Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2457
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: 59108
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:5314 original size:52 final size:52
Alignment explanation
Indices: 5258--5377 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
5248 CACCGATCTT
* *
5258 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
*
5310 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
5362 TGTATCGATACATGCA
1 TGTATCGATACATGCA
5378 AGTAACTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATAAAA
Found at i:9692 original size:79 final size:78
Alignment explanation
Indices: 9567--10009 Score: 374
Period size: 79 Copynumber: 5.6 Consensus size: 78
9557 TCTTTCAAAG
* * ** * *
9567 ATAACGGGGTTGGAGTATTCC-CGATGGTGGAAAATCGATGTTTTAGAAATAAAATCAAGGTTGG
1 ATAACGAGGTTGGAGTA-TCCTCAATGGTAAAAAATCTATGTTTTAGAAATAAAA-CAAGGTTAG
*
9631 AGTATCCCCTCAAAA
64 AGTATCCCCTCGAAA
* * * *** **
9646 ATAACAAGGTTGGAGTAACCCCAATGGTAAAAAAAT-TATGTTTTAGAAATAAAATTGGGGTGGG
1 ATAACGAGGTTGGAGTATCCTCAATGGT-AAAAAATCTATGTTTTAGAAATAAAA-CAAGGTTAG
* *
9710 ACTATCTCCTCGAAA
64 AGTATCCCCTCGAAA
* * * * *
9725 ATAATG-GGATTGGAGTATCCTCAATGTTGAAAAATCAATGTTTTAGAAATAAAACTAAGGTTAA
1 ATAACGAGG-TTGGAGTATCCTCAATGGTAAAAAATCTATGTTTTAGAAATAAAAC-AAGGTTAG
*
9789 AGTATCACCTCGAAA
64 AGTATCCCCTCGAAA
* * * * ** *
9804 TTAACGAGGTTAGAGTATCCTCGATGGTAGAAAATCGGTGTTTTAGAAATAAAACCGAGGTTAGA
1 ATAACGAGGTTGGAGTATCCTCAATGGTAAAAAATCTATGTTTTAGAAATAAAA-CAAGGTTAGA
9869 GTATCCCCTC-AAA
65 GTATCCCCTCGAAA
* * * * *
9882 AGTAACGGGGTTGGAGTATCCTCGATGGT-GAAAATTTGATATTTTAGAAATAAAACAAGAGTTA
1 A-TAACGAGGTTGGAGTATCCTCAATGGTAAAAAATCT-ATGTTTTAGAAATAAAACAAG-GTTA
* *
9946 GAGTGTTCCCTCGAAA
63 GAGTATCCCCTCGAAA
* * * * **
9962 ATAACGAGGCTAGAGTATCCTCAATGGTAGAAATTCGGTGTTTTAGAA
1 ATAACGAGGTTGGAGTATCCTCAATGGTAAAAAATCTATGTTTTAGAA
10010 GTAGAACATC
Statistics
Matches: 292, Mismatches: 60, Indels: 24
0.78 0.16 0.06
Matches are distributed among these distances:
78 22 0.08
79 253 0.87
80 17 0.06
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (78 bp):
ATAACGAGGTTGGAGTATCCTCAATGGTAAAAAATCTATGTTTTAGAAATAAAACAAGGTTAGAG
TATCCCCTCGAAA
Found at i:9759 original size:158 final size:158
Alignment explanation
Indices: 9563--10009 Score: 472
Period size: 158 Copynumber: 2.8 Consensus size: 158
9553 ATGTTCTTTC
* * *
9563 AAAGATAACGGGGTTGGAGTATTCC-CGATGGTGGAAAATCGATGTTTTAGAAATAAAATCAAGG
1 AAAG-TAACGGGATTGGAGTA-TCCTCAATGGTGAAAAATCGATGTTTTAGAAATAAAA-CAAGG
* * * * * * *
9627 TTGGAGTATCCCCTCAAAAATAACAAGGTTGGAGTAACCCCAATGGTAAAAAAAT-TATGTTTTA
63 TTAGAGTATCCCCTCGAAAATAACGAGGTTAGAGTATCCTCAATGGTAAAAAAATCGATGTTTTA
** * * *
9691 GAAATAAAATTGGGGTGGGACTATCTCCTCGA
128 GAAATAAAACCGAGGTGAGACTATCCCCTC-A
* * *
9723 AAA-TAATGGGATTGGAGTATCCTCAATGTTGAAAAATCAATGTTTTAGAAATAAAACTAAGGTT
1 AAAGTAACGGGATTGGAGTATCCTCAATGGTGAAAAATCGATGTTTTAGAAATAAAAC-AAGGTT
* * * * * *
9787 AAAGTATCACCTCGAAATTAACGAGGTTAGAGTATCCTCGATGGT-AGAAAATCGGTGTTTTAGA
65 AGAGTATCCCCTCGAAAATAACGAGGTTAGAGTATCCTCAATGGTAAAAAAATCGATGTTTTAGA
* *
9851 AATAAAACCGAGGTTAGAGTATCCCCTCA
130 AATAAAACCGAGGTGAGACTATCCCCTCA
* * * * *
9880 AAAGTAACGGGGTTGGAGTATCCTCGATGGTGAAAATTTGATATTTTAGAAATAAAACAAGAGTT
1 AAAGTAACGGGATTGGAGTATCCTCAATGGTGAAAAATCGATGTTTTAGAAATAAAACAAG-GTT
* * * * * *
9945 AGAGTGTTCCCTCGAAAATAACGAGGCTAGAGTATCCTCAATGGT-AGAAATTCGGTGTTTTAGA
65 AGAGTATCCCCTCGAAAATAACGAGGTTAGAGTATCCTCAATGGTAAAAAAATCGATGTTTTAGA
10009 A
130 A
10010 GTAGAACATC
Statistics
Matches: 240, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
157 17 0.07
158 220 0.92
160 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (158 bp):
AAAGTAACGGGATTGGAGTATCCTCAATGGTGAAAAATCGATGTTTTAGAAATAAAACAAGGTTA
GAGTATCCCCTCGAAAATAACGAGGTTAGAGTATCCTCAATGGTAAAAAAATCGATGTTTTAGAA
ATAAAACCGAGGTGAGACTATCCCCTCA
Found at i:15820 original size:67 final size:69
Alignment explanation
Indices: 15712--15850 Score: 255
Period size: 67 Copynumber: 2.0 Consensus size: 69
15702 CATTCGGCCA
15712 TATGCTTATATTACTAAGGAAATGCATTAGCTAAGTCAGCCCAACATTG-A-TTGAGTGCAATTA
1 TATGCTTATATTACTAAGGAAATGCATTAGCTAAGTCAGCCCAACATTGAATTTGAGTGCAATTA
15775 AAAT
66 AAAT
*
15779 TATGCTTATATTACTAAGGAAATGCATTAGCTAAGTTAGCCCAACATTGAATTTGAGTGCAATTA
1 TATGCTTATATTACTAAGGAAATGCATTAGCTAAGTCAGCCCAACATTGAATTTGAGTGCAATTA
15844 AAAT
66 AAAT
15848 TAT
1 TAT
15851 TATACCACTT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
67 48 0.70
68 1 0.01
69 20 0.29
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (69 bp):
TATGCTTATATTACTAAGGAAATGCATTAGCTAAGTCAGCCCAACATTGAATTTGAGTGCAATTA
AAAT
Found at i:16248 original size:48 final size:46
Alignment explanation
Indices: 16163--16265 Score: 118
Period size: 48 Copynumber: 2.2 Consensus size: 46
16153 CATTTTCTAA
* ** *
16163 TAGTGTTTTAGGTTGTACCCTTCAGATGTCCTAATAGGAATATCGC
1 TAGTATTTTAGGTTGTACCCCCCAGATGTCCTAATAGGAATACCGC
* *
16209 TAGTACTTTTAGGTTGTACTCCCCCAGATGT-CTCGATAGGAATGCCGC
1 TAGTA-TTTTAGGTTGTAC-CCCCCAGATGTCCT-AATAGGAATACCGC
16257 TAGTATTTT
1 TAGTATTTT
16266 CTTAGTGCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
46 4 0.08
47 19 0.40
48 25 0.52
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (46 bp):
TAGTATTTTAGGTTGTACCCCCCAGATGTCCTAATAGGAATACCGC
Found at i:21111 original size:154 final size:156
Alignment explanation
Indices: 20924--21272 Score: 350
Period size: 154 Copynumber: 2.2 Consensus size: 156
20914 AAAGTACCCG
* * ** * * * * *
20924 GTAATCCTAAAAGATACAAAAACATTATAAAAAGGATGAACCTCTCCTAAACATAT-TCCTTTGG
1 GTAATCCTAAAGGACATGAAAATATTAT-AAAAGGATGAACCTATCCTAAACAAATAT-CTTCGA
* * * * *
20988 CATAAAAGCAGCAT-GGTAACTACTTAGGA-TTTGATTCTAAAAAAAAAAAACTAAAATGC-TC-
64 CATAAAA-AAGCATCGGCAACTACCTAGGACTTAG-TTCT-AAAAAAAAAAACTAAAATGCGCCT
* * *
21049 TTAGGGTATACTTTTGAAGTGAGAGTAC-TA
126 TTAAGGTATACCTTTGAAGTGAAAGTACTTA
* * *
21079 GTAATCTTAAAGGACATGAAAATATTATAAAAGGATAAACCTATCCTAAGCAAATATCTTCGACA
1 GTAATCCTAAAGGACATGAAAATATTATAAAAGGATGAACCTATCCTAAACAAATATCTTCGACA
** * ***
21144 TAAAAAAGGTTCGGCAACTACCTAGGACTTAGTTCTAAAGAAATTTACTAAAATGCGCCTTTAAG
66 TAAAAAAGCATCGGCAACTACCTAGGACTTAGTTCTAAAAAAAAAAACTAAAATGCGCCTTTAAG
* *
21209 GTATACCTTTGACGTGAAAGTGCTTA
131 GTATACCTTTGAAGTGAAAGTACTTA
*
21235 GTAATCCTAAAGGACATGAAAATATTATAAAATGATGA
1 GTAATCCTAAAGGACATGAAAATATTATAAAAGGATGA
21273 CTTTTACCCT
Statistics
Matches: 157, Mismatches: 31, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
153 19 0.12
154 52 0.33
155 49 0.31
156 37 0.24
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (156 bp):
GTAATCCTAAAGGACATGAAAATATTATAAAAGGATGAACCTATCCTAAACAAATATCTTCGACA
TAAAAAAGCATCGGCAACTACCTAGGACTTAGTTCTAAAAAAAAAAACTAAAATGCGCCTTTAAG
GTATACCTTTGAAGTGAAAGTACTTA
Found at i:21477 original size:17 final size:18
Alignment explanation
Indices: 21459--21492 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21449 TAAAGGAAAT
21459 TTTAT-TATAT-ATTTTA
1 TTTATATATATAATTTTA
21475 TTTATATATATAATTTTA
1 TTTATATATATAATTTTA
21493 AAAGTGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATATATATAATTTTA
Found at i:22411 original size:27 final size:26
Alignment explanation
Indices: 22360--22411 Score: 61
Period size: 27 Copynumber: 1.9 Consensus size: 26
22350 TTCTAACAAG
*
22360 ACATAAATATTATCAAATAATATCAAA
1 ACATAAATATTAT-AAATAAAATCAAA
22387 ACATAAATTATTAT-AATGAAAATCA
1 ACATAAA-TATTATAAAT-AAAATCA
22412 GCCCAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 3 0.14
27 13 0.59
28 6 0.27
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (26 bp):
ACATAAATATTATAAATAAAATCAAA
Found at i:24615 original size:28 final size:27
Alignment explanation
Indices: 24583--24651 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
24573 TAAAGCCAGC
*
24583 GTTGGAGTGTCCCCTCA-GAAATAACGGG
1 GTTGGAGTATCCCC-CATG-AATAACGGG
* *
24611 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCCATGAATAACGGG
24638 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
24652 GATTGTGAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.25
Consensus pattern (27 bp):
GTTGGAGTATCCCCCATGAATAACGGG
Found at i:27139 original size:33 final size:33
Alignment explanation
Indices: 27101--27167 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
27091 AAAATTTCCA
***
27101 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
* *
27134 AATGTATCGGTACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
27167 A
1 A
27168 TTTCCTTGGC
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:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:27211 original size:19 final size:18
Alignment explanation
Indices: 27187--27254 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
27177 CAGTAGCTAA
27187 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
27206 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
27221 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
27238 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
27255 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:27227 original size:13 final size:13
Alignment explanation
Indices: 27209--27233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27199 ACAATACTTA
27209 TGTATCGATACAT
1 TGTATCGATACAT
27222 TGTATCGATACA
1 TGTATCGATACA
27234 AAACTTATGT
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:27231 original size:32 final size:32
Alignment explanation
Indices: 27190--27252 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
27180 TAGCTAATTA
*
27190 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
27222 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
27253 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:27334 original size:21 final size:21
Alignment explanation
Indices: 27310--27366 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
27300 CATTTGTAGG
27310 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
* *
27331 ATGTATTGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
27352 ATGTATCGATACATT
1 ATGTATCGATACATT
27367 TGGATAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:28688 original size:7 final size:7
Alignment explanation
Indices: 28678--28768 Score: 53
Period size: 7 Copynumber: 12.7 Consensus size: 7
28668 ACCTTGAACC
28678 AAAAAAG
1 AAAAAAG
28685 AAAAAA-
1 AAAAAAG
28691 AAAGGAAGGAG
1 AAA--AA--AG
*
28702 AAAAGAG
1 AAAAAAG
*
28709 AAAAGAG
1 AAAAAAG
28716 AAAAAAG
1 AAAAAAG
28723 AAAAAAG
1 AAAAAAG
*
28730 AAGAAA-
1 AAAAAAG
* *
28736 AAGAAGG
1 AAAAAAG
*
28743 AGAGAAA-
1 A-AAAAAG
28750 AAAAAAG
1 AAAAAAG
*
28757 AAGAAAG
1 AAAAAAG
28764 AAAAA
1 AAAAA
28769 TGATAGTTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
6 12 0.18
7 45 0.66
8 6 0.09
9 1 0.01
10 1 0.01
11 3 0.04
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:28721 original size:16 final size:17
Alignment explanation
Indices: 28688--28765 Score: 61
Period size: 16 Copynumber: 4.5 Consensus size: 17
28678 AAAAAAGAAA
*
28688 AAAAAAGGAAGGAGAAAAG
1 AAAAAA-GAA-GAAAAAAG
*
28707 AGAAAAG-AGAAAAAAG
1 AAAAAAGAAGAAAAAAG
28723 AAAAAAGAAG-AAAAAG
1 AAAAAAGAAGAAAAAAG
* * *
28739 AAGGAGAGAAAAAAAAAG
1 AA-AAAAGAAGAAAAAAG
*
28757 AAGAAAGAA
1 AAAAAAGAA
28766 AAATGATAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
16 21 0.43
17 14 0.29
18 9 0.18
19 5 0.10
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAGAAAAAAG
Found at i:28721 original size:31 final size:30
Alignment explanation
Indices: 28678--28768 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 30
28668 ACCTTGAACC
* * *
28678 AAAAAAGAAAAAAAAAGGAAGGAGAAAAGAG
1 AAAAGAGAAAAAAAAAGAAAGAAGAAAA-AG
28709 AAAAGAGAAAAAAGAAA-AAAGAAGAAAAAG
1 AAAAGAGAAAAAA-AAAGAAAGAAGAAAAAG
*
28739 AAGGAGAGAAAAAAAAAG-AAGAAAGAAAAA
1 AA-AAGAGAAAAAAAAAGAAAG-AAGAAAAA
28769 TGATAGTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
30 10 0.19
31 39 0.75
32 3 0.06
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (30 bp):
AAAAGAGAAAAAAAAAGAAAGAAGAAAAAG
Found at i:28754 original size:18 final size:17
Alignment explanation
Indices: 28716--28768 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
28706 GAGAAAAGAG
*
28716 AAAAAAGAAAAAAG-AA
1 AAAAAAGAAGAAAGAAA
* *
28732 GAAAAAGAAGGAGAGAAA
1 AAAAAAGAA-GAAAGAAA
28750 AAAAAAGAAGAAAGAAA
1 AAAAAAGAAGAAAGAAA
28767 AA
1 AA
28769 TGATAGTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 8 0.27
17 12 0.40
18 10 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAGAAAGAAA
Found at i:28767 original size:14 final size:14
Alignment explanation
Indices: 28707--28768 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
28697 AGGAGAAAAG
* *
28707 AGAAAAGAGAAAAA
1 AGAAAAAAGAAGAA
28721 AGAAAAAAGAAGAA
1 AGAAAAAAGAAGAA
* *
28735 A-AAGAAGGAGAGAA
1 AGAAAAAAGA-AGAA
28749 A-AAAAAAGAAGAA
1 AGAAAAAAGAAGAA
28762 AGAAAAA
1 AGAAAAA
28769 TGATAGTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.28
14 29 0.73
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAAAAAAGAAGAA
Found at i:31761 original size:18 final size:18
Alignment explanation
Indices: 31738--31842 Score: 131
Period size: 18 Copynumber: 5.8 Consensus size: 18
31728 TAAGATTACA
*
31738 AAAATCTATGATTTTTAG
1 AAAATCTATGATTCTTAG
*
31756 AAAATCTATGATTCCTAG
1 AAAATCTATGATTCTTAG
31774 AAAATCTAATGATTCTTAG
1 AAAATCT-ATGATTCTTAG
* * *
31793 AAAA-CATGTGATTCCTAA
1 AAAATC-TATGATTCTTAG
*
31811 AAAATCTAAGATTCTTAG
1 AAAATCTATGATTCTTAG
31829 AAAATCTATGATTC
1 AAAATCTATGATTC
31843 CTAAAATCAG
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
18 57 0.78
19 16 0.22
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (18 bp):
AAAATCTATGATTCTTAG
Found at i:31793 original size:37 final size:36
Alignment explanation
Indices: 31721--31848 Score: 165
Period size: 37 Copynumber: 3.6 Consensus size: 36
31711 TATTAAGGTT
* * *
31721 GAAAATCTAAGATTAC-AAAAATCT-ATGATTTTTA
1 GAAAATCTATGATTCCTAAAAATCTAATGATTCTTA
31755 GAAAATCTATGATTCCTAGAAAATCTAATGATTCTTA
1 GAAAATCTATGATTCCTA-AAAATCTAATGATTCTTA
*
31792 GAAAA-CATGTGATTCCTAAAAAATCTAA-GATTCTTA
1 GAAAATC-TATGATTCCT-AAAAATCTAATGATTCTTA
31828 GAAAATCTATGATTCCTAAAA
1 GAAAATCTATGATTCCTAAAA
31849 TCAGTGATTT
Statistics
Matches: 83, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
34 14 0.17
35 5 0.06
36 30 0.36
37 33 0.40
38 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (36 bp):
GAAAATCTATGATTCCTAAAAATCTAATGATTCTTA
Found at i:31831 original size:36 final size:36
Alignment explanation
Indices: 31721--31848 Score: 163
Period size: 36 Copynumber: 3.6 Consensus size: 36
31711 TATTAAGGTT
* * * *
31721 GAAAATCTAAGATTAC--AAAAATCTATGATTTTTA
1 GAAAATCTATGATTCCTAAAAAATCTAAGATTCTTA
*
31755 GAAAATCTATGATTCCTAGAAAATCTAATGATTCTTA
1 GAAAATCTATGATTCCTAAAAAATCTAA-GATTCTTA
*
31792 GAAAA-CATGTGATTCCTAAAAAATCTAAGATTCTTA
1 GAAAATC-TATGATTCCTAAAAAATCTAAGATTCTTA
31828 GAAAATCTATGATTCCTAAAA
1 GAAAATCTATGATTCCTAAAA
31849 TCAGTGATTT
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
34 14 0.17
36 35 0.43
37 32 0.40
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (36 bp):
GAAAATCTATGATTCCTAAAAAATCTAAGATTCTTA
Found at i:36714 original size:21 final size:21
Alignment explanation
Indices: 36681--36721 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36671 CTAAGTAAAA
36681 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
36702 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
36722 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:36927 original size:10 final size:10
Alignment explanation
Indices: 36908--36938 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
36898 AATCTCATTT
36908 TCACTGTTCA
1 TCACTGTTCA
*
36918 TCACTATTCA
1 TCACTGTTCA
36928 TCACTGTTCA
1 TCACTGTTCA
36938 T
1 T
36939 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:36960 original size:21 final size:22
Alignment explanation
Indices: 36926--36981 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
36916 CATCACTATT
36926 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
36948 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
36969 CATCACTGTTCAT
1 CATCACTGTTCAT
36982 CACTATTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:37013 original size:34 final size:32
Alignment explanation
Indices: 36948--37032 Score: 127
Period size: 34 Copynumber: 2.6 Consensus size: 32
36938 TGTATCGATA
* *
36948 CATCACT-TTCATGTATCGATACATCACTGTT
1 CATCACTATTCATGTATCGAAAAATCACTGTT
36979 CATCACTATTCATGTATCGTTAAAAATCACTGTT
1 CATCACTATTCATGTATCG--AAAAATCACTGTT
37013 CATCACTATTCATGTATCGA
1 CATCACTATTCATGTATCGA
37033 TACATATTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
31 7 0.14
32 12 0.24
34 30 0.61
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (32 bp):
CATCACTATTCATGTATCGAAAAATCACTGTT
Found at i:37062 original size:13 final size:13
Alignment explanation
Indices: 37044--37069 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37034 ACATATTTGT
37044 GTGTATCGATACA
1 GTGTATCGATACA
37057 GTGTATCGATACA
1 GTGTATCGATACA
37070 TCATAAATAG
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:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:37611 original size:34 final size:35
Alignment explanation
Indices: 37548--37614 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
37538 CTAAGTGATT
37548 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
37584 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
37615 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:38058 original size:93 final size:91
Alignment explanation
Indices: 37952--38163 Score: 237
Period size: 93 Copynumber: 2.3 Consensus size: 91
37942 GACTATTCTA
*
37952 AAGGGATACTCCAACCACATTTTTACACTAAAATTCAATTTAT-AGAAACATCAAATTATCATTT
1 AAGGGATACTCCAACC-CATTTTTACACTAAAATTCAATTTATGA-AAACATCAAATTATCATCT
* * *
38016 CCGAGGATACTCCAACCCCACTATCTCC
64 CCAAGAATACTCCAACCCCACCATCTCC
* * * * *
38044 AAGGCGATACTCCAACCCTATTTTTGCACTAAAATTCAATTTATGAAAATATTAATTTTTCATCT
1 AAGG-GATACTCCAACCC-ATTTTTACACTAAAATTCAATTTATGAAAACATCAAATTATCATCT
* *
38109 CCAAGAATACTCCAACCCTACCATCTCTG
64 CCAAGAATACTCCAACCCCACCATCTC-C
* * *
38138 AGGGGATGCTCCAACCTCGTTTTTAC
1 AAGGGATACTCCAACC-CATTTTTAC
38164 TACCAAAACA
Statistics
Matches: 100, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
92 5 0.05
93 90 0.90
94 5 0.05
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.31
Consensus pattern (91 bp):
AAGGGATACTCCAACCCATTTTTACACTAAAATTCAATTTATGAAAACATCAAATTATCATCTCC
AAGAATACTCCAACCCCACCATCTCC
Found at i:39468 original size:27 final size:27
Alignment explanation
Indices: 39433--39484 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
39423 GACAACAATA
*
39433 AAAAGAAAAGTAAAGAAAAAATAAAGC
1 AAAAGAAAAATAAAGAAAAAATAAAGC
* * *
39460 AAAATAAAAATCATGAAAAAATAAA
1 AAAAGAAAAATAAAGAAAAAATAAA
39485 AGGTAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.75, C:0.04, G:0.10, T:0.12
Consensus pattern (27 bp):
AAAAGAAAAATAAAGAAAAAATAAAGC
Found at i:41166 original size:19 final size:19
Alignment explanation
Indices: 41138--41200 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
41128 AAACAGTAAC
*
41138 TGTATTGATACATAAATGT
1 TGTATCGATACATAAATGT
41157 TGTATCGATAC---AA---
1 TGTATCGATACATAAATGT
*
41170 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAATGT
41189 TGTATCGATACA
1 TGTATCGATACA
41201 ATGTATTGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 11 0.31
16 3 0.08
19 22 0.61
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATAAATGT
Found at i:41175 original size:13 final size:13
Alignment explanation
Indices: 41157--41181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41147 ACATAAATGT
41157 TGTATCGATACAA
1 TGTATCGATACAA
41170 TGTATCGATACA
1 TGTATCGATACA
41182 TAAGTGTTGT
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:41180 original size:32 final size:32
Alignment explanation
Indices: 41138--41206 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
41128 AAACAGTAAC
*
41138 TGTATTGATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
*
41170 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
41202 TGTAT
1 TGTAT
41207 TGCTACGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAATGTTGTATCGATACAA
Found at i:41270 original size:13 final size:13
Alignment explanation
Indices: 41252--41279 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41242 CATTACTCAA
41252 TGTATCGATACAT
1 TGTATCGATACAT
41265 TGTATCGATACAT
1 TGTATCGATACAT
41278 TG
1 TG
41280 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:48280 original size:22 final size:22
Alignment explanation
Indices: 48255--48322 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 22
48245 CCTCAAAAGT
48255 ACAAACACAAAAAAAAAAAAAA
1 ACAAACACAAAAAAAAAAAAAA
*
48277 AC-AACACAAAAAAAACCAAAAA
1 ACAAACACAAAAAAAA-AAAAAA
48299 ACAAA-ACAAAAAAACAACAAAAA
1 ACAAACACAAAAAAA-AA-AAAAA
48322 A
1 A
48323 AAGTGCAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 13 0.32
22 18 0.45
23 9 0.22
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (22 bp):
ACAAACACAAAAAAAAAAAAAA
Found at i:48289 original size:13 final size:13
Alignment explanation
Indices: 48271--48324 Score: 64
Period size: 12 Copynumber: 4.5 Consensus size: 13
48261 ACAAAAAAAA
48271 AAAAAAACAACAC
1 AAAAAAACAACAC
48284 -AAAAAA-AAC-C
1 AAAAAAACAACAC
*
48294 -AAAAAACAAAAC
1 AAAAAAACAACAC
48306 AAAAAAACAACA-
1 AAAAAAACAACAC
48318 AAAAAAA
1 AAAAAAA
48325 GTGCAAAGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 7 0.19
11 5 0.14
12 14 0.39
13 10 0.28
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAACAC
Found at i:48321 original size:32 final size:32
Alignment explanation
Indices: 48257--48324 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
48247 TCAAAAGTAC
*
48257 AAACACAAAAAAAAAAAAAAACAACACAAAAA
1 AAACACAAAAAAAAAAAAAAAAAACACAAAAA
*
48289 AAAC-CAAAAAACAAAACAAAAAAACAACAAAAA
1 AAACACAAAAAA-AAAAAAAAAAAAC-ACAAAAA
48322 AAA
1 AAA
48325 GTGCAAAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 7 0.22
32 15 0.47
33 10 0.31
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (32 bp):
AAACACAAAAAAAAAAAAAAAAAACACAAAAA
Found at i:49588 original size:30 final size:30
Alignment explanation
Indices: 49510--49879 Score: 395
Period size: 31 Copynumber: 12.0 Consensus size: 30
49500 AATTCTTCAA
* *
49510 ATCTCTCTTCTCAAAGTCCACGATTTAGTGGC
1 ATCTCT-TTC-CAAAGTCCACGACTCAGTGGC
* *
49542 ATCTTTTTCTCAAAGTCCACAACTCAGTGGC
1 ATCTCTTTC-CAAAGTCCACGACTCAGTGGC
*
49573 ATCTCTTTCCAAAGTCCACGACTCAATGGC
1 ATCTCTTTCCAAAGTCCACGACTCAGTGGC
*
49603 ATCTCTTCTTCAAAGTCCACGACTCAGTGGC
1 ATCTCTT-TCCAAAGTCCACGACTCAGTGGC
* *
49634 GTCTTTTTTCCTAAAGTCCACGACTCAGTGGC
1 ATC-TCTTTCC-AAAGTCCACGACTCAGTGGC
* *
49666 ATCT-TTTCTTCCAAGTCCATGACTCAGTGGC
1 ATCTCTTTC--CAAAGTCCACGACTCAGTGGC
* * *
49697 ATCTCTTTCCGAAGTCCACGACTTAATGGC
1 ATCTCTTTCCAAAGTCCACGACTCAGTGGC
*
49727 ATCTC-TTCTCAAAGTCCACGATTCAGTGGC
1 ATCTCTTTC-CAAAGTCCACGACTCAGTGGC
* * *
49757 ATCTTTTTCTCAAAGTCCACAACTTAGTGGC
1 ATCTCTTTC-CAAAGTCCACGACTCAGTGGC
* * *
49788 ATCTCTTTTCAAAGTCCACAACTCACTGGC
1 ATCTCTTTCCAAAGTCCACGACTCAGTGGC
*
49818 ATCTCTTTTCAAAGTCCACGACTCAGTGGC
1 ATCTCTTTCCAAAGTCCACGACTCAGTGGC
* * *
49848 ATCT-TTTCTTCAAAGCCCACAACTCTGTGGC
1 ATCTCTTTC--CAAAGTCCACGACTCAGTGGC
49879 A
1 A
49880 CCCTTTTAAA
Statistics
Matches: 291, Mismatches: 37, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
29 6 0.02
30 124 0.43
31 126 0.43
32 35 0.12
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.32
Consensus pattern (30 bp):
ATCTCTTTCCAAAGTCCACGACTCAGTGGC
Found at i:49616 original size:61 final size:61
Alignment explanation
Indices: 49510--49937 Score: 458
Period size: 61 Copynumber: 7.0 Consensus size: 61
49500 AATTCTTCAA
* * *
49510 ATCTCTCTTCTCAAAGTCCACGATTTAGTGGCATCT-TTTTCTCAAAGTCCACAACTCAGTGGC
1 ATCTCT-TTC-CAAAGTCCACGACTCAGTGGCATCTCTTCT-TCAAAGTCCACAACTCAGTGGC
* *
49573 ATCTCTTTCCAAAGTCCACGACTCAATGGCATCTCTTCTTCAAAGTCCACGACTCAGTGGC
1 ATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACAACTCAGTGGC
* * * * **
49634 GTCTTTTTTCCTAAAGTCCACGACTCAGTGGCATCTTTTCTTCCAAGTCCATGACTCAGTGGC
1 ATC-TCTTTCC-AAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACAACTCAGTGGC
* * * * *
49697 ATCTCTTTCCGAAGTCCACGACTTAATGGCATCTCTTC-TCAAAGTCCACGATTCAGTGGC
1 ATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACAACTCAGTGGC
* * * *
49757 ATCTTTTTCTCAAAGTCCACAACTTAGTGGCATCTCTT-TTCAAAGTCCACAACTCACTGGC
1 ATCTCTTTC-CAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACAACTCAGTGGC
* * * *
49818 ATCTCTTTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGCCCACAACTCTGTGGC
1 ATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACAACTCAGTGGC
* * * * * * * *
49879 A-CCCTTT-TAAAGCCCACAACTCCGTGGCA-CCCTT-TT-AAAGCCCACAACTCCGTGGC
1 ATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACAACTCAGTGGC
49935 ATC
1 ATC
49938 CATTCAAGTC
Statistics
Matches: 315, Mismatches: 43, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
56 20 0.06
57 3 0.01
58 3 0.01
59 18 0.06
60 57 0.18
61 141 0.45
62 18 0.06
63 55 0.17
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (61 bp):
ATCTCTTTCCAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACAACTCAGTGGC
Found at i:49758 original size:91 final size:91
Alignment explanation
Indices: 49513--49937 Score: 450
Period size: 91 Copynumber: 4.7 Consensus size: 91
49503 TCTTCAAATC
* * * * *
49513 TCTCTTCTCAAAGTCCACGATTTAGTGGCATCTTTTTCTCAAAGTCCACAACTCAGTGGCATCTC
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCATC-TCTTCTCAAAGTCCACGACTCAGTGGCATCT-
*
49578 TTTC--CAAAGTCCACGACTCAATGGCA
64 TTTCTTCAAAGTCCACGACTCAGTGGCA
* * *
49604 TCTCTTCTTCAAAGTCCACGACTCAGTGGCGTCTTTTTTCCTAAAGTCCACGACTCAGTGGCATC
1 TCTCTT-TTCAAAGTCCACGACTCAGTGGCATCTCTTCT-C-AAAGTCCACGACTCAGTGGCATC
* *
49669 TTTTCTTCCAAGTCCATGACTCAGTGGCA
63 TTTTCTTCAAAGTCCACGACTCAGTGGCA
* * * * *
49698 TCTCTTTCCGAAGTCCACGACTTAATGGCATCTCTTCTCAAAGTCCACGATTCAGTGGCATCTTT
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTT
* *
49763 T-TCTCAAAGTCCACAACTTAGTGGCA
66 TCT-TCAAAGTCCACGACTCAGTGGCA
* * *
49789 TCTCTTTTCAAAGTCCACAACTCACTGGCATCTCTTTTCAAAGTCCACGACTCAGTGGCATCTTT
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTT
* * *
49854 TCTTCAAAGCCCACAACTCTGTGGCA
66 TCTTCAAAGTCCACGACTCAGTGGCA
* * * * * * * * *
49880 -CCCTTTT-AAAGCCCACAACTCCGTGGCA-CCCTT-TTAAAGCCCACAACTCCGTGGCATC
1 TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATC
49938 CATTCAAGTC
Statistics
Matches: 287, Mismatches: 40, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
87 21 0.07
88 4 0.01
89 18 0.06
90 7 0.02
91 135 0.47
92 29 0.10
93 48 0.17
94 25 0.09
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (91 bp):
TCTCTTTTCAAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTT
TCTTCAAAGTCCACGACTCAGTGGCA
Found at i:49893 original size:28 final size:30
Alignment explanation
Indices: 49513--49937 Score: 354
Period size: 30 Copynumber: 14.1 Consensus size: 30
49503 TCTTCAAATC
* * * * *
49513 TCTCTTCTCAAAGTCCACGATTTAGTGGCA
1 TCTCTTTTCAAAGCCCACAACTCAGTGGCA
* *
49543 TCTTTTTCTCAAAGTCCACAACTCAGTGGCA
1 TCTCTTT-TCAAAGCCCACAACTCAGTGGCA
* * * *
49574 TCTCTTTCCAAAGTCCACGACTCAATGGCA
1 TCTCTTTTCAAAGCCCACAACTCAGTGGCA
* * *
49604 TCTCTTCTTCAAAGTCCACGACTCAGTGGCG
1 TCTCTT-TTCAAAGCCCACAACTCAGTGGCA
* * *
49635 TCTTTTTTCCTAAAGTCCACGACTCAGTGGCA
1 TCTCTTTT-C-AAAGCCCACAACTCAGTGGCA
* * * **
49667 TCTTTTCTTCCAAGTCCATGACTCAGTGGCA
1 TCTCTT-TTCAAAGCCCACAACTCAGTGGCA
* * * * * *
49698 TCTCTTTCCGAAGTCCACGACTTAATGGCA
1 TCTCTTTTCAAAGCCCACAACTCAGTGGCA
* * * *
49728 TCTCTTCTCAAAGTCCACGATTCAGTGGCA
1 TCTCTTTTCAAAGCCCACAACTCAGTGGCA
* * *
49758 TCTTTTTCTCAAAGTCCACAACTTAGTGGCA
1 TCTCTTT-TCAAAGCCCACAACTCAGTGGCA
* *
49789 TCTCTTTTCAAAGTCCACAACTCACTGGCA
1 TCTCTTTTCAAAGCCCACAACTCAGTGGCA
* *
49819 TCTCTTTTCAAAGTCCACGACTCAGTGGCA
1 TCTCTTTTCAAAGCCCACAACTCAGTGGCA
* *
49849 TCTTTTCTTCAAAGCCCACAACTCTGTGGCA
1 TCTCTT-TTCAAAGCCCACAACTCAGTGGCA
* *
49880 -CCCTTTT-AAAGCCCACAACTCCGTGGCA
1 TCTCTTTTCAAAGCCCACAACTCAGTGGCA
* *
49908 -CCCTTTT-AAAGCCCACAACTCCGTGGCA
1 TCTCTTTTCAAAGCCCACAACTCAGTGGCA
49936 TC
1 TC
49938 CATTCAAGTC
Statistics
Matches: 342, Mismatches: 45, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
28 48 0.14
29 3 0.01
30 138 0.40
31 124 0.36
32 27 0.08
33 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (30 bp):
TCTCTTTTCAAAGCCCACAACTCAGTGGCA
Found at i:49985 original size:33 final size:33
Alignment explanation
Indices: 49943--50033 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 33
49933 GCATCCATTC
*
49943 AAGTCCACAACTCCGTGACACCTTGT-TCCTTTT
1 AAGTCCACAACTCAGTGACACCTT-TCTCCTTTT
* *
49976 AAGTCCACAACTCTA-TGGCATCTTTCTCCTTTT
1 AAGTCCACAACTC-AGTGACACCTTTCTCCTTTT
* *
50009 AAGCCCACAAGTCAGTGACAACCTT
1 AAGTCCACAACTCAGTGAC-ACCTT
50034 CAAAAGCACA
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
32 2 0.04
33 41 0.87
34 4 0.09
ACGTcount: A:0.25, C:0.32, G:0.12, T:0.31
Consensus pattern (33 bp):
AAGTCCACAACTCAGTGACACCTTTCTCCTTTT
Found at i:50045 original size:28 final size:29
Alignment explanation
Indices: 50009--50079 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
49999 TTCTCCTTTT
*
50009 AAGCCCACAAGTCAGTGACAA-CC-TTCAA
1 AAGCACACAAGTCAGT-ACAACCCTTTCAA
**
50037 AAGCACACAAGTTGGTACAACCCTTTCAA
1 AAGCACACAAGTCAGTACAACCCTTTCAA
50066 AAGTCCACACAAGT
1 AAG--CACACAAGT
50080 TGGTGGCGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.11
28 15 0.42
29 8 0.22
31 9 0.25
ACGTcount: A:0.39, C:0.30, G:0.14, T:0.17
Consensus pattern (29 bp):
AAGCACACAAGTCAGTACAACCCTTTCAA
Found at i:50214 original size:49 final size:49
Alignment explanation
Indices: 50093--51299 Score: 1145
Period size: 49 Copynumber: 24.8 Consensus size: 49
50083 TGGCGTCTTC
*
50093 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
*
50141 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * *
50190 CTTTAAGTCCAATATCGTTAGCCTTGAATCAGCATATTGGCACCTTTGTCAC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * *
50242 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTT-GT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * * *
50290 CTTTAAGACCAATGTTGTTGGCCTTGAATCAACACATTGG------CA-
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
50332 ---GAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * ** *
50378 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGTGCCTTTATTAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* *
50430 CTTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCAT
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
50480 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* *
50532 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* ** * *
50580 CTTTAAGACCAATGTCATTGGCCTTGAATCAACAAATTGG------CA-
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * *
50622 ---TAAGCCCAATGTCCCTGGCCTTGAATCAGCACATTGGCATCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
50668 CTTTAAGTCCAATATCGCTGGCCTTGAATCA--ATACATGGCACCTTTGTCCT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATA-TTGGCACC--T-TCAT
*
50719 CTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
50769 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTATCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * * *
50821 CTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTAGCACCTTTAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * **
50870 CTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGTGCCTTTATCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* *
50922 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
50971 CTTTAAGTCCAATATCGCTGGCCTTGAATCGGCATATTGGCACCTTTGTCAC
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCAT
* * *
51023 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGAACCTT-GT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * *
51071 CTTTAAGACCAATGTTGCTGGCCTTGAATCATCACATTGG------CA-
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * * *
51113 ---TAAGCCCAATGTCACTGGCCTTGAATCATCACATTGGCATCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
51159 CTTTAAGGCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
** * * * * *
51208 CTTTAAACCCAGTGTCGTTGGCTTTGAATCAGCACATTGGCATTCTTCTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA--CCT-TCAT
* * * * * *
51260 CTTCAAGTCTAAATGGCGCTAGCCATGAATCAGCACATTG
1 CTTTAAGTC-CAATGTCGCTGGCCTTGAATCAGCATATTG
51300 TCATTCTTTG
Statistics
Matches: 967, Mismatches: 128, Indels: 123
0.79 0.11 0.10
Matches are distributed among these distances:
39 98 0.10
45 6 0.01
47 2 0.00
48 150 0.16
49 348 0.36
50 14 0.01
51 14 0.01
52 264 0.27
53 69 0.07
54 2 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
Found at i:50286 original size:101 final size:101
Alignment explanation
Indices: 50093--51112 Score: 1221
Period size: 101 Copynumber: 10.4 Consensus size: 101
50083 TGGCGTCTTC
* *
50093 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC----TCATCTTTAAGACCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
*
50154 GTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
50190 CTTTAAGTCCAATATCGTTAGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
* * * *
50255 ATCGCTAGCCTTGAATCAGCATATTGGCACCTT-GT
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * * * *
50290 CTTTAAGACCAATGTTGTTGGCCTTGAATCAACACATTGGCA-----G--------AAGCCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
50342 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* ** * * *
50378 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGTGCCTTTATTATCTTTTAAGTCCAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCA-CCTTTAAGTCCAA
*
50443 TGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCAT
65 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
50480 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
* * *
50545 ATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GT
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * ** * * *
50580 CTTTAAGACCAATGTCATTGGCCTTGAATCAACA-A-----A---TTGGCA----TAAGCCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
* *
50632 GTCCCTGGCCTTGAATCAGCACATTGGCATCTTCAT
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
50668 CTTTAAGTCCAATATCGCTGGCCTTGAATCA--ATACATGGCACCTTTGTC-CTCTTTTAAGTCC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA-TTGGCACCTTTGTCAC-C-TTTAAGTCC
50730 AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
63 AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
50769 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTATCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
* * *
50834 GTTGCTGGCCTTGAATCAGCACATTAGCACCTTTAT
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* ** * *
50870 CTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGTGCCTTTATCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
*
50935 GTCGCTAGCCTTGAATCAGCACATTGGCACCTTCAT
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
50971 CTTTAAGTCCAATATCGCTGGCCTTGAATCGGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
* * * *
51036 ATCGCTGGCCTTGAATCAGCATATTGGAACCTT-GT
66 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
51071 CTTTAAGACCAATGTTGCTGGCCTTGAATCATCACATTGGCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
51113 TAAGCCCAAT
Statistics
Matches: 794, Mismatches: 90, Indels: 75
0.83 0.09 0.08
Matches are distributed among these distances:
86 1 0.00
87 77 0.10
88 62 0.08
91 5 0.01
93 1 0.00
95 1 0.00
96 4 0.01
97 42 0.05
99 1 0.00
100 104 0.13
101 391 0.49
102 102 0.13
103 3 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (101 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAAT
GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:50608 original size:290 final size:290
Alignment explanation
Indices: 50093--51111 Score: 1444
Period size: 290 Copynumber: 3.5 Consensus size: 290
50083 TGGCGTCTTC
*
50093 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC----TCATC-TTTAAGACCAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTTAAGTCCAA
* * *
50153 TGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGTTAGCCTTGAA
66 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAA
* *
50218 TCAGCATATTGGCACCTTTGTCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGC
131 TCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
* * *
50283 ACCTTGTCTTTAAGACCAATGTTGTTGGCCTTGAATCAACACATTGGCAGAAGCCCAATGTCGCT
196 ACCTTGTCTTTAAGACCAATGTCGTTGGCCTTGAATCAACAAATTGGCATAAGCCCAATGTCGCT
50348 GGCCTTGAATCAGCACATTGGCACCTTCAT
261 GGCCTTGAATCAGCACATTGGCACCTTCAT
* ** * *
50378 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGTGCCTTTATTATCTTTTAAGTCCAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTTAAGTCCAA
*
50443 TGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAA
66 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAA
50508 TCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
131 TCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
* *
50573 ACCTTGTCTTTAAGACCAATGTCATTGGCCTTGAATCAACAAATTGGCATAAGCCCAATGTCCCT
196 ACCTTGTCTTTAAGACCAATGTCGTTGGCCTTGAATCAACAAATTGGCATAAGCCCAATGTCGCT
*
50638 GGCCTTGAATCAGCACATTGGCATCTTCAT
261 GGCCTTGAATCAGCACATTGGCACCTTCAT
* *
50668 CTTTAAGTCCAATATCGCTGGCCTTGAATCA--ATACATGGCACCTTTGTCCTCTTTTAAGTCCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA-TTGGCACCTTTGTCATCTTTTAAGTCCA
50731 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGA
65 ATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGA
* * * * * *
50796 ATCAGCATATTGGCGCCTTTATCATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTAG
130 ATCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
* * * * *
50861 CACCTTTATCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGTGCCTTTATCATCTTT
195 CACC-TTGTCTTTAAGACCAATGTCGTTGGCCTTGAATCAACAAATT-G-G-------CA----T
* *
50926 AAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACCTTCAT
246 AAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
50971 CTTTAAGTCCAATATCGCTGGCCTTGAATCGGCATATTGGCACCTTTGTCA-CCTTTAAGTCCAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTTAAGTCCAA
* * * * * * *
51035 TATCGCTGGCCTTGAATCAGCATATTGGAACCTT-GTCTTTAAGACCAATGTTGCTGGCCTTGAA
66 TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAA
* *
51099 TCATCACATTGGC
131 TCAGCATATTGGC
51112 ATAAGCCCAA
Statistics
Matches: 658, Mismatches: 54, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
285 41 0.06
288 3 0.00
289 153 0.23
290 289 0.44
291 1 0.00
292 1 0.00
299 2 0.00
302 37 0.06
303 115 0.17
304 13 0.02
305 3 0.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.32
Consensus pattern (290 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTTAAGTCCAA
TGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAA
TCAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
ACCTTGTCTTTAAGACCAATGTCGTTGGCCTTGAATCAACAAATTGGCATAAGCCCAATGTCGCT
GGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:50642 original size:39 final size:39
Alignment explanation
Indices: 50583--50661 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
50573 ACCTTGTCTT
*
50583 TAAGACCAATGTCATTGGCCTTGAATCAACAAATTGGCA
1 TAAGACCAATGTCACTGGCCTTGAATCAACAAATTGGCA
* * * *
50622 TAAGCCCAATGTCCCTGGCCTTGAATCAGCACATTGGCA
1 TAAGACCAATGTCACTGGCCTTGAATCAACAAATTGGCA
50661 T
1 T
50662 CTTCATCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (39 bp):
TAAGACCAATGTCACTGGCCTTGAATCAACAAATTGGCA
Found at i:50973 original size:202 final size:199
Alignment explanation
Indices: 50622--51249 Score: 773
Period size: 202 Copynumber: 3.2 Consensus size: 199
50612 CAAATTGGCA
* * *
50622 TAAGCCCAATGTCCCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCT
1 TAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGCT
* * *
50687 GGCCTTGAATCAATACA-TGGCACCTTTGTCCTCTTTTAAGTCCAATGTCGCTGGCCTTGAATCA
66 GGCCTTGAATCAACACATTGG-GCCTTT-TCATC-TTTAAGTCCAATGTCGCTGGCCTTGAATCA
*
50751 GCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTT
128 GCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT
50816 ATCATCTT
193 -TCATCTT
* * *
50824 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTAGCACCTTTATCTTTAAGTCCAATATCGCT
1 TAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGCT
* *
50889 GGCCTTGAATCAACATATTGGTGCCTTTATCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAG
66 GGCCTTGAATCAACACATTGG-GCCTTT-TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAG
*
50954 CACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCGGCATATTGGCACCTTTG
129 CACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-
*
51019 TCACCTT
193 TCATCTT
* * * * * * * *
51026 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGAACC-TTGTCTTTAAGACCAATGTTGCT
1 TAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGCT
* * * *
51090 GGCCTTGAATCATCACATT-GG------CA----TAAGCCCAATGTCACTGGCCTTGAATCATCA
66 GGCCTTGAATCAACACATTGGGCCTTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
* * * * *
51144 CATTGGCATCTTCATCTTTAAGGCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACC--TTCA
131 CATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCA
51207 TCTT
196 TCTT
* * * *
51211 TAAACCCAGTGTCGTTGGCTTTGAATCAGCACATTGGCA
1 TAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
51250 TTCTTCTCAT
Statistics
Matches: 378, Mismatches: 47, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
185 37 0.10
186 1 0.00
188 80 0.21
192 2 0.01
199 1 0.00
200 1 0.00
201 36 0.10
202 208 0.55
203 12 0.03
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (199 bp):
TAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGCT
GGCCTTGAATCAACACATTGGGCCTTTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
CATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCA
TCTT
Found at i:51133 original size:39 final size:39
Alignment explanation
Indices: 51074--51152 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
51064 ACCTTGTCTT
**
51074 TAAGACCAATGTTGCTGGCCTTGAATCATCACATTGGCA
1 TAAGACCAATGTCACTGGCCTTGAATCATCACATTGGCA
*
51113 TAAGCCCAATGTCACTGGCCTTGAATCATCACATTGGCA
1 TAAGACCAATGTCACTGGCCTTGAATCATCACATTGGCA
51152 T
1 T
51153 CTTCATCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (39 bp):
TAAGACCAATGTCACTGGCCTTGAATCATCACATTGGCA
Found at i:51262 original size:491 final size:491
Alignment explanation
Indices: 50144--51299 Score: 1553
Period size: 491 Copynumber: 2.4 Consensus size: 491
50134 ACCTCATCTT
* * * * * *
50144 TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATCGTT
1 TAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGGCCAATATCGCT
* * * * ** * *
50209 AGCCTTGAATCAGCATATTGGCACCTTTGTCA-CCTTTAAGTCCAATATCGCTAGCCTTGAATCA
66 GGCCTTGAATCAACACA-TGGCACC-TTGTCATCTTTTAAACCCAATGTCGCTGGCCTTGAATCA
* * * * * * * * *
50273 GCATATTGGCACCTT-GTCTTTAAGACC-AATGTTGTTGGCCTTGAATCAACACATT-G-G----
129 GCACATTGGCACCTTCATCTTCAAGTCCAAATG-CGCTAGCCATGAATCAGCACATTGGCGCCTT
* * *
50330 ---CA----GAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCC
193 TATCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCC
* *
50388 AATATCGCTAGCCTTGAATCAGCATATTGGTGCCTTTATTATCTTTTAAGTCCAATGTCGCTAGC
258 AATATCGCTAGCCTTGAATCAACATATTGGTGCCTTTATCATCTTTTAAGTCCAATGTCGCTAGC
50453 CTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
323 CTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
* *
50518 GGCGCCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTT
388 GGCACCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGAACCTTGTCTT
*
50583 TAAGACCAATGTCATTGGCCTTGAATCAACAAATTGGCA
453 TAAGACCAATGTCACTGGCCTTGAATCAACAAATTGGCA
* *
50622 TAAGCCCAATGTCCCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCT
1 TAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGGCCAATATCGCT
* * **
50687 GGCCTTGAATCAATACATGGCACCTTTGTCCTCTTTTAAGTCCAATGTCGCTGGCCTTGAATCAG
66 GGCCTTGAATCAACACATGGCACC-TTGTCATCTTTTAAACCCAATGTCGCTGGCCTTGAATCAG
* * * *
50752 CACATTGGCACCTTCATCTTTAAGTCCAATAT-CGCTGGCCTTGAATCAGCATATTGGCGCCTTT
130 CACATTGGCACCTTCATCTTCAAGTCCAA-ATGCGCTAGCCATGAATCAGCACATTGGCGCCTTT
* *
50816 ATCATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTAGCACCTTTATCTTTAAGTCCA
194 ATCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCA
*
50881 ATATCGCTGGCCTTGAATCAACATATTGGTGCCTTTATCATC-TTTAAGTCCAATGTCGCTAGCC
259 ATATCGCTAGCCTTGAATCAACATATTGGTGCCTTTATCATCTTTTAAGTCCAATGTCGCTAGCC
*
50945 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCGGCATATTG
324 TTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
51010 GCACCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGAACCTTGTCTTT
389 GCACCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGAACCTTGTCTTT
** * *
51075 AAGACCAATGTTGCTGGCCTTGAATCATCACATTGGCA
454 AAGACCAATGTCACTGGCCTTGAATCAACAAATTGGCA
* * *
51113 TAAGCCCAATGTCACTGGCCTTGAATCATCACATTGGCATCTTCATCTTTAAGGCCAATGTCGTT
1 TAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGGCCAATATCGCT
* * * *
51178 GGCCTTGAATCAGCACATTGGCACC-T-TCATC-TTTAAACCCAGTGTCGTTGGCTTTGAATCAG
66 GGCCTTGAATCAACACA-TGGCACCTTGTCATCTTTTAAACCCAATGTCGCTGGCCTTGAATCAG
* *
51240 CACATTGGCATTCTTCTCATCTTCAAGTCTAAATGGCGCTAGCCATGAATCAGCACATTG
130 CACATTGGCA--CCT-TCATCTTCAAGTCCAAAT-GCGCTAGCCATGAATCAGCACATTG
51300 TCATTCTTTG
Statistics
Matches: 600, Mismatches: 55, Indels: 32
0.87 0.08 0.05
Matches are distributed among these distances:
477 13 0.02
478 116 0.19
479 29 0.05
480 2 0.00
481 3 0.00
488 38 0.06
489 4 0.01
490 5 0.01
491 271 0.45
492 119 0.20
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (491 bp):
TAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGGCCAATATCGCT
GGCCTTGAATCAACACATGGCACCTTGTCATCTTTTAAACCCAATGTCGCTGGCCTTGAATCAGC
ACATTGGCACCTTCATCTTCAAGTCCAAATGCGCTAGCCATGAATCAGCACATTGGCGCCTTTAT
CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCCAAT
ATCGCTAGCCTTGAATCAACATATTGGTGCCTTTATCATCTTTTAAGTCCAATGTCGCTAGCCTT
GAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
ACCTTTGTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGAACCTTGTCTTTAA
GACCAATGTCACTGGCCTTGAATCAACAAATTGGCA
Found at i:52799 original size:13 final size:13
Alignment explanation
Indices: 52781--52806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52771 CAATTTTTTG
52781 TGTATCGATACAT
1 TGTATCGATACAT
52794 TGTATCGATACAT
1 TGTATCGATACAT
52807 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:52871 original size:21 final size:21
Alignment explanation
Indices: 52845--52920 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
52835 CTGCCAAGAA
*
52845 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
52866 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
52886 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
52907 ATGTATCGATACAT
1 ATGTATCGATACAT
52921 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:52891 original size:20 final size:20
Alignment explanation
Indices: 52866--52938 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
52856 CATCTTTTTT
52866 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
52886 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
52907 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*
52927 ATGTATTGATAC
1 ATGTATCGATAC
52939 TTTGAATTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:52902 original size:41 final size:41
Alignment explanation
Indices: 52845--52938 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
52835 CTGCCAAGAA
*
52845 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
52886 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
*
52927 ATGTATTGATAC
1 ATGTATCGATAC
52939 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:55394 original size:13 final size:13
Alignment explanation
Indices: 55376--55414 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
55366 ATAATCACCC
*
55376 TGTATCGATACAG
1 TGTATCGATACAA
55389 TGTATCGATACAA
1 TGTATCGATACAA
55402 TGTATCGATACAA
1 TGTATCGATACAA
55415 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:55425 original size:20 final size:20
Alignment explanation
Indices: 55400--55478 Score: 79
Period size: 20 Copynumber: 3.7 Consensus size: 20
55390 GTATCGATAC
55400 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
55420 AATGTATCGATACAAAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
55445 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
55465 CATGTATCGATACA
1 AATGTATCGATACA
55479 TTTTGGACAT
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
20 33 0.65
25 16 0.31
26 2 0.04
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:57507 original size:15 final size:15
Alignment explanation
Indices: 57487--57517 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
57477 ATTTCGTTTG
*
57487 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
57502 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
57517 G
1 G
57518 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Done.