Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 48 of 51
Found at i:11927205 original size:16 final size:16
Alignment explanation
Indices: 11927184--11927222 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
11927174 TCAATTACAA
*
11927184 GTCAGGTTCATAACAT
1 GTCAGGTTCATAACAG
*
11927200 GTCAGGTTGATAACAG
1 GTCAGGTTCATAACAG
11927216 GTCAGGT
1 GTCAGGT
11927223 AATACCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (16 bp):
GTCAGGTTCATAACAG
Found at i:11931938 original size:182 final size:179
Alignment explanation
Indices: 11931635--11931996 Score: 681
Period size: 182 Copynumber: 2.0 Consensus size: 179
11931625 AAAAGCTCCA
11931635 TGTCTATTCGGCCACACACATGCCATGCACTGAGAGTTTTTGGCGCCAACATGAGGACACACACC
1 TGTCTATTCGGCCACACACATGCCATGCACTGAGAGTTTTTGGCGCCAACATGAGGACACACACC
11931700 ATTCGGCTAAGGGAGATGTTCCCTCATCATTGCCGAATCATCAAGCCCCTTCATGAAGGGTTAGT
66 ATTCGGCTAAGGGAGATGTTCCCTCATCATTGCCGAATCATCAAGCCCCTTCATGAAGGGTTAGT
11931765 CGAACCATCACAAGCCCAAAGGACTTAATC-TTCATTTGAAGCATTATG
131 CGAACCATCACAAGCCCAAAGGACTTAATCATTCATTTGAAGCATTATG
11931813 TGTCTATTCGGCCACACACATGCCATGCACATGAGAGTTTTTGGCGCCAACATGAGGAGACACAA
1 TGTCTATTCGGCCACACACATGCCATGCAC-TGAGAGTTTTTGGCGCCAACATGA-G-GACAC-A
11931878 CACCATTCGGCTAAGGGAGATGTTCCCTCATCATTGCCGAATCATCAAGCCCCTTCATGAAGGGT
62 CACCATTCGGCTAAGGGAGATGTTCCCTCATCATTGCCGAATCATCAAGCCCCTTCATGAAGGGT
11931943 TAGTCGAACCATCACAAGCCCAAAGGACTTAATCATTCATTTGAAGCATTATG
127 TAGTCGAACCATCACAAGCCCAAAGGACTTAATCATTCATTTGAAGCATTATG
11931996 T
1 T
11931997 ATCTTCCTAA
Statistics
Matches: 179, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
178 30 0.17
179 24 0.13
180 1 0.01
181 5 0.03
182 100 0.56
183 19 0.11
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.25
Consensus pattern (179 bp):
TGTCTATTCGGCCACACACATGCCATGCACTGAGAGTTTTTGGCGCCAACATGAGGACACACACC
ATTCGGCTAAGGGAGATGTTCCCTCATCATTGCCGAATCATCAAGCCCCTTCATGAAGGGTTAGT
CGAACCATCACAAGCCCAAAGGACTTAATCATTCATTTGAAGCATTATG
Found at i:11932715 original size:5 final size:5
Alignment explanation
Indices: 11932705--11932763 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
11932695 TTGGAGTGCC
11932705 AAAAG AAAAG AAAAAG ACAAAAG AAGAA- AAAAG AAAAG --AAG AAAAG
1 AAAAG AAAAG -AAAAG --AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG
11932751 AAAAG AAAAG AAA
1 AAAAG AAAAG AAA
11932764 TTCAAAAGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
3 3 0.06
4 2 0.04
5 30 0.64
6 7 0.15
7 5 0.11
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:11932739 original size:23 final size:24
Alignment explanation
Indices: 11932705--11932763 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
11932695 TTGGAGTGCC
11932705 AAAAGAAAAGAAAAAG-ACAAAAG
1 AAAAGAAAAGAAAAAGAACAAAAG
*
11932728 AAGAA-AAAAG-AAAAGAAGAAAAG
1 AA-AAGAAAAGAAAAAGAACAAAAG
11932751 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
11932764 TTCAAAAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 7 0.23
23 20 0.65
24 4 0.13
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (24 bp):
AAAAGAAAAGAAAAAGAACAAAAG
Found at i:11932755 original size:18 final size:18
Alignment explanation
Indices: 11932707--11932762 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
11932697 GGAGTGCCAA
*
11932707 AAGAAAAGAAAAAGACAA-
1 AAGAAAAG-AAAAGAAAAG
11932725 AAGAAGAA-AAAAGAAAAG
1 AAGAA-AAGAAAAGAAAAG
11932743 AAGAAAAGAAAAGAAAAG
1 AAGAAAAGAAAAGAAAAG
11932761 AA
1 AA
11932763 ATTCAAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 10 0.29
18 22 0.65
19 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAGAAAAGAAAAGAAAAG
Found at i:11936833 original size:13 final size:13
Alignment explanation
Indices: 11936815--11936859 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
11936805 CATAGCCATT
*
11936815 TCATCATCATCCA
1 TCATCAACATCCA
*
11936828 TCATCAACATCCT
1 TCATCAACATCCA
*
11936841 TCATCAAGA-CCA
1 TCATCAACATCCA
11936853 TCATCAA
1 TCATCAA
11936860 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:11942803 original size:26 final size:26
Alignment explanation
Indices: 11942690--11942806 Score: 73
Period size: 29 Copynumber: 4.4 Consensus size: 26
11942680 AAAATTAAAA
* * *
11942690 ATAATCATAATATATATAGTAT-ATA-
1 ATAAT-ATAATATATATTGAATGTTAT
*
11942715 ATAATATAATATGTATGATGAATGTTAT
1 ATAATATAATATATAT--TGAATGTTAT
* *
11942743 AATAATATGATATATATT-ATACTTGTAAT
1 -ATAATATAATATATATTGA-A--TGTTAT
11942772 AT-ATAT-ATATATATTGAATGTTAT
1 ATAATATAATATATATTGAATGTTAT
11942796 GATAATATAAT
1 -ATAATATAAT
11942807 GCATGTATAT
Statistics
Matches: 72, Mismatches: 8, Indels: 22
0.71 0.08 0.22
Matches are distributed among these distances:
24 15 0.21
25 7 0.10
26 18 0.25
27 11 0.15
28 2 0.03
29 19 0.26
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.44
Consensus pattern (26 bp):
ATAATATAATATATATTGAATGTTAT
Found at i:11943007 original size:21 final size:19
Alignment explanation
Indices: 11942969--11943014 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
11942959 AATTAATCCT
11942969 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
11942989 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
11943010 A-TAAT
1 ACTAAT
11943015 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:11944549 original size:16 final size:16
Alignment explanation
Indices: 11944518--11944550 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11944508 TTCTATGTAC
11944518 TATATAAACTATAAAG
1 TATATAAACTATAAAG
11944534 TATATAAACTATAAAG
1 TATATAAACTATAAAG
11944550 T
1 T
11944551 GTGTGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (16 bp):
TATATAAACTATAAAG
Found at i:11944611 original size:2 final size:2
Alignment explanation
Indices: 11944604--11944666 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
11944594 AAGTATAAAG
11944604 TA TA TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11944644 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
11944667 TGTCATGGGG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11944616 original size:16 final size:16
Alignment explanation
Indices: 11944597--11944665 Score: 95
Period size: 16 Copynumber: 4.2 Consensus size: 16
11944587 AAATAAAAAG
11944597 TATAAAGTATATATA-A
1 TATAAA-TATATATATA
11944613 TATAATATATATATATA
1 TATAA-ATATATATATA
*
11944630 TATATATATATATATA
1 TATAAATATATATATA
*
11944646 TATATATATATATATA
1 TATAAATATATATATA
11944662 TATA
1 TATA
11944666 TTGTCATGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
16 44 0.88
17 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (16 bp):
TATAAATATATATATA
Found at i:11947915 original size:11 final size:11
Alignment explanation
Indices: 11947901--11947925 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11947891 TTTAAAGCAA
11947901 CCTTAAGTTTT
1 CCTTAAGTTTT
11947912 CCTTAAGTTTT
1 CCTTAAGTTTT
11947923 CCT
1 CCT
11947926 AACACTTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (11 bp):
CCTTAAGTTTT
Found at i:11958996 original size:17 final size:19
Alignment explanation
Indices: 11958974--11959010 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
11958964 TATATATATA
11958974 TATATATATAAAGTATAAT
1 TATATATATAAAGTATAAT
11958993 TATATATATAAAGTATAA
1 TATATATATAAAGTATAA
11959011 ATTAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TATATATATAAAGTATAAT
Found at i:11962802 original size:18 final size:20
Alignment explanation
Indices: 11962781--11962827 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
11962771 TGTTTGTTGA
11962781 ATGCAAA-A-TGTTGAATTG
1 ATGCAAATACTGTTGAATTG
11962799 ATGCAATAATACTTGTTGAATTG
1 ATGC-A-AATAC-TGTTGAATTG
11962822 ATGCAA
1 ATGCAA
11962828 TGTCTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 4 0.17
19 1 0.04
20 2 0.08
21 2 0.08
22 1 0.04
23 14 0.58
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (20 bp):
ATGCAAATACTGTTGAATTG
Found at i:11962888 original size:25 final size:25
Alignment explanation
Indices: 11962858--11962915 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 25
11962848 TGTTGCCTTG
11962858 TAAATTATTGTTGGTCTAACTAAAA
1 TAAATTATTGTTGGTCTAACTAAAA
*
11962883 T-AA--ATTGTTGGTCTGACTAAAA
1 TAAATTATTGTTGGTCTAACTAAAA
*
11962905 TAAATTGTTGT
1 TAAATTATTGT
11962916 AACTTGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 19 0.68
23 2 0.07
24 2 0.07
25 5 0.18
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (25 bp):
TAAATTATTGTTGGTCTAACTAAAA
Found at i:11962891 original size:22 final size:22
Alignment explanation
Indices: 11962864--11962914 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
11962854 CTTGTAAATT
11962864 ATTGTTGGTCTAACTAAAATAA
1 ATTGTTGGTCTAACTAAAATAA
*
11962886 ATTGTTGGTCTGACTAAAATAA
1 ATTGTTGGTCTAACTAAAATAA
11962908 ATTGTTG
1 ATTGTTG
11962915 TAACTTGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (22 bp):
ATTGTTGGTCTAACTAAAATAA
Found at i:11963381 original size:21 final size:21
Alignment explanation
Indices: 11963357--11963409 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
11963347 TATTTAATGA
*
11963357 AATTAATAATT-TAATGATTAT
1 AATTAATAATTATAAT-ATAAT
* *
11963378 AATTAAGATTTATAATATAAT
1 AATTAATAATTATAATATAAT
11963399 AATT-ATAATTA
1 AATTAATAATTA
11963410 ATATAGAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 5 0.19
21 17 0.65
22 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
AATTAATAATTATAATATAAT
Found at i:11963556 original size:16 final size:16
Alignment explanation
Indices: 11963537--11963568 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11963527 GGTAACTTAT
11963537 AAGTCAGGTAAATATC
1 AAGTCAGGTAAATATC
*
11963553 AAGTTAGGTAAATATC
1 AAGTCAGGTAAATATC
11963569 GTACCAATTC
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:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (16 bp):
AAGTCAGGTAAATATC
Found at i:11963781 original size:15 final size:15
Alignment explanation
Indices: 11963761--11963797 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
11963751 GGTCAAGTTC
11963761 AGATCCACAATTTCT
1 AGATCCACAATTTCT
11963776 AGATCCACAATTTCT
1 AGATCCACAATTTCT
11963791 AGATCCA
1 AGATCCA
11963798 ACTCAGGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30
Consensus pattern (15 bp):
AGATCCACAATTTCT
Found at i:11965264 original size:41 final size:41
Alignment explanation
Indices: 11965077--11965499 Score: 342
Period size: 41 Copynumber: 10.3 Consensus size: 41
11965067 TAGCGGCACT
* * * * **
11965077 TTTAGCGGCGTTTTT-TGAACAAACGCCGGTAAATACTTGTGT
1 TTTAGTGGCGTTTTTAT--ACAAACGCCGCTAAATGCTCGTAC
* * ** *
11965119 TTTAGTGGCGTTTGTATATAAACGCCGCTACCTACT-GTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATGCTCGTAC
** * **
11965159 TTTAGTGGCGTTTTCGTATAAACGCCGCTAAATAAT-GTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATGCTCGTAC
** * *
11965199 AATAGTGGCGTTTTAAGCACAAACGCCGCTAAATGCTCGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATGCTCGTAC
* * **
11965241 TTTAGTGGCGTTTCTATATAAACGCCGCTAAATAAT-GTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATGCTCGTAC
* * * *
11965281 TATAGTGACGTTTTAAGCACAAACGCCGCTAAATGCTCGTAC
1 TTTAGTGGCGTTTTTA-TACAAACGCCGCTAAATGCTCGTAC
* *
11965323 TTTAGTGGCGTTTTTGTACAAACGCCGCCAAA-GACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATG-CTCGTAC
* * *
11965364 TTTAGCGACGTTTTTATACAAACGCCGCCAAA-GAC-CTGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATG-CTC-GTAC
* *
11965405 TTTAGTGGCGTTTTTATACAAACGCCGCCAAA-GACCCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATG-CTCGTAC
* * * *
11965446 TTTAGTTGCGTTTTTATGCAAACGCCGCCAAA-GACCCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAATG-CTCGTAC
*
11965487 TTTAGTGCCGTTT
1 TTTAGTGGCGTTT
11965500 CTGCGGCTAA
Statistics
Matches: 320, Mismatches: 53, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.21
41 207 0.65
42 46 0.14
43 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAATGCTCGTAC
Found at i:11965376 original size:123 final size:122
Alignment explanation
Indices: 11965077--11965501 Score: 426
Period size: 123 Copynumber: 3.5 Consensus size: 122
11965067 TAGCGGCACT
* * ** * * ** *
11965077 TTTAGCGGCGTTTTTTGAACAAACGCCGGTAAATACTTGTGTTTTAGTGGCGTTTGTATATAAAC
1 TTTAGTGGCG-TTTTTGTACAAACGCCGCCAAAGACTCGTACTTTAGTGGCGTTTCTATATAAAC
** * * **
11965142 GCCGCTACCTACTGTACTTTAGTGGCGTTTTCGTATAAACGCCGCTAAATAAT-GTAC
65 GCCGCTAAATACTGTACTTTAGTGGCGTTTTAGTACAAACGCCGCTAAATGCTCGTAC
** * * *
11965199 AATAGTGGCGTTTTAAGCACAAACGCCGCTAAATG-CTCGTACTTTAGTGGCGTTTCTATATAAA
1 TTTAGTGGCGTTTT-TGTACAAACGCCGCCAAA-GACTCGTACTTTAGTGGCGTTTCTATATAAA
* * * *
11965263 CGCCGCTAAATAATGTACTATAGTGACGTTTTAAGCACAAACGCCGCTAAATGCTCGTAC
64 CGCCGCTAAATACTGTACTTTAGTGGCGTTTT-AGTACAAACGCCGCTAAATGCTCGTAC
* * * *
11965323 TTTAGTGGCGTTTTTGTACAAACGCCGCCAAAGACTCGTACTTTAGCGACGTTTTTATACAAACG
1 TTTAGTGGCGTTTTTGTACAAACGCCGCCAAAGACTCGTACTTTAGTGGCGTTTCTATATAAACG
* * * *
11965388 CCGCCAAAGACCTGTACTTTAGTGGCGTTTTTA-TACAAACGCCGCCAAA-GACCCGTAC
66 CCGCTAAATA-CTGTACTTTAGTGGCG-TTTTAGTACAAACGCCGCTAAATG-CTCGTAC
* * * * *
11965446 TTTAGTTGCGTTTTTATGCAAACGCCGCCAAAGACCCGTACTTTAGTGCCGTTTCT
1 TTTAGTGGCGTTTTTGTACAAACGCCGCCAAAGACTCGTACTTTAGTGGCGTTTCT
11965502 GCGGCTAAAC
Statistics
Matches: 250, Mismatches: 45, Indels: 15
0.81 0.15 0.05
Matches are distributed among these distances:
121 4 0.02
122 76 0.30
123 136 0.54
124 30 0.12
125 4 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (122 bp):
TTTAGTGGCGTTTTTGTACAAACGCCGCCAAAGACTCGTACTTTAGTGGCGTTTCTATATAAACG
CCGCTAAATACTGTACTTTAGTGGCGTTTTAGTACAAACGCCGCTAAATGCTCGTAC
Found at i:11965387 original size:164 final size:163
Alignment explanation
Indices: 11965138--11965432 Score: 380
Period size: 164 Copynumber: 1.8 Consensus size: 163
11965128 GTTTGTATAT
** * * *
11965138 AAACGCCGCTACCTACTGTACTTTAGTGGCGTTTTCGTATAAACGCCGCTAAATAATGTACAATA
1 AAACGCCGCTAAATACTGTACTTTAGTGGCGTTTTCGTACAAACGCCGCCAAAGAATGTACAATA
* * * *
11965203 GTGGCGTTTTAAGCACAAACGCCGCTAAATG--CTCGTACTTTAGTGGCGTTTCTATATAAACGC
66 GCGACGTTTTAAGCACAAACGCCGCCAAA-GACCT-GTACTTTAGTGGCGTTTCTATACAAACGC
11965266 CGCTAAATAATGTACTATAGTGACGTTTTAAGCAC
129 CGCTAAATAATGTACTATAGTGACGTTTTAAGCAC
* * * **
11965301 AAACGCCGCTAAATGCTCGTACTTTAGTGGCGTTTTTGTACAAACGCCGCCAAAGACTCGTACTT
1 AAACGCCGCTAAATACT-GTACTTTAGTGGCGTTTTCGTACAAACGCCGCCAAAGAAT-GTACAA
* * *
11965366 TAGCGACGTTTTTA-TACAAACGCCGCCAAAGACCTGTACTTTAGTGGCGTTTTTATACAAACGC
64 TAGCGACGTTTTAAGCACAAACGCCGCCAAAGACCTGTACTTTAGTGGCGTTTCTATACAAACGC
11965430 CGC
129 CGC
11965433 CAAAGACCCG
Statistics
Matches: 111, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
163 15 0.14
164 79 0.71
165 17 0.15
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (163 bp):
AAACGCCGCTAAATACTGTACTTTAGTGGCGTTTTCGTACAAACGCCGCCAAAGAATGTACAATA
GCGACGTTTTAAGCACAAACGCCGCCAAAGACCTGTACTTTAGTGGCGTTTCTATACAAACGCCG
CTAAATAATGTACTATAGTGACGTTTTAAGCAC
Found at i:11965527 original size:82 final size:82
Alignment explanation
Indices: 11965299--11965527 Score: 234
Period size: 82 Copynumber: 2.8 Consensus size: 82
11965289 CGTTTTAAGC
* * * * * *
11965299 ACAAACGCCGCTAAATG-CTCGTACTTTAGTGGCGTTTTTG-TACAAACGCCGCCAAAGACTCGT
1 ACAAACGCCGCCAAA-GACCCGTACTTTAGTGCCG-TTTTGAGACAAACGCCCCCAAAGACACGT
11965362 ACTTTAGCGACGTTTTTAT
64 ACTTTAGCGACGTTTTTAT
* * * * * *
11965381 ACAAACGCCGCCAAAGACCTGTACTTTAGTGGCGTTTTTATACAAACGCCGCCAAAGACCCGTAC
1 ACAAACGCCGCCAAAGACCCGTACTTTAGTGCCGTTTTGAGACAAACGCCCCCAAAGACACGTAC
*
11965446 TTTAGTTG-CGTTTTTAT
66 TTTAG-CGACGTTTTTAT
* * *
11965463 GCAAACGCCGCCAAAGACCCGTACTTTAGTGCCGTTTCTGCGGCTAAAC-CCCCCAAA-ACACGT
1 ACAAACGCCGCCAAAGACCCGTACTTTAGTGCCGTTT-TGAGAC-AAACGCCCCCAAAGACACGT
11965526 AC
64 AC
11965528 GCACTTGAAT
Statistics
Matches: 127, Mismatches: 15, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
81 5 0.04
82 108 0.85
83 10 0.08
84 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (82 bp):
ACAAACGCCGCCAAAGACCCGTACTTTAGTGCCGTTTTGAGACAAACGCCCCCAAAGACACGTAC
TTTAGCGACGTTTTTAT
Found at i:11966121 original size:6 final size:6
Alignment explanation
Indices: 11966112--11966140 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
11966102 CAATAACAAT
11966112 ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
11966141 TTATAAATTA
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:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:11966522 original size:2 final size:2
Alignment explanation
Indices: 11966515--11966549 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
11966505 CACTTCCTGT
* *
11966515 TC TC TC TC TC TC TC TC TC CC TC TC TC CC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11966550 TTTTAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:11969557 original size:26 final size:26
Alignment explanation
Indices: 11969521--11969574 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
11969511 TGTATCTTGT
11969521 TTCCCTGCATTTTGTGATTTTAATCA
1 TTCCCTGCATTTTGTGATTTTAATCA
11969547 TTCCCTGCATTTTGTGATTTTAATCA
1 TTCCCTGCATTTTGTGATTTTAATCA
11969573 TT
1 TT
11969575 AATTATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.52
Consensus pattern (26 bp):
TTCCCTGCATTTTGTGATTTTAATCA
Found at i:11970469 original size:43 final size:42
Alignment explanation
Indices: 11970421--11970961 Score: 645
Period size: 43 Copynumber: 12.6 Consensus size: 42
11970411 GAATGGTAAT
* *
11970421 TATAGATCTGACTTTTTGCGGCGTTTGTGTCCAAAAACGTCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
*
11970464 TATAGATCTTACCTTTTGCGGCG-TTGTGTCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
11970506 TATAGATCTGACCTTTTGCGGCGTTTGTGTCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* *
11970549 TATAGATCCGTA-CTTTTGCAGCGTTTGTATCCAAAAACGCCGC
1 TATAGATCTG-ACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * * * *
11970592 TAAATATCTAACCTTTTGCGGCCTTTGTGTCCAAAAACGCCAC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * *
11970635 TATAGATCTGTCCTTTTGCAGCATTTGTATCCAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * * * *
11970678 TAAATATCTAACCTTTTGCGACGTTTGTTACAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
*
11970720 TATAGATCTCGACCTTTTGCGGCATTTGTATCCAAAAACGCCGC
1 TATAGATCT-GACCTTTTGCGGCGTTTGT-TCCAAAAACGCCGC
* * * * *
11970764 TAAATATCTAACCTTTTGCGACGTTTGTTACAAAAACGCCGC
1 TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* *
11970806 TATAGATCTCGACCTTTTGCGGCATTTGTTCCATAAACGCCGC
1 TATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* *
11970849 TAGAGATCTTGACCTTTTGCGGCGTTTGTTCTAAAAACGCCGC
1 TATAGATC-TGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* * *
11970892 TATATATATCGACCTTTTGCGACGTTTGTTCCAAAAACGCCGC
1 TATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
* * *
11970935 TATAGATCTTGAACTATAGCGGCGTTT
1 TATAGATC-TGACCTTTTGCGGCGTTT
11970962 TTGGTTCTCA
Statistics
Matches: 424, Mismatches: 65, Indels: 18
0.84 0.13 0.04
Matches are distributed among these distances:
42 82 0.19
43 319 0.75
44 23 0.05
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (42 bp):
TATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGC
Found at i:11975165 original size:18 final size:17
Alignment explanation
Indices: 11975142--11975176 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
11975132 GACCCGATCT
11975142 GACCGTTGACTGTTGACC
1 GACCGTTGACT-TTGACC
11975160 GACCGTTGACTTTGACC
1 GACCGTTGACTTTGACC
11975177 AAAAAGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.29
Consensus pattern (17 bp):
GACCGTTGACTTTGACC
Found at i:11976364 original size:2 final size:2
Alignment explanation
Indices: 11976357--11976388 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11976347 TGATATTTTG
11976357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11976389 GTTTATACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11978920 original size:14 final size:14
Alignment explanation
Indices: 11978901--11978933 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11978891 AGTACTTCAA
11978901 CTTTTCTTTCTT-TT
1 CTTTTCTTT-TTCTT
11978915 CTTTTCTTTTTCTT
1 CTTTTCTTTTTCTT
11978929 CTTTT
1 CTTTT
11978934 TTGAGTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTCTTTTTCTT
Found at i:11978972 original size:22 final size:22
Alignment explanation
Indices: 11978927--11978976 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
11978917 TTTCTTTTTC
*
11978927 TTCTTTTTTGAGTGTTTTCAAT
1 TTCTTTTTTGAGTGTCTTCAAT
*
11978949 TTCTTCTTTTGAGTG-CTTCGAT
1 TTCTT-TTTTGAGTGTCTTCAAT
11978971 TTCTTT
1 TTCTTT
11978977 ACTGGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.60
23 9 0.36
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.62
Consensus pattern (22 bp):
TTCTTTTTTGAGTGTCTTCAAT
Found at i:11983018 original size:15 final size:16
Alignment explanation
Indices: 11982986--11983022 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
11982976 GATAAACTGA
11982986 TTTATACTGAAGTATT
1 TTTATACTGAAGTATT
*
11983002 TTTATA-TGAA-TGTT
1 TTTATACTGAAGTATT
11983016 TTTATAC
1 TTTATAC
11983023 ATCGCAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 9 0.47
15 4 0.21
16 6 0.32
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (16 bp):
TTTATACTGAAGTATT
Found at i:11983744 original size:10 final size:10
Alignment explanation
Indices: 11983720--11983752 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
11983710 ATCTAATTAT
11983720 ATAATATTT-
1 ATAATATTTA
11983729 -TAATATTTA
1 ATAATATTTA
11983738 ATAATATTTA
1 ATAATATTTA
11983748 ATAAT
1 ATAAT
11983753 TAATTATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATATTTA
Found at i:11983749 original size:17 final size:17
Alignment explanation
Indices: 11983713--11983761 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
11983703 AAATATTATC
11983713 TAATTATATAATATTTTAA
1 TAATTA-ATAATA-TTTAA
*
11983732 TATTTAATAATATTTAA
1 TAATTAATAATATTTAA
*
11983749 TAATTAATTATAT
1 TAATTAATAATAT
11983762 GAAATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 16 0.59
18 6 0.22
19 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTAATAATATTTAA
Found at i:11986317 original size:2 final size:2
Alignment explanation
Indices: 11986310--11986336 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11986300 GTGCACTCTC
11986310 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
11986337 ATAGAATACT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11987424 original size:12 final size:12
Alignment explanation
Indices: 11987407--11987436 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
11987397 ACCCCACAAG
11987407 AGATCCGGAGCC
1 AGATCCGGAGCC
11987419 AGATCCGGAGCC
1 AGATCCGGAGCC
11987431 AGATCC
1 AGATCC
11987437 AGCTTCCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.33, G:0.30, T:0.10
Consensus pattern (12 bp):
AGATCCGGAGCC
Found at i:11995276 original size:78 final size:80
Alignment explanation
Indices: 11995136--11995291 Score: 298
Period size: 78 Copynumber: 2.0 Consensus size: 80
11995126 TCTTTCCCAT
11995136 GGCCATTGCTTATGCCTTTGTTATCAAACTTATCTGAAGCATATCCAGCCATGCTAAAATTCTGG
1 GGCCATTGCTTATGCCTTTGTTATCAAACTTATCTGAAGCATATCCAGCCATGCTAAAATTCTGG
11995201 TTAGCATTATCAATA
66 TTAGCATTATCAATA
11995216 GGCCATTGCTTATGCCTTTGTT-TCAAACTTATCTGAAGC-TATCCAGCCATGCTAAAATTCTGG
1 GGCCATTGCTTATGCCTTTGTTATCAAACTTATCTGAAGCATATCCAGCCATGCTAAAATTCTGG
11995279 TTAGCATTATCAA
66 TTAGCATTATCAA
11995292 CTTCATAACC
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
78 37 0.49
79 17 0.22
80 22 0.29
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (80 bp):
GGCCATTGCTTATGCCTTTGTTATCAAACTTATCTGAAGCATATCCAGCCATGCTAAAATTCTGG
TTAGCATTATCAATA
Found at i:11998871 original size:77 final size:78
Alignment explanation
Indices: 11998783--11998936 Score: 199
Period size: 77 Copynumber: 2.0 Consensus size: 78
11998773 AATTAATAAA
*
11998783 TAAAAAATTATTTAATTAATTC-AAATTAAATAT-ACATTA-AAGACTTATAATCTGAATTACAA
1 TAAAAAATTATTTAA-TAATTCTAAATTAAATATGA-ATTAGAAGACTTATAATCTAAATTACAA
11998845 TC-TTTAATGTTTAT
64 TCTTTTAATGTTTAT
* * * * *
11998859 TAAAAAACTTATTTAATCATTCTGAATTAAATATGAATTAGAAGAGTTGTAATCTAAATTACATT
1 TAAAAAA-TTATTTAATAATTCTAAATTAAATATGAATTAGAAGACTTATAATCTAAATTACAAT
11998924 CTTTTAATGTTTA
65 CTTTTAATGTTTA
11998937 CTTACTATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
76 12 0.18
77 22 0.33
78 22 0.33
79 11 0.16
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (78 bp):
TAAAAAATTATTTAATAATTCTAAATTAAATATGAATTAGAAGACTTATAATCTAAATTACAATC
TTTTAATGTTTAT
Found at i:12009839 original size:13 final size:13
Alignment explanation
Indices: 12009821--12009845 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12009811 AAATTGAATA
12009821 AAATATTAAATTG
1 AAATATTAAATTG
12009834 AAATATTAAATT
1 AAATATTAAATT
12009846 ATAAAAATAA
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AAATATTAAATTG
Found at i:12020793 original size:2 final size:2
Alignment explanation
Indices: 12020786--12020824 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
12020776 TGTATAATTA
*
12020786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
12020825 GTTGTTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 33 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12030333 original size:22 final size:21
Alignment explanation
Indices: 12030285--12030334 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
12030275 ATTAGGAATT
12030285 GATTTTTATTTGGATTTAAAA
1 GATTTTTATTTGGATTTAAAA
*
12030306 TATTTTTATTTGGATTTAAAA
1 GATTTTTATTTGGATTTAAAA
12030327 GACTTTTT
1 GA-TTTTT
12030335 CATTGTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (21 bp):
GATTTTTATTTGGATTTAAAA
Found at i:12034070 original size:15 final size:15
Alignment explanation
Indices: 12034050--12034087 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
12034040 AACCATAAGG
12034050 CAATCTTCAATATCT
1 CAATCTTCAATATCT
12034065 CAATCTTCAATATCT
1 CAATCTTCAATATCT
12034080 CAATCTTC
1 CAATCTTC
12034088 TAGGTAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (15 bp):
CAATCTTCAATATCT
Found at i:12034814 original size:14 final size:14
Alignment explanation
Indices: 12034792--12034830 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
12034782 GAGATTAGGT
* *
12034792 TGAATATAAACAAG
1 TGAACATAAACAAA
12034806 TGAACATAAACAAA
1 TGAACATAAACAAA
12034820 TGAACATAAAC
1 TGAACATAAAC
12034831 GAATATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.59, C:0.13, G:0.10, T:0.18
Consensus pattern (14 bp):
TGAACATAAACAAA
Found at i:12034971 original size:33 final size:33
Alignment explanation
Indices: 12034903--12035004 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
12034893 TTAAATGAAC
* *
12034903 ATAAAATATTGTTTATGTTTGTTCA--T-ATAA
1 ATAAAATCTTGTTTATCTTTGTTCATTTAATAA
12034933 ATAAAATCTTGTTTATCTTTGTTCATTTAATAA
1 ATAAAATCTTGTTTATCTTTGTTCATTTAATAA
12034966 ATAAAATCTTGTTTATCTTTGTTCATTTAATAA
1 ATAAAATCTTGTTTATCTTTGTTCATTTAATAA
12034999 ATAAAA
1 ATAAAA
12035005 GAACTTTCTG
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
30 23 0.34
32 1 0.01
33 43 0.64
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (33 bp):
ATAAAATCTTGTTTATCTTTGTTCATTTAATAA
Found at i:12040140 original size:46 final size:46
Alignment explanation
Indices: 12040073--12040496 Score: 731
Period size: 46 Copynumber: 9.2 Consensus size: 46
12040063 ATGAAAAGTT
* *
12040073 AAATGCCTAACGGTGCATTATCGGCATGAAAGAATGCCATAAATGA
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
12040119 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
* *
12040165 AAATGCATAACGGTGCATTATCGGCATGAAAGGATACCACAAATGA
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
*
12040211 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGTCATAAATGA
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
* * *
12040257 AAATGTATAACGGTGCATTATCGGAATGAAAGGATGTCATAAATGA
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
* *
12040303 AAATGCATAACGGTGCATTATCGGTATGAAATGATGCCATAAATGA
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
* *
12040349 AAATGTATAACGGTGCATTATCGGCATGAAAGGATGCTATAAATGA
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
12040395 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
*
12040441 AAATGCATAATGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
1 AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
12040487 AAATGCATAA
1 AAATGCATAA
12040497 ATGACATAAA
Statistics
Matches: 358, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 358 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (46 bp):
AAATGCATAACGGTGCATTATCGGCATGAAAGGATGCCATAAATGA
Found at i:12040448 original size:36 final size:36
Alignment explanation
Indices: 12040408--12040527 Score: 98
Period size: 46 Copynumber: 3.1 Consensus size: 36
12040398 TGCATAACGG
12040408 TGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAA
1 TGCATTATCGGCATGAAAGGATGCCATAAATG---A---A-AA
12040451 TGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAA
1 ---TGCATTATCGGCATGAAAGGATGCCATAAATGAAAA
* * * *
12040490 TGCATAAAT-GACATAAAAGGATGCCACAAATGAAAA
1 TGCAT-TATCGGCATGAAAGGATGCCATAAATGAAAA
12040526 TG
1 TG
12040528 TATAACTGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
36 31 0.45
37 2 0.03
39 2 0.03
40 1 0.01
43 1 0.01
46 32 0.46
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (36 bp):
TGCATTATCGGCATGAAAGGATGCCATAAATGAAAA
Found at i:12040662 original size:85 final size:85
Alignment explanation
Indices: 12040519--12040687 Score: 250
Period size: 85 Copynumber: 2.0 Consensus size: 85
12040509 GATGCCACAA
* *
12040519 ATGAAAATGTATAACTGTGTATTAACAACATATAAGGTGTCACTTATGTTAATTATAAAAGATAA
1 ATGAAAATGTATAACTGTGTATTAAAAACATATAAGGTGTCACTCATGTTAATTATAAAAGATAA
* * *
12040584 ATGATCATTTGGCATTTTGC
66 ATGACCATTTAGCACTTTGC
* * *
12040604 ATGAAAATGTATAA-TGGTGTATTAAAAACGTATAAGGTGTCTCTCATGTTGATTATAAAAGATA
1 ATGAAAATGTATAACT-GTGTATTAAAAACATATAAGGTGTCACTCATGTTAATTATAAAAGATA
12040668 AATGACCATTTAGCACTTTG
65 AATGACCATTTAGCACTTTG
12040688 GTGCAATACA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
84 1 0.01
85 74 0.99
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (85 bp):
ATGAAAATGTATAACTGTGTATTAAAAACATATAAGGTGTCACTCATGTTAATTATAAAAGATAA
ATGACCATTTAGCACTTTGC
Found at i:12044868 original size:16 final size:16
Alignment explanation
Indices: 12044847--12044879 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12044837 CCCATTTATC
12044847 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
12044863 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
12044879 A
1 A
12044880 AAACACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:12046597 original size:2 final size:2
Alignment explanation
Indices: 12046590--12046676 Score: 160
Period size: 2 Copynumber: 44.5 Consensus size: 2
12046580 TTGAGAAACA
12046590 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12046631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12046672 AT AT A
1 AT AT A
12046677 GTTTTCATAA
Statistics
Matches: 83, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.02
2 81 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12047141 original size:21 final size:21
Alignment explanation
Indices: 12047115--12047154 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12047105 CAGAACCCCA
*
12047115 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
12047136 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
12047155 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:12047186 original size:21 final size:23
Alignment explanation
Indices: 12047135--12047186 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
12047125 GATTCCCCTG
12047135 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTTCCCCTTCA
**
12047158 AAGGGGGAATCGGTT-CCC-TCA
1 TGGGGGGAATCGGTTCCCCTTCA
12047179 TGGGGGGA
1 TGGGGGGA
12047187 TTGATTCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCGGTTCCCCTTCA
Found at i:12054591 original size:20 final size:20
Alignment explanation
Indices: 12054568--12054721 Score: 150
Period size: 20 Copynumber: 7.7 Consensus size: 20
12054558 GTTTCCAGAT
12054568 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
** * *
12054588 TCGCATTGCGATTTTCCGAAT-
1 TCGCAACGCGA--TTCTGACTA
* * * *
12054609 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
*
12054629 TCGCAATGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
12054649 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
12054669 TCGCAACGTGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
*
12054689 TCGCAACGCGATGCTGACTA
1 TCGCAACGCGATTCTGACTA
*
12054709 TCGCAATGCGATT
1 TCGCAACGCGATT
12054722 TTCAAAGCGC
Statistics
Matches: 110, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.03
20 91 0.83
21 10 0.09
22 6 0.05
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:12055384 original size:20 final size:20
Alignment explanation
Indices: 12055297--12055386 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
12055287 TTAGTTTAGC
12055297 GTTGCGATTTTCA-TTTCGT
1 GTTGCGATTTTCATTTTCGT
** **
12055316 GTTGCGATAGTCAAATTC-T
1 GTTGCGATTTTCATTTTCGT
**
12055335 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCGT
*
12055356 ATTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
12055376 GTTGCGATTTT
1 GTTGCGATTTT
12055387 AAGTTTCAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
19 12 0.20
20 46 0.78
21 1 0.02
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.48
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:12059874 original size:20 final size:20
Alignment explanation
Indices: 12059850--12059956 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
12059840 AAATTCAGTG
* *
12059850 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* *
12059870 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCA
*
12059890 TTGCGATAATCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
*
12059910 TTGCGATAGTCAGAATCACA
1 TTGCGATAGTCAGAATCGCA
* *
12059930 TTGCGATAGTTATAATCGCA
1 TTGCGATAGTCAGAATCGCA
12059950 TTGCGAT
1 TTGCGAT
12059957 TTACATATTC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:12059968 original size:20 final size:20
Alignment explanation
Indices: 12059945--12060000 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
12059935 ATAGTTATAA
12059945 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
12059965 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
12059985 TCGCATTGCGAATTTA
1 TCGCATTGCG-ATTTA
12060001 GAAAATCGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 30 0.86
21 5 0.14
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:12060009 original size:21 final size:21
Alignment explanation
Indices: 12059943--12060037 Score: 86
Period size: 21 Copynumber: 4.6 Consensus size: 21
12059933 CGATAGTTAT
*
12059943 AATCGCATTGCG-ATTTACAT
1 AATCGCATTGCGAATTTACAA
* *
12059963 ATTCGCATTGCG-ATTTACAT
1 AATCGCATTGCGAATTTACAA
* *
12059983 ATTCGCATTGCGAATTTAGAA
1 AATCGCATTGCGAATTTACAA
** **
12060004 AATCGCAACGCGAATTTGGAA
1 AATCGCATTGCGAATTTACAA
*
12060025 AATCGCAATGCGA
1 AATCGCATTGCGA
12060038 TAGTCAGAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
20 31 0.47
21 35 0.53
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (21 bp):
AATCGCATTGCGAATTTACAA
Found at i:12060372 original size:21 final size:21
Alignment explanation
Indices: 12060339--12060391 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12060329 ATTCTGACTA
*
12060339 TCGCATTGTGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
12060360 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
12060381 TCGCAATGCGA
1 TCGCATTGCGA
12060392 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:12060436 original size:20 final size:20
Alignment explanation
Indices: 12060381--12060428 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
12060371 TTTTCCGAAT
*
12060381 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGACTATGTAAA
12060401 TCGCAATGCGACTATGTAAA
1 TCGCAATGCGACTATGTAAA
*
12060421 TCGTAATG
1 TCGCAATG
12060429 TGATTATGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGACTATGTAAA
Found at i:12060443 original size:20 final size:20
Alignment explanation
Indices: 12060430--12060523 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
12060420 ATCGTAATGT
* *
12060430 GATTATGACTATCGCAACGC
1 GATTCTGACTATCGCAACGA
12060450 GATTCTGACTATCGCAACGA
1 GATTCTGACTATCGCAACGA
*
12060470 GATTCTGACTATCGCAACGC
1 GATTCTGACTATCGCAACGA
* *
12060490 GATCCTGACTATCGCAACGT
1 GATTCTGACTATCGCAACGA
*
12060510 GATCCTGACTATCG
1 GATTCTGACTATCG
12060524 ATATACTTCT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (20 bp):
GATTCTGACTATCGCAACGA
Found at i:12060479 original size:40 final size:40
Alignment explanation
Indices: 12060430--12060523 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
12060420 ATCGTAATGT
* *
12060430 GATTATGACTATCGCAACGCGATTCTGACTATCGCAACGA
1 GATTCTGACTATCGCAACGCGATCCTGACTATCGCAACGA
*
12060470 GATTCTGACTATCGCAACGCGATCCTGACTATCGCAACGT
1 GATTCTGACTATCGCAACGCGATCCTGACTATCGCAACGA
*
12060510 GATCCTGACTATCG
1 GATTCTGACTATCG
12060524 ATATACTTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
GATTCTGACTATCGCAACGCGATCCTGACTATCGCAACGA
Found at i:12062516 original size:24 final size:24
Alignment explanation
Indices: 12062482--12062535 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
12062472 CTGAAACATC
12062482 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
12062506 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
12062530 ATCAAA
1 ATCAAA
12062536 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:12063341 original size:20 final size:20
Alignment explanation
Indices: 12063317--12063423 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
12063307 AAATTCAGTG
* *
12063317 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* *
12063337 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCA
*
12063357 TTGCGATAATCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
*
12063377 TTGCGATAGTCAGAATCGTA
1 TTGCGATAGTCAGAATCGCA
* *
12063397 TTGTGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
12063417 TTGCGAT
1 TTGCGAT
12063424 TTACATATTC
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:12063430 original size:20 final size:20
Alignment explanation
Indices: 12063407--12063485 Score: 113
Period size: 20 Copynumber: 4.0 Consensus size: 20
12063397 TTGTGATAGT
*
12063407 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
**
12063427 CATATTCGCATTTTGATTTA
1 CATATTCGCATTGCGATTTA
12063447 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
**
12063467 CATATTCATATTGCGATTT
1 CATATTCGCATTGCGATTT
12063486 CGGAAAATCG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.43
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:12063511 original size:21 final size:22
Alignment explanation
Indices: 12063482--12063524 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12063472 TCATATTGCG
12063482 ATTTCGGAAAATCGCAACGCGA
1 ATTTCGGAAAATCGCAACGCGA
*
12063504 ATTT-GGAAAATCGCAATGCGA
1 ATTTCGGAAAATCGCAACGCGA
12063525 TAGTTAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (22 bp):
ATTTCGGAAAATCGCAACGCGA
Found at i:12064870 original size:3 final size:3
Alignment explanation
Indices: 12064850--12064927 Score: 86
Period size: 3 Copynumber: 25.0 Consensus size: 3
12064840 ATTTAAAAAA
*
12064850 TAT TATT TATT TATT TAT TAT TAT TAT TAT AAT TAAT TAT TAT TAT TAT
1 TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
* *
12064899 TAT TAT TAT TAT T-T TAT TTT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12064928 AGGCCCCATA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.03
3 50 0.76
4 14 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:12066990 original size:11 final size:11
Alignment explanation
Indices: 12066974--12067002 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
12066964 TGTTCCTTTG
12066974 ATTTATTTATT
1 ATTTATTTATT
12066985 ATTTATTTATT
1 ATTTATTTATT
12066996 ATTTATT
1 ATTTATT
12067003 ATCTAACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:12070023 original size:13 final size:13
Alignment explanation
Indices: 12070005--12070068 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 13
12069995 TCAGAACAAA
12070005 AAAGAAAAAAAAC
1 AAAGAAAAAAAAC
*
12070018 AAAG--AAAAAGC
1 AAAGAAAAAAAAC
*
12070029 AAAGAGAAAATAAAA
1 AAAGA-AAAA-AAAC
12070044 AAGAGAAACAAAAAC
1 AA-AGAAA-AAAAAC
12070059 AAAGGAAAAA
1 AAA-GAAAAA
12070069 GTGAAGAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
11 10 0.25
13 4 0.10
14 6 0.15
15 15 0.38
16 5 0.12
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAAAC
Found at i:12070032 original size:24 final size:24
Alignment explanation
Indices: 12070007--12070055 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
12069997 AGAACAAAAA
*
12070007 AGAAAAAAAACAAAGAAAAAGCAAAG
1 AGAAAATAAA-AAAGAAAAA-CAAAG
*
12070033 AGAAAATAAAAAAGAGAAACAAA
1 AGAAAATAAAAAAGAAAAACAAA
12070056 AACAAAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 8 0.38
26 9 0.43
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (24 bp):
AGAAAATAAAAAAGAAAAACAAAG
Found at i:12070057 original size:31 final size:29
Alignment explanation
Indices: 12070004--12070067 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
12069994 TTCAGAACAA
*
12070004 AAAAGAAAAAAAACAAAGAAAAAGCAAAGAG
1 AAAAGAAAAAAAACAAACAAAAA-CAAAG-G
* * *
12070035 AAAATAAAAAAGAGAAACAAAAACAAAGG
1 AAAAGAAAAAAAACAAACAAAAACAAAGG
12070064 AAAA
1 AAAA
12070068 AGTGAAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 5 0.17
30 5 0.17
31 19 0.66
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (29 bp):
AAAAGAAAAAAAACAAACAAAAACAAAGG
Found at i:12071210 original size:32 final size:32
Alignment explanation
Indices: 12071140--12071226 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
12071130 AGGAACAATG
* *
12071140 GGGGCACCTTTGAAGATTCAACATCAAATGTT
1 GGGGCATCTTTGGAGATTCAACATCAAATGTT
* *
12071172 GGGGCATTTTTGGAGATTCAACATCGAATGTT
1 GGGGCATCTTTGGAGATTCAACATCAAATGTT
* *
12071204 GGGGCATCTTCGGGGATTCAACA
1 GGGGCATCTTTGGAGATTCAACA
12071227 CCCTGATGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (32 bp):
GGGGCATCTTTGGAGATTCAACATCAAATGTT
Found at i:12071715 original size:36 final size:36
Alignment explanation
Indices: 12071632--12071997 Score: 273
Period size: 36 Copynumber: 10.0 Consensus size: 36
12071622 TGGAATTAGG
* * *
12071632 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
* *
12071668 TTTTGTCTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAA
1 -----T-TTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
12071710 TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
*
12071746 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
* * * *
12071782 ------ATCT-TTGA-ATATGTTTTACATT-AAACAAA
1 TTTTGTCTCTCTTGAGACA-G-TTTCCCTTAAAACAAA
* * * * ** ** *
12071811 TTTCGTCTCCCTTGAGACAATATCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAAC-AAA
* * *
12071848 TTTTGTCTCTCTCGAGACAGTTTCTCTTAAGACAAATTTTA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAAC-AA----A
* * *
12071889 TCTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAA
1 T-TTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
* * *
12071926 TTTTGTCTCTCTTGAGAAAGTTTCACTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
*
12071962 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
12071998 ATCTTTGTAT
Statistics
Matches: 267, Mismatches: 40, Indels: 41
0.77 0.11 0.12
Matches are distributed among these distances:
28 2 0.01
29 12 0.04
30 9 0.03
35 6 0.02
36 141 0.53
37 33 0.12
41 4 0.01
42 60 0.22
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
Found at i:12071721 original size:21 final size:21
Alignment explanation
Indices: 12071696--12071758 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
12071686 TGAGACAATT
12071696 TCTCTTAAAACAAATTTTGTC
1 TCTCTTAAAACAAATTTTGTC
* * *
12071717 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTAAAACAAATTTTGTC
12071734 -C-CTTAAAACAAATTTTGTC
1 TCTCTTAAAACAAATTTTGTC
12071753 TCTCTT
1 TCTCTT
12071759 GAGACAGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 6 0.20
16 1 0.03
17 3 0.10
18 4 0.13
19 3 0.10
20 1 0.03
21 12 0.40
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (21 bp):
TCTCTTAAAACAAATTTTGTC
Found at i:12071974 original size:216 final size:217
Alignment explanation
Indices: 12071600--12072098 Score: 727
Period size: 216 Copynumber: 2.3 Consensus size: 217
12071590 CCAGATTTTA
* * * *
12071600 TCTCCCTTGAGACAGTGTCTTTTGGAATTAGGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAT
1 TCTCCCTTGAGACAGTATCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
* *
12071665 AAATTTTGTCTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
66 AAATTTTATCTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGAAAG
* *
12071730 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATG
131 TTTCACTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAAG
12071795 TTT-TACATT-AAAC-AAATTTCG
196 TTTCT-C-TTGAAACAAAATTTCG
* *
12071816 TCTCCCTTGAGACAATATCTTTTGGAACTAAGTTTTGTCTCTCTCGAGACAGTTTCTCTT-AAGA
1 TCTCCCTTGAGACAGTATCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAA-A
* * *
12071880 CAAATTTTATCTTTGTCTCTCTTGAGACAGTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGAAA
65 CAAATTTTATCTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGAAA
* *
12071945 GTTTCACTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGTATAA
130 GTTTCACTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAA
*
12072010 GTTTCTCTTGAAACAAAATTTTG
195 GTTTCTCTTGAAACAAAATTTCG
* * ** * * * *
12072033 TCTCCCTTAAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACTGCTTCTCTTGAAAC
1 TCTCCCTTGAGACAGTATCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
12072098 A
66 A
12072099 CCAATCTTTG
Statistics
Matches: 252, Mismatches: 26, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
215 4 0.02
216 185 0.73
217 61 0.24
218 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (217 bp):
TCTCCCTTGAGACAGTATCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
AAATTTTATCTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGAAAG
TTTCACTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAAG
TTTCTCTTGAAACAAAATTTCG
Found at i:12072059 original size:37 final size:37
Alignment explanation
Indices: 12072009--12072098 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
12071999 TCTTTGTATA
12072009 AGTTTCTCTTGAAACAAAATTTTGTCTCCCTTAAGAC
1 AGTTTCTCTTGAAACAAAATTTTGTCTCCCTTAAGAC
* * * *
12072046 AGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGAC
1 AGTTTCTCTTGAAACAAAATTTTGTCTCCCTTAAGAC
* *
12072083 TGCTTCTCTTGAAACA
1 AGTTTCTCTTGAAACA
12072099 CCAATCTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (37 bp):
AGTTTCTCTTGAAACAAAATTTTGTCTCCCTTAAGAC
Found at i:12072132 original size:103 final size:100
Alignment explanation
Indices: 12071901--12072164 Score: 350
Period size: 103 Copynumber: 2.6 Consensus size: 100
12071891 TTTGTCTCTC
* * *
12071901 TTGAGACAGTTTCTCTTGAAATAAATTTTGTCTCTCTTGAGAAAGTTTCACTTGAAACAAATTTT
1 TTGA-ACAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCACTTGAAACAAATTTT
*
12071966 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCT
65 GTCTCTCTTGAGACAGCTTCCCTTGAAACAAAATCT
* *
12072002 TTGTATA-AGTTTCTCTTGAAACAAAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAACAAAGT
1 TTG-A-ACAGTTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCACTTGAAACAAA-T
* * *
12072066 TTTGTCTCTCTTGAGACTGCTTCTCTTGAAACACCAATCT
62 TTTGTCTCTCTTGAGACAGCTTCCCTTGAAACA-AAATCT
* * *
12072106 TTGAACATGTTTCTCTTGAAACAAATTTTGCCTCCCTTGACACAGTTTCTCTTGAAACA
1 TTGAACA-GTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCACTTGAAACA
12072165 CAAAAAATCC
Statistics
Matches: 143, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
101 17 0.12
102 38 0.27
103 66 0.46
104 22 0.15
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (100 bp):
TTGAACAGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCACTTGAAACAAATTTTG
TCTCTCTTGAGACAGCTTCCCTTGAAACAAAATCT
Found at i:12072201 original size:30 final size:30
Alignment explanation
Indices: 12072166--12072223 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
12072156 CTTGAAACAC
*
12072166 AAAAAATCCTTTG-AAATCGTTTCTCTTGGA
1 AAAAAAACCTTTGAAAAT-GTTTCTCTTGGA
12072196 AAAAAAACCTTTGAAAATGTTTCTCTTG
1 AAAAAAACCTTTGAAAATGTTTCTCTTG
12072224 AAACACAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (30 bp):
AAAAAAACCTTTGAAAATGTTTCTCTTGGA
Found at i:12072579 original size:3 final size:3
Alignment explanation
Indices: 12072559--12072631 Score: 85
Period size: 3 Copynumber: 23.3 Consensus size: 3
12072549 GTTTAAAAAA
* *
12072559 TAT TATT TATT TATT TAT TAT TAC TAT TAT TAA TAT T-T TAT TAT TAT
1 TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12072606 TAT TAT TAT TATT TAT TAT TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT T
12072632 TTTGTAGGCC
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 2 0.03
3 47 0.75
4 14 0.22
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12075190 original size:43 final size:43
Alignment explanation
Indices: 12075137--12075219 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
12075127 TTAAATTTAA
* * * *
12075137 TCAAAGTAAAAAATCATGTCAAATTTATTTCATCATAATATTG
1 TCAAAATAAAAAATCATGACAAATTTATTTAATCAAAATATTG
**
12075180 TCAAAATAAAAAATTGTGACAAATTTATTTAATCAAAATA
1 TCAAAATAAAAAATCATGACAAATTTATTTAATCAAAATA
12075220 ACAATTTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (43 bp):
TCAAAATAAAAAATCATGACAAATTTATTTAATCAAAATATTG
Found at i:12076363 original size:24 final size:24
Alignment explanation
Indices: 12076336--12076405 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 24
12076326 AAATTGATCT
12076336 GAAGTGCCACGTAGAATTTGTCCC
1 GAAGTGCCACGTAGAATTTGTCCC
* *
12076360 GAAG-GACCGCGTAGAA-ATG-CACC
1 GAAGTG-CCACGTAGAATTTGTC-CC
** *
12076383 GAAGTGCCATATAAAATTTGTCC
1 GAAGTGCCACGTAGAATTTGTCC
12076406 ATAAGGACCA
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
22 1 0.03
23 15 0.44
24 17 0.50
25 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.21
Consensus pattern (24 bp):
GAAGTGCCACGTAGAATTTGTCCC
Found at i:12080102 original size:27 final size:24
Alignment explanation
Indices: 12080047--12080101 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
12080037 CGAAGATTCG
*
12080047 TCTTTTTGTTTCTTTGGTGGCGCA
1 TCTTCTTGTTTCTTTGGTGGCGCA
**
12080071 TCTTCTTGTTTCTTTGGTGGCGTG
1 TCTTCTTGTTTCTTTGGTGGCGCA
12080095 TCTTCTT
1 TCTTCTT
12080102 CCTTGGATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.02, C:0.18, G:0.24, T:0.56
Consensus pattern (24 bp):
TCTTCTTGTTTCTTTGGTGGCGCA
Found at i:12086354 original size:23 final size:21
Alignment explanation
Indices: 12086323--12086389 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
12086313 TTTGATCATT
12086323 ATTTCATTATCATTTATATATCTA
1 ATTT-ATTATCATTTAT-TAT-TA
12086347 ATTTATTAT--TTTATTATTA
1 ATTTATTATCATTTATTATTA
* *
12086366 TTTTATTTATCA-TTATTTTTA
1 ATTTA-TTATCATTTATTATTA
12086387 ATT
1 ATT
12086390 ATATAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 6 0.16
20 7 0.19
21 15 0.41
23 5 0.14
24 4 0.11
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTATTATCATTTATTATTA
Found at i:12091733 original size:29 final size:27
Alignment explanation
Indices: 12091700--12091791 Score: 107
Period size: 29 Copynumber: 3.3 Consensus size: 27
12091690 TCCAGCAAAG
12091700 AAAGAAGAAAGAAGGAAAAAAAGATAAAA
1 AAAGAA-AAAGAAGGAAAAAAAGA-AAAA
*
12091729 AAAGAAAAAGTGAGGAAAAAAAGAAAAA
1 AAAGAAAAAG-AAGGAAAAAAAGAAAAA
* *
12091757 AAAG-AAAA-AAGGGAAAAAGGAAAAAA
1 AAAGAAAAAGAAGGAAAAAAAG-AAAAA
12091783 AAAGAAAAA
1 AAAGAAAAA
12091792 ATTGAATCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
25 9 0.16
26 9 0.16
27 8 0.14
28 12 0.21
29 18 0.32
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (27 bp):
AAAGAAAAAGAAGGAAAAAAAGAAAAA
Found at i:12091734 original size:26 final size:25
Alignment explanation
Indices: 12091704--12091789 Score: 91
Period size: 26 Copynumber: 3.2 Consensus size: 25
12091694 GCAAAGAAAG
12091704 AAGAAAGAAGGAAAAAAAGATAAAAA
1 AAGAAAGAAGGAAAAAAAGA-AAAAA
*
12091730 AAGAAAAAGTGAGGAAAAAAAGAAAAAA
1 AAG--AAAG-AAGGAAAAAAAGAAAAAA
* * *
12091758 AAGAAAAAAGGGAAAAAGGAAAAAAA
1 AAGAAAGAAGGAAAAAAAG-AAAAAA
12091784 AAGAAA
1 AAGAAA
12091790 AAATTGAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
25 9 0.18
26 18 0.35
28 12 0.24
29 12 0.24
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (25 bp):
AAGAAAGAAGGAAAAAAAGAAAAAA
Found at i:12091765 original size:35 final size:34
Alignment explanation
Indices: 12091714--12091792 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 34
12091704 AAGAAAGAAG
* * *
12091714 GAAAAAAAGATAAAAAAAGAAAAAGTGAGGAAAAAAA
1 GAAAAAAA-AGAAAAAAGGAAAAAG-GA-AAAAAAAA
12091751 GAAAAAAAAGAAAAAAGGGAAAAAGGAAAAAAAAA
1 GAAAAAAAAGAAAAAA-GGAAAAAGGAAAAAAAAA
12091786 GAAAAAA
1 GAAAAAA
12091793 TTGAATCAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 14 0.37
36 9 0.24
37 15 0.39
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (34 bp):
GAAAAAAAAGAAAAAAGGAAAAAGGAAAAAAAAA
Found at i:12096349 original size:22 final size:22
Alignment explanation
Indices: 12096321--12096364 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12096311 GAAGGCCCAC
12096321 GTCAGTATGAATATTTGGGCAT
1 GTCAGTATGAATATTTGGGCAT
12096343 GTCAGTATGAATATTTGGGCAT
1 GTCAGTATGAATATTTGGGCAT
12096365 TTTTGAAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.36
Consensus pattern (22 bp):
GTCAGTATGAATATTTGGGCAT
Found at i:12097535 original size:54 final size:54
Alignment explanation
Indices: 12097470--12097573 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
12097460 CCTGAACAAA
* * * *
12097470 CATCTGGGCAGAAAG-CACATGAGATGATGAATGTGTTGTCAAATGTTTTATGAG
1 CATCTGAGCAG-AAGCCACAAGAAATGATGAATGTGTTGCCAAATGTTTTATGAG
*
12097524 CATCTGAGCAGAAGCCACAAGAAATGATGAATGTGTTGCCAAGTGTTTTA
1 CATCTGAGCAGAAGCCACAAGAAATGATGAATGTGTTGCCAAATGTTTTA
12097574 AGAACCAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 3 0.07
54 41 0.93
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (54 bp):
CATCTGAGCAGAAGCCACAAGAAATGATGAATGTGTTGCCAAATGTTTTATGAG
Found at i:12097970 original size:22 final size:22
Alignment explanation
Indices: 12097942--12098051 Score: 175
Period size: 22 Copynumber: 5.0 Consensus size: 22
12097932 TCTACATCTA
12097942 CACTCTTCAAAGATGATAGATT
1 CACTCTTCAAAGATGATAGATT
*
12097964 CTCTCTTCAAAGATGATAGATT
1 CACTCTTCAAAGATGATAGATT
12097986 CACTCTTCAAAGATGATAGATT
1 CACTCTTCAAAGATGATAGATT
* *
12098008 CTCTATTCAAAGATGATAGATT
1 CACTCTTCAAAGATGATAGATT
* *
12098030 CACTTTTCAAAGATGAAAGATT
1 CACTCTTCAAAGATGATAGATT
12098052 TATTGGATTT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 81 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (22 bp):
CACTCTTCAAAGATGATAGATT
Found at i:12098005 original size:44 final size:44
Alignment explanation
Indices: 12097942--12098051 Score: 193
Period size: 44 Copynumber: 2.5 Consensus size: 44
12097932 TCTACATCTA
*
12097942 CACTCTTCAAAGATGATAGATTCTCTCTTCAAAGATGATAGATT
1 CACTCTTCAAAGATGATAGATTCTCTATTCAAAGATGATAGATT
12097986 CACTCTTCAAAGATGATAGATTCTCTATTCAAAGATGATAGATT
1 CACTCTTCAAAGATGATAGATTCTCTATTCAAAGATGATAGATT
* *
12098030 CACTTTTCAAAGATGAAAGATT
1 CACTCTTCAAAGATGATAGATT
12098052 TATTGGATTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (44 bp):
CACTCTTCAAAGATGATAGATTCTCTATTCAAAGATGATAGATT
Found at i:12098891 original size:46 final size:46
Alignment explanation
Indices: 12098758--12099420 Score: 980
Period size: 46 Copynumber: 14.5 Consensus size: 46
12098748 TGGAGCTTTT
* * *
12098758 TGATATTTTC-AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
12098803 TGATGTTTTCAAAAACCCTTCGGGTCATTTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAA-CCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
12098850 TGATATTTTCAAAAACCTTTGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* * * *
12098896 TGATGTTTTC-AAAACCTTCAGGTCATCTATAAGCCCTTCAATGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
12098941 TGATGCTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
12098987 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
12099033 TGATGTTTTCAAAAACCTTCAGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* ** *
12099079 TGATGTTTTC-AAAATCTTCAAGTCATCTATAAG-CCATTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCC-TTCAGTGCA
*
12099124 TGATGTTTTCAAAAATCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
12099170 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
12099216 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* * *
12099262 TGATGTTTTC-AAAACCTTCGGGTCATCTATAAGCCCTTCATTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
12099307 TGATGTTTTC-AAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* * * * *
12099352 TGATGTTTTC-AAAACCCTCGGGTCATCCGTAAGCCCTGCAGTACA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
12099397 GGATATTTTCAAAAAGCCTTCGGG
1 TGATGTTTTCAAAAA-CCTTCGGG
12099421 AGCTTTTTGA
Statistics
Matches: 567, Mismatches: 43, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
44 2 0.00
45 209 0.37
46 304 0.54
47 52 0.09
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (46 bp):
TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:12099011 original size:137 final size:137
Alignment explanation
Indices: 12098758--12099420 Score: 1001
Period size: 137 Copynumber: 4.8 Consensus size: 137
12098748 TGGAGCTTTT
* * *
12098758 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCCTT
1 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAA-CCTT
* * *
12098823 CGGGTCATTTGTAAGTCCTTCAGTGCATGATATTTTCAAAAACCTTTGGGTCATCTGTAAGTCCT
65 CGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCT
12098888 TCAGTGCA
130 TCAGTGCA
* * *
12098896 TGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAATGCATGATGCTTTCAAAAACCTTC
1 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTC
*
12098961 GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTT
66 GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTT
12099026 CAGTGCA
131 CAGTGCA
* *
12099033 TGATGTTTTCAAAAACCTTCAGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAATCTT
1 TGATGTTTTC-AAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTT
** * *
12099097 CAAGTCATCTATAAG-CCATTCAGTGCATGATGTTTTCAAAAATCTTCGGGTCATCTGTAAGTCC
65 CGGGTCATCTGTAAGTCC-TTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCC
12099161 TTCAGTGCA
129 TTCAGTGCA
* *
12099170 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTT
1 TGATGTTTTC-AAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTT
* *
12099235 CGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGTCATCTATAAGCCCT
65 CGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCT
*
12099299 TCATTGCA
130 TCAGTGCA
*
12099307 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCCTC
1 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTC
* * * * * *
12099371 GGGTCATCCGTAAGCCCTGCAGTACAGGATATTTTCAAAAAGCCTTCGGG
66 GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAA-CCTTCGGG
12099421 AGCTTTTTGA
Statistics
Matches: 481, Mismatches: 38, Indels: 13
0.90 0.07 0.02
Matches are distributed among these distances:
135 38 0.08
136 49 0.10
137 259 0.54
138 133 0.28
139 2 0.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (137 bp):
TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTC
GGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTT
CAGTGCA
Found at i:12099072 original size:183 final size:182
Alignment explanation
Indices: 12098758--12099420 Score: 1058
Period size: 183 Copynumber: 3.6 Consensus size: 182
12098748 TGGAGCTTTT
* *
12098758 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAA-CCTT
* *
12098823 CGGGTCATTTGTAAGTCCTTCAGTGCATGATATTTTCAAAAACCTTTGGGTCATCTGTAAGTCCT
65 CGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGTCCT
12098888 TCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAATGCA
130 TCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAATGCA
* * *
12098941 TGATGCTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAACCTT
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTT
* *
12099006 CGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCAGGTCATCTGTAAGTCCT
65 CGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGTCCT
* * * *
12099071 TCAGTGCATGATGTTTTCAAAATCTTCAAGTCATCTATAAGCCATTCAGTGCA
130 TCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAATGCA
* *
12099124 TGATGTTTTCAAAAATCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTT
1 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTT
*
12099189 CGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCT
65 CGGGTCATCTGTAAGTCCTTCAGTGCATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGTCCT
* *
12099254 TCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCATTGCA
130 TCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAATGCA
* *
12099307 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCCTC
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTC
* * * * *
12099371 GGGTCATCCGTAAGCCCTGCAGTACAGGATATTTTCAAAAAGCCTTCGGG
66 GGGTCATCTGTAAGTCCTTCAGTGCATGATATTTTCAAAAA-CCTTCGGG
12099421 AGCTTTTTGA
Statistics
Matches: 446, Mismatches: 32, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
181 43 0.10
182 50 0.11
183 306 0.69
184 47 0.11
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (182 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTC
GGGTCATCTGTAAGTCCTTCAGTGCATGATATTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTT
CAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTATAAGCCCTTCAATGCA
Found at i:12099675 original size:15 final size:14
Alignment explanation
Indices: 12099632--12099675 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
12099622 CATTTTACTT
12099632 AAATTATTATTATTA
1 AAATTATTATTA-TA
12099647 AAATTATTATTATA
1 AAATTATTATTATA
*
12099661 AATATTATCATTATA
1 AA-ATTATTATTATA
12099676 TTATATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATTATTATTATA
Found at i:12099679 original size:20 final size:21
Alignment explanation
Indices: 12099649--12099698 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
12099639 TATTATTAAA
12099649 ATTATTATTATAAATATTATC
1 ATTATTATTATAAATATTATC
*
12099670 ATTA-TATTATATATATTAT-
1 ATTATTATTATAAATATTATC
*
12099689 ATCATTATTA
1 ATTATTATTA
12099699 AATAATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
21 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATTATTATAAATATTATC
Found at i:12105287 original size:2 final size:2
Alignment explanation
Indices: 12105282--12105320 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
12105272 TGGAACATAG
*
12105282 CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
12105321 AAGGGGAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:12107115 original size:29 final size:29
Alignment explanation
Indices: 12107070--12107142 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
12107060 CCCAAAATCA
12107070 TTCAAAAGTTTGAGAATAAATTTGGAACG
1 TTCAAAAGTTTGAGAATAAATTTGGAACG
*
12107099 TTCAAAAGTTTGGGAATAAATTTGGAACG
1 TTCAAAAGTTTGAGAATAAATTTGGAACG
*
12107128 TCCAAAAGTTT-AGAA
1 TTCAAAAGTTTGAGAA
12107143 ATGAATTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 3 0.07
29 38 0.93
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (29 bp):
TTCAAAAGTTTGAGAATAAATTTGGAACG
Found at i:12111009 original size:15 final size:15
Alignment explanation
Indices: 12110989--12111021 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12110979 CGTAGGACCC
*
12110989 CTACATCTCGAAGGA
1 CTACATCCCGAAGGA
12111004 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
12111019 CTA
1 CTA
12111022 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:12111183 original size:12 final size:12
Alignment explanation
Indices: 12111166--12111213 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
12111156 TATCATGTTC
*
12111166 TCATATCATATG
1 TCATATCACATG
12111178 TCATATCACATG
1 TCATATCACATG
*
12111190 TCATATCACATA
1 TCATATCACATG
12111202 TCATATCACATG
1 TCATATCACATG
12111214 AACATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (12 bp):
TCATATCACATG
Found at i:12111197 original size:24 final size:25
Alignment explanation
Indices: 12111166--12111227 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 25
12111156 TATCATGTTC
12111166 TCATATCATATGTCATATCACATG-
1 TCATATCATATGTCATATCACATGA
* *
12111190 TCATATCACATATCATATCACATGA
1 TCATATCATATGTCATATCACATGA
*
12111215 ACATAT-ATATGTC
1 TCATATCATATGTC
12111228 TTATGCATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 27 0.84
25 5 0.16
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (25 bp):
TCATATCATATGTCATATCACATGA
Found at i:12111609 original size:19 final size:19
Alignment explanation
Indices: 12111585--12111636 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
12111575 TATTGCTGGG
12111585 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
12111604 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
12111623 ATGCATCGATGCAC
1 ATGCATCGATGCAC
12111637 CAATTGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:12111660 original size:83 final size:83
Alignment explanation
Indices: 12111520--12111699 Score: 229
Period size: 83 Copynumber: 2.2 Consensus size: 83
12111510 TTAATGAAGG
* * * *
12111520 TATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATT-GCTGG
1 TATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTATTATTATTAACT-G
* *
12111584 GATGCATCGATGCACTCCT
65 GATGCATCGATACACTACT
* * * **
12111603 TATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAACTG
1 TATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTATT-ATTATTAACTG
12111667 GATGCATCGATACACTACT
65 GATGCATCGATACACTACT
12111686 TATGCATCGATGCA
1 TATGCATCGATGCA
12111700 TGAATTGTAT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
82 2 0.02
83 80 0.95
84 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (83 bp):
TATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTATTATTATTAACTGG
ATGCATCGATACACTACT
Found at i:12111672 original size:64 final size:62
Alignment explanation
Indices: 12111604--12111764 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 62
12111594 TGCACTCCTT
* **
12111604 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATT-TTAA-AAG
* ** * *
12111668 ATGCATCGATACACTACTTATGCATCGATGCATGAATTGTATTCGATGTTTTATTTTAAAAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTTTAAAAG
* * *
12111730 AGTGCATCGATGCACTACTAATGCATTGATACACC
1 A-TGCATCGATGCACTACTTATGCATCGATGCACC
12111765 TTCAAACAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
62 2 0.02
63 31 0.38
64 49 0.60
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTTTAAAAG
Found at i:12115517 original size:73 final size:72
Alignment explanation
Indices: 12115375--12115521 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 72
12115365 TTATGAATCG
12115375 TAGCAATAATATTATAATGGTAGATATTAATATTTGGTTTTGAAAACATCAATTACTATTACAGT
1 TAGCAATAATATTATAATGGTAGATATTAATATTTGGTTTTGAAAACATCAATTACTATTACAGT
12115440 ACTATGC
66 ACTATGC
12115447 TAGCAATAATATTATAATGGTAGATATTAATATTTAGGTTTTGAAAACATCAATTACTATTACAG
1 TAGCAATAATATTATAATGGTAGATATTAATATTT-GGTTTTGAAAACATCAATTACTATTACAG
12115512 TACTATGC
65 TACTATGC
12115520 TA
1 TA
12115522 TCATATATTT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 35 0.47
73 39 0.53
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (72 bp):
TAGCAATAATATTATAATGGTAGATATTAATATTTGGTTTTGAAAACATCAATTACTATTACAGT
ACTATGC
Found at i:12118322 original size:17 final size:17
Alignment explanation
Indices: 12118297--12118336 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
12118287 TTCAGCAACT
*
12118297 GACCCGATCCAGGATCC
1 GACCCGATCCAAGATCC
*
12118314 GACCTGATCCAAGATCC
1 GACCCGATCCAAGATCC
*
12118331 AACCCG
1 GACCCG
12118337 GCCCCTAGGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.40, G:0.20, T:0.12
Consensus pattern (17 bp):
GACCCGATCCAAGATCC
Found at i:12118424 original size:23 final size:23
Alignment explanation
Indices: 12118398--12118442 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12118388 CGCCGCATGC
*
12118398 GCCTCTGCTCCTTGTC-ACCGCCT
1 GCCTATGCTCC-TGTCAACCGCCT
*
12118421 GCCTATGCTGCTGTCAACCGCC
1 GCCTATGCTCCTGTCAACCGCC
12118443 CCATTTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.09, C:0.44, G:0.20, T:0.27
Consensus pattern (23 bp):
GCCTATGCTCCTGTCAACCGCCT
Found at i:12118940 original size:16 final size:16
Alignment explanation
Indices: 12118919--12118949 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12118909 GGGTCTCATA
12118919 AATGGTCATGCAGATG
1 AATGGTCATGCAGATG
12118935 AATGGTCATGCAGAT
1 AATGGTCATGCAGAT
12118950 ATGAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (16 bp):
AATGGTCATGCAGATG
Found at i:12125172 original size:17 final size:18
Alignment explanation
Indices: 12125150--12125186 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
12125140 TAAATGTTTA
12125150 TTTTAT-ATTTATAATTT
1 TTTTATAATTTATAATTT
12125167 TTTTATAATTTATAATTT
1 TTTTATAATTTATAATTT
12125185 TT
1 TT
12125187 ACTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATAATTTATAATTT
Found at i:12126304 original size:10 final size:10
Alignment explanation
Indices: 12126288--12126329 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
12126278 CCATTCATTT
12126288 CACACAAACA
1 CACACAAACA
*
12126298 AACACAAACA
1 CACACAAACA
*
12126308 CACACACACA
1 CACACAAACA
*
12126318 CACACACACA
1 CACACAAACA
12126328 CA
1 CA
12126330 TATATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00
Consensus pattern (10 bp):
CACACAAACA
Found at i:12126306 original size:6 final size:6
Alignment explanation
Indices: 12126288--12126329 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
12126278 CCATTCATTT
* * *
12126288 CACACA AACAAA CACAAA CACACA CACACA CACACA CACACA
1 CACACA CACACA CACACA CACACA CACACA CACACA CACACA
12126330 TATATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00
Consensus pattern (6 bp):
CACACA
Found at i:12126312 original size:4 final size:4
Alignment explanation
Indices: 12126288--12126329 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
12126278 CCATTCATTT
* * *
12126288 CACA CAAA CAAA CACA AACA CACA CACA CACA CACA CACA CA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CA
12126330 TATATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00
Consensus pattern (4 bp):
CACA
Found at i:12127247 original size:14 final size:14
Alignment explanation
Indices: 12127228--12127328 Score: 76
Period size: 14 Copynumber: 7.4 Consensus size: 14
12127218 CGCTGGGCTT
12127228 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
12127242 CCGAGGCCATCCAAAAGCA
1 CCGAGGCCATCC----G-A
12127261 TCCGAGGCCAT----
1 -CCGAGGCCATCCGA
12127272 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
12127286 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
12127300 CCGAGAG-CAT----
1 CCGAG-GCCATCCGA
12127310 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
12127324 CCGAG
1 CCGAG
12127329 CTATGCGAGG
Statistics
Matches: 71, Mismatches: 0, Indels: 32
0.69 0.00 0.31
Matches are distributed among these distances:
9 1 0.01
10 18 0.25
14 39 0.55
15 1 0.01
18 1 0.01
19 1 0.01
20 10 0.14
ACGTcount: A:0.25, C:0.40, G:0.28, T:0.08
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:12127299 original size:10 final size:10
Alignment explanation
Indices: 12127259--12127285 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
12127249 CATCCAAAAG
12127259 CATCCGAGGC
1 CATCCGAGGC
12127269 CATCCGAGGC
1 CATCCGAGGC
12127279 CATCCGA
1 CATCCGA
12127286 CCGAGGCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.41, G:0.26, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:12127349 original size:10 final size:11
Alignment explanation
Indices: 12127334--12127390 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 11
12127324 CCGAGCTATG
12127334 CGAGGG-AATC
1 CGAGGGCAATC
12127344 CGAGGGCAA-C
1 CGAGGGCAATC
* *
12127354 CGAGCGAGCTATG
1 CGAG-G-GCAATC
12127367 CGAGGG-AATC
1 CGAGGGCAATC
12127377 CGAGGGCAA-C
1 CGAGGGCAATC
12127387 CGAG
1 CGAG
12127391 TGAGGGTAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
10 24 0.63
11 6 0.16
12 4 0.11
13 4 0.11
ACGTcount: A:0.28, C:0.25, G:0.40, T:0.07
Consensus pattern (11 bp):
CGAGGGCAATC
Found at i:12127362 original size:33 final size:33
Alignment explanation
Indices: 12127308--12127390 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
12127298 GACCGAGAGC
* * *
12127308 ATCCGAGGCCATCCGACCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
12127341 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
12127374 ATCCGAGGGCAACCGAG
1 ATCCGAGGGCAACCGAG
12127391 TGAGGGTAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.27, C:0.28, G:0.36, T:0.10
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
Found at i:12127523 original size:33 final size:33
Alignment explanation
Indices: 12127482--12127568 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
12127472 GCGACCTACC
12127482 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
12127515 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
* * *
12127548 CTCGGTCGGATGGCCTCGGAT
1 CTCGCTCGGTTGCCCTCGGAT
12127569 GCTCTCGGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.09, C:0.37, G:0.28, T:0.26
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
Found at i:12127566 original size:43 final size:40
Alignment explanation
Indices: 12127519--12127607 Score: 97
Period size: 43 Copynumber: 2.1 Consensus size: 40
12127509 GCATAGCTCG
*
12127519 CTCGGTTGCCCTCGGATTCCCTCGCATAGCTCGGTCGGATGGC
1 CTCGGTTGCCCTCGGATGCCCTCGCAT-GCT--GTCGGATGGC
* * * * *
12127562 CTCGGATGCTCTCGGATGGCCTCGGATGCTTTCGGATGGC
1 CTCGGTTGCCCTCGGATGCCCTCGCATGCTGTCGGATGGC
12127602 CTCGGT
1 CTCGGT
12127608 CGGATAGCCT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
40 14 0.36
42 3 0.08
43 22 0.56
ACGTcount: A:0.09, C:0.31, G:0.33, T:0.27
Consensus pattern (40 bp):
CTCGGTTGCCCTCGGATGCCCTCGCATGCTGTCGGATGGC
Found at i:12127578 original size:20 final size:20
Alignment explanation
Indices: 12127553--12127606 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
12127543 CATAGCTCGG
12127553 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
12127573 TCGGATGGCCTCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
12127593 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
12127607 TCGGATAGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.09, C:0.28, G:0.37, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:12127622 original size:10 final size:10
Alignment explanation
Indices: 12127553--12127606 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
12127543 CATAGCTCGG
12127553 TCGGATGGCC
1 TCGGATGGCC
12127563 TCGGAT-GCTC
1 TCGGATGGC-C
12127573 TCGGATGGCC
1 TCGGATGGCC
*
12127583 TCGGAT-GCTT
1 TCGGATGGC-C
12127593 TCGGATGGCC
1 TCGGATGGCC
12127603 TCGG
1 TCGG
12127607 TCGGATAGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 4 0.11
10 30 0.79
11 4 0.11
ACGTcount: A:0.09, C:0.28, G:0.37, T:0.26
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:12127728 original size:29 final size:30
Alignment explanation
Indices: 12127671--12127743 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
12127661 CTGCATGGAT
12127671 TGCATGGCGACCTACCTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
**
12127701 TGCATGGCGACCT-GGTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
12127730 TGCATGGCGACCTA
1 TGCATGGCGACCTA
12127744 TATGGGGACT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.21
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAGGTCGCTGGGCG
Found at i:12129336 original size:20 final size:21
Alignment explanation
Indices: 12129306--12129345 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12129296 ACAATTCCAA
12129306 AAACATAAAATTCTAAACCCC
1 AAACATAAAATTCTAAACCCC
*
12129327 AAAC-TAAAATTTTAAACCC
1 AAACATAAAATTCTAAACCC
12129346 TATACTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (21 bp):
AAACATAAAATTCTAAACCCC
Found at i:12129391 original size:35 final size:34
Alignment explanation
Indices: 12129318--12129391 Score: 78
Period size: 35 Copynumber: 2.1 Consensus size: 34
12129308 ACATAAAATT
* * * *
12129318 CTAAACCCCAAACTAAAATTTTAAACCCTATACT
1 CTAAACCCCAAACTAAAACTTTAAAACCTACACC
*
12129352 CTAAACCCCAAA-TACTAAACTTTAAAACCTACCCC
1 CTAAACCCCAAACTA--AAACTTTAAAACCTACACC
12129387 CTAAA
1 CTAAA
12129392 TTCTAAATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
33 2 0.06
34 12 0.36
35 19 0.58
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (34 bp):
CTAAACCCCAAACTAAAACTTTAAAACCTACACC
Done.