Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006954.1 Hibiscus syriacus cultivar Beakdansim tig00017878_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: 100097
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:1295 original size:20 final size:22
Alignment explanation
Indices: 1250--1307 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1240 GCATGGGTAG
1250 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1274 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
1294 TGCATCGATGCACT
1 TGCATCGATGCACT
1308 TCAAGGGAAA
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:2064 original size:18 final size:18
Alignment explanation
Indices: 2036--2141 Score: 140
Period size: 18 Copynumber: 5.9 Consensus size: 18
2026 GAGGGTCTAC
*
2036 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
2054 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
2072 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* * *
2090 ATGGTTCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
*
2108 GTGGTCCTTCGAGACATA
1 GTGGTCCTTCGGGACATA
*
2126 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
2142 AATTCTACAC
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 74 1.00
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:2083 original size:36 final size:36
Alignment explanation
Indices: 2036--2141 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
2026 GAGGGTCTAC
*
2036 GTGGTCATTCGGGACATAATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATAATGGTCCTTCGGGACACA
*
2072 GTGGTCCTTCGGGACATAATGGTTCTTCGGGACACA
1 GTGGTCCTTCGGGACATAATGGTCCTTCGGGACACA
* * *
2108 GTGGTCCTTCGAGACATAGTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACATAATGGTCCTTCGGGACA
2142 AATTCTACAC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (36 bp):
GTGGTCCTTCGGGACATAATGGTCCTTCGGGACACA
Found at i:2402 original size:2 final size:2
Alignment explanation
Indices: 2397--2424 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2387 ATATATGTTA
2397 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
2425 GAATGAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5430 original size:24 final size:24
Alignment explanation
Indices: 5403--5463 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
5393 GTATGGGTAG
* *
5403 TGCATCAATGCATATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
*
5427 TGCATCGATGTACATGTTAAAGAA
1 TGCATCGATGCACATGTTAAAGAA
5451 TGCATCGATGCAC
1 TGCATCGATGCAC
5464 TTCAAGGGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAAGAA
Found at i:5862 original size:54 final size:54
Alignment explanation
Indices: 5798--5931 Score: 232
Period size: 54 Copynumber: 2.5 Consensus size: 54
5788 GAGGGTCTAC
* *
5798 GTGGTCCTTCGAGATATAGTGGTCCTTCGGGACATAATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACATAATGGTCCTTCGGGACACA
* *
5852 GTGGTCCTTCGGGACATAATGGTCCTTCGGGACATAATGGTTCTTCGGGACACA
1 GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACATAATGGTCCTTCGGGACACA
5906 GTGGTCCTTCGGGACATAGTGGTCCT
1 GTGGTCCTTCGGGACATAGTGGTCCT
5932 ATGGGATAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (54 bp):
GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACATAATGGTCCTTCGGGACACA
Found at i:5937 original size:18 final size:18
Alignment explanation
Indices: 5798--5931 Score: 196
Period size: 18 Copynumber: 7.4 Consensus size: 18
5788 GAGGGTCTAC
* *
5798 GTGGTCCTTCGAGATATA
1 GTGGTCCTTCGGGACATA
5816 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
5834 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
5852 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
5870 ATGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* * *
5888 ATGGTTCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
5906 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
5924 GTGGTCCT
1 GTGGTCCT
5932 ATGGGATAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 104 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:6199 original size:2 final size:2
Alignment explanation
Indices: 6194--6225 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6184 ATATATGTTA
6194 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
6226 GAATATCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10850 original size:15 final size:15
Alignment explanation
Indices: 10830--10862 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
10820 ACAATTTCTG
*
10830 TAAAATTATATTAAT
1 TAAAATTATATCAAT
10845 TAAAATTATATCAAT
1 TAAAATTATATCAAT
10860 TAA
1 TAA
10863 TATTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATTATATCAAT
Found at i:12005 original size:24 final size:24
Alignment explanation
Indices: 11961--12007 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11951 TTTGGTTATT
* * *
11961 TGATTTTATATTTTTTTAAATTTA
1 TGATTTTATATCTCTTAAAATTTA
11985 TGATTTTATATCTCTTAAAATTT
1 TGATTTTATATCTCTTAAAATTT
12008 TTATATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (24 bp):
TGATTTTATATCTCTTAAAATTTA
Found at i:12547 original size:26 final size:27
Alignment explanation
Indices: 12487--12548 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
12477 TCTTATATTT
*
12487 TAATTTTTTTTATTTTTATATTGATAA
1 TAATTTTTTATATTTTTATATTGATAA
*
12514 TATGTTTTTTATATTTTTATACTT-ATAA
1 TA-ATTTTTTATATTTTTATA-TTGATAA
12542 -AATTTTT
1 TAATTTTT
12549 AAAGTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 5 0.17
27 3 0.10
28 20 0.67
29 2 0.07
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (27 bp):
TAATTTTTTATATTTTTATATTGATAA
Found at i:13098 original size:15 final size:16
Alignment explanation
Indices: 13061--13100 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
13051 CAAAATTATA
*
13061 ATTTTATTTTTTAAGT
1 ATTTTATTTCTTAAGT
13077 ATTTTATTTCTTAA-T
1 ATTTTATTTCTTAAGT
*
13092 GTTTTATTT
1 ATTTTATTT
13101 TAAGATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (16 bp):
ATTTTATTTCTTAAGT
Found at i:28504 original size:22 final size:22
Alignment explanation
Indices: 28465--28528 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
28455 TTTTGGTGCA
*
28465 GAGGGAATCGA-TCACCCCCCAT
1 GAGGGAACCGATTC-CCCCCCAT
**
28487 GAGGGAACCGATT-CCCCCTTT
1 GAGGGAACCGATTCCCCCCCAT
28508 GAAGAGGAACCGATTCCCCCC
1 G-AG-GGAACCGATTCCCCCC
28529 ACAAGAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 7 0.20
22 12 0.34
23 11 0.31
24 5 0.14
ACGTcount: A:0.25, C:0.36, G:0.23, T:0.16
Consensus pattern (22 bp):
GAGGGAACCGATTCCCCCCCAT
Found at i:28547 original size:21 final size:22
Alignment explanation
Indices: 28509--28549 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28499 TCCCCCTTTG
*
28509 AAGAGGAACCGATTCCCCCCAC
1 AAGAGGAACCGATACCCCCCAC
*
28531 AAGA-GAATCGATACCCCCC
1 AAGAGGAACCGATACCCCCC
28550 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.34, C:0.39, G:0.17, T:0.10
Consensus pattern (22 bp):
AAGAGGAACCGATACCCCCCAC
Found at i:35488 original size:16 final size:16
Alignment explanation
Indices: 35467--35499 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35457 ATCTTATTGT
35467 CATATATGTAACTTAA
1 CATATATGTAACTTAA
35483 CATATATGTAACTTAA
1 CATATATGTAACTTAA
35499 C
1 C
35500 GGAAAGTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (16 bp):
CATATATGTAACTTAA
Found at i:38446 original size:16 final size:16
Alignment explanation
Indices: 38425--38486 Score: 124
Period size: 16 Copynumber: 3.9 Consensus size: 16
38415 ATCTTTTTGA
38425 TTCATCCATCTATTGG
1 TTCATCCATCTATTGG
38441 TTCATCCATCTATTGG
1 TTCATCCATCTATTGG
38457 TTCATCCATCTATTGG
1 TTCATCCATCTATTGG
38473 TTCATCCATCTATT
1 TTCATCCATCTATT
38487 TAGCCATCCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.19, C:0.26, G:0.10, T:0.45
Consensus pattern (16 bp):
TTCATCCATCTATTGG
Found at i:38495 original size:32 final size:32
Alignment explanation
Indices: 38427--38497 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
38417 CTTTTTGATT
* *
38427 CATCCATCTATTGGTTCATCCATCTATTGGTT
1 CATCCATCTATTGGTTCATCCATCTATTAGTC
38459 CATCCATCTATTGGTTCATCCATCTATTTAG-C
1 CATCCATCTATTGGTTCATCCATCTA-TTAGTC
38491 CATCCAT
1 CATCCAT
38498 GGATCAATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 33 0.92
33 3 0.08
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (32 bp):
CATCCATCTATTGGTTCATCCATCTATTAGTC
Found at i:42494 original size:60 final size:59
Alignment explanation
Indices: 42400--42578 Score: 198
Period size: 60 Copynumber: 3.0 Consensus size: 59
42390 CCATCATATG
* * * *
42400 TCCCCAAACTATGACCCTCATTTTAAATTGATCCTTAAACTTTTAAATATTTTAATTTCA
1 TCCCCAAACTATGA-TCTCAATTTAAATTAATCCTTAAACTTTTAAATATTTCAATTTCA
* * *
42460 TCCCCAAACTATGATACTCAATTTAAATTAATCCTTAAACATTTGAACATTTCAATTTCA
1 TCCCCAAACTATGAT-CTCAATTTAAATTAATCCTTAAACTTTTAAATATTTCAATTTCA
** * * * *
42520 TCGTCAAACTATGACTCTC-ATTCTAAATTAGTCCCTAAACTTCTAAATCTTTCAATTTC
1 TCCCCAAACTATGA-TCTCAATT-TAAATTAATCCTTAAACTTTTAAATATTTCAATTTC
42579 TTCCATACAT
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
59 3 0.03
60 96 0.96
61 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (59 bp):
TCCCCAAACTATGATCTCAATTTAAATTAATCCTTAAACTTTTAAATATTTCAATTTCA
Found at i:43227 original size:28 final size:28
Alignment explanation
Indices: 43194--43248 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
43184 CTGTTGTTGG
43194 TTTCAAGCATTGACTCGACAATATAATC
1 TTTCAAGCATTGACTCGACAATATAATC
* *
43222 TTTCAAGTATTGGCTCGACAATATAAT
1 TTTCAAGCATTGACTCGACAATATAAT
43249 GTAAATGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (28 bp):
TTTCAAGCATTGACTCGACAATATAATC
Found at i:47694 original size:27 final size:27
Alignment explanation
Indices: 47657--47778 Score: 203
Period size: 27 Copynumber: 4.6 Consensus size: 27
47647 TTGTAGGAAT
47657 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
47682 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
**
47709 TATAGAGATATGATTTGTTGTCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
47736 TATAGAGATATGATTTGTTGCCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
47763 TATAGAGATATGATTT
1 TATAGAGATATGATTT
47779 TGTAAATAGA
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
25 7 0.08
27 85 0.92
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:55849 original size:2 final size:2
Alignment explanation
Indices: 55844--55880 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
55834 AATGAAAAAA
55844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55881 ACAATGTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56291 original size:33 final size:33
Alignment explanation
Indices: 56254--56324 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
56244 AAAATGCTTC
56254 GGTTTTAGTGTTTCAAT-AGAACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAAG-ACTCAAATACGTT
56287 GGTTTTAGTGTTTCAATAAGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAAGACTCAAATACGTT
56320 GGTTT
1 GGTTT
56325 ATTTTCTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 35 0.95
34 2 0.05
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAAGACTCAAATACGTT
Found at i:56388 original size:3 final size:3
Alignment explanation
Indices: 56374--56437 Score: 75
Period size: 3 Copynumber: 22.7 Consensus size: 3
56364 GGCCTGTAAA
*
56374 AAT AAT AA- AAT AAT AAT ATT AAT AAT AAT AAT AAT AAAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
56418 AAT -AT AAT -AT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
56438 AATGTTTTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
2 10 0.19
3 40 0.75
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:56907 original size:84 final size:82
Alignment explanation
Indices: 56783--57383 Score: 534
Period size: 84 Copynumber: 7.2 Consensus size: 82
56773 CTAAATGGAA
* ** *
56783 TCGAACTCGAAGGTCTTTG--G-CAGATAACCATTCTTGCCTTGAGCTATGCTGTAAATGATAGT
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTC-TAACTTGAGTTATGCTGTAAATGAT-GT
* * * *
56845 GCCTTTGAGGTGAGTGGAG
64 GCCTTGGAGCTGAGCGTAG
*
56864 TCGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTAACCTTGAGTTATG-TCGTAAATGATGT
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAA-CTTGAGTTATGCT-GTAAATGATGT
* * * * *
56928 ACCCTCGAAGCTGAGTGTAA
64 -GCCTTGGAGCTGAGCGTAG
* * * * * * *
56948 TCGAACTCGAGGGTCTTTG--G-CAGATAACCCTTTTCGACTTAAGCTATGATGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCT-AACTTGAGTTATGCTGTAAATGATGTG
57010 CCTTGGAGCTGAGCGTAG
65 CCTTGGAGCTGAGCGTAG
** * * * * *
57028 TCGAACTCGAAGGTCTTTGGTTGGTAGATAACACTTCCTGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTT-CTAACTTGAGTTATGCTGTAAATGATGT
57093 GCCTTGGAGCTGAGCGTAG
64 GCCTTGGAGCTGAGCGTAG
* * * * * *
57112 TCGAACTCGAAGATCTTTTGGTCACAAATAACCCTTCTAGCATTGAGTTATGTTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAAC-TTGAGTTATGCTGTAAATGATGT
57177 GCCTTGGAGCTGAGCGTAG
64 GCCTTGGAGCTGAGCGTAG
* * * * *
57196 TCGAACTCGAAGGTCTTTTGGTCACAAATAACCCTTCTAGTCTTGAGTTATGTTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTA-ACTTGAGTTATGCTGTAAATGATGT
* * * *
57261 GCCCTCGAAGCTGAGTGTAA
64 G-CCTTGGAGCTGAGCGTAG
* * * * * *
57281 TAGAACTC-AAGGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATG
1 TCGAACTCGAA-GGTCTT-TGTTGACAGATAACCCTTC-TAACTTGAGTTATGCTGTAAATGATG
*
57345 TACCTTGGAGCTGAGCGTAG
63 TGCCTTGGAGCTGAGCGTAG
* *
57365 TCAAACTCGAAGGCCTTTG
1 TCGAACTCGAAGGTCTTTG
57384 GTGGGCACGA
Statistics
Matches: 429, Mismatches: 70, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
80 31 0.07
81 51 0.12
82 3 0.01
83 10 0.02
84 266 0.62
85 67 0.16
86 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (82 bp):
TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAACTTGAGTTATGCTGTAAATGATGTGC
CTTGGAGCTGAGCGTAG
Found at i:57191 original size:168 final size:162
Alignment explanation
Indices: 56781--57385 Score: 644
Period size: 168 Copynumber: 3.6 Consensus size: 162
56771 AGCTAAATGG
* * * *
56781 AATCGAACTCGAAGGTCTTTGGCAGATAACCATTCTTGCCTTGAGCTATGCTGTAAATGATAGTG
1 AATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGAT-GTG
* * * * * *
56846 CCTTTGAGGTGAGTGGAGTCGAACTCGAAGGTATTT-GTTGACAGATAACCCTTCTAACCTTGAG
65 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTGA-CTTGAG
*
56910 TTATGTCGTAAATGATGTACCCTCGAAGCTGAGTGT
129 TTATGT-GTAAATGATGT-GCCTCGAAGCTGAGTGT
* *
56946 AATCGAACTCGAGGGTCTTTGGCAGATAACCCTT-TTCGACTTAAGCTATGATGCAAATGATGTG
1 AATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTT-GACTTAAGCTATGCTGCAAATGATGTG
** * *
57010 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGTAGATAACACTTCCTGACTTAAG
65 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTT-CTGACTTGAG
* * * * *
57075 TTATGCTGCAAATGATATGCCTTGGAGCTGAGCGT
129 TTATG-TGTAAATGATGTGCCTCGAAGCTGAGTGT
* * * * * * * *
57110 AGTCGAACTCGAAGATCTTTTGGTCACAAATAACCCTTCTAG-CATTGAGTTATGTTGTAAATGA
1 AATCGAACTCGAAGGTC-TTTGG---CAGATAACCCTTCTTGAC-TTAAGCTATGCTGCAAATGA
* * *
57174 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TCACAAATAACCCTTCTAGTC
61 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGACAGATAACCCTTCT-GAC
57238 TTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGT
124 TTGAGTTATG-TGTAAATGATGTG-CCTCGAAGCTGAGTGT
* *
57279 AATAGAACTC-AAGGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGA
1 AATCGAACTCGAA-GGTC-T---TTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGA
* * *
57343 TGTACCTTGGAGCTGAGCGTAGTCAAACTCGAAGGCCTTTGGT
61 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
57386 GGGCACGATT
Statistics
Matches: 366, Mismatches: 55, Indels: 34
0.80 0.12 0.07
Matches are distributed among these distances:
164 63 0.17
165 90 0.25
166 4 0.01
167 3 0.01
168 104 0.28
169 97 0.27
170 1 0.00
172 4 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (162 bp):
AATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGC
CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATAACCCTTCTGACTTGAGTT
ATGTGTAAATGATGTGCCTCGAAGCTGAGTGT
Found at i:57342 original size:253 final size:248
Alignment explanation
Indices: 56785--57376 Score: 683
Period size: 253 Copynumber: 2.4 Consensus size: 248
56775 AAATGGAATC
* * * * *
56785 GAACTCGAAGGTC-T---TTGGCAGATAACCATTCTTGCCTTGAGCTATGCTGTAAATGATAGTG
1 GAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATA-TG
* * * * * * * * *
56846 CCTTTGAGGTGAGTGGAGTCGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTAACCTTGAGT
65 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGATATTTGGTCACAAATAACCCTTCTAACATTGAGT
* * *
56911 TATGTCGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAAC
130 TATGTCGTAAATGATGTACCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAAATAAC
* * * * * *
56976 CCTTTTCGACTTAAGCTATGATGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
195 CCTTCTAGACTTAAGCTATGATGCAAATGATGTGCCTCGAAGCTGAGCGTAATA
* * * *
57030 GAACTCGAAGGTCTTTGGTTGGTAGATAACACTTCCTGACTTAAGTTATGCTGCAAATGATATGC
1 GAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATATGC
* *
57095 CTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAAATAACCCTTCTAGCATTGAGT
66 CTTGGAGCTGAGCGTAGTCGAACTCGAAGAT-ATTTGGTCACAAATAACCCTTCTAACATTGAGT
* * * * *
57160 TATGTTGTAAATGATGT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAAA
130 TATGTCGTAAATGATGTACCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGG---CAAA
* * * * * *
57224 TAACCCTTCTAGTCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATA
191 TAACCCTTCTAGACTTAAGCTATGATGCAAATGATGTG-CCTCGAAGCTGAGCGTAATA
* *
57283 GAACTC-AAGGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTA
1 GAACTCGAA-GGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATATG
*
57347 CCTTGGAGCTGAGCGTAGTCAAACTCGAAG
65 CCTTGGAGCTGAGCGTAGTCGAACTCGAAG
57377 GCCTTTGGTG
Statistics
Matches: 290, Mismatches: 46, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
245 13 0.04
246 1 0.00
248 57 0.20
249 84 0.29
252 36 0.12
253 99 0.34
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (248 bp):
GAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATATGC
CTTGGAGCTGAGCGTAGTCGAACTCGAAGATATTTGGTCACAAATAACCCTTCTAACATTGAGTT
ATGTCGTAAATGATGTACCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGCAAATAACC
CTTCTAGACTTAAGCTATGATGCAAATGATGTGCCTCGAAGCTGAGCGTAATA
Found at i:57698 original size:110 final size:110
Alignment explanation
Indices: 57508--58147 Score: 1036
Period size: 110 Copynumber: 5.9 Consensus size: 110
57498 TGTTTTGAGA
*
57508 CCAATATCCTTCGCCGTGAAGTTGAAATTGACTC----TGAAACTGAAAAGTTATTTGTTGACAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAG
* * *
57569 CCAGTCGCCCATTCGCTGTGAAGTTGAGCTAGTGTTGTCTCGAGT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
* * * * *
57614 CCAATATTCTTCGCTGTAAAGTTGAAATTGACTTTGAAAGAAACTGAAAAGTTGTTTGTTGACAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAG
57679 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
* *
57724 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGAAAAGTTATTAGTTGACAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAG
* *
57789 TCAGTTGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
* * * *
57834 CCAATATCATTCCCTGTGAAATTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAG
57899 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
*
57944 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAA
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAG
* * *
58009 TCAGTCGCCCCTTCGCTGTGAAGTTGAGATTTTGTTGTCTTGAGT
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
* * *
58054 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACCG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAG
58119 TCAGTCGCCCCTTCGCTGTGAAGTTGAGC
66 TCAGTCGCCCCTTCGCTGTGAAGTTGAGC
58148 AACCACCATC
Statistics
Matches: 491, Mismatches: 39, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
106 30 0.06
110 461 0.94
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (110 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAG
TCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
Found at i:61765 original size:46 final size:41
Alignment explanation
Indices: 61709--61808 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 41
61699 AGAAAAGAAT
*
61709 AATAAAAAATATTAATATAATAATATTAATGAAAAATG-AAAAATA
1 AATAAAAAATATTAATAT-AT-ATA-T-AT-AAAAATGTAAAAAGA
*
61754 AATAAATAAATA-T-ATATATATATATAACAATGTAAAAAGA
1 AATAAA-AAATATTAATATATATATATAAAAATGTAAAAAGA
61794 AATAAAAAATATTAA
1 AATAAAAAATATTAA
61809 AATTAGGAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
39 11 0.22
40 15 0.31
41 2 0.04
42 3 0.06
43 2 0.04
44 4 0.08
45 7 0.14
46 5 0.10
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (41 bp):
AATAAAAAATATTAATATATATATATAAAAATGTAAAAAGA
Found at i:61845 original size:15 final size:15
Alignment explanation
Indices: 61818--61860 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
61808 AAATTAGGAG
* *
61818 AAAATAAAAAAATAT
1 AAAATAAATAAATAA
*
61833 AAAGTAAATAAATAA
1 AAAATAAATAAATAA
61848 AAAATGAAATAAA
1 AAAAT-AAATAAA
61861 AAGAATAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAATAA
Found at i:62252 original size:3 final size:3
Alignment explanation
Indices: 62238--62296 Score: 52
Period size: 3 Copynumber: 19.3 Consensus size: 3
62228 GGCTTACAAA
*
62238 AAT AAT AA- AAT AAT AAT ATAT AAT AAT AAT AAGA AAT AAAT ATAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA-T AAT -AAT A-AT AAT
62286 -AT AAT AA- AAT A
1 AAT AAT AAT AAT A
62297 TTTTTGTAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
2 6 0.13
3 30 0.64
4 11 0.23
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:62264 original size:13 final size:11
Alignment explanation
Indices: 62238--62296 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 11
62228 GGCTTACAAA
62238 AATAATAAAAT
1 AATAATAAAAT
62249 AATAATATATAAT
1 AATAATA-A-AAT
62262 AATAATAAGAAAT
1 AATAAT-A-AAAT
*
62275 AA-ATATATAAT
1 AATA-ATAAAAT
62286 -ATAATAAAAT
1 AATAATAAAAT
62296 A
1 A
62297 TTTTTGTAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
10 7 0.18
11 11 0.28
12 3 0.08
13 16 0.41
14 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:62269 original size:24 final size:25
Alignment explanation
Indices: 62238--62296 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 25
62228 GGCTTACAAA
62238 AATAATAAAATAAT-AATATATAAT
1 AATAATAAAATAATAAATATATAAT
*
62262 AATAATAAGA-AATAAATATATAAT
1 AATAATAAAATAATAAATATATAAT
62286 -ATAATAAAATA
1 AATAATAAAATA
62297 TTTTTGTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
AATAATAAAATAATAAATATATAAT
Found at i:73667 original size:21 final size:23
Alignment explanation
Indices: 73643--73713 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 23
73633 TGTATGTATG
73643 TTATGATA-A-TATACATTATAC
1 TTATGATACAGTATACATTATAC
* *
73664 TTATGTATACATTATA-AGTATA-
1 TTATG-ATACAGTATACATTATAC
*
73686 -TACTCATACAAGTATACATTATAC
1 TTA-TGATAC-AGTATACATTATAC
73710 TTAT
1 TTAT
73714 AATATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
21 11 0.29
22 9 0.24
23 11 0.29
24 5 0.13
25 2 0.05
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (23 bp):
TTATGATACAGTATACATTATAC
Found at i:73767 original size:26 final size:26
Alignment explanation
Indices: 73735--73785 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
73725 ATAATATGTG
* *
73735 TGATGAATGTCATGATAATATAATTA
1 TGATGAATGCCATGACAATATAATTA
73761 TGATGAATGCCATGACAATATAATT
1 TGATGAATGCCATGACAATATAATT
73786 TATGTGTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (26 bp):
TGATGAATGCCATGACAATATAATTA
Found at i:73888 original size:53 final size:51
Alignment explanation
Indices: 73831--74064 Score: 124
Period size: 53 Copynumber: 4.5 Consensus size: 51
73821 ATGCATTCAT
73831 TATATGTATATACTTATATAAGTATATAATATAAGTATACATTATACTTATAA
1 TATATGTATATAC--ATATAAGTATATAATATAAGTATACATTATACTTATAA
* ** ** * * **
73884 TATATGTAGGTATGCATATAAGTATATCTTAGTGTGTGTATATATATAAAGTAT-A
1 TATATGTA--TATACATATAAGTATATAATA-TAAGTATACAT-TAT-ACTTATAA
* * * * * *
73939 TAAAT-TATAAAGCATA-AA-TATATAATATATA-TATA-A-TATGCATACAT
1 TATATGTATATA-CATATAAGTATATAATATA-AGTATACATTATACTTATAA
* *
73986 TATATTTATATACTTATATAAGTATATAATACAAGTATACATTATACTTATAA
1 TATATGTATATAC--ATATAAGTATATAATATAAGTATACATTATACTTATAA
** *
74039 TATAAATATATATATATATA-TATATA
1 TATATGTATATACATATA-AGTATATA
74065 TGATGAATGT
Statistics
Matches: 132, Mismatches: 32, Indels: 36
0.66 0.16 0.18
Matches are distributed among these distances:
46 2 0.02
47 8 0.06
48 5 0.04
49 4 0.03
50 7 0.05
51 32 0.24
52 6 0.05
53 43 0.33
54 9 0.07
55 12 0.09
56 4 0.03
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (51 bp):
TATATGTATATACATATAAGTATATAATATAAGTATACATTATACTTATAA
Found at i:73968 original size:2 final size:2
Alignment explanation
Indices: 73956--74065 Score: 51
Period size: 2 Copynumber: 58.0 Consensus size: 2
73946 TAAAGCATAA
** * *
73956 AT AT AT A- AT AT AT AT AT A- AT AT GC AT AC AT -T AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
73995 AT ACT -T AT AT A- AGT AT AT A- AT AC A- AGT AT AC AT -T AT ACT
1 AT A-T AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T
*
74034 -T AT A- AT AT AA 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
74066 GATGAATGTC
Statistics
Matches: 81, Mismatches: 13, Indels: 28
0.66 0.11 0.23
Matches are distributed among these distances:
1 10 0.12
2 67 0.83
3 4 0.05
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:74145 original size:155 final size:155
Alignment explanation
Indices: 73752--74154 Score: 349
Period size: 155 Copynumber: 2.6 Consensus size: 155
73742 TGTCATGATA
* * * *
73752 ATATA-AT-TATGATGAATGCCATGACAATATAATTTATGTGTATATAATGTATATTATACATTT
1 ATATATATATATGATGAATGTCATGATAATATAA-TTATGTATATATAATGCATATTATACATTT
* *
73815 ATACTTATGCATTCATTATATG------TATATACTTATATAAGTATATAATATAAGTATACATT
65 ATATTTATGCATTCATTATATGTATATTTATATACTTATATAAGTATATAATACAAGTATACATT
** *
73874 ATACTTATAATATATGTAGGTATGCAT
130 ATACTTATAATATAAATA-GTATACAT
* * ** * * * *
73901 ATA-AGTATATCTTAGTGTGTGT-AT-AT-ATATAAAGTATATAAATTATAAAGCATAAATATAT
1 ATATA-TATATATGA-TGAATGTCATGATAATAT-AATTATGTATA-TATAATGCAT--AT-TAT
* * * *
73962 A-ATATATATATAAT--ATGCA-TACAT-TATATTTATATACTTATATAAGTATATAATACAAGT
59 ACATTTATAT-TTATGCATTCATTATATGTATATTTATATACTTATATAAGTATATAATACAAGT
*
74022 ATACATTATACTTATAATATAAATA-TATATAT
123 ATACATTATACTTATAATATAAATAGTATACAT
74054 ATATATATATATGATGAATGTCATGATAATATAATTCATGTATATCA-AATGCATATTATACATT
1 ATATATATATATGATGAATGTCATGATAATATAATT-ATGTATAT-ATAATGCATATTATACATT
74118 TATATTTATGCATTCATTATATGTATATACTTATATA
64 TATATTTATGCATTCATTATATGTATAT--TTATATA
74155 AGTGTAATGT
Statistics
Matches: 191, Mismatches: 34, Indels: 50
0.69 0.12 0.18
Matches are distributed among these distances:
148 1 0.01
149 12 0.06
150 17 0.09
151 16 0.08
152 26 0.14
153 28 0.15
154 17 0.09
155 67 0.35
157 7 0.04
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (155 bp):
ATATATATATATGATGAATGTCATGATAATATAATTATGTATATATAATGCATATTATACATTTA
TATTTATGCATTCATTATATGTATATTTATATACTTATATAAGTATATAATACAAGTATACATTA
TACTTATAATATAAATAGTATACAT
Found at i:74181 original size:2 final size:2
Alignment explanation
Indices: 74174--74260 Score: 67
Period size: 2 Copynumber: 45.5 Consensus size: 2
74164 TATACTTAAA
74174 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * * * * *
74215 AG AT AT GT GT AT AC AT -T AT AT -T AT AA AT AT -T GT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74254 AT AT AT A
1 AT AT AT A
74261 AAAAGTAATT
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
1 5 0.07
2 62 0.91
3 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:76574 original size:30 final size:30
Alignment explanation
Indices: 76538--76624 Score: 147
Period size: 30 Copynumber: 2.9 Consensus size: 30
76528 TGTCTAATTT
*
76538 AATAAAAAATAATTATTTGTGATTAATAAA
1 AATAAAAAATAATTATTTGTAATTAATAAA
76568 AATAAAAAATAATTATTTGTAATTAATAAA
1 AATAAAAAATAATTATTTGTAATTAATAAA
* *
76598 AATAAAAAATAAATACTTGTAATTAAT
1 AATAAAAAATAATTATTTGTAATTAAT
76625 TTATTTAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.36
Consensus pattern (30 bp):
AATAAAAAATAATTATTTGTAATTAATAAA
Found at i:78504 original size:60 final size:60
Alignment explanation
Indices: 78440--78555 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
78430 ATTTAGGGGT
* * * * * * *
78440 GAAATTGGAACATTCAAAATTTTGAGAACTATTTTAGAATGAAAATCATAGTTTAATGAA
1 GAAATTGGAACATTCAAAAATTTAAGAACCAATTTAAAATAAAAATAATAGTTTAATGAA
* * *
78500 GAAATTGGAATATTTAAAAATTTAATAACCAATTTAAAATAAAAATAATAGTTTAA
1 GAAATTGGAACATTCAAAAATTTAAGAACCAATTTAAAATAAAAATAATAGTTTAA
78556 GAATATGTGA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (60 bp):
GAAATTGGAACATTCAAAAATTTAAGAACCAATTTAAAATAAAAATAATAGTTTAATGAA
Found at i:80820 original size:104 final size:103
Alignment explanation
Indices: 80627--80888 Score: 490
Period size: 103 Copynumber: 2.5 Consensus size: 103
80617 TGAAGTATTG
* *
80627 TTGAAGATAAGCGCATATAAAGAAAAGTTCGAGAAAAAAAATGATAATTGTAATACTCAATCTTT
1 TTGAAGATAAGTGCATATAAAGAAAAGTTTGAG-AAAAAAATGATAATTGTAATACTCAATCTTT
80692 GTTTAGCCTTTGAATCTTAATTTTTTATTTAAAATTTAT
65 GTTTAGCCTTTGAATCTTAATTTTTTATTTAAAATTTAT
80731 TTGAAGATAAGTGCATATAAAGAAAAGTTTGAGAAAAAAATGATAATTGTAATACTCAATCTTTG
1 TTGAAGATAAGTGCATATAAAGAAAAGTTTGAGAAAAAAATGATAATTGTAATACTCAATCTTTG
80796 TTTAGCCTTTGAATCTTAATTTTTTATTTAAAATTTAT
66 TTTAGCCTTTGAATCTTAATTTTTTATTTAAAATTTAT
80834 TTGAAGATAAGTGCATATAAAGAAAAGTTTGAGAAAAAAATGATAATTGT-ATACT
1 TTGAAGATAAGTGCATATAAAGAAAAGTTTGAGAAAAAAATGATAATTGTAATACT
80889 TATTGAACCT
Statistics
Matches: 156, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
102 5 0.03
103 120 0.77
104 31 0.20
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (103 bp):
TTGAAGATAAGTGCATATAAAGAAAAGTTTGAGAAAAAAATGATAATTGTAATACTCAATCTTTG
TTTAGCCTTTGAATCTTAATTTTTTATTTAAAATTTAT
Found at i:81099 original size:18 final size:18
Alignment explanation
Indices: 81057--81091 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
81047 CAAATACTTT
*
81057 ATTATTATTTTTATATAA
1 ATTATAATTTTTATATAA
81075 ATTATAATTTTT-TATAA
1 ATTATAATTTTTATATAA
81092 CTTTATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATAATTTTTATATAA
Found at i:82884 original size:61 final size:62
Alignment explanation
Indices: 82810--82934 Score: 141
Period size: 61 Copynumber: 2.0 Consensus size: 62
82800 TTTAAAATAT
* *
82810 TAATATTGGTATATTTTATTGAAATAAAAATATT-ATAAAT-TATTTT-AAT-TATTTATTAAAA
1 TAATAGTGGTATATTATATT---ATAAAAATATTAATAAATATATTTTAAATATATTTATTAAAA
* * * *
82871 TAATAGTGTTATATTATATTTTAAAAATATTAATTAGTATATTTTAAATATATTTATTAAAA
1 TAATAGTGGTATATTATATTATAAAAATATTAATAAATATATTTTAAATATATTTATTAAAA
82933 TA
1 TA
82935 TTATTAGATT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
58 10 0.19
59 4 0.07
60 6 0.11
61 20 0.37
62 14 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.50
Consensus pattern (62 bp):
TAATAGTGGTATATTATATTATAAAAATATTAATAAATATATTTTAAATATATTTATTAAAA
Found at i:82914 original size:23 final size:23
Alignment explanation
Indices: 82885--82929 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
82875 AGTGTTATAT
82885 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
82908 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
82930 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:82935 original size:23 final size:23
Alignment explanation
Indices: 82886--82954 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
82876 GTGTTATATT
* * **
82886 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
82909 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
82932 ATATTATTAGAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
82955 TATTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:82948 original size:62 final size:58
Alignment explanation
Indices: 82834--82952 Score: 141
Period size: 62 Copynumber: 2.0 Consensus size: 58
82824 TTTATTGAAA
*
82834 TAAAAATATTATAAATTATTTTAATTATTTATTAAAATAATAGTGTTATATTATATTT
1 TAAAAATATTATAAATTATTTTAATTATTTATTAAAATAATAGTGATATATTATATTT
* * * *
82892 TAAAAATATTAATTAGTATATTTTAAATATATTTATTAAAATATTATTAGAT-TATTATATT
1 TAAAAATATT-ATAAAT-TATTTT-AAT-TATTTATTAAAATAATAGT-GATATATTATATT
82953 AATATTAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
58 10 0.20
59 4 0.08
60 6 0.12
61 3 0.06
62 26 0.51
63 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.51
Consensus pattern (58 bp):
TAAAAATATTATAAATTATTTTAATTATTTATTAAAATAATAGTGATATATTATATTT
Found at i:82992 original size:19 final size:19
Alignment explanation
Indices: 82924--83004 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
82914 TTAAATATAT
82924 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
82943 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
82962 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
82982 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
83000 -TATTA
1 TTATTA
83005 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:83089 original size:8 final size:8
Alignment explanation
Indices: 83078--83131 Score: 58
Period size: 8 Copynumber: 6.9 Consensus size: 8
83068 AAATATAATA
83078 TATTATAT
1 TATTATAT
*
83086 TATTATAA
1 TATTATAT
83094 TA-TA-AT
1 TATTATAT
*
83100 TGATTATTT
1 T-ATTATAT
*
83109 TATTATAA
1 TATTATAT
83117 TATTATAT
1 TATTATAT
83125 TATTATA
1 TATTATA
83132 AATATTAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 2 0.05
7 3 0.08
8 30 0.81
9 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (8 bp):
TATTATAT
Found at i:83099 original size:23 final size:23
Alignment explanation
Indices: 83069--83131 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
83059 TTAAAATAAA
83069 AATATAATATATTATATTATTAT
1 AATATAATATATTATATTATTAT
*
83092 AATATAAT-TGATTATTTTATTAT
1 AATATAATAT-ATTATATTATTAT
*
83115 AATATTATATTATTATA
1 AATATAATA-TATTATA
83132 AATATTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 1 0.03
23 27 0.79
24 5 0.15
25 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:86402 original size:36 final size:37
Alignment explanation
Indices: 86317--86420 Score: 160
Period size: 35 Copynumber: 2.9 Consensus size: 37
86307 GTTGATAATG
* *
86317 CTCAAATTAGGTCATCCCACTAATATTAGAAATATGT
1 CTCAAATTAGGTTATCCCACTAGTATTAGAAATATGT
86354 -T-AAATTAGGTTATCCCACTAGTATTAGAAATAT-T
1 CTCAAATTAGGTTATCCCACTAGTATTAGAAATATGT
*
86388 CTCAAATTAGGTTATCCCACTAGTATTGGAAAT
1 CTCAAATTAGGTTATCCCACTAGTATTAGAAAT
86421 GACAATTTTG
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
34 1 0.02
35 31 0.50
36 30 0.48
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (37 bp):
CTCAAATTAGGTTATCCCACTAGTATTAGAAATATGT
Found at i:87806 original size:66 final size:64
Alignment explanation
Indices: 87721--87883 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 64
87711 TTGTTGAAGG
* * * *
87721 TGCATCGATGCACATGGAGTGTATCGATGCA-CTCATTTAAAATAAATGAACATCGAAT-GACAT
1 TGCATCGATGCATAAGGAGTGCATCGATGCACCT-ACTTAAAATAAA--AACATCGAATAG-CAT
87784 TAA
62 TAA
* * * *
87787 TGCATCGATGCATAAGGAGTGCATCTATGCACCTACTTAAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCACCTACTTAAAATAAAAACATCGAATAGCATTAA
* *
87851 TGCACCGATGCAT-GGGTAGTGCATCGATGCACC
1 TGCATCGATGCATAAGG-AGTGCATCGATGCACC
87884 CGTCAAGGGA
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 2 0.02
64 41 0.49
65 1 0.01
66 37 0.45
67 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCACCTACTTAAAATAAAAACATCGAATAGCATTAA
Found at i:88454 original size:22 final size:22
Alignment explanation
Indices: 88429--88506 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
88419 TGGTATATTA
*
88429 GTCCTTTGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
88451 GTCCTTCGGGACGTATCGAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
88473 GTCCTTCAGGACATATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
88495 GTCCTTCGGGAC
1 GTCCTTCGGGAC
88507 ATAGTGGTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.15, C:0.26, G:0.31, T:0.28
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:88524 original size:40 final size:42
Alignment explanation
Indices: 88437--88525 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 42
88427 TAGTCCTTTG
*
88437 GGACGTATCCAGTGGTCCTTCGGGACGTATCGAGTGGTCCTTCA
1 GGACATATCCAGTGGTCCTTCGGGACG-ATC-AGTGGTCCTTCA
*
88481 GGACATATCCAGTGGTCCTTCGGGAC-AT-AGTGGTTCTTCA
1 GGACATATCCAGTGGTCCTTCGGGACGATCAGTGGTCCTTCA
88521 GGACA
1 GGACA
88526 AATATTGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 16 0.37
42 2 0.05
44 25 0.58
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (42 bp):
GGACATATCCAGTGGTCCTTCGGGACGATCAGTGGTCCTTCA
Found at i:92751 original size:66 final size:65
Alignment explanation
Indices: 92644--92807 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 65
92634 TTTGTTGAAG
* * * *
92644 GTGCATCGATGCACATGGAGTGTATCGATGCA-CTCATTTAAAATAAATGAACATCGAAT-GCCA
1 GTGCATCGATGCATAAGAAGTGCATCGATGCACCTCA-TTAAAATAAA--AACATCGAATAG-CA
92707 -TTA
62 TTTA
*
92710 GTGCATCGATGCATAAGAAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAATAGCATTT
1 GTGCATCGATGCATAAGAAGTGCATCGATGCACCT-CATTAAAATAAAAACATCGAATAGCATTT
92774 A
65 A
* ** *
92775 -TGCACCGATGCATGGGTAGTGCATCGATGCACC
1 GTGCATCGATGCATAAGAAGTGCATCGATGCACC
92808 CGTCAAGGGA
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
64 41 0.48
65 4 0.05
66 37 0.44
67 2 0.02
68 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (65 bp):
GTGCATCGATGCATAAGAAGTGCATCGATGCACCTCATTAAAATAAAAACATCGAATAGCATTTA
Found at i:93381 original size:22 final size:22
Alignment explanation
Indices: 93356--93411 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
93346 GGGTATATTA
93356 GTCATTTGGGACGTATCCAGTG
1 GTCATTTGGGACGTATCCAGTG
**
93378 GTCATTCAGGACGTATCCAGTG
1 GTCATTTGGGACGTATCCAGTG
*
93400 GTCCTTTGGGAC
1 GTCATTTGGGAC
93412 AAGTACTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.30
Consensus pattern (22 bp):
GTCATTTGGGACGTATCCAGTG
Found at i:94881 original size:23 final size:22
Alignment explanation
Indices: 94850--94894 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
94840 AGGTTGAACG
*
94850 ATTTATTAAATAGATATATAAAT
1 ATTTATT-AATAGATATAGAAAT
* *
94873 ATTTGTTAATAGCTATAGAAAT
1 ATTTATTAATAGATATAGAAAT
94895 GTTAGTGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (22 bp):
ATTTATTAATAGATATAGAAAT
Found at i:95424 original size:21 final size:20
Alignment explanation
Indices: 95400--95440 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
95390 GAGATAAAAC
*
95400 CACTAGTAAAGACTAAGGTAG
1 CACTACTAAAGA-TAAGGTAG
*
95421 CACTACTAAGGATAAGGTAG
1 CACTACTAAAGATAAGGTAG
95441 TGCAAGCTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (20 bp):
CACTACTAAAGATAAGGTAG
Done.