAGCTTTGCTACG
* *
3386672 ATGCTATTGATGGC
1 ATACTATTGCTGGC
3386686 TTTGTGTCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (26 bp):
ATACTATTGCTGGCAGCTTTGCTACG
Found at i:3386722 original size:32 final size:32
Alignment explanation
Indices: 3386679--3386954 Score: 231
Period size: 32 Copynumber: 8.6 Consensus size: 32
3386669 ATGATGCTAT
*
3386679 TGATGGCTTTGTGTCGATCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGATCATAGTACCGTTAC
*
3386711 TAATGGCTTTGTGCCGATCATAGTACCGTTAC
1 TGATGGCTTTGTGCCGATCATAGTACCGTTAC
* * *
3386743 TGATGGCTTTGTGTCGATCATAGTACCATCAC
1 TGATGGCTTTGTGCCGATCATAGTACCGTTAC
* * ***
3386775 TGATGGCTTTGTGCCAATCATATTAGAATTAC
1 TGATGGCTTTGTGCCGATCATAGTACCGTTAC
* * * *
3386807 CGATGG-TTGTGTGTCGATCAT-TTCACTGTTAC
1 TGATGGCTT-TGTGCCGATCATAGT-ACCGTTAC
* * ***
3386839 TGATGGCTATGTACCGATCATA-TCACTAATAC
1 TGATGGCTTTGTGCCGATCATAGT-ACCGTTAC
*
3386871 TGATAGCTTTGTGCCGATCAT-GTTACCGTTAC
1 TGATGGCTTTGTGCCGATCATAG-TACCGTTAC
* ***
3386903 TGATGGCTGTGTGCCGAAT-ATA-TCATTTTTAC
1 TGATGGCTTTGTGCCG-ATCATAGT-ACCGTTAC
*
3386935 TGATGGCTTTGTGCCAATCA
1 TGATGGCTTTGTGCCGATCA
3386955 CATTACTGTA
Statistics
Matches: 197, Mismatches: 37, Indels: 20
0.78 0.15 0.08
Matches are distributed among these distances:
31 7 0.04
32 186 0.94
33 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATAGTACCGTTAC
Found at i:3386949 original size:64 final size:64
Alignment explanation
Indices: 3386679--3386947 Score: 278
Period size: 64 Copynumber: 4.2 Consensus size: 64
3386669 ATGATGCTAT
* **
3386679 TGATGGCTTTGTGTCGATCATAGTACCGTTACTAATGGCTTTGTGCCGATCATAGT-ACCGTTAC
1 TGATGGCTTTGTGTCGATCATAGTACCGTTACTGATGGCTTTGTGCCGATCATA-TCACTATTAC
* * * * **
3386743 TGATGGCTTTGTGTCGATCATAGTACCATCACTGATGGCTTTGTGCCAATCATATTAGAATTAC
1 TGATGGCTTTGTGTCGATCATAGTACCGTTACTGATGGCTTTGTGCCGATCATATCACTATTAC
* * * * * *
3386807 CGATGG-TTGTGTGTCGATCAT-TTCACTGTTACTGATGGCTATGTACCGATCATATCACTAATA
1 TGATGGCTT-TGTGTCGATCATAGT-ACCGTTACTGATGGCTTTGTGCCGATCATATCACTATTA
3386870 C
64 C
* * * * *
3386871 TGATAGCTTTGTGCCGATCAT-GTTACCGTTACTGATGGCTGTGTGCCGAAT-ATATCATTTTTA
1 TGATGGCTTTGTGTCGATCATAG-TACCGTTACTGATGGCTTTGTGCCG-ATCATATCACTATTA
3386934 C
64 C
3386935 TGATGGCTTTGTG
1 TGATGGCTTTGTG
3386948 CCAATCACAT
Statistics
Matches: 169, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
63 4 0.02
64 160 0.95
65 5 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (64 bp):
TGATGGCTTTGTGTCGATCATAGTACCGTTACTGATGGCTTTGTGCCGATCATATCACTATTAC
Found at i:3387221 original size:27 final size:27
Alignment explanation
Indices: 3387180--3387235 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
3387170 CATACTTGCA
*
3387180 CCATACTGATACTGTATCGGGCTTAGG
1 CCATACTGATACTGTATCGGGCTAAGG
* * *
3387207 CCATACTGTTTCTGTATTGGGCTAAGG
1 CCATACTGATACTGTATCGGGCTAAGG
3387234 CC
1 CC
3387236 CACACTGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (27 bp):
CCATACTGATACTGTATCGGGCTAAGG
Found at i:3389164 original size:20 final size:21
Alignment explanation
Indices: 3389139--3389180 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3389129 AAATAAAAGA
* *
3389139 TGGAAACGAGCT-CATTGAGC
1 TGGAAACAAGCTAAATTGAGC
3389159 TGGAAACAAGCTAAATTGAGC
1 TGGAAACAAGCTAAATTGAGC
3389180 T
1 T
3389181 CAACAAGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (21 bp):
TGGAAACAAGCTAAATTGAGC
Found at i:3395523 original size:41 final size:41
Alignment explanation
Indices: 3395456--3395602 Score: 161
Period size: 41 Copynumber: 3.6 Consensus size: 41
3395446 TGCCAGCATA
* * * *
3395456 AAGCCTTCTAGGCACAAAGTCAGATATGATATACCGGCACG
1 AAGCCTGCTAGGCACAAAGCCTGATATGATATACCGGCAAG
* * * *
3395497 AAGCCTGCTAGGCATAAAGCCTGATATGGTACACCGGCATG
1 AAGCCTGCTAGGCACAAAGCCTGATATGATATACCGGCAAG
* * * *
3395538 AAGCCTGCTAGGCATAAAGCCTGCTATAAT-TCACCGGCAAA
1 AAGCCTGCTAGGCACAAAGCCTGATATGATAT-ACCGGCAAG
*
3395579 AAGCCTGCTAGGCACAGAGCCTGA
1 AAGCCTGCTAGGCACAAAGCCTGA
3395603 ATATCACTGT
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (41 bp):
AAGCCTGCTAGGCACAAAGCCTGATATGATATACCGGCAAG
Found at i:3395557 original size:16 final size:16
Alignment explanation
Indices: 3395532--3395563 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3395522 ATGGTACACC
*
3395532 GGCATGAAGCCTGCTA
1 GGCATAAAGCCTGCTA
3395548 GGCATAAAGCCTGCTA
1 GGCATAAAGCCTGCTA
3395564 TAATTCACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (16 bp):
GGCATAAAGCCTGCTA
Found at i:3404248 original size:22 final size:22
Alignment explanation
Indices: 3404223--3404265 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3404213 ATAAGGGGAA
3404223 TTGCTAACTATTGCCCTAAATT
1 TTGCTAACTATTGCCCTAAATT
**
3404245 TTGCTAACTATTTTCCTAAAT
1 TTGCTAACTATTGCCCTAAAT
3404266 GTTTTAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (22 bp):
TTGCTAACTATTGCCCTAAATT
Found at i:3405441 original size:27 final size:27
Alignment explanation
Indices: 3405411--3405905 Score: 553
Period size: 27 Copynumber: 18.3 Consensus size: 27
3405401 GGCCATAACA
* *
3405411 GTCATTTTACTCATCAAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
***
3405438 GTCATTTTACCCAGAAAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * * *
3405465 ATCATTTTACCCATTGAGGGCATTTCT
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
3405492 GTCATTTTAGCCA-CTGAGTGTATTTCA
1 GTCATTTTACCCATC-GAGGGTATTTCG
*
3405519 ATCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
** * *
3405546 GTCATTTTACCCATTAAGGGCATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
*
3405573 GTCATTTTACCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
3405600 GTCATTTTACCCATCAAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
**
3405627 GTCATTTTACCCATCGAGGGTATTTTT
1 GTCATTTTACCCATCGAGGGTATTTCG
* * **
3405654 GCCATTTTACTCATCGAGCATATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
3405681 ATCATTTTACCCATCAAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
3405708 GTCATTTTACCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
3405735 GTTATTTTACCCTTCGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTCG
*
3405762 GTCATTTTAGCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
3405789 GTCATTTTACCCATCGATGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
3405816 GTCATTTTACCTATCGAGGGCATTTTG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * * *
3405843 GTCATTTTACCTATCAAGAGCATGTT-G
1 GTCATTTTACCCATCGAGGGTAT-TTCG
* *
3405870 ATCATTTTACCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
3405897 GTCATTTTA
1 GTCATTTTA
3405906 GAATTCGGCC
Statistics
Matches: 391, Mismatches: 73, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
26 2 0.01
27 386 0.99
28 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTCG
Found at i:3409945 original size:37 final size:37
Alignment explanation
Indices: 3409894--3410005 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
3409884 ATTATCCGAA
* * * *
3409894 TTGAATCACAACATAATTAAAAAAAATACATAAATCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
3409931 TTGAATCACTACATAATTAAAAACATTAGATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
3409968 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
3410005 T
1 T
3410006 GAAATTAACA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.31
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:3409999 original size:17 final size:17
Alignment explanation
Indices: 3409940--3410000 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
3409930 TTTGAATCAC
3409940 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
* ** * *
3409957 TAGATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
3409977 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
3409994 TACATAA
1 TACATAA
3410001 GTCTTGAAAT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
17 19 0.61
20 12 0.39
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:3413618 original size:3 final size:3
Alignment explanation
Indices: 3413610--3413654 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3413600 GTTTCTCCAA
3413610 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3413655 GTCGTCGTCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3414290 original size:7 final size:7
Alignment explanation
Indices: 3414278--3414308 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3414268 AGGGCTAGGG
3414278 GTGTTAA
1 GTGTTAA
3414285 GTGTTAA
1 GTGTTAA
3414292 GTGTTAA
1 GTGTTAA
*
3414299 TTGTTAA
1 GTGTTAA
3414306 GTG
1 GTG
3414309 ACAGTGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (7 bp):
GTGTTAA
Found at i:3419003 original size:38 final size:38
Alignment explanation
Indices: 3418951--3419023 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
3418941 ACCTTTTAAC
* * *
3418951 TTTTGCTTAGAAGTGCAGTCGAGGTCATCCATTATAAA
1 TTTTGCTCAAAAGTGCAATCGAGGTCATCCATTATAAA
3418989 TTTTGCTCAAAAGTGCAATCGAGGTCATCCATTAT
1 TTTTGCTCAAAAGTGCAATCGAGGTCATCCATTAT
3419024 TCTCTCCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (38 bp):
TTTTGCTCAAAAGTGCAATCGAGGTCATCCATTATAAA
Found at i:3419583 original size:26 final size:26
Alignment explanation
Indices: 3419543--3419598 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
3419533 AGTTTCCTAT
3419543 AGTAACGCAGCAAAGCTGCCAGTAAC
1 AGTAACGCAGCAAAGCTGCCAGTAAC
* *
3419569 AGTAATGCAGTAAAGCTGCCAGTAAC
1 AGTAACGCAGCAAAGCTGCCAGTAAC
3419595 AGTA
1 AGTA
3419599 TATGTGGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (26 bp):
AGTAACGCAGCAAAGCTGCCAGTAAC
Found at i:3419734 original size:25 final size:26
Alignment explanation
Indices: 3419706--3419760 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
3419696 TCAGTAACGA
* * *
3419706 TCATATATATCATAAAGCAA-ATCAG
1 TCATACATAACATAAAGCAATAACAG
*
3419731 TCATACATAACATAATGCAATAACAG
1 TCATACATAACATAAAGCAATAACAG
3419757 TCAT
1 TCAT
3419761 TTTACTCGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.27
Consensus pattern (26 bp):
TCATACATAACATAAAGCAATAACAG
Found at i:3419799 original size:27 final size:26
Alignment explanation
Indices: 3419756--3420223 Score: 432
Period size: 27 Copynumber: 17.3 Consensus size: 26
3419746 TGCAATAACA
* * *
3419756 GTCATTTTACTCGTCGAGGGTGTTCTG
1 GTCATTTTACCCATCGAGGGTATT-TG
3419783 GTCATTTTACCCATCGAGGGTATTTAG
1 GTCATTTTACCCATCGAGGGTATTT-G
* *
3419810 GTTATTTTACCCATCAAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTT-G
* *
3419837 GTCATTTTACCCATTGAGGGCATTTTG
1 GTCATTTTACCCATCGAGGGTA-TTTG
* *
3419864 TTCATTTTACCTATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTT-G
* * *
3419891 ATCATTTTACCCATCGAGGGAATTTTA
1 GTCATTTTACCCATCGAGGGTA-TTTG
3419918 GTCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTT-G
* * * * *
3419945 ATCATTTTACCCATTGAAGGCATTTCA
1 GTCATTTTACCCATCGAGGGTATTT-G
*
3419972 GTCATTTTACCCATCGAGGGCATTTCG
1 GTCATTTTACCCATCGAGGGTATTT-G
* * *
3419999 ATCATTTTACCCATCGGGGGCATTTTG
1 GTCATTTTACCCATCGAGGGTA-TTTG
* * *
3420026 GTCATTTTACCCATTGAGGGCATTTTA
1 GTCATTTTACCCATCGAGGGTA-TTTG
3420053 GTCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTT-G
* * *
3420080 ATAATTTTACCCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTT-G
* *
3420107 GTCATTTTACCCATCAAGGGCATTTTG
1 GTCATTTTACCCATCGAGGGTA-TTTG
** **
3420134 GTCATTTTACCCATCGAGGACAATTCA
1 GTCATTTTACCCATCGAGG-GTATTTG
* * * *
3420161 GTCATTTTACCCATCAATGGCATTTTA
1 GTCATTTTACCCATCGAGGGTA-TTTG
* *
3420188 GTCATTTTAACCATCGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTT-G
3420215 GTCATTTTA
1 GTCATTTTA
3420224 GGCCCAATTC
Statistics
Matches: 369, Mismatches: 61, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
26 14 0.04
27 342 0.93
28 13 0.04
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (26 bp):
GTCATTTTACCCATCGAGGGTATTTG
Found at i:3419830 original size:54 final size:54
Alignment explanation
Indices: 3419756--3420223 Score: 530
Period size: 54 Copynumber: 8.7 Consensus size: 54
3419746 TGCAATAACA
* * * *
3419756 GTCATTTTACTCGTCGAGGGT-GTTCTGGTCATTTTACCCATCGAGGGTATTTAG
1 GTCATTTTACCCATCGAGGGTATTTC-GGTCATTTTACCCATCGAGGGCATTTAG
* * * *
3419810 GTTATTTTACCCATCAAGGGTATTTCGGTCATTTTACCCATTGAGGGCATTTTG
1 GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGCATTTAG
* * * *
3419864 TTCATTTTACCTATCGAGGGTATTTCGATCATTTTACCCATCGAGGGAATTTTA-
1 GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGCA-TTTAG
* * *
3419918 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATTGAAGGCATTTCA-
1 GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGCATTT-AG
* * * *
3419972 GTCATTTTACCCATCGAGGGCATTTCGATCATTTTACCCATCGGGGGCATTTTG
1 GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGCATTTAG
* * ** * *
3420026 GTCATTTTACCCATTGAGGGCATTTTAGTCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGCATTTAG
* * * * *
3420080 ATAATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATCAAGGGCATTTTG
1 GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGCATTTAG
** * * * *
3420134 GTCATTTTACCCATCGAGGACAATTCAGTCATTTTACCCATCAATGGCATTTTA-
1 GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGCA-TTTAG
* *
3420188 GTCATTTTAACCATCGAGGGTATTTCAGTCATTTTA
1 GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTA
3420224 GGCCCAATTC
Statistics
Matches: 357, Mismatches: 52, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
53 3 0.01
54 345 0.97
55 9 0.03
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (54 bp):
GTCATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCGAGGGCATTTAG
Found at i:3419898 original size:81 final size:81
Alignment explanation
Indices: 3419756--3420223 Score: 498
Period size: 81 Copynumber: 5.8 Consensus size: 81
3419746 TGCAATAACA
* * ** * * * *
3419756 GTCATTTTACTCGTCGAGGGTGTTCTGGTCATTTTACCCATCGAGGGTATTTAG-GTTATTTTAC
1 GTCATTTTACCCATCGAGGGCATT-TTGTCATTTTACCCATCGAGGGCATTTCGAGTCATTTTAC
* *
3419820 CCATCAAGGGTATTTCG
65 CCATCGAGGGCATTTCG
* * *
3419837 GTCATTTTACCCATTGAGGGCATTTTGTTCATTTTACCTATCGAGGGTATTTCGA-TCATTTTAC
1 GTCATTTTACCCATCGAGGGCATTTTG-TCATTTTACCCATCGAGGGCATTTCGAGTCATTTTAC
* **
3419901 CCATCGAGGGAATTTTA
65 CCATCGAGGGCATTTCG
* * * *
3419918 GTCATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATTGAAGGCATTTC-AGTCATTTTAC
1 GTCATTTTACCCATCGAGGGCATTTTG-TCATTTTACCCATCGAGGGCATTTCGAGTCATTTTAC
3419982 CCATCGAGGGCATTTCG
65 CCATCGAGGGCATTTCG
* * * *
3419999 ATCATTTTACCCATCGGGGGCATTTTGGTCATTTTACCCATTGAGGGCATTT-TAGTCATTTTAC
1 GTCATTTTACCCATCGAGGGCATTTT-GTCATTTTACCCATCGAGGGCATTTCGAGTCATTTTAC
*
3420063 CCATCGAGGGTATTTCG
65 CCATCGAGGGCATTTCG
* * * * * *
3420080 ATAATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATCAAGGGCATTTTG-GTCATTTTAC
1 GTCATTTTACCCATCGAGGGCATTT-TGTCATTTTACCCATCGAGGGCATTTCGAGTCATTTTAC
* * *
3420144 CCATCGAGGACAATTCA
65 CCATCGAGGGCATTTCG
* * * *
3420161 GTCATTTTACCCATCAATGGCATTTTAGTCATTTTAACCATCGAGGGTATTTC-AGTCATTTTA
1 GTCATTTTACCCATCGAGGGCATTTT-GTCATTTTACCCATCGAGGGCATTTCGAGTCATTTTA
3420224 GGCCCAATTC
Statistics
Matches: 327, Mismatches: 51, Indels: 18
0.83 0.13 0.05
Matches are distributed among these distances:
80 3 0.01
81 323 0.99
82 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (81 bp):
GTCATTTTACCCATCGAGGGCATTTTGTCATTTTACCCATCGAGGGCATTTCGAGTCATTTTACC
CATCGAGGGCATTTCG
Found at i:3460419 original size:23 final size:23
Alignment explanation
Indices: 3460387--3460452 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
3460377 TTTTTTGAAC
* *
3460387 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
3460410 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
3460433 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
3460453 CCCAAAACCG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:3467892 original size:25 final size:25
Alignment explanation
Indices: 3467864--3467919 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
3467854 ACCGATTCTC
3467864 AGCTCG-AGAGAGCTTACCGATATTT
1 AGCTCGCA-AGAGCTTACCGATATTT
* *
3467889 AGCTCGCATGAGCTTATCGATATTT
1 AGCTCGCAAGAGCTTACCGATATTT
3467914 AGCTCG
1 AGCTCG
3467920 TATGAGCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (25 bp):
AGCTCGCAAGAGCTTACCGATATTT
Found at i:3467924 original size:25 final size:25
Alignment explanation
Indices: 3467873--3467926 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
3467863 CAGCTCGAGA
3467873 GAGCTTACCGATATTTAGCTCGCAT
1 GAGCTTACCGATATTTAGCTCGCAT
* *
3467898 GAGCTTATCGATATTTAGCTCGTAT
1 GAGCTTACCGATATTTAGCTCGCAT
3467923 GAGC
1 GAGC
3467927 ATACATGTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (25 bp):
GAGCTTACCGATATTTAGCTCGCAT
Found at i:3477273 original size:26 final size:26
Alignment explanation
Indices: 3477237--3477317 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
3477227 AGAGCGTAGT
*
3477237 AGGCTTCGTGCTGGTGTATATTTAGC
1 AGGCTTTGTGCTGGTGTATATTTAGC
* * * *
3477263 AGGCTTTGTGCTAGTGTTTCTATAGC
1 AGGCTTTGTGCTGGTGTATATTTAGC
* *
3477289 AGACACTTTGTACTGGTGTTATATTTAGC
1 AG--GCTTTGTGCTGGTG-TATATTTAGC
3477318 CAGTACTCTG
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
26 23 0.56
28 11 0.27
29 7 0.17
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.41
Consensus pattern (26 bp):
AGGCTTTGTGCTGGTGTATATTTAGC
Found at i:3479540 original size:41 final size:41
Alignment explanation
Indices: 3479462--3479547 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
3479452 ATTTTCCAGG
* **
3479462 TATGATTTCGTGTAAGAATATGTCTGGGACATTGGCATCGTA
1 TATGATTTCGTGTAAGAACATGTCTGGGACAGAGGCATCG-A
* * *
3479504 TATGA-TTCGTGTAAGACCCTGTCTGGGATAGAGGCATCGA
1 TATGATTTCGTGTAAGAACATGTCTGGGACAGAGGCATCGA
3479544 TATG
1 TATG
3479548 TGATAACTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 5 0.13
41 28 0.74
42 5 0.13
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (41 bp):
TATGATTTCGTGTAAGAACATGTCTGGGACAGAGGCATCGA
Found at i:3482526 original size:50 final size:50
Alignment explanation
Indices: 3482453--3482607 Score: 179
Period size: 50 Copynumber: 3.1 Consensus size: 50
3482443 ACATTAAGAG
* *
3482453 GATGAGA--TCCCATGTTAGACCATGTTTGGGACATGGCGTTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAA
* * *
3482501 GATGAGAGGTCCCATGTAAGACCATGTTTGGGATACGGCGTTGACACCAA
1 GATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAA
* ** * * * *
3482551 GATAAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAA
*
3482601 TATGAGA
1 GATGAGA
3482608 ACTCTCATGC
Statistics
Matches: 88, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
48 7 0.08
50 81 0.92
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAA
Found at i:3486679 original size:39 final size:39
Alignment explanation
Indices: 3486592--3486741 Score: 140
Period size: 39 Copynumber: 3.8 Consensus size: 39
3486582 ATCCTATTAC
* * * ** *
3486592 ACATATAATCACCTAACATTCAAGCATATATCATGATAT
1 ACATATAATCTCATAACATTTAAGCATATATCACAACAT
* * * *
3486631 ATATTTAATCTTATAACATTTAAGCATATATCACAACCCT
1 ACATATAATCTCATAACATTTAAGCATATATCACAA-CAT
* * * * *
3486671 -CGTATAATCACATAACATTCAAGCATATACCACAATAT
1 ACATATAATCTCATAACATTTAAGCATATATCACAACAT
*
3486709 ACATATAATCTCACAACATTTAAGCATATATCA
1 ACATATAATCTCATAACATTTAAGCATATATCA
3486742 TAATACTCAA
Statistics
Matches: 85, Mismatches: 24, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
38 1 0.01
39 83 0.98
40 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.31
Consensus pattern (39 bp):
ACATATAATCTCATAACATTTAAGCATATATCACAACAT
Found at i:3486709 original size:78 final size:78
Alignment explanation
Indices: 3486595--3486741 Score: 222
Period size: 78 Copynumber: 1.9 Consensus size: 78
3486585 CTATTACACA
* * ** * * * *
3486595 TATAATCACCTAACATTCAAGCATATATCATGATATATATTTAATCTTATAACATTTAAGCATAT
1 TATAATCACATAACATTCAAGCATATACCACAATATACATATAATCTCACAACATTTAAGCATAT
3486660 ATCACAACCCTCG
66 ATCACAACCCTCG
3486673 TATAATCACATAACATTCAAGCATATACCACAATATACATATAATCTCACAACATTTAAGCATAT
1 TATAATCACATAACATTCAAGCATATACCACAATATACATATAATCTCACAACATTTAAGCATAT
3486738 ATCA
66 ATCA
3486742 TAATACTCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 61 1.00
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (78 bp):
TATAATCACATAACATTCAAGCATATACCACAATATACATATAATCTCACAACATTTAAGCATAT
ATCACAACCCTCG
Found at i:3486826 original size:17 final size:17
Alignment explanation
Indices: 3486783--3486827 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3486773 GCATAATGGT
3486783 CATATGTCAT-ATAAACA
1 CATAT-TCATAATAAACA
*
3486800 CATA-TCATAATACACA
1 CATATTCATAATAAACA
3486816 CATATTCATAAT
1 CATATTCATAAT
3486828 TTATGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 4 0.16
16 10 0.40
17 11 0.44
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (17 bp):
CATATTCATAATAAACA
Done.