Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003511.1 Hibiscus syriacus cultivar Beakdansim tig00007422_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: 68270
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:889 original size:24 final size:24
Alignment explanation
Indices: 861--911 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
851 CGACGCTATC
861 TCCCTATGACGTGCCACCACCTTT
1 TCCCTATGACGTGCCACCACCTTT
**
885 TCCCTATGACGTGCCACTGCCTTT
1 TCCCTATGACGTGCCACCACCTTT
909 TCC
1 TCC
912 ATCAAGGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.41, G:0.14, T:0.31
Consensus pattern (24 bp):
TCCCTATGACGTGCCACCACCTTT
Found at i:3060 original size:13 final size:14
Alignment explanation
Indices: 3044--3076 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3034 AAATGTTCGG
*
3044 AAAAAAAGAGA-GA
1 AAAAAAAGACATGA
3057 AAAAAAAGACATGA
1 AAAAAAAGACATGA
3071 AAAAAA
1 AAAAAA
3077 TGAAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (14 bp):
AAAAAAAGACATGA
Found at i:4173 original size:19 final size:17
Alignment explanation
Indices: 4137--4175 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
4127 ACTTTTCAAG
*
4137 TTATTTTCATTTTTCTT
1 TTATTTTCATTTTGCTT
4154 TTATTTTCAAGTTTTGCTT
1 TTATTTTC-A-TTTTGCTT
4173 TTA
1 TTA
4176 ATATGCTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (17 bp):
TTATTTTCATTTTGCTT
Found at i:9093 original size:95 final size:95
Alignment explanation
Indices: 8914--9142 Score: 280
Period size: 95 Copynumber: 2.4 Consensus size: 95
8904 ATACGATTGA
*
8914 GGTAGTATCGATACCACTGTAAGGGTATCGATACCAAGAAAACATCGAATCTAATATTGGTATCG
1 GGTAGTATCGATACCA-TGTAAGGGTATCGATACCAAGAAAACATCGAACCTAATATTGGTATCG
* *
8979 ATACCGCAAAGGGATATCGGTATCATATTAT
65 ATACCGCAAAGGGATATCGGTACCATACTAT
* *
9010 GGTAGTATCGATACCATGGTAAGGGTATCGATACCATG-CAACATCGAACCTAATATTGGTATCG
1 GGTAGTATCGATACCAT-GTAAGGGTATCGATACCAAGAAAACATCGAACCTAATATTGGTATCG
* ** * *
9074 ATACTGGTAGGGGGTATCGGTACCATACTAT
65 ATACCGCAAAGGGATATCGGTACCATACTAT
* * * *
9105 AGAAGTATCGGTACCATAGTATAGAAGTATCGATACCA
1 GGTAGTATCGATACCAT-GTA-AG-GGTATCGATACCA
9143 GGGTAGAAGT
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
95 66 0.57
96 37 0.32
97 12 0.10
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (95 bp):
GGTAGTATCGATACCATGTAAGGGTATCGATACCAAGAAAACATCGAACCTAATATTGGTATCGA
TACCGCAAAGGGATATCGGTACCATACTAT
Found at i:9113 original size:22 final size:22
Alignment explanation
Indices: 9087--9142 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
9077 CTGGTAGGGG
9087 GTATCGGTACCATACTATAGAA
1 GTATCGGTACCATACTATAGAA
*
9109 GTATCGGTACCATAGTATAGAA
1 GTATCGGTACCATACTATAGAA
*
9131 GTATCGATACCA
1 GTATCGGTACCA
9143 GGGTAGAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (22 bp):
GTATCGGTACCATACTATAGAA
Found at i:9686 original size:34 final size:34
Alignment explanation
Indices: 9642--9722 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
9632 AGTTGAAATA
* *
9642 CATATGGGTGCATTATTGGCATAAATGAATAATG
1 CATATGGGTGCATTATCGGCATAAAAGAATAATG
*
9676 TATATGGGTGCATTATCGGCATAAAAGAATAATG
1 CATATGGGTGCATTATCGGCATAAAAGAATAATG
9710 CATATGGGTGCAT
1 CATATGGGTGCAT
9723 GGCATGAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (34 bp):
CATATGGGTGCATTATCGGCATAAAAGAATAATG
Found at i:10218 original size:65 final size:65
Alignment explanation
Indices: 10130--10259 Score: 179
Period size: 65 Copynumber: 2.0 Consensus size: 65
10120 TAATTATATT
* * * *
10130 GATGTTTCAAAAGAGTCAGGAGTGCATCGATACATGGCTTGTGCATCGGTATAGAAAATGAATTC
1 GATGTTTCAAAAGAGTCAAGAGTGCATCGATACATGGCTTGTGAATCGGTACACAAAATGAATTC
* * * * *
10195 GATGTTTCAAAATATTCAAGAGTGCATCGATGCATGTCTTGTGAATCGGTACACAAAATGCATTC
1 GATGTTTCAAAAGAGTCAAGAGTGCATCGATACATGGCTTGTGAATCGGTACACAAAATGAATTC
10260 AAAATGGGTG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (65 bp):
GATGTTTCAAAAGAGTCAAGAGTGCATCGATACATGGCTTGTGAATCGGTACACAAAATGAATTC
Found at i:12153 original size:35 final size:35
Alignment explanation
Indices: 12102--12171 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
12092 AAAACAAGTA
12102 TGGTACCTATAGTAGAGATCTTGTCTACGACCAGG
1 TGGTACCTATAGTAGAGATCTTGTCTACGACCAGG
* *
12137 TGGTGCCTATGGTAGAGATCTTGTCTACGACCAGG
1 TGGTACCTATAGTAGAGATCTTGTCTACGACCAGG
12172 CACATTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (35 bp):
TGGTACCTATAGTAGAGATCTTGTCTACGACCAGG
Found at i:19501 original size:20 final size:20
Alignment explanation
Indices: 19478--19520 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
19468 ATTTCACCAC
*
19478 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
19498 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
19518 ATG
1 ATG
19521 GGCTCTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:20580 original size:65 final size:65
Alignment explanation
Indices: 20511--20644 Score: 214
Period size: 65 Copynumber: 2.1 Consensus size: 65
20501 ACACTAATTA
*
20511 CATTCGATGTTTCAAAAGAGCCAAGAGTGCATTGATGCATGGCTTGTGCAACGATACACAAAATG
1 CATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGCAACGATACACAAAATG
* ** * *
20576 CATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATG
1 CATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGCAACGATACACAAAATG
20641 CATT
1 CATT
20645 TGAAGTGGGT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (65 bp):
CATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGCAACGATACACAAAATG
Found at i:21025 original size:27 final size:27
Alignment explanation
Indices: 20995--21051 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
20985 CATGTTATAT
*
20995 GATATTCATGCATACAACATATACCCA
1 GATATTCATGCATACAACAAATACCCA
21022 GATATTCATGCATACAACAAATACCCA
1 GATATTCATGCATACAACAAATACCCA
21049 GAT
1 GAT
21052 CTTTATGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.09, T:0.25
Consensus pattern (27 bp):
GATATTCATGCATACAACAAATACCCA
Found at i:22976 original size:18 final size:18
Alignment explanation
Indices: 22945--22993 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
22935 GAATATTTAT
* * *
22945 CCGAAGAACAACTATGTC
1 CCGAAGGACCACTATATC
22963 CCGAAGGACCACTATATC
1 CCGAAGGACCACTATATC
*
22981 TCGAAGGACCACT
1 CCGAAGGACCACT
22994 GATAATCCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.35, C:0.31, G:0.18, T:0.16
Consensus pattern (18 bp):
CCGAAGGACCACTATATC
Found at i:28534 original size:10 final size:10
Alignment explanation
Indices: 28519--28543 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28509 ACATAAGTAA
28519 GGATTAGATG
1 GGATTAGATG
28529 GGATTAGATG
1 GGATTAGATG
28539 GGATT
1 GGATT
28544 CCATATGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.40, T:0.32
Consensus pattern (10 bp):
GGATTAGATG
Found at i:30459 original size:95 final size:96
Alignment explanation
Indices: 30326--30532 Score: 267
Period size: 95 Copynumber: 2.2 Consensus size: 96
30316 CAGTATCATT
* * *
30326 GTAAGGCTATCGATAACAAGCAAACATCGAATCTAATATTGGTATCGAT-GCCGTAAGGGGATAT
1 GTAAGGGTATCGATACCAAGCAAACATCGAACCTAATATTGGTATCGATAGCCGT-AGGGGATAT
* * *
30390 TGGTACCATAGTATGGTAGTATCGATACCATG
65 CGGTACCATAGTATAGAAGTATCGATACCATG
*** *
30422 GTAAGGGTATCGATACCAAG-AAACATCGAACCTAATATTGGTATCGATATTGGTAGGGGGTATC
1 GTAAGGGTATCGATACCAAGCAAACATCGAACCTAATATTGGTATCGATAGCCGTAGGGGATATC
*
30486 GGTACCATAGTATAGAAGTATCGGTACCATG
66 GGTACCATAGTATAGAAGTATCGATACCATG
*
30517 GT-AGAAGTATCGATAC
1 GTAAG-GGTATCGATAC
30533 TTTGGAGCCA
Statistics
Matches: 97, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
94 2 0.02
95 75 0.77
96 20 0.21
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (96 bp):
GTAAGGGTATCGATACCAAGCAAACATCGAACCTAATATTGGTATCGATAGCCGTAGGGGATATC
GGTACCATAGTATAGAAGTATCGATACCATG
Found at i:30523 original size:20 final size:22
Alignment explanation
Indices: 30481--30528 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
30471 TTGGTAGGGG
30481 GTATCGGTACCATAGTATAGAA
1 GTATCGGTACCATAGTATAGAA
*
30503 GTATCGGTACCAT-G-GTAGAA
1 GTATCGGTACCATAGTATAGAA
30523 GTATCG
1 GTATCG
30529 ATACTTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 13 0.52
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (22 bp):
GTATCGGTACCATAGTATAGAA
Found at i:30592 original size:2 final size:2
Alignment explanation
Indices: 30585--30646 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
30575 AAAGTTAATA
30585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30627 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
30647 CCTTTTGAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31084 original size:79 final size:79
Alignment explanation
Indices: 30993--31147 Score: 247
Period size: 79 Copynumber: 2.0 Consensus size: 79
30983 AGAACAAATG
* * * ** *
30993 ATAAAAGAATAATGCATATGGGTGTATTATTGGCATGAAATGATGCCTTAGCTGAAATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTAGCATGAAAGGATGCCAAAGCTGAAATGCATATG
31058 GGTGCATTATCGGC
66 GGTGCATTATCGGC
*
31072 ATAAAAGAATAATGCATATGGGTGCATTATTAGCATGAAAGGATGCCAAAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTAGCATGAAAGGATGCCAAAGCTGAAATGCATATG
31137 GGTGCATTATC
66 GGTGCATTATC
31148 AACATAAAGG
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTAGCATGAAAGGATGCCAAAGCTGAAATGCATATG
GGTGCATTATCGGC
Found at i:40131 original size:38 final size:35
Alignment explanation
Indices: 40092--40162 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
40082 ATCAATGAAG
*
40092 AAGAAGAAGCTATCATATGTTGAAATCACACGGAA
1 AAGAAGAAGCCATCATATGTTGAAATCACACGGAA
*
40127 AAGAAGTAGCCATCATATGTTGAAATCACACGGAA
1 AAGAAGAAGCCATCATATGTTGAAATCACACGGAA
40162 A
1 A
40163 CATGAAGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (35 bp):
AAGAAGAAGCCATCATATGTTGAAATCACACGGAA
Found at i:41649 original size:21 final size:22
Alignment explanation
Indices: 41625--41673 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
41615 TATAATTTTT
41625 AATAATT-AAAAAACTCAACAA
1 AATAATTAAAAAAACTCAACAA
*
41646 AATAATTAAAAAAACTCAATAA
1 AATAATTAAAAAAACTCAACAA
41668 AATAAT
1 AATAAT
41674 ATTTTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.22
Consensus pattern (22 bp):
AATAATTAAAAAAACTCAACAA
Found at i:45341 original size:15 final size:15
Alignment explanation
Indices: 45317--45347 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45307 AATCTTCATG
*
45317 TCCTATTCTCTAATC
1 TCCTAGTCTCTAATC
45332 TCCTAGTCTCTAATC
1 TCCTAGTCTCTAATC
45347 T
1 T
45348 TGCAAATGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.32, G:0.03, T:0.45
Consensus pattern (15 bp):
TCCTAGTCTCTAATC
Found at i:46179 original size:25 final size:25
Alignment explanation
Indices: 46126--46179 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
46116 GGCATGTGCC
* *
46126 ATGTCACCTAAAATGATAATGTCAC
1 ATGTCACCCAAAATGATAATGTCAA
* *
46151 ATGTCACCCAAAATGATATTGTGAA
1 ATGTCACCCAAAATGATAATGTCAA
46176 ATGT
1 ATGT
46180 GTCATGTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (25 bp):
ATGTCACCCAAAATGATAATGTCAA
Found at i:46468 original size:32 final size:32
Alignment explanation
Indices: 46338--46546 Score: 139
Period size: 32 Copynumber: 6.7 Consensus size: 32
46328 TGGGAAATGA
* ** *
46338 CACATCA-CCAAAGTGATGATATAACAAATGA
1 CACATCACCCAAAGTGATGATGTAACATGTGT
**
46369 CACATCATTCAAAGTGATG-TAGT---ATGTGT
1 CACATCACCCAAAGTGATGAT-GTAACATGTGT
* * * *
46398 CATATCACCCAAAGTGATGACATGT--TATAT-A
1 CACATCACCCAAAGTGATG--ATGTAACATGTGT
46429 CAACATCACCCAAAGTGATGATGTAACATGTGT
1 C-ACATCACCCAAAGTGATGATGTAACATGTGT
* * *
46462 CGCATCACCCAAAGTGATGATGTAACATATGC
1 CACATCACCCAAAGTGATGATGTAACATGTGT
* *
46494 CACATCACCCAAAGAT-ATGATGTGATATGTGT
1 CACATCACCCAAAG-TGATGATGTAACATGTGT
** * *
46526 CATGTCATCTAAAGTGATGAT
1 CACATCACCCAAAGTGATGAT
46547 ATGCCATATG
Statistics
Matches: 140, Mismatches: 26, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
29 19 0.14
30 4 0.03
31 12 0.09
32 103 0.74
33 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (32 bp):
CACATCACCCAAAGTGATGATGTAACATGTGT
Found at i:46499 original size:64 final size:62
Alignment explanation
Indices: 46338--46562 Score: 197
Period size: 64 Copynumber: 3.6 Consensus size: 62
46328 TGGGAAATGA
* * **
46338 CACATCA-CCAAAGTGATGATATAACAAATGACACATCATTCAAAGTGATG-TAGT-ATGTGT
1 CACATCACCCAAAGTGATGATATAACATATGCCACATCACCCAAAGTGATGAT-GTAATGTGT
* * *** * *
46398 CATATCACCCAAAGTGATGACATGTTATATACAACATCACCCAAAGTGATGATGTAACATGTGT
1 CACATCACCCAAAGTGATGATATAACATATGCCACATCACCCAAAGTGATGATGT-A-ATGTGT
* *
46462 CGCATCACCCAAAGTGATGATGTAACATATGCCACATCACCCAAAGAT-ATGATGTGATATGTGT
1 CACATCACCCAAAGTGATGATATAACATATGCCACATCACCCAAAG-TGATGATGT-A-ATGTGT
** * * **
46526 CATGTCATCTAAAGTGATGATATGCCATATGCCACAT
1 CACATCACCCAAAGTGATGATATAACATATGCCACAT
46563 ATGAATTATT
Statistics
Matches: 129, Mismatches: 30, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
60 6 0.05
61 35 0.27
62 1 0.01
64 86 0.67
65 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (62 bp):
CACATCACCCAAAGTGATGATATAACATATGCCACATCACCCAAAGTGATGATGTAATGTGT
Found at i:47083 original size:45 final size:44
Alignment explanation
Indices: 47015--47124 Score: 123
Period size: 44 Copynumber: 2.5 Consensus size: 44
47005 GGTAGATCTA
* * *
47015 GGTCACACAGCATCAG-CATCTCCCAAATATCTCAGGAGAGGTCCG
1 GGTCACATAGCATC-GTCACCTCCC-AATACCTCAGGAGAGGTCCG
* ** *
47060 GGTCACATAGCATCGTCACCTCCCAATACCTTAGGCTAGGTCTG
1 GGTCACATAGCATCGTCACCTCCCAATACCTCAGGAGAGGTCCG
*
47104 GGTAACATAGCATCGTCACCT
1 GGTCACATAGCATCGTCACCT
47125 TGCTTGGCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 36 0.64
45 20 0.36
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.22
Consensus pattern (44 bp):
GGTCACATAGCATCGTCACCTCCCAATACCTCAGGAGAGGTCCG
Found at i:47742 original size:2 final size:2
Alignment explanation
Indices: 47737--47784 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
47727 ACACACACAC
47737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47779 AT -T AT A
1 AT AT AT A
47785 GTTTGCAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47877 original size:37 final size:36
Alignment explanation
Indices: 47810--48190 Score: 376
Period size: 38 Copynumber: 10.5 Consensus size: 36
47800 TTAAAAATAC
*
47810 GTTTTTAAAATA-TTTTGAAAATATATATAATATATA
1 GTTTTTAAAACATTTTTGAAAAT-TATATAATATATA
*
47846 GTTTTTAAAACATTTTTAAAAATGTATATAATATATAA
1 GTTTTTAAAACATTTTTGAAAAT-TATATAATATAT-A
* *
47884 ATTTTTAAATCA-TTTTGAAAAATTATATAATATATA
1 GTTTTTAAAACATTTTTG-AAAATTATATAATATATA
47920 GTTTTTGAAAACATTTTTGAAAACTTATATAATATATA
1 GTTTTT-AAAACATTTTTGAAAA-TTATATAATATATA
*
47958 GTTTTGAAAACA--TTT----A-TATAT--TATATA
1 GTTTTTAAAACATTTTTGAAAATTATATAATATATA
47985 GTTTTTAAAAAACA-TTTTGAAAA-TATATAATATATA
1 GTTTTT--AAAACATTTTTGAAAATTATATAATATATA
*
48021 GATTTTTAAAACATTTTTGAAAATATATATATTATATA
1 G-TTTTTAAAACATTTTTGAAAAT-TATATAATATATA
48059 GTTTTTTAAAACATTTTTGAAAACTTATATAATATATA
1 G-TTTTTAAAACATTTTTGAAAA-TTATATAATATATA
* * *
48097 ATTTTTAAAATATTTTGGAAAATATATATAATATATA
1 GTTTTTAAAACATTTTTGAAAAT-TATATAATATATA
* * * *
48134 -ATTTTAAAATATGTTTTTGAAAATATATTATATTATATG
1 GTTTTTAAAACA--TTTTTGAAAAT-TA-TATAATATATA
*
48173 GTTTTGAAAAACATTTTT
1 GTTTT-TAAAACATTTTT
48191 TTAAAAAAAT
Statistics
Matches: 296, Mismatches: 23, Indels: 49
0.80 0.06 0.13
Matches are distributed among these distances:
27 11 0.04
29 11 0.04
30 3 0.01
31 1 0.00
34 6 0.02
35 9 0.03
36 44 0.15
37 89 0.30
38 99 0.33
39 15 0.05
40 3 0.01
41 5 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (36 bp):
GTTTTTAAAACATTTTTGAAAATTATATAATATATA
Found at i:47968 original size:25 final size:26
Alignment explanation
Indices: 47934--47994 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
47924 TTGAAAACAT
47934 TTTTGAAAAC-TTATATAATATATAG
1 TTTTGAAAACATTATATAATATATAG
*
47959 TTTTGAAAACATTTATATATTATATAG
1 TTTTGAAAACA-TTATATAATATATAG
*
47986 TTTTTAAAA
1 TTTTGAAAA
47995 AACATTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 10 0.31
27 22 0.69
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (26 bp):
TTTTGAAAACATTATATAATATATAG
Found at i:47983 original size:139 final size:138
Alignment explanation
Indices: 47821--48111 Score: 412
Period size: 139 Copynumber: 2.1 Consensus size: 138
47811 TTTTTAAAAT
*
47821 ATTTTG-AAA-ATATATATAATATATAGTTTTT-AAAACATTTTTAAAAATGTATATAATATATA
1 ATTTTGAAAACATTTATATAATATATAGTTTTTAAAAACA-TTTTAAAAA--TATATAATATATA
*
47883 AATTTTTAAATCA-TTTTGAAAA-ATTATATAATATATAGTTTTTGAAAACATTTTTGAAAACTT
63 AATTTTTAAAACATTTTTGAAAATA-TATATAATATATAGTTTTTGAAAACATTTTTGAAAACTT
47946 ATATAATATATA
127 ATATAATATATA
* * * *
47958 GTTTTGAAAACATTTATATATTATATAGTTTTTAAAAAACATTTTGAAAATATATAATATATAGA
1 ATTTTGAAAACATTTATATAATATATAGTTTTT-AAAAACATTTTAAAAATATATAATATATAAA
* *
48023 TTTTTAAAACATTTTTGAAAATATATATATTATATAGTTTTTTAAAACATTTTTGAAAACTTATA
65 TTTTTAAAACATTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAACTTATA
48088 TAATATATA
130 TAATATATA
* *
48097 ATTTTTAAAATATTT
1 ATTTTGAAAACATTT
48112 TGGAAAATAT
Statistics
Matches: 137, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
137 5 0.04
138 27 0.20
139 90 0.66
140 9 0.07
141 6 0.04
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (138 bp):
ATTTTGAAAACATTTATATAATATATAGTTTTTAAAAACATTTTAAAAATATATAATATATAAAT
TTTTAAAACATTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAACTTATAT
AATATATA
Found at i:47996 original size:29 final size:27
Alignment explanation
Indices: 47944--48001 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
47934 TTTTGAAAAC
*
47944 TTATATAATATATAGTTTTGAAAACAT
1 TTATATAATATATAGTTTTAAAAACAT
*
47971 TTATATATTATATAGTTTTTAAAAAACAT
1 TTATATAATATATAG-TTTT-AAAAACAT
48000 TT
1 TT
48002 TGAAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 14 0.52
28 4 0.15
29 9 0.33
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (27 bp):
TTATATAATATATAGTTTTAAAAACAT
Found at i:48011 original size:29 final size:27
Alignment explanation
Indices: 47944--48013 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 27
47934 TTTTGAAAAC
* *
47944 TTATATAATATATAGTTTTGAAAACAT
1 TTATAAAATATATAGTTTTAAAAACAT
* *
47971 TTATATATTATATAGTTTTTAAAAAACAT
1 TTATAAAATATATAG-TTTT-AAAAACAT
48000 TT-TGAAAATATATA
1 TTAT-AAAATATATA
48014 ATATATAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 14 0.39
28 5 0.14
29 17 0.47
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (27 bp):
TTATAAAATATATAGTTTTAAAAACAT
Found at i:48267 original size:18 final size:18
Alignment explanation
Indices: 48226--48269 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
48216 TTTTAAAAAA
*
48226 TATTTATTTATTTAATTT
1 TATTTATTTAGTTAATTT
*
48244 TTTTTATTT-GTTAATTGT
1 TATTTATTTAGTTAATT-T
48262 TATTTATT
1 TATTTATT
48270 ATTCATTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (18 bp):
TATTTATTTAGTTAATTT
Found at i:51874 original size:22 final size:22
Alignment explanation
Indices: 51827--51887 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
51817 ATATTTTATT
* * *
51827 TTAACTAATTTACATTTAGATT
1 TTAACTAATTTATAATTAGATG
*
51849 TTAACTAATTTATAATTATATG
1 TTAACTAATTTATAATTAGATG
* *
51871 TTAAGTACTTTATAATT
1 TTAACTAATTTATAATT
51888 TTAAAGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.51
Consensus pattern (22 bp):
TTAACTAATTTATAATTAGATG
Found at i:53548 original size:23 final size:23
Alignment explanation
Indices: 53533--53587 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
53523 GTCAACAATA
53533 AAAGTCAACATCGGTCAATGATC
1 AAAGTCAACATCGGTCAATGATC
53556 AAAGTCAACATCGGTCAATGATC
1 AAAGTCAACATCGGTCAATGATC
53579 AAAGTCAAC
1 AAAGTCAAC
53588 TTTAGTCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (23 bp):
AAAGTCAACATCGGTCAATGATC
Found at i:53595 original size:23 final size:23
Alignment explanation
Indices: 53533--53603 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
53523 GTCAACAATA
*
53533 AAAGTCAACATCGGTCAATGATC
1 AAAGTCAACATCAGTCAATGATC
*
53556 AAAGTCAACATCGGTCAATGATC
1 AAAGTCAACATCAGTCAATGATC
* * *
53579 AAAGTCAACTTTAGTCAACGATC
1 AAAGTCAACATCAGTCAATGATC
53602 AA
1 AA
53604 CAATAATCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (23 bp):
AAAGTCAACATCAGTCAATGATC
Found at i:57115 original size:55 final size:55
Alignment explanation
Indices: 57068--57432 Score: 404
Period size: 55 Copynumber: 6.7 Consensus size: 55
57058 TTCAAATGAT
* * * * *
57068 AAGTCTGCTCCCTATTCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAATAAAC
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAAC
** * * * *
57123 GGGTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCAAACAATCTTCATA-AAAT
1 AAGTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAAC
**
57178 GGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
* * *
57233 GAGTCCACTCTCTATTCCTTAAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
* * *
57288 AGGTTCGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
** *
57343 GGGTCCGCTCTCTATTCCTTCAGAGAGTATA-AGACTCG----ATCTTCAATAAAC
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAAC
** * *
57394 GTGTCCGCTCACTATTCCTTCAGAGAGTATAGGACTCGA
1 AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGA
57433 TATTCAACAA
Statistics
Matches: 276, Mismatches: 26, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
51 46 0.17
54 5 0.02
55 220 0.80
56 5 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (55 bp):
AAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
Found at i:57261 original size:110 final size:109
Alignment explanation
Indices: 57074--57467 Score: 461
Period size: 110 Copynumber: 3.7 Consensus size: 109
57064 TGATAAGTCT
* * * * *
57074 GCTCCCTATTCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAATAAACGGGTCCGCTCCCTA-
1 GCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTAT
* *
57137 TCCGTTCAGGGAGTATAGAACTCAAACAATCTTCATA-AAATGGGTCC
65 TCC-TTCAGAGAGTATAGAACTC-AACAATCTTCA-ACAAACGGGTCC
* *
57184 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGAGTCCACTCTCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATT
* * *
57249 CCTTAAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTTC
66 CCTTCAGAGAGTATAGAACTC-AACAATCTTCAACAAACGGGTCC
*
57294 GCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATT
* * *
57359 CCTTCAGAGAGTATA-AGACT---CGATCTTCAATAAACGTGTCC
66 CCTTCAGAGAGTATAGA-ACTCAACAATCTTCAACAAACGGGTCC
* * * *
57400 GCTCACTATTCCTTCAGAGAGTATAGGACTCG----ATATTCAACAAACGTGTCCGCTC-CTTAT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTC-TAT
57460 TCCTTCAG
65 TCCTTCAG
57468 TGTATGGAAC
Statistics
Matches: 252, Mismatches: 27, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
101 1 0.00
102 32 0.13
106 45 0.18
109 2 0.01
110 168 0.67
111 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (109 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTCAACAATCTTCAACAAACGGGTCC
Found at i:57332 original size:165 final size:161
Alignment explanation
Indices: 57079--57432 Score: 471
Period size: 165 Copynumber: 2.2 Consensus size: 161
57069 AGTCTGCTCC
* * * *
57079 CTATTCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAATAAACGGGTCCGCTCCCTATCCGTT
1 CTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTATCCGTT
* *
57143 CAGGGAGTATAGAACTCAAACAATCTTCATA-AAATGGGTCCGCTCTCTATTCCTTCAGAGAGTA
65 CAGAGAGTATAGAACTCAAACAATCTTCA-ACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTA
*
57207 T-AGAACTCGAACAATCTTCAACAAACGAGTCCACTCT
129 TAAG-ACTCG----ATCTTCAACAAACGAGTCCACTCA
* * * * *
57244 CTATTCCTTAAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTTCGCTCTCTATTCTTTC
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTATCCGTTC
*
57309 AGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
66 AGAGAGTATAGAACTCAAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
* * *
57374 AGACTCGATCTTCAATAAACGTGTCCGCTCA
131 AGACTCGATCTTCAACAAACGAGTCCACTCA
*
57405 CTATTCCTTCAGAGAGTATAGGACTCGA
1 CTATTCCTTCAGAGAGTATAGAACTCGA
57433 TATTCAACAA
Statistics
Matches: 168, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
161 46 0.27
164 1 0.01
165 118 0.70
166 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (161 bp):
CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAGGTCCGCTCCCTATCCGTTC
AGAGAGTATAGAACTCAAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATA
AGACTCGATCTTCAACAAACGAGTCCACTCA
Found at i:57637 original size:54 final size:54
Alignment explanation
Indices: 57469--57921 Score: 734
Period size: 54 Copynumber: 8.5 Consensus size: 54
57459 TTCCTTCAGT
* * *
57469 GTATGGAACTCAAACATCTTCTTCTTATGGGTTCGCT-CC-CTTTATCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
* *
57521 GTATGGAACTCGAACATCTTCTTCTTACGGATTTGCT-CC-CTTTCTCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
*
57573 GTATGGAACTCGAGCATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
* * *
57627 GTATGGAACTCAAACATATTCTTCTTACAGGTTCGCTCCCTCTTTCTCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
*
57681 GTATGGAACTCGAATATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
*
57735 GTATGGAACTCAAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
* *
57789 GTATGGAACTCGAACATCTTCTTCTTATGGGTTCGCTCCCTCTTTCTCTAGAGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
* * *
57843 GTATGAAACTCGAACATCTTCTTCTTACGGGTTCGCTCCTTCTTTCTTTAGGGA
1 GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
57897 GTATGGAACTCGAACATCTTCTTCT
1 GTATGGAACTCGAACATCTTCTTCT
57922 GCTTTACTAC
Statistics
Matches: 372, Mismatches: 27, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
52 81 0.22
53 2 0.01
54 289 0.78
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (54 bp):
GTATGGAACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGA
Found at i:58346 original size:37 final size:37
Alignment explanation
Indices: 58295--58418 Score: 144
Period size: 37 Copynumber: 3.4 Consensus size: 37
58285 TTGCTCCAAC
* * * *
58295 ACTCTTCCGAGAAGGCTTAAAAAGGATATT-ATTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGAT-TTGCTTCACT
*
58332 ACTCTTCGGTGAAGGCTTAAGATGG-TTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
* * *
58368 ACTCTTTGGTGAAGGCTCAAAATGGATTTGCTTCATT
1 ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
*
58405 ACTCTTTGGTGAAG
1 ACTCTTCGGTGAAG
58419 ACTTGACTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
35 2 0.03
36 29 0.38
37 45 0.59
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAAATGGATTTGCTTCACT
Found at i:58373 original size:36 final size:37
Alignment explanation
Indices: 58326--58418 Score: 143
Period size: 36 Copynumber: 2.5 Consensus size: 37
58316 AAGGATATTA
* * *
58326 TTCACTACTCTTCGGTGAAGGCTTAAGATGG-TTTGC
1 TTCACTACTCTTTGGTGAAGGCTCAAAATGGATTTGC
58362 TTCACTACTCTTTGGTGAAGGCTCAAAATGGATTTGC
1 TTCACTACTCTTTGGTGAAGGCTCAAAATGGATTTGC
*
58399 TTCATTACTCTTTGGTGAAG
1 TTCACTACTCTTTGGTGAAG
58419 ACTTGACTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 28 0.54
37 24 0.46
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (37 bp):
TTCACTACTCTTTGGTGAAGGCTCAAAATGGATTTGC
Found at i:63118 original size:72 final size:72
Alignment explanation
Indices: 63001--63151 Score: 248
Period size: 72 Copynumber: 2.1 Consensus size: 72
62991 CCCCTAATAG
* *
63001 GTTCTTGATAAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTT
1 GTTCTTGATAAGTTACTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
63066 TTCATAT
66 TTCATAT
* * *
63073 GTTCTTGATCATTTACTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATAAGTTACTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
63138 TTCATAT
66 TTCATAT
*
63145 TTTCTTG
1 GTTCTTG
63152 TGTAATAGGG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (72 bp):
GTTCTTGATAAGTTACTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:67405 original size:17 final size:19
Alignment explanation
Indices: 67364--67402 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
67354 TTTGGTTCAC
67364 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAG-G
67384 GGAATGT-AGATTACCAGG
1 GGAATGTAAGATTACCAGG
67402 G
1 G
67403 AATAGGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 10 0.53
20 7 0.37
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.23
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:67594 original size:16 final size:15
Alignment explanation
Indices: 67569--67602 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
67559 ATATATTTTC
67569 TTTAAAAAATTTAAA
1 TTTAAAAAATTTAAA
*
67584 TTTATAAAAATTTATA
1 TTTA-AAAAATTTAAA
67600 TTT
1 TTT
67603 TAACCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAAAAAATTTAAA
Done.