Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008072.1 Hibiscus syriacus cultivar Beakdansim tig00110570_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: 1263316
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 5 of 5
Found at i:1219825 original size:29 final size:29
Alignment explanation
Indices: 1219775--1219848 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
1219765 AAGACAATTT
* *
1219775 CTTTTGGA-AAAAATCTTTGAGTTTGTTC
1 CTTTTGAATAAAAATCTTGGAGTTTGTTC
1219803 CTTTTGAATAAAAATCTTGGAGTTTGTTC
1 CTTTTGAATAAAAATCTTGGAGTTTGTTC
*
1219832 CTTTGGAATAAAAATCT
1 CTTTTGAATAAAAATCT
1219849 GTGAGTTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 7 0.17
29 35 0.83
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (29 bp):
CTTTTGAATAAAAATCTTGGAGTTTGTTC
Found at i:1219950 original size:30 final size:29
Alignment explanation
Indices: 1219909--1220178 Score: 137
Period size: 30 Copynumber: 8.3 Consensus size: 29
1219899 GACAATTTTG
1219909 TGAAA-AAAAATCTTTGAGATTGTTTCCTT
1 TGAAACAAAAATCTTTGAGATTGTTT-CTT
*
1219938 TGAAACAAAAATCTTTGAGTTTGTTTCTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTT
* * **
1219967 TGGAAACAAAATTTTGTCTCTTTTAAGATAATTTCTTT
1 T-GAAACAAAA------ATC-TTTGAGATTGTTTC-TT
*
1220005 TGAAACAAAAATCTTTGAGTTTGTTTCTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTT
* * **
1220034 TGGAAACAAAATTTTGTCTCTTTTAAGATAATTTCTTT
1 T-GAAACAAAA------ATC-TTTGAGATTGTTTC-TT
*
1220072 TGAAACAAAAATCTTTGAGTTTGTTTCTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTT
* * *
1220101 TGGAAACAAAATTTTGTCTCTCTAAAGATAGTTTCTTT
1 T-GAAACAAAA----ATCT-T-T-GAGATTGTTTC-TT
*
1220139 TGAAACAAAAATCTTTGAGTTTGTTTCTT
1 TGAAACAAAAATCTTTGAGATTGTTTCTT
1220168 TGGAAACAAAA
1 T-GAAACAAAA
1220179 TTTTGTCTCT
Statistics
Matches: 183, Mismatches: 29, Indels: 57
0.68 0.11 0.21
Matches are distributed among these distances:
29 18 0.10
30 83 0.45
31 5 0.03
32 1 0.01
33 3 0.02
34 3 0.02
35 1 0.01
36 5 0.03
37 55 0.30
38 9 0.05
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (29 bp):
TGAAACAAAAATCTTTGAGATTGTTTCTT
Found at i:1219976 original size:94 final size:97
Alignment explanation
Indices: 1219857--1220044 Score: 251
Period size: 94 Copynumber: 2.0 Consensus size: 97
1219847 CTGTGAGTTG
* *
1219857 TTTGAGTCTATTTACTTTGAAACAAAGTTTTGTCTCTCTTGAGACAA-TT-TTGTGAAA-AAAAA
1 TTTGAGTCTATTTACTTTGAAACAAAATTTTGTCTCTCTTAAGACAATTTCTTGTGAAACAAAAA
1219919 TCTTTGAGATTGTTTCCTTT-GAAACAAAAATC
66 TCTTTGAGATTGTTT-CTTTGGAAACAAAAATC
* * * * *
1219951 TTTGAGTTTGTTT-CTTTGGAAACAAAATTTTGTCTCTTTTAAGATAATTTCTTTTGAAACAAAA
1 TTTGAGTCTATTTACTTT-GAAACAAAATTTTGTCTCTCTTAAGACAATTTCTTGTGAAACAAAA
*
1220015 ATCTTTGAGTTTGTTTCTTTGGAAACAAAA
65 ATCTTTGAGATTGTTTCTTTGGAAACAAAA
1220045 TTTTGTCTCT
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
93 4 0.05
94 36 0.44
95 2 0.02
96 11 0.14
97 28 0.35
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (97 bp):
TTTGAGTCTATTTACTTTGAAACAAAATTTTGTCTCTCTTAAGACAATTTCTTGTGAAACAAAAA
TCTTTGAGATTGTTTCTTTGGAAACAAAAATC
Found at i:1220044 original size:67 final size:67
Alignment explanation
Indices: 1219931--1220289 Score: 630
Period size: 67 Copynumber: 5.4 Consensus size: 67
1219921 TTTGAGATTG
* *
1219931 TTTCCTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1219996 AA
66 AA
*
1219998 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1220063 AA
66 AA
*
1220065 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTAAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
*
1220130 AG
66 AA
1220132 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1220197 AA
66 AA
* * * *
1220199 ATTCTTTTGAAACGAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAAAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1220264 AA
66 AA
1220266 TTTCTTTTGAAA-AAAAATCTTTGA
1 TTTCTTTTGAAACAAAAATCTTTGA
1220290 ACATGTTTCT
Statistics
Matches: 280, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
66 11 0.04
67 269 0.96
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:1220598 original size:63 final size:63
Alignment explanation
Indices: 1220520--1220643 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 63
1220510 GATGTGATTC
* * *
1220520 ATCTTTGAGTATGTTT-TTTTGAAACAAAATTTTATCTATTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCT-CTAAAGACAACTTCTTTTGAAAAAA
* * **
1220583 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
1220644 TACCAACCTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
63 34 0.64
64 19 0.36
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (63 bp):
ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:1220834 original size:14 final size:15
Alignment explanation
Indices: 1220800--1220841 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1220790 TTTTGAGTCG
*
1220800 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
1220815 TTTCTCTTGAAACA-
1 TTTCTCTTGAAACAT
1220829 TTTCTCTT-AAACA
1 TTTCTCTTGAAACA
1220842 AGATCATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 5 0.19
14 8 0.31
15 13 0.50
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:1221164 original size:66 final size:65
Alignment explanation
Indices: 1221043--1221181 Score: 172
Period size: 66 Copynumber: 2.1 Consensus size: 65
1221033 ACAAAACAAA
* * ** *
1221043 CATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCATTTGAGACAATTTCCCATGAAACGC
1 CATCTTTGAGAACGTTTCCCTTAAAACAAATTTTGTCTCACTTGAGACAATTTCCCATGAAACGC
* * * *
1221108 CGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAA-TTCCCTTTAAAT
1 C-ATCTTTGAGAACGTTTCCCTT-AAAACAAATTTTGTCTCACTTGAGACAATTTCCCATGAAAC
1221172 GC
64 GC
1221174 CATCTTTG
1 CATCTTTG
1221182 GGTTGTTTCC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
65 8 0.13
66 32 0.51
67 23 0.37
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (65 bp):
CATCTTTGAGAACGTTTCCCTTAAAACAAATTTTGTCTCACTTGAGACAATTTCCCATGAAACGC
Found at i:1221390 original size:28 final size:28
Alignment explanation
Indices: 1221340--1221393 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1221330 TCAAAATCCA
* *
1221340 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
1221368 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
1221394 CATTATCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:1221650 original size:130 final size:129
Alignment explanation
Indices: 1221406--1221659 Score: 420
Period size: 130 Copynumber: 2.0 Consensus size: 129
1221396 TTATCCCTAG
*
1221406 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGATATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGATATCACCTTAAGATGGCCAGAACTCTTCA
* * * *
1221471 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCAGTGTCAACCCCAGACCAGATCTCCTCATCACGTAGGAACCATGTCAACCAT
*
1221535 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAACTCTTC
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGATATCACCTTAAGATGGCC-AGAACTCTTC
*
1221600 ATCACGTATGAGCAGTGTCAACCCTC-GACCAGATTTCCTCATCACGTAGGAACCATGTCA
65 ATCACGTATGAGCAGTGTCAACCC-CAGACCAGATCTCCTCATCACGTAGGAACCATGTCA
1221660 CCCTTAGACG
Statistics
Matches: 116, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
129 52 0.45
130 63 0.54
131 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.23
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGATATCACCTTAAGATGGCCAGAACTCTTCA
TCACGTATGAGCAGTGTCAACCCCAGACCAGATCTCCTCATCACGTAGGAACCATGTCAACCAT
Found at i:1221686 original size:43 final size:43
Alignment explanation
Indices: 1221419--1221686 Score: 133
Period size: 40 Copynumber: 6.2 Consensus size: 43
1221409 TAACCAGCCG
* * *
1221419 TCCTCATCACGTAGGAACCGTGATATCACCTTTAGATGGCCAGAAC
1 TCCTCATCACGTAGGAACC---ATGTCACCCTTAGATGACCAGAAC
* * * * * *
1221465 TCTTCATCACGTATGAGCCGTGTCATCCC---CA-GACCAGATC
1 TCCTCATCACGTAGGAACCATGTCA-CCCTTAGATGACCAGAAC
* * * * * *
1221505 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCATGTCACCCTTAGATGACCAGAAC
* * *
1221547 GTCCTCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAAGAAC
1 -TCCTCATCACGTAGGAACCATGTCA-C-CCTT-AGATGACC-AGAAC
* * * * **
1221595 TCTTCATCACGTATG-AGCAGTGTCAACCC-T---CGACCAGATT
1 TCCTCATCACGTAGGAACCA-TGTC-ACCCTTAGATGACCAGAAC
*
1221635 TCCTCATCACGTAGGAACCATGTCACCCTTAGACGACCAGAAC
1 TCCTCATCACGTAGGAACCATGTCACCCTTAGATGACCAGAAC
*
1221678 TCTTCATCA
1 TCCTCATCA
1221687 TGTATGAGCA
Statistics
Matches: 167, Mismatches: 37, Indels: 39
0.69 0.15 0.16
Matches are distributed among these distances:
39 6 0.04
40 51 0.31
41 7 0.04
42 2 0.01
43 48 0.29
44 2 0.01
45 4 0.02
46 26 0.16
47 19 0.11
48 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (43 bp):
TCCTCATCACGTAGGAACCATGTCACCCTTAGATGACCAGAAC
Found at i:1221862 original size:3 final size:3
Alignment explanation
Indices: 1221854--1221930 Score: 84
Period size: 3 Copynumber: 24.0 Consensus size: 3
1221844 CGGGTCTTTT
1221854 TTA TTA TTA TTTA TATA TATA TTTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA T-TA T-TA -TTA TTA -TTA TTA TTA TTA TTA TTA
*
1221901 TTA TTTA TTA TTA TTA -TA TTA TTA ATA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
1221931 CATTTTACAT
Statistics
Matches: 66, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
2 2 0.03
3 46 0.70
4 17 0.26
5 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1221881 original size:19 final size:18
Alignment explanation
Indices: 1221857--1221922 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 18
1221847 GTCTTTTTTA
1221857 TTATTATTTATATATATAT
1 TTATTATTTAT-TATATAT
1221876 TTATTATTTATTAT-TA-
1 TTATTATTTATTATATAT
*
1221892 TTATTA-TTATTATTTA-
1 TTATTATTTATTATATAT
1221908 TTATTATTATATTAT
1 TTATTATT-TATTAT
1221923 TAATATTACA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.16
16 14 0.32
17 3 0.07
18 9 0.20
19 11 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTATTTATTATATAT
Found at i:1221881 original size:22 final size:20
Alignment explanation
Indices: 1221853--1221924 Score: 94
Period size: 19 Copynumber: 3.5 Consensus size: 20
1221843 CCGGGTCTTT
1221853 TTTATTATTATTTATATATATA
1 TTTATTATTATTTAT-TAT-TA
1221875 TTTATTATT-TATTATTATTA
1 TTTATTATTAT-TTATTATTA
1221895 -TTATTATTATTTATTATTA
1 TTTATTATTATTTATTATTA
1221914 TTATATTATTA
1 TT-TATTATTA
1221925 ATATTACATT
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
19 17 0.37
20 4 0.09
21 12 0.26
22 13 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTATTATTTATTATTA
Found at i:1224897 original size:13 final size:13
Alignment explanation
Indices: 1224870--1224910 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1224860 TAATTTTTAA
*
1224870 ATTTTTAATAATTT
1 ATTTTT-ATATTTT
*
1224884 ATTTTTATTTTTT
1 ATTTTTATATTTT
1224897 ATTTTTATATTTT
1 ATTTTTATATTTT
1224910 A
1 A
1224911 AATTTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTTTTATATTTT
Found at i:1230144 original size:30 final size:30
Alignment explanation
Indices: 1230108--1230167 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1230098 TGCTTTGACT
1230108 GACCTAGAATAGGAGTTTTCACGACCTTTC
1 GACCTAGAATAGGAGTTTTCACGACCTTTC
1230138 GACCTAGAATAGGAGTTTTCACGACCTTTC
1 GACCTAGAATAGGAGTTTTCACGACCTTTC
1230168 TTGCACTCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (30 bp):
GACCTAGAATAGGAGTTTTCACGACCTTTC
Found at i:1233970 original size:2 final size:2
Alignment explanation
Indices: 1233963--1233987 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1233953 TAATGAACAA
1233963 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
1233988 CTTTAGAAGC
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:1240899 original size:20 final size:20
Alignment explanation
Indices: 1240876--1240927 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1240866 AACGCGATCC
1240876 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1240896 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1240916 CCAAAATCGCAA
1 CCAGAATCGCAA
1240928 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1240944 original size:21 final size:20
Alignment explanation
Indices: 1240918--1241015 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1240908 ATCAGTTTCC
1240918 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * **
1240939 AAAATCGCGATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
1240958 ACAAATTCGCATTGCGATTTTCA
1 A-AAA-TCGCAACGCGATTTT-G
* *
1240981 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
1241001 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1241016 ACACATAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
19 1 0.02
20 19 0.32
21 36 0.60
22 3 0.05
23 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:1241044 original size:20 final size:20
Alignment explanation
Indices: 1240982--1241175 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1240972 CGATTTTCAA
* ** *
1240982 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1241002 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1241022 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1241042 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1241062 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1241082 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1241102 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1241122 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1241142 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1241163 AAATCGCAACGCG
1 AAATCGCAACGCG
1241176 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1241066 original size:60 final size:60
Alignment explanation
Indices: 1240982--1241175 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1240972 CGATTTTCAA
* ** * *
1240982 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1241042 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1241102 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1241163 AAATCGCAACGCG
1 AAATCGCAACGCG
1241176 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1241595 original size:33 final size:33
Alignment explanation
Indices: 1241556--1241626 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1241546 TTCACTTAGA
*
1241556 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1241589 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1241622 TTTCA
1 TTTCA
1241627 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1241766 original size:14 final size:14
Alignment explanation
Indices: 1241747--1241801 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1241737 AGAATGACTG
1241747 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1241761 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
1241780 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1241794 TCGCAACG
1 TCGCAACG
1241802 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1241784 original size:33 final size:33
Alignment explanation
Indices: 1241747--1241817 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1241737 AGAATGACTG
**
1241747 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1241780 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1241813 TCGCA
1 TCGCA
1241818 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1241835 original size:19 final size:19
Alignment explanation
Indices: 1241813--1241910 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1241803 GAAACCAAAA
*
1241813 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1241832 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1241846 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1241865 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1241879 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1241898 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1241911 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1241854 original size:14 final size:14
Alignment explanation
Indices: 1241835--1241924 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1241825 TTTCATTTCG
1241835 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1241849 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1241868 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1241882 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1241899 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1241915 CGTTGCGATT
1 CGTTGCGATT
1241925 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1241860 original size:33 final size:33
Alignment explanation
Indices: 1241818--1241932 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1241808 CAAAATCGCA
1241818 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1241851 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1241884 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1241917 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1241933 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1243860 original size:185 final size:186
Alignment explanation
Indices: 1243631--1244010 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
1243621 TAGATTGCTT
1243631 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243696 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1243761 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1243816 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243881 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1243946 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1244002 AGTAAATTT
1 AGTAAATTT
1244011 ATCCATTCAA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1243945 original size:93 final size:93
Alignment explanation
Indices: 1243631--1244010 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
1243621 TAGATTGCTT
1243631 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243696 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1243724 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243788 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1243816 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243881 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1243909 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1243974 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1244002 AGTAAATTT
1 AGTAAATTT
1244011 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1244094 original size:19 final size:19
Alignment explanation
Indices: 1244054--1244182 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1244044 TAGTTTACTT
* *
1244054 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1244074 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1244093 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1244112 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1244126 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1244145 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1244159 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1244178 TCGCA
1 TCGCA
1244183 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1244133 original size:33 final size:32
Alignment explanation
Indices: 1244090--1244182 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1244080 CGCGAAACCA
**
1244090 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1244122 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1244155 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1244183 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1244180 original size:52 final size:52
Alignment explanation
Indices: 1244054--1244182 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1244044 TAGTTTACTT
**
1244054 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1244106 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1244159 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1244183 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1244200 original size:19 final size:19
Alignment explanation
Indices: 1244178--1244312 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1244168 GAAACCAAAA
*
1244178 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1244197 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1244213 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1244230 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1244246 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1244263 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1244282 TCTCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1244302 TCGTGTTGCGA
1 TCGCGTTGCGA
1244313 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 45 0.48
20 11 0.12
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1244219 original size:14 final size:14
Alignment explanation
Indices: 1244200--1244256 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1244190 TTTCATTTCG
1244200 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1244214 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1244231 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1244247 CGTTGCGATT
1 CGTTGCGATT
1244257 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1244225 original size:33 final size:33
Alignment explanation
Indices: 1244183--1244275 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1244173 CAAAATCGCA
*
1244183 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1244216 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1244249 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1244276 TTGGTTTCTC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1246172 original size:38 final size:38
Alignment explanation
Indices: 1246129--1246201 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1246119 AATTGATTGT
*
1246129 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
1246167 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1246202 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:1246188 original size:19 final size:19
Alignment explanation
Indices: 1246124--1246188 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
1246114 AGTTTAATTG
*
1246124 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
1246143 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
1246161 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
1246181 ATTGATTT
1 ATTGATTT
1246189 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:1246202 original size:14 final size:14
Alignment explanation
Indices: 1246183--1246218 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1246173 ATTGTTTAAT
1246183 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1246197 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1246211 TGATTTGT
1 TGATTTGT
1246219 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1246341 original size:19 final size:19
Alignment explanation
Indices: 1246325--1246426 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1246315 AAAAATGACT
1246325 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1246344 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1246363 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1246377 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1246396 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1246416 ATCGCAATGCG
1 ATCGCAATGCG
1246427 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1246479 original size:19 final size:19
Alignment explanation
Indices: 1246455--1246780 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
1246445 GATTATCTCG
1246455 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246474 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246493 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1246507 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246526 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1246545 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1246564 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246583 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1246602 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1246616 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246635 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1246654 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1246668 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1246687 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1246706 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1246720 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1246740 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1246754 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1246773 TTGCGATT
1 TTGCGATT
1246781 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1246495 original size:52 final size:52
Alignment explanation
Indices: 1246433--1246752 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
1246423 TGCGTTTATA
*
1246433 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1246485 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1246537 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1246594 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1246646 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1246698 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1246751 AT
1 AT
1246753 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1246530 original size:71 final size:72
Alignment explanation
Indices: 1246455--1246780 Score: 389
Period size: 71 Copynumber: 4.6 Consensus size: 72
1246445 GATTATCTCG
1246455 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
1246519 TTTCGCA
66 TTTCGCA
* *
1246526 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGATT
1246591 TTCATTTCGCA
62 TTCATTTCGCA
*
1246602 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
1246660 TTC-TCTCG--
62 TTCATTTCGCA
*
1246668 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
1246732 TTTCCGCA
66 TTT-CGCA
* *
1246740 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1246781 GTATTTTCCG
Statistics
Matches: 227, Mismatches: 11, Indels: 38
0.82 0.04 0.14
Matches are distributed among these distances:
66 12 0.05
67 25 0.11
68 14 0.06
69 13 0.06
70 3 0.01
71 109 0.48
72 12 0.05
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTTCA
TTTCGCA
Found at i:1246698 original size:161 final size:157
Alignment explanation
Indices: 1246433--1246752 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
1246423 TGCGTTTATA
1246433 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
1246498 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
1246563 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
1246594 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1246659 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
1246724 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
1246751 AT
1 AT
1246753 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:1246724 original size:33 final size:33
Alignment explanation
Indices: 1246474--1246780 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
1246464 TCATTTCGCA
*
1246474 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1246507 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
1246543 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
1246581 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1246616 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
1246652 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
1246687 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1246720 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
1246754 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
1246781 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1249102 original size:13 final size:13
Alignment explanation
Indices: 1249084--1249108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1249074 CTTCGGGGAC
1249084 TTTTTCTTCTTCT
1 TTTTTCTTCTTCT
1249097 TTTTTCTTCTTC
1 TTTTTCTTCTTC
1249109 AGGATTATAT
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCTTCTTCT
Found at i:1249317 original size:24 final size:24
Alignment explanation
Indices: 1249283--1249329 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1249273 CTGAAACATC
1249283 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1249307 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1249330 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1250028 original size:20 final size:20
Alignment explanation
Indices: 1250000--1250368 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1249990 AAATTTCAGT
* * * *
1250000 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1250020 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1250040 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1250060 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1250080 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1250100 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1250120 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1250140 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1250160 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1250180 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1250200 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1250220 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1250240 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1250260 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1250280 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1250300 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1250320 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1250340 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1250360 GTTGCGATT
1 GTTGCGATT
1250369 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1253843 original size:20 final size:21
Alignment explanation
Indices: 1253793--1253844 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1253783 ATTATATATC
1253793 AATATACTTTTAATGAAAAACA
1 AATATA-TTTTAATGAAAAACA
* *
1253815 TATATTATTTTAAT-AAAAATA
1 AATA-TATTTTAATGAAAAACA
1253836 AATATATTT
1 AATATATTT
1253845 GACAAAACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.19
21 9 0.35
22 10 0.38
23 2 0.08
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (21 bp):
AATATATTTTAATGAAAAACA
Found at i:1258230 original size:83 final size:83
Alignment explanation
Indices: 1258078--1258240 Score: 236
Period size: 83 Copynumber: 2.0 Consensus size: 83
1258068 CGTATATTTG
* * * *
1258078 TTTAATATTTTAAATTTAAAAGATATTGTTATCTGTTTAAATTTAGATATTAAAACATATCTGGT
1 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAACAGATCTAGA
*
1258143 TGGAGTAAATCTCTCAGA
66 TGGAGTAAAACTCTCAGA
* * * * *
1258161 TTTAATATTTTAAATTTAAAATATATTATTATCTTTTTAAATTTAGTTATTAAAAGAGATTTAGA
1 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAACAGATCTAGA
1258226 TGGAGTAAAACTCTC
66 TGGAGTAAAACTCTC
1258241 TCGAAATTCC
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (83 bp):
TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAACAGATCTAGA
TGGAGTAAAACTCTCAGA
Done.