Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1930
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: 35626
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:372 original size:52 final size:51
Alignment explanation
Indices: 217--394 Score: 234
Period size: 53 Copynumber: 3.4 Consensus size: 51
207 AATATGAAAT
217 TTGCCTGCATGTATCGATACATTTCATAGTGGTATCGATACATCCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTCATAGT-GTATCGATACAT-CTGGGCAAA
* *
270 TGTGCCTGCA-GTATCGATACATTTCATAGT-TTTACGAGACATCTGGGCAAA
1 T-TGCCTGCATGTATCGATACATTTCATAGTGTAT-CGATACATCTGGGCAAA
*
321 TTGCCTGCATGTATCGATACAATTTTATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATAC-ATTTCATAGTGTATCGATACATCTGGGCAAA
* * *
373 CTTACTTGCATGTATCAATACA
1 -TTGCCTGCATGTATCGATACA
395 AAGATCAGTG
Statistics
Matches: 111, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
50 8 0.07
51 22 0.20
52 33 0.30
53 40 0.36
54 8 0.07
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:405 original size:52 final size:51
Alignment explanation
Indices: 220--414 Score: 162
Period size: 52 Copynumber: 3.7 Consensus size: 51
210 ATGAAATTTG
* * ** *
220 CCTGCATGTATCGATACATTTCATAGTGGTATCGATACATCCTGGGCAAATGTG
1 CCTGCATGTATCAATACAATAGATAGT-GTATCGATACAT-CTGGGCAAAT-TA
* * ** * * *
274 CCTGCA-GTATCGATACATTTCATAGT-TTTACGAGACATCTGGGCAAATTG
1 CCTGCATGTATCAATACAATAGATAGTGTAT-CGATACATCTGGGCAAATTA
* **
324 CCTGCATGTATCGATACAATTTTATAGTGTATCGATACATCTGGGCAAACTTA
1 CCTGCATGTATCAATACAA-TAGATAGTGTATCGATACATCTGGGCAAA-TTA
*
377 CTTGCATGTATCAATACAA-AGATCAGTGTATCGATACA
1 CCTGCATGTATCAATACAATAGAT-AGTGTATCGATACA
415 ATGTATCGAT
Statistics
Matches: 124, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
50 8 0.06
51 25 0.20
52 44 0.35
53 41 0.33
54 6 0.05
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (51 bp):
CCTGCATGTATCAATACAATAGATAGTGTATCGATACATCTGGGCAAATTA
Found at i:421 original size:13 final size:13
Alignment explanation
Indices: 403--427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
393 CAAAGATCAG
403 TGTATCGATACAA
1 TGTATCGATACAA
416 TGTATCGATACA
1 TGTATCGATACA
428 TGAGTAATGT
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:504 original size:13 final size:13
Alignment explanation
Indices: 486--572 Score: 68
Period size: 13 Copynumber: 5.9 Consensus size: 13
476 ACAAAACTTA
486 TGTATCGATACAT
1 TGTATCGATACAT
499 TGTATCGATACACACTT
1 TGTATCGAT--ACA--T
516 ATGTATCGATACAT
1 -TGTATCGATACAT
530 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
548 ATGTATCGATAC-T
1 -TGTATCGATACAT
561 TGTATCGATACA
1 TGTATCGATACA
573 ACACTTTATG
Statistics
Matches: 62, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
12 11 0.18
13 19 0.31
14 1 0.02
15 3 0.05
16 8 0.13
17 1 0.02
18 10 0.16
19 9 0.15
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:516 original size:31 final size:32
Alignment explanation
Indices: 462--592 Score: 230
Period size: 32 Copynumber: 4.1 Consensus size: 32
452 GGCAGTATCT
*
462 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
494 TACATTGTATCGATAC-ACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
525 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
557 TAC-TTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
589 TACA
1 TACA
593 AATCGTTGAA
Statistics
Matches: 95, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
31 47 0.49
32 48 0.51
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:548 original size:63 final size:64
Alignment explanation
Indices: 462--592 Score: 230
Period size: 63 Copynumber: 2.1 Consensus size: 64
452 GGCAGTATCT
462 TACATTGTATCGATACAAAACTTATGTATCGATACATTGTATCGATAC-ACAC-TTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGATAC-TTGTATCGATACAACACTTTATGTATCGA
*
525 TACATTGTATCGATACAACACTTATGTATCGATACTTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGATACTTGTATCGATACAACACTTTATGTATCGA
589 TACA
1 TACA
593 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
62 12 0.18
63 38 0.58
64 15 0.23
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (64 bp):
TACATTGTATCGATACAAAACTTATGTATCGATACTTGTATCGATACAACACTTTATGTATCGA
Found at i:1559 original size:93 final size:92
Alignment explanation
Indices: 1272--1917 Score: 800
Period size: 93 Copynumber: 6.9 Consensus size: 92
1262 TCATTGGGTT
* * **
1272 TTAAAGATGATGAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGGTGCCAAT
1 TTAAAGATGA--AGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGGAGGTGCCAAT
* *
1337 GTGCTGATTCAAGGCCAGCGACATTGGGC
64 GTGCTGATTCAAGGCCAGCTACATTGGAC
* * *
1366 TTAAAAGATGAGGGTGCCAATATGCTGATTTCAAGGCCAACGATATTGGGACTTGGAGTTGCCAA
1 TT-AAAGATGAAGGTGCCAATATGCTGA-TTCAAGGCCAGCGATATT-GGACTTGGAGGTGCCAA
1431 TGTGCTGATTCAAGGCCAAGCTACATTGGAC
63 TGTGCTGATTCAAGGCC-AGCTACATTGGAC
*
1462 TTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGGAGGTGCCAATGT
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGGAGGTGCCAATGT
1527 GCTGATTCAAGGCCAGCTACATTGGAC
66 GCTGATTCAAGGCCAGCTACATTGGAC
1554 TTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAAA
1 -TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TG-G----
* * * *
1619 AGGATGTCAATGTGCTAATTCAAGGCCAGCGATATTGGAC
54 AGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * * *
1659 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTGGAGGTGCCAATGT
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGGAGGTGCCAATGT
1718 GCTGATTCAAGGCCAGCTACATTGGAC
66 GCTGATTCAAGGCCAGCTACATTGGAC
* * * * ** *
1745 TTAAAGATGAAGGTGCCAATATGCTGGACTCTAGGCCTGCTATATTGGACTTAAAGGTGCCAAAG
1 TTAAAGATGAAGGTGCCAATATGCT-GATTCAAGGCCAGCGATATTGGACTTGGAGGTGCCAATG
*
1810 TGTTGATTCAAGGCCAGCTACATTGGAC
65 TGCTGATTCAAGGCCAGCTACATTGGAC
* * **
1838 TTAAAGATGAAGGTGCCAATATGCTGACTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGT
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGGAGGTGCCAATGT
1903 GCTGATTCAAGGCCA
66 GCTGATTCAAGGCCA
1918 AACGATATTG
Statistics
Matches: 491, Mismatches: 37, Indels: 50
0.85 0.06 0.09
Matches are distributed among these distances:
86 34 0.07
87 3 0.01
90 1 0.00
91 1 0.00
92 81 0.16
93 180 0.37
94 37 0.08
95 63 0.13
96 13 0.03
97 1 0.00
98 36 0.07
99 2 0.00
100 2 0.00
104 5 0.01
105 32 0.07
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (92 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGGAGGTGCCAATGT
GCTGATTCAAGGCCAGCTACATTGGAC
Found at i:1644 original size:55 final size:49
Alignment explanation
Indices: 1272--1938 Score: 572
Period size: 43 Copynumber: 14.1 Consensus size: 49
1262 TCATTGGGTT
* * *
1272 TTAAAGATGATGAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGAC
1 TTAAAGATGA--AGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
* *
1323 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
* * *
1366 TTAAAAGATGAGGGTGCCAATATGCTGATTTCAAGGCCAACGATATTGGGAC
1 TT-AAAGATGAAGGTGCCAATGTGCTGA-TTCAAGGCCAGCGATATT-GGAC
* * *
1418 TT---G--G-AGTTGCCAATGTGCTGATTCAAGGCCAAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC-AGCGATATTGGAC
* *
1462 TTAAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
* *
1511 TT---G--G-AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
*
1554 TTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 -TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
* *
1604 TTAAAGATGAGAAAAAGGATGTCAATGTGCTAATTCAAGGCCAGCGATATTGGAC
1 TTAAAGAT--G---AAGG-TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
* * *
1659 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
* *
1702 TT---G--G-AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
* * * * *
1745 TTAAAGATGAAGGTGCCAATATGCTGGACTCTAGGCCTGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCT-GATTCAAGGCCAGCGATATTGGAC
* * * *
1795 TT----A--AAGGTGCCAAAGTGTTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
* * *
1838 TTAAAGATGAAGGTGCCAATATGCTGACTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
*
1887 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAAACGATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC-AGCGATATTGGAC
1931 TTAGAAGA
1 TTA-AAGA
1939 AGATGCCACC
Statistics
Matches: 508, Mismatches: 58, Indels: 102
0.76 0.09 0.15
Matches are distributed among these distances:
43 191 0.38
44 48 0.09
45 22 0.04
46 4 0.01
47 4 0.01
48 3 0.01
49 75 0.15
50 97 0.19
51 20 0.04
52 5 0.01
54 4 0.01
55 35 0.07
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGAC
Found at i:1731 original size:191 final size:196
Alignment explanation
Indices: 1428--1917 Score: 604
Period size: 191 Copynumber: 2.6 Consensus size: 196
1418 TTGGAGTTGC
* *
1428 CAATGTGCTGATTCAAGGCCAAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATTCA
1 CAATGTGCTAATTCAAGGCCAAGCGACATTGGACTT-AAGA-GATGGTGCCAATATGCTGATTCA
* *
1493 AGGCCAGCGATATTGGACTTGGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTTA
64 AGGCCAGCGACATTAGACTTGGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC-TTA
*
1558 AAGATGAAGGTGCCAATATGCT-GATTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGG
128 AAGATGAAGGTGCCAATATGCTGGACTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGG
1622 ATGT
193 ATGT
* *
1626 CAATGTGCTAATTCAAGGCC-AGCGATATTGGACTT-A-A-A-GGTGCCAATGTGCTGATTCAAG
1 CAATGTGCTAATTCAAGGCCAAGCGACATTGGACTTAAGAGATGGTGCCAATATGCTGATTCAAG
*
1686 GCCAGCTACATTAGACTTGGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
66 GCCAGCGACATTAGACTTGGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * * * **
1751 ATGAAGGTGCCAATATGCTGGACTCTAGGCCTGCTATATTGGACTTAAAG--GTGCCAAA-G-TG
131 ATGAAGGTGCCAATATGCTGGACTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATG
1812 -
196 T
* * *
1812 ---T-TG---ATTCAAGGCC-AGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGACTCA
1 CAATGTGCTAATTCAAGGCCAAGCGACATTGGACTT-AAGA-GATGGTGCCAATATGCTGATTCA
* * * **
1869 AGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
64 AGGCCAGCGACATTAGACTTGGAGGTGCCAATGTGCTGATTCAAGGCCA
1918 AACGATATTG
Statistics
Matches: 263, Mismatches: 22, Indels: 27
0.84 0.07 0.09
Matches are distributed among these distances:
179 23 0.09
181 1 0.00
182 3 0.01
183 1 0.00
184 1 0.00
185 63 0.24
187 2 0.01
188 1 0.00
189 5 0.02
190 25 0.10
191 103 0.39
192 1 0.00
194 1 0.00
195 1 0.00
197 13 0.05
198 19 0.07
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (196 bp):
CAATGTGCTAATTCAAGGCCAAGCGACATTGGACTTAAGAGATGGTGCCAATATGCTGATTCAAG
GCCAGCGACATTAGACTTGGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
ATGAAGGTGCCAATATGCTGGACTCAAGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATG
T
Found at i:1748 original size:283 final size:284
Alignment explanation
Indices: 1238--1933 Score: 856
Period size: 283 Copynumber: 2.5 Consensus size: 284
1228 CGAAAAATGA
* * **
1238 CAATGTGTTGATTCATGACCAGCGT-CATTGGGTTTTAAAGATGATGAGGTGCCAATATGCTGAT
1 CAATGTGTTGATTCAAGGCCAGC-TACATTGGACTTTAAAGATGA--AGGTGCCAATATGCTGAT
* *
1302 TCAAGGCCAACAATATTGGAC-T----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT
63 TCAAGGCCAGCAATATTGGACTTAAAGTAAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATT
* * * *
1362 GGGCTTAAAAGATGAGGGTGCCAATATGCTGATTTCAAGGCCAACGATATTGGGACTTGGAGTTG
128 GGACTT--AAGA-GAGGGTGCCAATATGCTGATTTCAAGGCCAACGACATTGAGACTTGGAGGTG
* *
1427 CCAATGTGCTGATTCAAGGCCAAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCT-GATT
190 CCAATGTGCTGATTCAAGGCCAAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGGACT
**
1491 CAAGGCCAGCGATATTGGACTTGGAGGTGC
255 CAAGGCCAGCGATATTGGACTTAAAGGTGC
*
1521 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTTAAAGATGAAGGTGCCAATATGCTGATTCA
1 CAATGTGTTGATTCAAGGCCAGCTACATTGGACTTTAAAGATGAAGGTGCCAATATGCTGATTCA
* *
1586 AGGCCAGCGATATTGGACTTAAAGATGAGAAAAAGGATGTCAATGTGCTAATTCAAGGCCAGCGA
66 AGGCCAGCAATATTGGACTTAAAG-T-----AAAGG-TGCCAATGTGCTAATTCAAGGCCAGCGA
* * * *
1651 TATTGGACTT-A-A-A-GGTGCCAATGTGCTGA-TTCAAGGCCAGCTACATT-AGACTTGGAGGT
124 CATTGGACTTAAGAGAGGGTGCCAATATGCTGATTTCAAGGCCAACGACATTGAGACTTGGAGGT
1710 GCCAATGTGCTGATTCAAGGCC-AGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGGAC
189 GCCAATGTGCTGATTCAAGGCCAAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGGAC
* * *
1774 TCTAGGCCTGCTATATTGGACTTAAAGGTGC
254 TCAAGGCCAGCGATATTGGACTTAAAGGTGC
* *
1805 CAAAGTGTTGATTCAAGGCCAGCTACATTGGAC-TTAAAGATGAAGGTGCCAATATGCTGACTCA
1 CAATGTGTTGATTCAAGGCCAGCTACATTGGACTTTAAAGATGAAGGTGCCAATATGCTGATTCA
* * * *
1869 AGGCCAGCTATATTGGAC-T----TAAAGGTGCCAATGTGCTGATTCAAGGCCAAACGATATTGG
66 AGGCCAGCAATATTGGACTTAAAGTAAAGGTGCCAATGTGCTAATTCAAGGCC-AGCGACATTGG
1929 ACTTA
130 ACTTA
1934 GAAGAAGATG
Statistics
Matches: 366, Mismatches: 31, Indels: 42
0.83 0.07 0.10
Matches are distributed among these distances:
271 21 0.06
272 19 0.05
277 1 0.00
281 37 0.10
282 3 0.01
283 121 0.33
284 91 0.25
285 15 0.04
286 15 0.04
287 2 0.01
289 1 0.00
290 1 0.00
292 5 0.01
293 34 0.09
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (284 bp):
CAATGTGTTGATTCAAGGCCAGCTACATTGGACTTTAAAGATGAAGGTGCCAATATGCTGATTCA
AGGCCAGCAATATTGGACTTAAAGTAAAGGTGCCAATGTGCTAATTCAAGGCCAGCGACATTGGA
CTTAAGAGAGGGTGCCAATATGCTGATTTCAAGGCCAACGACATTGAGACTTGGAGGTGCCAATG
TGCTGATTCAAGGCCAAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGGACTCAAGGC
CAGCGATATTGGACTTAAAGGTGC
Found at i:1894 original size:136 final size:132
Alignment explanation
Indices: 1641--1933 Score: 358
Period size: 136 Copynumber: 2.2 Consensus size: 132
1631 TGCTAATTCA
*
1641 AGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTGG
1 AGGCCAGCGATATTGGACTTAAAGGTGCCAAAGTGCTGATTCAAGGCCAGCTACATTAGACTTGG
* *
1706 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTG
66 AGGTGCCAATATGCTGACTCAAGGCCAGCTACATTGGACTT--A-A-GAAGGTGCCAATATGCTG
1771 GACTCT
127 GACTCT
* * * *
1777 AGGCCTGCTATATTGGACTTAAAGGTGCCAAAGTGTTGATTCAAGGCCAGCTACATTGGACTTAA
1 AGGCCAGCGATATTGGACTTAAAGGTGCCAAAGTGCTGATTCAAGGCCAGCTACATTAGACTT--
* *
1842 AGATGAAGGTGCCAATATGCTGACTCAAGGCCAGCTATATTGGACTT-A-AAGGTGCCAATGTGC
64 -G--G-AGGTGCCAATATGCTGACTCAAGGCCAGCTACATTGGACTTAAGAAGGTGCCAATATGC
* *
1905 T-GATTCA
125 TGGACTCT
*
1912 AGGCCAAACGATATTGGACTTA
1 AGGCC-AGCGATATTGGACTTA
1934 GAAGAAGATG
Statistics
Matches: 136, Mismatches: 14, Indels: 14
0.83 0.09 0.09
Matches are distributed among these distances:
135 9 0.07
136 86 0.63
138 1 0.01
139 1 0.01
141 1 0.01
142 38 0.28
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (132 bp):
AGGCCAGCGATATTGGACTTAAAGGTGCCAAAGTGCTGATTCAAGGCCAGCTACATTAGACTTGG
AGGTGCCAATATGCTGACTCAAGGCCAGCTACATTGGACTTAAGAAGGTGCCAATATGCTGGACT
CT
Found at i:1983 original size:31 final size:31
Alignment explanation
Indices: 1942--2025 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 31
1932 TAGAAGAAGA
1942 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAA-GGT
1974 TG-CACCAACTTGTGT--GCTTTTG-AAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGT
*
2001 TGCCACTAAC-T-TGTGGGCTTTTGAA
1 TGCCACCAACTTGTGTGGGCTTTTGAA
2026 GAGATACCAT
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
26 3 0.06
27 6 0.13
28 15 0.32
29 8 0.17
31 13 0.28
32 2 0.04
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAAGGT
Found at i:2047 original size:29 final size:29
Alignment explanation
Indices: 1981--2114 Score: 162
Period size: 29 Copynumber: 4.6 Consensus size: 29
1971 GGTTGCACCA
* * * *
1981 ACTTGTGTGCTTTTGAAG-GTTGCCACTA
1 ACTTGTGGGCTTTGGAAGAGATGCCACTG
* * *
2009 ACTTGTGGGCTTTTGAAGAGATACCATTG
1 ACTTGTGGGCTTTGGAAGAGATGCCACTG
* *
2038 ACTTGTGGGCTTTGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTGGAAGA-GATGCCACTG
*
2068 ACTTGTGGGCTTTGGAAAAGATGCCACTG
1 ACTTGTGGGCTTTGGAAGAGATGCCACTG
2097 ACTTGTGGGCTTTGGAAG
1 ACTTGTGGGCTTTGGAAG
2115 GGTGAGGAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 17 0.18
29 49 0.53
30 26 0.28
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (29 bp):
ACTTGTGGGCTTTGGAAGAGATGCCACTG
Found at i:2064 original size:59 final size:59
Alignment explanation
Indices: 1996--2113 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 59
1986 TGTGCTTTTG
* * * *
1996 AAGGTTGCCACTAACTTGTGGGCTTTTGAAGAGATACCATTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTAACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAA
* *
2055 AAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAA
1 AAGGGTGCCACTAACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAA
2114 GGGTGAGGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (59 bp):
AAGGGTGCCACTAACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAA
Found at i:3520 original size:6 final size:5
Alignment explanation
Indices: 3507--3554 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
3497 TCCGGACCCT
* *
3507 TTTTG TTGTTG TTGT- TTTTG TTTTT TTTTG TTTTG TTTTG TTTT- TTTT
1 TTTTG TT-TTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
3555 CCTTCTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
4 7 0.19
5 25 0.68
6 5 0.14
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:3524 original size:15 final size:14
Alignment explanation
Indices: 3506--3551 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
3496 ATCCGGACCC
3506 TTTTTGTTGTTGTTG
1 TTTTTGTTGTT-TTG
3521 TTTTTGTT-TTTT-
1 TTTTTGTTGTTTTG
3533 TTTGTT-TTGTTTTG
1 TTT-TTGTTGTTTTG
3547 TTTTT
1 TTTTT
3552 TTTCCTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 5 0.18
15 8 0.29
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (14 bp):
TTTTTGTTGTTTTG
Found at i:3564 original size:30 final size:29
Alignment explanation
Indices: 3507--3585 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 29
3497 TCCGGACCCT
* * *
3507 TTTTGTTGTTGTTGTTTTTGTTTTTTTTTG
1 TTTTGTT-TTGTTTTTTTTCTTCTTTTTTG
*
3537 TTTTGTTTTGTTTTTTTTCCTTCTTTTTTT
1 TTTTGTTTTGTTTTTTTT-CTTCTTTTTTG
* *
3567 TGTTTATTTGGTTTTTTTT
1 T-TTTGTTTTGTTTTTTTT
3586 TTTTGTGTGG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 10 0.24
30 16 0.39
31 15 0.37
ACGTcount: A:0.01, C:0.04, G:0.14, T:0.81
Consensus pattern (29 bp):
TTTTGTTTTGTTTTTTTTCTTCTTTTTTG
Found at i:3565 original size:20 final size:19
Alignment explanation
Indices: 3521--3565 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3511 GTTGTTGTTG
**
3521 TTTTTGTTTTTTTTTGTTT
1 TTTTTGTTTTTTTTCCTTT
3540 TGTTTTGTTTTTTTTCCTTCT
1 T-TTTTGTTTTTTTTCCTT-T
3561 TTTTT
1 TTTTT
3566 TTGTTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 19 0.86
21 2 0.09
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (19 bp):
TTTTTGTTTTTTTTCCTTT
Found at i:21953 original size:61 final size:60
Alignment explanation
Indices: 21772--22133 Score: 406
Period size: 61 Copynumber: 6.0 Consensus size: 60
21762 ACCTTTCATC
*
21772 CTTTTAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
21832 CCTTTTAGTCCTCAAAGAGAAGGACGCCTTTTTCCTTTCAAAGCTCACACAAGTTAGTGGCA
1 -CTTTCAGTCCTCAAAGAGTAGGACGCC-TTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
21894 TCGTTCAATCCTCAAAAAGTAGGATGCCTTCTCCTTTTAAAACCCACACAAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
21955 CCTTCTAGTCCTCAAAGAGTAGGAC-ACTT-T-CTTTTCAAAGGCTACACAAGTTGGTGGCA
1 CTTTC-AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
* * * ** *
22014 CTTTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCAACGTAAGTTTGTGGCA
1 C-TTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* ** *
22075 CCTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCTTACATAAGTTGGTGG
1 -CTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGG
22134 TACCTGAAAG
Statistics
Matches: 252, Mismatches: 41, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
58 5 0.02
59 39 0.15
60 13 0.05
61 139 0.55
62 56 0.22
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (60 bp):
CTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:22067 original size:120 final size:119
Alignment explanation
Indices: 21772--22133 Score: 460
Period size: 120 Copynumber: 3.0 Consensus size: 119
21762 ACCTTTCATC
21772 CTTTT-AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1 CTTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACC-T
* * *
21836 TTAGTCCTCAAAGAGAAGGACGCCTTTTTCCTTTCAAAGCTCACACAAGTTAGTGGCA
65 TTAGTCCTCAAAGAGTAGGACGCC--TTTCTTTTCAAAGCT-ACACAAGTTGGTGGCA
* * * * *
21894 -TCGTTCAATCCTCAAAAAGTAGGATGCCTTCTCCTTTTAAAACCCACACAAGTTGGTGGCACCT
1 CT-TTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
*
21958 TCTAGTCCTCAAAGAGTAGGAC-ACTTTCTTTTCAAAGGCTACACAAGTTGGTGGCA
65 T-TAGTCCTCAAAGAGTAGGACGCCTTTCTTTTCAAA-GCTACACAAGTTGGTGGCA
* * * ** *
22014 CTTTTCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCAACGTAAGTTTGTGGCACCTT
1 CTTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* *
22079 TCAGTCCTCAAAGAGTAGGACGCCTTCTCTTTTTAAAGCTTACATAAGTTGGTGG
66 T-AGTCCTCAAAGAGTAGGACGCCTT-TCTTTTCAAAGC-TACACAAGTTGGTGG
22134 TACCTGAAAG
Statistics
Matches: 208, Mismatches: 23, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
119 1 0.00
120 97 0.47
121 10 0.05
122 28 0.13
123 72 0.35
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (119 bp):
CTTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
TAGTCCTCAAAGAGTAGGACGCCTTTCTTTTCAAAGCTACACAAGTTGGTGGCA
Found at i:22903 original size:13 final size:13
Alignment explanation
Indices: 22885--22910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22875 CAATTTTTTG
22885 TGTATCGATACAT
1 TGTATCGATACAT
22898 TGTATCGATACAT
1 TGTATCGATACAT
22911 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:22995 original size:20 final size:20
Alignment explanation
Indices: 22970--23042 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
22960 CAACTTTTTT
22970 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
22990 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
23011 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
23031 ATGTATCGATAC
1 ATGTATCGATAC
23043 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:23008 original size:41 final size:41
Alignment explanation
Indices: 22949--23042 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
22939 CTGCCAAGAA
*
22949 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
22990 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
23031 ATGTATCGATAC
1 ATGTATCGATAC
23043 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:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:23024 original size:21 final size:21
Alignment explanation
Indices: 22949--23024 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
22939 CTGCCAAGAA
* *
22949 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
22970 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
22990 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
23011 ATGTATCGATACAT
1 ATGTATCGATACAT
23025 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:23701 original size:21 final size:21
Alignment explanation
Indices: 23677--23718 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
23667 ATCTCCCCCT
23677 TAATCAAGTAATTCACAACAA
1 TAATCAAGTAATTCACAACAA
23698 TAATCAAGTAATTCACAACAA
1 TAATCAAGTAATTCACAACAA
23719 AAATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (21 bp):
TAATCAAGTAATTCACAACAA
Found at i:25524 original size:13 final size:13
Alignment explanation
Indices: 25506--25543 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
25496 ATAATCACCC
*
25506 TGTATCAATACAG
1 TGTATCGATACAG
*
25519 TGTATCGATACAT
1 TGTATCGATACAG
25532 TGTATCGATACA
1 TGTATCGATACA
25544 AAGAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:25557 original size:20 final size:20
Alignment explanation
Indices: 25532--25608 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
25522 ATCGATACAT
25532 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
25552 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
* *
25577 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAAA
25597 TGTATCGATACA
1 TGTATCGATACA
25609 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
20 30 0.62
25 18 0.38
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:27638 original size:15 final size:15
Alignment explanation
Indices: 27618--27648 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27608 ATTTCGTTTG
*
27618 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
27633 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
27648 G
1 G
27649 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
Found at i:29859 original size:51 final size:49
Alignment explanation
Indices: 29775--29879 Score: 165
Period size: 51 Copynumber: 2.1 Consensus size: 49
29765 TGGAGTACGT
* *
29775 TCCTCGATGGAAAATTTAATATTTTGGAGATAAAAATGGGGTTGGAGTA
1 TCCTCGATGGAAAAATTAATATTTTGGAAATAAAAATGGGGTTGGAGTA
*
29824 TCCTCGATAGTGAAAAATTAGTATTTTGGAAATAAAAATGGGGTTGGAGTA
1 TCCTCGAT-G-GAAAAATTAATATTTTGGAAATAAAAATGGGGTTGGAGTA
29875 TCCTC
1 TCCTC
29880 TTGGAAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
49 8 0.16
50 1 0.02
51 42 0.82
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (49 bp):
TCCTCGATGGAAAAATTAATATTTTGGAAATAAAAATGGGGTTGGAGTA
Found at i:30056 original size:78 final size:77
Alignment explanation
Indices: 29812--30255 Score: 465
Period size: 79 Copynumber: 5.6 Consensus size: 77
29802 AGATAAAAAT
* * * **
29812 GGGGTTGGAGTATCCTCGATAGTGAAAAATTAGTATTTTGGAAATAAAAATGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTAAAAAT-AAAATGGGGTTGGAGTATC
*
29877 CTCTTGGAAATAAC
65 C-CTTTGAAATAAC
* * *
29891 GGGGTTGGAGTATCCCCGATGGTGAAAAAATTGATATTTTAAAAATCGAACTGGGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATGGTG-AAAAATTAATATTTTAAAAAT-AAAATGGGGTTGGAGTAT
*** *
29956 CCTCTCAAAAATAAT
64 CC-CTTTGAAATAAC
* * * * * *
29971 GGTGTTGGAGTATCCCTGATGGCGAAAAGTTAATATTTTAAAAATAAAATCGGGTTAGAGTATCC
1 GGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTAAAAATAAAATGGGGTTGGAGTATCC
*
30036 CTTTAGGAATAAC
66 CTTT-GAAATAAC
* * * *
30049 GGGGTTGGAGTATCCCCGATGGCGAAAAATCAGTATTTTAAAAATAGAATTGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTAAAAATA-AAATGGGGTTGGAGTATC
*
30114 CCTTTGAAAATAAT
65 CCTTTG-AAATAAC
* * * * *
30128 GAGGTTGAAGTATCCCCGATGGTGAAAAATTGATATTTTGAAAATAAAACTGGGGTTAGAGTATC
1 GGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTAAAAATAAAA-TGGGGTTGGAGTATC
*
30193 CCTTCGAAATAAC
65 CCTTTGAAATAAC
* * * * **
30206 GGGGTTGGAGTGTCCCCAATGGTGAAGAAAATCATATTTTGGAAATAAAA
1 GGGGTTGGAGTATCCCCGATGGTGAA-AAATTAATATTTTAAAAATAAAA
30256 AAAATTAATG
Statistics
Matches: 304, Mismatches: 55, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
77 2 0.01
78 93 0.31
79 144 0.47
80 65 0.21
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (77 bp):
GGGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTAAAAATAAAATGGGGTTGGAGTATCC
CTTTGAAATAAC
Found at i:30149 original size:157 final size:156
Alignment explanation
Indices: 29813--30245 Score: 543
Period size: 157 Copynumber: 2.7 Consensus size: 156
29803 GATAAAAATG
* * * * *
29813 GGGTTGGAGTATCCTCGATAGTGAAAAATTAGTATTTTGGAAATAAAAATGGGGTTGGAGTAT-C
1 GGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGAAAAT-AAAATGGGGTTAGAGTATCC
* *
29877 CTCTTGGAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAAAT-TGATATTTTAAAAATCGAA
65 CT-TTGG-AATAACGGGGTTGGAGTATCCCCGATGGTGAAAAAATCAG-TATTTTAAAAATAGAA
29941 CTGGGGTTGGAGTATCCTCTCAAAAATAAT
127 CTGGGGTTGGAGTATCCTCTCAAAAATAAT
* * * * *
29971 GGTGTTGGAGTATCCCTGATGGCGAAAAGTTAATATTTTAAAAATAAAATCGGGTTAGAGTATCC
1 GG-GTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGAAAATAAAATGGGGTTAGAGTATCC
* *
30036 CTTTAGGAATAACGGGGTTGGAGTATCCCCGATGGCG-AAAAATCAGTATTTTAAAAATAGAATT
65 CTTT-GGAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAAATCAGTATTTTAAAAATAGAACT
**
30100 GGGGTTGGAGTATCC-CTTTGAAAATAAT
129 GGGGTTGGAGTATCCTC-TCAAAAATAAT
* *
30128 GAGGTTGAAGTATCCCCGATGGTGAAAAATTGATATTTTGAAAATAAAACTGGGGTTAGAGTATC
1 G-GGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGAAAATAAAA-TGGGGTTAGAGTATC
* * * *
30193 CCTTCGAAATAACGGGGTTGGAGTGTCCCCAATGGTGAAGAAAATCA-TATTTT
64 CCTTTGGAATAACGGGGTTGGAGTATCCCCGATGGTGAA-AAAATCAGTATTTT
30246 GGAAATAAAA
Statistics
Matches: 238, Mismatches: 28, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
156 1 0.00
157 115 0.48
158 76 0.32
159 46 0.19
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (156 bp):
GGGTTGGAGTATCCCCGATGGTGAAAAATTAATATTTTGAAAATAAAATGGGGTTAGAGTATCCC
TTTGGAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAAATCAGTATTTTAAAAATAGAACTGG
GGTTGGAGTATCCTCTCAAAAATAAT
Found at i:32216 original size:22 final size:20
Alignment explanation
Indices: 32165--32220 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
32155 CAAAATCCAG
32165 AATGTATCGATACAATGATA
1 AATGTATCGATACAATGATA
* *
32185 AATGTGTCGATACAATTATA
1 AATGTATCGATACAATGATA
32205 AGTATGTATCGATACA
1 A--ATGTATCGATACA
32221 TTTACTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 19 0.61
22 12 0.39
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACAATGATA
Found at i:32232 original size:20 final size:20
Alignment explanation
Indices: 32207--32248 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
32197 CAATTATAAG
*
32207 TATGTATCGATACATTTACT
1 TATGTATAGATACATTTACT
*
32227 TATGTATAGATACATTTCCT
1 TATGTATAGATACATTTACT
32247 TA
1 TA
32249 GTAATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (20 bp):
TATGTATAGATACATTTACT
Found at i:32313 original size:20 final size:20
Alignment explanation
Indices: 32288--32342 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
32278 CATTTTAGGC
*
32288 ATGTATTGATATATTCATTT
1 ATGTATCGATATATTCATTT
*
32308 ATGTATCAATATATTCATTT
1 ATGTATCGATATATTCATTT
32328 ATGTATCGATATATT
1 ATGTATCGATATATT
32343 TTTTGTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (20 bp):
ATGTATCGATATATTCATTT
Found at i:32988 original size:65 final size:67
Alignment explanation
Indices: 32838--33008 Score: 229
Period size: 65 Copynumber: 2.6 Consensus size: 67
32828 TAAAGTAGAT
* * * * *
32838 AGGTGCCACCAACTTGTGTGGGCTTTGAGATAGAAAAGGAGAGATGCGTCTTGCTCTTTGAAGAC
1 AGGTGCCACCAACTTGTGTGGGCTTTGA-AAAGAAAA-GAAAGAAGCGTCATGCTCTTTGAAAAC
*
32903 TAGA
64 TAAA
* *
32907 AGGTGCCACCAGCTTGTGTGGGCTTT-AAAAGAAAA-AAAGAAGTGTCATGCTCTTTGAAAACTA
1 AGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGAAAGAAGCGTCATGCTCTTTGAAAACTA
32970 AA
66 AA
*
32972 AGGTGCCACCAACTTGTATGGGCTTTGAAAAGAAAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAG
33009 GTGTCTTAGT
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
65 48 0.53
66 9 0.10
67 7 0.08
68 1 0.01
69 25 0.28
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.25
Consensus pattern (67 bp):
AGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGAAAGAAGCGTCATGCTCTTTGAAAACTA
AA
Found at i:33354 original size:20 final size:20
Alignment explanation
Indices: 33331--33403 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
33321 ACAATTCAAA
33331 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
33351 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
33372 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
33392 GTATCGATACAT
1 GTATCGATACAT
33404 AAAAAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:33382 original size:41 final size:40
Alignment explanation
Indices: 33331--33423 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 40
33321 ACAATTCAAA
33331 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAT
*
33372 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAT
33412 GTATCGATACAT
1 GTATCGATACAT
33424 TTTCTTGGCA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 19 0.37
41 32 0.63
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (40 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAT
Found at i:33414 original size:20 final size:19
Alignment explanation
Indices: 33350--33423 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
33340 CATGTTGCAA
33350 TGTATCGATACATGAAAAAG
1 TGTATCGATACAT-AAAAAG
***
33370 ATGTATCGATACATGTTGCAA-
1 -TGTATCGATACA--TAAAAAG
33391 TGTATCGATACATAAAAAG
1 TGTATCGATACATAAAAAG
33410 TTGTATCGATACAT
1 -TGTATCGATACAT
33424 TTTCTTGGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
18 3 0.07
20 25 0.58
21 12 0.28
22 2 0.05
23 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (19 bp):
TGTATCGATACATAAAAAG
Found at i:33481 original size:13 final size:13
Alignment explanation
Indices: 33463--33488 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33453 TACAGCAAGT
33463 ATGTATCGATACA
1 ATGTATCGATACA
33476 ATGTATCGATACA
1 ATGTATCGATACA
33489 CAAAAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:33486 original size:32 final size:32
Alignment explanation
Indices: 33445--33507 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
33435 TAGCCAAACT
**
33445 TGTATCGATACAGCAAGTA-TGTATCGATACAA
1 TGTATCGATACA-CAAAAATTGTATCGATACAA
33477 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
33508 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Done.