Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008734.1 Hibiscus syriacus cultivar Beakdansim tig00111807_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: 415630
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:93 original size:3 final size:3
Alignment explanation
Indices: 85--139 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
75 TTTTTATCCA
*
85 TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
132 TAT TAT TA
1 TAT TAT TA
140 ATAAATATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:157 original size:15 final size:15
Alignment explanation
Indices: 135--173 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
125 TTATTATTAT
135 TATT-AATAAATATA
1 TATTAAATAAATATA
*
149 TATTAAATATATATA
1 TATTAAATAAATATA
*
164 TAATAAATAA
1 TATTAAATAA
174 TTACAGACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATTAAATAAATATA
Found at i:637 original size:17 final size:17
Alignment explanation
Indices: 615--650 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
605 TCTGCAAGCA
615 AAAAAAAACG-GAGACAG
1 AAAAAAAA-GAGAGACAG
632 AAAAAAAAGAGAGACAG
1 AAAAAAAAGAGAGACAG
649 AA
1 AA
651 CCGAGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.69, C:0.08, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAGAGACAG
Found at i:673 original size:15 final size:15
Alignment explanation
Indices: 617--680 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 15
607 TGCAAGCAAA
* *
617 AAAAAACGGAGACAG
1 AAAAAACAGAGAAAG
*
632 AAAAAA-A-AGAGAG
1 AAAAAACAGAGAAAG
* * *
645 ACAGAACCGAGAAAG
1 AAAAAACAGAGAAAG
660 AAAAAACAGAGAAAG
1 AAAAAACAGAGAAAG
675 AAAAAA
1 AAAAAA
681 AACTACTAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
13 9 0.24
15 29 0.76
ACGTcount: A:0.69, C:0.09, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAAACAGAGAAAG
Found at i:1599 original size:30 final size:30
Alignment explanation
Indices: 1547--1608 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
1537 GTTTTAGTAG
* * * *
1547 TATTTTTATTTTTATTATTATAT-TATTAAA
1 TATTTTTATGTTCATAAATATATATA-TAAA
1577 TATTTTTATGTTCATAAATATATATATAAA
1 TATTTTTATGTTCATAAATATATATATAAA
1607 TA
1 TA
1609 GTAATTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (30 bp):
TATTTTTATGTTCATAAATATATATATAAA
Found at i:13061 original size:10 final size:10
Alignment explanation
Indices: 13046--13075 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
13036 TTATGCTTGA
13046 AAAAAAAAAT
1 AAAAAAAAAT
13056 AAAAAAAAAT
1 AAAAAAAAAT
13066 AATAAAAAAA
1 AA-AAAAAAA
13076 AGAGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:13063 original size:13 final size:13
Alignment explanation
Indices: 13045--13076 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
13035 ATTATGCTTG
13045 AAAAAAAAAATAA
1 AAAAAAAAAATAA
*
13058 AAAAAAATAATAA
1 AAAAAAAAAATAA
13071 AAAAAA
1 AAAAAA
13077 GAGAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAATAA
Found at i:13439 original size:16 final size:17
Alignment explanation
Indices: 13420--13465 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
13410 CTATTTCAAG
*
13420 TTCAATTTATT-GGAGA
1 TTCAATTTATTGGGAAA
13436 TTCAATTTATTTTGGGAAA
1 TTCAATTTA--TTGGGAAA
13455 TTCAATTTATT
1 TTCAATTTATT
13466 CTTCTATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 2 0.08
19 13 0.50
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (17 bp):
TTCAATTTATTGGGAAA
Found at i:14325 original size:83 final size:83
Alignment explanation
Indices: 14228--14778 Score: 841
Period size: 83 Copynumber: 6.7 Consensus size: 83
14218 AATTAAATGA
14228 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
14292 AA-CAATCATTGAGTTTTG
65 AACCAATCATTGAGTTTAG
14310 AAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 -AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
14374 GAA-CAATCATTGAGTTTAG
64 GAACCAATCATTGAGTTTAG
* *
14393 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
14456 GAA-CAATCATTGAGTTTAG
64 GAACCAATCATTGAGTTTAG
* * * *
14475 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTCGAGTTATATGATCTGGTTTGGCAG
1 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
* *
14539 AACCAATCATTGAATTTGG
65 AACCAATCATTGAGTTTAG
14558 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
14623 ACCAATCATTGAGTTTAG
66 ACCAATCATTGAGTTTAG
* *
14641 AAGATGAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
* **
14705 AACCAATCATTGAATTCGG
65 AACCAATCATTGAGTTTAG
*
14724 AAGATGAATGTGTTCATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
14779 ATTCAGTAGG
Statistics
Matches: 441, Mismatches: 21, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
81 1 0.00
82 138 0.31
83 300 0.68
84 2 0.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (83 bp):
AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAGTTTAG
Found at i:15719 original size:113 final size:113
Alignment explanation
Indices: 15521--16409 Score: 694
Period size: 117 Copynumber: 7.9 Consensus size: 113
15511 TCGAATCCAC
* *
15521 TTGATGGATC-ATTTCTTCCAGAAAAAGTTCATAATGAGAAGAA-CTCATCTGAAGAAGGAAGAA
1 TTGATGGATCAACTT-TTCCAG-AGAAGTTCATAATGAGAAGAACCTCATCTGAAGAAGGAAGAA
* ** *
15584 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
64 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTATTTGAATTCATCAT
**
15634 TTGATGGATCAGTTTTTCCAGATGAAGTTCATAATGAGAAGAA-CTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCAACTTTTCCAGA-GAAGTTCATAATGAGAAGAACCTCATCTGAAGAAGGAAGAAG
* * *
15698 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTATTTGAATTCATCAT
* * * * *
15747 TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA-AAACTCATCTAAATAAGGAAGAAT
1 TTGATGGATCAACTTTTCCAGAG-AAGTTCATAATGAGAAGAACCTCATCTGAAGAAGGAAGAAG
** * * * ** * * *
15811 TTGTTCA-AACCTTTTACATGAA-TCCATT--A-C-TTGA--TGGA-GCATCAT
65 AAGTTCATAA----TGAGAAGAACT-TGTTCAACCTTTTATTTGAATTCATCAT
*** * * * * *
15856 CCCCAGCGGA--AAGTTCAT-AATGAGAAGAACTCAT-AT--GAAG-A----A---G-A-AA-GA
1 -TTGA-TGGATCAACTT-TTCCA-GAGAAG--TTCATAATGAGAAGAACCTCATCTGAAGAAGGA
** *
15904 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTTGGTTTGAATTCATCAT
60 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-ATTTGAATTCATCAT
* * *
15959 TTGATGGATCAACATTTCCAG-GTAGAGTTCATAATAAGAAGAACTCATCATCTGAAGAAAGAAG
1 TTGATGGATCAACTTTTCCAGAG-A-AGTTCATAATGAGAAGAAC-C-TCATCTGAAGAAGGAAG
** *
16023 AAGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTTGGTTTGAATTCATCAT
62 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-ATTTGAATTCATCAT
* * *
16076 TTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAA
1 TTGATGGATCAACTTTTCCAGAG-A-AGTTCATAATGAGAAGAAC-C-TCATCTGAAGAAGGAAG
* *
16140 AAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCAT
62 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-ATTTGAATTCATCAT
* *
16193 TTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAG
1 TTGATGGATCAACTTTTCCAGAG-A-AGTTCATAATGAGAAGAAC-C-TCATCTGAAGAAGGAAG
* * *
16257 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTCATCAC
62 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTATTTGAATTCATCAT
* * * * *
16309 TGGATGGAT-TATTTCTTCCAGAGAAAGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAG
1 TTGATGGATCAACTT-TTCCAGAG-AAGTTCATAATGAGAAGAA--CCTCATCTGAAGAAGGAAG
* *
16373 AAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
62 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
16410 GCATAATTCT
Statistics
Matches: 651, Mismatches: 74, Indels: 99
0.79 0.09 0.12
Matches are distributed among these distances:
95 8 0.01
96 1 0.00
97 1 0.00
98 11 0.02
99 6 0.01
100 1 0.00
101 8 0.01
102 9 0.01
103 12 0.02
104 5 0.01
105 1 0.00
108 4 0.01
109 13 0.02
110 10 0.02
111 8 0.01
112 9 0.01
113 165 0.25
114 5 0.01
115 4 0.01
116 102 0.16
117 267 0.41
118 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
TTGATGGATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACCTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACCTTTTATTTGAATTCATCAT
Found at i:15834 original size:94 final size:94
Alignment explanation
Indices: 15711--15889 Score: 252
Period size: 94 Copynumber: 1.9 Consensus size: 94
15701 TTCATAATGA
* * * * **
15711 GAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAG-AGAAAGT
1 GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGCAGAAAGT
15775 TCATAATGAGAAAAACTCATCTAAATAAG
66 TCATAATGAGAAAAACTCATCTAAATAAG
* * *
15804 GAAGAATTTGTTCAAACCTTTTACATGAATCCATTACTTGATGGAGCATCATCCCCAGCGGAAAG
1 GAAGAATTTGTTC-AACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGCAGAAAG
*
15869 TTCATAATGAGAAGAACTCAT
65 TTCATAATGAGAAAAACTCAT
15890 ATGAAGAAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 13 0.18
94 36 0.49
95 25 0.34
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (94 bp):
GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGCAGAAAGT
TCATAATGAGAAAAACTCATCTAAATAAG
Found at i:16016 original size:117 final size:117
Alignment explanation
Indices: 15867--16410 Score: 776
Period size: 117 Copynumber: 4.7 Consensus size: 117
15857 CCCAGCGGAA
**
15867 AGTTCATAATGAGAAGAACTCAT-ATGAAGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTT
1 AGTTCATAATGAGAAGAACTCATCAT-CTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTT
* *
15931 GTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTTCCAGGTAG
65 GTTCAACTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAG
*
15984 AGTTCATAATAAGAAGAACTCATCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGTTCATAATGAGAAGAACTCATCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
*
16049 TTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAG
66 TTCAACTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAG
* * *
16101 AGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAACTTG
1 AGTTCATAATGAGAAGAACTCATCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
* *
16166 TTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAG
66 TTCAACTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAG
* * *
16218 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCATCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * * * * *
16283 TTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATTTC-TT-CCAGAG-AA
66 TTCAACTTTTTGGTTTGAATTCATCATTTGATGGATCA--ACATTGCCAG-GTAG
* * *
16334 AGTTCATAATGAGAAGAACTCCTCATATGAAG-AAGAAAGAAGAAGTTCATAATAAGAAGAACTT
1 AGTTCATAATGAGAAGAACTCATCATCTGAAGAAAG-AAGAAGAAGTTCATAATGAGAAGAACTT
16398 GTTCAACTTTTTG
65 GTTCAACTTTTTG
16411 CATAATTCTA
Statistics
Matches: 393, Mismatches: 28, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
115 2 0.01
116 93 0.24
117 295 0.75
118 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (117 bp):
AGTTCATAATGAGAAGAACTCATCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAG
Found at i:16650 original size:3 final size:3
Alignment explanation
Indices: 16637--16707 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
16627 TTTTTATCCA
*
16637 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
16685 TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
16708 ATAAATATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16722 original size:14 final size:14
Alignment explanation
Indices: 16703--16743 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
16693 TTATTATTAT
16703 TATTAATAAATATA
1 TATTAATAAATATA
16717 TATTAAATAAATATA
1 TATT-AATAAATATA
*
16732 TATAAATAAATA
1 TATTAATAAATA
16744 ATTACAGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATTAATAAATATA
Found at i:16727 original size:15 final size:15
Alignment explanation
Indices: 16703--16743 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
16693 TTATTATTAT
16703 TATT-AATAAATATA
1 TATTAAATAAATATA
16717 TATTAAATAAATATA
1 TATTAAATAAATATA
16732 TA-TAAATAAATA
1 TATTAAATAAATA
16744 ATTACAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTAAATAAATATA
Found at i:17219 original size:15 final size:15
Alignment explanation
Indices: 17199--17265 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
17189 TGCAAGCAAA
* *
17199 AAAAAACGGAGACAG
1 AAAAAACAGAGAAAG
* *
17214 AAAAAAAAGAGAGAG
1 AAAAAACAGAGAAAG
* * *
17229 ACAGAACCGGAGAAAG
1 A-AAAAACAGAGAAAG
17245 AAAAAACAGAGAAAG
1 AAAAAACAGAGAAAG
17260 AAAAAA
1 AAAAAA
17266 AACTACTAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
15 30 0.75
16 10 0.25
ACGTcount: A:0.67, C:0.09, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAAACAGAGAAAG
Found at i:17220 original size:19 final size:19
Alignment explanation
Indices: 17196--17234 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
17186 ATCTGCAAGC
*
17196 AAAAAAAAACG-GAGACAG
1 AAAAAAAAAAGAGAGACAG
*
17214 AAAAAAAAGAGAGAGACAG
1 AAAAAAAAAAGAGAGACAG
17233 AA
1 AA
17235 CCGGAGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAGAGACAG
Found at i:18560 original size:115 final size:113
Alignment explanation
Indices: 18322--18560 Score: 257
Period size: 115 Copynumber: 2.1 Consensus size: 113
18312 TTATTTAAAT
* * * * *
18322 TAATCAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGCTCTTTTCTGATATTTTTGAAT
1 TAAT-AATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTTCTAAAT
* * *
18387 AAATAAATATCTTACTATATTAAAATAAAATGTTTTTGATATTTATTTA
65 AAATAAATATCTTACTATATTAAAATAAAATATTTTTGAAAATTATTTA
**
18436 TTTTTTAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTTCTGATATTTCTAA
1 --TAATAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCC-TTTTCTGATATTTCTAA
* * * * * *
18501 ATAAGTAAATATCTTA-TTTATGTATATTAATATATTTTCTTAAAATTATTTGA
63 ATAAATAAATATCTTACTATAT-TAAAATAAAATATTTT-TGAAAATTATTT-A
18554 -AATAATA
1 TAATAATA
18561 AAATTATGAA
Statistics
Matches: 101, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
115 47 0.47
116 44 0.44
117 9 0.09
118 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (113 bp):
TAATAATATCAAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGCCCTTTTCTGATATTTCTAAATA
AATAAATATCTTACTATATTAAAATAAAATATTTTTGAAAATTATTTA
Found at i:21897 original size:91 final size:91
Alignment explanation
Indices: 21742--21924 Score: 312
Period size: 91 Copynumber: 2.0 Consensus size: 91
21732 CAGTTCAGGG
* *
21742 TCCCTGATGCATAAACATATCCAAAACTCAATCCGAGTCCGGGCGACGTAGCAACTAGAAACTTA
1 TCCCTGATGCAAAAACATATCCAAAACTCAATCCGAGTCCGGGCGAAGTAGCAACTAGAAACTTA
*
21807 AGAAAAATGTAGTAATACAGTAGCAT
66 AGAAAAATGCAGTAATACAGTAGCAT
* *
21833 TCCCTGATGCAAAAACATATCCAACACTCAATCCGAGTCCGGGCGAAGTAGCATCTAGAAACTTA
1 TCCCTGATGCAAAAACATATCCAAAACTCAATCCGAGTCCGGGCGAAGTAGCAACTAGAAACTTA
*
21898 AGGAAAATGCAGTAATACAGTAGCAT
66 AGAAAAATGCAGTAATACAGTAGCAT
21924 T
1 T
21925 GCAATGTGAG
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (91 bp):
TCCCTGATGCAAAAACATATCCAAAACTCAATCCGAGTCCGGGCGAAGTAGCAACTAGAAACTTA
AGAAAAATGCAGTAATACAGTAGCAT
Found at i:25488 original size:22 final size:22
Alignment explanation
Indices: 25460--25519 Score: 97
Period size: 20 Copynumber: 2.8 Consensus size: 22
25450 AGATTGTCCA
*
25460 GGGGTACAGATTCCCCCCCCAG
1 GGGGTACCGATTCCCCCCCCAG
25482 GGGGTACCGATT--CCCCCCAG
1 GGGGTACCGATTCCCCCCCCAG
25502 GGGGTACCGATTCCCCCC
1 GGGGTACCGATTCCCCCC
25520 TGTCTAACGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 20 0.57
22 15 0.43
ACGTcount: A:0.15, C:0.42, G:0.28, T:0.15
Consensus pattern (22 bp):
GGGGTACCGATTCCCCCCCCAG
Found at i:26792 original size:19 final size:20
Alignment explanation
Indices: 26768--26815 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
26758 AATGATTTTC
*
26768 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
26787 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
26807 TTTTGAAAA
1 TTTTGAAAA
26816 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:32204 original size:20 final size:20
Alignment explanation
Indices: 32177--32233 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
32167 TCATTCTGGA
32177 CAAGGGGTTTCAAAACCAAC
1 CAAGGGGTTTCAAAACCAAC
*
32197 CCAGGGGTTTCAAAACCAAC
1 CAAGGGGTTTCAAAACCAAC
32217 CAAGGGGTTTCAAAACC
1 CAAGGGGTTTCAAAACC
32234 TTTACTCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.16
Consensus pattern (20 bp):
CAAGGGGTTTCAAAACCAAC
Found at i:48635 original size:31 final size:30
Alignment explanation
Indices: 48575--48645 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
48565 TGTGACTCTT
*
48575 AGGTAGGCTCTGCGGCCCTGAGATCATTCTC
1 AGGTAGGC-CTGCGGCCCTAAGATCATTCTC
* * *
48606 GGGTAGGCCTGCGGCCCTAAGATGTATTCTT
1 AGGTAGGCCTGCGGCCCTAAGAT-CATTCTC
48637 AGGTAGGCC
1 AGGTAGGCC
48646 CCACGGCCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 14 0.41
31 20 0.59
ACGTcount: A:0.17, C:0.25, G:0.32, T:0.25
Consensus pattern (30 bp):
AGGTAGGCCTGCGGCCCTAAGATCATTCTC
Found at i:50194 original size:18 final size:18
Alignment explanation
Indices: 50168--50202 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
50158 TGGTCACAAC
50168 CCGAACCGACCCGTTGAG
1 CCGAACCGACCCGTTGAG
*
50186 CCGACCCGACCCGTTGA
1 CCGAACCGACCCGTTGA
50203 CCGGCGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.43, G:0.26, T:0.11
Consensus pattern (18 bp):
CCGAACCGACCCGTTGAG
Found at i:53094 original size:32 final size:31
Alignment explanation
Indices: 53024--53094 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
53014 AATGTGACTG
* * *
53024 TTAGGTAGGCTCTGCGGCCCTGAGATCATTC
1 TTAGGTAGACCCTGCGGCCCTAAGATCATTC
** *
53055 TCGGGTAGACCCTGCGGCCCTAAGATGTATTC
1 TTAGGTAGACCCTGCGGCCCTAAGAT-CATTC
53087 TTAGGTAG
1 TTAGGTAG
53095 GCCCCACGGC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (31 bp):
TTAGGTAGACCCTGCGGCCCTAAGATCATTC
Found at i:60428 original size:58 final size:57
Alignment explanation
Indices: 60314--60475 Score: 182
Period size: 58 Copynumber: 2.8 Consensus size: 57
60304 AGAATCAAGT
* * * * **
60314 ATATTATTTTAGCTAATTTAAAATATTAATTTATTTGTATCAAAATGGGGTTGGTCGA
1 ATATTATTTTAACTATTTTAAAATATTAATTTATTTGAATC-AAGTGGGGCGGGTCGA
*
60372 ATATTATTTTAACCATTTTAAAATATTAATTTATTTGAATCAAGTCGGGGCGGGTCGA
1 ATATTATTTTAACTATTTTAAAATATTAATTTATTTGAATCAAGT-GGGGCGGGTCGA
** * *
60430 ATATAATAAATT-ATTATTTTAAAATATTAATTTATTCGAATCAAGT
1 ATAT--TATTTTAACTATTTTAAAATATTAATTTATTTGAATCAAGT
60476 TGGGACATAT
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 3 0.03
58 51 0.57
59 31 0.35
60 4 0.04
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (57 bp):
ATATTATTTTAACTATTTTAAAATATTAATTTATTTGAATCAAGTGGGGCGGGTCGA
Found at i:66482 original size:18 final size:18
Alignment explanation
Indices: 66459--66519 Score: 104
Period size: 18 Copynumber: 3.4 Consensus size: 18
66449 ATCAAGGTCG
* *
66459 GCGGGCTCTTTTGCTTCA
1 GCGGGCTCTTCTACTTCA
66477 GCGGGCTCTTCTACTTCA
1 GCGGGCTCTTCTACTTCA
66495 GCGGGCTCTTCTACTTCA
1 GCGGGCTCTTCTACTTCA
66513 GCGGGCT
1 GCGGGCT
66520 GGGGACTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.08, C:0.31, G:0.28, T:0.33
Consensus pattern (18 bp):
GCGGGCTCTTCTACTTCA
Found at i:76726 original size:18 final size:19
Alignment explanation
Indices: 76689--76726 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
76679 ACTCGACGTG
*
76689 TTCACTAGATAAATATAAT
1 TTCACTAGATAAATAAAAT
*
76708 TTCATTAGA-AAATAAAAT
1 TTCACTAGATAAATAAAAT
76726 T
1 T
76727 AATAAATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
TTCACTAGATAAATAAAAT
Found at i:80806 original size:23 final size:25
Alignment explanation
Indices: 80762--80807 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
80752 AAGCATTAGA
*
80762 ACAAAAAAATATAGCAAGGAAAATC
1 ACAAAAAAATATAGCAAAGAAAATC
*
80787 ACAAAAAAA-A-AGGAAAGAAAA
1 ACAAAAAAATATAGCAAAGAAAA
80808 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 1 0.05
25 9 0.47
ACGTcount: A:0.72, C:0.09, G:0.13, T:0.07
Consensus pattern (25 bp):
ACAAAAAAATATAGCAAAGAAAATC
Found at i:83863 original size:17 final size:17
Alignment explanation
Indices: 83806--83863 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
83796 AATTTCGTCC
*
83806 TTATATTATATA-ATAT
1 TTATATTATATATTTAT
* *
83822 ATATATT-TATATTATAAA
1 TTATATTATATATT-T-AT
83840 TTATATTATATATTTAT
1 TTATATTATATATTTAT
83857 TTATATT
1 TTATATT
83864 TTTTTCTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
15 4 0.12
16 6 0.18
17 9 0.27
18 8 0.24
19 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATTATATATTTAT
Found at i:85320 original size:19 final size:21
Alignment explanation
Indices: 85274--85328 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
85264 ACTATTATAG
* **
85274 ATATATTATATATTTTATTTT
1 ATATTTTATATATTTTAGGTT
85295 ATATTTTATAT-TTTTAGGTT
1 ATATTTTATATATTTTAGGTT
*
85315 AT-TTTTATTTATTT
1 ATATTTTATATATTT
85329 ATTGGTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 7 0.24
20 12 0.41
21 10 0.34
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
ATATTTTATATATTTTAGGTT
Found at i:95886 original size:9 final size:8
Alignment explanation
Indices: 95872--95896 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
95862 AAGTCGAAAG
95872 AAAAAAAC
1 AAAAAAAC
95880 AAAAAAAC
1 AAAAAAAC
95888 AAAAAAAC
1 AAAAAAAC
95896 A
1 A
95897 TTTAGGGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:96844 original size:106 final size:106
Alignment explanation
Indices: 96715--97382 Score: 1059
Period size: 106 Copynumber: 6.3 Consensus size: 106
96705 AACATCCACG
**
96715 ATTTCAACTTCACAGCGAAGGATATCAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
96780 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
96821 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
96886 ACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
96927 ATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
96992 ACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
97033 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
97098 ACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
97139 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * *
97204 ACCGCTGGTTGTCAATAAACAATTTCCTAATTTCGGATCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* ** * * *
97245 ATTTCAACTTCACAGCGAAGGATATTAGACTTGAGACAGCACAAGCTCAACTTCAC-AGCGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA-CGAAGG
* * ** * * * *
97309 GGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCA
65 GACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
97351 ATTTCAACTTCACAGCGGAGGATATTGGACTC
1 ATTTCAACTTCACAGCGAAGGATATTGGACTC
97383 GGAACAATAC
Statistics
Matches: 526, Mismatches: 35, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
105 1 0.00
106 525 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
Found at i:99024 original size:21 final size:21
Alignment explanation
Indices: 98992--99049 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
98982 TTTTGTCTTC
98992 ATTACT-TATATATATTTTATT
1 ATTACTAT-TATATATTTTATT
* *
99013 ATTACTATTATAGATTATA-T
1 ATTACTATTATATATTTTATT
99033 ATTA-TATT-T-TATTTTAT
1 ATTACTATTATATATTTTAT
99050 ATTTATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 5 0.16
18 1 0.03
19 4 0.13
20 5 0.16
21 15 0.48
22 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTACTATTATATATTTTATT
Found at i:99044 original size:14 final size:14
Alignment explanation
Indices: 98998--99060 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 14
98988 CTTCATTACT
98998 TATA-TATATTTTA
1 TATATTATATTTTA
99011 T-TATTACTA--TTA
1 TATATTA-TATTTTA
* *
99023 TAGATTATATATTA
1 TATATTATATTTTA
99037 TAT-TT-TATTTTA
1 TATATTATATTTTA
99049 TAT-TTATATTTT
1 TATATTATATTTT
99061 TAGGTTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
12 19 0.46
13 15 0.37
14 7 0.17
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
TATATTATATTTTA
Found at i:99068 original size:19 final size:18
Alignment explanation
Indices: 99027--99074 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
99017 CTATTATAGA
**
99027 TTATATATTATATTTTATT
1 TTATAT-TTATATTTTAGG
99046 TTATATTTATATTTTTAGG
1 TTATATTTATA-TTTTAGG
*
99065 TTATTTTTAT
1 TTATATTTAT
99075 TTATTTATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
TTATATTTATATTTTAGG
Found at i:99129 original size:2 final size:2
Alignment explanation
Indices: 99122--99154 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
99112 CTTTTTATTA
99122 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 A
99155 CTTAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:101365 original size:24 final size:24
Alignment explanation
Indices: 101333--101381 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
101323 CTCATTGGAA
101333 AATTAATTCATAGATATTAGTCTT
1 AATTAATTCATAGATATTAGTCTT
101357 AATTAATTCATAGATATTAGTCTT
1 AATTAATTCATAGATATTAGTCTT
101381 A
1 A
101382 CATAAATACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (24 bp):
AATTAATTCATAGATATTAGTCTT
Found at i:103375 original size:84 final size:83
Alignment explanation
Indices: 103186--103352 Score: 207
Period size: 84 Copynumber: 2.0 Consensus size: 83
103176 TAATTTTATC
* * * * *
103186 TTTAGGAATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGGATATTATTTTTATTA
1 TTTAGAAATTTAAGTATAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTATGA
*
103251 TATTTTATCTTATATTTGT
66 TA-TTTATCTTATAGTTGT
* * *
103270 TTTAGAAATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAGATATTA-TTTTATGA
1 TTTAGAAATTTAAGTATAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTATGA
103334 -A-TTATCTT-TAGGTTGT
66 TATTTATCTTATA-GTTGT
103350 TTT
1 TTT
103353 TAAGAATTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
79 2 0.03
80 14 0.18
82 1 0.01
83 7 0.09
84 53 0.69
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (83 bp):
TTTAGAAATTTAAGTATAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTATTTTTATGA
TATTTATCTTATAGTTGT
Found at i:109425 original size:6 final size:5
Alignment explanation
Indices: 109400--109464 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
109390 GCGGCAACCC
* * **
109400 ATTTT GTTTT ATTTT CATTTT AATTTC GCTTT ATTTT ATATTT CA-TTT
1 ATTTT ATTTT ATTTT -ATTTT -ATTTT ATTTT ATTTT AT-TTT -ATTTT
109448 ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT AT
109465 CAGATGCTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
4 1 0.02
5 33 0.70
6 12 0.26
7 1 0.02
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (5 bp):
ATTTT
Found at i:109435 original size:16 final size:16
Alignment explanation
Indices: 109416--109454 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
109406 TTTTATTTTC
*
109416 ATTTTA-ATTTCGCTTT
1 ATTTTATATTTC-ATTT
109432 ATTTTATATTTCATTT
1 ATTTTATATTTCATTT
109448 ATTTTAT
1 ATTTTAT
109455 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTTATATTTCATTT
Found at i:113766 original size:42 final size:42
Alignment explanation
Indices: 113707--114068 Score: 528
Period size: 42 Copynumber: 8.6 Consensus size: 42
113697 AAAGAGCCTG
* *
113707 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* *
113749 GGGAAACTGTAAGGCTTACCCTTGTACACAGCAAAAGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
*
113791 -GGAGAACTGTAAGGCTTACCCTTGTACACAACAAAGTAACCT
1 GGGA-AACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* *
113833 GGGAAATTGTAAGGGTTACCCTTGTACACAACAAAGGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* *
113875 GGGAAACTATAAGGCTTACCCTTGTACAAAACAAAGGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* * *
113917 GGGAAACTGTAGGGCTTACCCTTGTACACAAAAAAGGGACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
*
113959 GGGAAACTATAAGGCTTACCCTTGTACACAACAAAGGAACCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* *
114001 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAGCCT
1 GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
* * *
114043 GCAGTAACGGTAAGGACTTACCCTTG
1 G-GGAAACTGTAAGG-CTTACCCTTG
114069 CACATAGCAG
Statistics
Matches: 289, Mismatches: 27, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
41 3 0.01
42 263 0.91
43 13 0.04
44 10 0.03
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.19
Consensus pattern (42 bp):
GGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGAACCT
Found at i:116845 original size:42 final size:42
Alignment explanation
Indices: 116761--117107 Score: 426
Period size: 42 Copynumber: 8.2 Consensus size: 42
116751 AGGTTTTATT
* * * * * *
116761 CTTGCACATAGCAAAAGAGCCTGAGGAAAATGTAAGGTTTACC
1 CTTGCACACAACAAAGGAACCTG-GGAAACTGTAAGGCTTACC
*
116804 CTTGCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACC
1 CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
* * * *
116846 CTTGCACACATCAAAGGAACCT-AGAGAACTATAAGACTTACC
1 CTTGCACACAACAAAGGAACCTGGGA-AACTGTAAGGCTTACC
* * **
116888 CTTGTACACAACAAAGTAACCTGGGAAACTGTAAGATTTACC
1 CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
* *
116930 CTTGTACACAACAAAGGAACATGGGAAACTGTAAGGCTTACC
1 CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
* *
116972 CTTGTACACAACAAAGGAACCTGGGAAACTGTAAGGCATACC
1 CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
*
117014 CTTGTACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
1 CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
* * * *
117056 CTTGCACACAACAAGGGAGCCTGCGGTAACGGTAAGGACTTACC
1 CTTGCACACAACAAAGGAACCTG-GGAAACTGTAAGG-CTTACC
*
117100 GTTGCACA
1 CTTGCACA
117108 TAGCAGAGAA
Statistics
Matches: 272, Mismatches: 28, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
41 2 0.01
42 224 0.82
43 33 0.12
44 13 0.05
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (42 bp):
CTTGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACC
Found at i:119744 original size:18 final size:18
Alignment explanation
Indices: 119721--119766 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
119711 ATCGGTCACA
*
119721 ACCCGACCCGACCCATTT
1 ACCCGACCCGACCCATTG
* **
119739 ACCCGACCCAACCTGTTG
1 ACCCGACCCGACCCATTG
119757 ACCCGACCCG
1 ACCCGACCCG
119767 TTGACCCGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.50, G:0.15, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCATTG
Found at i:119774 original size:8 final size:8
Alignment explanation
Indices: 119761--119807 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
119751 CTGTTGACCC
119761 GACCCGTT
1 GACCCGTT
119769 GACCCGTT
1 GACCCGTT
119777 GA-CCGTT
1 GACCCGTT
119784 GACCGGCGTT
1 GACC--CGTT
119794 GACCACTGTT
1 GACC-C-GTT
119804 GACC
1 GACC
119808 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 1 0.03
10 15 0.44
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:119784 original size:15 final size:16
Alignment explanation
Indices: 119764--119797 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
119754 TTGACCCGAC
119764 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
119779 CCGTTGACCGGCGTTGA
1 CCGTTGACC-GCGTTGA
119796 CC
1 CC
119798 ACTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:121122 original size:18 final size:18
Alignment explanation
Indices: 121096--121131 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
121086 TCAAAAGGAC
*
121096 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
121114 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
121132 CGGATGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:122282 original size:12 final size:11
Alignment explanation
Indices: 122255--122321 Score: 53
Period size: 12 Copynumber: 5.7 Consensus size: 11
122245 CGTTACTTGA
*
122255 ATTCTGTTCTG
1 ATTCTGATCTG
122266 ATTCTGATCTGG
1 ATTCTGATCT-G
*
122278 ATTCTGTTCTG
1 ATTCTGATCTG
*
122289 ATATCTGATATG
1 AT-TCTGATCTG
* *
122301 AATTCTGTTTTG
1 -ATTCTGATCTG
122313 ATTTCTGAT
1 A-TTCTGAT
122322 ATCTCCGTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
11 13 0.29
12 30 0.67
13 2 0.04
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (11 bp):
ATTCTGATCTG
Found at i:122282 original size:47 final size:48
Alignment explanation
Indices: 122214--122321 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 48
122204 AAATATTTTA
* * *
122214 TCTGATTTCCGAAT-TGAATTCTGTTCTGATA-C-GTTACTTGAATTCTGT
1 TCTGATTTCTG-ATCTGGATTCTGTTCTGATATCTGATA--TGAATTCTGT
122262 TCTGA-TTCTGATCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
*
122309 TTTGATTTCTGAT
1 TCTGATTTCTGAT
122322 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
46 2 0.04
47 34 0.65
48 13 0.25
49 3 0.06
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
Found at i:122305 original size:24 final size:24
Alignment explanation
Indices: 122228--122323 Score: 108
Period size: 24 Copynumber: 4.0 Consensus size: 24
122218 ATTTCCGAAT
*
122228 TGAATTCTGTTCTGATA-C-GTTA
1 TGAATTCTGTTCTGATATCTGATA
*
122250 CTTGAATTCTGTTCTGAT-TCTGATC
1 --TGAATTCTGTTCTGATATCTGATA
*
122275 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATATCTGATA
* *
122299 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATATCTGATA
122323 T
1 T
122324 CTCCGTTTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
23 15 0.24
24 45 0.73
25 2 0.03
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATA
Found at i:124564 original size:10 final size:10
Alignment explanation
Indices: 124549--124586 Score: 76
Period size: 10 Copynumber: 3.8 Consensus size: 10
124539 CTTTGAGAGA
124549 ATTTTAAAAC
1 ATTTTAAAAC
124559 ATTTTAAAAC
1 ATTTTAAAAC
124569 ATTTTAAAAC
1 ATTTTAAAAC
124579 ATTTTAAA
1 ATTTTAAA
124587 GAAGACCCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (10 bp):
ATTTTAAAAC
Found at i:132933 original size:22 final size:22
Alignment explanation
Indices: 132908--132949 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
132898 CAAACGCAAG
132908 TTTGAATCGAGTTCGACTTCAA
1 TTTGAATCGAGTTCGACTTCAA
132930 TTTGAATCGAGTTCGACTTC
1 TTTGAATCGAGTTCGACTTC
132950 GAGTTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (22 bp):
TTTGAATCGAGTTCGACTTCAA
Found at i:141552 original size:2 final size:2
Alignment explanation
Indices: 141545--141584 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
141535 TTCACCATTC
141545 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
141585 TATTTTAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142752 original size:16 final size:17
Alignment explanation
Indices: 142727--142760 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
142717 AAACTCATTA
*
142727 ATAATTAAATTA-AAAT
1 ATAATAAAATTACAAAT
142743 ATAATAAAATTACAAAT
1 ATAATAAAATTACAAAT
142760 A
1 A
142761 ATCACTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAAAATTACAAAT
Found at i:143287 original size:20 final size:19
Alignment explanation
Indices: 143232--143278 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
143222 TAACAAATTC
143232 ATAAAGTTATAAATTTTAAAA
1 ATAAA-TTAT-AATTTTAAAA
**
143253 ATATTTTATAATTTTAAAA
1 ATAAATTATAATTTTAAAA
143272 ATAAATT
1 ATAAATT
143279 GTGAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 15 0.68
20 4 0.18
21 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAAATTATAATTTTAAAA
Found at i:143702 original size:323 final size:326
Alignment explanation
Indices: 143188--143843 Score: 918
Period size: 323 Copynumber: 2.0 Consensus size: 326
143178 GAATCATACC
* *
143188 TAAATAAAAAAAATTATAAAATAATTTGATAAATTAACAAATTCATAAAGTTATAAATTTTAAAA
1 TAAATAAAAAAAATTATAAAATAAATTGATAAATTAACAAATTCATAAAGTGATAAA-TTTAAAA
* * ** * *
143253 ATATTTTATAATTTTAAAAATAAATTGTGAATTTTTTTACATTTAAATTTTTTTTTTAGGATTAT
65 ATATTTTATAATTATAAAAATAAATGGTGAATTTTTTTACATTTAAAAATATTTTTTAGAATTAT
* * *
143318 TACTTAGAAATGTTGAAAAATTATAAAAATTGAAACTTTATTTATAATTGAGGGTTAAATGAGAT
130 TACTTAGAAATGTTGAAAAAATATAAAAATTAAAACTTTATTTATAATTGAGGGGTAAATGAGAT
* * * *
143383 TATTTTATTAATTTAGTATGTCACTACACCCATTT-TA-TTA-TATA-AA-TTTTGAAAGTTTAA
195 CATTGTATTAATTTAATATCTCACTACACCCATTTATATTTATTATATAATTTTTGAAAGTTTAA
*
143443 TATCTAAAAA-ATTA-TAACATAATTTAGTGACCATTTACAAATTTTATCTTACAAAATTAGTGG
260 TATCTAAAAAGATTATTAACATAATTTAGTGACCATTTACAAATTTTATCTTACAAAACTAGTGG
143506 AT
325 AT
143508 TAAATAAAAAAAA-TATAAAATAAATTGATAAATTAACAAATTCATAAAGTGATAAA-TTAGAAA
1 TAAATAAAAAAAATTATAAAATAAATTGATAAATTAACAAATTCATAAAGTGATAAATTTA-AAA
** **
143571 ATATTTTATAATGTATAAAAATAAATGGTTCATTTTTATTATTTTTAAAAAAAATATTTTTTAGA
65 ATATTTTATAAT-TATAAAAATAAATGGTGAATTTTT-TTACATTT---AAAAATATTTTTTAGA
* * *
143636 ATTATTACTTATAAATGTTGAAAAAATATCAAAAA-TAAAACTTTGTTTATACTTGAGGGGTAAA
125 ATTATTACTTAGAAATGTTGAAAAAATAT-AAAAATTAAAACTTTATTTATAATTGAGGGGTAAA
* *
143700 TGAGATCATTGTATTAATTTAATATCTTACTTCACCCATTTAATATTTATTATATAATTTTTGAA
189 TGAGATCATTGTATTAATTTAATATCTCACTACACCCATTT-ATATTTATTATATAATTTTTGAA
143765 AGTTTAATATCTAAAAAGATTATTTTAACATAATTTAGTGACCATTTACAAATTTTATCTTACAA
253 AGTTTAATATCTAAAAAGATTA--TTAACATAATTTAGTGACCATTTACAAATTTTATCTTACAA
143830 AACTAGTGGAT
316 AACTAGTGGAT
143841 TAA
1 TAA
143844 TCATGGAGCG
Statistics
Matches: 294, Mismatches: 25, Indels: 21
0.86 0.07 0.06
Matches are distributed among these distances:
317 3 0.01
318 15 0.05
319 61 0.21
320 19 0.06
323 99 0.34
324 5 0.02
325 2 0.01
326 3 0.01
327 4 0.01
328 2 0.01
329 24 0.08
330 4 0.01
333 53 0.18
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (326 bp):
TAAATAAAAAAAATTATAAAATAAATTGATAAATTAACAAATTCATAAAGTGATAAATTTAAAAA
TATTTTATAATTATAAAAATAAATGGTGAATTTTTTTACATTTAAAAATATTTTTTAGAATTATT
ACTTAGAAATGTTGAAAAAATATAAAAATTAAAACTTTATTTATAATTGAGGGGTAAATGAGATC
ATTGTATTAATTTAATATCTCACTACACCCATTTATATTTATTATATAATTTTTGAAAGTTTAAT
ATCTAAAAAGATTATTAACATAATTTAGTGACCATTTACAAATTTTATCTTACAAAACTAGTGGA
T
Found at i:144587 original size:12 final size:12
Alignment explanation
Indices: 144570--144606 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
144560 TCAGAAAGAA
144570 AATAAAATAAAT
1 AATAAAATAAAT
144582 AATAAAAT-AAT
1 AATAAAATAAAT
*
144593 ACTAAAATAAAT
1 AATAAAATAAAT
144605 AA
1 AA
144607 AAATACACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:147829 original size:21 final size:21
Alignment explanation
Indices: 147798--147853 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
147788 AGTCGAGGGT
*
147798 TACATGAGGTCCTTCGGAACA
1 TACACGAGGTCCTTCGGAACA
* * *
147819 TATACGAGGTCCTTCGGGATA
1 TACACGAGGTCCTTCGGAACA
*
147840 TACATGAGGTCCTT
1 TACACGAGGTCCTT
147854 TGGGGCAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (21 bp):
TACACGAGGTCCTTCGGAACA
Found at i:151247 original size:2 final size:2
Alignment explanation
Indices: 151240--151273 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
151230 ACCATTCATA
151240 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
151274 TATTTTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153966 original size:7 final size:8
Alignment explanation
Indices: 153949--153973 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
153939 TCAATATATC
153949 AAATAAAA
1 AAATAAAA
153957 AAATAAAA
1 AAATAAAA
153965 AAATAAAA
1 AAATAAAA
153973 A
1 A
153974 CAAAATAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:176915 original size:216 final size:216
Alignment explanation
Indices: 176541--177191 Score: 1293
Period size: 216 Copynumber: 3.0 Consensus size: 216
176531 ATTACATGGG
176541 AAAATTATTTTAAAAATAATAAAGTTTTTATTTATTTCTTGGGTAAACTACACATTTAGTACCTA
1 AAAATTATTTTAAAAATAATAAAGTTTTTATTTATTTCTTGGGTAAACTACACATTTAGTACCTA
176606 AACTATTAATTTTGGTCGTTTTAGTACCTAAACTTTCATTTTTTTCAAAATCATACCTAACATTT
66 AACTATTAATTTTGGTCGTTTTAGTACCTAAACTTTCATTTTTTTCAAAATCATACCTAACATTT
176671 AGTTTTCACTTCATTTTAATACTCTGTCGTTAAAAACTTAACACGTTTAATTTCTAAACTATCAG
131 AGTTTTCACTTCATTTTAATACTCTGTCGTTAAAAACTTAACACGTTTAATTTCTAAACTATCAG
176736 TTTTGGTCCATTTTAGTACCC
196 TTTTGGTCCATTTTAGTACCC
*
176757 AAAATTATTTTTAAAATAATAAAGTTTTTATTTATTTCTTGGGTAAACTACACATTTAGTACCTA
1 AAAATTATTTTAAAAATAATAAAGTTTTTATTTATTTCTTGGGTAAACTACACATTTAGTACCTA
176822 AACTATTAATTTTGGTCGTTTTAGTACCTAAACTTTCATTTTTTTCAAAATCATACCTAACATTT
66 AACTATTAATTTTGGTCGTTTTAGTACCTAAACTTTCATTTTTTTCAAAATCATACCTAACATTT
176887 AGTTTTCACTTCATTTTAATACTCTGTCGTTAAAAACTTAACACGTTTAATTTCTAAACTATCAG
131 AGTTTTCACTTCATTTTAATACTCTGTCGTTAAAAACTTAACACGTTTAATTTCTAAACTATCAG
176952 TTTTGGTCCATTTTAGTACCC
196 TTTTGGTCCATTTTAGTACCC
176973 AAAATTATTTTAAAAATAATAAAGTTTTTATTTATTTCTTGGGTAAACTACACATTTAGTACCTA
1 AAAATTATTTTAAAAATAATAAAGTTTTTATTTATTTCTTGGGTAAACTACACATTTAGTACCTA
177038 AACTATTAATTTTGGTCGTTTTAGTACCTAAACTTTCATTTTTTTCAAAATCATACCTAACATTT
66 AACTATTAATTTTGGTCGTTTTAGTACCTAAACTTTCATTTTTTTCAAAATCATACCTAACATTT
177103 AGTTTTCACTTCATTTTAATACTCTGTCGTTAAAAACTTAACACGTTTAATTTCTAAACTATCAG
131 AGTTTTCACTTCATTTTAATACTCTGTCGTTAAAAACTTAACACGTTTAATTTCTAAACTATCAG
177168 TTTTGGTCCATTTTAGTACCC
196 TTTTGGTCCATTTTAGTACCC
177189 AAA
1 AAA
177192 CTTTCAATTT
Statistics
Matches: 433, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 433 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.44
Consensus pattern (216 bp):
AAAATTATTTTAAAAATAATAAAGTTTTTATTTATTTCTTGGGTAAACTACACATTTAGTACCTA
AACTATTAATTTTGGTCGTTTTAGTACCTAAACTTTCATTTTTTTCAAAATCATACCTAACATTT
AGTTTTCACTTCATTTTAATACTCTGTCGTTAAAAACTTAACACGTTTAATTTCTAAACTATCAG
TTTTGGTCCATTTTAGTACCC
Found at i:177281 original size:39 final size:39
Alignment explanation
Indices: 177237--177337 Score: 134
Period size: 39 Copynumber: 2.6 Consensus size: 39
177227 TGAACAGTGC
* *
177237 ACTAAAATGAAACAAAAACTATA-GTTTTAATGAT-GATTT
1 ACTAAAATGAAACAAAAACTAAATGTTTTAACGATAGA--T
* *
177276 TCTAAAATGAAACAAAAACTAAATTTTTTAACGATAGAT
1 ACTAAAATGAAACAAAAACTAAATGTTTTAACGATAGAT
177315 ACTAAAATGAAACAAAAACTAAA
1 ACTAAAATGAAACAAAAACTAAA
177338 ATTTAAGTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 44 0.80
40 9 0.16
41 2 0.04
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (39 bp):
ACTAAAATGAAACAAAAACTAAATGTTTTAACGATAGAT
Found at i:178134 original size:19 final size:18
Alignment explanation
Indices: 178101--178136 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
178091 ATATGAAGAT
*
178101 AAAGAAAATAAGATAAAC
1 AAAGAAAAGAAGATAAAC
178119 AAAGACAAAGAAGATAAA
1 AAAGA-AAAGAAGATAAA
178137 GATATGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.72, C:0.06, G:0.14, T:0.08
Consensus pattern (18 bp):
AAAGAAAAGAAGATAAAC
Found at i:178605 original size:51 final size:51
Alignment explanation
Indices: 178507--178618 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 51
178497 GTAACTACTA
* * * * * * * *
178507 AATAAAATAATAATAAATTGAATATAATGTTTTGATTTTATCCTAATTTTT
1 AATAAAATAATAATAAACTAAAAATAATATTTTAACTCTATCCTAATTATT
**
178558 AATAAAATAATAATAAACTAAAAATAATATTTTAACTCTATTTTAATTATT
1 AATAAAATAATAATAAACTAAAAATAATATTTTAACTCTATCCTAATTATT
*
178609 AATAAGATAA
1 AATAAAATAA
178619 GAAATATAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAAATAATATTTTAACTCTATCCTAATTATT
Found at i:179618 original size:23 final size:23
Alignment explanation
Indices: 179588--179635 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
179578 AGTCATACTT
179588 AACATATTTAAAAACAAAGCTTG
1 AACATATTTAAAAACAAAGCTTG
179611 AACATATTTAAAAACAAAGCTTG
1 AACATATTTAAAAACAAAGCTTG
179634 AA
1 AA
179636 AATAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.25
Consensus pattern (23 bp):
AACATATTTAAAAACAAAGCTTG
Found at i:179647 original size:24 final size:23
Alignment explanation
Indices: 179597--179648 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
179587 TAACATATTT
* ***
179597 AAAAACAAAGCTTGAACATATTT
1 AAAAACAAAGCTTGAAAATAAAG
179620 AAAAACAAAGCTTGAAAATAAAAG
1 AAAAACAAAGCTTGAAAAT-AAAG
179644 AAAAA
1 AAAAA
179649 TGAAAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (23 bp):
AAAAACAAAGCTTGAAAATAAAG
Found at i:179656 original size:19 final size:19
Alignment explanation
Indices: 179634--179675 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
179624 ACAAAGCTTG
*
179634 AAAATAAAAGA-AAAATGAA
1 AAAATAAAAAATAAAAT-AA
179653 AAAATAAAAAATAAAATAA
1 AAAATAAAAAATAAAATAA
179672 AAAA
1 AAAA
179676 GAAAGCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAATAAAAAATAAAATAA
Found at i:184395 original size:3 final size:3
Alignment explanation
Indices: 184387--184423 Score: 56
Period size: 3 Copynumber: 11.7 Consensus size: 3
184377 TCCAGATTTC
184387 TCT TCT TCT TCTT TCT TCT TCT TCTT TCT TCT TCT TC
1 TCT TCT TCT TC-T TCT TCT TCT TC-T TCT TCT TCT TC
184424 GCCGCGAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:184404 original size:10 final size:10
Alignment explanation
Indices: 184383--184422 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
184373 AGTTTCCAGA
184383 TTTC-TCTTC
1 TTTCTTCTTC
184392 -TTCTTCTT-
1 TTTCTTCTTC
184400 TCTTCTTCTTC
1 T-TTCTTCTTC
184411 TTTCTTCTTC
1 TTTCTTCTTC
184421 TT
1 TT
184423 CGCCGCGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 3 0.11
9 4 0.15
10 19 0.70
11 1 0.04
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTCTTCTTC
Found at i:184405 original size:13 final size:13
Alignment explanation
Indices: 184387--184423 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
184377 TCCAGATTTC
184387 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
184400 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
184413 TCTTCTTCTTC
1 TCTTCTTCTTC
184424 GCCGCGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
TCTTCTTCTTCTT
Found at i:185504 original size:30 final size:31
Alignment explanation
Indices: 185444--185507 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
185434 TTATATAAGC
*
185444 TATGTGATAAATTGATGGAACATGATATGTT
1 TATGTGATAAAGTGATGGAACATGATATGTT
*
185475 TATGTGATAAAG-GTATGGAA-ATTATATGTT
1 TATGTGATAAAGTG-ATGGAACATGATATGTT
185505 TAT
1 TAT
185508 ACAATATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.41
Consensus pattern (31 bp):
TATGTGATAAAGTGATGGAACATGATATGTT
Found at i:201487 original size:28 final size:30
Alignment explanation
Indices: 201446--201505 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 30
201436 TTGGCAACAT
* *
201446 AAATAAAGATAAAGCA-AAACAC-AAAGAA
1 AAATAAAGAAAAAGCATAAAAACAAAAGAA
* *
201474 AAATAAATAAAAAGGATAAAAACAAAAGAA
1 AAATAAAGAAAAAGCATAAAAACAAAAGAA
201504 AA
1 AA
201506 TGAAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 13 0.50
29 5 0.19
30 8 0.31
ACGTcount: A:0.75, C:0.07, G:0.10, T:0.08
Consensus pattern (30 bp):
AAATAAAGAAAAAGCATAAAAACAAAAGAA
Found at i:201492 original size:35 final size:35
Alignment explanation
Indices: 201444--201524 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
201434 AATTGGCAAC
*
201444 ATAAATAAAGAT-AAAGCAAAACACAAA-GAAAAATAA
1 ATAAA-AAAGATAAAAACAAAACA-AAATGAAAAA-AA
* *
201480 ATAAAAAGGATAAAAACAAAAGAAAATGAAAAAAA
1 ATAAAAAAGATAAAAACAAAACAAAATGAAAAAAA
201515 ATAAAAAAGA
1 ATAAAAAAGA
201525 AGAAATGGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
35 19 0.49
36 20 0.51
ACGTcount: A:0.75, C:0.05, G:0.10, T:0.10
Consensus pattern (35 bp):
ATAAAAAAGATAAAAACAAAACAAAATGAAAAAAA
Found at i:201529 original size:19 final size:18
Alignment explanation
Indices: 201472--201529 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
201462 AAACACAAAG
* *
201472 AAAAATAAATAAAAAGGAT
1 AAAAATAAA-AAAAAGAAA
*
201491 AAAAACAAAAGAAAATGAAA
1 AAAAATAAAA-AAAA-GAAA
201511 AAAAATAAAAAAGAAGAAA
1 AAAAATAAAAAA-AAGAAA
201530 TGGAGAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.03
19 18 0.56
20 13 0.41
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.09
Consensus pattern (18 bp):
AAAAATAAAAAAAAGAAA
Found at i:202844 original size:2 final size:2
Alignment explanation
Indices: 202831--202915 Score: 145
Period size: 2 Copynumber: 43.0 Consensus size: 2
202821 TGATAAAATA
*
202831 AT AT AC 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
*
202873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
202914 AT
1 AT
202916 TTTAGTTAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
1 1 0.01
2 77 0.99
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:203487 original size:116 final size:116
Alignment explanation
Indices: 203319--203529 Score: 316
Period size: 116 Copynumber: 1.8 Consensus size: 116
203309 TTAGGGTATG
*
203319 ATATCCTTCATTGTGAAGTCTAAATCGTAGATGGCTCCTTCATCGTGAAGTTGAGCTTTGAATTG
1 ATATCCTTCATTGTGAAGTCTAAATCGTAGATAGCTCCTTCATCGTGAAGTTGAGCTTTGAATTG
* **
203384 GATATCTTTCATTTTGAAGTTGAAATCCAATGGATGCTGCTTGTGGGCATT
66 GATATCCTTCATCATGAAGTTGAAATCCAATGGATGCTGCTTGTGGGCATT
* * * *
203435 ATATCCTTCGTTGTGAAGT-TGAAATCGTGGATAGCTCCTTCGTTGTGAAGTTGAGCTTTGAATT
1 ATATCCTTCATTGTGAAGTCT-AAATCGTAGATAGCTCCTTCATCGTGAAGTTGAGCTTTGAATT
* *
203499 TGATATCCTTCGTCATGAAGTTGAAATCCAA
65 GGATATCCTTCATCATGAAGTTGAAATCCAA
203530 GCTTGTGTAA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
115 1 0.01
116 83 0.99
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (116 bp):
ATATCCTTCATTGTGAAGTCTAAATCGTAGATAGCTCCTTCATCGTGAAGTTGAGCTTTGAATTG
GATATCCTTCATCATGAAGTTGAAATCCAATGGATGCTGCTTGTGGGCATT
Found at i:203628 original size:64 final size:64
Alignment explanation
Indices: 203553--203975 Score: 713
Period size: 64 Copynumber: 6.6 Consensus size: 64
203543 GCATTGTTTC
**
203553 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
203617 GAGTCCAATATCCTTCGCTCTGAAGTTGAAATTGACTATGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
203681 GTA-TCCAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAATGAATCTGGAAAGTTGTTTGTT
1 G-AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
*
203745 GAGTCCAATATCCTTAGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
203809 GAGTCTAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
*
203873 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTATTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * *
203937 GAGACCAATATCTTTCGCTATGAAGTTGAAATTGACTCT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
203976 AAAAGCAGCA
Statistics
Matches: 337, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
63 1 0.00
64 335 0.99
65 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:209054 original size:11 final size:10
Alignment explanation
Indices: 209035--209077 Score: 54
Period size: 9 Copynumber: 4.4 Consensus size: 10
209025 GGTTGATAAA
*
209035 ATAATAATAC
1 ATAATAATAT
209045 ATATATAATAT
1 ATA-ATAATAT
209056 AT-ATAATAT
1 ATAATAATAT
209065 AT-ATAATAT
1 ATAATAATAT
209074 ATAA
1 ATAA
209078 ATATATATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 18 0.60
10 4 0.13
11 8 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
ATAATAATAT
Found at i:209057 original size:2 final size:2
Alignment explanation
Indices: 209045--209091 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
209035 ATAATAATAC
*
209045 AT AT AT A- AT AT AT AT A- AT AT AT AT A- AT AT AT AA 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
*
209084 AT GT AT AT
1 AT AT AT AT
209092 TTCGGTTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:209059 original size:9 final size:9
Alignment explanation
Indices: 209045--209085 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
209035 ATAATAATAC
209045 ATATATAAT
1 ATATATAAT
209054 ATATATAAT
1 ATATATAAT
209063 ATATATAAT
1 ATATATAAT
209072 ATATA-AAT
1 ATATATAAT
209080 ATATAT
1 ATATAT
209086 GTATATTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.26
9 23 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATATAAT
Found at i:211614 original size:17 final size:17
Alignment explanation
Indices: 211574--211615 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
211564 GGAGAGAAAA
*
211574 AAAAGTAAAATAAAAGGT
1 AAAA-TAAAATAAAAGAT
*
211592 ATAATAAAATAAAAGAT
1 AAAATAAAATAAAAGAT
211609 AAAATAA
1 AAAATAA
211616 TAAATAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (17 bp):
AAAATAAAATAAAAGAT
Found at i:211685 original size:19 final size:19
Alignment explanation
Indices: 211661--211707 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
211651 AAAGTTGTTT
211661 TTAAAATAAAAGATAAA-AA
1 TTAAAATAAAAGA-AAATAA
*
211680 TTAAAATGAAAGAAAATAA
1 TTAAAATAAAAGAAAATAA
211699 TT-AAATAAA
1 TTAAAATAAA
211708 TAATCTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (19 bp):
TTAAAATAAAAGAAAATAA
Found at i:211924 original size:17 final size:17
Alignment explanation
Indices: 211884--211925 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
211874 AGGAGAGAAA
*
211884 AAAAGTAAAATAAAAGGT
1 AAAA-TAAAATAAAAGAT
*
211902 ATAATAAAATAAAAGAT
1 AAAATAAAATAAAAGAT
211919 AAAATAA
1 AAAATAA
211926 TAAATAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (17 bp):
AAAATAAAATAAAAGAT
Found at i:211995 original size:19 final size:19
Alignment explanation
Indices: 211971--212017 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
211961 AAAGTTGTTT
211971 TTAAAATAAAAGATAAA-AA
1 TTAAAATAAAAGA-AAATAA
*
211990 TTAAAATGAAAGAAAATAA
1 TTAAAATAAAAGAAAATAA
212009 TT-AAATAAA
1 TTAAAATAAA
212018 TAATCTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (19 bp):
TTAAAATAAAAGAAAATAA
Found at i:212073 original size:310 final size:311
Alignment explanation
Indices: 211510--212131 Score: 1174
Period size: 310 Copynumber: 2.0 Consensus size: 311
211500 AAAAAAGAAG
211510 TAGGAAAATAAAAATAAAATAGAAAAAGAAATGTTAAATTTTAAAAAAATACAAGGAGAGAAAAA
1 TAGGAAAATAAAAATAAAATAGAAAAAGAAATGTTAAATTTTAAAAAAATACAAGGAGAGAAAAA
*
211575 AAAGTAAAATAAAAGGTATAATAAAATAAAAGATAAAATAATAAATAATAGTAGTACAAATATAA
66 AAAGTAAAATAAAAGGTATAATAAAATAAAAGATAAAATAATAAATAATAGTAGTACAAATAAAA
*
211640 ATGGGTTTTTAAAAGTTGTTTTTAAAATAAAAGATAAAAATTAAAATGAAAGAAAATAATTAAAT
131 AGGGGTTTTTAAAAGTTGTTTTTAAAATAAAAGATAAAAATTAAAATGAAAGAAAATAATTAAAT
*
211705 AAATAATCTAAAGAGATTGAGATAAAGAGAAATTTATAGTGAAAACAGCCTCAGAAATTCCTCGG
196 AAATAATCTAAAGAGATTGAGATAAAGAGAAATTTATAGTGAAAACAGCATCAGAAATTCCTCGG
*
211770 ATTATCAAAACAGATTTTTACTTCAAAATTCACGTCAACTTACAATGACAA
261 ATTATCAAAACAGATTTTTACTTCAAAATTCACGTCAACTTACAAGGACAA
211821 TAGGAAAATAAAAATAAAATAGAAAAAGAAATGTTAAATTTTAAAAAAATACAAGGAGAG-AAAA
1 TAGGAAAATAAAAATAAAATAGAAAAAGAAATGTTAAATTTTAAAAAAATACAAGGAGAGAAAAA
211885 AAAGTAAAATAAAAGGTATAATAAAATAAAAGATAAAATAATAAATAATAGTAGTACAAATAAAA
66 AAAGTAAAATAAAAGGTATAATAAAATAAAAGATAAAATAATAAATAATAGTAGTACAAATAAAA
211950 AGGGGTTTTTAAAAGTTGTTTTTAAAATAAAAGATAAAAATTAAAATGAAAGAAAATAATTAAAT
131 AGGGGTTTTTAAAAGTTGTTTTTAAAATAAAAGATAAAAATTAAAATGAAAGAAAATAATTAAAT
*
212015 AAATAATCTAAAGAGATTGAGATAAAGAGAAATTTATAGTGAAAGCAGCATCAGAAATTCCTCGG
196 AAATAATCTAAAGAGATTGAGATAAAGAGAAATTTATAGTGAAAACAGCATCAGAAATTCCTCGG
* *
212080 ATTATCGAAACAGATTTTTACTTCAAAATTCACGTCAGCTTACAAGGACAA
261 ATTATCAAAACAGATTTTTACTTCAAAATTCACGTCAACTTACAAGGACAA
212131 T
1 T
212132 TCTTCGCTGA
Statistics
Matches: 304, Mismatches: 7, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
310 244 0.80
311 60 0.20
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.25
Consensus pattern (311 bp):
TAGGAAAATAAAAATAAAATAGAAAAAGAAATGTTAAATTTTAAAAAAATACAAGGAGAGAAAAA
AAAGTAAAATAAAAGGTATAATAAAATAAAAGATAAAATAATAAATAATAGTAGTACAAATAAAA
AGGGGTTTTTAAAAGTTGTTTTTAAAATAAAAGATAAAAATTAAAATGAAAGAAAATAATTAAAT
AAATAATCTAAAGAGATTGAGATAAAGAGAAATTTATAGTGAAAACAGCATCAGAAATTCCTCGG
ATTATCAAAACAGATTTTTACTTCAAAATTCACGTCAACTTACAAGGACAA
Found at i:213566 original size:270 final size:271
Alignment explanation
Indices: 213118--213728 Score: 872
Period size: 270 Copynumber: 2.3 Consensus size: 271
213108 AGTCGATCCA
* * *
213118 TTGGGCACGATATCCTTC-TTCGTGAAGT-TGAAATCGT-GAGTGGCTCCTTCGTTGTGAAGTTG
1 TTGGGTACGATATCCTTCATTCATGAAGTCT-AAATCGTAG-GTGGCTCATTCGTTGTGAAGTTG
* * * *
213180 TGCTTTGAACTAAAAAATCCTGAGCATGATATCCTTCGTCGTAAAGTTAAAACCGGGCTCAAAGC
64 AGCTTTGAACTAAAAAATCCTGAGCACGATATCATTCGTCGTAAAGTTAAAACAGGGCTCAAAGC
*
213245 ATTGGAAAGTCACTCATAGATCGTCTTCTAGACCAATATACTTCGTCGTGAAGCTGAAATTTGAC
129 ATTGGAAAGTCACTCATAGATCGTCTTCTAGACCAATATACTTCGTCGTGAAGCTAAAATTTGAC
* * * * **
213310 CTGAAAACTTTGTTATGAAATTGGTTTTTCATTGTTGTGTTACATATGACTCATTCGTTGTGAAG
194 CTGAAAACTTTGGTATGAAACTGGTTTTTCATTGTTGTGCTACAGATGACTCATTCGTCATGAAG
213375 TTGGGTCAATCTT
259 TTGGGTCAATCTT
*
213388 TTGGGTATGATATCCTTCATT-ATGAAGTCTAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAG
1 TTGGGTACGATATCCTTCATTCATGAAGTCTAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAG
* * * * * *
213452 CTTTGAACTGAAAAATCCTGAGTACGATATCATTTGTCGTGAAGTTGAAACATGGCTCAAAGCAT
66 CTTTGAACTAAAAAATCCTGAGCACGATATCATTCGTCGTAAAGTTAAAACAGGGCTCAAAGCAT
* * *
213517 TGGAAAGTCACTCCTGGATCGTCTTCTAGCCCAATATACTTCGTCGTGAAGCTAAAATTTGACCT
131 TGGAAAGTCACTCATAGATCGTCTTCTAGACCAATATACTTCGTCGTGAAGCTAAAATTTGACCT
* *
213582 GAAGACTTTGGTATGAAACTGGTTTTTCATTGTTGTGCTACAGATGACTCCTTCGTCATGAAGTT
196 GAAAACTTTGGTATGAAACTGGTTTTTCATTGTTGTGCTACAGATGACTCATTCGTCATGAAGTT
213647 GGGTCAATCTT
261 GGGTCAATCTT
* * * ** *
213658 TTGGGTACGATATCCTTAATTGA-GAAGTCGAAATCACAGGTGGCTCTTTCGTTGTGAAGTTGAG
1 TTGGGTACGATATCCTTCATTCATGAAGTCTAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAG
*
213722 TTTTGAA
66 CTTTGAA
213729 TTGGATATCC
Statistics
Matches: 304, Mismatches: 33, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
270 299 0.98
271 5 0.02
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (271 bp):
TTGGGTACGATATCCTTCATTCATGAAGTCTAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAG
CTTTGAACTAAAAAATCCTGAGCACGATATCATTCGTCGTAAAGTTAAAACAGGGCTCAAAGCAT
TGGAAAGTCACTCATAGATCGTCTTCTAGACCAATATACTTCGTCGTGAAGCTAAAATTTGACCT
GAAAACTTTGGTATGAAACTGGTTTTTCATTGTTGTGCTACAGATGACTCATTCGTCATGAAGTT
GGGTCAATCTT
Found at i:219522 original size:19 final size:19
Alignment explanation
Indices: 219498--219546 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
219488 GAATGTAGTT
219498 AGTGCATCGATGAATAAGA
1 AGTGCATCGATGAATAAGA
*
219517 AGTGCATCGATGCATAAGA
1 AGTGCATCGATGAATAAGA
*
219536 AGTGCAACGAT
1 AGTGCATCGAT
219547 ACACCCCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (19 bp):
AGTGCATCGATGAATAAGA
Found at i:219647 original size:20 final size:22
Alignment explanation
Indices: 219602--219659 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
219592 GCATGGGTAG
219602 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
219626 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
219646 TGTATCGATGCACT
1 TGCATCGATGCACT
219660 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:219718 original size:13 final size:13
Alignment explanation
Indices: 219700--219733 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
219690 TTGGTCTAAG
219700 GAATGATATATTA
1 GAATGATATATTA
219713 GAATGATATATTA
1 GAATGATATATTA
219726 GAAT-ATAT
1 GAATGATAT
219734 CAATTGGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
GAATGATATATTA
Found at i:222726 original size:59 final size:59
Alignment explanation
Indices: 222654--222922 Score: 493
Period size: 59 Copynumber: 4.6 Consensus size: 59
222644 AATCAATAAT
* *
222654 ATTTTCTTTCCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATG
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATG
*
222713 ATTTCCTTACCATTTTAGTACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATG
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATG
222772 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATG
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATG
* *
222831 ATTTCCTTACCATTTTAGCACACAAAGCGCCCTATCTAGAAATTCATACACTTAGTATG
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATG
222890 ATTTCCTTACCATTTTAGCACACAAAGTGCCCT
1 ATTTCCTTACCATTTTAGCACACAAAGTGCCCT
222923 TTGGTAATTT
Statistics
Matches: 203, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 203 1.00
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (59 bp):
ATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTGGAAATTCATACACTTAGTATG
Found at i:223298 original size:53 final size:53
Alignment explanation
Indices: 223235--223351 Score: 198
Period size: 53 Copynumber: 2.2 Consensus size: 53
223225 CTTCAGAACA
* *
223235 GTATCGATACACTACTGGGGTATTAGTACCCAAATTAACTTCGATGTTTACAG
1 GTATCGATACACTACTGAGGTATCAGTACCCAAATTAACTTCGATGTTTACAG
* *
223288 GTATCGATACACTACTGAGGTATCGGTACCCAAATTAACTTCGATGTTTATAG
1 GTATCGATACACTACTGAGGTATCAGTACCCAAATTAACTTCGATGTTTACAG
223341 GTATCGATACA
1 GTATCGATACA
223352 TGCCTGATGG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (53 bp):
GTATCGATACACTACTGAGGTATCAGTACCCAAATTAACTTCGATGTTTACAG
Found at i:228342 original size:45 final size:45
Alignment explanation
Indices: 228278--228363 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
228268 GTGCCCTATC
*
228278 TGGAAATTGAAACACTTAGTATAATTTCCTTACCATTTTAGTATA
1 TGGAAATTCAAACACTTAGTATAATTTCCTTACCATTTTAGTATA
* *
228323 TGGAAATTCATACACTTAGTATTATTTCCTTACCATTTTAG
1 TGGAAATTCAAACACTTAGTATAATTTCCTTACCATTTTAG
228364 CACACAAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (45 bp):
TGGAAATTCAAACACTTAGTATAATTTCCTTACCATTTTAGTATA
Found at i:228416 original size:60 final size:59
Alignment explanation
Indices: 228323--228497 Score: 296
Period size: 59 Copynumber: 2.9 Consensus size: 59
228313 TTTTAGTATA
* *
228323 TGGAAATTCATACACTTAGTATTATTTCCTTACCATTTTAGCACACAAAAGTGCCCTATT
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACAC-AAAGTGCCCTATC
* *
228383 TGGAAATTCATACACTTAGAATGATTTCCTTACCATTTTAGCACACAAAGTGCTCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
228442 TAGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
228498 TTGGTAATTT
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 64 0.59
60 44 0.41
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (59 bp):
TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:228883 original size:53 final size:53
Alignment explanation
Indices: 228826--228943 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
228816 CTTTCAAAAC
* *
228826 GGTATCGATACACTATTGGGGTATCGGTACCCAAATTAACTTCGATGTTTACA
1 GGTATCGATACACTACTGAGGTATCGGTACCCAAATTAACTTCGATGTTTACA
228879 GGTATCGATACACTACTGAGGTATCGGTACCCAAATTAACTTCGATGTTTACA
1 GGTATCGATACACTACTGAGGTATCGGTACCCAAATTAACTTCGATGTTTACA
*
228932 GGTATCAATACA
1 GGTATCGATACA
228944 TGCCTGATGG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (53 bp):
GGTATCGATACACTACTGAGGTATCGGTACCCAAATTAACTTCGATGTTTACA
Found at i:230434 original size:10 final size:10
Alignment explanation
Indices: 230421--230539 Score: 51
Period size: 11 Copynumber: 11.3 Consensus size: 10
230411 ATGTTAAAAG
230421 AAAAAAAT-A
1 AAAAAAATAA
230430 AAAAAAATGAA
1 AAAAAAAT-AA
*
230441 AAAAAATATTA
1 AAAAAA-ATAA
****
230452 AATTTCATAA
1 AAAAAAATAA
230462 AAGAAAAATAA
1 AA-AAAAATAA
* *
230473 TAAAATATAA
1 AAAAAAATAA
***
230483 AAAATGTTAA
1 AAAAAAATAA
230493 AAGAGAAAATAA
1 AA-A-AAAATAA
*
230505 AAACAAAACAA
1 AAA-AAAATAA
*
230516 AACAAAATAA
1 AAAAAAATAA
*
230526 AATAAAATTAA
1 AA-AAAAATAA
230537 AAA
1 AAA
230540 GAATTGGGAA
Statistics
Matches: 78, Mismatches: 25, Indels: 13
0.67 0.22 0.11
Matches are distributed among these distances:
9 8 0.10
10 29 0.37
11 33 0.42
12 8 0.10
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:230686 original size:18 final size:18
Alignment explanation
Indices: 230665--230707 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
230655 GTTGTTTTTA
*
230665 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
230683 AAATGAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
230701 AAATAAA
1 AAATAAA
230708 TAATCTAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:231285 original size:12 final size:12
Alignment explanation
Indices: 231268--231295 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
231258 AGATAAAATA
231268 AAATAATATTCT
1 AAATAATATTCT
231280 AAATAATATTCT
1 AAATAATATTCT
231292 AAAT
1 AAAT
231296 TCTAATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:237479 original size:14 final size:13
Alignment explanation
Indices: 237446--237485 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
237436 ACATAGATAC
*
237446 TATTTTATTAAAT
1 TATTTTGTTAAAT
*
237459 AATTTTGTTAATAT
1 TATTTTGTTAA-AT
237473 TATTTTGTTAAAT
1 TATTTTGTTAAAT
237486 GATTCAAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (13 bp):
TATTTTGTTAAAT
Found at i:244901 original size:330 final size:329
Alignment explanation
Indices: 244301--244956 Score: 1195
Period size: 330 Copynumber: 2.0 Consensus size: 329
244291 TCAACTATAT
244301 GCCAAGTTTAGGAAGTGTGAATTCTGGTTGACCGAAGTTGCATTTTTGAATAATGTAGTAATAGA
1 GCCAAGTTTAGGAAGTGTGAATTCTGGTTGACCGAAGTTGCATTTTTGAATAATGTAGTAATAGA
* *
244366 CAACGGTATCTGAGTAAACCCCTAAAAGATTAAAGTAATCTTCGAGTGAGAAGTACCTAAAAATT
66 CAACGGTATCTGAGTAAACCCCAAAAAGATTAAAGTAATCTTCGAGTGAGAACTACCTAAAAATT
*
244431 TCTCTGAGGTGCATAATTTATTAAACCTTGTAGGGTACTACTTTTGTAATGCCCTAATCCAGTTA
131 TCTCTGAGGTGCATAATTTATTAAACCTTGTAGGGTACTACTTTTGTAACGCCCTAATCCAGTTA
*
244496 GACCCAAAGTTCCATGGATTACAATGTTACACAAGATTACCGAAATAGTGACCCAAAAGTTTCTT
196 GACCCAAAATTCCATGGATTACAATGTTACACAAGATTACCGAAATAGTGACCCAAAAGTTTCTT
* *
244561 TTAAAATTGCTTGTAAATCTCTGAAATTTAGACATTCATAAAGTAATATAAACACTTAATAATAA
261 TTAAAATTGCTTGTAAATCTCTGAAATTTAGACATTCATAAAGTAATATAAAAACGTAATAATAA
244626 TCTA
326 TCTA
**
244630 GCCAAGTTTAGGAAGTGTGAATTCTGGTTGACCGAAGTTGCATTTTTGGGTAATGTAGTAATAGA
1 GCCAAGTTTAGGAAGTGTGAATTCTGGTTGACCGAAGTTGCATTTTTGAATAATGTAGTAATAGA
* * *
244695 CAACGGTATCTGAGTAAACCCCCAAAAAGATTAAAGTAATCTTTGAGTGGGAACTACCTAATAAT
66 CAACGGTATCTGAGTAAA-CCCCAAAAAGATTAAAGTAATCTTCGAGTGAGAACTACCTAAAAAT
244760 TTCTCTGAGGTGCATAATTTATTAAACCTTGTAGGGTACTACTTTTGTAACGCCCTAATCCAGTT
130 TTCTCTGAGGTGCATAATTTATTAAACCTTGTAGGGTACTACTTTTGTAACGCCCTAATCCAGTT
*
244825 AGACCCAAAATTCCATGGATTACAATGTTACACAAGATTACCGAAATAGTGACCCAAAATTTTCT
195 AGACCCAAAATTCCATGGATTACAATGTTACACAAGATTACCGAAATAGTGACCCAAAAGTTTCT
244890 TTTAAAATTGCTTGTAAATCTCTGAAATTTAGACATTCATAAAGTAATATAAAAACGTAATAATA
260 TTTAAAATTGCTTGTAAATCTCTGAAATTTAGACATTCATAAAGTAATATAAAAACGTAATAATA
244955 AT
325 AT
244957 ATAGGCTTAC
Statistics
Matches: 314, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
329 81 0.26
330 233 0.74
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (329 bp):
GCCAAGTTTAGGAAGTGTGAATTCTGGTTGACCGAAGTTGCATTTTTGAATAATGTAGTAATAGA
CAACGGTATCTGAGTAAACCCCAAAAAGATTAAAGTAATCTTCGAGTGAGAACTACCTAAAAATT
TCTCTGAGGTGCATAATTTATTAAACCTTGTAGGGTACTACTTTTGTAACGCCCTAATCCAGTTA
GACCCAAAATTCCATGGATTACAATGTTACACAAGATTACCGAAATAGTGACCCAAAAGTTTCTT
TTAAAATTGCTTGTAAATCTCTGAAATTTAGACATTCATAAAGTAATATAAAAACGTAATAATAA
TCTA
Found at i:248872 original size:18 final size:19
Alignment explanation
Indices: 248849--248894 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
248839 AATTTGGTAC
*
248849 CGATACTCATGGG-AGTAT
1 CGATACTCAAGGGAAGTAT
248867 CGATAC-CAAGGGTAAAGTAT
1 CGATACTCAAGGG--AAGTAT
248887 CGATACTC
1 CGATACTC
248895 CCCATAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
20 11 0.48
21 1 0.04
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (19 bp):
CGATACTCAAGGGAAGTAT
Found at i:249317 original size:38 final size:38
Alignment explanation
Indices: 249266--249355 Score: 180
Period size: 38 Copynumber: 2.4 Consensus size: 38
249256 TACGCATCTA
249266 ATGCATGTAAAATTCTGGATCGTACCAGTACATATCCG
1 ATGCATGTAAAATTCTGGATCGTACCAGTACATATCCG
249304 ATGCATGTAAAATTCTGGATCGTACCAGTACATATCCG
1 ATGCATGTAAAATTCTGGATCGTACCAGTACATATCCG
249342 ATGCATGTAAAATT
1 ATGCATGTAAAATT
249356 TCATATCGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (38 bp):
ATGCATGTAAAATTCTGGATCGTACCAGTACATATCCG
Found at i:249364 original size:38 final size:37
Alignment explanation
Indices: 249266--249368 Score: 163
Period size: 38 Copynumber: 2.7 Consensus size: 37
249256 TACGCATCTA
249266 ATGCATGTAAAATTCTGGATCGTACCAGTACATATCCG
1 ATGCATGTAAAATTCT-GATCGTACCAGTACATATCCG
249304 ATGCATGTAAAATTCTGGATCGTACCAGTACATATCCG
1 ATGCATGTAAAATTCT-GATCGTACCAGTACATATCCG
249342 ATGCATGTAAAATTTCAT-ATCGTACCA
1 ATGCATGTAAAA-TTC-TGATCGTACCA
249369 TATACTTGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
38 59 0.94
39 3 0.05
40 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (37 bp):
ATGCATGTAAAATTCTGATCGTACCAGTACATATCCG
Found at i:250800 original size:12 final size:12
Alignment explanation
Indices: 250778--250803 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
250768 TCACCACCAC
250778 CACCATCACCCT
1 CACCATCACCCT
250790 CACCATCACCCT
1 CACCATCACCCT
250802 CA
1 CA
250804 TCTGCATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.58, G:0.00, T:0.15
Consensus pattern (12 bp):
CACCATCACCCT
Found at i:250805 original size:21 final size:22
Alignment explanation
Indices: 250759--250805 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
250749 TTTATCAACA
250759 TCATCACCATCACCACCACCAC
1 TCATCACCATCACCACCACCAC
* *
250781 -CATCACCCTCACCATCACC-C
1 TCATCACCATCACCACCACCAC
250801 TCATC
1 TCATC
250806 TGCATATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.28, C:0.55, G:0.00, T:0.17
Consensus pattern (22 bp):
TCATCACCATCACCACCACCAC
Found at i:255805 original size:15 final size:15
Alignment explanation
Indices: 255782--255844 Score: 117
Period size: 15 Copynumber: 4.2 Consensus size: 15
255772 CGTAGGACTC
*
255782 CTACATCCCGAAGGA
1 CTACGTCCCGAAGGA
255797 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
255812 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
255827 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
255842 CTA
1 CTA
255845 TTATACCCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.29, C:0.33, G:0.24, T:0.14
Consensus pattern (15 bp):
CTACGTCCCGAAGGA
Found at i:262683 original size:15 final size:15
Alignment explanation
Indices: 262660--262692 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
262650 CGTAGGACTC
262660 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
262675 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
262690 CTA
1 CTA
262693 TTATACCCTC
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:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:262871 original size:12 final size:12
Alignment explanation
Indices: 262837--262871 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
262827 TATCATGTTC
**
262837 TCATATCACAGG
1 TCATATCACATA
262849 TCATATCACATA
1 TCATATCACATA
262861 TCATATCACAT
1 TCATATCACAT
262872 GAACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:264299 original size:21 final size:21
Alignment explanation
Indices: 264274--264317 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
264264 CCCCTTATGC
264274 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
264295 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
264316 CT
1 CT
264318 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:266589 original size:20 final size:20
Alignment explanation
Indices: 266564--266618 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
266554 GGTAGCGCTT
266564 TACCGGTTTTATCATTTTGA
1 TACCGGTTTTATCATTTTGA
266584 TACCGGTTTTATCATTTTGA
1 TACCGGTTTTATCATTTTGA
* *
266604 TACTGATTTTATCAT
1 TACCGGTTTTATCAT
266619 ATTTTCACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.51
Consensus pattern (20 bp):
TACCGGTTTTATCATTTTGA
Found at i:267010 original size:11 final size:12
Alignment explanation
Indices: 266994--267022 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
266984 TCCAGTAATG
266994 CCGTATATTAA-
1 CCGTATATTAAC
267005 CCGTATATTAAC
1 CCGTATATTAAC
267017 CCGTAT
1 CCGTAT
267023 TTTCTGAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (12 bp):
CCGTATATTAAC
Found at i:267873 original size:2 final size:2
Alignment explanation
Indices: 267866--267903 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
267856 CACCACAAAA
*
267866 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
267904 TATCTATCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:268122 original size:16 final size:15
Alignment explanation
Indices: 268093--268127 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
268083 GAGATTTCTT
268093 AAAA-ATATTTTTAA
1 AAAATATATTTTTAA
268107 AAAATATATATTTTAA
1 AAAATATAT-TTTTAA
268123 AAAAT
1 AAAAT
268128 TAAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 4 0.21
16 11 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATATATTTTTAA
Found at i:269497 original size:35 final size:35
Alignment explanation
Indices: 269450--269521 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
269440 ATATAACATA
* * *
269450 AACATTCTAATATG-TCTATATAAAGTAACTTCATT
1 AACATTCCAATATGCT-TATATAAACTAACTCCATT
269485 AACATTCCAATATGCTTATATAAACTAACTCCATT
1 AACATTCCAATATGCTTATATAAACTAACTCCATT
269520 AA
1 AA
269522 GCTCTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (35 bp):
AACATTCCAATATGCTTATATAAACTAACTCCATT
Found at i:269961 original size:43 final size:43
Alignment explanation
Indices: 269900--269981 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
269890 TTTTCTCGAA
* *
269900 CCACATGATTCTCACATTAAAGTATACGTAGGAGGTATGTGTT
1 CCACATGATTCTCACATTAAAGTAGACGTAAGAGGTATGTGTT
269943 CCACATGATTCTCACATTAAAGTAGACGTAAGAGGTATG
1 CCACATGATTCTCACATTAAAGTAGACGTAAGAGGTATG
269982 AATTTTACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (43 bp):
CCACATGATTCTCACATTAAAGTAGACGTAAGAGGTATGTGTT
Found at i:270011 original size:16 final size:16
Alignment explanation
Indices: 269990--270024 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
269980 TGAATTTTAC
*
269990 TCTCTTATTTTATTCA
1 TCTCTTATTTTACTCA
270006 TCTCTTATTTTACTCA
1 TCTCTTATTTTACTCA
270022 TCT
1 TCT
270025 ACAAAATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (16 bp):
TCTCTTATTTTACTCA
Found at i:270156 original size:25 final size:26
Alignment explanation
Indices: 270118--270166 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
270108 AATAATTACT
* * *
270118 TAAAATA-TTTTTTTATTTAAATATA
1 TAAAATACTATTTTGATTAAAATATA
270143 TAAAATACTATTTTGATTAAAATA
1 TAAAATACTATTTTGATTAAAATA
270167 AATATATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TAAAATACTATTTTGATTAAAATATA
Found at i:275745 original size:73 final size:73
Alignment explanation
Indices: 275643--275829 Score: 227
Period size: 73 Copynumber: 2.5 Consensus size: 73
275633 AAATATAAAA
*
275643 AAAAAGTTGA-AGATAAGATCAAAATTTAAAATATCGATACTCATGCGGTAATAATCAATACTTT
1 AAAAAGTTGATAGA-AAGATCAAAATTTAAAATATCGATACTCATGCGATAATAATCAATACTTT
275707 TAAA-AATTG
65 TAAATAA-TG
* * * * *
275716 AAAAAGTTGATAGAAAGATCAAAATTTAAAATATCGATATTTATGCGATGATGATCGATACTTTT
1 AAAAAGTTGATAGAAAGATCAAAATTTAAAATATCGATACTCATGCGATAATAATCAATACTTTT
275781 AAATAATG
66 AAATAATG
* * * *
275789 AATAAGTTAAT-GAATATGATCGATATTTAAAATATCGATAC
1 AAAAAGTTGATAGAA-A-GATCAAAATTTAAAATATCGATAC
275830 ATATGTTATG
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
72 3 0.03
73 70 0.71
74 26 0.26
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (73 bp):
AAAAAGTTGATAGAAAGATCAAAATTTAAAATATCGATACTCATGCGATAATAATCAATACTTTT
AAATAATG
Found at i:275851 original size:74 final size:73
Alignment explanation
Indices: 275643--275854 Score: 207
Period size: 73 Copynumber: 2.9 Consensus size: 73
275633 AAATATAAAA
* * * **
275643 AAAAAGTTGA-AGATAAGATCAAAATTTAAAATATCGATAC-TCATGCGGTAATAATCAATACTT
1 AAAAAGTTAATAGA-AAGATCAAAATTTAAAATATCGATACAT-ATGCGATGAGGATCAATACTT
275706 TTAAAAATTG
64 TTAAAAATTG
* ** * *
275716 AAAAAGTTGATAGAAAGATCAAAATTTAAAATATCGATATTTATGCGATGATGATCGATACTTTT
1 AAAAAGTTAATAGAAAGATCAAAATTTAAAATATCGATACATATGCGATGAGGATCAATACTTTT
275781 AAATAA-TG
66 AAA-AATTG
* * * ** *
275789 AATAAGTTAAT-GAATATGATCGATATTTAAAATATCGATACATATGTTATGAGGTTCAATACTT
1 AAAAAGTTAATAGAA-A-GATCAAAATTTAAAATATCGATACATATGCGATGAGGATCAATACTT
275853 TT
64 TT
275855 TTTATTTATA
Statistics
Matches: 118, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
72 3 0.03
73 69 0.58
74 46 0.39
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (73 bp):
AAAAAGTTAATAGAAAGATCAAAATTTAAAATATCGATACATATGCGATGAGGATCAATACTTTT
AAAAATTG
Found at i:275874 original size:42 final size:41
Alignment explanation
Indices: 275820--275905 Score: 145
Period size: 42 Copynumber: 2.1 Consensus size: 41
275810 GATATTTAAA
275820 ATATCGATACATATGTTATGAGGTTCAATACTTTTTTTATTT
1 ATATCGATACATATGTTATGAGGTTCAATAC-TTTTTTATTT
**
275862 ATATCGATACATATGTTATGAGGTTTGATACTTTTTTATTT
1 ATATCGATACATATGTTATGAGGTTCAATACTTTTTTATTT
275903 ATA
1 ATA
275906 CAAATACTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
41 13 0.31
42 29 0.69
ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50
Consensus pattern (41 bp):
ATATCGATACATATGTTATGAGGTTCAATACTTTTTTATTT
Found at i:275918 original size:41 final size:42
Alignment explanation
Indices: 275820--275921 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 42
275810 GATATTTAAA
*
275820 ATATCGATACATATGTTATGAGGTTCAATACTTTTTTTATTT
1 ATATCAATACATATGTTATGAGGTTCAATACTTTTTTTATTT
* **
275862 ATATCGATACATATGTTATGAGGTTTGATAC-TTTTTTATTT
1 ATATCAATACATATGTTATGAGGTTCAATACTTTTTTTATTT
*
275903 ATA-CAAATACTTATGTTAT
1 ATATC-AATACATATGTTAT
275922 TGTATTTGTG
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
40 1 0.02
41 25 0.45
42 29 0.53
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (42 bp):
ATATCAATACATATGTTATGAGGTTCAATACTTTTTTTATTT
Done.