Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 54 of 325
Found at i:19555521 original size:17 final size:18
Alignment explanation
Indices: 19555480--19555514 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19555470 TAATTATTAA
*
19555480 ATATATTTTAATTAAAAT
1 ATATAATTTAATTAAAAT
19555498 ATATAATTTAA-TAAAAT
1 ATATAATTTAATTAAAAT
19555515 TATTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATAATTTAATTAAAAT
Found at i:19556284 original size:13 final size:13
Alignment explanation
Indices: 19556266--19556295 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19556256 TTAAAAGCTA
*
19556266 AATTCAGAAAATC
1 AATTCAGAAAAAC
19556279 AATTCAGAAAAAC
1 AATTCAGAAAAAC
19556292 AATT
1 AATT
19556296 ACATGACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:19559400 original size:71 final size:71
Alignment explanation
Indices: 19559306--19559457 Score: 261
Period size: 71 Copynumber: 2.1 Consensus size: 71
19559296 TTTAAAATAT
* *
19559306 ATTTTTAAAAAATATATTGAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTTAATA
1 ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACA-TTTTTAATA
19559371 TATTT-A
65 TATTTAA
19559377 ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTAATAT
1 ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTAATAT
19559442 ATTTAAA
66 ATTT-AA
19559449 ATTTTTTAA
1 ATTTTTTAA
19559458 GTTTTTTAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
70 14 0.18
71 53 0.69
72 10 0.13
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (71 bp):
ATTTTTTAAAAATATATTAAATATATTAAAATTTTAAAATTGGTTATACTTAACATTTTTAATAT
ATTTAA
Found at i:19559405 original size:20 final size:20
Alignment explanation
Indices: 19559367--19559407 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19559357 AACATTTTTT
* * *
19559367 AATATATTTAATTTTTTAAA
1 AATATATTAAATATATTAAA
19559387 AATATATTAAATATATTAAA
1 AATATATTAAATATATTAAA
19559407 A
1 A
19559408 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATTAAATATATTAAA
Found at i:19559447 original size:18 final size:18
Alignment explanation
Indices: 19559362--19559482 Score: 65
Period size: 18 Copynumber: 6.8 Consensus size: 18
19559352 TACTTAACAT
*
19559362 TTTTTAATATATTT-AAT
1 TTTTTAATATATTTAAAA
*
19559379 TTTTTAAAAATATATT-AAA
1 TTTTT-AATATAT-TTAAAA
* *
19559398 TATATTAAAAT-TTTAAAA
1 T-TTTTAATATATTTAAAA
** * *
19559416 TTGGT--TATACTTAACA
1 TTTTTAATATATTTAAAA
19559432 TTTTTAATATATTTAAAA
1 TTTTTAATATATTTAAAA
*
19559450 TTTTTTAAGT-TTTTTAAAA
1 -TTTTTAA-TATATTTAAAA
*
19559469 TTTTAAATATATTT
1 TTTTTAATATATTT
19559483 CCCTAAACCC
Statistics
Matches: 79, Mismatches: 15, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
15 2 0.03
16 8 0.10
17 10 0.13
18 30 0.38
19 25 0.32
20 4 0.05
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTTAATATATTTAAAA
Found at i:19561002 original size:9 final size:9
Alignment explanation
Indices: 19560988--19561031 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
19560978 CAATAAGATG
19560988 AAAGTAAAA
1 AAAGTAAAA
19560997 AAAGTAAAA
1 AAAGTAAAA
*
19561006 AAAGAAAAGA
1 AAAGTAAA-A
19561016 AAAG-AAAA
1 AAAGTAAAA
19561024 TAAAGTAA
1 -AAAGTAA
19561032 CAGCAGGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
8 1 0.03
9 23 0.74
10 7 0.23
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (9 bp):
AAAGTAAAA
Found at i:19561019 original size:28 final size:30
Alignment explanation
Indices: 19560962--19561031 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
19560952 GAAAAAACTT
*
19560962 TAAAAAAA-TAAAGAAACAATAAGATGAAAG
1 TAAAAAAAGTAAAAAAACAATAAGA-GAAAG
*
19560992 TAAAAAAAGTAAAAAAAGAA-AAGA-AAAG
1 TAAAAAAAGTAAAAAAACAATAAGAGAAAG
19561020 -AAAATAAAGTAA
1 TAAAA-AAAGTAA
19561032 CAGCAGGGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 4 0.11
28 11 0.31
30 12 0.33
31 9 0.25
ACGTcount: A:0.74, C:0.01, G:0.13, T:0.11
Consensus pattern (30 bp):
TAAAAAAAGTAAAAAAACAATAAGAGAAAG
Found at i:19573186 original size:21 final size:22
Alignment explanation
Indices: 19573162--19573212 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
19573152 AATCTAAAGC
19573162 CTAGA-GCACAATCAACTATAG
1 CTAGACGCACAATCAACTATAG
*
19573183 CTAGAATCCTCACAATCAACTATAG
1 CTAG-A--CGCACAATCAACTATAG
19573208 CTAGA
1 CTAGA
19573213 ATCCTCACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.16
22 1 0.04
24 1 0.04
25 19 0.76
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (22 bp):
CTAGACGCACAATCAACTATAG
Found at i:19573202 original size:25 final size:25
Alignment explanation
Indices: 19573168--19573228 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
19573158 AAGCCTAGAG
19573168 CACAATCAACTATAGCTAGAATCCT
1 CACAATCAACTATAGCTAGAATCCT
19573193 CACAATCAACTATAGCTAGAATCCT
1 CACAATCAACTATAGCTAGAATCCT
19573218 CACAATCAACT
1 CACAATCAACT
19573229 TGTCTCCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.41, C:0.30, G:0.07, T:0.23
Consensus pattern (25 bp):
CACAATCAACTATAGCTAGAATCCT
Found at i:19575881 original size:3 final size:3
Alignment explanation
Indices: 19575873--19575899 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19575863 CCACTTTGAT
19575873 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
19575900 TCTGAATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:19577764 original size:4 final size:4
Alignment explanation
Indices: 19577755--19577779 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19577745 GAAGAAGAAG
19577755 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
19577780 CAAATCTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:19581048 original size:15 final size:15
Alignment explanation
Indices: 19581028--19581056 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19581018 GACTTCCCCC
19581028 GTTTACCCGAAACGA
1 GTTTACCCGAAACGA
19581043 GTTTACCCGAAACG
1 GTTTACCCGAAACG
19581057 CTTCATTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (15 bp):
GTTTACCCGAAACGA
Found at i:19583827 original size:17 final size:19
Alignment explanation
Indices: 19583805--19583843 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
19583795 TTAAAACTTG
19583805 AAAAATGAA-TAATTA-AA
1 AAAAATGAATTAATTATAA
*
19583822 AAAAATTAATTAATTATAA
1 AAAAATGAATTAATTATAA
19583841 AAA
1 AAA
19583844 GTGTATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAAATGAATTAATTATAA
Found at i:19593790 original size:20 final size:20
Alignment explanation
Indices: 19593761--19593828 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
19593751 AAAAATATAT
*
19593761 CAAATTTTCATAATCCGCAA
1 CAAATCTTCATAATCCGCAA
*
19593781 CAAATCTTCATTATCCG-ATTGCA
1 CAAATCTTCATAATCCGCA----A
*
19593804 CCAATCTTCATAATCCGCAA
1 CAAATCTTCATAATCCGCAA
19593824 CAAAT
1 CAAAT
19593829 TGATGCCTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
19 1 0.03
20 20 0.53
23 16 0.42
24 1 0.03
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.29
Consensus pattern (20 bp):
CAAATCTTCATAATCCGCAA
Found at i:19594277 original size:51 final size:51
Alignment explanation
Indices: 19594222--19594358 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 51
19594212 TATGGTAACT
*
19594222 AATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGG
1 AATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* * ** * * **
19594273 AATCTTATAAGATATTATTTTATAAGATTACATATCTTATCTAAGATATGG
1 AATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* *
19594324 AATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 AATCTTATAAGATATGATATTATAATCTTAGAGAT
19594359 TTGATGGTAG
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (51 bp):
AATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
Found at i:19597298 original size:51 final size:51
Alignment explanation
Indices: 19597243--19597379 Score: 175
Period size: 51 Copynumber: 2.7 Consensus size: 51
19597233 TATGGTAACT
*
19597243 AATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATATGATATGG
1 AATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* * ** * * **
19597294 AATCTTATAAGATATTATTTTATAAGATTACATATCTTATCTAAGATATGG
1 AATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* *
19597345 AATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 AATCTTATAAGATATGATATTATAATCTTAGAGAT
19597380 TTGATGGTAG
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (51 bp):
AATCTTATAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
Found at i:19602503 original size:21 final size:22
Alignment explanation
Indices: 19602477--19602518 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
19602467 ATCCTAGTCA
19602477 AGATTTAC-TCTT-AACTTTTAC
1 AGATTT-CTTCTTAAACTTTTAC
19602498 AGATTTCTTCTTAAACTTTTA
1 AGATTTCTTCTTAAACTTTTA
19602519 TTCAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 10 0.53
22 8 0.42
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.50
Consensus pattern (22 bp):
AGATTTCTTCTTAAACTTTTAC
Found at i:19603405 original size:43 final size:43
Alignment explanation
Indices: 19603344--19603430 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
19603334 TTCTGTTCAC
*
19603344 ATTCTCCATTGATTTTGTAGAATGTTATAAGAATTTACTAAAA
1 ATTCTCCATTGATTTTGTAGAATGTAATAAGAATTTACTAAAA
19603387 ATTCTCCATTGATTTTGTAGAATGTAATAAGAATTTACTAAAA
1 ATTCTCCATTGATTTTGTAGAATGTAATAAGAATTTACTAAAA
19603430 A
1 A
19603431 ATTACATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.40
Consensus pattern (43 bp):
ATTCTCCATTGATTTTGTAGAATGTAATAAGAATTTACTAAAA
Found at i:19615218 original size:27 final size:25
Alignment explanation
Indices: 19615153--19615219 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
19615143 ATTTATTTAT
*
19615153 TATTTATAATGTTAATCATTTAAATA
1 TATTTATAAT-TTAATAATTTAAATA
19615179 TGATTTATTAATTTAATAATTTAAAACTA
1 T-ATTTA-TAATTTAATAATTT-AAA-TA
*
19615208 TATTTACAATTT
1 TATTTATAATTT
19615220 TAACAGTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 1 0.03
27 19 0.54
28 12 0.34
29 3 0.09
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (25 bp):
TATTTATAATTTAATAATTTAAATA
Found at i:19616558 original size:34 final size:32
Alignment explanation
Indices: 19616510--19616593 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 32
19616500 TTTTATCAAT
* * * *
19616510 TTAATATTTAATATTTATATTTAAAAAAATTAAA
1 TTAAAATTTTATATTTAT-CTT-AAAAAATAAAA
19616544 TTAAAATTTTATATTT-TCTTAAAAAATAAAA
1 TTAAAATTTTATATTTATCTTAAAAAATAAAA
* *
19616575 ATATAATTTTATTATTTAT
1 TTAAAATTTTA-TATTTAT
19616594 TAATATAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
31 19 0.45
32 7 0.17
33 2 0.05
34 14 0.33
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (32 bp):
TTAAAATTTTATATTTATCTTAAAAAATAAAA
Found at i:19617000 original size:9 final size:11
Alignment explanation
Indices: 19616974--19617002 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
19616964 TAACAATTAA
19616974 AATATTTTTTT
1 AATATTTTTTT
19616985 AATATTTTTTT
1 AATATTTTTTT
19616996 AAT-TTTT
1 AATATTTT
19617003 AAGAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
AATATTTTTTT
Found at i:19618284 original size:13 final size:13
Alignment explanation
Indices: 19618266--19618290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19618256 AATAAATATC
19618266 ATTTTAATTTTTA
1 ATTTTAATTTTTA
19618279 ATTTTAATTTTT
1 ATTTTAATTTTT
19618291 CACTCCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTAATTTTTA
Found at i:19618610 original size:65 final size:65
Alignment explanation
Indices: 19618501--19618623 Score: 192
Period size: 65 Copynumber: 1.9 Consensus size: 65
19618491 TGTATTCTCC
* * * *
19618501 AACTGATCTAGTAGTCCCTCTACTGTTTCTAGGCAATTCTCAGCAATTTCGAGTTCTGCACTCTT
1 AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTGCACTCTT
* *
19618566 AACTAATCTAATAGTCTCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGGGTTCTG
1 AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTG
19618624 TGCCTTTCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (65 bp):
AACTAATCTAATAGTCCCTCTACTGTTTCTAAGCAATACTCAGCAATTTCGAGTTCTGCACTCTT
Found at i:19620231 original size:29 final size:30
Alignment explanation
Indices: 19620172--19620229 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19620162 TCCGAGCCTT
*
19620172 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
19620202 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
19620230 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:19620459 original size:13 final size:13
Alignment explanation
Indices: 19620441--19620472 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
19620431 TTTCCAGCAA
19620441 TTATGAATTTATT
1 TTATGAATTTATT
19620454 TTATGAATTTATT
1 TTATGAATTTATT
*
19620467 TGATGA
1 TTATGA
19620473 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:19620641 original size:50 final size:50
Alignment explanation
Indices: 19620566--19620758 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
19620556 CATTGGGTAA
19620566 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
19620616 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
19620666 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
19620716 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
19620759 TGTTATTATC
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 95 0.74
51 34 0.26
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:19627761 original size:29 final size:30
Alignment explanation
Indices: 19627702--19627759 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
19627692 TCCGAGCCTT
*
19627702 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
19627732 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
19627760 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:19627989 original size:13 final size:13
Alignment explanation
Indices: 19627971--19628002 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
19627961 TTTCCAGCAA
19627971 TTATGAATTTATT
1 TTATGAATTTATT
19627984 TTATGAATTTATT
1 TTATGAATTTATT
*
19627997 TGATGA
1 TTATGA
19628003 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:19628210 original size:50 final size:50
Alignment explanation
Indices: 19628097--19628338 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
19628087 ATTTGGGTAA
* * *
19628097 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
19628153 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
19628203 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
19628253 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
19628303 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
19628339 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:19628286 original size:100 final size:103
Alignment explanation
Indices: 19628097--19628346 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
19628087 ATTTGGGTAA
19628097 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
19628162 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
19628203 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
19628265 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
19628303 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
19628347 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:19637797 original size:31 final size:31
Alignment explanation
Indices: 19637759--19637821 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
19637749 TACAGATTGT
19637759 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
1 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
19637790 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
1 AAATGGCAAAAGAATTGACCTTCCCTTGAGA
19637821 A
1 A
19637822 TAATAACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (31 bp):
AAATGGCAAAAGAATTGACCTTCCCTTGAGA
Found at i:19648637 original size:47 final size:49
Alignment explanation
Indices: 19648520--19648699 Score: 173
Period size: 47 Copynumber: 3.8 Consensus size: 49
19648510 TGTAACCCGC
* * * * **
19648520 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC--A-GGCGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
* *
19648566 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
*
19648616 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATT-CACAT
*
19648660 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
19648700 TCAACCATCC
Statistics
Matches: 111, Mismatches: 10, Indels: 22
0.78 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 5 0.05
45 1 0.01
46 34 0.31
47 57 0.51
48 3 0.03
49 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:19648688 original size:94 final size:93
Alignment explanation
Indices: 19648528--19648699 Score: 274
Period size: 94 Copynumber: 1.8 Consensus size: 93
19648518 GCCCATAAGT
* **
19648528 GAACTCGGACTCAACTCAACGAGCTCAGGCGTTTGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGGCATTCACATCCATAAGTGAACTCAGACTCAACTCAA
19648593 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
19648621 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCCACATCCATAAGTGAACTCGGACTCAACTC
1 GAACTCGGACTCAACTCAACGAGCTCAGG-CATT-CACATCCATAAGTGAACTCAGACTCAACTC
19648685 AACGAGTTCGGATGC
64 AACGAGTTCGGATGC
19648700 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
92 2 0.03
93 28 0.39
94 42 0.58
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGGCATTCACATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:19650005 original size:6 final size:6
Alignment explanation
Indices: 19649994--19650018 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19649984 ATATTACAAG
19649994 AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT A
19650019 CGGTACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:19650063 original size:47 final size:47
Alignment explanation
Indices: 19650006--19650118 Score: 181
Period size: 47 Copynumber: 2.4 Consensus size: 47
19649996 CAGTAACAGT
*
19650006 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
* * *
19650053 AACAGTAACAGTACGGTACACGGAGTACCTCATTGGAACAAATCTGA
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
19650100 AACAGTAACAGTAACGGTA
1 AACAGTAACAGT-ACGGTA
19650119 GCAGTAACAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 55 0.90
48 6 0.10
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:19651462 original size:16 final size:15
Alignment explanation
Indices: 19651430--19651464 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
19651420 TTTTTATTAT
*
19651430 ATAATATATTATTTA
1 ATAATATATTATATA
19651445 ATAATATACTTATATA
1 ATAATATA-TTATATA
19651461 ATAA
1 ATAA
19651465 GTAAATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATATATTATATA
Found at i:19671063 original size:74 final size:74
Alignment explanation
Indices: 19670942--19671086 Score: 281
Period size: 74 Copynumber: 2.0 Consensus size: 74
19670932 CTTCAGTCAA
19670942 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
1 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
19671007 GTCATTCAG
66 GTCATTCAG
*
19671016 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTTG
1 AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
19671081 GTCATT
66 GTCATT
19671087 ATAAGGGTAC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (74 bp):
AGTTTAGAGATGACATTGAAAATGGAGAAACAATCAAAGTCTGTTATCCTATTCAGCCATTCTAG
GTCATTCAG
Found at i:19674158 original size:18 final size:18
Alignment explanation
Indices: 19674135--19674169 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19674125 TGTAATATCA
* *
19674135 ATTAATTTTTTTATTTTT
1 ATTAATTATTATATTTTT
19674153 ATTAATTATTATATTTT
1 ATTAATTATTATATTTT
19674170 AATTCCATAT
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTAATTATTATATTTTT
Found at i:19674430 original size:20 final size:20
Alignment explanation
Indices: 19674405--19674454 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
19674395 TGGCTTAAAA
19674405 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
19674425 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
19674442 GTGGTAGTGGATT
1 TTGGTAGTGGATT
19674455 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:19679068 original size:20 final size:20
Alignment explanation
Indices: 19679043--19679092 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
19679033 TGGCTTAAAA
19679043 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
19679063 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
19679080 GTGGTAGTGGATT
1 TTGGTAGTGGATT
19679093 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:19679905 original size:3 final size:3
Alignment explanation
Indices: 19679897--19679933 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
19679887 CAATAAACTA
19679897 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
19679934 GAATTAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19686237 original size:17 final size:16
Alignment explanation
Indices: 19686212--19686258 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
19686202 GTTTTATATG
19686212 AAAAT-TTAAAATTTA
1 AAAATATTAAAATTTA
19686227 TAAAATATTAAAAAATTTA
1 -AAAATATT--AAAATTTA
19686246 AAAA-ATTAAAATT
1 AAAATATTAAAATT
19686259 AAGTATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.21
16 5 0.18
17 5 0.18
18 4 0.14
19 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATATTAAAATTTA
Found at i:19686249 original size:10 final size:9
Alignment explanation
Indices: 19686219--19686256 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
19686209 ATGAAAATTT
*
19686219 AAAATTTAT
1 AAAATTTAA
19686228 AAAATATTAA
1 AAAAT-TTAA
19686238 AAAATTTAA
1 AAAATTTAA
19686247 AAAA-TTAA
1 AAAATTTAA
19686255 AA
1 AA
19686257 TTAAGTATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 6 0.22
9 13 0.48
10 8 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTTAA
Found at i:19686585 original size:14 final size:16
Alignment explanation
Indices: 19686557--19686589 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
19686547 TTACGGTAAT
19686557 AAAAATATAATATTTA
1 AAAAATATAATATTTA
19686573 AAAAAT-TAA-ATTTA
1 AAAAATATAATATTTA
19686587 AAA
1 AAA
19686590 TTTTATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATATAATATTTA
Found at i:19694888 original size:18 final size:19
Alignment explanation
Indices: 19694867--19694905 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19694857 ATTTTAGATT
*
19694867 TTTTATAAA-TATTTTAAA
1 TTTTAAAAATTATTTTAAA
*
19694885 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTAAA
19694904 TT
1 TT
19694906 ATTTTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:19703382 original size:11 final size:11
Alignment explanation
Indices: 19703368--19703412 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
19703358 AGATAAATAT
19703368 TATTTTATTAA
1 TATTTTATTAA
*
19703379 TATTTTAATATGA
1 TATTTT-AT-TAA
*
19703392 TATTTTATTAT
1 TATTTTATTAA
19703403 TATTTTATTA
1 TATTTTATTA
19703413 GTTTATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 17 0.59
12 4 0.14
13 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:19703481 original size:3 final size:3
Alignment explanation
Indices: 19703473--19703503 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
19703463 AACTAACGTG
19703473 AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
19703504 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19704795 original size:59 final size:61
Alignment explanation
Indices: 19704730--19704861 Score: 223
Period size: 62 Copynumber: 2.2 Consensus size: 61
19704720 TCATTGTATG
19704730 AAAATTGATGAAACATTG-ATA-TTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGAATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
*
19704789 AAAATTGATGAAACATTGATATATTTGATAAAAAGGGAAAGAAATCTCGGTTGAATGAAAGA
1 AAAATTGATGAAACATTGA-ATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
19704851 AAAATTCGATG
1 AAAATT-GATG
19704862 GATCTCTGAA
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
59 18 0.26
61 3 0.04
62 43 0.63
63 4 0.06
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.25
Consensus pattern (61 bp):
AAAATTGATGAAACATTGAATATTTGATAAAAAGGGAAAGAAATATCGGTTGAATGAAAGA
Found at i:19705236 original size:46 final size:46
Alignment explanation
Indices: 19705166--19705480 Score: 398
Period size: 46 Copynumber: 6.8 Consensus size: 46
19705156 GCTCTCTGAA
* * *
19705166 ATGAAATGTGTAAGACCATTGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
19705212 ATGAAATGTGTAAGACCATGGTTGAAAGATGCCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * ** **
19705258 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATACCAATGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
19705304 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
19705350 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
19705396 ATGAAAAGAATAAGACCCTGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
19705442 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
19705481 TCAATGTCAA
Statistics
Matches: 240, Mismatches: 28, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 239 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:19705237 original size:21 final size:21
Alignment explanation
Indices: 19705213--19705284 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
19705203 CAACATGATA
19705213 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* * * *
19705234 TGAAA-GATGCCATGGCAACATGAT
1 TGAAATG-TG-TA-AG-ACCATGGT
19705258 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
19705280 TGAAA
1 TGAAA
19705285 GATACTATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 1 0.03
21 12 0.32
22 7 0.19
23 2 0.05
24 7 0.19
25 7 0.19
26 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:19708446 original size:11 final size:11
Alignment explanation
Indices: 19708432--19708476 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
19708422 AGATAAATAT
19708432 TATTTTATTAA
1 TATTTTATTAA
*
19708443 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
19708456 TATTTTATTAT
1 TATTTTATTAA
19708467 TATTTTATTA
1 TATTTTATTA
19708477 GTATATGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:19710190 original size:21 final size:21
Alignment explanation
Indices: 19710166--19710237 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
19710156 CTCTCTGAAA
19710166 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
19710187 TGAAA-G-ATACCATGACAGCATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
19710211 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
19710233 TGAAA
1 TGAAA
19710238 GATACCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:19710217 original size:46 final size:46
Alignment explanation
Indices: 19710165--19710525 Score: 456
Period size: 46 Copynumber: 7.8 Consensus size: 46
19710155 GCTCTCTGAA
** * * *
19710165 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAGCATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
19710211 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
19710257 ATGAAAAAAATAAGACCATGGTTGAGAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
19710303 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCTGA-GTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGC-AACATGAC
*
19710349 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
19710395 ATGAAATGAATAAGATCATGGTTGAAAGAGACCATGACAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
19710441 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
19710487 A-GAAAATGAGTAAGATCATAGTTGAAAGAAACTATGGCA
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
19710526 TCAATGTCAA
Statistics
Matches: 278, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
45 2 0.01
46 275 0.99
47 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:19717836 original size:14 final size:13
Alignment explanation
Indices: 19717815--19717846 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
19717805 TTTTATGAGA
19717815 TATTTATTATTAT
1 TATTTATTATTAT
19717828 TA-TTA-TATTAT
1 TATTTATTATTAT
19717839 TATTTATT
1 TATTTATT
19717847 TAGTATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.47
12 6 0.35
13 3 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTATTATTAT
Found at i:19720035 original size:46 final size:46
Alignment explanation
Indices: 19719983--19720163 Score: 292
Period size: 46 Copynumber: 4.0 Consensus size: 46
19719973 AGTGTGCTCT
*
19719983 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
19720029 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
19720075 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
19720121 ATGACA-GAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
19720164 TCATGTCAAA
Statistics
Matches: 128, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 33 0.26
46 95 0.74
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:19720184 original size:45 final size:45
Alignment explanation
Indices: 19719998--19720186 Score: 146
Period size: 46 Copynumber: 4.2 Consensus size: 45
19719988 ATGAAATGTG
* * * * * ***
19719998 TAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATGTG
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACA-GAAATAAA
* * * * ***
19720044 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTG
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACA-GAAATAAA
* * * *
19720090 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAATGAG
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACAGAAATAAA
* * *
19720135 TAAGACCATAGTTGAAAGACACTATGGCATCATGTCA-AAGATAAA
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACAGAA-ATAAA
19720180 TAAGACC
1 TAAGACC
19720187 GTGGATGAGA
Statistics
Matches: 131, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 2 0.02
45 49 0.37
46 80 0.61
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.22
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACCATGGCAACATGACAGAAATAAA
Found at i:19721402 original size:43 final size:41
Alignment explanation
Indices: 19721328--19721407 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 41
19721318 TGGTAGAATG
19721328 TACATGTTGAGTCATCGTTTCTGGGCAACCCGGGGTGGTTA
1 TACATGTTGAGTCATCGTTTCTGGGCAACCCGGGGTGGTTA
* *
19721369 TACATGTTTAGAGTCATTGTTGTC-GGGCCACCCGGGGTG
1 TACATG-TT-GAGTCATCGTT-TCTGGGCAACCCGGGGTG
19721408 ACAAATCTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 6 0.18
42 2 0.06
43 24 0.71
44 2 0.06
ACGTcount: A:0.16, C:0.20, G:0.33, T:0.31
Consensus pattern (41 bp):
TACATGTTGAGTCATCGTTTCTGGGCAACCCGGGGTGGTTA
Found at i:19724032 original size:18 final size:18
Alignment explanation
Indices: 19724011--19724053 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
19724001 GAACAATTAT
* * *
19724011 TTATTCAGTAACAGTCAG
1 TTATTCAGCAACAATCAA
*
19724029 TTATTCGGCAACAATCAA
1 TTATTCAGCAACAATCAA
19724047 TTATTCA
1 TTATTCA
19724054 ATAATAACTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATTCAGCAACAATCAA
Found at i:19724201 original size:54 final size:54
Alignment explanation
Indices: 19724143--19724245 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
19724133 GTAGCAATTA
* * * *
19724143 AGTTATTCAGTGACAATC-AGTTATTCAGTAATGATCATTTATTCAGTAATATCC
1 AGTTATTCAGTAACAATCTA-TTATCCAGTAACGATCAATTATTCAGTAATATCC
* *
19724197 AGTTATTCAGTAACAGTCTATTATCCAGTAACGGTCAATTATTCAGTAA
1 AGTTATTCAGTAACAATCTATTATCCAGTAACGATCAATTATTCAGTAA
19724246 CAGTAAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 41 0.98
55 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (54 bp):
AGTTATTCAGTAACAATCTATTATCCAGTAACGATCAATTATTCAGTAATATCC
Found at i:19724220 original size:18 final size:18
Alignment explanation
Indices: 19724096--19724260 Score: 122
Period size: 18 Copynumber: 9.2 Consensus size: 18
19724086 ATTGGCTATC
19724096 CAGTAACAGTCAATTATT
1 CAGTAACAGTCAATTATT
* *
19724114 TAGTAA-AATCAGA-TATT
1 CAGTAACAGTCA-ATTATT
* * *
19724131 CAGTAGCAATTAAGTTATT
1 CAGTAACAGTCAA-TTATT
* * *
19724150 CAGTGACAATCAGTTATT
1 CAGTAACAGTCAATTATT
* *
19724168 CAGTAA-TGATCATTTATT
1 CAGTAACAG-TCAATTATT
* *
19724186 CAGTAATA-TCCAGTTATT
1 CAGTAACAGT-CAATTATT
* *
19724204 CAGTAACAGTCTATTATC
1 CAGTAACAGTCAATTATT
*
19724222 CAGTAACGGTCAATTATT
1 CAGTAACAGTCAATTATT
*
19724240 CAGTAACAGTAAATTATT
1 CAGTAACAGTCAATTATT
19724258 CAG
1 CAG
19724261 AAATAATCAG
Statistics
Matches: 115, Mismatches: 24, Indels: 16
0.74 0.15 0.10
Matches are distributed among these distances:
17 14 0.12
18 87 0.76
19 14 0.12
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
CAGTAACAGTCAATTATT
Found at i:19726460 original size:46 final size:49
Alignment explanation
Indices: 19726334--19726467 Score: 156
Period size: 46 Copynumber: 2.8 Consensus size: 49
19726324 AACTCGGACA
*
19726334 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT
1 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA-GACTAGTT
* * * *
19726384 ACAT-C-TCA-CGAACTCGGACTCAACTCAACGAGTTC-GA-AC-A-TT
1 GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAGACTAGTT
19726426 CGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1 -GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
19726468 TGCCCAAATA
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.03
43 4 0.06
44 2 0.03
45 2 0.03
46 27 0.39
47 27 0.39
48 2 0.03
49 1 0.01
50 3 0.04
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (49 bp):
GCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAGACTAGTT
Found at i:19726486 original size:46 final size:45
Alignment explanation
Indices: 19726343--19726486 Score: 112
Period size: 46 Copynumber: 3.1 Consensus size: 45
19726333 AGCATCCATA
* * *
19726343 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCA---ATATATC
* * * * * ** *
19726391 A-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGC-ATCCATA
1 AGTGAACTCGGACTCAACTCAACGAGCTCG--GATGCCCAATATATC
*
19726436 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAAATATTTC
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCC-AATATATC
19726482 AGTGA
1 AGTGA
19726487 CATGTCACTT
Statistics
Matches: 71, Mismatches: 20, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
44 4 0.06
45 3 0.04
46 34 0.48
47 26 0.37
48 1 0.01
49 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAATATATC
Found at i:19727921 original size:45 final size:44
Alignment explanation
Indices: 19727814--19727924 Score: 123
Period size: 45 Copynumber: 2.5 Consensus size: 44
19727804 ATTCTGAACA
* * *
19727814 GTAACAGTAACAGTAACAATACTCAACACACAAAGTGCTGAATCG
1 GTAACAGTAA-TGTAACAGTACTCAACACACAAAGTGCCGAATCG
* * * * *
19727859 ATAACGGTAAATATAACAGTATTCGACACACAAAGTGCCGAATCG
1 GTAACAGT-AATGTAACAGTACTCAACACACAAAGTGCCGAATCG
19727904 GTAACAGTAATGGTAACAGTA
1 GTAACAGTAAT-GTAACAGTA
19727925 ACAGTAGTCG
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
44 3 0.06
45 48 0.91
46 2 0.04
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (44 bp):
GTAACAGTAATGTAACAGTACTCAACACACAAAGTGCCGAATCG
Found at i:19728888 original size:31 final size:32
Alignment explanation
Indices: 19728832--19728894 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
19728822 CACACTTGTC
*
19728832 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
19728864 ATAATATAA-ATATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
19728895 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:19729296 original size:22 final size:24
Alignment explanation
Indices: 19729253--19729299 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
19729243 TGTATTACAA
19729253 ATGTATGTATATTATTTATCACAC
1 ATGTATGTATATTATTTATCACAC
*
19729277 ATGTAT-TTTATTA-TTATCACAC
1 ATGTATGTATATTATTTATCACAC
19729299 A
1 A
19729300 CTTGGCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.45
23 6 0.27
24 6 0.27
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (24 bp):
ATGTATGTATATTATTTATCACAC
Found at i:19731845 original size:14 final size:15
Alignment explanation
Indices: 19731817--19731850 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
19731807 GCCAACTTCA
19731817 TTTCAGGATTTTTTT
1 TTTCAGGATTTTTTT
19731832 TTTCAGGATTTTTTT
1 TTTCAGGATTTTTTT
19731847 TTTC
1 TTTC
19731851 TTATGGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.09, G:0.12, T:0.68
Consensus pattern (15 bp):
TTTCAGGATTTTTTT
Found at i:19746349 original size:29 final size:29
Alignment explanation
Indices: 19746307--19746373 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
19746297 CCCTAAAATG
19746307 GAAGGAATTTGAAACCAAAGTTGTTATTT
1 GAAGGAATTTGAAACCAAAGTTGTTATTT
19746336 GAAGGAATTTGAAACCAAAGTTGTTATTT
1 GAAGGAATTTGAAACCAAAGTTGTTATTT
19746365 GAAGGAATT
1 GAAGGAATT
19746374 AATATTAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (29 bp):
GAAGGAATTTGAAACCAAAGTTGTTATTT
Found at i:19754442 original size:15 final size:15
Alignment explanation
Indices: 19754422--19754529 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
19754412 TTTATGGAAA
*
19754422 ATCAAAGATATGGGT
1 ATCAAATATATGGGT
* **
19754437 ATCAAATA-ATAGAA
1 ATCAAATATATGGGT
*
19754451 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
19754467 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
19754481 AGTCAAATATATGGGT
1 A-TCAAATATATGGGT
**
19754497 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
19754511 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
19754527 ATC
1 ATC
19754530 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 12 0.17
15 45 0.65
16 12 0.17
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.27
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:19754459 original size:30 final size:30
Alignment explanation
Indices: 19754416--19754539 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
19754406 TCCATATTTA
* *
19754416 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
19754446 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
19754476 TGGAAAGTCAAATATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
19754506 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
19754537 TGG
1 TGG
19754540 CATAATAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 78 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:19759128 original size:15 final size:15
Alignment explanation
Indices: 19759108--19759215 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
19759098 TTTATGGAAA
*
19759108 ATCAAAGATATGGGT
1 ATCAAATATATGGGT
* **
19759123 ATCAAATA-ATAGAA
1 ATCAAATATATGGGT
*
19759137 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
19759153 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
19759167 AGTCAAATATATGGGT
1 A-TCAAATATATGGGT
**
19759183 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
19759197 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
19759213 ATC
1 ATC
19759216 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 12 0.17
15 45 0.65
16 12 0.17
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.27
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:19759145 original size:30 final size:30
Alignment explanation
Indices: 19759102--19759225 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
19759092 TCCATATTTA
* *
19759102 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
19759132 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
19759162 TGGAAAGTCAAATATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
19759192 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
19759223 TGG
1 TGG
19759226 CATAATAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 78 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:19792402 original size:7 final size:7
Alignment explanation
Indices: 19792390--19792415 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19792380 GATTCTTGCC
19792390 CTCAACT
1 CTCAACT
19792397 CTCAACT
1 CTCAACT
19792404 CTCAACT
1 CTCAACT
19792411 CTCAA
1 CTCAA
19792416 ATTACTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (7 bp):
CTCAACT
Found at i:19798081 original size:53 final size:53
Alignment explanation
Indices: 19797940--19798090 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
19797930 ATAAGTGCGC
* **
19797940 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
19797993 CCATATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
19798046 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
19798091 ACCGTGTAAG
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.01
53 79 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:19800450 original size:13 final size:13
Alignment explanation
Indices: 19800432--19800497 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 13
19800422 TTTACTTTTT
19800432 TTTTTAATAAAAA
1 TTTTTAATAAAAA
**
19800445 TTTTTAA-AAAGG
1 TTTTTAATAAAAA
*
19800457 TTTTTAA-AAGAA
1 TTTTTAATAAAAA
19800469 TTTTT-ATAAAAAA
1 TTTTTAAT-AAAAA
19800482 TTTATT--TAAAAA
1 TTT-TTAATAAAAA
19800494 TTTT
1 TTTT
19800498 AAATGTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
11 2 0.05
12 25 0.57
13 15 0.34
14 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (13 bp):
TTTTTAATAAAAA
Found at i:19800538 original size:19 final size:21
Alignment explanation
Indices: 19800507--19800565 Score: 86
Period size: 20 Copynumber: 2.8 Consensus size: 21
19800497 TAAATGTTTA
19800507 AATATTATTAAAAAT-ATATTT
1 AATATT-TTAAAAATAATATTT
19800528 AATA-TTTAAAAATAATATTT
1 AATATTTTAAAAATAATATTT
19800548 AATATTTTAAAAAATAAT
1 AATATTTT-AAAAATAAT
19800566 TTCAAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.23
20 11 0.31
21 7 0.20
22 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATTTTAAAAATAATATTT
Found at i:19800539 original size:20 final size:20
Alignment explanation
Indices: 19800507--19800560 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 20
19800497 TAAATGTTTA
19800507 AATATTATTAAAAATATATTT
1 AATATT-TTAAAAATATATTT
19800528 AATA-TTTAAAAATAATATTT
1 AATATTTTAAAAAT-ATATTT
19800548 AATATTTTAAAAA
1 AATATTTTAAAAA
19800561 ATAATTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.26
20 11 0.35
21 12 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTTAAAAATATATTT
Found at i:19800582 original size:15 final size:14
Alignment explanation
Indices: 19800549--19800586 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
19800539 ATAATATTTA
*
19800549 ATATTTTAAAAAAT
1 ATATTTCAAAAAAT
19800563 A-ATTTCAAAAATAT
1 ATATTTCAAAAA-AT
19800577 ATATTTCAAA
1 ATATTTCAAA
19800587 TTTAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 9 0.43
14 4 0.19
15 8 0.38
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATTTCAAAAAAT
Found at i:19800598 original size:21 final size:22
Alignment explanation
Indices: 19800563--19800609 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
19800553 TTTAAAAAAT
19800563 AATTTCAAAAATATATATTTCA
1 AATTTCAAAAATATATATTTCA
* * *
19800585 AATTT-AAAAGTATATTTTTGA
1 AATTTCAAAAATATATATTTCA
19800606 AATT
1 AATT
19800610 ATTTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (22 bp):
AATTTCAAAAATATATATTTCA
Found at i:19800644 original size:14 final size:13
Alignment explanation
Indices: 19800621--19800654 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
19800611 TTTTATTTTA
19800621 TTTTAAAATATAT
1 TTTTAAAATATAT
19800634 TTTTAAAA-ATAT
1 TTTTAAAATATAT
*
19800646 ATTTAAAAT
1 TTTTAAAAT
19800655 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAATATAT
Found at i:19800770 original size:21 final size:24
Alignment explanation
Indices: 19800741--19800794 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 24
19800731 AAATTTTTAA
19800741 AAAAATTT-AAAAATA-ATATT-T
1 AAAAATTTAAAAAATATATATTAT
*
19800762 AAAATTTTAAAAAATATATATTAT
1 AAAAATTTAAAAAATATATATTAT
19800786 AAAACATTT
1 AAAA-ATTT
19800795 CAAATATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.26
22 7 0.26
23 5 0.19
24 5 0.19
25 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAAATTTAAAAAATATATATTAT
Found at i:19800849 original size:13 final size:13
Alignment explanation
Indices: 19800819--19800867 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
19800809 AAAATTTTTA
* *
19800819 AAATTAATAACAAA
1 AAATAAATAA-AAT
19800833 AAATAAATAAAAT
1 AAATAAATAAAAT
*
19800846 AAATAAACAAAAT
1 AAATAAATAAAAT
*
19800859 AAAAAAATA
1 AAATAAATA
19800868 TAAAACTCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 21 0.70
14 9 0.30
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:19800867 original size:8 final size:8
Alignment explanation
Indices: 19800832--19800890 Score: 55
Period size: 9 Copynumber: 6.9 Consensus size: 8
19800822 TTAATAACAA
19800832 AAAATAAAT
1 AAAA-AAAT
19800841 AAAATAAAT
1 AAAA-AAAT
19800850 AAACAAAAT
1 AAA-AAAAT
19800859 AAAAAAAT
1 AAAAAAAT
* *
19800867 ATAAAACT
1 AAAAAAAT
*
19800875 CAAAAAAAG
1 -AAAAAAAT
19800884 AAAAAAA
1 AAAAAAA
19800891 ATTAAAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
8 18 0.42
9 24 0.56
10 1 0.02
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:19800910 original size:20 final size:21
Alignment explanation
Indices: 19800877--19800932 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
19800867 ATAAAACTCA
*
19800877 AAAAAAGAAAAAAAATTAAAG
1 AAAAAAGAACAAAAATTAAAG
* *
19800898 AAAAAAG-ACAAAAGTTAAAT
1 AAAAAAGAACAAAAATTAAAG
*
19800918 AAAAAAGTACAAAAA
1 AAAAAAGAACAAAAA
19800933 AAAAAGTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.77, C:0.04, G:0.09, T:0.11
Consensus pattern (21 bp):
AAAAAAGAACAAAAATTAAAG
Found at i:19801351 original size:23 final size:20
Alignment explanation
Indices: 19801319--19801367 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
19801309 AAGGGTTAGA
19801319 AAAATAGAAAGATAGAAAATAT
1 AAAATAGAAAGA-AGAAAA-AT
*
19801341 ATAAATGGAAAGAAGAAAAAT
1 A-AAATAGAAAGAAGAAAAAT
19801362 AAAATA
1 AAAATA
19801368 TAATTTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 3 0.12
22 7 0.29
23 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.16
Consensus pattern (20 bp):
AAAATAGAAAGAAGAAAAAT
Found at i:19814496 original size:13 final size:12
Alignment explanation
Indices: 19814478--19814514 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
19814468 TTATATATAT
19814478 TTTAAACTAAAAA
1 TTTAAAC-AAAAA
19814491 TTTAAACAAAAA
1 TTTAAACAAAAA
*
19814503 GTTAAACAAAAA
1 TTTAAACAAAAA
19814515 AGGAGAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.24
Consensus pattern (12 bp):
TTTAAACAAAAA
Found at i:19822774 original size:7 final size:7
Alignment explanation
Indices: 19822762--19822795 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
19822752 ATTTTTTTTA
19822762 AAAATTT
1 AAAATTT
19822769 AAAATTT
1 AAAATTT
19822776 AAAATTT
1 AAAATTT
*
19822783 AAATATAT
1 AAA-ATTT
19822791 AAAAT
1 AAAAT
19822796 GAATTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:19826629 original size:23 final size:23
Alignment explanation
Indices: 19826602--19826648 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
19826592 AAAATACATG
19826602 TGTAAAAA-TATTATACATATACT
1 TGTAAAAATTA-TATACATATACT
* *
19826625 TGTAATAATTATATACATTTACT
1 TGTAAAAATTATATACATATACT
19826648 T
1 T
19826649 ATTATTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (23 bp):
TGTAAAAATTATATACATATACT
Found at i:19826739 original size:18 final size:19
Alignment explanation
Indices: 19826704--19826754 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
19826694 AAATATAAAA
19826704 GAAACAAAACAAAAAGAAT
1 GAAACAAAACAAAAAGAAT
* *
19826723 GAAA-AAAAGAAACAGAAT
1 GAAACAAAACAAAAAGAAT
19826741 AGCAAACGAAAACA
1 -G-AAAC-AAAACA
19826755 GAGGAGAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 12 0.48
19 5 0.20
20 3 0.12
22 5 0.20
ACGTcount: A:0.71, C:0.12, G:0.14, T:0.04
Consensus pattern (19 bp):
GAAACAAAACAAAAAGAAT
Found at i:19834072 original size:15 final size:15
Alignment explanation
Indices: 19834052--19834080 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19834042 AGAAATTGAA
19834052 TAAAAATTTGAGAAC
1 TAAAAATTTGAGAAC
19834067 TAAAAATTTGAGAA
1 TAAAAATTTGAGAA
19834081 AATTGAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.14, T:0.28
Consensus pattern (15 bp):
TAAAAATTTGAGAAC
Found at i:19834640 original size:21 final size:21
Alignment explanation
Indices: 19834607--19834646 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19834597 CTAATAACTC
*
19834607 TATTTAAACATAATTAAATAA
1 TATTTAAACATAAATAAATAA
**
19834628 TATTTAATTATAAATAAAT
1 TATTTAAACATAAATAAAT
19834647 GCTGAAATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TATTTAAACATAAATAAATAA
Found at i:19835621 original size:42 final size:43
Alignment explanation
Indices: 19835566--19835673 Score: 119
Period size: 45 Copynumber: 2.5 Consensus size: 43
19835556 TAGGCAATAA
* * * * * *
19835566 GGGATGTGCAGGCAACGGTGG-TGGTGGTGGTTTTGGCAGGGG
1 GGGAGGTGTAGGCAATGGTGGTTGGTGGAGGTTTCGGCAGAGG
19835608 GGGAGGTGTAGGCAATGGTGGTCTTGGTGGAGGTTTCGGCAGAGG
1 GGGAGGTGTAGGCAATGGTGG--TTGGTGGAGGTTTCGGCAGAGG
**
19835653 GGGAGGCATAGGCAATGGTGG
1 GGGAGGTGTAGGCAATGGTGG
19835674 AACCGGGGGT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 18 0.33
45 37 0.67
ACGTcount: A:0.16, C:0.09, G:0.53, T:0.22
Consensus pattern (43 bp):
GGGAGGTGTAGGCAATGGTGGTTGGTGGAGGTTTCGGCAGAGG
Found at i:19835636 original size:45 final size:45
Alignment explanation
Indices: 19835587--19835673 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
19835577 GCAACGGTGG
* * * **
19835587 TGGTGGTGGTTTTGGCAGGGGGGGAGGTGTAGGCAATGGTGGTCT
1 TGGTGGAGGTTTCGGCAGAGGGGGAGGCATAGGCAATGGTGGTCT
19835632 TGGTGGAGGTTTCGGCAGAGGGGGAGGCATAGGCAATGGTGG
1 TGGTGGAGGTTTCGGCAGAGGGGGAGGCATAGGCAATGGTGG
19835674 AACCGGGGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.15, C:0.08, G:0.53, T:0.24
Consensus pattern (45 bp):
TGGTGGAGGTTTCGGCAGAGGGGGAGGCATAGGCAATGGTGGTCT
Found at i:19837225 original size:13 final size:13
Alignment explanation
Indices: 19837207--19837254 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 13
19837197 CAATTATTTT
19837207 TATTAAAAAATTA
1 TATTAAAAAATTA
*
19837220 TATTAAATAATGATA
1 TATTAAAAAAT--TA
19837235 TATTAAATAAAATTA
1 TATT-AA-AAAATTA
19837250 TATTA
1 TATTA
19837255 CGTGTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 10 0.34
14 1 0.03
15 12 0.41
16 2 0.07
17 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
TATTAAAAAATTA
Found at i:19837251 original size:15 final size:15
Alignment explanation
Indices: 19837213--19837254 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
19837203 TTTTTATTAA
19837213 AAAATTATATTAAAT
1 AAAATTATATTAAAT
*
19837228 AATGA-TATATTAAAT
1 AA-AATTATATTAAAT
19837243 AAAATTATATTA
1 AAAATTATATTA
19837255 CGTGTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.04
15 21 0.91
16 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAAATTATATTAAAT
Found at i:19843496 original size:17 final size:17
Alignment explanation
Indices: 19843476--19843509 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19843466 CTTGTGATTC
*
19843476 TTCTTTTCTTGTTTTTT
1 TTCTTTTCTTCTTTTTT
*
19843493 TTCTTTTTTTCTTTTTT
1 TTCTTTTCTTCTTTTTT
19843510 ACATATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (17 bp):
TTCTTTTCTTCTTTTTT
Found at i:19844235 original size:18 final size:18
Alignment explanation
Indices: 19844212--19844246 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19844202 TTTTAATATA
19844212 ATAATTATAATTATAAGT
1 ATAATTATAATTATAAGT
* *
19844230 ATAATTTTAATTTTAAG
1 ATAATTATAATTATAAG
19844247 AAAATAGTTT
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:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
ATAATTATAATTATAAGT
Found at i:19851969 original size:3 final size:3
Alignment explanation
Indices: 19851961--19851991 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
19851951 ATAGTTAAAG
19851961 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
19851992 AGTCTTATTC
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:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19854830 original size:25 final size:25
Alignment explanation
Indices: 19854802--19854862 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
19854792 TTAAGCTCTT
*
19854802 ATGAGCTTCCTAATACTCAGCTCGC
1 ATGAGCTTCCCAATACTCAGCTCGC
** * *
19854827 ATGAGCTTCCCCTTATTCATCTCGC
1 ATGAGCTTCCCAATACTCAGCTCGC
19854852 ATGAGCTTCCC
1 ATGAGCTTCCC
19854863 GTTATTCAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.20, C:0.34, G:0.15, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCAATACTCAGCTCGC
Found at i:19854867 original size:25 final size:25
Alignment explanation
Indices: 19854818--19854884 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
19854808 TTCCTAATAC
19854818 TCAGCTCGCATGAGCTTCCCCTTAT
1 TCAGCTCGCATGAGCTTCCCCTTAT
* *
19854843 TCATCTCGCATGAGCTTCCCGTTAT
1 TCAGCTCGCATGAGCTTCCCCTTAT
* *
19854868 TCAGCTCGGAAGAGCTT
1 TCAGCTCGCATGAGCTT
19854885 ATCGTTTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.31
Consensus pattern (25 bp):
TCAGCTCGCATGAGCTTCCCCTTAT
Found at i:19854890 original size:25 final size:25
Alignment explanation
Indices: 19854818--19854899 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
19854808 TTCCTAATAC
* * *
19854818 TCAGCTCGCATGAGCTTCCCCTTAT
1 TCAGCTCGCAAGAGCTTACCGTTAT
* * *
19854843 TCATCTCGCATGAGCTTCCCGTTAT
1 TCAGCTCGCAAGAGCTTACCGTTAT
* *
19854868 TCAGCTCGGAAGAGCTTATCGTT-T
1 TCAGCTCGCAAGAGCTTACCGTTAT
*
19854892 ACAGCTCG
1 TCAGCTCG
19854900 TATGAGCATA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 8 0.16
25 41 0.84
ACGTcount: A:0.18, C:0.30, G:0.20, T:0.32
Consensus pattern (25 bp):
TCAGCTCGCAAGAGCTTACCGTTAT
Found at i:19865027 original size:19 final size:20
Alignment explanation
Indices: 19865005--19865044 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
19864995 GGATGACAAT
19865005 GGAA-CTTACCACTGACATA
1 GGAACCTTACCACTGACATA
*
19865024 GGAACTCTTACTACTGACATA
1 GGAAC-CTTACCACTGACATA
19865045 TTAAATTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
21 14 0.78
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
GGAACCTTACCACTGACATA
Found at i:19869011 original size:14 final size:14
Alignment explanation
Indices: 19868992--19869018 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19868982 AGACAACATA
19868992 TATGTATGTATATG
1 TATGTATGTATATG
19869006 TATGTATGTATAT
1 TATGTATGTATAT
19869019 ATGTATAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (14 bp):
TATGTATGTATATG
Found at i:19871012 original size:17 final size:16
Alignment explanation
Indices: 19870987--19871030 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
19870977 AAAATTAAAT
* *
19870987 TTTAAATTTTATAATA
1 TTTAAATTTAAGAATA
19871003 TTTAATATTTAAGAATA
1 TTTAA-ATTTAAGAATA
*
19871020 TTTAAAATTAA
1 TTTAAATTTAA
19871031 AATTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTAAATTTAAGAATA
Found at i:19871144 original size:23 final size:23
Alignment explanation
Indices: 19871117--19871173 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
19871107 ACTATTTACT
19871117 AATGAATATTTT-ATAATATAAA
1 AATGAATATTTTAATAATATAAA
* *
19871139 ATATGAGTATTTTAATAGTATAAA
1 A-ATGAATATTTTAATAATATAAA
19871163 AATGAA-ATTTT
1 AATGAATATTTT
19871174 GTTTAACTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 6 0.20
23 14 0.47
24 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (23 bp):
AATGAATATTTTAATAATATAAA
Found at i:19889199 original size:41 final size:43
Alignment explanation
Indices: 19889147--19889241 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 43
19889137 TTTTGACTTT
*** *
19889147 TTTTTTTTATATATGTCATATATATTGAC-TTTTTTTGTTAA-
1 TTTTTTTTATATATAAAACATATATTGACATTTTTTTGTTAAG
* *
19889188 TTTTTTGTATATATAAAACATATGTTGACATTTTTTTGTTAAG
1 TTTTTTTTATATATAAAACATATATTGACATTTTTTTGTTAAG
19889231 TTTTTTTTATA
1 TTTTTTTTATA
19889242 CATGGATATT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 23 0.51
42 12 0.27
43 10 0.22
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (43 bp):
TTTTTTTTATATATAAAACATATATTGACATTTTTTTGTTAAG
Found at i:19889200 original size:32 final size:31
Alignment explanation
Indices: 19889129--19889202 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
19889119 GTATGCATAG
* * * *
19889129 TGTATCTATTTTGACTTTTTTTTTTTATATA
1 TGTATATATATTGACTTTTTTTGTTAATATA
* *
19889160 TGTCATATATATTGACTTTTTTTGTTAATTTTT
1 TGT-ATATATATTGACTTTTTTTGTTAA-TATA
19889193 TGTATATATA
1 TGTATATATA
19889203 AAACATATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
31 3 0.09
32 27 0.77
33 5 0.14
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (31 bp):
TGTATATATATTGACTTTTTTTGTTAATATA
Found at i:19896719 original size:6 final size:6
Alignment explanation
Indices: 19896708--19896734 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19896698 GCAATGCTGT
19896708 TCCACC TCCACC TCCACC TCCACC TCC
1 TCCACC TCCACC TCCACC TCCACC TCC
19896735 CTTTGTATCT
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:0.15, C:0.67, G:0.00, T:0.19
Consensus pattern (6 bp):
TCCACC
Found at i:19915711 original size:12 final size:12
Alignment explanation
Indices: 19915696--19915726 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19915686 TTCTCTTTTA
19915696 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
19915708 TTTTTCTTTCTC
1 TTTTTCTTTCCC
19915720 TTTTTCT
1 TTTTTCT
19915727 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:19915827 original size:16 final size:16
Alignment explanation
Indices: 19915806--19915836 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19915796 TTTATTGTTT
19915806 TATTAACATAATATAA
1 TATTAACATAATATAA
*
19915822 TATTAATATAATATA
1 TATTAACATAATATA
19915837 TTAAAATATC
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:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:19918588 original size:6 final size:6
Alignment explanation
Indices: 19918577--19918609 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
19918567 AAATTAAGCC
19918577 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAG
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAG
19918610 AAGTTAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:19925878 original size:90 final size:90
Alignment explanation
Indices: 19925725--19925917 Score: 300
Period size: 90 Copynumber: 2.2 Consensus size: 90
19925715 ATTTGCTTTG
* *
19925725 CCAAAATAGAATTCGACTCTCCCGCTCTCCCCCACTATCCCTTTTCCTCTGTTAATAATTTCTTG
1 CCAAAAAAGAATTCGACTCTCCCGCTCTCCCCCACTATCCCTTTCCCTCTGTTAATAATTTCTTG
*
19925790 TTTCTAGATCACCAAAAAAAGCAAC
66 TTTCTAGATAACCAAAAAAAGCAAC
* *
19925815 CCAAAAAAGAATTCGGCTCTCTCC-CTCTCCCCCACTATCCCTTTCCCTCTGTTAATCATTTCTT
1 CCAAAAAAGAATTCGACTCTC-CCGCTCTCCCCCACTATCCCTTTCCCTCTGTTAATAATTTCTT
* *
19925879 GTTTCTAGATAATCGAAAAAAGCAAC
65 GTTTCTAGATAACCAAAAAAAGCAAC
19925905 CCAAAAAA-AATTC
1 CCAAAAAAGAATTC
19925918 AATTTTTTGG
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 5 0.05
90 88 0.93
91 2 0.02
ACGTcount: A:0.31, C:0.32, G:0.08, T:0.30
Consensus pattern (90 bp):
CCAAAAAAGAATTCGACTCTCCCGCTCTCCCCCACTATCCCTTTCCCTCTGTTAATAATTTCTTG
TTTCTAGATAACCAAAAAAAGCAAC
Found at i:19928359 original size:23 final size:22
Alignment explanation
Indices: 19928307--19928359 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
19928297 TCCACGTCTT
*
19928307 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
19928329 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
19928352 TTTCTTTT
1 TTTCTTTT
19928360 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:19947733 original size:46 final size:46
Alignment explanation
Indices: 19947681--19947856 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
19947671 TGGTTGAGCA
*
19947681 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
19947727 TTCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * * *
19947772 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTAATTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
19947820 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
19947857 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 60 0.58
47 25 0.24
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:19947837 original size:93 final size:93
Alignment explanation
Indices: 19947678--19947848 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
19947668 GGATGGTTGA
* * * **
19947678 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTAACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
19947743 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
19947771 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTAATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTAACTTATGGATGCGAACGCCCGAACTCGTTGAGT
19947836 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
19947849 ACTTATGGGC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTAACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:19948034 original size:24 final size:24
Alignment explanation
Indices: 19948004--19948053 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
19947994 ATAAATGTTG
19948004 TGAAATGGATACTTTGAACAGGTA
1 TGAAATGGATACTTTGAACAGGTA
19948028 TGAAATGGATACTTTGAACAGGTA
1 TGAAATGGATACTTTGAACAGGTA
19948052 TG
1 TG
19948054 TACTTAACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (24 bp):
TGAAATGGATACTTTGAACAGGTA
Found at i:19950536 original size:17 final size:16
Alignment explanation
Indices: 19950512--19950547 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
19950502 TTCAATATCA
*
19950512 GTTTTAGTTTATTTTT
1 GTTTTAGTTCATTTTT
19950528 GTTTCTAGTTCATTTTT
1 GTTT-TAGTTCATTTTT
19950545 GTT
1 GTT
19950548 AATTGTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.11, C:0.06, G:0.14, T:0.69
Consensus pattern (16 bp):
GTTTTAGTTCATTTTT
Found at i:19957742 original size:12 final size:12
Alignment explanation
Indices: 19957725--19957751 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19957715 TCCGTCGAAG
19957725 CCCGAGAAACAC
1 CCCGAGAAACAC
19957737 CCCGAGAAACAC
1 CCCGAGAAACAC
19957749 CCC
1 CCC
19957752 ATTTTCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.48, G:0.15, T:0.00
Consensus pattern (12 bp):
CCCGAGAAACAC
Found at i:19960212 original size:74 final size:74
Alignment explanation
Indices: 19960101--19960242 Score: 250
Period size: 74 Copynumber: 1.9 Consensus size: 74
19960091 ACCAAAAATT
* *
19960101 AAAGAAACATTTTAAGTCAAAAGAAAGGTTTGGCTTAGAGATCAAAAATCAAAATAAATATAACA
1 AAAGAAACATTTTAAGTCAAAAGAAAGGTTTGACTTAGAGATAAAAAATCAAAATAAATATAACA
19960166 CTGCCAAAA
66 CTGCCAAAA
19960175 AAAGAAAACATTTTAAGTCAAAA-AAAGGTTTGACTTAGAGATAAAAAATCAAAATAAATATAAC
1 AAAG-AAACATTTTAAGTCAAAAGAAAGGTTTGACTTAGAGATAAAAAATCAAAATAAATATAAC
19960239 ACTG
65 ACTG
19960243 AAGATAATAG
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
74 47 0.72
75 18 0.28
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.23
Consensus pattern (74 bp):
AAAGAAACATTTTAAGTCAAAAGAAAGGTTTGACTTAGAGATAAAAAATCAAAATAAATATAACA
CTGCCAAAA
Found at i:19963172 original size:13 final size:13
Alignment explanation
Indices: 19963154--19963179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19963144 TTCCTTTCGC
19963154 CCCTTCTGTAGTA
1 CCCTTCTGTAGTA
19963167 CCCTTCTGTAGTA
1 CCCTTCTGTAGTA
19963180 GTACCTTTTC
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:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (13 bp):
CCCTTCTGTAGTA
Found at i:19963349 original size:29 final size:29
Alignment explanation
Indices: 19963316--19963372 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
19963306 AGCTCACAAT
*
19963316 TTCAGAGATAAATTATTAAGCATATCTGA
1 TTCAGAGATAAATTATTAAGCAAATCTGA
19963345 TTCAGAGATAAATTATTAAGCAAATCTG
1 TTCAGAGATAAATTATTAAGCAAATCTG
19963373 GTAAGACCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TTCAGAGATAAATTATTAAGCAAATCTGA
Done.