Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold211
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: 2157208
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 20444 characters in sequence are not A, C, G, or T
File 13 of 15
Found at i:1802844 original size:11 final size:11
Alignment explanation
Indices: 1802793--1802845 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
1802783 AAATTTATGA
*
1802793 ATATAAAATAT
1 ATATAATATAT
*
1802804 -TTTAATATA-
1 ATATAATATAT
1802813 ATTATAATATA-
1 A-TATAATATAT
1802824 ATAT-ATATAT
1 ATATAATATAT
1802834 ATATAATATAT
1 ATATAATATAT
1802845 A
1 A
1802846 AATGATCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
9 5 0.14
10 14 0.40
11 16 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATAATATAT
Found at i:1802999 original size:25 final size:25
Alignment explanation
Indices: 1802962--1803025 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
1802952 CGTGTAAGAG
* * *
1802962 AAATAGAGTTTTTCTTTTTAAATAA
1 AAATATAGATTTTATTTTTAAATAA
*
1802987 AAATATAGATTTTATTTTTATATAA
1 AAATATAGATTTTATTTTTAAATAA
1803012 AAATAATA-ATTTTA
1 AAAT-ATAGATTTTA
1803026 AAAAATTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 31 0.91
26 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
AAATATAGATTTTATTTTTAAATAA
Found at i:1803324 original size:52 final size:50
Alignment explanation
Indices: 1803179--1803328 Score: 164
Period size: 52 Copynumber: 2.9 Consensus size: 50
1803169 CTGTTTTAAA
* * ***
1803179 AAATTACTATTTAAAAATTAATAAAATTAAAAAAATATTTT-TATTAAATTTT
1 AAATTACTTTTTAAAAAAT-ATAAAA-T-AAAAAATATTTTATATTAAATCAC
1803231 AAATTA-TTATTTAAAATAATA-AAAAT-AAAAATATTTTATATTAAATCAC
1 AAATTACTT-TTTAAAA-AATATAAAATAAAAAATATTTTATATTAAATCAC
1803280 AAATTACTTTTTAAAAAATATTTAAAATAAAAAATATTTTATATTAAAT
1 AAATTACTTTTTAAAAAATA--TAAAATAAAAAATATTTTATATTAAAT
1803329 TATAAAAAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
48 15 0.18
49 21 0.25
50 3 0.04
51 10 0.12
52 34 0.40
53 2 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (50 bp):
AAATTACTTTTTAAAAAATATAAAATAAAAAATATTTTATATTAAATCAC
Found at i:1803781 original size:73 final size:73
Alignment explanation
Indices: 1803704--1803840 Score: 163
Period size: 73 Copynumber: 1.9 Consensus size: 73
1803694 TATATATATT
* *
1803704 ATATTATTATATTTTTAAAAATTATATATTTATA-TA-TTTTATTATA-ATAATAATTTATATTA
1 ATATTATTATATATTT-AAAATTA-A-ATTTATATTATTTTTATAATATATAATAATTTATATTA
1803766 TAACAAATTTA
63 TAACAAATTTA
* * ** *
1803777 ATATTTTTTTATATTTATTATTAAATTTATATTATTTTTATAATATATAATATTTTATATTATA
1 ATATTATTATATATTTAAAATTAAATTTATATTATTTTTATAATATATAATAATTTATATTATA
1803841 TTTTAATTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
70 7 0.13
71 3 0.06
72 14 0.26
73 30 0.56
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.58
Consensus pattern (73 bp):
ATATTATTATATATTTAAAATTAAATTTATATTATTTTTATAATATATAATAATTTATATTATAA
CAAATTTA
Found at i:1803825 original size:18 final size:18
Alignment explanation
Indices: 1803786--1803841 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 18
1803776 AATATTTTTT
*
1803786 TATAT-TTATTATTA-AA
1 TATATATTATTTTTATAA
*
1803802 TTTATATTATTTTTATAA
1 TATATATTATTTTTATAA
* *
1803820 TATATAATA-TTTTATAT
1 TATATATTATTTTTATAA
1803837 TATAT
1 TATAT
1803842 TTTAATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 4 0.12
17 20 0.61
18 9 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATATTATTTTTATAA
Found at i:1803855 original size:11 final size:12
Alignment explanation
Indices: 1803777--1803854 Score: 51
Period size: 12 Copynumber: 6.6 Consensus size: 12
1803767 AACAAATTTA
1803777 ATATTTT-T-TT
1 ATATTTTATATT
1803787 ATA-TTTATTATT
1 ATATTTTA-TATT
*
1803799 A-AATTTATATT
1 ATATTTTATATT
*
1803810 ATTTTTATAATATAT
1 ATATTT-T-ATAT-T
1803825 AATATTTTATATT
1 -ATATTTTATATT
1803838 ATATTTTA-ATT
1 ATATTTTATATT
1803849 AT-TTTT
1 ATATTTT
1803855 TTTTAATGAT
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
9 3 0.05
10 7 0.12
11 12 0.21
12 17 0.30
13 2 0.04
14 8 0.14
15 2 0.04
16 5 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:1809647 original size:14 final size:13
Alignment explanation
Indices: 1809628--1809732 Score: 63
Period size: 14 Copynumber: 7.7 Consensus size: 13
1809618 ACGTAATATA
1809628 ATTATATTTATTAT
1 ATTATATTT-TTAT
1809642 ATTATATTTTT-T
1 ATTATATTTTTAT
* *
1809654 AAATAAATTTTAATAT
1 -ATTATATTTT--TAT
1809670 ATTAATAATTTTT-T
1 ATT-AT-ATTTTTAT
* * *
1809684 ATAAAAATTTTA-
1 ATTATATTTTTAT
*
1809696 ATATATATATTTAT
1 AT-TATATTTTTAT
1809710 ATTATAATTTTTAT
1 ATTAT-ATTTTTAT
1809724 ATTATATTT
1 ATTATATTT
1809733 ATATTGTATA
Statistics
Matches: 69, Mismatches: 12, Indels: 21
0.68 0.12 0.21
Matches are distributed among these distances:
12 8 0.12
13 24 0.35
14 26 0.38
15 4 0.06
16 2 0.03
17 5 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTATATTTTTAT
Found at i:1809683 original size:30 final size:28
Alignment explanation
Indices: 1809634--1809732 Score: 100
Period size: 30 Copynumber: 3.6 Consensus size: 28
1809624 TATAATTATA
*
1809634 TTTATTATATTATATTTTTTA-AATAAAT
1 TTTAATATATTATATTTTTTATAA-AAAT
1809662 TTTAATATATTAATAATTTTTTATAAAAAT
1 TTTAATATATT-AT-ATTTTTTATAAAAAT
* * *
1809692 TTTAATATA-TATA-TTTATATTATAAT
1 TTTAATATATTATATTTTTTATAAAAAT
1809718 TTT--TATATTATATTT
1 TTTAATATATTATATTT
1809733 ATATTGTATA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
24 4 0.06
25 4 0.06
26 15 0.24
27 1 0.02
28 12 0.19
29 3 0.05
30 21 0.34
31 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTAATATATTATATTTTTTATAAAAAT
Found at i:1809702 original size:16 final size:16
Alignment explanation
Indices: 1809658--1809702 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 16
1809648 TTTTTTAAAT
1809658 AAATTTTAATATATTAA
1 AAATTTTAATATA-TAA
*
1809675 TAATTTT--T-TATAA
1 AAATTTTAATATATAA
1809688 AAATTTTAATATATA
1 AAATTTTAATATATA
1809703 TATTTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 2 0.09
16 4 0.17
17 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATTTTAATATATAA
Found at i:1809744 original size:27 final size:26
Alignment explanation
Indices: 1809689--1809737 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
1809679 TTTTTATAAA
1809689 AATTTTAATATATATATTTATATTAT
1 AATTTTAATATATATATTTATATTAT
*
1809715 AATTTTTATAT-TATATTTATATT
1 AATTTTAATATATATATTTATATT
1809738 GTATAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
AATTTTAATATATATATTTATATTAT
Found at i:1813301 original size:18 final size:18
Alignment explanation
Indices: 1813247--1813301 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
1813237 TATAATTTAT
* * *
1813247 ATTAAATAATATAATAAT
1 ATTAAATTATATATTAAA
1813265 ATT-AATT-TAT-TTAAA
1 ATTAAATTATATATTAAA
*
1813280 ATTAAATTATATATTAAG
1 ATTAAATTATATATTAAA
1813298 ATTA
1 ATTA
1813302 CTATATGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 6 0.20
16 7 0.23
17 6 0.20
18 11 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAATTATATATTAAA
Found at i:1813646 original size:16 final size:15
Alignment explanation
Indices: 1813621--1813693 Score: 65
Period size: 16 Copynumber: 4.6 Consensus size: 15
1813611 ATCGATTTAT
*
1813621 TTTAGATTATTTTTAA
1 TTTA-ATTATTTTAAA
*
1813637 TTTAAGTTATTTAAAA
1 TTTAA-TTATTTTAAA
*
1813653 TTTAATTATTTTGAA
1 TTTAATTATTTTAAA
* *
1813668 TTTAAATCATTTTATA
1 TTT-AATTATTTTAAA
1813684 TTTGAATTAT
1 TTT-AATTAT
1813694 ATTGTAATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.26
16 34 0.74
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (15 bp):
TTTAATTATTTTAAA
Found at i:1813664 original size:31 final size:31
Alignment explanation
Indices: 1813621--1813706 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
1813611 ATCGATTTAT
* *
1813621 TTTAGATTATTTTTAATTTAAGTTATTTAAAA
1 TTTA-ATTATTTTTAATTTAAATCATTTAAAA
* * *
1813653 TTTAATTATTTTGAATTTAAATCATTTTATA
1 TTTAATTATTTTTAATTTAAATCATTTAAAA
*
1813684 TTTGAATTATATTGTAATTTAAA
1 TTT-AATTAT-TTTTAATTTAAA
1813707 CGAGATGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 25 0.56
32 10 0.22
33 10 0.22
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (31 bp):
TTTAATTATTTTTAATTTAAATCATTTAAAA
Found at i:1819644 original size:2 final size:2
Alignment explanation
Indices: 1819637--1819663 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1819627 CTTCTCAACT
1819637 TA 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 TA T
1819664 TCATTTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1821703 original size:22 final size:22
Alignment explanation
Indices: 1821678--1821719 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1821668 TTTATAATAA
1821678 TTCTATCATTTACAATATGTAT
1 TTCTATCATTTACAATATGTAT
*
1821700 TTCTATCATTTACATTATGT
1 TTCTATCATTTACAATATGT
1821720 TACTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (22 bp):
TTCTATCATTTACAATATGTAT
Found at i:1824560 original size:142 final size:143
Alignment explanation
Indices: 1824303--1824582 Score: 454
Period size: 142 Copynumber: 2.0 Consensus size: 143
1824293 TTTAAGATTA
* * * * *
1824303 TCAAATAACTATGATATTTGTGTGAGTACATTGTATGTAGTTGGGATATTTGAAGGTACATAATC
1 TCAAATAACCATGATATTTGTGTGAGTACATTGCATGCAGTTGGGATATTTGAAAGTACACAATC
* * * *
1824368 ATCATGAATATCCTTTAGGTCAACATATAACAATTATATTGACATTCAAAAATTGTTGATGAGTA
66 ATCAAGAATATCCTCTAGGTCAACATATAACAATTATATTGACATTCAAAAATTGCTGATGAGCA
1824433 TGAAACATATATT
131 TGAAACATATATT
* *
1824446 TCAAATGACCATGATATTTGTGTGAGTACGTTGCATGCAGTTGGGAT-TTTGAAAGTACACAATC
1 TCAAATAACCATGATATTTGTGTGAGTACATTGCATGCAGTTGGGATATTTGAAAGTACACAATC
1824510 ATCAAGAATATCCTCTAGGTCAACATATAACAATTATATTGACATTCAAAAATTGCTGATGAGCA
66 ATCAAGAATATCCTCTAGGTCAACATATAACAATTATATTGACATTCAAAAATTGCTGATGAGCA
1824575 TGAAACAT
131 TGAAACAT
1824583 GCATTTTATA
Statistics
Matches: 126, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
142 84 0.67
143 42 0.33
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (143 bp):
TCAAATAACCATGATATTTGTGTGAGTACATTGCATGCAGTTGGGATATTTGAAAGTACACAATC
ATCAAGAATATCCTCTAGGTCAACATATAACAATTATATTGACATTCAAAAATTGCTGATGAGCA
TGAAACATATATT
Found at i:1825312 original size:92 final size:91
Alignment explanation
Indices: 1825216--1825484 Score: 215
Period size: 93 Copynumber: 2.9 Consensus size: 91
1825206 ACAGTGTAAA
* * *
1825216 ATTTATAATCAAATAATTTTTTTCCTTTTTTATAAAAAAGAATCTC-TTTTAAAAAAATAATTC-
1 ATTTATAATCAAATAATTTTTTTCCTTTTCTACAAAAAAGAAT-TCATTCT-AAAAAATAA-TCA
* * *
1825279 ATGCATTAATCTAATCTTTACAGTTTGAT
63 ATACATTAATCTAATCTTTACAATTTGAC
* * *
1825308 ATTTACAATC-AATCAAATTTTTTTTCTTTTCTACCAAAAAGAATTCGATTCTAAAAAATAATCA
1 ATTTATAATCAAAT--AATTTTTTTCCTTTTCTACAAAAAAGAATTC-ATTCTAAAAAATAATCA
* * *
1825372 ATATATTAATTTAATCTTTATAATTTGAC
63 ATACATTAATCTAATCTTTACAATTTGAC
* * * * * * *
1825401 ATTTATAATTAATTAACTTTTTTTTCC-CTTCTACTAAAAAA-ATTTTAATTCTTAAAATTAATC
1 ATTTATAATCAAATAA--TTTTTTTCCTTTTCTAC-AAAAAAGA-ATTCATTCTAAAAAATAATC
* * *
1825464 CATATATTAATTTAATCTTTA
62 AATACATTAATCTAATCTTTA
1825485 TAACTTAATA
Statistics
Matches: 144, Mismatches: 23, Indels: 19
0.77 0.12 0.10
Matches are distributed among these distances:
91 3 0.02
92 15 0.10
93 106 0.74
94 20 0.14
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (91 bp):
ATTTATAATCAAATAATTTTTTTCCTTTTCTACAAAAAAGAATTCATTCTAAAAAATAATCAATA
CATTAATCTAATCTTTACAATTTGAC
Found at i:1825365 original size:93 final size:93
Alignment explanation
Indices: 1825267--1825503 Score: 262
Period size: 93 Copynumber: 2.5 Consensus size: 93
1825257 ATCTCTTTTA
** * * *
1825267 AAAAAATAATTCATGCATTAATCTAATCTTTACAGTTTGATATTTACAATCAATCAAATTTTTTT
1 AAAAAATAATTCATATATTAATTTAATCTTTATAATTTGATATTTACAATCAATCAAATTTTTTT
** *
1825332 TCTTTTCTACCAAAAAGAA-TTCGATTCT
66 TCCCTTCTACCAAAAA-AATTTCAATTCT
* * * * *
1825360 AAAAAATAA-TCAATATATTAATTTAATCTTTATAATTTGACATTTATAATTAATTAACTTTTTT
1 AAAAAATAATTC-ATATATTAATTTAATCTTTATAATTTGATATTTACAATCAATCAAATTTTTT
* *
1825424 TTCCCTTCTACTAAAAAAATTTTAATTCT
65 TTCCCTTCTACCAAAAAAATTTCAATTCT
* * * * *
1825453 TAAAATTAATCCATATATTAATTTAATCTTTATAACTTAATATTTACAATC
1 AAAAAATAATTCATATATTAATTTAATCTTTATAATTTGATATTTACAATC
1825504 CATATATTAA
Statistics
Matches: 118, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
92 4 0.03
93 113 0.96
94 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.45
Consensus pattern (93 bp):
AAAAAATAATTCATATATTAATTTAATCTTTATAATTTGATATTTACAATCAATCAAATTTTTTT
TCCCTTCTACCAAAAAAATTTCAATTCT
Found at i:1826010 original size:22 final size:22
Alignment explanation
Indices: 1825945--1826004 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
1825935 ATCATAAAAT
1825945 TAAAAAATTATTTTT--T-TAAA
1 TAAAAAA-TATTTTTAATATAAA
1825965 TAAAAAATATTTTTAATATAAA
1 TAAAAAATATTTTTAATATAAA
1825987 TAAAAATATATATTTTAA
1 TAAAAA-ATAT-TTTTAA
1826005 AAAATATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.20
20 7 0.20
21 1 0.03
22 10 0.29
23 4 0.11
24 6 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAAAATATTTTTAATATAAA
Found at i:1828922 original size:20 final size:20
Alignment explanation
Indices: 1828894--1828931 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1828884 ATATCGAACG
1828894 AAATATAAA-ATTATTTTAAA
1 AAATATAAATA-TATTTTAAA
*
1828914 AAATTTAAATATATTTTA
1 AAATATAAATATATTTTA
1828932 TTTTACTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATATAAATATATTTTAAA
Found at i:1831543 original size:16 final size:16
Alignment explanation
Indices: 1831522--1831577 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
1831512 AGATTTAAAA
1831522 TTAAATTTATTCGAGT
1 TTAAATTTATTCGAGT
1831538 TTAAATTTATTCTGA-T
1 TTAAATTTATTC-GAGT
* * **
1831554 TTGAATTTTTTTAAGT
1 TTAAATTTATTCGAGT
1831570 TTAAATTT
1 TTAAATTT
1831578 TTTTAGATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.91
17 2 0.06
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (16 bp):
TTAAATTTATTCGAGT
Found at i:1831578 original size:16 final size:16
Alignment explanation
Indices: 1831535--1831598 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 16
1831525 AATTTATTCG
* *
1831535 AGTTTAAATTTATTCTG
1 AGTTTAAATTT-TTTTA
*
1831552 A-TTTGAATTTTTTTA
1 AGTTTAAATTTTTTTA
1831567 AGTTTAAATTTTTTT-
1 AGTTTAAATTTTTTTA
1831582 AGATTTAAATTTTTTTA
1 AG-TTTAAATTTTTTTA
1831599 TATTCGGATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 6 0.15
16 33 0.82
17 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.61
Consensus pattern (16 bp):
AGTTTAAATTTTTTTA
Found at i:1831587 original size:32 final size:32
Alignment explanation
Indices: 1831535--1831598 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1831525 AATTTATTCG
*
1831535 AGTTTAAATTTATTCTGATTTGAATTTTTTTA
1 AGTTTAAATTTATTCTGATTTAAATTTTTTTA
*
1831567 AGTTTAAATTT-TTTTAGATTTAAATTTTTTTA
1 AGTTTAAATTTATTCT-GATTTAAATTTTTTTA
1831599 TATTCGGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.61
Consensus pattern (32 bp):
AGTTTAAATTTATTCTGATTTAAATTTTTTTA
Found at i:1831781 original size:24 final size:22
Alignment explanation
Indices: 1831754--1831806 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
1831744 TTTATTATAC
1831754 TATTATATTT-TTAATATATTTAAT
1 TATTATATTTATTAA-A-ATTT-AT
1831778 TATT-TATTTATTAAAATTTAT
1 TATTATATTTATTAAAATTTAT
*
1831799 TTTTATAT
1 TATTATAT
1831807 ATAAAACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.19
22 7 0.27
23 6 0.23
24 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTATATTTATTAAAATTTAT
Found at i:1833255 original size:24 final size:26
Alignment explanation
Indices: 1833219--1833275 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 26
1833209 CTTGATAATA
* * *
1833219 TATACTAAGTTTAAATT-T-TTTTAT
1 TATATTAACTTTAAATTCTATTTTAC
*
1833243 TATATTAACTTTATATTCTATTTTAC
1 TATATTAACTTTAAATTCTATTTTAC
1833269 TATATTA
1 TATATTA
1833276 CTGTTTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 14 0.52
25 1 0.04
26 12 0.44
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (26 bp):
TATATTAACTTTAAATTCTATTTTAC
Found at i:1833752 original size:16 final size:16
Alignment explanation
Indices: 1833733--1833765 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1833723 TGAATCAATC
1833733 TCAAATTCTCTCAAAT
1 TCAAATTCTCTCAAAT
*
1833749 TCAAATTCTTTCAAAT
1 TCAAATTCTCTCAAAT
1833765 T
1 T
1833766 TGAGTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.42
Consensus pattern (16 bp):
TCAAATTCTCTCAAAT
Found at i:1834023 original size:87 final size:87
Alignment explanation
Indices: 1833877--1834052 Score: 325
Period size: 87 Copynumber: 2.0 Consensus size: 87
1833867 ATTTTCGAAT
* * *
1833877 TCAAATTCATTTTACCACCTTTAATAAGAACCCAACACCCACCTCTGATTTGCTACTTGTTCACT
1 TCAAATTCATTTTACCACCTCTAATAAAAACCCAACACCCACCTCCGATTTGCTACTTGTTCACT
1833942 ACCTAGTGTGTTTGGGAGGTCC
66 ACCTAGTGTGTTTGGGAGGTCC
1833964 TCAAATTCATTTTACCACCTCTAATAAAAACCCAACACCCACCTCCGATTTGCTACTTGTTCACT
1 TCAAATTCATTTTACCACCTCTAATAAAAACCCAACACCCACCTCCGATTTGCTACTTGTTCACT
1834029 ACCTAGTGTGTTTGGGAGGTCC
66 ACCTAGTGTGTTTGGGAGGTCC
1834051 TC
1 TC
1834053 GCTGTTGCAG
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (87 bp):
TCAAATTCATTTTACCACCTCTAATAAAAACCCAACACCCACCTCCGATTTGCTACTTGTTCACT
ACCTAGTGTGTTTGGGAGGTCC
Found at i:1837088 original size:22 final size:22
Alignment explanation
Indices: 1837038--1837088 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1837028 TTATTAATTT
1837038 TTTATTTAAATTTAATTTAAAA
1 TTTATTTAAATTTAATTTAAAA
** *
1837060 TAAATTTAGA-TTAATTTAAAAA
1 TTTATTTAAATTTAATTT-AAAA
1837082 TTTATTT
1 TTTATTT
1837089 TATTATTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTATTTAAATTTAATTTAAAA
Found at i:1837125 original size:17 final size:18
Alignment explanation
Indices: 1837103--1837148 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
1837093 ATTTATGATA
1837103 ATATTAAAATAT-TTTTT
1 ATATTAAAATATATTTTT
1837120 ATATTAATAAATATATTTTT
1 ATATT-A-AAATATATTTTT
1837140 ATAATTAAA
1 AT-ATTAAA
1837149 TTTAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.20
18 1 0.04
19 8 0.32
20 8 0.32
21 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTAAAATATATTTTT
Found at i:1837137 original size:21 final size:20
Alignment explanation
Indices: 1837107--1837147 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1837097 ATGATAATAT
1837107 TAAAATATTTTT-TATATTAA
1 TAAAATATTTTTATA-ATTAA
1837127 TAAATATATTTTTATAATTAA
1 TAAA-ATATTTTTATAATTAA
1837148 ATTTAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 13 0.68
22 2 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAAATATTTTTATAATTAA
Found at i:1837140 original size:20 final size:20
Alignment explanation
Indices: 1837109--1837147 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1837099 GATAATATTA
1837109 AAATATTTTTTAT-ATTAAT
1 AAATATTTTTTATAATTAAT
1837128 AAATATATTTTTATAATTAA
1 AAATAT-TTTTTATAATTAA
1837148 ATTTAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATATTTTTTATAATTAAT
Found at i:1837653 original size:3 final size:3
Alignment explanation
Indices: 1837645--1837674 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1837635 TTTCCACTAC
1837645 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1837675 GTCGACCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:1838767 original size:14 final size:13
Alignment explanation
Indices: 1838725--1838768 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
1838715 AGTTTGACTC
1838725 ATTTTTTTA-ATT
1 ATTTTTTTATATT
*
1838737 ATATTTTGTATATT
1 AT-TTTTTTATATT
1838751 ATTTTTTATATATT
1 ATTTTTT-TATATT
1838765 ATTT
1 ATTT
1838769 AACTTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 2 0.07
13 10 0.37
14 15 0.56
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
ATTTTTTTATATT
Found at i:1840880 original size:24 final size:24
Alignment explanation
Indices: 1840845--1840892 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1840835 AAAGTGGACA
1840845 TGAGATTGTAAAAGTTTAATGCAT
1 TGAGATTGTAAAAGTTTAATGCAT
*
1840869 TGAGATTTTAAAAGTTTAATGCAT
1 TGAGATTGTAAAAGTTTAATGCAT
1840893 GATTAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.40
Consensus pattern (24 bp):
TGAGATTGTAAAAGTTTAATGCAT
Found at i:1846900 original size:3 final size:3
Alignment explanation
Indices: 1846892--1846923 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1846882 CTTGGAGGAA
1846892 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1846924 TTGGCTTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1847406 original size:14 final size:14
Alignment explanation
Indices: 1847387--1847429 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1847377 TAAACTTTTT
1847387 TATTAAATTAATAA
1 TATTAAATTAATAA
1847401 TATTAAATATAAT-A
1 TATTAAAT-TAATAA
*
1847415 TATCTAAAATAATAA
1 TAT-TAAATTAATAA
1847430 AAAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
TATTAAATTAATAA
Found at i:1847503 original size:26 final size:26
Alignment explanation
Indices: 1847396--1847503 Score: 80
Period size: 24 Copynumber: 4.0 Consensus size: 26
1847386 TTATTAAATT
*
1847396 AATAATATTAAATATAATATA-TCTAA
1 AATAATA-TAAATATAATATATTTTAA
*
1847422 AATAATA-AAAAATAA-ATATTTTAA
1 AATAATATAAATATAATATATTTTAA
*
1847446 AAT-ATATATAATATAAATTATTGATAAATTAA
1 AATAATATA-AATAT-AA-TA-T-AT--TTTAA
*
1847478 ATTAATATAAATATAATATATTTTAA
1 AATAATATAAATATAATATATTTTAA
1847504 TACTCATAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
23 6 0.09
24 15 0.23
25 4 0.06
26 13 0.20
28 3 0.05
29 2 0.03
30 4 0.06
31 2 0.03
32 11 0.17
33 5 0.08
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (26 bp):
AATAATATAAATATAATATATTTTAA
Found at i:1848116 original size:17 final size:16
Alignment explanation
Indices: 1848094--1848131 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
1848084 TATGATTATC
1848094 AAAATTATTAAATCTA
1 AAAATTATTAAATCTA
1848110 GAAAATTATTAAATCTA
1 -AAAATTATTAAATCTA
1848127 AAAAT
1 AAAAT
1848132 AAACATGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (16 bp):
AAAATTATTAAATCTA
Found at i:1848975 original size:13 final size:13
Alignment explanation
Indices: 1848950--1848983 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1848940 TTGAGTTCAG
*
1848950 ATTAATTTAATTA
1 ATTAATATAATTA
*
1848963 ATTTATATAATTA
1 ATTAATATAATTA
1848976 ATTAATAT
1 ATTAATAT
1848984 TTAATAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTAATATAATTA
Found at i:1851983 original size:28 final size:28
Alignment explanation
Indices: 1851952--1852048 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 28
1851942 AATAATCTAA
* *
1851952 AAATACATGAAATTGCATAATAGTCCTT
1 AAATGCATGAAATAGCATAATAGTCCTT
* * *
1851980 AAATGCATGGAAAATACCTTAAGT-GAT-CTA
1 AAATGCAT-G-AAATAGCATAA-TAG-TCCTT
*
1852010 AAATGCATGAAATAGCATAATAGTCTTT
1 AAATGCATGAAATAGCATAATAGTCCTT
1852038 AAAT-CATGAAA
1 AAATGCATGAAA
1852049 ATTGACTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
27 9 0.17
28 22 0.41
29 2 0.04
30 19 0.35
31 2 0.04
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.29
Consensus pattern (28 bp):
AAATGCATGAAATAGCATAATAGTCCTT
Found at i:1852021 original size:58 final size:57
Alignment explanation
Indices: 1851783--1852167 Score: 208
Period size: 58 Copynumber: 6.8 Consensus size: 57
1851773 AAATGGCCTA
* * * * *
1851783 AAAATGTATAAAATTGTATAATATTCCTT-AATACGTGGAAAATACCTTAAATAACCT
1 AAAATGCATGAAATTGCATAATAATCCTTAAAT-CATGGAAAATACCTTAAATAACCT
* * * * * * *
1851840 --AATGC--GGAATTGCATAACAATCCCTAATTGCATGAAAAATGCCTTAAATGACCT
1 AAAATGCATGAAATTGCATAATAATCCTTAAAT-CATGGAAAATACCTTAAATAACCT
*** * *
1851894 AAAATGCATGAAA-TGACATAATAAT-CTCTAAATCACAAAAAAGGA-C-TAAATAATCT
1 AAAATGCATGAAATTG-CATAATAATCCT-TAAATCATGGAAAA-TACCTTAAATAACCT
* * * * *
1851950 AAAAATACATGAAATTGCATAATAGTCCTTAAATGCATGGAAAATACCTTAAGTGATCT
1 -AAAATGCATGAAATTGCATAATAATCCTTAAAT-CATGGAAAATACCTTAAATAACCT
* * * ***
1852009 AAAATGCATGAAATAGCATAATAGTCTTTAAATCAT-GAAAATTGA-C-TAAACGGCCTT
1 AAAATGCATGAAATTGCATAATAATCCTTAAATCATGGAAAA-T-ACCTTAAATAACC-T
* * * *
1852066 AAAATGCATGATATTGCATAAATGATCC-CAAATCATGGCAAATTA-C-TAGAATAAACCT
1 AAAATGCATGAAATTGCAT-AATAATCCTTAAATCATGG-AAAATACCTTA-AAT-AACCT
* *
1852124 AAAATGCATGAAATTGCATAAATAAT-ATCAAATCATGGCAAAAT
1 AAAATGCATGAAATTGCAT-AATAATCCTTAAATCATGG-AAAAT
1852168 TACTAGAATG
Statistics
Matches: 253, Mismatches: 52, Indels: 45
0.72 0.15 0.13
Matches are distributed among these distances:
53 14 0.06
54 22 0.09
55 4 0.02
56 23 0.09
57 71 0.28
58 106 0.42
59 13 0.05
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (57 bp):
AAAATGCATGAAATTGCATAATAATCCTTAAATCATGGAAAATACCTTAAATAACCT
Found at i:1852070 original size:115 final size:115
Alignment explanation
Indices: 1851847--1852086 Score: 275
Period size: 115 Copynumber: 2.1 Consensus size: 115
1851837 CCTAATGCGG
* *
1851847 AATTGCATAACAATCCCTAATTGCATGAAAAATGCCTTAAATGACCTAAAATGCATGAAATGACA
1 AATTGCATAACAATCCCTAAATGCATGAAAAATACCTTAAATGACCTAAAATGCATGAAATGACA
* *
1851912 TAATAATCTCTAAATCACAAAAAAGGACTAAATAATCTAAAAATACATGA
66 TAATAATCTCTAAATCACAAAAAAGGACTAAACAACCTAAAAATACATGA
* * * * * *
1851962 AATTGCATAATAGTCCTTAAATGCATGGAAAATACCTTAAGTGATCTAAAATGCATGAAAT-AGC
1 AATTGCATAACAATCCCTAAATGCATGAAAAATACCTTAAATGACCTAAAATGCATGAAATGA-C
* * ** ** ** * *
1852026 ATAATAGTCTTTAAATCATGAAAATTGACTAAACGGCCTTAAAATGCATGA
65 ATAATAATCTCTAAATCACAAAAAAGGACTAAACAACCTAAAAATACATGA
*
1852077 TATTGCATAA
1 AATTGCATAA
1852087 ATGATCCCAA
Statistics
Matches: 103, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
114 1 0.01
115 102 0.99
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (115 bp):
AATTGCATAACAATCCCTAAATGCATGAAAAATACCTTAAATGACCTAAAATGCATGAAATGACA
TAATAATCTCTAAATCACAAAAAAGGACTAAACAACCTAAAAATACATGA
Found at i:1852147 original size:29 final size:29
Alignment explanation
Indices: 1852065--1852148 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
1852055 TAAACGGCCT
* * *
1852065 TAAAATGCATGATATTGCATAAATGATCC
1 TAAAATGCATGAAATTGCATAAATAAACC
* *
1852094 -CAAAT-CATGGCAAATTAC-TAGAATAAACC
1 TAAAATGCAT-G-AAATTGCATA-AATAAACC
1852123 TAAAATGCATGAAATTGCATAAATAA
1 TAAAATGCATGAAATTGCATAAATAA
1852149 TATCAAATCA
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
27 3 0.07
28 7 0.17
29 22 0.52
30 7 0.17
31 3 0.07
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (29 bp):
TAAAATGCATGAAATTGCATAAATAAACC
Found at i:1852195 original size:58 final size:58
Alignment explanation
Indices: 1852078--1852195 Score: 148
Period size: 58 Copynumber: 2.0 Consensus size: 58
1852068 AATGCATGAT
* * * *
1852078 ATTGCATAAATGATCCCAAATCATGGCAAATTACTAGAATAAACCTAAAATGCATGAA
1 ATTGCATAAATAATACCAAATCATGGCAAATTACTAGAATAAACCTAAAATACACGAA
* * **
1852136 ATTGCATAAATAATATCAAATCATGGCAAAATTACTAGAATGATTCT-AAATACACGAA
1 ATTGCATAAATAATACCAAATCATGGC-AAATTACTAGAATAAACCTAAAATACACGAA
1852194 AT
1 AT
1852196 GACATGAAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 35 0.69
59 16 0.31
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.26
Consensus pattern (58 bp):
ATTGCATAAATAATACCAAATCATGGCAAATTACTAGAATAAACCTAAAATACACGAA
Found at i:1852348 original size:29 final size:30
Alignment explanation
Indices: 1852289--1852348 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1852279 AATTCACGGT
* *
1852289 AATCTTTAAACATGCAGGGAATGACATAAA
1 AATCTTTAAACATGCAGGAAATGACAAAAA
* *
1852319 AATCTTTAAA-ATGCATGAAATGATAAAAA
1 AATCTTTAAACATGCAGGAAATGACAAAAA
1852348 A
1 A
1852349 GTTTCTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (30 bp):
AATCTTTAAACATGCAGGAAATGACAAAAA
Found at i:1857110 original size:22 final size:22
Alignment explanation
Indices: 1857082--1857126 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1857072 AGTTTTTAAA
1857082 ATTTTAAAGTTAAAGCCTAGGT
1 ATTTTAAAGTTAAAGCCTAGGT
* *
1857104 ATTTTAAAGTTGAAGCCTTGGT
1 ATTTTAAAGTTAAAGCCTAGGT
1857126 A
1 A
1857127 AATGAGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (22 bp):
ATTTTAAAGTTAAAGCCTAGGT
Found at i:1857161 original size:39 final size:40
Alignment explanation
Indices: 1857104--1857199 Score: 135
Period size: 39 Copynumber: 2.5 Consensus size: 40
1857094 AAGCCTAGGT
* *
1857104 ATTTT-AAAGTTGAAGCCTTGGTAAATGAGTCTTTTC-AA
1 ATTTTAAAAGTTGAAGCCTTGGTAAAGGAGTCTTTCCAAA
*
1857142 ATTTTAAAAGTTGATGCCTTGGTAAAGGAGTCTTTCCAAA
1 ATTTTAAAAGTTGAAGCCTTGGTAAAGGAGTCTTTCCAAA
*
1857182 ATTTT-AAAGTTAAAGCCT
1 ATTTTAAAAGTTGAAGCCT
1857200 CGATGGAGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
38 5 0.10
39 39 0.76
40 7 0.14
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (40 bp):
ATTTTAAAAGTTGAAGCCTTGGTAAAGGAGTCTTTCCAAA
Found at i:1858099 original size:24 final size:24
Alignment explanation
Indices: 1858053--1858099 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1858043 AAAATTTTCC
* *
1858053 TTACTTTTATGTTTTTTTATATAA
1 TTACTTTTACGTTTTTCTATATAA
1858077 TTACATTTTACGTTTTTCT-TATA
1 TTAC-TTTTACGTTTTTCTATATA
1858100 CTTTTTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.23, C:0.09, G:0.04, T:0.64
Consensus pattern (24 bp):
TTACTTTTACGTTTTTCTATATAA
Found at i:1859492 original size:12 final size:12
Alignment explanation
Indices: 1859451--1859492 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1859441 TTAGGATTAT
* *
1859451 TTTATTTATTTA
1 TTTATTAATATA
*
1859463 TTTATCAATATA
1 TTTATTAATATA
1859475 TTTATTAATATA
1 TTTATTAATATA
1859487 TTTATT
1 TTTATT
1859493 TTTATTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTATTAATATA
Found at i:1859492 original size:16 final size:17
Alignment explanation
Indices: 1859453--1859493 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1859443 AGGATTATTT
*
1859453 TATTTATTTATTTATCA
1 TATTTATTTATTAATCA
*
1859470 -ATATATTTATTAAT-A
1 TATTTATTTATTAATCA
1859485 TATTTATTT
1 TATTTATTT
1859494 TTATTTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTATTTATTAATCA
Found at i:1861442 original size:12 final size:12
Alignment explanation
Indices: 1861427--1861454 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1861417 TATAAAAATA
1861427 TAAAAAAAATTT
1 TAAAAAAAATTT
1861439 TAAAAAAAATTT
1 TAAAAAAAATTT
1861451 TAAA
1 TAAA
1861455 TAATAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAAAAAAATTT
Found at i:1864625 original size:53 final size:52
Alignment explanation
Indices: 1864522--1864627 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 52
1864512 TTAAAATCAA
* * *
1864522 ATATATATATATATATATATTATATGCACATTCCTAATGCAAAAATCAAATAT
1 ATATATATATACATATATATTATATACACATTCCCAATGC-AAAATCAAATAT
1864575 ATATATATATACATATATCATATATATACACACTTCCCAATGC-AAA-CAAATAT
1 ATATATATATACATATAT-AT-TATATACACA-TTCCCAATGCAAAATCAAATAT
1864628 CATAAGAAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
53 24 0.51
54 5 0.11
55 9 0.19
56 9 0.19
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (52 bp):
ATATATATATACATATATATTATATACACATTCCCAATGCAAAATCAAATAT
Found at i:1869406 original size:2 final size:2
Alignment explanation
Indices: 1869394--1869428 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1869384 GATCTGGGTT
* *
1869394 TA TA TA CA TA TA TA TA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1869429 GTATTCCCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1869413 original size:14 final size:14
Alignment explanation
Indices: 1869394--1869427 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1869384 GATCTGGGTT
1869394 TATATACATATATA
1 TATATACATATATA
1869408 TATATACATATATA
1 TATATACATATATA
1869422 TATATA
1 TATATA
1869428 TGTATTCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATACATATATA
Found at i:1870908 original size:6 final size:6
Alignment explanation
Indices: 1870897--1870922 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1870887 TGACCCAATT
1870897 GAGTCA GAGTCA GAGTCA GAGTCA GA
1 GAGTCA GAGTCA GAGTCA GAGTCA GA
1870923 TAAATTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.35, T:0.15
Consensus pattern (6 bp):
GAGTCA
Found at i:1875702 original size:23 final size:24
Alignment explanation
Indices: 1875657--1875704 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1875647 ATATTTTTAT
* *
1875657 TTTTATTTAAAATTTTTAAATATA
1 TTTTATTTAAAAATTATAAATATA
*
1875681 TTTT-TTTAAAAATTATATATATA
1 TTTTATTTAAAAATTATAAATATA
1875704 T
1 T
1875705 AAACTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTATTTAAAAATTATAAATATA
Found at i:1876415 original size:24 final size:24
Alignment explanation
Indices: 1876385--1876430 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1876375 TATATTAAAG
1876385 TTTTATTTAAATATAAATTAAAAA
1 TTTTATTTAAATATAAATTAAAAA
*
1876409 TTTTATTTAGATATAAATTAAA
1 TTTTATTTAAATATAAATTAAA
1876431 TGATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTATTTAAATATAAATTAAAAA
Found at i:1876439 original size:31 final size:31
Alignment explanation
Indices: 1876403--1876497 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
1876393 AAATATAAAT
*
1876403 TAAAAATTTTATTTAGATATAAATTAAATGA
1 TAAAAATTTTATTTAAATATAAATTAAATGA
* *
1876434 TAAAAATTTTATTTAAATATAATTTTAATGA
1 TAAAAATTTTATTTAAATATAAATTAAATGA
* ** * *
1876465 AAAAAAACTTATTTAAGTGTAAA-TAAAT-A
1 TAAAAATTTTATTTAAATATAAATTAAATGA
1876494 TAAA
1 TAAA
1876498 TTTTATCTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 4 0.08
30 4 0.08
31 45 0.85
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (31 bp):
TAAAAATTTTATTTAAATATAAATTAAATGA
Found at i:1877747 original size:16 final size:16
Alignment explanation
Indices: 1877699--1877786 Score: 70
Period size: 16 Copynumber: 5.4 Consensus size: 16
1877689 TGATTAATCT
*
1877699 AATTCAAAATAATTTA
1 AATTTAAAATAATTTA
* * * *
1877715 AAATTGAAGTAACTTA
1 AATTTAAAATAATTTA
1877731 AATTTAAAATAATTTA
1 AATTTAAAATAATTTA
* *
1877747 AATTAAAAAAAATCTTAAA
1 AATTTAAAATAAT-TT--A
*
1877766 AATTTTAAA-AATTTA
1 AATTTAAAATAATTTA
1877781 AATTTA
1 AATTTA
1877787 CTCGATCTGA
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
15 6 0.11
16 34 0.62
17 4 0.07
18 3 0.05
19 8 0.15
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (16 bp):
AATTTAAAATAATTTA
Found at i:1878701 original size:17 final size:18
Alignment explanation
Indices: 1878674--1878707 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1878664 TGCATTCAAA
*
1878674 AAAATGTATAATATTATG
1 AAAATGTATAAAATTATG
1878692 AAAA-GTATAAAATTAT
1 AAAATGTATAAAATTAT
1878708 ATTTGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (18 bp):
AAAATGTATAAAATTATG
Found at i:1878739 original size:18 final size:19
Alignment explanation
Indices: 1878713--1878759 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
1878703 ATTATATTTG
* *
1878713 ATATTATTAAATAT-AATT
1 ATATAATTAAATATAAATA
1878731 ATATAATT-AATATAAATA
1 ATATAATTAAATATAAATA
*
1878749 AAATAATTAAA
1 ATATAATTAAA
1878760 ATATGAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 5 0.21
18 17 0.71
19 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAATTAAATATAAATA
Found at i:1880997 original size:20 final size:20
Alignment explanation
Indices: 1880972--1881015 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1880962 ATGAATTATT
*
1880972 AATTTTTTAATAAAATAAAA
1 AATTTTTAAATAAAATAAAA
* *
1880992 AA-TTTTAAATTAAATTAAA
1 AATTTTTAAATAAAATAAAA
1881011 AATTT
1 AATTT
1881016 AAAAAGTAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTTTTAAATAAAATAAAA
Found at i:1881261 original size:13 final size:13
Alignment explanation
Indices: 1881238--1881276 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1881228 GTTTAAGTTT
1881238 TAATATTTATTAAG
1 TAAT-TTTATTAAG
*
1881252 TAATTTTATTATG
1 TAATTTTATTAAG
*
1881265 TAATTTTTTTAA
1 TAATTTTATTAA
1881277 CATATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (13 bp):
TAATTTTATTAAG
Found at i:1881360 original size:26 final size:24
Alignment explanation
Indices: 1881324--1881405 Score: 89
Period size: 23 Copynumber: 3.5 Consensus size: 24
1881314 ATGATTATAT
*
1881324 AAATTTAATTTATTTTTATTTGTA
1 AAATATAATTTATTTTTATTTGTA
*
1881348 AAAGTTTAAATTTA-TTTTATTT-TA
1 AAA-TAT-AATTTATTTTTATTTGTA
* *
1881372 ATATATGATTTATTTTTATTTGTA
1 AAATATAATTTATTTTTATTTGTA
1881396 AAAT-TAATTT
1 AAATATAATTT
1881406 TATTAAAGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.10
23 15 0.31
24 12 0.24
25 11 0.22
26 6 0.12
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (24 bp):
AAATATAATTTATTTTTATTTGTA
Found at i:1881431 original size:40 final size:41
Alignment explanation
Indices: 1881355--1881435 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
1881345 GTAAAAGTTT
* * *
1881355 AAATTTATTTTATTTTAATATATGATTTATTTTTATTTGTA
1 AAATTAATTTTATTTAAAGATATGATTTATTTTTATTTGTA
*
1881396 AAATTAATTTTA-TTAAAGATATTATTTATTTTTATTTGTA
1 AAATTAATTTTATTTAAAGATATGATTTATTTTTATTTGTA
1881436 GAAGTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 25 0.69
41 11 0.31
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (41 bp):
AAATTAATTTTATTTAAAGATATGATTTATTTTTATTTGTA
Found at i:1881552 original size:70 final size:71
Alignment explanation
Indices: 1881424--1881565 Score: 196
Period size: 70 Copynumber: 2.0 Consensus size: 71
1881414 ATATTATTTA
* *
1881424 TTTTTATTTGTAGAAGTTTAAATTTGTTTGTAGAGTATGATTATATAAGTTTAAATTTTGAAGGT
1 TTTTTATTTATAGAAGTTTAAATTTGTTTGTAGAGTATGATTATATAAGTTTAAATTTTGAAGAT
1881489 ATAATT
66 ATAATT
* ** * * * *
1881495 TTTTTATTTATAGAAGTTTAAATTTGTTTTTTTA-TTTGATTATCTGAGTTTAAATTTTTAAGAT
1 TTTTTATTTATAGAAGTTTAAATTTGTTTGTAGAGTATGATTATATAAGTTTAAATTTTGAAGAT
1881559 ATAATT
66 ATAATT
1881565 T
1 T
1881566 ATTGTGATTC
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
70 32 0.52
71 30 0.48
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (71 bp):
TTTTTATTTATAGAAGTTTAAATTTGTTTGTAGAGTATGATTATATAAGTTTAAATTTTGAAGAT
ATAATT
Found at i:1881566 original size:143 final size:141
Alignment explanation
Indices: 1881414--1881857 Score: 376
Period size: 143 Copynumber: 3.1 Consensus size: 141
1881404 TTTATTAAAG
* * * *
1881414 ATATTATTTATTTTTATTTGTAGAAGTTTAAATTTGTTTGTAGAGTATGATTATATAAGTTTAAA
1 ATATAATTTATTTTTATTTGTAGAAATTTAAATTTATTT-TAGAGTATGATTATACAAGTTTAAA
* *
1881479 TTTTGAAGGTATAATT-TTTTTATTTATAGAAGTTTAAATTTGTTTTTTTATTTGATTAT-CTGA
65 TTTTTAAGGTATAATTATTTTTATTTATA-AAGTTTAAATTT-TTTTTTTATTTGATTATAC-AA
1881542 GTTTAAATTTTTA-A
127 GTTTAAATTTTTAGA
* * * * *
1881556 GATATAATTTATTGTGATTCGTA-AAATTTTAAGTATATTTTTAG-GTATG----TACAAGTTTA
1 -ATATAATTTATTTTTATTTGTAGAAA-TTTAAATTTA-TTTTAGAGTATGATTATACAAGTTTA
* * * *
1881615 AATTTTTAATAGTGTAATTTATTTTTATATGTATAAA-TTTAAATTTATATTTTATTTTGATTAT
63 AATTTTTAA-GGTATAA-TTATTTTTAT-T-TATAAAGTTTAAATTTTTTTTTTA-TTTGATTAT
*
1881679 ACAAGTTTATATTTTTAGA
123 ACAAGTTTAAATTTTTAGA
* * ** * *
1881698 ATATTAGTTAACTTTATTTGTAGAAATTTAAAACTTATTTTTGA-T-TGATTATACAAGTTTAAA
1 ATATAATTTATTTTTATTTGTAGAAATTT-AAATTTATTTTAGAGTATGATTATACAAGTTTAAA
* * *
1881761 TTTTTAAGATATTATTTATTTTTATTCGTA-AAAGTTTAAA-TTTATTTTTATGTATGATTATAC
65 TTTTTAAGGTA-TAATTATTTTTATT--TATAAAGTTTAAATTTTTTTTTTAT-T-TGATTATAC
*
1881824 AAGTTTAAAATTTTTAGT
125 AAGTTT-AAATTTTTAGA
*
1881842 GTATAATTTATTTTTA
1 ATATAATTTATTTTTA
1881858 GGTATGATTA
Statistics
Matches: 237, Mismatches: 41, Indels: 45
0.73 0.13 0.14
Matches are distributed among these distances:
138 17 0.07
139 5 0.02
140 10 0.04
141 63 0.27
142 31 0.13
143 67 0.28
144 44 0.19
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.54
Consensus pattern (141 bp):
ATATAATTTATTTTTATTTGTAGAAATTTAAATTTATTTTAGAGTATGATTATACAAGTTTAAAT
TTTTAAGGTATAATTATTTTTATTTATAAAGTTTAAATTTTTTTTTTATTTGATTATACAAGTTT
AAATTTTTAGA
Found at i:1881659 original size:212 final size:213
Alignment explanation
Indices: 1881419--1881857 Score: 473
Period size: 212 Copynumber: 2.1 Consensus size: 213
1881409 TAAAGATATT
* * * *
1881419 ATTTATTTTTATTTGTAGAAGTTTAAATTTGT-TTGTAGAGTATGATTATATAAGTTTA-AATTT
1 ATTTATTTTTATATGTAGAAATTTAAATTTATATT-T-GAGTATGATTATACAAGTTTATAATTT
** * * * * *
1881482 T-GAAGGTA-TAATT-TTTTTATTTATAGAAGTTT-AAATTTGTTTTTTTATTTGATTAT-CTGA
64 TAGAA--TATTAATTAACTTTATTTATAGAAATTTAAAACTT-ATTTTTGA-TTGATTATAC-AA
* *
1881542 GTTTAAATTTTTAAGATATAATTTATTGTGATTCGTAAAATTTTAAGTATATTTTTAGGTATG-T
124 GTTTAAATTTTTAAGATATAATTTATTGTGATTCGTAAAAGTTTAAATATATTTTTAGGTATGAT
*
1881606 ACAAGTTT-AAATTTTTAATAGTGTA
189 ACAAGTTTAAAATTTTTAAT-GTATA
* * * * *
1881631 ATTTATTTTTATATGTATAAATTTAAATTTATATTTTATTTTGATTATACAAGTTTATATTTTTA
1 ATTTATTTTTATATGTAGAAATTTAAATTTATATTTGAGTATGATTATACAAGTTTATAATTTTA
* *
1881696 GAATATTAGTTAACTTTATTTGTAGAAATTTAAAACTTATTTTTGATTGATTATACAAGTTTAAA
66 GAATATTAATTAACTTTATTTATAGAAATTTAAAACTTATTTTTGATTGATTATACAAGTTTAAA
* * * * *
1881761 TTTTTAAGATATTATTTATTTTTATTCGTAAAAGTTTAAATTTATTTTTATGTATGATTATACAA
131 TTTTTAAGATATAATTTATTGTGATTCGTAAAAGTTTAAATATATTTTTAGGTATG---ATACAA
*
1881826 GTTTAAAATTTTTAGTGTATA
193 GTTTAAAATTTTTAATGTATA
1881847 ATTTATTTTTA
1 ATTTATTTTTA
1881858 GGTATGATTA
Statistics
Matches: 188, Mismatches: 27, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
211 19 0.10
212 103 0.55
213 27 0.14
214 5 0.03
216 24 0.13
217 10 0.05
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (213 bp):
ATTTATTTTTATATGTAGAAATTTAAATTTATATTTGAGTATGATTATACAAGTTTATAATTTTA
GAATATTAATTAACTTTATTTATAGAAATTTAAAACTTATTTTTGATTGATTATACAAGTTTAAA
TTTTTAAGATATAATTTATTGTGATTCGTAAAAGTTTAAATATATTTTTAGGTATGATACAAGTT
TAAAATTTTTAATGTATA
Found at i:1881752 original size:71 final size:71
Alignment explanation
Indices: 1881652--1881840 Score: 206
Period size: 71 Copynumber: 2.6 Consensus size: 71
1881642 TATGTATAAA
* * *
1881652 TTTAAATTTATATTTTATTTTGATTATACAAGTTTATATTTTTAGA-ATATTAGTTAACTTTATT
1 TTTAAACTTAT-TTTTA-GTTGATTATACAAGTTTAAATTTTTAGAGATATTAGTTAACTTTATT
*
1881716 TGTAGAAA-
64 CGTA-AAAG
* **
1881724 TTTAAAACTTATTTTT-GATTGATTATACAAGTTTAAATTTTTA-AGATATTATTTATTTTTATT
1 TTT-AAACTTATTTTTAG-TTGATTATACAAGTTTAAATTTTTAGAGATATTAGTTAACTTTATT
1881787 CGTAAAAG
64 CGTAAAAG
*
1881795 TTTAAATTTATTTTTATGTATGATTATACAAGTTTAAAATTTTTAG
1 TTTAAACTTATTTTTA-GT-TGATTATACAAGTTT-AAATTTTTAG
1881841 TGTATAATTT
Statistics
Matches: 100, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
70 15 0.15
71 46 0.46
72 23 0.23
73 16 0.16
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.53
Consensus pattern (71 bp):
TTTAAACTTATTTTTAGTTGATTATACAAGTTTAAATTTTTAGAGATATTAGTTAACTTTATTCG
TAAAAG
Found at i:1881852 original size:47 final size:47
Alignment explanation
Indices: 1881799--1881905 Score: 205
Period size: 47 Copynumber: 2.3 Consensus size: 47
1881789 TAAAAGTTTA
1881799 AATTTATTTTTATGTATGATTATACAAGTTTAAAATTTTTAGTGTAT
1 AATTTATTTTTATGTATGATTATACAAGTTTAAAATTTTTAGTGTAT
*
1881846 AATTTATTTTTAGGTATGATTATACAAGTTTAAAATTTTTAGTGTAT
1 AATTTATTTTTATGTATGATTATACAAGTTTAAAATTTTTAGTGTAT
1881893 AATTTATTTTTAT
1 AATTTATTTTTAT
1881906 TTGTGAAAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (47 bp):
AATTTATTTTTATGTATGATTATACAAGTTTAAAATTTTTAGTGTAT
Found at i:1881902 original size:120 final size:121
Alignment explanation
Indices: 1881743--1881979 Score: 340
Period size: 120 Copynumber: 2.0 Consensus size: 121
1881733 TATTTTTGAT
* *
1881743 TGATTATACAAGTTTAAATTTTTAAGATATTATTTATTTTTATTCGTAAAAGTTTAAATTTATTT
1 TGATTATACAAGTTTAAATTTTTAAGATATAATTTATTTTTATTCGTAAAAGTTTAAATGTATTT
1881808 TTAT-G-TATGATTATACAAGTTTAAAATTTTT-AGT-GTATAATTTATTTTTAGGTA
66 TTATGGATATGATTATACAAGTTT-AAATTTTTGA-TAGTATAATTTATTTTTAGGTA
* * *
1881862 TGATTATACAAGTTTAAAATTTTT-AGTGTATAATTTATTTTTATTTGTGAAAGTTTAAATGTAT
1 TGATTATACAAGTTT-AAATTTTTAAG-ATATAATTTATTTTTATTCGTAAAAGTTTAAATGTAT
* *
1881926 TTTTTTGGATATGATTATATAAGTTTAAATTTTTGATAGTATAATTTATTTTTA
64 TTTTATGGATATGATTATACAAGTTTAAATTTTTGATAGTATAATTTATTTTTA
1881980 TTTATAAAAA
Statistics
Matches: 105, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
119 17 0.16
120 45 0.43
121 10 0.10
122 33 0.31
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.54
Consensus pattern (121 bp):
TGATTATACAAGTTTAAATTTTTAAGATATAATTTATTTTTATTCGTAAAAGTTTAAATGTATTT
TTATGGATATGATTATACAAGTTTAAATTTTTGATAGTATAATTTATTTTTAGGTA
Found at i:1881940 original size:75 final size:74
Alignment explanation
Indices: 1881852--1882141 Score: 342
Period size: 75 Copynumber: 3.9 Consensus size: 74
1881842 GTATAATTTA
* * * * *
1881852 TTTTTAGG-TATGATTATACAAGTTTAAAATTTTTAGTGTATAATTTATTTTTATTTGTGAAAGT
1 TTTTTTGGATATGATTATACAAGTTT-AAATTTTTAATGTATAATTTATTTTTATTTATAAAAAT
1881916 TTAAATGTAT
65 TTAAATGTAT
* *
1881926 TTTTTTGGATATGATTATATAAGTTTAAATTTTTGATAGTATAATTTATTTTTATTTATAAAAAT
1 TTTTTTGGATATGATTATACAAGTTTAAATTTTTAAT-GTATAATTTATTTTTATTTATAAAAAT
1881991 TTAAATGTA-
65 TTAAATGTAT
*
1882000 TTTTTTGAGATATGAATATACAAGTTTAAATTTTTAATGATATAATTTATTTTT-TTTATAAAAA
1 TTTTTTG-GATATGATTATACAAGTTTAAATTTTTAATG-TATAATTTATTTTTATTTATAAAAA
1882064 TTTAAAT-T-T
64 TTTAAATGTAT
** * * ** * *
1882073 AATTTTGGAT-TGATTATATGAA-TTTAAAATTTTAAAATATTATTTATTTTTATTTATAAAATT
1 TTTTTTGGATATGATTATA-CAAGTTTAAATTTTTAATGTATAATTTATTTTTATTTATAAAAAT
1882136 TTAAAT
65 TTAAAT
1882142 ATTTTAAATA
Statistics
Matches: 190, Mismatches: 19, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
70 13 0.07
71 35 0.18
72 5 0.03
73 6 0.03
74 41 0.22
75 90 0.47
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (74 bp):
TTTTTTGGATATGATTATACAAGTTTAAATTTTTAATGTATAATTTATTTTTATTTATAAAAATT
TAAATGTAT
Found at i:1882014 original size:150 final size:144
Alignment explanation
Indices: 1881852--1882141 Score: 377
Period size: 145 Copynumber: 2.0 Consensus size: 144
1881842 GTATAATTTA
* * * * * *
1881852 TTTTTAGGTATGATTATACAAGTTTAAAATTTTTAGTG-TATAATTTATTTTTATTTGTGAAAGT
1 TTTTTAGATATGAATATACAAGTTT-AAATTTTTAATGATATAATTTATTTTT-TTTATAAAAAT
** * * *
1881916 TTAAATGTATTTTTTTGGATATGATTATAT-AAGTTTAAATTTTTGATAGTATAATTTATTTTTA
64 TTAAAT-T-TAATTTTGGAT-TGATTATATGAA-TTTAAAATTTT-AAAATATAATTTATTTTTA
1881980 TTTATAAAAATTTAAATGTAT
124 TTTATAAAAATTTAAATGTAT
1882001 TTTTTGAGATATGAATATACAAGTTTAAATTTTTAATGATATAATTTATTTTTTTTATAAAAATT
1 TTTTT-AGATATGAATATACAAGTTTAAATTTTTAATGATATAATTTATTTTTTTTATAAAAATT
*
1882066 TAAATTTAATTTTGGATTGATTATATGAATTTAAAATTTTAAAATATTATTTATTTTTATTTATA
65 TAAATTTAATTTTGGATTGATTATATGAATTTAAAATTTTAAAATATAATTTATTTTTATTTATA
*
1882131 AAATTTTAAAT
130 AAAATTTAAAT
1882142 ATTTTAAATA
Statistics
Matches: 125, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
145 32 0.26
146 19 0.15
147 11 0.09
148 1 0.01
149 30 0.24
150 32 0.26
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (144 bp):
TTTTTAGATATGAATATACAAGTTTAAATTTTTAATGATATAATTTATTTTTTTTATAAAAATTT
AAATTTAATTTTGGATTGATTATATGAATTTAAAATTTTAAAATATAATTTATTTTTATTTATAA
AAATTTAAATGTAT
Found at i:1882511 original size:17 final size:17
Alignment explanation
Indices: 1882464--1882520 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 17
1882454 TATTAAACAC
1882464 TTAATATAATAA-ATTT
1 TTAATATAATAATATTT
*
1882480 TTAA-AAAAT-ATATTT
1 TTAATATAATAATATTT
*
1882495 TTAATATTATAATATTT
1 TTAATATAATAATATTT
1882512 TTAA-ATAAT
1 TTAATATAAT
1882521 GATTTGGGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 1 0.03
15 12 0.35
16 11 0.32
17 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAATATAATAATATTT
Found at i:1882914 original size:22 final size:22
Alignment explanation
Indices: 1882889--1882930 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1882879 TATTAAAAAA
*
1882889 ATATTTTTAT-ATTAATATTTTT
1 ATATTTTAATAATTAA-ATTTTT
1882911 ATATTTTAATAATTAAATTT
1 ATATTTTAATAATTAAATTT
1882931 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATTTTAATAATTAAATTTTT
Found at i:1882921 original size:16 final size:14
Alignment explanation
Indices: 1882888--1882915 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1882878 ATATTAAAAA
1882888 AATATTTTTATATT
1 AATATTTTTATATT
1882902 AATATTTTTATATT
1 AATATTTTTATATT
1882916 TTAATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:1883411 original size:15 final size:15
Alignment explanation
Indices: 1883380--1883526 Score: 54
Period size: 15 Copynumber: 9.5 Consensus size: 15
1883370 ATTAATTAGA
*
1883380 TAAA-TAAAATTTATT
1 TAAATTAAAATAT-TT
1883395 TAAATTAAAATATTT
1 TAAATTAAAATATTT
1883410 TAAATTTAAATCATATGATT
1 TAAA-TTAAA--ATAT--TT
* *
1883430 TAAATT-AATTAATT
1 TAAATTAAAATATTT
* *
1883444 TAATATTTAAAT-TAAT
1 TAA-ATTAAAATAT-TT
* *
1883460 TAAATTTTAATTATTT
1 TAAA-TTAAAATATTT
* *
1883476 TAAATTTAATTATTT
1 TAAATTAAAATATTT
* *
1883491 TAAATTTAAAT-TAAT
1 TAAATTAAAATAT-TT
*
1883506 TAAATT-TAATA-TT
1 TAAATTAAAATATTT
1883519 TAAATTAA
1 TAAATTAA
1883527 TTTATTTATG
Statistics
Matches: 105, Mismatches: 13, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
13 7 0.07
14 9 0.09
15 42 0.40
16 32 0.30
17 1 0.01
18 6 0.06
19 2 0.02
20 6 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (15 bp):
TAAATTAAAATATTT
Found at i:1883446 original size:5 final size:5
Alignment explanation
Indices: 1883427--1883635 Score: 64
Period size: 5 Copynumber: 41.4 Consensus size: 5
1883417 AAATCATATG
* * *
1883427 ATTTA AATTA A-TTA ATTTAA TATTTA AATTA ATTAA ATTTTA A-TTA
1 ATTTA ATTTA ATTTA ATTT-A -ATTTA ATTTA ATTTA A-TTTA ATTTA
* * * *
1883473 TTTTAA ATTTA A-TTA TTTTAA ATTTA AATTA ATTAA ATTTAA TATTTA
1 ATTT-A ATTTA ATTTA ATTT-A ATTTA ATTTA ATTTA ATTT-A -ATTTA
* * * * *
1883521 AATTA ATTT- ATTT- ATGATCA AGTAA ATGTATT ATTTGA ATTT- A-TTA
1 ATTTA ATTTA ATTTA AT--TTA ATTTA AT-T-TA ATTT-A ATTTA ATTTA
* *
1883567 ATTTA A-TTA TTTTA AGTTTA ATTTA A-TTA ATTTTA AATT- A-TTA ATTT-
1 ATTTA ATTTA ATTTA A-TTTA ATTTA ATTTA A-TTTA ATTTA ATTTA ATTTA
* *
1883614 TTTTA ATTTA TTTTA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA AT
1883636 AAAATAGAAC
Statistics
Matches: 150, Mismatches: 29, Indels: 50
0.66 0.13 0.22
Matches are distributed among these distances:
3 4 0.03
4 30 0.20
5 73 0.49
6 32 0.21
7 11 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (5 bp):
ATTTA
Found at i:1883453 original size:21 final size:21
Alignment explanation
Indices: 1883427--1883534 Score: 137
Period size: 21 Copynumber: 4.9 Consensus size: 21
1883417 AAATCATATG
1883427 ATTTAAATTAATTAATTTAAT
1 ATTTAAATTAATTAATTTAAT
1883448 ATTTAAATTAATTAAATTTTAATT
1 ATTTAAATTAATT-AA-TTTAA-T
*
1883472 ATTTTAAATTTAATTATTTTAA-
1 A-TTTAAA-TTAATTAATTTAAT
1883494 ATTTAAATTAATTAAATTTAAT
1 ATTTAAATTAATT-AATTTAAT
*
1883516 ATTTAAATTAATTTATTTA
1 ATTTAAATTAATTAATTTA
1883535 TGATCAAGTA
Statistics
Matches: 77, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
20 6 0.08
21 30 0.39
22 16 0.21
23 5 0.06
24 7 0.09
25 7 0.09
26 6 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAAATTAATTAATTTAAT
Found at i:1883498 original size:46 final size:44
Alignment explanation
Indices: 1883428--1883608 Score: 158
Period size: 46 Copynumber: 4.0 Consensus size: 44
1883418 AATCATATGA
*
1883428 TTTAAATTAATTAATTTAATATTTAAATTAATTAAATTTTAATTAT
1 TTTAAATTAATTATTTTAA-ATTTAAATTAATT-AATTTTAATTAT
*
1883474 TTTAAATTTAATTATTTTAAATTTAAATTAATTAAATTTAA-TA-
1 TTTAAA-TTAATTATTTTAAATTTAAATTAATTAATTTTAATTAT
* *
1883517 TTTAAATTAATTTATTTATGATCAA-GTAAATGT-ATT-ATTTGAATT-T
1 TTTAAATTAA-TTATTT-T-A--AATTTAAAT-TAATTAATTTTAATTAT
* * * *
1883563 ATTAATTTAATTATTTTAAGTTTAATTTAATTAATTTTAAATTAT
1 TTTAAATTAATTATTTTAAATTTAAATTAATTAATTTT-AATTAT
1883608 T
1 T
1883609 AATTTTTTTA
Statistics
Matches: 109, Mismatches: 12, Indels: 29
0.73 0.08 0.19
Matches are distributed among these distances:
41 2 0.02
42 11 0.10
43 17 0.16
44 8 0.07
45 20 0.18
46 36 0.33
47 15 0.14
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (44 bp):
TTTAAATTAATTATTTTAAATTTAAATTAATTAATTTTAATTAT
Found at i:1883580 original size:9 final size:9
Alignment explanation
Indices: 1883563--1883631 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
1883553 ATTTGAATTT
*
1883563 ATTAATTTA
1 ATTATTTTA
1883572 ATTATTTTA
1 ATTATTTTA
*
1883581 AGTTTAATTTA
1 A--TTATTTTA
1883592 ATTAATTTTA
1 ATT-ATTTTA
1883602 A--ATTATTA
1 ATTATT-TTA
*
1883610 ATTTTTTTA
1 ATTATTTTA
1883619 ATTTATTTTA
1 A-TTATTTTA
1883629 ATT
1 ATT
1883632 TAATAAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
9 17 0.35
10 16 0.33
11 8 0.17
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (9 bp):
ATTATTTTA
Found at i:1883596 original size:15 final size:14
Alignment explanation
Indices: 1883427--1883635 Score: 89
Period size: 15 Copynumber: 14.9 Consensus size: 14
1883417 AAATCATATG
*
1883427 ATTTAAATTAATTA
1 ATTTAATTTAATTA
1883441 ATTTAATATTTAAATTA
1 ATTT-A-ATTT-AATTA
*
1883458 ATTAAATTTTAATTA
1 ATTTAA-TTTAATTA
*
1883473 TTTTAAATTTAATTA
1 ATTT-AATTTAATTA
*
1883488 TTTTAAATTTAAATTA
1 ATTT-AATTT-AATTA
*
1883504 ATTAAATTTAA-T-
1 ATTTAATTTAATTA
* *
1883516 ATTTAAATTAATTT
1 ATTTAATTTAATTA
* *
1883530 ATTT-A--TGATCA
1 ATTTAATTTAATTA
* * *
1883541 AGTAAATGT-ATT-
1 ATTTAATTTAATTA
1883553 ATTTGAATTT-ATTA
1 ATTT-AATTTAATTA
*
1883567 ATTTAA-TTATTTTA
1 ATTTAATTTA-ATTA
1883581 AGTTTAATTTAATTA
1 A-TTTAATTTAATTA
*
1883596 ATTTTAAATT-ATTA
1 A-TTTAATTTAATTA
*
1883610 ATTT-TTTTAATTTA
1 ATTTAATTTAA-TTA
*
1883624 TTTTAATTTAAT
1 ATTTAATTTAAT
1883636 AAAATAGAAC
Statistics
Matches: 150, Mismatches: 25, Indels: 40
0.70 0.12 0.19
Matches are distributed among these distances:
11 5 0.03
12 16 0.11
13 18 0.12
14 31 0.21
15 53 0.35
16 19 0.13
17 8 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTTAATTTAATTA
Found at i:1884724 original size:25 final size:24
Alignment explanation
Indices: 1884670--1884724 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1884660 TATTTTATTT
1884670 TATTTTAGTTTTTTTATAAAATAA
1 TATTTTAGTTTTTTTATAAAATAA
* *
1884694 TTATTTTATTTTATTTTAATAAATTAA
1 -TATTTTAGTTT-TTTT-ATAAAATAA
1884721 -ATTT
1 TATTT
1884725 ATGATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 14 0.54
26 4 0.15
27 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TATTTTAGTTTTTTTATAAAATAA
Found at i:1885485 original size:3 final size:3
Alignment explanation
Indices: 1885477--1885507 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1885467 TAATTGGAAG
*
1885477 ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1885508 AATTTACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1886578 original size:80 final size:79
Alignment explanation
Indices: 1886428--1886586 Score: 248
Period size: 80 Copynumber: 2.0 Consensus size: 79
1886418 CAATAATATG
* * *
1886428 GTCCTTCAAAAGCACAATGTGATTTTCAGCTGAAAAAAAAAAAAATCATTTTTGCGATATGGAGA
1 GTCCTTCAAAAGCACAATGTGATTGTCAGCTGAAAAAAAAAAAAAACATTTTTGAGATATGGAGA
1886493 GGGAAAATTTGACC
66 GGGAAAATTTGACC
* *
1886507 GTCCTTC-AAAGCACAGTGTGATTGTCAGCTGAAAAAAAAAAAAAAAACTTTTTTGAGATATGGA
1 GTCCTTCAAAAGCACAATGTGATTGTCAGCTG--AAAAAAAAAAAAAACATTTTTGAGATATGGA
1886571 GAGGGAAAATTTGACC
64 GAGGGAAAATTTGACC
1886587 ATGATATGGA
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
78 22 0.30
79 7 0.10
80 44 0.60
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (79 bp):
GTCCTTCAAAAGCACAATGTGATTGTCAGCTGAAAAAAAAAAAAAACATTTTTGAGATATGGAGA
GGGAAAATTTGACC
Found at i:1892671 original size:72 final size:72
Alignment explanation
Indices: 1892549--1892693 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
1892539 TTTTGTTTAA
1892549 TCCTAAACTTAAAGCAAGATAAGATTCAGTGTTCATGGCTGCCACCGATTAGGTTGAGGACTGAA
1 TCCTAAACTTAAAGCAAGATAAGATTCAGTGTTCATGGCTGCCACCGATTAGGTTGAGGACTGAA
1892614 ATTTCTT
66 ATTTCTT
* * *
1892621 TCCTAAACTTAAAGCAAGATAAGATTCAGTGTTCATGGTTGCCGCTGATTAGGTTGAGGACTGAA
1 TCCTAAACTTAAAGCAAGATAAGATTCAGTGTTCATGGCTGCCACCGATTAGGTTGAGGACTGAA
1892686 ATTTCTT
66 ATTTCTT
1892693 T
1 T
1892694 TTCCTTTTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (72 bp):
TCCTAAACTTAAAGCAAGATAAGATTCAGTGTTCATGGCTGCCACCGATTAGGTTGAGGACTGAA
ATTTCTT
Found at i:1892774 original size:24 final size:24
Alignment explanation
Indices: 1892742--1892792 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1892732 TATCACTAAT
* *
1892742 TAAAAAATAATATATTAAATATTA
1 TAAAAAATAATAAATTAAATATAA
* * *
1892766 TAAATAATATTAAATTTAATATAA
1 TAAAAAATAATAAATTAAATATAA
1892790 TAA
1 TAA
1892793 TTTTATAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAAAAATAATAAATTAAATATAA
Found at i:1892777 original size:19 final size:20
Alignment explanation
Indices: 1892748--1892805 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
1892738 TAATTAAAAA
1892748 ATAAT-ATATTAAATATTAT
1 ATAATAATATTAAATATTAT
1892767 A-AATAATATTAAAT-TTAAT
1 ATAATAATATTAAATATT-AT
*
1892786 ATAATAATTTTATAATATTA
1 ATAATAATATTA-AATATTA
1892806 ATTACATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 5 0.15
19 13 0.39
20 9 0.27
21 4 0.12
22 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATAATATTAAATATTAT
Found at i:1893517 original size:17 final size:17
Alignment explanation
Indices: 1893491--1893530 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
1893481 ATTTAAAATG
1893491 TTAAATATAT-TT-ATA
1 TTAAATATATATTAATA
1893506 TTAAATATATATTAATA
1 TTAAATATATATTAATA
*
1893523 TTCAATAT
1 TTAAATAT
1893531 TCATTCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.45
16 2 0.09
17 10 0.45
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATATATATTAATA
Found at i:1895254 original size:2 final size:2
Alignment explanation
Indices: 1895247--1895283 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1895237 AACCATCTTA
1895247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1895284 AATGTTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1896756 original size:153 final size:150
Alignment explanation
Indices: 1896500--1897302 Score: 506
Period size: 153 Copynumber: 5.2 Consensus size: 150
1896490 TATACCTTCG
* * *
1896500 ACATGAAAGTATCTTAGTAATCC-TAAAAAAC-TAAAAAATGATCATAAAAAAAGTGAACCTATC
1 ACATGAAAGTATCTTAGTAA-CCTTAAAAGACAT-GAAAA-G---ATAAAAAAAGTGAACCTATT
* * * * *
1896563 CTAAATGTACACCTTCGGCAT-AAAG-GTATCTTAGTGACTACTTAAGTCTCAGTTTTAAAGAAA
60 CTAAATGCACACCTTTGGCATAAAAGCG-A-C-TCGTGACTACTTAAGACTCAGTTCTAAAGAAA
* *
1896626 TTAGCAAAATGCCCTTAGGGCATACCTTTA
122 TTACCAAAATGCCCTTAGGGTATA-CTTTA
* * * *
1896656 ACGTGAAAGTATCTTAGTAATCTTAAAGGACATGAAAAGATAACAAAATGTGAACCTATTCTAAA
1 ACATGAAAGTATCTTAGTAACCTTAAAAGACATGAAAAGATAA-AAAAAGTGAACCTATTCTAAA
* * **
1896721 TGCACACCTTTGGCATAAAAGCGACTCAGTAACTACTTAAGACTC-GATTATATTGAAATTACCA
65 TGCACACCTTTGGCATAAAAGCGACTC-GTGACTACTTAAGACTCAG-TTCTAAAGAAATTACCA
* * * * *
1896785 AAATACCTTTAGAGTATATTTTCG
128 AAATGCCCTTAGGGTATACTTT-A
* * *
1896809 ATATGAAAGTATC-TCGATAACCTTAAAAGATATGAAAAGATTAAAAAAAGTGATAAACCTATTC
1 ACATGAAAGTATCTTAG-TAACCTTAAAAGACATGAAAAGA-TAAAAAAAGTG---AACCTATTC
* * * * * *
1896873 CAAATGCACACCTTTGTCATATAAA-TGACCTCGTGACTACTTAGGACTTAGTTCTAAGGAAA-T
61 TAAATGCACACCTTTGGCATA-AAAGCGA-CTCGTGACTACTTAAGACTCAGTTCTAAAGAAATT
* *
1896936 ACGAAAATG-CCTCTA-GGTATATCTTTC
124 ACCAAAATGCCCT-TAGGGTATA-CTTTA
* ** * *
1896963 ACATGAAAGTAT-TATTGTAACCCCAAATGACATG-AAA-ATAAAGCTAGATAAGTGAACCTATC
1 ACATGAAAGTATCT-TAGTAACCTTAAAAGACATGAAAAGATAAA---A-A-AAGTGAACCTATT
** * * * * * *
1897025 CTAAACACATACTTTTGGCATAAAAGCGACTTGGTGACTAC-TAAGACTCAATTTTAAAAAAATT
60 CTAAATGCACACCTTTGGCATAAAAGCGAC-TCGTGACTACTTAAGACTCAGTTCTAAAGAAATT
* ** *
1897089 ACCATAATGCCCTTAAAGTATACTTTCG
124 ACCAAAATGCCCTTAGGGTATACTTT-A
** * * * ** *
1897117 ATGTGAAAGTATCCTAGTAGCC-TAAAGGACACAAAAATGATATTAAAAAAGATGAATCTA-TCA
1 ACATGAAAGTATCTTAGTAACCTTAAAAGACATGAAAA-GATA--AAAAAAG-TGAACCTATTC-
* * * * * *
1897180 TAAATGCACACCTTTGGCATAAAAACGACTCGCTAACTACCTAAGACTTAGATCTAGAGAAATTA
61 TAAATGCACACCTTTGGCATAAAAGCGACTCG-TGACTACTTAAGACTCAGTTCTAAAGAAATTA
* * * *
1897245 TCAAAATACACTT-GGGTATACCTTCA
125 CCAAAATGCCCTTAGGGTATA-CTTTA
* *
1897271 ACATGAAAATTTCTTAGTAACCTTAAAAGACA
1 ACATGAAAGTATCTTAGTAACCTTAAAAGACA
1897303 CAAAAATGAT
Statistics
Matches: 496, Mismatches: 108, Indels: 87
0.72 0.16 0.13
Matches are distributed among these distances:
151 4 0.01
152 31 0.06
153 178 0.36
154 126 0.25
155 58 0.12
156 89 0.18
157 8 0.02
158 2 0.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (150 bp):
ACATGAAAGTATCTTAGTAACCTTAAAAGACATGAAAAGATAAAAAAAGTGAACCTATTCTAAAT
GCACACCTTTGGCATAAAAGCGACTCGTGACTACTTAAGACTCAGTTCTAAAGAAATTACCAAAA
TGCCCTTAGGGTATACTTTA
Found at i:1898587 original size:13 final size:13
Alignment explanation
Indices: 1898569--1898594 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1898559 CATTTTTCTG
1898569 TGTATCGATACAT
1 TGTATCGATACAT
1898582 TGTATCGATACAT
1 TGTATCGATACAT
1898595 GGATCTTTGT
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:1898591 original size:33 final size:33
Alignment explanation
Indices: 1898549--1898615 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1898539 GCCAAGGAAA
***
1898549 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1898582 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1898615 T
1 T
1898616 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1901142 original size:28 final size:27
Alignment explanation
Indices: 1901075--1901143 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
1901065 CTTCACAATC
* *
1901075 GGGGGTACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1901102 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1901130 GGGGATACTCCAAC
1 GGGGATACTCCAAC
1901144 TCCGGTTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1901190 original size:52 final size:51
Alignment explanation
Indices: 1901130--1901299 Score: 157
Period size: 52 Copynumber: 3.3 Consensus size: 51
1901120 TTATTTCTGA
* *
1901130 GGGGATACTCCAACTCCGGTTTGATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATC-CTAAAACACCAATTTTTCCACAATC
** * * **
1901182 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCGA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATCCT-AAAACACCAATTTTTCC-ACAATC
* * *
1901234 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTA--TCCTAAAACACCAATTTTTCCACAATC
*
1901286 GAGGATACTCCAAC
1 GGGGATACTCCAAC
1901300 CTCGTTATTT
Statistics
Matches: 93, Mismatches: 18, Indels: 14
0.74 0.14 0.11
Matches are distributed among these distances:
51 10 0.11
52 67 0.72
53 11 0.12
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATCCTAAAACACCAATTTTTCCACAATC
Found at i:1901319 original size:28 final size:28
Alignment explanation
Indices: 1901283--1901359 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
1901273 ATTTTTCACA
* * *
1901283 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
1901311 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
1901339 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1901360 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:1901346 original size:212 final size:212
Alignment explanation
Indices: 1900960--1901360 Score: 601
Period size: 212 Copynumber: 1.9 Consensus size: 212
1900950 TTATCAATTC
* *
1900960 TCCACAATCGGCGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGCGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* * *
1901025 TACTCTAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGGTACTCCAACC
66 TACTCCAACTCCGATTTTATTTCC-AAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACC
* * *
1901090 CCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACTCCGGTTTGAT
130 CCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGTTTGAT
1901155 CGCTAAAACACTAATTTT
195 CGCTAAAACACTAATTTT
* * * * *
1901173 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCGATTTTCCTTTAATCGGG
1 TCCACAATCGGCGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
1901237 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
1901300 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGG
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGG
1901361 CTTTATTCCC
Statistics
Matches: 169, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
211 27 0.16
212 65 0.38
213 42 0.25
214 35 0.21
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (212 bp):
TCCACAATCGGCGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGTTTGATC
GCTAAAACACTAATTTT
Found at i:1901426 original size:107 final size:107
Alignment explanation
Indices: 1901020--1901438 Score: 255
Period size: 107 Copynumber: 3.9 Consensus size: 107
1901010 TTCTATAATC
* * * * * *
1901020 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGGTACTC
1 GGGGATACTCCAACCCCGACTTTATTTCC--AAAAATACCAATTTC-TCACAATCGAGGATACTC
* * * *
1901085 CAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGA
63 CAACCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
* * * * * * *
1901130 GGGGATACTCCAACTCCG-GTTTGA--TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTC
1 GGGGATACTCCAACCCCGACTTT-ATTTC-CAAAAATACCAATTTCT-CACAATCGAGGATACTC
* * * ***** * * *** * *
1901192 CAATCCTGGT-TTTATTTTCAAAACGCCGATTTTCCTTTA-AT-C--
63 CAACCCCGTTATTTATCGGGGATACTCC-A-ACCCCGTTACTTCCGA
* * *
1901234 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
1901299 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * * * *
1901342 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCTAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
1901406 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAACCCCG
1901439 ATTTTTTTTT
Statistics
Matches: 234, Mismatches: 59, Indels: 35
0.71 0.18 0.11
Matches are distributed among these distances:
104 46 0.20
105 25 0.11
106 19 0.08
107 94 0.40
108 28 0.12
109 4 0.02
110 18 0.08
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:1908354 original size:55 final size:55
Alignment explanation
Indices: 1907594--1908344 Score: 1179
Period size: 55 Copynumber: 13.6 Consensus size: 55
1907584 GACTCTGTGG
1907594 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
**
1907649 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTTAAAGAGCAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
* *
1907704 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGTAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCCCAAAGAGCAGGA
1907759 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
*** *
1907814 CACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCCTCAAAGAGCAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
*
1907869 CACCTCTTAAAGCCCACACAAGTTGGTGGTATTTTCCAGTCCCCAAAGAGCAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
1907924 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
*
1907979 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCCCAAAGAGCAGGA
*** *
1908034 CACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCCTCAAAGAGCAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
*
1908089 CATCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
**** *
1908144 CACCTCTTAAAGCCCACACAAGTTGGTGGTGCCTTCCAGTCCTCAAAGAGCAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
* *
1908199 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAACAGGA
1 CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
* *
1908254 CACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGA
1 CACCTCTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCCCAAAGAGCAGGA
* *
1908309 CGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTT
1 CACCTCTT-AAAGCCCACACAAGTTGGTGGCA-TTTT
1908345 TACTCCTCAA
Statistics
Matches: 647, Mismatches: 43, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
54 8 0.01
55 630 0.97
56 9 0.01
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (55 bp):
CACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
Found at i:1909226 original size:19 final size:19
Alignment explanation
Indices: 1909202--1909269 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1909192 AATTCAACGA
1909202 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1909221 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1909236 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1909253 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1909270 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1909240 original size:32 final size:32
Alignment explanation
Indices: 1909204--1909266 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1909194 TTCAACGATT
*
1909204 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1909236 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1909267 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1909241 original size:13 final size:13
Alignment explanation
Indices: 1909223--1909247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1909213 ACATAAGTTT
1909223 TGTATCGATACAA
1 TGTATCGATACAA
1909236 TGTATCGATACA
1 TGTATCGATACA
1909248 TAAGTATTGT
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:1909327 original size:13 final size:13
Alignment explanation
Indices: 1909309--1909334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1909299 CATTTTTCTG
1909309 TGTATCGATACAT
1 TGTATCGATACAT
1909322 TGTATCGATACAT
1 TGTATCGATACAT
1909335 GGATCTTTGT
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:1909331 original size:33 final size:33
Alignment explanation
Indices: 1909289--1909355 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1909279 GCCAAGGAAA
***
1909289 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1909322 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1909355 T
1 T
1909356 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1911883 original size:28 final size:27
Alignment explanation
Indices: 1911816--1911884 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
1911806 CTTCACAATC
* *
1911816 GGGGGTACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1911843 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1911871 GGGGATACTCCAAC
1 GGGGATACTCCAAC
1911885 TCCGGTTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1911931 original size:52 final size:51
Alignment explanation
Indices: 1911871--1912040 Score: 157
Period size: 52 Copynumber: 3.3 Consensus size: 51
1911861 TTATTTCTGA
* *
1911871 GGGGATACTCCAACTCCGGTTTGATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATC-CTAAAACACCAATTTTTCCACAATC
** * * **
1911923 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCGA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATCCT-AAAACACCAATTTTTCC-ACAATC
* * *
1911975 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTA--TCCTAAAACACCAATTTTTCCACAATC
*
1912027 GAGGATACTCCAAC
1 GGGGATACTCCAAC
1912041 CTCGTTATTT
Statistics
Matches: 93, Mismatches: 18, Indels: 14
0.74 0.14 0.11
Matches are distributed among these distances:
51 10 0.11
52 67 0.72
53 11 0.12
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATCCTAAAACACCAATTTTTCCACAATC
Found at i:1912060 original size:28 final size:28
Alignment explanation
Indices: 1912024--1912100 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
1912014 ATTTTTCACA
* * *
1912024 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
1912052 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
1912080 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1912101 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:1912087 original size:212 final size:212
Alignment explanation
Indices: 1911701--1912101 Score: 601
Period size: 212 Copynumber: 1.9 Consensus size: 212
1911691 TTATCAATTC
* *
1911701 TCCACAATCGGCGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGCGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* * *
1911766 TACTCTAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGGTACTCCAACC
66 TACTCCAACTCCGATTTTATTTCC-AAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACC
* * *
1911831 CCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACTCCGGTTTGAT
130 CCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGTTTGAT
1911896 CGCTAAAACACTAATTTT
195 CGCTAAAACACTAATTTT
* * * * *
1911914 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCGATTTTCCTTTAATCGGG
1 TCCACAATCGGCGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
1911978 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
1912041 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGG
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGG
1912102 CTTTATTCCC
Statistics
Matches: 169, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
211 27 0.16
212 65 0.38
213 42 0.25
214 35 0.21
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (212 bp):
TCCACAATCGGCGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGTTTGATC
GCTAAAACACTAATTTT
Found at i:1912167 original size:107 final size:107
Alignment explanation
Indices: 1911761--1912179 Score: 255
Period size: 107 Copynumber: 3.9 Consensus size: 107
1911751 TTCTATAATC
* * * * * *
1911761 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGGTACTC
1 GGGGATACTCCAACCCCGACTTTATTTCC--AAAAATACCAATTTC-TCACAATCGAGGATACTC
* * * *
1911826 CAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGA
63 CAACCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
* * * * * * *
1911871 GGGGATACTCCAACTCCG-GTTTGA--TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTC
1 GGGGATACTCCAACCCCGACTTT-ATTTC-CAAAAATACCAATTTCT-CACAATCGAGGATACTC
* * * ***** * * *** * *
1911933 CAATCCTGGT-TTTATTTTCAAAACGCCGATTTTCCTTTA-AT-C--
63 CAACCCCGTTATTTATCGGGGATACTCC-A-ACCCCGTTACTTCCGA
* * *
1911975 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
1912040 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * * * *
1912083 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCTAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
1912147 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAACCCCG
1912180 ATTTTTTTTT
Statistics
Matches: 234, Mismatches: 59, Indels: 35
0.71 0.18 0.11
Matches are distributed among these distances:
104 46 0.20
105 25 0.11
106 19 0.08
107 94 0.40
108 28 0.12
109 4 0.02
110 18 0.08
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:1913367 original size:20 final size:21
Alignment explanation
Indices: 1913342--1913385 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1913332 GTATATATGA
1913342 AAAAATCAAAATCATATC-AC
1 AAAAATCAAAATCATATCAAC
*
1913362 AAAAATCAACATCATATCAAC
1 AAAAATCAAAATCATATCAAC
1913383 AAA
1 AAA
1913386 TAACATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.18
Consensus pattern (21 bp):
AAAAATCAAAATCATATCAAC
Found at i:1913966 original size:13 final size:13
Alignment explanation
Indices: 1913950--1913974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1913940 AAAAATCAAA
1913950 TAAAATTAAAATC
1 TAAAATTAAAATC
1913963 TAAAATTAAAAT
1 TAAAATTAAAAT
1913975 TAATAATCAT
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAATTAAAATC
Found at i:1918793 original size:25 final size:24
Alignment explanation
Indices: 1918738--1918809 Score: 94
Period size: 25 Copynumber: 3.0 Consensus size: 24
1918728 CAACTTCCAT
*
1918738 ATTTTGATGATTCATCA-CTCATG
1 ATTTCGATGATTCATCATCTCATG
1918761 -TTTCCGATGATTCATCAGTCTCATG
1 ATTT-CGATGATTCATCA-TCTCATG
1918786 ATTTCGATGATTCATCAATCTCAT
1 ATTTCGATGATTCATC-ATCTCAT
1918810 TCTATTTGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
22 3 0.07
23 12 0.28
25 24 0.56
26 4 0.09
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (24 bp):
ATTTCGATGATTCATCATCTCATG
Found at i:1926925 original size:52 final size:52
Alignment explanation
Indices: 1926847--1927047 Score: 314
Period size: 52 Copynumber: 3.9 Consensus size: 52
1926837 CGAAATATGA
*
1926847 AAATTTGCCTGTATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1926899 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
** * * *
1926951 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATTTGGGA
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
**
1927003 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAAT-AGTGTATCGATACA
1927048 ATGTATCGAT
Statistics
Matches: 138, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
51 2 0.01
52 136 0.99
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
Found at i:1927054 original size:13 final size:13
Alignment explanation
Indices: 1927036--1927060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1927026 CAAAGATCAG
1927036 TGTATCGATACAA
1 TGTATCGATACAA
1927049 TGTATCGATACA
1 TGTATCGATACA
1927061 TTTAAGTGAT
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:1927141 original size:13 final size:13
Alignment explanation
Indices: 1927123--1927147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1927113 CAAAAAAAAA
1927123 TGTATCGATACAT
1 TGTATCGATACAT
1927136 TGTATCGATACA
1 TGTATCGATACA
1927148 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1928464 original size:23 final size:24
Alignment explanation
Indices: 1928438--1928483 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1928428 ATAGAATGGA
*
1928438 GAAAACGTAAAA-AAAAGAAAAAT
1 GAAAACGTAAAAGAAAAAAAAAAT
*
1928461 GAAAAGGTAAAAGAAAAAAAAAA
1 GAAAACGTAAAAGAAAAAAAAAA
1928484 GGCAAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (24 bp):
GAAAACGTAAAAGAAAAAAAAAAT
Found at i:1928608 original size:26 final size:25
Alignment explanation
Indices: 1928554--1928608 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
1928544 CATAAAATTT
*
1928554 AAAATTTAAAAAATACCAAAATAATA
1 AAAATTTAAAAAATACCAAAA-AAAA
* *
1928580 AAATTTTAAAAAGTACCAAAAAAAA
1 AAAATTTAAAAAATACCAAAAAAAA
1928605 AAAA
1 AAAA
1928609 GCAAGAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (25 bp):
AAAATTTAAAAAATACCAAAAAAAA
Found at i:1928850 original size:13 final size:13
Alignment explanation
Indices: 1928832--1928858 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1928822 AAAAGAATTC
1928832 TTTTATTTATTTT
1 TTTTATTTATTTT
1928845 TTTTATTTATTTT
1 TTTTATTTATTTT
1928858 T
1 T
1928859 ACATTGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTATTTT
Found at i:1930054 original size:2 final size:2
Alignment explanation
Indices: 1930041--1930076 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1930031 AATTTATCAA
*
1930041 AT AT AA AT 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 AT AT AT AT
1930077 TTAAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1938814 original size:12 final size:11
Alignment explanation
Indices: 1938773--1938828 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
1938763 ATCAATTTTT
*
1938773 TTATATTTTTA
1 TTATATTTATA
1938784 -TATATTTAAATA
1 TTATATTT--ATA
1938796 TTATATTTATA
1 TTATATTTATA
*
1938807 TCTATATTTAAA
1 T-TATATTTATA
1938819 TATATATTTA
1 T-TATATTTA
1938829 AATATAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.18
11 4 0.11
12 20 0.53
13 7 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTATATTTATA
Done.