Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3444
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: 30454
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Found at i:12953 original size:108 final size:110
Alignment explanation
Indices: 12808--13009 Score: 311
Period size: 108 Copynumber: 1.9 Consensus size: 110
12798 TATCCTATTG
* * * *
12808 AAACTTACCATTGACATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTCTG-AA-CTCACCA
1 AAACTTACCAATGACATGTCTTGACATGGTATTACATGATATCCTTGCCTT-AGAAACCTCACCA
12871 A-TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAA
65 ATTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAA
* * *
12916 AAACTTATCAATGTCATGTCTTGACATGGTATTACATGATATCCTTGCCTTAGAAACCTTACCAA
1 AAACTTACCAATGACATGTCTTGACATGGTATTACATGATATCCTTGCCTTAGAAACCTCACCAA
12981 TTGCCATGCCTTGGCATGGTCTTACATGG
66 TTGCCATGCCTTGGCATGGTCTTACATGG
13010 TACCCTTAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.57
109 7 0.08
110 28 0.33
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (110 bp):
AAACTTACCAATGACATGTCTTGACATGGTATTACATGATATCCTTGCCTTAGAAACCTCACCAA
TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAA
Found at i:12964 original size:55 final size:54
Alignment explanation
Indices: 12762--13016 Score: 227
Period size: 55 Copynumber: 4.8 Consensus size: 54
12752 ACACGGGTAC
* * * * * *
12762 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---AT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAAAA
* * * * *
12811 CTTACCATTGACATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTCT-GAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAAAA
* * *
12864 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAAAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-AAAA
* * * * * * *
12919 CTTATCAATGTCATGTCTTGACATGGTATTACATGATATCCTTGCCTTAGAAAC
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAAAA
* *
12973 CTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTACCCTT
1 CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
13017 AAACCCTAAT
Statistics
Matches: 165, Mismatches: 31, Indels: 14
0.79 0.15 0.07
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
52 2 0.01
53 43 0.26
54 11 0.07
55 69 0.42
56 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAAAA
Found at i:13134 original size:14 final size:14
Alignment explanation
Indices: 13115--13142 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13105 GAGTCTTCTT
13115 TGAATAATTTCATA
1 TGAATAATTTCATA
13129 TGAATAATTTCATA
1 TGAATAATTTCATA
13143 AAATAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TGAATAATTTCATA
Found at i:14646 original size:11 final size:11
Alignment explanation
Indices: 14630--14658 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
14620 CTCATTTTGC
14630 TATCAACTCGT
1 TATCAACTCGT
14641 TATCAACTCGT
1 TATCAACTCGT
14652 TATCAAC
1 TATCAAC
14659 CTTCTGGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (11 bp):
TATCAACTCGT
Found at i:16074 original size:6 final size:6
Alignment explanation
Indices: 16044--16230 Score: 125
Period size: 6 Copynumber: 30.3 Consensus size: 6
16034 AAGAAACATT
* *
16044 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAGA ATCAG-
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * * *
16091 GTGACAGA ATCAAA ATCAAA ATCAGA ATTAGA ATTAGGTA A-CAGA ATCAGA
1 AT--CAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
* * * *
16142 ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ACCAGA ATCAGA ATTAGGTA
1 ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
*
16193 A-CAGA ATCAGA ATCAGT ATCAGGTA AT-AGA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA AT
16231 GTGAATGCAA
Statistics
Matches: 144, Mismatches: 20, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
5 11 0.08
6 112 0.78
7 13 0.09
8 8 0.06
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:16152 original size:37 final size:37
Alignment explanation
Indices: 16065--16186 Score: 124
Period size: 37 Copynumber: 3.3 Consensus size: 37
16055 AATCAAAATG
*
16065 AGAATCAGAATCAGAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATCAGAATCAGAATCAGGTAACAGAATC
* * * *
16102 AAAATCAAAATCAGAATTAGAATTAGGTAACAGAATC
1 AGAATCAGAATCAGAATCAGAATCAGGTAACAGAATC
* * *
16139 AGAATCAGTATCAGGTAA-CAGAATCA--AAATCAGAACC
1 AGAATCAGAATCA-G-AATCAGAATCAGGTAA-CAGAATC
16176 AGAATCAGAAT
1 AGAATCAGAAT
16187 TAGGTAACAG
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
36 2 0.03
37 58 0.84
38 7 0.10
39 2 0.03
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (37 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAACAGAATC
Found at i:16152 original size:62 final size:62
Alignment explanation
Indices: 16070--16226 Score: 260
Period size: 62 Copynumber: 2.5 Consensus size: 62
16060 AAATGAGAAT
* * * *
16070 CAGAATCAGAATCAGAATCAGGTGACAGAATCAAAATCAAAATCAGAATTAGAATTAGGTAA
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAAAACCAGAATCAGAATTAGGTAA
*
16132 CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAACCAGAATCAGAATTAGGTAA
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAAAACCAGAATCAGAATTAGGTAA
*
16194 CAGAATCAGAATCAGTATCAGGTAATAGAATCA
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCA
16227 GAATGTGAAT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 89 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (62 bp):
CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAAAACCAGAATCAGAATTAGGTAA
Found at i:16192 original size:37 final size:37
Alignment explanation
Indices: 16132--16208 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
16122 AATTAGGTAA
* *
16132 CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAAT
1 CAGAACCAGAATCAGAATCAGGTAACAGAATCAAAAT
* *
16169 CAGAACCAGAATCAGAATTAGGTAACAGAATCAGAAT
1 CAGAACCAGAATCAGAATCAGGTAACAGAATCAAAAT
16206 CAG
1 CAG
16209 TATCAGGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.18, T:0.17
Consensus pattern (37 bp):
CAGAACCAGAATCAGAATCAGGTAACAGAATCAAAAT
Found at i:16203 original size:25 final size:25
Alignment explanation
Indices: 16070--16230 Score: 104
Period size: 25 Copynumber: 6.5 Consensus size: 25
16060 AAATGAGAAT
*
16070 CAGAATCAGAATCAGAATCAGGTGA
1 CAGAATCAGAATCAGAATCAGGTAA
* *
16095 CAGAATCAAAATCAAAATCA-G-AA
1 CAGAATCAGAATCAGAATCAGGTAA
* *
16118 TTAGAATTAGGTAA-CAGAATCA-G-AA
1 -CAGAATCA-G-AATCAGAATCAGGTAA
* *
16143 TCAGTATCAGGTAA-CAGAATCA--AAA
1 -CAGAATCA-G-AATCAGAATCAGGTAA
* *
16168 TCAGAACCAGAATCAGAATTAGGTAA
1 -CAGAATCAGAATCAGAATCAGGTAA
*
16194 CAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGGTAA
*
16219 TAGAATCAGAAT
1 CAGAATCAGAAT
16231 GTGAATGCAA
Statistics
Matches: 111, Mismatches: 18, Indels: 14
0.78 0.13 0.10
Matches are distributed among these distances:
23 3 0.03
24 15 0.14
25 89 0.80
26 4 0.04
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.19
Consensus pattern (25 bp):
CAGAATCAGAATCAGAATCAGGTAA
Found at i:16396 original size:27 final size:26
Alignment explanation
Indices: 16348--16407 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
16338 GCGAGGCTGC
*
16348 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
16375 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
16401 CAGATAT
1 CAGATAT
16408 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:16452 original size:71 final size:67
Alignment explanation
Indices: 16376--16512 Score: 193
Period size: 67 Copynumber: 2.0 Consensus size: 67
16366 CACCAGATAC
* * *
16376 AGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGTAGCGAG
1 AGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGTAGCGAG
16441 GCTGCT
62 GCTGCT
* *
16447 AGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGACGCCACCAGATTGTAGCGAGGCTG
1 AGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGTAGCGAGGCTG
16512 C
66 C
16513 CAGAACGCTT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
67 37 0.61
71 24 0.39
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.21
Consensus pattern (67 bp):
AGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGTAGCGAGGCTG
CT
Found at i:16494 original size:27 final size:26
Alignment explanation
Indices: 16447--16497 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
16437 CGAGGCTGCT
*
16447 AGATATTGTGACGAAGTCACCAGAAC
1 AGATATTGTGACGAAGCCACCAGAAC
* *
16473 AGATATATGTGGCGACGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
16498 TTGTAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAC
Found at i:16763 original size:27 final size:26
Alignment explanation
Indices: 16699--16764 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
16689 CAGTCACTTG
* *
16699 CCCACAAGGGAAAAATAGTCATTTAA
1 CCCACAAGGGTAAAATAGTAATTTAA
* * *
16725 CACACAAGGGGTAAAATGGTAATTTTAC
1 CCCACAA-GGGTAAAATAGTAA-TTTAA
16753 CCCACAAGGGTA
1 CCCACAAGGGTA
16765 TCTCGGTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 6 0.19
27 16 0.50
28 10 0.31
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (26 bp):
CCCACAAGGGTAAAATAGTAATTTAA
Found at i:16772 original size:27 final size:27
Alignment explanation
Indices: 16742--16858 Score: 130
Period size: 27 Copynumber: 4.3 Consensus size: 27
16732 GGGGTAAAAT
* *
16742 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTTTACCCTACAAGGGTATTTC
* * *
16769 GGTAATTCTACCTTA-TAGGAGTATTTC
1 GGTAATTTTACCCTACAAGG-GTATTTC
* *
16796 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTTTACCCTACAAGGGTATTTC
*
16823 GGT-ATTTCTACCCTACAAGGGTATTTT
1 GGTAATTT-TACCCTACAAGGGTATTTC
16850 GGTAATTTT
1 GGTAATTTT
16859 GTAAATCGAG
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
26 6 0.08
27 62 0.83
28 7 0.09
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (27 bp):
GGTAATTTTACCCTACAAGGGTATTTC
Found at i:16855 original size:54 final size:54
Alignment explanation
Indices: 16741--16856 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
16731 AGGGGTAAAA
* * *
16741 TGGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCTTATAGGAGTATTT
1 TGGTAATTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTAAAGGAGTATTT
** * * *
16795 CAGTAATTCTACCCTACAAGGGTATTTCGGTATTTCTACCCTACAAGG-GTATTT
1 TGGTAATTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTA-AAGGAGTATTT
16849 TGGTAATT
1 TGGTAATT
16857 TTGTAAATCG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 48 0.94
55 3 0.06
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (54 bp):
TGGTAATTCTACCCCACAAGGGTATCTCGGTAATTCTACCCTAAAGGAGTATTT
Found at i:16870 original size:27 final size:26
Alignment explanation
Indices: 16810--17154 Score: 235
Period size: 27 Copynumber: 12.8 Consensus size: 26
16800 ATTCTACCCT
* **
16810 ACAAGGGTATTTCGGT-ATTTCTACCCT
1 ACAAGGGTATTTTGGTAATTT-TA-CAA
**
16837 ACAAGGGTATTTTGGTAATTTTGTAA
1 ACAAGGGTATTTTGGTAATTTTACAA
* ****
16863 ATCGAGGGTAAAACGGTAATTCTGTA-AA
1 A-CAAGGGTATTTTGGTAATT-T-TACAA
* * *
16891 TCAAAGGTACTTTGGTAATTTTACAA
1 ACAAGGGTATTTTGGTAATTTTACAA
* * *** *
16917 GTCAAAGGTATTTCAATAATTTTACAGG
1 -ACAAGGGTATTTTGGTAATTTTACA-A
* * ** *
16945 TCGAGGGTATTTCAGTAATTTCACAA
1 ACAAGGGTATTTTGGTAATTTTACAA
*
16971 ATCAGGGGTATTTTGGTAATTTTACAA
1 A-CAAGGGTATTTTGGTAATTTTACAA
* *
16998 ACTAGGGGTATTTTGATAATTTTACAA
1 AC-AAGGGTATTTTGGTAATTTTACAA
*
17025 ACTAGGGGTATTTTGGTAATTTTACAA
1 AC-AAGGGTATTTTGGTAATTTTACAA
* * *
17052 ACTAGGGGTATTTTGGCAATTTTATAA
1 AC-AAGGGTATTTTGGTAATTTTACAA
*
17079 ACCAAGGGTATTTTAGTAATTTTACAA
1 A-CAAGGGTATTTTGGTAATTTTACAA
* **
17106 ACCAGGGATATTTTGGTAATTTTGTAA
1 ACAAGGG-TATTTTGGTAATTTTACAA
17133 ACTAAGGGTATTTTGGTAATTT
1 AC-AAGGGTATTTTGGTAATTT
17155 GGTAAACTAA
Statistics
Matches: 259, Mismatches: 47, Indels: 24
0.78 0.14 0.07
Matches are distributed among these distances:
25 2 0.01
26 10 0.04
27 234 0.90
28 12 0.05
29 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (26 bp):
ACAAGGGTATTTTGGTAATTTTACAA
Found at i:17166 original size:27 final size:27
Alignment explanation
Indices: 16948--17154 Score: 247
Period size: 27 Copynumber: 7.7 Consensus size: 27
16938 TTACAGGTCG
** *
16948 AGGGTATTTCAGTAATTTCACAAA-TCA
1 AGGGTATTTTGGTAATTTTACAAACT-A
*
16975 GGGGTATTTTGGTAATTTTACAAACTA
1 AGGGTATTTTGGTAATTTTACAAACTA
* *
17002 GGGGTATTTTGATAATTTTACAAACTA
1 AGGGTATTTTGGTAATTTTACAAACTA
*
17029 GGGGTATTTTGGTAATTTTACAAACTA
1 AGGGTATTTTGGTAATTTTACAAACTA
* * * *
17056 GGGGTATTTTGGCAATTTTATAAACCA
1 AGGGTATTTTGGTAATTTTACAAACTA
* *
17083 AGGGTATTTTAGTAATTTTACAAAC-C
1 AGGGTATTTTGGTAATTTTACAAACTA
**
17109 AGGGATATTTTGGTAATTTTGTAAACTA
1 AGGG-TATTTTGGTAATTTTACAAACTA
17137 AGGGTATTTTGGTAATTT
1 AGGGTATTTTGGTAATTT
17155 GGTAAACTAA
Statistics
Matches: 159, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
26 4 0.03
27 150 0.94
28 5 0.03
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTACAAACTA
Found at i:18788 original size:29 final size:29
Alignment explanation
Indices: 18755--18814 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
18745 ATAACCAAAC
*
18755 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
18784 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
18813 CT
1 CT
18815 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:18807 original size:15 final size:15
Alignment explanation
Indices: 18761--18808 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
18751 AAACCTACAA
*
18761 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
18776 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
18790 AAACTTCATATCCAT
1 AAACTTCATATCCAT
18805 AAAC
1 AAAC
18809 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:19049 original size:14 final size:13
Alignment explanation
Indices: 19030--19065 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
19020 AGTAAGTTTC
19030 AAAAAAAATCGAAA
1 AAAAAAAATC-AAA
*
19044 AAAAAAATTCAAA
1 AAAAAAAATCAAA
19057 AAAAAAAAT
1 AAAAAAAAT
19066 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.81, C:0.06, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAAAAATCAAA
Found at i:19078 original size:14 final size:14
Alignment explanation
Indices: 19030--19066 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
19020 AGTAAGTTTC
*
19030 AAAAAAAA-TCGAA
1 AAAAAAAATTCAAA
19043 AAAAAAAATTCAAA
1 AAAAAAAATTCAAA
19057 AAAAAAAATT
1 AAAAAAAATT
19067 TTGAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (14 bp):
AAAAAAAATTCAAA
Found at i:19089 original size:18 final size:17
Alignment explanation
Indices: 19041--19091 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
19031 AAAAAAATCG
*
19041 AAAAAAAAAAT-T-CAA
1 AAAAAAAAAATCTGAAA
* *
19056 AAAAAAAAATTTTGAAA
1 AAAAAAAAAATCTGAAA
19073 AAAAAACAAAATCTGAAA
1 AAAAAA-AAAATCTGAAA
19091 A
1 A
19092 TTTGAACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 10 0.34
16 1 0.03
17 8 0.28
18 10 0.34
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.16
Consensus pattern (17 bp):
AAAAAAAAAATCTGAAA
Found at i:20153 original size:30 final size:28
Alignment explanation
Indices: 20117--20172 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
20107 AAGCGAAAAA
* *
20117 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
20147 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
20173 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:23359 original size:48 final size:48
Alignment explanation
Indices: 23307--23412 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
23297 TTGTCTTTTC
*
23307 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
23355 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
23403 TTTCTTTTTC
1 TTTCTTTTTC
23413 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:24452 original size:13 final size:13
Alignment explanation
Indices: 24434--24475 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
24424 GACTTTTCAC
24434 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
*
24447 TTTTTTTACTTTT
1 TTTTTTTTCTTTT
*
24460 TTTTCTTTCTTTT
1 TTTTTTTTCTTTT
24473 TTT
1 TTT
24476 GCTCGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTT
Found at i:24452 original size:22 final size:23
Alignment explanation
Indices: 24427--24475 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
24417 CTCGCAAGAC
24427 TTTTCACTTTTTTTTCTTT-TTT
1 TTTTCACTTTTTTTTCTTTCTTT
*
24449 TTTTTACTTTTTTTTCTTTCTTT
1 TTTTCACTTTTTTTTCTTTCTTT
24472 TTTT
1 TTTT
24476 GCTCGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTCACTTTTTTTTCTTTCTTT
Found at i:24510 original size:11 final size:11
Alignment explanation
Indices: 24491--24521 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
24481 ATTTTTTCAC
24491 TTTTTTTTGAA
1 TTTTTTTTGAA
24502 TTTTTTTTGAA
1 TTTTTTTTGAA
24513 TTTCTTTTT
1 TTT-TTTTT
24522 TGATACTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.13, C:0.03, G:0.06, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:26011 original size:20 final size:20
Alignment explanation
Indices: 25988--26034 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25978 TGGTTAAGAT
*
25988 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
26008 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
26028 TGAGCTG
1 TGAGCTG
26035 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:29243 original size:29 final size:28
Alignment explanation
Indices: 29205--29263 Score: 100
Period size: 29 Copynumber: 2.1 Consensus size: 28
29195 ATAACCAAAC
*
29205 CTACAAAACTTTATATCCATAAACCCAT
1 CTACAAAACTTCATATCCATAAACCCAT
29233 CTACATAAACTTCATATCCATAAACCCAT
1 CTACA-AAACTTCATATCCATAAACCCAT
29262 CT
1 CT
29264 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.29
Consensus pattern (28 bp):
CTACAAAACTTCATATCCATAAACCCAT
Found at i:29256 original size:15 final size:15
Alignment explanation
Indices: 29210--29257 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
29200 CAAACCTACA
*
29210 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
29225 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
29239 AAACTTCATATCCAT
1 AAACTTCATATCCAT
29254 AAAC
1 AAAC
29258 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Done.