Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2389
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: 7093
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Found at i:218 original size:51 final size:52
Alignment explanation
Indices: 98--221 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
88 ATATGAAAAG
* *
98 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
150 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATC-GGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
201 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
222 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 29 0.42
52 40 0.58
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:234 original size:51 final size:51
Alignment explanation
Indices: 98--241 Score: 202
Period size: 51 Copynumber: 2.8 Consensus size: 51
88 ATATGAAAAG
*
98 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
150 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATC-GGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
201 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
242 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 42 0.50
52 40 0.48
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:248 original size:13 final size:13
Alignment explanation
Indices: 230--254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
220 CAAAGATCAG
230 TGTATCGATACAA
1 TGTATCGATACAA
243 TGTATCGATACA
1 TGTATCGATACA
255 TGGAGTCATG
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:251 original size:33 final size:33
Alignment explanation
Indices: 209--274 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
199 ATTTGCCTGC
209 ATGTATCGATACAAAGA-TCAGTGTATCGATACA
1 ATGTATCGATACAAAGAGTCA-TGTATCGATACA
**
242 ATGTATCGATACATGGAGTCATGTATCGATACA
1 ATGTATCGATACAAAGAGTCATGTATCGATACA
275 TTTTTTTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTCATGTATCGATACA
Found at i:1235 original size:55 final size:55
Alignment explanation
Indices: 1168--1471 Score: 179
Period size: 52 Copynumber: 5.6 Consensus size: 55
1158 GCCAATATGT
* * *
1168 TGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAACGTGC
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACGTGC
* * * * *
1223 TGATTCAAGGCCAGCTACATTGAACTTAAAGAT--G---AA-GATGCCAA--TGC
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACGTGC
* **
1270 TGATTCAAGG-CAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAGATGCCAATAT
1 TGATTCAAGGCCAACGATATTGGACTT--AAA-GATGA-GA-AAAAG-GAT---G-T--CAACGT
1334 G-
54 GC
* *
1335 TTATTCATGGCCAACGATATTAGG-CTTAAAGA-GAGAAAAAGGATGTCAACGTGC
1 TGATTCAAGGCCAACGATATT-GGACTTAAAGATGAGAAAAAGGATGTCAACGTGC
* * * * * * **
1389 TGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-AAAATG-TGCCAATATGC
1 TGATTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACGTGC
* *
1441 TGATTCAAGGCCAGCTATATTGGACTTAAAG
1 TGATTCAAGGCCAACGATATTGGACTTAAAG
1472 GTGCCAATGT
Statistics
Matches: 195, Mismatches: 29, Indels: 53
0.70 0.10 0.19
Matches are distributed among these distances:
46 13 0.07
47 13 0.07
48 3 0.02
49 10 0.05
50 2 0.01
52 38 0.19
53 12 0.06
54 25 0.13
55 28 0.14
56 3 0.02
58 3 0.02
59 3 0.02
60 5 0.03
61 3 0.02
62 2 0.01
63 2 0.01
64 6 0.03
65 8 0.04
66 14 0.07
67 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (55 bp):
TGATTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGGATGTCAACGTGC
Found at i:1279 original size:166 final size:168
Alignment explanation
Indices: 1085--1471 Score: 613
Period size: 166 Copynumber: 2.3 Consensus size: 168
1075 TTTTAGAGAT
*
1085 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
1150 GTGAT-A-ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGAT
66 GTGATAAGATGCCAATATGTT-ATTCATGGCCAACGATATTAGGCCTAAAGA-GAGAAAAAGGAT
1213 GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
129 GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* * *
1253 GATGAAGATGCC-A-ATGCTGATTCAAGG-CAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
1315 GTGATAAAGATGCCAATATGTTATTCATGGCCAACGATATTAGGCTTAAAGAGAGAAAAAGGATG
66 GTGAT-AAGATGCCAATATGTTATTCATGGCCAACGATATTAGGCCTAAAGAGAGAAAAAGGATG
1380 TCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
130 TCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
1419 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
1472 GTGCCAATGT
Statistics
Matches: 201, Mismatches: 9, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
165 37 0.18
166 69 0.34
167 34 0.17
168 24 0.12
169 4 0.02
170 1 0.00
171 14 0.07
172 18 0.09
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (168 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
GTGATAAGATGCCAATATGTTATTCATGGCCAACGATATTAGGCCTAAAGAGAGAAAAAGGATGT
CAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:1633 original size:49 final size:49
Alignment explanation
Indices: 1386--1946 Score: 679
Period size: 49 Copynumber: 11.7 Consensus size: 49
1376 GATGTCAACG
* *
1386 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
1438 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1481 TGCTGA-TCAAGGCCAGCTACATTGG-C-T-AAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
1526 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
1569 TGCTGAGTC-AGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * * *
1617 TGTTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
1666 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
1715 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
1764 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * ** *
1813 TGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGGGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
1862 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
* *
1914 TGCTGAGTCAAGGCCAGCTATATTGGACTTAAA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1947 CCGACTTGTG
Statistics
Matches: 440, Mismatches: 51, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
40 3 0.01
41 2 0.00
42 37 0.08
43 30 0.07
44 3 0.01
45 14 0.03
46 18 0.04
47 3 0.01
48 18 0.04
49 238 0.54
50 2 0.00
51 2 0.00
52 70 0.16
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:1709 original size:98 final size:98
Alignment explanation
Indices: 1321--1946 Score: 840
Period size: 98 Copynumber: 6.5 Consensus size: 98
1311 AAAAGTGATA
* * * * *
1321 AAGATGCCAATATG-TTATTCATGGCCAACGATATTAGG-CTTAAAGAGAGAAAAAGGATGTCAA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGA-TG---AAGG-TGCCAA
* * *
1384 CGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
60 TGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* *
1424 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTG
1 AAGA--TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
1483 CTGA-TCAAGGCCAGCTACATTGG-C-T-AAGATG
64 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1514 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1573 GAGTC-AGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
1605 AAGATGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1670 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1703 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1768 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
* * * * *
1801 GAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGGGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1866 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* * *
1900 AAAAGGTGCCAATATGCTGAGTCAAGGCCAGCTATATTGGACTTAAA
1 --AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1947 CCGACTTGTG
Statistics
Matches: 484, Mismatches: 21, Indels: 38
0.89 0.04 0.07
Matches are distributed among these distances:
88 72 0.15
89 3 0.01
90 5 0.01
91 52 0.11
92 1 0.00
93 1 0.00
94 18 0.04
95 13 0.03
96 4 0.01
97 21 0.04
98 216 0.45
99 1 0.00
101 41 0.08
102 1 0.00
103 3 0.01
105 12 0.02
106 20 0.04
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (98 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
Found at i:2052 original size:34 final size:34
Alignment explanation
Indices: 2009--2613 Score: 651
Period size: 34 Copynumber: 17.8 Consensus size: 34
1999 AAGAAGGGTG
* * *
2009 AAAGATGCCACGAAGTTGTGGAC-TTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
** *
2042 CGAGGTTGCCACAGAGTTGTGGGCTTTAAAAAGGAAAA
1 AAAGG-TGCCACGGAGTTGTGGGCTTTAAAAA-G--AA
* *
2080 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
2114 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
*
2148 AAAGAGTGCCACGGAGTTGTGGGCTTT--AAAGGA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
2181 AAAGAGTGCCACGGAGTCGTGGAC-TT-AAAAGGA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
2214 AAAGAGTGCCACGGAGTCGTGGACTTTGAAAAGGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTT-AAAA-AGAA
*
2251 AAAGAGTGCCACGGAGTTGTGGGCTTTAAATAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
*
2286 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAATAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
2320 AAAGGTGCCACGGAGTGGTGGAC-TTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAA-AAGAA
* *
2354 AAAAGTGCCACGGAG-T-TGGGCTTTGAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
2386 GAAGGCGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
2420 GAAGGTGCCACGGAGTTGTGGGCTTTAAACAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
*
2454 AAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
2488 AAAGGTGCCACGGAGTTGTGGAC-TTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAA-AAGAA
* *
2522 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
2556 GAAGGTGCCACGGAGTTGTGGGCTTT--AAAGGA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
2588 AAAGGTGCCACGAAGCTGTGGGCTTT
1 AAAGGTGCCACGGAGTTGTGGGCTTT
2614 GAAGAAAAAT
Statistics
Matches: 500, Mismatches: 54, Indels: 37
0.85 0.09 0.06
Matches are distributed among these distances:
32 50 0.10
33 73 0.15
34 295 0.59
35 20 0.04
36 8 0.02
37 32 0.06
38 21 0.04
39 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
Found at i:2627 original size:30 final size:29
Alignment explanation
Indices: 2079--2892 Score: 206
Period size: 34 Copynumber: 24.9 Consensus size: 29
2069 AAAAAGGAAA
*
2079 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
1 AAAAGA-TGCCAC-GAG-TGTGGGCTTTGAA-G
*
2112 AAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
1 -AAAAGA-TGCCAC-GAG-TGTGGGCTTTGAA-G
*
2146 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGG
1 -AAAAGA-TGCCAC-GAG-TGTGGGCTTTGAA-G
* **
2180 AAAAGAGTGCCACGGAGTCGTGGACTTAAAAGG
1 AAAAGA-TGCCAC-GAGT-GTGGGCTTTGAA-G
*
2213 AAAAGAGTGCCACGGAGTCGTGGACTTTGAAAAGGG
1 AAAAGA-TGCCAC-GAGT-GTGGGCTTTG--AA--G
*
2249 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAATAG
1 -AAAAGA-TGCCAC-GAG-TGTGGGCTTT-GA-AG
* * *
2284 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAATA
1 -AAAAGATGCCAC-GAG-TGTGGGCTTT--GAA-G
* * * *
2319 AAAAGGTGCCACGGAGTGGTGGACTTAAAGATG
1 AAAAGATGCCAC-GAGT-GTGGGCTT--TGAAG
*
2352 AAAAAAGTGCCACGGAGT-TGGGCTTTGAAAAG
1 AAAAGA-TGCCAC-GAGTGTGGGCTTTG--AAG
**
2384 AAGAAGGCGCCACGGAGTTGTGGGCTTTGAAAAG
1 AA-AAGATGCCAC-GAG-TGTGGGCTTTG--AAG
* *
2418 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAACAG
1 AA-AAGATGCCAC-GAG-TGTGGGCTTT-GA-AG
* *
2452 AAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAAG
1 -AAAAGATGCCAC-GAG-TGTGGGCTTT--GAAG
* * * *
2486 AAAAAGGTGCCACGGAGTTGTGGACTTAAAGATG
1 -AAAAGATGCCAC-GAG-TGTGGGCTT--TGAAG
*
2520 AAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAGA-TGCCAC-GAG-TGTGGGCTTTG--AAG
* *
2554 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGG
1 AA-AAGATGCCAC-GAG-TGTGGGCTTTGAA-G
*
2587 AAAAGGTGCCACGAAGCTGTGGGCTTTGAAG
1 AAAAGATGCCACG-AG-TGTGGGCTTTGAAG
*
2618 AAAA-ATGCCACTGAGTCGTGGACTTTG-AG
1 AAAAGATGCCAC-GAGT-GTGGGCTTTGAAG
*
2647 ACAAA-ATGCCACTGAGTCGTGGACTTTGAAGG
1 A-AAAGATGCCAC-GAGT-GTGGGCTTTGAA-G
*
2679 AAAAGATGCCACTGAGTCGTGGACTTTG-AG
1 AAAAGATGCCAC-GAGT-GTGGGCTTTGAAG
* * * *
2709 CAGAGATTGCCACTGGGTCGTGGACTTTG-AG
1 AAAAGA-TGCCAC-GAGT-GTGGGCTTTGAAG
* *
2740 AAGAGATTGCCACTGAGTCGTGGACTTTGAAGG
1 AAAAGA-TGCCAC-GAGT-GTGGGCTTTGAA-G
* *
2773 AAAAGATGCCACTAAGTCGTGGACTTTG-AG
1 AAAAGATGCCAC-GAGT-GTGGGCTTTGAAG
* * * *
2803 CAGAGATTGCCACTGGGTCGTGGACTTTG-AG
1 AAAAGA-TGCCAC-GAGT-GTGGGCTTTGAAG
* *
2834 AAGAGATTGCCACTGAGTCGTGGACTTTG-AG
1 AAAAGA-TGCCAC-GAGT-GTGGGCTTTGAAG
* *
2865 AAGAGATTGCCACTGAGTCGTGGACTTT
1 AAAAGA-TGCCAC-GAGT-GTGGGCTTT
2893 AAAAGGTATT
Statistics
Matches: 683, Mismatches: 56, Indels: 85
0.83 0.07 0.10
Matches are distributed among these distances:
29 4 0.01
30 54 0.08
31 142 0.21
32 94 0.14
33 78 0.11
34 262 0.38
35 19 0.03
36 3 0.00
37 26 0.04
38 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.21
Consensus pattern (29 bp):
AAAAGATGCCACGAGTGTGGGCTTTGAAG
Found at i:2723 original size:31 final size:31
Alignment explanation
Indices: 2623--2892 Score: 395
Period size: 31 Copynumber: 8.7 Consensus size: 31
2613 TGAAGAAAAA
*
2623 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGAT
*
2653 TGCCACTGAGTCGTGGACTTTGAAGGAAAAGA-
1 TGCCACTGAGTCGTGGACTTTG-A-GAAGAGAT
*
2685 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
*
2716 TGCCACTGGGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
*
2747 TGCCACTGAGTCGTGGACTTTGAAGGAAAAGA-
1 TGCCACTGAGTCGTGGACTTTG-A-GAAGAGAT
* *
2779 TGCCACTAAGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
*
2810 TGCCACTGGGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
2841 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
2872 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
2893 AAAAGGTATT
Statistics
Matches: 219, Mismatches: 13, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
30 32 0.15
31 133 0.61
32 47 0.21
33 7 0.03
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:2770 original size:94 final size:94
Alignment explanation
Indices: 2623--2892 Score: 458
Period size: 94 Copynumber: 2.9 Consensus size: 94
2613 TGAAGAAAAA
* *
2623 TGCCACTGAGTCGTGGACTTTGAGACA-A-AATGCCACTGAGTCGTGGACTTTGAAGGAAAAGAT
1 TGCCACTGGGTCGTGGACTTTGAGA-AGAGATTGCCACTGAGTCGTGGACTTTGAAGGAAAAGAT
2686 GCCACTGAGTCGTGGACTTTGAGCAGAGAT
65 GCCACTGAGTCGTGGACTTTGAGCAGAGAT
2716 TGCCACTGGGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTGAAGGAAAAGATG
1 TGCCACTGGGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTGAAGGAAAAGATG
*
2781 CCACTAAGTCGTGGACTTTGAGCAGAGAT
66 CCACTGAGTCGTGGACTTTGAGCAGAGAT
*
2810 TGCCACTGGGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTG-A-GAAGAGATT
1 TGCCACTGGGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTGAAGGAAAAGA-T
2873 GCCACTGAGTCGTGGACTTT
65 GCCACTGAGTCGTGGACTTT
2893 AAAAGGTATT
Statistics
Matches: 169, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
92 7 0.04
93 46 0.27
94 116 0.69
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (94 bp):
TGCCACTGGGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTGAAGGAAAAGATG
CCACTGAGTCGTGGACTTTGAGCAGAGAT
Found at i:4201 original size:14 final size:13
Alignment explanation
Indices: 4184--4262 Score: 70
Period size: 13 Copynumber: 5.6 Consensus size: 13
4174 GCCTTTACAC
4184 TTTTTTTTGTGCTT
1 TTTTTTTTGTG-TT
*
4198 TTTTTTTTGTTTT
1 TTTTTTTTGTGTT
4211 TTGTTTTTTGTGTTTTT
1 TT-TTTTTTGTG---TT
*
4228 TGTTTTTTTGTGTG
1 T-TTTTTTTGTGTT
4242 TTTTTTTTGT-TT
1 TTTTTTTTGTGTT
4254 TGTTTTTTT
1 T-TTTTTTT
4263 TTCATCACTT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
12 2 0.04
13 20 0.36
14 20 0.36
17 12 0.22
18 1 0.02
ACGTcount: A:0.00, C:0.01, G:0.15, T:0.84
Consensus pattern (13 bp):
TTTTTTTTGTGTT
Found at i:4203 original size:16 final size:15
Alignment explanation
Indices: 4184--4264 Score: 87
Period size: 14 Copynumber: 5.3 Consensus size: 15
4174 GCCTTTACAC
*
4184 TTTTTTTTGTG-CTT
1 TTTTTTTTGTGTTTT
4198 TTTTTTTTGT-TTTT
1 TTTTTTTTGTGTTTT
*
4212 TGTTTTTTGTGTTTTT
1 TTTTTTTTGTG-TTTT
4228 TGTTTTTTTGTGTGTTT
1 T-TTTTTTTGTGT-TTT
4245 TTTTTGTTT-TGTTTT
1 TTTTT-TTTGTGTTTT
4260 TTTTT
1 TTTTT
4265 CATCACTTCT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 21 0.36
15 8 0.14
16 13 0.22
17 16 0.28
ACGTcount: A:0.00, C:0.01, G:0.15, T:0.84
Consensus pattern (15 bp):
TTTTTTTTGTGTTTT
Found at i:4212 original size:21 final size:20
Alignment explanation
Indices: 4186--4254 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 20
4176 CTTTACACTT
4186 TTTTTTGTGCTTTTTTTTTTG
1 TTTTTTGTG-TTTTTTTTTTG
*
4207 TTTTTTGTTTTTTGTGTTTTTTG
1 TTTTTTG-TGTTT-T-TTTTTTG
*
4230 TTTTTTTGTGTGTTTTTTTTG
1 -TTTTTTGTGTTTTTTTTTTG
4251 TTTT
1 TTTT
4255 GTTTTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 4 0.10
21 17 0.41
22 3 0.07
23 10 0.24
24 7 0.17
ACGTcount: A:0.00, C:0.01, G:0.16, T:0.83
Consensus pattern (20 bp):
TTTTTTGTGTTTTTTTTTTG
Found at i:4217 original size:28 final size:27
Alignment explanation
Indices: 4186--4264 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 27
4176 CTTTACACTT
*
4186 TTTTTTGTGCTTTTTTTTTTGTTT-TTTG
1 TTTTTTGTG-TTTTTTTTTT-TTTGTGTG
4214 TTTTTTGTGTTTTTTGTTTTTTTGTGTG
1 TTTTTTGTGTTTTTT-TTTTTTTGTGTG
*
4242 TTTTTTTTGTTTTGTTTTTTTTT
1 TTTTTTGTGTTTT-TTTTTTTTT
4265 CATCACTTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 9 0.20
28 35 0.76
29 2 0.04
ACGTcount: A:0.00, C:0.01, G:0.15, T:0.84
Consensus pattern (27 bp):
TTTTTTGTGTTTTTTTTTTTTTGTGTG
Done.