Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007833.1 Hibiscus syriacus cultivar Beakdansim tig00110177_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: 816380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:624944 original size:16 final size:16
Alignment explanation
Indices: 624925--624980 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 16
624915 TTACTTTTTA
624925 TATTTAATTTTAATTT
1 TATTTAATTTTAATTT
624941 TATTT-ATTTTACTCATTGTT
1 TATTTAATTTTA---A-T-TT
624961 TATTTATATTTTAATTT
1 TATTTA-ATTTTAATTT
624978 TAT
1 TAT
624981 ATGTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 6 0.18
16 5 0.15
17 5 0.15
18 2 0.06
19 2 0.06
20 7 0.21
22 6 0.18
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTTAATTTTAATTT
Found at i:624996 original size:37 final size:36
Alignment explanation
Indices: 624925--624998 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
624915 TTACTTTTTA
* * *
624925 TATTTAATTTTAATTTTATTTATTTTACTCATTGTT
1 TATTTAATTTTAATTTTATATATTTAAATCATTGTT
* *
624961 TATTTATATTTTAATTTTATATGTTTAAATTATTGTT
1 TATTTA-ATTTTAATTTTATATATTTAAATCATTGTT
624998 T
1 T
624999 TCATAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (36 bp):
TATTTAATTTTAATTTTATATATTTAAATCATTGTT
Found at i:625836 original size:13 final size:14
Alignment explanation
Indices: 625813--625850 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
625803 TTACTATTTT
625813 TATTATTTTATTAA
1 TATTATTTTATTAA
*
625827 TATT-TTTTATTTA
1 TATTATTTTATTAA
625840 T-TTATTTTATT
1 TATTATTTTATT
625851 CAAGTATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 2 0.09
13 16 0.73
14 4 0.18
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTATTTTATTAA
Found at i:625841 original size:17 final size:17
Alignment explanation
Indices: 625791--625841 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 17
625781 TTTCTTTCAA
*
625791 ATTTTTTA-TTACTTACT
1 ATTTTTTATTTA-TTAAT
625808 ATTTTTATTATTTTATTAAT
1 A-TTTT-TTA-TTTATTAAT
625828 ATTTTTTATTTATT
1 ATTTTTTATTTATT
625842 TATTTTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 7 0.24
20 5 0.17
21 3 0.10
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTATTTATTAAT
Found at i:631075 original size:16 final size:16
Alignment explanation
Indices: 631052--631107 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
631042 AAAGAAAGAC
631052 AAAA-AAAAA-GATGAA
1 AAAAGAAAAATGA-GAA
*
631067 AAAGGAAAAATGAGAA
1 AAAAGAAAAATGAGAA
* *
631083 AAAAGAAAAAAG-GGA
1 AAAAGAAAAATGAGAA
631098 AAAAGAAAAA
1 AAAAGAAAAA
631108 GGAAAATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 15 0.43
16 18 0.51
17 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.04
Consensus pattern (16 bp):
AAAAGAAAAATGAGAA
Found at i:631084 original size:15 final size:15
Alignment explanation
Indices: 631052--631107 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
631042 AAAGAAAGAC
631052 AAAAA-AAAAGATGA-
1 AAAAAGAAAA-ATGAG
*
631066 AAAAGGAAAAATGAG
1 AAAAAGAAAAATGAG
* *
631081 AAAAAAGAAAAAAGGG
1 -AAAAAGAAAAATGAG
631097 AAAAAGAAAAA
1 AAAAAGAAAAA
631108 GGAAAATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 8 0.23
15 15 0.43
16 12 0.34
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAAATGAG
Found at i:631099 original size:9 final size:8
Alignment explanation
Indices: 631065--631113 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
631055 AAAAAAGATG
631065 AAAAAGGA
1 AAAAAGGA
*
631073 AAAATGAGA
1 AAAAAG-GA
631082 AAAAA-GA
1 AAAAAGGA
*
631089 AAAAAGGG
1 AAAAAGGA
631097 AAAAA-G-
1 AAAAAGGA
631103 AAAAAGGA
1 AAAAAGGA
631111 AAA
1 AAA
631114 TTGAATCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
6 5 0.15
7 9 0.26
8 14 0.41
9 6 0.18
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (8 bp):
AAAAAGGA
Found at i:635970 original size:22 final size:22
Alignment explanation
Indices: 635944--636020 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
635934 ATCTACACTC
635944 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* * *
635966 TTCAAAAATAATAGATTCTTTT
1 TTCAAAGATGATAGATTCTCTT
*
635988 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
636010 TTCAAAGATGA
1 TTCAAAGATGA
636021 AAGCTTTATG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:637190 original size:75 final size:76
Alignment explanation
Indices: 636865--637505 Score: 1126
Period size: 76 Copynumber: 8.5 Consensus size: 76
636855 CTATTTCCCA
636865 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
636930 AGCCTTAGGGT
66 AGCCTTAGGGT
636941 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
637006 AGCCTTAGGGT
66 AGCCTTAGGGT
*
637017 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
637082 AGCCTTAGGGT
66 AGCCTTAGGGT
637093 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
637157 AGCCTTAGGGT
66 AGCCTTAGGGT
*
637168 TATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
637233 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
637244 CATCTGTAAGTCCTGCAGTGTATGATGTTTCCAAAAAGCCTTCGGGAGCTTTATGATGTTTT-TA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
637308 AGCCTTAGGGT
66 AGCCTTAGGGT
637319 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
637384 A-CCTTCGGGT
66 AGCCTTAGGGT
* **
637394 CATCTATAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
637459 AAACCTTCGGGT
65 AAGCCTTAGGGT
* * *
637471 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAA
637506 CATTTTCATC
Statistics
Matches: 542, Mismatches: 19, Indels: 7
0.95 0.03 0.01
Matches are distributed among these distances:
75 214 0.39
76 289 0.53
77 39 0.07
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:637223 original size:151 final size:152
Alignment explanation
Indices: 636865--637505 Score: 1126
Period size: 151 Copynumber: 4.2 Consensus size: 152
636855 CTATTTCCCA
636865 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
636930 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
636995 GATGTTTTCAAAGCCTTAGGGT
131 GATGTTTTCAAAGCCTTAGGGT
*
637017 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
637082 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
637146 GATGTTTTCAAAGCCTTAGGGT
131 GATGTTTTCAAAGCCTTAGGGT
*
637168 TATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
637233 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGTATGATGTTTCCAAAAAGCCTTCGGGAGCTTTAT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
637298 GATGTTTT-TAAGCCTTAGGGT
131 GATGTTTTCAAAGCCTTAGGGT
637319 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * **
637384 A-CCTTCGGGTCATCTATAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* *
637448 GATGTTTTCAAAAACCTTCGGGT
131 GATGTTTTC-AAAGCCTTAGGGT
* * *
637471 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAA
637506 CATTTTCATC
Statistics
Matches: 467, Mismatches: 19, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
150 65 0.14
151 225 0.48
152 177 0.38
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (152 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGT
Found at i:637651 original size:19 final size:19
Alignment explanation
Indices: 637626--637668 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 19
637616 TTTTTTTTCA
637626 TAATAATAATTATAATTATTAT
1 TAAT-ATAA-TAT-ATTATTAT
637648 TAATATAATATATTATTAT
1 TAATATAATATATTATTAT
637667 TA
1 TA
637669 TTATTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 4 0.19
22 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATAATATATTATTAT
Found at i:637665 original size:22 final size:22
Alignment explanation
Indices: 637626--637696 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
637616 TTTTTTTTCA
*
637626 TAATAATAAT-TATAATTATTAT
1 TAAT-ATAATATATTATTATTAT
637648 TAATATAATATATTATTATTAT
1 TAATATAATATATTATTATTAT
* *
637670 TATTAAAATATATATATATATATAT
1 TAATATAATATAT-TAT-TAT-TAT
637695 TA
1 TA
637697 CAAATTACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 5 0.12
22 26 0.62
23 3 0.07
24 3 0.07
25 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATATAATATATTATTATTAT
Found at i:639059 original size:16 final size:16
Alignment explanation
Indices: 639040--639095 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 16
639030 TTACTTTTTA
639040 TATTTAATTTTAATTT
1 TATTTAATTTTAATTT
639056 TATTT-ATTTTACTCATTGTT
1 TATTTAATTTTA---A-T-TT
639076 TATTTATATTTTAATTT
1 TATTTA-ATTTTAATTT
639093 TAT
1 TAT
639096 ATGTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 6 0.18
16 5 0.15
17 5 0.15
18 2 0.06
19 2 0.06
20 7 0.21
22 6 0.18
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTTAATTTTAATTT
Found at i:640545 original size:200 final size:199
Alignment explanation
Indices: 640146--640718 Score: 758
Period size: 200 Copynumber: 2.9 Consensus size: 199
640136 AATACCAATG
* *
640146 TTCCAGTATGCTTATCAAACAATTTGAACGCAAAAAGTATCGATACACTTATATAAAGTATCGAT
1 TTCCAGTATGCTTCTCAAACAATTTGAACGCAAAAAGTATCGATACACATATATAAAGTATCGAT
*
640211 ACTTGG-AATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAG
66 AC-TGGTAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAG
* * * * *
640275 TTTACTGGTATAATGATAATAGGCGTAAACATAAAGTATCTATATTGTTTATATCGGTATCGATA
130 TATAC-GGTATAATGATAATAGGCGTAAACATAAAGTATCGATAGTGTTTATATCAGTATCGACA
640340 CTTTTA
194 CTTTTA
* * *
640346 TTCCAGTATGTTTCTCAAACAATTTGTACGCAACAAAGTATCGATACCCATATATAAAGTATCGA
1 TTCCAGTATGCTTCTCAAACAATTTGAACGCAA-AAAGTATCGATACACATATATAAAGTATCGA
* * *
640411 TACTGGTAATTTTGAAACCTATTACTTTAAAGTAATA-CTAAAATTTATAATGTAAACGGTAAAA
65 TACTGGTAATTTCGAAACCTATTACTTTAAAGTAATAGGT-AAATTTACAATGTAAACGGTAAAA
* * *
640475 GTCTACGGTATAGTGATAATAGGCATAAATCAT-AAGTATCGATACGT-TTTATATCAGTATCGA
129 GTATACGGTATAATGATAATAGGCGTAAA-CATAAAGTATCGATA-GTGTTTATATCAGTATCGA
640538 CACTTTTA
192 CACTTTTA
* * * *
640546 TTCCAGTATGCTTCTCAAACAATTTGCACGCAAAACGTATCAATACATATATATAAAGTATCGAT
1 TTCCAGTATGCTTCTCAAACAATTTGAACGCAAAAAGTATCGATACACATATATAAAGTATCGAT
** * * * * * **
640611 ACTTATAATTTCGAAATCTATTATTTTAAAATAATAGGTTAATTTACAATGAAAACAATAAAAGT
66 ACTGGTAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAGT
* * *
640676 ATATAGGTATAATGATAATAGGTGTAAACATCAAGTATCGATA
131 ATA-CGGTATAATGATAATAGGCGTAAACATAAAGTATCGATA
640719 TAAATGTATA
Statistics
Matches: 326, Mismatches: 39, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
199 84 0.26
200 150 0.46
201 92 0.28
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (199 bp):
TTCCAGTATGCTTCTCAAACAATTTGAACGCAAAAAGTATCGATACACATATATAAAGTATCGAT
ACTGGTAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAGT
ATACGGTATAATGATAATAGGCGTAAACATAAAGTATCGATAGTGTTTATATCAGTATCGACACT
TTTA
Found at i:640552 original size:20 final size:21
Alignment explanation
Indices: 640509--640554 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
640499 ATAAATCATA
*
640509 AGTATCGATACGTTTTATATC
1 AGTATCGACACGTTTTATATC
640530 AGTATCGACAC-TTTTAT-TCC
1 AGTATCGACACGTTTTATAT-C
640550 AGTAT
1 AGTAT
640555 GCTTCTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 12 0.52
21 10 0.43
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (21 bp):
AGTATCGACACGTTTTATATC
Found at i:646028 original size:15 final size:15
Alignment explanation
Indices: 646008--646038 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
645998 GATCACCTTG
646008 TTGTCCAGCCCCTCT
1 TTGTCCAGCCCCTCT
646023 TTGTCCAGCCCCTCT
1 TTGTCCAGCCCCTCT
646038 T
1 T
646039 AGATGAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.45, G:0.13, T:0.35
Consensus pattern (15 bp):
TTGTCCAGCCCCTCT
Found at i:646368 original size:29 final size:29
Alignment explanation
Indices: 646326--646382 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
646316 GGACTATCAA
646326 AGATAAATTTCCAATTCCTATAATAGAGT
1 AGATAAATTTCCAATTCCTATAATAGAGT
646355 AGATAAATTTCCAATTCCTATAATAGAG
1 AGATAAATTTCCAATTCCTATAATAGAG
646383 GACTTACTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (29 bp):
AGATAAATTTCCAATTCCTATAATAGAGT
Found at i:680822 original size:20 final size:22
Alignment explanation
Indices: 680794--680836 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
680784 TAATGTTTCC
*
680794 TTTTCTTTCTTT-C-TTTCTTT
1 TTTTATTTCTTTGCTTTTCTTT
680814 TTTTATTTCTTTGCTTTTCTTT
1 TTTTATTTCTTTGCTTTTCTTT
680836 T
1 T
680837 GATTGGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTATTTCTTTGCTTTTCTTT
Found at i:686548 original size:33 final size:32
Alignment explanation
Indices: 686506--686569 Score: 119
Period size: 33 Copynumber: 2.0 Consensus size: 32
686496 ACGATCCTTT
686506 AGGGGTTGTATTGTCCTGATTTGGAAGGAAAGA
1 AGGGGTTGTATTGTCCTGATTTGG-AGGAAAGA
686539 AGGGGTTGTATTGTCCTGATTTGGAGGAAAG
1 AGGGGTTGTATTGTCCTGATTTGGAGGAAAG
686570 GAACAGACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.25, C:0.06, G:0.38, T:0.31
Consensus pattern (32 bp):
AGGGGTTGTATTGTCCTGATTTGGAGGAAAGA
Found at i:687633 original size:47 final size:47
Alignment explanation
Indices: 687563--687663 Score: 157
Period size: 47 Copynumber: 2.1 Consensus size: 47
687553 AAACAAAAGA
* *
687563 AAATCCCTGATCAAAACCATTGTGCTTTTAACTAGAGACAAGCAAGC
1 AAATCCCTGATCAAAACCATTGTGCTTTAAACCAGAGACAAGCAAGC
** *
687610 AAATCCCTGATCAAAACTGTTGTGCTTTAAACCAGAGACATGCAAGC
1 AAATCCCTGATCAAAACCATTGTGCTTTAAACCAGAGACAAGCAAGC
687657 AAATCCC
1 AAATCCC
687664 ATCCATCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (47 bp):
AAATCCCTGATCAAAACCATTGTGCTTTAAACCAGAGACAAGCAAGC
Found at i:687794 original size:47 final size:47
Alignment explanation
Indices: 687725--687822 Score: 160
Period size: 47 Copynumber: 2.1 Consensus size: 47
687715 TCTCATTCCC
*
687725 TCCCTGATCAAAACCATTGTGCTTTTAACTAGAGACAAGCAAGCAAA
1 TCCCTGATCAAAACCATTGTGCTTTTAACCAGAGACAAGCAAGCAAA
** *
687772 TCCCTGATCAAAACTGTTGTGCTTTTAACCAGAGACATGCAAGCAAA
1 TCCCTGATCAAAACCATTGTGCTTTTAACCAGAGACAAGCAAGCAAA
687819 TCCC
1 TCCC
687823 ATCCATCAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (47 bp):
TCCCTGATCAAAACCATTGTGCTTTTAACCAGAGACAAGCAAGCAAA
Found at i:687855 original size:159 final size:160
Alignment explanation
Indices: 687566--687884 Score: 622
Period size: 159 Copynumber: 2.0 Consensus size: 160
687556 CAAAAGAAAA
687566 TCCCTGATCAAAACCATTGTGCTTTTAACTAGAGACAAGCAAGCAAATCCCTGATCAAAACTGTT
1 TCCCTGATCAAAACCATTGTGCTTTTAACTAGAGACAAGCAAGCAAATCCCTGATCAAAACTGTT
687631 GTGCTTTAAACCAGAGACATGCAAGCAAATCCCATCCATCAATAGAAATTTACAAGGTTTGGCAT
66 GTGCTTTAAACCAGAGACATGCAAGCAAATCCCATCCATCAATAGAAATTTACAAGGTTTGGCAT
687696 TTGAAATTAAATA-TCCTAATCTCATTCCC
131 TTGAAATTAAATATTCCTAATCTCATTCCC
687725 TCCCTGATCAAAACCATTGTGCTTTTAACTAGAGACAAGCAAGCAAATCCCTGATCAAAACTGTT
1 TCCCTGATCAAAACCATTGTGCTTTTAACTAGAGACAAGCAAGCAAATCCCTGATCAAAACTGTT
*
687790 GTGCTTTTAACCAGAGACATGCAAGCAAATCCCATCCATCAATAGAAATTTACAAGGTTTGGCAT
66 GTGCTTTAAACCAGAGACATGCAAGCAAATCCCATCCATCAATAGAAATTTACAAGGTTTGGCAT
687855 TTGAAATTAAATATTCCTAATCTCATTCCC
131 TTGAAATTAAATATTCCTAATCTCATTCCC
687885 AAACTAGATT
Statistics
Matches: 158, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
159 142 0.90
160 16 0.10
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (160 bp):
TCCCTGATCAAAACCATTGTGCTTTTAACTAGAGACAAGCAAGCAAATCCCTGATCAAAACTGTT
GTGCTTTAAACCAGAGACATGCAAGCAAATCCCATCCATCAATAGAAATTTACAAGGTTTGGCAT
TTGAAATTAAATATTCCTAATCTCATTCCC
Found at i:700422 original size:234 final size:227
Alignment explanation
Indices: 700011--700436 Score: 559
Period size: 234 Copynumber: 1.8 Consensus size: 227
700001 TTCCATAAAC
* *
700011 TCCTATCAAAGGCTGAACACTTGGTCCTTTTTTCCATGATCCTTCAGCAACATAAAGCATTACAG
1 TCCTATCAAAGGCAGAACACTAGGTCCTTTTTTCCATGATCCTTCAGCAACATAAAGCATTACAG
* * * * ** *
700076 AGATTATTCTAGCACATTGTTGTTTAGGGTGCACGGCAATCTAGGTGCTAGAACCTTTATATTGC
66 AGATTATTCTAGCACATTCTTGTTTAGGGTGAAAGACAATCTAGGCACTAGAACCGTTATATTGC
** * * * *
700141 TCAAGATGCAAGGCACAAGATAATGCACACACATGAGCAATGTAAGGCACCATATCTATGAGCGT
131 TCAAGACACAAGGCACAAGAAAAGGCACACACATGAGCAAGGTAAGGCACAATATCTATGAGCGT
700206 ATAACAGTACTACCCCCTGTATAGTCCTATGA
196 ATAACAGTACTACCCCCTGTATAGTCCTATGA
* *
700238 TCCTATCAAAGGCAGAACACTAGGTCC-TTTTTCCTTGATCCTTCTGCAACATAAAGCATAAGCA
1 TCCTATCAAAGGCAGAACACTAGGTCCTTTTTTCCATGATCCTTCAGCAACAT-----A-AAGCA
* *
700302 TTATAGAGGTTATTCTAGCACATTCTTGTTTAGGGTGAAAGACAAATTCTAGGCACTAGAACCGT
60 TTACAGAGATTATTCTAGCACATTCTTGTTTAGGGTGAAAGAC-AA-TCTAGGCACTAGAACCGT
* * *
700367 TATATTGCTCAAGGCACAAGGCA-AGAGAAAAGGCACTCGCATGAGCAAGGTAAGGCACAATATC
123 TATATTGCTCAAGACACAAGGCACA-AGAAAAGGCACACACATGAGCAAGGTAAGGCACAATATC
700431 TATGAG
187 TATGAG
700437 TGTTTATCTT
Statistics
Matches: 168, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
226 23 0.14
227 25 0.15
231 1 0.01
232 42 0.25
233 3 0.02
234 74 0.44
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (227 bp):
TCCTATCAAAGGCAGAACACTAGGTCCTTTTTTCCATGATCCTTCAGCAACATAAAGCATTACAG
AGATTATTCTAGCACATTCTTGTTTAGGGTGAAAGACAATCTAGGCACTAGAACCGTTATATTGC
TCAAGACACAAGGCACAAGAAAAGGCACACACATGAGCAAGGTAAGGCACAATATCTATGAGCGT
ATAACAGTACTACCCCCTGTATAGTCCTATGA
Found at i:704895 original size:116 final size:113
Alignment explanation
Indices: 704678--704905 Score: 250
Period size: 116 Copynumber: 2.0 Consensus size: 113
704668 AAAAATATAT
* * *
704678 ATTAATTTATATATTTATAATAAATATTTATTTATTAGAAATATCAGAAAAGGACTCTAGGTGCT
1 ATTAATATATATATTTATAATAAATATTTATTTATTAAAAATATCAGAAAAGGACTCCAGGTGCT
* *
704743 TAAGACAGCTCTTTTCTTTGATATTAAATAAATAAAT-AATAATTAAAC
66 TAAGACAGCTCCTTTCTTTAATATTAAATAAATAAATAAAT-ATTAAAC
704791 ATTAATATATA-ATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 ATTAATATATATATTTAT--AATAA-ATATTTATTTA-TTAAAAATATCAGAAAA-GGAC-TCCA
* ** * **
704855 GTTATTTTAAGACTGC-CCTTTC-TTAATATTGGA-AAATAAATAAATATTAAA
60 GGT-GCTTAAGACAGCTCCTTTCTTTAATATTAAATAAATAAATAAATATTAAA
704906 ATAGGATTAA
Statistics
Matches: 96, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
112 6 0.06
113 10 0.10
114 5 0.05
115 11 0.11
116 30 0.31
117 15 0.16
118 10 0.10
119 9 0.09
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (113 bp):
ATTAATATATATATTTATAATAAATATTTATTTATTAAAAATATCAGAAAAGGACTCCAGGTGCT
TAAGACAGCTCCTTTCTTTAATATTAAATAAATAAATAAATATTAAAC
Found at i:715545 original size:121 final size:119
Alignment explanation
Indices: 715339--715567 Score: 273
Period size: 121 Copynumber: 1.9 Consensus size: 119
715329 AATATATATT
* * * * *
715339 AATTTATATATATTTATAAATAAAATATTTATTTACTTAGAAATATCAGAAAAGGACTTCTAGGT
1 AATTAATATATATTTATAAATAAAATATTTATTTACTTAAAAATATCAGAAAAGAACATCCAGGT
* * *
715404 GCCTTAAGACAGCTCTTTTCTTTGATATT-AAATAAATAAATAAATAATTAAAAC
66 ACCTTAAGACAGCTCCTTTC-TTAATATTGAAATAAATAAATAAATAATTAAAAC
* *
715458 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGAACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTACTTAAAAATATCAGAAAA-GAACATCCA
* ** *
715523 GTTATTTTAAGACTGC-CCTTTCTTAATATTGGAAATAAATAAATA
63 GGTACCTTAAGACAGCTCCTTTCTTAATATT-GAAATAAATAAATA
715568 TTAAATAGGA
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
119 10 0.11
120 13 0.14
121 38 0.42
122 30 0.33
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (119 bp):
AATTAATATATATTTATAAATAAAATATTTATTTACTTAAAAATATCAGAAAAGAACATCCAGGT
ACCTTAAGACAGCTCCTTTCTTAATATTGAAATAAATAAATAAATAATTAAAAC
Found at i:715676 original size:3 final size:3
Alignment explanation
Indices: 715668--715705 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
715658 TTTATGGTTA
*
715668 AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
715706 CAAGTAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:717005 original size:3 final size:3
Alignment explanation
Indices: 716997--717043 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
716987 AGCCTGTTTG
**
716997 TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
717042 TA
1 TA
717044 GAAAATGGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:717427 original size:124 final size:123
Alignment explanation
Indices: 717241--717586 Score: 459
Period size: 124 Copynumber: 2.8 Consensus size: 123
717231 GGGATGATAA
* * * * * *
717241 TATCTCATTCTGTGAT-GTAAT-TTGGAAAAGGGTTGAACAAGTTCTTCTTATTATAAAATTCTT
1 TATCTCCTTCTGTGATAG-AATCATGCAAAA-GGTTGAACAAGTTCTTCTCATTATGAACTTCTT
*
717304 CTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCCTGGAAAAGTTGATGTTGACC
64 CTT-CTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCCTGGAAAAGTTGATGCTGACC
* * * *
717365 TATTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-
* * *
717430 TTCTTCTTCAAATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATGCTGATC
65 TTCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCCTGGAAAAGTTGATGCTGACC
* * *
717489 TATCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC-
1 TATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
*
717553 T-TT-TTCAGATGAGTTCTTCTCATTATGAACTTTC
66 TCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTC
717587 TGGGTAAAAC
Statistics
Matches: 196, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
120 29 0.15
121 2 0.01
122 1 0.01
124 156 0.80
125 8 0.04
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (123 bp):
TATCTCCTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
TCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCCTGGAAAAGTTGATGCTGACC
Found at i:718180 original size:6 final size:6
Alignment explanation
Indices: 718165--718204 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
718155 AAACGTAAAA
* * *
718165 AAATGC AAATGT AAATGC AAATGT AAATGC AAATGT AAAT
1 AAATGC AAATGC AAATGC AAATGC AAATGC AAATGC AAAT
718205 ATGTGAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.53, C:0.07, G:0.15, T:0.25
Consensus pattern (6 bp):
AAATGC
Found at i:718180 original size:12 final size:12
Alignment explanation
Indices: 718165--718204 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
718155 AAACGTAAAA
718165 AAATGCAAATGT
1 AAATGCAAATGT
718177 AAATGCAAATGT
1 AAATGCAAATGT
718189 AAATGCAAATGT
1 AAATGCAAATGT
718201 AAAT
1 AAAT
718205 ATGTGAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.53, C:0.07, G:0.15, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:719879 original size:28 final size:26
Alignment explanation
Indices: 719824--719881 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
719814 AAACATTAAT
*
719824 AAAATAATATAGATATAAATATTATG
1 AAAATAATATAGATATAAAAATTATG
* *
719850 AAAATAATAGGTATATATAAAAATTTTG
1 AAAATAATA--TAGATATAAAAATTATG
719878 AAAA
1 AAAA
719882 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (26 bp):
AAAATAATATAGATATAAAAATTATG
Found at i:720580 original size:121 final size:119
Alignment explanation
Indices: 720374--720607 Score: 285
Period size: 121 Copynumber: 1.9 Consensus size: 119
720364 AATATATATT
* * * *
720374 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAGGT
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGT
* * *
720439 GCCTTAAGACAGCTCTTTTCTTTGATATT-AAAA-AAATAAATAATTAATTAAAAC
66 ACCTTAAGACAGCTCCTTTC-TTAATATTGAAAATAAATAAAT-ATTAATTAAAAC
*
720493 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAAT-GACATCCA
* ** *
720558 GTTATGTTAAGACTGC-CCTTTCTTAATATTGGAAAATAAATAAATATTAA
63 GGTACCTTAAGACAGCTCCTTTCTTAATATT-GAAAATAAATAAATATTAA
720608 AATAGGATTA
Statistics
Matches: 97, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
119 10 0.10
120 13 0.13
121 40 0.41
122 26 0.27
123 8 0.08
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.38
Consensus pattern (119 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGT
ACCTTAAGACAGCTCCTTTCTTAATATTGAAAATAAATAAATATTAATTAAAAC
Found at i:720709 original size:3 final size:3
Alignment explanation
Indices: 720701--720732 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
720691 TTTATGGTTA
*
720701 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
720733 CAAGTAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:722076 original size:3 final size:3
Alignment explanation
Indices: 722068--722132 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
722058 GGCCTGTTTG
**
722068 TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
722113 TATA TAA -AA TAA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TA
722133 GAAAATGGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:722100 original size:24 final size:24
Alignment explanation
Indices: 722080--722132 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
722070 ATAATAATTT
722080 TAATAATAATAAATAAAATAATAA
1 TAATAATAATAAATAAAATAATAA
*
722104 TAATAATAATATATAAAATAATAA
1 TAATAATAATAAATAAAATAATAA
722128 TAATA
1 TAATA
722133 GAAAATGGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
TAATAATAATAAATAAAATAATAA
Found at i:724532 original size:21 final size:21
Alignment explanation
Indices: 724492--724532 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
724482 AGCATCATTT
* * *
724492 TTCATTAAAGCTATTGTGATG
1 TTCATTAAAACTACTATGATG
724513 TTCATTAAAACTACTATGAT
1 TTCATTAAAACTACTATGAT
724533 AAGTCACTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (21 bp):
TTCATTAAAACTACTATGATG
Found at i:729498 original size:83 final size:83
Alignment explanation
Indices: 729356--729522 Score: 289
Period size: 83 Copynumber: 2.0 Consensus size: 83
729346 CTTTGAGAAA
* * * *
729356 CAGATGCATCTGCTTTATTCAATTCCAATGAGCATTTTGAATAATATTGAATGATAAGAATAACG
1 CAGATGCATCTGCTTCATTCAATTCCAATGAGCATTTTGAATAATACTGAACGACAAGAATAACG
729421 TTAGAATTTAGATGCCTT
66 TTAGAATTTAGATGCCTT
*
729439 CAGATGTATCTGCTTCATTCAATTCCAATGAGCATTTTGAATAATACTGAACGACAAGAATAACG
1 CAGATGCATCTGCTTCATTCAATTCCAATGAGCATTTTGAATAATACTGAACGACAAGAATAACG
729504 TTAGAATTTAGATGCCTT
66 TTAGAATTTAGATGCCTT
729522 C
1 C
729523 CTAAATGCAA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (83 bp):
CAGATGCATCTGCTTCATTCAATTCCAATGAGCATTTTGAATAATACTGAACGACAAGAATAACG
TTAGAATTTAGATGCCTT
Found at i:737058 original size:30 final size:30
Alignment explanation
Indices: 737007--737114 Score: 96
Period size: 30 Copynumber: 3.6 Consensus size: 30
736997 CCCATGAAAG
* * *
737007 CAAATCAAAGAAAGA-AGAAACCCACCACAA
1 CAAAACAAAGAAA-ACAAAAACCCATCACAA
* *
737037 CAAACCAAAGAAAACAAAAACCC-TCACAG
1 CAAAACAAAGAAAACAAAAACCCATCACAA
* * *
737066 CAGAAGCAAAGGAAACAAAAGCCCATCACAA
1 CA-AAACAAAGAAAACAAAAACCCATCACAA
737097 CAAAAACAAAG-AAACAAA
1 C-AAAACAAAGAAAACAAA
737115 TATAGGGGTA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
29 7 0.11
30 44 0.68
31 13 0.20
32 1 0.02
ACGTcount: A:0.61, C:0.26, G:0.10, T:0.03
Consensus pattern (30 bp):
CAAAACAAAGAAAACAAAAACCCATCACAA
Found at i:737107 original size:31 final size:31
Alignment explanation
Indices: 737024--737114 Score: 98
Period size: 30 Copynumber: 3.0 Consensus size: 31
737014 AAGAAAGAAG
* * *
737024 AAACCCACCACAAC-AAACCAAAGAAAACAA
1 AAACCCATCACAACAAAAACAAAGGAAACAA
* * *
737054 AAACCC-TCACAGCAGAAGCAAAGGAAACAA
1 AAACCCATCACAACAAAAACAAAGGAAACAA
*
737084 AAGCCCATCACAACAAAAACAAA-GAAACAA
1 AAACCCATCACAACAAAAACAAAGGAAACAA
737114 A
1 A
737115 TATAGGGGTA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
29 5 0.10
30 32 0.64
31 13 0.26
ACGTcount: A:0.60, C:0.29, G:0.09, T:0.02
Consensus pattern (31 bp):
AAACCCATCACAACAAAAACAAAGGAAACAA
Found at i:739329 original size:34 final size:33
Alignment explanation
Indices: 739281--739356 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 33
739271 GGACTTGGGG
739281 ATCAGCTTTTCCCTTTGTACGCTTTGTATCCTAA
1 ATCAG-TTTTCCCTTTGTACGCTTTGTATCCTAA
** *
739315 ATCAGTTTTGCCCTTTGTGTGCTTTGTATCCTGA
1 ATCAGTTTT-CCCTTTGTACGCTTTGTATCCTAA
739349 ATCAGTTT
1 ATCAGTTT
739357 CTCATTTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 4 0.11
34 34 0.89
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.46
Consensus pattern (33 bp):
ATCAGTTTTCCCTTTGTACGCTTTGTATCCTAA
Found at i:740205 original size:34 final size:33
Alignment explanation
Indices: 740157--740232 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 33
740147 GGACTTGGGG
740157 ATCAGCTTTTCCCTTTGTACGCTTTGTATCCTAA
1 ATCAG-TTTTCCCTTTGTACGCTTTGTATCCTAA
** *
740191 ATCAGTTTTGCCCTTTGTGTGCTTTGTATCCTGA
1 ATCAGTTTT-CCCTTTGTACGCTTTGTATCCTAA
740225 ATCAGTTT
1 ATCAGTTT
740233 CTCATTTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 4 0.11
34 34 0.89
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.46
Consensus pattern (33 bp):
ATCAGTTTTCCCTTTGTACGCTTTGTATCCTAA
Found at i:740312 original size:876 final size:876
Alignment explanation
Indices: 738621--740374 Score: 3508
Period size: 876 Copynumber: 2.0 Consensus size: 876
738611 GGATCTTAAT
738621 TGCTCGGCAGCTATATTCAGAGGCGTTTATTTTAGTTTTTGGTTGTAAATGTTGGTTTTTATTGC
1 TGCTCGGCAGCTATATTCAGAGGCGTTTATTTTAGTTTTTGGTTGTAAATGTTGGTTTTTATTGC
738686 ATTAGAAGGTGTTGTTAGATGGGTTAATAGGACAACCATTTTAGAGGCTGATGTCTTAGCTTAAG
66 ATTAGAAGGTGTTGTTAGATGGGTTAATAGGACAACCATTTTAGAGGCTGATGTCTTAGCTTAAG
738751 AAGGAATTGGCTGAACTAGTGTTGCTGTTTATGGGTGGTTTAGGGTTTTTTCTTGTTTATCTGTT
131 AAGGAATTGGCTGAACTAGTGTTGCTGTTTATGGGTGGTTTAGGGTTTTTTCTTGTTTATCTGTT
738816 TCTGTTAAGGGTGTTTACTAGGTTGTATCTTATGTAATTTCTTATGTGCAATATAATCCAAAGGC
196 TCTGTTAAGGGTGTTTACTAGGTTGTATCTTATGTAATTTCTTATGTGCAATATAATCCAAAGGC
738881 ACTCTTTTCCTCCTTCCGTTGATTAAGGAGCTACCCTACTAGCTCCATTAATCAAGAAAGGGGTT
261 ACTCTTTTCCTCCTTCCGTTGATTAAGGAGCTACCCTACTAGCTCCATTAATCAAGAAAGGGGTT
738946 TTTAACGAGGCCTGAAATTCTTATAAAAAAATGAGAAGGAACCTGTGCGACTGAGAATTGGATCA
326 TTTAACGAGGCCTGAAATTCTTATAAAAAAATGAGAAGGAACCTGTGCGACTGAGAATTGGATCA
739011 ATGGGTGAATTTAATGTCAGTATTAACTAGAATAAATCCACGTGAGGAAGCTAAAGATAGTGTAG
391 ATGGGTGAATTTAATGTCAGTATTAACTAGAATAAATCCACGTGAGGAAGCTAAAGATAGTGTAG
739076 TGTGGACGGGAAACAGAGAAGGGATATAACTGCCAAATCCTGTAAGAGCCTGATCATGAGTATTA
456 TGTGGACGGGAAACAGAGAAGGGATATAACTGCCAAATCCTGTAAGAGCCTGATCATGAGTATTA
739141 ATGGGGAAGATTAGTGATGGAGTCAATGTGTTTGGAGAGGACTTGCTCCACCTAGGGTAGAAACA
521 ATGGGGAAGATTAGTGATGGAGTCAATGTGTTTGGAGAGGACTTGCTCCACCTAGGGTAGAAACA
739206 TTTTTGTGGCGTGTTTTTCATCATGGGGTGGCAATTAGAGTAATTTATCCAAAAGAGGAGTCCCT
586 TTTTTGTGGCGTGTTTTTCATCATGGGGTGGCAATTAGAGTAATTTATCCAAAAGAGGAGTCCCT
739271 GGACTTGGGGATCAGCTTTTCCCTTTGTACGCTTTGTATCCTAAATCAGTTTTGCCCTTTGTGTG
651 GGACTTGGGGATCAGCTTTTCCCTTTGTACGCTTTGTATCCTAAATCAGTTTTGCCCTTTGTGTG
739336 CTTTGTATCCTGAATCAGTTTCTCATTTGTTTATCTCCTGCAGAGTAACCTGGGGTTTGTGGAAT
716 CTTTGTATCCTGAATCAGTTTCTCATTTGTTTATCTCCTGCAGAGTAACCTGGGGTTTGTGGAAT
739401 CACTTTTTTCAATTCTGGGGTATCTCCTCTGCACTTCCATTAGAAATCCAGTCTTTGTGTTTAGC
781 CACTTTTTTCAATTCTGGGGTATCTCCTCTGCACTTCCATTAGAAATCCAGTCTTTGTGTTTAGC
739466 ATGGGATGCTTTAGTGCCCAACTCTCACATC
846 ATGGGATGCTTTAGTGCCCAACTCTCACATC
739497 TGCTCGGCAGCTATATTCAGAGGCGTTTATTTTAGTTTTTGGTTGTAAATGTTGGTTTTTATTGC
1 TGCTCGGCAGCTATATTCAGAGGCGTTTATTTTAGTTTTTGGTTGTAAATGTTGGTTTTTATTGC
739562 ATTAGAAGGTGTTGTTAGATGGGTTAATAGGACAACCATTTTAGAGGCTGATGTCTTAGCTTAAG
66 ATTAGAAGGTGTTGTTAGATGGGTTAATAGGACAACCATTTTAGAGGCTGATGTCTTAGCTTAAG
739627 AAGGAATTGGCTGAACTAGTGTTGCTGTTTATGGGTGGTTTAGGGTTTTTTCTTGTTTATCTGTT
131 AAGGAATTGGCTGAACTAGTGTTGCTGTTTATGGGTGGTTTAGGGTTTTTTCTTGTTTATCTGTT
739692 TCTGTTAAGGGTGTTTACTAGGTTGTATCTTATGTAATTTCTTATGTGCAATATAATCCAAAGGC
196 TCTGTTAAGGGTGTTTACTAGGTTGTATCTTATGTAATTTCTTATGTGCAATATAATCCAAAGGC
739757 ACTCTTTTCCTCCTTCCGTTGATTAAGGAGCTACCCTACTAGCTCCATTAATCAAGAAAGGGGTT
261 ACTCTTTTCCTCCTTCCGTTGATTAAGGAGCTACCCTACTAGCTCCATTAATCAAGAAAGGGGTT
739822 TTTAACGAGGCCTGAAATTCTTATAAAAAAATGAGAAGGAACCTGTGCGACTGAGAATTGGATCA
326 TTTAACGAGGCCTGAAATTCTTATAAAAAAATGAGAAGGAACCTGTGCGACTGAGAATTGGATCA
739887 ATGGGTGAATTTAATGTCAGTATTAACTAGAATAAATCCACGTGAGGAAGCTAAAGATAGTGTAG
391 ATGGGTGAATTTAATGTCAGTATTAACTAGAATAAATCCACGTGAGGAAGCTAAAGATAGTGTAG
739952 TGTGGACGGGAAACAGAGAAGGGATATAACTGCCAAATCCTGTAAGAGCCTGATCATGAGTATTA
456 TGTGGACGGGAAACAGAGAAGGGATATAACTGCCAAATCCTGTAAGAGCCTGATCATGAGTATTA
740017 ATGGGGAAGATTAGTGATGGAGTCAATGTGTTTGGAGAGGACTTGCTCCACCTAGGGTAGAAACA
521 ATGGGGAAGATTAGTGATGGAGTCAATGTGTTTGGAGAGGACTTGCTCCACCTAGGGTAGAAACA
740082 TTTTTGTGGCGTGTTTTTCATCATGGGGTGGCAATTAGAGTAATTTATCCAAAAGAGGAGTCCCT
586 TTTTTGTGGCGTGTTTTTCATCATGGGGTGGCAATTAGAGTAATTTATCCAAAAGAGGAGTCCCT
740147 GGACTTGGGGATCAGCTTTTCCCTTTGTACGCTTTGTATCCTAAATCAGTTTTGCCCTTTGTGTG
651 GGACTTGGGGATCAGCTTTTCCCTTTGTACGCTTTGTATCCTAAATCAGTTTTGCCCTTTGTGTG
740212 CTTTGTATCCTGAATCAGTTTCTCATTTGTTTATCTCCTGCAGAGTAACCTGGGGTTTGTGGAAT
716 CTTTGTATCCTGAATCAGTTTCTCATTTGTTTATCTCCTGCAGAGTAACCTGGGGTTTGTGGAAT
740277 CACTTTTTTCAATTCTGGGGTATCTCCTCTGCACTTCCATTAGAAATCCAGTCTTTGTGTTTAGC
781 CACTTTTTTCAATTCTGGGGTATCTCCTCTGCACTTCCATTAGAAATCCAGTCTTTGTGTTTAGC
740342 ATGGGATGCTTTAGTGCCCAACTCTCACATC
846 ATGGGATGCTTTAGTGCCCAACTCTCACATC
740373 TG
1 TG
740375 GTCGTTTATT
Statistics
Matches: 878, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
876 878 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (876 bp):
TGCTCGGCAGCTATATTCAGAGGCGTTTATTTTAGTTTTTGGTTGTAAATGTTGGTTTTTATTGC
ATTAGAAGGTGTTGTTAGATGGGTTAATAGGACAACCATTTTAGAGGCTGATGTCTTAGCTTAAG
AAGGAATTGGCTGAACTAGTGTTGCTGTTTATGGGTGGTTTAGGGTTTTTTCTTGTTTATCTGTT
TCTGTTAAGGGTGTTTACTAGGTTGTATCTTATGTAATTTCTTATGTGCAATATAATCCAAAGGC
ACTCTTTTCCTCCTTCCGTTGATTAAGGAGCTACCCTACTAGCTCCATTAATCAAGAAAGGGGTT
TTTAACGAGGCCTGAAATTCTTATAAAAAAATGAGAAGGAACCTGTGCGACTGAGAATTGGATCA
ATGGGTGAATTTAATGTCAGTATTAACTAGAATAAATCCACGTGAGGAAGCTAAAGATAGTGTAG
TGTGGACGGGAAACAGAGAAGGGATATAACTGCCAAATCCTGTAAGAGCCTGATCATGAGTATTA
ATGGGGAAGATTAGTGATGGAGTCAATGTGTTTGGAGAGGACTTGCTCCACCTAGGGTAGAAACA
TTTTTGTGGCGTGTTTTTCATCATGGGGTGGCAATTAGAGTAATTTATCCAAAAGAGGAGTCCCT
GGACTTGGGGATCAGCTTTTCCCTTTGTACGCTTTGTATCCTAAATCAGTTTTGCCCTTTGTGTG
CTTTGTATCCTGAATCAGTTTCTCATTTGTTTATCTCCTGCAGAGTAACCTGGGGTTTGTGGAAT
CACTTTTTTCAATTCTGGGGTATCTCCTCTGCACTTCCATTAGAAATCCAGTCTTTGTGTTTAGC
ATGGGATGCTTTAGTGCCCAACTCTCACATC
Found at i:766895 original size:68 final size:68
Alignment explanation
Indices: 766810--766938 Score: 195
Period size: 68 Copynumber: 1.9 Consensus size: 68
766800 AATTCTGGTA
* * * *
766810 AAAATGTTCAACAATAATAAAATCAATAGCGCCTAATAATATTTTCGATCATTTTTATCAAATTC
1 AAAACGTTCAACAATAATAAAATCAACAACGCCTAATAATATTTTCGATAATTTTTATCAAATTC
766875 GAT
66 GAT
* * *
766878 AAAACGTTCAATAATAATAAAATCGACAACGTCTAATAATATTTTCGATAATTTTTATCAA
1 AAAACGTTCAACAATAATAAAATCAACAACGCCTAATAATATTTTCGATAATTTTTATCAA
766939 TTTTATTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 54 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (68 bp):
AAAACGTTCAACAATAATAAAATCAACAACGCCTAATAATATTTTCGATAATTTTTATCAAATTC
GAT
Found at i:771256 original size:28 final size:28
Alignment explanation
Indices: 771216--771353 Score: 267
Period size: 28 Copynumber: 4.9 Consensus size: 28
771206 GTTTAGAGTA
771216 TGTATAATTCCTTGTATTCTAAGCAACG
1 TGTATAATTCCTTGTATTCTAAGCAACG
771244 TGTATAATTCCTTGTATTCTAAGCAACG
1 TGTATAATTCCTTGTATTCTAAGCAACG
*
771272 TGTATAATTCCTTGTATTCTAAGAAACG
1 TGTATAATTCCTTGTATTCTAAGCAACG
771300 TGTATAATTCCTTGTATTCTAAGCAACG
1 TGTATAATTCCTTGTATTCTAAGCAACG
771328 TGTATAATTCCTTGTATTCTAAGCAA
1 TGTATAATTCCTTGTATTCTAAGCAA
771354 TGCAACGGTA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 108 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.40
Consensus pattern (28 bp):
TGTATAATTCCTTGTATTCTAAGCAACG
Found at i:776669 original size:21 final size:21
Alignment explanation
Indices: 776643--776682 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
776633 TCTGCTGAAA
* *
776643 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGCTGTGGAGTATG
776664 CTCCACCTGCTGTGGAGTA
1 CTCCACCTGCTGTGGAGTA
776683 CTACTTGTCT
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:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGCTGTGGAGTATG
Found at i:781153 original size:16 final size:16
Alignment explanation
Indices: 781111--781155 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
781101 TAATACTATT
* *
781111 ATAAGATAAATATAAA
1 ATAATATAAAAATAAA
781127 ATAAT-TAAAAATAAA
1 ATAATATAAAAATAAA
*
781142 ATTATATAAAAATA
1 ATAATATAAAAATA
781156 CCTTAAGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (16 bp):
ATAATATAAAAATAAA
Found at i:796039 original size:19 final size:19
Alignment explanation
Indices: 796015--796057 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
796005 GTTTTTAATA
796015 AAATT-ACTACTTTACTTTT
1 AAATTAACTA-TTTACTTTT
* *
796034 AAATTAATTATTTTCTTTT
1 AAATTAACTATTTACTTTT
796053 AAATT
1 AAATT
796058 TAATATGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTAACTATTTACTTTT
Found at i:812070 original size:21 final size:21
Alignment explanation
Indices: 812046--812096 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
812036 TAAAATTGTT
812046 ATTTTTACTTGTAAGTTTTAA-
1 ATTTTTACTT-TAAGTTTTAAC
* *
812067 ATTTTTTAATTTAATTTTTAAC
1 A-TTTTTACTTTAAGTTTTAAC
812089 ATTTTTAC
1 ATTTTTAC
812097 AAGGTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (21 bp):
ATTTTTACTTTAAGTTTTAAC
Found at i:812072 original size:22 final size:22
Alignment explanation
Indices: 812047--812094 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
812037 AAAATTGTTA
*
812047 TTTTTACTTGTAAGTTTTAA-AT
1 TTTTTAATT-TAAGTTTTAACAT
*
812069 TTTTTAATTTAATTTTTAACAT
1 TTTTTAATTTAAGTTTTAACAT
812091 TTTT
1 TTTT
812095 ACAAGGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTTAATTTAAGTTTTAACAT
Done.