Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010508.1 Kokia drynarioides strain JFW-HI SEQ_125419, whole genome shotgun sequence
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: 255767
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:1430 original size:4 final size:4
Alignment explanation
Indices: 1410--1492 Score: 69
Period size: 4 Copynumber: 20.2 Consensus size: 4
1400 TACACATTAC
* * * * * *
1410 CTTT CTTT CCTT ATTT CTTT CCTCT CATT C-TT CTTT CTTTT CTCT CATT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT C-TTT CTTT CTTT
*
1459 CTTC CTTT CTTT CTTT CTTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT C
1493 CCGTTTATTT
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
3 3 0.05
4 48 0.77
5 11 0.18
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:1448 original size:20 final size:20
Alignment explanation
Indices: 1423--1488 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
1413 TCTTTCCTTA
1423 TTTCTTTCCTCTCATTCTTC
1 TTTCTTTCCTCTCATTCTTC
*
1443 TTTCTTTTCTCTCATTCTTCC
1 TTTCTTTCCTCTCATTCTT-C
*
1464 TTTCTTT-CTTTC-TT-TTC
1 TTTCTTTCCTCTCATTCTTC
1481 TTTCTTTC
1 TTTCTTTC
1489 TTTCCCGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
17 8 0.19
18 2 0.05
19 2 0.05
20 22 0.52
21 8 0.19
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTCTTTCCTCTCATTCTTC
Found at i:1480 original size:13 final size:13
Alignment explanation
Indices: 1440--1491 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
1430 CCTCTCATTC
1440 TTCTTTCTTTTCT
1 TTCTTTCTTTTCT
* *
1453 CTCATTCTTCCTTTCT
1 TTC--T-TTCTTTTCT
1469 TTCTTTCTTTTCT
1 TTCTTTCTTTTCT
1482 TTCTTTCTTT
1 TTCTTTCTTT
1492 CCCGTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 20 0.62
14 1 0.03
15 1 0.03
16 10 0.31
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (13 bp):
TTCTTTCTTTTCT
Found at i:1485 original size:25 final size:25
Alignment explanation
Indices: 1409--1492 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 25
1399 ATACACATTA
* * *
1409 CCTTTCTTTCCTT-ATTTCTTTCCT
1 CCTTTCTTTCTTTCTTTTCTTTCTT
*
1433 CTCATTC-TTCTTTCTTTTCTCTCATTCTT
1 C-CTTTCTTTCTTTC-TTT-TCT--TTCTT
1462 CCTTTCTTTCTTTCTTTTCTTTCTT
1 CCTTTCTTTCTTTCTTTTCTTTCTT
*
1487 TCTTTC
1 CCTTTC
1493 CCGTTTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
24 6 0.13
25 14 0.30
26 2 0.04
27 6 0.13
28 7 0.15
29 12 0.26
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (25 bp):
CCTTTCTTTCTTTCTTTTCTTTCTT
Found at i:4389 original size:6 final size:6
Alignment explanation
Indices: 4380--4409 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
4370 TGATATTGAA
*
4380 GATGAC GATGAG GATGAG GATGAG GATGAG
1 GATGAG GATGAG GATGAG GATGAG GATGAG
4410 AACGCTGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.03, G:0.47, T:0.17
Consensus pattern (6 bp):
GATGAG
Found at i:6532 original size:35 final size:35
Alignment explanation
Indices: 6488--6563 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
6478 TTGTGTGACC
*
6488 CAAATTCTAAGAGATTACTTGCAAGTCAAGTTAAA
1 CAAAATCTAAGAGATTACTTGCAAGTCAAGTTAAA
*
6523 CAAAATCTAAGAGATTGCTTGCAAGTCAAGTTAAA
1 CAAAATCTAAGAGATTACTTGCAAGTCAAGTTAAA
6558 CAAAAT
1 CAAAAT
6564 ATATTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.26
Consensus pattern (35 bp):
CAAAATCTAAGAGATTACTTGCAAGTCAAGTTAAA
Found at i:38243 original size:17 final size:16
Alignment explanation
Indices: 38204--38268 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 16
38194 ATATTTATGG
*
38204 AAATGCAATGACAATA
1 AAATGCAGTGACAATA
*
38220 TAGATGCAGCT-ACAATAA
1 -AAATGCAG-TGACAAT-A
38238 AAATGCAGTGACAATA
1 AAATGCAGTGACAATA
*
38254 AAATGCAGGGACAAT
1 AAATGCAGTGACAAT
38269 TATACTACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
16 16 0.39
17 23 0.56
18 2 0.05
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (16 bp):
AAATGCAGTGACAATA
Found at i:53973 original size:158 final size:158
Alignment explanation
Indices: 53685--53987 Score: 435
Period size: 158 Copynumber: 1.9 Consensus size: 158
53675 TTATAAGTTA
* * * * * *
53685 TATGGGTGCTTGTCTTAGATGTCCTAACGATGACTAAGATCTGTCAATTATTGCGGATTCTCCAT
1 TATGGGTGCTGGTCTTAGATGTCCTAACGATGACTAAGATCAGACAATTATTGCGAATTCTCAAC
* * * *
53750 AGCTTATGTGAGCAGCATCGTGTAGCTCAACATCTCGACCCACAGCTCATGTGAGTAGGCCCATT
66 AACTCATGTGAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACTCATGTGAGCAGGCCCATT
53815 TCACAGCTCGTGTGAACATTACAGGCTG
131 TCACAGCTCGTGTGAACATTACAGGCTG
* * ** * *
53843 TATGGGTGCTGGTCTTAGATGTCTTACCGATGGTTGAGATCAGACAATTATTGTGAATTCTCAAC
1 TATGGGTGCTGGTCTTAGATGTCCTAACGATGACTAAGATCAGACAATTATTGCGAATTCTCAAC
* *
53908 AACTCGTGTGAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACTCGTGTGAGCAGGCCCATT
66 AACTCATGTGAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACTCATGTGAGCAGGCCCATT
*
53973 TTACAGCTCGTGTGA
131 TCACAGCTCGTGTGA
53988 GCAATACAAG
Statistics
Matches: 126, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
158 126 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.29
Consensus pattern (158 bp):
TATGGGTGCTGGTCTTAGATGTCCTAACGATGACTAAGATCAGACAATTATTGCGAATTCTCAAC
AACTCATGTGAGCAGCATCGTGTAGCTCAACATCTCGACCCACAACTCATGTGAGCAGGCCCATT
TCACAGCTCGTGTGAACATTACAGGCTG
Found at i:55830 original size:72 final size:71
Alignment explanation
Indices: 55622--55830 Score: 213
Period size: 72 Copynumber: 2.9 Consensus size: 71
55612 TATCGACTAG
* * * * *
55622 CGCAGGACACATTTATTTGT-GGTTATACCAACCAGTGTCAGGCACACTCATTTGTTGGTTTTAC
1 CGCAGGGCGCATTTATTTTTCGGTTATACCGACCAGTGT-AGGCACACTCATTTTTTGGTTTTAC
* *
55686 GGACCAG
65 TGACCAA
* * * * * * *
55693 TGTAGGGCGCATTTATTTTTCGATTATATCGACCAGTTTTAGGCACACTCATTTTTCGATTTTAC
1 CGCAGGGCGCATTTATTTTTCGGTTATACCGACCAG-TGTAGGCACACTCATTTTTTGGTTTTAC
*
55758 TGACTAA
65 TGACCAA
* * * *
55765 CGCAGGGTGTATTTATTTTTCGGTTATACCGATCAGTGGTGGGCACACTCATTTTTTGGTTTTAC
1 CGCAGGGCGCATTTATTTTTCGGTTATACCGACCAGT-GTAGGCACACTCATTTTTTGGTTTTAC
55830 T
65 T
55831 AGCAAGGGCA
Statistics
Matches: 109, Mismatches: 26, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
71 16 0.15
72 91 0.83
73 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (71 bp):
CGCAGGGCGCATTTATTTTTCGGTTATACCGACCAGTGTAGGCACACTCATTTTTTGGTTTTACT
GACCAA
Found at i:56954 original size:43 final size:43
Alignment explanation
Indices: 56892--57343 Score: 265
Period size: 43 Copynumber: 10.5 Consensus size: 43
56882 ATTCTTGATA
* * *
56892 ATGCACTGTATGTGTCAGTATAATTGCTTCGACTTGTTCGATG
1 ATGCATTGTATGTGCCAGTATAATTGCTTCGACTTATTCGATG
* * * * *
56935 ATGCATTGTGTGTGCCAGTATAGTTACTTCG-GTATATCCGATG
1 ATGCATTGTATGTGCCAGTATAATTGCTTCGACT-TATTCGATG
* * * * * * * *
56978 GTGCACTGTGTGTGCCAATATAGTTACTTC-A-ATATATCTGACG
1 ATGCATTGTATGTGCCAGTATAATTGCTTCGACTTAT-TC-GATG
* * *
57021 ATGCATTGTATGTGCCAGTATAATTGCTTCAACTT-TTCCAATA
1 ATGCATTGTATGTGCCAGTATAATTGCTTCGACTTATT-CGATG
* * * * * *
57064 ATGCACTATGTGTGCCAGTATAGTTACTTC-AATATATTCGATG
1 ATGCATTGTATGTGCCAGTATAATTGCTTCGACT-TATTCGATG
* * * ** * * * *
57107 ATGTATTGTATGTGCTAGTGTAATTTTTTTGGCTTGTCCGATG
1 ATGCATTGTATGTGCCAGTATAATTGCTTCGACTTATTCGATG
* * * * *
57150 ATGCATTATGTGTGCCAGTATAGTTACTTCGA-TATATGCGATG
1 ATGCATTGTATGTGCCAGTATAATTGCTTCGACT-TATTCGATG
* * *
57193 ATGCACTGTATGTGCCAGTATAATTGC-TCTGGCTTGTTCGATG
1 ATGCATTGTATGTGCCAGTATAATTGCTTC-GACTTATTCGATG
* * * **
57236 ATGCACTTGTGTGTGCCAATATAATTGCTTTGGTTTA-TCTGATG
1 ATGCA-TTGTATGTGCCAGTATAATTGCTTCGACTTATTC-GATG
* * * * *
57280 ATGCATTGCATGTGTCAGTATAACTGCTTCGATTTATCCGATG
1 ATGCATTGTATGTGCCAGTATAATTGCTTCGACTTATTCGATG
* * *
57323 GTGCATT-TACGTGCTAGTATA
1 ATGCATTGTATGTGCCAGTATA
57344 TTTACATTGA
Statistics
Matches: 307, Mismatches: 85, Indels: 35
0.72 0.20 0.08
Matches are distributed among these distances:
41 3 0.01
42 17 0.06
43 245 0.80
44 40 0.13
45 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (43 bp):
ATGCATTGTATGTGCCAGTATAATTGCTTCGACTTATTCGATG
Found at i:57024 original size:86 final size:85
Alignment explanation
Indices: 56931--57327 Score: 359
Period size: 86 Copynumber: 4.6 Consensus size: 85
56921 CGACTTGTTC
* * * * *
56931 GATGATGCATTGTGTGTGCCAGTATAGTTACTTCGGTATATCCGATGGTGCACTGTGTGTGCCAA
1 GATGATGCATTGTATGTGCCAGTATAATTGCTTCGGT-TATCCGATGATGCACTATGTGTGCCAA
56996 TATAGTTACTTCAATATATCT
65 TATAGTTACTTCAATATATCT
* ** * * * *
57017 GACGATGCATTGTATGTGCCAGTATAATTGCTTCAACTTTTCCAATAATGCACTATGTGTGCCAG
1 GATGATGCATTGTATGTGCCAGTATAATTGCTTC-GGTTATCCGATGATGCACTATGTGTGCCAA
57082 TATAGTTACTTCAATATAT-T
65 TATAGTTACTTCAATATATCT
* * * ** * * *
57102 CGATGATGTATTGTATGTGCTAGTGTAATTTTTTTGGCTTGTCCGATGATGCATTATGTGTGCCA
1 -GATGATGCATTGTATGTGCCAGTATAATTGCTTCGG-TTATCCGATGATGCACTATGTGTGCCA
* *
57167 GTATAGTTACTTCGATATATGC-
64 ATATAGTTACTTCAATATAT-CT
* * * *
57189 GATGATGCACTGTATGTGCCAGTATAATTGC-TCTGGCTTGTTCGATGATGCACTTGTGTGTGCC
1 GATGATGCATTGTATGTGCCAGTATAATTGCTTC-GG-TTATCCGATGATGCAC-TATGTGTGCC
* * *** *
57253 AATATAATTGCTTTGGTTTATCT
63 AATATAGTTACTTCAATATATCT
* * * * *
57276 GATGATGCATTGCATGTGTCAGTATAACTGCTTCGATTTATCCGATGGTGCA
1 GATGATGCATTGTATGTGCCAGTATAATTGCTTCG-GTTATCCGATGATGCA
57328 TTTACGTGCT
Statistics
Matches: 251, Mismatches: 50, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
85 2 0.01
86 182 0.73
87 65 0.26
88 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (85 bp):
GATGATGCATTGTATGTGCCAGTATAATTGCTTCGGTTATCCGATGATGCACTATGTGTGCCAAT
ATAGTTACTTCAATATATCT
Found at i:60437 original size:27 final size:27
Alignment explanation
Indices: 60399--60455 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
60389 TTGTACTGCT
60399 TAAATTAAGTATGGGGAATAAATAGCA
1 TAAATTAAGTATGGGGAATAAATAGCA
60426 TAAATTAAGTATGGGGAATAAATAGCA
1 TAAATTAAGTATGGGGAATAAATAGCA
60453 TAA
1 TAA
60456 GTGGTGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (27 bp):
TAAATTAAGTATGGGGAATAAATAGCA
Found at i:75251 original size:9 final size:8
Alignment explanation
Indices: 75221--75251 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
75211 AAATTATTTC
75221 TTTTAATT
1 TTTTAATT
75229 TTTTAATT
1 TTTTAATT
75237 TTTTAATT
1 TTTTAATT
75245 TTATTAA
1 TT-TTAA
75252 CGTAACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTAATT
Found at i:93782 original size:32 final size:32
Alignment explanation
Indices: 93717--93782 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
93707 AAATTGATAT
* **
93717 ATGATCCTTTGCATTTTCTGTGAAATATTATG
1 ATGATCCTTTGCATTTTCTATGAAATACCATG
*
93749 ATGATCCTTTGCATTTTCTATGGAATACCATG
1 ATGATCCTTTGCATTTTCTATGAAATACCATG
93781 AT
1 AT
93783 AATATTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (32 bp):
ATGATCCTTTGCATTTTCTATGAAATACCATG
Found at i:97582 original size:7 final size:7
Alignment explanation
Indices: 97570--97640 Score: 60
Period size: 7 Copynumber: 10.6 Consensus size: 7
97560 GCTCGAGAAG
97570 AAAAAGA
1 AAAAAGA
97577 AAAAAGA
1 AAAAAGA
*
97584 AAGATA-A
1 AA-AAAGA
*
97591 AAAATG-
1 AAAAAGA
97597 AAAAAGA
1 AAAAAGA
97604 AAAAAGA
1 AAAAAGA
*
97611 AAGAA-A
1 AAAAAGA
97617 AAAAAGA
1 AAAAAGA
*
97624 AGAAA-A
1 AAAAAGA
*
97630 AAAAACA
1 AAAAAGA
97637 AAAA
1 AAAA
97641 CAAAAAGGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
6 16 0.31
7 33 0.65
8 2 0.04
ACGTcount: A:0.83, C:0.01, G:0.13, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:97585 original size:13 final size:12
Alignment explanation
Indices: 97567--97647 Score: 81
Period size: 13 Copynumber: 6.2 Consensus size: 12
97557 TTTGCTCGAG
97567 AAGAAAAAGAAAA
1 AAGAAAAA-AAAA
97580 AAGAAAGATAAAAA
1 AAGAAA-A-AAAAA
*
97594 ATGAAAAAGAAAA
1 AAGAAAAA-AAAA
97607 AAGAAAGAAAAAA
1 AAGAAA-AAAAAA
97620 AAGAAGAAAAAAA
1 AAGAA-AAAAAAA
* *
97633 AACAAAAACAAA
1 AAGAAAAAAAAA
97645 AAG
1 AAG
97648 GAGAGGTAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
12 9 0.16
13 35 0.60
14 13 0.22
15 1 0.02
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:97599 original size:27 final size:26
Alignment explanation
Indices: 97567--97647 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
97557 TTTGCTCGAG
97567 AAGAAAAAGAAAAAAGAAAGATAAAAA
1 AAGAAAAAGAAAAAAGAAAGA-AAAAA
*
97594 ATGAAAAAGAAAAAAGAAAGAAAAAA
1 AAGAAAAAGAAAAAAGAAAGAAAAAA
* *
97620 AAGAAGAAA-AAAAAACAAA-AACAAA
1 AAGAA-AAAGAAAAAAGAAAGAAAAAA
97645 AAG
1 AAG
97648 GAGAGGTAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.16
26 18 0.37
27 23 0.47
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (26 bp):
AAGAAAAAGAAAAAAGAAAGAAAAAA
Found at i:97620 original size:20 final size:20
Alignment explanation
Indices: 97565--97633 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
97555 CTTTTGCTCG
*
97565 AGAAGAAAAAGAAAAAAGAA
1 AGAAAAAAAAGAAAAAAGAA
*
97585 AGATAAAAAATG-AAAAAGAA
1 AGA-AAAAAAAGAAAAAAGAA
97605 A-AAAGAAAGAA-AAAAAAG-A
1 AGAAA-AAA-AAGAAAAAAGAA
97624 AGAAAAAAAA
1 AGAAAAAAAA
97634 ACAAAAACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 4 0.10
19 9 0.22
20 22 0.54
21 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (20 bp):
AGAAAAAAAAGAAAAAAGAA
Found at i:97639 original size:20 final size:18
Alignment explanation
Indices: 97570--97646 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 18
97560 GCTCGAGAAG
*
97570 AAAAAGAAAAAAGAAAGATA
1 AAAAAAAAAAAAGAAA-A-A
**
97590 AAAAATGAAAAAGAAAAA
1 AAAAAAAAAAAAGAAAAA
97608 AGAAAGAAAAAAAAGAAGAAA
1 A-AAA-AAAAAAAAGAA-AAA
* *
97629 AAAAAACAAAAACAAAAA
1 AAAAAAAAAAAAGAAAAA
97647 GGAGAGGTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 5 0.10
19 13 0.27
20 26 0.54
21 4 0.08
ACGTcount: A:0.83, C:0.03, G:0.12, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAAAGAAAAA
Found at i:97645 original size:16 final size:15
Alignment explanation
Indices: 97570--97646 Score: 57
Period size: 16 Copynumber: 4.7 Consensus size: 15
97560 GCTCGAGAAG
97570 AAAAAGAAAAAAGAAA
1 AAAAAGAAAAAA-AAA
*
97586 GATAAAA-AATGAAAAAGA
1 -A-AAAAGAA--AAAAAAA
97604 AAAAAGAAAGAAAAAA
1 AAAAAGAAA-AAAAAA
*
97620 AAGAAGAAAAAAAAA
1 AAAAAGAAAAAAAAA
*
97635 CAAAAACAAAAA
1 -AAAAAGAAAAA
97647 GGAGAGGTAG
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
15 7 0.14
16 26 0.53
17 6 0.12
18 6 0.12
19 4 0.08
ACGTcount: A:0.83, C:0.03, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAAAAAA
Found at i:98096 original size:112 final size:116
Alignment explanation
Indices: 97959--98175 Score: 291
Period size: 112 Copynumber: 1.9 Consensus size: 116
97949 TGGTCATTTT
* * * * * *
97959 TAATCTTTTCATTCAAACGAGCTTTGCCTCTAATAAAATTCAATTTTATCCA-CCTTACAACCTT
1 TAATCTTTTCATTCAAACAAACTTTGCCTCCAATAAAACTCAATTTCAT-CATCCTCACAACCTT
*
98023 G-TTCAAGCA-TT-TTTGCA-TTGAAATAACAGTTAGTGGACCAATGCTTCG
65 GATTCAAGCATTTCTTTGCATTTGAAATAAAAGTTAGTGGACCAATGCTTCG
* * *
98071 TAATCTTTTCATTCAAACAAACTTTGTCTCCAATAAAACTCAATTTCATTATGCTCACAACCTTG
1 TAATCTTTTCATTCAAACAAACTTTGCCTCCAATAAAACTCAATTTCATCATCCTCACAACCTTG
98136 ATTCAAGCATTTTCTTTGCATTTGAAATAAAAGTTAGTGG
66 ATTCAAGCA-TTTCTTTGCATTTGAAATAAAAGTTAGTGG
98176 TCTAACGATA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
111 1 0.01
112 54 0.61
113 8 0.09
115 2 0.02
116 6 0.07
117 18 0.20
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (116 bp):
TAATCTTTTCATTCAAACAAACTTTGCCTCCAATAAAACTCAATTTCATCATCCTCACAACCTTG
ATTCAAGCATTTCTTTGCATTTGAAATAAAAGTTAGTGGACCAATGCTTCG
Found at i:98730 original size:49 final size:49
Alignment explanation
Indices: 98603--98829 Score: 163
Period size: 50 Copynumber: 4.6 Consensus size: 49
98593 GGAAACATAG
* * * * * *
98603 AGATATAAAGGGAAAGGTTGAGG-CTGCAATGGCGAACCCGGA-ACCTTAGA
1 AGATATGAAGGGAAAGGTTGAGGTC-GCAACGACGAATCC-AATACCAT-GA
* * * * **
98653 AGATGTGATGGGAAAGATTGAGGCCGCAACGGTGAATCCAATACCATGA
1 AGATATGAAGGGAAAGGTTGAGGTCGCAACGACGAATCCAATACCATGA
* * * * *
98702 AGATATGAAGGGAAAGGTTGAAGTCGCAATGACAAACCCTATACCATAGA
1 AGATATGAAGGGAAAGGTTGAGGTCGCAACGACGAATCCAATACCAT-GA
* * * *
98752 AGATACGATGGG-AAGGATTGAGGTCGCAACGACGAATCTAGTACCATGA
1 AGATATGAAGGGAAAGG-TTGAGGTCGCAACGACGAATCCAATACCATGA
* * * *
98801 AGATTTGAAGGGAAAAGTTAAGGCCGCAA
1 AGATATGAAGGGAAAGGTTGAGGTCGCAA
98830 TAGCGAACCT
Statistics
Matches: 137, Mismatches: 35, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
49 64 0.47
50 72 0.53
51 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.30, T:0.18
Consensus pattern (49 bp):
AGATATGAAGGGAAAGGTTGAGGTCGCAACGACGAATCCAATACCATGA
Found at i:98774 original size:99 final size:99
Alignment explanation
Indices: 98603--98830 Score: 262
Period size: 99 Copynumber: 2.3 Consensus size: 99
98593 GGAAACATAG
* * * * **
98603 AGATATAAAGGGAAAGGTTGAGGCTGCAATGGCGAACCCGGAACCTTAGAAGATGTGATGGGAAA
1 AGATATGAAGGGAAAGGTTGAGGCTGCAATGACAAACCCGGAACCATAGAAGATACGATGGGAAA
**
98668 GATTGAGGCCGCAACGGTGAATCCAATACCATGA
66 GATTGAGGCCGCAACGACGAATCCAATACCATGA
* *
98702 AGATATGAAGGGAAAGGTTGAAG-TCGCAATGACAAACCC-TATACCATAGAAGATACGATGGGA
1 AGATATGAAGGGAAAGGTTGAGGCT-GCAATGACAAACCCGGA-ACCATAGAAGATACGATGGGA
* * * *
98765 AGGATTGAGGTCGCAACGACGAATCTAGTACCATGA
64 AAGATTGAGGCCGCAACGACGAATCCAATACCATGA
* * * *
98801 AGATTTGAAGGGAAAAGTTAAGGCCGCAAT
1 AGATATGAAGGGAAAGGTTGAGGCTGCAAT
98831 AGCGAACCTT
Statistics
Matches: 107, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
98 2 0.02
99 105 0.98
ACGTcount: A:0.37, C:0.15, G:0.29, T:0.18
Consensus pattern (99 bp):
AGATATGAAGGGAAAGGTTGAGGCTGCAATGACAAACCCGGAACCATAGAAGATACGATGGGAAA
GATTGAGGCCGCAACGACGAATCCAATACCATGA
Found at i:98797 original size:50 final size:48
Alignment explanation
Indices: 98651--98814 Score: 150
Period size: 49 Copynumber: 3.3 Consensus size: 48
98641 CGGAACCTTA
* * * ** *
98651 GAAGATGTGATGGGAAAGATTGAGGCCGCAACGGTGAATCCAATACCAT
1 GAAGATATGATGGGAAGGATTGAGGTCGCAACGACGAAT-CTATACCAT
* * * * *
98700 GAAGATATGAAGGGAAAGG-TTGAAGTCGCAATGACAAACCCTATACCAT
1 GAAGATATGATGGG-AAGGATTGAGGTCGCAACGACGAA-TCTATACCAT
*
98749 AGAAGATACGATGGGAAGGATTGAGGTCGCAACGACGAATCTAGTACCAT
1 -GAAGATATGATGGGAAGGATTGAGGTCGCAACGACGAATCTA-TACCAT
* *
98799 GAAGATTTGAAGGGAA
1 GAAGATATGATGGGAA
98815 AAGTTAAGGC
Statistics
Matches: 90, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
49 53 0.59
50 37 0.41
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.18
Consensus pattern (48 bp):
GAAGATATGATGGGAAGGATTGAGGTCGCAACGACGAATCTATACCAT
Found at i:99120 original size:78 final size:79
Alignment explanation
Indices: 99032--100511 Score: 1083
Period size: 78 Copynumber: 18.7 Consensus size: 79
99022 GCGACACACC
**
99032 AATCTCTTACCCCGATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATG-GGAC
1 AATCTCTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGAGG-C
*
99096 AGATCGAAGA-ATCT
65 AGATTGAAGACATCT
* * * * * * *
99110 AATCTTTTACCTTAATCA-GAAGGCAGAATGAAGACAATTCAATCTCTTACCTCGATCATGAGGC
1 AATCTCTTACCCTAATCATG-GGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGAGGC
* *
99174 AAATTGAAG-CATCC
65 AGATTGAAGACATCT
* * * *
99188 AATCTTTTACCCTAATTA-GAGGGCAAATTGAAGACATCATCCAATCTCTTACTCCGATCATGAG
1 AATCTCTTACCCTAATCATG-GGGCAGATTGAAGAC--CATCCAATCTCTTACCCCGATCATGAG
*
99252 GTAGATTGAAGACATCAT
63 GCAGATTGAAGACATC-T
* ** * *
99270 CCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCTGAT-ATTA
1 --AATCTCTTACCCTAATCATGGGGCAGATTGAAGAC--CATCCAATCTCTTACCCCGATCA-TG
99334 AGGCAGATTGAAGATATCATCT
61 AGGCAGATTGAAG--A-CATCT
* *
99356 AATCTCTTACCCTGATCATAGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGAGG
1 AATCTCTTACCCTAATCATGGGGCAGATTGAAGAC--CATCCAATCTCTTACCCCGATCATGAGG
99421 CAGATTGAAGACCAT-T
64 CAGATTGAAGA-CATCT
* * * * *** * *
99437 CAATCTCTTACCCCAATCATAGGGTAGATTGAAG--CATCCAATCTTTTACCTTAATTA-GAAAG
1 -AATCTCTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATG-AGG
* *
99499 TAGATTGAAGACAATCC
64 CAGATTGAAGAC-ATCT
* * * **
99516 AATCTCTTA-CCTCGATCATGAGGCAGATTGAAG--CATCCAATCTTTTACCCTAATCA-GAGGG
1 AATCTCTTACCCT-AATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGA-GG
*
99577 TAGATTGAAGACATCAT
64 CAGATTGAAGACATC-T
* * * * ** *
99594 CAATCTCTT-GCCTCGATCTTGGGGTAGATTGAAGACCATCCAATCTCTTACCTTGATCATGGGG
1 -AATCTCTTACCCT-AATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGAGG
*
99658 CAGATTGAAGA-ATCC
64 CAGATTGAAGACATCT
* * * * * * ** *
99673 AATCTTTTACCTTAATCA-GAAGGCATAATGAAGACAATCCAATCTCTTACCTTGATCATGAGGA
1 AATCTCTTACCCTAATCATG-GGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGAGGC
*
99737 AGATTGAAG-CATCC
65 AGATTGAAGACATCT
* * * *
99751 AATCTTTTACCCTAATTA-GAGGGCAGATTAAAGACATCATCCAATCTCTTACTCCGATCATTG-
1 AATCTCTTACCCTAATCATG-GGGCAGATTGAAGAC--CATCCAATCTCTTACCCCGATCA-TGA
99814 GGCAGATTGAAGACATCAT
62 GGCAGATTGAAGACATC-T
* * * *
99833 CCAATCTCTTACCCTAATCATGGGACAAATTGAAGATATCATCCAATCTCTTACCCCGATCTTGA
1 --AATCTCTTACCCTAATCATGGGGCAGATTGAAG--ACCATCCAATCTCTTACCCCGATCATGA
99898 GGCAGATTGAAGACATCAT
62 GGCAGATTGAAGACATC-T
99917 CCAATCTCTTA--C----CAT-GGGCAGATTGAAGACATCATCCAATCTCTTA---C---CATG-
1 --AATCTCTTACCCTAATCATGGGGCAGATTGAAGAC--CATCCAATCTCTTACCCCGATCATGA
*
99968 GGCATATTGAAGACATCAT
62 GGCAGATTGAAGACATC-T
* * * * *
99987 CCAATCTGTTACCCTGATCATGAGGCATATTGAAGACCATCCAATCTCTTACCCCGATCATGGGG
1 --AATCTCTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGAGG
* *
100052 TAGATT-AA-ACATCC
64 CAGATTGAAGACATCT
* * * *** * * *
100066 AATCTTTTACCTTAATTATAAAGCAGATTGAAGACAATCCAATCTCTTACCTCGATCATGAGACA
1 AATCTCTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGAGGCA
*
100131 GATTGAAG-CATCC
66 GATTGAAGACATCT
* * * *
100144 AATCTTTTACCCTAAT--TGGATGGCAGATTGAAGACATAATCCAATCTCTTACCCNGATCTTGA
1 AATCTCTTACCCTAATCATGG--GGCAGATTGAAGAC--CATCCAATCTCTTACCCCGATCATGA
100207 GGCAGATTGAAGACATCAT
62 GGCAGATTGAAGACATC-T
* ** * * * *
100226 CCAGTCTCTTACCCCGATCATAGGGCAGATTAAAGACCATCTAATCTTTTACCCCGATCATGAGG
1 --AATCTCTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGAGG
* * *
100291 CAAATTGAAG-CGTCC
64 CAGATTGAAGACATCT
* * * * * *
100306 AATCTTTTACCTTAATCA-GAAGGCAGATTGAAGACAATCCAATATCTTACCTCGATCATGAGGC
1 AATCTCTTACCCTAATCATG-GGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGAGGC
* *
100370 ATATTGAA-ACATTT
65 AGATTGAAGACATCT
* *** * * * * * *
100384 AATCTTTTACCCTAATCAAAAGGCAAATTAAAGA-CACGCCAATCTTTTACCCCGATCATGGGGT
1 AATCTCTTACCCTAATCATGGGGCAGATTGAAGACCA-TCCAATCTCTTACCCCGATCATGAGGC
*
100448 AGATTGAAG-CATCC
65 AGATTGAAGACATCT
*
100462 AATCTCTTATCCC-AATCATGGGGCAGATTGAAG--CATTCAATCTCTTACCC
1 AATCTCTTA-CCCTAATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCC
100512 TAATCAGAGG
Statistics
Matches: 1142, Mismatches: 185, Indels: 152
0.77 0.13 0.10
Matches are distributed among these distances:
70 28 0.02
71 3 0.00
72 1 0.00
74 1 0.00
75 15 0.01
76 16 0.01
77 108 0.09
78 452 0.40
79 36 0.03
80 104 0.09
81 56 0.05
82 74 0.06
83 3 0.00
84 233 0.20
85 3 0.00
86 5 0.00
87 4 0.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (79 bp):
AATCTCTTACCCTAATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGAGGCA
GATTGAAGACATCT
Found at i:99143 original size:38 final size:38
Alignment explanation
Indices: 99101--99221 Score: 104
Period size: 38 Copynumber: 3.1 Consensus size: 38
99091 GGGACAGATC
99101 GAAGAATCTAATCTTTTACCTTAATCAGAAGGCAGAA-T
1 GAAGAATCTAATCTTTTACCTTAATCAGAAGGCA-AATT
* **
99139 GAAGACAAT-TCAATCTCTTACCTCGATCATG-AGGCAAATT
1 GAAG--AATCT-AATCTTTTACCTTAATCA-GAAGGCAAATT
* * * * *
99179 GAAGCATCCAATCTTTTACCCTAATTAGAGGGCAAATT
1 GAAGAATCTAATCTTTTACCTTAATCAGAAGGCAAATT
99217 GAAGA
1 GAAGA
99222 CATCATCCAA
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
37 1 0.02
38 31 0.48
39 3 0.05
40 28 0.44
41 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (38 bp):
GAAGAATCTAATCTTTTACCTTAATCAGAAGGCAAATT
Found at i:99260 original size:42 final size:40
Alignment explanation
Indices: 99024--100511 Score: 999
Period size: 42 Copynumber: 37.5 Consensus size: 40
99014 AAAGCGAAGC
*
99024 GACACA-CCAATCTCTTACCCCGATCATGGGGCAGATTGAA
1 GACACATCCAATCTCTTA-CCCGATCATGAGGCAGATTGAA
*
99064 GAC-CATCCAATCTCTTACCCCGATCATG-GGACAGATCGAA
1 GACACATCCAATCTCTTA-CCCGATCATGAGG-CAGATTGAA
* * ** *
99104 G--A-ATCTAATCTTTTACCTTAATCA-GAAGGCAGAATGAA
1 GACACATCCAATCTCTTACC-CGATCATG-AGGCAGATTGAA
* *
99142 GACA-ATTCAATCTCTTACCTCGATCATGAGGCAAATTGAA
1 GACACATCCAATCTCTTACC-CGATCATGAGGCAGATTGAA
* * * *
99182 G---CATCCAATCTTTTACCCTAATTA-GAGGGCAAATTGAA
1 GACACATCCAATCTCTTACCC-GATCATGA-GGCAGATTGAA
*
99220 GACATCATCCAATCTCTTACTCCGATCATGAGGTAGATTGAA
1 GACA-CATCCAATCTCTTAC-CCGATCATGAGGCAGATTGAA
* *
99262 GACATCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAA
1 GACA-CATCCAATCTCTTA-CCCGATCATGAGGCAGATTGAA
*
99304 GACATCATCCAATCTCTTACCCTGAT-ATTAAGGCAGATTGAA
1 GACA-CATCCAATCTCTTACCC-GATCA-TGAGGCAGATTGAA
* *
99346 GATATCATCTAATCTCTTACCCTGATCAT-AGGGCAGATTGAA
1 GACA-CATCCAATCTCTTACCC-GATCATGA-GGCAGATTGAA
99388 GACATCATCCAATCTCTTACCCCGATCATGAGGCAGATTGAA
1 GACA-CATCCAATCTCTTA-CCCGATCATGAGGCAGATTGAA
* * *
99430 GAC-CATTCAATCTCTTACCCCAATCAT-AGGGTAGATTGAA
1 GACACATCCAATCTCTTA-CCCGATCATGA-GGCAGATTGAA
* ** * * *
99470 G---CATCCAATCTTTTACCTTAATTA-GAAAGTAGATTGAA
1 GACACATCCAATCTCTTACC-CGATCATG-AGGCAGATTGAA
99508 GACA-ATCCAATCTCTTACCTCGATCATGAGGCAGATTGAA
1 GACACATCCAATCTCTTACC-CGATCATGAGGCAGATTGAA
* * *
99548 G---CATCCAATCTTTTACCCTAATCA-GAGGGTAGATTGAA
1 GACACATCCAATCTCTTACCC-GATCATGA-GGCAGATTGAA
* * * *
99586 GACATCAT-CAATCTCTTGCCTCGATCTTGGGGTAGATTGAA
1 GACA-CATCCAATCTCTTACC-CGATCATGAGGCAGATTGAA
* *
99627 GAC-CATCCAATCTCTTACCTTGATCATGGGGCAGATTGAA
1 GACACATCCAATCTCTTACC-CGATCATGAGGCAGATTGAA
* ** * *
99667 G--A-ATCCAATCTTTTACCTTAATCA-GAAGGCATAATGAA
1 GACACATCCAATCTCTTACC-CGATCATG-AGGCAGATTGAA
* *
99705 GACA-ATCCAATCTCTTACCTTGATCATGAGGAAGATTGAA
1 GACACATCCAATCTCTTACC-CGATCATGAGGCAGATTGAA
* * * *
99745 G---CATCCAATCTTTTACCCTAATTA-GAGGGCAGATTAAA
1 GACACATCCAATCTCTTACCC-GATCATGA-GGCAGATTGAA
99783 GACATCATCCAATCTCTTACTCCGATCATTG-GGCAGATTGAA
1 GACA-CATCCAATCTCTTAC-CCGATCA-TGAGGCAGATTGAA
* *
99825 GACATCATCCAATCTCTTACCCTAATCATG-GGACAAATTGAA
1 GACA-CATCCAATCTCTTACCC-GATCATGAGG-CAGATTGAA
* *
99867 GATATCATCCAATCTCTTACCCCGATCTTGAGGCAGATTGAA
1 GACA-CATCCAATCTCTTA-CCCGATCATGAGGCAGATTGAA
99909 GACATCATCCAATCTCTTA--C---CATG-GGCAGATTGAA
1 GACA-CATCCAATCTCTTACCCGATCATGAGGCAGATTGAA
*
99944 GACATCATCCAATCTCTTA--C---CATG-GGCATATTGAA
1 GACA-CATCCAATCTCTTACCCGATCATGAGGCAGATTGAA
* *
99979 GACATCATCCAATCTGTTACCCTGATCATGAGGCATATTGAA
1 GACA-CATCCAATCTCTTACCC-GATCATGAGGCAGATTGAA
* *
100021 GAC-CATCCAATCTCTTACCCCGATCATGGGGTAGATT--A
1 GACACATCCAATCTCTTA-CCCGATCATGAGGCAGATTGAA
* ** * * *
100059 -A-ACATCCAATCTTTTACCTTAATTATAAAGCAGATTGAA
1 GACACATCCAATCTCTTACC-CGATCATGAGGCAGATTGAA
*
100098 GACA-ATCCAATCTCTTACCTCGATCATGAGACAGATTGAA
1 GACACATCCAATCTCTTACC-CGATCATGAGGCAGATTGAA
* *
100138 G---CATCCAATCTTTTACCC--TAATTGGATGGCAGATTGAA
1 GACACATCCAATCTCTTACCCGATCA-T-GA-GGCAGATTGAA
* *
100176 GACATAATCCAATCTCTTACCCNGATCTTGAGGCAGATTGAA
1 GACA-CATCCAATCTCTTACCC-GATCATGAGGCAGATTGAA
* *
100218 GACATCATCCAGTCTCTTACCCCGATCAT-AGGGCAGATTAAA
1 GACA-CATCCAATCTCTTA-CCCGATCATGA-GGCAGATTGAA
* * *
100260 GAC-CATCTAATCTTTTACCCCGATCATGAGGCAAATTGAA
1 GACACATCCAATCTCTTA-CCCGATCATGAGGCAGATTGAA
* * **
100300 G---CGTCCAATCTTTTACCTTAATCA-GAAGGCAGATTGAA
1 GACACATCCAATCTCTTACC-CGATCATG-AGGCAGATTGAA
* *
100338 GACA-ATCCAATATCTTACCTCGATCATGAGGCATATTG-A
1 GACACATCCAATCTCTTACC-CGATCATGAGGCAGATTGAA
** * * ** * *
100377 -A-ACATTTAATCTTTTACCCTAATCAAAAGGCAAATTAAA
1 GACACATCCAATCTCTTACCC-GATCATGAGGCAGATTGAA
* * * *
100416 GACAC-GCCAATCTTTTACCCCGATCATGGGGTAGATTGAA
1 GACACATCCAATCTCTTA-CCCGATCATGAGGCAGATTGAA
* *
100456 G---CATCCAATCTCTTATCCCAATCATGGGGCAGATTGAA
1 GACACATCCAATCTCTTA-CCCGATCATGAGGCAGATTGAA
*
100494 G---CATTCAATCTCTTACCC
1 GACACATCCAATCTCTTACCC
100512 TAATCAGAGG
Statistics
Matches: 1185, Mismatches: 160, Indels: 209
0.76 0.10 0.13
Matches are distributed among these distances:
35 65 0.05
36 6 0.01
37 51 0.04
38 286 0.24
39 15 0.01
40 323 0.27
41 57 0.05
42 357 0.30
43 22 0.02
44 2 0.00
45 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
GACACATCCAATCTCTTACCCGATCATGAGGCAGATTGAA
Found at i:99640 original size:197 final size:197
Alignment explanation
Indices: 99030--100278 Score: 1072
Period size: 197 Copynumber: 6.3 Consensus size: 197
99020 AAGCGACACA
* * *** * **
99030 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCCCGATCATGGGA
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAG--CATCCAATCTTTTACCTTAATTA-GAAA
* * * ** * * *
99095 -CAGATCGAAG--AATCTAATCTTTTACCTTAATCA-GAAGGCAGAATGAAGACAATTCAATCTC
63 GCAGATTGAAGACAATCCAATCTCTTACCTCGATCATG-AGGCAGATTGAAG-C-ATCCAATCTT
* * * * * *
99156 TTA-CCTCGATCATGA-GGCAAATTGAAG----CATCCAATCTTTTACCCTAAT-TAGAGGGCAA
125 TTACCCT-AATCA-GAGGGCAGATTGAAGACATCATCCAATCTCTTACCC-GATCTTGA-GGCAG
99214 ATTGAAGACATCAT
186 ATTGAAGAC--CAT
* * *** *
99228 CCAATCTCTTACTCCGATCAT-GAGGTAGATTGAAGACATCATCCAATCTTTTACCCCGATCATG
1 CCAATCTCTTACCCCGATCATAG-GGCAGATTGAAG----CATCCAATCTTTTACCTTAATTA-G
** *
99292 -GGGCAGATTGAAGACATCATCCAATCTCTTACC-CTGAT-ATTAAGGCAGATTGAAGATATCAT
60 AAAGCAGATTGAAGACA--ATCCAATCTCTTACCTC-GATCA-TGAGGCAGATTGAAG----CAT
* * * * *
99354 CTAATCTCTTACCCTGATCATAGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGA
117 CCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACATCATCCAATCTCTTA-CCCGATCTTGA
99419 GGCAGATTGAAGACCAT
181 GGCAGATTGAAGACCAT
* * * *
99436 TCAATCTCTTACCCCAATCATAGGGTAGATTGAAGCATCCAATCTTTTACCTTAATTAGAAAGTA
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTTTTACCTTAATTAGAAAGCA
99501 GATTGAAGACAATCCAATCTCTTACCTCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCC
66 GATTGAAGACAATCCAATCTCTTACCTCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCC
* * * *
99566 TAATCAGAGGGTAGATTGAAGACATCAT-CAATCTCTTGCCTCGATCTTGGGGTAGATTGAAGAC
131 TAATCAGAGGGCAGATTGAAGACATCATCCAATCTCTTACC-CGATCTTGAGGCAGATTGAAGAC
99630 CAT
195 CAT
** * * * *
99633 CCAATCTCTTACCTTGATCATGGGGCAGATTGAAGAATCCAATCTTTTACCTTAATCAGAAGGCA
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTTTTACCTTAATTAGAAAGCA
* * * *
99698 TAATGAAGACAATCCAATCTCTTACCTTGATCATGAGGAAGATTGAAGCATCCAATCTTTTACCC
66 GATTGAAGACAATCCAATCTCTTACCTCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCC
* *
99763 TAATTAGAGGGCAGATTAAAGACATCATCCAATCTCTTACTCCGATCATTG-GGCAGATTGAAGA
131 TAATCAGAGGGCAGATTGAAGACATCATCCAATCTCTTAC-CCGATC-TTGAGGCAGATTGAAGA
99827 CATCAT
194 C--CAT
** * * *** *
99833 CCAATCTCTTACCCTAATCAT-GGGACAAATTGAAGATATCATCCAATCTCTTACCCCGATCTTG
1 CCAATCTCTTACCCCGATCATAGGG-CAGATTGAAG----CATCCAATCTTTTACCTTAAT-TAG
*
99897 -AGGCAGATTGAAGACATCATCCAATCTCTTA---C---CATG-GGCAGATTGAAGACATCATCC
60 AAAGCAGATTGAAGACA--ATCCAATCTCTTACCTCGATCATGAGGCAGATTGAAG----CATCC
* * * *
99954 AATCTCTTA-CC--AT----GGGCATATTGAAGACATCATCCAATCTGTTACCCTGATCATGAGG
119 AATCTTTTACCCTAATCAGAGGGCAGATTGAAGACATCATCCAATCTCTTACCC-GATCTTGAGG
*
100012 CATATTGAAGACCAT
183 CAGATTGAAGACCAT
* * * *
100027 CCAATCTCTTACCCCGATCATGGGGTAGATT-AAACATCCAATCTTTTACCTTAATTATAAAGCA
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTTTTACCTTAATTAGAAAGCA
*
100091 GATTGAAGACAATCCAATCTCTTACCTCGATCATGAGACAGATTGAAGCATCCAATCTTTTACCC
66 GATTGAAGACAATCCAATCTCTTACCTCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCC
** * *
100156 TAATTGGATGGCAGATTGAAGACATAATCCAATCTCTTACCCNGATCTTGAGGCAGATTGAAGAC
131 TAATCAGAGGGCAGATTGAAGACATCATCCAATCTCTTACCC-GATCTTGAGGCAGATTGAAGAC
100221 ATCAT
195 --CAT
* * *
100226 CCAGTCTCTTACCCCGATCATAGGGCAGATTAAAGACCATCTAATCTTTTACC
1 CCAATCTCTTACCCCGATCATAGGGCAGATTGAAG--CATCCAATCTTTTACC
100279 CCGATCATGA
Statistics
Matches: 877, Mismatches: 107, Indels: 130
0.79 0.10 0.12
Matches are distributed among these distances:
187 13 0.01
188 1 0.00
189 32 0.04
190 14 0.02
191 2 0.00
193 8 0.01
194 37 0.04
195 7 0.01
196 48 0.05
197 224 0.26
198 99 0.11
199 50 0.06
200 73 0.08
202 50 0.06
203 17 0.02
204 89 0.10
205 2 0.00
206 40 0.05
207 4 0.00
208 33 0.04
209 1 0.00
210 28 0.03
211 5 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (197 bp):
CCAATCTCTTACCCCGATCATAGGGCAGATTGAAGCATCCAATCTTTTACCTTAATTAGAAAGCA
GATTGAAGACAATCCAATCTCTTACCTCGATCATGAGGCAGATTGAAGCATCCAATCTTTTACCC
TAATCAGAGGGCAGATTGAAGACATCATCCAATCTCTTACCCGATCTTGAGGCAGATTGAAGACC
AT
Found at i:99944 original size:35 final size:35
Alignment explanation
Indices: 99898--99999 Score: 186
Period size: 35 Copynumber: 2.9 Consensus size: 35
99888 CCGATCTTGA
99898 GGCAGATTGAAGACATCATCCAATCTCTTACCATG
1 GGCAGATTGAAGACATCATCCAATCTCTTACCATG
99933 GGCAGATTGAAGACATCATCCAATCTCTTACCATG
1 GGCAGATTGAAGACATCATCCAATCTCTTACCATG
* *
99968 GGCATATTGAAGACATCATCCAATCTGTTACC
1 GGCAGATTGAAGACATCATCCAATCTCTTACC
100000 CTGATCATGA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (35 bp):
GGCAGATTGAAGACATCATCCAATCTCTTACCATG
Found at i:103365 original size:42 final size:40
Alignment explanation
Indices: 103310--103622 Score: 216
Period size: 38 Copynumber: 8.0 Consensus size: 40
103300 NNNNNNNNNN
* *
103310 GATCTTGAGGCAGATTGAAGACATCATCCAGTCTCTTACCCC
1 GATCATGAGGCAGATTGAAGAC--CATCCAATCTCTTACCCC
* * *
103352 GATCAT-AGGGCAGATTAAAGACCATCTAATCTTTTACCCC
1 GATCATGA-GGCAGATTGAAGACCATCCAATCTCTTACCCC
* * * **
103392 GATCATGAGGCAAATTGAAG--CGTCCAATCTTTTACCTT
1 GATCATGAGGCAGATTGAAGACCATCCAATCTCTTACCCC
* * * *
103430 AATCA-GAAGGCAGATTGAAGACAATCCAATATCTTACCTC
1 GATCATG-AGGCAGATTGAAGACCATCCAATCTCTTACCCC
* ** * *
103470 GATCATGAGGCATATTGAA-A-CATTTAATCTTTTACCCT
1 GATCATGAGGCAGATTGAAGACCATCCAATCTCTTACCCC
* ** * * * *
103508 AATCAAAAGGCAAATTAAAGA-CACGCCAATCTTTTACCCC
1 GATCATGAGGCAGATTGAAGACCA-TCCAATCTCTTACCCC
* * *
103548 GATCATGGGGTAGATTGAAG--CATCCAATCTCTTATCCC
1 GATCATGAGGCAGATTGAAGACCATCCAATCTCTTACCCC
* * *
103586 AATCATGGGGCAGATTGAAG--CATTCAATCTCTTACCC
1 GATCATGAGGCAGATTGAAGACCATCCAATCTCTTACCC
103623 TAATCAGAGG
Statistics
Matches: 213, Mismatches: 50, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
37 1 0.00
38 101 0.47
39 6 0.03
40 84 0.39
41 3 0.01
42 18 0.08
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (40 bp):
GATCATGAGGCAGATTGAAGACCATCCAATCTCTTACCCC
Found at i:103441 original size:38 final size:39
Alignment explanation
Indices: 103399--103545 Score: 129
Period size: 40 Copynumber: 3.8 Consensus size: 39
103389 CCCGATCATG
*
103399 AGGCAAATTGAAG-CGTCCAATCTTTTACCTTAATCAGA
1 AGGCAAATTGAAGACATCCAATCTTTTACCTTAATCAGA
* * * **
103437 AGGCAGATTGAAGACAATCCAATATCTTACCTCGATCATG-
1 AGGCAAATTGAAGAC-ATCCAATCTTTTACCTTAATCA-GA
* ** * *
103477 AGGCATATTGAA-ACATTTAATCTTTTACCCTAATCAAA
1 AGGCAAATTGAAGACATCCAATCTTTTACCTTAATCAGA
* *
103515 AGGCAAATTAAAGACACGCCAATCTTTTACC
1 AGGCAAATTGAAGACA-TCCAATCTTTTACC
103546 CCGATCATGG
Statistics
Matches: 83, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
38 37 0.45
39 6 0.07
40 39 0.47
41 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (39 bp):
AGGCAAATTGAAGACATCCAATCTTTTACCTTAATCAGA
Found at i:103451 original size:78 final size:78
Alignment explanation
Indices: 103360--103590 Score: 259
Period size: 78 Copynumber: 3.0 Consensus size: 78
103350 CCGATCATAG
* *
103360 GGCAGATTAAAGACCATCTAATCTTTTACCCCGATCATGAGGCAAATTGAAGCGTCCAATCTTTT
1 GGCAGATTAAAGACCATCCAATCTTTTACCCCGATCATGAGGCAAATTGAAGCATCCAATCTTTT
* *
103425 ACCTTAATCAGAA
66 ACCCTAATCAAAA
* * * * * * * **
103438 GGCAGATTGAAGACAATCCAATATCTTACCTCGATCATGAGGCATATTGAAACATTTAATCTTTT
1 GGCAGATTAAAGACCATCCAATCTTTTACCCCGATCATGAGGCAAATTGAAGCATCCAATCTTTT
103503 ACCCTAATCAAAA
66 ACCCTAATCAAAA
* * * * * *
103516 GGCAAATTAAAGA-CACGCCAATCTTTTACCCCGATCATGGGGTAGATTGAAGCATCCAATCTCT
1 GGCAGATTAAAGACCA-TCCAATCTTTTACCCCGATCATGAGGCAAATTGAAGCATCCAATCTTT
103580 TATCCC-AATCA
65 TA-CCCTAATCA
103591 TGGGGCAGAT
Statistics
Matches: 124, Mismatches: 27, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
77 1 0.01
78 120 0.97
79 3 0.02
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (78 bp):
GGCAGATTAAAGACCATCCAATCTTTTACCCCGATCATGAGGCAAATTGAAGCATCCAATCTTTT
ACCCTAATCAAAA
Found at i:109456 original size:25 final size:25
Alignment explanation
Indices: 109428--109598 Score: 107
Period size: 25 Copynumber: 6.8 Consensus size: 25
109418 TTCTATCTCT
*
109428 CTCGTAAGAGCAATATTCTGTCTAG
1 CTCGTAAGAGCAATATTCTGTCTGG
* **
109453 CTCGCAAGAG-TGTAATTCTGTCTGG
1 CTCGTAAGAGCAAT-ATTCTGTCTGG
* ** *
109478 CTCATAAGAGTGATATTCTGTTTGG
1 CTCGTAAGAGCAATATTCTGTCTGG
* * *
109503 CTCGCAAGAGTGAA-ACTT-TGTTTGG
1 CTCGTAAGAG-CAATA-TTCTGTCTGG
* * *
109528 CTCGTAAGAGCGATACTCTGTCTGA
1 CTCGTAAGAGCAATATTCTGTCTGG
* **
109553 CTCGTATGAGTGATATTCTGTCTAGG
1 CTCGTAAGAGCAATATTCTGTCT-GG
*
109579 CTCGTTAGAGCTAA-ATTCTG
1 CTCGTAAGAGC-AATATTCTG
109599 GAATACTTGA
Statistics
Matches: 111, Mismatches: 27, Indels: 15
0.73 0.18 0.10
Matches are distributed among these distances:
24 3 0.03
25 88 0.79
26 19 0.17
27 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (25 bp):
CTCGTAAGAGCAATATTCTGTCTGG
Found at i:109529 original size:50 final size:50
Alignment explanation
Indices: 109405--109581 Score: 169
Period size: 50 Copynumber: 3.5 Consensus size: 50
109395 GATTCTGGCA
* * ** * *
109405 CGCAAGAGTGTAATTCTATCTCTCTCGTAAGAGCAATATTCTGTCTAGCT
1 CGCAAGAGTGAAATTCTGTCTGGCTCATAAGAGCGATATTCTGTCTAGCT
* * * *
109455 CGCAAGAGTGTAATTCTGTCTGGCTCATAAGAGTGATATTCTGTTTGGCT
1 CGCAAGAGTGAAATTCTGTCTGGCTCATAAGAGCGATATTCTGTCTAGCT
* * *
109505 CGCAAGAGTGAAACTT-TGTTTGGCTCGTAAGAGCGATACTCTGTCT-GACT
1 CGCAAGAGTGAAA-TTCTGTCTGGCTCATAAGAGCGATATTCTGTCTAG-CT
* * *
109555 CGTATGAGTGATATTCTGTCTAGGCTC
1 CGCAAGAGTGAAATTCTGTCT-GGCTC
109582 GTTAGAGCTA
Statistics
Matches: 105, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
49 3 0.03
50 95 0.90
51 7 0.07
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (50 bp):
CGCAAGAGTGAAATTCTGTCTGGCTCATAAGAGCGATATTCTGTCTAGCT
Found at i:110271 original size:21 final size:20
Alignment explanation
Indices: 110240--110295 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
110230 GAGTTTTTAG
*
110240 TATCAGTAGAAGTACAACTTA
1 TATCGGTAGAAGTAC-ACTTA
* *
110261 TTTCGGTAGAAGTTACACTTG
1 TATCGGTAGAAG-TACACTTA
110282 TATCGGTAGAAGTA
1 TATCGGTAGAAGTA
110296 TTTCAAGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 25 0.83
22 3 0.10
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (20 bp):
TATCGGTAGAAGTACACTTA
Found at i:112219 original size:21 final size:21
Alignment explanation
Indices: 112172--112302 Score: 99
Period size: 21 Copynumber: 6.2 Consensus size: 21
112162 TGGCCTTGTG
* *
112172 TTGCACTTCGATCCCCCTG-A
1 TTGCACTTCGGTGCCCCTGTA
112192 CTTGCACTTCGGTGCCCCTGTA
1 -TTGCACTTCGGTGCCCCTGTA
* * *
112214 TGGCACTAT-GGTTCCCCT-AA
1 TTGCACT-TCGGTGCCCCTGTA
* *
112234 CTCGCACTTCGGTGCCCCTATA
1 -TTGCACTTCGGTGCCCCTGTA
* *
112256 TTGCACTACGGTGCTCCTG-A
1 TTGCACTTCGGTGCCCCTGTA
* *
112276 CTTGCACTTTGGTGCCCTTGTA
1 -TTGCACTTCGGTGCCCCTGTA
112298 TTGCA
1 TTGCA
112303 TTATGGTGCC
Statistics
Matches: 87, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
20 3 0.03
21 80 0.92
22 4 0.05
ACGTcount: A:0.14, C:0.34, G:0.21, T:0.32
Consensus pattern (21 bp):
TTGCACTTCGGTGCCCCTGTA
Found at i:112241 original size:42 final size:42
Alignment explanation
Indices: 112185--112312 Score: 166
Period size: 42 Copynumber: 3.0 Consensus size: 42
112175 CACTTCGATC
* *
112185 CCCCTGACTTGCACTTCGGTGCCCCTGTATGGCACTATGGTT
1 CCCCTGACTTGCACTTCGGTGCCCCTGTATTGCACTATGGTG
* * * *
112227 CCCCTAACTCGCACTTCGGTGCCCCTATATTGCACTACGGTG
1 CCCCTGACTTGCACTTCGGTGCCCCTGTATTGCACTATGGTG
* * * *
112269 CTCCTGACTTGCACTTTGGTGCCCTTGTATTGCATTATGGTG
1 CCCCTGACTTGCACTTCGGTGCCCCTGTATTGCACTATGGTG
112311 CC
1 CC
112313 GTTATCTTGC
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.13, C:0.33, G:0.22, T:0.32
Consensus pattern (42 bp):
CCCCTGACTTGCACTTCGGTGCCCCTGTATTGCACTATGGTG
Found at i:112309 original size:21 final size:21
Alignment explanation
Indices: 112277--112337 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
112267 TGCTCCTGAC
112277 TTGCACTT-TGGTGCCCTTGTA
1 TTGCA-TTATGGTGCCCTTGTA
* * *
112298 TTGCATTATGGTGCCGTTATC
1 TTGCATTATGGTGCCCTTGTA
112319 TTGCATTATGGTGCCCTTG
1 TTGCATTATGGTGCCCTTG
112338 GAAATGCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 2 0.06
21 32 0.94
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.43
Consensus pattern (21 bp):
TTGCATTATGGTGCCCTTGTA
Found at i:118498 original size:50 final size:50
Alignment explanation
Indices: 118429--118573 Score: 182
Period size: 50 Copynumber: 2.9 Consensus size: 50
118419 ACATTCTAAT
* * * *
118429 TTTGGCACGCAAGAGCGTAATTCTATATGGCTCGTAAGAGCGATATTCTG
1 TTTGGCTCGCAAGAGCGTAATTCTGTCTAGCTCGTAAGAGCGATATTCTG
* * *
118479 TTTGGCTCGAAAGAGCGTAATTCTGTCTAGCTCGTAAGAGCAATATTTTG
1 TTTGGCTCGCAAGAGCGTAATTCTGTCTAGCTCGTAAGAGCGATATTCTG
* * * * *
118529 TCTAGCTCGCAAGAACGTAATTATGTCTAGCTTGTAAGAGCGATA
1 TTTGGCTCGCAAGAGCGTAATTCTGTCTAGCTCGTAAGAGCGATA
118574 CTCTATCGAC
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 81 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (50 bp):
TTTGGCTCGCAAGAGCGTAATTCTGTCTAGCTCGTAAGAGCGATATTCTG
Found at i:118530 original size:25 final size:25
Alignment explanation
Indices: 118439--118569 Score: 104
Period size: 25 Copynumber: 5.2 Consensus size: 25
118429 TTTGGCACGC
* * * *
118439 AAGAGCGTAATTCTATATGGCTCGT
1 AAGAGCATAATTCTGTCTAGCTCGT
* * *
118464 AAGAGCGAT-ATTCTGTTTGGCTCGA
1 AAGAGC-ATAATTCTGTCTAGCTCGT
*
118489 AAGAGCGTAATTCTGTCTAGCTCGT
1 AAGAGCATAATTCTGTCTAGCTCGT
* *
118514 AAGAGCA-ATATTTTGTCTAGCTCGC
1 AAGAGCATA-ATTCTGTCTAGCTCGT
* * * *
118539 AAGAACGTAATTATGTCTAGCTTGT
1 AAGAGCATAATTCTGTCTAGCTCGT
118564 AAGAGC
1 AAGAGC
118570 GATACTCTAT
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
24 2 0.02
25 81 0.95
26 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (25 bp):
AAGAGCATAATTCTGTCTAGCTCGT
Found at i:121105 original size:28 final size:28
Alignment explanation
Indices: 121074--121128 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
121064 GATTTATAAC
121074 TGCTTATAACTGCTTTTCTTATGATTAT
1 TGCTTATAACTGCTTTTCTTATGATTAT
121102 TGCTTATAACTGCTTTTCTTATGATTA
1 TGCTTATAACTGCTTTTCTTATGATTA
121129 CTCGACCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.53
Consensus pattern (28 bp):
TGCTTATAACTGCTTTTCTTATGATTAT
Found at i:125727 original size:15 final size:17
Alignment explanation
Indices: 125696--125729 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
125686 AAAATTTAGA
125696 TATTTTAAATGTATTTT
1 TATTTTAAATGTATTTT
125713 TATTTT-AAT-TATTTT
1 TATTTTAAATGTATTTT
125728 TA
1 TA
125730 AGAAGCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TATTTTAAATGTATTTT
Found at i:126754 original size:12 final size:11
Alignment explanation
Indices: 126726--126755 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
126716 ACTTGTCCAT
126726 ATTATTTTTAA
1 ATTATTTTTAA
126737 ATTATTTTTAA
1 ATTATTTTTAA
126748 ATATATTT
1 AT-TATTT
126756 ATATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTATTTTTAA
Found at i:132844 original size:29 final size:29
Alignment explanation
Indices: 132789--132844 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
132779 GTTTCAGAAT
*
132789 ATTATAAAAATTATTAAAATATGTAAACA
1 ATTATAAAAATTATTAAAATATATAAACA
*
132818 ATTATAAAAATTTATTAAATTA-ATAAA
1 ATTATAAAAA-TTATTAAAATATATAAA
132845 AATATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
ATTATAAAAATTATTAAAATATATAAACA
Found at i:132858 original size:19 final size:19
Alignment explanation
Indices: 132817--132855 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
132807 ATATGTAAAC
*
132817 AATT-ATAAAAATTTATTA
1 AATTAATAAAAATTTAATA
132835 AATTAATAAAAATATTAATA
1 AATTAATAAAAAT-TTAATA
132855 A
1 A
132856 TTACTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAATAAAAATTTAATA
Found at i:134323 original size:29 final size:30
Alignment explanation
Indices: 134258--134327 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
134248 TTTGTATTTA
* *
134258 GGACTAAATTGGAAATTTTGTGAAATTTAG
1 GGACTAATTTGGAAATTTTGTGAAACTTAG
* *
134288 GGTCTAATTTGTAAA-TTTGTGAAACTT-G
1 GGACTAATTTGGAAATTTTGTGAAACTTAG
134316 TGGACTAATTTG
1 -GGACTAATTTG
134328 ATCTTTAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 1 0.03
29 21 0.62
30 12 0.35
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (30 bp):
GGACTAATTTGGAAATTTTGTGAAACTTAG
Found at i:140221 original size:34 final size:34
Alignment explanation
Indices: 140178--140250 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
140168 GAAAAATGGA
140178 AACTTATAAGGTCAGACTTGTAGCAAAAGGTTAT
1 AACTTATAAGGTCAGACTTGTAGCAAAAGGTTAT
140212 AACTTATAAGGTCAGACTTGTAGCAAAAGGTTAT
1 AACTTATAAGGTCAGACTTGTAGCAAAAGGTTAT
140246 -ACTTA
1 AACTTA
140251 GAAAGAAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 5 0.13
34 34 0.87
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (34 bp):
AACTTATAAGGTCAGACTTGTAGCAAAAGGTTAT
Found at i:144153 original size:23 final size:22
Alignment explanation
Indices: 144107--144169 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
144097 TAACATACAA
* *
144107 AATATGGCACAAAGGCTTATTAG
1 AATATGCCACAAAGGC-TAATAG
*
144130 ATTATGCCACAAAGGCTAGATAG
1 AATATGCCACAAAGGCTA-ATAG
*
144153 AATACGCCACAAAGGCT
1 AATATGCCACAAAGGCT
144170 CTATTTGGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 2 0.06
23 32 0.94
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (22 bp):
AATATGCCACAAAGGCTAATAG
Found at i:145398 original size:21 final size:21
Alignment explanation
Indices: 145373--145430 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
145363 TAGTGCAGAC
145373 CTCTACCGATACAAGTGACCA
1 CTCTACCGATACAAGTGACCA
* *
145394 TTCTACCGATACAAGTGACTA
1 CTCTACCGATACAAGTGACCA
145415 CTCTACCGATACAAGT
1 CTCTACCGATACAAGT
145431 CTTGATTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (21 bp):
CTCTACCGATACAAGTGACCA
Found at i:146224 original size:52 final size:52
Alignment explanation
Indices: 146119--146298 Score: 236
Period size: 52 Copynumber: 3.5 Consensus size: 52
146109 TGTGTATTTG
* * * * *
146119 ATACTCACGATGACACAGAGTCATTGAACCT-TTAATCCGTAAAGAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* ** *** *
146170 ATACTCACGATAATGCATAGTCATCTTCCCTCATAATCCGTAAAGGATTTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
146222 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
146274 ATACTCACGATGACACATAGTCATC
1 ATACTCACGATGACACATAGTCATC
146299 AGAACTATTT
Statistics
Matches: 109, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 23 0.21
52 86 0.79
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:152125 original size:21 final size:21
Alignment explanation
Indices: 152101--152154 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
152091 AGTGTAGACC
*
152101 TCTACCGATATAAGTGAC-CAT
1 TCTACCGATACAAGTGACTC-T
152122 TCTACCGATACAAGTGACTCT
1 TCTACCGATACAAGTGACTCT
152143 TCTACCGATACA
1 TCTACCGATACA
152155 GTATTGATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTGACTCT
Found at i:158883 original size:21 final size:20
Alignment explanation
Indices: 158857--158925 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
158847 TTTAATTTTT
158857 ATAATTTTTAATGATTCTTTA
1 ATAATTTTTAATG-TTCTTTA
**
158878 ATAATTTAAAAT-TTC-TTA
1 ATAATTTTTAATGTTCTTTA
* *
158896 ATAAATTTTACA-GCTTTTTTA
1 ATAATTTTTA-ATG-TTCTTTA
158917 ATAATTTTT
1 ATAATTTTT
158926 TTTAATTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 10 0.27
19 4 0.11
20 2 0.05
21 21 0.57
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (20 bp):
ATAATTTTTAATGTTCTTTA
Found at i:158924 original size:10 final size:10
Alignment explanation
Indices: 158849--158925 Score: 54
Period size: 10 Copynumber: 7.8 Consensus size: 10
158839 AGTTATTTTT
158849 TAATTTTT-A
1 TAATTTTTAA
158858 TAATTTTTAA
1 TAATTTTTAA
*
158868 TGATTCTTTAA
1 TAATT-TTTAA
158879 TAA--TTTAA
1 TAATTTTTAA
158887 -AATTTCTTAA
1 TAATTT-TTAA
*
158897 TAAATTTTACA
1 TAATTTTTA-A
***
158908 GCTTTTTTAA
1 TAATTTTTAA
158918 TAATTTTT
1 TAATTTTT
158926 TTTAATTATT
Statistics
Matches: 51, Mismatches: 10, Indels: 13
0.69 0.14 0.18
Matches are distributed among these distances:
7 2 0.04
8 5 0.10
9 9 0.18
10 18 0.35
11 17 0.33
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:160711 original size:22 final size:22
Alignment explanation
Indices: 160686--160752 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
160676 TCTACCATTT
160686 AGTGGTATATTCATTAAGGGGA
1 AGTGGTATATTCATTAAGGGGA
* * ***
160708 AGTGAT-TCTATC-TTAA-TTTA
1 AGTGGTATAT-TCATTAAGGGGA
160728 -GTGGTATATTCATTAAGGGGA
1 AGTGGTATATTCATTAAGGGGA
160749 AGTG
1 AGTG
160753 ATTCTATCTT
Statistics
Matches: 30, Mismatches: 10, Indels: 10
0.60 0.20 0.20
Matches are distributed among these distances:
19 6 0.20
20 7 0.23
21 7 0.23
22 10 0.33
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (22 bp):
AGTGGTATATTCATTAAGGGGA
Found at i:160739 original size:41 final size:42
Alignment explanation
Indices: 160681--160768 Score: 169
Period size: 41 Copynumber: 2.1 Consensus size: 42
160671 GATCATCTAC
160681 CATTTAGTGGTATATTCATTAAGGGGAAGTGATTCTATCTTA
1 CATTTAGTGGTATATTCATTAAGGGGAAGTGATTCTATCTTA
160723 -ATTTAGTGGTATATTCATTAAGGGGAAGTGATTCTATCTTA
1 CATTTAGTGGTATATTCATTAAGGGGAAGTGATTCTATCTTA
160764 CATTT
1 CATTT
160769 GAAAAGATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
41 41 0.91
42 4 0.09
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (42 bp):
CATTTAGTGGTATATTCATTAAGGGGAAGTGATTCTATCTTA
Found at i:165211 original size:6 final size:6
Alignment explanation
Indices: 165200--165224 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
165190 AGAATCTTTC
165200 TCTAAT TCTAAT TCTAAT TCTAAT T
1 TCTAAT TCTAAT TCTAAT TCTAAT T
165225 ATGATTCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTAAT
Found at i:174754 original size:29 final size:28
Alignment explanation
Indices: 174717--174780 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 28
174707 GATCCAAAAT
*
174717 AAAATTTACCAACTTTTAGGGGCTCTAA
1 AAAATTTACCAACTTTTAGAGGCTCTAA
*
174745 AAATATTTACCAACTTTTAGAGGTTCTAA
1 AAA-ATTTACCAACTTTTAGAGGCTCTAA
174774 AAAATTT
1 AAAATTT
174781 TCTTCCACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (28 bp):
AAAATTTACCAACTTTTAGAGGCTCTAA
Found at i:176618 original size:9 final size:9
Alignment explanation
Indices: 176580--176618 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
176570 CTCATATCAT
176580 ATTCTCTCA
1 ATTCTCTCA
*
176589 ACTCTCTCA
1 ATTCTCTCA
* *
176598 AATCTCTTA
1 ATTCTCTCA
176607 ATTCTCTCA
1 ATTCTCTCA
176616 ATT
1 ATT
176619 TTATCAAGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTCTCTCA
Found at i:178829 original size:26 final size:27
Alignment explanation
Indices: 178779--178839 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
178769 ATGCATGAAT
*
178779 TAAATTGAATTATATATGACAATTAG-
1 TAAATTGAATTAAATATGACAATTAGC
178805 TAAATTGAATTAAAT-TG-CATTATTAGC
1 TAAATTGAATTAAATATGACA--ATTAGC
178832 TAAATTGA
1 TAAATTGA
178840 TCTTATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 2 0.06
25 2 0.06
26 19 0.61
27 8 0.26
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.39
Consensus pattern (27 bp):
TAAATTGAATTAAATATGACAATTAGC
Found at i:179088 original size:24 final size:24
Alignment explanation
Indices: 179056--179105 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
179046 ATGTTTCTTA
179056 TATTCATGCTGACGAGCGTAAACG
1 TATTCATGCTGACGAGCGTAAACG
179080 TATTCATGCTGACGAGCGTAAACG
1 TATTCATGCTGACGAGCGTAAACG
179104 TA
1 TA
179106 ATTAACTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (24 bp):
TATTCATGCTGACGAGCGTAAACG
Found at i:184395 original size:52 final size:52
Alignment explanation
Indices: 184328--184672 Score: 471
Period size: 52 Copynumber: 6.6 Consensus size: 52
184318 TTCCCATTTA
* *
184328 ATACTCACGATGACACAAAGTCATTGGACCTTA-AATCCGTAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGT-AAAGGATTCAT
* * * * *
184380 ATGCTCAC-AGTGACACGTAGTCATCGAACCTCATAATCCGTAAAGGATTCGT
1 ATACTCACGA-TGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
* * *
184432 ATACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
* *
184484 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
* ** *
184536 ATACTCACAATGACACATAGTCATCAAACCTTATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
*
184588 ATACTCACGATGACACATAGTCATCGGACCTT-TAATCTGTAATAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAA-AGGATTCAT
*
184640 ATAACTCACGATGACACAGAGTCATCGGACCTT
1 AT-ACTCACGATGACACATAGTCATCGGACCTT
184673 TTTGCATTTA
Statistics
Matches: 264, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
51 11 0.04
52 216 0.82
53 37 0.14
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
Found at i:189335 original size:52 final size:52
Alignment explanation
Indices: 189269--189610 Score: 494
Period size: 52 Copynumber: 6.6 Consensus size: 52
189259 TTCCCATTTA
* * * *
189269 ATACTCACGATGACACAAAGTCATTGGACCTTA-AATCCGTAAAAGGATCCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAAGGATTCAT
* * *
189321 ATGCTCACGGTGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCGT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
189373 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
189425 ATATTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
189477 ATACTCACGATGACAC--AGTCATCAGACCTCATAATCTGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
189527 ATACTCACGATGACATATAGTCATCGGACCT-TTAATCCGTAATAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAA-AGGATTCAT
*
189579 ATAACTCACGATGACACAGAGTCATCGGACCT
1 AT-ACTCACGATGACACATAGTCATCGGACCT
189611 GATTTCACTA
Statistics
Matches: 261, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
50 45 0.17
51 9 0.03
52 173 0.66
53 34 0.13
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:191079 original size:18 final size:18
Alignment explanation
Indices: 191058--191098 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
191048 TTGGTAAAAA
* *
191058 AATTATCCAAATTAACTG
1 AATTACCCAAATTAACCG
*
191076 AATTACCCGAATTAACCG
1 AATTACCCAAATTAACCG
191094 AATTA
1 AATTA
191099 AAGTATTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (18 bp):
AATTACCCAAATTAACCG
Found at i:194540 original size:22 final size:22
Alignment explanation
Indices: 194512--194573 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
194502 TGAGATCTTT
*
194512 TAGTTTCAGTCTTTTAGACTTC
1 TAGTTTCAGCCTTTTAGACTTC
194534 TAGTTTCAGCCTTTTAGACTTC
1 TAGTTTCAGCCTTTTAGACTTC
194556 TAGTTTCAGCCTTTTAGA
1 TAGTTTCAGCCTTTTAGA
194574 TTTTTATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.47
Consensus pattern (22 bp):
TAGTTTCAGCCTTTTAGACTTC
Found at i:194936 original size:15 final size:16
Alignment explanation
Indices: 194916--194946 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
194906 CAAACATTAA
194916 AAAATA-ATTAAATTT
1 AAAATACATTAAATTT
194931 AAAATACATTAAATTT
1 AAAATACATTAAATTT
194947 TTTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATACATTAAATTT
Found at i:195109 original size:12 final size:12
Alignment explanation
Indices: 195078--195188 Score: 53
Period size: 12 Copynumber: 8.8 Consensus size: 12
195068 ACATCCAAAT
*
195078 AACAAAAATAAC
1 AACAAAAACAAC
** *
195090 AATTAAAACAGC
1 AACAAAAACAAC
*
195102 AACAAAAATAAC
1 AACAAAAACAAC
195114 AACAAACAACATTAAAAC
1 AACAAA-AAC-----AAC
* *
195132 AACAAAAATATC
1 AACAAAAACAAC
* *
195144 AATAAAAATAAC
1 AACAAAAACAAC
195156 AACAAAAACAAC
1 AACAAAAACAAC
** *
195168 -ATGAAAATAAC
1 AACAAAAACAAC
195179 AACAAAAACA
1 AACAAAAACA
195189 GTAAAAAAAA
Statistics
Matches: 71, Mismatches: 21, Indels: 14
0.67 0.20 0.13
Matches are distributed among these distances:
11 8 0.11
12 50 0.70
13 2 0.03
17 2 0.03
18 9 0.13
ACGTcount: A:0.70, C:0.17, G:0.02, T:0.11
Consensus pattern (12 bp):
AACAAAAACAAC
Found at i:195111 original size:33 final size:32
Alignment explanation
Indices: 195074--195188 Score: 108
Period size: 33 Copynumber: 3.5 Consensus size: 32
195064 AATAACATCC
*
195074 AAATAACAAAAATAACAATTAAAACAGCAACAA
1 AAATAACAAAAATAACAATTAAAACAACAA-AA
*
195107 AAATAACAACAAACAAC-ATTAAAACAACAAAA
1 AAATAACAA-AAATAACAATTAAAACAACAAAA
* * ** **
195139 ATATCAATAAAAATAACAACAAAAACAACATGA
1 AAAT-AACAAAAATAACAATTAAAACAACAAAA
195172 AAATAACAACAAA-AACA
1 AAATAACAA-AAATAACA
195189 GTAAAAAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
32 19 0.28
33 42 0.63
34 6 0.09
ACGTcount: A:0.70, C:0.17, G:0.02, T:0.11
Consensus pattern (32 bp):
AAATAACAAAAATAACAATTAAAACAACAAAA
Found at i:195174 original size:23 final size:22
Alignment explanation
Indices: 195078--195253 Score: 91
Period size: 24 Copynumber: 8.1 Consensus size: 22
195068 ACATCCAAAT
*
195078 AACA-AAAATAACAATTAAAACAGC
1 AACATAAAATAACAA-CAAAA-A-C
195102 AACA-AAAATAACAAC--AAAC
1 AACATAAAATAACAACAAAAAC
* *
195121 AACAT-TAA-AACAACAAAAAT
1 AACATAAAATAACAACAAAAAC
*
195141 ATCAATAAAAATAACAACAAAAAC
1 AAC-AT-AAAATAACAACAAAAAC
195165 AACATGAAAATAACAACAAAAAC
1 AACAT-AAAATAACAACAAAAAC
** * * *
195188 AGTAAAAAAAAAGC-ACCAAAAC
1 AACATAAAATAA-CAACAAAAAC
** *
195210 -AGTTAAAAAAAC-ACAAAAAC
1 AACATAAAATAACAACAAAAAC
* * *
195230 AACAAAAAACAACAACCAAAAC
1 AACATAAAATAACAACAAAAAC
195252 AA
1 AA
195254 TAAAAAAAAT
Statistics
Matches: 119, Mismatches: 23, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
18 6 0.05
19 7 0.06
20 14 0.12
21 19 0.16
22 22 0.18
23 24 0.20
24 27 0.23
ACGTcount: A:0.70, C:0.18, G:0.03, T:0.09
Consensus pattern (22 bp):
AACATAAAATAACAACAAAAAC
Found at i:195194 original size:44 final size:42
Alignment explanation
Indices: 195105--195195 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 42
195095 AAACAGCAAC
* *
195105 AAAAATAACAACAAACAACATTAAAACAACAAAAATATCAAT
1 AAAAATAACAACAAACAACATGAAAACAACAAAAATAACAAT
* *
195147 AAAAATAACAACAAAAACAACATGAAAATAACAACAAA-AACAGT
1 AAAAATAACAAC--AAACAACATGAAAACAACAA-AAATAACAAT
195191 AAAAA
1 AAAAA
195196 AAAAGCACCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 12 0.29
44 27 0.64
45 3 0.07
ACGTcount: A:0.71, C:0.15, G:0.02, T:0.11
Consensus pattern (42 bp):
AAAAATAACAACAAACAACATGAAAACAACAAAAATAACAAT
Found at i:195227 original size:10 final size:10
Alignment explanation
Indices: 195214--195260 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
195204 CAAAACAGTT
195214 AAAAA-AACA
1 AAAAACAACA
195223 CAAAAACAACA
1 -AAAAACAACA
195234 AAAAACAACA
1 AAAAACAACA
*
195244 ACCAAAACAATA
1 A--AAAACAACA
195256 AAAAA
1 AAAAA
195261 AATCACCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 20 0.61
11 4 0.12
12 9 0.27
ACGTcount: A:0.79, C:0.19, G:0.00, T:0.02
Consensus pattern (10 bp):
AAAAACAACA
Found at i:195237 original size:42 final size:42
Alignment explanation
Indices: 195143--195274 Score: 63
Period size: 43 Copynumber: 3.1 Consensus size: 42
195133 ACAAAAATAT
* * * *
195143 CAATAAAAATAACAACAAAAACAACATGAAAATAACAACAAAAA
1 CAATAAAAAAAAC-ACAAAAACAACA-AAAAAAAACAACCAAAA
* * *** *
195187 CAGTAAAAAAAAAGCACCAAAAC-AGTTAAAAAAAC-ACAAAAA
1 CAAT-AAAAAAAA-CACAAAAACAACAAAAAAAAACAACCAAAA
* * * *
195229 CAACAAAAAACAACAACCAAAACAATAAAAAAAATC-ACCAAAA
1 CAATAAAAAA-AAC-ACAAAAACAACAAAAAAAAACAACCAAAA
195272 CAA
1 CAA
195275 CAATATATAT
Statistics
Matches: 69, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
41 7 0.10
42 19 0.28
43 24 0.35
44 4 0.06
45 14 0.20
46 1 0.01
ACGTcount: A:0.71, C:0.19, G:0.03, T:0.07
Consensus pattern (42 bp):
CAATAAAAAAAACACAAAAACAACAAAAAAAAACAACCAAAA
Found at i:195259 original size:21 final size:21
Alignment explanation
Indices: 195081--195259 Score: 109
Period size: 21 Copynumber: 8.2 Consensus size: 21
195071 TCCAAATAAC
* *
195081 AAAAATAACAATTAAAACAGCAAC
1 AAAAATAACAA-CAAAA-A-CAAT
195105 AAAAATAACAACAAACAAC-AT
1 AAAAATAACAACAAA-AACAAT
* * *
195126 TAAAACAACAA-AAATATCAAT
1 AAAAATAACAACAAA-AACAAT
195147 AAAAATAACAACAAAAACAACAT
1 AAAAATAACAACAAAAAC-A-AT
* *
195170 GAAAATAACAACAAAAACAGT
1 AAAAATAACAACAAAAACAAT
*
195191 AAAAA-AA-AAGCACCAAAACAGTT
1 AAAAATAACAA-CA--AAAACA-AT
*
195214 AAAAA-AAC-ACAAAAACAACA
1 AAAAATAACAACAAAAACAA-T
* *
195234 AAAAACAACAACCAAAACAAT
1 AAAAATAACAACAAAAACAAT
195255 AAAAA
1 AAAAA
195260 AAATCACCAA
Statistics
Matches: 125, Mismatches: 17, Indels: 29
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.02
20 20 0.16
21 36 0.29
22 23 0.18
23 32 0.26
24 12 0.10
ACGTcount: A:0.71, C:0.17, G:0.03, T:0.09
Consensus pattern (21 bp):
AAAAATAACAACAAAAACAAT
Found at i:195259 original size:23 final size:21
Alignment explanation
Indices: 195183--195274 Score: 96
Period size: 22 Copynumber: 4.3 Consensus size: 21
195173 AATAACAACA
*
195183 AAAACAGTAAAAAAAAAGCACC
1 AAAACAATAAAAAAAAA-CACC
* * *
195205 AAAACAGT-TAAAAAAACACA
1 AAAACAATAAAAAAAAACACC
* *
195225 AAAACAACAAAAAACAACAACC
1 AAAACAATAAAAAAAAAC-ACC
*
195247 AAAACAATAAAAAAAATCACC
1 AAAACAATAAAAAAAAACACC
195268 AAAACAA
1 AAAACAA
195275 CAATATATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.16
21 24 0.41
22 25 0.43
ACGTcount: A:0.72, C:0.20, G:0.03, T:0.05
Consensus pattern (21 bp):
AAAACAATAAAAAAAAACACC
Found at i:195262 original size:43 final size:43
Alignment explanation
Indices: 195143--195274 Score: 65
Period size: 42 Copynumber: 3.1 Consensus size: 43
195133 ACAAAAATAT
* * * *
195143 CAAT-AAAAATAACAACAAAAACAACATGAAAATAACAACAAAAA
1 CAATAAAAAAAAAC-ACAAAAACAACA-AAAAAAAACAACCAAAA
* * *** *
195187 CAGTAAAAAAAAAGCACCAAAAC-AGTTAAAAAAAC-ACAAAAA
1 CAATAAAAAAAAA-CACAAAAACAACAAAAAAAAACAACCAAAA
* * * * *
195229 CAACAAAAAACAACAACCAAAACAATAAAAAAAATC-ACCAAAA
1 CAATAAAAAAAAAC-ACAAAAACAACAAAAAAAAACAACCAAAA
195272 CAA
1 CAA
195275 CAATATATAT
Statistics
Matches: 69, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
41 1 0.01
42 25 0.36
43 24 0.35
44 4 0.06
45 14 0.20
46 1 0.01
ACGTcount: A:0.71, C:0.19, G:0.03, T:0.07
Consensus pattern (43 bp):
CAATAAAAAAAAACACAAAAACAACAAAAAAAAACAACCAAAA
Found at i:195268 original size:21 final size:20
Alignment explanation
Indices: 195192--195274 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 20
195182 AAAAACAGTA
*
195192 AAAAAAAAGCACCAAAACAGT
1 AAAAAAAA-CACCAAAACAAT
* * *
195213 TAAAAAAACACAAAAACAAC
1 AAAAAAAACACCAAAACAAT
195233 AAAAAACAACAACCAAAACAAT
1 AAAAAA-AAC-ACCAAAACAAT
195255 AAAAAAAATCACCAAAACAA
1 AAAAAAAA-CACCAAAACAA
195275 CAATATATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 14 0.27
21 22 0.42
22 16 0.31
ACGTcount: A:0.72, C:0.20, G:0.02, T:0.05
Consensus pattern (20 bp):
AAAAAAAACACCAAAACAAT
Found at i:206989 original size:2 final size:2
Alignment explanation
Indices: 206982--207006 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
206972 CAGACTTATT
206982 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
207007 GTGTTTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:213334 original size:23 final size:23
Alignment explanation
Indices: 213308--213366 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
213298 CTCATTGCTG
*
213308 AATGCGTCGACAATTTGTGCTTT
1 AATGCGTCGACAATCTGTGCTTT
*
213331 AATGCGTGGACAATCTGTGCTTT
1 AATGCGTCGACAATCTGTGCTTT
213354 AATGCGTCGACAA
1 AATGCGTCGACAA
213367 AAAGATGACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (23 bp):
AATGCGTCGACAATCTGTGCTTT
Found at i:213437 original size:14 final size:15
Alignment explanation
Indices: 213405--213437 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
213395 ATAAAACAAC
213405 ATAACTAAAAGTGAA
1 ATAACTAAAAGTGAA
*
213420 ATAACTGAAAGT-AA
1 ATAACTAAAAGTGAA
213434 ATAA
1 ATAA
213438 AGAAATGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.21
Consensus pattern (15 bp):
ATAACTAAAAGTGAA
Found at i:215730 original size:41 final size:41
Alignment explanation
Indices: 215669--215752 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
215659 AAAAGTCCCA
215669 AAAGGGCATGTAAATATGGTTTTTGCTTGATCTTCCGACGC
1 AAAGGGCATGTAAATATGGTTTTTGCTTGATCTTCCGACGC
*
215710 AAAGGGCATGTAAATGTGGTTTTTGCTTGATCTTCCGACGC
1 AAAGGGCATGTAAATATGGTTTTTGCTTGATCTTCCGACGC
215751 AA
1 AA
215753 TAGCTATTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (41 bp):
AAAGGGCATGTAAATATGGTTTTTGCTTGATCTTCCGACGC
Found at i:223258 original size:20 final size:20
Alignment explanation
Indices: 223233--223278 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
223223 TTTTAAAGAG
*
223233 AAAATATGAGTTTTATAGGA
1 AAAATATCAGTTTTATAGGA
* *
223253 ATAATATCATTTTTATAGGA
1 AAAATATCAGTTTTATAGGA
223273 AAAATA
1 AAAATA
223279 AATCTGCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (20 bp):
AAAATATCAGTTTTATAGGA
Found at i:224612 original size:14 final size:15
Alignment explanation
Indices: 224593--224622 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
224583 TTTGTGTTTT
224593 ACTATTCAT-TTATC
1 ACTATTCATCTTATC
224607 ACTATTCATCTTATC
1 ACTATTCATCTTATC
224622 A
1 A
224623 TTATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (15 bp):
ACTATTCATCTTATC
Found at i:229118 original size:24 final size:24
Alignment explanation
Indices: 229086--229349 Score: 375
Period size: 24 Copynumber: 11.0 Consensus size: 24
229076 GTTCATTACA
*
229086 TTTACGCTCGTCAGCATGAATACG
1 TTTACGCTCGCCAGCATGAATACG
*
229110 TTTACGCTCACCAGCATGAATACG
1 TTTACGCTCGCCAGCATGAATACG
229134 TTTACGCTCGCCAGCATGAATACG
1 TTTACGCTCGCCAGCATGAATACG
229158 TTTACGCTCGCCAGCATGAATACG
1 TTTACGCTCGCCAGCATGAATACG
* *
229182 TTTACGCTCGTCAGCATGAATACA
1 TTTACGCTCGCCAGCATGAATACG
* *
229206 TTTATGCTTGCCAGCATGAATACG
1 TTTACGCTCGCCAGCATGAATACG
* *
229230 TTTACGCTCGCTAGCATGAATACA
1 TTTACGCTCGCCAGCATGAATACG
* * *
229254 TTTATGCTTGCCAACATGAATACG
1 TTTACGCTCGCCAGCATGAATACG
* *
229278 TTTAAGCTCGTCAGCATGAATACG
1 TTTACGCTCGCCAGCATGAATACG
**
229302 TTTACGCTCATCAGCATGAATACG
1 TTTACGCTCGCCAGCATGAATACG
* *
229326 TTTACACTCGTCAGCATGAATACG
1 TTTACGCTCGCCAGCATGAATACG
229350 AGAAACATTG
Statistics
Matches: 214, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 214 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (24 bp):
TTTACGCTCGCCAGCATGAATACG
Found at i:229920 original size:9 final size:9
Alignment explanation
Indices: 229906--229964 Score: 50
Period size: 9 Copynumber: 6.2 Consensus size: 9
229896 GCAAATGATT
229906 TTAAAATTA
1 TTAAAATTA
229915 TTAAAATTA
1 TTAAAATTA
229924 TTTTAAAATTA
1 --TTAAAATTA
*
229935 TTTTTTAAA-TA
1 ---TTAAAATTA
229946 -TAAAATTA
1 TTAAAATTA
229954 TTAAAATTA
1 TTAAAATTA
229963 TT
1 TT
229965 TTATTATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
7 4 0.09
8 2 0.05
9 19 0.44
11 11 0.26
12 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTAAAATTA
Found at i:229944 original size:12 final size:11
Alignment explanation
Indices: 229898--229938 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
229888 TCTTATCAGC
*
229898 AAATGATTTTA
1 AAATTATTTTA
229909 AAATTA--TTA
1 AAATTATTTTA
229918 AAATTATTTTA
1 AAATTATTTTA
229929 AAATTATTTT
1 AAATTATTTT
229939 TTAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 9 0.33
11 18 0.67
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:230820 original size:9 final size:9
Alignment explanation
Indices: 230792--230825 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
230782 ATTAAAATTA
230792 TTTAATAAT
1 TTTAATAAT
230801 TTTAAATTAAT
1 TTT-AA-TAAT
230812 TTTAATAAT
1 TTTAATAAT
230821 TTTAA
1 TTTAA
230826 AACCATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 12 0.52
10 4 0.17
11 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTAATAAT
Found at i:230833 original size:20 final size:20
Alignment explanation
Indices: 230792--230833 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
230782 ATTAAAATTA
**
230792 TTTAATAATTTTAAATTAAT
1 TTTAATAATTTTAAAACAAT
*
230812 TTTAATAATTTTAAAACCAT
1 TTTAATAATTTTAAAACAAT
230832 TT
1 TT
230834 GCTGATGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAATAATTTTAAAACAAT
Found at i:236451 original size:24 final size:24
Alignment explanation
Indices: 236413--236458 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
236403 GAAAATTCAG
**
236413 TATTTATTAGTATAATATATTTTA
1 TATTTATTAACATAATATATTTTA
*
236437 TATTTATTAACATAATTTATTT
1 TATTTATTAACATAATATATTT
236459 GACATACGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
TATTTATTAACATAATATATTTTA
Found at i:237399 original size:24 final size:24
Alignment explanation
Indices: 237370--237454 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
237360 GACTAATAAA
* *
237370 AGTTTAACTCAAACAAATAAATAG
1 AGTTTAACTGAAACAAATAAACAG
* *
237394 AGTTTAATTGAAACACATAAACAG
1 AGTTTAACTGAAACAAATAAACAG
* *
237418 AGTTTAATTGAAACAATTAAACAG
1 AGTTTAACTGAAACAAATAAACAG
*
237442 AATTTAACTGAAA
1 AGTTTAACTGAAA
237455 GATTATTTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAG
Found at i:239403 original size:24 final size:24
Alignment explanation
Indices: 239371--239443 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
239361 CGACTCAAAC
239371 AAATAAACAGAGTTTAATCGAAAT
1 AAATAAACAGAGTTTAATCGAAAT
** *
239395 AAATAAACAGAGTTTAATTAAAAC
1 AAATAAACAGAGTTTAATCGAAAT
* *
239419 AATTAAATAGAGTTTAA-CTGAAAT
1 AAATAAACAGAGTTTAATC-GAAAT
239443 A
1 A
239444 TTATTTCTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (24 bp):
AAATAAACAGAGTTTAATCGAAAT
Found at i:241582 original size:3 final size:3
Alignment explanation
Indices: 241576--241609 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
241566 CTTCTTTTTC
241576 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
241610 GAAAAGTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:246785 original size:18 final size:17
Alignment explanation
Indices: 246737--246786 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
246727 CAAATGATAT
*
246737 TTTTATTAATAATAGTA
1 TTTTATTAATAATAATA
* *
246754 TTATAATAAGTAATAATA
1 TTTTATTAA-TAATAATA
246772 TTTTATTAATTAATA
1 TTTTATTAA-TAATA
246787 TTATAAAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTTTATTAATAATAATA
Found at i:247061 original size:16 final size:16
Alignment explanation
Indices: 247040--247070 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
247030 TTATGACTAA
247040 TTATATTAATTTTATT
1 TTATATTAATTTTATT
*
247056 TTATATTATTTTTAT
1 TTATATTAATTTTAT
247071 GAGTTTTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATATTAATTTTATT
Found at i:249720 original size:16 final size:16
Alignment explanation
Indices: 249685--249718 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
249675 TTGAATATAA
*
249685 GGTACCCGAAATTTCG
1 GGTACCCGAAATATCG
249701 GGTACCCGAAATAATCG
1 GGTACCCGAAAT-ATCG
249718 G
1 G
249719 TATCCGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (16 bp):
GGTACCCGAAATATCG
Found at i:250567 original size:16 final size:16
Alignment explanation
Indices: 250546--250581 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
250536 TCTATTTTTC
*
250546 TTATTTATTTATTATT
1 TTATTTATTTATTATA
250562 TTATTTATTTATTATA
1 TTATTTATTTATTATA
250578 TTAT
1 TTAT
250582 GAATATGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTTATTTATTATA
Found at i:250634 original size:3 final size:3
Alignment explanation
Indices: 250628--250667 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
250618 ACAAAATCCA
250628 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
250668 TCAAAAGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:250773 original size:25 final size:26
Alignment explanation
Indices: 250722--250779 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
250712 TTTACAAAAT
*
250722 CACAAGCCCAATACTCAAAATACACC
1 CACAAGCCCAATACTCAAAATAAACC
*
250748 CACAAGCCCAATAC-CCAAATAAACC
1 CACAAGCCCAATACTCAAAATAAACC
*
250773 CATAAGC
1 CACAAGC
250780 ACAAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.47, C:0.38, G:0.05, T:0.10
Consensus pattern (26 bp):
CACAAGCCCAATACTCAAAATAAACC
Found at i:252004 original size:9 final size:9
Alignment explanation
Indices: 251990--252014 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
251980 GATCCCCCTT
251990 ATTATTTTA
1 ATTATTTTA
251999 ATTATTTTA
1 ATTATTTTA
252008 ATTATTT
1 ATTATTT
252015 ATTTGTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTATTTTA
Found at i:255683 original size:2 final size:2
Alignment explanation
Indices: 255676--255703 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
255666 TTTTAACTTA
255676 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
255704 TAATGACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.