Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000250.1 Hibiscus syriacus cultivar Beakdansim tig00000452_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: 2850692
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1735528 original size:37 final size:37
Alignment explanation
Indices: 1735461--1735547 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
1735451 ATTGAAAACA
** * *
1735461 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1735497 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
1735534 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1735548 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:1735550 original size:102 final size:105
Alignment explanation
Indices: 1735366--1735613 Score: 360
Period size: 102 Copynumber: 2.4 Consensus size: 105
1735356 TTTTTCTTAA
* * * *
1735366 AACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
*
1735431 GTTTCTCTTTAAACATAAACATTGAAAACATTTCCCTT-G
66 GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* * *
1735470 AA-ATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGAC
1 AACA-AAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGAC
1735532 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
65 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* * *
1735573 AACAAAATTTTGTCTCCCTTGAGACATTTTCTCTTGAAACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
1735614 TAAACATTGA
Statistics
Matches: 129, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
102 55 0.43
103 39 0.30
104 35 0.27
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (105 bp):
AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
Found at i:1735604 original size:66 final size:66
Alignment explanation
Indices: 1735497--1735676 Score: 269
Period size: 66 Copynumber: 2.8 Consensus size: 66
1735487 CTTGAGATAG
*
1735497 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1735562 A
66 A
* *
1735563 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACATTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1735628 A
66 A
* * *
1735629 TTTCCCTT-GAA-ATAAA--TTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1735677 AAATTTTGTC
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
63 28 0.26
64 1 0.01
65 6 0.06
66 71 0.67
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (66 bp):
TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
A
Found at i:1735672 original size:34 final size:36
Alignment explanation
Indices: 1735628--1735713 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 36
1735618 CATTGAAAGC
* * *
1735628 ATTTCCCTTGAAA-TAAA-TTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACA
*
1735662 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAAA-TTTGTCTCCCTTGAGACA
*
1735699 ATTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
1735714 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
34 12 0.28
35 3 0.07
37 28 0.65
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACA
Found at i:1735690 original size:100 final size:99
Alignment explanation
Indices: 1735563--1735909 Score: 465
Period size: 100 Copynumber: 3.5 Consensus size: 99
1735553 ATTGAAAACA
* * *
1735563 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACATTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1735628 ATTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
65 ATTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
*
1735663 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
*
1735728 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
65 ATTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAG
* * *
1735765 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAGTTTCTATTGAAACATAAACTTTGAAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
1735830 GTTTCCCTTGAAACAAA----ATCT-TTGA-ATATG
66 -TTTCCCTTGAAATAAATTGTCTCTCTTGAGATA-G
* * *
1735860 TTTTACATT-AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 -TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1735910 AATTTTGTCT
Statistics
Matches: 226, Mismatches: 16, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
94 3 0.01
95 43 0.19
96 9 0.04
100 76 0.34
101 52 0.23
102 43 0.19
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (99 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
TTTCCCTTGAAATAAATTGTCTCTCTTGAGATAG
Found at i:1735706 original size:166 final size:169
Alignment explanation
Indices: 1735393--1735778 Score: 613
Period size: 166 Copynumber: 2.3 Consensus size: 169
1735383 CTTGAGATAG
* * *
1735393 TTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCTCTTTAAACATAAACATTGAAA
1 TTTCCCTTGGAACAGAAA-TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
*
1735458 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
65 ACATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
*
1735523 CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
130 CCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* * *
1735563 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACATTTTCTCTTGAAACATAAACATTGAAAG
1 TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
1735627 CATTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
66 CATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
1735690 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
131 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* * *
1735729 TTTCCCTT-GAA-ATG-AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-GAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACA
1735779 AATTTTGTCT
Statistics
Matches: 202, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
164 1 0.00
165 35 0.17
166 91 0.45
167 2 0.01
168 58 0.29
169 3 0.01
170 12 0.06
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (169 bp):
TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
CATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
Found at i:1735776 original size:36 final size:36
Alignment explanation
Indices: 1735729--1735983 Score: 127
Period size: 36 Copynumber: 7.4 Consensus size: 36
1735719 ATTGAAAACA
** *
1735729 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
1735765 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
** * *
1735801 TTTCTATTGAAACATAA--------ACTTTGAAAACAG
1 TTTCCCTTGAAACA-AATTTTGTCTCCTTTG-AGACAG
* *
1735831 TTTCCCTTGAAACAAA------AT-CTTTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACA-G
* *
1735860 TTTTACATT-AAACAAATTTTGTCT-CTCTTGAGACAG
1 -TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
* *
1735896 TTTCTCTTGAAACAAATTTTGTCT-CTCTTAAGACATG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACA-G
** * *
1735933 TTTTTCTTAAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCCTTTGAGACAG
*
1735970 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
1735984 CAAAATCTTT
Statistics
Matches: 176, Mismatches: 24, Indels: 38
0.74 0.10 0.16
Matches are distributed among these distances:
28 2 0.01
29 16 0.09
30 28 0.16
35 8 0.05
36 73 0.41
37 30 0.17
38 18 0.10
39 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:1735832 original size:30 final size:30
Alignment explanation
Indices: 1735797--1735855 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1735787 CTCCTTTGAG
*
1735797 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
1735827 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
1735856 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:1735951 original size:38 final size:36
Alignment explanation
Indices: 1735869--1735983 Score: 167
Period size: 36 Copynumber: 3.1 Consensus size: 36
1735859 GTTTTACATT
*
1735869 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTA
* *
1735905 AAACAAATTTTGTCTCTCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTA
* *
1735942 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTA
1735979 AAACA
1 AAACA
1735984 CAAAATCTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
36 26 0.37
37 24 0.34
38 20 0.29
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTA
Found at i:1736598 original size:106 final size:107
Alignment explanation
Indices: 1736407--1736658 Score: 337
Period size: 106 Copynumber: 2.4 Consensus size: 107
1736397 GGTTTTAGCT
*
1736407 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
** *
1736472 CGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCCCAATTTC
66 CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
* ** * *
1736513 GGAGCCAATTTCAACTTCACATTGAAGGGCATTGGACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
* * *
1736578 CGAAGGGATGGCTGACTGTCAACAAAATAATTTCCCAGTTCC
66 CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
* * * *
1736620 AGAACCAACTTCAACTTCACGACAGAA-GATATTGGACTC
1 AGAGCCAATTTCAACTTCACAAC-GAAGGACATTGGACTC
1736659 GGAACAGCAG
Statistics
Matches: 124, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
106 79 0.64
107 42 0.34
108 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.22
Consensus pattern (107 bp):
AGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
Found at i:1737752 original size:14 final size:14
Alignment explanation
Indices: 1737733--1737771 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
1737723 TTTAAAGTTA
1737733 TTATA-TATATATAT
1 TTATATTAT-TATAT
1737747 TTATATTATTATAT
1 TTATATTATTATAT
1737761 TTATTATTATT
1 TTA-TATTATT
1737772 GTACTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATATTATTATAT
Found at i:1739648 original size:18 final size:17
Alignment explanation
Indices: 1739587--1739666 Score: 65
Period size: 18 Copynumber: 4.6 Consensus size: 17
1739577 TATTTGCAAT
1739587 AAAACTATATATATTATA
1 AAAACTATATATATT-TA
* *
1739605 TATATA-TATATATATATA
1 -A-AAACTATATATATTTA
* *
1739623 TATA-TATATATATTTA
1 AAAACTATATATATTTA
*
1739639 AAAAGCTATATATATTTT
1 AAAA-CTATATATATTTA
1739657 AAAACTATAT
1 AAAACTATAT
1739667 GTTTTCAGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
16 16 0.31
17 6 0.12
18 17 0.33
19 10 0.20
20 2 0.04
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
AAAACTATATATATTTA
Found at i:1739653 original size:2 final size:2
Alignment explanation
Indices: 1739592--1739635 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1739582 GCAATAAAAC
1739592 TA TA TA TA T- TA TA TA 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
1739633 TA T
1 TA T
1739636 TTAAAAAGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1748118 original size:3 final size:3
Alignment explanation
Indices: 1748082--1748107 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1748072 AAGATAATGG
1748082 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1748108 GTGGAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1748158 original size:21 final size:20
Alignment explanation
Indices: 1748132--1748215 Score: 77
Period size: 19 Copynumber: 4.2 Consensus size: 20
1748122 AAAATATATA
1748132 ATATATATTTTTAATAAAACT
1 ATATATATTTTT-ATAAAACT
1748153 ATATATA-TTTTA-AAATA-T
1 ATATATATTTTTATAAA-ACT
* *
1748171 AATATATATATATATAAAAACT
1 -ATATATATTTTTAT-AAAACT
*
1748193 ATGTATATTTTT-TAAAACT
1 ATATATATTTTTATAAAACT
1748212 ATAT
1 ATAT
1748216 GTTTTCAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
18 4 0.08
19 18 0.35
20 8 0.16
21 17 0.33
22 4 0.08
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (20 bp):
ATATATATTTTTATAAAACT
Found at i:1748166 original size:17 final size:17
Alignment explanation
Indices: 1748146--1748235 Score: 56
Period size: 19 Copynumber: 4.9 Consensus size: 17
1748136 ATATTTTTAA
1748146 TAAAACTATATATATTT
1 TAAAACTATATATATTT
*
1748163 TAAAATATAATATATATATAT
1 TAAAA-CT-ATATATAT-T-T
*
1748184 ATAAAAACTATGTATATTTTT
1 -T-AAAACTA--TATATATTT
*
1748205 TAAAACTATATGT-TTT
1 TAAAACTATATATATTT
* *
1748221 CAAAACAATATATAT
1 TAAAACTATATATAT
1748236 ACATACATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
16 13 0.23
17 10 0.18
18 1 0.02
19 15 0.26
20 2 0.04
21 3 0.05
22 3 0.05
23 10 0.18
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAAACTATATATATTT
Found at i:1748171 original size:40 final size:40
Alignment explanation
Indices: 1748127--1748203 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
1748117 TATTCAAAAT
* *
1748127 ATATAATATATATTTTTA-ATAAAACTATATATATTTTAAA
1 ATATAATATATATATATATA-AAAACTATATATATTTTAAA
*
1748167 ATATAATATATATATATATAAAAACTATGTATATTTT
1 ATATAATATATATATATATAAAAACTATATATATTTT
1748204 TTAAAACTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (40 bp):
ATATAATATATATATATATAAAAACTATATATATTTTAAA
Found at i:1748591 original size:14 final size:14
Alignment explanation
Indices: 1748572--1748604 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1748562 TGGGGAGTAA
*
1748572 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
1748586 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
1748600 TCCCT
1 TCCCT
1748605 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:1752249 original size:24 final size:25
Alignment explanation
Indices: 1752208--1752255 Score: 80
Period size: 24 Copynumber: 1.9 Consensus size: 25
1752198 TCTTCCAGAT
1752208 GATGTATAAAAAACATCTATGTACAC
1 GATGTAT-AAAAACATCTATGTACAC
1752234 GATGTAT-AAAACATCTATGTAC
1 GATGTATAAAAACATCTATGTAC
1752256 CATATCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 15 0.68
26 7 0.32
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (25 bp):
GATGTATAAAAACATCTATGTACAC
Found at i:1752632 original size:10 final size:10
Alignment explanation
Indices: 1752619--1752644 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1752609 ATGATTTTGC
1752619 TCGATTTGAT
1 TCGATTTGAT
1752629 TCGATTTGAT
1 TCGATTTGAT
1752639 TCGATT
1 TCGATT
1752645 CAAACATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (10 bp):
TCGATTTGAT
Found at i:1758628 original size:22 final size:22
Alignment explanation
Indices: 1758596--1758644 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1758586 ATTTTTTTAT
*
1758596 AGTGATAAACAGTACCGTAAAC
1 AGTGATAAACAATACCGTAAAC
* *
1758618 AGTGATGAACAATACCGTCAAC
1 AGTGATAAACAATACCGTAAAC
1758640 AGTGA
1 AGTGA
1758645 ACAGTGTACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (22 bp):
AGTGATAAACAATACCGTAAAC
Found at i:1759485 original size:24 final size:24
Alignment explanation
Indices: 1759453--1759498 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1759443 TCTTCCAGAT
1759453 GATGTATAAAAAATCTATGTACAC
1 GATGTATAAAAAATCTATGTACAC
*
1759477 GATGTATAAAACATCTATGTAC
1 GATGTATAAAAAATCTATGTAC
1759499 CATATCATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAAAATCTATGTACAC
Found at i:1760726 original size:30 final size:30
Alignment explanation
Indices: 1760692--1760763 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
1760682 AAATTACATT
*
1760692 TTGGTCCCTAAACTTT-TCAAAGTTTATACC
1 TTGGTCCCTAAACTTTATCAAA-TTTATAAC
* *
1760722 TTGGTCACC-AAATTTTATCAAATTTATAAT
1 TTGGTC-CCTAAACTTTATCAAATTTATAAC
*
1760752 TTGGTCACTAAA
1 TTGGTCCCTAAA
1760764 GAATTTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 1 0.03
30 27 0.77
31 7 0.20
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (30 bp):
TTGGTCCCTAAACTTTATCAAATTTATAAC
Found at i:1772318 original size:23 final size:26
Alignment explanation
Indices: 1772269--1772324 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
1772259 AGAAAAAAGA
*
1772269 AGAAAAAAAATAATTTATATATATTT
1 AGAAATAAAATAATTTATATATATTT
*
1772295 ATAAATAAAAT-ATTTAT-T-TATTT
1 AGAAATAAAATAATTTATATATATTT
1772318 AGAAATA
1 AGAAATA
1772325 TCAGAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 6 0.22
26 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
AGAAATAAAATAATTTATATATATTT
Found at i:1773913 original size:3 final size:3
Alignment explanation
Indices: 1773907--1773970 Score: 103
Period size: 3 Copynumber: 21.3 Consensus size: 3
1773897 TTATTTAAAT
1773907 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
*
1773952 ATT ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
1773971 ATAAAAATGG
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 1 0.02
3 55 0.96
4 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1774333 original size:120 final size:120
Alignment explanation
Indices: 1774130--1774406 Score: 409
Period size: 120 Copynumber: 2.3 Consensus size: 120
1774120 CTTCTCTTTT
*
1774130 TTCAGATGAGTTCTTCTCATTATGAACCTTC-CGTTGG---GGATGATGCTAATATATCTCCTTC
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTC--TGGAAAGGATGATGCTAATATATCTCCTTC
* * *
1774191 TGTGATAAAATTATGTAAAAGGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTTC
64 TATGATAAAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTC
* * * **
1774248 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTGTTTCTA
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAATATATCTCCTTCTA
*
1774313 TGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTC
66 TGATAAAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTC
*
1774368 TTGAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1774407 TGTTGATCCA
Statistics
Matches: 144, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
117 3 0.02
118 30 0.21
119 1 0.01
120 110 0.76
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (120 bp):
TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAATATATCTCCTTCTA
TGATAAAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTC
Found at i:1774521 original size:113 final size:113
Alignment explanation
Indices: 1774326--1774885 Score: 724
Period size: 113 Copynumber: 5.0 Consensus size: 113
1774316 TAGAATTATG
* * *
1774326 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAA---CTTCTT-CTTCTTGAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
1774387 TTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAA
66 TTATGAACTCTATCTGGAAATGTTGATCCATCAAGTGATGAATTTGAA
* *
1774435 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
1774500 TTATGAACTCGAACTGGAAATGTTGATCCATCAAGTGATGAATTTGAA
66 TTATGAACTCTATCTGGAAATGTTGATCCATCAAGTGATGAATTTGAA
* *
1774548 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
1774613 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAA-TTCAA
66 TTATGAACTCTATCTGGAAATGTTGATCCATCAAGTGATGAATTTGAA
* * * * * *
1774660 GCAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-TTTCTTTAAATGAGTTC-T-T-
1 -CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * *
1774721 ATTATGAACTCTTTCTGGCAATGTTAATCCATCAAATAATGAATTTAAA
65 ATTATGAACTCTATCTGGAAATGTTGATCCATCAAGTGATGAATTTGAA
*
1774770 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTC
* * * *
1774835 TCATTATGAACTCTATCTGGTAATGCTGATCCATCAATTGATGGATTTGAA
63 TCATTATGAACTCTATCTGGAAATGTTGATCCATCAAGTGATGAATTTGAA
1774886 TCTTTGCTAA
Statistics
Matches: 390, Mismatches: 48, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
109 103 0.26
110 10 0.03
111 1 0.00
112 25 0.06
113 208 0.53
114 1 0.00
115 1 0.00
116 41 0.11
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTATCTGGAAATGTTGATCCATCAAGTGATGAATTTGAA
Found at i:1774571 original size:222 final size:220
Alignment explanation
Indices: 1774326--1774885 Score: 721
Period size: 222 Copynumber: 2.5 Consensus size: 220
1774316 TAGAATTATG
* *
1774326 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTT-CTTCTTGAGATGAGTTCTTCTCATTA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTTCTTGAGATGAGTTCTTCTCATTA
* * *
1774390 TGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAA-CAAAAGGTTAAACAAGTTC
66 TGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTTGAAGCAAAAAGTTAAACAAATTC
*
1774454 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCGAACTGGAA
131 TTCTCATTATGAACTTCTTCTT-CTTCTTCAAATGAATTC-T-T-ATTATGAACTCGAACTGGAA
* * * *
1774519 ATGTTGATCCATCAAGTGATGAATTTGAA
192 ATGTTAATCCATCAAATAATGAATTTAAA
* *
1774548 CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC---TTCCTTCTTGAGATGAGTTCTTCTCA
* * *
1774613 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAA-TTCAAGCAAAAAGTTGAACAAA
63 TTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTTGAAGCAAAAAGTTAAACAAA
* * * * *** *
1774677 TTCTTCTCATTATGAATTTCTTCTTTTTCTTTAAATGAGTTCTTATTATGAACTCTTTCTGGCAA
128 TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAAATGAATTCTTATTATGAACTCGAACTGGAAA
1774742 TGTTAATCCATCAAATAATGAATTTAAA
193 TGTTAATCCATCAAATAATGAATTTAAA
*
1774770 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAA---CTTCTTCCTTCTT--GA-GATGAGTTCTTC
* * * * *
1774835 TCATTATGAACTCTATCTGGTAATGCTGATCCATCAATTGATGGATTTGAA
60 TCATTATGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTTGAA
1774886 TCTTTGCTAA
Statistics
Matches: 293, Mismatches: 33, Indels: 20
0.85 0.10 0.06
Matches are distributed among these distances:
222 113 0.39
223 1 0.00
224 2 0.01
225 74 0.25
226 103 0.35
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (220 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTTCTTGAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAATGCTGATCCATCAAGTGATGAATTTGAAGCAAAAAGTTAAACAAATTC
TTCTCATTATGAACTTCTTCTTCTTCTTCAAATGAATTCTTATTATGAACTCGAACTGGAAATGT
TAATCCATCAAATAATGAATTTAAA
Found at i:1775830 original size:92 final size:92
Alignment explanation
Indices: 1775673--1776612 Score: 1661
Period size: 92 Copynumber: 10.2 Consensus size: 92
1775663 CTTATTTCTA
* *
1775673 CTATGAGCACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAATCAAATCAGA
1 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1775738 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
*
1775765 CTATGAGCACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
*
1775830 TAACTCAAAGAACACTTCCAGAAAATG
66 TAACTCAAAGAACACTTCCAGAAGATG
*
1775857 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTATGTGGTTCATACCAAACCAAATCAGA
1 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
*
1775922 TAACTCAAAGAACACTTCCAGAAAATG
66 TAACTCAAAGAACACTTCCAGAAGATG
* *
1775949 CTATGAGTACATTTATCTTCTAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
*
1776014 TAACTCAAAGAACACTTTCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
*
1776041 TTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1776106 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
* *
1776133 TTATGAGCACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1776198 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
*
1776225 CTATGAGCACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
* *
1776290 TAACTCAAAGAACACTTATCAGAAAATG
66 TAACTCAAAGAACACTT-CCAGAAGATG
*
1776318 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTATGTGGTTCATACCAAACCAAATCAGA
1 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
*
1776383 TAACTCAAAGAACACTTCCAGAAAATG
66 TAACTCAAAGAACACTTCCAGAAGATG
1776410 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1776475 TAACTCAAAGAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
*
1776502 TTATGAGTACATTCATCTTCCAA---CAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
1 CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
*
1776564 TAACTCAAATAACACTTCCAGAAGATG
66 TAACTCAAAGAACACTTCCAGAAGATG
* *
1776591 TTATGAGCACATTCATCTTCCA
1 CTATGAGTACATTCATCTTCCA
1776613 CTTGAATCTG
Statistics
Matches: 822, Mismatches: 25, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
89 86 0.10
92 648 0.79
93 88 0.11
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (92 bp):
CTATGAGTACATTCATCTTCCAATTTCAATGATTGGTTCTGTGGTTCATACCAAACCAAATCAGA
TAACTCAAAGAACACTTCCAGAAGATG
Found at i:1777609 original size:9 final size:9
Alignment explanation
Indices: 1777595--1777667 Score: 80
Period size: 9 Copynumber: 8.3 Consensus size: 9
1777585 ATCTTGACCC
1777595 CTTTTTTTT
1 CTTTTTTTT
1777604 C-TTTTTTT
1 CTTTTTTTT
1777612 CTTTTTTTT
1 CTTTTTTTT
*
1777621 -TCTTTCTTT
1 CT-TTTTTTT
*
1777630 CTTTTCTTT
1 CTTTTTTTT
1777639 CTTTTTTTT
1 CTTTTTTTT
*
1777648 C-TTTCTTT
1 CTTTTTTTT
*
1777656 CTTTCTTTT
1 CTTTTTTTT
1777665 CTT
1 CTT
1777668 CAAGCATAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
8 16 0.29
9 38 0.69
10 1 0.02
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:1777621 original size:13 final size:13
Alignment explanation
Indices: 1777599--1777667 Score: 75
Period size: 13 Copynumber: 5.2 Consensus size: 13
1777589 TGACCCCTTT
1777599 TTTTTCTTTTTTTC
1 TTTTT-TTTTTTTC
1777613 TTTTTTTTTCTTTC
1 TTTTTTTTT-TTTC
* *
1777627 TTTCTTTTCTTTC
1 TTTTTTTTTTTTC
*
1777640 TTTTTTTTCTTTC
1 TTTTTTTTTTTTC
* *
1777653 TTTCTTTCTTTTC
1 TTTTTTTTTTTTC
1777666 TT
1 TT
1777668 CAAGCATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
13 32 0.67
14 16 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:1777630 original size:26 final size:26
Alignment explanation
Indices: 1777601--1777667 Score: 109
Period size: 26 Copynumber: 2.5 Consensus size: 26
1777591 ACCCCTTTTT
1777601 TTTCTTTTTTTCTTTTTTTTTCTTTC
1 TTTCTTTTTTTCTTTTTTTTTCTTTC
1777627 TTTCTTTTCTTTC-TTTTTTTTCTTTC
1 TTTCTTTT-TTTCTTTTTTTTTCTTTC
1777653 TTTCTTTCTTTTCTT
1 TTTCTTT-TTTTCTT
1777668 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 32 0.84
27 6 0.16
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (26 bp):
TTTCTTTTTTTCTTTTTTTTTCTTTC
Found at i:1777652 original size:4 final size:4
Alignment explanation
Indices: 1777601--1777663 Score: 76
Period size: 4 Copynumber: 15.8 Consensus size: 4
1777591 ACCCCTTTTT
* *
1777601 TTTC TTTT TTTC TTT- TTT- TTTC TTTC TTTC TTTTC TTTC TTTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC -TTTC TTTC
1777649 TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTT
1777664 TCTTCAAGCA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
3 6 0.12
4 39 0.75
5 7 0.13
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (4 bp):
TTTC
Found at i:1784807 original size:15 final size:15
Alignment explanation
Indices: 1784784--1784815 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1784774 AATAATGAAT
1784784 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1784799 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1784814 AA
1 AA
1784816 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1788156 original size:30 final size:30
Alignment explanation
Indices: 1788113--1788198 Score: 70
Period size: 30 Copynumber: 2.9 Consensus size: 30
1788103 ATGAAATATT
* * *
1788113 AATAAGAAAATATATAAATACTATGAAAAG
1 AATAAGAAAATATAAAAAAAATATGAAAAG
* * *
1788143 AATAAGTATATATAAAAAAAATTTGAAAAG
1 AATAAGAAAATATAAAAAAAATATGAAAAG
*
1788173 -A-AAG-AATTATAAATAAAATATATGAA
1 AATAAGAAAATATAAA-AAAA-ATATGAA
1788199 TTTTTAATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
27 7 0.16
28 7 0.16
29 7 0.16
30 24 0.53
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (30 bp):
AATAAGAAAATATAAAAAAAATATGAAAAG
Found at i:1788198 original size:29 final size:31
Alignment explanation
Indices: 1788128--1788198 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 31
1788118 GAAAATATAT
*
1788128 AAATACTATGAAAAGAATAAGTATATATAAAA
1 AAATA-TATGAAAAGAATAAGAATATATAAAA
*
1788160 AAA-ATTTGAAAAG-A-AAGAAT-TATAAATA
1 AAATATATGAAAAGAATAAGAATATATAAA-A
1788188 AAATATATGAA
1 AAATATATGAA
1788199 TTTTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 6 0.18
28 9 0.26
29 7 0.21
30 8 0.24
31 1 0.03
32 3 0.09
ACGTcount: A:0.63, C:0.01, G:0.10, T:0.25
Consensus pattern (31 bp):
AAATATATGAAAAGAATAAGAATATATAAAA
Found at i:1788714 original size:23 final size:26
Alignment explanation
Indices: 1788665--1788720 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
1788655 AGAAAAAAGA
*
1788665 AGAAAAAAAATAATTTATATATATTT
1 AGAAATAAAATAATTTATATATATTT
*
1788691 ATAAATAAAAT-ATTTAT-T-TATTT
1 AGAAATAAAATAATTTATATATATTT
1788714 AGAAATA
1 AGAAATA
1788721 TCAGAAAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 6 0.22
26 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
AGAAATAAAATAATTTATATATATTT
Found at i:1790316 original size:3 final size:3
Alignment explanation
Indices: 1790310--1790361 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1790300 TTATTTAAAT
1790310 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1790358 ATA A
1 ATA A
1790362 ATAAAAATGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1791889 original size:26 final size:28
Alignment explanation
Indices: 1791842--1791893 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
1791832 AACTGTTCAC
1791842 TCTACTATTATATGATACTTTTGATATA
1 TCTACTATTATATGATACTTTTGATATA
1791870 TCTA-TATT-TATGGATA-TTTTGATA
1 TCTACTATTATAT-GATACTTTTGATA
1791894 AATGAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 11 0.48
27 8 0.35
28 4 0.17
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.52
Consensus pattern (28 bp):
TCTACTATTATATGATACTTTTGATATA
Found at i:1792427 original size:23 final size:24
Alignment explanation
Indices: 1792401--1792454 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
1792391 AGTCAGATTT
*
1792401 ATATTATCATATGCTAT-TATATG
1 ATATTATCATATGATATATATATG
* *
1792424 ATATTTTTCATATTATATATATATG
1 ATA-TTATCATATGATATATATATG
1792449 AT-TTAT
1 ATATTAT
1792455 TTTATATACT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 6 0.24
24 11 0.44
25 8 0.32
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.54
Consensus pattern (24 bp):
ATATTATCATATGATATATATATG
Found at i:1808854 original size:59 final size:59
Alignment explanation
Indices: 1808782--1809179 Score: 647
Period size: 59 Copynumber: 6.8 Consensus size: 59
1808772 TATATTTCCC
* * *
1808782 ATACGGAAATTCATACACATAGTATGAATTTCTTATCCTTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
* *
1808841 ATATGGAAATTCATACACTTAGTATGAATTTATTAACATTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
* * *
1808900 ATACAGAAATTTATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCTA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
*
1808959 ATACGGAAATTCAGACACTTAGTATGAATTTCTTAACA-TTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
* *
1809017 ATACGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACATAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
* *
1809076 ATACGAAAATTCATACACTTAGTATGAATTTCTTAGCATTTTTGCACACAAAGTGCCCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
* *
1809135 ATACAGAAATTCATACACTTAATATGAATTTCTTAAC-TTTTTGCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCA
1809180 AACTTAGTGC
Statistics
Matches: 315, Mismatches: 23, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
58 63 0.20
59 252 0.80
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (59 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
Found at i:1809077 original size:176 final size:176
Alignment explanation
Indices: 1808782--1809179 Score: 654
Period size: 176 Copynumber: 2.3 Consensus size: 176
1808772 TATATTTCCC
* * * *
1808782 ATACGGAAATTCATACACATAGTATGAATTTCTTATCCTTTTTGCACACAAAGTGCCCAATATGG
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTA-ACTTTTTGCACACAAAGTGCCCAATACGA
1808847 AAATTCATACACTTAGTATGAATTTATTAACATTTTTGCACACAAAGTGCCCAATAC-AGAAATT
65 AAATTCATACACTTAGTATGAATTTATTAACATTTTTGCACACAAAGTGCCCAATACGA-AAATT
* *
1808911 TATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCTA
129 CATACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
* *
1808959 ATACGGAAATTCAGACACTTAGTATGAATTTCTTAACATTTTGCACACAAAGTGCCCAATACGAA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGAA
* *
1809024 AATTCATACACTTAGTATGAATTTCTTAACATTTTTGCACATAAAGTGCCCAATACGAAAATTCA
66 AATTCATACACTTAGTATGAATTTATTAACATTTTTGCACACAAAGTGCCCAATACGAAAATTCA
*
1809089 TACACTTAGTATGAATTTCTTAGCATTTTTGCACACAAAGTGCCCA
131 TACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
* *
1809135 ATACAGAAATTCATACACTTAATATGAATTTCTTAACTTTTTGCA
1 ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCA
1809180 AACTTAGTGC
Statistics
Matches: 205, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
176 171 0.83
177 34 0.17
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (176 bp):
ATACGGAAATTCATACACTTAGTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCAATACGAA
AATTCATACACTTAGTATGAATTTATTAACATTTTTGCACACAAAGTGCCCAATACGAAAATTCA
TACACTTAGTATGAATTTCTTAACATTTTTGCACACAAAGTGCCCA
Found at i:1809566 original size:19 final size:19
Alignment explanation
Indices: 1809542--1809585 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1809532 GTATCAATAT
1809542 TACCATACTATGGTACCGA
1 TACCATACTATGGTACCGA
*
1809561 TACCATACTATGGTATCGA
1 TACCATACTATGGTACCGA
1809580 TACCAT
1 TACCAT
1809586 TTTTTCTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (19 bp):
TACCATACTATGGTACCGA
Found at i:1816809 original size:24 final size:24
Alignment explanation
Indices: 1816772--1816824 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1816762 TTATGTGTTA
**
1816772 TATGATTTTTTATCTG-TTATGAAT
1 TATGATTTGCTATCTGATT-TGAAT
*
1816796 TATGATTTGCTATCTGATTTGAGT
1 TATGATTTGCTATCTGATTTGAAT
1816820 TATGA
1 TATGA
1816825 ATATTTTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.53
Consensus pattern (24 bp):
TATGATTTGCTATCTGATTTGAAT
Found at i:1818206 original size:2 final size:2
Alignment explanation
Indices: 1818199--1818224 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1818189 AAACAAATAG
1818199 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
1818225 GTATGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1818542 original size:27 final size:28
Alignment explanation
Indices: 1818512--1818594 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 28
1818502 TTAGTCATAC
* *
1818512 TTTTAAATAAACTTTAACAA-AAAATATTT
1 TTTTAAATAAAC-ATAAAAATAAAATA-TT
*
1818541 TTTTAAATGAACATAAAAATAAAATA-T
1 TTTTAAATAAACATAAAAATAAAATATT
* ** *
1818568 TTTTAAATTAAGTTAATAATAAAATAT
1 TTTTAAATAAACATAAAAATAAAATAT
1818595 ATTTAATACT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 23 0.51
28 5 0.11
29 17 0.38
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (28 bp):
TTTTAAATAAACATAAAAATAAAATATT
Found at i:1818544 original size:29 final size:29
Alignment explanation
Indices: 1818512--1818571 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1818502 TTAGTCATAC
* *
1818512 TTTTAAATAAACTTTAACAA-AAAATATTT
1 TTTTAAATAAAC-ATAAAAATAAAATATTT
*
1818541 TTTTAAATGAACATAAAAATAAAATATTT
1 TTTTAAATAAACATAAAAATAAAATATTT
1818570 TT
1 TT
1818572 AAATTAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (29 bp):
TTTTAAATAAACATAAAAATAAAATATTT
Found at i:1818596 original size:29 final size:29
Alignment explanation
Indices: 1818532--1818598 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 29
1818522 ACTTTAACAA
*
1818532 AAAATATTTTTTTAAATGAACATAAAAAT
1 AAAATATATTTTTAAATGAACATAAAAAT
* ** *
1818561 -AAA-ATATTTTTAAATTAAGTTAATAAT
1 AAAATATATTTTTAAATGAACATAAAAAT
1818588 AAAATATATTT
1 AAAATATATTT
1818599 AATACTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 19 0.61
28 6 0.19
29 6 0.19
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (29 bp):
AAAATATATTTTTAAATGAACATAAAAAT
Found at i:1831100 original size:17 final size:17
Alignment explanation
Indices: 1831054--1831122 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
1831044 TAAGAGTTAA
* *
1831054 TTTAATAAATGAACTTG
1 TTTAATTAATGAACTAG
* * *
1831071 TTTGATGATTGAACTAG
1 TTTAATTAATGAACTAG
*
1831088 TTTAATTAATGAACTAAC
1 TTTAATTAATGAACT-AG
1831106 TTT-ATTCAATGAACTAG
1 TTTAATT-AATGAACTAG
1831123 ATGCATGAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
17 29 0.71
18 12 0.29
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.41
Consensus pattern (17 bp):
TTTAATTAATGAACTAG
Found at i:1836730 original size:2 final size:2
Alignment explanation
Indices: 1836723--1836747 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1836713 AAATAAATAA
1836723 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 A
1836748 ATTCATGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1837523 original size:16 final size:17
Alignment explanation
Indices: 1837502--1837534 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1837492 TACTTATCTC
*
1837502 CATTTA-AACAAAAAAT
1 CATTTACAAAAAAAAAT
1837518 CATTTACAAAAAAAAAT
1 CATTTACAAAAAAAAAT
1837535 AAAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (17 bp):
CATTTACAAAAAAAAAT
Found at i:1838291 original size:40 final size:36
Alignment explanation
Indices: 1838182--1838314 Score: 133
Period size: 37 Copynumber: 3.5 Consensus size: 36
1838172 GTTTTTTAAG
1838182 ATATATAATATAGTTTTTGCAAACATTTTTTT-AAAAC
1 ATATAT-ATATAGTTTTTG-AAACATTTTTTTGAAAAC
* **
1838219 ATATAATATATAGTTTTTAAAATGGTTTTTTTGAAAAC
1 ATAT-ATATATAGTTTTTGAAA-CATTTTTTTGAAAAC
* *
1838257 ATATATGATATAGTTTTTGAAAACATATTATTTTGAATAT
1 ATATAT-ATATAGTTTTTG-AAACAT-TT-TTTTGAAAAC
1838297 ATATATATATAGCTTTTT
1 ATATATATATAG-TTTTT
1838315 TTAAACGGTT
Statistics
Matches: 80, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
36 3 0.04
37 24 0.30
38 23 0.29
39 11 0.14
40 19 0.24
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (36 bp):
ATATATATATAGTTTTTGAAACATTTTTTTGAAAAC
Found at i:1848537 original size:30 final size:30
Alignment explanation
Indices: 1848502--1848593 Score: 148
Period size: 30 Copynumber: 3.1 Consensus size: 30
1848492 CCCGAATTCT
1848502 AGAAGAAAAAGTCGCACATCAAGAAGAACA
1 AGAAGAAAAAGTCGCACATCAAGAAGAACA
* * *
1848532 AGAAGAAAAATTTGAACATCAAGAAGAACA
1 AGAAGAAAAAGTCGCACATCAAGAAGAACA
*
1848562 AGAAGAAAAAGTCTCACATCAAGAAGAACA
1 AGAAGAAAAAGTCGCACATCAAGAAGAACA
1848592 AG
1 AG
1848594 GTACATCTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (30 bp):
AGAAGAAAAAGTCGCACATCAAGAAGAACA
Found at i:1857684 original size:54 final size:54
Alignment explanation
Indices: 1857626--1858049 Score: 577
Period size: 54 Copynumber: 7.9 Consensus size: 54
1857616 CAAAGTATGG
* * *
1857626 AATTCATCATATGTTAATGAATAATCGTTTCGACACTAAGTGTGCAATTCACGA
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAATTCACGA
* * *
1857680 AATTCATCATATGTTGATGAATAACCGTTTTGGCACTAAGTGTGCAATTCATGG
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAATTCACGA
* *
1857734 AATTCATCATATGTTGATGAATAACCATTTCGACACTAAGTGTGCAATTCAC-A
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAATTCACGA
* * * * *
1857787 GAATTCATCATATG-TGATGAATAACCGTTTCGGAACTAAATGTACAAAGT-ACAA
1 -AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGC-AATTCACGA
* * * *
1857841 AATTCATCATATATTGATGAATAACCATTTCGGCACTAAGTGTGCAATTCATGG
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAATTCACGA
* * * *
1857895 AATTCATCATATGTTGATGAATAGCCGTTTTGGCACTAAATGTGCAAAGT-ACGA
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGC-AATTCACGA
* *
1857949 AATTCATCATATGTTGATGAATAACCATTTCGGCACTAAGTGTGCAATTCACGG
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAATTCACGA
*
1858003 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTATGTGTGCAA
1 AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAA
1858050 CCCACAGAAT
Statistics
Matches: 321, Mismatches: 42, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
53 46 0.14
54 272 0.85
55 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (54 bp):
AATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAATTCACGA
Found at i:1857988 original size:215 final size:216
Alignment explanation
Indices: 1857626--1858040 Score: 672
Period size: 215 Copynumber: 1.9 Consensus size: 216
1857616 CAAAGTATGG
* * *
1857626 AATTCATCATATGTTAATGAATAATCGTTTCGACACTAAGTGTGCAATTCACGAAATTCATCATA
1 AATTCATCATATATTAATGAATAACCATTTCGACACTAAGTGTGCAATTCACGAAATTCATCATA
* * * *
1857691 TGTTGATGAATAACCGTTTTGGCACTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAAT
66 TGTTGATGAATAACCGTTTTGGCACTAAATGTGCAAGTCACGAAATTCATCATATGTTGATGAAT
1857756 AACCATTTCGACACTAAGTGTGCAATTCACAGAATTCATCATATG-TGATGAATAACCGTTTCGG
131 AACCATTTCGACACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
1857820 AACTAAATGTACAAAGTACAA
196 AACTAAATGTACAAAGTACAA
* * * *
1857841 AATTCATCATATATTGATGAATAACCATTTCGGCACTAAGTGTGCAATTCATGGAATTCATCATA
1 AATTCATCATATATTAATGAATAACCATTTCGACACTAAGTGTGCAATTCACGAAATTCATCATA
*
1857906 TGTTGATGAATAGCCGTTTTGGCACTAAATGTGCAAAGT-ACGAAATTCATCATATGTTGATGAA
66 TGTTGATGAATAACCGTTTTGGCACTAAATGTGC-AAGTCACGAAATTCATCATATGTTGATGAA
* *
1857970 TAACCATTTCGGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCG
130 TAACCATTTCGACACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTCG
*
1858035 GCACTA
195 GAACTA
1858041 TGTGTGCAAC
Statistics
Matches: 183, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
215 157 0.86
216 26 0.14
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (216 bp):
AATTCATCATATATTAATGAATAACCATTTCGACACTAAGTGTGCAATTCACGAAATTCATCATA
TGTTGATGAATAACCGTTTTGGCACTAAATGTGCAAGTCACGAAATTCATCATATGTTGATGAAT
AACCATTTCGACACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTCGG
AACTAAATGTACAAAGTACAA
Found at i:1860735 original size:24 final size:22
Alignment explanation
Indices: 1860700--1860744 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1860690 TTTCAAAAAT
1860700 ATATAATATATATTGTTTTTGAAG
1 ATATAATATATA--GTTTTTGAAG
1860724 ATAT-ATAGTATAGTTTTTGAA
1 ATATAATA-TATAGTTTTTGAA
1860745 AACATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (22 bp):
ATATAATATATAGTTTTTGAAG
Found at i:1860751 original size:22 final size:21
Alignment explanation
Indices: 1860705--1860751 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1860695 AAAATATATA
* * *
1860705 ATATATATTGTTTTTGAAGAT
1 ATATATATAGTTTTTGAAAAC
1860726 ATATAGTATAGTTTTTGAAAAC
1 ATATA-TATAGTTTTTGAAAAC
1860748 ATAT
1 ATAT
1860752 TTTTGAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (21 bp):
ATATATATAGTTTTTGAAAAC
Found at i:1860774 original size:38 final size:37
Alignment explanation
Indices: 1860721--1860915 Score: 143
Period size: 38 Copynumber: 5.5 Consensus size: 37
1860711 ATTGTTTTTG
1860721 AAGATATATAGTATAGTTTTTGAAAACATATTTTTGAA
1 AAGATATATA-TATAGTTTTTGAAAACATATTTTTGAA
**
1860759 AAGATATAATATATAGTTTTT-AAAATGGT-TTTTTGAA
1 AAGATAT-ATATATAGTTTTTGAAAA-CATATTTTTGAA
* *
1860796 AACATATATAACATAGTTTTTGAAAACATA----T---
1 AAGATATAT-ATATAGTTTTTGAAAACATATTTTTGAA
***
1860827 -A-ATATATAGT-T--TTTCAAAAAACA-ATTTTTGAA
1 AAGATATATA-TATAGTTTTTGAAAACATATTTTTGAA
*
1860859 AACATATATAATATAGTTTTTGAAAACATATTTTTGAA
1 AAGATATAT-ATATAGTTTTTGAAAACATATTTTTGAA
*
1860897 AACATATA-ATATAGTTTTT
1 AAGATATATATATAGTTTTT
1860916 TTAAAGCGGA
Statistics
Matches: 124, Mismatches: 13, Indels: 42
0.69 0.07 0.23
Matches are distributed among these distances:
25 1 0.01
26 9 0.07
28 2 0.02
29 7 0.06
30 1 0.01
33 1 0.01
34 8 0.06
35 2 0.02
36 13 0.10
37 38 0.31
38 39 0.31
39 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (37 bp):
AAGATATATATATAGTTTTTGAAAACATATTTTTGAA
Found at i:1860819 original size:24 final size:24
Alignment explanation
Indices: 1860788--1860845 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
1860778 TTAAAATGGT
1860788 TTTTTGAAAACATAT-ATAACATAG
1 TTTTTGAAAACATATAAT-ACATAG
*
1860812 TTTTTGAAAACATATAATATATAG
1 TTTTTGAAAACATATAATACATAG
*
1860836 TTTTTCAAAA
1 TTTTTGAAAA
1860846 AACAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 29 0.94
25 2 0.06
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (24 bp):
TTTTTGAAAACATATAATACATAG
Found at i:1860830 original size:61 final size:62
Alignment explanation
Indices: 1860745--1860889 Score: 213
Period size: 63 Copynumber: 2.4 Consensus size: 62
1860735 AGTTTTTGAA
* ****
1860745 AACATA-TTTTTGAAAAGATATAATATATAGTTTTT-AAAATGGTTTTTTGAAAACATATAT
1 AACATAGTTTTTGAAAACATATAATATATAGTTTTTAAAAAACAATTTTTGAAAACATATAT
1860805 AACATAGTTTTTGAAAACATATAATATATAGTTTTTCAAAAAACAATTTTTGAAAACATATAT
1 AACATAGTTTTTGAAAACATATAATATATAGTTTTT-AAAAAACAATTTTTGAAAACATATAT
*
1860868 AATATAGTTTTTGAAAACATAT
1 AACATAGTTTTTGAAAACATAT
1860890 TTTTGAAAAC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
60 6 0.08
61 28 0.37
63 42 0.55
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.41
Consensus pattern (62 bp):
AACATAGTTTTTGAAAACATATAATATATAGTTTTTAAAAAACAATTTTTGAAAACATATAT
Found at i:1860866 original size:39 final size:38
Alignment explanation
Indices: 1860805--1860909 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 38
1860795 AAACATATAT
1860805 AACATAGTTTTTGAAAACATATAATATATAGTTTTTCAAAA
1 AACATA-TTTTTGAAAACATATAATATATAGTTTTT--AAA
*
1860846 AACA-ATTTTTGAAAACATAT-ATAATATAGTTTTTGAA
1 AACATATTTTTGAAAACATATAAT-ATATAGTTTTTAAA
1860883 AACATATTTTTGAAAACATATAATATA
1 AACATATTTTTGAAAACATATAATATA
1860910 GTTTTTTTAA
Statistics
Matches: 60, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
37 6 0.10
38 21 0.35
39 28 0.47
40 1 0.02
41 4 0.07
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (38 bp):
AACATATTTTTGAAAACATATAATATATAGTTTTTAAA
Found at i:1860894 original size:14 final size:14
Alignment explanation
Indices: 1860875--1860903 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1860865 TATAATATAG
1860875 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1860889 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1860903 T
1 T
1860904 AATATAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACATA
Found at i:1860943 original size:38 final size:37
Alignment explanation
Indices: 1860812--1860947 Score: 127
Period size: 39 Copynumber: 3.6 Consensus size: 37
1860802 TATAACATAG
*
1860812 TTTTTGAAAAC-ATATAATATATAGTTTTTCAAAAAACA-A
1 TTTTTGAAAACTATAT-A-ATATAGTTTTT--GAAAACAGA
*
1860851 TTTTTGAAAACATATATAATATAGTTTTTGAAAACATA
1 TTTTTGAAAAC-TATATAATATAGTTTTTGAAAACAGA
* * *
1860889 TTTTTGAAAAC-ATATAATATAGTTTTTTTAAAGCGGA
1 TTTTTGAAAACTATATAATATAG-TTTTTGAAAACAGA
*
1860926 -TTTTGAAAACGTTTATAATATA
1 TTTTTGAAAAC-TATATAATATA
1860948 TATAATCTTT
Statistics
Matches: 85, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
36 21 0.25
37 16 0.19
38 21 0.25
39 22 0.26
40 1 0.01
41 4 0.05
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (37 bp):
TTTTTGAAAACTATATAATATAGTTTTTGAAAACAGA
Found at i:1862562 original size:12 final size:12
Alignment explanation
Indices: 1862545--1862571 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1862535 ACCTTATTTT
1862545 AAAATTAAGTCG
1 AAAATTAAGTCG
1862557 AAAATTAAGTCG
1 AAAATTAAGTCG
1862569 AAA
1 AAA
1862572 TCTGATTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (12 bp):
AAAATTAAGTCG
Found at i:1862907 original size:11 final size:12
Alignment explanation
Indices: 1862889--1862918 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1862879 ATAGTATTAC
1862889 ATAATTAGATCA
1 ATAATTAGATCA
1862901 A-AATTAGATCA
1 ATAATTAGATCA
1862912 ATAATTA
1 ATAATTA
1862919 TAATATTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (12 bp):
ATAATTAGATCA
Found at i:1863915 original size:126 final size:126
Alignment explanation
Indices: 1863690--1863942 Score: 506
Period size: 126 Copynumber: 2.0 Consensus size: 126
1863680 AACAATATGG
1863690 GTTTCGGTGTGGACCATCGCCGATGAGCGACGGCGAGGCAGTGGCCACCAACCGGAATATGGGAA
1 GTTTCGGTGTGGACCATCGCCGATGAGCGACGGCGAGGCAGTGGCCACCAACCGGAATATGGGAA
1863755 CCAGCGGCGGCGTTCATCTCTCGGATGAACAAATGAGAGAACTCTGAAGATGGGAGGGGAA
66 CCAGCGGCGGCGTTCATCTCTCGGATGAACAAATGAGAGAACTCTGAAGATGGGAGGGGAA
1863816 GTTTCGGTGTGGACCATCGCCGATGAGCGACGGCGAGGCAGTGGCCACCAACCGGAATATGGGAA
1 GTTTCGGTGTGGACCATCGCCGATGAGCGACGGCGAGGCAGTGGCCACCAACCGGAATATGGGAA
1863881 CCAGCGGCGGCGTTCATCTCTCGGATGAACAAATGAGAGAACTCTGAAGATGGGAGGGGAA
66 CCAGCGGCGGCGTTCATCTCTCGGATGAACAAATGAGAGAACTCTGAAGATGGGAGGGGAA
1863942 G
1 G
1863943 CGTTTTGTGA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 127 1.00
ACGTcount: A:0.26, C:0.22, G:0.36, T:0.16
Consensus pattern (126 bp):
GTTTCGGTGTGGACCATCGCCGATGAGCGACGGCGAGGCAGTGGCCACCAACCGGAATATGGGAA
CCAGCGGCGGCGTTCATCTCTCGGATGAACAAATGAGAGAACTCTGAAGATGGGAGGGGAA
Found at i:1864223 original size:35 final size:36
Alignment explanation
Indices: 1864157--1864236 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 36
1864147 TATATATACT
1864157 TATATACATTTTATATCTCTATTATGCTTTATGTA-AA
1 TATATAC-TTTTATATCTCTATTATGCTTTAT-TACAA
* * *
1864194 TATATACTTTTAATATTTTTA-TATG-TTTATTACTA
1 TATATACTTTT-ATATCTCTATTATGCTTTATTACAA
1864229 TATATACT
1 TATATACT
1864237 CTAGTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
34 2 0.05
35 14 0.37
36 8 0.21
37 14 0.37
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.55
Consensus pattern (36 bp):
TATATACTTTTATATCTCTATTATGCTTTATTACAA
Found at i:1865906 original size:21 final size:22
Alignment explanation
Indices: 1865853--1865909 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
1865843 AAATAGATTT
1865853 TTAGCGGCGTTTTCTCAGTCATA
1 TTAGCGGCGTTTT-TCAGTCATA
* *
1865876 TTA-CGACGTTTTTCAGTTATA
1 TTAGCGGCGTTTTTCAGTCATA
1865897 -TAGCGGCGTTTTT
1 TTAGCGGCGTTTTT
1865910 AAGCGTCGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 17 0.57
22 8 0.27
23 3 0.10
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (22 bp):
TTAGCGGCGTTTTTCAGTCATA
Found at i:1866547 original size:5 final size:5
Alignment explanation
Indices: 1866537--1866846 Score: 521
Period size: 5 Copynumber: 63.2 Consensus size: 5
1866527 GACTTGACCT
1866537 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1866587 TATAA TATAA TAT-A TA-AA TATAA TATAA TATAA TATAA TATAA TA-AA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1866634 TATAA TATAA -ATAA TATAA -ATAA TATAA TATAAA TATAA TATAA TAT-A
1 TATAA TATAA TATAA TATAA TATAA TATAA TAT-AA TATAA TATAA TATAA
*
1866682 -ATAA TATAA TAATAAA TATAA TATAA TATAA TATAA TATAA AAT-A -ATAA
1 TATAA TATAA T-AT-AA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1866731 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1866781 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1866831 TATAA TATAA TATAA T
1 TATAA TATAA TATAA T
1866847 GCCTATTATA
Statistics
Matches: 292, Mismatches: 1, Indels: 24
0.92 0.00 0.08
Matches are distributed among these distances:
3 4 0.01
4 22 0.08
5 254 0.87
6 9 0.03
7 3 0.01
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:1867108 original size:19 final size:19
Alignment explanation
Indices: 1867084--1867131 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1867074 TAACATATAT
1867084 ACTATATATATTTTCAAAA
1 ACTATATATATTTTCAAAA
* *
1867103 ACTATATGTATTTTCAAAT
1 ACTATATATATTTTCAAAA
1867122 A-TATATATAT
1 ACTATATATAT
1867132 ATATGGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (19 bp):
ACTATATATATTTTCAAAA
Found at i:1868031 original size:2 final size:2
Alignment explanation
Indices: 1868024--1868061 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1868014 ACTTCTCAGG
1868024 AT AT AT 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 AT AT AT
1868062 TGGAACAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1869163 original size:21 final size:20
Alignment explanation
Indices: 1869131--1869178 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1869121 CTATTTTATA
* *
1869131 TATTTATTTATTTGTT-TTTT
1 TATTTTTTTATTT-TTATTCT
1869151 TATTTTTTCTATTTTTATTCT
1 TATTTTTT-TATTTTTATTCT
1869172 TATTTTT
1 TATTTTT
1869179 GTTCCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (20 bp):
TATTTTTTTATTTTTATTCT
Found at i:1878701 original size:61 final size:63
Alignment explanation
Indices: 1878630--1878750 Score: 165
Period size: 61 Copynumber: 1.9 Consensus size: 63
1878620 AGTACTTCGC
* *
1878630 TTAGGATGAAAACCCGAAAGGGCATCCTAAGTT-GAAA-AAAAAGAAAAAAAGAAAAAGACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTAGAAAGAAAAAGAAAAAAAGAAAAAGACGT
* * *
1878691 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAAGAAAGAAAAAGAAAAAGAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATT--AGAAAGAAAAAGAAAAAAAGAAAAA
1878751 AGAGAAAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 29 0.57
64 4 0.08
65 18 0.35
ACGTcount: A:0.54, C:0.12, G:0.23, T:0.12
Consensus pattern (63 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTAGAAAGAAAAAGAAAAAAAGAAAAAGACGT
Found at i:1878749 original size:8 final size:7
Alignment explanation
Indices: 1878728--1878787 Score: 77
Period size: 8 Copynumber: 8.1 Consensus size: 7
1878718 TAAATTGAAG
1878728 AAAG-AA
1 AAAGAAA
1878734 AAAGAAA
1 AAAGAAA
1878741 AAGAGAAA
1 AA-AGAAA
1878749 AAAGAGAA
1 AAAGA-AA
1878757 AAAGAACA
1 AAAGAA-A
1878765 AAAGAACA
1 AAAGAA-A
1878773 AAAGAAA
1 AAAGAAA
1878780 AAAGAAA
1 AAAGAAA
1878787 A
1 A
1878788 GAAAAATAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
6 4 0.08
7 17 0.34
8 29 0.58
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:1878759 original size:23 final size:23
Alignment explanation
Indices: 1878730--1878787 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 23
1878720 AATTGAAGAA
1878730 AGAAAAAGAAAAAGAGAA-AAAAG
1 AGAAAAAGAAAAA-AGAACAAAAG
1878753 AGAAAAAGAACAAAAGAACAAAAG
1 AGAAAAAGAA-AAAAGAACAAAAG
1878777 A-AAAAAGAAAA
1 AGAAAAAGAAAA
1878788 GAAAAATAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
22 2 0.06
23 22 0.67
24 9 0.27
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.00
Consensus pattern (23 bp):
AGAAAAAGAAAAAAGAACAAAAG
Found at i:1883833 original size:21 final size:21
Alignment explanation
Indices: 1883784--1883839 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
1883774 AACAGATTTT
1883784 TAGCGGCGTTTTCTCAGTCATA
1 TAGCGGCGTTTT-TCAGTCATA
* *
1883806 TCA-CGGCGTTTTTTAGTTATA
1 T-AGCGGCGTTTTTCAGTCATA
1883827 TAGCGGCGTTTTT
1 TAGCGGCGTTTTT
1883840 AAGCGCCGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 18 0.60
22 10 0.33
23 1 0.03
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (21 bp):
TAGCGGCGTTTTTCAGTCATA
Found at i:1884489 original size:5 final size:5
Alignment explanation
Indices: 1884479--1884663 Score: 319
Period size: 5 Copynumber: 38.0 Consensus size: 5
1884469 AAAAATAACA
1884479 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1884529 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT AT-AT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1884577 AT-A- ATAAT ATAAT ATAAT ATAAT ATAAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT
1884626 ATAAT AT-AT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1884664 GCCTATTATA
Statistics
Matches: 174, Mismatches: 0, Indels: 12
0.94 0.00 0.06
Matches are distributed among these distances:
3 2 0.01
4 18 0.10
5 149 0.86
6 5 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:1884906 original size:7 final size:9
Alignment explanation
Indices: 1884878--1884910 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1884868 TAATACGTAC
1884878 TATATACCA
1 TATATACCA
1884887 TATATACCA
1 TATATACCA
*
1884896 TATATACTA
1 TATATACCA
1884905 TATATA
1 TATATA
1884911 TTTTCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (9 bp):
TATATACCA
Found at i:1884925 original size:19 final size:19
Alignment explanation
Indices: 1884901--1884948 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1884891 TACCATATAT
1884901 ACTATATATATTTTCAAAA
1 ACTATATATATTTTCAAAA
* *
1884920 ACTATATGTATTTTCAAAT
1 ACTATATATATTTTCAAAA
1884939 A-TATATATAT
1 ACTATATATAT
1884949 ATATGTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (19 bp):
ACTATATATATTTTCAAAA
Found at i:1894439 original size:22 final size:22
Alignment explanation
Indices: 1894411--1894466 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1894401 GTCAGAGTTA
*
1894411 ACCGTTGATTTTGACCGGTTTG
1 ACCGTTGACTTTGACCGGTTTG
1894433 ACCGTTGACTTTGACCGGTTTG
1 ACCGTTGACTTTGACCGGTTTG
**
1894455 ATAGTTGACTTT
1 ACCGTTGACTTT
1894467 TACCCAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (22 bp):
ACCGTTGACTTTGACCGGTTTG
Found at i:1895780 original size:95 final size:95
Alignment explanation
Indices: 1895681--1895853 Score: 213
Period size: 95 Copynumber: 1.8 Consensus size: 95
1895671 AACATGAAAC
* * * * * *
1895681 CTAATTTTGGTATCGATACCATATA-GGTGTATCGGTACCATAGTATAGTAGTATCGATACCATG
1 CTAATTTTGATATCGATACCAGA-AGGGGGTATCGATACCAAAGTAGAGTAGTATCGATACCATG
1895745 ATAAGGGTATCGATTCTGGCCCACATCGAAT
65 ATAAGGGTATCGATTCTGGCCCACATCGAAT
* ** * * *
1895776 CTAATTTTGATATTGATACTGGAAGGGGGTATTGATACCAAAGTAGGGTAGTATCGATACCATGG
1 CTAATTTTGATATCGATACCAGAAGGGGGTATCGATACCAAAGTAGAGTAGTATCGATACCATGA
*
1895841 TAGGGGTATCGAT
66 TAAGGGTATCGAT
1895854 ACTGAATGAC
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
94 1 0.02
95 63 0.98
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (95 bp):
CTAATTTTGATATCGATACCAGAAGGGGGTATCGATACCAAAGTAGAGTAGTATCGATACCATGA
TAAGGGTATCGATTCTGGCCCACATCGAAT
Found at i:1895851 original size:20 final size:20
Alignment explanation
Indices: 1895801--1895855 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
1895791 ATACTGGAAG
*
1895801 GGGGTATTGATACCAAAGTA
1 GGGGTATCGATACCAAAGTA
**
1895821 GGGTAGTATCGATACCATGGTA
1 GGG--GTATCGATACCAAAGTA
1895843 GGGGTATCGATAC
1 GGGGTATCGATAC
1895856 TGAATGACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.43
22 17 0.57
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGTATCGATACCAAAGTA
Found at i:1896255 original size:59 final size:59
Alignment explanation
Indices: 1896178--1896642 Score: 731
Period size: 59 Copynumber: 7.9 Consensus size: 59
1896168 ATTACCAACT
* * * * *
1896178 GGCACTTTGTGTGTTAAAATTGTAAGGAAATCATAATAAGTGTATGAATTTCAAGATAA
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
*
1896237 GGCACTTTGTGTGCTAAAATGGTTAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
1896296 GGCACTTTGTGTGCTAAAATGGAAAAGAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
*
1896355 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
1896414 GGCACTTTGTGTGCTAAAATGGGAA--AAATCATACTAAGTGTATGAATTTCTAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
1896471 GGAACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
*
1896530 GGCACTTTGTGTGCTAAAATGTTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* * *
1896589 GGCACTTCT-TGTGTTAAAA-GGATAAGGAAATCATACTGATTGTATGAATTTCCA
1 GGCACTT-TGTGTGCTAAAATGG-TAAGGAAATCATACTAAGTGTATGAATTTCCA
1896643 AATGAATTTA
Statistics
Matches: 376, Mismatches: 26, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
57 53 0.14
58 1 0.00
59 321 0.85
60 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (59 bp):
GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
Found at i:1896617 original size:234 final size:235
Alignment explanation
Indices: 1896178--1896642 Score: 747
Period size: 234 Copynumber: 2.0 Consensus size: 235
1896168 ATTACCAACT
* * * *
1896178 GGCACTTTGTGTGTTAAAATTGTAAGGAAATCATAATAAGTGTATGAATTTCAAGATAAGGCACT
1 GGCACTTTGTGTGCTAAAATGGGAA-GAAATCATAATAAGTGTATGAATTTCAAGATAAGGAACT
*
1896243 TTGTGTGCTAAAATGGTTAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
65 TTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGT
1896308 GCTAAAATGGAAAAGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAA
130 GCTAAAATGGAAAAGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAA
1896373 ATGGTAAGGAAATCATACTAAGTGTATGAATTTCCATATAG
195 ATGGTAAGGAAATCATACTAAGTGTATGAATTTCCATATAG
* * *
1896414 GGCACTTTGTGTGCTAAAATGGGAA-AAATCATACTAAGTGTATGAATTTCTAGATAGGGAACTT
1 GGCACTTTGTGTGCTAAAATGGGAAGAAATCATAATAAGTGTATGAATTTCAAGATAAGGAACTT
*
1896478 TGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCATATAGGGCACTTTGTGTG
66 TGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTG
** * *
1896543 CTAAAATGTTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTCT-TGTGTTAAA
131 CTAAAATGGAAAAGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTT-TGTGTGCTAAA
* *
1896607 A-GGATAAGGAAATCATACTGATTGTATGAATTTCCA
195 ATGG-TAAGGAAATCATACTAAGTGTATGAATTTCCA
1896643 AATGAATTTA
Statistics
Matches: 212, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
233 2 0.01
234 187 0.88
235 1 0.00
236 22 0.10
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (235 bp):
GGCACTTTGTGTGCTAAAATGGGAAGAAATCATAATAAGTGTATGAATTTCAAGATAAGGAACTT
TGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTG
CTAAAATGGAAAAGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAA
TGGTAAGGAAATCATACTAAGTGTATGAATTTCCATATAG
Found at i:1898997 original size:31 final size:30
Alignment explanation
Indices: 1898962--1899046 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 30
1898952 GGAGTACATT
* *
1898962 GGGGCCTGCAAGCCTACCCAAGAATATTCTC
1 GGGGCC-GCAAGCCTACCCAAGAAAAATCTC
*
1898993 GGGGCCACAAAGGCCTACCCAAGAAAAATCTC
1 GGGGCCGC-AA-GCCTACCCAAGAAAAATCTC
* *
1899025 AGGGCCGCAGAGCTTACCCAAG
1 GGGGCCGCA-AGCCTACCCAAG
1899047 GGTCTCCTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 1 0.02
31 19 0.42
32 25 0.56
ACGTcount: A:0.31, C:0.32, G:0.25, T:0.13
Consensus pattern (30 bp):
GGGGCCGCAAGCCTACCCAAGAAAAATCTC
Found at i:1899187 original size:12 final size:12
Alignment explanation
Indices: 1899164--1899258 Score: 86
Period size: 12 Copynumber: 7.9 Consensus size: 12
1899154 CCGGAGATAT
*
1899164 CAGAAATTAGAA
1 CAGAAATCAGAA
*
1899176 CATAAATCAGAA
1 CAGAAATCAGAA
*
1899188 CAGAAATAAGAA
1 CAGAAATCAGAA
*
1899200 CA-AAATTCAGAG
1 CAGAAA-TCAGAA
*
1899212 TAGAAATCAGAA
1 CAGAAATCAGAA
* *
1899224 CA-AAATTCATAG
1 CAGAAA-TCAGAA
*
1899236 CAGAAATCATAA
1 CAGAAATCAGAA
1899248 CAGAAATCAGA
1 CAGAAATCAGA
1899259 TAAAATATTC
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
11 6 0.09
12 54 0.82
13 6 0.09
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:1899192 original size:24 final size:24
Alignment explanation
Indices: 1899164--1899258 Score: 104
Period size: 24 Copynumber: 4.0 Consensus size: 24
1899154 CCGGAGATAT
* *
1899164 CAGAAATTAGAACATAAA-TCAGAA
1 CAGAAATCAGAACA-AAATTCAGAG
*
1899188 CAGAAATAAGAACAAAATTCAGAG
1 CAGAAATCAGAACAAAATTCAGAG
* *
1899212 TAGAAATCAGAACAAAATTCATAG
1 CAGAAATCAGAACAAAATTCAGAG
*
1899236 CAGAAATCATAACAGAAA-TCAGA
1 CAGAAATCAGAACA-AAATTCAGA
1899259 TAAAATATTC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 3 0.05
24 55 0.90
25 3 0.05
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (24 bp):
CAGAAATCAGAACAAAATTCAGAG
Found at i:1904352 original size:59 final size:59
Alignment explanation
Indices: 1904275--1904679 Score: 643
Period size: 59 Copynumber: 6.9 Consensus size: 59
1904265 ATTACCAACT
* *
1904275 GGCACTTTGTGTGTTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
*
1904334 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCACATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
*
1904393 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATAGTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
1904452 GGCACTTTGTGTGCTAAAATGGTAAGGAAATTATACTATGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
**
1904511 GGCACTTTGTGTGCTAAAATGGTAAGGAACCCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* * *
1904570 GGAACTTTGTGTGCTAAAATGTTAA-GAAATCATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* * * * *
1904628 GGCACTTCT-TGTGTTAAAATGATAAGGAAATCATATTGATTGTATGAATTTC
1 GGCACTT-TGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTC
1904680 TAATTGAATT
Statistics
Matches: 321, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
58 50 0.16
59 271 0.84
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (59 bp):
GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
Found at i:1906363 original size:26 final size:25
Alignment explanation
Indices: 1906328--1906383 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
1906318 TTAGCATATT
*
1906328 TAAAAAC-AAAACTTTAAAAATAAAG
1 TAAAAACAAAAAC-TTAAAAATAAAA
*
1906353 TAAAAACCAAAAACTTGAAAATAAAA
1 TAAAAA-CAAAAACTTAAAAATAAAA
1906379 TAAAA
1 TAAAA
1906384 GAGAGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 6 0.22
26 16 0.59
27 5 0.19
ACGTcount: A:0.70, C:0.09, G:0.04, T:0.18
Consensus pattern (25 bp):
TAAAAACAAAAACTTAAAAATAAAA
Found at i:1919717 original size:13 final size:13
Alignment explanation
Indices: 1919699--1919739 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1919689 GCGTAAAGGA
1919699 ATATACTCTTTGT
1 ATATACTCTTTGT
*
1919712 ATATACGCTTTTGT
1 ATATACTC-TTTGT
*
1919726 ATATACTTTTTGT
1 ATATACTCTTTGT
1919739 A
1 A
1919740 GACACGTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.54
Consensus pattern (13 bp):
ATATACTCTTTGT
Found at i:1922898 original size:43 final size:44
Alignment explanation
Indices: 1922834--1922920 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 44
1922824 CCGTGCATCA
*
1922834 AACAAAACTTTTACATGTAGGGGACAACTTTCAGTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCAGTCCTAACTTC
* **
1922878 AACAAAAC-TTTACATATAGGGGATAACTTTCCTTCCTAACTTC
1 AACAAAACTTTTACATATAGGGGACAACTTTCAGTCCTAACTTC
1922921 TGTAAAGCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 31 0.79
44 8 0.21
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (44 bp):
AACAAAACTTTTACATATAGGGGACAACTTTCAGTCCTAACTTC
Found at i:1927556 original size:24 final size:24
Alignment explanation
Indices: 1927520--1927565 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1927510 TAAAGAGAAT
* * *
1927520 ACGTGTCATAAGAGCAGAAAGATA
1 ACGTGCCACAAGAACAGAAAGATA
*
1927544 ACGTGCCACAAGAACATAAAGA
1 ACGTGCCACAAGAACAGAAAGA
1927566 ACCAGTGAGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (24 bp):
ACGTGCCACAAGAACAGAAAGATA
Found at i:1928546 original size:21 final size:20
Alignment explanation
Indices: 1928520--1928675 Score: 102
Period size: 20 Copynumber: 7.7 Consensus size: 20
1928510 GTTTCCAGAT
*
1928520 TCGCAACGCGATTTTAGAAAA
1 TCGCAACGCGATTAT-GAAAA
* * *
1928541 TCGCAATGCGAATATGTAAA
1 TCGCAACGCGATTATGAAAA
* **
1928561 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGAAAA
*
1928581 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGA-A-AA
*
1928602 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGA-A-AA
* * **
1928623 TCGCAACTCGATTCTGACTA
1 TCGCAACGCGATTATGAAAA
* *
1928643 TCGCAACGCGATTCTGACTAA
1 TCGCAACGCGATTATGA-AAA
1928664 -CGCAACGCGATT
1 TCGCAACGCGATT
1928676 CTGACTGTCG
Statistics
Matches: 109, Mismatches: 22, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
19 1 0.01
20 60 0.55
21 47 0.43
22 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATTATGAAAA
Found at i:1928583 original size:20 final size:20
Alignment explanation
Indices: 1928560--1928691 Score: 151
Period size: 20 Copynumber: 6.5 Consensus size: 20
1928550 GAATATGTAA
1928560 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
1928580 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
**
1928600 AATCGCAACGCGATAAT-ACAT
1 -ATCGCAACGCGATTCTGAC-T
*
1928621 AATCGCAACTCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
1928642 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1928662 AACGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1928682 GTCGCAACGC
1 ATCGCAACGC
1928692 TGAATTTCAA
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
19 2 0.02
20 61 0.61
21 35 0.35
22 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1929561 original size:24 final size:24
Alignment explanation
Indices: 1929510--1929563 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1929500 GTATTCAAAA
*
1929510 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1929534 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1929558 TTTGAT
1 TTTGAT
1929564 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1931849 original size:18 final size:18
Alignment explanation
Indices: 1931826--1931860 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1931816 AGAAAAAGAC
*
1931826 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1931844 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1931861 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1932170 original size:140 final size:140
Alignment explanation
Indices: 1931918--1932318 Score: 729
Period size: 140 Copynumber: 2.9 Consensus size: 140
1931908 GCAGACGTTG
*
1931918 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTAAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1931983 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
1932048 TGAATTTGAC
131 CGAATTTGAC
1932058 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1932123 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1932188 CGAATTTGAC
131 CGAATTTGAC
* *
1932198 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTTAGTTAGGCATGTATT--TTA--TGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1932259 TTGAACATTGCTATGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCG
1932319 TAACTCAAAA
Statistics
Matches: 256, Mismatches: 5, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
136 64 0.25
138 2 0.01
140 190 0.74
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:1932354 original size:20 final size:20
Alignment explanation
Indices: 1932329--1932457 Score: 195
Period size: 20 Copynumber: 6.5 Consensus size: 20
1932319 TAACTCAAAA
1932329 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
1932349 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAATTTGACT
1932369 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
1932389 ATCACAACGCGAATTTAACT
1 ATCGCAACGCGAATTTGACT
* *
1932409 ATCGCAACGTGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* *
1932429 ATTGCAACGGGAATTTGACT
1 ATCGCAACGCGAATTTGACT
1932449 ATCGCAACG
1 ATCGCAACG
1932458 AGAAAATCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 97 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:1932559 original size:20 final size:20
Alignment explanation
Indices: 1932496--1932573 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
1932486 GCAATGCGAA
*
1932496 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
1932516 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
*
1932536 TTGACTTTCACATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
1932556 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
1932574 AAGTGTACCT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:1932714 original size:14 final size:14
Alignment explanation
Indices: 1932695--1932729 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1932685 TCAATTAAAA
1932695 AAATCAACTTTTAC
1 AAATCAACTTTTAC
1932709 AAATCAACTTTTAC
1 AAATCAACTTTTAC
1932723 AAATCAA
1 AAATCAA
1932730 TTAAACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:1934097 original size:21 final size:21
Alignment explanation
Indices: 1934032--1934148 Score: 92
Period size: 21 Copynumber: 5.6 Consensus size: 21
1934022 GTGAATCGGG
* *
1934032 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGATGGGAGGGGC
* ** **
1934053 CTCTTCAACAATGACA-GGGC
1 CTCTTGAATGATGGGAGGGGC
* *
1934073 CTCTTGAACGATGGGAGGGGA
1 CTCTTGAATGATGGGAGGGGC
** **
1934094 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGATGGGAGGGGC
* *
1934115 CTCTTGAATGATAGGAGAGGC
1 CTCTTGAATGATGGGAGGGGC
1934136 CTCTTGAATGATG
1 CTCTTGAATGATG
1934149 ACAGGTGAGT
Statistics
Matches: 71, Mismatches: 24, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
20 15 0.21
21 56 0.79
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (21 bp):
CTCTTGAATGATGGGAGGGGC
Found at i:1934149 original size:42 final size:42
Alignment explanation
Indices: 1934069--1934149 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
1934059 AACAATGACA
* * *
1934069 GGGCCTCTTGAACGATGGGAGGGGACTCTTGAGGGATGATAG
1 GGGCCTCTTGAACGATAGGAGAGGACTCTTGAAGGATGATAG
* * *
1934111 GGGCCTCTTGAATGATAGGAGAGGCCTCTTGAATGATGA
1 GGGCCTCTTGAACGATAGGAGAGGACTCTTGAAGGATGA
1934150 CAGGTGAGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.23
Consensus pattern (42 bp):
GGGCCTCTTGAACGATAGGAGAGGACTCTTGAAGGATGATAG
Found at i:1934654 original size:20 final size:20
Alignment explanation
Indices: 1934629--1934672 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1934619 AATAGTTTCT
*
1934629 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCACAACAC
*
1934649 GAAACTTAAAATCACAACGC
1 GAAACTTAAAATCACAACAC
1934669 GAAA
1 GAAA
1934673 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.23, G:0.11, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCACAACAC
Found at i:1934686 original size:20 final size:20
Alignment explanation
Indices: 1934663--1934707 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1934653 CTTAAAATCA
1934663 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
** **
1934683 CAACTTGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
1934703 CAACG
1 CAACG
1934708 GGATAATCGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:1934764 original size:20 final size:20
Alignment explanation
Indices: 1934741--1934778 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1934731 AATTGCAACG
1934741 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAATGCGAAAA
1934761 TGAAAATCGCAATGCGAA
1 TGAAAATCGCAATGCGAA
1934779 TTTAGTTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (20 bp):
TGAAAATCGCAATGCGAAAA
Found at i:1934816 original size:19 final size:19
Alignment explanation
Indices: 1934773--1934818 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1934763 AAAATCGCAA
* *
1934773 TGCGAATTTAGTTTCGCGT
1 TGCGATTTTAGTTTCACGT
*
1934792 TGCGATTTTGGTTTCACGT
1 TGCGATTTTAGTTTCACGT
1934811 TGCGATTT
1 TGCGATTT
1934819 CTCATTATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.13, C:0.15, G:0.26, T:0.46
Consensus pattern (19 bp):
TGCGATTTTAGTTTCACGT
Found at i:1934908 original size:20 final size:19
Alignment explanation
Indices: 1934856--1934910 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1934846 GATTATCCTG
*
1934856 TTGCGATAGTCAAATTCGCT
1 TTGCGATAGTC-ATTTCGCT
*
1934876 TTGCAATAGTCATTTCCGCT
1 TTGCGATAGTCATTT-CGCT
1934896 TTGCGATAGTCATTT
1 TTGCGATAGTCATTT
1934911 TCGCCTTGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (19 bp):
TTGCGATAGTCATTTCGCT
Found at i:1936870 original size:20 final size:20
Alignment explanation
Indices: 1936847--1936952 Score: 99
Period size: 20 Copynumber: 5.4 Consensus size: 20
1936837 TCTGAAACTT
*
1936847 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
* *
1936867 AAAATCACAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
1936887 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
** *
1936907 ACTATCGCAATGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
1936926 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
1936945 AAAATCGC
1 AAAATCGC
1936953 GTTGCGATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
19 22 0.31
20 49 0.69
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:1936934 original size:19 final size:19
Alignment explanation
Indices: 1936910--1936952 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1936900 GAATTTGACT
*
1936910 ATCGCAATGCGAAA-TGAAA
1 ATCGCAACGCGAAACT-AAA
1936929 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
1936948 ATCGC
1 ATCGC
1936953 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.44, C:0.23, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:1937372 original size:22 final size:22
Alignment explanation
Indices: 1937342--1937400 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
1937332 AGATGGAGAT
1937342 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
* *
1937364 AGACAGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
* *
1937386 GGACGGATATCGCCG
1 AGACGGATTTCGCCG
1937401 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.24, C:0.19, G:0.39, T:0.19
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:1937591 original size:20 final size:20
Alignment explanation
Indices: 1937568--1937633 Score: 89
Period size: 20 Copynumber: 3.2 Consensus size: 20
1937558 TTATCGCAAC
1937568 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
**
1937588 GCGATTATGT-ATTATCGCGTT
1 GCGA-TA-GTCAGAATCGCGTT
1937609 GCGATAGTCAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
1937629 GCGAT
1 GCGAT
1937634 TATGTATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 2 0.05
20 20 0.51
21 15 0.38
22 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:1937605 original size:21 final size:21
Alignment explanation
Indices: 1937580--1937651 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
1937570 GATAGTCAGA
1937580 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
1937601 ATCGCGTTGCGA-TA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
1937621 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
1937642 ATCGCGTTGC
1 ATCGCGTTGC
1937652 AATAGTCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
19 2 0.05
20 15 0.34
21 25 0.57
22 2 0.05
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:1937647 original size:41 final size:41
Alignment explanation
Indices: 1937538--1937659 Score: 181
Period size: 41 Copynumber: 3.0 Consensus size: 41
1937528 GCGCTTTAAA
* * * ***
1937538 AATCGCATTGAGATTTTGTATTATCGCAACGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
1937579 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
*
1937620 AATCGCGTTGCGATTATGTATTATCGCGTTGCAATAGTCA
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCA
1937660 AAATTGTATT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (41 bp):
AATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAG
Found at i:1937672 original size:41 final size:41
Alignment explanation
Indices: 1937536--1937673 Score: 159
Period size: 41 Copynumber: 3.4 Consensus size: 41
1937526 TGGCGCTTTA
* * *** *
1937536 AAAATCGCATTGAGATTTTGTATTATCGCAACGCGATAGTC
1 AAAATCGCATTGCGATTATGTATTATCGCGTTGCAATAGTC
* * *
1937577 AGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTC
1 AAAATCGCATTGCGATTATGTATTATCGCGTTGCAATAGTC
* *
1937618 AGAATCGCGTTGCGATTATGTATTATCGCGTTGCAATAGTC
1 AAAATCGCATTGCGATTATGTATTATCGCGTTGCAATAGTC
* *
1937659 AAAATTGTATTGCGA
1 AAAATCGCATTGCGA
1937674 ATCTGAAAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (41 bp):
AAAATCGCATTGCGATTATGTATTATCGCGTTGCAATAGTC
Found at i:1942903 original size:131 final size:131
Alignment explanation
Indices: 1942633--1942969 Score: 358
Period size: 131 Copynumber: 2.6 Consensus size: 131
1942623 TTCGGTCGGA
* * * * *
1942633 GTAATAAATGACTGCTTTAA-G-ACATAAGAGGTCATTTATTCTCGATCGAAAATAATTTGATAT
1 GTAATAAATGACTGTTTTAATGCAC-GAA-AGGTCATTTATTCCCGATTGAAAATAATTAGATAT
** * * ** ** * * * * *
1942696 TGCCGTTTTCTCTCAAATTAATATCG-ATTTTTAGACGAAATATTAATATCTCTTTGTTTCGATT
64 TATCATTTTCACTTGAATCGATATTGAATTTTAAGACGAAATAGTAATATCTCTTTATTTCAATT
1942760 AGG
129 AGG
* * * * ** *
1942763 GTAATAAATGATTGTTTTAATGCATGAAAGGTCGTTTATTCCCGATTGGAAATCTTTAGTTATTA
1 GTAATAAATGACTGTTTTAATGCACGAAAGGTCATTTATTCCCGATTGAAAATAATTAGATATTA
* * *
1942828 TTATTTTCACTTGAATCGATATTGAATTTTAAGATGAAATAGTAATATCTTTTTATTTCAATT-G
66 TCATTTTCACTTGAATCGATATTGAATTTTAAGACGAAATAGTAATATCTCTTTATTTCAATTAG
1942892 G
131 G
*
1942893 AGTAATAAATGACTGTTTTAATGCACGAAAGGTCATTTATTCTCGATTGAAAATAATTAGATATT
1 -GTAATAAATGACTGTTTTAATGCACGAAAGGTCATTTATTCCCGATTGAAAATAATTAGATATT
1942958 ATCATTTTCACT
65 ATCATTTTCACT
1942970 CTTAAGATCA
Statistics
Matches: 166, Mismatches: 37, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
130 63 0.38
131 102 0.61
132 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (131 bp):
GTAATAAATGACTGTTTTAATGCACGAAAGGTCATTTATTCCCGATTGAAAATAATTAGATATTA
TCATTTTCACTTGAATCGATATTGAATTTTAAGACGAAATAGTAATATCTCTTTATTTCAATTAG
G
Found at i:1944723 original size:16 final size:16
Alignment explanation
Indices: 1944702--1944738 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1944692 ATGTAAGATT
1944702 GAAGCCTAAGACTGAA
1 GAAGCCTAAGACTGAA
1944718 GAAGCCTAAGACTGAA
1 GAAGCCTAAGACTGAA
1944734 GAAGC
1 GAAGC
1944739 TCAGAAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.27, T:0.11
Consensus pattern (16 bp):
GAAGCCTAAGACTGAA
Found at i:1949054 original size:113 final size:112
Alignment explanation
Indices: 1948743--1949117 Score: 479
Period size: 112 Copynumber: 3.3 Consensus size: 112
1948733 GTGATAGCGG
* * * **
1948743 AATGGATCAACCTCCCCCATATATGATATTCCCTTCAGAAAAAGTGGAACATATCCCTTTCTTTT
1 AATGGATCAA-CTCCCCCAAATATGATATTCCCTTTAGAAAAAGTGGAACATATCCCTCTCTTAC
* * * *
1948808 AAGATTTGATATCCCCTGAGTGACAGCAGAACAAGTTTGCCCCGATTC
65 AAGATTTGATATTCCCAGAGTGACAGCGGAACAAGTCTGCCCCGATTC
* * *
1948856 AATGGATCAACTCTCCCAAATATGCTATTCCCGTTAGAAAAAGTGGAACATATCTCC-CTCTTAC
1 AATGGATCAACTCCCCCAAATATGATATTCCCTTTAGAAAAAGTGGAACATATC-CCTCTCTTAC
1948920 AAGATTTGATATT-CCATGAGTGACAGCGGAACAAGTCTGCCCCGATTC
65 AAGATTTGATATTCCCA-GAGTGACAGCGGAACAAGTCTGCCCCGATTC
* * * * * *
1948968 AATGGATTAACTCCCCCAAGATCTGATATTCCCTTTAGAAGAAGTGGAATAGATCCCTCTCTTCC
1 AATGGATCAACTCCCCCAA-ATATGATATTCCCTTTAGAAAAAGTGGAACATATCCCTCTCTTAC
* * *
1949033 AAGATTTGATATTCCCAGAGTGA-A-CGAAACAAGTCTTCCCTGATTC
65 AAGATTTGATATTCCCAGAGTGACAGCGGAACAAGTCTGCCCCGATTC
* *
1949079 AATAGATCAACTCCCCCAAATATAATATTCCCTTTAGAA
1 AATGGATCAACTCCCCCAAATATGATATTCCCTTTAGAA
1949118 GAAGCGGAGA
Statistics
Matches: 229, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
110 18 0.08
111 38 0.17
112 104 0.45
113 66 0.29
114 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (112 bp):
AATGGATCAACTCCCCCAAATATGATATTCCCTTTAGAAAAAGTGGAACATATCCCTCTCTTACA
AGATTTGATATTCCCAGAGTGACAGCGGAACAAGTCTGCCCCGATTC
Found at i:1950328 original size:159 final size:162
Alignment explanation
Indices: 1950145--1950467 Score: 616
Period size: 159 Copynumber: 2.0 Consensus size: 162
1950135 TATAAACATA
1950145 TATAACTCATGCATGTATATATATAATGATTATAACATATGCATGTCCATAACTACTATACCATG
1 TATAACTCATGCATGTATATATATAATGATTATAACATATGCATGTCCATAACTACTATACCATG
1950210 AAAAGTAATATAGGAAATAAACTTATCACAAGTCTTATTTCCATTGGACTACACCTATAGTAT-C
66 AAAAGTAATATAGGAAATAAACTTATCACAAGTCTTATTTCCATTGGACTACACCTATAGTATAC
1950274 ACTAACCTGTCCTCACTA-T-ATACCGATCAC
131 ACTAACCTGTCCTCACTAGTAATACCGATCAC
1950304 TATAACTCATGCATGTATATATATAATGATTATAACATATGCATGTCCATAACTACTATACCATG
1 TATAACTCATGCATGTATATATATAATGATTATAACATATGCATGTCCATAACTACTATACCATG
1950369 AAAAGTAATATAGGAAATAAACTTATCACAAGTCTTATTTCCATTGGACTACACCTATAGTATAC
66 AAAAGTAATATAGGAAATAAACTTATCACAAGTCTTATTTCCATTGGACTACACCTATAGTATAC
1950434 ACTAACCTGTCCTCACTAGTCAATACCGATCAC
131 ACTAACCTGTCCTCACTAGT-AATACCGATCAC
1950467 T
1 T
1950468 TACTTCTTCC
Statistics
Matches: 160, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
159 128 0.80
160 19 0.12
161 1 0.01
163 12 0.08
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.32
Consensus pattern (162 bp):
TATAACTCATGCATGTATATATATAATGATTATAACATATGCATGTCCATAACTACTATACCATG
AAAAGTAATATAGGAAATAAACTTATCACAAGTCTTATTTCCATTGGACTACACCTATAGTATAC
ACTAACCTGTCCTCACTAGTAATACCGATCAC
Found at i:1954072 original size:15 final size:15
Alignment explanation
Indices: 1954052--1954085 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1954042 ATATCATTTC
*
1954052 ATTATTCTTATTATT
1 ATTATTCTTATCATT
1954067 ATTATTCTTATCATT
1 ATTATTCTTATCATT
1954082 ATTA
1 ATTA
1954086 ACCAAACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATTCTTATCATT
Found at i:1956247 original size:12 final size:12
Alignment explanation
Indices: 1956210--1956255 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
1956200 TTTACTATTA
*
1956210 TATTTTTAATAT
1 TATTATTAATAT
*
1956222 ATATTACTTCATAT
1 -TATTA-TTAATAT
1956236 TATTATTAATAT
1 TATTATTAATAT
1956248 TATTATTA
1 TATTATTA
1956256 TTTTTCAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 14 0.48
13 9 0.31
14 6 0.21
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTAATAT
Done.