Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005202.1 Hibiscus syriacus cultivar Beakdansim tig00011756_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: 99623
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2036 original size:18 final size:18
Alignment explanation
Indices: 2013--2051 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2003 TACTAAATTT
* *
2013 ATGAAATGAATGTAAAGA
1 ATGAAACGAATGTAAAAA
2031 ATGAAACGAATGTAAAAA
1 ATGAAACGAATGTAAAAA
2049 ATG
1 ATG
2052 TGAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (18 bp):
ATGAAACGAATGTAAAAA
Found at i:4313 original size:103 final size:103
Alignment explanation
Indices: 3985--4305 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
3975 GTCGAGGGTC
* *
3985 TATGTGGTCTTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
4050 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
4088 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
4153 TTGATCCTTGGCATATGTATATGATGCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
4191 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
4256 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
4294 TATGTGGTCCTT
1 TATGTGGTCCTT
4306 ATGGACATTA
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:4361 original size:23 final size:23
Alignment explanation
Indices: 4322--4387 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
4312 ATTATTATAT
* * *
4322 GGCACTACAGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTATACGC
* * *
4345 GGTACTCCGGTGCAATTATATGT
1 GGCACTCCGGTGCAATTATACGC
*
4368 GGCACTTCGGTGCAATTATA
1 GGCACTCCGGTGCAATTATA
4388 TGAGCTGTGG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTATACGC
Found at i:10036 original size:103 final size:103
Alignment explanation
Indices: 9708--10028 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
9698 GTCGAGGGTC
9708 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
9773 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
9811 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
9876 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
9914 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
9979 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
10017 TATGTGGTCCTT
1 TATGTGGTCCTT
10029 AAGGACATTA
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:10094 original size:23 final size:23
Alignment explanation
Indices: 10035--10112 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
10025 CCTTAAGGAC
* *
10035 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTCCGGTGCA
* *** *
10059 ATTCTACACGGCAGTCCGGTGCA
1 ATTATATGTGGCACTCCGGTGCA
*
10082 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTCCGGTGCA
10105 ATTATATG
1 ATTATATG
10113 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 40 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTCCGGTGCA
Found at i:13990 original size:29 final size:29
Alignment explanation
Indices: 13957--14014 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
13947 TTCAATAGAA
13957 CATAGTTATGTGGGATAAGGGACAAGTGG
1 CATAGTTATGTGGGATAAGGGACAAGTGG
* *
13986 CATAGTTATGTGGGATGAGGGATAAGTGG
1 CATAGTTATGTGGGATAAGGGACAAGTGG
14015 TCCCATCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.05, G:0.40, T:0.26
Consensus pattern (29 bp):
CATAGTTATGTGGGATAAGGGACAAGTGG
Found at i:18614 original size:137 final size:136
Alignment explanation
Indices: 18440--18753 Score: 416
Period size: 137 Copynumber: 2.3 Consensus size: 136
18430 CTAAAAATGT
* * * * *
18440 AGGCTCTAATATTAA-CTTAAATCATTTTTAATGAATTATTGAGTCGAATAGTTAAAACGAAACA
1 AGGCTCTAATATTAATCCT-AATTAATTTTAATCAATTATTGAGTCGAATAATTAAAACGAAACA
*
18504 TCGAGCAAAAACGAAGACCAAATTAAGAATTCACCTAATTTAAAGACTAAAT-TTATAATTAGGC
65 TCGAGCAAAAACGAAGACCAAATTAAGAATTCACCTAATTTAAAGA-TAAATGTGA-AATTAGGC
*
18568 CTAAGATGG
128 CTAAGATGA
* * ** * * *
18577 AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATGCGATTCGAATAATTAAATTGGATCC
1 AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTAT-TGAGTCGAATAATTAAAACGAAACA
* **
18642 TCGAGCAAAAGCGTGGACCAAATTAAGAATTCACCTAATTTAAAGATAAATGTGAAATTAGGCCT
65 TCGAGCAAAAACGAAGACCAAATTAAGAATTCACCTAATTTAAAGATAAATGTGAAATTAGGCCT
18707 AAGATGA
130 AAGATGA
*
18714 AGGCTCTAATATTGATCCTAATTAATTTTAATCAATTATT
1 AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATT
18754 TATTCAAATC
Statistics
Matches: 155, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
137 91 0.59
138 64 0.41
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (136 bp):
AGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATTGAGTCGAATAATTAAAACGAAACAT
CGAGCAAAAACGAAGACCAAATTAAGAATTCACCTAATTTAAAGATAAATGTGAAATTAGGCCTA
AGATGA
Found at i:18677 original size:138 final size:137
Alignment explanation
Indices: 18504--18752 Score: 419
Period size: 137 Copynumber: 1.8 Consensus size: 137
18494 AAACGAAACA
*
18504 TCGAGCAAAAACGAAGACCAAATTAAGAATTCACCTAATTTAAAGACTAAAT-TTATAATTAGGC
1 TCGAGCAAAAACGAAGACCAAATTAAGAATTCACCTAATTTAAAGA-TAAATGTGA-AATTAGGC
*
18568 CTAAGATGGAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATGCGATTCGAATAATTAA
64 CTAAGATGAAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATGCGATTCGAATAATTAA
18633 ATTGGATCC
129 ATTGGATCC
* **
18642 TCGAGCAAAAGCGTGGACCAAATTAAGAATTCACCTAATTTAAAGATAAATGTGAAATTAGGCCT
1 TCGAGCAAAAACGAAGACCAAATTAAGAATTCACCTAATTTAAAGATAAATGTGAAATTAGGCCT
*
18707 AAGATGAAGGCTCTAATATTGATCCTAATTAATTTTAATCAATTAT
66 AAGATGAAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTAT
18753 TTATTCAAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
137 59 0.57
138 45 0.43
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (137 bp):
TCGAGCAAAAACGAAGACCAAATTAAGAATTCACCTAATTTAAAGATAAATGTGAAATTAGGCCT
AAGATGAAGGCTCTAATATTAATCCTAATTAATTTTAATCAATTATGCGATTCGAATAATTAAAT
TGGATCC
Found at i:19208 original size:16 final size:16
Alignment explanation
Indices: 19187--19222 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
19177 CAGAGTAAAA
19187 CATAAATAACGCGAAT
1 CATAAATAACGCGAAT
*
19203 CATAAATAACGTGAAT
1 CATAAATAACGCGAAT
19219 CATA
1 CATA
19223 CCCCAGGGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (16 bp):
CATAAATAACGCGAAT
Found at i:20990 original size:3 final size:3
Alignment explanation
Indices: 20961--21122 Score: 104
Period size: 3 Copynumber: 54.3 Consensus size: 3
20951 TTTATATTGA
* *
20961 AAT AGT AAT AAAT ACT AAT AA- AAT AAT AAT AAT -AT AAT -AT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
21004 AA- AAA AAT ACT AAT AA- AAT AAT AAT AAC AA- CAT AAT AAAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
** * *
21047 AAT TGT AAT AAT AAT AAGGT AAT AGT AA- AAT AAT AAC AAT AAAT AAT
1 AAT AAT AAT AAT AAT AA--T AAT AAT AAT AAT AAT AAT AAT -AAT AAT
* *
21094 AAT AAT AAT AAT AGGT AAA AAT AAT AAT A
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT A
21123 GGATATGGCA
Statistics
Matches: 122, Mismatches: 24, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
2 13 0.11
3 95 0.78
4 11 0.09
5 3 0.02
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:21116 original size:19 final size:18
Alignment explanation
Indices: 20980--21122 Score: 78
Period size: 19 Copynumber: 7.7 Consensus size: 18
20970 AAATACTAAT
20980 AAAATAATAATAATA-TA
1 AAAATAATAATAATAGTA
* *
20997 ATATAATAA-AAAAATACTA
1 A-A-AATAATAATAATAGTA
* **
21016 ATAA-AATAATAATAACA
1 AAAATAATAATAATAGTA
* *
21033 ACATAATAAATGATAATTGTA
1 A-A-AAT-AATAATAATAGTA
*
21054 ATAATAATAAGGTAATAGT-
1 AAAATAATAA--TAATAGTA
* *
21073 AAAATAATAACAATAAATA
1 AAAATAATAATAAT-AGTA
*
21092 ATAATAATAATAATAGGTA
1 AAAATAATAATAATA-GTA
21111 AAAATAATAATA
1 AAAATAATAATA
21123 GGATATGGCA
Statistics
Matches: 93, Mismatches: 20, Indels: 24
0.68 0.15 0.18
Matches are distributed among these distances:
16 2 0.02
17 14 0.15
18 14 0.15
19 47 0.51
20 6 0.06
21 10 0.11
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAATAATAATAATAGTA
Found at i:21135 original size:22 final size:19
Alignment explanation
Indices: 21094--21137 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
21084 AATAAATAAT
*
21094 AATAATAATAATAGGTAAA
1 AATAATAATAATAGGCAAA
21113 AATAATAATAGGATATGGCAAA
1 AATAATAATA--ATA-GGCAAA
21135 AAT
1 AAT
21138 GGTGATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (19 bp):
AATAATAATAATAGGCAAA
Found at i:22337 original size:18 final size:18
Alignment explanation
Indices: 22314--22349 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
22304 AAAATCAAAC
*
22314 AAGATGATGAATATTAGA
1 AAGATGATGAATAATAGA
22332 AAGATGATGAATAATAGA
1 AAGATGATGAATAATAGA
22350 TAATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (18 bp):
AAGATGATGAATAATAGA
Found at i:22466 original size:3 final size:3
Alignment explanation
Indices: 22460--22501 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
22450 GTGAGCGATT
* * *
22460 TGA TGA TGA TGA TGA TGA TGA TGA TGA TAA TGG TGG TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
22502 AGATAAATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:23292 original size:23 final size:24
Alignment explanation
Indices: 23260--23331 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
23250 TAATTGATCA
23260 AATTGTAGATGTTCATTTTGTTCG
1 AATTGTAGATGTTCATTTTGTTCG
* * * *
23284 ACTTG-AGA--TCCATTAATTGATCA
1 AATTGTAGATGTTCATT--TTGTTCG
23307 AATTGTAGATGTTCATTTTGTTCG
1 AATTGTAGATGTTCATTTTGTTCG
23331 A
1 A
23332 GGCTTCATTC
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
21 5 0.14
23 12 0.34
24 13 0.37
26 5 0.14
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.44
Consensus pattern (24 bp):
AATTGTAGATGTTCATTTTGTTCG
Found at i:23306 original size:47 final size:47
Alignment explanation
Indices: 23237--23370 Score: 192
Period size: 47 Copynumber: 3.0 Consensus size: 47
23227 ACGTATAAGT
23237 ACTTGAGATCCATTAATTGATCAAATTGTAGATGTTCATTTTGTTCG
1 ACTTGAGATCCATTAATTGATCAAATTGTAGATGTTCATTTTGTTCG
23284 ACTTGAGATCCATTAATTGATCAAATTGTAGATGTTCATTTTGTTCG
1 ACTTGAGATCCATTAATTGATCAAATTGTAGATGTTCATTTTGTTCG
* * *
23331 A---G-GCTTCATTCA---ATCAAATTGTAGATGTTCATTTTGTTCG
1 ACTTGAGATCCATTAATTGATCAAATTGTAGATGTTCATTTTGTTCG
23371 GGGCTTCATT
Statistics
Matches: 84, Mismatches: 3, Indels: 7
0.89 0.03 0.07
Matches are distributed among these distances:
40 28 0.33
43 7 0.08
44 1 0.01
47 48 0.57
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (47 bp):
ACTTGAGATCCATTAATTGATCAAATTGTAGATGTTCATTTTGTTCG
Found at i:23316 original size:24 final size:24
Alignment explanation
Indices: 23242--23316 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
23232 TAAGTACTTG
23242 AGATCCATTAATTGATCAAATTGT
1 AGATCCATTAATTGATCAAATTGT
* * * *
23266 AGATGTTCATT--TTGTTCGACTTG-
1 AGA--TCCATTAATTGATCAAATTGT
23289 AGATCCATTAATTGATCAAATTGT
1 AGATCCATTAATTGATCAAATTGT
23313 AGAT
1 AGAT
23317 GTTCATTTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
21 5 0.13
23 12 0.32
24 16 0.42
26 5 0.13
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (24 bp):
AGATCCATTAATTGATCAAATTGT
Found at i:23347 original size:40 final size:40
Alignment explanation
Indices: 23303--23381 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
23293 CCATTAATTG
23303 ATCAAATTGTAGATGTTCATTTTGTTCGAGGCTTCATTCA
1 ATCAAATTGTAGATGTTCATTTTGTTCGAGGCTTCATTCA
*
23343 ATCAAATTGTAGATGTTCATTTTGTTCGGGGCTTCATTC
1 ATCAAATTGTAGATGTTCATTTTGTTCGAGGCTTCATTC
23382 TAGTTTCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (40 bp):
ATCAAATTGTAGATGTTCATTTTGTTCGAGGCTTCATTCA
Found at i:23446 original size:7 final size:7
Alignment explanation
Indices: 23428--23460 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
23418 TAGTTAGTTT
23428 AAATATAA
1 AAATA-AA
23436 AAATAAA
1 AAATAAA
23443 AAATAAA
1 AAATAAA
23450 AAATAAA
1 AAATAAA
23457 AAAT
1 AAAT
23461 TTAAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAATAAA
Found at i:23453 original size:14 final size:15
Alignment explanation
Indices: 23428--23465 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
23418 TAGTTAGTTT
23428 AAATATAAAAATAAA
1 AAATATAAAAATAAA
23443 AAATA-AAAAATAAA
1 AAATATAAAAATAAA
*
23457 AAATTTAAA
1 AAATATAAA
23466 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATATAAAAATAAA
Found at i:23685 original size:22 final size:21
Alignment explanation
Indices: 23660--23720 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 21
23650 ATTGTGCCTA
23660 TTATTATTGGTTATATCATTAG
1 TTATTATTGGTTA-ATCATTAG
* * * *
23682 TTATATATAGTTTAATTATTGG
1 TTAT-TATTGGTTAATCATTAG
*
23704 TTATTATT-ATTAATCAT
1 TTATTATTGGTTAATCAT
23721 GCGTGTGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 7 0.23
21 3 0.10
22 14 0.45
23 7 0.23
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (21 bp):
TTATTATTGGTTAATCATTAG
Found at i:23799 original size:2 final size:2
Alignment explanation
Indices: 23792--23817 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23782 AAAAATAAAA
23792 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
23818 TATTTACAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26796 original size:23 final size:23
Alignment explanation
Indices: 26755--26802 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
26745 TAAAATGTTG
*
26755 TTTTAATAAAATTAAAATTATTT
1 TTTTAATAAAATGAAAATTATTT
* * *
26778 TTTTATTAAAATGACAATTGTTT
1 TTTTAATAAAATGAAAATTATTT
26801 TT
1 TT
26803 GGGTGCTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTTAATAAAATGAAAATTATTT
Found at i:27378 original size:16 final size:16
Alignment explanation
Indices: 27357--27394 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
27347 TGTGCAAATC
27357 CGGGTACCCAGATTTT
1 CGGGTACCCAGATTTT
*
27373 CGGGTA-CCTGATTTT
1 CGGGTACCCAGATTTT
*
27388 TGGGTAC
1 CGGGTAC
27395 TCGGAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (16 bp):
CGGGTACCCAGATTTT
Found at i:27467 original size:15 final size:15
Alignment explanation
Indices: 27447--27503 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
27437 TCGAATGTTA
27447 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
27462 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
*
27478 GCGAGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
27494 CGGGTACCCG
1 CGGGTACCCG
27504 ATACCCGATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:29052 original size:6 final size:6
Alignment explanation
Indices: 29038--29071 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
29028 GATAACTTTT
*
29038 ATTAAA ATTACA ATTACA ATTACA ATTACA ATTA
1 ATTACA ATTACA ATTACA ATTACA ATTACA ATTA
29072 TCCTTGTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTACA
Found at i:29724 original size:31 final size:31
Alignment explanation
Indices: 29650--29727 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
29640 ACAGTACGTC
* * * *
29650 GGGGGCCATATTACAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATATTA
*
29681 GGGGACCATATTGCAAATGGACTAAATATTA
1 GGGGACCATATTGCAAACGGACTAAATATTA
**
29712 GGGGACTGTATTGCAA
1 GGGGACCATATTGCAA
29728 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGCAAACGGACTAAATATTA
Found at i:32781 original size:18 final size:18
Alignment explanation
Indices: 32758--32793 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
32748 AAAATCAAAC
*
32758 AAGATGATGAATATTAGA
1 AAGATGATGAATAATAGA
32776 AAGATGATGAATAATAGA
1 AAGATGATGAATAATAGA
32794 TAATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (18 bp):
AAGATGATGAATAATAGA
Found at i:32823 original size:29 final size:30
Alignment explanation
Indices: 32781--32840 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
32771 TTAGAAAGAT
* *
32781 GATGAATAATAGAT-AATAAATATATAAAA
1 GATGAATAAAAGATAAATAAAGATATAAAA
*
32810 GATGAATAAAAGATAAATAAAGATATGAAA
1 GATGAATAAAAGATAAATAAAGATATAAAA
32840 G
1 G
32841 TATTTGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (30 bp):
GATGAATAAAAGATAAATAAAGATATAAAA
Found at i:33256 original size:51 final size:51
Alignment explanation
Indices: 33187--33285 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 51
33177 TGTAACATAA
* * *
33187 TAAACTAAAGATAATGTTTCGATTCTATCCTT-ATTCCTAAAAAAATAATAG
1 TAAACTAAAGATAATGTTTCAACTCGAT-CTTAATTCCTAAAAAAATAATAG
*
33238 TAAACT-AAGCATAATGTTTTAACTCGATCTTAATTCCTAAAAAAATAA
1 TAAACTAAAG-ATAATGTTTCAACTCGATCTTAATTCCTAAAAAAATAA
33286 ATCTTATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
50 6 0.14
51 36 0.86
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.34
Consensus pattern (51 bp):
TAAACTAAAGATAATGTTTCAACTCGATCTTAATTCCTAAAAAAATAATAG
Found at i:43385 original size:21 final size:21
Alignment explanation
Indices: 43360--43401 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43350 TGGGTTGGGG
**
43360 ATTTGAGGATTTTTGTTTTTA
1 ATTTGAGGATTTGGGTTTTTA
*
43381 ATTTGGGGATTTGGGTTTTTA
1 ATTTGAGGATTTGGGTTTTTA
43402 TCCCTAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (21 bp):
ATTTGAGGATTTGGGTTTTTA
Found at i:44353 original size:16 final size:14
Alignment explanation
Indices: 44316--44349 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44306 ACTTGAATAT
* *
44316 AATACCTCTGAAAA
1 AATAACTCTAAAAA
44330 AATAACTCTAAAAA
1 AATAACTCTAAAAA
44344 AATAAC
1 AATAAC
44350 ACTCCCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.18, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAACTCTAAAAA
Found at i:46293 original size:3 final size:3
Alignment explanation
Indices: 46285--46339 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
46275 CCGTAGATTG
*
46285 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TATA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA
46332 TT- TTA TTA
1 TTA TTA TTA
46340 CTTTTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:48779 original size:18 final size:17
Alignment explanation
Indices: 48758--48792 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48748 AAATTTATTG
48758 TTTTAATTAAAATTAATA
1 TTTTAATTAAAA-TAATA
*
48776 TTTTTATTAAAATAATA
1 TTTTAATTAAAATAATA
48793 AATATGTTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTAATTAAAATAATA
Found at i:54660 original size:59 final size:61
Alignment explanation
Indices: 54537--54700 Score: 149
Period size: 59 Copynumber: 2.7 Consensus size: 61
54527 TCAATATGCC
* * * *
54537 TTTTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTATTGACATGATATTTTCAAATGAA-
1 TTTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGTTTATTGACAAGATATCTCCAAATGAAT
* * * *
54597 -TTTTTAAAGAAGCTAAGTCTGATTTTCAGAAGTTTTTTGATAAG-T-TCTCCATAT-AAGTTTT
1 TTTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGTTTATTGACAAGATATCTCCAAATGAA----T
* * *
54658 TTTTTTAAAAAAAGCTAAGTCTAATTTTCAGAGGTTTCTTGAC
1 TTTTTT-AAAGAAGCTAAGTCTGATTTTCAGAGGTTTATTGAC
54701 GGTCAGCCAA
Statistics
Matches: 84, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
56 2 0.02
57 6 0.07
58 1 0.01
59 39 0.46
62 5 0.06
63 31 0.37
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (61 bp):
TTTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGTTTATTGACAAGATATCTCCAAATGAAT
Found at i:54881 original size:41 final size:42
Alignment explanation
Indices: 54775--54886 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
54765 TCTTACTTAG
* *
54775 TAAGTTCTTCGGGCCAT-CAGTAAGCCTTTCAAGCATGATGAT
1 TAAGTCCTTCGGGCCATCCA-TAAGCCTTTCAAGCAAGATGAT
* * * *
54817 TAAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGA-
1 TAAGTCCTTCGGGCCATCCATAAGCCTTTCAAGCAAGATGAT
*
54858 TAAGTCCTTTGGGCCATCCATAAGACCTT
1 TAAGTCCTTCGGGCCATCCATAAG-CCTT
54887 CGGGTAGGAT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
41 20 0.34
42 37 0.64
43 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCCATAAGCCTTTCAAGCAAGATGAT
Found at i:55114 original size:41 final size:42
Alignment explanation
Indices: 55013--55119 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
55003 TCTTACTTAG
* * * *
55013 TAAGTCCTTTGAGCCATC-AGTAAGTCTTTCGAGCATGATGTT
1 TAAGTCCTTCGAGCCATCTA-TAAGTCTTTCAAGCAAGATGTA
* * *
55055 TAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATG-A
1 TAAGTCCTTCGAGCCATCTATAAGTCTTTCAAGCAAGATGTA
55096 TAAGTCCTTCGAGCCATCTATAAG
1 TAAGTCCTTCGAGCCATCTATAAG
55120 ACCTTCAGGA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 21 0.39
42 32 0.59
43 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (42 bp):
TAAGTCCTTCGAGCCATCTATAAGTCTTTCAAGCAAGATGTA
Found at i:55225 original size:20 final size:22
Alignment explanation
Indices: 55186--55225 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
55176 AATCTTTTCT
*
55186 GAAAATTGATTTTGAAAAGTAA
1 GAAAATTGATTTTCAAAAGTAA
55208 GAAAA-TGA-TTTCAAAAGT
1 GAAAATTGATTTTCAAAAGT
55226 TTCTTACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (22 bp):
GAAAATTGATTTTCAAAAGTAA
Found at i:55307 original size:42 final size:40
Alignment explanation
Indices: 55241--55341 Score: 103
Period size: 42 Copynumber: 2.5 Consensus size: 40
55231 ACTTAGTAAG
* * *
55241 TCCTTCGGGTCATCAACAATTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGTCATCTA-TATTCTTTCGAGCAAGATGA-TAAA
* * *
55283 TCCTTCGGGTCATCTATATGTCTTTTGAGTAAGATGATAAG
1 TCCTTCGGGTCATCTATAT-TCTTTCGAGCAAGATGATAAA
* *
55324 TCCTTTGGGCCATCTATA
1 TCCTTCGGGTCATCTATA
55342 AGACCTTTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 21 0.42
42 29 0.58
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (40 bp):
TCCTTCGGGTCATCTATATTCTTTCGAGCAAGATGATAAA
Found at i:55319 original size:224 final size:226
Alignment explanation
Indices: 54907--55348 Score: 656
Period size: 224 Copynumber: 2.0 Consensus size: 226
54897 CTTTTCACAT
* * *
54907 ATTTTCGAAAAATGAGAAAACGATTTCTAAAGTTTCTCATTTAAATTTTTTTCTAAAAATAAAAT
1 ATTTTCGAAAAATGAAAAAACGATTTCCAAAGTTTCTCATTTAAATTCTTTTCTAAAAATAAAAT
* * **
54972 TTTTGAAAATAAGAAAATGATATCCAAAGTTTCTTACTTAGTAAGTCCTTTGAGCCATCAGTAAG
66 TTTTGAAAATAAGAAAATGATATCAAAAGTTTCTTACTTAGTAAGTCCTTCGAGCCATCAACAAG
*
55037 TCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTC
131 TCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTC
55102 CTTCGAGCCATCTATAAGACCTTCAGGAAGG
196 CTTCGAGCCATCTATAAGACCTTCAGGAAGG
* * **
55133 ATTTTTGAAAAATGAAAAAACGATTTCCAAAGTTTCTCATTTAAA-TCTTTTCTGAAAAT-TGA-
1 ATTTTCGAAAAATGAAAAAACGATTTCCAAAGTTTCTCATTTAAATTCTTTTCTAAAAATAAAAT
* * *
55195 TTTTGAAAAGTAAGAAAATGATTTCAAAAGTTTCTTACTTAGTAAGTCCTTCGGGTCATCAACAA
66 TTTTGAAAA-TAAGAAAATGATATCAAAAGTTTCTTACTTAGTAAGTCCTTCGAGCCATCAACAA
* * ** *
55260 TTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATATGTCTTTTGAGTAAGATGATAAGT
130 GTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGT
* *
55325 CCTTTGGGCCATCTATAAGACCTT
195 CCTTCGAGCCATCTATAAGACCTT
55349 TGACCAGGAT
Statistics
Matches: 193, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
223 9 0.05
224 130 0.67
225 12 0.06
226 42 0.22
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (226 bp):
ATTTTCGAAAAATGAAAAAACGATTTCCAAAGTTTCTCATTTAAATTCTTTTCTAAAAATAAAAT
TTTTGAAAATAAGAAAATGATATCAAAAGTTTCTTACTTAGTAAGTCCTTCGAGCCATCAACAAG
TCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTC
CTTCGAGCCATCTATAAGACCTTCAGGAAGG
Found at i:55351 original size:41 final size:42
Alignment explanation
Indices: 55273--55351 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 42
55263 TTTCGAGCAT
* * * *
55273 GATGATTAAATCCTTCGGGTCATCTATATGTCTTTTGAGTAA
1 GATGATTAAATCCTTCGGGCCATCTATAAGACCTTTGAGTAA
* *
55315 GATGA-TAAGTCCTTTGGGCCATCTATAAGACCTTTGA
1 GATGATTAAATCCTTCGGGCCATCTATAAGACCTTTGA
55352 CCAGGATGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
41 26 0.84
42 5 0.16
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (42 bp):
GATGATTAAATCCTTCGGGCCATCTATAAGACCTTTGAGTAA
Found at i:55906 original size:132 final size:132
Alignment explanation
Indices: 55662--56395 Score: 722
Period size: 132 Copynumber: 5.6 Consensus size: 132
55652 AAGAAAATAT
* * ** *
55662 AACAAGTCTGCCTTGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTTCAGATCTG
1 AACAAGTCTACCTTGATTCAATCTTCCCTGAAGAGCAGTGGAATGAATCAATGTTTCCAGATCTG
* * * * * * *
55727 ATCTACCCTGAAGAGCAA-TGGAGCCGATCC-TCTTTTTCCAGATTTGATTTTCCCTGAGGACCA
66 ATCTCCCCTAAAGAG-AAGTGAAGCAGATCCATCTTTTT-CAGATTTGATCTTCCCTGAAGAGCA
55790 GTGG
129 GTGG
* * * * * *
55794 AATAAGTCTTCCTCGATCCAATCTTCCCTGAAGAGCAGTGGAATAAATCAATGTTTCCAAATCTG
1 AACAAGTCTACCTTGATTCAATCTTCCCTGAAGAGCAGTGGAATGAATCAATGTTTCCAGATCTG
* * * * *
55859 ATTTCCCCTAAAGAGAAGTGAAGCAGATCCATCTTTTTTAGACTTGATCTTCCCTAAAGAGAAGT
66 ATCTCCCCTAAAGAGAAGTGAAGCAGATCCATCTTTTTCAGATTTGATCTTCCCTGAAGAGCAGT
55924 GG
131 GG
* * * * * *
55926 AACAAATCTACCTTGATTTAATCTTCCCTGAAGAGAAGTGGAATAAATCAATGTTTCCATATCTA
1 AACAAGTCTACCTTGATTCAATCTTCCCTGAAGAGCAGTGGAATGAATCAATGTTTCCAGATCTG
* * ** * * **
55991 ATATCCCCTAAAGAGAAG-CAGAGCAGATCCCCCTTTTCCAGATTTGATCTTCCTTGTGGAGCAG
66 ATCTCCCCTAAAGAGAAGTGA-AGCAGATCCATCTTTTTCAGATTTGATCTTCCCTGAAGAGCAG
*
56055 TAG
130 TGG
* * * **
56058 AACAAGTCTGCCTTGATTCAAGCTTCCCTGAAGAGCAGTGGAATGAATCAACGTTTCTTGATCTG
1 AACAAGTCTACCTTGATTCAATCTTCCCTGAAGAGCAGTGGAATGAATCAATGTTTCCAGATCTG
* * * * *
56123 GTCTCCCCTAAAGAGAAGCGAAGCAGGTCCATCTTTTTCAGATTTGATCTTCCCTGAAGAACAAT
66 ATCTCCCCTAAAGAGAAGTGAAGCAGATCCATCTTTTTCAGATTTGATCTTCCCTGAAGAGCAGT
56188 GG
131 GG
* *
56190 AACAAATCTACCTTGATTCAATCTTCCCTGAAGAGCAGTGGAATGAATAAATGTTTCCAGATCTG
1 AACAAGTCTACCTTGATTCAATCTTCCCTGAAGAGCAGTGGAATGAATCAATGTTTCCAGATCTG
* * * * * * * * **
56255 ATCTCCCCTGAACAGAAG-CAGAGTAGATCCCTCTCTTTCAGATTTGATCTACCATG-AGAAATA
66 ATCTCCCCTAAAGAGAAGTGA-AGCAGATCCATCTTTTTCAGATTTGATCTTCCCTGAAG-AGCA
**
56318 GTAA
129 GTGG
* * * * * * * * * * *
56322 AACAAATCTGCCTCGATTCAATATACTCTAAAGAGTAGTGGAGTAAATCAACGTTTCCAGATCTG
1 AACAAGTCTACCTTGATTCAATCTTCCCTGAAGAGCAGTGGAATGAATCAATGTTTCCAGATCTG
*
56387 ATCTACCCT
66 ATCTCCCCT
56396 GAAAAATAGC
Statistics
Matches: 495, Mismatches: 101, Indels: 12
0.81 0.17 0.02
Matches are distributed among these distances:
131 6 0.01
132 481 0.97
133 8 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (132 bp):
AACAAGTCTACCTTGATTCAATCTTCCCTGAAGAGCAGTGGAATGAATCAATGTTTCCAGATCTG
ATCTCCCCTAAAGAGAAGTGAAGCAGATCCATCTTTTTCAGATTTGATCTTCCCTGAAGAGCAGT
GG
Found at i:56148 original size:264 final size:264
Alignment explanation
Indices: 55662--56416 Score: 849
Period size: 264 Copynumber: 2.9 Consensus size: 264
55652 AAGAAAATAT
* * ** *
55662 AACAAGTCTGCCTTGATTCAATCTTCCCTGAAGA-ACAGTGGAATGAATCAACATTTTCAGATCT
1 AACAAATCTACCTTGATTCAATCTTCCCTGAAGAGA-AGTGGAATGAATCAATGTTTCCAGATCT
* * * * *
55726 GATCTACCCTGAAGAGCAATG--GAGCCGATCCTCTTTTTCCAGATTTGATTTTCCCTGAGGACC
65 GATCTCCCCTGAAGAG-AA-GCAGAGCAGATCCCCCTTTTCCAGATTTGATCTTCCCTGAGGACC
* * * * *
55789 AGTGGAATAAGTCTTCCTCGATCCAATCTTCCCTGAAGAGCAGTGGAATAAATCAATGTTTCCAA
128 AGTAGAACAAGTCTGCCTCGATCCAAGCTTCCCTGAAGAGCAGTGGAATAAATCAACGTTTCCAA
* * *
55854 ATCTGATTTCCCCTAAAGAGAAGTGAAGCAGATCCATCTTTTTTAGACTTGATCTTCCCTAAAGA
193 ATCTGATCTCCCCTAAAGAGAAGCGAAGCAGATCCATCTTTTTCAGACTTGATCTTCCCTAAAGA
*
55919 GA-AGTGG
258 -ACAATGG
* * * *
55926 AACAAATCTACCTTGATTTAATCTTCCCTGAAGAGAAGTGGAATAAATCAATGTTTCCATATCTA
1 AACAAATCTACCTTGATTCAATCTTCCCTGAAGAGAAGTGGAATGAATCAATGTTTCCAGATCTG
* * * * *
55991 ATATCCCCTAAAGAGAAGCAGAGCAGATCCCCCTTTTCCAGATTTGATCTTCCTTGTGGAGCAGT
66 ATCTCCCCTGAAGAGAAGCAGAGCAGATCCCCCTTTTCCAGATTTGATCTTCCCTGAGGACCAGT
* * * ***
56056 AGAACAAGTCTGCCTTGATTCAAGCTTCCCTGAAGAGCAGTGGAATGAATCAACGTTTCTTGATC
131 AGAACAAGTCTGCCTCGATCCAAGCTTCCCTGAAGAGCAGTGGAATAAATCAACGTTTCCAAATC
* * * *
56121 TGGTCTCCCCTAAAGAGAAGCGAAGCAGGTCCATCTTTTTCAGATTTGATCTTCCCTGAAGAACA
196 TGATCTCCCCTAAAGAGAAGCGAAGCAGATCCATCTTTTTCAGACTTGATCTTCCCTAAAGAACA
56186 ATGG
261 ATGG
* *
56190 AACAAATCTACCTTGATTCAATCTTCCCTGAAGAGCAGTGGAATGAATAAATGTTTCCAGATCTG
1 AACAAATCTACCTTGATTCAATCTTCCCTGAAGAGAAGTGGAATGAATCAATGTTTCCAGATCTG
* * * * * * **
56255 ATCTCCCCTGAACAGAAGCAGAGTAGATCCCTCTCTTT-CAGATTTGATCTACCATGAGAAATAG
66 ATCTCCCCTGAAGAGAAGCAGAGCAGATCCCCCT-TTTCCAGATTTGATCTTCCCTGAGGACCAG
* * * ** * * * * * *
56319 TAAAACAAATCTGCCTCGATTCAATATACTCTAAAGAGTAGTGGAGTAAATCAACGTTTCCAGAT
130 TAGAACAAGTCTGCCTCGATCCAAGCTTCCCTGAAGAGCAGTGGAATAAATCAACGTTTCCAAAT
* *
56384 CTGATCTACCCTGAAA-A-ATAGCGAAGCAAATCC
195 CTGATCTCCCCT-AAAGAGA-AGCGAAGCAGATCC
56417 CTTTTTAAAT
Statistics
Matches: 412, Mismatches: 72, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
262 1 0.00
263 4 0.01
264 400 0.97
265 7 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (264 bp):
AACAAATCTACCTTGATTCAATCTTCCCTGAAGAGAAGTGGAATGAATCAATGTTTCCAGATCTG
ATCTCCCCTGAAGAGAAGCAGAGCAGATCCCCCTTTTCCAGATTTGATCTTCCCTGAGGACCAGT
AGAACAAGTCTGCCTCGATCCAAGCTTCCCTGAAGAGCAGTGGAATAAATCAACGTTTCCAAATC
TGATCTCCCCTAAAGAGAAGCGAAGCAGATCCATCTTTTTCAGACTTGATCTTCCCTAAAGAACA
ATGG
Found at i:59052 original size:18 final size:19
Alignment explanation
Indices: 59020--59056 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
59010 GTGGACCGTA
*
59020 TAATTTTTTTAATTAAAAT
1 TAATATTTTTAATTAAAAT
59039 TAATATTTTT-ATTAAAAT
1 TAATATTTTTAATTAAAAT
59057 GACAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATATTTTTAATTAAAAT
Found at i:61711 original size:25 final size:22
Alignment explanation
Indices: 61668--61719 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
61658 AGGTTTGTTG
* *
61668 TTTTAATTAAAATTAAAATTAATA
1 TTTTTATTAAAATGAAAA-T-ATA
61692 TTTTTATTAAAATGACAAATATA
1 TTTTTATTAAAATGA-AAATATA
61715 TTTTT
1 TTTTT
61720 GGGTGTCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 14 0.56
25 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTTATTAAAATGAAAATATA
Found at i:62037 original size:18 final size:18
Alignment explanation
Indices: 62014--62049 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
62004 AAAATCAAAC
*
62014 AAGATGATGAATATTAGA
1 AAGATGATGAATAATAGA
62032 AAGATGATGAATAATAGA
1 AAGATGATGAATAATAGA
62050 TAATAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (18 bp):
AAGATGATGAATAATAGA
Found at i:62516 original size:51 final size:50
Alignment explanation
Indices: 62447--62546 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 50
62437 TATAACATAA
*
62447 TAAACTAAAGATAATGTTTCGAA-TCTATCCTAATTCCTAAAAAAATAATAG
1 TAAACTAAAGATAATGTTT-GAACTCGATCCTAATTCCT-AAAAAATAATAG
* *
62498 TAAACT-AAGAATAATGTTTTAACTCGATCTTAATTCCTAAAAAATAATA
1 TAAACTAAAG-ATAATGTTTGAACTCGATCCTAATTCCTAAAAAATAATA
62547 AATCTTATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
50 16 0.36
51 28 0.64
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (50 bp):
TAAACTAAAGATAATGTTTGAACTCGATCCTAATTCCTAAAAAATAATAG
Found at i:64969 original size:31 final size:31
Alignment explanation
Indices: 64869--65006 Score: 156
Period size: 31 Copynumber: 4.5 Consensus size: 31
64859 GAGTAACTTG
*
64869 GGCCTACCCAAGAAAGTTCTCA-GGCCACG-
1 GGCCTACCCAAGAAAGATCTCAGGGCCACGA
* *
64898 GAGCCTACCCAAGAAAGATCTCAAAGGCCGC-A
1 G-GCCTACCCAAGAAAGATCTC-AGGGCCACGA
*
64930 GGGCCTACCCAAGAATGATCTCAGGGCCACGA
1 -GGCCTACCCAAGAAAGATCTCAGGGCCACGA
* ***
64962 GGCCTACCCAAGAAAAATCTCAGGGCCGTAA
1 GGCCTACCCAAGAAAGATCTCAGGGCCACGA
64993 GGCCTACCCAAGAA
1 GGCCTACCCAAGAA
65007 TAATCTAGGG
Statistics
Matches: 93, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.01
30 19 0.20
31 47 0.51
32 25 0.27
33 1 0.01
ACGTcount: A:0.33, C:0.32, G:0.24, T:0.12
Consensus pattern (31 bp):
GGCCTACCCAAGAAAGATCTCAGGGCCACGA
Found at i:64989 original size:62 final size:63
Alignment explanation
Indices: 64868--65037 Score: 204
Period size: 62 Copynumber: 2.7 Consensus size: 63
64858 GGAGTAACTT
* * *
64868 GGGCCTACCCAAGAAAGTTCTCA-GGCCACGGAGCCTACCCAAGAAAGATCTCAAAGGCCGCA
1 GGGCCTACCCAAGAATGATCTCAGGGCCACGGAGCCTACCCAAGAAAAATCTCAAAGGCCGCA
* *
64930 GGGCCTACCCAAGAATGATCTCAGGGCCAC-GAGGCCTACCCAAGAAAAATCTC-AGGGCCGTA
1 GGGCCTACCCAAGAATGATCTCAGGGCCACGGA-GCCTACCCAAGAAAAATCTCAAAGGCCGCA
* * * * *
64992 AGGCCTACCCAAGAATAATCT-AGGGGCCGCAGAGCCTACCTAAGAA
1 GGGCCTACCCAAGAATGATCTCA-GGGCCACGGAGCCTACCCAAGAA
65038 TCACATTAGG
Statistics
Matches: 95, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
61 1 0.01
62 67 0.71
63 27 0.28
ACGTcount: A:0.32, C:0.31, G:0.25, T:0.12
Consensus pattern (63 bp):
GGGCCTACCCAAGAATGATCTCAGGGCCACGGAGCCTACCCAAGAAAAATCTCAAAGGCCGCA
Found at i:65012 original size:31 final size:31
Alignment explanation
Indices: 64900--65038 Score: 149
Period size: 31 Copynumber: 4.5 Consensus size: 31
64890 AGGCCACGGA
* *
64900 GCCTACCCAAGAA-AGATCTCAAAGGCCGCAGG
1 GCCTACCCAAGAATA-ATCTC-AGGGCCGCAAG
* * *
64932 GCCTACCCAAGAATGATCTCAGGGCCACGAG
1 GCCTACCCAAGAATAATCTCAGGGCCGCAAG
* *
64963 GCCTACCCAAGAAAAATCTCAGGGCCGTAAG
1 GCCTACCCAAGAATAATCTCAGGGCCGCAAG
64994 GCCTACCCAAGAATAATCT-AGGGGCCGC-AG
1 GCCTACCCAAGAATAATCTCA-GGGCCGCAAG
*
65024 AGCCTACCTAAGAAT
1 -GCCTACCCAAGAAT
65039 CACATTAGGT
Statistics
Matches: 91, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.03
31 70 0.77
32 18 0.20
ACGTcount: A:0.33, C:0.30, G:0.24, T:0.13
Consensus pattern (31 bp):
GCCTACCCAAGAATAATCTCAGGGCCGCAAG
Found at i:65029 original size:93 final size:93
Alignment explanation
Indices: 64869--65038 Score: 220
Period size: 93 Copynumber: 1.8 Consensus size: 93
64859 GAGTAACTTG
** * *
64869 GGCCTACCCAAGAAAGTTCTCAGGCCACGGAGCCTACCCAAGAAAGATCTCAAAGGCCGCAGGGC
1 GGCCTACCCAAGAAAAATCTCAGGCCACGAAGCCTACCCAAGAAAGATCTCAAAGGCCGCAGAGC
64934 CTACCCAAGAATGATCTCAGGGCCACGA
66 CTACCCAAGAATGATCTCAGGGCCACGA
* **
64962 GGCCTACCCAAGAAAAATCTCAGGGC-CGTAAGGCCTACCCAAGAATA-ATCT-AGGGGCCGCAG
1 GGCCTACCCAAGAAAAATCTCAGGCCACG-AA-GCCTACCCAAGAA-AGATCTCAAAGGCCGCAG
*
65024 AGCCTACCTAAGAAT
63 AGCCTACCCAAGAAT
65039 CACATTAGGT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
92 2 0.03
93 46 0.70
94 17 0.26
95 1 0.02
ACGTcount: A:0.32, C:0.31, G:0.24, T:0.13
Consensus pattern (93 bp):
GGCCTACCCAAGAAAAATCTCAGGCCACGAAGCCTACCCAAGAAAGATCTCAAAGGCCGCAGAGC
CTACCCAAGAATGATCTCAGGGCCACGA
Found at i:69529 original size:31 final size:30
Alignment explanation
Indices: 69494--69671 Score: 130
Period size: 31 Copynumber: 5.7 Consensus size: 30
69484 AAGCATCTTG
*
69494 GGGCCTATGGGCCTACCCAAGAAAGTTCTCA
1 GGGCC-ATGGGCCTACCCAAGAAAGATCTCA
*
69525 GGGCCACGGGGCCTACCCAAGAAAGATCTCAA
1 GGGCCA-TGGGCCTACCCAAGAAAGATCTC-A
* *
69557 GGCCGCATGGGCCTACCCAA-AAATGATGTCA
1 GGGC-CATGGGCCTACCCAAGAAA-GATCTCA
*** * *
69588 GGGCCACAAAGCCTACCCAAGAAAAATCCCA
1 GGGCCA-TGGGCCTACCCAAGAAAGATCTCA
*
69619 GGGCCGCAT-GGCCTACCCAAGAATA-ATCTCG
1 GGG-C-CATGGGCCTACCCAAGAA-AGATCTCA
*
69650 GGGCCGGA-GAGCCTACCCAAGA
1 GGGCC--ATGGGCCTACCCAAGA
69672 GTTACATTAG
Statistics
Matches: 118, Mismatches: 17, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
29 1 0.01
30 4 0.03
31 83 0.70
32 26 0.22
33 4 0.03
ACGTcount: A:0.30, C:0.31, G:0.26, T:0.12
Consensus pattern (30 bp):
GGGCCATGGGCCTACCCAAGAAAGATCTCA
Found at i:69602 original size:63 final size:63
Alignment explanation
Indices: 69500--69671 Score: 204
Period size: 63 Copynumber: 2.7 Consensus size: 63
69490 CTTGGGGCCT
* * * * *
69500 ATGGGCCTACCCAAGAAA-GTTCTCAGGGCCACGGGGCCTACCCAAGAAAGATCTCAAGGCCGC
1 ATGGGCCTACCCAA-AAATGATCTCAGGGCCACAGAGCCTACCCAAGAAAAATCCCAAGGCCGC
* * *
69563 ATGGGCCTACCCAAAAATGATGTCAGGGCCACAAAGCCTACCCAAGAAAAATCCCAGGGCCGC
1 ATGGGCCTACCCAAAAATGATCTCAGGGCCACAGAGCCTACCCAAGAAAAATCCCAAGGCCGC
* * * **
69626 AT-GGCCTACCCAAGAATAATCTCGGGGCCGGAGAGCCTACCCAAGA
1 ATGGGCCTACCCAAAAATGATCTCAGGGCCACAGAGCCTACCCAAGA
69672 GTTACATTAG
Statistics
Matches: 93, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
62 40 0.43
63 53 0.57
ACGTcount: A:0.31, C:0.31, G:0.25, T:0.12
Consensus pattern (63 bp):
ATGGGCCTACCCAAAAATGATCTCAGGGCCACAGAGCCTACCCAAGAAAAATCCCAAGGCCGC
Found at i:78324 original size:13 final size:13
Alignment explanation
Indices: 78300--78334 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
78290 TATTTATTAT
78300 ATATTT-ATAAAA
1 ATATTTAATAAAA
78312 ATATTTAAT-AAA
1 ATATTTAATAAAA
78324 ATATTTAATAA
1 ATATTTAATAA
78335 TAAAAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTAATAAAA
Found at i:79783 original size:3 final size:3
Alignment explanation
Indices: 79775--79854 Score: 115
Period size: 3 Copynumber: 26.7 Consensus size: 3
79765 TAATATAAAT
* *
79775 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
79823 TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
79855 TGGAAAAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:80370 original size:113 final size:113
Alignment explanation
Indices: 80146--80786 Score: 948
Period size: 113 Copynumber: 5.7 Consensus size: 113
80136 TCAGATAATA
**
80146 TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * * * *
80210 TTTCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAAT
66 TCTCATT-ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
* * * * *
80259 TTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCATTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * * * *
80324 TCTCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAAT
66 TCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
* * *
80372 TTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
80437 TCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
66 TCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
*** * *
80485 TCAGGTAAAAGGTTGAAAAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
80550 TCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
66 TCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
***
80598 TCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
80663 TCTCATTATGAACTTTCTCTGG-AAA-A-GATCCACCAAATGATGGAT
66 TCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
***
80708 TCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
80773 TCTCATTATGAACT
66 TCTCATTATGAACT
80787 CTACCTTGCA
Statistics
Matches: 501, Mismatches: 26, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
110 98 0.20
111 1 0.00
112 3 0.01
113 339 0.68
114 60 0.12
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
Found at i:81539 original size:84 final size:84
Alignment explanation
Indices: 81398--82229 Score: 1331
Period size: 84 Copynumber: 10.0 Consensus size: 84
81388 GGTTCTGTAA
81398 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
*
81463 CTTCTAAATTCAATGATTG
66 CTTCCAAATTCAATGATTG
81482 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
*
81547 CTTCTAAATTCAATGATTG
66 CTTCCAAATTCAATGATTG
81566 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
*
81631 CTTCTAAATTCAATGATTG
66 CTTCCAAATTCAATGATTG
81650 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
*
81715 CTTCTAAATTCAATGATTG
66 CTTCCAAATTCAATGATTG
**
81734 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCAT
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
81798 CTTCCAAATTCAATGATTG
66 CTTCCAAATTCAATGATTG
* *
81817 GTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGGAGCACATTCA
1 GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG-GCACATTCA
81881 TCTTCCAAATTCAATGATTG
65 TCTTCCAAATTCAATGATTG
* * * *
81901 ATTCTGTCC-AATCAGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATT-GGCAAATTCA
1 GTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCA
*
81964 TCTTCCAAATTCAATGCTTG
65 TCTTCCAAATTCAATGATTG
* * * *
81984 ATTCTGTCC-AATCAGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATT-GGCAAATTCA
1 GTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCA
*
82047 TCTTCCAAATTCAATGCTTG
65 TCTTCCAAATTCAATGATTG
* *
82067 ATTCTGTCC-AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCA
1 GTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCA
* *
82131 TCTTCTAAATTCAATGCTTG
65 TCTTCCAAATTCAATGATTG
* * *
82151 ATTCTGTCC-AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-GGCAAATTCA
1 GTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCA
82214 TCTTCCAAATTCAATG
65 TCTTCCAAATTCAATG
82230 CTTGAACTGG
Statistics
Matches: 725, Mismatches: 19, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
83 266 0.37
84 457 0.63
85 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (84 bp):
GTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
CTTCCAAATTCAATGATTG
Found at i:82230 original size:167 final size:167
Alignment explanation
Indices: 81399--82234 Score: 1333
Period size: 167 Copynumber: 5.0 Consensus size: 167
81389 GTTCTGTAAG
81399 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATC
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATC
81464 TTCTAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
66 TTCTAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
* *
81528 TGCTATTGGGCACATTCATCTTCTAAATTCAATGATTGG
130 TGCTATT-GGCACATTCATCTTCCAAATTCAATGATTGA
81567 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATC
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATC
81632 TTCTAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
66 TTCTAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
* *
81696 TGCTATTGGGCACATTCATCTTCTAAATTCAATGATTGG
130 TGCTATT-GGCACATTCATCTTCCAAATTCAATGATTGA
**
81735 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATC
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATC
* * *
81799 TTCCAAATTCAATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
66 TTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
*
81864 GCTATGGAGCACATTCATCTTCCAAATTCAATGATTGA
131 GCTATTG-GCACATTCATCTTCCAAATTCAATGATTGA
* * *
81902 TTCTGTCC-AATCAGATCAGATAACTTAAAGAACACTTCCAGAAGATGCTATT-GGCAAATTCAT
1 TTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
* * * * *
81965 CTTCCAAATTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTTAAAGAACACTTCCAGAAGA
65 CTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
* *
82030 TGCTATTGGCAAATTCATCTTCCAAATTCAATGCTTGA
130 TGCTATTGGCACATTCATCTTCCAAATTCAATGATTGA
*
82068 TTCTGTCC-AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
1 TTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCAT
* * *
82132 CTTCTAAATTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
65 CTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
* *
82197 TGCTATTGGCAAATTCATCTTCCAAATTCAATGCTTGA
130 TGCTATTGGCACATTCATCTTCCAAATTCAATGATTGA
82235 ACTGGGATAT
Statistics
Matches: 637, Mismatches: 26, Indels: 11
0.95 0.04 0.02
Matches are distributed among these distances:
166 80 0.13
167 335 0.53
168 222 0.35
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (167 bp):
TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATC
TTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
GCTATTGGCACATTCATCTTCCAAATTCAATGATTGA
Found at i:83376 original size:16 final size:17
Alignment explanation
Indices: 83355--83394 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
83345 ACCCCCTTTC
*
83355 TTTTTCTT-CTCTTTTT
1 TTTTTCTTACTATTTTT
*
83371 TTTTTCTTATTATTTTT
1 TTTTTCTTACTATTTTT
83388 TTTTTCT
1 TTTTTCT
83395 ATTCTCTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTACTATTTTT
Found at i:94742 original size:12 final size:12
Alignment explanation
Indices: 94725--94759 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
94715 TATTTATTAT
94725 ATATTT-ATAAAA
1 ATATTTAAT-AAA
94737 ATATTTAATAAA
1 ATATTTAATAAA
94749 ATATTTAATAA
1 ATATTTAATAA
94760 TAAAATACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 20 0.91
13 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATTTAATAAA
Found at i:96170 original size:3 final size:3
Alignment explanation
Indices: 96156--96239 Score: 81
Period size: 3 Copynumber: 29.7 Consensus size: 3
96146 TTTAATATTT
*
96156 TAA TAA -AA TAA TAA TAA TAA T-A TAA TAA T-A TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
96201 T-A TAA -ATA TAA TAA GGA TAA TAA TAA TAT TAA T-A TAA TA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
96240 TGGATAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
2 11 0.17
3 54 0.82
4 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:96172 original size:11 final size:11
Alignment explanation
Indices: 96156--96226 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
96146 TTTAATATTT
96156 TAATAAAATAA
1 TAATAAAATAA
96167 TAATAATAAT-A
1 TAATAA-AATAA
*
96178 TAATAATATAA
1 TAATAAAATAA
*
96189 TAAT--AATGA
1 TAATAAAATAA
96198 TAATATAAAT-A
1 TAATA-AAATAA
*
96209 TAATAAGGATAA
1 TAATAA-AATAA
96221 TAATAA
1 TAATAA
96227 TATTAATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
9 7 0.14
10 3 0.06
11 26 0.53
12 13 0.27
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.32
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:96177 original size:25 final size:25
Alignment explanation
Indices: 96156--96234 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
96146 TTTAATATTT
96156 TAATAAAATAATAATAATAATATAA
1 TAATAAAATAATAATAATAATATAA
* *
96181 TAATATAATAATAATGATAATATAA
1 TAATAAAATAATAATAATAATATAA
**
96206 -ATATAATAAGGATAATAATAATATTAA
1 TA-ATAA-AATAATAATAATAATA-TAA
96233 TA
1 TA
96235 TAATATGGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 1 0.02
25 26 0.59
26 13 0.30
27 3 0.07
28 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (25 bp):
TAATAAAATAATAATAATAATATAA
Found at i:96239 original size:11 final size:11
Alignment explanation
Indices: 96155--96240 Score: 55
Period size: 11 Copynumber: 7.1 Consensus size: 11
96145 ATTTAATATT
*
96155 TTAATAAAATA
1 TTAATATAATA
*
96166 ATAATAATAATA
1 TTAAT-ATAATA
96178 TAATAATATAATA
1 T--TAATATAATA
*
96191 ATAATGATAATA
1 TTAAT-ATAATA
*
96203 TAAATATAATAA
1 TTAATATAAT-A
*
96215 GGATAATAATAATA
1 --TTAAT-ATAATA
96229 TTAATATAATA
1 TTAATATAATA
96240 T
1 T
96241 GGATAAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
11 20 0.34
12 19 0.33
13 6 0.10
14 8 0.14
15 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
TTAATATAATA
Done.