Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_pilon, 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: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 23
Found at i:2790925 original size:42 final size:42
Alignment explanation
Indices: 2790832--2790925 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
2790822 ATTTATATGT
* *
2790832 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
** * *
2790873 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGCAAAA
2790915 TCGCGTTGCGA
1 TCGCGTTGCGA
2790926 TTATGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGCAAAA
Found at i:2791132 original size:2 final size:2
Alignment explanation
Indices: 2791125--2791154 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2791115 ACCTTAAATT
2791125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2791155 ATCCTTACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2791761 original size:8 final size:8
Alignment explanation
Indices: 2791748--2791780 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2791738 ATGATTATTC
2791748 AATTTACT
1 AATTTACT
2791756 AATTTACT
1 AATTTACT
2791764 -ATTTCACT
1 AATTT-ACT
2791772 AATTTACT
1 AATTTACT
2791780 A
1 A
2791781 GTTTGATGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 4 0.17
8 15 0.65
9 4 0.17
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTACT
Found at i:2792136 original size:24 final size:23
Alignment explanation
Indices: 2792099--2792152 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
2792089 TCACGAAATA
*
2792099 TGTTCATTTAATGTTCGTGAACG
1 TGTTCATTTAATGTTCATGAACG
* *
2792122 TGTTCGTTTATATGTTCATGAATG
1 TGTTCATTTA-ATGTTCATGAACG
2792146 TGTTCAT
1 TGTTCAT
2792153 AAGCATGTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.48
Consensus pattern (23 bp):
TGTTCATTTAATGTTCATGAACG
Found at i:2792180 original size:70 final size:70
Alignment explanation
Indices: 2792100--2792262 Score: 184
Period size: 76 Copynumber: 2.2 Consensus size: 70
2792090 CACGAAATAT
* * *
2792100 GTTCATTTAATGTTCGTGAACGTGTTCGTTTATATGTTCATGAATGTGTTCAT-AAGCATGTTCG
1 GTTCATTTAATGTTCGTGAACGTGTTCGTTTATATGTTCATGAACGTGATCATGAA-CATGTTCA
2792164 TTTAGC
65 TTTAGC
* *
2792170 GTTCGTTTAATGTTTGCGAACGTGTACGTGTTCGTTTATATGTTCATGAACGTGATCATGAACAT
1 GTTCATTTAATG-TT-----CGTGAACGTGTTCGTTTATATGTTCATGAACGTGATCATGAACAT
* *
2792235 GTTCATTTCGT
60 GTTCATTTAGC
*
2792246 GTTCATTTAATCTTCGT
1 GTTCATTTAATGTTCGT
2792263 TTAGCATTGT
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
70 14 0.18
71 2 0.03
75 2 0.03
76 57 0.74
77 2 0.03
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (70 bp):
GTTCATTTAATGTTCGTGAACGTGTTCGTTTATATGTTCATGAACGTGATCATGAACATGTTCAT
TTAGC
Found at i:2792211 original size:76 final size:76
Alignment explanation
Indices: 2792114--2792256 Score: 207
Period size: 76 Copynumber: 1.9 Consensus size: 76
2792104 ATTTAATGTT
* * * *
2792114 CGTGAACGTGTTCGTTTATATGTTCATGAATGTGTTCAT-AAGCATGTTCGTTTAGCGTTCGTTT
1 CGTGAACGTGTTCGTTTATATGTTCATGAACGTGATCATGAA-CATGTTCATTTAGCGTTCATTT
2792178 AATGTTTGCGAA
65 AATGTTTGCGAA
* * *
2792190 CGTGTACGTGTTCGTTTATATGTTCATGAACGTGATCATGAACATGTTCATTTCGTGTTCATTTA
1 CGTGAACGTGTTCGTTTATATGTTCATGAACGTGATCATGAACATGTTCATTTAGCGTTCATTTA
2792255 AT
66 AT
2792257 CTTCGTTTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
76 57 0.97
77 2 0.03
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.43
Consensus pattern (76 bp):
CGTGAACGTGTTCGTTTATATGTTCATGAACGTGATCATGAACATGTTCATTTAGCGTTCATTTA
ATGTTTGCGAA
Found at i:2792533 original size:12 final size:12
Alignment explanation
Indices: 2792518--2792581 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
2792508 TTGATAAACG
*
2792518 AGCTCATAAATA
1 AGCTTATAAATA
2792530 AGCTTATAAACT-
1 AGCTTATAAA-TA
* **
2792542 AGCTCATAAACG
1 AGCTTATAAATA
*
2792554 AGCTTATAAATG
1 AGCTTATAAATA
*
2792566 AGCTTATAAACA
1 AGCTTATAAATA
2792578 AGCT
1 AGCT
2792582 AACTCATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 42 0.98
13 1 0.02
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (12 bp):
AGCTTATAAATA
Found at i:2792545 original size:24 final size:24
Alignment explanation
Indices: 2792511--2792581 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
2792501 GAATGAGTTG
* *
2792511 ATAAACGAGCTCATAAATAAGCTT
1 ATAAACTAGCTCATAAACAAGCTT
*
2792535 ATAAACTAGCTCATAAACGAGCTT
1 ATAAACTAGCTCATAAACAAGCTT
*
2792559 ATAAA-TGAGCTTATAAACAAGCT
1 ATAAACT-AGCTCATAAACAAGCT
2792582 AACTCATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (24 bp):
ATAAACTAGCTCATAAACAAGCTT
Found at i:2792554 original size:36 final size:36
Alignment explanation
Indices: 2792511--2792581 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
2792501 GAATGAGTTG
*
2792511 ATAAACGAGCTCATAAATAAGCTTATAAACTAGCTC
1 ATAAACGAGCTCATAAATAAGCTTATAAACAAGCTC
* *
2792547 ATAAACGAGCTTATAAATGAGCTTATAAACAAGCT
1 ATAAACGAGCTCATAAATAAGCTTATAAACAAGCT
2792582 AACTCATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (36 bp):
ATAAACGAGCTCATAAATAAGCTTATAAACAAGCTC
Found at i:2798610 original size:123 final size:118
Alignment explanation
Indices: 2798391--2798631 Score: 412
Period size: 123 Copynumber: 2.0 Consensus size: 118
2798381 AAATTGACAA
2798391 TTAAAATATAAGAATCATATTTACATAAGTCATGGGCAATTGCATGCTTGTCATGGGCTTTGAGG
1 TTAAAATATAAGAATCATATTTACATAAGTCATGGGCAATTGCATGCTTGTCATGGGCTTTGAGG
2798456 TCTTCATCATAATCTCATAAATAGGTCTAATTACTTGAACCCAAAATCTCTTT
66 TCTTCATCATAATCTCATAAATAGGTCTAATTACTTGAACCCAAAATCTCTTT
*
2798509 TTAATATATAAGAATCATATTTACATAAGTCAT-GGCATACTTGCATGCACTTGTCATGGAGGCT
1 TTAAAATATAAGAATCATATTTACATAAGTCATGGGCA-A-TTGCATG--CTTGTCAT-G-GGCT
2798573 TTGAGGTCTTCATCATAATCTCATAAATAGGTCTAATTACTTGAACCCAAAATCTCTTT
60 TTGAGGTCTTCATCATAATCTCATAAATAGGTCTAATTACTTGAACCCAAAATCTCTTT
2798632 GAAAGAACAA
Statistics
Matches: 116, Mismatches: 1, Indels: 7
0.94 0.01 0.06
Matches are distributed among these distances:
117 4 0.03
118 33 0.28
119 7 0.06
121 8 0.07
122 1 0.01
123 63 0.54
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (118 bp):
TTAAAATATAAGAATCATATTTACATAAGTCATGGGCAATTGCATGCTTGTCATGGGCTTTGAGG
TCTTCATCATAATCTCATAAATAGGTCTAATTACTTGAACCCAAAATCTCTTT
Found at i:2800317 original size:31 final size:31
Alignment explanation
Indices: 2800282--2800377 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
2800272 CCAACCTAAG
2800282 GGAATAACTTGGGGCCTTAA-AGCCTACCCAA
1 GGAATAACTTGGGGCC-TAAGAGCCTACCCAA
*
2800313 GGAATACCTTGGGGCCTAAGAGCCTACCCAA
1 GGAATAACTTGGGGCCTAAGAGCCTACCCAA
* * * * *
2800344 GAGAGTATCTCGAGGCCTAATAGCCTACCCAA
1 G-GAATAACTTGGGGCCTAAGAGCCTACCCAA
2800376 GG
1 GG
2800378 GTCACCTTAG
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.05
31 28 0.49
32 26 0.46
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (31 bp):
GGAATAACTTGGGGCCTAAGAGCCTACCCAA
Found at i:2800369 original size:32 final size:30
Alignment explanation
Indices: 2800294--2800377 Score: 96
Period size: 32 Copynumber: 2.7 Consensus size: 30
2800284 AATAACTTGG
* *
2800294 GGCCTTAAAGCCTACCCAAGGAATACCTTGG
1 GGCC-TAAAGCCTACCCAAGGAATACCTCGA
* *
2800325 GGCCTAAGAGCCTACCCAAGAGAGTATCTCGA
1 GGCCTAA-AGCCTACCCAAG-GAATACCTCGA
2800357 GGCCTAATAGCCTACCCAAGG
1 GGCCTAA-AGCCTACCCAAGG
2800378 GTCACCTTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 3 0.07
31 17 0.37
32 26 0.57
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.17
Consensus pattern (30 bp):
GGCCTAAAGCCTACCCAAGGAATACCTCGA
Found at i:2810400 original size:57 final size:58
Alignment explanation
Indices: 2810312--2810427 Score: 225
Period size: 57 Copynumber: 2.0 Consensus size: 58
2810302 TAGCGATAAA
2810312 GGTTAGCTCCATTCGGCCTTGGGGTATGATTTATTTGGAGCAAGGTTAG-AAATTTGT
1 GGTTAGCTCCATTCGGCCTTGGGGTATGATTTATTTGGAGCAAGGTTAGAAAATTTGT
2810369 GGTTAGCTCCATTCGGCCTTGGGGTATGATTTATTTGGAGCAAGGTTAGAAAATTTGT
1 GGTTAGCTCCATTCGGCCTTGGGGTATGATTTATTTGGAGCAAGGTTAGAAAATTTGT
2810427 G
1 G
2810428 AAGTCTTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 49 0.84
58 9 0.16
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (58 bp):
GGTTAGCTCCATTCGGCCTTGGGGTATGATTTATTTGGAGCAAGGTTAGAAAATTTGT
Found at i:2812335 original size:21 final size:21
Alignment explanation
Indices: 2812311--2812378 Score: 127
Period size: 21 Copynumber: 3.2 Consensus size: 21
2812301 TTCAAAAAAA
2812311 ATGCTAAGTATGATTTCTATC
1 ATGCTAAGTATGATTTCTATC
*
2812332 ATGCTAAGTATGATTTCTATA
1 ATGCTAAGTATGATTTCTATC
2812353 ATGCTAAGTATGATTTCTATC
1 ATGCTAAGTATGATTTCTATC
2812374 ATGCT
1 ATGCT
2812379 TAGCTAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (21 bp):
ATGCTAAGTATGATTTCTATC
Found at i:2813376 original size:3 final size:3
Alignment explanation
Indices: 2813368--2813399 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2813358 TTGTTCAAAC
2813368 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2813400 CGTAATTTCT
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:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:2814175 original size:19 final size:19
Alignment explanation
Indices: 2814151--2814189 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2814141 AATAGAAAAT
2814151 GCAAAACAGAGAAAAGAAA
1 GCAAAACAGAGAAAAGAAA
2814170 GCAAAACAGAGAAAAGAAA
1 GCAAAACAGAGAAAAGAAA
2814189 G
1 G
2814190 GAATAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.10, G:0.23, T:0.00
Consensus pattern (19 bp):
GCAAAACAGAGAAAAGAAA
Found at i:2814485 original size:26 final size:26
Alignment explanation
Indices: 2814416--2814492 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
2814406 CTCACCTTTA
* * **
2814416 AAAATTTATAATTTAATCCTTATTTT
1 AAAATGTAAAATTTAATTTTTATTTT
2814442 AAAATGTAAAATTTAATTTTTATTTT
1 AAAATGTAAAATTTAATTTTTATTTT
2814468 AAAATGTAAAATTTAATTTTTATTT
1 AAAATGTAAAATTTAATTTTTATTT
2814493 AATTTAATCC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (26 bp):
AAAATGTAAAATTTAATTTTTATTTT
Found at i:2815386 original size:38 final size:38
Alignment explanation
Indices: 2815335--2815410 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
2815325 TCTGTTCTTC
2815335 GGTGACTGGAAGAAAAGGGATACCGCAATGTACATTTT
1 GGTGACTGGAAGAAAAGGGATACCGCAATGTACATTTT
2815373 GGTGACTGGAAGAAAAGGGATACCGCAATGTACATTTT
1 GGTGACTGGAAGAAAAGGGATACCGCAATGTACATTTT
2815411 TTCCAGTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (38 bp):
GGTGACTGGAAGAAAAGGGATACCGCAATGTACATTTT
Found at i:2817367 original size:13 final size:13
Alignment explanation
Indices: 2817344--2817377 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2817334 GGTATGTTAA
2817344 TGATA-TTTTGTT
1 TGATATTTTTGTT
2817356 TGATATTTTTGTT
1 TGATATTTTTGTT
2817369 TGATATTTT
1 TGATATTTT
2817378 GTTATATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (13 bp):
TGATATTTTTGTT
Found at i:2817386 original size:12 final size:12
Alignment explanation
Indices: 2817344--2817380 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
2817334 GGTATGTTAA
2817344 TGATATTTTGTT
1 TGATATTTTGTT
2817356 TGATATTTTTGTT
1 TGATA-TTTTGTT
2817369 TGATATTTTGTT
1 TGATATTTTGTT
2817381 ATATATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TGATATTTTGTT
Found at i:2817768 original size:11 final size:11
Alignment explanation
Indices: 2817752--2817814 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
2817742 TAAATTACCT
2817752 TATTAAAAATA
1 TATTAAAAATA
2817763 TATTAAAAATA
1 TATTAAAAATA
* * ***
2817774 CACTATTGATA
1 TATTAAAAATA
2817785 -ATTATAAAAT-
1 TATTA-AAAATA
2817795 T-TTAAAAATA
1 TATTAAAAATA
2817805 TATTAAAAAT
1 TATTAAAAAT
2817815 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:2817898 original size:21 final size:21
Alignment explanation
Indices: 2817872--2817933 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
2817862 CCCTAAACCT
* * **
2817872 TAAACCTTAAACCATATATCC
1 TAAACCCTAAACCATAAATAA
2817893 TAAACCCTAAACCATAAATAA
1 TAAACCCTAAACCATAAATAA
*
2817914 TAAACCCTAAACCCTAAATA
1 TAAACCCTAAACCATAAATA
2817934 GTACTTATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAACCCTAAACCATAAATAA
Found at i:2817901 original size:7 final size:7
Alignment explanation
Indices: 2817862--2817931 Score: 59
Period size: 7 Copynumber: 10.0 Consensus size: 7
2817852 TTGCATTGAG
2817862 CCCTAAA
1 CCCTAAA
*
2817869 CCTTAAA
1 CCCTAAA
*
2817876 CCTTAAA
1 CCCTAAA
* *
2817883 CCATATA
1 CCCTAAA
*
2817890 TCCTAAA
1 CCCTAAA
2817897 CCCTAAA
1 CCCTAAA
*
2817904 CCATAAA
1 CCCTAAA
***
2817911 TAATAAA
1 CCCTAAA
2817918 CCCTAAA
1 CCCTAAA
2817925 CCCTAAA
1 CCCTAAA
2817932 TAGTACTTAT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAA
Found at i:2817922 original size:28 final size:28
Alignment explanation
Indices: 2817862--2817931 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
2817852 TTGCATTGAG
* * * *
2817862 CCCTAAACCTTAAACCTTAAACCATATA
1 CCCTAAACCCTAAACCATAAACAATAAA
* *
2817890 TCCTAAACCCTAAACCATAAATAATAAA
1 CCCTAAACCCTAAACCATAAACAATAAA
2817918 CCCTAAACCCTAAA
1 CCCTAAACCCTAAA
2817932 TAGTACTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.21
Consensus pattern (28 bp):
CCCTAAACCCTAAACCATAAACAATAAA
Found at i:2831157 original size:21 final size:20
Alignment explanation
Indices: 2831124--2831162 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2831114 GAATCAAGGC
*
2831124 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
2831145 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
2831163 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:2837170 original size:3 final size:3
Alignment explanation
Indices: 2837162--2837203 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
2837152 ACCTTCACTC
* *
2837162 TCA TCA TCA TCG TCA TCT TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
2837204 CTCTCATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:2839146 original size:14 final size:14
Alignment explanation
Indices: 2839127--2839157 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2839117 AAAAATTATT
2839127 TAAATAAATTATAA
1 TAAATAAATTATAA
*
2839141 TAAATAAATTCTAA
1 TAAATAAATTATAA
2839155 TAA
1 TAA
2839158 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAATAAATTATAA
Found at i:2848596 original size:19 final size:19
Alignment explanation
Indices: 2848574--2848611 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2848564 CATTTTTTAA
2848574 ATTTGTTATCA-ATTTTTTT
1 ATTT-TTATCATATTTTTTT
*
2848593 ATTTTTCTCATATTTTTTT
1 ATTTTTATCATATTTTTTT
2848612 TACTGTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (19 bp):
ATTTTTATCATATTTTTTT
Found at i:2859756 original size:80 final size:79
Alignment explanation
Indices: 2859623--2859785 Score: 272
Period size: 80 Copynumber: 2.1 Consensus size: 79
2859613 GTTTCTGTTT
* * * *
2859623 TCTCAATTGGAAACTTCTTGAAATCCACCACTGTTGTGCCTATCTTCTGCTGCAACATGGACTGT
1 TCTCAACTGGAAACTGCTCGAAATCCACCACTGTTGTGCCTATCTTCTACTGCAACATGGACTGT
2859688 TCATCAAAAACAACA
66 TCAT-AAAAACAACA
*
2859703 TCTCAACTGGAAACTGCTCGAAATCCACCACTGTTGTGCCTATCTTCTACTGCAACATGGATTGT
1 TCTCAACTGGAAACTGCTCGAAATCCACCACTGTTGTGCCTATCTTCTACTGCAACATGGACTGT
2859768 TCATAAAAACAACA
66 TCATAAAAACAACA
2859782 TCTC
1 TCTC
2859786 TACTTATAAC
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 14 0.18
80 64 0.82
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.29
Consensus pattern (79 bp):
TCTCAACTGGAAACTGCTCGAAATCCACCACTGTTGTGCCTATCTTCTACTGCAACATGGACTGT
TCATAAAAACAACA
Found at i:2865424 original size:22 final size:22
Alignment explanation
Indices: 2865374--2865438 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
2865364 CTATTGGAAT
* * *
2865374 AATTACATCTCTTCATATGGAT
1 AATTACATCTATTCATATGAAA
**
2865396 ACCTACATCTATTCATATGAAA
1 AATTACATCTATTCATATGAAA
2865418 AATTACATCTA-TCGATATGAA
1 AATTACATCTATTC-ATATGAA
2865439 TTGTCACACC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 2 0.06
22 33 0.94
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (22 bp):
AATTACATCTATTCATATGAAA
Found at i:2868739 original size:29 final size:30
Alignment explanation
Indices: 2868686--2868745 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 30
2868676 CATACTTAGC
*
2868686 ATAAAAATGAAACTTGAAAATAAAGA-AAA
1 ATAAAAATGAAACTTGAAAAAAAAGAGAAA
2868715 ATAAAAA-G-AACTTGAAAAGGAAAAGAGAAA
1 ATAAAAATGAAACTTGAAAA--AAAAGAGAAA
2868745 A
1 A
2868746 CTTTTATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 10 0.37
28 1 0.04
29 12 0.44
30 4 0.15
ACGTcount: A:0.68, C:0.03, G:0.15, T:0.13
Consensus pattern (30 bp):
ATAAAAATGAAACTTGAAAAAAAAGAGAAA
Found at i:2871481 original size:14 final size:14
Alignment explanation
Indices: 2871462--2871489 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2871452 GCAGCAAAGT
2871462 ATGCGTGAATAGAC
1 ATGCGTGAATAGAC
2871476 ATGCGTGAATAGAC
1 ATGCGTGAATAGAC
2871490 TCACGTAAAT
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:0.14, G:0.29, T:0.21
Consensus pattern (14 bp):
ATGCGTGAATAGAC
Found at i:2879886 original size:3 final size:3
Alignment explanation
Indices: 2879878--2879947 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
2879868 AATAGTATAG
2879878 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2879926 TAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
2879948 CATATACATA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2880507 original size:12 final size:12
Alignment explanation
Indices: 2880475--2880514 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2880465 TTCAAAGAAA
2880475 TTAAAA-TTA-T
1 TTAAAATTTATT
*
2880485 TT-AAATCTATT
1 TTAAAATTTATT
2880496 TTAAAATTTATT
1 TTAAAATTTATT
2880508 TTAAAAT
1 TTAAAAT
2880515 ATGGATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:2880526 original size:22 final size:22
Alignment explanation
Indices: 2880501--2880944 Score: 559
Period size: 22 Copynumber: 20.6 Consensus size: 22
2880491 CTATTTTAAA
2880501 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2880523 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
* * ***
2880545 ATTTATTTTGAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
* ***
2880567 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
2880589 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2880611 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
* * *
2880633 A-TT-TTAT-AGAT-T-GATTT
1 ATTTATTTTAAAATATGGATTG
2880650 A-TT-TT--AAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2880668 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2880690 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2880712 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2880734 ATTTATTTAAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
2880756 ATTTATTTTAAAAAATGGATTA
1 ATTTATTTTAAAATATGGATTG
2880778 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
2880800 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
2880821 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
2880844 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
2880866 ATTTATATTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
2880888 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
2880909 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
2880932 ATTTATTTAAAAA
1 ATTTATTTTAAAA
2880945 ATTTTATTAT
Statistics
Matches: 378, Mismatches: 33, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
16 3 0.01
17 9 0.02
18 6 0.02
19 5 0.01
20 5 0.01
21 4 0.01
22 344 0.91
23 2 0.01
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:2880638 original size:18 final size:17
Alignment explanation
Indices: 2880609--2880671 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
2880599 AAATATGGAT
*
2880609 TGATTTATTTTAAAATA
1 TGATTGATTTTAAAATA
*
2880626 TGAATTGATTTTATAGAT-
1 TG-ATTGATTTTA-AAATA
*
2880644 TGATTTATTTTAAAATA
1 TGATTGATTTTAAAATA
2880661 TGGATTGATTT
1 T-GATTGATTT
2880672 ATTTAAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 3 0.08
17 12 0.32
18 19 0.51
19 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (17 bp):
TGATTGATTTTAAAATA
Found at i:2881025 original size:31 final size:31
Alignment explanation
Indices: 2880968--2881026 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2880958 AGTTGTATGG
*
2880968 ATTATTTAAATTTCATTATTATAAAACTAAA
1 ATTATTTAAATTTCATTATTACAAAACTAAA
*
2880999 ATTATTTAAATTTCATTATTGCAAAACT
1 ATTATTTAAATTTCATTATTACAAAACT
2881027 CATTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (31 bp):
ATTATTTAAATTTCATTATTACAAAACTAAA
Found at i:2884105 original size:5 final size:6
Alignment explanation
Indices: 2884090--2884124 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
2884080 GATAAAATTA
2884090 AAAAAT AAAAAT AAAAAT AAAAATAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT -AAAA-AT AAAAAT AAA
2884125 GGTGAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 17 0.63
7 8 0.30
8 2 0.07
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:2884106 original size:14 final size:12
Alignment explanation
Indices: 2884090--2884124 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
2884080 GATAAAATTA
2884090 AAAAATAAAAAT
1 AAAAATAAAAAT
2884102 AAAAATAAAAATAT
1 AAAAAT-AAAA-AT
2884116 AAAAATAAA
1 AAAAATAAA
2884125 GGTGAGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 7 0.33
14 8 0.38
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:2884107 original size:12 final size:13
Alignment explanation
Indices: 2884081--2884124 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
2884071 TTGGATAGGG
2884081 ATAAAAT-TAAAAA
1 ATAAAATAT-AAAA
2884094 ATAAAA-ATAAAA
1 ATAAAATATAAAA
2884106 ATAAAAATATAAAA
1 AT-AAAATATAAAA
2884120 ATAAA
1 ATAAA
2884125 GGTGAGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.21
13 14 0.50
14 8 0.29
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
ATAAAATATAAAA
Found at i:2884112 original size:20 final size:20
Alignment explanation
Indices: 2884083--2884124 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2884073 GGATAGGGAT
*
2884083 AAAATTAAAAAATAAAAATA
1 AAAATAAAAAAATAAAAATA
*
2884103 AAAATAAAAATATAAAAATA
1 AAAATAAAAAAATAAAAATA
2884123 AA
1 AA
2884125 GGTGAGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAATAAAAAAATAAAAATA
Found at i:2887364 original size:26 final size:26
Alignment explanation
Indices: 2887319--2887375 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2887309 TCATTAAGCA
* *
2887319 AAAATAAAATATACTGAAAATTAAAT
1 AAAATAAAACATACTGAAAATAAAAT
*
2887345 GAAATAAAACATA-TGAAAAATAAAAT
1 AAAATAAAACATACTG-AAAATAAAAT
2887371 AAAAT
1 AAAAT
2887376 TGAGTGGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.68, C:0.04, G:0.05, T:0.23
Consensus pattern (26 bp):
AAAATAAAACATACTGAAAATAAAAT
Found at i:2887368 original size:25 final size:26
Alignment explanation
Indices: 2887320--2887368 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2887310 CATTAAGCAA
* *
2887320 AAATAAAATATACTGAAAATTAAATG
1 AAATAAAACATACTGAAAAATAAATG
2887346 AAATAAAACATA-TGAAAAATAAA
1 AAATAAAACATACTGAAAAATAAA
2887369 ATAAAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.22
Consensus pattern (26 bp):
AAATAAAACATACTGAAAAATAAATG
Found at i:2889636 original size:74 final size:74
Alignment explanation
Indices: 2889548--2889696 Score: 253
Period size: 74 Copynumber: 2.0 Consensus size: 74
2889538 AAAGACTTTG
** *
2889548 ATGTCATTCTCCACATAGTTGGAAAATATACTAAACATGCATCTTTGGAAGGTGGCTGGTGCAAT
1 ATGTCATTCTCCACATAGTCAGAAAATATACTAAACATGCATCTTTGGAAGGTGGCTGGAGCAAT
2889613 ACAAAGGCT
66 ACAAAGGCT
*
2889622 ATGTCATTCTCCACATAGTCAGAAAATATACTAAACATGCATCTTTGGAAGGTGGCTGGAGCATT
1 ATGTCATTCTCCACATAGTCAGAAAATATACTAAACATGCATCTTTGGAAGGTGGCTGGAGCAAT
*
2889687 ATAAAGGCT
66 ACAAAGGCT
2889696 A
1 A
2889697 AAGTGAATTC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (74 bp):
ATGTCATTCTCCACATAGTCAGAAAATATACTAAACATGCATCTTTGGAAGGTGGCTGGAGCAAT
ACAAAGGCT
Found at i:2891398 original size:26 final size:26
Alignment explanation
Indices: 2891369--2891431 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
2891359 CTGGACAGGT
**
2891369 CTGAGCCGAGCCGCCAAGCTGCTGAG
1 CTGAGCCGAGCCGCCAAGCCACTGAG
** * *
2891395 CTGAGATGAGCCGTCGAGCCACTGAG
1 CTGAGCCGAGCCGCCAAGCCACTGAG
*
2891421 CGGAGCCGAGC
1 CTGAGCCGAGC
2891432 TAAGCCGACT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.21, C:0.32, G:0.37, T:0.11
Consensus pattern (26 bp):
CTGAGCCGAGCCGCCAAGCCACTGAG
Found at i:2895978 original size:13 final size:13
Alignment explanation
Indices: 2895962--2896023 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
2895952 CGCCGAGCCA
2895962 AGCCGAGCCACTG
1 AGCCGAGCCACTG
** **
2895975 AGCCGAGCTGCCA
1 AGCCGAGCCACTG
2895988 AGCCGAGCCACTG
1 AGCCGAGCCACTG
*
2896001 ATCCGAGCCACTG
1 AGCCGAGCCACTG
*
2896014 AGCTGAGCCA
1 AGCCGAGCCA
2896024 AACTGACTGA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.24, C:0.37, G:0.29, T:0.10
Consensus pattern (13 bp):
AGCCGAGCCACTG
Found at i:2895987 original size:26 final size:26
Alignment explanation
Indices: 2895958--2896008 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
2895948 GAACCGCCGA
2895958 GCCAAGCCGAGCCACTGAGCCGAGCT
1 GCCAAGCCGAGCCACTGAGCCGAGCT
*
2895984 GCCAAGCCGAGCCACTGATCCGAGC
1 GCCAAGCCGAGCCACTGAGCCGAGC
2896009 CACTGAGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.39, G:0.29, T:0.08
Consensus pattern (26 bp):
GCCAAGCCGAGCCACTGAGCCGAGCT
Found at i:2899242 original size:21 final size:21
Alignment explanation
Indices: 2899195--2899243 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2899185 GCTTTGGAAT
*
2899195 TTTTCCTGGGATGCAACTAGC
1 TTTTCTTGGGATGCAACTAGC
*
2899216 TTTTCTTGGGATGTAACTAGC
1 TTTTCTTGGGATGCAACTAGC
2899237 TTTTCTT
1 TTTTCTT
2899244 ATGAAATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.45
Consensus pattern (21 bp):
TTTTCTTGGGATGCAACTAGC
Found at i:2900181 original size:23 final size:23
Alignment explanation
Indices: 2900155--2900205 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
2900145 AAGATGAATA
2900155 AGTCCTATCTTTAATTGAAATGG
1 AGTCCTATCTTTAATTGAAATGG
*
2900178 AGTCCTGTCTTTAATTGAAATGG
1 AGTCCTATCTTTAATTGAAATGG
2900201 AGTCC
1 AGTCC
2900206 CACCATTAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (23 bp):
AGTCCTATCTTTAATTGAAATGG
Found at i:2902626 original size:14 final size:13
Alignment explanation
Indices: 2902597--2902633 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2902587 TCTTAAGCTC
2902597 AAAA-TTCACA-T
1 AAAAGTTCACATT
2902608 AAAAGTTTCACATT
1 AAAAG-TTCACATT
2902622 AAAAGTTCACAT
1 AAAAGTTCACAT
2902634 GGATCATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
13 13 0.57
14 6 0.26
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (13 bp):
AAAAGTTCACATT
Found at i:2906501 original size:2 final size:2
Alignment explanation
Indices: 2906494--2906521 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2906484 CACTTCTAGG
2906494 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2906522 GGTGAATTCA
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):
TA
Found at i:2906860 original size:29 final size:29
Alignment explanation
Indices: 2906810--2906918 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
2906800 AGGAATAGAG
* *
2906810 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
2906839 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2906868 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2906897 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
2906919 CCATTCCCAT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:2907025 original size:27 final size:27
Alignment explanation
Indices: 2906993--2907045 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2906983 CCTACAGCTC
2906993 CCAATGCATGCATGTGAACCATTTGAA
1 CCAATGCATGCATGTGAACCATTTGAA
2907020 CCAATGCATGCATGTGAACCATTTGA
1 CCAATGCATGCATGTGAACCATTTGA
2907046 TTATTGGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (27 bp):
CCAATGCATGCATGTGAACCATTTGAA
Found at i:2907185 original size:23 final size:23
Alignment explanation
Indices: 2907157--2907202 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2907147 AAAAGAAAGA
2907157 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
2907180 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
2907203 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:2907217 original size:25 final size:23
Alignment explanation
Indices: 2907157--2907217 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
2907147 AAAAGAAAGA
**
2907157 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
2907180 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
2907203 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
2907218 AGGAGAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:2907231 original size:21 final size:21
Alignment explanation
Indices: 2907207--2907270 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
2907197 TTGCAGCCGA
2907207 GAAAGAAAGAAAGGAGAAAGG
1 GAAAGAAAGAAAGGAGAAAGG
2907228 GAAAGAAAGAAAGGGAGAAA-G
1 GAAAGAAAGAAA-GGAGAAAGG
* *
2907249 GAAAGTAAG-AAGAAGAAAGG
1 GAAAGAAAGAAAGGAGAAAGG
2907269 GA
1 GA
2907271 GATAAGGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.15
20 5 0.13
21 21 0.54
22 7 0.18
ACGTcount: A:0.61, C:0.00, G:0.38, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGAGAAAGG
Found at i:2907438 original size:40 final size:40
Alignment explanation
Indices: 2907394--2907480 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
2907384 TATATGATTG
*
2907394 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAATAATTAA
* * * *
2907434 TTAGTATATGTTTGATAGTTATATAGTTAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAATAATTAA
2907474 TTAGTTT
1 TTAGTTT
2907481 GTTTTGTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 28 0.72
41 6 0.15
42 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (40 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAATAATTAA
Found at i:2907494 original size:34 final size:39
Alignment explanation
Indices: 2907420--2907496 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
2907410 TATACATAAA
*
2907420 TTAAAAATTATTAATTAGTATATGTTTGATAGTTATATAG
1 TTAAAAATAATTAATTAGTATATGTTT-ATAGTTATATAG
2907460 TTAAAAATAATTAATTAGT-T-TGTTT-T-GTTA-ATAG
1 TTAAAAATAATTAATTAGTATATGTTTATAGTTATATAG
2907494 TTA
1 TTA
2907497 GTTATAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
34 7 0.19
35 4 0.11
36 1 0.03
38 5 0.14
39 1 0.03
40 18 0.50
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (39 bp):
TTAAAAATAATTAATTAGTATATGTTTATAGTTATATAG
Found at i:2907525 original size:44 final size:46
Alignment explanation
Indices: 2907462--2907549 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 46
2907452 TTATATAGTT
*
2907462 AAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAAA
1 AAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAAA
*
2907505 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
1 AAAAA-TAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
2907550 TTTGTTTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 5 0.13
44 15 0.38
45 5 0.13
46 7 0.18
47 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (46 bp):
AAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAAA
Found at i:2908963 original size:18 final size:18
Alignment explanation
Indices: 2908940--2908975 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2908930 TTTTTTTAAT
2908940 TATTATTTAAATTAAATA
1 TATTATTTAAATTAAATA
* *
2908958 TATTATTTGATTTAAATA
1 TATTATTTAAATTAAATA
2908976 AATTTTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTATTTAAATTAAATA
Found at i:2909914 original size:17 final size:17
Alignment explanation
Indices: 2909892--2909924 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2909882 CAATGATTTT
*
2909892 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
2909909 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
2909925 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:2910062 original size:14 final size:14
Alignment explanation
Indices: 2910043--2910082 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2910033 TAGTAATAAT
2910043 TATTAAATCATTAG
1 TATTAAATCATTAG
*
2910057 TATTAAATCATTAT
1 TATTAAATCATTAG
*
2910071 TA-TAAATAATTA
1 TATTAAATCATTA
2910083 CTAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:2910136 original size:26 final size:25
Alignment explanation
Indices: 2910028--2910270 Score: 82
Period size: 26 Copynumber: 9.8 Consensus size: 25
2910018 GTATTCTATA
* *
2910028 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTA-TAAATCATTATTATAATG
*
2910052 ATTAGTATTAAATCATTATTATAA--
1 ATTATTA-TAAATCATTATTATAATG
* * * * *
2910076 ATAATTACTAAATAATAACTA-AATA
1 ATTATTA-TAAATCATTATTATAATG
2910101 ATTATTATAAAATCATTATTATAATG
1 ATTATTAT-AAATCATTATTATAATG
*
2910127 ATTATTAT-AATGATTATTATCAA--
1 ATTATTATAAATCATTATTAT-AATG
* * * * *
2910150 ATCATTACTAAATCATCA-AATCATTA
1 ATTATTA-TAAATCATTATTAT-AATG
* *
2910176 AATATT-TAAATCATTATTA-AATC
1 ATTATTATAAATCATTATTATAATG
* * *
2910199 ATTTTTAT-AATGATTATTACTAAATC
1 ATTATTATAAATCATTATTA-T-AATG
* *
2910225 ATTATTAT-AATGATTATTATCAAATC
1 ATTATTATAAATCATTATTAT--AATG
* *
2910251 ATTACTAT-AATGATTATTAT
1 ATTATTATAAATCATTATTAT
2910271 CAAATCATTA
Statistics
Matches: 171, Mismatches: 31, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
23 24 0.14
24 49 0.29
25 35 0.20
26 63 0.37
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (25 bp):
ATTATTATAAATCATTATTATAATG
Found at i:2910143 original size:98 final size:97
Alignment explanation
Indices: 2910041--2910338 Score: 268
Period size: 98 Copynumber: 3.0 Consensus size: 97
2910031 ATTAGTAATA
* * *
2910041 ATTATTAAATCATTAGTATTAAATCATTATTATAAATAATTACTAAATAATAACTAAATAATTAT
1 ATTATCAAATCATTA-TA-TAAATCATTATTATAAAT-ATTACTAAATCATAAATAAATAATTAT
*
2910106 TATAAAATCATTATTATAATGATTATTATAATGATT
63 T-TAAAATCATTATTATAATCATTATTATAATGATT
* * * * * *
2910142 ATTATCAAATCATTA-CTAAATCATCAAATCATTAAATATT--TAAATCATTATTAAATCATT-T
1 ATTATCAAATCATTATATAAATCAT--TATTA-TAAATATTACTAAATCATAAATAAATAATTAT
* *
2910203 TTATAATGATTATTACTAAATCATTATTATAATGATT
63 TTAAAATCATTATTA-T-AATCATTATTATAATGATT
* * * *
2910240 ATTATCAAATCATTACTAT-AATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA
1 ATTATCAAATCATTA-TATAAATCATTATTAT-AAAT-ATTACTAAATCAT-AAATAAATAATTA
* *
2910304 TTT-AAATCATTATTA-AATTATTTTTATAATGATT
62 TTTAAAATCATTATTATAATCATTATTATAATGATT
2910338 A
1 A
2910339 ATAAATACAT
Statistics
Matches: 159, Mismatches: 25, Indels: 29
0.75 0.12 0.14
Matches are distributed among these distances:
96 13 0.08
97 10 0.06
98 78 0.49
99 5 0.03
100 15 0.09
101 35 0.22
102 3 0.02
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (97 bp):
ATTATCAAATCATTATATAAATCATTATTATAAATATTACTAAATCATAAATAAATAATTATTTA
AAATCATTATTATAATCATTATTATAATGATT
Found at i:2910263 original size:124 final size:123
Alignment explanation
Indices: 2910093--2910338 Score: 413
Period size: 124 Copynumber: 2.0 Consensus size: 123
2910083 CTAAATAATA
* *
2910093 ACTAAATAATTATTATAAAATCATTATTATAATGATTATTATAATGATTATTATCAAATCATTAC
1 ACTAAATAATTATTAT-AAATCATTATTATAATCATTACTATAATGATTATTATCAAATCATTAC
2910158 TAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATT
65 TAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATT
* *
2910217 ACTAAATCATTATTAT-AATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTA
1 ACTAAATAATTATTATAAATCATTATTAT--AATCATTACTATAATGATTATTATCAAATCATTA
*
2910281 CTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATTATTTTTATAATGATTA
64 CTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTA
2910339 ATAAATACAT
Statistics
Matches: 115, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
122 11 0.10
124 104 0.90
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (123 bp):
ACTAAATAATTATTATAAATCATTATTATAATCATTACTATAATGATTATTATCAAATCATTACT
AAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATT
Found at i:2910271 original size:26 final size:26
Alignment explanation
Indices: 2910188--2910283 Score: 140
Period size: 26 Copynumber: 3.7 Consensus size: 26
2910178 TATTTAAATC
* **
2910188 ATTATTAAATCATTTTTATAATGATT
1 ATTATCAAATCATTACTATAATGATT
*
2910214 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTACTATAATGATT
2910240 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTACTATAATGATT
2910266 ATTATCAAATCATTACTA
1 ATTATCAAATCATTACTA
2910284 AATCATCAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
26 64 0.98
27 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (26 bp):
ATTATCAAATCATTACTATAATGATT
Found at i:2913493 original size:15 final size:15
Alignment explanation
Indices: 2913446--2913496 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 15
2913436 ACAATGTAAA
*
2913446 TTAAACAAAATATTT
1 TTAAACACAATATTT
2913461 TTAAAACAACTAAATATTT
1 TT-AAAC-AC--AATATTT
2913480 TTAAACACAATATTT
1 TTAAACACAATATTT
2913495 TT
1 TT
2913497 TAAAACGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
15 11 0.35
16 4 0.13
17 3 0.10
18 4 0.13
19 9 0.29
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAACACAATATTT
Found at i:2914004 original size:13 final size:13
Alignment explanation
Indices: 2913986--2914024 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
2913976 TATATAATAT
2913986 ATAACTTAAACTA
1 ATAACTTAAACTA
2913999 ATAAC-TAATA-TA
1 ATAACTTAA-ACTA
2914011 ATAACTTAAACTA
1 ATAACTTAAACTA
2914024 A
1 A
2914025 CAAACTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAACTTAAACTA
Found at i:2914014 original size:25 final size:25
Alignment explanation
Indices: 2913980--2914054 Score: 88
Period size: 21 Copynumber: 3.2 Consensus size: 25
2913970 TTTTTATATA
*
2913980 TAATATATAACTTAAACTAA-TAAC
1 TAATATATAACTTAAACTAACAAAC
2914004 TAATATAATAACTTAAACTAACAAAC
1 TAATAT-ATAACTTAAACTAACAAAC
*
2914030 TAATA-AT---TTATACTAACAAAC
1 TAATATATAACTTAAACTAACAAAC
2914051 TAAT
1 TAAT
2914055 TAACTAGATT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
21 17 0.36
24 8 0.17
25 14 0.30
26 8 0.17
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (25 bp):
TAATATATAACTTAAACTAACAAAC
Found at i:2914463 original size:25 final size:25
Alignment explanation
Indices: 2914435--2914508 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
2914425 ACACCGTTCG
2914435 ACGTGCATGGCCATGCACAGTTCCC
1 ACGTGCATGGCCATGCACAGTTCCC
* *
2914460 ACGT-C----CCATGCACAGCAT-GC
1 ACGTGCATGGCCATGCACAG-TTCCC
2914480 ATC-TGCATGGCCATGCACAGTTCCC
1 A-CGTGCATGGCCATGCACAGTTCCC
2914505 ACGT
1 ACGT
2914509 CCCATGCACA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
20 13 0.36
21 3 0.08
24 3 0.08
25 17 0.47
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.20
Consensus pattern (25 bp):
ACGTGCATGGCCATGCACAGTTCCC
Found at i:2914470 original size:20 final size:20
Alignment explanation
Indices: 2914445--2914519 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
2914435 ACGTGCATGG
2914445 CCATGCACAGTTCCCACGTC
1 CCATGCACAGTTCCCACGTC
* * *
2914465 CCATGCACAGCAT-GCATCTGCATGG
1 CCATGCACAG-TTCCCA-C-G--T-C
2914490 CCATGCACAGTTCCCACGTC
1 CCATGCACAGTTCCCACGTC
2914510 CCATGCACAG
1 CCATGCACAG
2914520 CATGCATCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
20 22 0.52
21 3 0.07
22 1 0.02
23 1 0.02
24 3 0.07
25 12 0.29
ACGTcount: A:0.23, C:0.40, G:0.19, T:0.19
Consensus pattern (20 bp):
CCATGCACAGTTCCCACGTC
Found at i:2914488 original size:45 final size:45
Alignment explanation
Indices: 2914438--2914527 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
2914428 CCGTTCGACG
2914438 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
1 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
2914483 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
1 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
2914528 CCCTCCCCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (45 bp):
TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
Found at i:2914529 original size:25 final size:25
Alignment explanation
Indices: 2914456--2914529 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
2914446 CATGCACAGT
2914456 TCCCACGTCCCATGCACAGCATGCA
1 TCCCACGTCCCATGCACAGCATGCA
* * *
2914481 TCTGCATG-GCCATGCACAG--T---
1 TC-CCACGTCCCATGCACAGCATGCA
2914501 TCCCACGTCCCATGCACAGCATGCA
1 TCCCACGTCCCATGCACAGCATGCA
2914526 TCCC
1 TCCC
2914530 CTCCCCCATG
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.08
20 12 0.33
22 1 0.03
23 1 0.03
25 16 0.44
26 3 0.08
ACGTcount: A:0.22, C:0.42, G:0.18, T:0.19
Consensus pattern (25 bp):
TCCCACGTCCCATGCACAGCATGCA
Found at i:2914539 original size:45 final size:45
Alignment explanation
Indices: 2914445--2914556 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
2914435 ACGTGCATGG
* **
2914445 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCTGCATGG
1 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCTCCATCC
*
2914490 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC-CCCTCCC
1 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCTCCAT-CC
2914535 CCATG--CA-TTCCCACGTCCCATG
1 CCATGCACAGTTCCCACGTCCCATG
2914557 TTGATTGCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
42 15 0.24
43 2 0.03
44 2 0.03
45 43 0.69
ACGTcount: A:0.21, C:0.44, G:0.16, T:0.20
Consensus pattern (45 bp):
CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCTCCATCC
Found at i:2914637 original size:29 final size:29
Alignment explanation
Indices: 2914594--2914669 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
2914584 ACACACAGGG
***
2914594 CGCCCGGA-TGCCATGGCGACCTTGGAGGT
1 CGCCCGGATTG-CATGGCGACCTCCAAGGT
2914623 CGCCCGGATTGCATGGCGACCTCCAAGGT
1 CGCCCGGATTGCATGGCGACCTCCAAGGT
*
2914652 CGCCTGGATTGCATGGCG
1 CGCCCGGATTGCATGGCG
2914670 TCCTATGGCG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 40 0.95
30 2 0.05
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (29 bp):
CGCCCGGATTGCATGGCGACCTCCAAGGT
Found at i:2917039 original size:6 final size:6
Alignment explanation
Indices: 2917030--2917056 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2917020 TCTTTCATGA
2917030 ATGCAG ATGCAG ATGCAG ATGCAG ATG
1 ATGCAG ATGCAG ATGCAG ATGCAG ATG
2917057 ATGATGGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19
Consensus pattern (6 bp):
ATGCAG
Found at i:2921629 original size:3 final size:3
Alignment explanation
Indices: 2921621--2921741 Score: 152
Period size: 3 Copynumber: 38.0 Consensus size: 3
2921611 TGTTATTACC
* *
2921621 TAT TAT TAT CATT TAT TAG TAT TACT TAT TAT TAT TAT TAAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT T-AT TAT TAT
*
2921669 TAT TAAT TAC TAT TAT TAGT TAT TAT TAT TAT TAT TAAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TA-T TAT TAT TAT TAT TAT T-AT TAT TAT TAT
2921717 TAT TAT TAAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT
2921742 AAATAAAATA
Statistics
Matches: 105, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
3 85 0.81
4 20 0.19
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2921637 original size:13 final size:12
Alignment explanation
Indices: 2921621--2921741 Score: 152
Period size: 13 Copynumber: 9.5 Consensus size: 12
2921611 TGTTATTACC
*
2921621 TATTATTATCATT
1 TATTATTATTA-T
*
2921634 TATTAGTATTACT
1 TATTATTATTA-T
2921647 TATTATTATTAT
1 TATTATTATTAT
2921659 TAATTATTATTAT
1 T-ATTATTATTAT
*
2921672 TAATTACTATTAT
1 T-ATTATTATTAT
2921685 TAGTTATTATTAT
1 TA-TTATTATTAT
2921698 TATTATTAATTAT
1 TATTATT-ATTAT
2921711 TATTATTATTAT
1 TATTATTATTAT
2921723 TAATTATTATTAT
1 T-ATTATTATTAT
2921736 TATTAT
1 TATTAT
2921742 AAATAAAATA
Statistics
Matches: 98, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
12 19 0.19
13 79 0.81
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (12 bp):
TATTATTATTAT
Found at i:2921643 original size:16 final size:15
Alignment explanation
Indices: 2921621--2921741 Score: 109
Period size: 16 Copynumber: 7.6 Consensus size: 15
2921611 TGTTATTACC
2921621 TATTATTATCATTTAT
1 TATTATTATCA-TTAT
* *
2921637 TAGTATTACTTATTAT
1 TATTATTA-TCATTAT
*
2921653 TATTATTAATTATTAT
1 TATTATT-ATCATTAT
2921669 TATTAATTA-CTATTAT
1 TATT-ATTATC-ATTAT
*
2921685 TAGTTATTATTATTAT
1 TA-TTATTATCATTAT
*
2921701 TATTAATTATTATTAT
1 TATT-ATTATCATTAT
*
2921717 TATTATTAATTATTAT
1 TATTATT-ATCATTAT
2921733 TATTATTAT
1 TATTATTAT
2921742 AAATAAAATA
Statistics
Matches: 92, Mismatches: 5, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.08
16 77 0.84
17 8 0.09
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (15 bp):
TATTATTATCATTAT
Found at i:2925488 original size:14 final size:14
Alignment explanation
Indices: 2925469--2925520 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
2925459 CTTCGTTGCA
2925469 TTTTCATTTTCATT
1 TTTTCATTTTCATT
** *
2925483 TTTTCATTCGCACT
1 TTTTCATTTTCATT
* *
2925497 TTTTCATTTTTATA
1 TTTTCATTTTCATT
2925511 TTTTCATTTT
1 TTTTCATTTT
2925521 TTACAGTATG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTTCATTTTCATT
Found at i:2928563 original size:10 final size:10
Alignment explanation
Indices: 2928520--2928612 Score: 77
Period size: 10 Copynumber: 9.4 Consensus size: 10
2928510 GGTTGAATAT
2928520 AAAAA-AAGA
1 AAAAATAAGA
*
2928529 AAAAATAAGG
1 AAAAATAAGA
*
2928539 AAAAATAAGG
1 AAAAATAAGA
2928549 AAAAATAAGA
1 AAAAATAAGA
* *
2928559 AAAAAGAATA
1 AAAAATAAGA
*
2928569 AGAAA-AAGA
1 AAAAATAAGA
*
2928578 AAAAATGAATA
1 AAAAAT-AAGA
2928589 AAAGAA-AAG-
1 AAA-AATAAGA
2928598 AAAAATAACGA
1 AAAAATAA-GA
2928609 AAAA
1 AAAA
2928613 GAAAATAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
8 2 0.03
9 17 0.25
10 37 0.54
11 10 0.15
12 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (10 bp):
AAAAATAAGA
Found at i:2928570 original size:13 final size:13
Alignment explanation
Indices: 2928552--2928602 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
2928542 AATAAGGAAA
2928552 AATAAGAAAAAAG
1 AATAAGAAAAAAG
2928565 AATAAG-AAAAAG
1 AATAAGAAAAAAG
*
2928577 AAAAAATGAATAAAAG
1 -AATAA-GAA-AAAAG
2928593 AA-AAGAAAAA
1 AATAAGAAAAA
2928603 TAACGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
12 9 0.27
13 13 0.39
14 3 0.09
15 3 0.09
16 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (13 bp):
AATAAGAAAAAAG
Found at i:2928587 original size:20 final size:20
Alignment explanation
Indices: 2928555--2928602 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
2928545 AAGGAAAAAT
*
2928555 AAGAAAAAAGAATAAGA-AA
1 AAGAAAAAAGAATAAAAGAA
2928574 AAGAAAAAATGAATAAAAGAA
1 AAGAAAAAA-GAATAAAAGAA
2928595 AAGAAAAA
1 AAGAAAAA
2928603 TAACGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.35
20 7 0.27
21 10 0.38
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (20 bp):
AAGAAAAAAGAATAAAAGAA
Found at i:2928601 original size:49 final size:49
Alignment explanation
Indices: 2928521--2928622 Score: 120
Period size: 49 Copynumber: 2.1 Consensus size: 49
2928511 GTTGAATATA
*
2928521 AAAAAAGAAAAAATAAGGAAAAATAAGGAAAAATAA-GAAAAAAGAATA
1 AAAAAAGAAAAAATAAGGAAAAATAAAGAAAAATAACGAAAAAAGAATA
* *
2928569 AGAAAAAGAAAAAATGAA-TAAAAGA-AAAGAAAAATAACGAAAAAGAAAATA
1 A-AAAAAGAAAAAAT-AAGGAAAA-ATAAAGAAAAATAACGAAAAA-AGAATA
2928620 AAA
1 AAA
2928623 TTGAAAGGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
48 1 0.02
49 28 0.61
50 11 0.24
51 6 0.13
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (49 bp):
AAAAAAGAAAAAATAAGGAAAAATAAAGAAAAATAACGAAAAAAGAATA
Found at i:2928604 original size:16 final size:16
Alignment explanation
Indices: 2928548--2928622 Score: 52
Period size: 16 Copynumber: 4.7 Consensus size: 16
2928538 GAAAAATAAG
2928548 GAAAAATAAGAA-AAAA
1 GAAAAATAA-AAGAAAA
2928564 GAATAAGA-AAAAGAAAA
1 GAA-AA-ATAAAAGAAAA
*
2928581 -AATGAATAAAAGAAAA
1 GAA-AAATAAAAGAAAA
*
2928597 GAAAAAT-AACGAAAA
1 GAAAAATAAAAGAAAA
2928612 -AGAAAATAAAA
1 GA-AAAATAAAA
2928623 TTGAAAGGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
14 1 0.02
15 13 0.27
16 23 0.48
17 10 0.21
18 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.08
Consensus pattern (16 bp):
GAAAAATAAAAGAAAA
Found at i:2928611 original size:20 final size:19
Alignment explanation
Indices: 2928520--2928622 Score: 63
Period size: 21 Copynumber: 5.2 Consensus size: 19
2928510 GGTTGAATAT
2928520 AAAAA-AAGAAAA-AATAAGG
1 AAAAATAAGAAAAGAA-AA-G
*
2928539 AAAAATAAGGAAAA-ATAAG
1 AAAAATAA-GAAAAGAAAAG
2928558 -AAAA-AAGAATAAGAAAAAG
1 AAAAATAAGAA-AAG-AAAAG
*
2928577 AAAAAATGAATAAAAGAAAAG
1 -AAAAAT-AAGAAAAGAAAAG
*
2928598 AAAAATAACGAAAAAGAAAAT
1 AAAAATAA-G-AAAAGAAAAG
2928619 AAAA
1 AAAA
2928623 TTGAAAGGAG
Statistics
Matches: 68, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
16 3 0.04
17 4 0.06
18 4 0.06
19 12 0.18
20 10 0.15
21 28 0.41
22 3 0.04
23 4 0.06
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAAATAAGAAAAGAAAAG
Found at i:2936058 original size:137 final size:138
Alignment explanation
Indices: 2935917--2936214 Score: 429
Period size: 137 Copynumber: 2.2 Consensus size: 138
2935907 TCCTTTACGT
* * * *
2935917 GAAGGAGTAGTGTCATCCTCAA-ACAATTAGACTTCCTCAACATGAAGGAACCGTATTGTCTTCA
1 GAAGGAGTAGTATCATCCTCAAGACAATTAGACTTCCTCAACACGAAGGAACCATATTGTCTCCA
* *
2935981 AATTATCCAAATACGACTAGACATCCTCAACACGAAGGAACAATGTCGTCCACCGACCAGACCTT
66 AATTATCCAAATACGACTAAACATCCTCAACACGAAGGAACAATGTCGTCCACCGACCAGACCTC
**
2936046 CTCAATGC
131 CTCAACAC
* * * *
2936054 GAAGGAATAGTTTCATCCT-AAGACAATTAGACTTCCTCAACACGAATGAACCATGTTGTCTCCA
1 GAAGGAGTAGTATCATCCTCAAGACAATTAGACTTCCTCAACACGAAGGAACCATATTGTCTCCA
* * * *
2936118 AATTATCCAAATATGTCTAAACATCCTCAATACGAAGGAACAATGTCGTCCACCGACCAGATCTC
66 AATTATCCAAATACGACTAAACATCCTCAACACGAAGGAACAATGTCGTCCACCGACCAGACCTC
2936183 CTCAACAC
131 CTCAACAC
*
2936191 GAAGGAGTAGTATCATACTCAAGA
1 GAAGGAGTAGTATCATCCTCAAGA
2936215 TAGTAAGAAT
Statistics
Matches: 141, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
136 2 0.01
137 135 0.96
138 4 0.03
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (138 bp):
GAAGGAGTAGTATCATCCTCAAGACAATTAGACTTCCTCAACACGAAGGAACCATATTGTCTCCA
AATTATCCAAATACGACTAAACATCCTCAACACGAAGGAACAATGTCGTCCACCGACCAGACCTC
CTCAACAC
Found at i:2936821 original size:3 final size:3
Alignment explanation
Indices: 2936806--2936913 Score: 110
Period size: 3 Copynumber: 33.3 Consensus size: 3
2936796 GTTATTTTTG
*
2936806 TTA TTA CTTA TTA TTA TCGT- TTA TTA TTC TTA CTTA TTA TTA TTAA
1 TTA TTA -TTA TTA TTA T--TA TTA TTA TTA TTA -TTA TTA TTA TT-A
*
2936852 TTA TTA TTA TTCA TTA CTA TTA TTA GTTA TTA TTA TTTA TTA TTAA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TT-A TTA
2936901 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
2936914 AAAAAAAATA
Statistics
Matches: 91, Mismatches: 4, Indels: 20
0.79 0.03 0.17
Matches are distributed among these distances:
2 1 0.01
3 67 0.74
4 22 0.24
5 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2936842 original size:13 final size:12
Alignment explanation
Indices: 2936806--2936913 Score: 110
Period size: 13 Copynumber: 8.3 Consensus size: 12
2936796 GTTATTTTTG
2936806 TTATTACTTATTA
1 TTATTA-TTATTA
2936819 TTATCGT-TTATTA
1 TTAT--TATTATTA
*
2936832 TTCTTACTTATTA
1 TTATTA-TTATTA
2936845 TTATTAATTATTA
1 TTATT-ATTATTA
*
2936858 TTATTCATTACTA
1 TTATT-ATTATTA
2936871 TTATTAGTTATTA
1 TTATTA-TTATTA
2936884 TTATTTATTATTAA
1 TTA-TTATTATT-A
2936898 TTATTATTATTA
1 TTATTATTATTA
2936910 TTAT
1 TTAT
2936914 AAAAAAAATA
Statistics
Matches: 82, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
11 1 0.01
12 6 0.07
13 66 0.80
14 8 0.10
15 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (12 bp):
TTATTATTATTA
Found at i:2938585 original size:6 final size:5
Alignment explanation
Indices: 2938544--2938586 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
2938534 ATGATAGTAA
* * *
2938544 TATTT TATTC AATTT TATTT TATTT TATTT CTATTT TAATT TA
1 TATTT TATTT TATTT TATTT TATTT TATTT -TATTT TATTT TA
2938587 AGTATTGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:2944178 original size:56 final size:56
Alignment explanation
Indices: 2944113--2944226 Score: 192
Period size: 56 Copynumber: 2.0 Consensus size: 56
2944103 ACTAATGTAC
* * *
2944113 CACCCTAATTTTTATTTTACAGAAAATTTTAATTTATCTTCAAGTGGATTCTCGAT
1 CACCCTAATTTTTATTTTACAAAAAAATTTAATTTATCATCAAGTGGATTCTCGAT
*
2944169 CACCCTAATTTTTATTTTACAAAAAAATTTAATTTATCATCAAGTGGCTTCTCGAT
1 CACCCTAATTTTTATTTTACAAAAAAATTTAATTTATCATCAAGTGGATTCTCGAT
2944225 CA
1 CA
2944227 AACATTCTAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (56 bp):
CACCCTAATTTTTATTTTACAAAAAAATTTAATTTATCATCAAGTGGATTCTCGAT
Found at i:2946475 original size:148 final size:148
Alignment explanation
Indices: 2946279--2946573 Score: 574
Period size: 149 Copynumber: 2.0 Consensus size: 148
2946269 AAGGGTGGCA
2946279 TCTGCTATGTGCATTGGGTAAGGCTTATAGGCCTGAGGGCACACCCCTCAGGTGGGCACCTATGA
1 TCTGCTATGTGCATTGGGTAAGGCTTATAGGCCTGAGGGCACACCCCTCAGGTGGGCACCTATGA
2946344 TTCGGCTAGGGTAAGACC-TATGAACCCAAGGTGCTCCCTTAGGTTGGAACCTACGCCCTTCAGA
66 TTCGGCTAGGGTAAGACCTTATGAACCCAAGGTGCTCCCTTAGGTTGGAACCTACGCCCTTCAGA
2946408 CCTAGGGTAAGTACTTAC
131 CCTAGGGTAAGTACTTAC
2946426 TCTGCTATGTGCATTGGGTAAGTGCTTATAGGCCTGAGGGCACACCCCTCAGGTGGGCACCTATG
1 TCTGCTATGTGCATTGGGTAAG-GCTTATAGGCCTGAGGGCACACCCCTCAGGTGGGCACCTATG
2946491 ATTCGGCTAGGGTAAGACCTTATGAACCCAAGGTGCTCCCTTAGGTTGGAACCTACGCCCTTCAG
65 ATTCGGCTAGGGTAAGACCTTATGAACCCAAGGTGCTCCCTTAGGTTGGAACCTACGCCCTTCAG
2946556 ACCTAGGGTAAGTACTTA
130 ACCTAGGGTAAGTACTTA
2946574 TGGGTTTAGT
Statistics
Matches: 146, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
147 22 0.15
148 61 0.42
149 63 0.43
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (148 bp):
TCTGCTATGTGCATTGGGTAAGGCTTATAGGCCTGAGGGCACACCCCTCAGGTGGGCACCTATGA
TTCGGCTAGGGTAAGACCTTATGAACCCAAGGTGCTCCCTTAGGTTGGAACCTACGCCCTTCAGA
CCTAGGGTAAGTACTTAC
Found at i:2970415 original size:22 final size:22
Alignment explanation
Indices: 2970385--2970437 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
2970375 ACATGACCCA
2970385 AACTGTTGATCGGTCTGACCGTT
1 AACT-TTGATCGGTCTGACCGTT
*
2970408 GACTTTGATCGGTCTGACCGTT
1 AACTTTGATCGGTCTGACCGTT
2970430 AACTTTGA
1 AACTTTGA
2970438 CAAAAAAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.36
Consensus pattern (22 bp):
AACTTTGATCGGTCTGACCGTT
Found at i:2971176 original size:31 final size:30
Alignment explanation
Indices: 2971141--2971212 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
2971131 TAAGGCGACC
** *
2971141 CTTGGGTAGGCTCTACGGCCATGAGATCTTT
1 CTTGGGTAGGCTC-ACAACCACGAGATCTTT
** *
2971172 CTTGGGTATTCTCACAACCCCGAGATCTTT
1 CTTGGGTAGGCTCACAACCACGAGATCTTT
2971202 CTTGGGTAGGC
1 CTTGGGTAGGC
2971213 CCCGTAGCCC
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 22 0.67
31 11 0.33
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (30 bp):
CTTGGGTAGGCTCACAACCACGAGATCTTT
Found at i:2974523 original size:13 final size:13
Alignment explanation
Indices: 2974486--2974531 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
2974476 TCAAAGGTCT
2974486 GAGTTAACTCAACAC
1 GAGTTAACTC-A-AC
* *
2974501 GAGTTGACTCAAT
1 GAGTTAACTCAAC
2974514 GAGTTAACTCAAC
1 GAGTTAACTCAAC
2974527 GAGTT
1 GAGTT
2974532 GACTACTCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 17 0.63
14 1 0.04
15 9 0.33
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (13 bp):
GAGTTAACTCAAC
Found at i:2983159 original size:19 final size:19
Alignment explanation
Indices: 2983135--2983205 Score: 124
Period size: 19 Copynumber: 3.7 Consensus size: 19
2983125 GAATGGCCTT
2983135 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
*
2983154 AGTGCATCGATACATAAGG
1 AGTGCATCGATGCATAAGG
*
2983173 AGTACATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
2983192 AGTGCATCGATGCA
1 AGTGCATCGATGCA
2983206 CCCCCTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:2984235 original size:18 final size:18
Alignment explanation
Indices: 2984076--2984227 Score: 196
Period size: 18 Copynumber: 8.4 Consensus size: 18
2984066 GAGGGTCTAC
* *
2984076 GTGGTCCTTTGGGATATA
1 GTGGTCCTTCGGGACATA
*
2984094 ATGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
2984112 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* * * *
2984130 ATGGTCTTTCAGGACACA
1 GTGGTCCTTCGGGACATA
* * *
2984148 GTAGTCCTTCGGGATACA
1 GTGGTCCTTCGGGACATA
2984166 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
2984184 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
*
2984202 GTGGTCCTTCGAGACATA
1 GTGGTCCTTCGGGACATA
2984220 GTGGTCCT
1 GTGGTCCT
2984228 ACAGGACAAA
Statistics
Matches: 115, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 115 1.00
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:2986258 original size:50 final size:50
Alignment explanation
Indices: 2986178--2986277 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
2986168 TTTATTTGAG
2986178 ATTGTCCACTTATGACTGAGGAGACAATGCAAAGAGAAAGATATAGTACA
1 ATTGTCCACTTATGACTGAGGAGACAATGCAAAGAGAAAGATATAGTACA
* *
2986228 ATTGTCCACTTATGACTGAGGAGACGATGCAAAGAGAAAGATCTAGTACA
1 ATTGTCCACTTATGACTGAGGAGACAATGCAAAGAGAAAGATATAGTACA
2986278 GTACCTCAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (50 bp):
ATTGTCCACTTATGACTGAGGAGACAATGCAAAGAGAAAGATATAGTACA
Found at i:2988084 original size:18 final size:18
Alignment explanation
Indices: 2988061--2988162 Score: 159
Period size: 18 Copynumber: 5.7 Consensus size: 18
2988051 GTCTACGTTT
2988061 TCCTTCGGGACATAGTGG
1 TCCTTCGGGACATAGTGG
* **
2988079 TCCTTCGGGACATAATTA
1 TCCTTCGGGACATAGTGG
2988097 TCCTTCGGGACATAGTGG
1 TCCTTCGGGACATAGTGG
*
2988115 TCCTTCGGGACACAGTGG
1 TCCTTCGGGACATAGTGG
2988133 TCCTTCGGGACATAGTGG
1 TCCTTCGGGACATAGTGG
*
2988151 TCCTACGGGACA
1 TCCTTCGGGACA
2988163 AATTCTACGC
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 75 1.00
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.26
Consensus pattern (18 bp):
TCCTTCGGGACATAGTGG
Found at i:2989193 original size:22 final size:22
Alignment explanation
Indices: 2989168--2989216 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2989158 CCTCACGAGT
*
2989168 TCACTTCAAGGAAACTTGAATG
1 TCACTTCAAGGAAACTTGAATC
2989190 TCACTTCAAGGAAACTTGAATC
1 TCACTTCAAGGAAACTTGAATC
2989212 TCACT
1 TCACT
2989217 CAATCCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (22 bp):
TCACTTCAAGGAAACTTGAATC
Found at i:2992196 original size:13 final size:13
Alignment explanation
Indices: 2992176--2992210 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2992166 GACTCGACAC
2992176 GAGTTGACTCAGT
1 GAGTTGACTCAGT
*
2992189 GGGTTGACTCAGT
1 GAGTTGACTCAGT
2992202 GAGTTGACT
1 GAGTTGACT
2992211 ACTCGGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.31
Consensus pattern (13 bp):
GAGTTGACTCAGT
Found at i:2995894 original size:21 final size:23
Alignment explanation
Indices: 2995860--2995917 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
2995850 TTACCCTAAA
2995860 TAAAAAATATATATGAATTATGT
1 TAAAAAATATATATGAATTATGT
*
2995883 TAAACAATATATATGAATTATGT
1 TAAAAAATATATATGAATTATGT
2995906 TAAAAAATATAT
1 TAAAAAATATAT
2995918 TGATTCGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
TAAAAAATATATATGAATTATGT
Found at i:2996209 original size:22 final size:22
Alignment explanation
Indices: 2996179--2996227 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2996169 TTTCTTTTCC
*
2996179 TCTTCTCAATTGCTCTGATTTT
1 TCTTATCAATTGCTCTGATTTT
2996201 TCTTATCAATTGCTCTGATTTT
1 TCTTATCAATTGCTCTGATTTT
2996223 TCTTA
1 TCTTA
2996228 GAAAACTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.55
Consensus pattern (22 bp):
TCTTATCAATTGCTCTGATTTT
Found at i:3000974 original size:203 final size:203
Alignment explanation
Indices: 3000625--3001030 Score: 812
Period size: 203 Copynumber: 2.0 Consensus size: 203
3000615 AATTGATATC
3000625 TAAACATGTAAAAACAACACATATGCACTCTAAAATAAGAATTTGGAACCCGAAATAAAAATATT
1 TAAACATGTAAAAACAACACATATGCACTCTAAAATAAGAATTTGGAACCCGAAATAAAAATATT
3000690 CTAATTTAGGGTTTATGGATTAAGAATTACAACTCTTGGGTTGAGAAAAGAAAAATACCAAATTG
66 CTAATTTAGGGTTTATGGATTAAGAATTACAACTCTTGGGTTGAGAAAAGAAAAATACCAAATTG
3000755 AAGCTTTGAATGAGTACATCAGACATATGGTACTGGGTTTATTTTTTTATGGCTACAATAAGCAT
131 AAGCTTTGAATGAGTACATCAGACATATGGTACTGGGTTTATTTTTTTATGGCTACAATAAGCAT
3000820 TCAAGCTT
196 TCAAGCTT
3000828 TAAACATGTAAAAACAACACATATGCACTCTAAAATAAGAATTTGGAACCCGAAATAAAAATATT
1 TAAACATGTAAAAACAACACATATGCACTCTAAAATAAGAATTTGGAACCCGAAATAAAAATATT
3000893 CTAATTTAGGGTTTATGGATTAAGAATTACAACTCTTGGGTTGAGAAAAGAAAAATACCAAATTG
66 CTAATTTAGGGTTTATGGATTAAGAATTACAACTCTTGGGTTGAGAAAAGAAAAATACCAAATTG
3000958 AAGCTTTGAATGAGTACATCAGACATATGGTACTGGGTTTATTTTTTTATGGCTACAATAAGCAT
131 AAGCTTTGAATGAGTACATCAGACATATGGTACTGGGTTTATTTTTTTATGGCTACAATAAGCAT
3001023 TCAAGCTT
196 TCAAGCTT
3001031 GGGAGTGAGA
Statistics
Matches: 203, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
203 203 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (203 bp):
TAAACATGTAAAAACAACACATATGCACTCTAAAATAAGAATTTGGAACCCGAAATAAAAATATT
CTAATTTAGGGTTTATGGATTAAGAATTACAACTCTTGGGTTGAGAAAAGAAAAATACCAAATTG
AAGCTTTGAATGAGTACATCAGACATATGGTACTGGGTTTATTTTTTTATGGCTACAATAAGCAT
TCAAGCTT
Found at i:3001138 original size:22 final size:21
Alignment explanation
Indices: 3001093--3001134 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3001083 ATTTTGTATT
3001093 TTTTTTTCAAAAAATTGATCC
1 TTTTTTTCAAAAAATTGATCC
*
3001114 TTTTTTT-AGAAAGATTGATCC
1 TTTTTTTCA-AAAAATTGATCC
3001135 CTTTGACCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (21 bp):
TTTTTTTCAAAAAATTGATCC
Found at i:3007680 original size:42 final size:42
Alignment explanation
Indices: 3007584--3007742 Score: 171
Period size: 42 Copynumber: 3.8 Consensus size: 42
3007574 AAAACATCCC
* * * * *
3007584 GCTCGAAGGTCTTATGGATGGCCTGAAGGACTT-ATCATCTT
1 GCTCGAAAGACTTATAGATGGCCCGAAGGACTTAATCATCAT
* * * *
3007625 GCTCGAAATACTTATAGATGACCCGAAGGATTTAAGCATCAT
1 GCTCGAAAGACTTATAGATGGCCCGAAGGACTTAATCATCAT
*
3007667 GCTCGAAAGACTTACTA-ATGGCCCGAAGGACTTACTCATCAT
1 GCTCGAAAGACTTA-TAGATGGCCCGAAGGACTTAATCATCAT
* *
3007709 GCTTGAAAGACTTACT-GATGGCCTGAAGGACTTA
1 GCTCGAAAGACTTA-TAGATGGCCCGAAGGACTTA
3007743 TGCTGATTTG
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
41 26 0.26
42 71 0.72
43 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (42 bp):
GCTCGAAAGACTTATAGATGGCCCGAAGGACTTAATCATCAT
Found at i:3007698 original size:20 final size:20
Alignment explanation
Indices: 3007670--3007742 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
3007660 GCATCATGCT
3007670 CGAAAGACTTACTAATGGCC
1 CGAAAGACTTACTAATGGCC
* *
3007690 CGAAGGACTTACTCATCAT-GCT
1 CGAAAGACTTACT-A--ATGGCC
* *
3007712 TGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTAATGGCC
* *
3007732 TGAAGGACTTA
1 CGAAAGACTTA
3007743 TGCTGATTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 24 0.57
21 1 0.02
22 13 0.31
23 2 0.05
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (20 bp):
CGAAAGACTTACTAATGGCC
Found at i:3007723 original size:22 final size:22
Alignment explanation
Indices: 3007661--3007724 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 22
3007651 AGGATTTAAG
3007661 CATCATGCTCGAAAGACTTACT
1 CATCATGCTCGAAAGACTTACT
* *
3007683 -A--ATGGCCCGAAGGACTTACT
1 CATCAT-GCTCGAAAGACTTACT
*
3007703 CATCATGCTTGAAAGACTTACT
1 CATCATGCTCGAAAGACTTACT
3007725 GATGGCCTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 2 0.06
20 14 0.42
21 2 0.06
22 13 0.39
23 2 0.06
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (22 bp):
CATCATGCTCGAAAGACTTACT
Found at i:3007986 original size:53 final size:52
Alignment explanation
Indices: 3007889--3007994 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 52
3007879 AAGGACTTAA
* * * *
3007889 GCTGATTCGAAGTGTCGTGAATCGAGCAATAGTAAATGTTAACCCCTCTGGTG
1 GCTGATTCGAAATGTCGAGAATCGACCAATAGGAAATGTTAA-CCCTCTGGTG
*
3007942 GCTGATTCGAAATGTTGAGAATCGACCAA-AGGAAATGTTAAACCCTCTGGTG
1 GCTGATTCGAAATGTCGAGAATCGACCAATAGGAAATGTT-AACCCTCTGGTG
3007994 G
1 G
3007995 GGCATTGCTG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
52 20 0.43
53 27 0.57
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (52 bp):
GCTGATTCGAAATGTCGAGAATCGACCAATAGGAAATGTTAACCCTCTGGTG
Found at i:3008039 original size:197 final size:196
Alignment explanation
Indices: 3007744--3008123 Score: 557
Period size: 197 Copynumber: 1.9 Consensus size: 196
3007734 AAGGACTTAT
* * * * * * * * *
3007744 GCTGATTTGAAGTGTTGTGAATCTAGCAATAGGAAATGTTAACCCCTTTGGTGGGGCGTTGTTGA
1 GCTGATTCGAAATGTTGAGAATCGACCAATAGGAAATGTTAAACCCTCTGGTGGGGCATTGCTGA
* *
3007809 TTCGAAGTGTTGTGAATCGAGCAAAGAAAATGTTGAAAACATCCTGC-CTGAAGGTCTTATGGAT
66 TTCAAAGTATTGTGAATCGAGCAAAGAAAATGTTGAAAACATCCTGCTC-GAAGGTCTTATGGAT
* * * *
3007873 GGCCCGAAGGACTTAAGCTGATTCGAAGTGTCGTGAATCGAGCAATAGTAAATGTTAACCCCTCT
130 GGCCCGAAGGACTTAAGCTGATTCAAAGTAT-GTAAATCGAGCAAT-GGAAATGTTAACCCCTCT
3007938 GGTG
193 GGTG
3007942 GCTGATTCGAAATGTTGAGAATCGACCAA-AGGAAATGTTAAACCCTCTGGTGGGGCATTGCTGA
1 GCTGATTCGAAATGTTGAGAATCGACCAATAGGAAATGTTAAACCCTCTGGTGGGGCATTGCTGA
* * *
3008006 TTCAAAGTATTGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCTCGAAGGTTTTATGGATG
66 TTCAAAGTATTGTGAATCGAGCAAAGAAAATGTTGAAAACATCCTGCTCGAAGGTCTTATGGATG
3008071 GCCCGAAGGACTTAAGCTGATTCAAAGTATGTAAATCGAGCAATGGAAATGTT
131 GCCCGAAGGACTTAAGCTGATTCAAAGTATGTAAATCGAGCAATGGAAATGTT
3008124 GCAAACATCC
Statistics
Matches: 163, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
195 8 0.05
196 13 0.08
197 117 0.72
198 25 0.15
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (196 bp):
GCTGATTCGAAATGTTGAGAATCGACCAATAGGAAATGTTAAACCCTCTGGTGGGGCATTGCTGA
TTCAAAGTATTGTGAATCGAGCAAAGAAAATGTTGAAAACATCCTGCTCGAAGGTCTTATGGATG
GCCCGAAGGACTTAAGCTGATTCAAAGTATGTAAATCGAGCAATGGAAATGTTAACCCCTCTGGT
G
Found at i:3008119 original size:84 final size:85
Alignment explanation
Indices: 3008001--3008168 Score: 241
Period size: 84 Copynumber: 2.0 Consensus size: 85
3007991 GTGGGGCATT
* * *
3008001 GCTGATTCAAAGTATTGTGAATCGAGCAAAGGAAATGTTGAAAACATCTTGCT-CGAAGGTTTTA
1 GCTGATTCAAAGTATTGTAAATCGAGCAAAGGAAATGTTGAAAACATC-CGCTCCGAAGGTCTTA
*
3008065 TGGATGGCCCGAAGGACTTAA
65 TGGATGGCCCAAAGGACTTAA
* * *
3008086 GCTGATTCAAAGTA-TGTAAATCGAGCAATGGAAATGTTGCAAACATCCGGTCCGAAGGTCTTAT
1 GCTGATTCAAAGTATTGTAAATCGAGCAAAGGAAATGTTGAAAACATCCGCTCCGAAGGTCTTAT
*
3008150 GGATGGCCTAAAGGACTTA
66 GGATGGCCCAAAGGACTTA
3008169 TCATCTTGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
83 2 0.03
84 58 0.78
85 14 0.19
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (85 bp):
GCTGATTCAAAGTATTGTAAATCGAGCAAAGGAAATGTTGAAAACATCCGCTCCGAAGGTCTTAT
GGATGGCCCAAAGGACTTAA
Found at i:3008258 original size:42 final size:41
Alignment explanation
Indices: 3008145--3008258 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 41
3008135 GTCCGAAGGT
* * *
3008145 CTTATGGATGGCCTAAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCTGAAGGACTTATCATCATGCTCGAAAGA
* * * *
3008186 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCTGAAGGACTT-ATCATCATGCTCGAAAGA
*
3008228 CTTACT-GATGGCCTGAAGAACTTACTCATCA
1 CTTA-TAGATGGCCTGAAGGACTTA-TCATCA
3008259 AGAAACCCTT
Statistics
Matches: 58, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
41 19 0.33
42 38 0.66
43 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (41 bp):
CTTATAGATGGCCTGAAGGACTTATCATCATGCTCGAAAGA
Found at i:3008490 original size:52 final size:53
Alignment explanation
Indices: 3008394--3008541 Score: 217
Period size: 52 Copynumber: 2.8 Consensus size: 53
3008384 TCTAAAAACT
* * *
3008394 TTTGAAAACATCAAGAAATCCCTAAAAATTTGGCTTAATTTCTTTGAAATTCA
1 TTTGAAAACATCAAGAAATCCCTAAAAATTAGGCTTAGTTTCTTTCAAATTCA
* * * *
3008447 TTTGAAAACATTAAGAAACCCCT-TAAATTAGGCTTAGCTTCTTTCAAATTCA
1 TTTGAAAACATCAAGAAATCCCTAAAAATTAGGCTTAGTTTCTTTCAAATTCA
*
3008499 TTTGAAAACATCAAGAAATCCCTGAAAATTAGGCTTAGTTTCT
1 TTTGAAAACATCAAGAAATCCCTAAAAATTAGGCTTAGTTTCT
3008542 AAAAATCTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
52 45 0.54
53 38 0.46
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (53 bp):
TTTGAAAACATCAAGAAATCCCTAAAAATTAGGCTTAGTTTCTTTCAAATTCA
Found at i:3008591 original size:39 final size:39
Alignment explanation
Indices: 3008543--3008651 Score: 146
Period size: 39 Copynumber: 2.8 Consensus size: 39
3008533 TTAGTTTCTA
* *
3008543 AAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCTAGAT
1 AAAATCTTTTGTTTCGAGTGAAACAATCTCAAGCGAGAT
*
3008582 AAAATCTTTTGTTTTGAGTGAAACAATCTCAAGCGAGAT
1 AAAATCTTTTGTTTCGAGTGAAACAATCTCAAGCGAGAT
* * **
3008621 AAAATCTTCTGGTTTCAAGAAAAACAATCTC
1 AAAATCTT-TTGTTTCGAGTGAAACAATCTC
3008652 GAGTGTGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
39 44 0.72
40 17 0.28
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (39 bp):
AAAATCTTTTGTTTCGAGTGAAACAATCTCAAGCGAGAT
Found at i:3008944 original size:36 final size:36
Alignment explanation
Indices: 3008817--3008945 Score: 86
Period size: 38 Copynumber: 3.5 Consensus size: 36
3008807 GTTTAAAGAG
* * * *
3008817 AAACTATCTCAAGGGAGACAAACTTTGT-TTTGAGTA
1 AAACTATCTC-AGTGAGACAAAATTTGTATTTTAGGA
* *
3008853 GAAA-TCGTCTCAAGTGAGACAAAATTTGTATTTTAATGA
1 -AAACT-ATCTC-AGTGAGACAAAATTTGTATTTT-AGGA
* *
3008892 AAATTGTCTCCAGTGAGACAAAATTTGT-TCTTT-GGA
1 AAACTATCT-CAGTGAGACAAAATTTGTAT-TTTAGGA
3008928 AAACTATCTCATGTGAGA
1 AAACTATCTCA-GTGAGA
3008946 TCAATTTTGT
Statistics
Matches: 76, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
35 2 0.03
36 16 0.21
37 24 0.32
38 30 0.39
39 4 0.05
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (36 bp):
AAACTATCTCAGTGAGACAAAATTTGTATTTTAGGA
Found at i:3009194 original size:104 final size:103
Alignment explanation
Indices: 3009050--3009277 Score: 359
Period size: 104 Copynumber: 2.2 Consensus size: 103
3009040 TGGTTAATGT
* *
3009050 AAAACAACTTTGAAATTTTTGGTCCAAAGGAAAATATCTCAAATGAGACGAAATTCGTTTTGAGA
1 AAAACAACTTTGAAATTTGTGGTCCAAAGGAAAATATCTCAAATGAGACGAAATTCGTTTTAAGA
3009115 GAAAAATGTCTAAAGTGAGA-AAAATTTGTTTTTTTAAGA
66 GAAAAATGTCTAAAGTGAGACAAAATTTG--TTTTTAAGA
* * * * *
3009154 AAAACAACTTTCAAATTTGTGTTTCAAAGGAAAATGTCTCAAATGAGACGAAATTTGTTTTAAGA
1 AAAACAACTTTGAAATTTGTGGTCCAAAGGAAAATATCTCAAATGAGACGAAATTCGTTTTAAGA
*
3009219 GAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGA
66 GAAAAATGTCTAAAGTGAGACAAAATTTGTTTTTAAGA
3009257 AAAACAACTTTGAAATTTGTG
1 AAAACAACTTTGAAATTTGTG
3009278 CTTCGATCTT
Statistics
Matches: 114, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
103 29 0.25
104 77 0.68
105 8 0.07
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (103 bp):
AAAACAACTTTGAAATTTGTGGTCCAAAGGAAAATATCTCAAATGAGACGAAATTCGTTTTAAGA
GAAAAATGTCTAAAGTGAGACAAAATTTGTTTTTAAGA
Found at i:3009230 original size:37 final size:36
Alignment explanation
Indices: 3009166--3009260 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 36
3009156 AACAACTTTC
* *
3009166 AAATTTGTGTTTCAAAGGAAAATGTCTCAAATGAGACG
1 AAATTTGT-TTT-AAAGAAAAATGTCTCAAATGAGACA
*
3009204 AAATTTGTTTTAAGAGAAAAATGTCTCAAGTGAGACA
1 AAATTTGTTTTAA-AGAAAAATGTCTCAAATGAGACA
*
3009241 AAATTTGTTTTTAAGAAAAA
1 AAATTTGTTTTAAAGAAAAA
3009261 CAACTTTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
36 9 0.17
37 35 0.67
38 8 0.15
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (36 bp):
AAATTTGTTTTAAAGAAAAATGTCTCAAATGAGACA
Found at i:3013481 original size:2 final size:2
Alignment explanation
Indices: 3013474--3013499 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3013464 TGAAACATGC
3013474 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
3013500 TCATATGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3015156 original size:3 final size:3
Alignment explanation
Indices: 3015148--3015203 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
3015138 AACAGATGTA
3015148 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3015196 AAT AAT AA
1 AAT AAT AA
3015204 ATATTTTTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3016475 original size:21 final size:22
Alignment explanation
Indices: 3016451--3016494 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3016441 CATTTGATTC
*
3016451 AATTGAAATTAGAATCCT-AAT
1 AATTCAAATTAGAATCCTGAAT
* *
3016472 AATTCAATTTATAATCCTGAAT
1 AATTCAAATTAGAATCCTGAAT
3016494 A
1 A
3016495 CCCCTGATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (22 bp):
AATTCAAATTAGAATCCTGAAT
Done.