Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold160
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: 5021213
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 92036 characters in sequence are not A, C, G, or T
File 18 of 30
Found at i:2845063 original size:59 final size:58
Alignment explanation
Indices: 2844957--2845068 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 58
2844947 ACCCTGTCAA
*
2844957 AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCACCCTTTTTCG
1 AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTTTTTCG
* * * *
2845015 AAGCCCATAAGTCAGTGGCATCTTTTCCAAAGCCCACAAG-CTAGTGGCAACCTT
1 AAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTC-AGTGGCAACCTT
2845069 CAAAAGTCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
58 21 0.45
59 26 0.55
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (58 bp):
AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAACCTTTTTCG
Found at i:2845237 original size:29 final size:29
Alignment explanation
Indices: 2845204--2845354 Score: 81
Period size: 34 Copynumber: 4.9 Consensus size: 29
2845194 ACTCTTTTTC
*
2845204 CTTTTTAAAGCCCACAACTCTGTGGCACT
1 CTTTTTAAAGCCCACAACTCAGTGGCACT
* * *
2845233 CTTTTTCCTTTTAAGCCTACAACTCCGTGGCACT
1 C---TT--TTTAAAGCCCACAACTCAGTGGCACT
* * *
2845267 CTTTTTCCTTTTAAGTCCACAACTCTGTGGCAC-
1 C---TT--TTTAAAGCCCACAACTCAGTGGCACT
* * *
2845300 CCTTTT-AAGCCCACAAGTCAGTGGCACC
1 CTTTTTAAAGCCCACAACTCAGTGGCACT
* * *
2845328 CCTTTCAAAGCCCACAAGTCAGTGGCA
1 CTTTTTAAAGCCCACAACTCAGTGGCA
2845355 ACCTTCAAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
27 18 0.17
28 8 0.08
29 21 0.20
30 1 0.01
32 2 0.02
33 1 0.01
34 53 0.51
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.30
Consensus pattern (29 bp):
CTTTTTAAAGCCCACAACTCAGTGGCACT
Found at i:2845255 original size:34 final size:35
Alignment explanation
Indices: 2845071--2845305 Score: 293
Period size: 34 Copynumber: 6.8 Consensus size: 35
2845061 GCAACCTTCA
* * *
2845071 AAAGTCCACAACTCCGTGGCACAT-TTTTTCTTTTT
1 AAAGCCCACAACTCTGTGGCAC-TCTTTTTCCTTTT
* *
2845106 AAAGCCCACAACTCTATGGCACTC-TTTTCCTTCT
1 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
* * *
2845140 -AAGTCCACAACTCCGTGGCAC-CTTTCTTCTTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTT-TTCCTTTT
2845174 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTTTCC-TTTT
2845210 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
* *
2845245 -AAGCCTACAACTCCGTGGCACTCTTTTTCCTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
* *
2845279 -AAGTCCACAACTCTGTGGCACCCTTTT
1 AAAGCCCACAACTCTGTGGCACTCTTTT
2845306 AAGCCCACAA
Statistics
Matches: 175, Mismatches: 19, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.01
33 20 0.11
34 70 0.40
35 45 0.26
36 39 0.22
ACGTcount: A:0.20, C:0.31, G:0.11, T:0.37
Consensus pattern (35 bp):
AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
Found at i:2845287 original size:104 final size:103
Alignment explanation
Indices: 2845071--2845305 Score: 343
Period size: 104 Copynumber: 2.3 Consensus size: 103
2845061 GCAACCTTCA
*
2845071 AAAGTCCACAACTCCGTGGCACAT-TTTTTCTTTTTAAAGCCCACAACTCTATGGCACTCTTTTC
1 AAAGTCCACAACTCTGTGGCAC-TCTTTTTCTTTTTAAAGCCCACAACTCTATGGCACTCTTTTC
*
2845135 CTTCTAAGTCCACAACTCCGTGGCACCTTTCTTCTTTTT
65 CTTCTAAGTCCACAACTCCGTGGCACCTTTCTTCCTTTT
* *
2845174 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 AAAGTCCACAACTCTGTGGCACTCTTTTT-CTTTTTAAAGCCCACAACTCTATGGCACTC-TTTT
*
2845239 CCTTTTAAG-CCTACAACTCCGTGGCACTCTTT-TTCCTTTT
64 CCTTCTAAGTCC-ACAACTCCGTGGCAC-CTTTCTTCCTTTT
*
2845279 -AAGTCCACAACTCTGTGGCACCCTTTT
1 AAAGTCCACAACTCTGTGGCACTCTTTT
2845306 AAGCCCACAA
Statistics
Matches: 120, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
102 1 0.01
103 25 0.21
104 56 0.47
105 34 0.28
106 4 0.03
ACGTcount: A:0.20, C:0.31, G:0.11, T:0.37
Consensus pattern (103 bp):
AAAGTCCACAACTCTGTGGCACTCTTTTTCTTTTTAAAGCCCACAACTCTATGGCACTCTTTTCC
TTCTAAGTCCACAACTCCGTGGCACCTTTCTTCCTTTT
Found at i:2845304 original size:27 final size:27
Alignment explanation
Indices: 2845273--2845359 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 27
2845263 CACTCTTTTT
* *
2845273 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGCCCACAACTCAGTGGCAC
*
2845300 CCTTTTAAGCCCACAAGTCAGTGGCACC
1 CCTTTTAAGCCCACAACTCAGTGGCA-C
* * *
2845328 CCTTTCAAAGCCCACAAGTCAGTGGCAA
1 CCTTT-TAAGCCCACAACTCAGTGGCAC
2845356 CCTT
1 CCTT
2845360 CAAAAGCACA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
27 23 0.43
28 10 0.19
29 20 0.38
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.24
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCAGTGGCAC
Found at i:2845382 original size:27 final size:30
Alignment explanation
Indices: 2845327--2845410 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 30
2845317 TCAGTGGCAC
*
2845327 CCCTTTC-AAAGCC-CACAAG-TCAGTGGCAA
1 CCCTTTCAAAAGCCACACAAGTTGA-T-GCAA
2845356 -CC-TTCAAAAG-CACACAAGTTGATGCAA
1 CCCTTTCAAAAGCCACACAAGTTGATGCAA
2845383 CCCTTTCAAAAGCCCACACAAGTTGATG
1 CCCTTTCAAAAG-CCACACAAGTTGATG
2845411 GCGTCTTCTT
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
27 8 0.17
28 15 0.32
29 10 0.21
31 14 0.30
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.19
Consensus pattern (30 bp):
CCCTTTCAAAAGCCACACAAGTTGATGCAA
Found at i:2845541 original size:21 final size:21
Alignment explanation
Indices: 2845477--2845541 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
2845467 TCTTTAAAAC
2845477 CCAATATCGCTGGCCTTGAAT
1 CCAATATCGCTGGCCTTGAAT
* *
2845498 -CAGCATATTGAC--ACCTTGAAAT
1 CCA--ATATCG-CTGGCCTTG-AAT
2845520 CCAATATCGCTGGCCTTGAAT
1 CCAATATCGCTGGCCTTGAAT
2845541 C
1 C
2845542 AGTATACTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
20 3 0.09
21 14 0.42
22 13 0.39
23 3 0.09
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (21 bp):
CCAATATCGCTGGCCTTGAAT
Found at i:2845592 original size:91 final size:93
Alignment explanation
Indices: 2845429--2845696 Score: 237
Period size: 91 Copynumber: 2.9 Consensus size: 93
2845419 TTCTAAGTCT
* * * *
2845429 AATATCGCTGGCCTTGAACCAGCATATTGGCACCTTTATCTTTAAAACCCAATATCGCTGGCCTT
1 AATATCGCTGGCCTTGAACCAGCATACTGACACCTTTATCTCTAAAACCCAATATCGCTAGCCTT
*
2845494 GAATCAGCATATTGACACCTTGAAATCC
66 GAATCAGCACATTGACACCTTGAAATCC
* * * * * *
2845522 AATATCGCTGGCCTTGAATCAGTATACTGACA-CTTTGTCTCTAAGA-CCAATGTTGCTAGCCTT
1 AATATCGCTGGCCTTGAACCAGCATACTGACACCTTTATCTCTAAAACCCAATATCGCTAGCCTT
*
2845585 GAATCAGCACATTGGCA-C---AAGA-CC
66 GAATCAGCACATTGACACCTTGAA-ATCC
* * * * * * * * * *
2845609 AATGTCGCTGGCCATGAATCAGCATATTGGCACCTTAACCATCTTTAAGA-CCAATGTCGCTGGC
1 AATATCGCTGGCCTTGAACCAGCATACTGACACCTT---TATCTCTAAAACCCAATATCGCTAGC
*
2845673 CTTGAATCAGCACATTGGCACCTT
63 CTTGAATCAGCACATTGACACCTT
2845697 TATCTTTTAG
Statistics
Matches: 145, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
87 31 0.21
88 4 0.03
90 1 0.01
91 69 0.48
92 12 0.08
93 28 0.19
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (93 bp):
AATATCGCTGGCCTTGAACCAGCATACTGACACCTTTATCTCTAAAACCCAATATCGCTAGCCTT
GAATCAGCACATTGACACCTTGAAATCC
Found at i:2845627 original size:39 final size:39
Alignment explanation
Indices: 2845564--2845641 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
2845554 CTTTGTCTCT
* *
2845564 AAGACCAATGTTGCTAGCCTTGAATCAGCACATTGGCAC
1 AAGACCAATGTCGCTAGCCATGAATCAGCACATTGGCAC
* *
2845603 AAGACCAATGTCGCTGGCCATGAATCAGCATATTGGCAC
1 AAGACCAATGTCGCTAGCCATGAATCAGCACATTGGCAC
2845642 CTTAACCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (39 bp):
AAGACCAATGTCGCTAGCCATGAATCAGCACATTGGCAC
Found at i:2845722 original size:49 final size:49
Alignment explanation
Indices: 2845603--2845837 Score: 170
Period size: 52 Copynumber: 4.7 Consensus size: 49
2845593 ACATTGGCAC
* * *
2845603 AAGACCAATGTCGCTGGCCATGAATCAGCATATTGGCACCTTAACCATCTTT
1 AAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT---TATCTTT
* *
2845655 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTT
1 AAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTT
* * * * * * *
2845704 TAGTCCAATATTGTTGGCCTTGAATCAGTATATTGGCATCTTTAACATTTCT
1 AAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC--TT-T
* * * * * *
2845756 AAGCCCAATGTCGCTGGCCTT-ATCTCAGCACATTGGCA--TTTTTCTTC
1 AAGACCAATATCGCTGGCCTTGA-ATCAGCATATTGGCACCTTTATCTTT
* * * * * *
2845803 AAGTCTAATGTCACTGGTCATGAATCAGCATATTG
1 AAGACCAATATCGCTGGCCTTGAATCAGCATATTG
2845838 TCATTCTTCG
Statistics
Matches: 148, Mismatches: 30, Indels: 15
0.77 0.16 0.08
Matches are distributed among these distances:
47 26 0.18
48 3 0.02
49 43 0.29
50 4 0.03
51 3 0.02
52 69 0.47
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (49 bp):
AAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTT
Found at i:2845794 original size:52 final size:51
Alignment explanation
Indices: 2845603--2845794 Score: 203
Period size: 52 Copynumber: 3.8 Consensus size: 51
2845593 ACATTGGCAC
* * *
2845603 AAGACCAATGTCGCTGGCCATGAATCAGCATATTGGCA-CCTTAACCATCTTT
1 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTAA-CAT-TTT
* *
2845655 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATC-TTTT
1 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTAACATTTT
* * * * * *
2845705 -AGTCCAATATTGTTGGCCTTGAATCAGTATATTGGCATCTTTAACATTTCT
1 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTAACATTT-T
* *
2845756 AAGCCCAATGTCGCTGGCCTT-ATCTCAGCACATTGGCAT
1 AAGACCAATGTCGCTGGCCTTGA-ATCAGCACATTGGCAT
2845795 TTTTCTTCAA
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
49 37 0.32
50 6 0.05
51 3 0.03
52 66 0.57
53 4 0.03
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (51 bp):
AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTAACATTTT
Found at i:2846580 original size:13 final size:13
Alignment explanation
Indices: 2846562--2846650 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
2846552 TTCAACAATT
2846562 TGTATCGATACAA
1 TGTATCGATACAA
2846575 TGTATCGATACATAA
1 TGTATCGATAC--AA
2846590 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2846607 TGTATCGATACATAA
1 TGTATCGATAC--AA
2846622 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2846639 TGTATCGATACA
1 TGTATCGATACA
2846651 TAAGTTTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2846599 original size:19 final size:18
Alignment explanation
Indices: 2846575--2846669 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
2846565 ATCGATACAA
2846575 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
2846594 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
2846607 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
2846626 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
2846639 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
*
2846658 TTTATCGATACA
1 TGTATCGATACA
2846670 ATGTATCGCT
Statistics
Matches: 63, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 22 0.35
15 4 0.06
17 4 0.06
19 33 0.52
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:2846602 original size:32 final size:32
Alignment explanation
Indices: 2846561--2846682 Score: 217
Period size: 32 Copynumber: 3.8 Consensus size: 32
2846551 TTTCAACAAT
2846561 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
2846593 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
2846625 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
* *
2846657 TTTTATCGATACAATGTATCGCTACA
1 TTGTATCGATACAATGTATCGATACA
2846683 AAGCTACTGC
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 87 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:2852141 original size:3 final size:3
Alignment explanation
Indices: 2852133--2852163 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2852123 CAATTATCTC
*
2852133 ATG ATG ATG ATG ATG ATG ATG ATT ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
2852164 AATAATGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:2854558 original size:89 final size:89
Alignment explanation
Indices: 2854447--2854616 Score: 234
Period size: 89 Copynumber: 1.9 Consensus size: 89
2854437 ATGAGGTTGA
* * * * *
2854447 AGTATCCCCTCGAAGTAGTGGGGATGAAG-TTTCTCCAAGGATAAAATTATATGAAGGAAAATTT
1 AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTC-CCAAGGACAAAATTATACGAAGGAAAATTT
* *
2854511 AAATTTTTGATAGAACAAGGGTTAG
65 AAATTTTTAATAAAACAAGGGTTAG
* * *
2854536 AGTATCCCCTCGGAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAGATTTG
1 AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAAATTTA
2854601 AATTTTTAATAAAACA
66 AATTTTTAATAAAACA
2854617 GAGTTGGAGT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
89 66 0.94
90 4 0.06
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (89 bp):
AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAAATTTA
AATTTTTAATAAAACAAGGGTTAG
Found at i:2861914 original size:12 final size:12
Alignment explanation
Indices: 2861897--2861921 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2861887 TTAAGATTAC
2861897 GGAGTTAGTTTA
1 GGAGTTAGTTTA
2861909 GGAGTTAGTTTA
1 GGAGTTAGTTTA
2861921 G
1 G
2861922 TGAAAACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (12 bp):
GGAGTTAGTTTA
Found at i:2863691 original size:3 final size:3
Alignment explanation
Indices: 2863683--2863713 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2863673 CAATTATCTC
*
2863683 ATG ATG ATG ATG ATG ATG ATG ATT ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
2863714 AATAATGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:2866108 original size:89 final size:89
Alignment explanation
Indices: 2865997--2866166 Score: 234
Period size: 89 Copynumber: 1.9 Consensus size: 89
2865987 ATGAGGTTGA
* * * * *
2865997 AGTATCCCCTCGAAGTAGTGGGGATGAAG-TTTCTCCAAGGATAAAATTATATGAAGGAAAATTT
1 AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTC-CCAAGGACAAAATTATACGAAGGAAAATTT
* *
2866061 AAATTTTTGATAGAACAAGGGTTAG
65 AAATTTTTAATAAAACAAGGGTTAG
* * *
2866086 AGTATCCCCTCGGAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAGATTTG
1 AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAAATTTA
2866151 AATTTTTAATAAAACA
66 AATTTTTAATAAAACA
2866167 GAGTTGGAGT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
89 66 0.94
90 4 0.06
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (89 bp):
AGTATCCCCTCGAAGGAATGGGGATAAAGTTTTCCCAAGGACAAAATTATACGAAGGAAAATTTA
AATTTTTAATAAAACAAGGGTTAG
Found at i:2873465 original size:12 final size:12
Alignment explanation
Indices: 2873448--2873472 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2873438 TTAAGATTAC
2873448 GGAGTTAGTTTA
1 GGAGTTAGTTTA
2873460 GGAGTTAGTTTA
1 GGAGTTAGTTTA
2873472 G
1 G
2873473 TGAAAACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (12 bp):
GGAGTTAGTTTA
Found at i:2874863 original size:20 final size:20
Alignment explanation
Indices: 2874792--2874883 Score: 85
Period size: 20 Copynumber: 4.6 Consensus size: 20
2874782 AAAAACCCAA
* * *
2874792 AATGTATTGATACATTGAGT
1 AATGTATCGATACATTAACT
* *
2874812 AATTTATCGATACATTAAGT
1 AATGTATCGATACATTAACT
* *
2874832 AATATATCGATACATTTACT
1 AATGTATCGATACATTAACT
* * *
2874852 TATGTATTGATACATTCACT
1 AATGTATCGATACATTAACT
*
2874872 TATGTATCGATA
1 AATGTATCGATA
2874884 TAATTTTTCC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTAACT
Found at i:2874985 original size:20 final size:21
Alignment explanation
Indices: 2874946--2874991 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
2874936 ATAAGCCTGA
*
2874946 GTATCAATACATTCACTTA-T
1 GTATCAATACATTAACTTATT
*
2874966 GTATCAATACATTAATTTATT
1 GTATCAATACATTAACTTATT
2874987 GTATC
1 GTATC
2874992 GATATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (21 bp):
GTATCAATACATTAACTTATT
Found at i:2876042 original size:29 final size:29
Alignment explanation
Indices: 2875957--2876203 Score: 243
Period size: 29 Copynumber: 8.6 Consensus size: 29
2875947 TGCCAGCTAG
*
2875957 TATGGGCTTTAAAAA-GGTGCCATTGACT
1 TATGGGCTTTAAAAAGGGTGCCACTGACT
* * * * * *
2875985 TGTAGTCTTT-GAAAGAGTGCCATTGACT
1 TATGGGCTTTAAAAAGGGTGCCACTGACT
* *
2876013 TGTGGGCTTTAAAAAGGGTGCCACTAACT
1 TATGGGCTTTAAAAAGGGTGCCACTGACT
* *
2876042 TGTGGGCTTTGAAAAGGGTGCCACTGACT
1 TATGGGCTTTAAAAAGGGTGCCACTGACT
* * *
2876071 TATGGGCTTTGAAAAGGGTGCCATTAACT
1 TATGGGCTTTAAAAAGGGTGCCACTGACT
* *
2876100 TATGGGCTTT-GAAAGTGGTGCCACTTACT
1 TATGGGCTTTAAAAAG-GGTGCCACTGACT
**
2876129 TATGGGCTTTGAAAAA-GGTGCCACTGGTT
1 TATGGGCTTT-AAAAAGGGTGCCACTGACT
*
2876158 TATGGGC-TTAGAAAAGGGTGCCACTAACT
1 TATGGGCTTTA-AAAAGGGTGCCACTGACT
* *
2876187 TGTGGGCTTTGAAAAGG
1 TATGGGCTTTAAAAAGG
2876204 TTCAACTCCC
Statistics
Matches: 183, Mismatches: 28, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
27 4 0.02
28 37 0.20
29 137 0.75
30 2 0.01
31 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
TATGGGCTTTAAAAAGGGTGCCACTGACT
Found at i:2876086 original size:58 final size:57
Alignment explanation
Indices: 2875957--2876203 Score: 280
Period size: 58 Copynumber: 4.3 Consensus size: 57
2875947 TGCCAGCTAG
* * * * * * * *
2875957 TATGGGCTTT-AAAAAGGTGCCATTGACTTGTAGTCTTTGAAAGAGTGCCATTGACT
1 TATGGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTGACT
* * *
2876013 TGTGGGCTTTAAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
1 TATGGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTG-AAAGGGTGCCACTGACT
* *
2876071 TATGGGCTTTGAAAAGGGTGCCATTAACTTATGGGCTTTGAAAGTGGTGCCACTTACT
1 TATGGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTGAAAG-GGTGCCACTGACT
* *** * *
2876129 TATGGGCTTTGAAAAAGGTGCCACTGGTTTATGGGCTTAGAAAAGGGTGCCACTAACT
1 TATGGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTG-AAAGGGTGCCACTGACT
*
2876187 TGTGGGCTTTGAAAAGG
1 TATGGGCTTTGAAAAGG
2876204 TTCAACTCCC
Statistics
Matches: 165, Mismatches: 22, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
56 9 0.05
57 28 0.17
58 124 0.75
59 4 0.02
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (57 bp):
TATGGGCTTTGAAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTGACT
Found at i:2876109 original size:87 final size:86
Alignment explanation
Indices: 2875957--2876203 Score: 318
Period size: 87 Copynumber: 2.9 Consensus size: 86
2875947 TGCCAGCTAG
* * * * * *
2875957 TATGGGCTTT-AAAAAGGTGCCATTGACTTGTAGTCTTTG-AAAGAGTGCCATTGACTTGTGGGC
1 TATGGGCTTTGAAAAAGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCATTAACTTGTGGGC
2876020 TTTAAAAAGGGTGCCACTAACT
66 TTT-AAAAGGGTGCCACTAACT
* * *
2876042 TGTGGGCTTTGAAAAGGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCATTAACTTATGGGC
1 TATGGGCTTTGAAAAAGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCATTAACTTGTGGGC
* *
2876107 TTTGAAAGTGGTGCCACTTACT
66 TTTAAAAG-GGTGCCACTAACT
** * *
2876129 TATGGGCTTTGAAAAAGGTGCCACTGGTTTATGGGCTTAGAAAAGGGTGCCACTAACTTGTGGGC
1 TATGGGCTTTGAAAAAGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCATTAACTTGTGGGC
2876194 TTTGAAAAGG
66 TTT-AAAAGG
2876204 TTCAACTCCC
Statistics
Matches: 139, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
85 9 0.06
86 28 0.20
87 98 0.71
88 4 0.03
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (86 bp):
TATGGGCTTTGAAAAAGGTGCCACTGACTTATGGGCTTTGAAAAGGGTGCCATTAACTTGTGGGC
TTTAAAAGGGTGCCACTAACT
Found at i:2876623 original size:24 final size:24
Alignment explanation
Indices: 2876591--2876636 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2876581 AGTTTCCTAA
2876591 TGAAAAAA-TCTTAACACAAGTTCT
1 TGAAAAAATTCTTAACA-AAGTTCT
*
2876615 TGAAAAAATTCTTGACAAAGTT
1 TGAAAAAATTCTTAACAAAGTT
2876637 TCTGACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (24 bp):
TGAAAAAATTCTTAACAAAGTTCT
Found at i:2882607 original size:32 final size:33
Alignment explanation
Indices: 2882544--2882608 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
2882534 CAGACCCAGA
*
2882544 TGTATCAATACATTATGCTTTGTATCAATACAT
1 TGTATCAATACATTATGCATTGTATCAATACAT
* * *
2882577 TGTATCGATACA-TATTCATTGTATCGATACAT
1 TGTATCAATACATTATGCATTGTATCAATACAT
2882609 GGATAATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (33 bp):
TGTATCAATACATTATGCATTGTATCAATACAT
Found at i:2882619 original size:20 final size:20
Alignment explanation
Indices: 2882575--2882630 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
2882565 GTATCAATAC
*
2882575 ATTGTATCGATACAT-ATTC
1 ATTGTATCGATACATGATTA
2882594 ATTGTATCGATACATGGA-TA
1 ATTGTATCGATACAT-GATTA
*
2882614 ATTGTATCAATACATGA
1 ATTGTATCGATACATGA
2882631 AACTGGCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.52
20 15 0.45
21 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (20 bp):
ATTGTATCGATACATGATTA
Found at i:2884215 original size:20 final size:20
Alignment explanation
Indices: 2884190--2884246 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
2884180 TTTTACCCAG
* *
2884190 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
2884210 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
2884230 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
2884247 GTCTTTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:2890802 original size:19 final size:19
Alignment explanation
Indices: 2890756--2890809 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
2890746 TGCTAGTTTC
**
2890756 ATGTATCGATACAATTGTCT
1 ATGTATCGATACAA-TGAAT
*
2890776 ATGCATCGATACAATGAAT
1 ATGTATCGATACAATGAAT
2890795 ATGTATCGATACAAT
1 ATGTATCGATACAAT
2890810 TTATTGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGAAT
Found at i:2891435 original size:22 final size:22
Alignment explanation
Indices: 2891407--2891448 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2891397 ATCGAAATAT
2891407 ATTTCTCCCACTTTATCAAAGC
1 ATTTCTCCCACTTTATCAAAGC
* *
2891429 ATTTCTCCCATTTTGTCAAA
1 ATTTCTCCCACTTTATCAAA
2891449 TCTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTTCTCCCACTTTATCAAAGC
Found at i:2893379 original size:33 final size:33
Alignment explanation
Indices: 2893337--2893402 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
2893327 ATAGTAACCC
*
2893337 ATGTATCGATACAAGGAATGTTGTATTGATACA
1 ATGTATCGATACAAGGAATGTTGTATCGATACA
2893370 ATGTATCGATACAAGGAATGTTGTATCGATACA
1 ATGTATCGATACAAGGAATGTTGTATCGATACA
2893403 TTTGGGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAGGAATGTTGTATCGATACA
Found at i:2893396 original size:20 final size:20
Alignment explanation
Indices: 2893338--2893402 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
2893328 TAGTAACCCA
2893338 TGTATCGATACAAGGAATGT
1 TGTATCGATACAAGGAATGT
*
2893358 TGTATTGATAC----AA---
1 TGTATCGATACAAGGAATGT
2893371 TGTATCGATACAAGGAATGT
1 TGTATCGATACAAGGAATGT
2893391 TGTATCGATACA
1 TGTATCGATACA
2893403 TTTGGGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 10 0.28
16 2 0.06
17 2 0.06
20 22 0.61
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (20 bp):
TGTATCGATACAAGGAATGT
Found at i:2896131 original size:139 final size:139
Alignment explanation
Indices: 2895873--2896153 Score: 508
Period size: 139 Copynumber: 2.0 Consensus size: 139
2895863 GCTTTCGCCC
*
2895873 AAAAATATCTTGGTAAATTATTTTCGCAAAGCATGGTTCTAGCCATTTCTTCCAAAGTCCAATTT
1 AAAAATATCTTGGTAAATTATTTTCACAAAGCATGGTTCTAGCCATTTCTTCCAAAGTCCAATTT
2895938 TTCCTCTCAACAACTCTATTTTGTTGAGGAGTTCTAGGAGCTGAAAAATCATGGCTAATACTATT
66 TTCCTCTCAACAACTCTATTTTGTTGAGGAGTTCTAGGAGCTGAAAAATCATGGCTAATACTATT
2896003 TTCATTACA
131 TTCATTACA
* *
2896012 AAAAATATCTTGGTAAATTATTTTCACAAAGCATGGTTCTAGCCATTTCTTCGAAAGTCCGATTT
1 AAAAATATCTTGGTAAATTATTTTCACAAAGCATGGTTCTAGCCATTTCTTCCAAAGTCCAATTT
* * *
2896077 TTCCTCTCAACAACTCTATTTTGTTGAGGAGTTCTAGGAGCTGAGAAATTATGGCTAATACTGTT
66 TTCCTCTCAACAACTCTATTTTGTTGAGGAGTTCTAGGAGCTGAAAAATCATGGCTAATACTATT
2896142 TTCATTACA
131 TTCATTACA
2896151 AAA
1 AAA
2896154 TTTATCAAAA
Statistics
Matches: 136, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (139 bp):
AAAAATATCTTGGTAAATTATTTTCACAAAGCATGGTTCTAGCCATTTCTTCCAAAGTCCAATTT
TTCCTCTCAACAACTCTATTTTGTTGAGGAGTTCTAGGAGCTGAAAAATCATGGCTAATACTATT
TTCATTACA
Found at i:2899710 original size:20 final size:20
Alignment explanation
Indices: 2899685--2899734 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2899675 CAAGCAATGT
*
2899685 ATCGATATAAT-TCATCATGC
1 ATCGATATAATGT-ACCATGC
* *
2899705 ATCGATACAATGTACCATGT
1 ATCGATATAATGTACCATGC
2899725 ATCGATATAA
1 ATCGATATAA
2899735 ACATTGGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (20 bp):
ATCGATATAATGTACCATGC
Found at i:2899802 original size:13 final size:13
Alignment explanation
Indices: 2899784--2899843 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
2899774 ACAATTGTCC
2899784 ATGTATCGATACA
1 ATGTATCGATACA
2899797 ATGTATCGATACA
1 ATGTATCGATACA
*
2899810 A---AGC-AT--A
1 ATGTATCGATACA
2899817 ATGTATCGATACA
1 ATGTATCGATACA
2899830 ATGTATCGATACA
1 ATGTATCGATACA
2899843 A
1 A
2899844 AGCATTCTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 2 0.05
9 2 0.05
10 4 0.10
11 2 0.05
13 29 0.74
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2899848 original size:33 final size:33
Alignment explanation
Indices: 2899784--2899848 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
2899774 ACAATTGTCC
2899784 ATGTATCGATACAATGTATCGATACAAAGCATA
1 ATGTATCGATACAATGTATCGATACAAAGCATA
2899817 ATGTATCGATACAATGTATCGATACAAAGCAT
1 ATGTATCGATACAATGTATCGATACAAAGCAT
2899849 TCTGGGTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAATGTATCGATACAAAGCATA
Found at i:2905549 original size:17 final size:17
Alignment explanation
Indices: 2905527--2905561 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2905517 TTGTTTGCTT
2905527 AAAAATACTCTAAAAAC
1 AAAAATACTCTAAAAAC
2905544 AAAAATACTCTAAAAAC
1 AAAAATACTCTAAAAAC
2905561 A
1 A
2905562 TGTTCTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAATACTCTAAAAAC
Found at i:2914698 original size:34 final size:33
Alignment explanation
Indices: 2914642--2914846 Score: 211
Period size: 34 Copynumber: 6.5 Consensus size: 33
2914632 ATGATGCAAA
2914642 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGG
1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGG
*
2914675 AGTTGTGGGCTTTGAAAAGAAGAAAGTGCCACGG
1 AGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGG
*
2914709 AGTTGTGGGC-TT--AA-ACG--GGTGCCACGG
1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGG
* * *
2914736 AGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACGG
1 AGTTGTGGGCTTTAAA-A-GAAGAAGGTGCCACGG
*
2914770 AATTGTGGGCTTT--AA-AAG--GGTGCCACGG
1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGG
* *
2914798 AGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGG
1 AGTTGTGGGCTTTAAAA-GAAGAAGGTGCCACGG
2914831 AGTTGTGGGCTTTAAA
1 AGTTGTGGGCTTTAAA
2914847 GAAAAAATGC
Statistics
Matches: 141, Mismatches: 15, Indels: 31
0.75 0.08 0.17
Matches are distributed among these distances:
27 22 0.16
28 17 0.12
29 5 0.04
30 5 0.04
31 2 0.01
32 2 0.01
33 35 0.25
34 51 0.36
35 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.22
Consensus pattern (33 bp):
AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGG
Found at i:2914738 original size:27 final size:26
Alignment explanation
Indices: 2914700--2914812 Score: 100
Period size: 27 Copynumber: 3.9 Consensus size: 26
2914690 AAAGAAGAAA
*
2914700 GTGCCACGGAGTTGTGGGCTTAAACGG
1 GTGCCACGGAGTTGTGGACTTAAA-GG
2914727 GTGCCACGGAGTTGTGGACTTAAAGATG
1 GTGCCACGGAGTTGTGGACTTAAAG--G
* *
2914755 AAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGG
1 ------GTGCCACGGAGTTGTGGAC-TT-AAAGG
2914789 GTGCCACGGAGTTGTGGACTTAAA
1 GTGCCACGGAGTTGTGGACTTAAA
2914813 AGGAACAAGG
Statistics
Matches: 71, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
26 4 0.06
27 25 0.35
28 18 0.25
34 18 0.25
35 2 0.03
36 4 0.06
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.23
Consensus pattern (26 bp):
GTGCCACGGAGTTGTGGACTTAAAGG
Found at i:2914740 original size:61 final size:60
Alignment explanation
Indices: 2914665--2914847 Score: 251
Period size: 61 Copynumber: 3.0 Consensus size: 60
2914655 AAAAGAAGAA
* * *
2914665 GGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAAGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGAC-TT-AAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAG
* *
2914726 GGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAA-AGGAAAAAAGTGCCACGGAGTTGTGGGC-TTAAAAG
* * *
2914788 GGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAG
2914848 AAAAAATGCC
Statistics
Matches: 110, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
59 3 0.03
60 9 0.08
61 67 0.61
62 31 0.28
ACGTcount: A:0.28, C:0.14, G:0.36, T:0.22
Consensus pattern (60 bp):
GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAAG
Found at i:2914885 original size:30 final size:31
Alignment explanation
Indices: 2914790--2914907 Score: 112
Period size: 30 Copynumber: 3.8 Consensus size: 31
2914780 TTTAAAAGGG
* * * **
2914790 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 TGCCACTGAGTCGTGGACTTTAAA-GAA-AAAA
* * *
2914823 TGCCACGGAGTTGTGGGCTTTAAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
* *
2914854 TGCCACTGAGTCGTGGACTTT-GAGACAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
*
2914884 TGCCACTGAGTCGTGGACGTTAAA
1 TGCCACTGAGTCGTGGACTTTAAA
2914908 AAGGTATTTG
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
30 27 0.37
31 21 0.29
32 3 0.04
33 22 0.30
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
Found at i:2914907 original size:122 final size:122
Alignment explanation
Indices: 2914665--2914908 Score: 257
Period size: 122 Copynumber: 2.0 Consensus size: 122
2914655 AAAAGAAGAA
* * **
2914665 GGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAAGTGCCACGGAGTTGTGGGCTTAAACGGGTG
1 GGTGCCACGGAGTTGTGGACTTTGAAAAGAACAAAGTGCCACGGAGTTGTGGGCTTAAACGAATG
* * * *
2914730 CCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAG
66 CCACGGAGTCGTGGACTT-AAGATGAAAAAAGTGCCACGGAATCGTGGACGTTAAAAG
*
2914788 GGTGCCACGGAGTTGTGGAC-TT-AAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAA-GAA
1 GGTGCCACGGAGTTGTGGACTTTGAAAA-GAACAAAGTGCCACGGAGTTGTGGGC-TTAAACG--
* * * * *
2914850 AAAATGCCACTGAGTCGTGGACTT-TGA-GACAAAA-TGCCACTGAGTCGTGGACGTTAAAA
62 --AATGCCACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACGGAATCGTGGACGTTAAAA
2914909 AGGTATTTGA
Statistics
Matches: 101, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
121 4 0.04
122 47 0.47
123 30 0.30
124 2 0.02
126 18 0.18
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (122 bp):
GGTGCCACGGAGTTGTGGACTTTGAAAAGAACAAAGTGCCACGGAGTTGTGGGCTTAAACGAATG
CCACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACGGAATCGTGGACGTTAAAAG
Found at i:2916219 original size:14 final size:14
Alignment explanation
Indices: 2916202--2916241 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2916192 CCTTTGCACT
2916202 TTTTTTTTGTTTTG
1 TTTTTTTTGTTTTG
*
2916216 TTTTTTTTTTTTTG
1 TTTTTTTTGTTTTG
*
2916230 TTTTTTGTGTTT
1 TTTTTTTTGTTT
2916242 ACTTTTGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Found at i:2916223 original size:9 final size:9
Alignment explanation
Indices: 2916202--2916241 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
2916192 CCTTTGCACT
2916202 TTTTTTTTG
1 TTTTTTTTG
*
2916211 TTTTGTTTTT
1 TTTT-TTTTG
2916221 TTTTTTTTG
1 TTTTTTTTG
*
2916230 TTTTTTGTG
1 TTTTTTTTG
2916239 TTT
1 TTT
2916242 ACTTTTGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:2923215 original size:52 final size:52
Alignment explanation
Indices: 2923134--2923254 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
2923124 TGAAAAGTTA
*
2923134 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
2923186 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
2923238 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
2923255 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:2923267 original size:52 final size:51
Alignment explanation
Indices: 2923134--2923274 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
2923124 TGAAAAGTTA
2923134 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
2923186 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
2923238 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2923275 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:2923281 original size:13 final size:13
Alignment explanation
Indices: 2923263--2923287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2923253 CAAAGATCAG
2923263 TGTATCGATACAA
1 TGTATCGATACAA
2923276 TGTATCGATACA
1 TGTATCGATACA
2923288 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2923369 original size:33 final size:33
Alignment explanation
Indices: 2923327--2923396 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2923317 GGCAGTAGCT
2923327 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
2923360 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
2923393 TACA
1 TACA
2923397 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:2923370 original size:13 final size:13
Alignment explanation
Indices: 2923352--2923376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2923342 CAAAAAAATA
2923352 TGTATCGATACAT
1 TGTATCGATACAT
2923365 TGTATCGATACA
1 TGTATCGATACA
2923377 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2928851 original size:39 final size:39
Alignment explanation
Indices: 2928797--2928875 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
2928787 CGCCAACGGT
*
2928797 GCCCGACGAAAAAGTACTTTTAGATTTTTTGAGCTTTTC
1 GCCCGACGAAAAAGTACTTTTAGATTTTTTAAGCTTTTC
2928836 GCCCGACGAAAAAGTACTTTTAGATTTTTTAAGCTTTTC
1 GCCCGACGAAAAAGTACTTTTAGATTTTTTAAGCTTTTC
2928875 G
1 G
2928876 GCTAATACGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (39 bp):
GCCCGACGAAAAAGTACTTTTAGATTTTTTAAGCTTTTC
Found at i:2935175 original size:32 final size:33
Alignment explanation
Indices: 2935113--2935176 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2935103 TACACCCAGA
*
2935113 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCAATACATATTGCTTAGTATCGATACAT
* *
2935146 TGTATCAATACATGTT-CTTGGTATCGATACA
1 TGTATCAATACATATTGCTTAGTATCGATACA
2935177 CAATGAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCAATACATATTGCTTAGTATCGATACAT
Found at i:2935262 original size:13 final size:13
Alignment explanation
Indices: 2935225--2935262 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2935215 AACTTACTCA
*
2935225 GTATCGATACAGT
1 GTATCGATACATT
*
2935238 GTATTGATACATT
1 GTATCGATACATT
2935251 GTATCGATACAT
1 GTATCGATACAT
2935263 GGTGAAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2943281 original size:16 final size:16
Alignment explanation
Indices: 2943262--2943311 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
2943252 ATAAATTTGT
2943262 AAAAAAAGGAGAGATA
1 AAAAAAAGGAGAGATA
* *
2943278 AAAAAAAGGGGGGAGAGA
1 AAAAAAA--GGAGAGATA
*
2943296 AAAAAAGGGAGAGATA
1 AAAAAAAGGAGAGATA
2943312 TTTTGAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 14 0.52
18 13 0.48
ACGTcount: A:0.62, C:0.00, G:0.34, T:0.04
Consensus pattern (16 bp):
AAAAAAAGGAGAGATA
Found at i:2947991 original size:13 final size:13
Alignment explanation
Indices: 2947973--2947997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2947963 TCAAAGAGCT
2947973 TTTGTATTCTTTA
1 TTTGTATTCTTTA
2947986 TTTGTATTCTTT
1 TTTGTATTCTTT
2947998 GAAAGCTCAT
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:0.12, C:0.08, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTGTATTCTTTA
Found at i:2948683 original size:18 final size:19
Alignment explanation
Indices: 2948646--2948683 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2948636 GTTGTTCAAA
*
2948646 TCCACTACTTTAATTAACT
1 TCCACGACTTTAATTAACT
2948665 TCCACGACTTTAA-TAACT
1 TCCACGACTTTAATTAACT
2948683 T
1 T
2948684 TATCAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (19 bp):
TCCACGACTTTAATTAACT
Found at i:2948953 original size:20 final size:19
Alignment explanation
Indices: 2948930--2948984 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
2948920 TTTTTATTAA
2948930 TTATTTGTTATATTTAACAC
1 TTATTTGTTATATTTAA-AC
*
2948950 TTA-TT-TAATA-TTAAAC
1 TTATTTGTTATATTTAAAC
2948966 TTATTTGTTAATATTTAAA
1 TTATTTGTT-ATATTTAAA
2948985 ACTATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 5 0.17
17 6 0.21
18 5 0.17
19 5 0.17
20 8 0.28
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (19 bp):
TTATTTGTTATATTTAAAC
Found at i:2948972 original size:36 final size:35
Alignment explanation
Indices: 2948930--2949001 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
2948920 TTTTTATTAA
*
2948930 TTATTTGTT-ATATTTAACACTTATTTAATATTAAAC
1 TTATTTGTTAATATTTAAAAC-TATTTAA-ATTAAAC
*
2948966 TTATTTGTTAATATTTAAAACTATTTTAATTAAAC
1 TTATTTGTTAATATTTAAAACTATTTAAATTAAAC
2949001 T
1 T
2949002 GATCAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 8 0.24
36 15 0.45
37 10 0.30
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (35 bp):
TTATTTGTTAATATTTAAAACTATTTAAATTAAAC
Found at i:2948990 original size:20 final size:20
Alignment explanation
Indices: 2948931--2948991 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 20
2948921 TTTTATTAAT
*
2948931 TATTTGTT-ATATTTAACAC
1 TATTTGTTAATATTTAAAAC
*
2948950 T-TAT-TTAATA-TT-AAAC
1 TATTTGTTAATATTTAAAAC
2948966 TTATTTGTTAATATTTAAAAC
1 -TATTTGTTAATATTTAAAAC
2948987 TATTT
1 TATTT
2948992 TAATTAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
16 3 0.09
17 5 0.15
18 7 0.21
19 7 0.21
20 7 0.21
21 4 0.12
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (20 bp):
TATTTGTTAATATTTAAAAC
Found at i:2949454 original size:13 final size:13
Alignment explanation
Indices: 2949436--2949466 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2949426 TGATACATGG
*
2949436 TACATTGTATCGA
1 TACATTATATCGA
2949449 TACATTATATCGA
1 TACATTATATCGA
2949462 TACAT
1 TACAT
2949467 GATCAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTATATCGA
Found at i:2955469 original size:13 final size:13
Alignment explanation
Indices: 2955451--2955489 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
2955441 TACAGCAAGT
2955451 ATGTATCGATACA
1 ATGTATCGATACA
2955464 ATGTATCGATACA
1 ATGTATCGATACA
2955477 ATGTATCGATACA
1 ATGTATCGATACA
2955490 CAAAAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2957741 original size:21 final size:21
Alignment explanation
Indices: 2957708--2957752 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2957698 TTGCAAGTTG
*
2957708 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2957730 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2957750 AAA
1 AAA
2957753 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2959576 original size:15 final size:15
Alignment explanation
Indices: 2959556--2959586 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2959546 TAAAAATGTC
*
2959556 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2959571 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2959586 C
1 C
2959587 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2961683 original size:13 final size:13
Alignment explanation
Indices: 2961665--2961703 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
2961655 ACATTTTTCT
2961665 TTGTATCGATACA
1 TTGTATCGATACA
2961678 TTGTATCGATACA
1 TTGTATCGATACA
2961691 TTGTATCGATACA
1 TTGTATCGATACA
2961704 GGCTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2964269 original size:13 final size:13
Alignment explanation
Indices: 2964251--2964276 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2964241 TACAGCAAGT
2964251 ATGTATCGATACA
1 ATGTATCGATACA
2964264 ATGTATCGATACA
1 ATGTATCGATACA
2964277 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2965950 original size:20 final size:20
Alignment explanation
Indices: 2965925--2965981 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
2965915 TACTGCCAGT
2965925 TTCATGTATCGATACAATTG
1 TTCATGTATCGATACAATTG
2965945 TTCATGTATCGATACAA-TG
1 TTCATGTATCGATACAATTG
**
2965964 AACATGTATCGATACAAT
1 TTCATGTATCGATACAAT
2965982 GTATCTATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
TTCATGTATCGATACAATTG
Found at i:2974206 original size:13 final size:13
Alignment explanation
Indices: 2974188--2974213 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2974178 CAATTTTTTG
2974188 TGTATCGATACAT
1 TGTATCGATACAT
2974201 TGTATCGATACAT
1 TGTATCGATACAT
2974214 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2976778 original size:13 final size:13
Alignment explanation
Indices: 2976760--2976798 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2976750 ATAATCACCC
*
2976760 TGTATCGATACAG
1 TGTATCGATACAA
*
2976773 TGTATCGATAGAA
1 TGTATCGATACAA
2976786 TGTATCGATACAA
1 TGTATCGATACAA
2976799 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2976809 original size:20 final size:20
Alignment explanation
Indices: 2976784--2976862 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
2976774 GTATCGATAG
2976784 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
2976804 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
2976829 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
2976849 CATGTATCGATACA
1 AATGTATCGATACA
2976863 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:2980741 original size:21 final size:21
Alignment explanation
Indices: 2980712--2980756 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2980702 AAGTTTTCAT
*
2980712 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2980732 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2980754 TTT
1 TTT
2980757 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2982996 original size:13 final size:13
Alignment explanation
Indices: 2982978--2983003 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2982968 CAATTTTTTG
2982978 TGTATCGATACAT
1 TGTATCGATACAT
2982991 TGTATCGATACAT
1 TGTATCGATACAT
2983004 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2984598 original size:13 final size:13
Alignment explanation
Indices: 2984580--2984607 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2984570 TACAATTATT
2984580 AATGTATCGATAC
1 AATGTATCGATAC
2984593 AATGTATCGATAC
1 AATGTATCGATAC
2984606 AA
1 AA
2984608 AGCATAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2984603 original size:33 final size:33
Alignment explanation
Indices: 2984561--2984626 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2984551 TGCCAGTTTC
**
2984561 ATGTATCGATAC-AATTATTAATGTATCGATACA
1 ATGTATCGATACAAAGCA-TAATGTATCGATACA
2984594 ATGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
2984627 TTTGAAAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATACA
Found at i:2986012 original size:20 final size:20
Alignment explanation
Indices: 2985987--2986037 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2985977 CCACTGTTTA
*
2985987 TATCGATACATGGT-ACATTG
1 TATCGATACATGATGA-ATTG
2986007 TATCGATACATGATGAATTG
1 TATCGATACATGATGAATTG
*
2986027 TATTGATACAT
1 TATCGATACAT
2986038 TGCTTCTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (20 bp):
TATCGATACATGATGAATTG
Found at i:2988155 original size:21 final size:22
Alignment explanation
Indices: 2988131--2988191 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
2988121 GAATTAAAGG
2988131 AGAAAATGAATGAGTTAG-AAA
1 AGAAAATGAATGAGTTAGCAAA
2988152 AGAAAA-GAAATGAGTT-GCAAA
1 AGAAAATG-AATGAGTTAGCAAA
2988173 ATGAAAATG-ATGAGTTAGC
1 A-GAAAATGAATGAGTTAGC
2988192 TAATAAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 2 0.06
21 25 0.71
22 7 0.20
23 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.25, T:0.20
Consensus pattern (22 bp):
AGAAAATGAATGAGTTAGCAAA
Found at i:2990207 original size:31 final size:31
Alignment explanation
Indices: 2990172--2990231 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
2990162 GGAGAGATTG
2990172 TTGTTCATAAATTTGGTTTTATCAAACTTTA
1 TTGTTCATAAATTTGGTTTTATCAAACTTTA
2990203 TTGTTCATAAATTTGGTTTTATCAAACTT
1 TTGTTCATAAATTTGGTTTTATCAAACTT
2990232 AGCTTATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (31 bp):
TTGTTCATAAATTTGGTTTTATCAAACTTTA
Found at i:2991133 original size:20 final size:20
Alignment explanation
Indices: 2991081--2991136 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2991071 CACACCCATA
*
2991081 TGTATCGATACACTATGCTT
1 TGTATCGATACATTATGCTT
2991101 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
2991121 TGTATCGATACATTAT
1 TGTATCGATACATTAT
2991137 ATTGATACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:2991249 original size:13 final size:13
Alignment explanation
Indices: 2991231--2991294 Score: 86
Period size: 13 Copynumber: 5.4 Consensus size: 13
2991221 CGATACATGG
2991231 TACATTGTATCGA
1 TACATTGTATCGA
2991244 TACATTGTATCGA
1 TACATTGTATCGA
2991257 TACA-TG-AT-G-
1 TACATTGTATCGA
2991266 -A-ATTGTATCGA
1 TACATTGTATCGA
2991277 TACATTGTATCGA
1 TACATTGTATCGA
2991290 TACAT
1 TACAT
2991295 GCTTCTAACG
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
7 1 0.02
8 3 0.07
9 2 0.04
10 2 0.04
11 2 0.04
12 3 0.07
13 32 0.71
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:2991255 original size:33 final size:33
Alignment explanation
Indices: 2991215--2991295 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
2991205 TTACCATTGT
*
2991215 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
2991248 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
2991281 TTGTATCGATACATG
1 TTGTATCGATACATG
2991296 CTTCTAACGG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 45 0.98
34 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.37
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:2991370 original size:13 final size:13
Alignment explanation
Indices: 2991352--2991386 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2991342 ATCGATACAT
2991352 GGTACATTGTATC
1 GGTACATTGTATC
2991365 GGTACATTGTATC
1 GGTACATTGTATC
*
2991378 GATACATTG
1 GGTACATTG
2991387 CTTCTAACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (13 bp):
GGTACATTGTATC
Found at i:2991484 original size:52 final size:53
Alignment explanation
Indices: 2991372--2991491 Score: 197
Period size: 52 Copynumber: 2.3 Consensus size: 53
2991362 ATCGGTACAT
* * * *
2991372 TGTATCGATACATTGCTTCTAACGGCTATAAAATGGCTATAATTTTAAATGCA
1 TGTATCGATACATTACTTCTAACGACTATAAAACGGCTATAATTTCAAATGCA
2991425 TGTATCGATACATTACTTCTAACGACTAT-AAACGGCTATAATTTCAAATGCA
1 TGTATCGATACATTACTTCTAACGACTATAAAACGGCTATAATTTCAAATGCA
2991477 TGTATCGATACATTA
1 TGTATCGATACATTA
2991492 TGAATTGTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 36 0.57
53 27 0.43
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (53 bp):
TGTATCGATACATTACTTCTAACGACTATAAAACGGCTATAATTTCAAATGCA
Found at i:2993667 original size:21 final size:21
Alignment explanation
Indices: 2993641--2993685 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2993631 ATCTTTTATT
*
2993641 AATTTAAAAAACGT-AATAAAA
1 AATTT-AAAAACATAAATAAAA
*
2993662 AATTTAATAACATAAATAAAA
1 AATTTAAAAACATAAATAAAA
2993683 AAT
1 AAT
2993686 ACTAATAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
AATTTAAAAACATAAATAAAA
Found at i:2993804 original size:41 final size:42
Alignment explanation
Indices: 2993697--2993789 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 42
2993687 CTAATAGTTA
* * *
2993697 TATAA-AAT-TAACAATAATAATATAAATAAAAATATTAACAT
1 TATAATAATATAA-AATAAGAATATAAATAAAAATAATAACAC
*
2993738 TATAATAATATAAAATTAAGAATATAAATAAATATTAATAACAC
1 TATAATAATATAAAA-TAAGAATATAAATAAA-AATAATAACAC
2993782 TATAATAA
1 TATAATAA
2993790 GTTTAATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
41 5 0.11
42 5 0.11
43 18 0.41
44 16 0.36
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (42 bp):
TATAATAATATAAAATAAGAATATAAATAAAAATAATAACAC
Found at i:3000103 original size:17 final size:17
Alignment explanation
Indices: 3000081--3000131 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
3000071 ATAATTAATT
*
3000081 TAAAATATTATATATAA
1 TAAAATATTTTATATAA
3000098 TAAAAT-TTTTAATATAA
1 TAAAATATTTT-ATATAA
**
3000115 TAATTTATTTTATATAA
1 TAAAATATTTTATATAA
3000132 ATTTTAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 3 0.10
17 22 0.76
18 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATATTTTATATAA
Found at i:3000111 original size:24 final size:24
Alignment explanation
Indices: 3000058--3000112 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
3000048 TTATTTTTTA
* *
3000058 TTAATATTTTATTATAATTAATTT
1 TTAATATTATATTATAATAAATTT
**
3000082 AAAATATTATA-TATAATAAAATTT
1 TTAATATTATATTATAAT-AAATTT
3000106 TTAATAT
1 TTAATAT
3000113 AATAATTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAATATTATATTATAATAAATTT
Found at i:3000157 original size:10 final size:9
Alignment explanation
Indices: 3000138--3000179 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
3000128 ATAAATTTTA
3000138 ATTTATTTAT
1 ATTTA-TTAT
3000148 ATATTATTAT
1 AT-TTATTAT
3000158 ATTT-TTAT
1 ATTTATTAT
3000166 ATTATATTAT
1 ATT-TATTAT
3000176 ATTT
1 ATTT
3000180 TAATTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.24
9 4 0.14
10 15 0.52
11 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTATTAT
Found at i:3000160 original size:16 final size:15
Alignment explanation
Indices: 3000141--3000187 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
3000131 AATTTTAATT
3000141 TATTTATATATTATTA
1 TATTT-TATATTATTA
3000157 TATTTTTATATTATATTA
1 TA-TTTTATA-T-TATTA
3000175 TATTTTA-ATTATT
1 TATTTTATATTATT
3000188 TTTTTGTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 4 0.14
15 1 0.04
16 7 0.25
17 9 0.32
18 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTATATTATTA
Found at i:3000164 original size:18 final size:18
Alignment explanation
Indices: 3000143--3000180 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
3000133 TTTTAATTTA
3000143 TTTATA-TATTATTATATT
1 TTTATATTA-TATTATATT
3000161 TTTATATTATATTATATT
1 TTTATATTATATTATATT
3000179 TT
1 TT
3000181 AATTATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATATTATATTATATT
Found at i:3000408 original size:16 final size:16
Alignment explanation
Indices: 3000352--3000410 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
3000342 TAATTTGTAT
*
3000352 ATTTTAAATTCAGATTA
1 ATTTTAAATTAAGA-TA
*
3000369 A-TTTAAATTTAA-ATC
1 ATTTTAAA-TTAAGATA
* *
3000384 GTTTCAAATTAAGATA
1 ATTTTAAATTAAGATA
3000400 ATTTTAAATTA
1 ATTTTAAATTA
3000411 TTAACTTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
15 5 0.16
16 23 0.72
17 4 0.12
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTTTAAATTAAGATA
Found at i:3000903 original size:30 final size:28
Alignment explanation
Indices: 3000848--3000919 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 28
3000838 AATAAATAAA
3000848 ATATTATATATTTTATATAAATTTTAAT
1 ATATTATATATTTTATATAAATTTTAAT
*
3000876 ATATTA-ATAATTTATATTATAATTTTTAAT
1 ATATTATAT-ATTT-TA-TATAAATTTTAAT
3000906 ATATT-T-TATTTTAT
1 ATATTATATATTTTAT
3000920 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
26 1 0.03
27 4 0.10
28 14 0.36
29 3 0.08
30 17 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATATTATATATTTTATATAAATTTTAAT
Found at i:3000917 original size:15 final size:15
Alignment explanation
Indices: 3000899--3000953 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
3000889 ATATTATAAT
3000899 TTTTAATATATTTTA
1 TTTTAATATATTTTA
* *
3000914 TTTTATTTTATTTTA
1 TTTTAATATATTTTA
3000929 TTTT--TATA-TTTA
1 TTTTAATATATTTTA
3000941 TTTTAAT-TATTTT
1 TTTTAATATATTTT
3000954 TTATTATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 8 0.24
13 5 0.15
14 4 0.12
15 17 0.50
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTAATATATTTTA
Found at i:3000933 original size:21 final size:21
Alignment explanation
Indices: 3000899--3000963 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 21
3000889 ATATTATAAT
*
3000899 TTTTAA-TATATTTTATTTTA
1 TTTTAATTATTTTTTATTTTA
*
3000919 TTTT-ATTTTATTTTTATATTTA
1 TTTTAATTAT-TTTTTAT-TTTA
*
3000941 TTTTAATTATTTTTTATTATA
1 TTTTAATTATTTTTTATTTTA
3000962 TT
1 TT
3000964 CATTAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 6 0.16
21 11 0.30
22 15 0.41
23 4 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTAATTATTTTTTATTTTA
Found at i:3000935 original size:6 final size:5
Alignment explanation
Indices: 3000907--3000963 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
3000897 ATTTTTAATA
3000907 TATTT TATTT TATTT TATTT TATTTT TATATT TATTT TAATTAT T-TTT
1 TATTT TATTT TATTT TATTT TA-TTT TAT-TT TATTT T-ATT-T TATTT
*
3000955 TATTA TATT
1 TATTT TATT
3000964 CATTAAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
4 2 0.04
5 29 0.63
6 13 0.28
7 2 0.04
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:3000973 original size:25 final size:26
Alignment explanation
Indices: 3000921--3000975 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
3000911 TTATTTTATT
* * **
3000921 TTATTTTATTTTTATATTTATTTTAA
1 TTATTTTATTATTATATTCATTAAAA
3000947 TTATTTT-TTATTATATTCATTAAAA
1 TTATTTTATTATTATATTCATTAAAA
3000972 TTAT
1 TTAT
3000976 ATGATCCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TTATTTTATTATTATATTCATTAAAA
Found at i:3002180 original size:17 final size:17
Alignment explanation
Indices: 3002126--3002192 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
3002116 AGTTTAATTA
3002126 AAATAAA-TTTAAATATT
1 AAATAAATTTTAAATA-T
* *
3002143 AAATAAGTAATTAAAATTAT
1 AAATAA--ATTTTAAA-TAT
3002163 AAATAAATTTTAAATAT
1 AAATAAATTTTAAATAT
3002180 -AATAAATATTTAA
1 AAATAAAT-TTTAA
3002193 TAAATTATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
16 7 0.17
17 14 0.33
18 6 0.14
19 1 0.02
20 12 0.29
21 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
AAATAAATTTTAAATAT
Found at i:3002184 original size:20 final size:19
Alignment explanation
Indices: 3002126--3002187 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
3002116 AGTTTAATTA
3002126 AAATAAA-TTTAAATAT-T
1 AAATAAATTTTAAATATAT
* *
3002143 AAATAAGTAATTAAA-ATTAT
1 AAATAAAT-TTTAAATA-TAT
3002163 AAATAAATTTTAAATATAAT
1 AAATAAATTTTAAATAT-AT
3002183 AAATA
1 AAATA
3002188 TTTAATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
17 6 0.17
18 1 0.03
19 12 0.34
20 16 0.46
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATAAATTTTAAATATAT
Found at i:3003368 original size:2 final size:2
Alignment explanation
Indices: 3003361--3003404 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
3003351 TCTGTGATTT
* * * *
3003361 TA TA TA TA TA TA TA TA TA TA TA TG TT TA TA TT TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3003403 TA
1 TA
3003405 AGTATATTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (2 bp):
TA
Found at i:3004364 original size:2 final size:2
Alignment explanation
Indices: 3004316--3004350 Score: 52
Period size: 2 Copynumber: 16.5 Consensus size: 2
3004306 TTAGACTTGT
3004316 AG AG AG AG AG AG AG AG AG AG AG AG TAG AG TAG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG -AG AG -AG AG A
3004351 AGGTTTGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 27 0.87
3 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.46, T:0.06
Consensus pattern (2 bp):
AG
Found at i:3004811 original size:22 final size:22
Alignment explanation
Indices: 3004796--3004839 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3004786 AAATAGTAAT
3004796 TTATCAAAAAATAAATTATATC
1 TTATCAAAAAATAAATTATATC
3004818 TTATCAAAAAATAAATTATATC
1 TTATCAAAAAATAAATTATATC
3004840 ATGAGCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (22 bp):
TTATCAAAAAATAAATTATATC
Found at i:3005257 original size:13 final size:13
Alignment explanation
Indices: 3005239--3005269 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3005229 ATAAAGTACT
3005239 TTCAAAAACTATA
1 TTCAAAAACTATA
3005252 TTCAAAAACTATA
1 TTCAAAAACTATA
3005265 TTCAA
1 TTCAA
3005270 TACTATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCAAAAACTATA
Found at i:3006354 original size:21 final size:20
Alignment explanation
Indices: 3006328--3006378 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3006318 TCTACAATTG
*
3006328 TATCGATATAAACAGTGAATA
1 TATCGATACAAA-AGTGAATA
* *
3006349 TATCGATACATAAGTGAATG
1 TATCGATACAAAAGTGAATA
3006369 TATCGATACA
1 TATCGATACA
3006379 TGTCTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (20 bp):
TATCGATACAAAAGTGAATA
Found at i:3006386 original size:20 final size:20
Alignment explanation
Indices: 3006343--3006399 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
3006333 ATATAAACAG
* *
3006343 TGAATATATCGATACATAAG
1 TGAATGTATCGATACATAAC
**
3006363 TGAATGTATCGATACATGTC
1 TGAATGTATCGATACATAAC
3006383 TGAAATGTATCGATACA
1 TG-AATGTATCGATACA
3006400 AAACCATGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (20 bp):
TGAATGTATCGATACATAAC
Found at i:3006464 original size:20 final size:20
Alignment explanation
Indices: 3006437--3006491 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
3006427 CTGGAAAGAA
3006437 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
*
3006457 ATTGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
3006477 AATGTATCGATACAT
1 AATGTATCGATACAT
3006492 GTAGCCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:3010240 original size:16 final size:15
Alignment explanation
Indices: 3010219--3010248 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3010209 TTATTACACT
3010219 TAGAATAGTAATATAG
1 TAGAATAG-AATATAG
3010235 TAGAATAGAATATA
1 TAGAATAGAATATA
3010249 AAGTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:3013102 original size:24 final size:23
Alignment explanation
Indices: 3013074--3013121 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
3013064 TTTAGTTAAG
*
3013074 ATTAAATAAATTTTTAAATATTTT
1 ATTAAATAAATTTTAAAAT-TTTT
*
3013098 ATTAAATATATTTTAAAATTTTT
1 ATTAAATAAATTTTAAAATTTTT
3013121 A
1 A
3013122 AATATTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTAAATAAATTTTAAAATTTTT
Found at i:3013120 original size:9 final size:10
Alignment explanation
Indices: 3013083--3013127 Score: 56
Period size: 11 Copynumber: 4.3 Consensus size: 10
3013073 GATTAAATAA
3013083 ATTTTTAAAT
1 ATTTTTAAAT
3013093 ATTTTATTAAAT
1 A-TTT-TTAAAT
3013105 ATATTTTAAA-
1 AT-TTTTAAAT
3013115 ATTTTTAAAT
1 ATTTTTAAAT
3013125 ATT
1 ATT
3013128 AAGTCGGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 7 0.23
10 6 0.19
11 9 0.29
12 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTTTAAAT
Found at i:3013568 original size:16 final size:17
Alignment explanation
Indices: 3013523--3013597 Score: 77
Period size: 16 Copynumber: 4.6 Consensus size: 17
3013513 CTCAAAAAAA
3013523 CCCGAACCCG-TATAAG
1 CCCGAACCCGATATAAG
** * *
3013539 ATCGAGCTCG-TATAAG
1 CCCGAACCCGATATAAG
3013555 CCCGAACCC-ATATAAG
1 CCCGAACCCGATATAAG
*
3013571 CCCGAACCCGA-ATGAG
1 CCCGAACCCGATATAAG
3013587 CCCGAACCCGA
1 CCCGAACCCGA
3013598 ACCCGAACGA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
16 47 0.98
17 1 0.02
ACGTcount: A:0.32, C:0.36, G:0.20, T:0.12
Consensus pattern (17 bp):
CCCGAACCCGATATAAG
Found at i:3013596 original size:22 final size:22
Alignment explanation
Indices: 3013571--3013616 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3013561 CCCATATAAG
* *
3013571 CCCGAACCCGAATGAGCCCGAA
1 CCCGAACCCGAACGAGCCCAAA
3013593 CCCGAACCCGAACGAGCCCAAA
1 CCCGAACCCGAACGAGCCCAAA
3013615 CC
1 CC
3013617 AGAATGAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.46, G:0.20, T:0.02
Consensus pattern (22 bp):
CCCGAACCCGAACGAGCCCAAA
Found at i:3016088 original size:20 final size:22
Alignment explanation
Indices: 3016059--3016101 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3016049 ATTAGCTGTC
3016059 GTATA-TTTT-TACTGATACTT
1 GTATAGTTTTATACTGATACTT
3016079 GTATAGTTTTATACTGATACTT
1 GTATAGTTTTATACTGATACTT
3016101 G
1 G
3016102 CCACAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (22 bp):
GTATAGTTTTATACTGATACTT
Found at i:3017173 original size:13 final size:13
Alignment explanation
Indices: 3017155--3017179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3017145 CATTATGCTT
3017155 TGTATCGATACAA
1 TGTATCGATACAA
3017168 TGTATCGATACA
1 TGTATCGATACA
3017180 TGATCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3017176 original size:33 final size:32
Alignment explanation
Indices: 3017134--3017196 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
3017124 ACACATCCAG
* *
3017134 ATGTATCGATACATTATGCTTTGTATCGATACA
1 ATGTATCGATACATGAT-CATTGTATCGATACA
3017167 ATGTATCGATACATGATCATTGTATCGATA
1 ATGTATCGATACATGATCATTGTATCGATA
3017197 TATGAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATGATCATTGTATCGATACA
Found at i:3017264 original size:13 final size:13
Alignment explanation
Indices: 3017246--3017272 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3017236 GATAAATGGC
3017246 ACATTGTATCGAT
1 ACATTGTATCGAT
3017259 ACATTGTATCGAT
1 ACATTGTATCGAT
3017272 A
1 A
3017273 GATTCATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:3017331 original size:95 final size:95
Alignment explanation
Indices: 3017154--3017357 Score: 284
Period size: 95 Copynumber: 2.1 Consensus size: 95
3017144 ACATTATGCT
* * * * * *
3017154 TTGTATCGATACAATGTATCGATACATGATCATTGTATCGATATATGAAACTAGCAGTAGCTACC
1 TTGTATCGATACATTGTATCGATACATCATAATTATATCGATACATAAAACTAGCAGTAGCTACC
* *
3017219 GTACCGCTGTTTGTATCGATAAATGGCACA
66 CTACCACTGTTTGTATCGATAAATGGCACA
* *
3017249 TTGTATCGATACATTGTATCGATAGATTCATAATTATATCGATACATAAAACTGGCAGTAGCTAC
1 TTGTATCGATACATTGTATCGATACA-TCATAATTATATCGATACATAAAACTAGCAGTAGCTAC
*
3017314 CCTACCATTGTTT-TATCGATAAATGGCACA
65 CCTACCACTGTTTGTATCGATAAATGGCACA
*
3017344 TTTTATCGATACAT
1 TTGTATCGATACAT
3017358 GAAGAATTGT
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 54 0.56
96 42 0.44
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (95 bp):
TTGTATCGATACATTGTATCGATACATCATAATTATATCGATACATAAAACTAGCAGTAGCTACC
CTACCACTGTTTGTATCGATAAATGGCACA
Found at i:3018953 original size:21 final size:21
Alignment explanation
Indices: 3018927--3018968 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3018917 CAAGAGCCAC
3018927 CAAAGAAAGCAAGTGTCACCT
1 CAAAGAAAGCAAGTGTCACCT
3018948 CAAAGAAAGCAAGTGTCACCT
1 CAAAGAAAGCAAGTGTCACCT
3018969 TCAAGTCAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.14
Consensus pattern (21 bp):
CAAAGAAAGCAAGTGTCACCT
Found at i:3025734 original size:13 final size:13
Alignment explanation
Indices: 3025716--3025742 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3025706 ATATTATGCT
3025716 TTGTATCGATACA
1 TTGTATCGATACA
3025729 TTGTATCGATACA
1 TTGTATCGATACA
3025742 T
1 T
3025743 GCATAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3027085 original size:11 final size:11
Alignment explanation
Indices: 3027069--3027105 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
3027059 AAACTTGGAG
3027069 AAAAAAAGAGA
1 AAAAAAAGAGA
3027080 AAAAAAAGAGA
1 AAAAAAAGAGA
*
3027091 GAAAAAAGA-A
1 AAAAAAAGAGA
3027101 AAAAA
1 AAAAA
3027106 TCTAAATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAGA
Found at i:3027090 original size:21 final size:20
Alignment explanation
Indices: 3027066--3027105 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3027056 TGGAAACTTG
3027066 GAGAAAAAAAGAGAAAAAAAA
1 GAGAAAAAAA-AGAAAAAAAA
*
3027087 GAGAGAAAAAAGAAAAAAA
1 GAGAAAAAAAAGAAAAAAA
3027106 TCTAAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
GAGAAAAAAAAGAAAAAAAA
Found at i:3028512 original size:16 final size:17
Alignment explanation
Indices: 3028486--3028519 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3028476 TCTTGTCTGA
3028486 AAAATTAAAAAAATAAT
1 AAAATTAAAAAAATAAT
*
3028503 AAAA-TAAAAATATAAT
1 AAAATTAAAAAAATAAT
3028519 A
1 A
3028520 TTCTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATTAAAAAAATAAT
Found at i:3030885 original size:2 final size:2
Alignment explanation
Indices: 3030878--3030920 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3030868 TCTTTTCTTT
3030878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3030920 T
1 T
3030921 TACTGAAAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3031771 original size:20 final size:21
Alignment explanation
Indices: 3031726--3031778 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3031716 CTGCCAAGAA
* **
3031726 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTGTAAC
3031747 ATGTATCGATACAT-TGTAAC
1 ATGTATCGATACATCTGTAAC
3031767 ATGTATCGATAC
1 ATGTATCGATAC
3031779 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATCTGTAAC
Done.