Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 27 of 153
Found at i:9465035 original size:24 final size:24
Alignment explanation
Indices: 9464986--9465036 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
9464976 CGGTGTTATC
**
9464986 TATCAGGCTTTGTGCCGGTGTATT
1 TATCAGGCTTTGTGCCAATGTATT
* *
9465010 TATCAGGCTTTGTGTCAATGTGTT
1 TATCAGGCTTTGTGCCAATGTATT
9465034 TAT
1 TAT
9465037 TGGGCTCTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.14, G:0.25, T:0.45
Consensus pattern (24 bp):
TATCAGGCTTTGTGCCAATGTATT
Found at i:9465082 original size:25 final size:25
Alignment explanation
Indices: 9465065--9465124 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
9465055 GGCTTTGTGT
9465065 TGGTGTTATCTATCAGGCCTTGAGC
1 TGGTGTTATCTATCAGGCCTTGAGC
* * *
9465090 TGGTGTTGTCTATCAAGCATTGAGC
1 TGGTGTTATCTATCAGGCCTTGAGC
9465115 TGGTGGTTAT
1 TGGT-GTTAT
9465125 TTAGCAAGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (25 bp):
TGGTGTTATCTATCAGGCCTTGAGC
Found at i:9486792 original size:40 final size:41
Alignment explanation
Indices: 9486678--9486792 Score: 128
Period size: 40 Copynumber: 2.8 Consensus size: 41
9486668 AGCGGCATTT
* **
9486678 TTAGTGGCGTTTGGCCAAAAAAGCGCCGCTAAAAATCGAGCA
1 TTAGCGGCGTTTTTCCAAAAAA-CGCCGCTAAAAATCGAGCA
* * *
9486720 TTAGCGGCG-CTTTACATAAAAA-GTCGCTAAAAAT-GAGCA
1 TTAGCGGCGTTTTTCCA-AAAAACGCCGCTAAAAATCGAGCA
*
9486759 TTAGCGGCGTTTTTCCAAAAAACGCCGCAAAAAA
1 TTAGCGGCGTTTTTCCAAAAAACGCCGCTAAAAA
9486793 CCTAAGCCGA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
39 19 0.32
40 25 0.42
41 3 0.05
42 13 0.22
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGTTTTTCCAAAAAACGCCGCTAAAAATCGAGCA
Found at i:9486933 original size:20 final size:19
Alignment explanation
Indices: 9486905--9486950 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
9486895 CCGCAAAAAC
*
9486905 ATTTTATTTGTCTATTTACT
1 ATTTAATTTGTCTATTTA-T
*
9486925 ATTTAATTTGTTTATTTAT
1 ATTTAATTTGTCTATTTAT
9486944 A-TTAATT
1 ATTTAATT
9486951 AAAATTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.25
19 2 0.08
20 16 0.67
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (19 bp):
ATTTAATTTGTCTATTTAT
Found at i:9487320 original size:14 final size:15
Alignment explanation
Indices: 9487292--9487321 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9487282 AAGGTTAATA
9487292 GATTATGGAATTAGG
1 GATTATGGAATTAGG
9487307 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
9487321 G
1 G
9487322 GTTCTAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:9487522 original size:7 final size:7
Alignment explanation
Indices: 9487450--9487548 Score: 51
Period size: 7 Copynumber: 14.1 Consensus size: 7
9487440 TATTAAATAT
9487450 GGTTTAG
1 GGTTTAG
*
9487457 GGGTTAG
1 GGTTTAG
* *
9487464 GGGTTGG
1 GGTTTAG
9487471 GGTTTAG
1 GGTTTAG
*
9487478 AG-TTAG
1 GGTTTAG
*
9487484 GGATTCA-
1 GG-TTTAG
*
9487491 GGTTCAG
1 GGTTTAG
9487498 TGG-TTAG
1 -GGTTTAG
*
9487505 GGGTTATG
1 GGTTTA-G
9487513 GGTTTAG
1 GGTTTAG
*
9487520 GGTTTAT
1 GGTTTAG
* *
9487527 GTTTTAT
1 GGTTTAG
*
9487534 GGTTTAA
1 GGTTTAG
9487541 GGTTTAG
1 GGTTTAG
9487548 G
1 G
9487549 AGATAGGGGT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
6 11 0.15
7 51 0.71
8 10 0.14
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:9487523 original size:21 final size:20
Alignment explanation
Indices: 9487450--9487523 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
9487440 TATTAAATAT
*
9487450 GGTTTAGGGGTTAGGGGTTGG
1 GGTTTA-GGGTTAGGGGTTAG
* *
9487471 GGTTTAGAGTTAGGGATTCA-
1 GGTTTAGGGTTAGGGGTT-AG
*
9487491 GGTTCAGTGGTTAGGGGTTATG
1 GGTTTAG-GGTTAGGGGTTA-G
9487513 GGTTTAGGGTT
1 GGTTTAGGGTT
9487524 TATGTTTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 17 0.40
21 19 0.45
22 6 0.14
ACGTcount: A:0.15, C:0.03, G:0.46, T:0.36
Consensus pattern (20 bp):
GGTTTAGGGTTAGGGGTTAG
Found at i:9490887 original size:43 final size:43
Alignment explanation
Indices: 9490840--9490993 Score: 143
Period size: 43 Copynumber: 3.6 Consensus size: 43
9490830 TCTTTAGCAA
* *
9490840 CATTTTTTAGAAAAGCGCCGCTAAAGATCATGGTTTATAACGG
1 CATTTTTTAGAAAAGCGCCGCTAAAGATCATGGTCTATAGCGG
* ** *
9490883 CA-TTTTTAGTAGAAGCATCGCTAAAGGTCATGGTCTATAGCGG
1 CATTTTTTAG-AAAAGCGCCGCTAAAGATCATGGTCTATAGCGG
* * * ** *
9490926 CATTTGTGAGAAAAACGCCATTACAA-ATCATGGTCTATAGCGA
1 CATTTTTTAGAAAAGCGCCGCTA-AAGATCATGGTCTATAGCGG
* *
9490969 CGTTTTTT-TAAAAGCGCCGCTAAAG
1 CATTTTTTAGAAAAGCGCCGCTAAAG
9490994 GCCTAAAAAG
Statistics
Matches: 84, Mismatches: 23, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
41 2 0.02
42 17 0.20
43 58 0.69
44 7 0.08
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
CATTTTTTAGAAAAGCGCCGCTAAAGATCATGGTCTATAGCGG
Found at i:9490930 original size:86 final size:85
Alignment explanation
Indices: 9490750--9490944 Score: 207
Period size: 86 Copynumber: 2.3 Consensus size: 85
9490740 GCCATGTTTT
* *** *
9490750 TAGCGGCGTTTGTTA-AAAAGCGCCGCTAAAAGTCATCTTTATTGTGGCATTTGTTGTAGAAGCG
1 TAGCGGCATTTGTTAGAAAAGCGCCGCTAAAAGTCATCTTTATAACGGCATTTGTTGTAGAAGCA
* *
9490814 TCGCTAAAAGTCATATTCTT
66 TCGCTAAAAGTCATAGTCTA
** * *
9490834 TAGCAACATTTTTTAGAAAAGCGCCGCT-AAAGATCATGGTTTATAACGGCATTT-TTAGTAGAA
1 TAGCGGCATTTGTTAGAAAAGCGCCGCTAAAAG-TCAT-CTTTATAACGGCATTTGTT-GTAGAA
* *
9490897 GCATCGCTAAAGGTCATGGTCTA
63 GCATCGCTAAAAGTCATAGTCTA
* *
9490920 TAGCGGCATTTGTGAGAAAAACGCC
1 TAGCGGCATTTGTTAGAAAAGCGCC
9490945 ATTACAAATC
Statistics
Matches: 89, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
84 15 0.17
85 18 0.20
86 56 0.63
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (85 bp):
TAGCGGCATTTGTTAGAAAAGCGCCGCTAAAAGTCATCTTTATAACGGCATTTGTTGTAGAAGCA
TCGCTAAAAGTCATAGTCTA
Found at i:9490956 original size:86 final size:86
Alignment explanation
Indices: 9490795--9490964 Score: 191
Period size: 86 Copynumber: 2.0 Consensus size: 86
9490785 TCTTTATTGT
* * * * * * *
9490795 GGCATTTGTTGTAGAAGCGTCGCTAAAAGTCATATTCTTTAGCAACATTTTTTAGAAAAGCGCCG
1 GGCATTTGTTGTAGAAGCATCGCTAAAAGTCATAGTCTATAGCAACATTTGTGAGAAAAACGCCA
*
9490860 CTAAAGATCATGGTTTATAAC
66 CTAAAGATCATGGTCTATAAC
* * **
9490881 GGCATTT-TTAGTAGAAGCATCGCTAAAGGTCATGGTCTATAGCGGCATTTGTGAGAAAAACGCC
1 GGCATTTGTT-GTAGAAGCATCGCTAAAAGTCATAGTCTATAGCAACATTTGTGAGAAAAACGCC
*
9490945 ATTACAA-ATCATGGTCTATA
65 ACTA-AAGATCATGGTCTATA
9490965 GCGACGTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
85 2 0.03
86 65 0.94
87 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (86 bp):
GGCATTTGTTGTAGAAGCATCGCTAAAAGTCATAGTCTATAGCAACATTTGTGAGAAAAACGCCA
CTAAAGATCATGGTCTATAAC
Found at i:9493599 original size:93 final size:93
Alignment explanation
Indices: 9493440--9493625 Score: 327
Period size: 93 Copynumber: 2.0 Consensus size: 93
9493430 AAGGGTCCAC
*
9493440 AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTAGATG
1 AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTACATG
9493505 GATATGATATTTAGACTACTAATACATT
66 GATATGATATTTAGACTACTAATACATT
* * * *
9493533 AAAAATTACAAGATAGGTTAAGTACTTATGACGCTTACATGTACAAGTTTAATTATTATTACATG
1 AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTACATG
9493598 GATATGATATTTAGACTACTAATACATT
66 GATATGATATTTAGACTACTAATACATT
9493626 GAGAAAGCAA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (93 bp):
AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTACATG
GATATGATATTTAGACTACTAATACATT
Found at i:9496437 original size:21 final size:21
Alignment explanation
Indices: 9496411--9496464 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
9496401 AATAGCAGTG
9496411 GCGGTGAGATTAGTTACTATA
1 GCGGTGAGATTAGTTACTATA
*
9496432 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGTTACTATA
9496453 GCGGTGAGATTA
1 GCGGTGAGATTA
9496465 AAAACAATGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.31
Consensus pattern (21 bp):
GCGGTGAGATTAGTTACTATA
Found at i:9496713 original size:33 final size:32
Alignment explanation
Indices: 9496676--9496739 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
9496666 AATAATTTAT
9496676 ATAATTAATTTAAATTATTTATTAGATAAAATA
1 ATAATTAATTTAAATTATTTA-TAGATAAAATA
* * *
9496709 ATAATTATTTTAAATTTTTTATAGTTAAAAT
1 ATAATTAATTTAAATTATTTATAGATAAAAT
9496740 TTTTTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 9 0.32
33 19 0.68
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (32 bp):
ATAATTAATTTAAATTATTTATAGATAAAATA
Found at i:9500710 original size:41 final size:41
Alignment explanation
Indices: 9500653--9500797 Score: 179
Period size: 41 Copynumber: 3.5 Consensus size: 41
9500643 TTTAACATAT
*
9500653 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAA
* *
9500694 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAA
* * **
9500735 TCACCGGCACTTAGCCTGCT-GGACTTAAAGTCC-GAATCATT
1 TCACCGGCACTTAGCCTGCTAGG-CTTATAG-CCTGATTCAAA
9500776 TCACCGGC-CTTAAGCCTGCTAG
1 TCACCGGCACTT-AGCCTGCTAG
9500798 ACATAAAGTC
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
40 5 0.05
41 83 0.91
42 3 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAA
Found at i:9500805 original size:41 final size:41
Alignment explanation
Indices: 9500735--9500920 Score: 241
Period size: 41 Copynumber: 4.5 Consensus size: 41
9500725 CTGATTCAAA
* * * *
9500735 TCACCGGCACTT-AGCCTGCTGGACTTAAAGTCCG-AATCATT
1 TCACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGAAAT-AAT
*
9500776 TCACCGGCCTTAAGCCTGCTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
* * *
9500817 TCACCGACATTAAGCCTGGTAGACATAAAGTTTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
9500858 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
* * *
9500899 TCATCGGTATTAAACCTGCTAG
1 TCACCGGCATTAAGCCTGCTAG
9500921 GCATCGAGCC
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
40 2 0.02
41 123 0.96
42 3 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
Found at i:9501713 original size:196 final size:196
Alignment explanation
Indices: 9501253--9501679 Score: 669
Period size: 199 Copynumber: 2.2 Consensus size: 196
9501243 AATTCAATAC
* ** *
9501253 ATACATTCGGCTAACATATATGTAATTCATTAAATTTCATTCAACTTACAAAACTCAGCATATAT
1 ATACATTCAGCTAACATATATACAATTCATTAAATTTCATTCAACTTACAAAAC-CAACATATAT
*
9501318 ATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTATCTTATAAACTCAAATATACATT
65 ATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTATAAACTCAAATATACATT
9501383 GACTAACACACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACAT
130 GACT-A-ACACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACAT
9501448 ATAT
193 ATAT
**
9501452 ATACATTCAGCTAACATATATGTAATTCATTAAATTTCATTCAACTTACAAAACCCAACATATAT
1 ATACATTCAGCTAACATATATACAATTCATTAAATTTCATTCAACTTACAAAA-CCAACATATAT
* *
9501517 ATATTCGGCTAAATATATATAGAATTTCTGTAATTTATTTTAACTTATAAAACTCAAATATACAT
65 ATATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTAT-AAACTCAAATATACAT
*
9501582 TGACT-A-ACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATT
129 TGACTAACACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATA
9501645 TAT
194 TAT
* *
9501648 ATACATTCGGCTAACATTTTTATACAATTCAT
1 ATACATTCAGCTAACA--TATATACAATTCAT
9501680 ACCATTATAT
Statistics
Matches: 214, Mismatches: 10, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
196 74 0.35
197 1 0.00
198 11 0.05
199 106 0.50
200 22 0.10
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (196 bp):
ATACATTCAGCTAACATATATACAATTCATTAAATTTCATTCAACTTACAAAACCAACATATATA
TATTCGGCTAAATATATATAGAATTTATGCAATTTATTTTAACTTATAAACTCAAATATACATTG
ACTAACACACATATATATATACAATTCATACATTTTATTTTAACTTATAAAATTCAAAACATATA
T
Found at i:9507842 original size:41 final size:41
Alignment explanation
Indices: 9507785--9507929 Score: 188
Period size: 41 Copynumber: 3.5 Consensus size: 41
9507775 TTTAACATAT
9507785 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* *
9507826 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * **
9507867 TCACCGGCACTTAGCCTGCT-GGACTTAAAGTCC-GAATCATT
1 TCACCGGCACTTAGCCTGCTAGG-CTTATAG-CCTGATTCAGA
9507908 TCACCGGC-CTTAAGCCTGCTAG
1 TCACCGGCACTT-AGCCTGCTAG
9507930 ACATAAAGTC
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
40 5 0.05
41 84 0.91
42 3 0.03
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:9508066 original size:41 final size:41
Alignment explanation
Indices: 9507867--9508052 Score: 268
Period size: 41 Copynumber: 4.5 Consensus size: 41
9507857 CTGATTCAGA
* * * *
9507867 TCACCGGCACTT-AGCCTGCTGGACTTAAAGTCCG-AATCATT
1 TCACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGAAAT-AAT
*
9507908 TCACCGGCCTTAAGCCTGCTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
*
9507949 TCACCGGCATTAAGCCTGGTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
9507990 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
* *
9508031 TCACCGGTATTAAACCTGCTAG
1 TCACCGGCATTAAGCCTGCTAG
9508053 GCATCGAGCC
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 2 0.02
41 128 0.96
42 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
Found at i:9509287 original size:13 final size:13
Alignment explanation
Indices: 9509269--9509293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9509259 ACAAACGATA
9509269 AAATTTTCACACG
1 AAATTTTCACACG
9509282 AAATTTTCACAC
1 AAATTTTCACAC
9509294 AAGTAAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:9510851 original size:9 final size:9
Alignment explanation
Indices: 9510837--9510930 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
9510827 TTTGGTTAAA
9510837 AATTAACCG
1 AATTAACCG
*
9510846 AATTAACCA
1 AATTAACCG
*
9510855 AATTAACCA
1 AATTAACCG
*
9510864 AATTACCCG
1 AATTAACCG
9510873 AATTAACCG
1 AATTAACCG
*
9510882 AATTACCCG
1 AATTAACCG
9510891 AATTAACCG
1 AATTAACCG
*
9510900 AATTACCCG
1 AATTAACCG
*
9510909 AATTACCCG
1 AATTAACCG
*
9510918 AATTAACCT
1 AATTAACCG
9510927 AATT
1 AATT
9510931 GAATCATACA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 76 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:9514915 original size:274 final size:272
Alignment explanation
Indices: 9514428--9514980 Score: 1038
Period size: 274 Copynumber: 2.0 Consensus size: 272
9514418 TTAACATTAA
9514428 ATGTATATATGAAAATGAAAACGTATATATAGGACATATATAATATAAGGTATAAAATATGATAT
1 ATGTATATATGAAAATGAAAACGTATATATAGGACATATATAATATAAGGTATAAAATATGATAT
9514493 ATATATTAGGGAAGTAGATAAATACATAAATATGTACATAAATAATAATGAAGGGACAAATGTAT
66 ATATATTAGGGAAGTAGATAAATACATAAATATGTACATAAATAATAATGAAGGGACAAATGTAT
*
9514558 GCCTATATATATTCTAAAATATGTATGTATATATGAAGATAATAAAAATGCATGCATATATACGT
131 GCCTATATATATCCTAAAATATGTATGTATATATGAAGATAATAAAAATGCATGCATATATACGT
*
9514623 AGATTATAAAATATAGATATGTATGTATATATGTATGTGTTTTAAAATATGTATATAATAACAAA
196 AGATTATAAAATATAGATATGTATATATATATGTATGTGTTTTAAAATATGTATATAATAACAAA
9514688 ATACATTAATAC
261 ATACATTAATAC
9514700 ATGTATATATGAAAATGAAAACGTATATATAGGACATATATAATATAAGGTATAAAATATGATAT
1 ATGTATATATGAAAATGAAAACGTATATATAGGACATATATAATATAAGGTATAAAATATG--AT
*
9514765 ATATATATTAGGGAAGTAGATAAATACATAAATATGTACATAAATAATAATGAAGGGATAAATGT
64 ATATATATTAGGGAAGTAGATAAATACATAAATATGTACATAAATAATAATGAAGGGACAAATGT
9514830 ATGCCTATATATATCCTAAAATATGTATGTATATATGAAGATAATAAAAATGCATGCATATATAC
129 ATGCCTATATATATCCTAAAATATGTATGTATATATGAAGATAATAAAAATGCATGCATATATAC
*
9514895 GTAGATTATAAAATATAGATATGTATATATATATGTATGTGTTTTAAAATATGTATGTAATAACA
194 GTAGATTATAAAATATAGATATGTATATATATATGTATGTGTTTTAAAATATGTATATAATAACA
9514960 AAATACATTAATAC
259 AAATACATTAATAC
9514974 --GTATATA
1 ATGTATATA
9514981 GGATACAACA
Statistics
Matches: 275, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
272 68 0.25
274 207 0.75
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.34
Consensus pattern (272 bp):
ATGTATATATGAAAATGAAAACGTATATATAGGACATATATAATATAAGGTATAAAATATGATAT
ATATATTAGGGAAGTAGATAAATACATAAATATGTACATAAATAATAATGAAGGGACAAATGTAT
GCCTATATATATCCTAAAATATGTATGTATATATGAAGATAATAAAAATGCATGCATATATACGT
AGATTATAAAATATAGATATGTATATATATATGTATGTGTTTTAAAATATGTATATAATAACAAA
ATACATTAATAC
Found at i:9518300 original size:24 final size:24
Alignment explanation
Indices: 9518273--9518324 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
9518263 TTAGTAAGTC
*
9518273 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
9518297 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
9518321 AAAT
1 AAAT
9518325 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:9520270 original size:24 final size:24
Alignment explanation
Indices: 9520243--9520294 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
9520233 TTAGTAAGTC
*
9520243 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
9520267 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
9520291 AAAT
1 AAAT
9520295 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:9525599 original size:26 final size:24
Alignment explanation
Indices: 9525535--9525604 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 24
9525525 ATGCTCAAGG
9525535 ATTTAAAATAA-TTTAAAATATTT
1 ATTTAAAATAATTTTAAAATATTT
* *
9525558 GTTAAAAATAGAAATTTTAAAATACTATT
1 ATTTAAAAT---AATTTTAAAATA-T-TT
9525587 ATTTAAAATAATTTTAAA
1 ATTTAAAATAATTTTAAA
9525605 GTTTTTTGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
23 7 0.19
26 11 0.30
27 9 0.24
28 1 0.03
29 9 0.24
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (24 bp):
ATTTAAAATAATTTTAAAATATTT
Found at i:9525797 original size:22 final size:21
Alignment explanation
Indices: 9525772--9525819 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
9525762 GTGTTACCAT
*
9525772 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGGTTATGGATTAT-GG
*
9525794 TTTAAGGGTTATGGTTTATGG
1 TTTAAGGGTTATGGATTATGG
9525815 TTTAA
1 TTTAA
9525820 AGGCCGGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (21 bp):
TTTAAGGGTTATGGATTATGG
Found at i:9525874 original size:15 final size:14
Alignment explanation
Indices: 9525856--9525904 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
9525846 ATGTGTTAAT
9525856 GGTTTATGGTTTTAG
1 GGTTTATGG-TTTAG
*
9525871 GGTTTTAGGGTTTA-
1 GG-TTTATGGTTTAG
*
9525885 GGTTTATAGTTTAG
1 GGTTTATGGTTTAG
9525899 GGTTTA
1 GGTTTA
9525905 GATTAACTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 9 0.31
14 8 0.28
15 6 0.21
16 6 0.21
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (14 bp):
GGTTTATGGTTTAG
Found at i:9525943 original size:16 final size:16
Alignment explanation
Indices: 9525922--9525954 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9525912 TAGTGGTTTC
9525922 TAATTTA-TATATTAAT
1 TAATTTATTATA-TAAT
9525938 TAATTTATTATATAAT
1 TAATTTATTATATAAT
9525954 T
1 T
9525955 GTAAAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTATTATATAAT
Found at i:9526222 original size:20 final size:20
Alignment explanation
Indices: 9526200--9526262 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
9526190 TTAGTGATTT
9526200 AAAATTTTAAAATGAATTTTA
1 AAAATTTTAAAATG-ATTTTA
**
9526221 AAAGATTTT-AAATTTTTTTA
1 AAA-ATTTTAAAATGATTTTA
*
9526241 AAAATTTTAAAAAGATTTTA
1 AAAATTTTAAAATGATTTTA
9526261 AA
1 AA
9526263 CTTTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.14
20 18 0.51
21 7 0.20
22 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAATTTTAAAATGATTTTA
Found at i:9526230 original size:10 final size:10
Alignment explanation
Indices: 9526203--9526262 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
9526193 GTGATTTAAA
9526203 ATTTTAAAATG
1 ATTTTAAAA-G
9526214 AATTTTAAAAG
1 -ATTTTAAAAG
**
9526225 ATTTTAAATT
1 ATTTTAAAAG
*
9526235 TTTTTAAAA-
1 ATTTTAAAAG
9526244 ATTTTAAAAAG
1 ATTTT-AAAAG
9526255 ATTTTAAA
1 ATTTTAAA
9526263 CTTTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 4 0.10
10 22 0.54
11 6 0.15
12 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (10 bp):
ATTTTAAAAG
Found at i:9526710 original size:32 final size:27
Alignment explanation
Indices: 9526648--9526702 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
9526638 AGTTAGGAAT
*
9526648 AAATATCTCTAATAAAATGAAGATTAG
1 AAATATCTCTAATAAAATAAAGATTAG
9526675 AAATATCTCTAATAAAATAAAGATTAG
1 AAATATCTCTAATAAAATAAAGATTAG
9526702 A
1 A
9526703 TCGGAAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.29
Consensus pattern (27 bp):
AAATATCTCTAATAAAATAAAGATTAG
Found at i:9530585 original size:43 final size:43
Alignment explanation
Indices: 9530515--9530658 Score: 225
Period size: 43 Copynumber: 3.3 Consensus size: 43
9530505 AAATATTTTT
* * * *
9530515 TAAATGTCTTGTTCTTTAGCGGAGTTTGTGGGAAAAACGCTGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
9530558 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * *
9530601 TAAAGGTCTTGTTCTATAACGGCGTTTGTGTGAAAAGCGCCGC
1 TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
9530644 TAAAGGTCTTGTTCT
1 TAAAGGTCTTGTTCT
9530659 ATAGTGAAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
TAAAGGTCTTGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:9536049 original size:27 final size:28
Alignment explanation
Indices: 9536003--9536125 Score: 151
Period size: 28 Copynumber: 4.5 Consensus size: 28
9535993 CGTGTGAGGT
* *
9536003 AGCCTTTGTGGCGATATATG-AAAAGGA
1 AGCCTTTGTGGCGATCTATGAAAAAAGA
* * *
9536030 AGCCTTTGTAGCAATTTATGAAAAAAGA
1 AGCCTTTGTGGCGATCTATGAAAAAAGA
*
9536058 AGTCTTTGTGGCGATCTATGAAAAAAGA
1 AGCCTTTGTGGCGATCTATGAAAAAAGA
* *
9536086 AGCCTTTGTGGCTATCTAT-AAAAAGGA
1 AGCCTTTGTGGCGATCTATGAAAAAAGA
*
9536113 AGCATTTGTGGCG
1 AGCCTTTGTGGCG
9536126 CACTCTAAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
27 35 0.43
28 47 0.57
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.28
Consensus pattern (28 bp):
AGCCTTTGTGGCGATCTATGAAAAAAGA
Found at i:9536109 original size:55 final size:54
Alignment explanation
Indices: 9536006--9536125 Score: 152
Period size: 55 Copynumber: 2.2 Consensus size: 54
9535996 GTGAGGTAGC
* *
9536006 CTTTGTGGCGATATATGAAAAGGAAGCCTTTGTAGCAATTTATGAAAAAAGAAG
1 CTTTGTGGCGATATATGAAAAAGAAGCCTTTGTAGCAATCTATGAAAAAAGAAG
* * * *
9536060 TCTTTGTGGCGATCTATGAAAAAAGAAGCCTTTGTGGCTATCTAT-AAAAAGGAAG
1 -CTTTGTGGCGATATATG-AAAAAGAAGCCTTTGTAGCAATCTATGAAAAAAGAAG
9536115 CATTTGTGGCG
1 C-TTTGTGGCG
9536126 CACTCTAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 1 0.02
55 34 0.60
56 22 0.39
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (54 bp):
CTTTGTGGCGATATATGAAAAAGAAGCCTTTGTAGCAATCTATGAAAAAAGAAG
Found at i:9538916 original size:25 final size:25
Alignment explanation
Indices: 9538794--9538916 Score: 94
Period size: 25 Copynumber: 5.0 Consensus size: 25
9538784 TGAGTGTCCT
*
9538794 GATATATGGCTCTTCGGAGCTTCCC
1 GATATATGGCTCTTTGGAGCTTCCC
* *
9538819 GAT-TAAGGCTTTTTGTGAGCTTCCC
1 GATATATGGCTCTTTG-GAGCTTCCC
* ** * *
9538844 GTTA-ATGGCTCTTCAGACCTTCTC
1 GATATATGGCTCTTTGGAGCTTCCC
* *
9538868 G--ATATGGCTCACTT-GAACTTCCC
1 GATATATGGCTC-TTTGGAGCTTCCC
*
9538891 GATATATGGCTCTTTGGAGCTACCC
1 GATATATGGCTCTTTGGAGCTTCCC
9538916 G
1 G
9538917 TTTTTGGCTC
Statistics
Matches: 74, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
22 1 0.01
23 15 0.20
24 20 0.27
25 38 0.51
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (25 bp):
GATATATGGCTCTTTGGAGCTTCCC
Found at i:9538938 original size:72 final size:73
Alignment explanation
Indices: 9538813--9538950 Score: 165
Period size: 72 Copynumber: 1.9 Consensus size: 73
9538803 CTCTTCGGAG
* * *
9538813 CTTCCCGATTAAGGCTTTTTGTGAGCTTCCCGTTAATGGCTCTTCAGACCTTCTCG-ATATGGCT
1 CTTCCCGATTAAGGCTCTTTGTGAGCTACCCGTTAATGGCTCTTCAAACCTTCTCGAATATGGCT
9538877 CACTTGAA
66 CACTTGAA
* ** * *
9538885 CTTCCCGATATATGGCTCTTTG-GAGCTACCCGTTTTTGGCTC-TCACAAGCTTCTTGAATATGG
1 CTTCCCGAT-TAAGGCTCTTTGTGAGCTACCCGTTAATGGCTCTTCA-AACCTTCTCGAATATGG
9538948 CTC
64 CTC
9538951 TTATGAGCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
71 3 0.05
72 33 0.60
73 19 0.35
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (73 bp):
CTTCCCGATTAAGGCTCTTTGTGAGCTACCCGTTAATGGCTCTTCAAACCTTCTCGAATATGGCT
CACTTGAA
Found at i:9540282 original size:14 final size:13
Alignment explanation
Indices: 9540240--9540296 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
9540230 AATAAAACAC
*
9540240 TAAAAAATTATTT
1 TAAAAAAATATTT
* *
9540253 TAAAAATAAAAATT
1 TAAAAA-AATATTT
9540267 TAAAAAAAGTATTT
1 TAAAAAAA-TATTT
9540281 T--AAAAATATTT
1 TAAAAAAATATTT
9540292 TAAAA
1 TAAAA
9540297 TTAAAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
11 6 0.17
12 5 0.14
13 10 0.29
14 14 0.40
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
TAAAAAAATATTT
Found at i:9540310 original size:15 final size:17
Alignment explanation
Indices: 9540280--9540312 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
9540270 AAAAAGTATT
9540280 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
9540297 TTAAAAA-A-TTTAAAA
1 TTAAAAATATTTTAAAA
9540312 T
1 T
9540313 ATATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:9541218 original size:189 final size:189
Alignment explanation
Indices: 9540898--9541275 Score: 747
Period size: 189 Copynumber: 2.0 Consensus size: 189
9540888 CAAAGTCAGA
9540898 ATGGGGGAACCCGAAATCATTCTGATCTTGTCTCACAAAATTTATTATATCTCATGATTTACAAT
1 ATGGGGGAACCCGAAATCATTCTGATCTTGTCTCACAAAATTTATTATATCTCATGATTTACAAT
9540963 TCCATAACTTACACTGTTTATTCTATGAGAAACTAGACTAAATAAGCTTTAATTCCATATTTTTT
66 TCCATAACTTACACTGTTTATTCTATGAGAAACTAGACTAAATAAGCTTTAATTCCATATTTTTT
*
9541028 CATCCTCTAATTCGATTTCCACAATTTATGGTGATTTTTAAAATTTAACCTACTGCTGC
131 CATCCTCTAATTCGATTTCCACAATTTATGGTGATTTTTAAAATTTAACCTACTACTGC
9541087 ATGGGGGAACCCGAAATCATTCTGATCTTGTCTCACAAAATTTATTATATCTCATGATTTACAAT
1 ATGGGGGAACCCGAAATCATTCTGATCTTGTCTCACAAAATTTATTATATCTCATGATTTACAAT
9541152 TCCATAACTTACACTGTTTATTCTATGAGAAACTAGACTAAATAAGCTTTAATTCCATATTTTTT
66 TCCATAACTTACACTGTTTATTCTATGAGAAACTAGACTAAATAAGCTTTAATTCCATATTTTTT
9541217 CATCCTCTAATTCGATTTCCACAATTTATGGTGATTTTTAAAATTTAACCTACTACTGC
131 CATCCTCTAATTCGATTTCCACAATTTATGGTGATTTTTAAAATTTAACCTACTACTGC
9541276 TGTCCAAAAC
Statistics
Matches: 188, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 188 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (189 bp):
ATGGGGGAACCCGAAATCATTCTGATCTTGTCTCACAAAATTTATTATATCTCATGATTTACAAT
TCCATAACTTACACTGTTTATTCTATGAGAAACTAGACTAAATAAGCTTTAATTCCATATTTTTT
CATCCTCTAATTCGATTTCCACAATTTATGGTGATTTTTAAAATTTAACCTACTACTGC
Found at i:9553322 original size:81 final size:81
Alignment explanation
Indices: 9553218--9553380 Score: 308
Period size: 81 Copynumber: 2.0 Consensus size: 81
9553208 TTTTCTAAGC
*
9553218 AGATTTGAATCTCACACTTGAAAGGAAACTTTTAAATTAGTTGAAACCATAACATAGGATGCCTT
1 AGATTTGAATCTCACACTTGAAAGGAAACTTTTAAATTAGTTGAAACCATAACATAGGATACCTT
9553283 CAGTTTGCCTTAGTTA
66 CAGTTTGCCTTAGTTA
*
9553299 AGATTTGAATCTCACACTTGAAAGGAAACTTTTAAATTTGTTGAAACCATAACATAGGATACCTT
1 AGATTTGAATCTCACACTTGAAAGGAAACTTTTAAATTAGTTGAAACCATAACATAGGATACCTT
9553364 CAGTTTGCCTTAGTTA
66 CAGTTTGCCTTAGTTA
9553380 A
1 A
9553381 TACTGTGTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (81 bp):
AGATTTGAATCTCACACTTGAAAGGAAACTTTTAAATTAGTTGAAACCATAACATAGGATACCTT
CAGTTTGCCTTAGTTA
Found at i:9580103 original size:21 final size:21
Alignment explanation
Indices: 9580077--9580117 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9580067 AGACGAGCAA
* *
9580077 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
9580098 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
9580118 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:9585618 original size:18 final size:18
Alignment explanation
Indices: 9585595--9585631 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9585585 TCAGAAAAAC
9585595 TAATTAATAGGACAAGAT
1 TAATTAATAGGACAAGAT
9585613 TAATTAATAGGACAAGAT
1 TAATTAATAGGACAAGAT
9585631 T
1 T
9585632 CTAATGCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (18 bp):
TAATTAATAGGACAAGAT
Found at i:9585731 original size:18 final size:19
Alignment explanation
Indices: 9585690--9585733 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
9585680 TATTAGAATT
9585690 TTTTTCATAATTATTAATAG
1 TTTTT-ATAATTATTAATAG
*
9585710 -TTTTATAATTTTTAA-AG
1 TTTTTATAATTATTAATAG
9585727 TTTTTAT
1 TTTTTAT
9585734 TTTTATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 16 0.73
19 4 0.18
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTATAATTATTAATAG
Found at i:9588991 original size:23 final size:23
Alignment explanation
Indices: 9588965--9589011 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
9588955 GTAATTATAA
9588965 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
9588988 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
9589011 A
1 A
9589012 CATACTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:9589583 original size:18 final size:17
Alignment explanation
Indices: 9589551--9589586 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
9589541 TAAATGAGTT
*
9589551 AATTAGGATTAAATTGA
1 AATTAAGATTAAATTGA
9589568 AATTAAGATATAAATTGA
1 AATTAAGAT-TAAATTGA
9589586 A
1 A
9589587 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (17 bp):
AATTAAGATTAAATTGA
Found at i:9590341 original size:21 final size:20
Alignment explanation
Indices: 9590317--9590365 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
9590307 GCACCTCGTA
*
9590317 TGTCGTATCAGGCACATTGTG
1 TGTCGTATCAGGCAC-TTATG
* *
9590338 TGTCATTTCAGGCACTTATG
1 TGTCGTATCAGGCACTTATG
*
9590358 TGACGTAT
1 TGTCGTAT
9590366 ACTGATCAGG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
TGTCGTATCAGGCACTTATG
Found at i:9590778 original size:25 final size:25
Alignment explanation
Indices: 9590750--9590800 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
9590740 AATGAAATTG
*
9590750 AGATAGTGAAATATTGCTTATTGAT
1 AGATAGTGAAATATTGCCTATTGAT
9590775 AGATAGTGAAATATTGCCTATTGAT
1 AGATAGTGAAATATTGCCTATTGAT
9590800 A
1 A
9590801 TTAATGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (25 bp):
AGATAGTGAAATATTGCCTATTGAT
Found at i:9593354 original size:22 final size:21
Alignment explanation
Indices: 9593324--9593368 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
9593314 ACACCAAAAC
* *
9593324 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCAGCG-TTTTTT
9593346 AGGCCTTTAGCAGCGTTTTTT
1 AGGCCTTTAGCAGCGTTTTTT
9593367 AG
1 AG
9593369 CGCCGCTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.13, C:0.18, G:0.27, T:0.42
Consensus pattern (21 bp):
AGGCCTTTAGCAGCGTTTTTT
Found at i:9593504 original size:43 final size:43
Alignment explanation
Indices: 9593450--9593838 Score: 580
Period size: 43 Copynumber: 9.0 Consensus size: 43
9593440 TTAGCGGCAC
* *
9593450 TTTCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCT
1 TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCT
* * * *
9593493 TTTCCCACAAACGACGCTAAAGACCATGATCTTTAACGACGCT
1 TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCT
*
9593536 TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCT
1 TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCT
* *
9593579 TTTCCGACAAACGCCGCTAAAGACCATGATCTTTAACGACGCT
1 TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCT
*
9593622 TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCT
1 TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCT
* * *
9593665 TTTCCCACAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCT
1 TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCT
* *
9593708 TTTCCGACAAACGCCGCTAAAGACGATGACTTTTAGCGACGCT
1 TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCT
* *
9593751 TTTCCGACAAACGCCACTAAAGACCCTGACCTTTAGCGACGCT
1 TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCT
* * **
9593794 TTTCCCAAAAACGGCCGCTAAAGACCACAACCTTTAGCGACGCT
1 TTTCCGACAAAC-GCCGCTAAAGACCATGACCTTTAGCGACGCT
9593838 T
1 T
9593839 AAACAACAAA
Statistics
Matches: 313, Mismatches: 32, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
43 285 0.91
44 28 0.09
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
TTTCCGACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCT
Found at i:9593865 original size:129 final size:128
Alignment explanation
Indices: 9593438--9593899 Score: 517
Period size: 129 Copynumber: 3.6 Consensus size: 128
9593428 GCGTCGCTAA
* * * * *
9593438 CTTTAGCGGCAC-TTTCCCACAAACGCCGC--TAAAGACCATGACCTTTAGCGGCGCTTTTCCCA
1 CTTTAGCGGCGCTTTTCCGACAAACGCCGCAATAAAG---ATGACTTTTAGCGACGCTTTTCCGA
* * * *
9593500 CAAACGACGCTAAAGACCATGATCTTTAACGACGCTTTTCCGACAAACGCCGCTAAAGACCATGA
63 CAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATGA
9593565 C
128 C
*
9593566 CTTTAGCGGCGCTTTTCCGACAAACGCCGC--TAAAGACCATGA-TCTTTAACGACGCTTTTCCG
1 CTTTAGCGGCGCTTTTCCGACAAACGCCGCAATAAAG---ATGACT-TTTAGCGACGCTTTTCCG
*
9593628 ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCATG
62 ACAAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATG
*
9593693 AT
127 AC
*
9593695 CTTTAGCGGCGCTTTTCCGACAAACGCCGCTAA-AGACGATGACTTTTAGCGACGCTTTTCCGAC
1 CTTTAGCGGCGCTTTTCCGACAAACGCCGC-AATA-AAGATGACTTTTAGCGACGCTTTTCCGAC
* * * **
9593759 AAACGCCACTAAAGACCCTGACCTTTAGCGACGCTTTTCCCAAAAACGGCCGCTAAAGACCACAA
64 AAACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTCCCACAAAC-GCCGCTAAAGACCATGA
9593824 C
128 C
* *** * * * * **
9593825 CTTTAGCGACGCTTAAACAACAAACGCCACAATAAAGATGAGTTTTAGCGGCGCTTTT-TAACAA
1 CTTTAGCGGCGCTTTTCCGACAAACGCCGCAATAAAGATGACTTTTAGCGACGCTTTTCCGACAA
*
9593889 ACACCGCTAAA
66 ACGCCGCTAAA
9593900 ACATGGCTTT
Statistics
Matches: 291, Mismatches: 34, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
128 24 0.08
129 223 0.77
130 41 0.14
131 1 0.00
132 2 0.01
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.22
Consensus pattern (128 bp):
CTTTAGCGGCGCTTTTCCGACAAACGCCGCAATAAAGATGACTTTTAGCGACGCTTTTCCGACAA
ACGCCGCTAAAGACCATGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGACCATGAC
Found at i:9598875 original size:39 final size:39
Alignment explanation
Indices: 9598826--9598910 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
9598816 TGGGCCTAGT
* *
9598826 TTTTTTGCGGCGCTTTT-CTAAAAACGCCACTAATGCTCA
1 TTTTTAGCGGCG-TTTTCCGAAAAACGCCACTAATGCTCA
* * *
9598865 TTTTTAGCGGCGTTTTCCGAAAAGCGCCGCTAATGCTTA
1 TTTTTAGCGGCGTTTTCCGAAAAACGCCACTAATGCTCA
9598904 TTTTTAG
1 TTTTTAG
9598911 TGATTTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 4 0.10
39 36 0.90
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTCCGAAAAACGCCACTAATGCTCA
Found at i:9598948 original size:22 final size:22
Alignment explanation
Indices: 9598913--9598957 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
9598903 ATTTTTAGTG
9598913 ATTTTATTTATTTATTTGTTAA
1 ATTTTATTTATTTATTTGTTAA
9598935 ATTTT-TTTATTTTATTTGTTAA
1 ATTTTATTTA-TTTATTTGTTAA
9598957 A
1 A
9598958 AATTATTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
ATTTTATTTATTTATTTGTTAA
Found at i:9599322 original size:8 final size:8
Alignment explanation
Indices: 9599311--9599339 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
9599301 AAATATAACT
9599311 CTAAACCC
1 CTAAACCC
9599319 CTAAACCC
1 CTAAACCC
9599327 CT-AACCC
1 CTAAACCC
9599334 CTAAAC
1 CTAAAC
9599340 TTTAAATCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.38, C:0.48, G:0.00, T:0.14
Consensus pattern (8 bp):
CTAAACCC
Found at i:9599359 original size:21 final size:22
Alignment explanation
Indices: 9599320--9599360 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
9599310 TCTAAACCCC
9599320 TAAACCCCTAACCCCTAAACTT
1 TAAACCCCTAACCCCTAAACTT
* *
9599342 TAAATCCC-AACCCTTAAAC
1 TAAACCCCTAACCCCTAAAC
9599361 AATAAACCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACCCCTAACCCCTAAACTT
Found at i:9599580 original size:16 final size:17
Alignment explanation
Indices: 9599547--9599585 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
9599537 AAGAACACTA
9599547 TATTTAATATATTAAAT
1 TATTTAATATATTAAAT
9599564 TATTTAATATA-TAAAT
1 TATTTAATATATTAAAT
9599580 TATTTA
1 TATTTA
9599586 TAAAGAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTTAATATATTAAAT
Found at i:9599734 original size:21 final size:20
Alignment explanation
Indices: 9599696--9599763 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
9599686 AATTAATCTA
* *
9599696 AACCCTAAATCCTAAACCCCT
1 AACCTTAAA-CCTCAACCCCT
9599717 AACTCTT-AACTCTCAACCCCT
1 AAC-CTTAAAC-CTCAACCCCT
*
9599738 AAACCTTAAACCTCAACCCTT
1 -AACCTTAAACCTCAACCCCT
9599759 AACCT
1 AACCT
9599764 ATAACATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 6 0.15
21 26 0.65
22 8 0.20
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (20 bp):
AACCTTAAACCTCAACCCCT
Found at i:9599822 original size:7 final size:7
Alignment explanation
Indices: 9599771--9599859 Score: 61
Period size: 7 Copynumber: 12.6 Consensus size: 7
9599761 CCTATAACAT
9599771 TAAACCA
1 TAAACCA
*
9599778 TAAACCG
1 TAAACCA
* * *
9599785 CAACCCT
1 TAAACCA
*
9599792 TAAACCC
1 TAAACCA
* *
9599799 TAAATCT
1 TAAACCA
9599806 TAAACCA
1 TAAACCA
*
9599813 TAAACTA
1 TAAACCA
9599820 TAAACCA
1 TAAACCA
* *
9599827 TAACCCT
1 TAAACCA
9599834 TAAACTCA
1 TAAAC-CA
*
9599842 TAATCCA
1 TAAACCA
*
9599849 TAAACCT
1 TAAACCA
9599856 TAAA
1 TAAA
9599860 ATAGTAACTA
Statistics
Matches: 61, Mismatches: 20, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
7 56 0.92
8 5 0.08
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:9599849 original size:22 final size:21
Alignment explanation
Indices: 9599770--9599917 Score: 82
Period size: 21 Copynumber: 7.0 Consensus size: 21
9599760 ACCTATAACA
* ** *
9599770 TTAAACCATAAACCGCAACCC
1 TTAAACTATAAACCATAAACC
** * *
9599791 TTAAACCCTAAATCTTAAACC
1 TTAAACTATAAACCATAAACC
* *
9599812 ATAAACTATAAACCATAACCC
1 TTAAACTATAAACCATAAACC
*
9599833 TTAAACTCATAATCCATAAACC
1 TTAAACT-ATAAACCATAAACC
* *
9599855 TTAAAATAGT-AACTATTAAACC
1 TTAAACTA-TAAACCA-TAAACC
* * *
9599877 TTAAACTCTAAATCATATACC
1 TTAAACTATAAACCATAAACC
* * * *
9599898 CTAAACCAAAAACCTTAAAC
1 TTAAACTATAAACCATAAAC
9599918 TATAGAGATA
Statistics
Matches: 94, Mismatches: 29, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
21 60 0.64
22 34 0.36
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.24
Consensus pattern (21 bp):
TTAAACTATAAACCATAAACC
Found at i:9600199 original size:19 final size:20
Alignment explanation
Indices: 9600173--9600218 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
9600163 ATAGAATTTT
9600173 AATT-AATA-TAAATAAACA
1 AATTAAATAGTAAATAAACA
* *
9600191 AATTAAATAGTAATTAGACA
1 AATTAAATAGTAAATAAACA
*
9600211 AATAAAAT
1 AATTAAAT
9600219 GTTTTTGCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (20 bp):
AATTAAATAGTAAATAAACA
Found at i:9600286 original size:41 final size:41
Alignment explanation
Indices: 9600229--9600333 Score: 174
Period size: 41 Copynumber: 2.6 Consensus size: 41
9600219 GTTTTTGCGA
* *
9600229 CGCTTTTCCAAAAACGCTGCTAAAGACCAGAGCATTAGCGG
1 CGCTTTTCCAAAAACGCCGCTAAAAACCAGAGCATTAGCGG
*
9600270 CGCTTCTCCAAAAACGCCGCTAAAAACCAGAGCATTAGCGG
1 CGCTTTTCCAAAAACGCCGCTAAAAACCAGAGCATTAGCGG
*
9600311 CGCTTTTCTAAAAACGCCGCTAA
1 CGCTTTTCCAAAAACGCCGCTAA
9600334 TGTCCCGAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (41 bp):
CGCTTTTCCAAAAACGCCGCTAAAAACCAGAGCATTAGCGG
Found at i:9603503 original size:2 final size:2
Alignment explanation
Indices: 9603496--9603522 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9603486 GCAAAAGCAG
9603496 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9603523 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9603527 original size:2 final size:2
Alignment explanation
Indices: 9603522--9603549 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9603512 ATATATATAT
9603522 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9603550 GTTATAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9611591 original size:9 final size:9
Alignment explanation
Indices: 9611577--9611607 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
9611567 GTTCAACGAA
9611577 TCGAGTTAT
1 TCGAGTTAT
*
9611586 TCGAGTTAA
1 TCGAGTTAT
9611595 TCGAGTTAT
1 TCGAGTTAT
9611604 TCGA
1 TCGA
9611608 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:9614385 original size:23 final size:24
Alignment explanation
Indices: 9614358--9614413 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
9614348 TCCAGGTTGT
9614358 ATAATGGGAAACTCATA-AGAGCC-
1 ATAATGGGAAACTCA-AGAGAGCCA
* *
9614381 ATAATTGGGAAGCTCAAGCGAGCCA
1 ATAA-TGGGAAACTCAAGAGAGCCA
9614406 ATAATGGG
1 ATAATGGG
9614414 TAGCTCCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 5 0.18
24 19 0.68
25 4 0.14
ACGTcount: A:0.39, C:0.16, G:0.27, T:0.18
Consensus pattern (24 bp):
ATAATGGGAAACTCAAGAGAGCCA
Found at i:9614427 original size:24 final size:24
Alignment explanation
Indices: 9614400--9614559 Score: 74
Period size: 24 Copynumber: 6.5 Consensus size: 24
9614390 AAGCTCAAGC
* *
9614400 GAGCCAATAATGGGTAGCTCCGAA
1 GAGCCAATAACGGGAAGCTCCGAA
* * *
9614424 GAGCTATTAACGGGAAGCTCCGGA
1 GAGCCAATAACGGGAAGCTCCGAA
* * **
9614448 TAGCCATATATCGGGAAG-T-TTAA
1 GAGCCA-ATAACGGGAAGCTCCGAA
* * *
9614471 GCAAGCC-ATATCGGGAAGCTTCGGA
1 G--AGCCAATAACGGGAAGCTCCGAA
* *
9614496 GAGCCATTAACGGGAAGCTCACAAA
1 GAGCCAATAACGGGAAGCTC-CGAA
** * *
9614521 GAGCCTTTAATCAGGAAGCTCACAAA
1 GAGCCAATAA-CGGGAAGCTC-CGAA
9614547 GAGCCATATAACG
1 GAGCCA-ATAACG
9614560 AGACGCTCAT
Statistics
Matches: 101, Mismatches: 26, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
23 16 0.16
24 36 0.36
25 26 0.26
26 20 0.20
27 3 0.03
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (24 bp):
GAGCCAATAACGGGAAGCTCCGAA
Found at i:9614455 original size:72 final size:72
Alignment explanation
Indices: 9614377--9614515 Score: 174
Period size: 72 Copynumber: 1.9 Consensus size: 72
9614367 AACTCATAAG
* * * *
9614377 AGCCATA-ATTGGGAAGCTCAAGCGAGCCAATAAT-GGGTAGCTCCGAAGAGCTATTAACGGGAA
1 AGCCATATATCGGGAAGCTCAAGCAAGCC-AT-ATCGGGAAGCTCCGAAGAGCCATTAACGGGAA
9614440 GCTCCGGAT
64 GCTCCGGAT
* * * *
9614449 AGCCATATATCGGGAAGTTTAAGCAAGCCATATCGGGAAGCTTCGGAGAGCCATTAACGGGAAGC
1 AGCCATATATCGGGAAGCTCAAGCAAGCCATATCGGGAAGCTCCGAAGAGCCATTAACGGGAAGC
9614514 TC
66 TC
9614516 ACAAAGAGCC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
71 2 0.04
72 38 0.67
73 17 0.30
ACGTcount: A:0.32, C:0.21, G:0.29, T:0.19
Consensus pattern (72 bp):
AGCCATATATCGGGAAGCTCAAGCAAGCCATATCGGGAAGCTCCGAAGAGCCATTAACGGGAAGC
TCCGGAT
Found at i:9614500 original size:23 final size:22
Alignment explanation
Indices: 9614434--9614514 Score: 63
Period size: 23 Copynumber: 3.4 Consensus size: 22
9614424 GAGCTATTAA
*
9614434 CGGGAAGCTCCGGATAGCCATATAT
1 CGGGAAGCTTCGGA-AGCC--ATAT
* * *
9614459 CGGGAAGTTTAAGCAAGCCATAT
1 CGGGAAGCTT-CGGAAGCCATAT
*
9614482 CGGGAAGCTTCGGAGAGCCATTAA
1 CGGGAAGCTTCGGA-AGCCA-TAT
9614506 CGGGAAGCT
1 CGGGAAGCT
9614515 CACAAAGAGC
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
22 2 0.04
23 18 0.40
24 11 0.24
25 12 0.27
26 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.31, T:0.19
Consensus pattern (22 bp):
CGGGAAGCTTCGGAAGCCATAT
Found at i:9614530 original size:25 final size:26
Alignment explanation
Indices: 9614495--9614553 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
9614485 GAAGCTTCGG
*
9614495 AGAGCCATTAA-CGGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
*
9614520 AGAGCCTTTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
9614546 AGAGCCAT
1 AGAGCCAT
9614554 ATAACGAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:9614567 original size:26 final size:25
Alignment explanation
Indices: 9614495--9614568 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
9614485 GAAGCTTCGG
*
9614495 AGAGCCATTAACGGGAAGCTCACAA
1 AGAGCCATTAACGAGAAGCTCACAA
*
9614520 AGAGCCTTTAATC-AGGAAGCTCACAA
1 AGAGCCATTAA-CGA-GAAGCTCACAA
*
9614546 AGAGCCATATAACGAGACGCTCA
1 AGAGCCAT-TAACGAGAAGCTCA
9614569 TAGGAGTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
25 10 0.24
26 27 0.66
27 4 0.10
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (25 bp):
AGAGCCATTAACGAGAAGCTCACAA
Found at i:9619344 original size:17 final size:17
Alignment explanation
Indices: 9619322--9619354 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9619312 CTACATATGT
9619322 TTTTCATTTTCTTTCAC
1 TTTTCATTTTCTTTCAC
*
9619339 TTTTCATTTTGTTTCA
1 TTTTCATTTTCTTTCA
9619355 TTTAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.18, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTCATTTTCTTTCAC
Found at i:9620356 original size:20 final size:19
Alignment explanation
Indices: 9620331--9620376 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
9620321 AATATATATG
9620331 TACACATGCATGTTTT-AAAA
1 TACACATG--TGTTTTCAAAA
*
9620351 TACACATGTTTTTTCAAAA
1 TACACATGTGTTTTCAAAA
9620370 TACACAT
1 TACACAT
9620377 TTTTTTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 11 0.46
20 8 0.33
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (19 bp):
TACACATGTGTTTTCAAAA
Found at i:9620388 original size:17 final size:18
Alignment explanation
Indices: 9620343--9620388 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
9620333 CACATGCATG
9620343 TTTTAAAATACACATGTT
1 TTTTAAAATACACATGTT
9620361 TTTTCAAAATACACAT-TT
1 TTTT-AAAATACACATGTT
*
9620379 TTTTATAATA
1 TTTTAAAATA
9620389 TACCTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 10 0.38
19 11 0.42
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTTAAAATACACATGTT
Found at i:9621635 original size:11 final size:11
Alignment explanation
Indices: 9621619--9621675 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
9621609 AAGTAAATCC
9621619 TAATCTAATAT
1 TAATCTAATAT
*
9621630 TAATCTAACAT
1 TAATCTAATAT
* *
9621641 TGATCTCTAATGT
1 T-A-ATCTAATAT
9621654 TAATCTAATAT
1 TAATCTAATAT
*
9621665 TTATCTTAATA
1 TAATC-TAATA
9621676 CTGCCGGAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
11 22 0.61
12 7 0.19
13 7 0.19
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.46
Consensus pattern (11 bp):
TAATCTAATAT
Found at i:9621649 original size:24 final size:24
Alignment explanation
Indices: 9621622--9621675 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
9621612 TAAATCCTAA
9621622 TCTAATATTAATCTAACATTGATC
1 TCTAATATTAATCTAACATTGATC
* * *
9621646 TCTAATGTTAATCTAATATTTATC
1 TCTAATATTAATCTAACATTGATC
9621670 T-TAATA
1 TCTAATA
9621676 CTGCCGGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (24 bp):
TCTAATATTAATCTAACATTGATC
Found at i:9628745 original size:28 final size:27
Alignment explanation
Indices: 9628714--9628766 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
9628704 CTTTTGAATA
*
9628714 AATAAATTCTCTTTGAGTTTTTTTTTTC
1 AATAAATTCTC-TTGAGTTTTCTTTTTC
*
9628742 AATAATTTCTCTTGAGTTTTCTTTT
1 AATAAATTCTCTTGAGTTTTCTTTT
9628767 AAAAGAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (27 bp):
AATAAATTCTCTTGAGTTTTCTTTTTC
Found at i:9630470 original size:6 final size:6
Alignment explanation
Indices: 9630459--9630515 Score: 53
Period size: 6 Copynumber: 8.8 Consensus size: 6
9630449 ACTAGGATAG
*
9630459 GAAAAA GAAAAA GAAGAAAA GAAAAA GAGGAAGAT GAAAAA G-AAAA GAAAAA
1 GAAAAA GAAAAA G-A-AAAA GAAAAA GA--AA-AA GAAAAA GAAAAA GAAAAA
9630511 GAAAA
1 GAAAA
9630516 GAGGCCAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
5 5 0.12
6 24 0.56
7 4 0.09
8 7 0.16
9 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:9630484 original size:20 final size:20
Alignment explanation
Indices: 9630459--9630513 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
9630449 ACTAGGATAG
9630459 GAAAAAGAAAAAGAAGAAAA
1 GAAAAAGAAAAAGAAGAAAA
** *
9630479 GAAAAAGAGGAAGATGAAAA
1 GAAAAAGAAAAAGAAGAAAA
9630499 -AGAAAAGAAAAAGAA
1 GA-AAAAGAAAAAGAA
9630514 AAGAGGCCAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
GAAAAAGAAAAAGAAGAAAA
Found at i:9630637 original size:33 final size:29
Alignment explanation
Indices: 9630615--9630670 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
9630605 AGTGAACAGA
9630615 AAAAAAAGTT-TAAGTATCAATATGGAAC
1 AAAAAAAGTTATAAGTATCAATATGGAAC
*
9630643 AAAAAAATTTATAAGTATCAATATGGAA
1 AAAAAAAGTTATAAGTATCAATATGGAA
9630671 AAAGTGAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.27
Consensus pattern (29 bp):
AAAAAAAGTTATAAGTATCAATATGGAAC
Found at i:9633554 original size:45 final size:45
Alignment explanation
Indices: 9633409--9633858 Score: 308
Period size: 44 Copynumber: 10.0 Consensus size: 45
9633399 ATAAGACTTG
* * *
9633409 TATCTTCGATCTACTTCACCACCAGTAGGGGAAGACAAGATCTGCT
1 TATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-T
* * * ***
9633455 T-TCTTCGATCTACTTC-ACGCCAGTACATGAAGACAAGA-CTTGT
1 TATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATC-TGT
* ** * *
9633498 T-TTTTTCGATCTGTTTCGCCACCAGTATGGGAGGACCAGATCTGT
1 TATCTTT-GATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGT
* * *** *
9633543 TATCTTTGATCTACTTC-ACGCCAGTACATGAAGAAAAGATTTACT-T
1 TATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGA--T-CTGT
* * ** *
9633589 TTTCCTTCGATC-AGCTTCGCCACCAGTATGGGAAGGTAAGATATGT
1 TAT-CTTTGATCTA-CTTCGCCACCAGTATGGGAAGACAAGATCTGT
* * ***
9633635 TATCTTTGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTT
1 TATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG--T
* * * *
9633681 TTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGT
1 TAT-CTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGT
* * * **
9633727 TACCTTTGATCTACTTC-ACGCCAGTATATGAAGACAAGATCTGT
1 TATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGT
*
9633771 TTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-
1 TATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGT
* * * * * * *
9633815 TATATTCGATCCACTTCGCTACCAATATAGGAAGACATGATCTG
1 TATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG
9633859 CTGCTTTTCA
Statistics
Matches: 307, Mismatches: 79, Indels: 38
0.72 0.19 0.09
Matches are distributed among these distances:
43 6 0.02
44 132 0.43
45 88 0.29
46 21 0.07
47 25 0.08
48 35 0.11
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (45 bp):
TATCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGT
Found at i:9633851 original size:181 final size:180
Alignment explanation
Indices: 9633411--9633831 Score: 577
Period size: 181 Copynumber: 2.3 Consensus size: 180
9633401 AAGACTTGTA
* * *
9633411 TCTTCGATCTACTTCACCACCAGTAGGGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
* *
9633476 AGTACATGAAGACAAGA-CTTG-TTTTTTTCGATCTGTTTCGCCACCAGTATGGGAGGACCAGAT
66 AGTACATGAAGACAAGATC-TGCTTTTTTTCGATCTGCTTCGCCACCAGTATGGGAGGACAAGAT
*
9633539 CTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGAAAAGATTTACTTTT
130 CTGTTACCTTTGATCTACTTCACGCCAGTACATGAAGAAAAGA-TTACTTTT
** * * *
9633591 TCCTTCGATC-AGCTTCGCCACCAGTATGGGAAGGTAAGATATGTTATCTTTGATCTACTTCACG
1 T-CTTCGATCTA-CTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
9633655 CCAGTACATGAAGACAAGATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGG-CA
64 CCAGTACATGAAGACAAGATCTGCTTTTT--TTCGATCTGCTTCGCCACCAGTATGGG-AGGACA
* *
9633719 AGATCTGTTACCTTTGATCTACTTCACGCCAGTATATGAAGACAAGA-T-CTGTTT
126 AGATCTGTTACCTTTGATCTACTTCACGCCAGTACATGAAGAAAAGATTACT-TTT
* * *
9633773 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-TATATTCGATCCACTTC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTC
9633832 GCTACCAATA
Statistics
Matches: 212, Mismatches: 20, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
180 16 0.08
181 110 0.52
182 12 0.06
184 71 0.33
185 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (180 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
AGTACATGAAGACAAGATCTGCTTTTTTTCGATCTGCTTCGCCACCAGTATGGGAGGACAAGATC
TGTTACCTTTGATCTACTTCACGCCAGTACATGAAGAAAAGATTACTTTT
Found at i:9633858 original size:89 final size:89
Alignment explanation
Indices: 9633411--9633815 Score: 539
Period size: 92 Copynumber: 4.5 Consensus size: 89
9633401 AAGACTTGTA
* * *
9633411 TCTTCGATCTACTTCACCACCAGTAGGGGAAGACAAGATCTGCTT-TCTTCGATCTACTTCACGC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-TTATCTTTGATCTACTTCACGC
9633475 CAGTACATGAAGACAAGA-CTTGTTT
65 CAGTACATGAAGACAAGATC-TGTTT
* ** * *
9633500 TTTTCGATCTGTTTCGCCACCAGTATGGGAGGACCAGATCTGTTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
*
9633565 AGTACATGAAGAAAAGATTTACT-TTT
66 AGTACATGAAGACAAGA--T-CTGTTT
** *
9633591 TCCTTCGATC-AGCTTCGCCACCAGTATGGGAAGGTAAGATATGTTATCTTTGATCTACTTCACG
1 T-CTTCGATCTA-CTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACG
9633655 CCAGTACATGAAGACAAGATCTGCTTTT
64 CCAGTACATGAAGACAAGATCTG--TTT
* * *
9633683 TCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTACCTTTGATCTACTTCACGC
1 T-CTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGC
*
9633748 CAGTATATGAAGACAAGATCTGTTT
65 CAGTACATGAAGACAAGATCTGTTT
*
9633773 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGT
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGT
9633816 ATATTCGATC
Statistics
Matches: 279, Mismatches: 26, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
88 2 0.01
89 111 0.40
90 5 0.02
91 4 0.01
92 156 0.56
93 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (89 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTTGATCTACTTCACGCC
AGTACATGAAGACAAGATCTGTTT
Found at i:9641554 original size:20 final size:20
Alignment explanation
Indices: 9641529--9641568 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9641519 TGAAGGTCTT
*
9641529 TAATGCATATGATGTGATGC
1 TAATGCATATGATGCGATGC
9641549 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
9641569 ATGAGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:9645461 original size:14 final size:14
Alignment explanation
Indices: 9645442--9645481 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
9645432 TCAACATACA
*
9645442 CAAATACATATTTG
1 CAAATACATATATG
*
9645456 CAAATATATATATG
1 CAAATACATATATG
9645470 CAAATACA-ATAT
1 CAAATACATATAT
9645482 AACAATAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (14 bp):
CAAATACATATATG
Found at i:9650724 original size:15 final size:15
Alignment explanation
Indices: 9650704--9650733 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9650694 ATTACTGCTC
9650704 TTCGCACAGTTGGAA
1 TTCGCACAGTTGGAA
9650719 TTCGCACAGTTGGAA
1 TTCGCACAGTTGGAA
9650734 ATATTGTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (15 bp):
TTCGCACAGTTGGAA
Found at i:9658828 original size:20 final size:20
Alignment explanation
Indices: 9658803--9658852 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
9658793 TGGCTTAAAA
9658803 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
9658823 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
9658840 GTGGTAGTGGATT
1 TTGGTAGTGGATT
9658853 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:9663540 original size:18 final size:19
Alignment explanation
Indices: 9663511--9663546 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
9663501 TAATAAATAT
9663511 TAAAAAATTATTTTAAAAA
1 TAAAAAATTATTTTAAAAA
9663530 TAAAAAA-TATTTTAAAA
1 TAAAAAATTATTTTAAAA
9663547 GTATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAAATTATTTTAAAAA
Found at i:9663546 original size:29 final size:29
Alignment explanation
Indices: 9663505--9663567 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
9663495 ATTTTTTAAT
*
9663505 AAATATTAAAAAATTATTTTAAAAATAAA
1 AAATATTAAAAAAGTATTTTAAAAATAAA
** *
9663534 AAATATTTTAAAAGTATTTTAAAATTAAA
1 AAATATTAAAAAAGTATTTTAAAAATAAA
9663563 AAATA
1 AAATA
9663568 AAAATAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (29 bp):
AAATATTAAAAAAGTATTTTAAAAATAAA
Found at i:9667144 original size:31 final size:31
Alignment explanation
Indices: 9667106--9667165 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
9667096 TTTAATTTAA
* *
9667106 TCAATTTTTGTCCAGGTACTTTTCAAATTGG
1 TCAATTTTAGTCCAGATACTTTTCAAATTGG
**
9667137 TCAATTTTAGTCCTTATACTTTTCAAATT
1 TCAATTTTAGTCCAGATACTTTTCAAATT
9667166 TTGAAGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (31 bp):
TCAATTTTAGTCCAGATACTTTTCAAATTGG
Found at i:9668748 original size:16 final size:18
Alignment explanation
Indices: 9668717--9668749 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
9668707 TCTAGAGTCA
9668717 AAGAAAAGCTTTAATAAG
1 AAGAAAAGCTTTAATAAG
9668735 AAGAAAA-C-TTAATAA
1 AAGAAAAGCTTTAATAA
9668750 AACTCTACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.21
Consensus pattern (18 bp):
AAGAAAAGCTTTAATAAG
Found at i:9668960 original size:14 final size:14
Alignment explanation
Indices: 9668941--9668971 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9668931 GGTAGGCAAC
*
9668941 TTTTTTTTGCGGTT
1 TTTTTTTTGCGCTT
9668955 TTTTTTTTGCGCTT
1 TTTTTTTTGCGCTT
9668969 TTT
1 TTT
9668972 ACTTCTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.16, T:0.74
Consensus pattern (14 bp):
TTTTTTTTGCGCTT
Found at i:9669595 original size:31 final size:32
Alignment explanation
Indices: 9669536--9669600 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
9669526 GGAAAATTAC
9669536 AAGAGTAACTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAACTGAATCCTAATAAAAACTCTTTA
*
9669568 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAACTGAATCCTAATAAAAACTCTTTA
9669599 AA
1 AA
9669601 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.41
32 19 0.59
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (32 bp):
AAGAGTAACTGAATCCTAATAAAAACTCTTTA
Found at i:9672823 original size:39 final size:39
Alignment explanation
Indices: 9672769--9672882 Score: 228
Period size: 39 Copynumber: 2.9 Consensus size: 39
9672759 ATGTATATAT
9672769 ATTTTATGGCATTAAATTCACTTCAAAGAAAACATACAC
1 ATTTTATGGCATTAAATTCACTTCAAAGAAAACATACAC
9672808 ATTTTATGGCATTAAATTCACTTCAAAGAAAACATACAC
1 ATTTTATGGCATTAAATTCACTTCAAAGAAAACATACAC
9672847 ATTTTATGGCATTAAATTCACTTCAAAGAAAACATA
1 ATTTTATGGCATTAAATTCACTTCAAAGAAAACATA
9672883 TCATACATTC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.32
Consensus pattern (39 bp):
ATTTTATGGCATTAAATTCACTTCAAAGAAAACATACAC
Found at i:9678959 original size:25 final size:26
Alignment explanation
Indices: 9678925--9678973 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
9678915 ACATATTTTC
9678925 TCAAAGTTTTACTA-GGGTAAAATCA
1 TCAAAGTTTTACTAGGGGTAAAATCA
*
9678950 TCAAATTTTTACTAGGGGTAAAAT
1 TCAAAGTTTTACTAGGGGTAAAAT
9678974 AAGGATGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (26 bp):
TCAAAGTTTTACTAGGGGTAAAATCA
Found at i:9685352 original size:32 final size:31
Alignment explanation
Indices: 9685302--9685361 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
9685292 ATGAATTATC
*
9685302 AAATTAAAATAATTAATTTATAATCAGTTACT
1 AAATTAAAATAATCAATTTATAAT-AGTTACT
* *
9685334 AAATTCAAGTAATCAATTTATAATAGTT
1 AAATTAAAATAATCAATTTATAATAGTT
9685362 TATGATGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (31 bp):
AAATTAAAATAATCAATTTATAATAGTTACT
Found at i:9688269 original size:44 final size:47
Alignment explanation
Indices: 9688178--9688270 Score: 129
Period size: 45 Copynumber: 2.0 Consensus size: 47
9688168 GCTGTCCCTC
* *
9688178 ATAAAGCAATAAAATTGAAATGAAAAGACAAGTGAAAACGTAAAGCAA
1 ATAAAGCAATAAAA-TGAAATGAAAAGACAAATGAAAACATAAAGCAA
*
9688226 ATAAAGCAAT-AAA-GAAATGAAAAGGCAAAT-AAAACATAAAGCAA
1 ATAAAGCAATAAAATGAAATGAAAAGACAAATGAAAACATAAAGCAA
9688270 A
1 A
9688271 GCCGCAGTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
44 14 0.33
45 15 0.36
47 3 0.07
48 10 0.24
ACGTcount: A:0.63, C:0.09, G:0.15, T:0.13
Consensus pattern (47 bp):
ATAAAGCAATAAAATGAAATGAAAAGACAAATGAAAACATAAAGCAA
Found at i:9709434 original size:42 final size:42
Alignment explanation
Indices: 9709375--9709499 Score: 232
Period size: 42 Copynumber: 3.0 Consensus size: 42
9709365 ATCAAATCCT
*
9709375 CAACAGCTGAAAGTGGGTTCGAAAGCTCTGTACCGTCTACTG
1 CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACTG
9709417 CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACTG
1 CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACTG
*
9709459 CAACAGCTGAAAATGGGTTCGAAAGCTCCGTACCGTCTACT
1 CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACT
9709500 ACGTTACAGT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (42 bp):
CAACAGCTGAAAGTGGGTTCGAAAGCTCCGTACCGTCTACTG
Found at i:9720227 original size:41 final size:38
Alignment explanation
Indices: 9720124--9720227 Score: 111
Period size: 41 Copynumber: 2.7 Consensus size: 38
9720114 TTCGAAGAAA
* *
9720124 TAAATTGACACCCAGTGTTTTATCG-GCTAAACTAAAG
1 TAAATTGACACCCAGTGTCTTATCGAACTAAACTAAAG
** * * *
9720161 TAAATTGACACCCAGTACCTCATCGAATTAATCTAAAGTAG
1 TAAATTGACACCCAGTGTCTTATCGAACTAAACT-AA--AG
9720202 TAAATTGACACCCAGTGTCTTATCGA
1 TAAATTGACACCCAGTGTCTTATCGA
9720228 CTCGAAGTCG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
37 21 0.40
38 5 0.09
39 2 0.04
41 25 0.47
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (38 bp):
TAAATTGACACCCAGTGTCTTATCGAACTAAACTAAAG
Found at i:9721123 original size:17 final size:18
Alignment explanation
Indices: 9721091--9721126 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
9721081 GAAACCCTAA
9721091 CTTTTTCTCCTTTCTTTCT
1 CTTTTTCT-CTTTCTTTCT
9721110 CTTTTTCT-TTTCTTTCT
1 CTTTTTCTCTTTCTTTCT
9721127 TTCCTTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTTTCTCTTTCTTTCT
Found at i:9721227 original size:20 final size:20
Alignment explanation
Indices: 9721180--9721245 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
9721170 TTCTATTTCT
*
9721180 TTATTTGTTTTGTTTTAATTA
1 TTATTTATTTTGTTTT-ATTA
9721201 CTTATTTATTTTGTTTTATTA
1 -TTATTTATTTTGTTTTATTA
**
9721222 TTATTTCA-TTTACTTTATTA
1 TTATTT-ATTTTGTTTTATTA
9721242 TTAT
1 TTAT
9721246 AATAATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
20 20 0.50
21 5 0.12
22 15 0.38
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (20 bp):
TTATTTATTTTGTTTTATTA
Found at i:9721321 original size:19 final size:20
Alignment explanation
Indices: 9721279--9721328 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
9721269 ATATTAAGTA
*
9721279 ATACATAT-TTTATTATTAT
1 ATACATATGTATATTATTAT
9721298 ATACATATGTATATTATT-T
1 ATACATATGTATATTATTAT
* *
9721317 TTACACATGTAT
1 ATACATATGTAT
9721329 TCACCAACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (20 bp):
ATACATATGTATATTATTAT
Found at i:9722039 original size:18 final size:17
Alignment explanation
Indices: 9722016--9722051 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
9722006 AAAATAAACA
9722016 TAATTAATTAATTTAAAT
1 TAATTAATTAA-TTAAAT
9722034 TAATTAATTAATTAAAT
1 TAATTAATTAATTAAAT
9722051 T
1 T
9722052 CTTAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTAATTAATTAAAT
Found at i:9723569 original size:3 final size:3
Alignment explanation
Indices: 9723548--9723625 Score: 68
Period size: 3 Copynumber: 25.7 Consensus size: 3
9723538 ACAGTAAATG
* * *
9723548 ATA ATA ATGA A-A ATG ATA ATA ATA GTA ATA ATA ATA TTA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
9723593 ACA AAA ATA ATA AAA ATA ATA CTA ATAA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA AT
9723626 TTTTAGAGTT
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
2 2 0.03
3 52 0.88
4 5 0.08
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:9723707 original size:15 final size:14
Alignment explanation
Indices: 9723681--9723734 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 14
9723671 ATGGAGTAAT
9723681 AATAACAATAATAAA
1 AATAA-AATAATAAA
9723696 AGATAAAATAATATAAA
1 A-ATAAAAT-A-ATAAA
*
9723713 AATAAAAATAATATA
1 AAT-AAAATAATAAA
9723728 AATAAAA
1 AATAAAA
9723735 GAATGCACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
14 4 0.12
15 11 0.32
16 8 0.24
17 11 0.32
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (14 bp):
AATAAAATAATAAA
Found at i:9723713 original size:17 final size:17
Alignment explanation
Indices: 9723681--9723729 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
9723671 ATGGAGTAAT
*
9723681 AATAACAATAATA-AAA
1 AATAAAAATAATATAAA
*
9723697 GAT-AAAATAATATAAA
1 AATAAAAATAATATAAA
9723713 AATAAAAATAATATAAA
1 AATAAAAATAATATAAA
9723730 TAAAAGAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 13 0.46
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (17 bp):
AATAAAAATAATATAAA
Found at i:9723880 original size:17 final size:18
Alignment explanation
Indices: 9723853--9723886 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9723843 GAAAATAAAT
9723853 AAATAAATAAATCAAACA
1 AAATAAATAAATCAAACA
*
9723871 AAAT-AATAAATGAAAC
1 AAATAAATAAATCAAAC
9723887 TGTTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATAAATAAATCAAACA
Found at i:9736589 original size:26 final size:26
Alignment explanation
Indices: 9736546--9736597 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
9736536 GCAATTACAA
9736546 AGTATTATTTTTACAAG-TATTAATTT
1 AGTATTATTTTTACAAGTTA-TAATTT
9736572 AGTATTATTTTTTA-AAGTTATAATTT
1 AGTATTA-TTTTTACAAGTTATAATTT
9736598 TTTTGTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (26 bp):
AGTATTATTTTTACAAGTTATAATTT
Found at i:9747921 original size:10 final size:10
Alignment explanation
Indices: 9747906--9747978 Score: 50
Period size: 10 Copynumber: 7.5 Consensus size: 10
9747896 TTTAAAATAC
9747906 TTTTTTAAAA
1 TTTTTTAAAA
9747916 TTTTTT-AAA
1 TTTTTTAAAA
*
9747925 -TTTTAAAAA
1 TTTTTTAAAA
*
9747934 ATTTTTAAACTA
1 TTTTTTAAA--A
9747946 CTTTTTT--AA
1 -TTTTTTAAAA
9747955 --TTTTAAAA
1 TTTTTTAAAA
9747963 TATTTTTAAAA
1 T-TTTTTAAAA
9747974 TTTTT
1 TTTTT
9747979 GTTTTAATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 20
0.68 0.04 0.27
Matches are distributed among these distances:
6 4 0.08
8 6 0.12
9 7 0.14
10 17 0.34
11 10 0.20
12 1 0.02
13 5 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:9747921 original size:30 final size:28
Alignment explanation
Indices: 9747885--9747996 Score: 125
Period size: 30 Copynumber: 3.7 Consensus size: 28
9747875 AAATATTTTT
9747885 ATTTTTTTAATTTTAAAATACTTTTTTAAA
1 ATTTTTTTAATTTTAAAATA--TTTTTAAA
* *
9747915 ATTTTTTAAATTTTAAAAAATTTTTAAA
1 ATTTTTTTAATTTTAAAATATTTTTAAA
*
9747943 CTACTTTTTTAATTTTAAAATATTTTTAAA
1 --ATTTTTTTAATTTTAAAATATTTTTAAA
9747973 ATTTTTGTTTTAATTTTTAAAATA
1 A--TTT-TTTTAA-TTTTAAAATA
9747997 AATTTTTGGT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
28 9 0.13
30 45 0.64
31 6 0.09
32 10 0.14
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (28 bp):
ATTTTTTTAATTTTAAAATATTTTTAAA
Found at i:9747970 original size:41 final size:40
Alignment explanation
Indices: 9747895--9747978 Score: 100
Period size: 39 Copynumber: 2.1 Consensus size: 40
9747885 ATTTTTTTAA
**
9747895 TTTTAAAATACTTTTTTAAAATTTTTTAAATTTTAAAAAAT
1 TTTTAAAATACTTTTTT-AAATTTTAAAAATTTTAAAAAAT
* *
9747936 TTTTAAACTACTTTTTT-AATTTTAAAATATTTT-TAAAAT
1 TTTTAAAATACTTTTTTAAATTTTAAAA-ATTTTAAAAAAT
9747975 TTTT
1 TTTT
9747979 GTTTTAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 17 0.45
40 5 0.13
41 16 0.42
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (40 bp):
TTTTAAAATACTTTTTTAAATTTTAAAAATTTTAAAAAAT
Found at i:9750092 original size:28 final size:28
Alignment explanation
Indices: 9750059--9750156 Score: 117
Period size: 28 Copynumber: 3.5 Consensus size: 28
9750049 TAATGAGATT
* *
9750059 AGCACTAAGTGTGCGAGTTTAATTG-AA
1 AGCACTAAGTGTGCGAGTATAATGGTAA
9750086 ATGCACTAAGTGTGCGAGTATAATGGTAA
1 A-GCACTAAGTGTGCGAGTATAATGGTAA
* * ** *
9750115 AGCACTAAGTGTGCGAGTGTGATTATTA
1 AGCACTAAGTGTGCGAGTATAATGGTAA
9750143 AGCACTAAGTGTGC
1 AGCACTAAGTGTGC
9750157 TTACTTATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
27 1 0.02
28 58 0.94
29 3 0.05
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTATAATGGTAA
Found at i:9762639 original size:6 final size:6
Alignment explanation
Indices: 9762628--9762657 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
9762618 AAGGAGCTAG
9762628 AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
9762658 TGCATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:9766811 original size:3 final size:3
Alignment explanation
Indices: 9766805--9766833 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9766795 CGAAGAGGAT
9766805 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
9766834 TGATGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9766884 original size:3 final size:3
Alignment explanation
Indices: 9766878--9766902 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9766868 GACGACGACC
9766878 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
9766903 CAAATATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:9767176 original size:3 final size:3
Alignment explanation
Indices: 9767170--9767308 Score: 278
Period size: 3 Copynumber: 46.3 Consensus size: 3
9767160 CATTTTCAGC
9767170 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
9767218 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
9767266 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
9767309 AGCAAAAAGA
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 136 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9769938 original size:9 final size:9
Alignment explanation
Indices: 9769924--9769981 Score: 82
Period size: 9 Copynumber: 6.4 Consensus size: 9
9769914 GTAGTGATTC
9769924 AATTCGGTT
1 AATTCGGTT
9769933 AATTCGGTT
1 AATTCGGTT
9769942 AATTCTGG-T
1 AATTC-GGTT
*
9769951 AATCCGGTT
1 AATTCGGTT
*
9769960 AATTCGGGT
1 AATTCGGTT
9769969 AATTCGGTT
1 AATTCGGTT
9769978 AATT
1 AATT
9769982 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 2 0.05
9 39 0.91
10 2 0.05
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:9778280 original size:34 final size:35
Alignment explanation
Indices: 9778236--9778302 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
9778226 CAGTAAAATA
9778236 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
9778270 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
9778303 CTGCTGCTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:9779617 original size:16 final size:16
Alignment explanation
Indices: 9779596--9779627 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9779586 AAATATATTT
*
9779596 TTTTTAAATTTTTTTA
1 TTTTTAAATCTTTTTA
9779612 TTTTTAAATCTTTTTA
1 TTTTTAAATCTTTTTA
9779628 ATTAATAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTAAATCTTTTTA
Found at i:9785651 original size:28 final size:26
Alignment explanation
Indices: 9785620--9785682 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 26
9785610 AATATTAAAT
9785620 ATTATTTTAATATAATATAATATAATTA
1 ATTATTTTAATAT-AT-TAATATAATTA
* *
9785648 ATTA-TTTAA-ATATTGATCTAATTA
1 ATTATTTTAATATATTAATATAATTA
9785672 ATTATTTTAAT
1 ATTATTTTAAT
9785683 GAAATTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 13 0.42
25 7 0.23
26 2 0.06
27 5 0.16
28 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTATTTTAATATATTAATATAATTA
Found at i:9787744 original size:31 final size:32
Alignment explanation
Indices: 9787709--9787770 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
9787699 AAAAACAAAG
* *
9787709 ATAATGATAAATGATATTTAAA-TAATTTAAT
1 ATAATGATAAATGAAATATAAATTAATTTAAT
*
9787740 ATAATGATATATGAAATATAAATTAATTTAA
1 ATAATGATAAATGAAATATAAATTAATTTAA
9787771 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (32 bp):
ATAATGATAAATGAAATATAAATTAATTTAAT
Found at i:9792654 original size:29 final size:32
Alignment explanation
Indices: 9792589--9792654 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 32
9792579 AAATGTGAAA
*
9792589 ATTAAACCAAAATTAAAGTTTGATATATATAC
1 ATTACACCAAAATTAAAGTTTGATATATATAC
*
9792621 A-TACACC-AAATTAAAG-TTGATGTATA-AC
1 ATTACACCAAAATTAAAGTTTGATATATATAC
9792649 ATTACA
1 ATTACA
9792655 AATTGTAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 3 0.10
29 13 0.42
30 9 0.29
31 5 0.16
32 1 0.03
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (32 bp):
ATTACACCAAAATTAAAGTTTGATATATATAC
Found at i:9795511 original size:30 final size:32
Alignment explanation
Indices: 9795458--9795521 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 32
9795448 GCTAAGTTTC
*
9795458 TAATCAATCTTAATTTCTTCAAGTGTTTGTAT
1 TAATCAATCTTAATTTCTTCAAGTATTTGTAT
*
9795490 TAATCAATTTTAA-TT-TTCAAGTATTTGTAT
1 TAATCAATCTTAATTTCTTCAAGTATTTGTAT
9795520 TA
1 TA
9795522 TTTATCCTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.53
31 2 0.07
32 12 0.40
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (32 bp):
TAATCAATCTTAATTTCTTCAAGTATTTGTAT
Done.