Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008943.1 Hibiscus syriacus cultivar Beakdansim tig00112264_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1742779
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 4 of 5
Found at i:1065209 original size:20 final size:20
Alignment explanation
Indices: 1065184--1065221 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1065174 TTTTGGTGCA
*
1065184 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
1065204 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
1065222 TTTAAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:1065253 original size:21 final size:21
Alignment explanation
Indices: 1065206--1065266 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
1065196 ACCCCCATGA
*
1065206 GGGAACCGATTCCCCCTTTAAAG
1 GGGAACCGATTCCCCC--CAAAG
*
1065229 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCAAAG
* *
1065250 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
1065267 TGGGGTTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 18 0.53
23 16 0.47
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCAAAG
Found at i:1067264 original size:33 final size:31
Alignment explanation
Indices: 1067211--1067275 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
1067201 TATTAACATT
*
1067211 TTGATTATTTTGGAATGTTTGCATTTGTGGA
1 TTGATTATTTTGGAATGTTTGCATTTATGGA
*
1067242 TTGATTGATTTT-GAATTTGTTTGGATTTATGGA
1 TTGATT-ATTTTGGAA--TGTTTGCATTTATGGA
1067275 T
1 T
1067276 GGTGAGAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 9 0.31
32 5 0.17
33 15 0.52
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.54
Consensus pattern (31 bp):
TTGATTATTTTGGAATGTTTGCATTTATGGA
Found at i:1078938 original size:49 final size:51
Alignment explanation
Indices: 1078822--1078938 Score: 118
Period size: 49 Copynumber: 2.4 Consensus size: 51
1078812 TTGGGCATCC
* * * * *
1078822 TTTCATACC-CATTATGTATTGTTTACATTTTCTTTTCCTTTATGACATTCA
1 TTTCATACCAC-TTATGCATTGTTTACATTTTCATATCCTATATGACATACA
* *
1078873 -TTCATACCAATAATGCATTGTTGTACATTTT-ATAT-CTATATGACA-ACA
1 TTTCATACCACTTATGCATTGTT-TACATTTTCATATCCTATATGACATACA
1078921 TTTCATACCACTTATGCA
1 TTTCATACCACTTATGCA
1078939 CCGTTTATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
48 2 0.04
49 24 0.44
50 20 0.37
51 8 0.15
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (51 bp):
TTTCATACCACTTATGCATTGTTTACATTTTCATATCCTATATGACATACA
Found at i:1079087 original size:81 final size:80
Alignment explanation
Indices: 1078998--1079531 Score: 572
Period size: 81 Copynumber: 6.6 Consensus size: 80
1078988 CATTTAACTT
* * *
1078998 TTCATCTAACTTGCATGATTGACACTTTCCTTCCAAATGCACAGTTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACTTT-CTGCCAAATGCACAGTTAGGCCATTTATCTTTTACT
* *
1079063 CAATGGTCTTTAACCA
65 CAACGGTCTTTAACCG
* * * * *
1079079 TTCATCTAATTGGCAAAATTGACACCTTTCTACCAAATGCATAGCTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGTTAGGCCATTTATCTTTTACT
**
1079144 CAATAGTCTTTAACCG
65 CAACGGTCTTTAACCG
* * *
1079160 TTCATCTAAGTTGCATAATTGACATCTTTCTGCCAAATGCAC-TTCTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGT-TAGGCCATTTATCTTTTAC
* * *
1079224 TTAACTGTCTTTAATCG
64 TCAACGGTCTTTAACCG
* * * * * *
1079241 TTCATCTAACAGGCATAATTGACATATTTCTGCAAAATGCACAGCTAAGCCATTTATCTTTTATT
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAGTTAGGCCATTTATCTTTTACT
* *
1079306 CAACGGTATTTAACCA
65 CAACGGTCTTTAACCG
* *
1079322 TTCATCTAACTGGCATAATTGATACCTTTCTGCCAAATGCATAGCTT-GGCCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACA-CTTTCTGCCAAATGCACAG-TTAGGCCATTTATCTTTTAC
*
1079386 TCAACGATCTTTAACCG
64 TCAACGGTCTTTAACCG
* * * **
1079403 TTCATCTAACTGGTATAATTGAC-CTATTTCTACCAAATGCTCAACTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACAC--TTTCTGCCAAATGCACAGTTAGGCCATTTATCTTTTAC
* * * *
1079467 TCGACAGTTTTTAACTG
64 TCAACGGTCTTTAACCG
* * *
1079484 TTCATCAAACTAGCACAATTGACACATTTCTTG-CAAATGCACAGTTAG
1 TTCATCTAACTGGCATAATTGACAC-TTTC-TGCCAAATGCACAGTTAG
1079532 TCCTCAAAGG
Statistics
Matches: 377, Mismatches: 67, Indels: 18
0.82 0.15 0.04
Matches are distributed among these distances:
79 1 0.00
80 1 0.00
81 368 0.98
82 7 0.02
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (80 bp):
TTCATCTAACTGGCATAATTGACACTTTCTGCCAAATGCACAGTTAGGCCATTTATCTTTTACTC
AACGGTCTTTAACCG
Found at i:1079401 original size:243 final size:243
Alignment explanation
Indices: 1078990--1079527 Score: 699
Period size: 243 Copynumber: 2.2 Consensus size: 243
1078980 TCCAAAGGCA
* * * ** * * *
1078990 TTTAACTTTTCATCTAACTTGCATGATTGACAC-TTTCCTTCCAAATGCACAGTTAGGCCATTTA
1 TTTAACTGTTCATCAAACTAGCACAATTGACACATTT-CTTGCAAATGCACAGCTAAGCCATTTA
* * *
1079054 TCTTTTACTCAATGGTCTTTAACCATTCATCTAATTGGCAAAATTGACACCTTTCTACCAAATGC
65 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCAAAATTGACACCTTTCTACCAAATGC
* * *
1079119 ATAGCTAGGCCATTTATCTTTTACTCAATAGTCTTTAACCGTTCATCTAAGTTGCATAATTGACA
130 ATAGCTAGGCCATTTATCTTTTACTCAAGAGTCTTTAACCGTTCATCTAACTGGCATAATTGACA
* * ** * *
1079184 TCTTTCTGCCAAATGCACTTCTAGGCCATTTATCTTTTACTTAACTGTC
195 TATTTCTACCAAATGCACAACTAGGCCATTTATCTTTTACTCAACAGTC
* * *
1079233 TTTAA-TCGTTCATCTAAC-AGGCATAATTGACATATTTC-TGCAAAATGCACAGCTAAGCCATT
1 TTTAACT-GTTCATCAAACTA-GCACAATTGACACATTTCTTGC-AAATGCACAGCTAAGCCATT
* * * *
1079295 TATCTTTTATTCAACGGTATTTAACCATTCATCTAACTGGCATAATTGATACCTTTCTGCCAAAT
63 TATCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCAAAATTGACACCTTTCTACCAAAT
* *
1079360 GCATAGCTTGGCCATTTATCTTTTACTCAACGA-TCTTTAACCGTTCATCTAACTGGTATAATTG
128 GCATAGCTAGGCCATTTATCTTTTACTCAA-GAGTCTTTAACCGTTCATCTAACTGGCATAATTG
* * * *
1079424 ACCTATTTCTACCAAATGCTCAACTAGGCCATTTATCTTTTACTCGACAGTT
192 ACATATTTCTACCAAATGCACAACTAGGCCATTTATCTTTTACTCAACAGTC
1079476 TTTAACTGTTCATCAAACTAGCACAATTGACACATTTCTTGCAAATGCACAG
1 TTTAACTGTTCATCAAACTAGCACAATTGACACATTTCTTGCAAATGCACAG
1079528 TTAGTCCTCA
Statistics
Matches: 255, Mismatches: 32, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
242 3 0.01
243 243 0.95
244 9 0.04
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (243 bp):
TTTAACTGTTCATCAAACTAGCACAATTGACACATTTCTTGCAAATGCACAGCTAAGCCATTTAT
CTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCAAAATTGACACCTTTCTACCAAATGCA
TAGCTAGGCCATTTATCTTTTACTCAAGAGTCTTTAACCGTTCATCTAACTGGCATAATTGACAT
ATTTCTACCAAATGCACAACTAGGCCATTTATCTTTTACTCAACAGTC
Found at i:1079590 original size:68 final size:68
Alignment explanation
Indices: 1079500--1079671 Score: 229
Period size: 68 Copynumber: 2.5 Consensus size: 68
1079490 AAACTAGCAC
* * *
1079500 AATTGACACATTTCTTG-CAAATGCACAGTTAGTCCTCAAAGGCATTTAACCTTTCATCTAACTG
1 AATTGACACCTTT-TTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAACCTTTCATCTAACTG
1079564 GAAT
65 GAAT
* * * **
1079568 AATTGGCACCTTTTTGTCAAATGCACGGTTTGGCCTCAAAGGCACTTAGTCTTTCATCTAACTGG
1 AATTGACACCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAACCTTTCATCTAACTGG
*
1079633 TAT
66 AAT
* *
1079636 AATTGACACCTTTCTGTTAAATGCACAGTTAGGCCT
1 AATTGACACCTTTTTGTCAAATGCACAGTTAGGCCT
1079672 ATTAATCTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
67 3 0.03
68 86 0.97
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (68 bp):
AATTGACACCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAACCTTTCATCTAACTGG
AAT
Found at i:1081669 original size:10 final size:11
Alignment explanation
Indices: 1081642--1081674 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1081632 ACCCGAAAAA
1081642 AGTCAACGGTC
1 AGTCAACGGTC
1081653 AGTCAACGG-C
1 AGTCAACGGTC
*
1081663 GGTCAACGGTC
1 AGTCAACGGTC
1081674 A
1 A
1081675 ACGATTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.15
Consensus pattern (11 bp):
AGTCAACGGTC
Found at i:1088880 original size:6 final size:6
Alignment explanation
Indices: 1088839--1088882 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
1088829 AAAAGCAACA
*
1088839 AAAAGAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
1088883 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1099127 original size:13 final size:13
Alignment explanation
Indices: 1099106--1099144 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1099096 CGAATATCGT
*
1099106 TAGTAAGGCATAA
1 TAGTGAGGCATAA
1099119 TAGTGAGGCATAA
1 TAGTGAGGCATAA
1099132 TAGGTGAGTGCAT
1 TA-GTGAG-GCAT
1099145 TTTATTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.61
14 5 0.22
15 4 0.17
ACGTcount: A:0.36, C:0.08, G:0.31, T:0.26
Consensus pattern (13 bp):
TAGTGAGGCATAA
Found at i:1137607 original size:478 final size:481
Alignment explanation
Indices: 1136648--1137610 Score: 1400
Period size: 478 Copynumber: 2.0 Consensus size: 481
1136638 GATGAATTCT
* *
1136648 AGAAGAATTCAAAAATAGTAGTCATTTTAAGTATTATTTTGTAGAAAATGTTAGTAAGAATACTA
1 AGAAGAATTCAAAAACAGAAGTCATTTTAAGTATTATTTTGTAGAAAATGTTAGTAAGAATACTA
*
1136713 ACATGTATTTTATATTTGTATGTGCTATGTGTTTATGCTTGTGTAGATCATGATCGAACTCACGG
66 ACATGTATTTTATATTTGTATGTGCTATGTGTTTATGCTTGTGTAGATCATGATCAAACTCACGG
*
1136778 TACAATCAATTCGAAAGGCAATGAAAAAGTCCATCAATAATCGGATATCGTTAGTAAGGCATAAT
131 TACAATCAAATCGAAAGGCAATGAAAAAGTCCATCAATAATCGGATA-C-TTAGTAAGG-ATAAT
* *
1136843 AGCGAGGCATACCAGGTGAGTGCATTTTATTATGTTTTGGTGGCAATTATATTATTGATTCAGAA
193 AGC---GCATACCAGGTGACTGCATTTTATTATGTTTTGGTGGCAATTAGATTATTGATTCAGAA
* * *
1136908 TTTGTGTTAAAAGCTAGAAAGTGTTAAAGTCCGAAAAAAATCAGAAAATCAGATCGAATAGAAAT
255 TTTGTGTTAAAAGCTAGAAAGTGTTAAAGTCAGAAAAAAATAAGAAAATCAGATCGAAAAGAAAT
* * ** **
1136973 TTTGAGAAAATTTGAAGGATATTAAATTAAGATTAGAAATATTATTTCCATGATTCAAAATGACC
320 TTTAAGAAAATTTGAAGGATATTAAATTAAGATTAGAAATATTATTTACACAATTCAAAATGAAA
* *
1137038 TAAAATAATATAAATCATTGGATTTAAGAATTTATTTCCATGTTCAAATTGGACTGTTGGGTGAA
385 GAAAATAATATAAATCATTGGATTTAAGAATTTATTTCCATGTTCAAATTGGACTGTTGGATGAA
* * *
1137103 AATGGCAAGATTGAAGTTTGTGGAAAAGAGAA
450 AAAGGCAAGATTGAAATTTATGGAAAAGAGAA
* *
1137135 AGAAGAATTCAAAAACAGAAGTCCTTTTAAGTATTATTTCTGTGTATAAAATGTTAGTAAGAATA
1 AGAAGAATTCAAAAACAGAAGTCATTTTAAGTATTA-TT-T-TGTAGAAAATGTTAGTAAGAATA
* * *
1137200 CTAACATGTATTTTATATTTGTATGTGTTATGTGTTTATGCTTGTGTAGATCGTGATCAAACTCG
63 CTAACATGTATTTTATATTTGTATGTGCTATGTGTTTATGCTTGTGTAGATCATGATCAAACTCA
* * * *
1137265 TGGTATAATCAAATCGAATGGCAATGAAAAAGTCCATCAATAATCGGATA-TT-GTTA-G-T-A-
128 CGGTACAATCAAATCGAAAGGCAATGAAAAAGTCCATCAATAATCGGATACTTAGTAAGGATAAT
* * *
1137324 AGC-CATACTAGGTGACTGCATTTTATTATGTTTTGGTGGTAATTAGATTATTGATTCGGAATTT
193 AGCGCATACCAGGTGACTGCATTTTATTATGTTTTGGTGGCAATTAGATTATTGATTCAGAATTT
* * * *
1137388 GTGTTAAAAGCTATAAAGTGTTAAAGTTCAGTAAAAATTAAGTAAATCAGATCGAAAAGAAATTT
258 GTGTTAAAAGCTAGAAAGTGTTAAAG-TCAGAAAAAAATAAGAAAATCAGATCGAAAAGAAATTT
* *
1137453 TAAGAAAATTTGAAGGATATTAAATTAAGATTAGAAATTTTATTTACACAATTTAAAATGAAAGA
322 TAAGAAAATTTGAAGGATATTAAATTAAGATTAGAAATATTATTTACACAATTCAAAATGAAAGA
* * * * *
1137518 AAATAATATAAATCATTGGATTTGATAATTTATTTCCATGTTCAATTTTGAGTGTTGGATGAAAA
387 AAATAATATAAATCATTGGATTTAAGAATTTATTTCCATGTTCAAATTGGACTGTTGGATGAAAA
1137583 AGGCAAGATTGAAATTTATGGAAAAGAG
452 AGGCAAGATTGAAATTTATGGAAAAGAG
1137611 CAATGGTAAA
Statistics
Matches: 429, Mismatches: 43, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
477 81 0.19
478 172 0.40
481 3 0.01
482 1 0.00
483 1 0.00
485 1 0.00
486 3 0.01
487 35 0.08
488 2 0.00
489 1 0.00
490 129 0.30
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (481 bp):
AGAAGAATTCAAAAACAGAAGTCATTTTAAGTATTATTTTGTAGAAAATGTTAGTAAGAATACTA
ACATGTATTTTATATTTGTATGTGCTATGTGTTTATGCTTGTGTAGATCATGATCAAACTCACGG
TACAATCAAATCGAAAGGCAATGAAAAAGTCCATCAATAATCGGATACTTAGTAAGGATAATAGC
GCATACCAGGTGACTGCATTTTATTATGTTTTGGTGGCAATTAGATTATTGATTCAGAATTTGTG
TTAAAAGCTAGAAAGTGTTAAAGTCAGAAAAAAATAAGAAAATCAGATCGAAAAGAAATTTTAAG
AAAATTTGAAGGATATTAAATTAAGATTAGAAATATTATTTACACAATTCAAAATGAAAGAAAAT
AATATAAATCATTGGATTTAAGAATTTATTTCCATGTTCAAATTGGACTGTTGGATGAAAAAGGC
AAGATTGAAATTTATGGAAAAGAGAA
Found at i:1139439 original size:14 final size:14
Alignment explanation
Indices: 1139420--1139451 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1139410 AGAGAATTGT
1139420 TCTATTCGATGAGC
1 TCTATTCGATGAGC
*
1139434 TCTATTCGATGAGT
1 TCTATTCGATGAGC
1139448 TCTA
1 TCTA
1139452 GGATTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (14 bp):
TCTATTCGATGAGC
Found at i:1141032 original size:38 final size:38
Alignment explanation
Indices: 1140981--1141076 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
1140971 GCTCGTAAAA
*
1140981 TGTCCCGAAGGACCTATCATCCCGAAGGATGTTATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
** *
1141019 TGTCCCGAAGGACCTGCCATCCTGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
* *
1141057 TGTTCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
1141077 ATGTCTTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:1141281 original size:46 final size:46
Alignment explanation
Indices: 1141225--1141336 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
1141215 ATGTGTAACC
1141225 ATGT-ATTTCATATCATATCACACGTATCACGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACACGTATCACGTATTACATATTCAT
* *
1141270 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACACGTATCACGTATTACATATTCAT
*
1141316 ATATCATTTCATAT-AT-TCACA
1 ATGTCATTTCATATCATATCACA
1141337 TTGGTCATGT
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
44 5 0.08
45 6 0.10
46 52 0.83
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACACGTATCACGTATTACATATTCAT
Found at i:1142715 original size:20 final size:20
Alignment explanation
Indices: 1142692--1142747 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
1142682 AATTATTTTG
1142692 TTCATCATTGAATTTTGGAA
1 TTCATCATTGAATTTTGGAA
1142712 TTCATCATTGAATTTTGGAA
1 TTCATCATTGAATTTTGGAA
1142732 TTCATCATTGAATTTT
1 TTCATCATTGAATTTT
1142748 AGAAGATGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (20 bp):
TTCATCATTGAATTTTGGAA
Found at i:1170850 original size:126 final size:126
Alignment explanation
Indices: 1170683--1170937 Score: 510
Period size: 126 Copynumber: 2.0 Consensus size: 126
1170673 GCCGAAAATT
1170683 TATTAAGTTGTTTGAGACTTGAAATGAAGAAATAATAGCAATGGGTCATTATGAGTAAAAAGGAA
1 TATTAAGTTGTTTGAGACTTGAAATGAAGAAATAATAGCAATGGGTCATTATGAGTAAAAAGGAA
1170748 AAGTTAAGATGAATTCTAGAAAAATTCAAAAATAGTAGTCCTTTTAAGAATTATTATTGTG
66 AAGTTAAGATGAATTCTAGAAAAATTCAAAAATAGTAGTCCTTTTAAGAATTATTATTGTG
1170809 TATTAAGTTGTTTGAGACTTGAAATGAAGAAATAATAGCAATGGGTCATTATGAGTAAAAAGGAA
1 TATTAAGTTGTTTGAGACTTGAAATGAAGAAATAATAGCAATGGGTCATTATGAGTAAAAAGGAA
1170874 AAGTTAAGATGAATTCTAGAAAAATTCAAAAATAGTAGTCCTTTTAAGAATTATTATTGTG
66 AAGTTAAGATGAATTCTAGAAAAATTCAAAAATAGTAGTCCTTTTAAGAATTATTATTGTG
1170935 TAT
1 TAT
1170938 GAAATGTTAT
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 129 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (126 bp):
TATTAAGTTGTTTGAGACTTGAAATGAAGAAATAATAGCAATGGGTCATTATGAGTAAAAAGGAA
AAGTTAAGATGAATTCTAGAAAAATTCAAAAATAGTAGTCCTTTTAAGAATTATTATTGTG
Found at i:1173849 original size:123 final size:124
Alignment explanation
Indices: 1173708--1173933 Score: 341
Period size: 123 Copynumber: 1.8 Consensus size: 124
1173698 AAAATGTGAA
* * * *
1173708 ATTGGACTATTTTTTGTAATTTATCAAAGTTTGATCATCAA-ATGGTAATTATTGAGAAAGTTAG
1 ATTGGACTATTTTTTGTAAGTTAGCAAAGGTTGATCATCAAGA-GGTAATTACTGAGAAAGTTAG
1173772 TAACCTAAGTCACAATAATTGCGA-TGTTAA-GGTAATTACTGAGAAAGTTAGTTACTGAG
65 TAACCTAAGTCACAATAATTGC-ATTGTTAATGGTAATTACTGAGAAAGTTAGTTACTGAG
*
1173831 ATTGGATTATTTTTTGTAAGTTAGCAAAGGTTGATCATCAAGAGGTAATTACTGAGAAAGTTAGT
1 ATTGGACTATTTTTTGTAAGTTAGCAAAGGTTGATCATCAAGAGGTAATTACTGAGAAAGTTAGT
* * *
1173896 TACTTAAGTTACAATAATTGCATTGTTAATGGTAATTA
66 AACCTAAGTCACAATAATTGCATTGTTAATGGTAATTA
1173934 GATTCTTGAT
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
122 1 0.01
123 82 0.89
124 9 0.10
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (124 bp):
ATTGGACTATTTTTTGTAAGTTAGCAAAGGTTGATCATCAAGAGGTAATTACTGAGAAAGTTAGT
AACCTAAGTCACAATAATTGCATTGTTAATGGTAATTACTGAGAAAGTTAGTTACTGAG
Found at i:1174498 original size:17 final size:17
Alignment explanation
Indices: 1174476--1174511 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1174466 CAAATTCTAG
1174476 GTTTGGTCTAAGCCCTA
1 GTTTGGTCTAAGCCCTA
*
1174493 GTTTGGTCTAAGCTCTA
1 GTTTGGTCTAAGCCCTA
1174510 GT
1 GT
1174512 GTAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (17 bp):
GTTTGGTCTAAGCCCTA
Found at i:1179091 original size:17 final size:17
Alignment explanation
Indices: 1179069--1179104 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1179059 CAAATTCTAG
1179069 GTTTGGTCTAAGCCCTA
1 GTTTGGTCTAAGCCCTA
*
1179086 GTTTGGTCTAAGCTCTA
1 GTTTGGTCTAAGCCCTA
1179103 GT
1 GT
1179105 GTAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (17 bp):
GTTTGGTCTAAGCCCTA
Found at i:1181795 original size:17 final size:17
Alignment explanation
Indices: 1181756--1181796 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1181746 GATCTCAAAT
*
1181756 TCTAGGTTTGGTCTAAGC
1 TCTA-GTTTGGTCTAAGA
*
1181774 CCTAGTTTGGTCTAAGA
1 TCTAGTTTGGTCTAAGA
1181791 TCTAGT
1 TCTAGT
1181797 GTAGAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (17 bp):
TCTAGTTTGGTCTAAGA
Found at i:1194603 original size:17 final size:18
Alignment explanation
Indices: 1194572--1194611 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1194562 ATCTCAAATT
*
1194572 CTAGGTTTGGTCTAAGCC
1 CTAGTTTTGGTCTAAGCC
1194590 CTAGTTTTGG-CTAAGCC
1 CTAGTTTTGGTCTAAGCC
1194607 CTAGT
1 CTAGT
1194612 GTAGAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (18 bp):
CTAGTTTTGGTCTAAGCC
Found at i:1197227 original size:28 final size:28
Alignment explanation
Indices: 1197187--1197278 Score: 184
Period size: 28 Copynumber: 3.3 Consensus size: 28
1197177 GTCATTTTAA
1197187 CACAAATTCTGAATGAATTATCAAGTTT
1 CACAAATTCTGAATGAATTATCAAGTTT
1197215 CACAAATTCTGAATGAATTATCAAGTTT
1 CACAAATTCTGAATGAATTATCAAGTTT
1197243 CACAAATTCTGAATGAATTATCAAGTTT
1 CACAAATTCTGAATGAATTATCAAGTTT
1197271 CACAAATT
1 CACAAATT
1197279 GTGGAAATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (28 bp):
CACAAATTCTGAATGAATTATCAAGTTT
Found at i:1197293 original size:14 final size:14
Alignment explanation
Indices: 1197274--1197306 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1197264 CAAGTTTCAC
1197274 AAATTGTGGAAATA
1 AAATTGTGGAAATA
1197288 AAATTGTGGAAATA
1 AAATTGTGGAAATA
1197302 AAATT
1 AAATT
1197307 TGTCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (14 bp):
AAATTGTGGAAATA
Found at i:1198668 original size:17 final size:16
Alignment explanation
Indices: 1198644--1198678 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1198634 ATTTGTGTTA
1198644 AAAGCTAGAAAATATT
1 AAAGCTAGAAAATATT
*
1198660 AAAGTCTAGTAAATATT
1 AAAG-CTAGAAAATATT
1198677 AA
1 AA
1198679 GTAACTCGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (16 bp):
AAAGCTAGAAAATATT
Found at i:1201050 original size:839 final size:844
Alignment explanation
Indices: 1199639--1201242 Score: 2289
Period size: 839 Copynumber: 1.9 Consensus size: 844
1199629 TTGAGACTTG
* * *
1199639 AAATGAAGAAATAATAGCAAGGTGTCATTGTGAGTAAAAAGGAAAAGTTAAGATGAATTCAAGAA
1 AAATGAAGAAATAATAACAAGGTGCCATTGTGAGTAAAAAGGAAAAGTTAACATGAATTCAAGAA
** * *
1199704 GAATTCAAAAGTAGTAGTCATTTTAAATATTATTATTGTGTATAAAATGTTAGTAAGAATACTAA
66 GAATAAAAAAATAGTAGTCATTTTAAATATTATTATTGTGTATAAAATGTTAGTAAAAATACTAA
* * *
1199769 CATTTATTTTATATTTGTATGTATTTTGTATTTATGCTTGTGTAGATCGTGATCAAACTAGTGGT
131 CATATATTTTATATTTGTATGTATTTTGCATTTATGCTTGTGTAGATCGTGACCAAACTAGTGGT
* *
1199834 ACAAGCAAATCGAAAGGAAATGAAAAAGTCCATTAATAATCGGATATCGTTAGTAAGGCATAATA
196 ACAAGCAAATCGAAAGGAAATGAAAAAGTCCATCAATAATCGGATATCATTAGTAAGGCATAATA
* * ***
1199899 GTGAGGCATATCAGGTGAGTTTTATAATGTTTTGGTGGTAATTAGATTCTTGATTTGGAATGTGT
261 GTGAGG---AT-A-GTCAGTTTTATAATGATTTGGTGGTAATTAGATTCTTGATTCACAATGTGT
* *
1199964 TAAAAGATAGAAAGTGTTAAAGTCTAGTAAAAATTAAGTAAATCTGATCGAAAAGAAATTTTGAG
321 TAAAAGATAGAAAGTGTTAAAGTCCAGTAAAAATCAAGTAAATCTGATCGAAAAGAAATTTTGAG
* * * *
1200029 AAAATTTGAAGGATATTCAATTAATATTAGAAATTTTATTTCGACAATTTAAAATGACAGAAAAT
386 AAAATTAGAAGGATATTCAATTAAGATTAGAAATTTTATTTCCACAATTTAAAATGACAGAAAAA
* * * * *
1200094 AATATAAATCTTTGGATTTGAAAATTTATTCCCATGTTCAATTTGGACTGTTGGGTGAAAATGGC
451 AATATAAACCTATGGATTTGAAAATTTATTCCCATGTTCAATTTGGACTATTGGATGAAAATGGA
* * * *
1200159 AAGATTGAAGTTTATTGAAAAGAGCAAGGGTAAAGTTGTAAATGGTAAATTATTTTGTTCATCAT
516 AAGATTGAAGTTTATGGAAAAGAGCAAGGGTAAAGTTGTAAATGGAAAATTATATTATTCATCAT
* * * *
1200224 TGAATTTTAGAAGATGATAAGTGTTATGTGGCTTATTATTGATGTAATTATCAAGTTTCATTAAT
581 TGAATTTGAGAAAATGATAAGTATTATGTGGCTTATTATGGATGTAATTATCAAGTTTCATTAAT
* *
1200289 TGTAAATTTGACATTTCT-AAGTTAAATGAATTTTAAACTCATTTAAGCTTAAATAAAATAAAAA
646 GGTAAATTTGACATTTCTCAA-TTAAATGAATTTTAAACTCATTTAAGCTTAAATAAAAGAAAAA
* *
1200353 TTAAATTAAAAGTACTTAAAAAAATTTCATGAAAGCTTTGTGATTTCCTCCATTTATTGATCATC
710 TTAAATTAAAAGTACTTAAAAAAA-AT--TGAAACCTTTGTGATTTCCTCCATTTATTGATCATC
1200418 AAGAGGTAATTACTGAGAAAGTTAGTTACTTAAGTGACAATAATTGCATTGTTGAGGTATTGGGC
772 AAGAGGTAATTACTGAGAAAGTTAGTTACTTAAGTGACAATAATTGCATTGTTGAGGTATTGGGC
1200483 TAGAATTT
837 TAGAATTT
* *
1200491 AAATGAAGAAATAATAACAAGG-GCCATTGTGAGTAAAAAGGAAAAGTTAACATGAATTCTAGGA
1 AAATGAAGAAATAATAACAAGGTGCCATTGTGAGTAAAAAGGAAAAGTTAACATGAATTCAAGAA
1200555 GAATAAAAAAATAGTAGTCATTTTAAATATTATTATTGTGTATAAAATGTTAGTAAAAATACTAA
66 GAATAAAAAAATAGTAGTCATTTTAAATATTATTATTGTGTATAAAATGTTAGTAAAAATACTAA
* * * * * *
1200620 CATATA-TTT-T-TTTGTATGTGTTTTGCGTTTATGTTTTTGTAGATCGTGACCAAATTTGTGGT
131 CATATATTTTATATTTGTATGTATTTTGCATTTATGCTTGTGTAGATCGTGACCAAACTAGTGGT
* *
1200682 ACAAGCAAATCGAAAGGCAATGAAAAAGTCCATCAATAATTGGATATCATTAGTAAGGCATACCA
196 ACAAGCAAATCGAAAGGAAATGAAAAAGTCCATCAATAATCGGATATCATTAGTAAGGCATA--A
* *
1200747 T-GTGA-G-T-G-CA-TTTTATTATGATTTGGTGGTGATTAGATTCTTGATTCACAATTTGTGTT
259 TAGTGAGGATAGTCAGTTTTATAATGATTTGGTGGTAATTAGATTCTTGATTCACAA--TGTGTT
* * * *** ** * *
1200806 AAAAGGTAGAAAGTGTTAAAGTCCAGTAAAAATCATGTAAATTTGATC-ACTTG-TTTTTTTATA
322 AAAAGATAGAAAGTGTTAAAGTCCAGTAAAAATCAAGTAAATCTGATCGAAAAGAAATTTTGAGA
* * *
1200869 AAATTAGAAGGTTATTTAATTAAGATTAGAAATTTTATTTCCATAATTTAAAATGACAGAAAAAA
387 AAATTAGAAGGATATTCAATTAAGATTAGAAATTTTATTTCCACAATTTAAAATGACAGAAAAAA
* * *
1200934 ATATAAACCTATGGATTTGAGAATTTATTTCCATGTTCAATTTGGACTATTGGATTAAAATGGAA
452 ATATAAACCTATGGATTTGAAAATTTATTCCCATGTTCAATTTGGACTATTGGATGAAAATGGAA
* * *
1200999 AGATTGAAGTTTGTGGAAAATAGTAAGGGTAAAGTTGTAAATGGAAAATTATATTATTCATCATT
517 AGATTGAAGTTTATGGAAAAGAGCAAGGGTAAAGTTGTAAATGGAAAATTATATTATTCATCATT
* *
1201064 GAATTTGGGAAAATGATAAGTATTATGTGGCTTATTATGGATGTAATTATCAAGTTTCATTTATG
582 GAATTTGAGAAAATGATAAGTATTATGTGGCTTATTATGGATGTAATTATCAAGTTTCATTAATG
* *
1201129 GTAAATTTGACATTTCTCAATTAAATGAATTTTAAATTCATTTAAGCTTAAATAAAAGATAAATT
647 GTAAATTTGACATTTCTCAATTAAATGAATTTTAAACTCATTTAAGCTTAAATAAAAGAAAAATT
* * * *
1201194 AACTTGAAATTACTTAAAAAAAATTGAAACCTTTGTGATTTCTTCCATT
712 AAATTAAAAGTACTTAAAAAAAATTGAAACCTTTGTGATTTCCTCCATT
1201243 GTGTCCCTGT
Statistics
Matches: 668, Mismatches: 79, Indels: 26
0.86 0.10 0.03
Matches are distributed among these distances:
836 23 0.03
838 1 0.00
839 350 0.52
840 5 0.01
841 50 0.07
844 1 0.00
848 103 0.15
849 5 0.01
850 5 0.01
851 104 0.16
852 21 0.03
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.36
Consensus pattern (844 bp):
AAATGAAGAAATAATAACAAGGTGCCATTGTGAGTAAAAAGGAAAAGTTAACATGAATTCAAGAA
GAATAAAAAAATAGTAGTCATTTTAAATATTATTATTGTGTATAAAATGTTAGTAAAAATACTAA
CATATATTTTATATTTGTATGTATTTTGCATTTATGCTTGTGTAGATCGTGACCAAACTAGTGGT
ACAAGCAAATCGAAAGGAAATGAAAAAGTCCATCAATAATCGGATATCATTAGTAAGGCATAATA
GTGAGGATAGTCAGTTTTATAATGATTTGGTGGTAATTAGATTCTTGATTCACAATGTGTTAAAA
GATAGAAAGTGTTAAAGTCCAGTAAAAATCAAGTAAATCTGATCGAAAAGAAATTTTGAGAAAAT
TAGAAGGATATTCAATTAAGATTAGAAATTTTATTTCCACAATTTAAAATGACAGAAAAAAATAT
AAACCTATGGATTTGAAAATTTATTCCCATGTTCAATTTGGACTATTGGATGAAAATGGAAAGAT
TGAAGTTTATGGAAAAGAGCAAGGGTAAAGTTGTAAATGGAAAATTATATTATTCATCATTGAAT
TTGAGAAAATGATAAGTATTATGTGGCTTATTATGGATGTAATTATCAAGTTTCATTAATGGTAA
ATTTGACATTTCTCAATTAAATGAATTTTAAACTCATTTAAGCTTAAATAAAAGAAAAATTAAAT
TAAAAGTACTTAAAAAAAATTGAAACCTTTGTGATTTCCTCCATTTATTGATCATCAAGAGGTAA
TTACTGAGAAAGTTAGTTACTTAAGTGACAATAATTGCATTGTTGAGGTATTGGGCTAGAATTT
Found at i:1206512 original size:30 final size:30
Alignment explanation
Indices: 1206476--1206539 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1206466 CAAACTCTAG
1206476 AAAATATTTGGG-CC-ATTTTGTAATATTTCA
1 AAAATA-TTGGGACCTATTTTGTAA-ATTTCA
*
1206506 AAAATATTGGGAACCTATTTTGTAAATTTGA
1 AAAATATTGGG-ACCTATTTTGTAAATTTCA
1206537 AAA
1 AAA
1206540 GTTTGAGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.17
30 6 0.20
31 10 0.33
32 9 0.30
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (30 bp):
AAAATATTGGGACCTATTTTGTAAATTTCA
Found at i:1209981 original size:37 final size:37
Alignment explanation
Indices: 1209928--1210032 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
1209918 CCTTTTCGTC
*
1209928 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * ** *
1209965 TTGCTAGGATTTAAACTCCTAAAAATAGGATTTAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
1210002 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
1210033 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:1210614 original size:3 final size:3
Alignment explanation
Indices: 1210599--1210695 Score: 50
Period size: 3 Copynumber: 33.7 Consensus size: 3
1210589 TTGCATTTTA
* * *
1210599 ATT ATT ATAT ATT ATT ATT ATT TTT ACT ATT A-T ATT -TT CCTT -TT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
*
1210643 ATT -CT ACTT ATT ATT ATAT ATGT A-T ATT -TT -TT A-T ATT -TT ATT
1 ATT ATT A-TT ATT ATT AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT
1210685 ATT ATT ATT AT
1 ATT ATT ATT AT
1210696 ATTTTTTACT
Statistics
Matches: 75, Mismatches: 7, Indels: 24
0.71 0.07 0.23
Matches are distributed among these distances:
2 17 0.23
3 46 0.61
4 12 0.16
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1210621 original size:25 final size:25
Alignment explanation
Indices: 1210593--1210695 Score: 72
Period size: 25 Copynumber: 4.1 Consensus size: 25
1210583 TTTTCTTTGC
1210593 ATTTTAATTATTATATATTATTATT
1 ATTTTAATTATTATATATTATTATT
* * * *
1210618 ATTTTTACTATTATATTTTCCTT-TT
1 ATTTTAATTATTATATATT-ATTATT
*
1210643 ATTCTACTTATTATTATATATGTA-TATT
1 ATT-T--TAATTATTATATAT-TATTATT
1210671 -TTTTATATT-TTAT-TATTATTATT
1 ATTTTA-ATTATTATATATTATTATT
1210694 AT
1 AT
1210696 ATTTTTTACT
Statistics
Matches: 61, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
22 2 0.03
23 7 0.11
24 6 0.10
25 24 0.39
26 4 0.07
27 3 0.05
28 14 0.23
29 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (25 bp):
ATTTTAATTATTATATATTATTATT
Found at i:1210741 original size:12 final size:11
Alignment explanation
Indices: 1210719--1210757 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
1210709 TCTTTCTTTT
1210719 TATTATTCTTG
1 TATTATTCTTG
1210730 TATTATTACTTG
1 TATTATT-CTTG
1210742 TATTATT-TT-
1 TATTATTCTTG
1210751 TATTATT
1 TATTATT
1210758 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 7 0.26
12 11 0.41
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:1210754 original size:9 final size:9
Alignment explanation
Indices: 1210650--1210758 Score: 53
Period size: 9 Copynumber: 11.0 Consensus size: 9
1210640 TTTATTCTAC
1210650 TTATTATTAT
1 TTATTATT-T
*
1210660 ATATGTATATT
1 TTAT-TAT-TT
1210671 TT-TTATATT
1 TTATTAT-TT
*
1210680 TTATTATTA
1 TTATTATTT
1210689 TTATTATATT
1 TTATTAT-TT
1210699 TT-TTACTTT
1 TTATTA-TTT
*
1210708 CTCT-TTCTTT
1 -T-TATTATTT
1210718 TTATTATTCT
1 TTATTATT-T
1210728 TGTATTATTACT
1 T-TATTATT--T
1210740 TGTATTATTT
1 T-TATTATTT
1210750 TTATTATTT
1 TTATTATTT
1210759 ATTTTGTTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
8 1 0.01
9 34 0.41
10 20 0.24
11 15 0.18
12 12 0.15
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.69
Consensus pattern (9 bp):
TTATTATTT
Found at i:1211303 original size:33 final size:31
Alignment explanation
Indices: 1211234--1211305 Score: 85
Period size: 34 Copynumber: 2.3 Consensus size: 31
1211224 TCGTCATTTA
* *
1211234 ATTTATTA-ATTTATATATATTTACTTTTTT
1 ATTTATTATATATATATATATTTACTTTGTT
1211264 ATTTATTATATATATATATTATTCGTACTTTGTT
1 ATTTATTATATATATATA-TATT--TACTTTGTT
1211298 A-TTATTAT
1 ATTTATTAT
1211306 TTTGTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 8 0.22
31 8 0.22
32 4 0.11
33 7 0.19
34 9 0.25
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (31 bp):
ATTTATTATATATATATATATTTACTTTGTT
Found at i:1211378 original size:27 final size:26
Alignment explanation
Indices: 1211299--1211386 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 26
1211289 TACTTTGTTA
*
1211299 TTATTATTTTGTTTTATTTATTTTCT-TT
1 TTATTA-TTTGTTTT-TTTA-TTACTATT
*
1211327 TTCTT-TTT-TCTTTTTTATATA-TATT
1 TTATTATTTGT-TTTTTTAT-TACTATT
1211352 TTATTATTTGTTTTTTTACTTACTATT
1 TTATTATTTGTTTTTTTA-TTACTATT
1211379 TTA-TATTT
1 TTATTATTT
1211387 TCTTTCTTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
24 2 0.04
25 12 0.24
26 23 0.46
27 9 0.18
28 4 0.08
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (26 bp):
TTATTATTTGTTTTTTTATTACTATT
Found at i:1212410 original size:250 final size:250
Alignment explanation
Indices: 1211967--1212467 Score: 977
Period size: 250 Copynumber: 2.0 Consensus size: 250
1211957 CATTTTTTAA
1211967 TGATTTCGGCCCTTAAAGATTTTTCATCCAAAGGCTCTATACCCGAGCTCCGAACCCGTTTTAAG
1 TGATTTCGGCCCTTAAAGATTTTTCATCCAAAGGCTCTATACCCGAGCTCCGAACCCGTTTTAAG
1212032 TGGGGGTGAAAGCGACACCTTCATATGAATTTATTCATCGTATGGGCCTAGCAAGTAACCTTCGG
66 TGGGGGTGAAAGCGACACCTTCA-ATGAATTTATTCATCGTATGGGCCTAGCAAGTAACCTTCGG
1212097 GATTCATATACCTTATGCCTTCGTGTGAATTTATTCTCCGTATGGGCATAAGGGAATGTTTTCTC
130 GATTCATATACCTTATGCCTTCGTGTGAATTTATTCTCCGTATGGGCATAAGGGAATGTTTTCTC
1212162 TCGAGTTTAACTTAGGTCCACAAAAGCTTGTGATGGGTTTATGACTAAGGGTCTGGT
195 TCGAGTTTAACTTA-GTCCACAAAAGCTTGTGATGGGTTTATGACTAAGGGTCTGGT
1212219 TGATTTCGGCCCTTAAAGATTTTTCATCCAAAGGCTCTATACCCGAGCTCCGAACCCGTTTTAAG
1 TGATTTCGGCCCTTAAAGATTTTTCATCCAAAGGCTCTATACCCGAGCTCCGAACCCGTTTTAAG
1212284 TGGGGGTGAAAGCGACACCTTC-ATGAATTTATTCATCGTATGGGCCTAGCAAGTAACCTTCGGG
66 TGGGGGTGAAAGCGACACCTTCAATGAATTTATTCATCGTATGGGCCTAGCAAGTAACCTTCGGG
1212348 ATTCATATACCTTATGCCTTCGTGTGAATTTATTCTCCGTATGGGCATAAGGGAATGTTTTCTCT
131 ATTCATATACCTTATGCCTTCGTGTGAATTTATTCTCCGTATGGGCATAAGGGAATGTTTTCTCT
1212413 CGAGTTTAACTTAGTCCACAAAAGCTTGTGATGGGTTTATGACTAAGGGTCTGGT
196 CGAGTTTAACTTAGTCCACAAAAGCTTGTGATGGGTTTATGACTAAGGGTCTGGT
1212468 AAGCCCAAGG
Statistics
Matches: 249, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
249 42 0.17
250 120 0.48
252 87 0.35
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (250 bp):
TGATTTCGGCCCTTAAAGATTTTTCATCCAAAGGCTCTATACCCGAGCTCCGAACCCGTTTTAAG
TGGGGGTGAAAGCGACACCTTCAATGAATTTATTCATCGTATGGGCCTAGCAAGTAACCTTCGGG
ATTCATATACCTTATGCCTTCGTGTGAATTTATTCTCCGTATGGGCATAAGGGAATGTTTTCTCT
CGAGTTTAACTTAGTCCACAAAAGCTTGTGATGGGTTTATGACTAAGGGTCTGGT
Found at i:1216219 original size:16 final size:15
Alignment explanation
Indices: 1216195--1216236 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1216185 AAAAAGGGCA
*
1216195 AAAATAAAAAAGAA-
1 AAAACAAAAAAGAAG
1216209 AAGAAGCAAAAAAGAAG
1 AA-AA-CAAAAAAGAAG
1216226 AAAACAAAAAA
1 AAAACAAAAAA
1216237 AACCTAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 9 0.38
16 11 0.46
17 2 0.08
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (15 bp):
AAAACAAAAAAGAAG
Found at i:1218015 original size:106 final size:106
Alignment explanation
Indices: 1217814--1219492 Score: 2324
Period size: 106 Copynumber: 16.0 Consensus size: 106
1217804 ATATCGTGCC
* * * *
1217814 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGATTGGTTGTCAAC--A-AACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
1217875 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1217917 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTAGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1217982 AATTTCAGATCCAATATCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
1218023 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTTTCAATAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1218088 AATTTCAGAGCCACTTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1218129 ACTCAAGACAACGCAAGTTCAACTTCATC-ACGAA-GGACCGCTGGTTGTTAATAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCA-CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* *
1218192 CAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1218234 ACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1218299 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * **
1218340 ACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTATC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1218405 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1218446 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGAACTGCTGGTTGTC-A-ATA-AA-----C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1218503 AATTTC----CTAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1218540 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1218605 ATTTTCACAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1218646 ACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1218711 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
1218752 ACTCCAGACAACACAAGTTCAACTTCATGATGAA-GGACCACTGGTTGTCAACAAACAACTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1218816 AATTTCAGAGCCAATTTCAATTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * ** * *
1218857 ACTCGAGACAACACAAGTTCAATTTCACAACAAAGGGATGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
1218922 AATTTCGGAGCCAATTTCAACTTCATAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1218963 ACTCCAGACAACACAAGTTCAACTTCACGA--AAGGGACTGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * **
1219026 AATTTCGGAGCCAATTTTAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1219067 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1219132 AAATTCAGAGCCAATTTCATCTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1219173 ACTCCAGGCAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1219238 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* **
1219279 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAACAAACAACTTCAA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1219344 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
1219385 ACTCGAGACAACACAAGTTCAACTTCACAACGAA-GGA-CGCTAGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * *
1219448 AGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1219489 ACTC
1 ACTC
1219493 AGAACAATGC
Statistics
Matches: 1413, Mismatches: 141, Indels: 43
0.88 0.09 0.03
Matches are distributed among these distances:
94 74 0.05
95 1 0.00
96 2 0.00
97 2 0.00
98 7 0.00
102 6 0.00
103 46 0.03
104 160 0.11
105 191 0.14
106 923 0.65
107 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1218443 original size:317 final size:317
Alignment explanation
Indices: 1217814--1219492 Score: 2317
Period size: 317 Copynumber: 5.3 Consensus size: 317
1217804 ATATCGTGCC
* * *
1217814 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGATTGGTTGTC-A-ACA-AACTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAA-GGACCG-CTGGTTGTCAATAAACAACTTCC
*
1217875 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
64 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
* * * *
1217940 TTCACGACAAAGGGACCGCTAGTTGTCAACAAACAACTTCCCAATTTCAGATCCAATATCAACTT
129 TTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTT
* *
1218005 CACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTT
194 CACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT
* * * *
1218070 TTCAATAAACAA-TT-TCCTAATTTCAGAGCCACTTTCAACTTCACAGCGAAGGATATTGG
259 GTCAACAAACAACTTAT-C-AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1218129 ACTCAAGACAACGCAAGTTCAACTTCATC-ACGAAGGACCGCTGGTTGTTAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCA-CAACGAAGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
1218193 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGGAAGTTCAACT
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
1218258 TCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTC
130 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
*
1218323 ACAACGAAGGATATTGGACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
195 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
*
1218388 TCAACAAATAACTTATCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
260 TCAACAAACAACTTATCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1218446 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGAACTGCTGGTTGTCAAT--A-AA-----C
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGG-ACCGCTGGTTGTCAATAAACAACTTCCC
* *
1218503 AATTTC----CTAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * * *
1218564 TCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCATTTTCACAGCCAATTTCAACTTC
130 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* *
1218629 ACAGCGAAGGATATTGGACTCCAGACAACGGAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
195 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* * *
1218694 TCAACAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
260 TCAACAAACAACTTATCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * * * *
1218752 ACTCCAGACAACACAAGTTCAACTTCATGATGAAGGACCACTGGTTGTCAACAAACAACTTCCAA
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGACCGCTGGTTGTCAATAAACAACTTCCCA
* * * * * *
1218817 ATTTCAGAGCCAATTTCAATTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAATTT
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
* * ** * * *
1218882 CACAACAAAGGGATGGCTGGTTGTCAACAAATAATTTCCCAATTTCGGAGCCAATTTCAACTTCA
131 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
* * * * *
1218947 TAGCGAAAGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA--AAGGGACTGCTGGTTGT
196 CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
* * ** * * **
1219010 CAATAAACAATTTCCCAATTTCGGAGCCAATTTTAACTTCACAGTGAAGGATATTGG
261 CAACAAACAACTTATCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
1219067 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAA-GGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
1219132 AAATTCAGAGCCAATTTCATCTTCACAGCGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACT
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
1219197 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
130 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* *
1219262 ACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGAACCGCTGGTTG
195 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* *
1219327 TCAACAAACAACTTCA-AAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
260 TCAACAAACAACTT-ATCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1219385 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGA-CGCTAGTTGTCAATAAACAATTTCCCA
1 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGACCGCTGGTTGTCAATAAACAACTTCCCA
* * * *
1219449 GTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGTACTC
66 ATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
1219493 AGAACAATGC
Statistics
Matches: 1213, Mismatches: 125, Indels: 51
0.87 0.09 0.04
Matches are distributed among these distances:
305 13 0.01
306 264 0.22
307 1 0.00
308 2 0.00
310 7 0.01
313 6 0.00
314 10 0.01
315 133 0.11
316 248 0.20
317 418 0.34
318 110 0.09
319 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (317 bp):
ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGACCGCTGGTTGTCAATAAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
CAACAAACAACTTATCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1218575 original size:43 final size:42
Alignment explanation
Indices: 1218415--1218575 Score: 119
Period size: 43 Copynumber: 3.6 Consensus size: 42
1218405 AATTTCAGAG
* * *
1218415 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAA
1 CCAAGTTCAACTTCACGACGAAGGATATTGGACTCAAGACAA
** *
1218457 CACAAGTTCAACTTCACGACGAAGGA-ACTGCTGGTTGTCAATAAACAA
1 C-CAAGTTCAACTTCACGACGAAGGATA-T--TGG-ACTC-A-AGACAA
*
1218505 TTTCCTAATTTCAACTTCAC-AGCGAAGGATATTGGACTCAAGACAA
1 ---CC-AAGTTCAACTTCACGA-CGAAGGATATTGGACTCAAGACAA
*
1218551 CGCAAGTTCAACTTCATGACGAAGG
1 C-CAAGTTCAACTTCACGACGAAGG
1218576 GACCGCTGGT
Statistics
Matches: 92, Mismatches: 12, Indels: 29
0.69 0.09 0.22
Matches are distributed among these distances:
42 2 0.02
43 42 0.46
44 2 0.02
45 3 0.03
46 7 0.08
47 1 0.01
48 7 0.08
49 3 0.03
50 2 0.02
51 22 0.24
52 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (42 bp):
CCAAGTTCAACTTCACGACGAAGGATATTGGACTCAAGACAA
Found at i:1220276 original size:37 final size:37
Alignment explanation
Indices: 1220223--1220327 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
1220213 CCTTTTCGTC
*
1220223 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * *
1220260 TTGCTAGGATTTAAACTCCTAAAAATAGGATTGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* *
1220297 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
1220328 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:1220897 original size:17 final size:16
Alignment explanation
Indices: 1220854--1221032 Score: 64
Period size: 17 Copynumber: 10.6 Consensus size: 16
1220844 TACCCATATA
1220854 TATATTTATT-TTCTT
1 TATATTTATTATTCTT
** *
1220869 TGCATTTTTTATTCTAT
1 TATATTTATTATTCT-T
*
1220886 TATATTTATTATTTTT
1 TATATTTATTATTCTT
1220902 TACTATTATATT-TTCCTT
1 TA-TATT-TATTATT-CTT
* *
1220920 T-TATTCTACTATT-TA
1 TATATT-TATTATTCTT
* * *
1220935 TATATATGTGTATTTTT
1 TATATTTAT-TATTCTT
*
1220952 TATATTTTATTATT-AT
1 TATA-TTTATTATTCTT
*
1220968 TATATTTTTTACTTTCTT
1 TATATTTATTA--TTCTT
* *
1220986 TCTTTTTATTATTCTTGT
1 TATATTTATTATTC-T-T
1221004 TATTACTTGTATTATT-TT
1 TA-TA-TT-TATTATTCTT
1221022 TATTATTTATT
1 TA-TATTTATT
1221033 TTGTTATATA
Statistics
Matches: 121, Mismatches: 25, Indels: 35
0.67 0.14 0.19
Matches are distributed among these distances:
15 16 0.13
16 33 0.27
17 34 0.28
18 27 0.22
19 2 0.02
20 2 0.02
21 7 0.06
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.68
Consensus pattern (16 bp):
TATATTTATTATTCTT
Found at i:1221196 original size:19 final size:18
Alignment explanation
Indices: 1221167--1221202 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1221157 ATTAATTTTC
1221167 TATATTTTATTATCTTTA
1 TATATTTTATTATCTTTA
*
1221185 TATATATTTATTTTCTTT
1 TATAT-TTTATTATCTTT
1221203 TTTATTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TATATTTTATTATCTTTA
Found at i:1221629 original size:32 final size:31
Alignment explanation
Indices: 1221568--1221632 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
1221558 GTTATTATTA
* *
1221568 TTTTGTTATATTTATTTTCTTTTTCTTTTTC
1 TTTTGTTATATATATTTTATTTTTCTTTTTC
*
1221599 TTTT-TTATATATATTTTATTATTTGTTTTT-
1 TTTTGTTATATATATTTTATT-TTTCTTTTTC
1221629 TTTT
1 TTTT
1221633 ACTTACTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (31 bp):
TTTTGTTATATATATTTTATTTTTCTTTTTC
Found at i:1221836 original size:13 final size:13
Alignment explanation
Indices: 1221798--1221838 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
1221788 GGATCGTTAT
*
1221798 TTAAACTTTCAAT
1 TTAAACTTTCAAC
1221811 TTAAACTTTCAAC
1 TTAAACTTTCAAC
1221824 TTAAACTTTCAAC
1 TTAAACTTTCAAC
1221837 TT
1 TT
1221839 TCTTAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAACTTTCAAC
Found at i:1227781 original size:13 final size:13
Alignment explanation
Indices: 1227760--1227801 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1227750 TATTGTATAC
*
1227760 AATGAGCGTCATA
1 AATGCGCGTCATA
1227773 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
1227786 AATACGCTTCATA
1 AATGCGCGTCATA
1227799 AAT
1 AAT
1227802 AAATGTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:1227802 original size:13 final size:13
Alignment explanation
Indices: 1227765--1227802 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1227755 TATACAATGA
*
1227765 GCGTCATAAATGC
1 GCGTCATAAATAC
1227778 GCGTCATAAATAC
1 GCGTCATAAATAC
*
1227791 GCTTCATAAATA
1 GCGTCATAAATA
1227803 AATGTCATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (13 bp):
GCGTCATAAATAC
Found at i:1228188 original size:23 final size:23
Alignment explanation
Indices: 1228162--1228206 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1228152 TTAAATTCAT
1228162 TTAAGCTT-AAATAAAATAAAAAA
1 TTAA-CTTGAAATAAAATAAAAAA
* *
1228185 TTAACTTGAAATTAATTAAAAA
1 TTAACTTGAAATAAAATAAAAA
1228207 TTTCATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (23 bp):
TTAACTTGAAATAAAATAAAAAA
Found at i:1236522 original size:22 final size:21
Alignment explanation
Indices: 1236487--1236530 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
1236477 CCCTATGTAA
1236487 GAGAAGATTTATTTATGATTTT
1 GAGAAGATTTATTTAT-ATTTT
*
1236509 GAGAA-ATTTAATTTGTATTTT
1 GAGAAGATTT-ATTTATATTTT
1236530 G
1 G
1236531 GATTAAGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (21 bp):
GAGAAGATTTATTTATATTTT
Found at i:1248536 original size:65 final size:65
Alignment explanation
Indices: 1248442--1248589 Score: 199
Period size: 65 Copynumber: 2.3 Consensus size: 65
1248432 TATACTAGGG
* * ** *
1248442 GTGCATCGGTACACTAATTACATTCGATGTTTCAAAAAATCCAGGAGTGCATTGATGCATGG-TA
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAAAAAATCCAAAAGTGCATCGATGCATGGCT-
1248506 T
65 T
* * * *
1248507 GTGCATCGGTACACAAAATGCATTTGATGTTTCAAAATATTCAAAAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAAAAAATCCAAAAGTGCATCGATGCATGGCTT
1248572 GTGCATCGGTACACAAAA
1 GTGCATCGGTACACAAAA
1248590 ATGGGTGTGC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 72 0.99
66 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATACATTCGATGTTTCAAAAAATCCAAAAGTGCATCGATGCATGGCTT
Found at i:1249280 original size:18 final size:21
Alignment explanation
Indices: 1249257--1249297 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
1249247 TTAAACATCT
1249257 AACATCCAA-A-A-CAATTCA
1 AACATCCAACATATCAATTCA
1249275 AACATCCAACATATCAATTCA
1 AACATCCAACATATCAATTCA
1249296 AA
1 AA
1249298 AGCATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 1 0.05
21 9 0.45
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.20
Consensus pattern (21 bp):
AACATCCAACATATCAATTCA
Found at i:1287627 original size:10 final size:9
Alignment explanation
Indices: 1287595--1287681 Score: 57
Period size: 10 Copynumber: 9.1 Consensus size: 9
1287585 GCTGCTGGAA
*
1287595 ACCGGTTTA
1 ACCGGTTTG
* *
1287604 ACCGTTTTCA
1 ACCGGTTT-G
1287614 ACCGGTTCTG
1 ACCGGTT-TG
1287624 ACCGGTTTG
1 ACCGGTTTG
*
1287633 ACCGGTTTCA
1 ACCGGTTT-G
* *
1287643 AACGGTTCG
1 ACCGGTTTG
1287652 AACCGGTTTG
1 -ACCGGTTTG
*
1287662 ACCGGTCTG
1 ACCGGTTTG
*
1287671 AATCGGTTTG
1 -ACCGGTTTG
1287681 A
1 A
1287682 GGTCTGACTG
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
9 26 0.43
10 34 0.56
11 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1287641 original size:29 final size:29
Alignment explanation
Indices: 1287594--1287667 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
1287584 GGCTGCTGGA
* * *
1287594 AACCGGTTTAACCGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGGTTTCAAACGGTTC-G
1287624 -ACCGGTTTGACCGGTTTCAAACGGTTCG
1 AACCGGTTTGACCGGTTTCAAACGGTTCG
1287652 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
1287668 CTGAATCGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 39 0.98
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTTCAAACGGTTCG
Found at i:1287667 original size:19 final size:19
Alignment explanation
Indices: 1287594--1287681 Score: 65
Period size: 19 Copynumber: 4.6 Consensus size: 19
1287584 GGCTGCTGGA
* *
1287594 AACCGGTTTAACCGTTTTC-
1 AACCGGTTTGACCG-GTTCG
*
1287613 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTTCG
* *
1287633 -ACCGGTTTCAAACGGTTCG
1 AACCGGTTT-GACCGGTTCG
1287652 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
1287671 AATCGGTTTGA
1 AACCGGTTTGA
1287682 GGTCTGACTG
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
18 3 0.05
19 39 0.71
20 13 0.24
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:1287677 original size:29 final size:29
Alignment explanation
Indices: 1287595--1287678 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
1287585 GCTGCTGGAA
* * * *
1287595 ACCGGTTTAACCGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGGTCTCAAACGGTTCTG
*
1287624 ACCGGTTTGACCGGTTTCAAACGGTTC-G
1 ACCGGTTTGACCGGTCTCAAACGGTTCTG
* *
1287652 AACCGGTTTGACCGGTCTGAATCGGTT
1 -ACCGGTTTGACCGGTCTCAAACGGTT
1287679 TGAGGTCTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
28 1 0.02
29 47 0.98
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (29 bp):
ACCGGTTTGACCGGTCTCAAACGGTTCTG
Found at i:1287716 original size:17 final size:18
Alignment explanation
Indices: 1287691--1287737 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
1287681 AGGTCTGACT
*
1287691 GACCCTTGACCCGACC-C
1 GACCGTTGACCCGACCGC
*
1287708 GACCGTTGACCCGACCGTT
1 GACCGTTGACCCGACCG-C
1287727 GACCGTTGACC
1 GACCGTTGACC
1287738 GTTGACTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
19 11 0.42
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
GACCGTTGACCCGACCGC
Found at i:1287718 original size:12 final size:12
Alignment explanation
Indices: 1287703--1287730 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1287693 CCCTTGACCC
1287703 GACCCGACCGTT
1 GACCCGACCGTT
1287715 GACCCGACCGTT
1 GACCCGACCGTT
1287727 GACC
1 GACC
1287731 GTTGACCGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.43, G:0.25, T:0.14
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:1294825 original size:9 final size:9
Alignment explanation
Indices: 1294811--1294884 Score: 60
Period size: 9 Copynumber: 7.8 Consensus size: 9
1294801 GGCTGCTGGA
1294811 AACCGGTTT
1 AACCGGTTT
1294820 AACCGGTTTT
1 AACCGG-TTT
1294830 CAACCGGTTCT
1 -AACCGGTT-T
*
1294841 GA-CGGTTT
1 AACCGGTTT
*
1294849 GACCGGTTT
1 AACCGGTTT
*
1294858 CAACCGGTTCG
1 -AACCGGTT-T
1294869 AACCGGTTT
1 AACCGGTTT
*
1294878 GACCGGT
1 AACCGGT
1294885 CTGAATCGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
8 3 0.06
9 23 0.43
10 21 0.39
11 7 0.13
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1294836 original size:11 final size:10
Alignment explanation
Indices: 1294811--1294877 Score: 50
Period size: 10 Copynumber: 6.9 Consensus size: 10
1294801 GGCTGCTGGA
1294811 AACCGG-TTT
1 AACCGGTTTT
1294820 AACCGGTTTT
1 AACCGGTTTT
*
1294830 CAACCGGTTCT
1 -AACCGGTTTT
*
1294841 GA-CGG-TTT
1 AACCGGTTTT
* *
1294849 GACCGGTTTC
1 AACCGGTTTT
**
1294859 AACCGGTTCG
1 AACCGGTTTT
1294869 AACCGGTTT
1 AACCGGTTT
1294878 GACCGGTCTG
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
8 4 0.09
9 12 0.26
10 21 0.46
11 9 0.20
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.31
Consensus pattern (10 bp):
AACCGGTTTT
Found at i:1294856 original size:29 final size:30
Alignment explanation
Indices: 1294811--1294884 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
1294801 GGCTGCTGGA
*
1294811 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGGTTTTCAACCGGTTC-G
1294842 -A-CGGTTTGACCGG-TTTCAACCGGTTCG
1 AACCGGTTTGACCGGTTTTCAACCGGTTCG
1294869 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
1294885 CTGAATCGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 1 0.03
28 14 0.36
29 23 0.59
30 1 0.03
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTTCAACCGGTTCG
Found at i:1294882 original size:19 final size:19
Alignment explanation
Indices: 1294811--1294899 Score: 69
Period size: 19 Copynumber: 4.6 Consensus size: 19
1294801 GGCTGCTGGA
*
1294811 AACCGGTTTAACCGGTTTTC-
1 AACCGGTTTGACCGG--TTCG
*
1294831 AACCGGTTCTGA-CGGTTTG
1 AACCGGTT-TGACCGGTTCG
*
1294850 -ACCGGTTTCAACCGGTTCG
1 AACCGGTTT-GACCGGTTCG
1294869 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
1294888 AATCGGTTTGAC
1 AACCGGTTTGAC
1294900 TGGTCTGACC
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.02
18 12 0.21
19 23 0.40
20 19 0.33
21 2 0.04
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:1294928 original size:12 final size:12
Alignment explanation
Indices: 1294911--1294960 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
1294901 GGTCTGACCC
1294911 GACCCGACCGTT
1 GACCCGACCGTT
*
1294923 GACCCGACC--C
1 GACCCGACCGTT
1294933 GACCCGACCGTT
1 GACCCGACCGTT
1294945 GACCCGACCGTT
1 GACCCGACCGTT
1294957 GACC
1 GACC
1294961 GTTGACCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 9 0.26
12 25 0.74
ACGTcount: A:0.18, C:0.46, G:0.24, T:0.12
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:1294934 original size:22 final size:22
Alignment explanation
Indices: 1294906--1294953 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1294896 TGACTGGTCT
1294906 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1294928 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1294950 GACC
1 GACC
1294954 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:1311825 original size:14 final size:13
Alignment explanation
Indices: 1311797--1311854 Score: 57
Period size: 13 Copynumber: 4.3 Consensus size: 13
1311787 AAATTTTCTA
1311797 TTTTTAAAGTATTT
1 TTTTTAAA-TATTT
*
1311811 TTTTCAAATATTT
1 TTTTTAAATATTT
1311824 TTTTTAAA-ATCTGT
1 TTTTTAAATAT-T-T
1311838 TTTTT-AATAATTT
1 TTTTTAAAT-ATTT
1311851 TTTT
1 TTTT
1311855 GGGAATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 2 0.05
13 20 0.53
14 14 0.37
15 2 0.05
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (13 bp):
TTTTTAAATATTT
Found at i:1314394 original size:396 final size:398
Alignment explanation
Indices: 1313661--1314446 Score: 1486
Period size: 396 Copynumber: 2.0 Consensus size: 398
1313651 TTCAGGTCCG
1313661 TCAGTATTGGCACTGGAAGAACAATACTGATATTGTTCTTCATGAAAAGCAAAAACCAAACATGT
1 TCAGTATTGGCACTGGAAGAACAATACTGATATTGTTCTTCATGAAAAGCAAAAACCAAACATGT
*
1313726 TGTAAGGGAAGTATCGATACTTAACTGGTCAATATCGATACCGAGACATTTTCGAAAACATCAAA
66 TGTAAGGGAAGTATCGATACTCAACTGGTCAATATCGATACCGAGACATTTTCGAAAACATCAAA
1313791 GTTGATTTTGGTATCAATATTCCCAATAGGAGTATAGATACCCAGTTATTTTTTAAAACATTGAA
131 GTTGATTTTGGTATCAATATTCCCAATAGGAGTATAGATACCCAGTTATTTTTTAAAACATTGAA
*
1313856 GCAAATTTTTGTATCGATACTCGAGTATTAATATTATTGGCCCAATATCGATATCCACGGTGAAT
196 GCAAATTTTTGTATCGATACTCGAGTATTAATATTACTGGCCCAATATCGATATCCACGGTGAAT
1313921 TTTGGGTAATTTTAGTTAATTTGTTTTTGTGTTCAGAATGAGGTGTTTTGAGTTCGTATAAACCA
261 TTTGGGTAATTTTAGTTAATTTGTTTTTGTGTTCAGAATGAGGTGTTTTGAGTTCGTATAAACCA
1313986 CAAGTATTCAACACAAGTGAAAACAATCAATATAACTCAATTCTCACCTAAAAATCATGC-AAGA
326 CAAGTATTCAACACAAGTGAAAACAATCAATATAACTCAATTCTCACCTAAAAATCATGCTAAGA
1314050 TAGTACCA
391 TAGTACCA
* *
1314058 TCAGTATTGGCACTGGAAGAACAATACTGATATTGTTCTTCGTGAAAGGCAAAAACCAAACATGT
1 TCAGTATTGGCACTGGAAGAACAATACTGATATTGTTCTTCATGAAAAGCAAAAACCAAACATGT
*
1314123 TGTAAGGGAAGTATCGATACTCAACTGGTCAGTATCGATACCGAGACATTTT-GAAAACATCAAA
66 TGTAAGGGAAGTATCGATACTCAACTGGTCAATATCGATACCGAGACATTTTCGAAAACATCAAA
*
1314187 GTTGATTTTGGTATCAATATTCCCCATAGGAGTATAGATACCCAGTTATTTTTTAAAACATTGAA
131 GTTGATTTTGGTATCAATATTCCCAATAGGAGTATAGATACCCAGTTATTTTTTAAAACATTGAA
*
1314252 GCAAATTTTTGTATCGATACTCGAGTATTGATATTACTGGCCCAATATCGATATCCACGGTGAAT
196 GCAAATTTTTGTATCGATACTCGAGTATTAATATTACTGGCCCAATATCGATATCCACGGTGAAT
*
1314317 TTTGGGTAATTTTAGTTAATTTGTTTTTGTGTTCAGGATGAGGTGTTTTGAGTTCGTATAAACCA
261 TTTGGGTAATTTTAGTTAATTTGTTTTTGTGTTCAGAATGAGGTGTTTTGAGTTCGTATAAACCA
1314382 CAAGTATTCAACACAAGTGAAAACAATCAATATAACTCAATTCTCACCTAAAAATCATGCTAAGA
326 CAAGTATTCAACACAAGTGAAAACAATCAATATAACTCAATTCTCACCTAAAAATCATGCTAAGA
1314447 CACTCGGGTT
Statistics
Matches: 380, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
396 263 0.69
397 117 0.31
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (398 bp):
TCAGTATTGGCACTGGAAGAACAATACTGATATTGTTCTTCATGAAAAGCAAAAACCAAACATGT
TGTAAGGGAAGTATCGATACTCAACTGGTCAATATCGATACCGAGACATTTTCGAAAACATCAAA
GTTGATTTTGGTATCAATATTCCCAATAGGAGTATAGATACCCAGTTATTTTTTAAAACATTGAA
GCAAATTTTTGTATCGATACTCGAGTATTAATATTACTGGCCCAATATCGATATCCACGGTGAAT
TTTGGGTAATTTTAGTTAATTTGTTTTTGTGTTCAGAATGAGGTGTTTTGAGTTCGTATAAACCA
CAAGTATTCAACACAAGTGAAAACAATCAATATAACTCAATTCTCACCTAAAAATCATGCTAAGA
TAGTACCA
Found at i:1331000 original size:6 final size:6
Alignment explanation
Indices: 1330989--1331017 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1330979 AAGACCTATG
1330989 GGTCAT GGTCAT GGTCAT GGTCAT GGTCA
1 GGTCAT GGTCAT GGTCAT GGTCAT GGTCA
1331018 CAGTCATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.31
Consensus pattern (6 bp):
GGTCAT
Found at i:1331023 original size:18 final size:18
Alignment explanation
Indices: 1330989--1331025 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1330979 AAGACCTATG
**
1330989 GGTCATGGTCATGGTCAT
1 GGTCATGGTCACAGTCAT
1331007 GGTCATGGTCACAGTCAT
1 GGTCATGGTCACAGTCAT
1331025 G
1 G
1331026 ATACAAGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (18 bp):
GGTCATGGTCACAGTCAT
Found at i:1332150 original size:18 final size:17
Alignment explanation
Indices: 1332127--1332202 Score: 75
Period size: 18 Copynumber: 4.4 Consensus size: 17
1332117 ATAGAAAACG
*
1332127 AAAATGAAAACGAAGAAA
1 AAAATGAAAATG-AGAAA
*
1332145 AAAATGAATATGAGAAA
1 AAAATGAAAATGAGAAA
1332162 GAAAA-G-AAATAGAGAAA
1 -AAAATGAAAAT-GAGAAA
*
1332179 AAAATGAGAAATGAAAAA
1 AAAATGA-AAATGAGAAA
1332197 AAAATG
1 AAAATG
1332203 CGAGACTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
16 7 0.14
17 13 0.27
18 25 0.51
19 4 0.08
ACGTcount: A:0.70, C:0.01, G:0.18, T:0.11
Consensus pattern (17 bp):
AAAATGAAAATGAGAAA
Found at i:1332160 original size:17 final size:16
Alignment explanation
Indices: 1332140--1332202 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 16
1332130 ATGAAAACGA
1332140 AGAAAAAAATGAATATG
1 AGAAAAAAATGAA-ATG
1332157 AGAAAGAAAA-GAAATAG
1 AGAAA-AAAATGAAAT-G
1332174 AGAAAAAAATGAGAAATG
1 AGAAAAAAAT--GAAATG
*
1332192 AAAAAAAAATG
1 AGAAAAAAATG
1332203 CGAGACTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
16 7 0.17
17 14 0.35
18 14 0.35
19 5 0.12
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (16 bp):
AGAAAAAAATGAAATG
Found at i:1336202 original size:44 final size:46
Alignment explanation
Indices: 1336152--1336261 Score: 134
Period size: 47 Copynumber: 2.4 Consensus size: 46
1336142 GTAACCATGC
* * *
1336152 AAATAAGCTAATGAGCTTACGGAA-T-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTACAGAATTAAATGGCAAGTATATTGGAA
* * * *
1336196 AAATAAGCTTACGAGCTTATAGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTACAGAA-TTAAATGGCAAGTATATTGGAA
1336243 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
1336262 TGGGATGAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
44 20 0.36
46 1 0.02
47 35 0.62
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTACAGAATTAAATGGCAAGTATATTGGAA
Found at i:1336747 original size:22 final size:22
Alignment explanation
Indices: 1336722--1336774 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
1336712 AAAGGGGTAC
1336722 CGATTCCCCTGCTACTGGGAAT
1 CGATTCCCCTGCTACTGGGAAT
1336744 CGATTCCCCTGCTACTGGGAAT
1 CGATTCCCCTGCTACTGGGAAT
1336766 CGATTCCCC
1 CGATTCCCC
1336775 CACTGTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.36, G:0.21, T:0.26
Consensus pattern (22 bp):
CGATTCCCCTGCTACTGGGAAT
Found at i:1339232 original size:44 final size:45
Alignment explanation
Indices: 1339112--1339237 Score: 191
Period size: 47 Copynumber: 2.8 Consensus size: 45
1339102 TATAAAATCT
1339112 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1339157 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1339204 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1339238 GTATGCTTAC
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
44 24 0.32
45 10 0.13
46 2 0.03
47 39 0.52
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1339438 original size:59 final size:59
Alignment explanation
Indices: 1339346--1339474 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 59
1339336 CGTAGTGCTA
* * **
1339346 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
1339405 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
1339464 TCCCGAATATG
1 TCCCGAATATG
1339475 CAGCCTGCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:1341784 original size:7 final size:6
Alignment explanation
Indices: 1341747--1341781 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
1341737 CAATACAAAG
*
1341747 TTTTCC TTTGCC TTTTCC TTTTCC TTTTTCC TTTT
1 TTTTCC TTTTCC TTTTCC TTTTCC -TTTTCC TTTT
1341782 TCCCTCTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.69
Consensus pattern (6 bp):
TTTTCC
Found at i:1342410 original size:60 final size:60
Alignment explanation
Indices: 1342334--1342511 Score: 205
Period size: 60 Copynumber: 3.0 Consensus size: 60
1342324 AAACATACCC
* * * * *
1342334 AAACTATAACTTTCATTCTAAATTGGTCTTTAAACTTTTGGACATTTTAATTTCATCCCT
1 AAACTATAGCTCTCATTCTAAATTGGTCCTTAAACTTTTGAACATTCTAATTTCATCCCT
* * *
1342394 AAACTATCAG-TCTCATTCTAAATTAGTCCTTAAACTCTTGAACATTCTAATTTCATTCCT
1 AAACTAT-AGCTCTCATTCTAAATTGGTCCTTAAACTTTTGAACATTCTAATTTCATCCCT
* * * * * * *
1342454 AAACTATGGCTCTCTTTATAAATTGGTCCCTAAACTTTTGCATATTCCAATTTCATCC
1 AAACTATAGCTCTCATTCTAAATTGGTCCTTAAACTTTTGAACATTCTAATTTCATCC
1342512 AAATTTCATC
Statistics
Matches: 98, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.01
60 96 0.98
61 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.42
Consensus pattern (60 bp):
AAACTATAGCTCTCATTCTAAATTGGTCCTTAAACTTTTGAACATTCTAATTTCATCCCT
Found at i:1342518 original size:11 final size:11
Alignment explanation
Indices: 1342502--1342528 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1342492 TGCATATTCC
1342502 AATTTCATCCA
1 AATTTCATCCA
1342513 AATTTCATCCA
1 AATTTCATCCA
1342524 AATTT
1 AATTT
1342529 GTAATTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (11 bp):
AATTTCATCCA
Found at i:1351560 original size:40 final size:41
Alignment explanation
Indices: 1351475--1351565 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 41
1351465 GATTACACAC
1351475 ATATATATATATGTTAATTTTCATTATCTGTTTTATTAATT
1 ATATATATATATGTTAATTTTCATTATCTGTTTTATTAATT
* * *
1351516 -TATATATATAT-TTACTATTTT-TTTATGT-TTTTATTTATT
1 ATATATATATATGTTA--ATTTTCATTATCTGTTTTATTAATT
1351555 ATATATATATA
1 ATATATATATA
1351566 CATATTATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
39 13 0.30
40 26 0.59
41 5 0.11
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (41 bp):
ATATATATATATGTTAATTTTCATTATCTGTTTTATTAATT
Found at i:1351757 original size:12 final size:13
Alignment explanation
Indices: 1351719--1351764 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
1351709 TTTTATGGAC
*
1351719 TTTATTTTTTTTA
1 TTTATTTATTTTA
1351732 TGTCT-TTTATTTTA
1 T-T-TATTTATTTTA
1351746 TTTATTTA-TTTA
1 TTTATTTATTTTA
1351758 TTTATTT
1 TTTATTT
1351765 TTCTTTTCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 12 0.41
13 6 0.21
14 10 0.34
15 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:1356004 original size:183 final size:183
Alignment explanation
Indices: 1355696--1356049 Score: 627
Period size: 183 Copynumber: 1.9 Consensus size: 183
1355686 ATTAAATCCG
*
1355696 TAAAGCTGAGCTATTCCACTAAGGCAATTTGTTATAGAGGAAACTCGAAAGCCCTGACTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGACTTTATGA
* * *
1355761 ATATATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACATTGCTCAGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
*
1355826 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGGCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
*
1355879 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGACTTTATGA
* *
1355944 ATAGATTACATTCAAACCATGACATTGCTCAGACTCTTGGCAATTCAGTGTTTTCTCCACTACTT
66 ATAGATTACATTCAAACCATGACATTGCTCAGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
*
1356009 TTGGCAGGCCAAAGACTTTGTGATGATACGAACCCTTCAGT
131 TTGGCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGT
1356050 TAAACTTGGT
Statistics
Matches: 162, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 162 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGACTTTATGA
ATAGATTACATTCAAACCATGACATTGCTCAGACACTTGGCAATTCAGTGTTTGCTCCACTACTT
TTGGCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
Found at i:1357251 original size:72 final size:75
Alignment explanation
Indices: 1357175--1357317 Score: 220
Period size: 72 Copynumber: 1.9 Consensus size: 75
1357165 TTGAGATTAT
* **
1357175 TTTTCTTAAAACATAATTTGTCTCACTTGAGACTGTTTT-ACTCGAAAGAAG-ATTT-ATTTCAC
1 TTTTCTTAAAACAGAATTTGTCTCACTTGAGACCATTTTCACTCGAAAGAAGCATTTCATTTCAC
1357237 TCAAGTTTTC
66 TCAAGTTTTC
*
1357247 TTTTCTTAAAACAGACTTTGTCTCACTTGAGACCATTTTCACTCGAAAGAAGTCATTTCATTTCA
1 TTTTCTTAAAACAGAATTTGTCTCACTTGAGACCATTTTCACTCGAAAGAAG-CATTTCATTTCA
1357312 CTCAAG
65 CTCAAG
1357318 ACTATTTTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
72 35 0.56
73 12 0.19
75 4 0.06
76 12 0.19
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (75 bp):
TTTTCTTAAAACAGAATTTGTCTCACTTGAGACCATTTTCACTCGAAAGAAGCATTTCATTTCAC
TCAAGTTTTC
Found at i:1357504 original size:37 final size:37
Alignment explanation
Indices: 1357444--1357529 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 37
1357434 TTGAAAAAAT
** * *
1357444 TTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAGG
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGG
*
1357480 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGT
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGG
*
1357517 TTCTCTTGAAACA
1 TTCCCTTGAAACA
1357530 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 11 0.26
37 32 0.74
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (37 bp):
TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGG
Found at i:1357522 original size:102 final size:102
Alignment explanation
Indices: 1357398--1357595 Score: 351
Period size: 102 Copynumber: 1.9 Consensus size: 102
1357388 ACTAGGTTTC
* *
1357398 GTCTCTCTTGAGACGGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTT
1 GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTT
1357463 GTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATTTT
66 GTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATTTT
*
1357500 GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTT
1 GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTT
* *
1357565 GTCTCTCTTGAGATAGTTTCTCTTGAAACAA
66 GTCTCTCTTGAGATAGGTTCCCTTGAAACAA
1357596 CATCTTTGAA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 91 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (102 bp):
GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTT
GTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATTTT
Found at i:1357605 original size:65 final size:65
Alignment explanation
Indices: 1357480--1357650 Score: 200
Period size: 65 Copynumber: 2.6 Consensus size: 65
1357470 TTGAGATAGG
1357480 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
1 TTCCCTTGAAA-AAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
1357545 T
65 T
** * * * * ****
1357546 TTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-ACATCTTTGAATTTG
1 TTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA-AACATTGAAAACA
1357610 T
65 T
* * *
1357611 TTCCCTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCT
1 TTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTCT
1357651 TTTGGAACTA
Statistics
Matches: 88, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 1 0.01
65 76 0.86
66 11 0.12
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (65 bp):
TTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACAT
Found at i:1357679 original size:167 final size:167
Alignment explanation
Indices: 1357398--1357758 Score: 463
Period size: 167 Copynumber: 2.2 Consensus size: 167
1357388 ACTAGGTTTC
** ** *
1357398 GTCTCTCTTGAGACGGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTT
1 GTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAACAAATTTC
* * *
1357463 GTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
66 GTCTCCCTTGAGACAGGTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAA
*
1357528 CATAAACATTGAAAACATTTCCCTTGAAATGAATTTT
131 CATAAACATTAAAAACATTTCCCTTGAAATGAATTTT
* * ****
1357565 GTCTCTCTTGAGATAGTTTCTCTTGAAACA-ACATCTTTGAATTTGTTTCCCTTGAAACAAATTT
1 GTCTCTCTTGAGATAGTTTCTCTTGAAACATA-AACATTGAAAAAATTTCCCTTGAAACAAATTT
** ** * * * * *
1357629 CGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTATCTCTCTTGAGATAGTTTCTCTTGAA
65 CGTCTCCCTTGAGACAGGTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAA
1357694 ACATAAACATTAAAAACATTTCCCTTGAAATGAATTTT
130 ACATAAACATTAAAAACATTTCCCTTGAAATGAATTTT
* * *
1357732 ATCTCTCTTGAGATAGGTTCCCTTGAA
1 GTCTCTCTTGAGATAGTTTCTCTTGAA
1357759 GCAAAATTTT
Statistics
Matches: 166, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
166 1 0.01
167 165 0.99
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (167 bp):
GTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAACAAATTTC
GTCTCCCTTGAGACAGGTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAA
CATAAACATTAAAAACATTTCCCTTGAAATGAATTTT
Found at i:1357700 original size:269 final size:269
Alignment explanation
Indices: 1357346--1357864 Score: 914
Period size: 269 Copynumber: 1.9 Consensus size: 269
1357336 TTTTATCTCT
* * *
1357346 CTTGAAACCAATTTCGTCTCCCTTGAGACATTTTCTTTTAGAACTAGGTTTCGTCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTAGAACTAAGTTTCATCTCTCTTGAGA
* *
1357411 CGGTTTCTCTTGAAACATAAACATTGAAAAA-ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAG
66 CAGTTTCTCTTGAAACATAAACATT-AAAAACATTTCCCTTGAAATGAATTTTATCTCTCTTGAG
1357475 ATAGGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
130 ATAGGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGA
* * *
1357540 AAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAACATCTTTGA
195 AAACATTTCCCTTGAAATGAATTTTGTCACTCATGAGATAGTTTCCCTTGAAACAACATCTTTGA
1357605 ATTTGTTTCC
260 ATTTGTTTCC
* *
1357615 CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTATCTCTCTTGAGA
1 CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTAGAACTAAGTTTCATCTCTCTTGAGA
*
1357680 TAGTTTCTCTTGAAACATAAACATTAAAAACATTTCCCTTGAAATGAATTTTATCTCTCTTGAGA
66 CAGTTTCTCTTGAAACATAAACATTAAAAACATTTCCCTTGAAATGAATTTTATCTCTCTTGAGA
*
1357745 TAGGTTCCCTTGAAGCAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAA
131 TAGGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAA
1357810 AACATTTCCCTTGAAATGAATTTTGTCACTCATGAGATAGTTTCCCTTGAAACAA
196 AACATTTCCCTTGAAATGAATTTTGTCACTCATGAGATAGTTTCCCTTGAAACAA
1357865 ATTTTGTCTC
Statistics
Matches: 237, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
268 5 0.02
269 232 0.98
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (269 bp):
CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCTTTTAGAACTAAGTTTCATCTCTCTTGAGA
CAGTTTCTCTTGAAACATAAACATTAAAAACATTTCCCTTGAAATGAATTTTATCTCTCTTGAGA
TAGGTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAA
AACATTTCCCTTGAAATGAATTTTGTCACTCATGAGATAGTTTCCCTTGAAACAACATCTTTGAA
TTTGTTTCC
Found at i:1357716 original size:102 final size:101
Alignment explanation
Indices: 1357545--1357931 Score: 409
Period size: 102 Copynumber: 3.8 Consensus size: 101
1357535 ATTGAAAACA
* ** * * * * ***
1357545 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-ACATCTTTGAATTT
1 TTTCCCTTGGAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA-AACATTGAAAAC
* * * * *
1357609 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAT
65 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
** * * * * *
1357646 TTTCTTTTGGAACTAAGTTTTATCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTAAAAAC
1 TTTCCCTTGGAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
** *
1357711 ATTTCCCTTGAAATGAATTTTATCTCTCTTGAGATAG
65 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
*
1357748 GTTCCCTT-GAAGCAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
1 TTTCCCTTGGAA-C-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
** * *
1357812 CATTTCCCTTGAAATGAATTTTGTCACTCATGAGATAG
64 CATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
* * *
1357850 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAGCATAAACTTTGAAAACA
1 TTTCCCTTGGAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC-
*
1357915 ATTTCCTTTGAAACAAA
65 ATTTCCCTTGAAACAAA
1357932 ATCTTTGAAT
Statistics
Matches: 241, Mismatches: 40, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
101 61 0.25
102 177 0.73
103 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (101 bp):
TTTCCCTTGGAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
Found at i:1357769 original size:204 final size:204
Alignment explanation
Indices: 1357559--1357927 Score: 463
Period size: 204 Copynumber: 1.8 Consensus size: 204
1357549 CCTTGAAATG
* * * * ****
1357559 AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-ACATCTTTGAATTTGTTTCCCTTGAAAC
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATA-AACATTGAAAACATTTCCCTTGAAAC
* * * ** * * * *
1357623 AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACTAAGTTTTATCTCTCTTGAGATAGTTTCT
65 AAATTTCGTCACCCATGAGACAGTTTCCCTTGAAAC-AAATTTTATCTCCCTTGAGACAGTTTCT
1357688 CTTGAAACATAAACATTAAAAAC-ATTTCCCTTGAAATGAATTTTATCTCTCTTGAGATAGGTTC
129 CTTGAAACATAAACATTAAAAACAATTTCCCTTGAAATGAATTTTATCTCTCTTGAGATAGGTTC
1357752 CCTTGAAGCAA
194 CCTTGAAGCAA
**
1357763 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAACA
* * * *
1357828 AATTTTGTCACTCATGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCT
66 AATTTCGTCACCCATGAGACAGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTTTCTCT
* * * *
1357893 TGAAGCATAAACTTTGAAAACAATTTCCTTTGAAA
131 TGAAACATAAACATTAAAAACAATTTCCCTTGAAA
1357928 CAAAATCTTT
Statistics
Matches: 136, Mismatches: 27, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
203 44 0.32
204 91 0.67
205 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (204 bp):
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAACA
AATTTCGTCACCCATGAGACAGTTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTAAAAACAATTTCCCTTGAAATGAATTTTATCTCTCTTGAGATAGGTTCCC
TTGAAGCAA
Found at i:1357861 original size:36 final size:36
Alignment explanation
Indices: 1357814--1357896 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
1357804 ATTGAAAACA
** * *
1357814 TTTCCCTTGAAATGAATTTTGTCACTCATGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCACCCATGAGACAG
* *
1357850 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCACCCATGAGACAG
*
1357886 TTTCTCTTGAA
1 TTTCCCTTGAA
1357897 GCATAAACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCACCCATGAGACAG
Found at i:1358046 original size:36 final size:36
Alignment explanation
Indices: 1357995--1358063 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1357985 TTTTGGAAGT
*
1357995 TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAA
* *
1358031 TTTTGTCTCTGTTGAGACAGTTTCCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAAC
1358064 TTCAATCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAA
Found at i:1359367 original size:43 final size:43
Alignment explanation
Indices: 1359320--1359404 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
1359310 TTTATTAATT
* * * *
1359320 TATATATATAT-TTA-CTATTTT-TTTATTTTTTATTTATTTTA
1 TATATATACATATTATC-ATTTTATTTATCTTATATCTATTTTA
1359361 TATATATACATATTATCATTTTATTTATCTTATATCTATTTTA
1 TATATATACATATTATCATTTTATTTATCTTATATCTATTTTA
1359404 T
1 T
1359405 TTATTTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
41 10 0.27
42 8 0.22
43 19 0.51
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (43 bp):
TATATATACATATTATCATTTTATTTATCTTATATCTATTTTA
Found at i:1359383 original size:39 final size:39
Alignment explanation
Indices: 1359308--1359404 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 39
1359298 TCATTATCTG
* ** **
1359308 TTTTTA-TTAATTTATATATATATTTACTATTTTTTTAT
1 TTTTTATTTATTTTATATATATACATACTATCATTTTAT
*
1359346 TTTTTATTTATTTTATATATATACATATTATCATTTTAT
1 TTTTTATTTATTTTATATATATACATACTATCATTTTAT
1359385 TTATCTTATATCTATTTTAT
1 TT-T-TTAT-T-TATTTTAT
1359405 TTATTTAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
38 6 0.12
39 28 0.58
40 1 0.02
41 4 0.08
42 1 0.02
43 8 0.17
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (39 bp):
TTTTTATTTATTTTATATATATACATACTATCATTTTAT
Found at i:1359579 original size:29 final size:30
Alignment explanation
Indices: 1359521--1359582 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1359511 TTTTATGGAC
*
1359521 TTTATTTTTTTATGTCTTTTATTTTATTTA
1 TTTATTTTTTTATGTCTTTTAGTTTATTTA
* *
1359551 TTTATTTTTCTT-T-TCTTTTCGTTTCTTTA
1 TTTATTTTT-TTATGTCTTTTAGTTTATTTA
1359580 TTT
1 TTT
1359583 TTATTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 16 0.57
30 10 0.36
31 2 0.07
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.77
Consensus pattern (30 bp):
TTTATTTTTTTATGTCTTTTAGTTTATTTA
Found at i:1364899 original size:29 final size:31
Alignment explanation
Indices: 1364843--1364901 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
1364833 AATTTAAGGT
*
1364843 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAATGGTATTTGGACTTGAATTGAATTTAC
1364874 AAAAT-GTATTTGGACTT-AATTGAATTTA
1 AAAATGGTATTTGGACTTGAATTGAATTTA
1364902 TGAAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAATGGTATTTGGACTTGAATTGAATTTAC
Found at i:1364999 original size:19 final size:19
Alignment explanation
Indices: 1364971--1365031 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
1364961 TTTTATAAAT
* *
1364971 AGTAATTTACTATTTGAAA
1 AGTAAATTACTATTTGAAC
1364990 AGTAAATTACTATTTGAAC
1 AGTAAATTACTATTTGAAC
* *
1365009 AGTAAATCACTGTTTGAAC
1 AGTAAATTACTATTTGAAC
1365028 AGTA
1 AGTA
1365032 CCCCCCGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
AGTAAATTACTATTTGAAC
Found at i:1365167 original size:21 final size:21
Alignment explanation
Indices: 1365141--1365182 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1365131 ATTTGAATAT
*
1365141 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1365162 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1365183 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1366197 original size:3 final size:3
Alignment explanation
Indices: 1366191--1366253 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
1366181 AATATTATTC
*
1366191 TAT TAT TAT TTT TAT TAT TA- TATT TAT TAT TA- TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
1366234 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1366254 CACGTTTTGC
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
2 6 0.11
3 46 0.85
4 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1369031 original size:32 final size:32
Alignment explanation
Indices: 1368993--1369069 Score: 145
Period size: 32 Copynumber: 2.4 Consensus size: 32
1368983 ATGGGTACAA
*
1368993 ATTTTCAAATCCACACCCGCCCACGCGGGTAC
1 ATTTTCAAATCCACACCCGCCCACGCGAGTAC
1369025 ATTTTCAAATCCACACCCGCCCACGCGAGTAC
1 ATTTTCAAATCCACACCCGCCCACGCGAGTAC
1369057 ATTTTCAAATCCA
1 ATTTTCAAATCCA
1369070 TCCCCACACC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.29, C:0.38, G:0.12, T:0.22
Consensus pattern (32 bp):
ATTTTCAAATCCACACCCGCCCACGCGAGTAC
Found at i:1369599 original size:15 final size:15
Alignment explanation
Indices: 1369579--1369615 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1369569 ATATTTAGTT
*
1369579 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
1369594 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
1369609 GGGCGGG
1 GGGCGGG
1369616 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:1371112 original size:20 final size:20
Alignment explanation
Indices: 1371087--1371135 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1371077 TGACCCTAGG
*
1371087 GTATCGATATTGCTAGTAGA
1 GTATCGATATTGCGAGTAGA
1371107 GTATCGATATTGCGAGTAGA
1 GTATCGATATTGCGAGTAGA
1371127 GTATCGATA
1 GTATCGATA
1371136 CTACTCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.33
Consensus pattern (20 bp):
GTATCGATATTGCGAGTAGA
Found at i:1372555 original size:17 final size:17
Alignment explanation
Indices: 1372510--1372556 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1372500 CATTTATATT
*
1372510 TTTTTATATATTTACTTT
1 TTTTTATAT-TTTACTTA
1372528 TTTTTATTATTTTA-TTCA
1 TTTTTA-TATTTTACTT-A
1372546 TTTTTATATTT
1 TTTTTATATTT
1372557 ACTGCTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.27
18 16 0.62
19 3 0.12
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTATATTTTACTTA
Found at i:1384473 original size:13 final size:13
Alignment explanation
Indices: 1384455--1384502 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
1384445 AGGCATGAGA
1384455 ATGGTGATGGAAG
1 ATGGTGATGGAAG
*
1384468 ATGGTGAT-G-AT
1 ATGGTGATGGAAG
1384479 ATAGGTGATGGAAG
1 AT-GGTGATGGAAG
*
1384493 ATGGCGATGG
1 ATGGTGATGG
1384503 TATAGGCGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 3 0.10
12 7 0.24
13 16 0.55
14 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.44, T:0.25
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:1384485 original size:25 final size:25
Alignment explanation
Indices: 1384457--1384525 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
1384447 GCATGAGAAT
1384457 GGTGATGGAAGATGGTGATGATATA
1 GGTGATGGAAGATGGTGATGATATA
* *
1384482 GGTGATGGAAGATGGCGATGGTATA
1 GGTGATGGAAGATGGTGATGATATA
* *
1384507 GGCG-T-GAAAATGGTGATGA
1 GGTGATGGAAGATGGTGATGA
1384526 ACAGATAGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 11 0.29
24 1 0.03
25 26 0.68
ACGTcount: A:0.30, C:0.03, G:0.42, T:0.25
Consensus pattern (25 bp):
GGTGATGGAAGATGGTGATGATATA
Found at i:1388089 original size:19 final size:19
Alignment explanation
Indices: 1388058--1388100 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1388048 ATGTAGGAGT
1388058 CTTTTTTCTTTTCTTTTTG
1 CTTTTTTCTTTTCTTTTTG
*
1388077 CTTTTATTC-TTTCTTTTTT
1 CTTTT-TTCTTTTCTTTTTG
1388096 CTTTT
1 CTTTT
1388101 GTTGAAGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (19 bp):
CTTTTTTCTTTTCTTTTTG
Found at i:1388538 original size:35 final size:35
Alignment explanation
Indices: 1388468--1388585 Score: 155
Period size: 36 Copynumber: 3.3 Consensus size: 35
1388458 ATGGTAATGG
* *
1388468 GATGGTAATAATATAGGTGTGAGAATGGTGATGGAA
1 GATGGTGATGATATAGGTGTGA-AATGGTGATGGAA
* *
1388504 GATGTTGATGATATAGGTGTGATATGGTGATGGAA
1 GATGGTGATGATATAGGTGTGAAATGGTGATGGAA
* * *
1388539 GATGGTGATTATATAGGCGTGAAAATGTTGATGGAA
1 GATGGTGATGATATAGGTGTG-AAATGGTGATGGAA
1388575 GATGGTGATGA
1 GATGGTGATGA
1388586 ACAATTAGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
35 30 0.42
36 41 0.58
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.31
Consensus pattern (35 bp):
GATGGTGATGATATAGGTGTGAAATGGTGATGGAA
Found at i:1396439 original size:16 final size:15
Alignment explanation
Indices: 1396414--1396460 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 15
1396404 GCTATTTTTT
1396414 AAAAAAAAAAAAAAGC
1 AAAAAAAAAAAAAA-C
1396430 AAAAACAAAAAAAAAC
1 AAAAA-AAAAAAAAAC
1396446 AAAAAAAAAACAAAA
1 AAAAAAAAAA-AAAA
1396461 AAAGCCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.17
16 15 0.52
17 9 0.31
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:1396470 original size:16 final size:14
Alignment explanation
Indices: 1396415--1396463 Score: 64
Period size: 15 Copynumber: 3.5 Consensus size: 14
1396405 CTATTTTTTA
1396415 AAAAAAAAAAAAAGC
1 AAAAAAAAAAAAA-C
*
1396430 AAAAACAAAAAAA-
1 AAAAAAAAAAAAAC
*
1396443 AACAAAAAAAAAAC
1 AAAAAAAAAAAAAC
1396457 AAAAAAA
1 AAAAAAA
1396464 GCCAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 11 0.38
14 6 0.21
15 12 0.41
ACGTcount: A:0.90, C:0.08, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:1396470 original size:21 final size:21
Alignment explanation
Indices: 1396414--1396463 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 21
1396404 GCTATTTTTT
1396414 AAAAAAAAA-AAAAAGCAAAAAC
1 AAAAAAAAACAAAAA--AAAAAC
1396436 AAAAAAAAACAAAAAAAAAAC
1 AAAAAAAAACAAAAAAAAAAC
1396457 AAAAAAA
1 AAAAAAA
1396464 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.48
22 9 0.33
23 5 0.19
ACGTcount: A:0.90, C:0.08, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAAAAAAACAAAAAAAAAAC
Found at i:1396481 original size:1 final size:1
Alignment explanation
Indices: 1396414--1396463 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
1396404 GCTATTTTTT
** * * *
1396414 AAAAAAAAAAAAAAGCAAAAACAAAAAAAAACAAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1396464 GCCAAAATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.90, C:0.08, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1403932 original size:8 final size:8
Alignment explanation
Indices: 1403919--1403944 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1403909 CATTAATGGC
1403919 ATCATATA
1 ATCATATA
1403927 ATCATATA
1 ATCATATA
1403935 ATCATATA
1 ATCATATA
1403943 AT
1 AT
1403945 TAACATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
ATCATATA
Found at i:1411325 original size:32 final size:31
Alignment explanation
Indices: 1411287--1411374 Score: 79
Period size: 32 Copynumber: 2.8 Consensus size: 31
1411277 TACACATATA
1411287 TAAATGTAATTCTGACTCTACTATGTG-TTATC
1 TAAATGTAATTCTGACTCTA-T-TGTGATTATC
* * * *
1411319 TGAATGTCATGCTAACTCTATTGTGCATTATC
1 TAAATGTAATTCTGACTCTATTGTG-ATTATC
** *
1411351 TAAATACAATTCTGACTCTGTTGT
1 TAAATGTAATTCTGACTCTATTGT
1411375 AACTCACATA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
30 4 0.09
31 1 0.02
32 38 0.88
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (31 bp):
TAAATGTAATTCTGACTCTATTGTGATTATC
Found at i:1413037 original size:9 final size:9
Alignment explanation
Indices: 1413023--1413047 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1413013 ATCACCTTTT
1413023 GCTTGAGAG
1 GCTTGAGAG
1413032 GCTTGAGAG
1 GCTTGAGAG
1413041 GCTTGAG
1 GCTTGAG
1413048 GGGGAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.12, G:0.44, T:0.24
Consensus pattern (9 bp):
GCTTGAGAG
Found at i:1428343 original size:23 final size:23
Alignment explanation
Indices: 1428313--1428392 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
1428303 GCATAGCCTT
*
1428313 GTGCATCGATGCACATTCAAATA
1 GTGCATCGATGCACATTCAAATG
*
1428336 GTGCATCGATGCACCTTC--ATG
1 GTGCATCGATGCACATTCAAATG
* * *
1428357 GTGTATTGATGCACATTCAAAGG
1 GTGCATCGATGCACATTCAAATG
1428380 GATGCATCGATGC
1 G-TGCATCGATGC
1428393 GTTGTTCAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 17 0.37
23 20 0.43
24 9 0.20
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAATG
Found at i:1433755 original size:21 final size:21
Alignment explanation
Indices: 1433729--1433776 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1433719 TGGGAGCGTT
1433729 TGGTGCATCGATGCATAAGGC
1 TGGTGCATCGATGCATAAGGC
1433750 TGGTGCATCGATGCATAAGGC
1 TGGTGCATCGATGCATAAGGC
*
1433771 TAGTGC
1 TGGTGC
1433777 GTCGGTACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (21 bp):
TGGTGCATCGATGCATAAGGC
Found at i:1433912 original size:45 final size:46
Alignment explanation
Indices: 1433843--1433949 Score: 137
Period size: 45 Copynumber: 2.3 Consensus size: 46
1433833 GGTGCACTAA
* * * *
1433843 GAGTGCATCGATGCATGAAGTGCATTCGACG-TTTCA-AACAAGCCT
1 GAGTGCATCGATGCATCAAATGCATTCGACGTTTTCATAA-AAACAT
* *
1433888 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAATAT
1 GAGTGCATCGATGCATCAAATGCATTCGACGTTTTCATAAAAACAT
1433934 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
1433950 GGTATGTGCA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 28 0.52
46 24 0.44
47 2 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (46 bp):
GAGTGCATCGATGCATCAAATGCATTCGACGTTTTCATAAAAACAT
Found at i:1458412 original size:22 final size:24
Alignment explanation
Indices: 1458385--1458429 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1458375 AAAATCAACA
*
1458385 AAGAAA-TTG-AAGCACTCAAAAG
1 AAGAAATTTGTAAGAACTCAAAAG
1458407 AAGAAATTTGTAAGAACTCAAAA
1 AAGAAATTTGTAAGAACTCAAAA
1458430 AGGAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.56, C:0.11, G:0.16, T:0.18
Consensus pattern (24 bp):
AAGAAATTTGTAAGAACTCAAAAG
Found at i:1458447 original size:14 final size:15
Alignment explanation
Indices: 1458428--1458456 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1458418 AAGAACTCAA
1458428 AAAGGAAAA-AAAAG
1 AAAGGAAAAGAAAAG
1458442 AAAGGAAAAGAAAAG
1 AAAGGAAAAGAAAAG
1458457 TTGAAACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAGGAAAAGAAAAG
Found at i:1460849 original size:35 final size:37
Alignment explanation
Indices: 1460780--1460859 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1460770 ATACTATTTC
*
1460780 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
1460817 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
1460852 CATCACCA
1 CATCACCA
1460860 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:1461487 original size:43 final size:44
Alignment explanation
Indices: 1461419--1461506 Score: 169
Period size: 43 Copynumber: 2.0 Consensus size: 44
1461409 GTTTCTTGTG
1461419 AAGGAAGATAATAAGTGTTGCAACTTGAGTTGTAAGTTATCTTC
1 AAGGAAGATAATAAGTGTTGCAACTTGAGTTGTAAGTTATCTTC
1461463 AAGGAAGATAAT-AGTGTTGCAACTTGAGTTGTAAGTTATCTTC
1 AAGGAAGATAATAAGTGTTGCAACTTGAGTTGTAAGTTATCTTC
1461506 A
1 A
1461507 TTTTCTTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 32 0.73
44 12 0.27
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (44 bp):
AAGGAAGATAATAAGTGTTGCAACTTGAGTTGTAAGTTATCTTC
Found at i:1464738 original size:35 final size:37
Alignment explanation
Indices: 1464670--1464749 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
1464660 ATACTATTTC
* *
1464670 CATCATCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
1464707 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
1464742 CATCACCA
1 CATCACCA
1464750 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:1465150 original size:20 final size:20
Alignment explanation
Indices: 1465121--1465158 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1465111 TAATAAATGG
1465121 AAGAAAGAAAT-GAAATGAT
1 AAGAAAGAAATGGAAATGAT
1465140 AAGAAAGGAAATGGAAATG
1 AAGAAA-GAAATGGAAATG
1465159 GAAATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (20 bp):
AAGAAAGAAATGGAAATGAT
Found at i:1470518 original size:40 final size:46
Alignment explanation
Indices: 1470446--1470545 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 46
1470436 AGGATTAGAT
*
1470446 TTATTATTTTATTAGGAATTAAGGTTGGGTTAA-A-ATATTTAG-TTA
1 TTATTATTTTATTAGGAATTAA-G-TGAGTTAAGACATATTTAGTTTA
*
1470491 TTATTATTTTATTAGGAATT-A-T-AGTTAAGACATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGTGAGTTAAGACATATTTAGTTTA
1470534 TTATT-TTTTATT
1 TTATTATTTTATT
1470546 CATTAGTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
40 5 0.10
41 2 0.04
42 14 0.28
43 8 0.16
44 1 0.02
45 20 0.40
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAAGTGAGTTAAGACATATTTAGTTTA
Found at i:1471345 original size:19 final size:18
Alignment explanation
Indices: 1471303--1471358 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
1471293 TACTATTTTT
1471303 AAAAAAAA-CAAAAAAA-
1 AAAAAAAAGCAAAAAAAC
1471319 AAGGAAAAAAGGCAAAAAAAC
1 AA--AAAAAA-GCAAAAAAAC
1471340 AAAAAAAAGCCAAAAAAAC
1 AAAAAAAAG-CAAAAAAAC
1471359 CAGAATTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.06
18 7 0.21
19 15 0.44
20 8 0.24
21 2 0.06
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGCAAAAAAAC
Done.