Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold881
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: 21956
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Found at i:62 original size:29 final size:29
Alignment explanation
Indices: 2--320 Score: 205
Period size: 30 Copynumber: 10.6 Consensus size: 29
1 A
*
2 AAAGCCTACAAGTCAGTGGGCATCTTTTTC
1 AAAGCCCACAAGTCAGT-GGCATCTTTTTC
32 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
61 AAAGTCCACAAGTCAGTGGCAAC-CTTT-
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
88 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
118 GAATCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
147 AAAGTCCGCAACTCCA-TGGCACTCTTTTTC
1 AAAGCCCACAAGT-CAGTGGCA-TCTTTTTC
* * * * *
177 TTTTGTAAGCTCACAACTCCGTAGCACTCTTTTTCC
1 -----AAAGCCCACAAGTCAGTGGCA-TCTTTTT-C
* * * *
213 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
245 AAAAGCCCACAAGTTAGTGGCACCCTTTTC
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
275 AAAAGCCCACAAGTTAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
304 AAAGCCCACAAGTCAGT
1 AAAGCCCACAAGTCAGT
321 AACAACCTTC
Statistics
Matches: 236, Mismatches: 41, Indels: 26
0.78 0.14 0.09
Matches are distributed among these distances:
27 19 0.08
28 20 0.08
29 58 0.25
30 92 0.39
32 1 0.00
33 5 0.02
34 19 0.08
35 21 0.09
36 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:103 original size:27 final size:28
Alignment explanation
Indices: 2--369 Score: 129
Period size: 30 Copynumber: 12.3 Consensus size: 28
1 A
* * *
2 AAAGCCTACAAGTCAGTGGGCATCTTTTTC
1 AAAGCCCACAAGTCAGT-GGCAAC-CTTTC
* *
32 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTTC
*
61 AAAGTCCACAAGTCAGTGGCAACCTTT-
1 AAAGCCCACAAGTCAGTGGCAACCTTTC
* *
88 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAACC--TTTC
* * * * *
118 GAATCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACCTTT-C
* * *
147 AAAGTCCGCAACTCCA-TGGC-ACTCTTTTTC
1 AAAGCCCACAAGT-CAGTGGCAAC-C--TTTC
* * * * *
177 TTTTGTAAGCTCACAACTCCGTAGC-ACTCTTTTTCC
1 -----AAAGCCCACAAGTCAGTGGCAAC-C--TTT-C
* * *
213 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCAACC-TTTC
* *
245 AAAAGCCCACAAGTTAGTGGCACCCTTTTC
1 -AAAGCCCACAAGTCAGTGGCAACC-TTTC
* *
275 AAAAGCCCACAAGTTAGTGGCAACCTTTA
1 -AAAGCCCACAAGTCAGTGGCAACCTTTC
**
304 AAAGCCCACAAGTCAGTAACAACC-TTC
1 AAAGCCCACAAGTCAGTGGCAACCTTTC
* *
331 AAAGGCACACAAGT-TGAT-GCAAACCTTTC
1 AAA-GCCCACAAGTCAG-TGGC-AACCTTTC
360 AAAAGCCCAC
1 -AAAGCCCAC
370 TCAAGTTGGT
Statistics
Matches: 271, Mismatches: 46, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
27 28 0.10
28 42 0.15
29 60 0.22
30 91 0.34
31 3 0.01
32 1 0.00
33 4 0.01
34 19 0.07
35 22 0.08
36 1 0.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTTC
Found at i:137 original size:57 final size:56
Alignment explanation
Indices: 9--138 Score: 154
Period size: 57 Copynumber: 2.2 Consensus size: 56
1 AAAAGCCT
* * * *
9 ACAAGTCAGTGGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGTCC
1 ACAAGTCAGT-GGCAAC-CTTT-AAAGCCCACAAATCAGTGGCACCTTTTTCAAAGTCC
*
68 ACAAGTCAGTGGCAACCTTTAAAGCCCACAAATCAGTGGCACCCTTTTTCGAA-TCCC
1 ACAAGTCAGTGGCAACCTTTAAAGCCCACAAATCAGTGGCA-CCTTTTTCAAAGT-CC
*
125 ACAAGTCGGTGGCA
1 ACAAGTCAGTGGCA
139 TCTTTTCCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
56 21 0.33
57 27 0.43
58 5 0.08
59 10 0.16
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (56 bp):
ACAAGTCAGTGGCAACCTTTAAAGCCCACAAATCAGTGGCACCTTTTTCAAAGTCC
Found at i:167 original size:86 final size:86
Alignment explanation
Indices: 2--160 Score: 221
Period size: 86 Copynumber: 1.8 Consensus size: 86
1 A
* * * *
2 AAAGCCTACAAGTCAGTGGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGTC
1 AAAGCCCACAAATCAGTGGGCACCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGTC
*
67 CACAAGTCAGTGGCAACCTTT
66 CACAACTCAGTGGCAACCTTT
* * *
88 AAAGCCCACAAATCAGT-GGCACCCTTTTTCGAATCCCACAAGTCGGTGGCATCTTTTCCAAAGT
1 AAAGCCCACAAATCAGTGGGCA-CCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGT
*
152 CCGCAACTC
65 CCACAACTC
161 CATGGCACTC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 4 0.06
86 59 0.94
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (86 bp):
AAAGCCCACAAATCAGTGGGCACCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGTC
CACAACTCAGTGGCAACCTTT
Found at i:226 original size:34 final size:35
Alignment explanation
Indices: 155--226 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
145 CCAAAGTCCG
* * *
155 CAACTCCATGGCACTCTTTTTCTTTTGTAAGCTCA
1 CAACTCCATAGCACTCTTTTTCCTTTGTAAGCCCA
*
190 CAACTCCGTAGCACTCTTTTTCCTTT-TAAGCCCA
1 CAACTCCATAGCACTCTTTTTCCTTTGTAAGCCCA
224 CAA
1 CAA
227 GTTAGTGGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 10 0.30
35 23 0.70
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.36
Consensus pattern (35 bp):
CAACTCCATAGCACTCTTTTTCCTTTGTAAGCCCA
Found at i:315 original size:28 final size:29
Alignment explanation
Indices: 217--369 Score: 179
Period size: 30 Copynumber: 5.3 Consensus size: 29
207 TTTTCCTTTT
*
217 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTTAGTGGCAACC-TTTCAA
*
247 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTTAGTGGCAACC-TTTCAA
277 AAGCCCACAAGTTAGTGGCAACCTTT-AA
1 AAGCCCACAAGTTAGTGGCAACCTTTCAA
* **
305 AAGCCCACAAGTCAGTAACAACC-TTCAA
1 AAGCCCACAAGTTAGTGGCAACCTTTCAA
* *
333 AGGCACACAAGTT-GAT-GCAAACCTTTCAA
1 AAGCCCACAAGTTAG-TGGC-AACCTTTCAA
362 AAGCCCAC
1 AAGCCCAC
370 TCAAGTTGGT
Statistics
Matches: 109, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
27 4 0.04
28 39 0.36
29 14 0.13
30 52 0.48
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (29 bp):
AAGCCCACAAGTTAGTGGCAACCTTTCAA
Found at i:516 original size:49 final size:46
Alignment explanation
Indices: 390--571 Score: 217
Period size: 48 Copynumber: 3.9 Consensus size: 46
380 GGCGTCTCCT
* *
390 TTTAAGCCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCTTGCC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTT-CC
* *
438 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACTTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC-TTC--C
* * * * *
487 TTTAAGTCAAATGTAGCTGACCTTGAATCAACACATTGGCA---CC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTCC
530 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
572 CTTTTTTAGA
Statistics
Matches: 114, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
43 37 0.32
45 1 0.01
47 2 0.02
48 39 0.34
49 35 0.31
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (46 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTCC
Found at i:547 original size:43 final size:44
Alignment explanation
Indices: 390--575 Score: 180
Period size: 43 Copynumber: 4.1 Consensus size: 44
380 GGCGTCTCCT
*
390 TTTAAGCCCAATATAGCT-AGCCTTGAATCAGCATATTGGCACCTTGCC
1 TTTAAGTCCAATATAGCTGA-CCTTGAATCAGCATATTGGCA---T-CC
* * *
438 TTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCACTTTCATC
1 TTTAAGTCCAATATAGCTGACCTTGAATCAGCATATTGGCA---TC--C
* * * *
487 TTTAAGTCAAATGTAGCTGACCTTGAATCAACACATTGGCA-CC
1 TTTAAGTCCAATATAGCTGACCTTGAATCAGCATATTGGCATCC
*
530 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC
1 TTTAAGTCCAATATAGCTGACCTTGAATCAGCATATTGGCATCC
573 TTT
1 TTT
576 TTTAGATTTT
Statistics
Matches: 118, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
43 42 0.36
45 1 0.01
47 1 0.01
48 39 0.33
49 35 0.30
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (44 bp):
TTTAAGTCCAATATAGCTGACCTTGAATCAGCATATTGGCATCC
Found at i:800 original size:33 final size:33
Alignment explanation
Indices: 756--822 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
746 TTCAACGATT
*
756 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCAATACATAAAGTGTTGTATCGATACAA
*** *
789 TGTATCAATACATATTTTTTTGTATCGATACAA
1 TGTATCAATACATAAAGTGTTGTATCGATACAA
822 T
1 T
823 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCAATACATAAAGTGTTGTATCGATACAA
Found at i:864 original size:21 final size:21
Alignment explanation
Indices: 839--897 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
829 TACTACCAAA
839 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTACTC
860 AAATGTATCGATACATTACTC
1 AAATGTATCGATACATTACTC
881 AAATGTATCGATACATT
1 AAATGTATCGATACATT
898 GTATCGATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (21 bp):
AAATGTATCGATACATTACTC
Found at i:902 original size:13 final size:13
Alignment explanation
Indices: 884--908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
874 ATTACTCAAA
884 TGTATCGATACAT
1 TGTATCGATACAT
897 TGTATCGATACA
1 TGTATCGATACA
909 CTGATCTTTG
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:8082 original size:1 final size:1
Alignment explanation
Indices: 8076--8127 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
8066 AAGTAAACAC
* * * * * *
8076 AAAAAAAAAAAGAAAAAAAAAACAAAACAAAACAAAAAAAAACATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8128 GGTGCAAAGT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:8093 original size:10 final size:10
Alignment explanation
Indices: 8078--8127 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
8068 GTAAACACAA
*
8078 AAAAAAAAAGA
1 AAAAAAAAA-C
8089 AAAAAAAAAC
1 AAAAAAAAAC
*
8099 AAAACAAAAC
1 AAAAAAAAAC
8109 AAAAAAAAAC
1 AAAAAAAAAC
8119 ATAAAAAAA
1 A-AAAAAAA
8128 GGTGCAAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
10 19 0.54
11 16 0.46
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:9462 original size:33 final size:33
Alignment explanation
Indices: 9414--9632 Score: 186
Period size: 33 Copynumber: 6.7 Consensus size: 33
9404 TTTTCAAAGC
*
9414 CCACAACTACGTGGCACTCTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCACTCTTTTCCTTTTAAGT
* * * *
9447 CCACAATTCCATGGCACAT-TTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCAC-TCTTTTCCTTTT-AAGT
*
9481 CCACAACTCTGTGGCACTCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCACTC-TTTTCCTTTTAAGT
**
9515 CCACAACTCCGTGGCA--C----CCTTTTAAAAC
1 CCACAACTCCGTGGCACTCTTTTCCTTTT-AAGT
* * *
9543 CCACAACTCCGTGGCACTCATTTCCCCTCTTAAAGC
1 CCACAACTCCGTGGCACTC-TTT-TCCT-TTTAAGT
9579 CCACAACTCCGTGGCAC-CTTATTCCTTTTAAGT
1 CCACAACTCCGTGGCACTCTT-TTCCTTTTAAGT
**
9612 CCACAACTTTGTGGCA-TCTTT
1 CCACAACTCCGTGGCACTCTTT
9633 CACCCCTTCA
Statistics
Matches: 150, Mismatches: 20, Indels: 33
0.74 0.10 0.16
Matches are distributed among these distances:
27 6 0.04
28 18 0.12
30 1 0.01
32 2 0.01
33 46 0.31
34 41 0.27
35 11 0.07
36 23 0.15
37 2 0.01
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (33 bp):
CCACAACTCCGTGGCACTCTTTTCCTTTTAAGT
Found at i:9486 original size:67 final size:68
Alignment explanation
Indices: 9376--9632 Score: 218
Period size: 64 Copynumber: 3.9 Consensus size: 68
9366 AAATACCTTC
* * *
9376 TTTAAGTCCACGACTCTATGGCAC---CTTCTTTTCAAAGCCCACAACTAC-GTGGCACTC-TTT
1 TTTAAGTCCACAACTCCATGGCACATTTTTCTTTTCAAAGCCCACAACT-CTGTGGCACTCTTTT
9436 TCCT
65 TCCT
* *
9440 TTTAAGTCCACAATTCCATGGCACATTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 TTTAAGTCCACAACTCCATGGCACATTTTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTTTT
9505 CCT
66 CCT
* * * * *
9508 TTTAAGTCCACAACTCCGTGGCAC-----CCTTTT-AAAACCCACAACTCCGTGGCACTCATTTC
1 TTTAAGTCCACAACTCCATGGCACATTTTTCTTTTCAAAGCCCACAACTCTGTGGCACTC-TTTT
*
9567 CCCT
65 TCCT
* * * * * * *
9571 CTTAAAGCCCACAACTCCGTGGCACCTTATTCCTTTT--AAGTCCACAACTTTGTGGCA-TCTTT
1 -TTTAAGTCCACAACTCCATGGCACATT-TTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTT
9633 CACCCCTTCA
Statistics
Matches: 162, Mismatches: 18, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
62 22 0.14
63 11 0.07
64 43 0.27
66 1 0.01
67 32 0.20
68 31 0.19
69 16 0.10
70 6 0.04
ACGTcount: A:0.23, C:0.32, G:0.12, T:0.33
Consensus pattern (68 bp):
TTTAAGTCCACAACTCCATGGCACATTTTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTTTT
CCT
Found at i:9496 original size:34 final size:33
Alignment explanation
Indices: 9403--9619 Score: 189
Period size: 34 Copynumber: 6.5 Consensus size: 33
9393 ATGGCACCTT
*
9403 CTTTTCAAAGCCCACAACTACGTGGCACTCTTTTC
1 CTTTT-AAAGCCCACAACTCCGTGGCACT-TTTTC
* * *
9438 CTTTT-AAGTCCACAATTCCATGGCACATTTTTC
1 CTTTTAAAGCCCACAACTCCGTGGCAC-TTTTTC
* *
9471 TTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTC
1 CTTTTAAAGCCCACAACTCCGTGGCA--CTTTTTC
*
9506 CTTTT-AAGTCCACAACTCCGTGGCAC-----C
1 CTTTTAAAGCCCACAACTCCGTGGCACTTTTTC
* *
9533 CTTTTAAAACCCACAACTCCGTGGCACTCATTTCCC
1 CTTTTAAAGCCCACAACTCCGTGGCACT--TTT-TC
* *
9569 CTCTTAAAGCCCACAACTCCGTGGCACCTTATTC
1 CTTTTAAAGCCCACAACTCCGTGGCA-CTTTTTC
*
9603 CTTTT-AAGTCCACAACT
1 CTTTTAAAGCCCACAACT
9620 TTGTGGCATC
Statistics
Matches: 148, Mismatches: 20, Indels: 30
0.75 0.10 0.15
Matches are distributed among these distances:
27 6 0.04
28 19 0.13
32 1 0.01
33 37 0.25
34 40 0.27
35 17 0.11
36 26 0.18
37 2 0.01
ACGTcount: A:0.24, C:0.34, G:0.11, T:0.32
Consensus pattern (33 bp):
CTTTTAAAGCCCACAACTCCGTGGCACTTTTTC
Found at i:9675 original size:32 final size:32
Alignment explanation
Indices: 9639--9793 Score: 215
Period size: 33 Copynumber: 4.8 Consensus size: 32
9629 CTTTCACCCC
9639 TTCAAAGCCCACACAAGTCGGTGGCAACCCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCTT
* *
9671 TTCAAAGCCCACACAAGTCGGTGACAACCTTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCTT
* * *
9703 TTCTAAAGCCCACATAAGTCAGTGGCAACCCCT
1 TTC-AAAGCCCACACAAGTCGGTGGCAACCCTT
9736 TT-AAAGCCCACACAAGTCGGTGGCAA-CCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCCTT
*
9766 CTTCAAAAGCCCACACAAGTTGGTGGCA
1 -TTC-AAAGCCCACACAAGTCGGTGGCA
9794 TCTTCCTTTA
Statistics
Matches: 108, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
30 3 0.03
31 24 0.22
32 33 0.31
33 48 0.44
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (32 bp):
TTCAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:9792 original size:64 final size:64
Alignment explanation
Indices: 9638--9793 Score: 233
Period size: 64 Copynumber: 2.4 Consensus size: 64
9628 TCTTTCACCC
*
9638 CTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGACAACCTT
1 CTTCAAAGCCCACACAAGTCGGTGGCAACCCCTTTCAAAGCCCACACAAGTCGGTGACAACCTT
* * * *
9702 TTTCTAAAGCCCACATAAGTCAGTGGCAACCCCTTT-AAAGCCCACACAAGTCGGTGGCAACCTT
1 CTTC-AAAGCCCACACAAGTCGGTGGCAACCCCTTTCAAAGCCCACACAAGTCGGTGACAACCTT
*
9766 CTTCAAAAGCCCACACAAGTTGGTGGCA
1 CTTC-AAAGCCCACACAAGTCGGTGGCA
9794 TCTTCCTTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 53 0.65
65 28 0.35
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (64 bp):
CTTCAAAGCCCACACAAGTCGGTGGCAACCCCTTTCAAAGCCCACACAAGTCGGTGACAACCTT
Found at i:9854 original size:43 final size:43
Alignment explanation
Indices: 9798--10164 Score: 358
Period size: 43 Copynumber: 8.1 Consensus size: 43
9788 GTGGCATCTT
*
9798 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
* * *
9841 CCTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
*
9884 CCTTTGTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
1 -C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
** * *
9933 CCTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
*
9976 CCTTCATCTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGGCA
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
** * * * *
10025 CCTCCAAG-CCTAATATCGTTGGCCTTTAATCAGCATATTGGTATCTTCA
1 CCTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCACATTGG------CA
* * * *
10074 TCTTTAAGTCCAATGTAGGTGGCCTTGAATTAGCACATTGGCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
* *
10117 CCTTTAAGTCCAATATAACTGGCCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
10160 CCTTT
1 CCTTT
10165 TCCATCTTTA
Statistics
Matches: 264, Mismatches: 40, Indels: 40
0.77 0.12 0.12
Matches are distributed among these distances:
42 1 0.00
43 151 0.57
44 1 0.00
45 1 0.00
47 1 0.00
48 1 0.00
49 106 0.40
50 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (43 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
Found at i:9961 original size:92 final size:92
Alignment explanation
Indices: 9799--10208 Score: 615
Period size: 92 Copynumber: 4.4 Consensus size: 92
9789 TGGCATCTTC
**
9799 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
* **
9864 TTTGAATCAGCATATTGGCACCTTTGT
66 CTTGAATCAGCATATTGGCACCTTCAT
9891 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
9956 CTTGAATCAGCATATTGGCACCTTCAT
66 CTTGAATCAGCATATTGGCACCTTCAT
* * *
9983 CTTTAAGTTCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAG-CCTAATATCGTTGG
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCC-AATATCGCTGG
* * *
10047 CCTTTAATCAGCATATTGGTATCTTCAT
65 CCTTGAATCAGCATATTGGCACCTTCAT
* * ** **
10075 CTTTAAGTCCAATGTAGGTGGCCTTGAATTAGCACATTGGCACCTTTAAGTCCAATATAACTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
10140 CTTGAATCAGCATATTGGCACCTTTTCCAT
66 CTTGAATCAGCATATTGGCACC--TT-CAT
*
10170 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
10209 ACATCTTTTT
Statistics
Matches: 287, Mismatches: 26, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
91 2 0.01
92 242 0.84
93 2 0.01
94 2 0.01
95 39 0.14
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
CTTGAATCAGCATATTGGCACCTTCAT
Found at i:10196 original size:52 final size:53
Alignment explanation
Indices: 10118--10271 Score: 166
Period size: 52 Copynumber: 2.9 Consensus size: 53
10108 ACATTGGCAC
*
10118 CTTTAAGTCCAATATAACTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * * *
10170 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCTTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-CTTTTCTCAT
* * * * * * *
10225 CTTTTAGCCCAATATTGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
10272 ATCACTTTTC
Statistics
Matches: 81, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
52 37 0.46
53 4 0.05
54 5 0.06
55 35 0.43
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:10366 original size:49 final size:49
Alignment explanation
Indices: 10286--10776 Score: 525
Period size: 49 Copynumber: 10.2 Consensus size: 49
10276 CTTTTCTCAT
*
10286 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCGTATTGGCAC
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
* ** * *
10335 CTTCATTTTTAAGTCCAACGTAGCTGTCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
* * * * *
10384 CTTCTTCTTTAAGTCCAATGTAGCTGGTCTTGAATCAGCACATTGGCA-
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
10432 ---C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
* * * * * * *
10476 CATCATCTTTAAGTCTAATGTAGCCGACCTTGAATCAGCACATTGGCA-
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
*
10524 ATTC--C---AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
* * *
10568 CCTCATCTTTTAAG-CACAATGTCGCTGGCCTTGAATCAGCACATTGGCA-
1 CTTCATC-TTTAAGTC-CAATATCGCTGGCCTTGAATCAGCATATTGGCAC
**
10617 ---C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGC
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
*
10661 CTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTC
1 C--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC
* * *
10714 TTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 -CT-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
10765 CTTCATCTTTAA
1 CTTCATCTTTAA
10777 CATTCCTAAG
Statistics
Matches: 371, Mismatches: 45, Indels: 52
0.79 0.10 0.11
Matches are distributed among these distances:
43 105 0.28
44 4 0.01
45 1 0.00
46 3 0.01
47 1 0.00
48 2 0.01
49 132 0.36
50 36 0.10
51 1 0.00
52 85 0.23
53 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:10453 original size:43 final size:43
Alignment explanation
Indices: 10390--10767 Score: 283
Period size: 43 Copynumber: 8.1 Consensus size: 43
10380 GCACCTTCTT
* * *
10390 CTTTAAGTCCAATGTAGCTGGTCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
*
10433 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGG---CA-C
* * * * *
10480 ATCTTTAAGTCTAATGTAGCCGACCTTGAATCAGCACATTGGCA-
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
10524 ATTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTC
1 CTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA----C
*
10572 ATCTTTTAAG-CACAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 --C-TTTAAGTC-CAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* *
10618 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACA-T--TG-----G-CAC
* *
10670 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT---G-----G-CAC
*
10722 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
10765 CTT
1 CTT
10768 CATCTTTAAC
Statistics
Matches: 277, Mismatches: 29, Indels: 58
0.76 0.08 0.16
Matches are distributed among these distances:
42 2 0.01
43 104 0.38
44 4 0.01
46 7 0.03
47 1 0.00
49 37 0.13
50 34 0.12
51 4 0.01
52 84 0.30
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:10487 original size:92 final size:92
Alignment explanation
Indices: 10342--10776 Score: 523
Period size: 92 Copynumber: 4.6 Consensus size: 92
10332 CACCTTCATT
** * * *
10342 TTTAAGTCCAACGTAGCTGTCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
10407 CTGGTCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
10434 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGTCTAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
* * *
10499 CCGACCTTGAATCAGCACATTGGCA-A
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
10525 TTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTCATCTTTTAAG-CACAATG
1 TT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTC-CAATG
*
10589 TCGCTGGCCTTGAATCAGCACATTGGCACC
63 TAGCTGGCCTTGAATCAGCACATTGGCACC
** *
10619 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTAAGTCCAATA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATG
* * *
10684 TCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATC
63 TAGCTGGCCTTGAATCAGCACATT---G-----G-CACC
* *
10723 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAA
10777 CATTCCTAAG
Statistics
Matches: 297, Mismatches: 29, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
91 2 0.01
92 126 0.42
93 73 0.25
94 2 0.01
95 33 0.11
96 6 0.02
98 1 0.00
101 10 0.03
102 1 0.00
103 1 0.00
104 42 0.14
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:10696 original size:52 final size:52
Alignment explanation
Indices: 10618--10767 Score: 255
Period size: 52 Copynumber: 2.9 Consensus size: 52
10608 ACATTGGCAC
*
10618 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
*
10670 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
* * *
10722 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTT
10768 CATCTTTAAC
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 92 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
Found at i:11634 original size:20 final size:20
Alignment explanation
Indices: 11609--11707 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 20
11599 TTTCAATGAT
11609 TTGTATCGATACATAAAGTG
1 TTGTATCGATACATAAAGTG
11629 TTGTATCGATAC---AA---
1 TTGTATCGATACATAAAGTG
11643 -TGTATCGATACATAAAGTG
1 TTGTATCGATACATAAAGTG
11662 TTGTATCGATAC---AA---
1 TTGTATCGATACATAAAGTG
11676 -TGTATCGATACATAAAGTG
1 TTGTATCGATACATAAAGTG
11695 TTGTATCGATACA
1 TTGTATCGATACA
11708 ATGTATCGAT
Statistics
Matches: 65, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 22 0.34
16 4 0.06
17 4 0.06
20 35 0.54
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (20 bp):
TTGTATCGATACATAAAGTG
Found at i:11648 original size:13 final size:13
Alignment explanation
Indices: 11630--11720 Score: 56
Period size: 13 Copynumber: 5.9 Consensus size: 13
11620 CATAAAGTGT
11630 TGTATCGATACAA
1 TGTATCGATACAA
11643 TGTATCGATACATAAA
1 TGTATCGATAC---AA
11659 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
11676 TGTATCGATACATAAA
1 TGTATCGATAC---AA
11692 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
11709 TGTATCGATACA
1 TGTATCGATACA
11721 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 34 0.53
16 4 0.06
17 4 0.06
20 22 0.34
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11652 original size:33 final size:33
Alignment explanation
Indices: 11610--11741 Score: 248
Period size: 33 Copynumber: 4.0 Consensus size: 33
11600 TTCAATGATT
11610 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
11643 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
11676 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
11709 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
11741 T
1 T
11742 TTAAGCTACT
Statistics
Matches: 98, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 19 0.19
33 79 0.81
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:11768 original size:66 final size:66
Alignment explanation
Indices: 11632--11773 Score: 155
Period size: 66 Copynumber: 2.2 Consensus size: 66
11622 TAAAGTGTTG
* ****
11632 TATCGATACAATGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATAAAGTGTT
1 TATCGATACAATGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACATAAAAAAAT
*
11697 G
66 A
* * *
11698 TATCGATACAATGTATCGATACAT-AAGTTTTGTATCGATACAATTTA-AGCTAC-TGCCAAAAA
1 TATCGATACAATGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACAT---AAAAA
11760 AATA
63 AATA
11764 TATCGATACA
1 TATCGATACA
11774 TTACTCAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
63 1 0.02
64 4 0.06
65 21 0.33
66 38 0.59
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (66 bp):
TATCGATACAATGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACATAAAAAAAT
A
Found at i:11801 original size:13 final size:13
Alignment explanation
Indices: 11783--11807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11773 ATTACTCAAA
11783 TATATCGATACAT
1 TATATCGATACAT
11796 TATATCGATACA
1 TATATCGATACA
11808 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:11860 original size:52 final size:50
Alignment explanation
Indices: 11796--11944 Score: 199
Period size: 52 Copynumber: 2.9 Consensus size: 50
11786 ATCGATACAT
*
11796 TATATCGATACACTGATCTTTGTATCGATACATGCAAGCAAATTTGCCCAGA
1 TATATCGATACACT-AT-TATGTATCGATACATGCAAGCAAATTTGCCCAGA
* * *
11848 TGTATCGATACACTATAAAATGTATCGATACATGCAAGCAAATTTGCCCATA
1 TATATCGATACACTAT--TATGTATCGATACATGCAAGCAAATTTGCCCAGA
*
11900 TATATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTT
1 TATATCGATACACTATT--ATGTATCGATACATGCAAGCAAATTT
11945 TCATATTTCG
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (50 bp):
TATATCGATACACTATTATGTATCGATACATGCAAGCAAATTTGCCCAGA
Found at i:15284 original size:18 final size:19
Alignment explanation
Indices: 15261--15300 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
15251 TAGTTATGCT
*
15261 TAAAATATT-TTATATTTA
1 TAAAATATTGTTATATTAA
*
15279 TAAAATTTTGTTATATTAA
1 TAAAATATTGTTATATTAA
15298 TAA
1 TAA
15301 TTTGTGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TAAAATATTGTTATATTAA
Found at i:15294 original size:19 final size:19
Alignment explanation
Indices: 15261--15312 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
15251 TAGTTATGCT
*
15261 TAAAATATT-TTATATTTA
1 TAAAATTTTGTTATATTTA
15279 TAAAATTTTGTTATA-TTA
1 TAAAATTTTGTTATATTTA
*
15297 -ATAATTTGTGTTATAT
1 TAAAATTT-TGTTATAT
15313 AAATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 18 0.62
19 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TAAAATTTTGTTATATTTA
Found at i:15691 original size:16 final size:18
Alignment explanation
Indices: 15660--15695 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
15650 AATAATTAAA
15660 ATAAATATGATGAAAAAT
1 ATAAATATGATGAAAAAT
15678 ATAAATAT-AT-AAAAAT
1 ATAAATATGATGAAAAAT
15694 AT
1 AT
15696 CAAAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAAATATGATGAAAAAT
Found at i:19603 original size:2 final size:2
Alignment explanation
Indices: 19598--19651 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
19588 GAGAGCACTC
* *
19598 AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
19640 AC AT AT AC AT AT
1 AT AT AT AT AT AT
19652 TTGAAACTAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Done.