Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008217.1 Hibiscus syriacus cultivar Beakdansim tig00110847_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: 2417150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2131620 original size:18 final size:18
Alignment explanation
Indices: 2131597--2131631 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2131587 TAACTTTAAT
*
2131597 CAAATAAATGAACGAATA
1 CAAATAAATAAACGAATA
*
2131615 CAAATAATTAAACGAAT
1 CAAATAAATAAACGAAT
2131632 GAAATTTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (18 bp):
CAAATAAATAAACGAATA
Found at i:2134109 original size:13 final size:13
Alignment explanation
Indices: 2134091--2134115 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2134081 ATATCTTCTT
2134091 TTTTTTATTTTTA
1 TTTTTTATTTTTA
2134104 TTTTTTATTTTT
1 TTTTTTATTTTT
2134116 CAAAAAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:2144584 original size:35 final size:35
Alignment explanation
Indices: 2144538--2144613 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
2144528 AAAACAGTCC
* *
2144538 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
2144573 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
2144608 TCAATT
1 TCAATT
2144614 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:2145151 original size:130 final size:130
Alignment explanation
Indices: 2145010--2145257 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
2145000 TATTTATATA
* **
2145010 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
2145075 TTAGCACATGATCATGACACGTGTCATTGATGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGATGACACATGTCACCACCTAATTATTTATATATGCT
2145140 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
2145205 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGATGACACATGTCACCACCTAATTA
2145258 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGATGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:2145288 original size:130 final size:129
Alignment explanation
Indices: 2145024--2145288 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
2145014 ATTTGGTCCT
* ** *
2145024 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
2145089 TGACACGTGTCATTGATGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGATGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
2145154 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
2145219 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGATGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
2145283 -A
128 CA
2145284 AAATT
1 AAATT
2145289 TGGGTCTTGA
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGATGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:2145745 original size:16 final size:18
Alignment explanation
Indices: 2145724--2145757 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
2145714 ATTTCTTATT
2145724 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
2145740 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
2145758 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:2154765 original size:49 final size:49
Alignment explanation
Indices: 2154672--2154765 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
2154662 GGCCCTACAT
* * *
2154672 TTATATATGAATCGTATTAATTTAAATTATAATAAATTAAAAAAAATTA
1 TTATATATGAATCATATTAATTTAAATTATAAAAAAATAAAAAAAATTA
* *
2154721 TTATATATGAATTATATTAATTTAAATTATAAAAAAATATAAAAA
1 TTATATATGAATCATATTAATTTAAATTATAAAAAAATAAAAAAA
2154766 TATAAACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (49 bp):
TTATATATGAATCATATTAATTTAAATTATAAAAAAATAAAAAAAATTA
Found at i:2154771 original size:18 final size:18
Alignment explanation
Indices: 2154748--2154795 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
2154738 TAATTTAAAT
2154748 TATAAAAAAATATAAAAA
1 TATAAAAAAATATAAAAA
* *
2154766 TATAAACAAAA-ATATAAT
1 TATAAA-AAAATATAAAAA
2154784 TATAATAAAAAT
1 TATAA-AAAAAT
2154796 CTATTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
TATAAAAAAATATAAAAA
Found at i:2157510 original size:31 final size:31
Alignment explanation
Indices: 2157463--2157533 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
2157453 TACTATTTTT
2157463 TAAAATAAAAAAGAAAACAG-AGTTC-AATTAAC
1 TAAAA-AAAAAAGAAAA-AGTAGTTCGAA-TAAC
* *
2157495 TAAAAAACAAAGAAAATGTAGTTCGAATAAC
1 TAAAAAAAAAAGAAAAAGTAGTTCGAATAAC
2157526 TAAAAAAA
1 TAAAAAAA
2157534 TTATAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 1 0.03
31 26 0.76
32 7 0.21
ACGTcount: A:0.63, C:0.08, G:0.10, T:0.18
Consensus pattern (31 bp):
TAAAAAAAAAAGAAAAAGTAGTTCGAATAAC
Found at i:2157662 original size:6 final size:6
Alignment explanation
Indices: 2157651--2157681 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2157641 CATCACTCTG
*
2157651 ATCACC ACCACC ATCACC ATCACC ATCACC A
1 ATCACC ATCACC ATCACC ATCACC ATCACC A
2157682 ACAAAATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.35, C:0.52, G:0.00, T:0.13
Consensus pattern (6 bp):
ATCACC
Found at i:2157973 original size:27 final size:27
Alignment explanation
Indices: 2157935--2157987 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2157925 GTTGGTGGCG
*
2157935 CCATATGCTGAAATGATGACAGAGTCT
1 CCATATGATGAAATGATGACAGAGTCT
* *
2157962 CCATATGATGAAATGTTGACTGAGTC
1 CCATATGATGAAATGATGACAGAGTC
2157988 GAGTGGGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (27 bp):
CCATATGATGAAATGATGACAGAGTCT
Found at i:2158606 original size:19 final size:19
Alignment explanation
Indices: 2158582--2158620 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2158572 TTACAAAAAC
2158582 TCGAATAAAAAAATAATAT
1 TCGAATAAAAAAATAATAT
*
2158601 TCGAATAAAAAATTAATAT
1 TCGAATAAAAAAATAATAT
2158620 T
1 T
2158621 TAATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
TCGAATAAAAAAATAATAT
Found at i:2160835 original size:23 final size:23
Alignment explanation
Indices: 2160798--2160909 Score: 93
Period size: 22 Copynumber: 5.0 Consensus size: 23
2160788 GTCGAGGGTT
* **
2160798 CTATGTGGTCCTTCGGGACAATC
1 CTATGTAGTCCTTCGGGACAAAA
* *
2160821 CTTTGTAGTCCTTCGGGATAAAA
1 CTATGTAGTCCTTCGGGACAAAA
*
2160844 CTATGTAGACCTTCGGGAC-AAA
1 CTATGTAGTCCTTCGGGACAAAA
* * **
2160866 TTATGTGGTTTTTCGGGAC-AAA
1 CTATGTAGTCCTTCGGGACAAAA
* * *
2160888 TTATGTGGTTCTTCGGGACAAA
1 CTATGTAGTCCTTCGGGACAAA
2160910 TATGTGGTAC
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
22 38 0.51
23 36 0.49
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (23 bp):
CTATGTAGTCCTTCGGGACAAAA
Found at i:2160915 original size:21 final size:22
Alignment explanation
Indices: 2160854--2160917 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
2160844 CTATGTAGAC
2160854 CTTCGGGACAAATTATGTGGTT
1 CTTCGGGACAAATTATGTGGTT
*
2160876 TTTCGGGACAAATTATGTGGTT
1 CTTCGGGACAAATTATGTGGTT
2160898 CTTCGGGACAAA-TATGTGGT
1 CTTCGGGACAAATTATGTGGT
2160918 ACTTTAGTGC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 8 0.20
22 32 0.80
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.36
Consensus pattern (22 bp):
CTTCGGGACAAATTATGTGGTT
Found at i:2160931 original size:43 final size:44
Alignment explanation
Indices: 2160854--2160937 Score: 118
Period size: 43 Copynumber: 1.9 Consensus size: 44
2160844 CTATGTAGAC
* *
2160854 CTTCGGGACAAATTATGTGGTTTTTCGGGACAAATTATGTGGTT
1 CTTCGGGACAAATTATGTGGTCTTTAGGGACAAATTATGTGGTT
*
2160898 CTTCGGGACAAA-TATGTGGTACTTTAGTG-CAAATTATGTG
1 CTTCGGGACAAATTATGTGGT-CTTTAGGGACAAATTATGTG
2160938 AGTTGTGGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 19 0.53
44 17 0.47
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (44 bp):
CTTCGGGACAAATTATGTGGTCTTTAGGGACAAATTATGTGGTT
Found at i:2161390 original size:20 final size:19
Alignment explanation
Indices: 2161365--2161414 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 19
2161355 GCATTATTAT
2161365 CGATACCCCTCCTACAGTAC
1 CGATACCCC-CCTACAGTAC
*
2161385 CGATACTTCTCCCCTATAGTAC
1 CGATAC--C-CCCCTACAGTAC
2161407 CGATACCC
1 CGATACCC
2161415 GAATCAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.04
20 7 0.27
22 16 0.62
23 2 0.08
ACGTcount: A:0.24, C:0.42, G:0.10, T:0.24
Consensus pattern (19 bp):
CGATACCCCCCTACAGTAC
Found at i:2168636 original size:23 final size:23
Alignment explanation
Indices: 2168602--2168711 Score: 121
Period size: 23 Copynumber: 4.8 Consensus size: 23
2168592 CCACTTATTT
* *
2168602 TCCCGAAGGACCACATAGTTTTG
1 TCCCAAAGGACCACATAGGTTTG
* ***
2168625 TCCCAAATGACCACATTTTTTTG
1 TCCCAAAGGACCACATAGGTTTG
* *
2168648 TCCTAAAGGACCACATAGGATTG
1 TCCCAAAGGACCACATAGGTTTG
*
2168671 TCCCGAAGGACCACATAGGTTTG
1 TCCCAAAGGACCACATAGGTTTG
* *
2168694 TCCCGAAGGACCATATAG
1 TCCCAAAGGACCACATAG
2168712 AACCCTTGAC
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (23 bp):
TCCCAAAGGACCACATAGGTTTG
Found at i:2171947 original size:13 final size:13
Alignment explanation
Indices: 2171929--2171954 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2171919 TTTAATTTTA
2171929 AAAAATTTAAAAT
1 AAAAATTTAAAAT
2171942 AAAAATTTAAAAT
1 AAAAATTTAAAAT
2171955 TAATACAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATTTAAAAT
Found at i:2175160 original size:22 final size:22
Alignment explanation
Indices: 2175133--2175188 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 22
2175123 GACACTTAAT
*
2175133 TAATAATAATATTGCTATAAATAAA
1 TAATAATAATA-T-ATAT-AATAAA
*
2175158 TAAAAATAATATATATAATAAA
1 TAATAATAATATATATAATAAA
2175180 TAGATAATA
1 TA-ATAATA
2175189 GATACTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 8 0.30
23 8 0.30
24 1 0.04
25 10 0.37
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (22 bp):
TAATAATAATATATATAATAAA
Found at i:2177459 original size:7 final size:7
Alignment explanation
Indices: 2177447--2177472 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2177437 TCATGTCATG
2177447 AACTTGA
1 AACTTGA
2177454 AACTTGA
1 AACTTGA
2177461 AACTTGA
1 AACTTGA
2177468 AACTT
1 AACTT
2177473 TTTGTAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (7 bp):
AACTTGA
Found at i:2184963 original size:30 final size:29
Alignment explanation
Indices: 2184929--2185048 Score: 107
Period size: 30 Copynumber: 4.1 Consensus size: 29
2184919 TCCACATTCG
* *
2184929 AAAATTACAAAAATATCACCTTTATTAAAA
1 AAAATTACCAAAATATCACCATT-TTAAAA
*
2184959 AAAATTACCAAAATATCACCATTTTACAA
1 AAAATTACCAAAATATCACCATTTTAAAA
* * **
2184988 ATAATTCCCAAAATATCA-TGTTTTAAAA
1 AAAATTACCAAAATATCACCATTTTAAAA
* * * **
2185016 ATAATTACCAGAATGTCATTAATTTTAAAA
1 AAAATTACCAAAATATCA-CCATTTTAAAA
2185046 AAA
1 AAA
2185049 TCCCAAAATG
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
28 22 0.30
29 21 0.28
30 31 0.42
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAATTACCAAAATATCACCATTTTAAAA
Found at i:2185001 original size:29 final size:28
Alignment explanation
Indices: 2184938--2185238 Score: 255
Period size: 29 Copynumber: 10.4 Consensus size: 28
2184928 GAAAATTACA
* * * *
2184938 AAAATATCACCTTTATTAAAAAAAATTACC
1 AAAATGTCACCTTT-TT-CAAATAATTCCC
* *
2184968 AAAATATCACCATTTTACAAATAATTCCC
1 AAAATGTCACC-TTTTTCAAATAATTCCC
* ** ** *
2184997 AAAATATCATGTTTTAAAAATAATTACC
1 AAAATGTCACCTTTTTCAAATAATTCCC
* * * *
2185025 AGAATGTCA--TTAATTTTAAAAAAATCCC
1 AAAATGTCACCTT--TTTCAAATAATTCCC
*** *
2185053 AAAATGTCTTTTTTTTTCAAAATAATTCCT
1 AAAATGTC-ACCTTTTTC-AAATAATTCCC
*
2185083 AAAATGTAACCTTTTTCAACATAATTCCC
1 AAAATGTCACCTTTTTCAA-ATAATTCCC
2185112 AAAATGTCACCTTTTTCAACATAATTCCC
1 AAAATGTCACCTTTTTCAA-ATAATTCCC
2185141 AAAATGTCACCTTTTTCAATATAATTCCC
1 AAAATGTCACCTTTTTCAA-ATAATTCCC
2185170 AAAATGTCACCTTTTTCAAAATAATTCCCC
1 AAAATGTCACCTTTTTC-AAATAATT-CCC
* * *
2185200 AAACTATCACCTTTTTCAAAATAATTTCC
1 AAAATGTCACCTTTTTC-AAATAATTCCC
2185229 AAAATGTCAC
1 AAAATGTCAC
2185239 TAGGTCAGGT
Statistics
Matches: 228, Mismatches: 33, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.01
28 41 0.18
29 124 0.54
30 56 0.25
31 5 0.02
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATGTCACCTTTTTCAAATAATTCCC
Found at i:2185231 original size:59 final size:58
Alignment explanation
Indices: 2184938--2185238 Score: 290
Period size: 58 Copynumber: 5.2 Consensus size: 58
2184928 GAAAATTACA
* * * * * *
2184938 AAAATATCACCTTTATTAAAAAAAATTACCAAAATATCACCATTTT-ACAAATAATTCCC
1 AAAATGTCACCTTT-TTCAAAATAATTCCCAAAATGTCACCTTTTTCA-AAATAATTCCC
* * * * * *
2184997 AAAATATCA--TGTTTTAAAAATAATTACCAGAATGTCA--TTAATTTTAAAA-AAATCCC
1 AAAATGTCACCT-TTTTCAAAATAATTCCCAAAATGTCACCTT--TTTCAAAATAATTCCC
*** * * *
2185053 AAAATGTCTTTTTTTTTCAAAATAATTCCTAAAATGTAACCTTTTTCAACATAATTCCC
1 AAAATGTC-ACCTTTTTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAATAATTCCC
* *
2185112 AAAATGTCACCTTTTTCAACATAATTCCCAAAATGTCACCTTTTTCAATATAATTCCC
1 AAAATGTCACCTTTTTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAATAATTCCC
* * *
2185170 AAAATGTCACCTTTTTCAAAATAATTCCCCAAACTATCACCTTTTTCAAAATAATTTCC
1 AAAATGTCACCTTTTTCAAAATAATT-CCCAAAATGTCACCTTTTTCAAAATAATTCCC
2185229 AAAATGTCAC
1 AAAATGTCAC
2185239 TAGGTCAGGT
Statistics
Matches: 204, Mismatches: 27, Indels: 22
0.81 0.11 0.09
Matches are distributed among these distances:
55 1 0.00
56 13 0.06
57 28 0.14
58 98 0.48
59 62 0.30
60 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAATGTCACCTTTTTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAATAATTCCC
Found at i:2187787 original size:30 final size:30
Alignment explanation
Indices: 2187746--2187849 Score: 122
Period size: 29 Copynumber: 3.5 Consensus size: 30
2187736 CACATTCGAA
* *
2187746 AATTACAAAAATATCACCTTTATTAAAAAT
1 AATTACCAAAATATCACCGTTATTAAAAAT
* *
2187776 AGTTACCAAAATATCACCGTTA-TACAAAT
1 AATTACCAAAATATCACCGTTATTAAAAAT
* * *
2187805 AATTCCCAAAATGTCATCGTT-TTAAAAAT
1 AATTACCAAAATATCACCGTTATTAAAAAT
*
2187834 AATTACCAGAATATCA
1 AATTACCAAAATATCA
2187850 TTAATTTTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
29 42 0.69
30 19 0.31
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (30 bp):
AATTACCAAAATATCACCGTTATTAAAAAT
Found at i:2187918 original size:29 final size:29
Alignment explanation
Indices: 2187801--2188001 Score: 174
Period size: 29 Copynumber: 6.8 Consensus size: 29
2187791 ACCGTTATAC
* *
2187801 AAATAATTCCCAAAATGTCA-TCGTTTTAA
1 AAATAATTCCCAAAATGTCACT-TTTTTCA
* * * * *
2187830 AAATAATTACCAGAATATCATTAATTTTTTA
1 AAATAATTCCCAAAATGTCACT--TTTTTCA
*
2187861 AAA-AAATCCCAAAATGTC-CTTTTTTTTTCA
1 AAATAATTCCCAAAATGTCAC---TTTTTTCA
*
2187891 AAATAATTTCCAAAATGTCACTTTTTTCA
1 AAATAATTCCCAAAATGTCACTTTTTTCA
* *
2187920 ACATAATTCCCAAAATGTGTCACATTTTTCA
1 AAATAATTCCCAAAA--TGTCACTTTTTTCA
* **
2187951 AAATAATTCCCAAAATATCAGATTTTTCA
1 AAATAATTCCCAAAATGTCACTTTTTTCA
*
2187980 AAATAATTTCCAAAATGTCACT
1 AAATAATTCCCAAAATGTCACT
2188002 AGGTCGGGTC
Statistics
Matches: 139, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
29 68 0.49
30 21 0.15
31 48 0.35
32 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.37
Consensus pattern (29 bp):
AAATAATTCCCAAAATGTCACTTTTTTCA
Found at i:2187937 original size:60 final size:61
Alignment explanation
Indices: 2187801--2187998 Score: 174
Period size: 60 Copynumber: 3.3 Consensus size: 61
2187791 ACCGTTATAC
* * * * * * *
2187801 AAATAATTCCCAAAATGTCAT--C-GTTTTAAAAATAATTACCAGAATATCATTAATTTTTTA
1 AAATAATTCCCAAAATGTCCTCACATTTTTCAAAATAATTCCCAAAATATCA--CATTTTTCA
* *** * * *
2187861 AAA-AAATCCCAAAATGTCCT-TTTTTTTTCAAAATAATTTCCAAAATGTCACTTTTTTCA
1 AAATAATTCCCAAAATGTCCTCACATTTTTCAAAATAATTCCCAAAATATCACATTTTTCA
* * *
2187920 ACATAATTCCCAAAATGT-GTCACATTTTTCAAAATAATTCCCAAAATATCAGATTTTTCA
1 AAATAATTCCCAAAATGTCCTCACATTTTTCAAAATAATTCCCAAAATATCACATTTTTCA
*
2187980 AAATAATTTCCAAAATGTC
1 AAATAATTCCCAAAATGTC
2187999 ACTAGGTCGG
Statistics
Matches: 110, Mismatches: 23, Indels: 9
0.77 0.16 0.06
Matches are distributed among these distances:
59 24 0.22
60 64 0.58
61 22 0.20
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (61 bp):
AAATAATTCCCAAAATGTCCTCACATTTTTCAAAATAATTCCCAAAATATCACATTTTTCA
Found at i:2188030 original size:13 final size:13
Alignment explanation
Indices: 2188006--2188043 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2187996 GTCACTAGGT
2188006 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
* *
2188019 CTGGTTGGGTCAA
1 CGGGTCGGGTCAA
2188032 CGGGTCGGGTCA
1 CGGGTCGGGTCA
2188044 GACCGGTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.45, T:0.21
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:2188063 original size:19 final size:19
Alignment explanation
Indices: 2188036--2188073 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2188026 GGTCAACGGG
2188036 TCGGGTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
* *
2188055 TCGGTTCAGATCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
2188074 CCGATTCACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (19 bp):
TCGGGTCAGACCGGTCAAA
Found at i:2188081 original size:19 final size:19
Alignment explanation
Indices: 2188041--2188081 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2188031 ACGGGTCGGG
* *
2188041 TCAGACCGGTCAAATCGGT
1 TCAGACCGGTCAAACCGAT
*
2188060 TCAGATCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGAT
2188079 TCA
1 TCA
2188082 CCGGTCACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGAT
Found at i:2193516 original size:22 final size:21
Alignment explanation
Indices: 2193504--2193549 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
2193494 TATGTATGAG
2193504 TGTATGTTGATATATTGTCAAA
1 TGTATGTTGATATA-TGTCAAA
2193526 TGTATGTTGATATATTGTCAAA
1 TGTATGTTGATATA-TGTCAAA
2193548 TG
1 TG
2193550 AGTAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (21 bp):
TGTATGTTGATATATGTCAAA
Found at i:2206387 original size:16 final size:16
Alignment explanation
Indices: 2206366--2206396 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2206356 GGTTAGCAAC
*
2206366 CAACTATTCCAGCTGA
1 CAACTACTCCAGCTGA
2206382 CAACTACTCCAGCTG
1 CAACTACTCCAGCTG
2206397 GCATCACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.35, G:0.13, T:0.23
Consensus pattern (16 bp):
CAACTACTCCAGCTGA
Found at i:2209527 original size:23 final size:23
Alignment explanation
Indices: 2209501--2209615 Score: 158
Period size: 23 Copynumber: 5.0 Consensus size: 23
2209491 CACCACAGCT
*
2209501 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
2209524 CGTAGAATTGCAGCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
2209547 CGTAGAATTGCACCGGAGTGTCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
2209570 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
2209593 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
2209616 TATAATAATG
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:2212068 original size:16 final size:18
Alignment explanation
Indices: 2212047--2212085 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2212037 ATTTTCACTG
2212047 CATGCCTT-T-ATATTAT
1 CATGCCTTCTAATATTAT
*
2212063 CATGCCTTCTAATATTTT
1 CATGCCTTCTAATATTAT
2212081 CATGC
1 CATGC
2212086 TGCTTCCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 11 0.55
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (18 bp):
CATGCCTTCTAATATTAT
Found at i:2214613 original size:23 final size:23
Alignment explanation
Indices: 2214587--2214639 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
2214577 AAGTGCCACC
*
2214587 TAGAATTGCACTGGAGTACTGCG
1 TAGAATTGCACTAGAGTACTGCG
*
2214610 TAGAATTGCACTAGAGTGCTGCG
1 TAGAATTGCACTAGAGTACTGCG
2214633 TAGAATT
1 TAGAATT
2214640 ATACCGTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (23 bp):
TAGAATTGCACTAGAGTACTGCG
Found at i:2219551 original size:16 final size:16
Alignment explanation
Indices: 2219526--2219565 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2219516 AATTAGTAAC
2219526 CAACTACTCCAGCTAG
1 CAACTACTCCAGCTAG
* *
2219542 CAACTGCTCCAGCTAA
1 CAACTACTCCAGCTAG
2219558 CAA-TACTC
1 CAACTACTC
2219566 TACTTCTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.33, C:0.38, G:0.10, T:0.20
Consensus pattern (16 bp):
CAACTACTCCAGCTAG
Found at i:2219629 original size:2 final size:2
Alignment explanation
Indices: 2219622--2219658 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2219612 CATGTACTAC
2219622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2219659 ACCTCAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2221628 original size:7 final size:7
Alignment explanation
Indices: 2221616--2221853 Score: 137
Period size: 7 Copynumber: 31.7 Consensus size: 7
2221606 TAATAATATA
2221616 ATATAAT
1 ATATAAT
2221623 ATATAAT
1 ATATAAT
*
2221630 AAATAGAT
1 ATATA-AT
2221638 ACTAT-AT
1 A-TATAAT
2221645 ATATATAT
1 ATATA-AT
2221653 ATATATAT
1 ATATA-AT
2221661 ATATAAT
1 ATATAAT
*
2221668 GTAATATAT
1 AT-ATA-AT
*
2221677 ATTATAAC
1 A-TATAAT
2221685 ATATAAT
1 ATATAAT
*
2221692 ATA-AGT
1 ATATAAT
*
2221698 ATATACT
1 ATATAAT
2221705 AATATAAT
1 -ATATAAT
*
2221713 ATAAAACT
1 ATATAA-T
2221721 ATAT-AT
1 ATATAAT
2221727 ATATATAT
1 ATATA-AT
2221735 ACTATTAA-
1 A-TA-TAAT
2221743 ATATAAT
1 ATATAAT
*
2221750 ATATTAT
1 ATATAAT
*
2221757 ATATAGT
1 ATATAAT
2221764 ATATATAT
1 ATATA-AT
*
2221772 ATTATAAC
1 A-TATAAT
2221780 ATATACTAT
1 ATATA--AT
2221789 ATATAAT
1 ATATAAT
2221796 ATAT-A-
1 ATATAAT
2221801 ATATAAT
1 ATATAAT
*
2221808 AGTATACT
1 A-TATAAT
2221816 ATATAAT
1 ATATAAT
*
2221823 ACAATATAT
1 A-TATA-AT
2221832 ATACTATAT
1 ATA-TA-AT
2221841 ACTATAAT
1 A-TATAAT
2221849 ATATA
1 ATATA
2221854 CTGTCACAGA
Statistics
Matches: 184, Mismatches: 21, Indels: 52
0.72 0.08 0.20
Matches are distributed among these distances:
5 4 0.02
6 18 0.10
7 72 0.39
8 54 0.29
9 31 0.17
10 5 0.03
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:2221645 original size:2 final size:2
Alignment explanation
Indices: 2221611--2221853 Score: 154
Period size: 2 Copynumber: 127.5 Consensus size: 2
2221601 ATTAATAATA
* *
2221611 AT AT A- AT AT A- AT AT AT A- AT AA AT AG AT ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
2221651 AT AT AT AT AT AT AT A- AT GT A- AT AT AT AT -T AT A- AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2221689 A- AT AT A- AGT AT AT ACT A- AT AT A- AT AT A- AA ACT AT AT AT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT
*
2221727 AT AT AT AT ACT AT -T AA AT AT A- AT AT AT -T AT AT AT AGT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
2221768 AT AT AT -T AT A- AC AT AT ACT AT AT AT A- AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
2221806 AT AGT AT ACT AT AT A- AT AC A- AT AT AT AT ACT AT AT ACT AT A-
1 AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT
2221847 AT AT AT A
1 AT AT AT A
2221854 CTGTCACAGA
Statistics
Matches: 195, Mismatches: 12, Indels: 68
0.71 0.04 0.25
Matches are distributed among these distances:
1 23 0.12
2 152 0.78
3 20 0.10
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2221725 original size:25 final size:24
Alignment explanation
Indices: 2221611--2221851 Score: 136
Period size: 23 Copynumber: 10.4 Consensus size: 24
2221601 ATTAATAATA
* *
2221611 ATATAATATAATATATA-ATAAAT
1 ATATAATATAAAATATATATATAT
* * *
2221634 AGATACTAT-ATATATATATATAT
1 ATATAATATAAAATATATATATAT
**
2221657 ATAT-ATATAATGTA-ATATATAT
1 ATATAATATAAAATATATATATAT
* *
2221679 -TATAACATATAATATAAGTATATACT
1 ATATAATATAAAATAT-A-TATATA-T
2221705 AATATAATATAAAACTATATATATAT
1 -ATATAATATAAAA-TATATATATAT
* *
2221731 ATATACTATTAAATATA-ATATAT
1 ATATAATATAAAATATATATATAT
*
2221754 -TAT-ATAT--AGTATATATATAT
1 ATATAATATAAAATATATATATAT
* * *
2221774 -TATAACATATACTATATATA-AT
1 ATATAATATAAAATATATATATAT
* *
2221796 ATATAATAT--AATA-GTATA-CT
1 ATATAATATAAAATATATATATAT
* *
2221816 ATATAATACAATATATATACTATAT
1 ATATAATATAAAATATATA-TATAT
2221841 ACTATAATATA
1 A-TATAATATA
2221852 TACTGTCACA
Statistics
Matches: 170, Mismatches: 27, Indels: 39
0.72 0.11 0.17
Matches are distributed among these distances:
19 5 0.03
20 22 0.13
21 12 0.07
22 32 0.19
23 43 0.25
24 7 0.04
25 19 0.11
26 10 0.06
27 6 0.04
28 11 0.06
29 3 0.02
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (24 bp):
ATATAATATAAAATATATATATAT
Found at i:2221775 original size:95 final size:96
Alignment explanation
Indices: 2221599--2221853 Score: 287
Period size: 95 Copynumber: 2.6 Consensus size: 96
2221589 GAAAATATTA
* * *
2221599 ATAT-TAATA-ATAATATAATATAATA-TATA-ATAAATAGATACTATATATATATATATATATA
1 ATATATAATATATAATATAATATAATACTATATATATATATATACTATAAATATA-ATATATATA
2221660 TATATAATGTAATATATATTATAACATATAAT
65 TATATAATGTAATATATATTATAACATATAAT
*
2221692 ATA-AGT-ATATACTAATATAATATAAAACTATATATATATATATACTATTAAATATAATATAT-
1 ATATA-TAATATA-TAATATAATATAATACTATATATATATATATACTA-TAAATATAATATATA
*
2221754 TATATAT-A-GTATATATATATTATAACATATACT
63 TATATATAATGTA-ATATATATTATAACATATAAT
*
2221787 ATATATAATATATAATATAATAGT-ATACTATATAATACAATATATATACTATATACTATAATAT
1 ATATATAATATATAATATAATA-TAATACTATAT-AT---ATATATATACTATA-AATATAATAT
2221851 ATA
60 ATA
2221854 CTGTCACAGA
Statistics
Matches: 138, Mismatches: 7, Indels: 27
0.80 0.04 0.16
Matches are distributed among these distances:
93 6 0.04
94 5 0.04
95 57 0.41
96 20 0.14
97 18 0.13
98 9 0.07
99 23 0.17
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (96 bp):
ATATATAATATATAATATAATATAATACTATATATATATATATACTATAAATATAATATATATAT
ATATAATGTAATATATATTATAACATATAAT
Found at i:2235154 original size:21 final size:20
Alignment explanation
Indices: 2235130--2235168 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2235120 CATCGAGGTC
*
2235130 TTCGTGGAGGCCATGAAATCT
1 TTCGTGGAAGCCAT-AAATCT
*
2235151 TTCGTTGAAGCCATAAAT
1 TTCGTGGAAGCCATAAAT
2235169 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (20 bp):
TTCGTGGAAGCCATAAATCT
Found at i:2238921 original size:4 final size:4
Alignment explanation
Indices: 2238912--2238952 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
2238902 TATCAACTTG
2238912 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA C-AA CT
1 CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CTAA CT
2238953 GATCCATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CTAA
Found at i:2242356 original size:21 final size:21
Alignment explanation
Indices: 2242324--2242372 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2242314 AAAAGAAATG
* *
2242324 AGAAGAAGGAGAAGAACAAGA
1 AGAAGAAAGAGAAGAAAAAGA
*
2242345 AGGAGAAAGAGAAGAAAAAGA
1 AGAAGAAAGAGAAGAAAAAGA
2242366 AGAAGAA
1 AGAAGAA
2242373 TGAAGAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (21 bp):
AGAAGAAAGAGAAGAAAAAGA
Found at i:2242359 original size:15 final size:15
Alignment explanation
Indices: 2242317--2242360 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2242307 GGAGTTGAAA
2242317 AGAAATGAGAAGAAGG
1 AGAAA-GAGAAGAAGG
*
2242333 AG-AAGAACAAGAAGG
1 AGAAAG-AGAAGAAGG
2242348 AGAAAGAGAAGAA
1 AGAAAGAGAAGAA
2242361 AAAGAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.61, C:0.02, G:0.34, T:0.02
Consensus pattern (15 bp):
AGAAAGAGAAGAAGG
Found at i:2243821 original size:15 final size:16
Alignment explanation
Indices: 2243801--2243831 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2243791 ATTTAATATA
2243801 AAACCTAAA-TAACCT
1 AAACCTAAACTAACCT
2243816 AAACCTAAACTAACCT
1 AAACCTAAACTAACCT
2243832 CACGCAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (16 bp):
AAACCTAAACTAACCT
Found at i:2245121 original size:55 final size:55
Alignment explanation
Indices: 2244972--2245429 Score: 421
Period size: 55 Copynumber: 8.3 Consensus size: 55
2244962 GGGATAAATG
* ** * * *
2244972 AGACTTGAACAATCTTCGAATGAA-GGGTCCGCTCCCTATTCTTTCA-AGGAGTGTA
1 AGACTCGAACAATCTTC-AACAAACGGGTCCGCTCTCTATTCCTTCAGA-GAGTATA
** ** ** * *
2245027 AGACTCGAACAATCTTTGACAAACATGTATGCTCCCTATTCGTTCA-AGGAGTATA
1 AGACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGA-GAGTATA
* *
2245082 AGACTCGAACAATCTTCAATAAACGGGTCCGCTCTCTATTCTTTCAGAGAGTAT-
1 AGACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
* * *
2245136 AGAACTTGAACAATCTTAAACAAACGGGTCCGCTCTCTATTCCTTGAGAGAGTATA
1 AG-ACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
* * * * *
2245192 GGACTCTAACAATTTTCAACAAACGAGTCCGCTCTCTATTCCCTCAGAGAGTAT-
1 AGACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
* *
2245246 AGAACTCGAACAATCTTCAACAAATGGGTTCGCTC-CATATT-CTATCAGAGAGTATA
1 AG-ACTCGAACAATCTTCAACAAACGGGTCCGCTCTC-TATTCCT-TCAGAGAGTATA
* * ** *
2245302 GGACTCGAATAATCTTCAACAAACGGGTATGCTCTCTATTCCTTCAGAGAGTATG
1 AGACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
* * * * * * *
2245357 GGACTTGAATAATCTTCATA-AAATGGGTCTGCTC-CTTATTCATTCAGGGAGTATA
1 AGACTCGAACAATCTTCA-ACAAACGGGTCCGCTCTC-TATTCCTTCAGAGAGTATA
*
2245412 AGACTTGAACAATCTTCA
1 AGACTCGAACAATCTTCA
2245430 TTTGCTTCAC
Statistics
Matches: 337, Mismatches: 54, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
54 9 0.03
55 321 0.95
56 7 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (55 bp):
AGACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
Found at i:2245479 original size:37 final size:37
Alignment explanation
Indices: 2245429--2245511 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
2245419 AACAATCTTC
** *
2245429 ATTTGCTTCACTACTCTTTTGTAAAGGATTTAGTTTG
1 ATTTGCTTCACTACTCTTCCGTAAAGGATTAAGTTTG
* *
2245466 ATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTG
1 ATTTGCTTCACTACTCTTCCGTAAAGGATTAAGTTTG
*
2245503 ATTTACTTC
1 ATTTGCTTC
2245512 GAATGTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (37 bp):
ATTTGCTTCACTACTCTTCCGTAAAGGATTAAGTTTG
Found at i:2246758 original size:45 final size:43
Alignment explanation
Indices: 2246690--2246773 Score: 114
Period size: 45 Copynumber: 1.9 Consensus size: 43
2246680 TAAACAAAAC
* *
2246690 TCAAGATGCCCTTTACGAGTTTTCAACTTGAGACCTCCTTTGGTT
1 TCAAGACGCCCTTTACGAATTTTCAACTTGA-ACC-CCTTTGGTT
* *
2246735 TCAAGACGCCCTTTGCGAATTTTCATCTTGAACCCCTTT
1 TCAAGACGCCCTTTACGAATTTTCAACTTGAACCCCTTT
2246774 TATTTCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 5 0.14
44 3 0.09
45 27 0.77
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.37
Consensus pattern (43 bp):
TCAAGACGCCCTTTACGAATTTTCAACTTGAACCCCTTTGGTT
Found at i:2246787 original size:6 final size:6
Alignment explanation
Indices: 2246776--2246954 Score: 91
Period size: 7 Copynumber: 28.5 Consensus size: 6
2246766 ACCCCTTTTA
* *
2246776 TTTCTT TTTCTTT TTTCATCAT TTTCCT TTTATT TTTCCTT TTTCCTT
1 TTTCTT TTTC-TT TTTC-T--T TTTCTT TTTCTT TTT-CTT TTT-CTT
* ** * *
2246824 TTTCATT TTTC-- TTTCAT TTTCCA TTT-TT TTTCTT TTTTTCT TTTCAT
1 TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* * *
2246871 TTT-TT TTTCATT TTTCATT TTTCATT TTTCATT TTTCCT TTTCCT TTCCTTT
1 TTTCTT TTTC-TT TTTC-TT TTTC-TT TTTC-TT TTTCTT TTTCTT TTTC-TT
*
2246923 TTTCAT TTTC-T TTT-TT TTTCGTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTT
2246955 TCATTTATTC
Statistics
Matches: 140, Mismatches: 18, Indels: 30
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.03
5 15 0.11
6 50 0.36
7 66 0.47
9 5 0.04
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:2246881 original size:87 final size:87
Alignment explanation
Indices: 2246786--2246960 Score: 216
Period size: 87 Copynumber: 2.0 Consensus size: 87
2246776 TTTCTTTTTC
*
2246786 TTTTTTCATCATTTTC-CTTTT-ATTTTTCCTTTTTCCTTTTTCATTT-TTCTTTCATTTTCCAT
1 TTTTTTCAT--TTTTCACTTTTCATTTTTCATTTTTCC-TTTTCATTTCTTCTTTCATTTT-CAT
2246848 TTTTTTTC-TTTTT-TTCTTTTCATTT
62 TTTTTTTCGTTTTTCTT-TTTTCATTT
* * * *
2246873 TTTTTTCATTTTTCATTTTTCATTTTTCATTTTTCCTTTTCCTTTCCTTTTTTCATTTTCTTTTT
1 TTTTTTCATTTTTCACTTTTCATTTTTCATTTTTCCTTTTCATTT-CTTCTTTCATTTTCATTTT
2246938 TTTTCGTTTTTCTTTTTTCATTT
65 TTTTCGTTTTTCTTTTTTCATTT
2246961 ATTCTTCAAG
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
85 5 0.06
86 12 0.16
87 33 0.43
88 25 0.32
89 2 0.03
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (87 bp):
TTTTTTCATTTTTCACTTTTCATTTTTCATTTTTCCTTTTCATTTCTTCTTTCATTTTCATTTTT
TTTCGTTTTTCTTTTTTCATTT
Found at i:2246924 original size:73 final size:73
Alignment explanation
Indices: 2246769--2246938 Score: 190
Period size: 73 Copynumber: 2.3 Consensus size: 73
2246759 ATCTTGAACC
* * *
2246769 CCTTTTATTTCTTTTTCTTTTTTCATCATTTTCCTTTTATTTTTCCTTTTTCCTTTTTCATTTTT
1 CCTTTTTTTTCTTTTTCTTTTTTCAT-ATTTT-CTTTTATTTTTCATTTTTCATTTTTCATTTTT
*
2246834 CTTTCATTTT
64 CTTTCACTTT
2246844 CCATTTTTTTTCTTTTT-TTCTTTTCAT-TTTT-TTTTCATTTTTCATTTTTCATTTTTCATTTT
1 CC-TTTTTTTTCTTTTTCTT-TTTTCATATTTTCTTTT-ATTTTTCATTTTTCATTTTTCATTTT
2246906 TCCTTTTC-CTTT
63 T-C-TTTCACTTT
*
2246918 CC--TTTTTTCATTTTCTTTTTT
1 CCTTTTTTTTCTTTTTCTTTTTT
2246939 TTTCGTTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
71 15 0.18
72 6 0.07
73 25 0.30
74 10 0.12
75 8 0.10
76 20 0.24
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.74
Consensus pattern (73 bp):
CCTTTTTTTTCTTTTTCTTTTTTCATATTTTCTTTTATTTTTCATTTTTCATTTTTCATTTTTCT
TTCACTTT
Found at i:2246937 original size:63 final size:62
Alignment explanation
Indices: 2246815--2246960 Score: 185
Period size: 63 Copynumber: 2.4 Consensus size: 62
2246805 TTATTTTTCC
* * *
2246815 TTTTTCCTTTTTCATTTTTC---TTTCATTTTCCATTTTTTTTCTTTTTTTCTTTTCATTTT
1 TTTTTCATTTTTCATTTTTCATTTTTCATTTTCCATTTTCTTTCCTTTTTTCTTTTCATTTT
2246874 TTTTTCATTTTTCATTTTTCATTTTTCATTTTTCC-TTTTCCTTTCCTTTTTTCATTTTC-TTTT
1 TTTTTCATTTTTCATTTTTCATTTTTCA-TTTTCCATTTT-CTTTCCTTTTTTC-TTTTCATTTT
* *
2246937 TTTTTCGTTTTTCTTTTTTCATTT
1 TTTTTCATTTTTCATTTTTCATTT
2246961 ATTCTTCAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
59 19 0.25
62 9 0.12
63 43 0.57
64 5 0.07
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (62 bp):
TTTTTCATTTTTCATTTTTCATTTTTCATTTTCCATTTTCTTTCCTTTTTTCTTTTCATTTT
Found at i:2246948 original size:73 final size:71
Alignment explanation
Indices: 2246776--2246960 Score: 175
Period size: 73 Copynumber: 2.5 Consensus size: 71
2246766 ACCCCTTTTA
** * * *
2246776 TTTCTTTTTCTTTTTTCATCATTTTCCTTTTATTTTTCCTTTTTCCTTTTTCATTTTTCTTTCAT
1 TTTC-TTTTCTTTTTTTTTCATTTT--TTTTATTTTTCATTTTTCATTTTTCATTTTTCTTTCAC
2246841 TTTCCATTT
63 TTTCCATTT
2246850 TTT-TTCTT-TTTTTCTTTTCATTTTTTTTTCATTTTTCATTTTTCATTTTTCATTTTTCCTTTT
1 TTTCTT-TTCTTTTT-TTTTCA-TTTTTTTT-ATTTTTCATTTTTCATTTTTCATTTTT-C-TTT
2246913 C-CTTTCC-TTT
60 CACTTTCCATTT
* *
2246923 TTTCATTTTCTTTTTTTTTC-GTTTTTCT-TTTTTCATTT
1 TTTC-TTTTCTTTTTTTTTCATTTTTTTTATTTTTCATTT
2246961 ATTCTTCAAG
Statistics
Matches: 95, Mismatches: 7, Indels: 22
0.77 0.06 0.18
Matches are distributed among these distances:
70 10 0.11
72 17 0.18
73 37 0.39
74 20 0.21
75 11 0.12
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.75
Consensus pattern (71 bp):
TTTCTTTTCTTTTTTTTTCATTTTTTTTATTTTTCATTTTTCATTTTTCATTTTTCTTTCACTTT
CCATTT
Found at i:2246954 original size:80 final size:79
Alignment explanation
Indices: 2246803--2246955 Score: 186
Period size: 80 Copynumber: 1.9 Consensus size: 79
2246793 ATCATTTTCC
* * * *
2246803 TTTTATTTTTCCTTTTTCCTTTTTCATTTTTCTTTCATTTTCCATTTTTTTTCTTTTTTTCTTTT
1 TTTTATTTTTCATTTTTCATTTTTCATTTTCCTTTCATTTTCCATTTTTTTTCTTTTTGTCTTTT
2246868 CATTTTTTTTTCAT
66 CATTTTTTTTTCAT
* * *
2246882 TTTTCATTTTTCATTTTTCATTTTTCCTTTTCCTTTCCTTTTTTCATTTTCTTTT-TTTTTCGT-
1 TTTT-ATTTTTCATTTTTCATTTTTCATTTTCCTTT-CATTTTCCATTTT-TTTTCTTTTT-GTC
2246945 TTTTC-TTTTTT
62 TTTTCATTTTTT
2246956 CATTTATTCT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
79 4 0.06
80 33 0.52
81 21 0.33
82 5 0.08
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.76
Consensus pattern (79 bp):
TTTTATTTTTCATTTTTCATTTTTCATTTTCCTTTCATTTTCCATTTTTTTTCTTTTTGTCTTTT
CATTTTTTTTTCAT
Found at i:2258567 original size:16 final size:16
Alignment explanation
Indices: 2258546--2258578 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2258536 ACATTTAATA
2258546 TAAAACCTAAA-TAACC
1 TAAAA-CTAAACTAACC
2258562 TAAAACTAAACTAACC
1 TAAAACTAAACTAACC
2258578 T
1 T
2258579 CACGCAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAACTAAACTAACC
Found at i:2262319 original size:27 final size:25
Alignment explanation
Indices: 2262288--2262350 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 25
2262278 ATGCAATAAT
* *
2262288 ATAAATGGTAAATTAAAGGGTACACAC
1 ATAAATGGTAAA-AAAAGGG-AAACAC
* *
2262315 ATAAATGCTAAAAAAAGGGAAAGAC
1 ATAAATGGTAAAAAAAGGGAAACAC
2262340 ATAAAT-GTAAA
1 ATAAATGGTAAA
2262351 GGTGTTAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 4 0.13
25 10 0.32
26 6 0.19
27 11 0.35
ACGTcount: A:0.56, C:0.08, G:0.17, T:0.19
Consensus pattern (25 bp):
ATAAATGGTAAAAAAAGGGAAACAC
Found at i:2272764 original size:14 final size:14
Alignment explanation
Indices: 2272741--2272782 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
2272731 TCTGGTCCAG
2272741 TCAT-TGAGTCAAC
1 TCATCTGAGTCAAC
2272754 TCATCTGAGTCAAC
1 TCATCTGAGTCAAC
*
2272768 TCGTCTGAGTCAAC
1 TCATCTGAGTCAAC
2272782 T
1 T
2272783 TGTTGATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (14 bp):
TCATCTGAGTCAAC
Found at i:2283136 original size:3 final size:3
Alignment explanation
Indices: 2283128--2283244 Score: 152
Period size: 3 Copynumber: 39.3 Consensus size: 3
2283118 CCCCCGGATC
2283128 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2283175 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TCTA TTG TT- TTAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TT-A TTA
* *
2283222 TAA TTA -TA TTT TTA TT- TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2283245 ATGCCCTTAC
Statistics
Matches: 102, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
2 8 0.08
3 86 0.84
4 8 0.08
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2287982 original size:46 final size:46
Alignment explanation
Indices: 2287929--2288017 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
2287919 GGTTTAGTGT
*
2287929 TTAATTTGAATTAATTTGCATGGTATCTTCATAAGCAATACTTGAA
1 TTAATTTGAATTAATTTGCATGGTATCCTCATAAGCAATACTTGAA
*
2287975 TTAATTTGAATTAATTTGCATGGTATCCTCATAAGCATTACTT
1 TTAATTTGAATTAATTTGCATGGTATCCTCATAAGCAATACTT
2288018 ATGTGGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (46 bp):
TTAATTTGAATTAATTTGCATGGTATCCTCATAAGCAATACTTGAA
Found at i:2290687 original size:36 final size:36
Alignment explanation
Indices: 2290600--2290694 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
2290590 CAAAATTTGC
* *
2290600 GTTTCAAAGGAAAACTATCTCAAGTGAGGTGAAATTT
1 GTTTC-AAGAAAAACAATCTCAAGTGAGGTGAAATTT
** * *
2290637 GTTTTTAGAAAAACAATCTCAAGTGAGGTTAATTTT
1 GTTTCAAGAAAAACAATCTCAAGTGAGGTGAAATTT
** *
2290673 GTTTCAAGTGAAACAATTTCAA
1 GTTTCAAGAAAAACAATCTCAA
2290695 AATTTGTGTT
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
36 43 0.91
37 4 0.09
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (36 bp):
GTTTCAAGAAAAACAATCTCAAGTGAGGTGAAATTT
Found at i:2290706 original size:102 final size:101
Alignment explanation
Indices: 2290549--2290892 Score: 395
Period size: 102 Copynumber: 3.4 Consensus size: 101
2290539 AAGATAAGCT
* * * **
2290549 ATCTCAGGTGAGATAAGATTTTGTTTTAACCGAAACAATTTCAAAATTTGCGTTTCAAAGGAAAA
1 ATCTCAAGTGAGATCA-ATTTTGTTTCAAGTGAAACAATTTCAAAATTTGCGTTTCAAAGGAAAA
* ***
2290614 CTATCTCAAGTGAGGTGAAATTTGTTTTTAGAAAAACA
65 CTATCTCAAGCGAGACAAAATTTGTTTTTAGAAAAA-A
* * * * *
2290652 ATCTCAAGTGAGGTTAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCGAGGGAAAAC
1 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGCGTTTCAAAGGAAAAC
* *
2290717 TATCTTAAGCGAGACAAAATTTGTTTTTAGGAAAAA
66 TATCTCAAGCGAGACAAAATTTGTTTTTAGAAAAAA
* * * * * *
2290753 ATCTCACGTGAGATCAATTTTGTTTCAAGTAAAACAACTTT-GAAATTTGGGCTT-AAAGGGAAA
1 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAA-TTTCAAAATTTGCGTTTCAAAGGAAAA
* **
2290816 CTGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAAATA
65 CTATCTCAAGCGAGACAAAA-TTTGTTTTTAGA-AAAA-A
2290856 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAA
1 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAA
2290893 CTCTGAAATT
Statistics
Matches: 205, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
100 24 0.12
101 53 0.26
102 79 0.39
103 49 0.24
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (101 bp):
ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAATTTGCGTTTCAAAGGAAAAC
TATCTCAAGCGAGACAAAATTTGTTTTTAGAAAAAA
Found at i:2290813 original size:101 final size:101
Alignment explanation
Indices: 2290549--2290933 Score: 407
Period size: 103 Copynumber: 3.8 Consensus size: 101
2290539 AAGATAAGCT
* * * ** * * * *
2290549 ATCTCAGGTGAGATAAGATTTTGTTTTAACCGAAACAA-TTTCAAAATTTGCGTTTCAAAGGAAA
1 ATCTCAAGTGAGATCA-ATTTTGTTTCAAGTGAAACAACTTT-GAAATTTGGGCTTC-AAGGGAA
* *** *
2290613 ACTATCTCAAGTGAGGTGAAATTTGTTTTTAGAAAAACA
63 ACTATCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACA
* * * * * *
2290652 ATCTCAAGTGAGGTTAATTTTGTTTCAAGTGAAACAA-TTTCAAAATTTGTGTTTCGAGGGAAAA
1 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTTT-GAAATTTGGGCTTCAAGGG-AAA
*
2290716 CTATCTTAAGCGAGACAAAATTTGTTTTTAGGAAAA-A
64 CTATCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACA
* * *
2290753 ATCTCACGTGAGATCAATTTTGTTTCAAGTAAAACAACTTTGAAATTTGGGCTTAAAGGGAAACT
1 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTTTGAAATTTGGGCTTCAAGGGAAACT
* ** *
2290818 GTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAAATA
66 ATCTCAAGCGAGACAAAA-TTTGTTTTTAG-GAAAACA
* *
2290856 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTCTGAAATTTAGGCTTCAAGGGAAACT
1 ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTTTGAAATTTGGGCTTCAAGGGAAACT
*
2290921 GTCTCAAGCGAGA
66 ATCTCAAGCGAGA
2290934 TGAAACTTTC
Statistics
Matches: 244, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
100 21 0.09
101 60 0.25
102 76 0.31
103 87 0.36
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (101 bp):
ATCTCAAGTGAGATCAATTTTGTTTCAAGTGAAACAACTTTGAAATTTGGGCTTCAAGGGAAACT
ATCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACA
Found at i:2293229 original size:15 final size:14
Alignment explanation
Indices: 2293209--2293251 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2293199 ATTTGTTCTA
2293209 TTTCTTCTTATTTTC
1 TTTCTTCTT-TTTTC
*
2293224 TTTCTTTTTTCTTTC
1 TTTCTTCTTT-TTTC
*
2293239 TTTTTTCTTTTTT
1 TTTCTTCTTTTTT
2293252 TTATATCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTCTTTTTTC
Found at i:2293251 original size:20 final size:20
Alignment explanation
Indices: 2293209--2293280 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
2293199 ATTTGTTCTA
2293209 TTTCT-TCTTATTTTCTTTCTTT
1 TTTCTATCTT-TTTTC-TT-TTT
*
2293231 TTTCTTTCTTTTTTCTTTTT
1 TTTCTATCTTTTTTCTTTTT
* *
2293251 TTTATATCTTTTATCTTTTT
1 TTTCTATCTTTTTTCTTTTT
2293271 TTTCTATCTT
1 TTTCTATCTT
2293281 GAATATGAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 29 0.64
21 2 0.04
22 10 0.22
23 4 0.09
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTCTATCTTTTTTCTTTTT
Found at i:2293262 original size:11 final size:10
Alignment explanation
Indices: 2293209--2293280 Score: 67
Period size: 11 Copynumber: 6.9 Consensus size: 10
2293199 ATTTGTTCTA
2293209 TTTCTTCTTAT
1 TTTCTTCTT-T
2293220 TTTCTTTCTTT
1 TTTC-TTCTTT
2293231 TTTCTTTCTTT
1 TTTC-TTCTTT
2293242 TTTCTT-TTT
1 TTTCTTCTTT
*
2293251 TTTATATCTTT
1 TTTCT-TCTTT
*
2293262 TATCTT-TTT
1 TTTCTTCTTT
2293271 TTTCTATCTT
1 TTTCT-TCTT
2293281 GAATATGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
9 14 0.27
10 5 0.10
11 28 0.54
12 5 0.10
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTTCTTT
Found at i:2300006 original size:21 final size:20
Alignment explanation
Indices: 2299982--2300040 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 20
2299972 ACCTCCTCGC
2299982 TATGTATCGATACACTATGAA
1 TATGTATCGATACACT-TGAA
*
2300003 TATGTACCGATACATTCCTTGAA
1 TATGTATCGATACA---CTTGAA
*
2300026 TGTGTATCGATACAC
1 TATGTATCGATACAC
2300041 CTGTGGGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.03
21 13 0.41
23 16 0.50
24 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (20 bp):
TATGTATCGATACACTTGAA
Found at i:2302270 original size:13 final size:13
Alignment explanation
Indices: 2302248--2302281 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2302238 AGGGGTAGTA
*
2302248 ATTTTCAAAATTG
1 ATTTTCAAAAATG
2302261 A-TTTCAAAAATG
1 ATTTTCAAAAATG
2302273 ATTTTCAAA
1 ATTTTCAAA
2302282 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:2302653 original size:234 final size:232
Alignment explanation
Indices: 2302261--2302730 Score: 823
Period size: 234 Copynumber: 2.0 Consensus size: 232
2302251 TTCAAAATTG
*
2302261 ATTTCAAAAATGATTTTCAAAGAAAATCTTAAAATTACAAATGTTTTGTTATATCAAAAAGGAGG
1 ATTTCAAAAATGATTTTCAAAGAAAATCTTAAAATTACAAATGTTTTCTTATATCAAAAAGGAGG
* *
2302326 AGATTGTTGAAAGCATTTTGATGTTTCGATATAACAAATAAAGTACTTTTGAATTTTAAGATTTT
66 AGATTGTTGAAAACATTTTGATGTTTCGATATAACAAATAAAGTACTATTGAATTTTAAGATTTT
*
2302391 ATTCAATTTTACTCCAAGTTTTCAAATGTCAATTTTAATTCTTACTTAAGTGTAAAATTGTGTTT
131 ATTCAATTTTACTCCAAGTTTTCAAATGTCAATTTTAATCCTTACTTAAGTGTAAAATTGTGTTT
*
2302456 TAATCTTAAAATAATTTTGAAATAATTTTTACAAAGT
196 TAATCTTAAAATAATTTTGAAACAATTTTTACAAAGT
*
2302493 ATTTCAAAAATGATTTTCAAAGAAAATCTTAAAATTACTTAAATGTTTTCTTATATCAAAAAGGG
1 ATTTCAAAAATGATTTTCAAAGAAAATCTTAAAATTAC--AAATGTTTTCTTATATCAAAAAGGA
*
2302558 GGAGATTGTTGAAAATATTTTGATGTTTCGATATAACAAATAAAGTACTATTGAATTTTAAGATT
64 GGAGATTGTTGAAAACATTTTGATGTTTCGATATAACAAATAAAGTACTATTGAATTTTAAGATT
* *
2302623 TTATTCAATTTTACTCCATGTTTTCAAATGTCAATTTTAATCCTTACTTAAGTGTAAAATTTTGT
129 TTATTCAATTTTACTCCAAGTTTTCAAATGTCAATTTTAATCCTTACTTAAGTGTAAAATTGTGT
* *
2302688 TTTAATCTTAGAATATTTTTGAAACAATTTTTACAAAGT
194 TTTAATCTTAAAATAATTTTGAAACAATTTTTACAAAGT
2302727 ATTT
1 ATTT
2302731 TGAACCTTAA
Statistics
Matches: 225, Mismatches: 11, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
232 38 0.17
234 187 0.83
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (232 bp):
ATTTCAAAAATGATTTTCAAAGAAAATCTTAAAATTACAAATGTTTTCTTATATCAAAAAGGAGG
AGATTGTTGAAAACATTTTGATGTTTCGATATAACAAATAAAGTACTATTGAATTTTAAGATTTT
ATTCAATTTTACTCCAAGTTTTCAAATGTCAATTTTAATCCTTACTTAAGTGTAAAATTGTGTTT
TAATCTTAAAATAATTTTGAAACAATTTTTACAAAGT
Found at i:2307583 original size:2 final size:2
Alignment explanation
Indices: 2307576--2307614 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2307566 AAAATTAGTA
2307576 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2307615 CAAGGGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2311926 original size:38 final size:38
Alignment explanation
Indices: 2311836--2311926 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
2311826 TTTTAGGCTC
* * * *
2311836 GTTTCTCTGGAAACCTCAATTTAGTCTTTCTTAAGATT
1 GTTTCTCTAGAAACCTCAACTTAGTCTTTCATAAGATG
* * *
2311874 ATTTCCCTAAAAACCTCAACCTT-GTCTTTCATAAGATG
1 GTTTCTCTAGAAACCTCAA-CTTAGTCTTTCATAAGATG
2311912 GTTTCTCTAGAAACC
1 GTTTCTCTAGAAACC
2311927 AACTTTATCT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
38 40 0.95
39 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.38
Consensus pattern (38 bp):
GTTTCTCTAGAAACCTCAACTTAGTCTTTCATAAGATG
Found at i:2312605 original size:134 final size:133
Alignment explanation
Indices: 2312361--2312976 Score: 551
Period size: 131 Copynumber: 4.7 Consensus size: 133
2312351 TGAAACATAT
* * * * * * *
2312361 CATTTTCCTCCAAATTTGATCATCCCTGAAGAGAATTGGAA-CAAATCTACCTTGATTCAATCCT
1 CATTTTCCTTCAGATTTGATCTTCCCTGAAGAGTAGT-GAAGCAAATCTACCTCGATTCAATCTT
* * * * * * * *
2312425 CTCTGAAGAGTAATGAAGTCAATCAAACTTTCCAGATTTAATCTACCCTGGAACA-CAGCGGAGC
65 CCCTGAAGAGTAGTGAAGTGAATCAAACTTTCAAGATCTGATCTACCCT-GAAGAGCAGCAGAGC
*
2312489 ATATCC
129 AGAT-C
* * *
2312495 CATTTTCCTTCAGATTTGATCTTCCCTGAAGAGAAATGGAA-CAAATCTACCTCAATTCAATCTT
1 CATTTTCCTTCAGATTTGATCTTCCCTGAAGAGTAGT-GAAGCAAATCTACCTCGATTCAATCTT
* *
2312559 CCCTGAAGAGTAGTGAAGTGAATCAAACTTTCAAGATCT-AGCCTACCCTGAAGAGCAG-GGAGC
65 CCCTGAAGAGTAGTGAAGTGAATCAAACTTTCAAGATCTGA-TCTACCCTGAAGAGCAGCAGAGC
2312622 AGAT-
129 AGATC
* * * * * *
2312626 CATTTT-TTTCATATTTGATCTTCTCT-ACAAAGTAGTGAAGCAAATCTACCTCAATTCAATCAT
1 CATTTTCCTTCAGATTTGATCTTCCCTGA-AGAGTAGTGAAGCAAATCTACCTCGATTCAATCTT
* * * ** * * ** *
2312689 CCTTGAA-AGGCAGTGAAGTGAATCAAAGTTTTTATATATGATCTATGCTGAAGA-CTAGTAGAG
65 CCCTGAAGA-GTAGTGAAGTGAATCAAACTTTCAAGATCTGATCTACCCTGAAGAGC-AGCAGAG
*
2312752 TAGATC
128 CAGATC
* *
2312758 C-TTTT--TTCCATATTTGATCTTCTCTGAAGAGTAGTGAAGCAAATCTACCTCGATTCAATCTT
1 CATTTTCCTT-CAGATTTGATCTTCCCTGAAGAGTAGTGAAGCAAATCTACCTCGATTCAATCTT
* * * * * *
2312820 CCCTAAAGAGAAGTGTAGTGAATCAAAGTTT-ATAGATCTGATATACCCTGAAGAGCAGCAGAAC
65 CCCTGAAGAGTAGTGAAGTGAATCAAACTTTCA-AGATCTGATCTACCCTGAAGAGCAGCAGAGC
*
2312884 ATATC
129 AGATC
* * * *
2312889 C-TTTTCTTTCTAGTTTTGATCTTCCCTAAAGAGTAGTGAAGCAAATCTACCTCGATTGAATCTT
1 CATTTTCCTTC-AGATTTGATCTTCCCTGAAGAGTAGTGAAGCAAATCTACCTCGATTCAATCTT
* *
2312953 CCCTAAAGAGTAGTGAAGCGAATC
65 CCCTGAAGAGTAGTGAAGTGAATC
2312977 TACCTCGATT
Statistics
Matches: 406, Mismatches: 59, Indels: 35
0.81 0.12 0.07
Matches are distributed among these distances:
129 6 0.01
130 88 0.22
131 122 0.30
132 5 0.01
133 84 0.21
134 101 0.25
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (133 bp):
CATTTTCCTTCAGATTTGATCTTCCCTGAAGAGTAGTGAAGCAAATCTACCTCGATTCAATCTTC
CCTGAAGAGTAGTGAAGTGAATCAAACTTTCAAGATCTGATCTACCCTGAAGAGCAGCAGAGCAG
ATC
Found at i:2313010 original size:41 final size:41
Alignment explanation
Indices: 2312907--2313002 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
2312897 TCTAGTTTTG
*
2312907 ATCTTCCCTAAAGAGTAGTGAAGCAAATCTACCTCGATTGA
1 ATCTTCCCTAAAGAGTAGTGAAGCAAATCTACCTCGATTCA
*
2312948 ATCTTCCCTAAAGAGTAGTGAAGCGAATCTACCTCGATTCA
1 ATCTTCCCTAAAGAGTAGTGAAGCAAATCTACCTCGATTCA
*
2312989 ATCTTCCCTCAAGA
1 ATCTTCCCTAAAGA
2313003 CCAGTGAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (41 bp):
ATCTTCCCTAAAGAGTAGTGAAGCAAATCTACCTCGATTCA
Found at i:2313278 original size:131 final size:130
Alignment explanation
Indices: 2312947--2313278 Score: 346
Period size: 131 Copynumber: 2.5 Consensus size: 130
2312937 ACCTCGATTG
* * * * * * * *
2312947 AATCTTCCCTAAAGAGTAGTGAAGCGAATCTACCTCGATTCAATCTTCCCTCAAGACCAGTGAAT
1 AATCTTCCCTGAAGAGTAGTGAAGCAAATCAACCCCAATTCAATCTTCCCTGAAGAGCAGT-AAA
* * * *
2313012 TGAATCAATGTTTCCAGAGTTGGCCTACCCTGAAGAGTAGCAGAGCAAATCCATTTTTCCATATT
65 TGAATCAAAGTTTCCAGAGTTGACCTACCCTGAAGAGCAGCAGAGCAAATCCATTTTTCCAAATT
2313077 T
130 T
* * * *
2313078 GATCTTCTCTGAAGAGCAGTGAAACAAAT-ATA-CCCATATTCAATCTTCCCTGAAGAGCAGTGA
1 AATCTTCCCTGAAGAGTAGTGAAGCAAATCA-ACCCCA-ATTCAATCTTCCCTGAAGAGCAGT-A
* * * * * * *
2313141 AATGAATCAAAGTTTCCAGATTTGATCTACCCTAGAA-CGCAGTAGAGCATATCCGTTTTTTCAA
63 AATGAATCAAAGTTTCCAGAGTTGACCTACCCT-GAAGAGCAGCAGAGCAAATCCATTTTTCCAA
2313205 ATTT
127 ATTT
** * *
2313209 AATCTTCCCTGAAGAGTAACGAAGCAAATCAACCCCAATTCAATCTTCCCTGAATAGTAGTAAAG
1 AATCTTCCCTGAAGAGTAGTGAAGCAAATCAACCCCAATTCAATCTTCCCTGAAGAGCAGTAAA-
2313274 TGAAT
65 TGAAT
2313279 TGAACTTTTA
Statistics
Matches: 164, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
130 5 0.03
131 151 0.92
132 8 0.05
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (130 bp):
AATCTTCCCTGAAGAGTAGTGAAGCAAATCAACCCCAATTCAATCTTCCCTGAAGAGCAGTAAAT
GAATCAAAGTTTCCAGAGTTGACCTACCCTGAAGAGCAGCAGAGCAAATCCATTTTTCCAAATTT
Found at i:2313368 original size:130 final size:131
Alignment explanation
Indices: 2312948--2313387 Score: 331
Period size: 131 Copynumber: 3.4 Consensus size: 131
2312938 CCTCGATTGA
* ** * * * * * *
2312948 ATCTTCCCTAAAGAGTAGTGAAGCGAATCTACCTCGATTCAATCTTCCCTCAAGACCAGTGAATT
1 ATCTTCCCTGAAGAGTAGTGAAGAAAATCAACCCCAATTCAATCTTCCCTGAAGAGCAGTGAAAT
** * *** * *
2313013 GAATCAATGTTTCCAGAGT-TGGCCTACCCT-GAA-G-AGTAGCAGAGCAAATCCATTTTTCCAT
66 GAATCAAACTTTCCA-AATATGATATACCCTAGAACGCAGTAG-A-A-CAGATCCATTTTTACAT
2313074 ATTTG
127 ATTTG
* *
2313079 ATCTTCTCTGAAGAGCAGTGAA-ACAAAT-ATA-CCCATATTCAATCTTCCCTGAAGAGCAGTGA
1 ATCTTCCCTGAAGAGTAGTGAAGA-AAATCA-ACCCCA-ATTCAATCTTCCCTGAAGAGCAGTGA
* * * * * * * * *
2313141 AATGAATCAAAGTTTCCAGATTTGATCTACCCTAGAACGCAGTAGAGCATATCCGTTTTTTCAAA
63 AATGAATCAAACTTTCCAAATATGATATACCCTAGAACGCAGTAGAACAGATCCATTTTTACATA
*
2313206 TTTA
128 TTTG
** * * *
2313210 ATCTTCCCTGAAGAGTAACGAAGCAAATCAACCCCAATTCAATCTTCCCTGAATAGTAGT-AAAG
1 ATCTTCCCTGAAGAGTAGTGAAGAAAATCAACCCCAATTCAATCTTCCCTGAAGAGCAGTGAAA-
** * * * * * * *
2313274 TGAATTGAACTTT-TAAATATGATATATCTTGGAACGCAGTGGAATAGATCCCTTTTTACATATT
65 TGAATCAAACTTTCCAAATATGATATACCCTAGAACGCAGTAGAACAGATCCATTTTTACATATT
2313338 TG
130 TG
* * *
2313340 ATCTTCCCTGAAGAATAGTGAAGAAAATCAACCCCGATTCAATATTCC
1 ATCTTCCCTGAAGAGTAGTGAAGAAAATCAACCCCAATTCAATCTTCC
2313388 TTAGAAAATA
Statistics
Matches: 245, Mismatches: 53, Indels: 23
0.76 0.17 0.07
Matches are distributed among these distances:
130 86 0.35
131 144 0.59
132 8 0.03
133 2 0.01
134 5 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (131 bp):
ATCTTCCCTGAAGAGTAGTGAAGAAAATCAACCCCAATTCAATCTTCCCTGAAGAGCAGTGAAAT
GAATCAAACTTTCCAAATATGATATACCCTAGAACGCAGTAGAACAGATCCATTTTTACATATTT
G
Found at i:2315346 original size:3 final size:3
Alignment explanation
Indices: 2315338--2315380 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
2315328 TTAATCCGAG
*
2315338 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2315381 ATATTATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2315884 original size:21 final size:21
Alignment explanation
Indices: 2315809--2315903 Score: 63
Period size: 21 Copynumber: 4.4 Consensus size: 21
2315799 GGTTAAGACC
* *
2315809 TTTCGATGATAGGACTTAATC-
1 TTTC-ATGAAAGGATTTAATCT
* *
2315830 TTTCAATTAAAGGACTT-ATCCT
1 TTTC-ATGAAAGGATTTAAT-CT
*
2315852 TTTTATGAAAAGTG-TTTAA-CAT
1 TTTCATG-AAAG-GATTTAATC-T
2315874 TTTCATGAAAGGATTTAATCT
1 TTTCATGAAAGGATTTAATCT
2315895 TTTCATGAA
1 TTTCATGAA
2315904 GAGAATTGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
20 3 0.05
21 37 0.63
22 17 0.29
23 2 0.03
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (21 bp):
TTTCATGAAAGGATTTAATCT
Found at i:2319369 original size:21 final size:21
Alignment explanation
Indices: 2319288--2319382 Score: 61
Period size: 21 Copynumber: 4.4 Consensus size: 21
2319278 GGTTAAGACC
2319288 TTTCGATGAAAGGATTTAA--T
1 TTTC-ATGAAAGGATTTAACCT
* * *
2319308 ATTTCAATTAAAGGACTTATCCT
1 -TTTC-ATGAAAGGATTTAACCT
* *
2319331 TCTGATGAAAAGTG-TTTAACCT
1 TTTCATG-AAAG-GATTTAACCT
**
2319353 TTTCATGAAAGGATTTAATTT
1 TTTCATGAAAGGATTTAACCT
2319374 TTTCATGAA
1 TTTCATGAA
2319383 GAGAATTGTT
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
20 1 0.02
21 36 0.64
22 17 0.30
23 2 0.04
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.41
Consensus pattern (21 bp):
TTTCATGAAAGGATTTAACCT
Found at i:2319489 original size:21 final size:21
Alignment explanation
Indices: 2319413--2319502 Score: 60
Period size: 21 Copynumber: 4.2 Consensus size: 21
2319403 GATTGAATGG
2319413 ATGAAAGGATTTAA--TATTTC
1 ATGAAAGGATTTAACCT-TTTC
* * * * *
2319433 AATTAAAGGACTTATCCTTCTG
1 -ATGAAAGGATTTAACCTTTTC
2319455 ATGAAAAGTG-TTTAACCTTTTC
1 ATG-AAAG-GATTTAACCTTTTC
**
2319477 ATGAAAGGATTTAATTTTTTC
1 ATGAAAGGATTTAACCTTTTC
2319498 ATGAA
1 ATGAA
2319503 GAGAATTGTT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
20 1 0.02
21 32 0.62
22 17 0.33
23 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (21 bp):
ATGAAAGGATTTAACCTTTTC
Found at i:2319505 original size:120 final size:120
Alignment explanation
Indices: 2319292--2319534 Score: 486
Period size: 120 Copynumber: 2.0 Consensus size: 120
2319282 AAGACCTTTC
2319292 GATGAAAGGATTTAATATTTCAATTAAAGGACTTATCCTTCTGATGAAAAGTGTTTAACCTTTTC
1 GATGAAAGGATTTAATATTTCAATTAAAGGACTTATCCTTCTGATGAAAAGTGTTTAACCTTTTC
2319357 ATGAAAGGATTTAATTTTTTCATGAAGAGAATTGTTGAATAAGTATGATTGAATG
66 ATGAAAGGATTTAATTTTTTCATGAAGAGAATTGTTGAATAAGTATGATTGAATG
2319412 GATGAAAGGATTTAATATTTCAATTAAAGGACTTATCCTTCTGATGAAAAGTGTTTAACCTTTTC
1 GATGAAAGGATTTAATATTTCAATTAAAGGACTTATCCTTCTGATGAAAAGTGTTTAACCTTTTC
2319477 ATGAAAGGATTTAATTTTTTCATGAAGAGAATTGTTGAATAAGTATGATTGAATG
66 ATGAAAGGATTTAATTTTTTCATGAAGAGAATTGTTGAATAAGTATGATTGAATG
2319532 GAT
1 GAT
2319535 CCAACTTTAA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 123 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (120 bp):
GATGAAAGGATTTAATATTTCAATTAAAGGACTTATCCTTCTGATGAAAAGTGTTTAACCTTTTC
ATGAAAGGATTTAATTTTTTCATGAAGAGAATTGTTGAATAAGTATGATTGAATG
Found at i:2331249 original size:76 final size:77
Alignment explanation
Indices: 2331132--2331330 Score: 280
Period size: 76 Copynumber: 2.6 Consensus size: 77
2331122 CTGTTGTACA
* * *
2331132 AGGGGGGAATCGGTACCCCCT-TGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
**
2331195 -CAAAACTGTTT
66 CCAAAACCATTT
* *
2331206 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
2331271 CCAAAACCATTT
66 CCAAAACCATTT
* *
2331283 A-GGGGGAATCGGTTCCTCCGATGGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
2331331 ATCTGTAATT
Statistics
Matches: 112, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
74 19 0.17
75 7 0.06
76 52 0.46
77 34 0.30
ACGTcount: A:0.20, C:0.24, G:0.34, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
CCAAAACCATTT
Found at i:2331695 original size:30 final size:30
Alignment explanation
Indices: 2331649--2331720 Score: 126
Period size: 30 Copynumber: 2.3 Consensus size: 30
2331639 TCCCCCTTAC
2331649 TTTAACACTTCTTCAATTTATTATGTAAAACA
1 TTTAACAC--CTTCAATTTATTATGTAAAACA
2331681 TTTAACACCTTCAATTTATTATGTAAAACA
1 TTTAACACCTTCAATTTATTATGTAAAACA
2331711 TTTAACACCT
1 TTTAACACCT
2331721 ATTCTTCTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 32 0.80
32 8 0.20
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.42
Consensus pattern (30 bp):
TTTAACACCTTCAATTTATTATGTAAAACA
Found at i:2333950 original size:21 final size:21
Alignment explanation
Indices: 2333924--2333963 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2333914 CAGAACCCCA
*
2333924 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2333945 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2333964 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2337854 original size:22 final size:21
Alignment explanation
Indices: 2337812--2337851 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2337802 GAGTTTGTTT
*
2337812 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2337833 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2337852 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2339859 original size:76 final size:76
Alignment explanation
Indices: 2339775--2339973 Score: 249
Period size: 76 Copynumber: 2.6 Consensus size: 76
2339765 GTTGTACAAG
* * *
2339775 GGGGGAATCGGTACCCCCTTGGGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-
1 GGGGGAATCGGTTCCCCCTT-GGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
**
2339839 CAAAACTGTTTA
65 CAAAACCATTTA
* * * *
2339851 GGGGGAATCGATTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 GGGGGAATCGGTTCCCCCT-TGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
2339915 CAAAACCATTTA
65 CAAAACCATTTA
** *
2339927 GGGGGAATCGGTTCCTCCGATGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCC-CCCTTGGGGGGGAATCGGTTCCCTCCGAGCA
2339974 ATCTGTAATT
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
75 38 0.36
76 41 0.39
77 26 0.25
ACGTcount: A:0.20, C:0.24, G:0.34, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCCCCTTGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
AAAACCATTTA
Found at i:2339876 original size:75 final size:76
Alignment explanation
Indices: 2339797--2339973 Score: 257
Period size: 75 Copynumber: 2.3 Consensus size: 76
2339787 ACCCCCTTGG
* **
2339797 GGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-CAAAACTGTTTAGGGGGAATCG
1 GGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTAGGGGGAATCG
*
2339861 ATTCCTCCTAT
66 ATTCCTCCGAT
* * *
2339872 GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCCAAAACCATTTAGGGGGAATCG
1 GGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTAGGGGGAATCG
*
2339937 GTTCCTCCGAT
66 ATTCCTCCGAT
*
2339948 GGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGGG-ATCGGTTCCCTCCGAGCA
2339974 ATCTGTAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 38 0.42
76 35 0.39
77 17 0.19
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (76 bp):
GGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCCAAAACCATTTAGGGGGAATCG
ATTCCTCCGAT
Found at i:2340667 original size:71 final size:71
Alignment explanation
Indices: 2340543--2340686 Score: 252
Period size: 71 Copynumber: 2.0 Consensus size: 71
2340533 GAGGCCTTAA
* *
2340543 CACTCTTTAGAAGAAAGGGTGAGTTAGTCAGGGGTATGGTTTCTGATATAGAGACTTCTAGGGGT
1 CACTCTTTAGAAGAAAGGGTGAGTTAGTCAGGGGTATGGTTTCCGATACAGAGACTTCTAGGGGT
2340608 AATATC
66 AATATC
* *
2340614 CACTCTTTAGAAGAAAGGGTGAGTTAGTCAGGGGTATGGTTTCCGATGCAGAGACTTCTAGGTGT
1 CACTCTTTAGAAGAAAGGGTGAGTTAGTCAGGGGTATGGTTTCCGATACAGAGACTTCTAGGGGT
2340679 AATATC
66 AATATC
2340685 CA
1 CA
2340687 GGGAAAACTA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (71 bp):
CACTCTTTAGAAGAAAGGGTGAGTTAGTCAGGGGTATGGTTTCCGATACAGAGACTTCTAGGGGT
AATATC
Found at i:2341517 original size:47 final size:48
Alignment explanation
Indices: 2341466--2341558 Score: 109
Period size: 47 Copynumber: 1.9 Consensus size: 48
2341456 AAGTGTCACG
**
2341466 TAGAATATG-CACCGAAGTGCCACATAG-ATTTGTCCCGAAAGACCGCA
1 TAGAATATGTC-CCGAAGAACCACATAGAATTTGTCCCGAAAGACCGCA
* * *
2341513 TAGAATTTGTCCCGAAGAACCACGTAGAAATTTGTCCCGAATGACC
1 TAGAATATGTCCCGAAGAACCACATAG-AATTTGTCCCGAAAGACC
2341559 ACGTAGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
47 21 0.55
48 1 0.03
49 16 0.42
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (48 bp):
TAGAATATGTCCCGAAGAACCACATAGAATTTGTCCCGAAAGACCGCA
Found at i:2341550 original size:25 final size:25
Alignment explanation
Indices: 2341493--2341570 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
2341483 TGCCACATAG
* *
2341493 ATTTGTCCCGAA-AGACCGCATAG-A
1 ATTTGTCCCGAAGA-ACCACGTAGAA
2341517 ATTTGTCCCGAAGAACCACGTAGAA
1 ATTTGTCCCGAAGAACCACGTAGAA
2341542 ATTTGTCCCGAATG-ACCACGTAGAA
1 ATTTGTCCCGAA-GAACCACGTAGAA
2341567 ATTT
1 ATTT
2341571 TAAATTTGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
24 19 0.39
25 29 0.59
26 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (25 bp):
ATTTGTCCCGAAGAACCACGTAGAA
Found at i:2342306 original size:21 final size:20
Alignment explanation
Indices: 2342264--2342313 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
2342254 CTTACCCTTG
2342264 GTATCGATACCTTCACATCA
1 GTATCGATACCTTCACATCA
2342284 GTATCGATACTACTTCA-ATCA
1 GTATCGATAC--CTTCACATCA
2342305 GTATCGATA
1 GTATCGATA
2342314 TTGTTCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.36
21 13 0.46
22 5 0.18
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (20 bp):
GTATCGATACCTTCACATCA
Found at i:2342861 original size:3 final size:3
Alignment explanation
Indices: 2342848--2342882 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2342838 GAGTCACGGT
2342848 AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2342883 GAGGATAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2347230 original size:25 final size:28
Alignment explanation
Indices: 2347193--2347265 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
2347183 ACAACTCCGA
* *
2347193 ATTAACTTGAGAT-TAAAT-AAT-GAAG
1 ATTAAATTAAGATATAAATCAATAGAAG
*
2347218 ATTAAATTAAGATATAAATCAATAACGAAT
1 ATTAAATTAAGATATAAATCAAT-A-GAAG
2347248 ATTAAATTAAGATATAAA
1 ATTAAATTAAGATATAAA
2347266 GACAATATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 11 0.28
26 5 0.12
27 3 0.08
30 21 0.52
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.32
Consensus pattern (28 bp):
ATTAAATTAAGATATAAATCAATAGAAG
Found at i:2347242 original size:30 final size:30
Alignment explanation
Indices: 2347208--2347265 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
2347198 CTTGAGATTA
*
2347208 AATAATGAAGATTAAATTAAGATATAAATC
1 AATAACGAAGATTAAATTAAGATATAAATC
*
2347238 AATAACGAATATTAAATTAAGATATAAA
1 AATAACGAAGATTAAATTAAGATATAAA
2347266 GACAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (30 bp):
AATAACGAAGATTAAATTAAGATATAAATC
Found at i:2350549 original size:21 final size:22
Alignment explanation
Indices: 2350523--2350569 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2350513 TAAAATTTTC
2350523 TAAAATTCGAA-TTTTCTTCAT
1 TAAAATTCGAAGTTTTCTTCAT
* *
2350544 TAAAATTTGAAGTTTTTTTTCAT
1 TAAAATTCGAAG-TTTTCTTCAT
2350567 TAA
1 TAA
2350570 TACACGTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
23 12 0.55
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (22 bp):
TAAAATTCGAAGTTTTCTTCAT
Found at i:2352771 original size:60 final size:59
Alignment explanation
Indices: 2352657--2352771 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 59
2352647 ATTTGACACG
* * * * *
2352657 ATGCCTTCAAGTTCCAGGGGAGGCATTCAACTGCGAGCTTCTTCGACCTTAATGTCAAA
1 ATGCCTTCAAGTTCAAGGGGAGGCATTCAACTACCAACTTCTTCGACCTAAATGTCAAA
* * *
2352716 ATGCCTTCAAGTTCAAGGGGAAGGCATTCAAGTACCAACTTGTTTGACCTAAATGT
1 ATGCCTTCAAGTTCAAGGGG-AGGCATTCAACTACCAACTTCTTCGACCTAAATGT
2352772 TGGCATTGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 19 0.40
60 28 0.60
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (59 bp):
ATGCCTTCAAGTTCAAGGGGAGGCATTCAACTACCAACTTCTTCGACCTAAATGTCAAA
Found at i:2363899 original size:19 final size:20
Alignment explanation
Indices: 2363848--2363898 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
2363838 GATCTAAATC
2363848 ATTTTTCAAAAATTCATTTT
1 ATTTTTCAAAAATTCATTTT
2363868 ATTTTTCAAAAATTCATTTT
1 ATTTTTCAAAAATTCATTTT
2363888 ATTTTTCAAAA
1 ATTTTTCAAAA
2363899 TCAACTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTTCAAAAATTCATTTT
Found at i:2363907 original size:20 final size:19
Alignment explanation
Indices: 2363848--2363921 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 19
2363838 GATCTAAATC
2363848 ATTTTTCAAAAATTC-ATTTT
1 ATTTTTC-AAAA-TCAATTTT
2363868 ATTTTTCAAAAATTC-ATTTT
1 ATTTTTC-AAAA-TCAATTTT
2363888 ATTTTTCAAAATCAACTTTT
1 ATTTTTCAAAATCAA-TTTT
*
2363908 A-CTTTCAAAATCAA
1 ATTTTTCAAAATCAA
2363922 ATCATTTCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
18 2 0.04
19 17 0.33
20 32 0.63
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTTCAAAATCAATTTT
Found at i:2364699 original size:23 final size:22
Alignment explanation
Indices: 2364660--2364709 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
2364650 CAACTCGTAT
*
2364660 AAATGCATCGAAATGCCACATA
1 AAATGCATCCAAATGCCACATA
*
2364682 GAAATGCA-CCAAAGTGCCATATA
1 -AAATGCATCCAAA-TGCCACATA
2364705 AAATG
1 AAATG
2364710 TCCACAAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (22 bp):
AAATGCATCCAAATGCCACATA
Found at i:2365378 original size:19 final size:19
Alignment explanation
Indices: 2365354--2365401 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
2365344 CCTTATAATG
*
2365354 GTATCGATACTATACCCGA
1 GTATCGATACTATACCCAA
2365373 GTATCGATACTATACCCAA
1 GTATCGATACTATACCCAA
2365392 GTATCGATAC
1 GTATCGATAC
2365402 CCAATTTCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (19 bp):
GTATCGATACTATACCCAA
Found at i:2371680 original size:23 final size:23
Alignment explanation
Indices: 2371649--2371717 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2371639 CACCATAACT
*
2371649 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
2371672 CGTAGAAATACACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
2371695 CATAGAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2371718 TATAAAATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2371740 original size:22 final size:22
Alignment explanation
Indices: 2371715--2371765 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2371705 CATCGAAGTG
*
2371715 CCATATAAAATGTCCA-TAAGAA
1 CCATATAAAATCT-CATTAAGAA
*
2371737 CCATATAGAATCTCATTAAGAA
1 CCATATAAAATCTCATTAAGAA
2371759 CCATATA
1 CCATATA
2371766 CATATTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (22 bp):
CCATATAAAATCTCATTAAGAA
Found at i:2371818 original size:21 final size:19
Alignment explanation
Indices: 2371763--2371821 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 19
2371753 TAAGAACCAT
*
2371763 ATACATATTCCAAAGGACC
1 ATACATGTTCCAAAGGACC
* *
2371782 AAATATGTGTCTCAAAGGACCC
1 ATACATGT-TC-CAAAGGA-CC
2371804 GATACATGTTCCAAAGGA
1 -ATACATGTTCCAAAGGA
2371822 TTATATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 5 0.16
20 2 0.06
21 14 0.45
22 4 0.13
23 6 0.19
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (19 bp):
ATACATGTTCCAAAGGACC
Found at i:2376338 original size:20 final size:20
Alignment explanation
Indices: 2376287--2376340 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
2376277 TTTGGGCTGG
2376287 GAGTATCGATACTTGTTCAT
1 GAGTATCGATACTTGTTCAT
* * *
2376307 GTGGCATTGATA-TTGTTCAAT
1 G-AGTATCGATACTTGTTC-AT
2376328 GAGTATCGATACT
1 GAGTATCGATACT
2376341 CTAGGCGTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (20 bp):
GAGTATCGATACTTGTTCAT
Found at i:2377381 original size:2 final size:2
Alignment explanation
Indices: 2377374--2377416 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2377364 TCAATACTCA
2377374 AT AT 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 AT AT
2377416 A
1 A
2377417 CCTTCTATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2377510 original size:13 final size:13
Alignment explanation
Indices: 2377492--2377516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2377482 CAAGTATATA
2377492 TATATATTATTAT
1 TATATATTATTAT
2377505 TATATATTATTA
1 TATATATTATTA
2377517 AGAATTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATATTATTAT
Found at i:2380248 original size:18 final size:18
Alignment explanation
Indices: 2380224--2380271 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2380214 TGTAGTCATT
2380224 CGGGACATAGTGGTCCAC
1 CGGGACATAGTGGTCCAC
*
2380242 TGGGACATAGTGGTCCAC
1 CGGGACATAGTGGTCCAC
2380260 CGGGACATAGTG
1 CGGGACATAGTG
2380272 ATCTTTCGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.35, T:0.19
Consensus pattern (18 bp):
CGGGACATAGTGGTCCAC
Found at i:2383621 original size:30 final size:30
Alignment explanation
Indices: 2383580--2383669 Score: 146
Period size: 30 Copynumber: 3.0 Consensus size: 30
2383570 CAATTTAAGG
*
2383580 CAAAATGGTTTTTGGACTTGAATTAAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
2383611 CAATATGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2383641 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2383670 TTCAAAGTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 11 0.20
30 40 0.71
31 5 0.09
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:2383806 original size:36 final size:36
Alignment explanation
Indices: 2383766--2383837 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
2383756 ATTACCCAGG
* * *
2383766 GGGTATAGATTCCCCCCTAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
2383802 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
2383838 TCTGCAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.33, G:0.28, T:0.15
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:2383807 original size:15 final size:15
Alignment explanation
Indices: 2383787--2383816 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2383777 CCCCCCTAGG
2383787 GGGTACAGATACCCC
1 GGGTACAGATACCCC
2383802 GGGTACAGATACCCC
1 GGGTACAGATACCCC
2383817 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:2383826 original size:21 final size:21
Alignment explanation
Indices: 2383760--2383837 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 21
2383750 TTCAAGATTA
* *
2383760 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
*
2383781 CCTAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
2383799 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
2383817 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
2383838 TCTGCAGGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 11 0.23
18 7 0.15
21 29 0.62
ACGTcount: A:0.23, C:0.35, G:0.28, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:2383955 original size:21 final size:21
Alignment explanation
Indices: 2383929--2383970 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2383919 ATTTGAATAT
*
2383929 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2383950 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2383971 GCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2384038 original size:20 final size:22
Alignment explanation
Indices: 2384000--2384039 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2383990 TTTAGTATAA
2384000 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
2384022 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
2384040 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:2384297 original size:34 final size:32
Alignment explanation
Indices: 2384252--2384323 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 32
2384242 CCTTTTGTAA
*
2384252 AGGGAAAAGGTTCTAGCTTAGCCCGTGTAAAATCT
1 AGGG-AAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
2384287 AGGGAAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
2384319 AGGGA
1 AGGGA
2384324 GTTTGTAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 11 0.31
33 1 0.03
34 19 0.54
35 4 0.11
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.22
Consensus pattern (32 bp):
AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:2385207 original size:19 final size:20
Alignment explanation
Indices: 2385183--2385230 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2385173 AATGATTTTC
*
2385183 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
2385202 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
2385222 TTTTGAAAA
1 TTTTGAAAA
2385231 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:2386511 original size:30 final size:30
Alignment explanation
Indices: 2386470--2386559 Score: 146
Period size: 30 Copynumber: 3.0 Consensus size: 30
2386460 CAATTTAAGG
*
2386470 CAAAATGGTTTTTGGACTTGAATTAAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
2386501 CAATATGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2386531 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
2386560 TTCAAAGTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 11 0.20
30 40 0.71
31 5 0.09
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:2386679 original size:21 final size:21
Alignment explanation
Indices: 2386650--2386692 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2386640 TTCAAGATTA
* *
2386650 CCCAAGGGGTATAGATTCCCC
1 CCCAAGGGGTACAGATACCCC
*
2386671 CCCAGGGGGTACAGATACCCC
1 CCCAAGGGGTACAGATACCCC
2386692 C
1 C
2386693 TGTAGGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.37, G:0.26, T:0.14
Consensus pattern (21 bp):
CCCAAGGGGTACAGATACCCC
Found at i:2386766 original size:20 final size:21
Alignment explanation
Indices: 2386726--2386768 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2386716 AACAGAATGT
2386726 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
2386747 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
2386768 C
1 C
2386769 TGTTCAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:2386830 original size:21 final size:21
Alignment explanation
Indices: 2386804--2386845 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2386794 ATTTGAATAT
*
2386804 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2386825 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2386846 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2386906 original size:21 final size:21
Alignment explanation
Indices: 2386875--2386914 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2386865 TTTAGTATAA
*
2386875 AAAATCATCCCTTAACGGCTCC
1 AAAATCATCCC-CAACGGCTCC
2386897 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2386915 ATATTCGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.35, C:0.38, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2387170 original size:34 final size:32
Alignment explanation
Indices: 2387127--2387197 Score: 106
Period size: 34 Copynumber: 2.2 Consensus size: 32
2387117 CCTTTTGTAA
*
2387127 AGGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCT
1 AGGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
2387161 AGGGAAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
2387193 AGGGA
1 AGGGA
2387198 GTTTGTAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 11 0.31
33 1 0.03
34 23 0.66
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.21
Consensus pattern (32 bp):
AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:2390335 original size:20 final size:20
Alignment explanation
Indices: 2390310--2390359 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2390300 ATTCATGAGG
2390310 TATCGATACCTGAAGAACAA
1 TATCGATACCTGAAGAACAA
* * *
2390330 TATCGATACCTTAAGGACGA
1 TATCGATACCTGAAGAACAA
2390350 TATCGATACC
1 TATCGATACC
2390360 ATATTTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
TATCGATACCTGAAGAACAA
Done.