Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 8 of 196
Found at i:2376674 original size:90 final size:90
Alignment explanation
Indices: 2376579--2376837 Score: 423
Period size: 90 Copynumber: 2.9 Consensus size: 90
2376569 TTAATTTGAT
* *
2376579 TCGTGATGCCATAGCGTCTTTCAG-CTATGGTCTTACTTGATAGAATTGTGATGCCATAACGTCT
1 TCGTGATGCCATAACGTCTTTCAGTC-ATGGTCTTACTTGATAGAATCGTGATGCCATAACGTCT
*
2376643 TTCAGTCATGGTCTTCCTCGATAGAA
65 TTCAGTCATGGTCTTACTCGATAGAA
*
2376669 TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGCCATAACGTCTT
1 TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTTGATAGAATCGTGATGCCATAACGTCTT
2376734 TCAGTCATGGTCTTACTCGATAGAA
66 TCAGTCATGGTCTTACTCGATAGAA
* **
2376759 TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTAC-TCATTAGAATCGTGATGCCATAACACCT
1 TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTTGA-TAGAATCGTGATGCCATAACGTCT
2376823 TTCAGTCATGGTCTT
65 TTCAGTCATGGTCTT
2376838 GTTTCTAGTA
Statistics
Matches: 159, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
89 1 0.01
90 157 0.99
91 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (90 bp):
TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTTGATAGAATCGTGATGCCATAACGTCTT
TCAGTCATGGTCTTACTCGATAGAA
Found at i:2376737 original size:135 final size:135
Alignment explanation
Indices: 2376579--2376837 Score: 432
Period size: 135 Copynumber: 1.9 Consensus size: 135
2376569 TTAATTTGAT
* * *
2376579 TCGTGATGCCATAGCGTCTTTCAG-CTATGGTCTTACTTGATAGAATTGTGATGCCATAACGTCT
1 TCGTGATGCCATAACGTCTTTCAGTC-ATGGTCTTACTCGATAGAATCGTGATGCCATAACGTCT
* **
2376643 TTCAGTCATGGTCTTCCTCGA-TAGAATCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTC
65 TTCAGTCATGGTCTTACTC-ATTAGAATCGTGATGCCATAACACCTTTCAGTCATGGTCTTACTC
2376707 GATAGAA
129 GATAGAA
2376714 TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGCCATAACGTCTT
1 TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGCCATAACGTCTT
2376779 TCAGTCATGGTCTTACTCATTAGAATCGTGATGCCATAACACCTTTCAGTCATGGTCTT
66 TCAGTCATGGTCTTACTCATTAGAATCGTGATGCCATAACACCTTTCAGTCATGGTCTT
2376838 GTTTCTAGTA
Statistics
Matches: 116, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
134 1 0.01
135 114 0.98
136 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (135 bp):
TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGCCATAACGTCTT
TCAGTCATGGTCTTACTCATTAGAATCGTGATGCCATAACACCTTTCAGTCATGGTCTTACTCGA
TAGAA
Found at i:2382230 original size:3 final size:3
Alignment explanation
Indices: 2382222--2382252 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2382212 ATAGATTTAA
2382222 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2382253 CCACTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2386214 original size:27 final size:27
Alignment explanation
Indices: 2386176--2386229 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
2386166 TTGCTTTGTA
*
2386176 ACACCGTTAAATATACATAGCAGAAAT
1 ACACCGTTAAATATACACAGCAGAAAT
*
2386203 ACACTGTTAAATATACACAGCAGAAAT
1 ACACCGTTAAATATACACAGCAGAAAT
2386230 CGTAATTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (27 bp):
ACACCGTTAAATATACACAGCAGAAAT
Found at i:2390546 original size:19 final size:19
Alignment explanation
Indices: 2390522--2390588 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
2390512 AATTGAGCAC
2390522 AATCAAACATACATACACA
1 AATCAAACATACATACACA
*
2390541 AATCAAAACCA-A-TTGAGCAC-
1 AATC-AAA-CATACAT-A-CACA
*
2390561 AATCAAACATACATAAACA
1 AATCAAACATACATACACA
2390580 AATCAAACA
1 AATCAAACA
2390589 CATAAATACC
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
18 4 0.11
19 19 0.50
20 10 0.26
21 5 0.13
ACGTcount: A:0.58, C:0.24, G:0.03, T:0.15
Consensus pattern (19 bp):
AATCAAACATACATACACA
Found at i:2390551 original size:39 final size:39
Alignment explanation
Indices: 2390499--2390586 Score: 149
Period size: 39 Copynumber: 2.3 Consensus size: 39
2390489 CACCTTTCAT
* * *
2390499 ACAATTCACAACCAATTGAGCACAATCAAACATACATAC
1 ACAAATCAAAACCAATTGAGCACAATCAAACATACATAA
2390538 ACAAATCAAAACCAATTGAGCACAATCAAACATACATAA
1 ACAAATCAAAACCAATTGAGCACAATCAAACATACATAA
2390577 ACAAATCAAA
1 ACAAATCAAA
2390587 CACATAAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.55, C:0.25, G:0.05, T:0.16
Consensus pattern (39 bp):
ACAAATCAAAACCAATTGAGCACAATCAAACATACATAA
Found at i:2394150 original size:19 final size:20
Alignment explanation
Indices: 2394100--2394144 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
2394090 ACCTTACTAA
*
2394100 TATTAATAATTTT--AGATT
1 TATTAATACTTTTAAAGATT
2394118 TATTAATACTTTTAAAGATT
1 TATTAATACTTTTAAAGATT
2394138 T-TTAATA
1 TATTAATA
2394145 TATTTATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 6 0.25
20 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (20 bp):
TATTAATACTTTTAAAGATT
Found at i:2396208 original size:4 final size:4
Alignment explanation
Indices: 2396199--2396225 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2396189 TCTCCACTTG
2396199 TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TAT
2396226 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:2398917 original size:19 final size:19
Alignment explanation
Indices: 2398893--2398934 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
2398883 ACTATCAAGC
2398893 TAACCAAATTCAAGCTTAG
1 TAACCAAATTCAAGCTTAG
2398912 TAACCAAATTCAAGCTTAG
1 TAACCAAATTCAAGCTTAG
2398931 TAAC
1 TAAC
2398935 ACGTAACTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
TAACCAAATTCAAGCTTAG
Found at i:2401231 original size:23 final size:23
Alignment explanation
Indices: 2401205--2401298 Score: 125
Period size: 23 Copynumber: 4.1 Consensus size: 23
2401195 AAGTTAGAAG
*
2401205 AGTGAAGAGACTTGAATACGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
2401228 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
2401251 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
2401274 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
2401297 AG
1 AG
2401299 ATACACACAT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.48, C:0.05, G:0.26, T:0.21
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:2405741 original size:23 final size:23
Alignment explanation
Indices: 2405706--2405799 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
2405696 AAGTTAGAAG
2405706 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
2405729 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
2405752 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
2405775 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
2405798 AG
1 AG
2405800 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:2414208 original size:133 final size:133
Alignment explanation
Indices: 2413970--2414220 Score: 448
Period size: 133 Copynumber: 1.9 Consensus size: 133
2413960 AGTAGGTACA
2413970 TGAGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTTTATTATCTGTTTTGATAA
1 TGAGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTTTATTATCTGTTTTGATAA
*
2414035 GCTAATTGATTCAATTGTGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTACATTG
66 GCTAATTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTACATTG
2414100 GGG
131 GGG
*
2414103 TGAGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTTTGTTATCTGTTTTGATAA
1 TGAGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTTTATTATCTGTTTTGATAA
* * * *
2414168 GCTATTTGGTTCAATTATGTAATATGAATATATGATATTATGATTTTGCATGT
66 GCTAATTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGT
2414221 GCATTGGGCT
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 112 1.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (133 bp):
TGAGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTTTATTATCTGTTTTGATAA
GCTAATTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTACATTG
GGG
Found at i:2414396 original size:6 final size:6
Alignment explanation
Indices: 2414382--2414432 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
2414372 TAGACTAAGT
* ** *
2414382 TTTTTG TTTTGG TTTT-G TTTTGG GCTTGG TTTTGG TTTTGG TTTTTG
1 TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG TTTTGG
2414429 TTTT
1 TTTT
2414433 ATTTTTTGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.02, G:0.27, T:0.71
Consensus pattern (6 bp):
TTTTGG
Found at i:2414397 original size:12 final size:12
Alignment explanation
Indices: 2414382--2414442 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
2414372 TAGACTAAGT
2414382 TTTTTGTTTTGG
1 TTTTTGTTTTGG
2414394 -TTTTGTTTTGG
1 TTTTTGTTTTGG
** *
2414405 GCTTGGTTTTGG
1 TTTTTGTTTTGG
* *
2414417 TTTTGGTTTTTG
1 TTTTTGTTTTGG
*
2414429 TTTTATTTTTTGG
1 TTTT-TGTTTTGG
2414442 T
1 T
2414443 ATTGATATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
11 11 0.28
12 22 0.56
13 6 0.15
ACGTcount: A:0.02, C:0.02, G:0.26, T:0.70
Consensus pattern (12 bp):
TTTTTGTTTTGG
Found at i:2414680 original size:14 final size:14
Alignment explanation
Indices: 2414661--2414709 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
2414651 CGACTTTGAA
2414661 TTTGAATTTTGGGT
1 TTTGAATTTTGGGT
** *
2414675 TTTGAATAAAT-GTT
1 TTTGAAT-TTTGGGT
2414689 TTTGAATTTTGGGT
1 TTTGAATTTTGGGT
2414703 TTTGAAT
1 TTTGAAT
2414710 AAATGTTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.55
Consensus pattern (14 bp):
TTTGAATTTTGGGT
Found at i:2414701 original size:28 final size:28
Alignment explanation
Indices: 2414661--2414733 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
2414651 CGACTTTGAA
2414661 TTTGAATTTTGGGTTTTGAATAAATGTT
1 TTTGAATTTTGGGTTTTGAATAAATGTT
2414689 TTTGAATTTTGGGTTTTGAATAAATGTT
1 TTTGAATTTTGGGTTTTGAATAAATGTT
* *
2414717 TTCGAACTTTGGGTTTT
1 TTTGAATTTTGGGTTTT
2414734 CAAATCATCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.22, C:0.03, G:0.22, T:0.53
Consensus pattern (28 bp):
TTTGAATTTTGGGTTTTGAATAAATGTT
Found at i:2417221 original size:192 final size:192
Alignment explanation
Indices: 2416894--2417267 Score: 622
Period size: 192 Copynumber: 1.9 Consensus size: 192
2416884 GATAAATGTG
* *
2416894 GCTTAATGGAGTTTCCTAAGCCTAGGCCTCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
1 GCTTAATGGAGTTTCCTAAGCCTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
* * *
2416959 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTTTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGCTTGCTCAGAACTAGCCATCTTCTCTTTCTC
* *
2417024 TAATTTTGATTTGTGTTTAACTAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
131 TAATTTTGATTTGTGTTTAACCAAAATTTGATCCAGACTACCCTGATCATCCGCCACCTGTT
*
2417086 GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
1 GCTTAATGGAGTTTCCTAAGCCTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
* * * * * *
2417151 CTACGAGATACAGATAATCTAATTTGCTCGCTTGCTTGCTCAGAACTTGTCATTTTCTCTTTCTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGCTTGCTCAGAACTAGCCATCTTCTCTTTCTC
2417216 TAATTTTGATTTGTGTTTAACCAAAATTTGATCCAGACTACCCTGATCATCC
131 TAATTTTGATTTGTGTTTAACCAAAATTTGATCCAGACTACCCTGATCATCC
2417268 ACTTGTGGCA
Statistics
Matches: 168, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
192 168 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (192 bp):
GCTTAATGGAGTTTCCTAAGCCTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
CTACGAGATACAGAGAATCTAATCTGCTCACTTGCTTGCTCAGAACTAGCCATCTTCTCTTTCTC
TAATTTTGATTTGTGTTTAACCAAAATTTGATCCAGACTACCCTGATCATCCGCCACCTGTT
Found at i:2421465 original size:13 final size:13
Alignment explanation
Indices: 2421449--2421474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2421439 CCGTGGAAAT
2421449 GTGCTTTTGAGAA
1 GTGCTTTTGAGAA
2421462 GTGCTTTTGAGAA
1 GTGCTTTTGAGAA
2421475 ATTTGAGTGT
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:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
GTGCTTTTGAGAA
Found at i:2421668 original size:28 final size:30
Alignment explanation
Indices: 2421636--2421701 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 30
2421626 ATTATAACTT
2421636 ATTTTTAATATTT-TAA-T-ATATAATATTA
1 ATTTTTAATATTTCTAAGTAAT-TAATATTA
*
2421664 ATTTTAAATATTTCTAAGTAATTAATATTA
1 ATTTTTAATATTTCTAAGTAATTAATATTA
2421694 ATTATTTA
1 ATT-TTTA
2421702 TTAAATTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 12 0.38
29 3 0.09
30 12 0.38
31 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (30 bp):
ATTTTTAATATTTCTAAGTAATTAATATTA
Found at i:2421692 original size:30 final size:28
Alignment explanation
Indices: 2421636--2421696 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
2421626 ATTATAACTT
*
2421636 ATTTTTAATATTTTAATATATAATATTA
1 ATTTTAAATATTTTAATATATAATATTA
2421664 ATTTTAAATATTTCTAAGTA-ATTAATATTA
1 ATTTTAAATATTT-TAA-TATA-TAATATTA
2421694 ATT
1 ATT
2421697 ATTTATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 12 0.41
29 4 0.14
30 13 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTTAAATATTTTAATATATAATATTA
Found at i:2424787 original size:22 final size:22
Alignment explanation
Indices: 2424742--2424810 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 22
2424732 CTTTTATTAT
* *
2424742 TTTATTTC-TTTCTTTTTCTTTC
1 TTTATTTCTTTTCATTTTC-CTC
2424764 TTTATTTCTTTTCATTTTCCTC
1 TTTATTTCTTTTCATTTTCCTC
*
2424786 TTCTATTTTCTTTTCATTTTTCTC
1 TT-TA-TTTCTTTTCATTTTCCTC
2424810 T
1 T
2424811 ATTTCCTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
22 12 0.29
23 11 0.27
24 18 0.44
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTATTTCTTTTCATTTTCCTC
Found at i:2424829 original size:21 final size:21
Alignment explanation
Indices: 2424761--2424829 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
2424751 TTCTTTTTCT
*
2424761 TTCTTTATTT-CTTTTCATTTTC
1 TTCTCTATTTCCTTTTCA--TTC
* * *
2424783 CTCTTCTATTTTCTTTTCATTT
1 TTC-TCTATTTCCTTTTCATTC
2424805 TTCTCTATTTCCTTTTTC-TTC
1 TTCTCTATTTCC-TTTTCATTC
2424826 TTCT
1 TTCT
2424830 TCTAACCCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
21 14 0.37
22 11 0.29
23 6 0.16
24 7 0.18
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (21 bp):
TTCTCTATTTCCTTTTCATTC
Found at i:2432163 original size:20 final size:20
Alignment explanation
Indices: 2432138--2432181 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2432128 TTGCATAGAT
2432138 TAAAAACTAAATTCAAAATA
1 TAAAAACTAAATTCAAAATA
* * *
2432158 TAAAAAGTTAATTTAAAATA
1 TAAAAACTAAATTCAAAATA
2432178 -AAAA
1 TAAAA
2432182 TATGTTACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAAAACTAAATTCAAAATA
Found at i:2432691 original size:17 final size:17
Alignment explanation
Indices: 2432662--2432710 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
2432652 TAATAAATAA
2432662 AATTATCCAACCCAACCC
1 AATTAT-CAACCCAACCC
2432680 AATTATCAACCCAACCC
1 AATTATCAACCCAACCC
*
2432697 AATTACCAACCCAA
1 AATTATCAACCCAA
2432711 TAAAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 24 0.80
18 6 0.20
ACGTcount: A:0.43, C:0.41, G:0.00, T:0.16
Consensus pattern (17 bp):
AATTATCAACCCAACCC
Found at i:2432919 original size:9 final size:9
Alignment explanation
Indices: 2432902--2432932 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2432892 GTAGTGATTC
*
2432902 AATTCGGGT
1 AATTTGGGT
2432911 AATTTGGGT
1 AATTTGGGT
2432920 AATTTGGGT
1 AATTTGGGT
2432929 AATT
1 AATT
2432933 CGGTTAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (9 bp):
AATTTGGGT
Found at i:2432958 original size:9 final size:9
Alignment explanation
Indices: 2432902--2432940 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2432892 GTAGTGATTC
2432902 AATTCGGGT
1 AATTCGGGT
*
2432911 AATTTGGGT
1 AATTCGGGT
*
2432920 AATTTGGGT
1 AATTCGGGT
*
2432929 AATTCGGTT
1 AATTCGGGT
2432938 AAT
1 AAT
2432941 CAATTAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.26, C:0.05, G:0.28, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:2434210 original size:11 final size:11
Alignment explanation
Indices: 2434196--2434251 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
2434186 AAAATTAAAA
2434196 AAAAGTATTTT
1 AAAAGTATTTT
*
2434207 AAAATTATTTT
1 AAAAGTATTTT
2434218 -AAA--A-TTT
1 AAAAGTATTTT
2434225 AAATAGTATTTT
1 AAA-AGTATTTT
*
2434237 AAAAATATTTT
1 AAAAGTATTTT
2434248 AAAA
1 AAAA
2434252 TTAAAAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
9 1 0.03
10 3 0.08
11 22 0.58
12 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:2434257 original size:17 final size:17
Alignment explanation
Indices: 2434235--2434279 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
2434225 AAATAGTATT
2434235 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
2434252 TTAAAAA-AATTTAAAA
1 TTAAAAATATTTTAAAA
* *
2434268 ATAAATATATTT
1 TTAAAAATATTT
2434280 ATTATGTCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:2439170 original size:18 final size:18
Alignment explanation
Indices: 2439130--2439173 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2439120 AATTTTTATG
**
2439130 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
2439148 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
2439166 CTTGGGTT
1 ATTGGGTT
2439174 TGGATTAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:2448038 original size:16 final size:16
Alignment explanation
Indices: 2448017--2448048 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2448007 CGCTAATTAG
2448017 ATTTTAAAAAATTAAA
1 ATTTTAAAAAATTAAA
*
2448033 ATTTTAACAAATTAAA
1 ATTTTAAAAAATTAAA
2448049 CTTGGACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTTAAAAAATTAAA
Found at i:2448179 original size:19 final size:19
Alignment explanation
Indices: 2448155--2448194 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2448145 ACCATAGTTG
*
2448155 TAGTTTAGTTATATTTTTT
1 TAGTTTAGTTAGATTTTTT
* *
2448174 TAGTTTTGTTAGGTTTTTT
1 TAGTTTAGTTAGATTTTTT
2448193 TA
1 TA
2448195 CCAAAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (19 bp):
TAGTTTAGTTAGATTTTTT
Found at i:2449242 original size:17 final size:16
Alignment explanation
Indices: 2449220--2449275 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 16
2449210 TAAAATTTTA
2449220 ATAAATGATAAAAATAT
1 ATAAAT-ATAAAAATAT
*
2449237 ATAAAT-TATTAAATAT
1 ATAAATATA-AAAATAT
2449253 -TAAAT-TAAAAATAAT
1 ATAAATATAAAAAT-AT
2449268 ATAAATAT
1 ATAAATAT
2449276 TGTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 4 0.12
15 11 0.33
16 11 0.33
17 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
ATAAATATAAAAATAT
Found at i:2454426 original size:18 final size:19
Alignment explanation
Indices: 2454399--2454439 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
2454389 TTAAACCCTT
2454399 AAAAATCCCT-AACCTTAAC
1 AAAAATCCCTAAACC-TAAC
2454418 AAAAA-CCCTAAACCTAAC
1 AAAAATCCCTAAACCTAAC
2454436 AAAA
1 AAAA
2454440 TTAAAAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAAATCCCTAAACCTAAC
Found at i:2455644 original size:18 final size:18
Alignment explanation
Indices: 2455617--2455651 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2455607 TAAAATTATA
2455617 AAATAAAATAATTATTTC
1 AAATAAAATAATTATTTC
*
2455635 AAATATAATAATTATTT
1 AAATAAAATAATTATTT
2455652 TTATATGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAAAATAATTATTTC
Found at i:2460523 original size:24 final size:24
Alignment explanation
Indices: 2460496--2460547 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2460486 TTAGTAAGTC
*
2460496 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2460520 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2460544 AAAT
1 AAAT
2460548 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2462444 original size:24 final size:24
Alignment explanation
Indices: 2462417--2462468 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2462407 TTAGTAAGTC
*
2462417 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2462441 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2462465 AAAT
1 AAAT
2462469 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2470761 original size:152 final size:149
Alignment explanation
Indices: 2470248--2470877 Score: 677
Period size: 152 Copynumber: 4.2 Consensus size: 149
2470238 CAAAATGATC
* * * * * * * *
2470248 TTTAGAAAAAATCATTAATTTTCTTAAAAATCAAAAC-CTTA-TTTCGAAATAGTTAAAAAATTT
1 TTTAAAAAAAAACACTATTTTTCTTAAAAATTAAAACTTTTACTTT-GAAATAGTTAAAAAAATC
* * * * * *
2470311 AAAACTTTGTTTTAAAAAGTTAAACTTTCCTTTAAAATGACTTAAAAACATAGATTTTTAATTTT
65 AAAACTTTATTTTAAAAATTTAAACTTTCCTTTAAAATAAC-TAAAAAAACAGATTTTTATTTTT
2470376 CAAAATCTAAACATTCTCTTTTT
129 CAAAATCTAAAC-TT-TCTTTTT
* * * *
2470399 TTTATTTATTAAAAAACACTA-TTTTCTTAAAAATTAAAGCTTTTTATTTTGAAGTAGTTAAAAA
1 TTTA---A-AAAAAAACACTATTTTTCTTAAAAATTAAAAC-TTTTACTTTGAAATAGTTAAAAA
* * * * *
2470463 AATAAAAATTTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAATTAAAAAAACAAATTTTTATT
61 AATCAAAACTTTATTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAACAGATTTTTATT
* **
2470528 TTTTAAAATCTAAACTTTC--TCC
126 TTTCAAAATCTAAACTTTCTTTTT
* ** *
2470550 TTTAAAAAAAAATACTATTTTTCTTAAGGATTAAAGCTTTTACTTTGAAATAGTTGAAAAAAAAA
1 TTTAAAAAAAAACACTATTTTTCTTAAAAATTAAAACTTTTACTTTGAAATAGTT---AAAAAAA
2470615 TCAAAACTTTATTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAACAGATTTTTATTTT
63 TCAAAACTTTATTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAACAGATTTTTATTTT
2470680 TCAAAATCTAAACTTTCTTTTT
128 TCAAAATCTAAACTTTCTTTTT
* * *
2470702 TTTAAAAAAAAAGATTATTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTGAAAAGAAAA
1 TTTAAAAAAAAACACTATTTTTCTTAAAAATTAAAACTTTTACTTTGAAATAGTT--AAA-AAAA
* *
2470767 TCAAAACTTTATTTTAAAAAATTAAAC-TTCTCTTTAAAATAACTAAAAAAACCATATTATTATT
63 TCAAAACTTTATTTTAAAAATTTAAACTTTC-CTTTAAAATAACTAAAAAAA-CAGA-T-TT-TT
2470831 ATTATTTCAAAATCTAAACTTTC---TT
123 ATT-TTTCAAAATCTAAACTTTCTTTTT
*
2470856 CTT-AAAAAAAACACTATTTTTC
1 TTTAAAAAAAAACACTATTTTTC
2470878 CCAAAATCAA
Statistics
Matches: 414, Mismatches: 45, Indels: 38
0.83 0.09 0.08
Matches are distributed among these distances:
147 26 0.06
148 18 0.04
150 83 0.20
151 16 0.04
152 102 0.25
153 22 0.05
154 24 0.06
155 41 0.10
156 60 0.14
157 22 0.05
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.41
Consensus pattern (149 bp):
TTTAAAAAAAAACACTATTTTTCTTAAAAATTAAAACTTTTACTTTGAAATAGTTAAAAAAATCA
AAACTTTATTTTAAAAATTTAAACTTTCCTTTAAAATAACTAAAAAAACAGATTTTTATTTTTCA
AAATCTAAACTTTCTTTTT
Found at i:2472992 original size:12 final size:12
Alignment explanation
Indices: 2472975--2473010 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2472965 TTAATTATAA
2472975 TACTATTATTAT
1 TACTATTATTAT
*
2472987 TACTATTATTAC
1 TACTATTATTAT
2472999 TACTATTATTAT
1 TACTATTATTAT
2473011 AGATGTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (12 bp):
TACTATTATTAT
Found at i:2473527 original size:18 final size:18
Alignment explanation
Indices: 2473495--2473872 Score: 108
Period size: 17 Copynumber: 20.9 Consensus size: 18
2473485 ATATTTTGAG
2473495 AACACGAAAATTTTTTTAA
1 AACACGAAAA-TTTTTTAA
*
2473514 AACACGAGAA--TTTTAGA
1 AACACGAAAATTTTTTA-A
* *
2473531 AACACGAAAATTCTTAAA
1 AACACGAAAATTTTTTAA
*
2473549 AACACGAAAATTTTTGAA
1 AACACGAAAATTTTTTAA
**
2473567 AACACGAAAA-TTTTTGG
1 AACACGAAAATTTTTTAA
* * *
2473584 ATCGCCG-AAATTTTTGAA
1 AAC-ACGAAAATTTTTTAA
*
2473602 AGCACG-AAATTTTTTGAA
1 AACACGAAAATTTTTT-AA
* *
2473620 AA-ATCTG--AATTTATTGAG
1 AACA-C-GAAAATTT-TTTAA
*
2473638 AA-ACGAAAA-TTTTGAA
1 AACACGAAAATTTTTTAA
*
2473654 AAC-CTGAAAA-TTTTTAC
1 AACAC-GAAAATTTTTTAA
** **
2473671 AACACGGTAA-TTTGCAA
1 AACACGAAAATTTTTTAA
* * *
2473688 AACATGGGAATTTTTTTGAAA
1 AACA-CGAAAATTTTTT--AA
* *
2473709 AACATGAAAA-TTTTTGA
1 AACACGAAAATTTTTTAA
* *
2473726 AATACGAAAATTTTTAGAA
1 AACACGAAAATTTTT-TAA
**
2473745 AACACGAATTTTTTTTGAA
1 AACACGAAAATTTTTT-AA
*
2473764 AACACGAAGATTTTTTTTTGAA
1 AACACGAA-A--ATTTTTT-AA
* *
2473786 AACACGGAAA-CTTTTAA
1 AACACGAAAATTTTTTAA
* *
2473803 AACAC-AGGAA-TTTTTGA
1 AACACGA-AAATTTTTTAA
* *
2473820 AACACGAAATTTTTTTTTCA
1 AACACGAAA--ATTTTTTAA
* *
2473840 AACATGAAAA-TTTTTGA
1 AACACGAAAATTTTTTAA
* *
2473857 AATACGAGAATTTTTT
1 AACACGAAAATTTTTT
2473873 TAATACGGAA
Statistics
Matches: 267, Mismatches: 62, Indels: 61
0.68 0.16 0.16
Matches are distributed among these distances:
16 13 0.05
17 99 0.37
18 68 0.25
19 46 0.17
20 17 0.06
21 7 0.03
22 17 0.06
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (18 bp):
AACACGAAAATTTTTTAA
Found at i:2473527 original size:36 final size:36
Alignment explanation
Indices: 2473487--2473581 Score: 122
Period size: 36 Copynumber: 2.6 Consensus size: 36
2473477 ATATAATTAT
* *
2473487 ATTTTGAGAACACGAAAATTTTTTTAAAACACGAGA
1 ATTTTGAGAACACGAAAATTTTTTAAAAACACGAAA
*
2473523 ATTTT-AGAAACACGAAAA-TTCTTAAAAACACGAAA
1 ATTTTGAG-AACACGAAAATTTTTTAAAAACACGAAA
*
2473558 ATTTTTGAAAACACGAAAATTTTT
1 A-TTTTGAGAACACGAAAATTTTT
2473582 GGATCGCCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 17 0.34
36 29 0.58
37 4 0.08
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.31
Consensus pattern (36 bp):
ATTTTGAGAACACGAAAATTTTTTAAAAACACGAAA
Found at i:2473710 original size:21 final size:21
Alignment explanation
Indices: 2473681--2473780 Score: 63
Period size: 19 Copynumber: 5.1 Consensus size: 21
2473671 AACACGGTAA
* **
2473681 TTTGCAAAACATGGGAATTTT
1 TTTGAAAAACATGAAAATTTT
2473702 TTTGAAAAACATGAAAA--TT
1 TTTGAAAAACATGAAAATTTT
*
2473721 TTTGAAATAC--GAAAA-TTT
1 TTTGAAAAACATGAAAATTTT
* * *
2473739 TTAG-AAAACACG-AATTTTT
1 TTTGAAAAACATGAAAATTTT
* *
2473758 TTTG-AAAACACGAAGATTTT
1 TTTGAAAAACATGAAAATTTT
2473778 TTT
1 TTT
2473781 TTGAAAACAC
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
17 9 0.14
18 7 0.11
19 26 0.41
20 8 0.12
21 14 0.22
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (21 bp):
TTTGAAAAACATGAAAATTTT
Found at i:2473800 original size:22 final size:20
Alignment explanation
Indices: 2473698--2473791 Score: 81
Period size: 19 Copynumber: 4.8 Consensus size: 20
2473688 AACATGGGAA
*
2473698 TTTTTTTGAAAAACATGAAA-
1 TTTTTTTG-AAAACACGAAAT
* *
2473718 -ATTTTTG-AAATACGAAA-
1 TTTTTTTGAAAACACGAAAT
* *
2473735 ATTTTTAGAAAACACG-AAT
1 TTTTTTTGAAAACACGAAAT
2473754 TTTTTTTGAAAACACGAAGATT
1 TTTTTTTGAAAACACGAA-A-T
2473776 TTTTTTTGAAAACACG
1 TTTTTTTGAAAACACG
2473792 GAAACTTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.13
18 7 0.12
19 26 0.43
20 1 0.02
21 1 0.02
22 17 0.28
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (20 bp):
TTTTTTTGAAAACACGAAAT
Found at i:2473800 original size:23 final size:22
Alignment explanation
Indices: 2473736--2473791 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
2473726 AATACGAAAA
*
2473736 TTTTTAGAAAACACG-A-A-TT
1 TTTTTTGAAAACACGAAGATTT
2473755 TTTTTTGAAAACACGAAGATTT
1 TTTTTTGAAAACACGAAGATTT
2473777 TTTTTTGAAAACACG
1 TTTTTTGAAAACACG
2473792 GAAACTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 14 0.42
20 1 0.03
21 1 0.03
22 17 0.52
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (22 bp):
TTTTTTGAAAACACGAAGATTT
Found at i:2473842 original size:20 final size:21
Alignment explanation
Indices: 2473813--2473854 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2473803 AACACAGGAA
*
2473813 TTTTTGAAACACG-AAATTTT
1 TTTTTCAAACACGAAAATTTT
*
2473833 TTTTTCAAACATGAAAATTTT
1 TTTTTCAAACACGAAAATTTT
2473854 T
1 T
2473855 GAAATACGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (21 bp):
TTTTTCAAACACGAAAATTTT
Found at i:2473843 original size:37 final size:38
Alignment explanation
Indices: 2473797--2473873 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 38
2473787 ACACGGAAAC
*
2473797 TTTTAAAACACAG-GAATTTTTGAAACACGA-AATTTTT
1 TTTTAAAACA-AGAAAATTTTTGAAACACGAGAATTTTT
* * *
2473834 TTTTCAAACATGAAAATTTTTGAAATACGAGAATTTTT
1 TTTTAAAACAAGAAAATTTTTGAAACACGAGAATTTTT
2473872 TT
1 TT
2473874 AATACGGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 1 0.03
37 24 0.71
38 9 0.26
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (38 bp):
TTTTAAAACAAGAAAATTTTTGAAACACGAGAATTTTT
Found at i:2473877 original size:17 final size:16
Alignment explanation
Indices: 2473857--2473888 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
2473847 AAATTTTTGA
2473857 AATACGAGAATTTTTTT
1 AATACG-GAATTTTTTT
2473874 AATACGGAATTTTTT
1 AATACGGAATTTTTT
2473889 GAAATACTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (16 bp):
AATACGGAATTTTTTT
Found at i:2473894 original size:17 final size:18
Alignment explanation
Indices: 2473850--2473901 Score: 72
Period size: 17 Copynumber: 3.0 Consensus size: 18
2473840 AACATGAAAA
2473850 TTTTTGAAATACGAGAAT
1 TTTTTGAAATACGAGAAT
*
2473868 TTTTT-TAATACG-GAAT
1 TTTTTGAAATACGAGAAT
*
2473884 TTTTTGAAATACTAGAAT
1 TTTTTGAAATACGAGAAT
2473902 ATTAGAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.31
17 11 0.38
18 9 0.31
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (18 bp):
TTTTTGAAATACGAGAAT
Found at i:2474617 original size:20 final size:20
Alignment explanation
Indices: 2474592--2474638 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2474582 GGCCTGGGCG
*
2474592 CTGGGCCGAATGCTGGTGCA
1 CTGGGCCGAACGCTGGTGCA
* *
2474612 CTGGGCCGGACGCTGGTGCG
1 CTGGGCCGAACGCTGGTGCA
2474632 CTGGGCC
1 CTGGGCC
2474639 TGGGCGCTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.09, C:0.30, G:0.45, T:0.17
Consensus pattern (20 bp):
CTGGGCCGAACGCTGGTGCA
Found at i:2474941 original size:5 final size:6
Alignment explanation
Indices: 2474895--2474945 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
2474885 TTTTAAAATT
** * *
2474895 TTTTTC TGTTTTC TTCCTC TTTTTC TTTCTA TTTTTC TTTTTC TTTTTC
1 TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
2474944 TT
1 TT
2474946 CTTCGGGCGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:2475561 original size:30 final size:29
Alignment explanation
Indices: 2475522--2475628 Score: 110
Period size: 30 Copynumber: 3.6 Consensus size: 29
2475512 TATGGGGCTA
2475522 AAATGTAATTTTCAAAAAGTTTAGAGGTC
1 AAATGTAATTTTCAAAAAGTTTAGAGGTC
* * * *
2475551 AAAGTGTAATTTTGAAAAAGATTAGATGTTG
1 AAA-TGTAATTTTCAAAAAGTTTAGA-GGTC
*
2475582 AAATGTAATTTT-AGAAAAGTTT-GGGGTC
1 AAATGTAATTTTCA-AAAAGTTTAGAGGTC
*
2475610 AAAATGTAAATTTCAAAAA
1 -AAATGTAATTTTCAAAAA
2475629 ATACAAGGGT
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.03
29 20 0.31
30 37 0.58
31 5 0.08
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.34
Consensus pattern (29 bp):
AAATGTAATTTTCAAAAAGTTTAGAGGTC
Found at i:2475628 original size:29 final size:29
Alignment explanation
Indices: 2475483--2475628 Score: 84
Period size: 30 Copynumber: 5.0 Consensus size: 29
2475473 ACGCAAAATA
* *
2475483 TTTGGGGTAAAAATGT-AATTTTAGGAAAA-
1 TTTGGGGTCAAAATGTAAATTTCA--AAAAG
* *
2475512 TATGGGG-CTAAAATGTAATTTTCAAAAAG
1 TTTGGGGTC-AAAATGTAAATTTCAAAAAG
* * * *
2475541 TTTAGAGGTCAAAGTGTAATTTTGAAAAAG
1 TTT-GGGGTCAAAATGTAAATTTCAAAAAG
* ** ** *
2475571 ATTAGATGTTGAAATGT-AATTTTAGAAAAG
1 -TTTGGGGTCAAAATGTAAATTTCA-AAAAG
2475601 TTTGGGGTCAAAATGTAAATTTCAAAAA
1 TTTGGGGTCAAAATGTAAATTTCAAAAA
2475629 ATACAAGGGT
Statistics
Matches: 88, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
28 4 0.05
29 35 0.40
30 46 0.52
31 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (29 bp):
TTTGGGGTCAAAATGTAAATTTCAAAAAG
Found at i:2475645 original size:59 final size:60
Alignment explanation
Indices: 2475520--2475652 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 60
2475510 AATATGGGGC
* * * * *
2475520 TAAAATGTAATTTTCAAAAAGTTTAGAGGTCAAAGTGTAATTTTGAAAAAGATTAGATGT
1 TAAAATGTAATTTTCAAAAAGTTTAGAGGTCAAAATGTAAATTTCAAAAAGATAAGAGGT
* *
2475580 TGAAATGTAATTTT-AGAAAAGTTT-GGGGTCAAAATGTAAATTTCAAAAA-ATACA-AGGGT
1 TAAAATGTAATTTTCA-AAAAGTTTAGAGGTCAAAATGTAAATTTCAAAAAGATA-AGA-GGT
2475639 TAAAATGTAATTTT
1 TAAAATGTAATTTT
2475653 TATTTTTTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
58 3 0.05
59 38 0.61
60 21 0.34
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.35
Consensus pattern (60 bp):
TAAAATGTAATTTTCAAAAAGTTTAGAGGTCAAAATGTAAATTTCAAAAAGATAAGAGGT
Found at i:2478274 original size:29 final size:29
Alignment explanation
Indices: 2478235--2478300 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
2478225 ACCAATAAAA
*
2478235 GCCGTTTTTTTCAAAATTTATCGAAATGG
1 GCCGATTTTTTCAAAATTTATCGAAATGG
* ** *
2478264 GCCGATTTTTTGATTATTTATCGGAATGG
1 GCCGATTTTTTCAAAATTTATCGAAATGG
*
2478293 TCC-ATTTT
1 GCCGATTTT
2478301 CCGAGAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (29 bp):
GCCGATTTTTTCAAAATTTATCGAAATGG
Found at i:2478597 original size:51 final size:51
Alignment explanation
Indices: 2478538--2478645 Score: 180
Period size: 51 Copynumber: 2.1 Consensus size: 51
2478528 TTTCATTCCA
* * *
2478538 AATTTCCTTCCAAAATTCTGTCAAACCCATATTTAATTTCAATTTCCTCTC
1 AATTTCCTTACAAAATTCTCTCAAACCCATATTTAATTTCAATTTCCCCTC
*
2478589 AATTTCCTTACAAAATTCTCTCAAATCCATATTTAATTTCAATTTCCCCTC
1 AATTTCCTTACAAAATTCTCTCAAACCCATATTTAATTTCAATTTCCCCTC
2478640 AATTTC
1 AATTTC
2478646 ATTTTTTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.31, C:0.27, G:0.01, T:0.42
Consensus pattern (51 bp):
AATTTCCTTACAAAATTCTCTCAAACCCATATTTAATTTCAATTTCCCCTC
Found at i:2478679 original size:29 final size:31
Alignment explanation
Indices: 2478646--2478709 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
2478636 CCTCAATTTC
2478646 ATTTTTT-AAAATAA-TTTAAA-TTTTTTAT
1 ATTTTTTAAAAATAATTTTAAATTTTTTTAT
2478674 ATTTTTTAAAAATAATTTTAAATTTTTTTAT
1 ATTTTTTAAAAATAATTTTAAATTTTTTTAT
2478705 ATTTT
1 ATTTT
2478710 CATCAATGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 7 0.21
29 7 0.21
30 6 0.18
31 13 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTTTTTAAAAATAATTTTAAATTTTTTTAT
Found at i:2480492 original size:18 final size:18
Alignment explanation
Indices: 2480466--2480500 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2480456 AGGTGTGTTT
* *
2480466 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
2480484 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
2480501 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:2480795 original size:21 final size:21
Alignment explanation
Indices: 2480759--2480808 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2480749 CAGATGCCAA
*
2480759 ACCGGAAGAACCACAATCA-CC
1 ACCGGAAGAACAACAA-CAGCC
*
2480780 ACCGGAAGAAGAACAACAGCC
1 ACCGGAAGAACAACAACAGCC
*
2480801 GCCGGAAG
1 ACCGGAAG
2480809 CTAGAGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.42, C:0.32, G:0.24, T:0.02
Consensus pattern (21 bp):
ACCGGAAGAACAACAACAGCC
Found at i:2481054 original size:29 final size:29
Alignment explanation
Indices: 2481021--2481285 Score: 407
Period size: 29 Copynumber: 9.3 Consensus size: 29
2481011 TAATAAAAAC
2481021 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
2481050 CCTAATTTAATTAAAAATCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
2481079 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
2481108 CCTAATTTAATTAAAAACCTTAAACCTTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
2481138 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
2481168 CCTAATTTAATTAAAAACCTTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
2481197 CCTAATTTAATTAAAAACCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
2481226 CCTAATTTAATT--AAA----AACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
2481249 CCTAATTTAATTAAAAACCCTAACTCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
2481278 CCTAATTT
1 CCTAATTT
2481286 TACATAATTT
Statistics
Matches: 216, Mismatches: 13, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
23 19 0.09
25 3 0.01
27 3 0.01
29 136 0.63
30 55 0.25
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:2481271 original size:18 final size:20
Alignment explanation
Indices: 2481225--2481267 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
2481215 CCTAACTCTA
2481225 ACCTAATTTAATTAAAAACCC
1 ACCTAATTTAATTAAAAA-CC
2481246 TAACCTAATTTAATTAAAAACC
1 --ACCTAATTTAATTAAAAACC
2481268 CTAACTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:2481341 original size:55 final size:55
Alignment explanation
Indices: 2481280--2481405 Score: 252
Period size: 55 Copynumber: 2.3 Consensus size: 55
2481270 AACTCTAACC
2481280 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
2481335 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
2481390 TAATTTTACATAATTT
1 TAATTTTACATAATTT
2481406 TACATAATGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 71 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (55 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
Found at i:2481404 original size:10 final size:10
Alignment explanation
Indices: 2481389--2481413 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2481379 TTTGGACTTA
2481389 ATAATTTTAC
1 ATAATTTTAC
2481399 ATAATTTTAC
1 ATAATTTTAC
2481409 ATAAT
1 ATAAT
2481414 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:2481498 original size:9 final size:9
Alignment explanation
Indices: 2481484--2481518 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2481474 AATTTTACTA
2481484 ACAATTAAT
1 ACAATTAAT
2481493 ACAATTAAT
1 ACAATTAAT
2481502 ACAATT-AT
1 ACAATTAAT
2481510 -CAATTAAT
1 ACAATTAAT
2481518 A
1 A
2481519 ATTGAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 5 0.21
8 4 0.17
9 15 0.62
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (9 bp):
ACAATTAAT
Found at i:2481515 original size:16 final size:18
Alignment explanation
Indices: 2481484--2481518 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2481474 AATTTTACTA
2481484 ACAATTAATACAATTAAT
1 ACAATTAATACAATTAAT
2481502 ACAATT-AT-CAATTAAT
1 ACAATTAATACAATTAAT
2481518 A
1 A
2481519 ATTGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 2 0.12
18 6 0.35
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
ACAATTAATACAATTAAT
Found at i:2484749 original size:124 final size:124
Alignment explanation
Indices: 2484529--2484876 Score: 554
Period size: 124 Copynumber: 2.8 Consensus size: 124
2484519 CAAACTTGCT
* * *
2484529 ACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGTATCTTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCCCTATTTCACAATTTCTTCTCAAATAGTATCCTGGTA
* *
2484594 GAAGCAATTTTATACTATTTGCTCAAAAACGTCAAAAAAAATTATTTCTTACATGACCA
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
2484653 ACTGTAGCAAAATCGCGTCCACGAGGGCCCTATTTCACAATTTCTTCTCAAATAGTATCCTGGTA
1 ACTGTAGCAAAATCGCGTCCACGAGGGCCCTATTTCACAATTTCTTCTCAAATAGTATCCTGGTA
*
2484718 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCT
66 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
* * ** * * *
2484777 ACTGTAGAAAAATCACGTCCACGAGGG-TGTGATTTCATAATTTCTTCTTAAATAGCATCCTGGT
1 ACTGTAGCAAAATCGCGTCCACGAGGGCCCT-ATTTCACAATTTCTTCTCAAATAGTATCCTGGT
*
2484841 AGAAGCGATTTTATACTATTTACTCAGAAACGTCAA
65 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
2484877 CTCGAAATAA
Statistics
Matches: 209, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
123 1 0.00
124 208 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (124 bp):
ACTGTAGCAAAATCGCGTCCACGAGGGCCCTATTTCACAATTTCTTCTCAAATAGTATCCTGGTA
GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCA
Found at i:2500130 original size:3 final size:3
Alignment explanation
Indices: 2500122--2500156 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2500112 ACCATATGAT
2500122 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
2500157 ATCATTGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:2513647 original size:55 final size:58
Alignment explanation
Indices: 2513581--2513707 Score: 170
Period size: 55 Copynumber: 2.2 Consensus size: 58
2513571 TTCAAAAATA
* *
2513581 ATATTATTTTAATAGTTTTAATATTAAATTAAAT-TAA-ATTTA-ATAGATAACTATT
1 ATATTAATTTAATAGATTTAATATTAAATTAAATCTAATATTTATATAGATAACTATT
* * * * *
2513636 CTATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATT
1 ATATTAATTTAATAGATTTAATATTAAATTAAATCTAATATTTATATAGATAACTATT
2513694 ATATTAATTTAATA
1 ATATTAATTTAATA
2513708 TTAAAGTGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
55 30 0.49
56 3 0.05
57 5 0.08
58 23 0.38
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (58 bp):
ATATTAATTTAATAGATTTAATATTAAATTAAATCTAATATTTATATAGATAACTATT
Found at i:2515844 original size:17 final size:16
Alignment explanation
Indices: 2515818--2515850 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
2515808 TAAATCCCAG
2515818 ATTTTGATACCCATAT
1 ATTTTGATACCCATAT
2515834 ATTTCTGATACCCATAT
1 ATTT-TGATACCCATAT
2515851 CTTTGACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTTGATACCCATAT
Found at i:2518932 original size:36 final size:36
Alignment explanation
Indices: 2518885--2518959 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
2518875 CTCATTCTAC
*
2518885 TAATATAAACATACCAAGCTAAATAAGTTCATGTTT
1 TAATATAAACATACCAAGCTAAAGAAGTTCATGTTT
*
2518921 TAATATAAACATACCAAGTTAAAGAAGTTCATGTTT
1 TAATATAAACATACCAAGCTAAAGAAGTTCATGTTT
2518957 TAA
1 TAA
2518960 CTTCCCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (36 bp):
TAATATAAACATACCAAGCTAAAGAAGTTCATGTTT
Found at i:2519721 original size:16 final size:16
Alignment explanation
Indices: 2519700--2519732 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2519690 GAATTTTTAA
2519700 TAATTA-TTAAGTAGTT
1 TAATTATTTAA-TAGTT
2519716 TAATTATTTAATAGTT
1 TAATTATTTAATAGTT
2519732 T
1 T
2519733 TATGTCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (16 bp):
TAATTATTTAATAGTT
Found at i:2519954 original size:26 final size:27
Alignment explanation
Indices: 2519901--2519954 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
2519891 TTGAGTTAAT
*
2519901 AAATTCTCTTTGAGTTTTTCTTTAAAA
1 AAATTCTCTTTGAGTTTCTCTTTAAAA
*
2519928 AAATTCTC-TTGAGTTTCT-TTTAGAA
1 AAATTCTCTTTGAGTTTCTCTTTAAAA
2519953 AA
1 AA
2519955 GTTTTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.32
26 9 0.36
27 8 0.32
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (27 bp):
AAATTCTCTTTGAGTTTCTCTTTAAAA
Found at i:2520182 original size:13 final size:13
Alignment explanation
Indices: 2520166--2520202 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2520156 TTATTCTATT
2520166 TTATTTATCTTAG
1 TTATTTATCTTAG
*
2520179 TTATTTATTTTAG
1 TTATTTATCTTAG
2520192 TTATTTTATCT
1 TTA-TTTATCT
2520203 GACTATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (13 bp):
TTATTTATCTTAG
Found at i:2529522 original size:14 final size:14
Alignment explanation
Indices: 2529505--2529538 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2529495 ATTAATAAAA
2529505 ATTCAATGAAAATG
1 ATTCAATGAAAATG
* *
2529519 ATTCAATGGAAATT
1 ATTCAATGAAAATG
2529533 ATTCAA
1 ATTCAA
2529539 ACTAATAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (14 bp):
ATTCAATGAAAATG
Found at i:2540039 original size:21 final size:21
Alignment explanation
Indices: 2540013--2540052 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2540003 TTGTACAAAC
2540013 TAAGCCTTTAAGCAAAGAAAT
1 TAAGCCTTTAAGCAAAGAAAT
2540034 TAAGCCTTTAAGCAAAGAA
1 TAAGCCTTTAAGCAAAGAA
2540053 GTTGATTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (21 bp):
TAAGCCTTTAAGCAAAGAAAT
Found at i:2560392 original size:19 final size:18
Alignment explanation
Indices: 2560370--2560409 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2560360 AGTTTTGTTG
*
2560370 TTATATTACTAATTTTTAA
1 TTATATTACTAA-ATTTAA
*
2560389 TTATATTATTAAATTTAA
1 TTATATTACTAAATTTAA
2560407 TTA
1 TTA
2560410 ATCATGCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATATTACTAAATTTAA
Found at i:2560675 original size:6 final size:6
Alignment explanation
Indices: 2560664--2560700 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
2560654 ATATTATAGA
2560664 ATGGAG ATGGAG ATGGAG ATGGAG ATGGAG ATGGAG A
1 ATGGAG ATGGAG ATGGAG ATGGAG ATGGAG ATGGAG A
2560701 AAGGTGTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.49, T:0.16
Consensus pattern (6 bp):
ATGGAG
Found at i:2562851 original size:309 final size:306
Alignment explanation
Indices: 2561993--2563191 Score: 1512
Period size: 309 Copynumber: 3.9 Consensus size: 306
2561983 CTGAACCCAT
* * * * * * **
2561993 ATGATGAAATCACTTTCATGGCAAGACCTTAATAGGAATGCGACAATGGAAAAG-CTCAGAATGA
1 ATGACGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGG-AGGGCCTCAGAATGA
* * * * *
2562057 ATTCAAGGTTCTGATTAAAAGGAAAATAAGATTATTCGGAC-AGAACATTTGGGGAGAGGTCATG
65 ATTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAG-ACATTTGGGGAGAGGTCATG
* ** * * * ** ** **
2562121 ATGTAAATTGTCAAAAGGTTTTTATGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAGTAGGTA
129 GTGTAAATTACCAAAAGCTTTTTACGCCATTGTTGGTGGGAGCCGCTAGAAAATAAGAACAAATA
* ** * **
2562186 CTAAAGCTATGTCTTTCATGTACTGAAT-ATTTCTTCATATTGAATAAAACCCGTGGTTCCAAAT
194 CTAAAGTTATGTCTTTCATGTACCAAATGTTTTC-TCATATTGAATAAAATTC-TGGTTCCAAAT
2562250 ATATATTAATTATCTTCTCCCTTTTATTCATTACAAATA-----T----A
257 ATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
*
2562291 AT---GAAATCACTCTCATGGCAAGACCTCAACACGAAGGCGACAATGGAGGGCCTCAGAATGAA
1 ATGACGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAGGGCCTCAGAATGAA
*
2562353 TTCAAGATTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTGTGGGGAGAGGTCATGG
66 TTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATT-TGGGGAGAGGTCATGG
* ** **
2562418 TGTAAATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAACAGGTAC
130 TGTAAATTACCAAAAGCTTTTTACGCCATTGTTGGTGGGAGCCGCTAGAAAATAAGAACAAATAC
* *
2562483 TAAAGTTATGTCTTTCATATACCAAATGTTTTCTCATATTGAATAAAACTCGTGGTTCCAAATAT
195 TAAAGTTATGTCTTTCATGTACCAAATGTTTTCTCATATTGAATAAAATTC-TGGTTCCAAATAT
2562548 ATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
259 ATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
* * *
2562596 ATTACGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAAGGCCTCAGAATGAT
1 ATGACGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAGGGCCTCAGAATGA-
* * * * * *
2562661 TTTTAAGGTTTTTATTAAAAGGAAAATAAGATTATTTAGGCAAGACATTTGGGGAGAGGTCATCG
65 ATTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTGGGGAGAGGTCATGG
* * *
2562726 TGTAAATTATCAAAAAGCTTTTTATGCCATTGTTGGTAGGAGCCGCTAGAAAATAAGAACAAATA
130 TGTAAATTA-CCAAAAGCTTTTTACGCCATTGTTGGTGGGAGCCGCTAGAAAATAAGAACAAATA
* * * *
2562791 CTAAAGTTATGTCTTTTATGTACCAAATATTTCCTTATATTGAATAAAATTCATGGTTCCAAATA
194 CTAAAGTTATGTCTTTCATGTACCAAATGTTTTCTCATATTGAATAAAATTC-TGGTTCCAAATA
* *
2562856 TATATTAATTATCTTATCCCTTTTATTCATTACAAATATTGGCTACCAT
258 TATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
* * ** *
2562905 ATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGTGACCTTGGAGGGCCTTAGAATGAA
1 ATGACGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAGGGCCTCAGAATGAA
* * * * *
2562970 TCCAAGGTTCTGATTAAAAGGAAAATAAGATTGTTTGGGCAAAAAATTTGGGGAGAGGTCATGGT
66 TTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTGGGGAGAGGTCATGGT
* * *
2563035 ATAAATTACCAAAAGCTTTTTACGCCGTTGTTGGTGGGAGCTGCTAGAAAATAAGAACAAATACT
131 GTAAATTACCAAAAGCTTTTTACGCCATTGTTGGTGGGAGCCGCTAGAAAATAAGAACAAATACT
* * * *
2563100 AAAGCTATGTCTTTCATGTACCAAATGTTTTCTCGTATTGAACAAAACTT-TGGTTCCAAATAGA
196 AAAGTTATGTCTTTCATGTACCAAATGTTTTCTCATATTGAATAAAA-TTCTGGTTCCAAATATA
*
2563164 TATTAATTATCTTCTCCCTTTTAATCAT
260 TATTAATTATCTTCTCCCTTTTATTCAT
2563192 CGAGTGAATT
Statistics
Matches: 795, Mismatches: 87, Indels: 30
0.87 0.10 0.03
Matches are distributed among these distances:
294 2 0.00
295 89 0.11
296 167 0.21
297 4 0.01
298 2 0.00
301 1 0.00
305 3 0.00
306 39 0.05
307 92 0.12
308 145 0.18
309 251 0.32
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (306 bp):
ATGACGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGACAATGGAGGGCCTCAGAATGAA
TTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTGGGGAGAGGTCATGGT
GTAAATTACCAAAAGCTTTTTACGCCATTGTTGGTGGGAGCCGCTAGAAAATAAGAACAAATACT
AAAGTTATGTCTTTCATGTACCAAATGTTTTCTCATATTGAATAAAATTCTGGTTCCAAATATAT
ATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCAA
Found at i:2563852 original size:78 final size:76
Alignment explanation
Indices: 2563716--2563946 Score: 266
Period size: 78 Copynumber: 3.0 Consensus size: 76
2563706 TTTCACAGTA
* * * * *
2563716 TTTTCATGTTGTTGACCATTCTGGACCTTCTCTCTTGTTTCAGACAACATAAAGCATAAGCATAC
1 TTTTCATGTTGTTGACCATCCTAGACCTTCTCCCCTGTTTCAGACTACATAAAGCATAAGCATAC
2563781 TACTTAAAATG
66 TACTTAAAATG
* * * *
2563792 TTTTCTATGTTGTTGACCATCCTAGACCCTCCTCCCCTGTCTCAGACTACATTAAGCATAAACAT
1 TTTTC-ATGTTGTTGACCATCCTAGA-CCTTCTCCCCTGTTTCAGACTACATAAAGCATAAGCAT
2563857 ACTACTTAAAATATG
64 ACTACTT-AAA-ATG
** * * **
2563872 TTTTCCATGTTGTTGATTATCCTAGATCTTC-CCCCTGTTTCAAACTACATAAAGTGTAAGCATA
1 TTTT-CATGTTGTTGACCATCCTAGACCTTCTCCCCTGTTTCAGACTACATAAAGCATAAGCATA
*
2563936 CTACTTTAAAT
65 CTACTTAAAAT
2563947 ATATTAATGA
Statistics
Matches: 130, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
76 7 0.05
77 20 0.15
78 71 0.55
79 6 0.05
80 25 0.19
81 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (76 bp):
TTTTCATGTTGTTGACCATCCTAGACCTTCTCCCCTGTTTCAGACTACATAAAGCATAAGCATAC
TACTTAAAATG
Found at i:2565230 original size:9 final size:9
Alignment explanation
Indices: 2565216--2565280 Score: 62
Period size: 9 Copynumber: 7.2 Consensus size: 9
2565206 TTTACATTTA
2565216 TATATTAAT
1 TATATTAAT
2565225 TATATTAAT
1 TATATTAAT
2565234 TATATT-AT
1 TATATTAAT
*
2565242 TATATTACT
1 TATATTAAT
* *
2565251 AATTTTTAAT
1 TA-TATTAAT
2565261 TATATT-AT
1 TATATTAAT
*
2565269 TAATTTTAAT
1 T-ATATTAAT
2565279 TA
1 TA
2565281 ATCATGCTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
8 11 0.24
9 25 0.56
10 9 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (9 bp):
TATATTAAT
Found at i:2565264 original size:19 final size:18
Alignment explanation
Indices: 2565220--2565280 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
2565210 CATTTATATA
* * *
2565220 TTAATTATATTAATTATA
1 TTAATTATATTACTAATT
2565238 TT-ATTATATTACTAATTT
1 TTAATTATATTACTAA-TT
*
2565256 TTAATTATATTATTAATT
1 TTAATTATATTACTAATT
2565274 TTAATTA
1 TTAATTA
2565281 ATCATGCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 11 0.30
18 14 0.38
19 12 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATTATATTACTAATT
Found at i:2565281 original size:22 final size:21
Alignment explanation
Indices: 2565227--2565282 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
2565217 ATATTAATTA
*
2565227 TATTAATTATATT-ATTATAT
1 TATTAATTTTATTAATTATAT
*
2565247 TACTAA-TTT-TTAATTATAT
1 TATTAATTTTATTAATTATAT
2565266 TATTAATTTTAATTAAT
1 TATTAATTTT-ATTAAT
2565283 CATGCTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.07
19 14 0.48
20 8 0.28
22 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTAATTTTATTAATTATAT
Found at i:2565455 original size:12 final size:12
Alignment explanation
Indices: 2565438--2565462 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2565428 AAACTTTTTT
2565438 CCCAATTAAAAA
1 CCCAATTAAAAA
2565450 CCCAATTAAAAA
1 CCCAATTAAAAA
2565462 C
1 C
2565463 AAATATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (12 bp):
CCCAATTAAAAA
Found at i:2565744 original size:84 final size:84
Alignment explanation
Indices: 2565603--2565772 Score: 241
Period size: 84 Copynumber: 2.0 Consensus size: 84
2565593 ATCAATAACA
*
2565603 TCCATAAAAAACAAACGCCATTCTTGAAACTCAAAAAATGAAGCAACAGACATGAAAGGAAAAAA
1 TCCATAAAAAACAAACACCATTCTTGAAACTCAAAAAATGAAGCAACAGACATGAAAGGAAAAAA
*
2565668 TAGTATGCATCATTCTACT
66 CAGTATGCATCATTCTACT
* * * * * *
2565687 TCCATGAAAAACAAGCACTATTCTTGAAACTCGAAAAATGCAGCAACAGACATGAAAGGGAAAAA
1 TCCATAAAAAACAAACACCATTCTTGAAACTCAAAAAATGAAGCAACAGACATGAAAGGAAAAAA
* * *
2565752 CGGTATGCATCGTTTTACT
66 CAGTATGCATCATTCTACT
2565771 TC
1 TC
2565773 GCTTTGAATC
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (84 bp):
TCCATAAAAAACAAACACCATTCTTGAAACTCAAAAAATGAAGCAACAGACATGAAAGGAAAAAA
CAGTATGCATCATTCTACT
Found at i:2573195 original size:6 final size:6
Alignment explanation
Indices: 2573186--2573216 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2573176 ATATTATAGA
2573186 ATGGAG ATGGAG ATGGAG ATGGAG ATGGAG A
1 ATGGAG ATGGAG ATGGAG ATGGAG ATGGAG A
2573217 AAGGTGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.48, T:0.16
Consensus pattern (6 bp):
ATGGAG
Found at i:2575078 original size:308 final size:306
Alignment explanation
Indices: 2574514--2575350 Score: 1133
Period size: 308 Copynumber: 2.7 Consensus size: 306
2574504 GACTAAAATC
* * * * * *
2574514 ATATGATGAAATCACTTTCATGGCAAGATCTTAACAAGAATGCGACAATAGAGAGG-CTCAGAAT
1 ATATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAG-GGCCTCAGAAT
* * ** *
2574578 GAATTCAAAATTCTAATTAAAAGGAAAATAAGATTGTTCGTAC-AGA-ATATTTGGGAAGAGTTC
65 GAATTCAAAGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACAT-TTTGGG-AGAGATC
** * * ** *
2574641 ATGGTGTAAATTGTCAAAAGTTTTTTATGCCATTGTTGGGGGGAGCCATTAGAAAATAAGAGTAG
128 ATGGTGTAAATTACCAAAAGCTTTTTATGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAA
*
2574706 GTACTAAAGCTATGTCTTTCATGTACCGAATATTTCTTCATATTGAATAAAACCCGTTGTTCCAA
193 GTACTAAAGCTATGTCTTTCATGTACC-AATATTTCTTCATATTGAATAAAACCCGTGGTTCCAA
*
2574771 ATATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTGCA
257 ATATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACA
* * * *
2574821 ATATGATGAAATCACTCCCATGGTAAGACCTCAACACGAAGGCGGCAATGGAGGGCCCCAGAATG
1 ATATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAGGGCCTCAGAATG
* * * * * *
2574886 AACTCAAGGTTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTATGAGGAGAGGTCAT
66 AATTCAAAGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTG-GGAGAGATCAT
* * *
2574951 GGTGTAAATTACCAAAAGCTTTTTATGTCATTGTTGGGGGGAGCCACTAGAAAGTAAGAACATGT
130 GGTGTAAATTACCAAAAGCTTTTTATGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAGT
* * *
2575016 ACTAAAGCTATGTCTTTCATATACCAACTGTTT-TATCATATTGAATAAAACTCGTGGTTCCAAA
195 ACTAAAGCTATGTCTTTCATGTACCAA-TATTTCT-TCATATTGAATAAAACCCGTGGTTCCAAA
*
2575080 TATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACC
258 TATATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACA
* * * *
2575129 ATATGATGAAATCACTCTCATGACAAGACCTCAACAAGAAGGTGGCAATGGAGGGCCTTAGAAAG
1 ATATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAGGGCCTCAGAATG
*
2575194 AATTCAATGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTGGGAGAGATCATG
66 AATTCAAAGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTGGGAGAGATCATG
* * * * * * *
2575259 GTGTAAAATACCAAAAAGCTTTTTAAGCCATTGTTGGTGGTAGGCGCTAGAAAATAAGAACAAAT
131 GTGTAAATTACC-AAAAGCTTTTTATGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAGT
2575324 ACTAAAGCTATGTCTTTCATGTACCAA
195 ACTAAAGCTATGTCTTTCATGTACCAA
2575351 ATGTGAAATA
Statistics
Matches: 463, Mismatches: 60, Indels: 13
0.86 0.11 0.02
Matches are distributed among these distances:
306 2 0.00
307 111 0.24
308 346 0.75
309 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (306 bp):
ATATGATGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCGGCAATGGAGGGCCTCAGAATG
AATTCAAAGTTCTAATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTGGGAGAGATCATG
GTGTAAATTACCAAAAGCTTTTTATGCCATTGTTGGGGGGAGCCACTAGAAAATAAGAACAAGTA
CTAAAGCTATGTCTTTCATGTACCAATATTTCTTCATATTGAATAAAACCCGTGGTTCCAAATAT
ATATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACA
Found at i:2577427 original size:10 final size:10
Alignment explanation
Indices: 2577412--2577436 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2577402 GTCCCTAAGA
2577412 TTTTTTATTT
1 TTTTTTATTT
2577422 TTTTTTATTT
1 TTTTTTATTT
2577432 TTTTT
1 TTTTT
2577437 GGAATTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:2586872 original size:27 final size:25
Alignment explanation
Indices: 2586818--2586873 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
2586808 AAGGACAAAA
* *
2586818 AAAACCCATTCTTTATAGGATGGTC
1 AAAACCCATTCTTTATAGGAAGGAC
2586843 AAAACCCATTCTTTATAGGACAAGGAC
1 AAAACCCATTCTTTATAGG--AAGGAC
2586870 AAAA
1 AAAA
2586874 AAATTCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 19 0.70
27 8 0.30
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (25 bp):
AAAACCCATTCTTTATAGGAAGGAC
Found at i:2591666 original size:16 final size:16
Alignment explanation
Indices: 2591645--2591675 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2591635 GTTTCCTTAA
*
2591645 AAATTTTTATAAATTC
1 AAATTTTTAAAAATTC
2591661 AAATTTTTAAAAATT
1 AAATTTTTAAAAATT
2591676 TGTCTAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTTTAAAAATTC
Found at i:2593806 original size:56 final size:56
Alignment explanation
Indices: 2593730--2593839 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
2593720 ATGTTATAAT
*
2593730 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTATAAAATGA
1 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTACAAAATGA
2593786 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTACAAAAT
1 GTAACTACCTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTACAAAAT
2593840 AAGTGTGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (56 bp):
GTAACTACCTATAATTTTAAATAACTTTGATTTAATTGCAATTTAGTACAAAATGA
Found at i:2594584 original size:23 final size:24
Alignment explanation
Indices: 2594553--2594607 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
2594543 TAGGTTAGAT
2594553 AATT-AAATAATTAGGAATAATTA-
1 AATTAAAATAATTA-GAATAATTAG
2594576 AA-TAAAATAATTAGAATAATTAG
1 AATTAAAATAATTAGAATAATTAG
2594599 AATTAAAAT
1 AATTAAAAT
2594608 TTTGGGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 10 0.34
23 13 0.45
24 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (24 bp):
AATTAAAATAATTAGAATAATTAG
Found at i:2595987 original size:15 final size:14
Alignment explanation
Indices: 2595958--2596005 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
2595948 TGTTGTTTTC
*
2595958 TTAAAGCTTTTGATG
1 TTAAAGC-TTAGATG
*
2595973 TTAAATGGTTAGATG
1 TTAAA-GCTTAGATG
2595988 TT-AAGCTTAGATG
1 TTAAAGCTTAGATG
2596001 TTAAA
1 TTAAA
2596006 AATGACTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.36
14 4 0.14
15 13 0.46
16 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (14 bp):
TTAAAGCTTAGATG
Found at i:2598757 original size:82 final size:82
Alignment explanation
Indices: 2598616--2598777 Score: 252
Period size: 82 Copynumber: 2.0 Consensus size: 82
2598606 GAATGTAAGG
* * * *
2598616 GGTTGCTAAGTGTAGATTCTCCGAGTCATTGATCAAAAAAGAGTTGCTAAGTGCCGATTCCCTAA
1 GGTTGCTAAGTGCAGATTCTCCGAATCATTGATCAAAAAAGAGTTGCTAAGTGCAGATTCCCAAA
2598681 ATCATAGATCAAAAAAT
66 ATCATAGATCAAAAAAT
* *
2598698 GGTTGCTAAGTGCAGATTCTCCGAATCATTGATCAAAAAGGGGTTGCTAAGTGCAGATTCCCAAA
1 GGTTGCTAAGTGCAGATTCTCCGAATCATTGATCAAAAAAGAGTTGCTAAGTGCAGATTCCCAAA
* *
2598763 ATTATTGATCAAAAA
66 ATCATAGATCAAAAA
2598778 GGGGTTACTA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (82 bp):
GGTTGCTAAGTGCAGATTCTCCGAATCATTGATCAAAAAAGAGTTGCTAAGTGCAGATTCCCAAA
ATCATAGATCAAAAAAT
Found at i:2598778 original size:41 final size:41
Alignment explanation
Indices: 2598612--2598783 Score: 213
Period size: 41 Copynumber: 4.2 Consensus size: 41
2598602 CTTTGAATGT
* * *
2598612 AAGGGGTTGCTAAGTGTAGATTCTCCGAGTCATTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCTCCAAATCATTGATCAAA
* * * *
2598653 AAAGAGTTGCTAAGTGCCGATTC-CCTAAATCATAGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCTCC-AAATCATTGATCAAA
** *
2598694 AAATGGTTGCTAAGTGCAGATTCTCCGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCTCCAAATCATTGATCAAA
*
2598735 AAGGGGTTGCTAAGTGCAGATTC-CCAAAATTATTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCTCC-AAATCATTGATCAAA
2598776 AAGGGGTT
1 AAGGGGTT
2598784 ACTATGTGTT
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 4 0.04
41 106 0.95
42 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCTCCAAATCATTGATCAAA
Found at i:2598869 original size:43 final size:41
Alignment explanation
Indices: 2598816--2599013 Score: 215
Period size: 43 Copynumber: 4.7 Consensus size: 41
2598806 CGCTAACTAC
2598816 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGATGGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCCACCGTATCAC-TGAT-GT-A
* * *
2598860 AAGGGGTTGCTATGTGTTGATTCC-CCGTATCACTGAATATA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTG-ATGTA
* *
2598901 AAGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATGGTGA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTGAT-GT-A
* *
2598944 AAGGGGTTGCTATGTGTTGATTCC-CCGTATCACTGAT-TA
1 AAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTGATGTA
*
2598983 TAAGGTGGTTGCTAAGTACTGATTCCACCGT
1 -AAGG-GGTTGCTAAGTGCTGATTCCACCGT
2599014 GTAATGGTTA
Statistics
Matches: 131, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
39 1 0.01
40 5 0.04
41 41 0.31
42 37 0.28
43 43 0.33
44 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTGATGTA
Found at i:2598878 original size:84 final size:83
Alignment explanation
Indices: 2598775--2599013 Score: 370
Period size: 84 Copynumber: 2.8 Consensus size: 83
2598765 TATTGATCAA
* * * * *
2598775 AAAGGGGTTACTATGTGTTGATTTCCCATATCGCTAACTACAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACTAA-TATAAGGTGGTTGCTAAGTGCTGATTC
*
2598840 CACCGTATCCTTGATGGTG
65 CACCGTATCATTGATGGTG
*
2598859 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACTGAATATAAAGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACT-AATATAAGGTGGTTGCTAAGTGCTGATTC
2598924 CACCGTATCATTGATGGTG
65 CACCGTATCATTGATGGTG
* *
2598943 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACTGATTATAAGGTGGTTGCTAAGTACTGATTC
1 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACT-AATATAAGGTGGTTGCTAAGTGCTGATTC
2599008 CACCGT
65 CACCGT
2599014 GTAATGGTTA
Statistics
Matches: 144, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
84 142 0.99
85 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (83 bp):
AAAGGGGTTGCTATGTGTTGATTCCCCGTATCACTAATATAAGGTGGTTGCTAAGTGCTGATTCC
ACCGTATCATTGATGGTG
Found at i:2598922 original size:41 final size:43
Alignment explanation
Indices: 2598819--2599013 Score: 222
Period size: 41 Copynumber: 4.6 Consensus size: 43
2598809 TAACTACAAG
*
2598819 GTGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGATGGTGAAA
1 GTGGTTGCTAAGTGCTGATTCCACCGTATCAC-TGATGATGAAA
* * *
2598862 GGGGTTGCTATGTGTTGATTCC-CCGTATCACTGAAT-AT-AAA
1 GTGGTTGCTAAGTGCTGATTCCACCGTATCACTG-ATGATGAAA
* *
2598903 GTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATGGTGAAA
1 GTGGTTGCTAAGTGCTGATTCCACCGTATCACTGATGATGAAA
* * * * *
2598946 GGGGTTGCTATGTGTTGATTCC-CCGTATCACTGATTAT-AAG
1 GTGGTTGCTAAGTGCTGATTCCACCGTATCACTGATGATGAAA
*
2598987 GTGGTTGCTAAGTACTGATTCCACCGT
1 GTGGTTGCTAAGTGCTGATTCCACCGT
2599014 GTAATGGTTA
Statistics
Matches: 126, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
41 44 0.35
42 38 0.30
43 44 0.35
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (43 bp):
GTGGTTGCTAAGTGCTGATTCCACCGTATCACTGATGATGAAA
Found at i:2604249 original size:29 final size:29
Alignment explanation
Indices: 2604193--2604249 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
2604183 CAACGGTGCC
* * *
2604193 TTCGAACCAATAACTCAGATATCTCTTGG
1 TTCGAACCAACAACTCAGATACCACTTGG
* *
2604222 TTCGAACCAACAGCTCGGATACCACTTG
1 TTCGAACCAACAACTCAGATACCACTTG
2604250 TCACGGGGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (29 bp):
TTCGAACCAACAACTCAGATACCACTTGG
Found at i:2607117 original size:101 final size:101
Alignment explanation
Indices: 2606935--2607137 Score: 334
Period size: 101 Copynumber: 2.0 Consensus size: 101
2606925 ATTTTCCATA
* * *
2606935 ATAAATTGAATGGCTAAACAAGATTCGAAAGCAGAAGCAACTCAGCTTCTAGCACCTATTAAAAC
1 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
* * *
2607000 AGTATAGATTAGGATGGAACTATAACTAAAGATGAC
66 AGGATAGACTAAGATGGAACTATAACTAAAGATGAC
*
2607036 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTTAGCTTCTAGCACATACTAAAAC
1 ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
*
2607101 AGGATAGACTAAGATGGAATTATAACTAAAGATGAC
66 AGGATAGACTAAGATGGAACTATAACTAAAGATGAC
2607137 A
1 A
2607138 AACTAAAAAG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.22
Consensus pattern (101 bp):
ATAAATTGAATGGCTAAACAAGATTCAAAAGCAGAAGCAACTCAGCTTCTAGCACATACTAAAAC
AGGATAGACTAAGATGGAACTATAACTAAAGATGAC
Found at i:2613074 original size:23 final size:24
Alignment explanation
Indices: 2613043--2613097 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
2613033 TAGGTTAGAT
2613043 AATT-AAATAATTAGGAATAATTA-
1 AATTAAAATAATTA-GAATAATTAG
2613066 AA-TAAAATAATTAGAATAATTAG
1 AATTAAAATAATTAGAATAATTAG
2613089 AATTAAAAT
1 AATTAAAAT
2613098 TTTGGGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 10 0.34
23 13 0.45
24 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (24 bp):
AATTAAAATAATTAGAATAATTAG
Found at i:2613136 original size:15 final size:15
Alignment explanation
Indices: 2613116--2613159 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
2613106 AAGAAATTAA
2613116 AATTAAGTTTTTGGG
1 AATTAAGTTTTTGGG
2613131 AATTAA---TTTGGG
1 AATTAAGTTTTTGGG
2613143 AATTAAGTTTTTGGG
1 AATTAAGTTTTTGGG
2613158 AA
1 AA
2613160 ATAATTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.46
15 14 0.54
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (15 bp):
AATTAAGTTTTTGGG
Found at i:2613179 original size:27 final size:27
Alignment explanation
Indices: 2613114--2613180 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
2613104 TTAAGAAATT
* *
2613114 AAAATTAAGTTTTTGGGAATTAATTTGG
1 AAAA-TAAGTTTTTGGGAAATAATTTAG
* *
2613142 GAATTAAGTTTTTGGGAAATAATTTAG
1 AAAATAAGTTTTTGGGAAATAATTTAG
*
2613169 AAAATATGTTTT
1 AAAATAAGTTTT
2613181 AATTGAACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 30 0.94
28 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.43
Consensus pattern (27 bp):
AAAATAAGTTTTTGGGAAATAATTTAG
Found at i:2618426 original size:12 final size:12
Alignment explanation
Indices: 2618409--2618433 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2618399 AGACCTGATA
2618409 AAATAAGAAAAC
1 AAATAAGAAAAC
2618421 AAATAAGAAAAC
1 AAATAAGAAAAC
2618433 A
1 A
2618434 TCTCCTGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAATAAGAAAAC
Found at i:2624878 original size:21 final size:21
Alignment explanation
Indices: 2624854--2624906 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2624844 CATTGTTTCT
*
2624854 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
2624875 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
2624896 AATCTCACCGC
1 AATCTCACCGC
2624907 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.40, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:2631527 original size:22 final size:22
Alignment explanation
Indices: 2631502--2631543 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2631492 GCATCGAAAT
* *
2631502 GAGGCACTGTAGTGCAAATACA
1 GAGGCACTGAAGTGAAAATACA
2631524 GAGGCACTGAAGTGAAAATA
1 GAGGCACTGAAGTGAAAATA
2631544 AAGACACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (22 bp):
GAGGCACTGAAGTGAAAATACA
Found at i:2631576 original size:20 final size:20
Alignment explanation
Indices: 2631532--2631577 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2631522 CAGAGGCACT
*
2631532 GAAGTGAAAATAAAGACACC
1 GAAGTGAAAACAAAGACACC
* * *
2631552 AAAGTGAAAACAAAGTCATC
1 GAAGTGAAAACAAAGACACC
2631572 GAAGTG
1 GAAGTG
2631578 CGATCTAGTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.13, G:0.22, T:0.13
Consensus pattern (20 bp):
GAAGTGAAAACAAAGACACC
Found at i:2635700 original size:21 final size:21
Alignment explanation
Indices: 2635653--2635700 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2635643 TTTCGTTTGC
*
2635653 TATTCTGTTTCTTTTCTTCTA
1 TATTTTGTTTCTTTTCTTCTA
* *
2635674 TCTTTTGTTTC-TTTCTTTCTT
1 TATTTTGTTTCTTTTC-TTCTA
2635695 TATTTT
1 TATTTT
2635701 ACTTACTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (21 bp):
TATTTTGTTTCTTTTCTTCTA
Found at i:2635886 original size:24 final size:25
Alignment explanation
Indices: 2635844--2635890 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2635834 TATTTGTTAC
* *
2635844 AATTTAATTTATTTTATAACATAAT
1 AATTTAATTAATTTAATAACATAAT
2635869 AATTTAA-TAATTTAATAACATA
1 AATTTAATTAATTTAATAACATA
2635891 TTTTAACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTTAATTAATTTAATAACATAAT
Found at i:2638627 original size:21 final size:23
Alignment explanation
Indices: 2638585--2638627 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2638575 TATTATTCCG
*
2638585 GGTGTGTTTAGGTTGGATATTCT
1 GGTGTGTTTAGGGTGGATATTCT
2638608 GGTGTGTTT-GGGTGGA-ATTC
1 GGTGTGTTTAGGGTGGATATTC
2638628 GCGTATCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.12, C:0.05, G:0.40, T:0.44
Consensus pattern (23 bp):
GGTGTGTTTAGGGTGGATATTCT
Found at i:2640543 original size:20 final size:20
Alignment explanation
Indices: 2640485--2640544 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
2640475 TATTTATTTA
* *
2640485 TACACATATTAACTATTTTT
1 TACATATATTAAATATTTTT
* * *
2640505 TATATTTA-TAAGTATTTTTT
1 TACATATATTAAATA-TTTTT
2640525 TACATATATTAAATATTTTT
1 TACATATATTAAATATTTTT
2640545 AAAAATATCG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 5 0.16
20 21 0.68
21 5 0.16
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (20 bp):
TACATATATTAAATATTTTT
Found at i:2641073 original size:32 final size:32
Alignment explanation
Indices: 2641037--2641099 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
2641027 CCATAAACTT
*
2641037 ATAAACTAATTACTTGAATTT-AGTAACTCATG
1 ATAAACTAATTAATTGAATTTGA-TAACTCATG
* *
2641069 ATAAATTAATTAATTTAATTTGATAACTCAT
1 ATAAACTAATTAATTGAATTTGATAACTCAT
2641100 ATTGATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (32 bp):
ATAAACTAATTAATTGAATTTGATAACTCATG
Found at i:2642661 original size:16 final size:17
Alignment explanation
Indices: 2642630--2642667 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2642620 GCGTTTCTTC
*
2642630 TTCTTCCATTTCTTTGT
1 TTCTTCCATCTCTTTGT
2642647 TTCTTCCA-CTCTTTGT
1 TTCTTCCATCTCTTTGT
2642663 TTCTT
1 TTCTT
2642668 TCCGACGCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.05, C:0.26, G:0.05, T:0.63
Consensus pattern (17 bp):
TTCTTCCATCTCTTTGT
Found at i:2649346 original size:47 final size:47
Alignment explanation
Indices: 2649277--2649371 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
2649267 CAAATAAGAA
2649277 TGATTGTCAGATTCTCTATTTATAGTATTTAAGATGTTGTTGGCATT
1 TGATTGTCAGATTCTCTATTTATAGTATTTAAGATGTTGTTGGCATT
2649324 TGATTGTCAGATTCTCTATTTATAGTATTTAAGATGTTGTTGGCATT
1 TGATTGTCAGATTCTCTATTTATAGTATTTAAGATGTTGTTGGCATT
2649371 T
1 T
2649372 CATACTAGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.49
Consensus pattern (47 bp):
TGATTGTCAGATTCTCTATTTATAGTATTTAAGATGTTGTTGGCATT
Found at i:2651152 original size:5 final size:6
Alignment explanation
Indices: 2651135--2651176 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
2651125 ATTTTTTTCG
*
2651135 ATAAAA ATAAAA ATAAAA AT-AAA ATAAATA CTAAAA AGTAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAA-A ATAAAA A-TAAA
2651177 TAGCTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 5 0.16
6 17 0.55
7 9 0.29
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:2651160 original size:17 final size:19
Alignment explanation
Indices: 2651138--2651176 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
2651128 TTTTTCGATA
2651138 AAAATAAA-AATAAAAA-T
1 AAAATAAATAATAAAAAGT
*
2651155 AAAATAAATACTAAAAAGT
1 AAAATAAATAATAAAAAGT
2651174 AAA
1 AAA
2651177 TAGCTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAATAAATAATAAAAAGT
Found at i:2657539 original size:14 final size:15
Alignment explanation
Indices: 2657520--2657562 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
2657510 TTAACCCAAT
2657520 ATTTTATTTATTAA-
1 ATTTTATTTATTAAC
*
2657534 ATTTTATATTTTTAAC
1 ATTTTAT-TTATTAAC
2657550 A-TTTATTTATTAA
1 ATTTTATTTATTAA
2657563 GTTTAGGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 13 0.52
15 11 0.44
16 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTATTTATTAAC
Found at i:2659321 original size:28 final size:28
Alignment explanation
Indices: 2659282--2659346 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
2659272 ATAAAAATTA
2659282 ACCAAAATATTATAAC-TTTTTT-TTATTT
1 ACCAAAATATT-T-ACTTTTTTTATTATTT
2659310 ACCAAAATA-TTACTTTTTTTATTATTT
1 ACCAAAATATTTACTTTTTTTATTATTT
*
2659337 ACGAAAATAT
1 ACCAAAATAT
2659347 ACCAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 2 0.06
26 7 0.21
27 15 0.45
28 9 0.27
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (28 bp):
ACCAAAATATTTACTTTTTTTATTATTT
Found at i:2659446 original size:27 final size:27
Alignment explanation
Indices: 2659416--2659467 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2659406 GGCCAATCAC
2659416 ATTGGCGACACCAAAGGTGCCAAAGAG
1 ATTGGCGACACCAAAGGTGCCAAAGAG
* *
2659443 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGACACCAAAGGTGCCAAAG
2659468 GACTAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.31, T:0.13
Consensus pattern (27 bp):
ATTGGCGACACCAAAGGTGCCAAAGAG
Found at i:2659568 original size:19 final size:19
Alignment explanation
Indices: 2659541--2659610 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
2659531 TCAACTCATT
*
2659541 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
2659560 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
2659578 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
2659597 TTTTAATTTAATAA
1 TTTTAATTTAATAA
2659611 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:2659591 original size:37 final size:37
Alignment explanation
Indices: 2659546--2659616 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
2659536 TCATTTTTTT
2659546 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
2659583 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
2659617 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:2659863 original size:19 final size:19
Alignment explanation
Indices: 2659836--2659905 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
2659826 TCAACTCATT
*
2659836 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
2659855 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
2659873 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
2659892 TTTTAATTTAATAA
1 TTTTAATTTAATAA
2659906 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:2659886 original size:37 final size:37
Alignment explanation
Indices: 2659841--2659911 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
2659831 TCATTTTTTT
2659841 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
2659878 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
2659912 AAGTAATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Done.