Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002032.1 Hibiscus syriacus cultivar Beakdansim tig00004147_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: 72940
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:759 original size:22 final size:23
Alignment explanation
Indices: 725--769 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
715 TTAAAAAGTA
725 AGAGTCATATATGCA-ATAAGCTG
1 AGAGTCATATATGCATA-AAGCTG
748 AGAGTC-TATATGCATAAAGCTG
1 AGAGTCATATATGCATAAAGCTG
770 CACCTCTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (23 bp):
AGAGTCATATATGCATAAAGCTG
Found at i:3949 original size:18 final size:18
Alignment explanation
Indices: 3926--3960 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3916 TTCCAACCCG
*
3926 ACCCGACCCGATCCGTTT
1 ACCCGACCCGACCCGTTT
3944 ACCCGACCCGACCCGTT
1 ACCCGACCCGACCCGTT
3961 GACCGACATT
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:0.17, C:0.49, G:0.17, T:0.17
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:4813 original size:17 final size:19
Alignment explanation
Indices: 4791--4831 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
4781 TTTTACAAAC
4791 ATATTGATCTG-ATAA-AA
1 ATATTGATCTGCATAAGAA
*
4808 ATATTGATGTGCATAAGAA
1 ATATTGATCTGCATAAGAA
4827 ATATT
1 ATATT
4832 AGTTTTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 4 0.19
19 7 0.33
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (19 bp):
ATATTGATCTGCATAAGAA
Found at i:6338 original size:24 final size:24
Alignment explanation
Indices: 6311--6425 Score: 142
Period size: 24 Copynumber: 4.8 Consensus size: 24
6301 TCGATTTGAT
*
6311 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
*
6335 TTCTGATATGATA-TCTAACATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
6359 TTCTGATATGATATTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* * *
6383 TTCTGATCTAATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
6407 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
6426 GTGAATTATG
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.01
24 76 0.97
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:6655 original size:2 final size:2
Alignment explanation
Indices: 6642--6690 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
6632 CGGATGGGGG
*
6642 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6684 TA TA TA T
1 TA TA TA T
6691 GATTTAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7417 original size:20 final size:20
Alignment explanation
Indices: 7389--7457 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
7379 TTTCCCACAG
* * *
7389 ATTTATAAAACCTCCGGGTT
1 ATTTGTAAAGCCTCCGGGTA
* *
7409 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTCCGGGTA
**
7429 ATTTGTAAAGCCTCCAAGTA
1 ATTTGTAAAGCCTCCGGGTA
7449 ATTTGTAAA
1 ATTTGTAAA
7458 TCCTTCAAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (20 bp):
ATTTGTAAAGCCTCCGGGTA
Found at i:7466 original size:20 final size:20
Alignment explanation
Indices: 7409--7467 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
7399 CCTCCGGGTT
** *
7409 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTTCAAGTA
*
7429 ATTTGTAAAGCCTCCAAGTA
1 ATTTGTAAAGCCTTCAAGTA
*
7449 ATTTGTAAATCCTTCAAGT
1 ATTTGTAAAGCCTTCAAGT
7468 CATCTGTCAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (20 bp):
ATTTGTAAAGCCTTCAAGTA
Found at i:7601 original size:36 final size:36
Alignment explanation
Indices: 7561--7725 Score: 208
Period size: 36 Copynumber: 4.6 Consensus size: 36
7551 CTTTGAATCT
7561 AACCTTCACGGAAGAGTAGTGGAGTAATGCAAATTC
1 AACCTTCACGGAAGAGTAGTGGAGTAATGCAAATTC
*
7597 AACCTTCACGGAATAGTAGTGGAGTAATGCAAATTC
1 AACCTTCACGGAAGAGTAGTGGAGTAATGCAAATTC
* ** *
7633 AGCCTTCATAGAAGAGTAGTGAAGTAGAT-CAAATTC
1 AACCTTCACGGAAGAGTAGTGGAGTA-ATGCAAATTC
* * * *
7669 AACCTTAACGGAAGAGTAATAGAGTAATGC-AAGTC
1 AACCTTCACGGAAGAGTAGTGGAGTAATGCAAATTC
*
7704 AAGCCTTCACTGAAGAGTAGTG
1 AA-CCTTCACGGAAGAGTAGTG
7726 AAGCTGGAGC
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
35 8 0.07
36 98 0.91
37 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.23
Consensus pattern (36 bp):
AACCTTCACGGAAGAGTAGTGGAGTAATGCAAATTC
Found at i:9213 original size:26 final size:28
Alignment explanation
Indices: 9193--9256 Score: 100
Period size: 26 Copynumber: 2.4 Consensus size: 28
9183 TTTTAGTTTG
9193 TTATATATATATATATATTTAGGTTAAA
1 TTATATATATATATATATTTAGGTTAAA
9221 -T-TATATATATATATA--TAGGTTAAA
1 TTATATATATATATATATTTAGGTTAAA
9245 TTATATATATAT
1 TTATATATATAT
9257 TTAGGTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.26
25 1 0.03
26 23 0.68
27 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (28 bp):
TTATATATATATATATATTTAGGTTAAA
Found at i:9225 original size:22 final size:22
Alignment explanation
Indices: 9200--9274 Score: 132
Period size: 22 Copynumber: 3.3 Consensus size: 22
9190 TTGTTATATA
9200 TATATATATATTTAGGTTAAAT
1 TATATATATATTTAGGTTAAAT
9222 TATATATATATATATAGGTTAAAT
1 TATATATATAT-T-TAGGTTAAAT
9246 TATATATATATTTAGGTTAAAT
1 TATATATATATTTAGGTTAAAT
9268 TATATAT
1 TATATAT
9275 TTAGTTCTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
22 28 0.55
23 2 0.04
24 21 0.41
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (22 bp):
TATATATATATTTAGGTTAAAT
Found at i:9230 original size:24 final size:24
Alignment explanation
Indices: 9198--9274 Score: 131
Period size: 24 Copynumber: 3.3 Consensus size: 24
9188 GTTTGTTATA
9198 TATATATATATATTTAGGTTAAAT
1 TATATATATATATTTAGGTTAAAT
*
9222 TATATATATATATATAGGTTAAA-
1 TATATATATATATTTAGGTTAAAT
9245 T-TATATATATATTTAGGTTAAAT
1 TATATATATATATTTAGGTTAAAT
9268 TATATAT
1 TATATAT
9275 TTAGTTCTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.41
23 2 0.04
24 27 0.55
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (24 bp):
TATATATATATATTTAGGTTAAAT
Found at i:10329 original size:25 final size:25
Alignment explanation
Indices: 10293--10355 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
10283 AGGTTTTTTT
* *
10293 TCTCAATTTTTTAACTTAGATTTGC
1 TCTCAATATTTTAACTTAAATTTGC
*
10318 TCTCAATATTTTAACTTAAATTTTC
1 TCTCAATATTTTAACTTAAATTTGC
*
10343 TATCAATAATTTT
1 TCTCAAT-ATTTT
10356 TATTTTTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 28 0.85
26 5 0.15
ACGTcount: A:0.30, C:0.14, G:0.03, T:0.52
Consensus pattern (25 bp):
TCTCAATATTTTAACTTAAATTTGC
Found at i:11354 original size:65 final size:65
Alignment explanation
Indices: 11226--11379 Score: 186
Period size: 65 Copynumber: 2.4 Consensus size: 65
11216 CTAAGAGTGA
* * *
11226 CGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTACATCGATGCATGATTGGTGCAT
1 CGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTACATCGATGCATGATTGGTGCAT
* * * * * *
11290 CGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCAGTGCATCGGTGCATGGTAT-GTGCA
1 CGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTACATCGATGCATGAT-TGGTGCA
11354 T
65 T
* *
11355 CGATGCATGAAATGCATTCTATGTT
1 CGATGCATCAAATGCATTCGATGTT
11380 CAATTTAATT
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 22 0.29
65 54 0.70
66 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (65 bp):
CGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTACATCGATGCATGATTGGTGCAT
Found at i:11909 original size:2 final size:2
Alignment explanation
Indices: 11902--11942 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11892 AATTGATTAA
11902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11943 GCTTAAGCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20013 original size:18 final size:17
Alignment explanation
Indices: 19959--20007 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
19949 TTGGACCCTT
* *
19959 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
19977 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
19995 AGTGCATTCGATG
1 AGTGCA-TCGATG
20008 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:20061 original size:45 final size:45
Alignment explanation
Indices: 19976--20062 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
19966 CGGTGCACTA
**
19976 AGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCC
1 AGAGTGCATCGATGCATCAAGTGCATTCGATGCATCAAAATAGCC
**
20021 AGAGTGCATCGATGCATGACTGGTGCA-TCGATGCAT-AAAATA
1 AGAGTGCATCGATGCAT--CAAGTGCATTCGATGCATCAAAATA
20063 TTCGATGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 23 0.64
46 7 0.19
47 6 0.17
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (45 bp):
AGAGTGCATCGATGCATCAAGTGCATTCGATGCATCAAAATAGCC
Found at i:20100 original size:63 final size:64
Alignment explanation
Indices: 19979--20136 Score: 162
Period size: 63 Copynumber: 2.5 Consensus size: 64
19969 TGCACTAAGA
* * * * *
19979 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCAT-G-AC
1 GTGCATCGATGCATAAAAT-CATTCGATGTTTTCAAAACAGCCACAGTGCAGCGATGCATGGTA-
20041 T
64 T
* * * *
20042 GGTGCATCGATGCATAAAAT-ATTCGATGTTTTCATAACATCCTCAGTGCAGCGGTGCATGGTAT
1 -GTGCATCGATGCATAAAATCATTCGATGTTTTCAAAACAGCCACAGTGCAGCGATGCATGGTAT
*
20106 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAAT-CATTCGATGTT
20137 CAATTTAATT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
62 8 0.10
63 41 0.52
64 19 0.24
65 11 0.14
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATCATTCGATGTTTTCAAAACAGCCACAGTGCAGCGATGCATGGTAT
Found at i:20929 original size:182 final size:181
Alignment explanation
Indices: 20618--21096 Score: 687
Period size: 182 Copynumber: 2.6 Consensus size: 181
20608 CGATCCAAAT
* * *
20618 TAAAAATGTATCGATC-CATATCAATATAACAGGTAAAAATATGATAAAACCGGTCA-CGAAAAG
1 TAAAAATGTATCGATCACA-A-CGATATAACAGGTAAAAATATGATAAAACCGAT-ATCGAAATG
* * * *
20681 -TCAATACCGGTAAAGCCCTACCGGATATATTGAACGTGTCGATACTTTAATATAAGGATTGACA
63 AT-AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACA
*
20745 CTTTGTGAATTTAAAAGAGAATCAGTTTTAACGCCTATAAAGTGTCAATACTTTA
127 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCAATACTTTA
* *
20800 TAAAAATGTATCGATACACAACGATATAACATGTAAAAATATGACAAAACCGATATCGAAATGAT
1 TAAAAATGTATCGAT-CACAACGATATAACAGGTAAAAATATGATAAAACCGATATCGAAATGAT
* * *
20865 AAAACCGGTAAAGCGCTACCGGATATATTTAAAGTGTTTG-TACTTTAATATAAGTATCGACACT
65 AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTG-TCGATACTTTAATATAAGGATCGACACT
* *
20929 TTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
129 TTGTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCAATACTTTA
* *
20982 TAAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACTGATATCAAAATGAT
1 TAAAAATGTATCGATC-ACAACGATATAACAGGTAAAAATATGATAAAACCGATATCGAAATGAT
** *
21047 AAAACTTGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
65 AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
21097 AGTACGTGTA
Statistics
Matches: 266, Mismatches: 24, Indels: 14
0.88 0.08 0.05
Matches are distributed among these distances:
181 4 0.02
182 255 0.96
183 5 0.02
184 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (181 bp):
TAAAAATGTATCGATCACAACGATATAACAGGTAAAAATATGATAAAACCGATATCGAAATGATA
AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTT
GTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCAATACTTTA
Found at i:23323 original size:21 final size:21
Alignment explanation
Indices: 23299--23364 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
23289 AAGACAATCA
23299 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
**
23320 AGAGTTAAAGAGAAACTTTGAG
1 AGAGTCGAAGAGAAAC-TTGAG
* *
23342 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
23363 AG
1 AG
23365 GCATAAGGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 17 0.45
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:23343 original size:22 final size:21
Alignment explanation
Indices: 23306--23364 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
23296 TCAAGAGTCG
23306 AAGAGAAACTTGAGAGAGTTA
1 AAGAGAAACTTGAGAGAGTTA
**
23327 AAGAGAAACTTTGAGAGAGTCG
1 AAGAGAAAC-TTGAGAGAGTTA
* *
23349 AAGATACACTTGAGAG
1 AAGAGAAACTTGAGAG
23365 GCATAAGGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.44, C:0.08, G:0.29, T:0.19
Consensus pattern (21 bp):
AAGAGAAACTTGAGAGAGTTA
Found at i:23670 original size:21 final size:21
Alignment explanation
Indices: 23644--23698 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
23634 GAAAAAATAT
23644 GAAGAAGAAAAGAGGGAGGAG
1 GAAGAAGAAAAGAGGGAGGAG
23665 GAAGAAGAAAAGAGGGAGGAG
1 GAAGAAGAAAAGAGGGAGGAG
23686 GAAGAAGAAAAGA
1 GAAGAAGAAAAGA
23699 TGGAAGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (21 bp):
GAAGAAGAAAAGAGGGAGGAG
Found at i:25295 original size:19 final size:19
Alignment explanation
Indices: 25268--25316 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
25258 AATGTAGGGT
*
25268 TAATGTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
25287 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
25306 TAATTTTGTAT
1 TAATTTTGTAT
25317 GTGAATGTTA
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:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:26040 original size:199 final size:200
Alignment explanation
Indices: 25528--26705 Score: 1732
Period size: 200 Copynumber: 5.8 Consensus size: 200
25518 GTAAGCATAT
* * * * *
25528 GTGTCGATCCATATATAAAAATTATCGATCACAGAAACATCGAAACCAATAAGTATAAAGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* ** * *
25593 GGTAATTTTTCAATGTAACCAGTATAAATATAGTGGTTTTATGAGAGAATAGGTCTACAACATTT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
*
25658 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACA
131 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
25723 ATAAA
196 ATAAA
** *
25728 GTGTCGATATATATATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * *
25793 GGTAATTTTTCAATGTAACCGGTATAAATTTACCAGTTTTACGAGAGAATAGGTCTAAAACATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
* *
25858 ATCGACACTTTTTAATTTTGTGTCGATACTTTAGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
131 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
25923 ATAAA
196 ATAAA
* *
25928 GTGTTGATCCATTTAT-AAAAGTATCGATCTCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* *
25992 GGTAATTTTTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
*
26057 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCATAATGAATGCCAAAAAGGGTGCAACC
131 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
26122 ATAAA
196 ATAAA
** * *
26127 GTGTCGATATATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATAAGTGTAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* *
26192 GGTAATTTTTCAATGTAACCGATATAAATTTACCGGTTTTACGAGAGAATAGGTCTACAACATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
* * *
26257 ATCGACAATTTTTAAATTTT-TGTCGATACTTTTGGTCCATAATGAATGCCAAAAAGGGTGCAAC
131 ATCGACACTTTTT-AATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAAC
26321 CATAAA
195 CATAAA
26327 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAG--T-A--TAAT-
* *
26392 GATAATTTTTCAATGTAATAGATAATTTTTCAATGTAATCGGTATAAATATACCGGTTTTACAAG
60 G-TAA----T--A-G-----G-TAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAG
*
26457 ATAATAGGTCTACAACATGTATCGACACTTTTTAA-TTTGTCTCGATACTTTTGGTCCAGAATGA
111 AGAATAGGTCTACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGA
* *
26521 ATCCCAAAAAGGGTGCAACCATAGA
176 ATGCCAAAAAGGGTGCAACCATAAA
*
26546 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCTATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
* * * ** *
26611 GGTAAATTTTCAATGTAACCAGTATAAATATACTGGTTTTATAAGAGAATATGTCTACAACATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
*
26676 ATCGACACTTTTTAATTTTGTGTCGATACT
131 ATCGACACTTTTTAATTTTGTCTCGATACT
26706 AATTTAAATA
Statistics
Matches: 891, Mismatches: 63, Indels: 48
0.89 0.06 0.05
Matches are distributed among these distances:
199 260 0.29
200 426 0.48
201 6 0.01
202 1 0.00
205 5 0.01
206 2 0.00
207 3 0.00
208 1 0.00
211 1 0.00
212 3 0.00
213 2 0.00
214 5 0.01
216 1 0.00
217 1 0.00
218 3 0.00
219 101 0.11
220 70 0.08
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (200 bp):
GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTACGAGAGAATAGGTCTACAACATGT
ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
ATAAA
Found at i:26211 original size:399 final size:400
Alignment explanation
Indices: 25528--26705 Score: 1795
Period size: 399 Copynumber: 2.9 Consensus size: 400
25518 GTAAGCATAT
* * * *
25528 GTGTCGATCCATATATAAAAATTATCGATCACAGAAACATCGAAACCAATAAGTATAAAGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCACAGAAACATCGAAACCCATAAGTATAATGTAATA
* ** *
25593 GGTAATTTTTCAATGTAACCAGTATAAATATAGTGGTTTTATGAGAGAATAGGTCTACAACATTT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
*
25658 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACA
131 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
*
25723 ATAAAGTGTCGATATATATATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATG
196 ATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATG
* *
25788 TAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCAGTTTTACGAGAGAATAGGTCTAAAA
261 TAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAGAATAGGTCTACAA
25853 CATGTATCGACACTTTTTAATTTTGTGTCGATACTTTAGGTCCAGAATGAATGCCAAAAAGGGTG
326 CATGTATCGACACTTTTTAATTTTGTGTCGATACTTTAGGTCCAGAATGAATGCCAAAAAGGGTG
25918 CAACCATAAA
391 CAACCATAAA
* *
25928 GTGTTGATCCATTTAT-AAAAGTATCGATCTCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCACAGAAACATCGAAACCCATAAGTATAATGTAATA
*
25992 GGTAATTTTTCAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACAACATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
*
26057 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCATAATGAATGCCAAAAAGGGTGCAACC
131 ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
* *
26122 ATAAAGTGTCGATATATTTATAAAAAGTATTGATCCCAGAAACATCGAAACCCATAAGTGTAATG
196 ATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATG
*
26187 TAATAGGTAATTTTTCAATGTAACCGATATAAATTTACCGGTTTTACGAGAGAATAGGTCTACAA
261 TAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAGAATAGGTCTACAA
* * *
26252 CATGTATCGACAATTTTTAAATTTT-TGTCGATACTTTTGGTCCATAATGAATGCCAAAAAGGGT
326 CATGTATCGACACTTTTT-AATTTTGTGTCGATACTTTAGGTCCAGAATGAATGCCAAAAAGGGT
26316 GCAACCATAAA
390 GCAACCATAAA
*
26327 GTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATCCATTTATAAAAAGTATCGATCACAGAAACATCGAAACCCATAAG--T-A--TAAT-
* **
26392 GATAATTTTTCAATGTAATAGATAATTTTTCAATGTAATCGGTATAAATATACCGGTTTTACAAG
60 G-TAA----T--A-G-----G-TAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAG
*
26457 ATAATAGGTCTACAACATGTATCGACACTTTTTAA-TTTGTCTCGATACTTTTGGTCCAGAATGA
111 AGAATAGGTCTACAACATGTATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGA
* * **
26521 ATCCCAAAAAGGGTGCAACCATAGAGTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACAT
176 ATGCCAAAAAGGGTGCAACCATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAGAAACAT
* * * * *
26586 CGAAACCTATAAGTATAATGTAATAGGTAAATTTTCAATGTAACCAGTATAAATATACTGGTTTT
241 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTT
** *
26651 ATAAGAGAATATGTCTACAACATGTATCGACACTTTTTAATTTTGTGTCGATACT
306 ACGAGAGAATAGGTCTACAACATGTATCGACACTTTTTAATTTTGTGTCGATACT
26706 AATTTAAATA
Statistics
Matches: 709, Mismatches: 46, Indels: 27
0.91 0.06 0.03
Matches are distributed among these distances:
399 371 0.52
400 55 0.08
402 1 0.00
403 1 0.00
405 4 0.01
406 1 0.00
407 3 0.00
411 1 0.00
413 1 0.00
414 1 0.00
418 6 0.01
419 191 0.27
420 73 0.10
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (400 bp):
GTGTCGATCCATTTATAAAAAGTATCGATCACAGAAACATCGAAACCCATAAGTATAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
ATCGACACTTTTTAATTTTGTCTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTGCAACC
ATAAAGTGTCGATATATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATG
TAATAGGTAATTTTTCAATGTAACCGGTATAAATTTACCGGTTTTACGAGAGAATAGGTCTACAA
CATGTATCGACACTTTTTAATTTTGTGTCGATACTTTAGGTCCAGAATGAATGCCAAAAAGGGTG
CAACCATAAA
Found at i:26408 original size:20 final size:20
Alignment explanation
Indices: 26383--26430 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
26373 CCATAAGTAT
26383 AATGTAATAGATAATTTTTC
1 AATGTAATAGATAATTTTTC
26403 AATGTAATAGATAATTTTTC
1 AATGTAATAGATAATTTTTC
26423 AATGTAAT
1 AATGTAAT
26431 CGGTATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (20 bp):
AATGTAATAGATAATTTTTC
Found at i:26577 original size:219 final size:220
Alignment explanation
Indices: 26183--26628 Score: 750
Period size: 219 Copynumber: 2.0 Consensus size: 220
26173 CCATAAGTGT
* * *
26183 AATGTAATAGGTAATTTTTCAATGTAACCGATATAAATTTACCGGTTTTACGAGAGAATAGGTCT
1 AATGTAATAGATAATTTTTCAATGTAACCGATATAAATATACCGGTTTTACAAGAGAATAGGTCT
* * * *
26248 ACAACATGTATCGACAATTTTTAAATTTTTGTCGATACTTTTGGTCCATAATGAATGCCAAAAAG
66 ACAACATGTATCGACAATTTTTAAATTTGTCTCGATACTTTTGGTCCAGAATGAATCCCAAAAAG
26313 GGTGCAACCATAAAGTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATA
131 GGTGCAACCATAAAGTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATA
*
26378 AGTATAATGTAATAGATAATTTTTC
196 AGTATAATGTAATAGATAAATTTTC
* * *
26403 AATGTAATAGATAATTTTTCAATGTAATCGGTATAAATATACCGGTTTTACAAGATAATAGGTCT
1 AATGTAATAGATAATTTTTCAATGTAACCGATATAAATATACCGGTTTTACAAGAGAATAGGTCT
*
26468 ACAACATGTATCGACACTTTTT-AATTTGTCTCGATACTTTTGGTCCAGAATGAATCCCAAAAAG
66 ACAACATGTATCGACAATTTTTAAATTTGTCTCGATACTTTTGGTCCAGAATGAATCCCAAAAAG
* *
26532 GGTGCAACCATAGAGTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCTATA
131 GGTGCAACCATAAAGTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATA
*
26597 AGTATAATGTAATAGGTAAATTTTC
196 AGTATAATGTAATAGATAAATTTTC
26622 AATGTAA
1 AATGTAA
26629 CCAGTATAAA
Statistics
Matches: 211, Mismatches: 15, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
219 131 0.62
220 80 0.38
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (220 bp):
AATGTAATAGATAATTTTTCAATGTAACCGATATAAATATACCGGTTTTACAAGAGAATAGGTCT
ACAACATGTATCGACAATTTTTAAATTTGTCTCGATACTTTTGGTCCAGAATGAATCCCAAAAAG
GGTGCAACCATAAAGTGTCGATCCATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATA
AGTATAATGTAATAGATAAATTTTC
Found at i:28211 original size:12 final size:12
Alignment explanation
Indices: 28194--28252 Score: 82
Period size: 12 Copynumber: 4.9 Consensus size: 12
28184 GGTCAATAAA
28194 GATGAAGATGAC
1 GATGAAGATGAC
28206 GATGAAGATGAC
1 GATGAAGATGAC
28218 GATGAAGATGAC
1 GATGAAGATGAC
* * *
28230 GACGACGACGAC
1 GATGAAGATGAC
*
28242 GATGATGATGA
1 GATGAAGATGA
28253 TGGTGATGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.39, C:0.12, G:0.34, T:0.15
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:28248 original size:3 final size:3
Alignment explanation
Indices: 28194--28268 Score: 51
Period size: 3 Copynumber: 25.0 Consensus size: 3
28184 GGTCAATAAA
* * * * * * * * * *
28194 GAT GAA GAT GAC GAT GAA GAT GAC GAT GAA GAT GAC GAC GAC GAC GAC
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
28242 GAT GAT GAT GAT GGT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
28269 CCAAACAAGT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.36, C:0.09, G:0.35, T:0.20
Consensus pattern (3 bp):
GAT
Found at i:28254 original size:6 final size:6
Alignment explanation
Indices: 28194--28252 Score: 64
Period size: 6 Copynumber: 9.8 Consensus size: 6
28184 GGTCAATAAA
* * * * *
28194 GATGAA GATGAC GATGAA GATGAC GATGAA GATGAC GACGAC GACGAC
1 GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC
*
28242 GATGAT GATGA
1 GATGAC GATGA
28253 TGGTGATGAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.39, C:0.12, G:0.34, T:0.15
Consensus pattern (6 bp):
GATGAC
Found at i:29043 original size:24 final size:24
Alignment explanation
Indices: 29016--29064 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29006 TACCTTTGAC
29016 GTTACTTCCCATTCGAACGACAGT
1 GTTACTTCCCATTCGAACGACAGT
29040 GTTACTTCCCATTCGAACGACAGT
1 GTTACTTCCCATTCGAACGACAGT
29064 G
1 G
29065 CTCTAGGTAT
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:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (24 bp):
GTTACTTCCCATTCGAACGACAGT
Found at i:29811 original size:51 final size:52
Alignment explanation
Indices: 29756--29865 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 52
29746 AGAATGAATG
29756 CCAAAAAAGG-TG-AGCGCACAAAGTGTCGATACATTT-TCAAAGAGTGTCGAT
1 CCAAAAAAGGTTGCA-CGCACAAAGTGTCGATACATTTATCAAA-AGTGTCGAT
* * * * *
29807 CC-AAAAGGGTTGCATGCATAAAGTTTCGATACATTTATTAAAAGTGTCGAT
1 CCAAAAAAGGTTGCACGCACAAAGTGTCGATACATTTATCAAAAGTGTCGAT
29858 CCAAAAAA
1 CCAAAAAA
29866 CATCGAAACC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
50 6 0.12
51 34 0.69
52 9 0.18
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (52 bp):
CCAAAAAAGGTTGCACGCACAAAGTGTCGATACATTTATCAAAAGTGTCGAT
Found at i:30435 original size:200 final size:198
Alignment explanation
Indices: 29826--30582 Score: 1005
Period size: 200 Copynumber: 3.8 Consensus size: 198
29816 TTGCATGCAT
* * *
29826 AAAGTTTCGATACATTTAT-TAAAAGTGTCGATCCAAAAAACATCGAAACCCCATAATTATAATG
1 AAAGTGTCGATACATTT-TCAAAAAGTGTCGATCCCAAAAACATCGAAA-CCCATAATTATAATG
* *
29890 TAATA-G------GTAATATAACTGGTATACATATACCGGTTTTATGAGAGAATAGGTCTATAAC
64 TAATAGGAAATTTGTAATATAAC-GGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAAC
* *
29948 ATGTATCGACACTTCTTAATATTGTGTCGATAATTTTTGTCCAGAATGGATGCCAAAAAGGGTGA
128 ATGTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTGA
*
30013 ACGCAT
193 ACGCAC
* * **
30019 AAAGTGTCGATACATTTTCAAAAAGTGTTGATCCCGACGACATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTA
** * *
30084 ATAGGTAAATTTACAATGTAATCGGTATAAATATACCGGTTTTTATGAGAGAATAGGTCTATAAC
66 ATAGG-AAATTTGTAATATAA-CGGTATAAATATACCGG-TTTTATGAGAGAATAGGTCTACAAC
* * * * * * *
30149 ATGTATTGACACTATATAA-ATTTGTATCGATATTTTTTGTCCAGAATGGATGCCAAAAATGATG
128 ATGTATCGACACTTTTTAATA-TTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTG
30213 AACGCAC
192 AACGCAC
*
30220 AAAGTGTCGATACATTTAT-TAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
1 AAAGTGTCGATACATTT-TCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGT
* *
30284 AATAGGAAATTTTGTAATATAACAAGTATAAATATATCGGTTTTATGAGAGAATAGGTCTACAAC
65 AATAGGAAA-TTTGTAATATAAC-GGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAAC
*
30349 ATGTATCGACACTTTTTAATATTGTGTCGATACTTTATGTCCAGAATGGATGCCAAAAAGGGTGA
128 ATGTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTGA
30414 ACGCAC
193 ACGCAC
*
30420 AAAGTGTCAATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTA
* * * * *
30485 ATAGGTAATTTTTTAATATAACCGGTATAAATATACC-ATTTTATAAGAGAATAGGTCTACAATA
66 ATAGG-AAATTTGTAATATAA-CGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACA
* * *
30549 TGTAACGACACTTTTTTATTTTGTGTCGATACTT
129 TGTATCGACACTTTTTAATATTGTGTCGATACTT
30583 ACAATATATG
Statistics
Matches: 494, Mismatches: 51, Indels: 32
0.86 0.09 0.06
Matches are distributed among these distances:
192 21 0.04
193 40 0.08
199 56 0.11
200 200 0.40
201 176 0.36
202 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (198 bp):
AAAGTGTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTA
ATAGGAAATTTGTAATATAACGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATG
TATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAAAAGGGTGAACG
CAC
Found at i:33416 original size:201 final size:197
Alignment explanation
Indices: 32956--33664 Score: 747
Period size: 200 Copynumber: 3.5 Consensus size: 197
32946 ACCTAAATAT
* * *
32956 GTGTCGATACATTT-TATACAAGTATCGA-CCCAAAAAATATCAAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTATA-AAAAGTATCGATCCC-AAAAACATCGAAACCAATAATTATAATGTAA
* * * * *
33019 TAGGT-AATTTAACAATGAAACTGGTATAAATATATCGGTTAATTA-G-AAAACAGGTCAACATA
64 TAGGTAAATTT-ACAATGTAACCGGTATAAATATACCGGTT-TTTATGAAAAATAGGTC-ACATA
* * * *
33081 ATGTATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGGATGAATG-CACAAACGAGGT
126 ATGTATCGACACTTGT-AAATTTGTGTCGATACTT-TTGTCCAGAATAAATGCCA-AAAAG-GGT
33145 GC-ACGCATAAA
187 GCAAC-CATAAA
* * * *
33156 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAATATTGAAACCAATAATTATAATGTATTA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
*** * *
33221 GGTAAATTTACAATGTAACTAATATAAATATATCGGTTTTTATGATAAAATAGGTCAGCATAAAG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTTATGA-AAAATAGGTCA-CATAATG
33286 TATCGACACTTGCTAAATTTGTGTCGATACTTTTGGTCCAGAATAAATGCCAAAAAGGGTGCAAC
129 TATCGACACTTG-TAAATTTGTGTCGATACTTTT-GTCCAGAATAAATGCCAAAAAGGGTGCAAC
33351 CATAAA
192 CATAAA
* * *
33357 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAAGTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
* * * *
33422 GGTAAATTTTCAATGTGACCGGTATAAATATACCGG-TTTTATGAGAGAATAGGTCTAAATAATG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTTATGA-AAAATAGGTC-ACATAATG
* * * **
33486 TATCGACACTTTGTTATTTTGTGTCGATACTTTTTTCCAGAATGAAATATGAATGCCCAACCA-G
129 TATCGACAC-TTGTAAATTTGTGTCGATACTTTTGTCC---A-G-AATA--AATG-CCAAAAAGG
*
33550 GTGCAAGCATAAA
185 GTGCAACCATAAA
* ** * *
33563 GTGTTGATACATTTA-AAATTGTATCGAT-CTAAAAACATCGAAACCAATAATAATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
* *
33626 GGTAAATTTGCAATGTTACCGGTATAAATATACCGGTTT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTT
33665 ACTTCGAAAA
Statistics
Matches: 439, Mismatches: 48, Indels: 39
0.83 0.09 0.07
Matches are distributed among these distances:
199 6 0.01
200 134 0.31
201 115 0.26
202 63 0.14
203 4 0.01
204 68 0.15
205 13 0.03
206 31 0.07
207 5 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (197 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTTATGAAAAATAGGTCACATAATGTA
TCGACACTTGTAAATTTGTGTCGATACTTTTGTCCAGAATAAATGCCAAAAAGGGTGCAACCATA
AA
Found at i:33816 original size:23 final size:23
Alignment explanation
Indices: 33766--33810 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
33756 TGCCTATTTT
*
33766 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
33789 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
33811 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:34227 original size:26 final size:27
Alignment explanation
Indices: 34169--34225 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
34159 ATTTTAAATA
* * *
34169 AAAATAAAAATATTATTATATTTTATT
1 AAAATAAAAATAATATTAAATTATATT
34196 AAAATAAAAA-AATATTACAATTATATT
1 AAAATAAAAATAATATTA-AATTATATT
34223 AAA
1 AAA
34226 TATGTATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
AAAATAAAAATAATATTAAATTATATT
Found at i:34281 original size:36 final size:35
Alignment explanation
Indices: 34241--34310 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
34231 ATTAAAATAA
*
34241 AAAATAAT-ATATTATTAAGTATATTAAATACTTATT
1 AAAATAATAATATTATTAA-AATATTAAA-ACTTATT
34277 AAAATAATAATATTATTAAAATATTAAAACTTAT
1 AAAATAATAATATTATTAAAATATTAAAACTTAT
34311 AATATTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 6 0.19
36 16 0.50
37 10 0.31
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (35 bp):
AAAATAATAATATTATTAAAATATTAAAACTTATT
Found at i:34294 original size:17 final size:17
Alignment explanation
Indices: 34241--34299 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
34231 ATTAAAATAA
34241 AAAATAAT-ATATTATT
1 AAAATAATAATATTATT
* *
34257 AAGTATATTAAATACTTATT
1 AA-AATAAT-AATA-TTATT
34277 AAAATAATAATATTATT
1 AAAATAATAATATTATT
34294 AAAATA
1 AAAATA
34300 TTAAAACTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.06
17 15 0.43
18 4 0.11
19 7 0.20
20 7 0.20
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAATAATAATATTATT
Found at i:34323 original size:37 final size:37
Alignment explanation
Indices: 34239--34310 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
34229 GTATTAAAAT
*
34239 AAAAAATAATATATTATTAAGTATATTAAATACTTATTA
1 AAAAAAT-A-ATATTATTAAGAATATTAAATACTTATTA
*
34278 AAATAATAATATTATTAA-AATATTAAA-ACTTAT
1 AAAAAATAATATTATTAAGAATATTAAATACTTAT
34311 AATATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 6 0.19
36 8 0.26
37 10 0.32
38 1 0.03
39 6 0.19
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (37 bp):
AAAAAATAATATTATTAAGAATATTAAATACTTATTA
Found at i:34520 original size:30 final size:29
Alignment explanation
Indices: 34472--34543 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 29
34462 AATATAATTT
*
34472 AATAACTAATATTTTTATTAAAATGATATTAA
1 AATAA-TAATATTATTATTAAAAT-ATA-TAA
34504 AATAAT-ATATTATTATTAAAATATATAA
1 AATAATAATATTATTATTAAAATATATAA
34532 AATAATAATATT
1 AATAATAATATT
34544 TTGAGTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
28 9 0.24
29 8 0.21
30 15 0.39
31 1 0.03
32 5 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (29 bp):
AATAATAATATTATTATTAAAATATATAA
Found at i:40116 original size:12 final size:12
Alignment explanation
Indices: 40099--40125 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40089 AACACCATCT
40099 CCAACCCCGACC
1 CCAACCCCGACC
40111 CCAACCCCGACC
1 CCAACCCCGACC
40123 CCA
1 CCA
40126 TCTCCAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.67, G:0.07, T:0.00
Consensus pattern (12 bp):
CCAACCCCGACC
Found at i:40701 original size:31 final size:30
Alignment explanation
Indices: 40666--40758 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 30
40656 GGTGATGGAA
*
40666 TAAAATCAAATTGATCGATAATATTAGAGAC
1 TAAAATCAAA-TGATCGATAAAATTAGAGAC
* * *
40697 TAAAATTAAAATAATCGATAACATTATG-GAC
1 TAAAA-TCAAATGATCGATAAAATTA-GAGAC
* * *
40728 TATAATCGAAATGATTGATAAAATTAAAGAC
1 TAAAATC-AAATGATCGATAAAATTAGAGAC
40759 AATGTACTCT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
30 1 0.02
31 43 0.88
32 5 0.10
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.29
Consensus pattern (30 bp):
TAAAATCAAATGATCGATAAAATTAGAGAC
Found at i:42126 original size:23 final size:24
Alignment explanation
Indices: 42100--42150 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
42090 TATGTCACGC
* *
42100 TTTTCTTTATATTTATGATAT-AT
1 TTTTCTCTATATTTATGACATAAT
*
42123 TTTTCTCTATCTTTATGACATAAT
1 TTTTCTCTATATTTATGACATAAT
42147 TTTT
1 TTTT
42151 TTCGTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.24, C:0.10, G:0.04, T:0.63
Consensus pattern (24 bp):
TTTTCTCTATATTTATGACATAAT
Found at i:45069 original size:29 final size:29
Alignment explanation
Indices: 44996--45183 Score: 184
Period size: 29 Copynumber: 6.6 Consensus size: 29
44986 CCGTTGACCG
* **
44996 GGTGGTATTTTGGTAATTATTTAAAAAAT
1 GGTGATATTTTGGTAATTATTTTGAAAAT
* *
45025 GGTGGTATTCTGGTAATTATTTTGAAAAT
1 GGTGATATTTTGGTAATTATTTTGAAAAT
* * * *
45054 GGTGCTATTTTTGTAAATT-TTTTTAAAAA
1 GGTGATATTTTGGT-AATTATTTTGAAAAT
* * * *
45083 AGTGATAATTTCGTAATT-TTTTTAAAA-
1 GGTGATATTTTGGTAATTATTTTGAAAAT
* *
45110 AGTGATATTTTAGTAATTATTTTGAAAAT
1 GGTGATATTTTGGTAATTATTTTGAAAAT
*
45139 TGTGATATTTTGGTAATTATTTTGAAAAT
1 GGTGATATTTTGGTAATTATTTTGAAAAT
* *
45168 GATGATATTTTCGTAA
1 GGTGATATTTTGGTAA
45184 AATGGTTGAT
Statistics
Matches: 136, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 16 0.12
28 21 0.15
29 95 0.70
30 4 0.03
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (29 bp):
GGTGATATTTTGGTAATTATTTTGAAAAT
Found at i:51702 original size:35 final size:35
Alignment explanation
Indices: 51654--51723 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
51644 TTAAAAACTC
* *
51654 TATTAATATACTAAATTAAAAGTAGGG-TCCATAAA
1 TATTAATAAACTAAATTAAAAATAGGGCT-CATAAA
51689 TATTAATAAACTAAATTAAAAATAGGGCTCATAAA
1 TATTAATAAACTAAATTAAAAATAGGGCTCATAAA
51724 CTTATTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (35 bp):
TATTAATAAACTAAATTAAAAATAGGGCTCATAAA
Found at i:61826 original size:22 final size:21
Alignment explanation
Indices: 61800--61840 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
61790 GTTGACTTTT
61800 TGGTCAAAGTCAACAGTCAAAC
1 TGGTCAAAGTCAA-AGTCAAAC
61822 TGGTCAAAGTCAAAGTCAA
1 TGGTCAAAGTCAAAGTCAA
61841 CGGGCAGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (21 bp):
TGGTCAAAGTCAAAGTCAAAC
Done.