Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold149
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: 2538714
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 122877 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:423175 original size:6 final size:6
Alignment explanation
Indices: 423164--423209 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
423154 GCTGAACTCG
423164 TTTCTT TTTCTT TTTCTT TTTCATT TTTC-T TTTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT TTTC
423210 ACTCGACTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.13
6 27 0.71
7 6 0.16
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:423196 original size:24 final size:25
Alignment explanation
Indices: 423164--423210 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
423154 GCTGAACTCG
423164 TTTCTTTTTCTTTTTCTTTTTCATT
1 TTTCTTTTTCTTTTTCTTTTTCATT
423189 TTTC-TTTTCTTTTTCTTTTTCA
1 TTTCTTTTTCTTTTTCTTTTTCA
423211 CTCGACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTCTTTTTCTTTTTCTTTTTCATT
Found at i:423219 original size:24 final size:24
Alignment explanation
Indices: 423169--423221 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
423159 ACTCGTTTCT
* ***
423169 TTTTCTTTTTCTTTTTCATTTTTC
1 TTTTCTTTTTCTTTTTCACTCGAC
423193 TTTTCTTTTTCTTTTTCACTCGAC
1 TTTTCTTTTTCTTTTTCACTCGAC
423217 TTTTC
1 TTTTC
423222 AACAGAAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTTCTTTTTCTTTTTCACTCGAC
Found at i:426060 original size:34 final size:34
Alignment explanation
Indices: 426017--426090 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
426007 TTGAGGTGGC
** *
426017 CGAACAGCCTTGTTGGTATGTC-TATTGATGTGCA
1 CGAACAGCCTTGAAGATATGTCAT-TTGATGTGCA
*
426051 CGAATAGCCTTGAAGATATGTCATTTGATGTGCA
1 CGAACAGCCTTGAAGATATGTCATTTGATGTGCA
426085 CGAACA
1 CGAACA
426091 ACTTTTGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (34 bp):
CGAACAGCCTTGAAGATATGTCATTTGATGTGCA
Found at i:427024 original size:21 final size:21
Alignment explanation
Indices: 426998--427052 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
426988 ACTAGGTACC
*
426998 TCGATTAAATCTTGACTGGCT
1 TCGATTGAATCTTGACTGGCT
427019 TCGATTGAATCTTGACTGGCT
1 TCGATTGAATCTTGACTGGCT
427040 TCGATTGAATCTT
1 TCGATTGAATCTT
427053 TAGGCGAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (21 bp):
TCGATTGAATCTTGACTGGCT
Found at i:432170 original size:6 final size:6
Alignment explanation
Indices: 432124--432169 Score: 67
Period size: 6 Copynumber: 7.7 Consensus size: 6
432114 GCTGAACTCG
*
432124 TTTCTT TTTCTT TTTCTT TTTCATT TTTC-T TTTCTT TTTCAT TTTC
1 TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT TTTC
432170 ACTCGACTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
5 5 0.14
6 26 0.70
7 6 0.16
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:432179 original size:24 final size:24
Alignment explanation
Indices: 432129--432181 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
432119 ACTCGTTTCT
* * ***
432129 TTTTCTTTTTCTTTTTCATTTTTC
1 TTTTCTTTTTCATTTTCACTCGAC
432153 TTTTCTTTTTCATTTTCACTCGAC
1 TTTTCTTTTTCATTTTCACTCGAC
432177 TTTTC
1 TTTTC
432182 AACAGAAGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.21, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTTCTTTTTCATTTTCACTCGAC
Found at i:435022 original size:34 final size:33
Alignment explanation
Indices: 434972--435057 Score: 109
Period size: 34 Copynumber: 2.5 Consensus size: 33
434962 ATTAGCTGTC
* * ** *
434972 CATTGAGGTGCTCGAACAGCCTTGTTGGTATGT
1 CATTGATGTGCACGAACAGCCTTGAAGATATGT
435005 CTATTGATGTGCACGAACAGCCTTGAAGATATGT
1 C-ATTGATGTGCACGAACAGCCTTGAAGATATGT
435039 CATTTGATGTGCACGAACA
1 CA-TTGATGTGCACGAACA
435058 ACTTTTGATG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.04
34 44 0.96
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (33 bp):
CATTGATGTGCACGAACAGCCTTGAAGATATGT
Found at i:488725 original size:18 final size:19
Alignment explanation
Indices: 488684--488725 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
488674 ATCTTACACG
* *
488684 AAAAATACTTCAACAAAGA
1 AAAAATACTTCAAAAAAAA
*
488703 CAAAATAC-TCAAAAAAAA
1 AAAAATACTTCAAAAAAAA
488721 AAAAA
1 AAAAA
488726 ACATGTTACA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.71, C:0.14, G:0.02, T:0.12
Consensus pattern (19 bp):
AAAAATACTTCAAAAAAAA
Found at i:490367 original size:40 final size:40
Alignment explanation
Indices: 490312--490401 Score: 162
Period size: 40 Copynumber: 2.2 Consensus size: 40
490302 TATACGAATA
*
490312 AATTTTAATTTTGATTTAATATGTAAAGGGTGGTGGCATG
1 AATTTTAATTTTGATTTAATATGTAAAGGGTGGTCGCATG
*
490352 AATTTTAATTTTGATTTAATATGTGAAGGGTGGTCGCATG
1 AATTTTAATTTTGATTTAATATGTAAAGGGTGGTCGCATG
490392 AATTTTAATT
1 AATTTTAATT
490402 AATGTAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.44
Consensus pattern (40 bp):
AATTTTAATTTTGATTTAATATGTAAAGGGTGGTCGCATG
Found at i:491684 original size:28 final size:28
Alignment explanation
Indices: 491644--491701 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
491634 AATTGGTCAC
491644 ACAACCGTTATATGGCAACAGGAGACTA
1 ACAACCGTTATATGGCAACAGGAGACTA
491672 ACAACCGTTATATGGCAACAGGAGACTA
1 ACAACCGTTATATGGCAACAGGAGACTA
491700 AC
1 AC
491702 CGTGCATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (28 bp):
ACAACCGTTATATGGCAACAGGAGACTA
Found at i:511174 original size:1 final size:1
Alignment explanation
Indices: 511168--511236 Score: 75
Period size: 1 Copynumber: 69.0 Consensus size: 1
511158 TACTTCTTTG
****** *
511168 TTTTTTTTTTTTTTTTTTTTTTGGGAGGTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
511233 TTTT
1 TTTT
511237 GGGAAGGTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.01, C:0.00, G:0.09, T:0.90
Consensus pattern (1 bp):
T
Found at i:512440 original size:4 final size:4
Alignment explanation
Indices: 512433--512457 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
512423 TATATATCAT
512433 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
512458 GATGGATGGA
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:513030 original size:162 final size:164
Alignment explanation
Indices: 512845--513176 Score: 641
Period size: 162 Copynumber: 2.0 Consensus size: 164
512835 ATATTTAATT
512845 TGAGATATAATATTATTTATTTATTTAAATCATGATATTAGTAACTAGCATTTTGGATGATATTG
1 TGAG-TATAATATTATTTATTTATTTAAATCATGATATTAGTAACTAGCATTTTGGATGATATTG
512910 ATGAAACATCATTTTCATTGCTAAAACTGAAAGTTTGTAGGTGATCATGTAATATAAAATAATTT
65 ATGAAACATCATTTTCATTGCTAAAACTGAAAGTTTGTAGGTGATCATGTAATATAAAATAATTT
512975 TGGTTATTTTTTTTGTTAAATAACCTT-A-CTAAA
130 TGGTTATTTTTTTTGTTAAATAACCTTAAGCTAAA
513008 TGAGTATAATATTATTTATTTATTTAAATCATGATATTAGTAACTAGCATTTTGGATGATATTGA
1 TGAGTATAATATTATTTATTTATTTAAATCATGATATTAGTAACTAGCATTTTGGATGATATTGA
513073 TGAAACATCATTTTCATTGCTAAAACTGAAAGTTTGTAGGTGATCATGTAATATAAAATAATTTT
66 TGAAACATCATTTTCATTGCTAAAACTGAAAGTTTGTAGGTGATCATGTAATATAAAATAATTTT
513138 GGTTATTTTTTTTGTTAAATAACCTTAAGCTAAA
131 GGTTATTTTTTTTGTTAAATAACCTTAAGCTAAA
513172 TGAGT
1 TGAGT
513177 TTTATATATG
Statistics
Matches: 167, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
162 152 0.91
163 5 0.03
164 10 0.06
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (164 bp):
TGAGTATAATATTATTTATTTATTTAAATCATGATATTAGTAACTAGCATTTTGGATGATATTGA
TGAAACATCATTTTCATTGCTAAAACTGAAAGTTTGTAGGTGATCATGTAATATAAAATAATTTT
GGTTATTTTTTTTGTTAAATAACCTTAAGCTAAA
Found at i:520173 original size:21 final size:23
Alignment explanation
Indices: 520126--520175 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
520116 AATTTTAAAT
**
520126 ATTAAAAATATAAAGACTAAATT
1 ATTAAAAATATAAAGACTAAAAA
*
520149 ATTAAAAATA-AAA-ATTAAAAA
1 ATTAAAAATATAAAGACTAAAAA
520170 ATTAAA
1 ATTAAA
520176 TTTAAAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.46
22 3 0.12
23 10 0.42
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
ATTAAAAATATAAAGACTAAAAA
Found at i:521291 original size:21 final size:23
Alignment explanation
Indices: 521244--521293 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
521234 AATTTTAAAT
**
521244 ATTAAAAATATAAAGACTAAATT
1 ATTAAAAATATAAAGACTAAAAA
*
521267 ATTAAAAATA-AAA-ATTAAAAA
1 ATTAAAAATATAAAGACTAAAAA
521288 ATTAAA
1 ATTAAA
521294 TTTAAAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.46
22 3 0.12
23 10 0.42
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
ATTAAAAATATAAAGACTAAAAA
Found at i:522363 original size:42 final size:42
Alignment explanation
Indices: 522317--522400 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
522307 AGTGTAGGGA
522317 AATTTAGTGAGATATACAATTTATATTTAATTTGTGTAATTT
1 AATTTAGTGAGATATACAATTTATATTTAATTTGTGTAATTT
522359 AATTTAGTGAGATATACAATTTATATTTAATTTGTGTAATTT
1 AATTTAGTGAGATATACAATTTATATTTAATTTGTGTAATTT
522401 TTCCCTTGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (42 bp):
AATTTAGTGAGATATACAATTTATATTTAATTTGTGTAATTT
Found at i:523424 original size:19 final size:19
Alignment explanation
Indices: 523395--523446 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
523385 TTGAATCGAT
523395 TTTATAATTTTTAA-TATA
1 TTTATAATTTTTAATTATA
* *
523413 TTTCTAATTTTTAATTATT
1 TTTATAATTTTTAATTATA
523432 TTTATAATTTTTAAT
1 TTTATAATTTTTAAT
523447 GAATTTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATAATTTTTAATTATA
Found at i:523434 original size:10 final size:10
Alignment explanation
Indices: 523394--523454 Score: 58
Period size: 9 Copynumber: 6.4 Consensus size: 10
523384 GTTGAATCGA
523394 TTTT-ATAAT
1 TTTTAATAAT
523403 TTTTAAT-AT
1 TTTTAATAAT
* *
523412 ATTT-CTAAT
1 TTTTAATAAT
*
523421 TTTTAATTAT
1 TTTTAATAAT
523431 TTTT-ATAAT
1 TTTTAATAAT
523440 TTTTAATGAAT
1 TTTTAAT-AAT
523451 TTTT
1 TTTT
523455 CAATTATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
8 1 0.02
9 22 0.54
10 11 0.27
11 7 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:523453 original size:19 final size:18
Alignment explanation
Indices: 523393--523453 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
523383 AGTTGAATCG
523393 ATTTTATAATTTTTAAT-
1 ATTTTATAATTTTTAATA
*
523410 ATATTTCTAATTTTTAATTA
1 AT-TTTATAATTTTTAA-TA
*
523430 TTTTTATAATTTTTAATGA
1 ATTTTATAATTTTTAAT-A
523449 ATTTT
1 ATTTT
523454 TCAATTATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.06
18 14 0.39
19 19 0.53
20 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
ATTTTATAATTTTTAATA
Found at i:525036 original size:21 final size:22
Alignment explanation
Indices: 525012--525055 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
525002 TTTTTTTTAT
525012 AGTGAGAATATA-AAAAGTTAA
1 AGTGAGAATATATAAAAGTTAA
525033 AGTGAGAATATATAAAAGTTAA
1 AGTGAGAATATATAAAAGTTAA
525055 A
1 A
525056 TAAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.25
Consensus pattern (22 bp):
AGTGAGAATATATAAAAGTTAA
Found at i:525049 original size:23 final size:20
Alignment explanation
Indices: 525012--525055 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 20
525002 TTTTTTTTAT
525012 AGTGAGAATATAAAAAGTTAA
1 AGTGAGAATAT-AAAAGTTAA
525033 AGTGAGAATATATAAAAGTTAA
1 AGTGAG-A-ATATAAAAGTTAA
525055 A
1 A
525056 TAAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.25
Consensus pattern (20 bp):
AGTGAGAATATAAAAGTTAA
Found at i:529765 original size:15 final size:15
Alignment explanation
Indices: 529736--529769 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
529726 TACCAAAAGG
529736 GTATTTACAAAAATC
1 GTATTTACAAAAATC
**
529751 GTATTTACACCAATC
1 GTATTTACAAAAATC
529766 GTAT
1 GTAT
529770 ATTCGAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (15 bp):
GTATTTACAAAAATC
Found at i:535595 original size:27 final size:28
Alignment explanation
Indices: 535564--535618 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
535554 CACTTAATCA
535564 AGTGGCCTAAGATATTA-TCTCATTATG
1 AGTGGCCTAAGATATTACTCTCATTATG
535591 AGTGGCCTAAGATATTACTCTCATTATG
1 AGTGGCCTAAGATATTACTCTCATTATG
535619 TAGGAGAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (28 bp):
AGTGGCCTAAGATATTACTCTCATTATG
Found at i:537788 original size:25 final size:24
Alignment explanation
Indices: 537707--537793 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
537697 TTAGGAAAAC
* *
537707 TTTATTTCTA-TTAATTTATCCATTT
1 TTTATTT-TATTTAATTTTTACA-TT
* *
537732 TTTATTTTATTTCATTTTTATATT
1 TTTATTTTATTTAATTTTTACATT
*
537756 TTTGTTTTAATTTAATTTTTACATT
1 TTTATTTT-ATTTAATTTTTACATT
*
537781 TTAATTTTTATTT
1 TTTA-TTTTATTT
537794 TGTTTGCTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 11 0.22
25 35 0.70
26 4 0.08
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (24 bp):
TTTATTTTATTTAATTTTTACATT
Found at i:544221 original size:6 final size:6
Alignment explanation
Indices: 544196--544232 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
544186 CCTATTATTA
544196 TTTTA- TTTTAT TTATTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TT-TTAT TTTTAT TTTTAT TTTTAT T
544233 ATTACTGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:544228 original size:24 final size:23
Alignment explanation
Indices: 544188--544236 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
544178 GCCCCTCCCC
544188 TATTATTATTTTA-TTTTATTTAT
1 TATTATTATTTTATTTTTA-TTAT
*
544211 TATTTTTATTTTTATTTTTATTAT
1 TATTATTA-TTTTATTTTTATTAT
544235 TA
1 TA
544237 CTGTTATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 11 0.48
25 5 0.22
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (23 bp):
TATTATTATTTTATTTTTATTAT
Found at i:544243 original size:24 final size:24
Alignment explanation
Indices: 544196--544244 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
544186 CCTATTATTA
* *
544196 TTTTATTTTATTTATTATTTTTAT
1 TTTTATTTTATTTATTACTGTTAT
544220 TTTTATTTT-TATTATTACTGTTAT
1 TTTTATTTTAT-TTATTACTGTTAT
544244 T
1 T
544245 ACTAGTGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTTATTTTATTTATTACTGTTAT
Found at i:544397 original size:97 final size:97
Alignment explanation
Indices: 544231--544427 Score: 376
Period size: 97 Copynumber: 2.0 Consensus size: 97
544221 TTTATTTTTA
*
544231 TTATTACTGTTATTACTAGTGTAATAGGCCCAATTTGCCCGGCCCGTCATAAAAAAATATAAACC
1 TTATTACTGTTATTACTAGTGTAATAGGCCCAATTTGCCCGGCCCGTAATAAAAAAATATAAACC
544296 AAACAAATTAATAACAGTCCAAAATAGTCTAG
66 AAACAAATTAATAACAGTCCAAAATAGTCTAG
*
544328 TTATTACTGTTATTATTAGTGTAATAGGCCCAATTTGCCCGGCCCGTAATAAAAAAATATAAACC
1 TTATTACTGTTATTACTAGTGTAATAGGCCCAATTTGCCCGGCCCGTAATAAAAAAATATAAACC
544393 AAACAAATTAATAACAGTCCAAAATAGTCTAG
66 AAACAAATTAATAACAGTCCAAAATAGTCTAG
544425 TTA
1 TTA
544428 CACGGCCCAG
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (97 bp):
TTATTACTGTTATTACTAGTGTAATAGGCCCAATTTGCCCGGCCCGTAATAAAAAAATATAAACC
AAACAAATTAATAACAGTCCAAAATAGTCTAG
Found at i:548490 original size:15 final size:16
Alignment explanation
Indices: 548465--548495 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
548455 TCTGAGTGGT
548465 TCACTTGTTTTGAGCA
1 TCACTTGTTTTGAGCA
548481 TCAC-TGTTTTGAGCA
1 TCACTTGTTTTGAGCA
548496 GTTCGACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (16 bp):
TCACTTGTTTTGAGCA
Found at i:555988 original size:15 final size:16
Alignment explanation
Indices: 555954--555989 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
555944 AATTAAGGTC
555954 ATTTTGAGTTCAAGTT
1 ATTTTGAGTTCAAGTT
*
555970 ATTTTGAGTTGAA-TT
1 ATTTTGAGTTCAAGTT
555985 ATTTT
1 ATTTT
555990 AAATTTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.56
Consensus pattern (16 bp):
ATTTTGAGTTCAAGTT
Found at i:558176 original size:24 final size:24
Alignment explanation
Indices: 558148--558199 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
558138 TTTCTAGAAG
* *
558148 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
558172 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
558196 ATTT
1 ATTT
558200 GACCTATGAA
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:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:565887 original size:31 final size:31
Alignment explanation
Indices: 565849--565910 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
565839 GGGTAACACA
565849 CTTACGACAAGGTCGTTGGACAAGCACTGAT
1 CTTACGACAAGGTCGTTGGACAAGCACTGAT
*
565880 CTTACGACAAGGTCGTTGGACAATCACTGAT
1 CTTACGACAAGGTCGTTGGACAAGCACTGAT
565911 TAAGTTACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (31 bp):
CTTACGACAAGGTCGTTGGACAAGCACTGAT
Found at i:569391 original size:27 final size:27
Alignment explanation
Indices: 569345--569419 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 27
569335 CAATTGTTTA
* * *
569345 TACACAAACTCGCCAGACCTTTTGGTG
1 TACACAAACTCACCAAACCTATTGGTG
*
569372 TACACGAACTCACCAAACCTATTGGTG
1 TACACAAACTCACCAAACCTATTGGTG
* * * *
569399 TACGCTAGCTCACCCAACCTA
1 TACACAAACTCACCAAACCTA
569420 CTAGTGAACA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (27 bp):
TACACAAACTCACCAAACCTATTGGTG
Found at i:570256 original size:23 final size:23
Alignment explanation
Indices: 570230--570273 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
570220 GAATATTAAA
570230 TGTACTCCAATTATTT-TATAACT
1 TGTACTCCAATT-TTTCTATAACT
* *
570253 TGTATTCCCATTTTTCTATAA
1 TGTACTCCAATTTTTCTATAA
570274 TAGTCATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50
Consensus pattern (23 bp):
TGTACTCCAATTTTTCTATAACT
Found at i:580897 original size:3 final size:3
Alignment explanation
Indices: 580877--580930 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
580867 CCTCTACTTG
* * *
580877 TTC TTG TTC TTG TTC TTC TTC ATC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
580925 TTC TTC
1 TTC TTC
580931 GACTATTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.02, C:0.30, G:0.04, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:581758 original size:20 final size:20
Alignment explanation
Indices: 581733--581793 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
581723 TATAACTAAG
581733 TCATTGCAATATGCATATAA
1 TCATTGCAATATGCATATAA
** * *
581753 TCATTGTTATA-AC-TA-AG
1 TCATTGCAATATGCATATAA
581770 TCATTGCAATATGTCATATAA
1 TCATTGCAATATG-CATATAA
581791 TCA
1 TCA
581794 ATTAAATTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 7
0.66 0.18 0.16
Matches are distributed among these distances:
17 10 0.34
18 2 0.07
19 2 0.07
20 11 0.38
21 4 0.14
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (20 bp):
TCATTGCAATATGCATATAA
Found at i:581769 original size:37 final size:38
Alignment explanation
Indices: 581719--581793 Score: 143
Period size: 37 Copynumber: 2.0 Consensus size: 38
581709 TTGCTTTAAT
581719 TTGTTATAACTAAGTCATTGCAATATG-CATATAATCA
1 TTGTTATAACTAAGTCATTGCAATATGTCATATAATCA
581756 TTGTTATAACTAAGTCATTGCAATATGTCATATAATCA
1 TTGTTATAACTAAGTCATTGCAATATGTCATATAATCA
581794 ATTAAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 27 0.73
38 10 0.27
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (38 bp):
TTGTTATAACTAAGTCATTGCAATATGTCATATAATCA
Found at i:581775 original size:17 final size:17
Alignment explanation
Indices: 581719--581775 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
581709 TTGCTTTAAT
581719 TTGTTATAACTAAGTCA
1 TTGTTATAACTAAGTCA
** * *
581736 TTGCAATATGCATATAATCA
1 TTGTTATA-AC-TA-AGTCA
581756 TTGTTATAACTAAGTCA
1 TTGTTATAACTAAGTCA
581773 TTG
1 TTG
581776 CAATATGTCA
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 13 0.45
18 3 0.10
19 3 0.10
20 10 0.34
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (17 bp):
TTGTTATAACTAAGTCA
Found at i:586253 original size:50 final size:50
Alignment explanation
Indices: 586176--586422 Score: 314
Period size: 50 Copynumber: 4.9 Consensus size: 50
586166 TCCTGTACTA
* * * * * ** * *
586176 CCAATGCCATATCCCAGATATGATCTTACATGGGAGTTCTCATATCGATG
1 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * * ** *
586226 CCCATGCCATGCCCCAAACATGGTCTTACGGGGGACCTCTCATCTTGGTG
1 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
586276 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTTGGTG
1 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * *
586326 CAAACGCCATGTCCCAGACATGGTCCTACATGGGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
586376 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
1 CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG
586423 TGTTGACATG
Statistics
Matches: 173, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 173 1.00
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (50 bp):
CCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:586504 original size:44 final size:44
Alignment explanation
Indices: 586440--586535 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
586430 ATGGATCAAC
*
586440 CATGGTACTTTTCCGTCAATTCTTTATTAATTGCCATGTTATAAA
1 CATGG-ACTTTTCCGTCAATTCTTCATTAATTGCCATGTTATAAA
*
586485 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCATTAATTGCCATGTTATAAA
586529 CATGGAC
1 CATGGAC
586536 CTTGAGATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 44 0.90
45 5 0.10
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
CATGGACTTTTCCGTCAATTCTTCATTAATTGCCATGTTATAAA
Found at i:595199 original size:41 final size:42
Alignment explanation
Indices: 595154--595235 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 42
595144 TATCACAAAA
* *
595154 CTCACAAAAGCCCATGCTCTC-GAGGAGCACGCAGAGTGAGG
1 CTCACAAAAGCCCATGCTCTCAAAGGAACACGCAGAGTGAGG
* *
595195 CTCACAAAAGCTCATGTTCTCAAAGGAACACGCAGAGTGAG
1 CTCACAAAAGCCCATGCTCTCAAAGGAACACGCAGAGTGAG
595236 ACTTAACATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 19 0.53
42 17 0.47
ACGTcount: A:0.33, C:0.27, G:0.26, T:0.15
Consensus pattern (42 bp):
CTCACAAAAGCCCATGCTCTCAAAGGAACACGCAGAGTGAGG
Found at i:607888 original size:259 final size:260
Alignment explanation
Indices: 607587--608107 Score: 1035
Period size: 259 Copynumber: 2.0 Consensus size: 260
607577 TACAAAAATT
607587 TATATTATTTAAATTCTAAAAAATTCTAAATTTATGACTAAAAAATTATTATATAAAATAATTTA
1 TATATTATTTAAATTCTAAAAAATTCTAAATTTATGACTAAAAAATTATTATATAAAATAATTTA
607652 CATGTTATAAAAGTGTTATAATATATTTATTTAAAAAATTTTATGGTCAAGAAGCATGAATATAA
66 CATGTTATAAAAGTGTTATAATATATTTATTTAAAAAATTTTATGGTCAAGAAGCATGAATATAA
607717 TTTATTTACATGTCCATCCTATATATTATAAAAATAATACACTTATTCATAAAAATTATCATAAT
131 TTTATTTACATGTCCATCCTATATATTATAAAAATAATACACTTATTCATAAAAATTATCATAAT
607782 TTTTTTATTGTAACTTATTTGTGAAAAATAACTTTTGAAATTTATGATAAAAAC-ATATTATTTA
196 TTTTTTATTGTAACTTATTTGTGAAAAATAACTTTTGAAATTTATGATAAAAACTATATTATTTA
607846 TATATTATTTAAATTCTAAAAAATTCTAAATTTATGACTAAAAAATTATTATATAAAATAATTTA
1 TATATTATTTAAATTCTAAAAAATTCTAAATTTATGACTAAAAAATTATTATATAAAATAATTTA
607911 CATGTTATAAAAGTGTTATAATATATTTATTTAAAAAATTTTATGGTCAAGAAGCATGAATATAA
66 CATGTTATAAAAGTGTTATAATATATTTATTTAAAAAATTTTATGGTCAAGAAGCATGAATATAA
607976 TTTATTTACATGTCCATCCTATATATTATAAAAATAATACACTTATTCATAAAAATTATCATAAT
131 TTTATTTACATGTCCATCCTATATATTATAAAAATAATACACTTATTCATAAAAATTATCATAAT
608041 TTTTTTATTGTAACTTATTTGTGAAAAATAACTTTTGAAATTTATGATAAAAACTATATTATTTA
196 TTTTTTATTGTAACTTATTTGTGAAAAATAACTTTTGAAATTTATGATAAAAACTATATTATTTA
608106 TA
1 TA
608108 AGAATTTCTA
Statistics
Matches: 261, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
259 249 0.95
260 12 0.05
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (260 bp):
TATATTATTTAAATTCTAAAAAATTCTAAATTTATGACTAAAAAATTATTATATAAAATAATTTA
CATGTTATAAAAGTGTTATAATATATTTATTTAAAAAATTTTATGGTCAAGAAGCATGAATATAA
TTTATTTACATGTCCATCCTATATATTATAAAAATAATACACTTATTCATAAAAATTATCATAAT
TTTTTTATTGTAACTTATTTGTGAAAAATAACTTTTGAAATTTATGATAAAAACTATATTATTTA
Found at i:611320 original size:19 final size:19
Alignment explanation
Indices: 611287--611334 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
611277 TAAACAATTC
611287 AATAATATAAA--TAATAT
1 AATAATATAAATTTAATAT
*
611304 AA-AATATGAAATTTAATTT
1 AATAATAT-AAATTTAATAT
611323 AATAATATAAAT
1 AATAATATAAAT
611335 AGTAGATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
19 11 0.42
20 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATATAAATTTAATAT
Found at i:619482 original size:39 final size:39
Alignment explanation
Indices: 619439--619572 Score: 207
Period size: 39 Copynumber: 3.4 Consensus size: 39
619429 TTTTGTGTAC
*
619439 TGTGATATATGCTTGAATGTTATGTGATTATATGAGTAT
1 TGTGATATATGCTTAAATGTTATGTGATTATATGAGTAT
*
619478 TGTGATATATGTTTAAATGTTATGTGATTATATGAGTAT
1 TGTGATATATGCTTAAATGTTATGTGATTATATGAGTAT
* * *
619517 TGTGATATATGATTAAATGTTATATGATTATAT-ATGTAA
1 TGTGATATATGCTTAAATGTTATGTGATTATATGA-GTAT
619556 TGTGATATATGCTTAAA
1 TGTGATATATGCTTAAA
619573 AGTGAATATG
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
38 1 0.01
39 87 0.99
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.46
Consensus pattern (39 bp):
TGTGATATATGCTTAAATGTTATGTGATTATATGAGTAT
Found at i:619549 original size:8 final size:8
Alignment explanation
Indices: 619458--619549 Score: 57
Period size: 8 Copynumber: 11.8 Consensus size: 8
619448 TGCTTGAATG
*
619458 TTATGTGA
1 TTATATGA
619466 TTATATGA
1 TTATATGA
* *
619474 GTATTGTGA
1 TTA-TATGA
*
619483 -TATATGT
1 TTATATGA
*
619490 TTAAATG-
1 TTATATGA
*
619497 TTATGTGA
1 TTATATGA
619505 TTATATGA
1 TTATATGA
* *
619513 GTATTGTGA
1 TTA-TATGA
619522 -TATATGA
1 TTATATGA
*
619529 TTAAATG-
1 TTATATGA
619536 TTATATGA
1 TTATATGA
619544 TTATAT
1 TTATAT
619550 ATGTAATGTG
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
7 18 0.28
8 38 0.59
9 8 0.12
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (8 bp):
TTATATGA
Found at i:619593 original size:39 final size:39
Alignment explanation
Indices: 619434--619594 Score: 103
Period size: 39 Copynumber: 4.1 Consensus size: 39
619424 CATGTTTTTG
* * * * * * *
619434 TGTACTGTGATATATGCTTGAATGTTATGTGATTATATGA
1 TGTAATGTGATATATGATTAAAAGTAATATGATTATA-CA
* * * * * *
619474 -GTATTGTGATATATGTTTAAATGTTATGTGATTATATGA
1 TGTAATGTGATATATGATTAAAAGTAATATGATTATA-CA
* * * *
619513 -GTATTGTGATATATGATTAAATGTTATATGATTATATA
1 TGTAATGTGATATATGATTAAAAGTAATATGATTATACA
* *
619551 TGTAATGTGATATATGCTTAAAAGTGAATATGATTA-CCA
1 TGTAATGTGATATATGATTAAAAGT-AATATGATTATACA
619590 TGTAA
1 TGTAA
619595 ATGAACTAGC
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
38 1 0.01
39 97 0.91
40 9 0.08
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (39 bp):
TGTAATGTGATATATGATTAAAAGTAATATGATTATACA
Found at i:622563 original size:30 final size:29
Alignment explanation
Indices: 622527--622600 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 29
622517 ACCGTCAGAC
622527 TTAAATTTAAAAATATAAAAAGTA-AAAAAA
1 TTAAATTTAAAAATA-AAAAA-TATAAAAAA
*
622557 TTAAATTCTTGAAAATAAAAAATATAAAAAA
1 TTAAA-T-TTAAAAATAAAAAATATAAAAAA
*
622588 TTAAATTTCAAAA
1 TTAAATTTAAAAA
622601 GAGTGCAGCG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
29 6 0.15
30 8 0.21
31 17 0.44
32 8 0.21
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
TTAAATTTAAAAATAAAAAATATAAAAAA
Found at i:622925 original size:20 final size:20
Alignment explanation
Indices: 622879--622925 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
622869 TGAATTAATC
*
622879 AAGGTGCAATGCGGATATCT
1 AAGGTGTAATGCGGATATCT
*
622899 AAGGTGTAATGTGGATA-CT
1 AAGGTGTAATGCGGATATCT
622918 AGAGGTGT
1 A-AGGTGT
622926 TTATGGGACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.30, C:0.09, G:0.34, T:0.28
Consensus pattern (20 bp):
AAGGTGTAATGCGGATATCT
Found at i:623371 original size:11 final size:11
Alignment explanation
Indices: 623350--623406 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
623340 AAAAAACAAC
*
623350 AACAACAAGAA
1 AACAGCAAGAA
*
623361 AATAGCAAGAA
1 AACAGCAAGAA
* *
623372 AACAGTAAAAAA
1 AACAG-CAAGAA
*
623384 AAGAGCAAGAA
1 AACAGCAAGAA
623395 AACAGCAA-AA
1 AACAGCAAGAA
623405 AA
1 AA
623407 GACAATAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
10 4 0.11
11 24 0.67
12 8 0.22
ACGTcount: A:0.70, C:0.12, G:0.14, T:0.04
Consensus pattern (11 bp):
AACAGCAAGAA
Found at i:623390 original size:23 final size:23
Alignment explanation
Indices: 623359--623406 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
623349 CAACAACAAG
* *
623359 AAAATAGCAAGAAAACAGTAAAA
1 AAAAGAGCAAGAAAACAGCAAAA
623382 AAAAGAGCAAGAAAACAGCAAAA
1 AAAAGAGCAAGAAAACAGCAAAA
623405 AA
1 AA
623407 GACAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.71, C:0.10, G:0.15, T:0.04
Consensus pattern (23 bp):
AAAAGAGCAAGAAAACAGCAAAA
Found at i:624389 original size:21 final size:20
Alignment explanation
Indices: 624363--624438 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 20
624353 ATTATATATT
624363 AAATATATATATTTTTTAATC
1 AAATATATAT-TTTTTTAATC
624384 AAATATATATTTTATTTTTAATC
1 AAATATATA--TT-TTTTTAATC
* *
624407 AAATATAT-TTTTTATATATT
1 AAATATATATTTTTTTA-ATC
624427 AAATATATATTT
1 AAATATATATTT
624439 AATATGAGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.10
20 12 0.25
21 12 0.25
22 1 0.02
23 18 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATATATATTTTTTTAATC
Found at i:624401 original size:23 final size:23
Alignment explanation
Indices: 624363--624421 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
624353 ATTATATATT
*
624363 AAATATATA-TAT-TTTTTAATC
1 AAATATATATTTTATTTTTAATC
624384 AAATATATATTTTATTTTTAATC
1 AAATATATATTTTATTTTTAATC
*
624407 AAATATATTTTTTAT
1 AAATATATATTTTAT
624422 ATATTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 9 0.26
22 2 0.06
23 23 0.68
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATATATATTTTATTTTTAATC
Found at i:624846 original size:17 final size:17
Alignment explanation
Indices: 624824--624858 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
624814 AATATAGAAA
*
624824 GTAATCTTAGAAGATTT
1 GTAATCTGAGAAGATTT
*
624841 GTAATCTGATAAGATTT
1 GTAATCTGAGAAGATTT
624858 G
1 G
624859 ATTTTATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (17 bp):
GTAATCTGAGAAGATTT
Found at i:635497 original size:18 final size:18
Alignment explanation
Indices: 635430--635500 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 18
635420 TTGAGCAGAT
*
635430 ATTCTTTTAAGATTCTTTC
1 ATTCTTTTGA-ATTCTTTC
* *** *
635449 ATTCTTTTGTA-TGAGTA
1 ATTCTTTTGAATTCTTTC
* *
635466 ATTATTTTGGATTCTTTC
1 ATTCTTTTGAATTCTTTC
635484 ATTCTTTTGAATTCTTT
1 ATTCTTTTGAATTCTTT
635501 GTCAAATTAT
Statistics
Matches: 37, Mismatches: 14, Indels: 3
0.69 0.26 0.06
Matches are distributed among these distances:
17 11 0.30
18 18 0.49
19 8 0.22
ACGTcount: A:0.20, C:0.11, G:0.10, T:0.59
Consensus pattern (18 bp):
ATTCTTTTGAATTCTTTC
Found at i:636981 original size:3 final size:3
Alignment explanation
Indices: 636920--636965 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
636910 TATCATCATC
636920 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
636966 AGGTTACTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:643087 original size:44 final size:44
Alignment explanation
Indices: 643016--643324 Score: 246
Period size: 44 Copynumber: 6.9 Consensus size: 44
643006 AGAAGATGGC
* *
643016 AAATCTTATTTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCAA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA
* * ** ** *
643060 AAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAGTTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA
* * * ** *
643104 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCA-A
* * * * *
643149 GAATCTTATTTCCCTGAAGTTGTAGTGGAACAAATTAAAGCTATAAA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGC---CAA
* * ** * * *
643196 TCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGC-AGGTCATGGC--
1 --A-A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA
*
643241 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA
* * *
643285 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAG
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAG
643325 TTACAAGTCT
Statistics
Matches: 205, Mismatches: 49, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
41 27 0.13
42 5 0.02
43 1 0.00
44 108 0.53
45 34 0.17
48 1 0.00
50 5 0.02
51 24 0.12
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCAA
Found at i:643259 original size:41 final size:44
Alignment explanation
Indices: 643202--643315 Score: 144
Period size: 41 Copynumber: 2.7 Consensus size: 44
643192 TAAATCACAG
* * * * *
643202 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAG-GTCATGGC-A-A
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAGTAAAGCCAATA
*
643243 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAGTAAAGCCAATA
*
643287 ATCCTATCTCCCTGAAGTTGCAGTGGAGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC
643316 GAATTAAAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 29 0.46
42 4 0.06
43 1 0.02
44 29 0.46
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAGTAAAGCCAATA
Found at i:643650 original size:44 final size:44
Alignment explanation
Indices: 643602--643806 Score: 159
Period size: 44 Copynumber: 4.7 Consensus size: 44
643592 AAGTTACAAG
643602 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
* * * * ** * *** *
643646 TCTTATTTCTCTGAAATTACAGTAAAGTAGA-TCGCATCA-GG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
* * ***
643687 TCTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAGAA--ACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-AATGATGGA
* * *
643731 TCCTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAATGATGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
* * *
643775 TCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
643807 CGCATCAGAC
Statistics
Matches: 116, Mismatches: 38, Indels: 14
0.69 0.23 0.08
Matches are distributed among these distances:
41 23 0.20
42 6 0.05
43 6 0.05
44 81 0.70
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGA
Found at i:643867 original size:129 final size:129
Alignment explanation
Indices: 643596--643888 Score: 383
Period size: 129 Copynumber: 2.3 Consensus size: 129
643586 GGATTAAAGT
* *
643596 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATGATGGATCTTATTTCTCTGAA
1 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATGATGGATCTTATCTCTCTGAA
** * * * *
643661 ATTACAGTAAAGTAGATCGCATCAGGTCTTATCTCCTTGAAGTTGCAGTGGAGAAGATTGAAGA
66 ATTACAGTAAAGTAGATCGCATCAGACCTTATCTCCTTGAAATTACAGTGAAGAAGATGGAAGA
* * *
643725 AACCAA-TCCTATCTCCCTGAAGTTGCAATGGAGCAAATTAAAATGATGGATCTTATCTCTCTGA
1 TA-CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATGATGGATCTTATCTCTCTGA
* * * * *
643789 AGTTGCAGTAGAGTAGATCGCATCAGACCTTATTTCCTTGAAATTACAGTGAAATAAG-TGGAAG
65 AATTACAGTAAAGTAGATCGCATCAGACCTTATCTCCTTGAAATTACAGTG-AAGAAGATGGAAG
*
643853 C
129 A
* *
643854 TACAAGTCTTATCTCCCTAAAGTTGTAGTGGAGCA
1 TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
643889 GACTGAAGAA
Statistics
Matches: 139, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
128 3 0.02
129 129 0.93
130 7 0.05
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (129 bp):
TACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAATGATGGATCTTATCTCTCTGAA
ATTACAGTAAAGTAGATCGCATCAGACCTTATCTCCTTGAAATTACAGTGAAGAAGATGGAAGA
Found at i:644302 original size:14 final size:15
Alignment explanation
Indices: 644274--644322 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
644264 AGGGTCCGTT
*
644274 TGTTTGCTAGTAAAA
1 TGTTTTCTAGTAAAA
*
644289 TGTTTTC-CGTAAAA
1 TGTTTTCTAGTAAAA
*
644303 TGATTTCTAG-AAAA
1 TGTTTTCTAGTAAAA
644317 TGTTTT
1 TGTTTT
644323 ACTTTTCTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (15 bp):
TGTTTTCTAGTAAAA
Found at i:644335 original size:34 final size:35
Alignment explanation
Indices: 644291--644357 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
644281 TAGTAAAATG
*
644291 TTTTCCGTAAAATGATTT-CTAGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
* *
644325 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
644358 TTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:644749 original size:43 final size:43
Alignment explanation
Indices: 644688--644774 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
644678 TACTAGAAAT
* * * *
644688 TAATAATAATATTATCCAAATGCATAATTAGTAGTACACCACA
1 TAATAACAACATTATCCAAATGCATAACTAATAGTACACCACA
* * *
644731 TAATAACAACATTGTCCAAGTGCATAACTAATATTACACCACA
1 TAATAACAACATTATCCAAATGCATAACTAATAGTACACCACA
644774 T
1 T
644775 TAAAAAAGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.29
Consensus pattern (43 bp):
TAATAACAACATTATCCAAATGCATAACTAATAGTACACCACA
Found at i:657803 original size:26 final size:26
Alignment explanation
Indices: 657772--657836 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
657762 TTCAAACTTT
657772 ATTATGGTTTGTTAGCTTTTGGAAAA
1 ATTATGGTTTGTTAGCTTTTGGAAAA
657798 ATTATGGTTTGTTAGCTTTTGGAAAA
1 ATTATGGTTTGTTAGCTTTTGGAAAA
*
657824 ATTATGATTTGTT
1 ATTATGGTTTGTT
657837 TAGTTCATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.49
Consensus pattern (26 bp):
ATTATGGTTTGTTAGCTTTTGGAAAA
Found at i:658378 original size:16 final size:15
Alignment explanation
Indices: 658352--658382 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
658342 TTTTAGAAAC
658352 ACTTTGTATATGATA
1 ACTTTGTATATGATA
658367 ACTTTAGTATATGATA
1 ACTTT-GTATATGATA
658383 TGACCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
ACTTTGTATATGATA
Found at i:658427 original size:7 final size:7
Alignment explanation
Indices: 658415--658439 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
658405 AAGAAAATGT
658415 GTTTAAA
1 GTTTAAA
658422 GTTTAAA
1 GTTTAAA
658429 GTTTAAA
1 GTTTAAA
658436 GTTT
1 GTTT
658440 GTATATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (7 bp):
GTTTAAA
Found at i:658490 original size:12 final size:12
Alignment explanation
Indices: 658473--658498 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
658463 ACACGTGAGT
658473 TGCATCTAGCAA
1 TGCATCTAGCAA
658485 TGCATCTAGCAA
1 TGCATCTAGCAA
658497 TG
1 TG
658499 AGTGGCATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (12 bp):
TGCATCTAGCAA
Found at i:676250 original size:37 final size:37
Alignment explanation
Indices: 676182--676265 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
676172 TGCCACATAT
* *
676182 TGGTTTGATTAGATGGATGGACTCTATTAGTCCAATA
1 TGGTGTGATTAGATGGATCGACTCTATTAGTCCAATA
*
676219 TGGTGTGATTAGATGGATCGACTAT-TATAGTCCAATA
1 TGGTGTGATTAGATGGATCGACTCTAT-TAGTCCAATA
676256 TGGTGTGATT
1 TGGTGTGATT
676266 GGTTGGACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 1 0.02
37 42 0.98
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (37 bp):
TGGTGTGATTAGATGGATCGACTCTATTAGTCCAATA
Found at i:707463 original size:24 final size:24
Alignment explanation
Indices: 707436--707486 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
707426 TGGGTAAGGT
* * *
707436 ATATACATATATTTGAAATGAATA
1 ATATACATAAACTTGAAATAAATA
*
707460 ATATATATAAACTTGAAATAAATA
1 ATATACATAAACTTGAAATAAATA
707484 ATA
1 ATA
707487 ATAAATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
ATATACATAAACTTGAAATAAATA
Found at i:709053 original size:44 final size:44
Alignment explanation
Indices: 708983--709099 Score: 164
Period size: 44 Copynumber: 2.7 Consensus size: 44
708973 TGGTTTTAGT
* * *
708983 CTGCTCCACTACAACTTTAGGGAGATAAGACTTGTATCTTCAAC
1 CTGCTCCACTGCAACTCTAGGAAGATAAGACTTGTATCTTCAAC
709027 CTGCTCCACTGCAACGTCT-GGAAGATAAGACTTGTATCTTCAAC
1 CTGCTCCACTGCAAC-TCTAGGAAGATAAGACTTGTATCTTCAAC
* * *
709071 CTGCTCCATTGCAACTTTAGGGAGATAAG
1 CTGCTCCACTGCAACTCTAGGAAGATAAG
709100 GTTTGATATG
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
43 2 0.03
44 61 0.94
45 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
CTGCTCCACTGCAACTCTAGGAAGATAAGACTTGTATCTTCAAC
Found at i:709258 original size:44 final size:44
Alignment explanation
Indices: 709160--709689 Score: 235
Period size: 44 Copynumber: 12.2 Consensus size: 44
709150 GATTCATCGT
* * * *
709160 TTTAATCCGCTCCACTGCAACTTCA-AGGAGATAGGATTAGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAGA-GAGATAAGATTGGTATC
*
709204 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGGTATC
1 TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGGTATC
* ** * * * * *
709248 TTTAACCTGCTTAACTACAACTTTAGTGAGATAAAACTT-GTAGC
1 TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGGTATC
* * ** * * * * *
709292 TTCAA-CTTGTTTTACTGCATCTTTA-AGAAAATAAAATTTGGT-GC
1 TTTAATC-TGCTCCACTGCAACTTCAGAG-AGATAAGA-TTGGTATC
** * * ***
709336 ---GGTCTGCTCTACTGCAACTTCAAAGAGATAAGATCCATAT-
1 TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGGTATC
* * *
709376 TTTAAT-TCGCTTCACTGCAACTTCAG-GAAGATAGGATTGGTTTC
1 TTTAATCT-GCTCCACTGCAACTTCAGAG-AGATAAGATTGGTATC
* * * *
709420 TTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGACTGG-ATGC
1 TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGGTAT-C
* * * ** * *
709464 ---GATCTGCTCTACTACAACTTCAGAGAGATAAGATCTATTTTT
1 TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGGTATC
* * * *
709506 TTTAATCTGCTCCACTGCAACTTTAGCGACG-TAGGATTGGTTTC
1 TTTAATCTGCTCCACTGCAACTTCAGAGA-GATAAGATTGGTATC
* * *
709550 TTCT-GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGG-ATGC
1 TT-TAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGGTAT-C
* * *
709594 ---AATCTGCTCTACTGAAACTTCAGAGAGATAAGATCT-GTGGT-
1 TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGGT-ATC
* * * *
709635 TTTAATCTACTCCACTGCAACTTTAGGGAGATAGGATTGGCT-TC
1 TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGG-TATC
*
709679 TTTGATCTGCT
1 TTTAATCTGCT
709690 TCGCCGTCAG
Statistics
Matches: 361, Mismatches: 89, Indels: 72
0.69 0.17 0.14
Matches are distributed among these distances:
40 2 0.01
41 77 0.21
42 7 0.02
43 35 0.10
44 204 0.57
45 35 0.10
46 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGGTATC
Found at i:709559 original size:130 final size:128
Alignment explanation
Indices: 709333--709689 Score: 463
Period size: 130 Copynumber: 2.8 Consensus size: 128
709323 TAAAATTTGG
* * * * *
709333 TGCGGTCTGCTCTACTGCAACTTCAAAGAGATAAGATCCA-TATTTTAAT-TCGCTTCACTGCAA
1 TGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTATTATTTTAATCT-GCTCCACTGCAA
* ** *
709396 CTTCAGGAAGATAGGATTGGTTTCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGACTGGA
65 CTTTAGG-AGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGA
*
709461 TGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTATTTTTTTTAATCTGCTCCACTGCAA
1 TGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTA-TTATTTTAATCTGCTCCACTGCAA
709526 CTTTAGCGACG-TAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGG
65 CTTTAG-GA-GATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGG
709590 A
128 A
* * ** *
709591 TGCAATCTGCTCTACTGA-AACTTCAGAGAGATAAGATCTGTGGTTTTAATCTACTCCACTGCAA
1 TGCGATCTGCTCTACT-ACAACTTCAGAGAGATAAGATCTATTATTTTAATCTGCTCCACTGCAA
*
709655 CTTTAGGGAGATAGGATTGGCTTCTT-TGATCTGCT
65 CTTTA-GGAGATAGGATTGGTTTCTTCTG-TCTGCT
709690 TCGCCGTCAG
Statistics
Matches: 204, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
128 39 0.19
129 48 0.24
130 113 0.55
131 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (128 bp):
TGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTATTATTTTAATCTGCTCCACTGCAAC
TTTAGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGA
Found at i:709787 original size:44 final size:45
Alignment explanation
Indices: 709683--710070 Score: 354
Period size: 44 Copynumber: 8.7 Consensus size: 45
709673 GGCTTCTTTG
* * * *
709683 ATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCCGCTATCTTCA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGCTGGTATCTTCA
* * * *
709728 GTATGCTTCACTGTCAGTACAGGAAGGCAAG-GCTGGTGTCTTCA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGCTGGTATCTTCA
* * * *
709772 ATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTTA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGCTGGTATCTTCA
* * * *
709817 GTCTGCTCCGTTGTCAGTACAGGAAGGCAAG-GCTGGTATCTTCG
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGCTGGTATCTTCA
* * ** * *
709861 ATCTGTTTCGCTGTTAGTACAGGAAGGCAAGATTTGCTATATTCA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGCTGGTATCTTCA
* * * * * * *
709906 GTCTGCTCCACTGTCAGTACAGAAAAGCAAG-GCTGGTGTCTTCG
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGCTGGTATCTTCA
* * * **
709950 ATCTGCTTTGCTGTTAGTACAGGAAGGCAAGATCTACTATCTTCA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGCTGGTATCTTCA
* * * * * * *
709995 GTCTGCTCCGCTGCCAGTA-TGAGAAGGTAAG-GCTGGTGTCTTCG
1 ATCTGCTTCGCTGTCAGTACAG-GAAGGCAAGAGCTGGTATCTTCA
*
710039 ATCTGCTTCGCTGTCAGTATAGGAAGGCAAGA
1 ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGA
710071 TTCGCTATCT
Statistics
Matches: 261, Mismatches: 76, Indels: 12
0.75 0.22 0.03
Matches are distributed among these distances:
44 135 0.52
45 126 0.48
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (45 bp):
ATCTGCTTCGCTGTCAGTACAGGAAGGCAAGAGCTGGTATCTTCA
Found at i:709799 original size:89 final size:89
Alignment explanation
Indices: 709677--710083 Score: 548
Period size: 89 Copynumber: 4.6 Consensus size: 89
709667 AGGATTGGCT
* * * * *
709677 TCTTTGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCCGCTATCTTCAGTATGCTTCACTGT
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGT
709742 CAGTACAGGAAGGCAAGGCTGGTG
66 CAGTACAGGAAGGCAAGGCTGGTG
* * * * **
709766 TCTTCAATCTACTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATCTTTAGTCTGCTCCGTTGT
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGT
*
709831 CAGTACAGGAAGGCAAGGCTGGTA
66 CAGTACAGGAAGGCAAGGCTGGTG
* * * *
709855 TCTTCGATCTGTTTCGCTGTTAGTACAGGAAGGCAAGATTTGCTATATTCAGTCTGCTCCACTGT
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGT
* *
709920 CAGTACAGAAAAGCAAGGCTGGTG
66 CAGTACAGGAAGGCAAGGCTGGTG
* * * * *
709944 TCTTCGATCTGCTTTGCTGTTAGTACAGGAAGGCAAGATCTACTATCTTCAGTCTGCTCCGCTGC
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGT
* *
710009 CAGTA-TGAGAAGGTAAGGCTGGTG
66 CAGTACAG-GAAGGCAAGGCTGGTG
*
710033 TCTTCGATCTGCTTCGCTGTCAGTATAGGAAGGCAAGAT-TCGCTATCTTCA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCT-GCTATCTTCA
710084 TTGATCTTTT
Statistics
Matches: 276, Mismatches: 40, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
88 2 0.01
89 274 0.99
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (89 bp):
TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGT
CAGTACAGGAAGGCAAGGCTGGTG
Found at i:710384 original size:24 final size:24
Alignment explanation
Indices: 710357--710413 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
710347 GGATTTCCCA
*
710357 CACTGTAATCTTCAAAGTTTAATC
1 CACTGTAATCTTCAAAGTTCAATC
* *
710381 CACTATAATCTTCAAGGTTCAATC
1 CACTGTAATCTTCAAAGTTCAATC
710405 CACTGTAAT
1 CACTGTAAT
710414 TTTGGGACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (24 bp):
CACTGTAATCTTCAAAGTTCAATC
Found at i:711320 original size:19 final size:19
Alignment explanation
Indices: 711294--711346 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
711284 TTGGCCTCTG
711294 CTTTTTCTTTTTTCGTTCTT
1 CTTTTTCTTTTTT-GTTCTT
*
711314 C-TTTTCTTTTCTTTTTCTT
1 CTTTTTCTTTT-TTGTTCTT
711333 CTTGTTTCTTTTTT
1 CTT-TTTCTTTTTT
711347 TTCAAGTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 15 0.52
20 6 0.21
21 8 0.28
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (19 bp):
CTTTTTCTTTTTTGTTCTT
Found at i:716488 original size:24 final size:23
Alignment explanation
Indices: 716461--716507 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
716451 AAATCAATTA
716461 TATG-CAAAACAATTTTAGAAATAC
1 TATGACAAAA-AATTTTA-AAATAC
716485 TATGTACAAAAAATTTTAAAATA
1 TATG-ACAAAAAATTTTAAAATA
716508 AATAATATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 9 0.43
25 7 0.33
26 5 0.24
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (23 bp):
TATGACAAAAAATTTTAAAATAC
Found at i:718161 original size:18 final size:18
Alignment explanation
Indices: 718112--718165 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
718102 ATTCACCTAA
*
718112 ACCCAATCTAAACCCAAGT
1 ACCCAATCT-AACCCAATT
** * *
718131 ATTCAACCCAACCCAATT
1 ACCCAATCTAACCCAATT
718149 ACCCAATCTAACCCAAT
1 ACCCAATCTAACCCAAT
718166 CATAAAAATT
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.41, C:0.39, G:0.02, T:0.19
Consensus pattern (18 bp):
ACCCAATCTAACCCAATT
Found at i:718278 original size:9 final size:9
Alignment explanation
Indices: 718261--718327 Score: 98
Period size: 9 Copynumber: 7.4 Consensus size: 9
718251 TGTATGATTC
*
718261 AATTAGGTT
1 AATTCGGTT
718270 AATTCGGTT
1 AATTCGGTT
*
718279 AATTCGGGT
1 AATTCGGTT
*
718288 AATTCGGGT
1 AATTCGGTT
*
718297 AATTCGGGT
1 AATTCGGTT
718306 AATTCGGTT
1 AATTCGGTT
718315 AATTCGGTT
1 AATTCGGTT
718324 AATT
1 AATT
718328 TTTAACCAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:724649 original size:45 final size:45
Alignment explanation
Indices: 724593--724723 Score: 235
Period size: 45 Copynumber: 2.9 Consensus size: 45
724583 TACTATGTGA
* * *
724593 ACCGAACATCATTAATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGATTCC
724638 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGATTCC
724683 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGA
1 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGA
724724 ATCTACCGAG
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 83 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGATTCC
Found at i:727820 original size:18 final size:18
Alignment explanation
Indices: 727797--727832 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
727787 GTGGACACAA
727797 AAGCTACCATCACTTACT
1 AAGCTACCATCACTTACT
727815 AAGCTACCATCACTTACT
1 AAGCTACCATCACTTACT
727833 CTATCATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.28
Consensus pattern (18 bp):
AAGCTACCATCACTTACT
Found at i:732648 original size:88 final size:87
Alignment explanation
Indices: 732545--732719 Score: 237
Period size: 88 Copynumber: 2.0 Consensus size: 87
732535 ATTAAGTCCC
* *
732545 TTTTTTCCACTCAATTGAGCACTTGGACTTTCAAAATGTATCAAAAAGAC-CTTCGAACTTCTTT
1 TTTTTTCCACTCAATTGAGCACATGAACTTTCAAAATGTATCAAAAAGACAC-TC-AACTTCTTT
732609 AAAAAAAGCAATTAATCCC-CTGCT
64 AAAAAAAGCAATTAA-CCCTCTGCT
* * * * * *
732633 TTTTTTTCACTCAATTGGGTACATGAACTTTCAAAATGTATCAAAAAGACACTCAATTTTTTTCA
1 TTTTTTCCACTCAATTGAGCACATGAACTTTCAAAATGTATCAAAAAGACACTCAACTTCTTTAA
732698 AAAAAGCAATTAACCCTCTGCT
66 AAAAAGCAATTAACCCTCTGCT
732720 CTTATTAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
86 3 0.04
87 26 0.34
88 47 0.61
89 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (87 bp):
TTTTTTCCACTCAATTGAGCACATGAACTTTCAAAATGTATCAAAAAGACACTCAACTTCTTTAA
AAAAAGCAATTAACCCTCTGCT
Found at i:732912 original size:56 final size:59
Alignment explanation
Indices: 732852--732973 Score: 153
Period size: 56 Copynumber: 2.1 Consensus size: 59
732842 ATTTACGAAA
* *
732852 TTTATATTTCTTTACATTTTGT-A-TTTCTTATGAC-TTTATAAAAAATTT-TAATTTTT
1 TTTATATTTCTATACATTTTGTAATTTTCTTATGACTTTTAT-AAAAATTTACAATTTTT
* * *
732908 TTTATATTTCTATATATTTTGTAATTTTTTTATGGCTTTTATAAAAATTTACAATTTTT
1 TTTATATTTCTATACATTTTGTAATTTTCTTATGACTTTTATAAAAATTTACAATTTTT
*
732967 TATATAT
1 TTTATAT
732974 ATTTTACTAC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
56 20 0.36
57 1 0.02
58 17 0.30
59 18 0.32
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.61
Consensus pattern (59 bp):
TTTATATTTCTATACATTTTGTAATTTTCTTATGACTTTTATAAAAATTTACAATTTTT
Found at i:733015 original size:20 final size:18
Alignment explanation
Indices: 732990--733036 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
732980 CTACTTTTAT
732990 ATTTTTTCTAATTTTTAATA
1 ATTTTTT-TAATTTTTAA-A
* *
733010 ATTTTTTTTATTTTTGAA
1 ATTTTTTTAATTTTTAAA
733028 ATTTTTTTA
1 ATTTTTTTA
733037 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
20 7 0.29
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTTTTTTAATTTTTAAA
Found at i:733243 original size:87 final size:88
Alignment explanation
Indices: 733104--733324 Score: 241
Period size: 87 Copynumber: 2.5 Consensus size: 88
733094 TAAAAGCAGT
* * * *
733104 GGCTTAATTGCTTTTTTTGAAAATATTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTACT
1 GGCTTAATTGCTTTTTTTGAAAAGATTTGAAGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
* *
733169 CAATTGAGTGCAGAAAAAAGTACA
66 CAAATGAGTCCA-AAAAAAGTACA
* * *
733193 GGCTTAATTGC-TTTTTTGAAAAGGTTT-AAGGTTTTTTTTATGCATTTTGAAAGTTCAAGTACC
1 GGCTTAATTGCTTTTTTTGAAAAGATTTGAAGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
*
733256 CAAATGAGTCCAAAAAAAGAAAAAGCAA
66 CAAATGAGTCCAAAAAAAG---TA-C-A
* * *
733284 TGGCTTAATTACTTTTTTTGAAAAAATTTG-AGGGCTTTTTG
1 -GGCTTAATTGCTTTTTTTGAAAAGATTTGAAGGTCTTTTTG
733325 CACCCTGAAG
Statistics
Matches: 108, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
86 7 0.06
87 41 0.38
88 14 0.13
89 12 0.11
90 1 0.01
91 1 0.01
92 10 0.09
93 22 0.20
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (88 bp):
GGCTTAATTGCTTTTTTTGAAAAGATTTGAAGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACC
CAAATGAGTCCAAAAAAAGTACA
Found at i:734567 original size:6 final size:6
Alignment explanation
Indices: 734527--734556 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
734517 AGTAACCTCA
734527 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
734557 ATGCTTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:744047 original size:68 final size:68
Alignment explanation
Indices: 743957--744527 Score: 615
Period size: 68 Copynumber: 8.4 Consensus size: 68
743947 GAGGTTTAAG
* * * * *
743957 GTGTAAGACCATAACTCAGCTATGGAAACATGTGGAGTCTACTAGGACATTAAACATTAGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
744022 ATT
66 ATT
* *
744025 GTGTAAGACCATAGCCCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
744090 ATT
66 ATT
** ** ** *
744093 GTGTAAGACCATAGCTCAACTATGGCAACACATGGAGTCCGCTAGGACATTAAACATTGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
744158 ATT
66 ATT
* * *
744161 CTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
744226 ATT
66 ATT
* ** * ** *
744229 GTGTAAGATCATAGCTCGAATATGGCAACATGTAGAGTCCGCTAGGACATTAAACA-TGGGTTTA
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGG-TTA
*
744293 CACT
65 CATT
* * * * * *
744297 GTGTAAGATCATAGCTTGGCTATGGAAATATGTGGAGTGTGCCAGGACATTAAACA-TGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
*
744361 AAT
66 ATT
* ** * ** * *
744364 GTGTAAGATCATAGCTCGATTACGAAAACATGTGGAGTCCACCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
744429 ATT
66 ATT
* ** *** * * * * * *
744432 GTGTAAGACCGTAAATTAACTATGGCAACATGTAGAGTTTGCCAAGACATTAAACATGGGGCTAC
1 GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
*
744497 AAT
66 ATT
* * *
744500 GTGTAAAACCATAGCTCGACTGTGGCAA
1 GTGTAAGACCATAGCTCGGCTATGGCAA
744528 AGTATGGAGC
Statistics
Matches: 419, Mismatches: 82, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
67 56 0.13
68 363 0.87
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (68 bp):
GTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATTGGGTTAC
ATT
Found at i:744201 original size:136 final size:136
Alignment explanation
Indices: 743957--744527 Score: 698
Period size: 136 Copynumber: 4.2 Consensus size: 136
743947 GAGGTTTAAG
* * * * *
743957 GTGTAAGACCATAACTCAGCTATGGAAACATGTGGAGTCTACTAGGACATTAAACATTAGGTTAC
1 GTGTAAGACCATAGCTCAACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
* *
744022 ATTGTGTAAGACCATAGCCCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGT
66 ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
*
744087 TACATT
131 TACAAT
** *
744093 GTGTAAGACCATAGCTCAACTATGGCAACACATGGAGTCCGCTAGGACATTAAACATTGGGTTAC
1 GTGTAAGACCATAGCTCAACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
*
744158 ATTCTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
66 ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
*
744223 TACATT
131 TACAAT
* * *
744229 GTGTAAGATCATAGCTCGAA-TATGGCAACATGTAGAGTCCGCTAGGACATTAAACA-TGGGTTT
1 GTGTAAGACCATAGCTC-AACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGG-TT
* * * * * * * *
744292 ACACTGTGTAAGATCATAGCTTGGCTATGGAAATATGTGGAGTGTGCCAGGACATTAAACAT-GG
64 ACATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGG
744356 GTTACAAT
129 GTTACAAT
* * * * ** * *
744364 GTGTAAGATCATAGCTCGATTACGAAAACATGTGGAGTCCACCAGGACATTAAACATGGGGTTAC
1 GTGTAAGACCATAGCTCAACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
* ** *** * * * *
744429 ATTGTGTAAGACCGTAAATTAACTATGGCAACATGTAGAGTTTGCCAAGACATTAAACATGGGGC
66 ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
744494 TACAAT
131 TACAAT
* * *
744500 GTGTAAAACCATAGCTCGACTGTGGCAA
1 GTGTAAGACCATAGCTCAACTATGGCAA
744528 AGTATGGAGC
Statistics
Matches: 377, Mismatches: 53, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
134 1 0.00
135 112 0.30
136 262 0.69
137 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (136 bp):
GTGTAAGACCATAGCTCAACTATGGCAACATGTGGAGTCCACTAGGACATTAAACATTGGGTTAC
ATTGTGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGT
TACAAT
Found at i:744312 original size:204 final size:203
Alignment explanation
Indices: 743958--744527 Score: 701
Period size: 204 Copynumber: 2.8 Consensus size: 203
743948 AGGTTTAAGG
* * * **
743958 TGTAAGACCATAACTCAGCTATGGAAACATGTGGAGTCTACTAGGACATTAAACATTAGGTTACA
1 TGTAAGACCATAGCTCGGCTATGGAAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTACA
* ** * *
744023 TTGTGTAAGACCATAGCCCGGCTATGGCAACATGTGGAGTCTACCAGGACATTAAACATGGGGTT
66 TTGTGTAAGACCATAGCTCGAATATGGCAACATGTAGAGTCTGCCAGGACATTAAACATGGGGTT
* * *
744088 ACATTGTGTAAGACCATAGCTCAACTATGGCAACACATGGAGTCCGCTAGGACATTAAACATTGG
131 ACAATGTGTAAGACCATAGCTCGACTATGGCAACACATGGAGTCCGCCAGGACATTAAACA-TGG
*
744153 GTTACATTC
195 GTTACAATC
* *
744162 TGTAAGACCATAGCTCGGCTATGGCAACATGTGGAGTCTACCAAGACATTAAACATGGGGTTACA
1 TGTAAGACCATAGCTCGGCTATGGAAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTACA
* * * *
744227 TTGTGTAAGATCATAGCTCGAATATGGCAACATGTAGAGTCCGCTAGGACATTAAACATGGGTTT
66 TTGTGTAAGACCATAGCTCGAATATGGCAACATGTAGAGTCTGCCAGGACATTAAACATGGGGTT
* * * * * * ** **
744292 ACACTGTGTAAGATCATAGCTTGGCTATGGAAATATGTGGAGTGTGCCAGGACATTAAACATGGG
131 ACAATGTGTAAGACCATAGCTCGACTATGGCAACACATGGAGTCCGCCAGGACATTAAACATGGG
*
744357 TTACAATG
196 TTACAATC
* ** * * *
744365 TGTAAGATCATAGCTCGATTACGAAAACATGTGGAGTCCACCAGGACATTAAACATGGGGTTACA
1 TGTAAGACCATAGCTCGGCTATGGAAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTACA
* ** * * * *
744430 TTGTGTAAGACCGTAAAT-TAACTATGGCAACATGTAGAGTTTGCCAAGACATTAAACATGGGGC
66 TTGTGTAAGACCATAGCTCGAA-TATGGCAACATGTAGAGTCTGCCAGGACATTAAACATGGGGT
* *
744494 TACAATGTGTAAAACCATAGCTCGACTGTGGCAA
130 TACAATGTGTAAGACCATAGCTCGACTATGGCAA
744528 AGTATGGAGC
Statistics
Matches: 309, Mismatches: 56, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
202 2 0.01
203 144 0.47
204 163 0.53
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (203 bp):
TGTAAGACCATAGCTCGGCTATGGAAACATGTGGAGTCTACCAGGACATTAAACATGGGGTTACA
TTGTGTAAGACCATAGCTCGAATATGGCAACATGTAGAGTCTGCCAGGACATTAAACATGGGGTT
ACAATGTGTAAGACCATAGCTCGACTATGGCAACACATGGAGTCCGCCAGGACATTAAACATGGG
TTACAATC
Found at i:752179 original size:21 final size:19
Alignment explanation
Indices: 752153--752201 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
752143 TGTAAAAGAC
752153 TAATGATTCCCTTCAGTGGTA
1 TAATGATTCCCTT-AG-GGTA
*
752174 TAATGATATTCCCTTTGGGTA
1 TAATG--ATTCCCTTAGGGTA
752195 TAATGAT
1 TAATGAT
752202 ATCCAAGCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
21 14 0.56
22 1 0.04
23 8 0.32
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (19 bp):
TAATGATTCCCTTAGGGTA
Found at i:752187 original size:23 final size:21
Alignment explanation
Indices: 752158--752203 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
752148 AAGACTAATG
752158 ATTCCCTTCAGTGGTATAATGAT
1 ATTCCCTT-AG-GGTATAATGAT
*
752181 ATTCCCTTTGGGTATAATGAT
1 ATTCCCTTAGGGTATAATGAT
752202 AT
1 AT
752204 CCAAGCCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.59
22 1 0.05
23 8 0.36
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (21 bp):
ATTCCCTTAGGGTATAATGAT
Found at i:754111 original size:15 final size:15
Alignment explanation
Indices: 754091--754120 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
754081 TTCCAAATGA
754091 TTTCATTTTCTCCAT
1 TTTCATTTTCTCCAT
*
754106 TTTCATTTTGTCCAT
1 TTTCATTTTCTCCAT
754121 GCAATTCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTCATTTTCTCCAT
Found at i:755579 original size:239 final size:239
Alignment explanation
Indices: 755154--755615 Score: 728
Period size: 239 Copynumber: 1.9 Consensus size: 239
755144 GATATGAGCT
*
755154 TGTGTCTATTCCATGTTGTATGAACCCGTAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
1 TGTGTCTATTCCATGTTGTATGAACCCATAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
* *
755219 TGTATGTATGTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
66 TGCATATATGTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
* * *
755284 ATAGAAATAAATACAATATATTGCATGAAATGCTTTTATGTATATGATGAGGAGAAAGGAGGAAT
131 ATAGAAATAAATACAATAAATTGCATGAAATGCTTGTATGAATATGATGAGGAGAAAGGAGGAAT
755349 ATACTTTGATGGGGTAGTTAAAGATAGGAACACTTTGATGAGTC
196 ATACTTTGATGGGGTAGTTAAAGATAGGAACACTTTGATGAGTC
* * * *
755393 TGTGTCTATTTCGTGTTGTATGAACCCATAGTTGTGTATGAACCTGGTGACTGAGTATGCTTGCA
1 TGTGTCTATTCCATGTTGTATGAACCCATAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
* * * * *
755458 TGCATATATGTTGGATGTTTATTTAGTTATAATTTGAAGTGTTAATGGGTGGTGTATTGTATGCT
66 TGCATATATGTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
* * *
755523 ATAGAAATAAATACAATAAATTG-ATTGAAATGCTTGTATGAATATGATGCGGAGAAATGAGGGA
131 ATAGAAATAAATACAATAAATTGCA-TGAAATGCTTGTATGAATATGATGAGGAGAAAGGAGGAA
* *
755587 TATACTTTGATGGGGTGGTTGAAGATAGG
195 TATACTTTGATGGGGTAGTTAAAGATAGG
755616 TGAAAGCTCG
Statistics
Matches: 202, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
238 1 0.00
239 201 1.00
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (239 bp):
TGTGTCTATTCCATGTTGTATGAACCCATAGTTGTGTATAAACCTGGTGACTAAGTATGCTTGCA
TGCATATATGTCGAATGTTTATTTAGTTATAAATTGAAGTGTTAATGGGTGGCGTACTGTATGCT
ATAGAAATAAATACAATAAATTGCATGAAATGCTTGTATGAATATGATGAGGAGAAAGGAGGAAT
ATACTTTGATGGGGTAGTTAAAGATAGGAACACTTTGATGAGTC
Found at i:758231 original size:21 final size:20
Alignment explanation
Indices: 758186--758231 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
758176 TTGTTGGAAT
758186 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
758205 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
758226 GGTTGA
1 GGTTGA
758232 TTGCATTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:765203 original size:50 final size:50
Alignment explanation
Indices: 765087--765278 Score: 208
Period size: 50 Copynumber: 3.8 Consensus size: 50
765077 GATAACAACA
* * * ** * *
765087 TGCCAAAGCCATGTCCCAGACATGATCTTATATGGGATGTTCTCATATCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
765138 TGTCC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TG-CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
765188 TGCCAACGCCATGTCCCAAACACGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** *
765238 AT-TTAACGCCATGTCCCAGACATGGTCTTACATAGGACCTC
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
765279 ATTACCCAAA
Statistics
Matches: 119, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
49 2 0.02
50 85 0.71
51 30 0.25
52 2 0.02
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:771908 original size:11 final size:11
Alignment explanation
Indices: 771888--772006 Score: 71
Period size: 11 Copynumber: 11.4 Consensus size: 11
771878 CAAAAATTAA
771888 AAAAAGTATTTT
1 AAAAA-TATTTT
771900 AAAAATATTTT
1 AAAAATATTTT
771911 --AAA-A--TT
1 AAAAATATTTT
* * *
771917 AAAAAAAATTA
1 AAAAATATTTT
771928 AAAAAGTATTTTT
1 AAAAA-TA-TTTT
771941 AAAAA-A-TTT
1 AAAAATATTTT
771950 -AAAA-A-TTT
1 AAAAATATTTT
771958 AAAAA-ATTTT
1 AAAAATATTTT
771968 AAAAAAGTATTTT
1 -AAAAA-TATTTT
*
771981 AAAAGTATTTT
1 AAAAATATTTT
*
771992 AAAAGTATTTT
1 AAAAATATTTT
772003 AAAA
1 AAAA
772007 TTAAAAAAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 25
0.75 0.04 0.21
Matches are distributed among these distances:
6 2 0.02
8 12 0.13
9 12 0.13
10 3 0.03
11 39 0.43
12 10 0.11
13 12 0.13
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:771931 original size:41 final size:40
Alignment explanation
Indices: 771855--771995 Score: 176
Period size: 41 Copynumber: 3.4 Consensus size: 40
771845 ATAAATACCA
771855 AAAAATTATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTT
1 AAAAA-TATTTT-AAAATT-AAA-AAAAATT-AAAAAAGTATTTT
771900 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTT
1 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAGTA-TTTT
* **
771941 AAAAA-ATTTAAAAATTTAAAAAATTTTAAAAAAGTATTTT
1 AAAAATATTTTAAAA-TTAAAAAAAATTAAAAAAGTATTTT
*
771981 AAAAGTATTTTAAAA
1 AAAAATATTTTAAAA
771996 GTATTTTAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
40 25 0.28
41 43 0.49
42 3 0.03
43 6 0.07
44 6 0.07
45 5 0.06
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (40 bp):
AAAAATATTTTAAAATTAAAAAAAATTAAAAAAGTATTTT
Found at i:771960 original size:17 final size:18
Alignment explanation
Indices: 771938--771972 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
771928 AAAAAGTATT
771938 TTTAAAAAA-TTTAAAAA
1 TTTAAAAAATTTTAAAAA
771955 TTTAAAAAATTTTAAAAA
1 TTTAAAAAATTTTAAAAA
771973 AGTATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTAAAAAATTTTAAAAA
Found at i:771963 original size:10 final size:10
Alignment explanation
Indices: 771911--771973 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
771901 AAAATATTTT
771911 AAAA-TTAAA
1 AAAATTTAAA
*
771920 AAAAATTAAA
1 AAAATTTAAA
*
771930 AAAGTATTTTTAA
1 AAA--A-TTTAAA
771943 AAAATTT--A
1 AAAATTTAAA
771951 AAAATTTAAA
1 AAAATTTAAA
*
771961 AAATTTTAAA
1 AAAATTTAAA
771971 AAA
1 AAA
771974 GTATTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 8 0.18
9 4 0.09
10 24 0.53
11 1 0.02
12 1 0.02
13 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:776023 original size:8 final size:8
Alignment explanation
Indices: 776010--776041 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
776000 TTTTCAGATC
776010 TTATTATT
1 TTATTATT
776018 TTATTATT
1 TTATTATT
776026 TTATTATT
1 TTATTATT
776034 TTATTATT
1 TTATTATT
776042 CTGAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTATT
Found at i:782845 original size:9 final size:8
Alignment explanation
Indices: 782816--782866 Score: 59
Period size: 9 Copynumber: 6.0 Consensus size: 8
782806 CTAATCTTTG
782816 ATTTA-TT
1 ATTTATTT
782823 ATTCTATTTT
1 ATT-TA-TTT
782833 ATTTATCTT
1 ATTTAT-TT
782842 ATTTATTT
1 ATTTATTT
782850 ATCTTATTT
1 AT-TTATTT
782859 ATTTATTT
1 ATTTATTT
782867 TGACTTGGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.08
8 13 0.33
9 18 0.46
10 5 0.13
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (8 bp):
ATTTATTT
Found at i:782846 original size:13 final size:13
Alignment explanation
Indices: 782830--782864 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
782820 ATTATTCTAT
782830 TTTATTTATCTTA
1 TTTATTTATCTTA
782843 TTTATTTATCTTA
1 TTTATTTATCTTA
782856 TTTATTTAT
1 TTTATTTAT
782865 TTTGACTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTATCTTA
Found at i:782847 original size:4 final size:4
Alignment explanation
Indices: 782816--782866 Score: 59
Period size: 4 Copynumber: 12.0 Consensus size: 4
782806 CTAATCTTTG
782816 ATTT A-TT ATTCT ATTTT ATTT ATCTT ATTT ATTT ATCTT ATTT ATTT
1 ATTT ATTT ATT-T A-TTT ATTT AT-TT ATTT ATTT AT-TT ATTT ATTT
782863 ATTT
1 ATTT
782867 TGACTTGGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
3 3 0.07
4 25 0.60
5 12 0.29
6 2 0.05
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:783320 original size:14 final size:14
Alignment explanation
Indices: 783262--783320 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
783252 TAAATTACAT
*
783262 TAGCCCAACAAGCC
1 TAGCCCAACTAGCC
* *
783276 TAAACCCAATTAGCC
1 T-AGCCCAACTAGCC
*
783291 TAAGCCCAA-TACCC
1 T-AGCCCAACTAGCC
783305 TAGCCCAACTAGCC
1 TAGCCCAACTAGCC
783319 TA
1 TA
783321 AACCAGAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 7 0.19
14 12 0.32
15 18 0.49
ACGTcount: A:0.36, C:0.39, G:0.10, T:0.15
Consensus pattern (14 bp):
TAGCCCAACTAGCC
Found at i:784463 original size:20 final size:20
Alignment explanation
Indices: 784440--784488 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
784430 TTGTTTAAGT
* *
784440 TTAATATATTTTTAATTTTA
1 TTAATATATTTTCAATATTA
784460 TTAATACTA-TTTCAATATTA
1 TTAATA-TATTTTCAATATTA
784480 -TAATATATT
1 TTAATATATT
784489 ATTATTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 15 0.60
21 2 0.08
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATATATTTTCAATATTA
Found at i:789774 original size:3 final size:3
Alignment explanation
Indices: 789766--789791 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
789756 AATTTATAAT
789766 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
789792 TCAAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:792721 original size:23 final size:23
Alignment explanation
Indices: 792695--792766 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
792685 TGTTTGTTTG
792695 ATAAAGAAATATTACTATTTTTT
1 ATAAAGAAATATTACTATTTTTT
* * *
792718 ATAAAGTAGTATTACT-GTTTTT
1 ATAAAGAAATATTACTATTTTTT
792740 ATAAA-ATATATATATAACTATTTTTT
1 ATAAAGA-A-ATAT-T-ACTATTTTTT
792766 A
1 A
792767 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
22 11 0.29
23 17 0.45
24 1 0.03
25 3 0.08
26 6 0.16
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (23 bp):
ATAAAGAAATATTACTATTTTTT
Found at i:794519 original size:15 final size:16
Alignment explanation
Indices: 794487--794520 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
794477 CCTTTTTCCA
*
794487 TTAAAATATTATTTTT
1 TTAAAATATTATTATT
794503 TTAAAAT-TTATTATT
1 TTAAAATATTATTATT
794518 TTA
1 TTA
794521 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAAAATATTATTATT
Found at i:794626 original size:22 final size:22
Alignment explanation
Indices: 794600--794642 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
794590 AACATTTTAA
*
794600 ATATTACATGTACCTTTTATTG
1 ATATTACATGTACATTTTATTG
794622 ATATTACATGTACATTTTATT
1 ATATTACATGTACATTTTATT
794643 AAAAGACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (22 bp):
ATATTACATGTACATTTTATTG
Found at i:795491 original size:19 final size:17
Alignment explanation
Indices: 795456--795497 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
795446 GTTTTTTCAC
795456 AAAA-ATATATATATTA
1 AAAATATATATATATTA
795472 AAAATATATATTATATTTA
1 AAAATATATA-TATA-TTA
795491 AAAATAT
1 AAAATAT
795498 TTATCTTNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.17
17 5 0.22
18 4 0.17
19 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATATATATATATTA
Found at i:795961 original size:16 final size:16
Alignment explanation
Indices: 795931--795981 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
795921 GGTTCATTGG
795931 AATGGAATA-AGGTTGT
1 AATGGAATAGA-GTTGT
*
795947 AATTGAATAGAGTTGT
1 AATGGAATAGAGTTGT
*
795963 AATGGAATAGAGCTGT
1 AATGGAATAGAGTTGT
795979 AAT
1 AAT
795982 CAGTAATTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 30 0.97
17 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.31
Consensus pattern (16 bp):
AATGGAATAGAGTTGT
Found at i:796381 original size:31 final size:29
Alignment explanation
Indices: 796312--796385 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
796302 ACAAAATAAT
**
796312 AACATAAGTGACTAAAACGTAACTTTTCA
1 AACATAAGTGACTAAAACGTAACTTGGCA
*
796341 AACATAAGTGACTAAAATGTAACTTGAGGCA
1 AACATAAGTGACTAAAACGTAACTT--GGCA
*
796372 AACAAAAGTGACTA
1 AACATAAGTGACTA
796386 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACTTGGCA
Found at i:805836 original size:30 final size:30
Alignment explanation
Indices: 805800--805860 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
805790 ATTTTTGAAT
805800 TCCTTGAACTTTTCAAGGGACTCAGACTTA
1 TCCTTGAACTTTTCAAGGGACTCAGACTTA
*
805830 TCCTTGAACTTTTCAAGGGACTTAGACTTA
1 TCCTTGAACTTTTCAAGGGACTCAGACTTA
805860 T
1 T
805861 GGCGTATGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (30 bp):
TCCTTGAACTTTTCAAGGGACTCAGACTTA
Found at i:816754 original size:9 final size:9
Alignment explanation
Indices: 816717--816918 Score: 87
Period size: 9 Copynumber: 21.9 Consensus size: 9
816707 AATATGTGGC
816717 AAAAATTAT
1 AAAAATTAT
* *
816726 AAAAA-AAG
1 AAAAATTAT
*
816734 AAAAATAAAT
1 AAAAAT-TAT
816744 AAAAATTAT
1 AAAAATTAT
816753 AAAAATTATT
1 AAAAATTA-T
**
816763 AAATTTTAAT
1 AAAAATT-AT
816773 AAAAA-TAT
1 AAAAATTAT
816781 AAAAA-TATT
1 AAAAATTA-T
816790 AAAAATTAT
1 AAAAATTAT
**
816799 AAAAATCGT
1 AAAAATTAT
816808 AAAAA-TAT
1 AAAAATTAT
*
816816 AAAAA-AAT
1 AAAAATTAT
*
816824 ATAAAATTGT
1 A-AAAATTAT
*
816834 AAAATTTTAT
1 AAAA-ATTAT
*
816844 AAAATTTTAT
1 AAAA-ATTAT
816854 AATGTCAAA--AT
1 AA----AAATTAT
816865 -AAAATTAT
1 AAAAATTAT
* *
816873 AAAAAATGT
1 AAAAATTAT
*
816882 AAAGAAATAT
1 AAA-AATTAT
*
816892 AAAATTTAT
1 AAAAATTAT
*
816901 AAAAAAATAT
1 -AAAAATTAT
816911 AAAAATTA
1 AAAAATTA
816919 ACTTACCAAA
Statistics
Matches: 149, Mismatches: 26, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
6 3 0.02
8 26 0.17
9 62 0.42
10 53 0.36
11 3 0.02
14 2 0.01
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:816756 original size:18 final size:18
Alignment explanation
Indices: 816717--816837 Score: 97
Period size: 18 Copynumber: 6.7 Consensus size: 18
816707 AATATGTGGC
*
816717 AAAAATTATAAAAA-AAG
1 AAAAATTATAAAAATAAT
* *
816734 AAAAATAAATAAAAATTAT
1 AAAAAT-TATAAAAATAAT
**
816753 AAAAATTATTAAATTTTAAT
1 AAAAATTA-TAAA-AATAAT
*
816773 AAAAA-TATAAAAATATT
1 AAAAATTATAAAAATAAT
**
816790 AAAAATTATAAAAATCGT
1 AAAAATTATAAAAATAAT
816808 AAAAA-TATAAAAA-AAT
1 AAAAATTATAAAAATAAT
*
816824 ATAAAATTGTAAAA
1 A-AAAATTATAAAA
816838 TTTTATAAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
16 2 0.02
17 26 0.32
18 33 0.40
19 13 0.16
20 8 0.10
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAAATTATAAAAATAAT
Found at i:816892 original size:19 final size:19
Alignment explanation
Indices: 816865--816915 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
816855 ATGTCAAAAT
* *
816865 AAAATTATAAAAAATGTAA
1 AAAAATATAAAAAATATAA
* **
816884 AGAAATATAAAATTTATAA
1 AAAAATATAAAAAATATAA
816903 AAAAATATAAAAA
1 AAAAATATAAAAA
816916 TTAACTTACC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (19 bp):
AAAAATATAAAAAATATAA
Found at i:819069 original size:229 final size:229
Alignment explanation
Indices: 818668--819118 Score: 875
Period size: 229 Copynumber: 2.0 Consensus size: 229
818658 AAACACAAGC
818668 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
1 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
818733 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
66 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
*
818798 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTGTTTCT
131 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTATTTCT
818863 ATATATTCCCTTTTATTCACATTTTATCATTTGA
196 ATATATTCCCTTTTATTCACATTTTATCATTTGA
*
818897 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGATTTGAATGCCATTGGTGAAAAA
1 ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
*
818962 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATTTCC
66 CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
819027 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTATTTCT
131 CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTATTTCT
819092 ATATATTCCCTTTTATTCACATTTTAT
196 ATATATTCCCTTTTATTCACATTTTAT
819119 TTAAGAAAAT
Statistics
Matches: 219, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 219 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (229 bp):
ATCTCAAATTGAGATATTGTAGCTTTTGTTTAAGATGCTCAGAGTTGAATGCCATTGGTGAAAAA
CTAAATCATTGAAAAACCAGCAAACTGGTGACATGCGAGGATGCAAGGTTGTCTTGAAAATGTCC
CTGAAAGTTTATCACAAACGGAAATTTTCTTCTATTGCTTTGTAGTAACTACTATTTTTATTTCT
ATATATTCCCTTTTATTCACATTTTATCATTTGA
Found at i:822286 original size:79 final size:80
Alignment explanation
Indices: 822155--822316 Score: 290
Period size: 79 Copynumber: 2.0 Consensus size: 80
822145 TTTAAGAGAA
* **
822155 AGTATCAGTTTGCCCTTTGATATAATATTATATAATATTTTGGGAATAATTTATAGAAGTGCAAA
1 AGTATCAGATTGCCCTTTGATATAATATTATATAATATGCTGGGAATAATTTATAGAAGTGCAAA
822220 ATACTCTTGA-TCAG
66 ATACTCTTGATTCAG
822234 AGTATCAGATTGCCCTTTGATATAATATTATATAATATGCTGGGAATAATTTATAGAAGTGCAAA
1 AGTATCAGATTGCCCTTTGATATAATATTATATAATATGCTGGGAATAATTTATAGAAGTGCAAA
822299 ATACTCTTGATTCAG
66 ATACTCTTGATTCAG
822314 AGT
1 AGT
822317 TAAGTGGAAA
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 72 0.91
80 7 0.09
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (80 bp):
AGTATCAGATTGCCCTTTGATATAATATTATATAATATGCTGGGAATAATTTATAGAAGTGCAAA
ATACTCTTGATTCAG
Found at i:822567 original size:18 final size:18
Alignment explanation
Indices: 822524--822569 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
822514 CTACTAGATC
*
822524 TTAATTTTTTTTATATAA
1 TTAATTATTTTTATATAA
*
822542 TTACTTATTTTTAT-TAA
1 TTAATTATTTTTATATAA
822559 TTTAATTATTT
1 -TTAATTATTT
822570 ACAAACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAATTATTTTTATATAA
Found at i:828560 original size:9 final size:9
Alignment explanation
Indices: 828546--828574 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
828536 TTGGTTATAA
828546 TTACAGTAT
1 TTACAGTAT
828555 TTACAGTAT
1 TTACAGTAT
828564 TTACAGTAT
1 TTACAGTAT
828573 TT
1 TT
828575 GTGATTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTACAGTAT
Done.