Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001055.1 Hibiscus syriacus cultivar Beakdansim tig00002087_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: 87686
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2004 original size:2 final size:2
Alignment explanation
Indices: 1999--2023 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1989 TACATGTGTG
1999 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2024 GAATGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5862 original size:16 final size:16
Alignment explanation
Indices: 5843--5875 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5833 TACCTTATAA
5843 CCCTAATCCTTATTAT
1 CCCTAATCCTTATTAT
*
5859 CCCTAATCTTTATTAT
1 CCCTAATCCTTATTAT
5875 C
1 C
5876 TATTTATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.30, G:0.00, T:0.45
Consensus pattern (16 bp):
CCCTAATCCTTATTAT
Found at i:13271 original size:20 final size:20
Alignment explanation
Indices: 13248--13298 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
13238 GGTTAAAACT
** *
13248 GAGTTGACTTGATTCGGTTC
1 GAGTTGACTCAATTCGATTC
13268 GAGTTGACTCAATTCGATTC
1 GAGTTGACTCAATTCGATTC
*
13288 AAGTTGACTCA
1 GAGTTGACTCA
13299 GACCGGTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
GAGTTGACTCAATTCGATTC
Found at i:14992 original size:29 final size:30
Alignment explanation
Indices: 14959--15024 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
14949 AGTGAACCGA
* *
14959 CGGTTCAAACCGGTTTTGCC-GTTTTCAAC
1 CGGTTCAAACCGGATTTACCGGTTTTCAAC
** *
14988 CGGTTCACCCCGGATTTACCGGTTTTCAGC
1 CGGTTCAAACCGGATTTACCGGTTTTCAAC
15018 CGGTTCA
1 CGGTTCA
15025 TTGCCAGACC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.15, C:0.30, G:0.23, T:0.32
Consensus pattern (30 bp):
CGGTTCAAACCGGATTTACCGGTTTTCAAC
Found at i:17419 original size:20 final size:22
Alignment explanation
Indices: 17374--17431 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
17364 GCATGGGTAG
17374 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
17398 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
17418 TGCATCGATGCACT
1 TGCATCGATGCACT
17432 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:24738 original size:33 final size:33
Alignment explanation
Indices: 24691--24762 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
24681 GTCATAGTAC
*
24691 AGGAGTGCTGGTAGAGTAGATTCTCCGTCGGTT
1 AGGAATGCTGGTAGAGTAGATTCTCCGTCGGTT
24724 AGGAATGCTGGTAGAGTAGATTCTCCGTCGGTT
1 AGGAATGCTGGTAGAGTAGATTCTCCGTCGGTT
24757 AGGAAT
1 AGGAAT
24763 TCATCAAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.22, C:0.14, G:0.35, T:0.29
Consensus pattern (33 bp):
AGGAATGCTGGTAGAGTAGATTCTCCGTCGGTT
Found at i:27615 original size:45 final size:45
Alignment explanation
Indices: 27551--27643 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
27541 AACTATCAAA
**
27551 CCTAAAGATGATGGATTGAGAGGAGAGCGGGTAGGAACGCTCGTT
1 CCTAAAGATGATGGATTGAGAGGAGAGCAAGTAGGAACGCTCGTT
27596 CCTAAAGATGATGGATTGAGAGGAGAGCAAGTAGGAACGCTCGTT
1 CCTAAAGATGATGGATTGAGAGGAGAGCAAGTAGGAACGCTCGTT
27641 CCT
1 CCT
27644 CCTAAACATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.20
Consensus pattern (45 bp):
CCTAAAGATGATGGATTGAGAGGAGAGCAAGTAGGAACGCTCGTT
Found at i:27684 original size:16 final size:17
Alignment explanation
Indices: 27651--27693 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
27641 CCTCCTAAAC
27651 ATTTTAAATTTTTATAT
1 ATTTTAAATTTTTATAT
*
27668 ATTTTAGATTTTT-TAT
1 ATTTTAAATTTTTATAT
27684 ATTTTCAAAT
1 ATTTT-AAAT
27694 CCTTCGGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTTAAATTTTTATAT
Found at i:27802 original size:76 final size:76
Alignment explanation
Indices: 27676--28610 Score: 1690
Period size: 76 Copynumber: 12.3 Consensus size: 76
27666 ATATTTTAGA
* * *
27676 TTTTTTATATTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
27741 CCTTCGGGAGC
66 CCTTCGGGAGC
27752 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
27817 CCTTCGGGAGC
66 CCTTCGGGAGC
*
27828 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAGAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
*
27893 CCTTCGGAAGC
66 CCTTCGGGAGC
* *
27904 TTTTTGATATTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
27969 CCTTCGGGAGC
66 CCTTCGGGAGC
27980 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
28045 CCTTCGGGAGC
66 CCTTCGGGAGC
*
28056 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAGAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
*
28121 CCTTCGGAAGC
66 CCTTCGGGAGC
* *
28132 TTTTTGATATTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
28197 CCTTCGGGAGC
66 CCTTCGGGAGC
28208 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
28273 CCTTCGGGAGC
66 CCTTCGGGAGC
*
28284 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAGAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
*
28349 CCTTCGGAAGC
66 CCTTCGGGAGC
* *
28360 TTTTTGATATTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
28425 CCTTCGGGAGC
66 CCTTCGGGAGC
28436 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
*
28501 CCTTCGGAAGC
66 CCTTCGGGAGC
*
28512 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAGAAG
1 TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
*
28577 CCTTCGGAAGC
66 CCTTCGGGAGC
* *
28588 TTTTTGATATTTTCAAATCCTTC
1 TTTTTGATGTTTTCAAAGCCTTC
28611 AGCTGTCGTA
Statistics
Matches: 828, Mismatches: 31, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 828 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (76 bp):
TTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAG
CCTTCGGGAGC
Found at i:29773 original size:13 final size:13
Alignment explanation
Indices: 29755--29783 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29745 CCACCGTACT
29755 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
29768 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
29781 CCG
1 CCG
29784 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:30520 original size:14 final size:14
Alignment explanation
Indices: 30501--30574 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 14
30491 TTGGGCTTTG
*
30501 TAATATTTAATAAA
1 TAATATATAATAAA
30515 TAATATATAATAATTA
1 TAATATATAATAA--A
30531 TAATA-ATAATACTAA
1 TAATATATAATA--AA
*
30546 TAATA-ATAATTTTAA
1 TAATATATAA--TAAA
30561 TAATA-ATAATAAA
1 TAATATATAATAAA
30574 T
1 T
30575 TTAAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
13 4 0.08
14 12 0.24
15 27 0.53
16 6 0.12
17 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATATATAATAAA
Found at i:30527 original size:3 final size:3
Alignment explanation
Indices: 30508--30572 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
30498 TTGTAATATT
* *
30508 TAA TAAA TAA TATA TAA TAA TTA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
30555 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
30573 ATTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:30577 original size:18 final size:18
Alignment explanation
Indices: 30543--30578 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
30533 ATAATAATAC
*
30543 TAATAATAATAATTTTAA
1 TAATAATAATAAATTTAA
30561 TAATAATAATAAATTTAA
1 TAATAATAATAAATTTAA
30579 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAATAATAATAAATTTAA
Found at i:30832 original size:76 final size:76
Alignment explanation
Indices: 30701--32178 Score: 2663
Period size: 76 Copynumber: 19.5 Consensus size: 76
30691 GATGGAAATG
* *
30701 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
30766 CCCGAAGGCTT
66 CCCGAAGGCTT
30777 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
30842 CCCGAAGGCTT
66 CCCGAAGGCTT
30853 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
30918 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
30929 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
30994 TCCGAAGGCTT
66 CCCGAAGGCTT
*
31005 CTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
31070 TCCGAAGGCTT
66 CCCGAAGGCTT
31081 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
31146 -CCGAAGGCTT
66 CCCGAAGGCTT
* *
31156 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
31221 TCCGAAGGCTT
66 CCCGAAGGCTT
*
31232 CTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
31297 CCCGAAGGCTT
66 CCCGAAGGCTT
31308 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
31373 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
31384 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
31449 TCCGAAGGCTT
66 CCCGAAGGCTT
*
31460 CTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
31525 CCCGAAGGCTT
66 CCCGAAGGCTT
31536 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
31601 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
31612 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
31677 TCCGAAGGCTT
66 CCCGAAGGCTT
*
31688 CTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
31753 CCCGAAGGC-T
66 CCCGAAGGCTT
*
31763 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
31828 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
31839 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
31904 TCCGAAGGCTT
66 CCCGAAGGCTT
*
31915 CTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
31980 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
31991 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
32056 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
32067 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
32132 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* *
32144 TTTAGAAACATCATGCACTGAAGGGCTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
32179 TAAGAAATAG
Statistics
Matches: 1351, Mismatches: 48, Indels: 5
0.96 0.03 0.00
Matches are distributed among these distances:
75 146 0.11
76 1141 0.84
77 64 0.05
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:31557 original size:455 final size:456
Alignment explanation
Indices: 30701--32178 Score: 2780
Period size: 455 Copynumber: 3.2 Consensus size: 456
30691 GATGGAAATG
* * *
30701 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
30766 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTCTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
30831 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
30896 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
30961 ATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTCTTGGAAACATCATGCACTGA
261 ATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTCTTGGAAACATCATGCACTGA
*
31026 AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGAAGGCTTTTTGGAAACA
326 AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
31091 TCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT-CCGAAGGCT
391 TCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
31155 T
456 T
*
31156 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
31221 TCCGAAGGCTTCTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTCTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
31286 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
31351 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
31416 ATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTCTTGGAAACATCATGCACTGA
261 ATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTCTTGGAAACATCATGCACTGA
31481 AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
326 AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
31546 TCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
391 TCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
31611 T
456 T
*
31612 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
31677 TCCGAAGGCTTCTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTCTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
31742 ATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
31806 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
31871 ATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTCTTGGAAACATCATGCACTGA
261 ATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTCTTGGAAACATCATGCACTGA
31936 AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
326 AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
* *
32001 TCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCTCCCGAAGGCT
391 TCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
32066 T
456 T
* *
32067 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-ATTTGAAAACATCAAAAAGC
* * *
32132 TCCCGAAGGCTTTTTAGAAACATCATGCACTGAAGGGCTTACAGATG
65 TCCCGAAGGCTTCTTGGAAACATCATGCACTGAAGGACTTACAGATG
32179 TAAGAAATAG
Statistics
Matches: 1004, Mismatches: 17, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
455 783 0.78
456 221 0.22
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (456 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
CCCGAAGGCTTCTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAG
ATGACCCGAAGGATTTGAAAATATCAAAAAGCTTCCGAAGGCTTCTTGGAAACATCATGCACTGA
AGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACA
TCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCT
T
Found at i:32872 original size:22 final size:22
Alignment explanation
Indices: 32847--32901 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
32837 CATAAAGCTT
* *
32847 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAAAATCTA
* * *
32869 TCATCTTTAAAAAGAAAATTTG
1 TCATCTTTGAAAAGAAAATCTA
32891 TCATCTTTGAA
1 TCATCTTTGAA
32902 GAGTGTAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:34509 original size:75 final size:75
Alignment explanation
Indices: 34385--34549 Score: 303
Period size: 75 Copynumber: 2.2 Consensus size: 75
34375 GGTTTTCAGC
34385 ATGCCCCAATATTTGCTTCTTGTTAATATGAGTCTTCAAAATACACCACATGGATATGTCTGAAG
1 ATGCCCCAATA-TTGCTTCTTGTTAATATGAGTCTTCAAAATACACCACATGGATATGTCTGAAG
34450 TAAGCTCTAAA
65 TAAGCTCTAAA
*
34461 ATGCCCCAATATTGCTTCTTGTTAATATGAGTCTTCAAAATACACCACATGGATCTGTCTGAAGT
1 ATGCCCCAATATTGCTTCTTGTTAATATGAGTCTTCAAAATACACCACATGGATATGTCTGAAGT
*
34526 GAGCTCTAAA
66 AAGCTCTAAA
34536 ATGCCCCAATATTG
1 ATGCCCCAATATTG
34550 GCTGATACAG
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
75 76 0.87
76 11 0.13
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (75 bp):
ATGCCCCAATATTGCTTCTTGTTAATATGAGTCTTCAAAATACACCACATGGATATGTCTGAAGT
AAGCTCTAAA
Found at i:34537 original size:36 final size:36
Alignment explanation
Indices: 34422--34537 Score: 85
Period size: 36 Copynumber: 3.1 Consensus size: 36
34412 ATGAGTCTTC
* *
34422 AAAATACACCACATGGATATGTCTGAAGTAAGCTCT
1 AAAATACACCACATGGATCTGTCTGAAGTGAGCTCT
* * * ** *
34458 AAAATGCCCCAATATTGCTTCTTGT-T-AATATGAG-TCTT
1 AAAATACACC-ACA-TGGATC-TGTCTGAA-GTGAGCTC-T
34496 CAAAATACACCACATGGATCTGTCTGAAGTGAGCTCT
1 -AAAATACACCACATGGATCTGTCTGAAGTGAGCTCT
34533 AAAAT
1 AAAAT
34538 GCCCCAATAT
Statistics
Matches: 57, Mismatches: 14, Indels: 18
0.64 0.16 0.20
Matches are distributed among these distances:
36 16 0.28
37 16 0.28
38 14 0.25
39 11 0.19
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (36 bp):
AAAATACACCACATGGATCTGTCTGAAGTGAGCTCT
Found at i:35702 original size:83 final size:83
Alignment explanation
Indices: 35563--35781 Score: 393
Period size: 83 Copynumber: 2.6 Consensus size: 83
35553 GTTCCTACTG
*
35563 AACCAGATCAGATAACTCAAAGAACACTTCGAGAAGATGCTATGAGCACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
35628 CAATGATTTGTTCTGCCA
66 CAATGATTTGTTCTGCCA
* *
35646 AACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTATGAGTACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
35711 CAATGATTTGTTCTGCCA
66 CAATGATTTGTTCTGCCA
*
35729 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-GAGCACATT
35782 ACATTTGTTC
Statistics
Matches: 130, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
83 122 0.94
84 8 0.06
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
CAATGATTTGTTCTGCCA
Found at i:43889 original size:13 final size:13
Alignment explanation
Indices: 43871--43899 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
43861 CCACCGTACT
43871 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
43884 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
43897 CCG
1 CCG
43900 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:44635 original size:14 final size:14
Alignment explanation
Indices: 44616--44686 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
44606 TTGGGCTTTG
*
44616 TAATATTTAATAAA
1 TAATATATAATAAA
44630 TAATATATAATAATTA
1 TAATATATAATAA--A
44646 TAATAATACTAAT-AA
1 TAAT-ATA-TAATAAA
* *
44661 TAATA-AT-TTTAA
1 TAATATATAATAAA
44673 TAATA-ATAATAAA
1 TAATATATAATAAA
44686 T
1 T
44687 TTAAATGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
11 1 0.02
12 10 0.21
13 5 0.11
14 13 0.28
15 5 0.11
16 5 0.11
17 4 0.09
18 4 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATATATAATAAA
Found at i:44642 original size:3 final size:3
Alignment explanation
Indices: 44623--44684 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
44613 TTGTAATATT
* * **
44623 TAA TAAA TAA TATA TAA TAA TTA TAA TAA TAC TAA TAA TAA TAA TTT
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44670 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
44685 ATTTAAATGA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:44818 original size:17 final size:17
Alignment explanation
Indices: 44793--44841 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
44783 TAAACACTAC
44793 ATTAGATATTTTATCAA
1 ATTAGATATTTTATCAA
* *
44810 ATTATATATATTAT--A
1 ATTAGATATTTTATCAA
44825 A-TAGATATTTTATCAA
1 ATTAGATATTTTATCAA
44841 A
1 A
44842 AAATATTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 10 0.38
15 2 0.08
16 2 0.08
17 12 0.46
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (17 bp):
ATTAGATATTTTATCAA
Found at i:47130 original size:16 final size:16
Alignment explanation
Indices: 47111--47142 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
47101 GGCTTTGTTA
47111 GTGCTGAGGAAGAGAG
1 GTGCTGAGGAAGAGAG
47127 GTGCTGAGGAAGAGAG
1 GTGCTGAGGAAGAGAG
47143 ATACTGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.50, T:0.12
Consensus pattern (16 bp):
GTGCTGAGGAAGAGAG
Found at i:64849 original size:27 final size:24
Alignment explanation
Indices: 64819--64885 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
64809 CTCCAACAAG
64819 GGAATTGAATTCCATCCATTTTTTGAT
1 GGAATTGAATTCCATCCA---TTTGAT
* * *
64846 GGAATTCACTTTCCCT-CATTTGAT
1 GGAATTGA-ATTCCATCCATTTGAT
64870 GGAATTGAATTCCATC
1 GGAATTGAATTCCATC
64886 AGGGATTCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
23 5 0.16
24 13 0.41
27 9 0.28
28 5 0.16
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (24 bp):
GGAATTGAATTCCATCCATTTGAT
Found at i:70238 original size:60 final size:61
Alignment explanation
Indices: 70159--70297 Score: 165
Period size: 61 Copynumber: 2.3 Consensus size: 61
70149 GTTTGGAATA
* * * *
70159 AAATTAGAATGTTCAAAAAGTTTGA-GATTGATTTAGAATGA-AGGTCATAGTTTAAGGACG
1 AAATTAAAATATTCAAAAAGTTTGAGGACTAATTTAGAATGATA-GTCATAGTTTAAGGACG
* * ** *
70219 AAATTGAAATATTCAAAAAGTTTGAGGACTAATTTAGAATGATAGTTATAGTTTGGGGATG
1 AAATTAAAATATTCAAAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAAGGACG
*
70280 AAATTAAAATATTTAAAA
1 AAATTAAAATATTCAAAA
70298 GTTCATAGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
60 22 0.33
61 43 0.65
62 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (61 bp):
AAATTAAAATATTCAAAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAAGGACG
Found at i:75679 original size:6 final size:6
Alignment explanation
Indices: 75668--75694 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
75658 TAATTACAAA
75668 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
75695 AATTCAATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:77113 original size:11 final size:11
Alignment explanation
Indices: 77093--77151 Score: 75
Period size: 11 Copynumber: 5.3 Consensus size: 11
77083 TTGTTGTGCA
*
77093 AAAATGTTAAT
1 AAAATATTAAT
77104 AAAATATTAAT
1 AAAATATTAAT
77115 AAAATATTAAT
1 AAAATATTAAT
*
77126 AAAATAATAAT
1 AAAATATTAAT
77137 AATAAT-TTATAT
1 AA-AATATTA-AT
77149 AAA
1 AAA
77152 TGTATATTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
11 36 0.84
12 7 0.16
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
AAAATATTAAT
Found at i:77382 original size:12 final size:12
Alignment explanation
Indices: 77365--77392 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
77355 ATCTGAATTA
77365 AATCTCGAAATG
1 AATCTCGAAATG
77377 AATCTCGAAATG
1 AATCTCGAAATG
77389 AATC
1 AATC
77393 CCTCGTCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (12 bp):
AATCTCGAAATG
Found at i:77956 original size:106 final size:106
Alignment explanation
Indices: 77761--78141 Score: 503
Period size: 106 Copynumber: 3.6 Consensus size: 106
77751 TCCAAGTAAG
* * * * * * *
77761 TTGTATTGTTTCGAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTATGGAACTGGGAAATT
1 TTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAACTGGGAAGTT
* ** * *
77826 ATTTGTTGACAGCCAGCCACCCCTTCGCTGTGAAGTTGAGC
66 GTTTGTTGACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGC
* * * * * *
77867 TTGTGCTGTCTCGAGTCTAATATCTTTTGCTGTGAAGTTGAAATTGACTCTGAAACTGAGAAGTT
1 TTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAACTGGGAAGTT
*
77932 GTTTGTTGACAATCAGCCGCCCCTTCATTGTGAAGTTGAGC
66 GTTTGTTGACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGC
* *
77973 TTGTGTTGTCTGGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTT
1 TTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAACTGGGAAGTT
* *
78038 GTTTGTTGAC-ATCCAGCAGCCCCTTCGTTGTGAAGTTGAGT
66 GTTTGTTGACAAT-CAGCCGCCCCTTCGTTGTGAAGTTGAGC
* * * *
78079 TTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGTCTCTGAAACTGGGAAG
1 TTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAACTGGGAAG
78142 CCCCTTCGTC
Statistics
Matches: 239, Mismatches: 35, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
105 2 0.01
106 237 0.99
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
TTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAACTGGGAAGTT
GTTTGTTGACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGC
Found at i:79944 original size:27 final size:27
Alignment explanation
Indices: 79884--79935 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
79874 TTTTTCTTCA
79884 CTTTTTCCTTTGTTTTGGTTTCTCTTTG
1 CTTTTTCCTTTGTTTT-GTTTCTCTTTG
79912 CTTTTT-CTTTGTTTT-TTTCTCTTT
1 CTTTTTCCTTTGTTTTGTTTCTCTTT
79936 TTTCTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 9 0.38
27 9 0.38
28 6 0.25
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.73
Consensus pattern (27 bp):
CTTTTTCCTTTGTTTTGTTTCTCTTTG
Found at i:85079 original size:43 final size:42
Alignment explanation
Indices: 85019--85103 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 42
85009 TCGAAACTCA
*
85019 CTGCTTGTGCTAGTATTGCTCTTGAATTGCGTAGGTAATATT
1 CTGCTTGTGCCAGTATTGCTCTTGAATTGCGTAGGTAATATT
*
85061 CTGCTTTGTGCCAGTATTGCTCTTGAATTGCGTAGGTGATATT
1 CTGC-TTGTGCCAGTATTGCTCTTGAATTGCGTAGGTAATATT
85104 GTTGAAAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 4 0.10
43 36 0.90
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.42
Consensus pattern (42 bp):
CTGCTTGTGCCAGTATTGCTCTTGAATTGCGTAGGTAATATT
Found at i:85617 original size:55 final size:54
Alignment explanation
Indices: 85558--86052 Score: 332
Period size: 55 Copynumber: 9.2 Consensus size: 54
85548 GTCAGGATAA
* * *
85558 ATAAGACTTGAAAAATCTTCAAATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGT
1 ATAAGACTCGAAAAATCTTCAAA-AACGAGCCTGCTCTCTATTCCTTCAGAG-AGT
* * * * *
85613 ATAAGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTATTCATTCAGAGAGT
1 ATAAGACTCGAAAAATCTTCA-AAAACGAGCCTGCTCTCTATTCCTTCAGAGAGT
* * * *
85668 ATAAGACTTGAACAATCTTCAATAAAACGGGCCCGCTCTCTATTCCTTCAGAGAGT
1 ATAAGACTCGAAAAATCTTC-A-AAAACGAGCCTGCTCTCTATTCCTTCAGAGAGT
* * *
85724 AT-AGAACTCGAAAAATCTTCAATAAAC-AGGTCAGCTCTCTATTCTTTCAGAGAGT
1 ATAAG-ACTCGAAAAATCTTCAA-AAACGA-GCCTGCTCTCTATTCCTTCAGAGAGT
* * * *
85779 ATAGGACTC----AATCTTTAACAAAC-ATG-TTCGCTCCCTATTCCTTCAGAGAGT
1 ATAAGACTCGAAAAATCTTCAA-AAACGA-GCCT-GCTCTCTATTCCTTCAGAGAGT
** **
85830 AT-AGAACTCGAGCAATCTTCATAAAACG-GGTTCGCTCTCTATTCCTTCAGA-AGT
1 ATAAG-ACTCGAAAAATCTTCA-AAAACGAGCCT-GCTCTCTATTCCTTCAGAGAGT
* *
85884 AT-AGAACTCGAACAATCTTCAACAAACG-TCC-GCTCTCTATTCCTTCAG-GAGT
1 ATAAG-ACTCGAAAAATCTTCAA-AAACGAGCCTGCTCTCTATTCCTTCAGAGAGT
* *
85936 AT-AGAACTCG-AACATCTTCATGAAACG-GTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTCGAAAAATCTTCA-AAAACGAG-CCTGCTCTCTATTCCTTCAGAGAGT
* * ** * *
85989 AT-AGAACTCGAACAATCTTCAACGAACTTGTCC-GCTCCCTATTCATTCAGAGAGT
1 ATAAG-ACTCGAAAAATCTTCAA-AAACGAG-CCTGCTCTCTATTCCTTCAGAGAGT
*
86044 ATAGGACTC
1 ATAAGACTC
86053 AATCTTCAAC
Statistics
Matches: 368, Mismatches: 47, Indels: 50
0.79 0.10 0.11
Matches are distributed among these distances:
50 1 0.00
51 53 0.14
52 49 0.13
53 15 0.04
54 41 0.11
55 158 0.43
56 51 0.14
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (54 bp):
ATAAGACTCGAAAAATCTTCAAAAACGAGCCTGCTCTCTATTCCTTCAGAGAGT
Found at i:85847 original size:106 final size:105
Alignment explanation
Indices: 85591--86052 Score: 487
Period size: 106 Copynumber: 4.3 Consensus size: 105
85581 TGACGAGCCT
*
85591 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAA-TGTGTCTGCTCTCT
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACAG-GTC-GCTCTCT
* * * *
85653 ATTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGGGCCC
62 ATTCCTTCAGAGAGTATAGA-AC-T--ACAATCTTCAA-CAAAC-TGTCC
* *
85702 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCA-ATAAACAGGTCAGCTCTCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACAGGTC-GCTCTCTAT
* * * *
85766 TCTTTCAGAGAGTATAGGACT-CAATCTTTAACAAACATGTTC
64 TCCTTCAGAGAGTATAGAACTACAATCTTCAACAAAC-TGTCC
* *
85808 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTTCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGG-TCGCTCTCTATT
85873 CCTTCAGA-AGTATAGAACTCGAACAATCTTCAACAAAC-GTCC
65 CCTTCAGAGAGTATAGAACT---ACAATCTTCAACAAACTGTCC
* *
85915 GCTCTCTATTCCTTCAG-GAGTATAGAACTCGAAC-ATCTTCATGAAAC-GGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGGT-CGCTCTCTATT
*
85977 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCC
65 CCTTCAGAGAGTATAGAACT---ACAATCTTCAACAAAC-TGTCC
* *
86022 GCTCCCTATTCATTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC
86053 AATCTTCAAC
Statistics
Matches: 308, Mismatches: 27, Indels: 35
0.83 0.07 0.09
Matches are distributed among these distances:
103 1 0.00
104 21 0.07
105 51 0.17
106 85 0.28
107 50 0.16
108 12 0.04
109 14 0.05
110 2 0.01
111 69 0.22
112 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (105 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACAGGTCGCTCTCTATTC
CTTCAGAGAGTATAGAACTACAATCTTCAACAAACTGTCC
Found at i:86068 original size:55 final size:51
Alignment explanation
Indices: 85646--86070 Score: 346
Period size: 55 Copynumber: 8.0 Consensus size: 51
85636 AAATGTGTCT
* * * *
85646 GCTCTCTATTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGGGCCC
1 GCTCTCTATTCCTTCAGAGAGTATAGA-AC-T---CAATCTTCAA-CAAACGAGTCC
* *
85702 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAAC-AGGTCA
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTC----AATCTTCAACAAACGA-GTCC
* * * *
85757 GCTCTCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAACAAAC-ATGTTC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAATCTTCAACAAACGA-GTCC
* * *
85808 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATA-AAACGGGTTC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACT----CAATCTTCA-ACAAACGAGTCC
85863 GCTCTCTATTCCTTCAGA-AGTATAGAACTCGAACAATCTTCAACAAAC--GTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACT----CAATCTTCAACAAACGAGTCC
**
85915 GCTCTCTATTCCTTCAG-GAGTATAGAACTCGAACATCTTCATGAAACG-GTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTC--A-ATCTTCAACAAACGAGTCC
* **
85967 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACT----CAATCTTCAACAAACGAGTCC
* * *
86022 GCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACAAACGAGT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCAATCTTCAACAAACGAGT
86071 TTGCTTCACT
Statistics
Matches: 313, Mismatches: 32, Indels: 53
0.79 0.08 0.13
Matches are distributed among these distances:
48 1 0.00
50 1 0.00
51 69 0.22
52 53 0.17
53 13 0.04
54 37 0.12
55 101 0.32
56 36 0.12
57 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (51 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCAATCTTCAACAAACGAGTCC
Found at i:86124 original size:38 final size:38
Alignment explanation
Indices: 86071--86175 Score: 201
Period size: 38 Copynumber: 2.8 Consensus size: 38
86061 ACAAACGAGT
*
86071 TTGCTTCACTACTCTTTCGTGAAGGCTTATAGATTTAA
1 TTGCTTCACTGCTCTTTCGTGAAGGCTTATAGATTTAA
86109 TTGCTTCACTGCTCTTTCGTGAAGGCTTATAGATTTAA
1 TTGCTTCACTGCTCTTTCGTGAAGGCTTATAGATTTAA
86147 TTGCTTCACTGCTCTTTCGTGAAGGCTTA
1 TTGCTTCACTGCTCTTTCGTGAAGGCTTA
86176 AAATTTACTT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (38 bp):
TTGCTTCACTGCTCTTTCGTGAAGGCTTATAGATTTAA
Found at i:87556 original size:51 final size:49
Alignment explanation
Indices: 87447--87580 Score: 141
Period size: 45 Copynumber: 2.7 Consensus size: 49
87437 CTTTTCTCTC
* * *
87447 TTTTTTTCATTTTTCTCTTTTTGTTTTTC-TCTT-TCATTTTTCCATCA
1 TTTTTTTCATTTTTTTCTTTTTCTTTTTCTTCTTCTCATTTTTACATCA
* * *
87494 TTTTCTT--TTTTTTTCTTTTTCTTTTTCTTCTTCTCATTTTATTATATTA
1 TTTTTTTCATTTTTTTCTTTTTCTTTTTCTTCTTCTCA-TTT-TTACATCA
*
87543 TTTTTTTCATTTTTTTCTTTTTCTCTTTTATTTCTTCT
1 TTTTTTTCATTTTTTTCTTTTTCT-TTTT-CTTCTTCT
87581 TCAAGCGAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
45 18 0.25
46 4 0.06
47 9 0.13
48 3 0.04
49 11 0.15
51 15 0.21
52 4 0.06
53 7 0.10
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.75
Consensus pattern (49 bp):
TTTTTTTCATTTTTTTCTTTTTCTTTTTCTTCTTCTCATTTTTACATCA
Found at i:87578 original size:9 final size:8
Alignment explanation
Indices: 87445--87578 Score: 56
Period size: 8 Copynumber: 15.5 Consensus size: 8
87435 TCCTTTTCTC
87445 TCTTTTTT
1 TCTTTTTT
*
87453 TCATTTTTC
1 TC-TTTTTT
87462 TCTTTTTGT
1 TCTTTTT-T
87471 T-TTTCTCTT
1 TCTTT-T-TT
*
87480 TCATTTTT
1 TCTTTTTT
* **
87488 CCATCATTT
1 TC-TTTTTT
87497 TCTTTTTT
1 TCTTTTTT
87505 T-TTCTTTT
1 TCTT-TTTT
87513 TCTTTTTCT
1 TCTTTTT-T
87522 TCTTCTCATTT
1 TCTT-T--TTT
* * *
87533 TATTATAT
1 TCTTTTTT
*
87541 TATTTTTT
1 TCTTTTTT
87549 TCATTTTTT
1 TC-TTTTTT
*
87558 TCTTTTTC
1 TCTTTTTT
87566 TCTTTTATT
1 TCTTTT-TT
87575 TCTT
1 TCTT
87579 CTTCAAGCGA
Statistics
Matches: 94, Mismatches: 18, Indels: 27
0.68 0.13 0.19
Matches are distributed among these distances:
7 2 0.02
8 46 0.49
9 36 0.38
10 4 0.04
11 4 0.04
12 2 0.02
ACGTcount: A:0.08, C:0.16, G:0.01, T:0.75
Consensus pattern (8 bp):
TCTTTTTT
Done.