Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004666.1 Hibiscus syriacus cultivar Beakdansim tig00010464_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: 118415
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3251 original size:14 final size:12
Alignment explanation
Indices: 3237--3284 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
3227 AAATACGGTA
3237 TGAACAATACTG
1 TGAACAATACTG
* *
3249 TATGAACAGTACCG
1 --TGAACAATACTG
*
3263 TGAACAGTACTG
1 TGAACAATACTG
3275 TGAACAATAC
1 TGAACAATAC
3285 CGGATTCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 20 0.67
14 10 0.33
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (12 bp):
TGAACAATACTG
Found at i:3268 original size:12 final size:12
Alignment explanation
Indices: 3251--3286 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3241 CAATACTGTA
3251 TGAACAGTACCG
1 TGAACAGTACCG
*
3263 TGAACAGTACTG
1 TGAACAGTACCG
*
3275 TGAACAATACCG
1 TGAACAGTACCG
3287 GATTCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (12 bp):
TGAACAGTACCG
Found at i:4214 original size:22 final size:22
Alignment explanation
Indices: 4189--4252 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
4179 GAAGAACCAC
4189 TATGTCCCGAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
* *
4211 TATGCCCCGAAGGACTAC----
1 TATGTCCCGAAGGACCACTGTA
*
4229 TATGTCCTGAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
4251 TA
1 TA
4253 ACCCTCGATC
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 15 0.45
22 18 0.55
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (22 bp):
TATGTCCCGAAGGACCACTGTA
Found at i:4220 original size:40 final size:40
Alignment explanation
Indices: 4176--4252 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
4166 TGAAATTTCT
4176 CCCGAAGAACCACTATGTCCCGAAGGACCACTGTATATGC
1 CCCGAAGAACCACTATGTCCCGAAGGACCACTGTATATGC
* * *
4216 CCCGAAGGACTACTATGTCCTGAAGGACCACTGTATA
1 CCCGAAGAACCACTATGTCCCGAAGGACCACTGTATA
4253 ACCCTCGATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (40 bp):
CCCGAAGAACCACTATGTCCCGAAGGACCACTGTATATGC
Found at i:4653 original size:16 final size:16
Alignment explanation
Indices: 4629--4671 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
4619 TAACATATTG
*
4629 CATATCACATAATTTA
1 CATAGCACATAATTTA
4645 CATAGCACATAATTTA
1 CATAGCACATAATTTA
4661 CATAGCACATA
1 CATAGCACATA
4672 TCAGTTCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (16 bp):
CATAGCACATAATTTA
Found at i:9133 original size:18 final size:18
Alignment explanation
Indices: 9110--9179 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 18
9100 GTTACACAGG
9110 GGTCATTCGGGACATAGT
1 GGTCATTCGGGACATAGT
9128 GGTCATTCGGGACATATACAGT
1 GGTCATTCGGGAC--AT--AGT
* *
9150 GGTCTTTCGGGATATAGT
1 GGTCATTCGGGACATAGT
*
9168 GGTCCTTCGGGA
1 GGTCATTCGGGA
9180 GAAATTTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 27 0.60
20 4 0.09
22 14 0.31
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (18 bp):
GGTCATTCGGGACATAGT
Found at i:14417 original size:51 final size:51
Alignment explanation
Indices: 14348--14462 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
14338 ATAATTAGAT
* * * * *
14348 TTATTATTTTATTAGGAATTAATATAGATTTAAAATATCAT-TTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGATAAAATTAAAACATCATCTTATA-TTTA
* * *
14399 TTATTATTTTATTTGGAATTAGGATAAAATTAAAACATTATCTTATATTTA
1 TTATTATTTTATTAGGAATTAAGATAAAATTAAAACATCATCTTATATTTA
14450 TTATTATTTTATT
1 TTATTATTTTATT
14463 CAGTAGTTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 51 0.93
52 4 0.07
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.54
Consensus pattern (51 bp):
TTATTATTTTATTAGGAATTAAGATAAAATTAAAACATCATCTTATATTTA
Found at i:15243 original size:8 final size:9
Alignment explanation
Indices: 15204--15242 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
15194 ATTTTTAATC
15204 AAAA-ATAA
1 AAAAGATAA
*
15212 AAAAGAAAGA
1 AAAAGATA-A
15222 AAAAGATAA
1 AAAAGATAA
15231 AAAAGATAA
1 AAAAGATAA
15240 AAA
1 AAA
15243 GGTGAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 4 0.15
9 15 0.56
10 8 0.30
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (9 bp):
AAAAGATAA
Found at i:22247 original size:25 final size:25
Alignment explanation
Indices: 22205--22252 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
22195 TATCATATAA
* * *
22205 TTTTTGAAAGAAATTTTTTAAAATT
1 TTTTTGAAACAAAGTTTTAAAAATT
*
22230 TTTTTGAAACATAGTTTTAAAAA
1 TTTTTGAAACAAAGTTTTAAAAA
22253 AAATCGGTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (25 bp):
TTTTTGAAACAAAGTTTTAAAAATT
Found at i:22346 original size:12 final size:12
Alignment explanation
Indices: 22329--22353 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22319 TAATATATAG
22329 TTTTTGAAAATA
1 TTTTTGAAAATA
22341 TTTTTGAAAATA
1 TTTTTGAAAATA
22353 T
1 T
22354 ATATAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTTTGAAAATA
Found at i:22382 original size:36 final size:36
Alignment explanation
Indices: 22261--22559 Score: 352
Period size: 36 Copynumber: 7.9 Consensus size: 36
22251 AAAAATCGGT
*
22261 TTTTGAAATATATATATATATAATATAGTTTTTTAAAAAACA
1 TTTTGAAA-ATATATATA-AT-ATATAG--TTTT-GAAAACA
*
22303 TTTTGAAAA-ATATTGATAATATATAGTTTTTGAAAATA
1 TTTTGAAAATATA-T-ATAATATATAG-TTTTGAAAACA
22341 TTTTTGAAAATATATATAATATATTA-TTTTGAAAACA
1 -TTTTGAAAATATATATAATATA-TAGTTTTGAAAACA
* *
22378 TTTTGAAAACT-TATATAAGATATAGTTTTTAAAAACA
1 TTTTGAAAA-TATATATAATATATAG-TTTTGAAAACA
* * *
22415 TTTTTAAAACATATATATTATATAGTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
22451 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
**
22487 TTTTGAAAATATATATGTTATATAGTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
22523 TTTTGAAAAAAATATATATAATATATAGTTTTGAAAA
1 TTTTG---AAAATATATATAATATATAGTTTTGAAAA
22560 TATATATTAT
Statistics
Matches: 228, Mismatches: 17, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
35 2 0.01
36 101 0.44
37 41 0.18
38 13 0.06
39 44 0.19
40 12 0.05
41 4 0.02
42 11 0.05
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACA
Found at i:22470 original size:109 final size:107
Alignment explanation
Indices: 22274--22559 Score: 346
Period size: 109 Copynumber: 2.6 Consensus size: 107
22264 TGAAATATAT
* *
22274 ATATATATA-ATATAGTTTTTTAAAAAACATTTTGAAAAATATTGATAATATATAGTTTTTGAAA
1 ATATATA-AGATATAG-TTTTT-AAAAACATTTTAAAAAATA-T-ATATTATATAG-TTTTGAAA
*
22338 ATATTTTTGAAAATATATATAATATATTA-TTTTGAAAACATTTTGAAA
60 ACATTTTTGAAAATATATATAATATA-TAGTTTTGAAAACATTTTGAAA
*
22386 ACTTATATAAGATATAGTTTTTAAAAACATTTTTAAAACATATATATTATATAGTTTTGAAAACA
1 A--TATATAAGATATAGTTTTTAAAAACA-TTTTAAAAAATATATATTATATAGTTTTGAAAACA
22451 -TTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAA
63 TTTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAA
* *
22495 ATATATATGTTATATAG-TTTTGAAAACATTTTGAAAAAAATATATATAATATATAGTTTTGAAA
1 ATATATAAG--ATATAGTTTTTAAAAACATTTT--AAAAAATATATAT--TATATAGTTTTGAAA
22559 A
60 A
22560 TATATATTAT
Statistics
Matches: 156, Mismatches: 7, Indels: 23
0.84 0.04 0.12
Matches are distributed among these distances:
107 11 0.07
108 12 0.08
109 60 0.38
110 10 0.06
111 26 0.17
112 9 0.06
113 16 0.10
114 12 0.08
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (107 bp):
ATATATAAGATATAGTTTTTAAAAACATTTTAAAAAATATATATTATATAGTTTTGAAAACATTT
TTGAAAATATATATAATATATAGTTTTGAAAACATTTTGAAA
Found at i:22574 original size:23 final size:24
Alignment explanation
Indices: 22531--22585 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
22521 CATTTTGAAA
22531 AAAATATATATAATATATAGTTTTG
1 AAAATATATAT-ATATATAGTTTTG
*
22556 AAAATATATAT-TATGTAGTTTTG
1 AAAATATATATATATATAGTTTTG
*
22579 ATAATAT
1 AAAATAT
22586 TTTTGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 17 0.61
25 11 0.39
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (24 bp):
AAAATATATATATATATAGTTTTG
Found at i:22595 original size:62 final size:63
Alignment explanation
Indices: 22487--22621 Score: 184
Period size: 62 Copynumber: 2.1 Consensus size: 63
22477 TTTGAAAACA
*
22487 TTTTGAAAATATATATGTTATATAGTTTTGAAAACATTTTGAAAAAAATATATATAATATATAG
1 TTTTGAAAATATATA-GTTATATAGTTTTGAAAACATTTTGAAAAAAAAATATATAATATATAG
* * * *
22551 TTTTGAAAATATATA-TTATGTAGTTTTGATAATATTTTTG-AAAAAAAATATATATTATATAG
1 TTTTGAAAATATATAGTTATATAGTTTTGAAAACA-TTTTGAAAAAAAAATATATAATATATAG
*
22613 TTTTAAAAA
1 TTTTGAAAA
22622 CAATTTTTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
62 44 0.69
63 5 0.08
64 15 0.23
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.44
Consensus pattern (63 bp):
TTTTGAAAATATATAGTTATATAGTTTTGAAAACATTTTGAAAAAAAAATATATAATATATAG
Found at i:22710 original size:20 final size:20
Alignment explanation
Indices: 22683--22749 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
22673 TTTAAAAATG
22683 ATTT-TTATTTTTTTTCATT
1 ATTTATTATTTTTTTTCATT
*
22702 ATATATTATATTTTTTT-ATT
1 ATTTATTAT-TTTTTTTCATT
22722 ATTTTATTAATTTTTTTTC-TT
1 A-TTTATT-ATTTTTTTTCATT
22743 ATTTATT
1 ATTTATT
22750 TAATTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
19 3 0.07
20 14 0.34
21 22 0.54
22 2 0.05
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (20 bp):
ATTTATTATTTTTTTTCATT
Found at i:22715 original size:21 final size:21
Alignment explanation
Indices: 22687--22738 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
22677 AAAATGATTT
22687 TTAT-TTTTTTTCATTA-TATA
1 TTATATTTTTTT-ATTATTATA
*
22707 TTATATTTTTTTATTATTTTA
1 TTATATTTTTTTATTATTATA
22728 TTA-ATTTTTTT
1 TTATATTTTTTT
22739 TCTTATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATATTTTTTTATTATTATA
Found at i:22739 original size:21 final size:20
Alignment explanation
Indices: 22689--22761 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
22679 AATGATTTTT
*
22689 ATTTTTTTTCATTATATATT-
1 ATTTTTTTT-ATTATTTATTA
22709 ATATTTTTTTATTATTTTATTA
1 AT-TTTTTTTATTA-TTTATTA
*
22731 ATTTTTTTTCTTATTTATTTA
1 ATTTTTTTTATTATTTA-TTA
22752 ATTTTATTTT
1 ATTTT-TTTT
22762 TCTTTGTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
20 10 0.22
21 30 0.65
22 6 0.13
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTTTTTATTATTTATTA
Found at i:23959 original size:7 final size:7
Alignment explanation
Indices: 23947--23972 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23937 TTTTCCTTTA
23947 TTTTTTC
1 TTTTTTC
23954 TTTTTTC
1 TTTTTTC
23961 TTTTTTC
1 TTTTTTC
23968 TTTTT
1 TTTTT
23973 AACATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:23998 original size:5 final size:5
Alignment explanation
Indices: 23984--24042 Score: 59
Period size: 5 Copynumber: 12.0 Consensus size: 5
23974 ACATTTATAC
* * * *
23984 ATTTT ATTTT TTTTT AATTT -TTTT ATTATT -TTTC ATCTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATT-TT ATTTT ATTTT ATTTT ATTTT
24033 ATTTT ATTTT
1 ATTTT ATTTT
24043 TCTCTTTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
4 4 0.09
5 37 0.86
6 2 0.05
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:25254 original size:140 final size:140
Alignment explanation
Indices: 25077--25336 Score: 457
Period size: 140 Copynumber: 1.9 Consensus size: 140
25067 ATCGTTATGT
*
25077 GATCGTTATGTATCAGAGCTTTTGGTTGTGAATTTTGTCAATTTTTTTGCGAGATTACTATTCAT
1 GATCGTTATGTATCAGAGCTTTTGATTGTGAATTTTGTCAATTTTTTTGCGAGATTACTATTCAT
* * *
25142 TACTATTCACGTGAATAGTTAATTTCTTGAATTGTAAAATTGTGTCGGCGATACATAAATAATTT
66 TACTATTCACATGAATAATTAATTTCGTGAATTGTAAAATTGTGTCGGCGATACATAAATAATTT
25207 AGGACGTTTG
131 AGGACGTTTG
* *
25217 GATCGTTATGTATTAGAGCTTTTGATTGTGAATTTTGTCAATTTTTTTGTGAGATTACTATTCAT
1 GATCGTTATGTATCAGAGCTTTTGATTGTGAATTTTGTCAATTTTTTTGCGAGATTACTATTCAT
*
25282 TACTATTCACATGAATAATTAATTTCGTGAATTGTATAATTGTGTCGGCGATACA
66 TACTATTCACATGAATAATTAATTTCGTGAATTGTAAAATTGTGTCGGCGATACA
25337 AATTTGTCAA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 113 1.00
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.44
Consensus pattern (140 bp):
GATCGTTATGTATCAGAGCTTTTGATTGTGAATTTTGTCAATTTTTTTGCGAGATTACTATTCAT
TACTATTCACATGAATAATTAATTTCGTGAATTGTAAAATTGTGTCGGCGATACATAAATAATTT
AGGACGTTTG
Found at i:29416 original size:30 final size:31
Alignment explanation
Indices: 29356--29416 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
29346 TGAAAGCCAA
*
29356 GGTTGGCACCGAATGGTGCTTAATTTCAATG
1 GGTTGGCACCGAATGGTGCATAATTTCAATG
29387 GGTTGGCACCGAATGGTGCATAA-TTCAATG
1 GGTTGGCACCGAATGGTGCATAATTTCAATG
29417 TGTTTGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (31 bp):
GGTTGGCACCGAATGGTGCATAATTTCAATG
Found at i:30561 original size:16 final size:16
Alignment explanation
Indices: 30536--30594 Score: 93
Period size: 16 Copynumber: 3.8 Consensus size: 16
30526 AACTGGTATT
* *
30536 AACC-GACCTGTTTTC
1 AACCTGACCTGTTATA
30551 AACCTGACCTGTTATA
1 AACCTGACCTGTTATA
30567 AACCTGACCTGTTATA
1 AACCTGACCTGTTATA
30583 AACCTGACCTGT
1 AACCTGACCTGT
30595 AATTGACTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 4 0.10
16 37 0.90
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.31
Consensus pattern (16 bp):
AACCTGACCTGTTATA
Found at i:30766 original size:23 final size:22
Alignment explanation
Indices: 30739--30806 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 22
30729 TTACTTTTTG
30739 AAATTTAGTTTTTATATTAATT
1 AAATTTAGTTTTTATATTAATT
*
30761 ATAATTTA---TATATATT-A-T
1 A-AATTTAGTTTTTATATTAATT
*
30779 AAATTTGGTTTTTATATTAATT
1 AAATTTAGTTTTTATATTAATT
30801 ACAATT
1 A-AATT
30807 CTTTATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 13
0.69 0.06 0.25
Matches are distributed among these distances:
17 5 0.14
18 2 0.06
19 1 0.03
20 14 0.39
21 1 0.03
22 3 0.08
23 10 0.28
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (22 bp):
AAATTTAGTTTTTATATTAATT
Found at i:30832 original size:18 final size:19
Alignment explanation
Indices: 30789--30835 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
30779 AAATTTGGTT
*
30789 TTTATATTAATTACAATTC
1 TTTATATTATTTACAATTC
* *
30808 TTTATATTATTTATATTTC
1 TTTATATTATTTACAATTC
30827 -TTATATTAT
1 TTTATATTAT
30836 AAATTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATTATTTACAATTC
Found at i:31454 original size:23 final size:23
Alignment explanation
Indices: 31428--31481 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
31418 CAACAATCTG
*
31428 CAAGCATCAATGTACCAATTCAT
1 CAAGCATCAATATACCAATTCAT
31451 CAAGCATCAATATACCAATTCAT
1 CAAGCATCAATATACCAATTCAT
31474 CAAGCATC
1 CAAGCATC
31482 CTGCAGTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (23 bp):
CAAGCATCAATATACCAATTCAT
Found at i:31599 original size:20 final size:20
Alignment explanation
Indices: 31574--31618 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
31564 AATCCTTATA
**
31574 AATATCAAGTAAAAGCAAAC
1 AATATCAAACAAAAGCAAAC
*
31594 AATATCAAACAGAAGCAAAC
1 AATATCAAACAAAAGCAAAC
31614 AATAT
1 AATAT
31619 AAAATAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.16, G:0.09, T:0.16
Consensus pattern (20 bp):
AATATCAAACAAAAGCAAAC
Found at i:31627 original size:20 final size:20
Alignment explanation
Indices: 31586--31627 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
31576 TATCAAGTAA
*
31586 AAGCAAACAATATCAAACAG
1 AAGCAAACAATATAAAACAG
*
31606 AAGCAAACAATATAAAATAG
1 AAGCAAACAATATAAAACAG
31626 AA
1 AA
31628 TAATGCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (20 bp):
AAGCAAACAATATAAAACAG
Found at i:34386 original size:61 final size:61
Alignment explanation
Indices: 34296--34442 Score: 206
Period size: 61 Copynumber: 2.4 Consensus size: 61
34286 TTGTCTCTTA
* * * *
34296 ATTTTAAATTTATTCAATTTAGTCTAAATTTAATGATT-TAATATATTAATTTAAGCTTCAT
1 ATTTAAAATTTTTTCAATTTAATCCAAATTTAATG-TTATAATATATTAATTTAAGCTTCAT
* * *
34357 ATTTCAACTTTTTTCAATTTAATCCAAATTTAATGTTATAATTTATTAATTTAAGCTTCAT
1 ATTTAAAATTTTTTCAATTTAATCCAAATTTAATGTTATAATATATTAATTTAAGCTTCAT
*
34418 ATTTAAAATTTTTTCAATTTGATCC
1 ATTTAAAATTTTTTCAATTTAATCC
34443 TTATATATTT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
60 2 0.03
61 74 0.97
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (61 bp):
ATTTAAAATTTTTTCAATTTAATCCAAATTTAATGTTATAATATATTAATTTAAGCTTCAT
Found at i:34506 original size:20 final size:20
Alignment explanation
Indices: 34481--34522 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
34471 TATATATGTT
34481 TATATTAATAAATTAATATA
1 TATATTAATAAATTAATATA
34501 TATATTAATAAATTAATATA
1 TATATTAATAAATTAATATA
34521 TA
1 TA
34523 GTTTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATTAATAAATTAATATA
Found at i:34565 original size:33 final size:33
Alignment explanation
Indices: 34528--34645 Score: 117
Period size: 33 Copynumber: 3.8 Consensus size: 33
34518 ATATAGTTTA
* *
34528 TATATACTGTATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
34561 TATATAATATATAGTTTGTATATAC-CAT--A-
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
34590 TA-CT-ATATAT-G-TTATATATACTAATGAAT
1 TATATAATATATAGTTTATATATACTAATGAAC
*
34619 TGTATAATATATAGTTTATATATACTA
1 TATATAATATATAGTTTATATATACTA
34646 TATAGTTTAT
Statistics
Matches: 68, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
25 9 0.13
26 3 0.04
27 6 0.09
28 2 0.03
29 3 0.04
30 2 0.03
31 6 0.09
32 3 0.04
33 34 0.50
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.45
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:34572 original size:51 final size:51
Alignment explanation
Indices: 34514--34657 Score: 182
Period size: 58 Copynumber: 2.7 Consensus size: 51
34504 ATTAATAAAT
*
34514 TAATATATAGTTTATATATACTGTATAGTTTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATA
* *
34565 TAATATATAGTTTGTATATACCATATACTATATA-TGTTATATATACTAATGAATTGTA
1 TAATATATAG--T-T-TAT---ATATACTATATAGT-TTATATATACTAATGAACTATA
34623 TAATATATAGTTTATATATACTATATAGTTTATAT
1 TAATATATAGTTTATATATACTATATAGTTTATAT
34658 GTAATGTATA
Statistics
Matches: 81, Mismatches: 3, Indels: 18
0.79 0.03 0.18
Matches are distributed among these distances:
51 28 0.35
52 1 0.01
53 1 0.01
54 4 0.05
55 4 0.05
56 1 0.01
57 1 0.01
58 41 0.51
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (51 bp):
TAATATATAGTTTATATATACTATATAGTTTATATATACTAATGAACTATA
Found at i:34605 original size:58 final size:58
Alignment explanation
Indices: 34529--34659 Score: 183
Period size: 58 Copynumber: 2.3 Consensus size: 58
34519 TATAGTTTAT
* *
34529 ATATACTGTATA-GTTTATATATACTAATGAACTATATAATATATAGTTTGTATATACC
1 ATATACTATATATG-TTATATATACTAATGAACTATATAATATATAGTTTATATATACC
* * *
34587 ATATACTATATATGTTATATATACTAATGAATTGTATAATATATAGTTTATATATACT
1 ATATACTATATATGTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
* *
34645 ATATAGTTTATATGT
1 ATATACTATATATGT
34660 AATGTATAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 64 0.98
59 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (58 bp):
ATATACTATATATGTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
Found at i:34607 original size:25 final size:25
Alignment explanation
Indices: 34514--34610 Score: 65
Period size: 25 Copynumber: 3.8 Consensus size: 25
34504 ATTAATAAAT
**
34514 TAATATATAGTTTATATATACTGTA
1 TAATATATAGTTTATATATACCATA
* * * *
34539 TAGTTTATA-TATACTA-ATGAACTATA
1 TAATATATAGTTTA-TATAT--ACCATA
*
34565 TAATATATAGTTTGTATATACCATA
1 TAATATATAGTTTATATATACCATA
*
34590 TACTATATA-TGTTATATATAC
1 TAATATATAGT-TTATATATAC
34611 TAATGAATTG
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
24 6 0.11
25 31 0.56
26 14 0.25
27 4 0.07
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (25 bp):
TAATATATAGTTTATATATACCATA
Found at i:34640 original size:2 final size:2
Alignment explanation
Indices: 34621--34812 Score: 79
Period size: 2 Copynumber: 91.0 Consensus size: 2
34611 TAATGAATTG
* * *
34621 TA TA -A TA TA TA GTT TA TA TA TA CTA TA TA GTT TA TA TG TA -A
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* * * * *
34662 TG TA TA GTT TA TA TA TA CCA TA TA -A TC TA TA TA GTT TA TA TA
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* *
34704 TA TA -A TA TA TA GTA TA TA AA TA TA AA CTA TA GTA 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
** * * *
34746 TA GG TCA TA TG TA AA CTA TA TA GTA TA TA AA TA TCA -A CTA TA GTA
1 TA TA T-A TA TA TA TA -TA TA TA -TA TA TA TA TA T-A TA -TA TA -TA
34791 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
34813 GGTCATATGT
Statistics
Matches: 140, Mismatches: 30, Indels: 40
0.67 0.14 0.19
Matches are distributed among these distances:
1 5 0.04
2 115 0.82
3 20 0.14
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (2 bp):
TA
Found at i:34685 original size:18 final size:18
Alignment explanation
Indices: 34517--34685 Score: 105
Period size: 18 Copynumber: 9.3 Consensus size: 18
34507 AATAAATTAA
34517 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
*
34535 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
34553 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
*
34568 TATATAGTTTGTATATAC
1 TATATAGTTTATATATAC
* * *
34586 CATATACTATATATGTTATA-
1 TATATAGT-T-TAT-ATATAC
* ** * *
34606 TATACTAATGAATTGTATAA
1 TATA-TAGTTTA-TATATAC
34626 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
34644 TATATAGTTTATATGTAA
1 TATATAGTTTATATATAC
*
34662 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
*
34680 CATATA
1 TATATA
34686 ATCTATATAG
Statistics
Matches: 112, Mismatches: 28, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
14 1 0.01
15 8 0.07
16 3 0.03
17 3 0.03
18 70 0.62
19 10 0.09
20 10 0.09
21 7 0.06
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:34693 original size:36 final size:36
Alignment explanation
Indices: 34623--34693 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
34613 ATGAATTGTA
* * *
34623 TAATATATAGTTTATATATACTATATAGTTTATATG
1 TAATATATAGTTTATATATACCATATAATCTATATG
*
34659 TAATGTATAGTTTATATATACCATATAATCTATAT
1 TAATATATAGTTTATATATACCATATAATCTATAT
34694 AGTTTATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (36 bp):
TAATATATAGTTTATATATACCATATAATCTATATG
Found at i:34709 original size:22 final size:21
Alignment explanation
Indices: 34621--34845 Score: 67
Period size: 18 Copynumber: 11.2 Consensus size: 21
34611 TAATGAATTG
34621 TATAA-TATATAGT-T-TATA
1 TATAACTATATAGTATATATA
34639 TAT-ACTATATAGT-T-TATA
1 TATAACTATATAGTATATATA
* *
34657 TGTAA-TGTATAGT-T-TATA
1 TATAACTATATAGTATATATA
* * *
34675 TAT-ACCATATAATCTATATA
1 TATAACTATATAGTATATATA
* *
34695 GTTTATA-TATATAATATATAGTA
1 -TATA-ACTATATAGTATATA-TA
* * *
34718 TATAAATATAAACTATAGTATA
1 TATAACTATATAGTATA-TATA
* * *
34740 TAT-A-TATA-GGT-CATATG
1 TATAACTATATAGTATATATA
*
34757 TA-AACTATATAGTATATAAA
1 TATAACTATATAGTATATATA
34777 TATCAAC--TATAGTATATATA
1 TAT-AACTATATAGTATATATA
34797 TATATA-TATATA-TATAGGTCATA
1 TATA-ACTATATAGTATA--T-ATA
* * *
34820 TGTAAACTATGTAGTTTATATA
1 TAT-AACTATATAGTATATATA
34842 TATA
1 TATA
34846 GTATATAAAT
Statistics
Matches: 156, Mismatches: 25, Indels: 49
0.68 0.11 0.21
Matches are distributed among these distances:
17 8 0.05
18 42 0.27
19 6 0.04
20 33 0.21
21 9 0.06
22 37 0.24
23 12 0.08
24 6 0.04
25 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (21 bp):
TATAACTATATAGTATATATA
Found at i:34712 original size:20 final size:20
Alignment explanation
Indices: 34621--34747 Score: 93
Period size: 20 Copynumber: 6.2 Consensus size: 20
34611 TAATGAATTG
34621 TATAATATATAG-TT-TATA
1 TATAATATATAGTTTATATA
*
34639 TATACTATATAG-TT-TATA
1 TATAATATATAGTTTATATA
* *
34657 TGTAATGTATAGTTTATATATACCA
1 TATAATATATAG-TT-TATAT---A
34682 TATAATCTATATAGTTTATATA
1 TATAA--TATATAGTTTATATA
* *
34704 TATAATATATAGTATATAAA
1 TATAATATATAGTTTATATA
*
34724 TATAA-ACTATAGTATATATA
1 TATAATA-TATAGTTTATATA
34744 TATA
1 TATA
34748 GGTCATATGT
Statistics
Matches: 90, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
18 26 0.29
19 1 0.01
20 35 0.39
21 1 0.01
22 9 0.10
25 10 0.11
26 2 0.02
27 6 0.07
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (20 bp):
TATAATATATAGTTTATATA
Found at i:34719 original size:27 final size:27
Alignment explanation
Indices: 34664--34774 Score: 77
Period size: 27 Copynumber: 4.1 Consensus size: 27
34654 ATATGTAATG
** *
34664 TATAGTTTATATATACCATATA-ATCTA
1 TATAGTTTATATATATAATATATA-GTA
34691 TATAGTTTATATATATAATATATAGTA
1 TATAGTTTATATATATAATATATAGTA
** * *
34718 TATA-AATATAAACTATAGTATATA-TA
1 TATAGTTTATATA-TATAATATATAGTA
* * *
34744 TATAGGTCATATGTA-AACTATATAGTA
1 TATAGTTTATATATATAA-TATATAGTA
34771 TATA
1 TATA
34775 AATATCAACT
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
25 1 0.02
26 19 0.29
27 45 0.68
28 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (27 bp):
TATAGTTTATATATATAATATATAGTA
Found at i:34745 original size:33 final size:32
Alignment explanation
Indices: 34698--34890 Score: 102
Period size: 33 Copynumber: 5.9 Consensus size: 32
34688 CTATATAGTT
34698 TATATATATAATATATAGTATATAAATATAAAC
1 TATATATAT-ATATATAGTATATAAATATAAAC
* *
34731 TATAGTATATATATATAGGT-CAT--ATGTAAAC
1 TATA-TATATATATATA-GTATATAAATATAAAC
* * *
34762 TATATAGTATATAAATA-TCAACTATAGTATATATA-
1 TATATA-TATATATATAGT--A-TATA-AATATAAAC
*
34797 TATATATATATATATAGGTCATATGTAAACTAT---G
1 TATATATATATATATA-GT-ATA--TAAA-TATAAAC
34831 TAGT-T-TATATATATAGTATATAAATATAAAC
1 TA-TATATATATATATAGTATATAAATATAAAC
* *
34862 TATAGTTTATATAAATAGTATA-AAATATA
1 TATA-TATATATATATAGTATATAAATATA
34891 GTATATAAAT
Statistics
Matches: 126, Mismatches: 11, Indels: 47
0.68 0.06 0.26
Matches are distributed among these distances:
28 3 0.02
29 5 0.04
30 3 0.02
31 25 0.20
32 10 0.08
33 39 0.31
34 21 0.17
35 9 0.07
36 11 0.09
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (32 bp):
TATATATATATATATAGTATATAAATATAAAC
Found at i:34867 original size:20 final size:20
Alignment explanation
Indices: 34841--34914 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
34831 TAGTTTATAT
34841 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
34861 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
34886 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
34906 TTATAGTAT
1 ATATAGTAT
34915 GTAGTTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 19 0.41
21 1 0.02
22 7 0.15
23 7 0.15
24 1 0.02
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:34893 original size:12 final size:13
Alignment explanation
Indices: 34854--34903 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
34844 TAGTATATAA
34854 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
34868 TTATATAA-ATAGT
1 ATATA-AATATAGT
34881 ATA-AAATATAGT
1 ATATAAATATAGT
34893 ATATAAATATA
1 ATATAAATATA
34904 AATTATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:35081 original size:13 final size:11
Alignment explanation
Indices: 34965--35083 Score: 64
Period size: 11 Copynumber: 10.6 Consensus size: 11
34955 ATATATAAAC
34965 TATATAATTTA
1 TATATAATTTA
**
34976 TAT-TAATAAA
1 TATATAATTTA
34986 CTATATAATTTA
1 -TATATAATTTA
*
34998 TACAATATATATTA
1 TA-TATA-AT-TTA
*
35012 TTTATAA-TTA
1 TATATAATTTA
* *
35022 TACATAATATA
1 TATATAATTTA
* **
35033 TAAAT-ATAAA
1 TATATAATTTA
* *
35043 TCGTATAGTTTA
1 T-ATATAATTTA
*
35055 TATATAATTCA
1 TATATAATTTA
35066 TATATAATTTA
1 TATATAATTTA
35077 TATATAA
1 TATATAA
35084 ACTATGTAGT
Statistics
Matches: 79, Mismatches: 21, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
10 18 0.23
11 40 0.51
12 12 0.15
13 5 0.06
14 4 0.05
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (11 bp):
TATATAATTTA
Found at i:35171 original size:27 final size:28
Alignment explanation
Indices: 35108--35185 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
35098 ATATAGTTCA
* *
35108 ATAGTTCATATATAA-ACTATATAGTATT
1 ATAGTTTATACATAATA-TATATAGTATT
**
35136 ATAGTTTATACATGGTATATATAGT-TT
1 ATAGTTTATACATAATATATATAGTATT
35163 AT-GCTTTATACATAATATATATA
1 ATAG-TTTATACATAATATATATA
35186 TATAAACTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
26 1 0.02
27 21 0.50
28 19 0.45
29 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (28 bp):
ATAGTTTATACATAATATATATAGTATT
Found at i:35184 original size:2 final size:2
Alignment explanation
Indices: 35177--35280 Score: 88
Period size: 2 Copynumber: 51.0 Consensus size: 2
35167 TTTATACATA
* * *
35177 AT AT AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT A- AT AC AT AT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * *
35220 ACT TT AT AT AT AA ACT AT AT AGT TT AT AT -T AT AT -T AT AT AT
1 A-T AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT
35261 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
35281 TAGTTGTTTT
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
1 3 0.04
2 74 0.90
3 5 0.06
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35216 original size:42 final size:43
Alignment explanation
Indices: 35170--35275 Score: 153
Period size: 42 Copynumber: 2.5 Consensus size: 43
35160 TTTATGCTTT
35170 ATACATAATATATATATATAAACTATATAGTTTATA-TATATA
1 ATACATAATATATATATATAAACTATATAGTTTATATTATATA
* *
35212 ATACAT-ATACTTTATATATAAACTATATAGTTTATATTATATT
1 ATACATAATA-TATATATATAAACTATATAGTTTATATTATATA
*
35255 ATATATATATATATATATATA
1 ATACATA-ATATATATATATA
35276 TATATTAGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
41 3 0.05
42 31 0.55
43 10 0.18
44 9 0.16
45 3 0.05
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (43 bp):
ATACATAATATATATATATAAACTATATAGTTTATATTATATA
Found at i:35258 original size:10 final size:11
Alignment explanation
Indices: 35177--35280 Score: 69
Period size: 11 Copynumber: 9.5 Consensus size: 11
35167 TTTATACATA
35177 ATATATATATAT
1 ATATATATAT-T
*
35189 AAACTATATAGTT
1 ATA-TATATA-TT
*
35202 -TATATATATA
1 ATATATATATT
*
35212 ATACATATACTT
1 ATATATATA-TT
*
35224 -TATATATA-A
1 ATATATATATT
35233 ACTATATAGT-TT
1 A-TATATA-TATT
35245 ATAT-TATATT
1 ATATATATATT
35255 ATATATATA-T
1 ATATATATATT
35265 ATATATATA-T
1 ATATATATATT
35275 ATATAT
1 ATATAT
35281 TAGTTGTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
9 1 0.01
10 26 0.35
11 33 0.45
12 6 0.08
13 7 0.09
14 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (11 bp):
ATATATATATT
Found at i:35285 original size:42 final size:41
Alignment explanation
Indices: 35168--35285 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 41
35158 AGTTTATGCT
*
35168 TTATACATA-ATATATATATATAAACTATATAGTTTATATATA
1 TTATACATATATATATATATATATA-TAT-TAGTTTATATATA
* * *
35210 TAATACATATACTTTATATATAAACTATA-TAGTTTATATTATA
1 TTATACATATA-TATATATATATA-TATATTAGTTTATA-TATA
*
35253 TTATATATATATATATATATATATATATTAGTT
1 TTATACATATATATATATATATATATATTAGTT
35286 GTTTTAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
41 4 0.06
42 32 0.51
43 14 0.22
44 12 0.19
45 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (41 bp):
TTATACATATATATATATATATATATATTAGTTTATATATA
Found at i:35666 original size:210 final size:213
Alignment explanation
Indices: 35304--36120 Score: 1238
Period size: 210 Copynumber: 3.8 Consensus size: 213
35294 TTTTTTCTCA
*
35304 ACTTATTACTTATTTATATTTATT-AATTGGCCCATAACTTTTTAAATGAGTATAATTTAGTA-T
1 ACTTATTACTTATTTATATTT-TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
* ** *
35367 ATTTTTGTATTAATTTCAACCTTAAAATTTAAAATTATTTCGATTCAATCCCT-T-T-TGTGATG
65 -TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTTATCCCTATATGTGTGTTG
*
35429 TTTAATATATTTAATTTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATT
129 TTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATT
* *
35494 TGCACCTGAAATTTACCCAT
194 TGCATCTGAAATTGACCCAT
35514 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* *
35579 TTTTGTATTAATTTCAACCTCAAAATTTTAAATTATTTTGATTTTATCCCT-T-T-TGTGTTGTT
66 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTTATCCCTATATGTGTGTTGTT
*
35641 TAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATCTG
131 TAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTG
35706 CATCTGAAATTGACCCAT
196 CATCTGAAATTGACCCAT
* * *
35724 ACTTATTACTTATTTCTATTTTTAAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTAATT
1 ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* * *
35789 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTTGATTTTATCCCTCATCAATGTGTGTT
66 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTTATCCCT-AT--ATGTGTGTT
* * *
35854 GTTTAATTTATTTAAATTTTTGTTTGTAATTTAATATTTGTTCAATTTAGTCCTCCAAATTTTAT
128 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
* *
35919 TTGCATATGAAATTGATCCAT
193 TTGCATCTGAAATTGACCCAT
*
35940 ACTTATTACTTAATTCTAT-TTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAC
1 ACTTATTACTT-ATT-TATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAC
* *
36004 TTTTTTTGTATTAATTTCAACCTCATAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGT
64 -TTTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTTATCCCT-AT--ATGTGT
*
36069 GTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
125 GTTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
36121 ATTCTTAAAT
Statistics
Matches: 563, Mismatches: 33, Indels: 14
0.92 0.05 0.02
Matches are distributed among these distances:
209 2 0.00
210 304 0.54
211 1 0.00
212 1 0.00
215 1 0.00
216 97 0.17
217 45 0.08
218 112 0.20
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (213 bp):
ACTTATTACTTATTTATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTTATCCCTATATGTGTGTTGTT
TAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTG
CATCTGAAATTGACCCAT
Found at i:39031 original size:20 final size:20
Alignment explanation
Indices: 38974--39032 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
38964 GTTTTGCCAA
* **
38974 TATCTGTACTACCTCAGCAG
1 TATCGGTACTACCTCAATAG
38994 TATCGGTACTACCTCAATAG
1 TATCGGTACTACCTCAATAG
*
39014 TATCGGTACTACTTCAATA
1 TATCGGTACTACCTCAATA
39033 TTTTGGGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (20 bp):
TATCGGTACTACCTCAATAG
Found at i:39171 original size:103 final size:103
Alignment explanation
Indices: 38991--39227 Score: 350
Period size: 103 Copynumber: 2.3 Consensus size: 103
38981 ACTACCTCAG
* *
38991 CAGTATCGGTACTACCTCAATAGTATCGGTACTACTTCAATATTTTGGGTTTTAGTATCAATATC
1 CAGTATCGGTACTGCCTCAGTAGTATCGGTACTACTTCAATATTTTGGGTTTTAGTATCAATATC
* *
39056 ATATATGGTATCGGTACCATTTTAGT-ATTCTATTTTGA
66 ATATATGGTATCGATACCATTTTA-TCATTATATTTTGA
* * *
39094 CAGTATCGGTATTGCCTCAGTAGTATCGGTACTACTTCATTATTTTGGGTTTTAGTATCGATATC
1 CAGTATCGGTACTGCCTCAGTAGTATCGGTACTACTTCAATATTTTGGGTTTTAGTATCAATATC
* *
39159 ATATATGTTATCGATACCATTTTATCATTATGTTTTGA
66 ATATATGGTATCGATACCATTTTATCATTATATTTTGA
* * *
39197 CAGTATCGTTACTGTCTCAGAAGTATCGGTA
1 CAGTATCGGTACTGCCTCAGTAGTATCGGTA
39228 TTGTCTCAGA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
102 1 0.01
103 119 0.99
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.42
Consensus pattern (103 bp):
CAGTATCGGTACTGCCTCAGTAGTATCGGTACTACTTCAATATTTTGGGTTTTAGTATCAATATC
ATATATGGTATCGATACCATTTTATCATTATATTTTGA
Found at i:39223 original size:20 final size:20
Alignment explanation
Indices: 39198--39249 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
39188 ATGTTTTGAC
*
39198 AGTATCGTTACTGTCTCAGA
1 AGTATCGGTACTGTCTCAGA
*
39218 AGTATCGGTATTGTCTCAGA
1 AGTATCGGTACTGTCTCAGA
*
39238 AGTATCAGTACT
1 AGTATCGGTACT
39250 ACTTCATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (20 bp):
AGTATCGGTACTGTCTCAGA
Found at i:44934 original size:8 final size:8
Alignment explanation
Indices: 44923--44956 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
44913 ATATTTTATA
44923 TATTTAAT
1 TATTTAAT
*
44931 TATTCAAT
1 TATTTAAT
*
44939 TATTTAAC
1 TATTTAAT
44947 TATTTAAT
1 TATTTAAT
44955 TA
1 TA
44957 CTTATCCGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAT
Found at i:45311 original size:55 final size:54
Alignment explanation
Indices: 45220--45377 Score: 178
Period size: 55 Copynumber: 2.9 Consensus size: 54
45210 ATATTCGGAA
* * *
45220 AACGAGCTCGCTCCCTCATTT-TTAGGGAGTATAGAACTCGAACAATTTTCTG-C
1 AACGAGTTCACTCCCTC-TTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
*
45273 GAACGAGTTCACTCCCTCTTTCTTCGGGGAGTATAGAACTCGAACAATCTTCTGTC
1 -AACGAGTTCACTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACAATCTTCTGTC
* ** * * *
45329 AACGGGTTCGTTCCCTCTTTCTTAGGGAGTA-GGAACTTGAAGAATCTTC
1 AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTC
45378 ATCAATCGTG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
53 18 0.20
54 24 0.27
55 47 0.52
56 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (54 bp):
AACGAGTTCACTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
Found at i:45432 original size:55 final size:55
Alignment explanation
Indices: 45371--45923 Score: 801
Period size: 55 Copynumber: 10.1 Consensus size: 55
45361 GAACTTGAAG
* *
45371 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* * * * *
45426 AATCTTCAACAAATCTTGTCTGCTCCCTATTTCTTCAGAGAGTAT-AGACCCAAAC
1 AATCTTCATC-AATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* * *
45481 AATCTTCATCAATCGTGTCTGCTCCCCA-TTCTTTCAGAGAGTATAAGACTTGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTC-CTCAGAGAGTATAAGACTCGAAC
*
45536 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
45591 AATCTTCATCAATCGTGTCTGCTCCCTATTT-CTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
45646 AATCTTCATCAATCGTGTCTGCTCCCTATTT-CTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
* * * *
45701 AATCTTCAACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTACAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* *
45756 AATCTTCATCCATCGTGTCTGCTCCATATTT-CTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCT-CAGAGAGTATAAGACTCGAAC
* * **
45811 AATTTTCAACAATCGTGTCTGCTCCCTATTTTTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
* * * *
45866 AATCTTCAACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
45921 AAT
1 AAT
45924 TTTCGATTAT
Statistics
Matches: 457, Mismatches: 33, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
53 3 0.01
54 30 0.07
55 387 0.85
56 37 0.08
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (55 bp):
AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACTCGAAC
Found at i:46950 original size:7 final size:8
Alignment explanation
Indices: 46930--46988 Score: 77
Period size: 8 Copynumber: 7.5 Consensus size: 8
46920 GAACCCTTCT
46930 TTTTTTCCA
1 TTTTTT-CA
46939 TTTTTTCA
1 TTTTTTCA
*
46947 TTTTTTTA
1 TTTTTTCA
*
46955 TTTTTTTA
1 TTTTTTCA
46963 TTTTTTC-
1 TTTTTTCA
46970 TTTTTTC-
1 TTTTTTCA
46977 TTTTTTCA
1 TTTTTTCA
46985 TTTT
1 TTTT
46989 CACTCATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
7 14 0.30
8 27 0.57
9 6 0.13
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCA
Found at i:46973 original size:6 final size:7
Alignment explanation
Indices: 46956--47016 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
46946 ATTTTTTTAT
*
46956 TTTTTTA
1 TTTTTTC
46963 TTTTTTC
1 TTTTTTC
46970 TTTTTTC
1 TTTTTTC
46977 TTTTTTC
1 TTTTTTC
*
46984 ATTTTCACTC
1 -TTTT--TTC
46994 ATTTTTTC
1 -TTTTTTC
*
47002 -TTCTTC
1 TTTTTTC
47008 TTTTTTC
1 TTTTTTC
47015 TT
1 TT
47017 CAAGCAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
6 5 0.11
7 27 0.60
8 6 0.13
10 7 0.16
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:56991 original size:16 final size:16
Alignment explanation
Indices: 56970--57007 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
56960 AACCTTATTC
56970 ACATGATATCTACCCA
1 ACATGATATCTACCCA
56986 ACATGATATCTACCCA
1 ACATGATATCTACCCA
57002 ATCATG
1 A-CATG
57008 CTTTAGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.29, G:0.08, T:0.26
Consensus pattern (16 bp):
ACATGATATCTACCCA
Found at i:58467 original size:8 final size:8
Alignment explanation
Indices: 58456--58489 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
58446 ATATTTTATA
58456 TATTTAAT
1 TATTTAAT
*
58464 TATTCAAT
1 TATTTAAT
*
58472 TATTTAAC
1 TATTTAAT
58480 TATTTAAT
1 TATTTAAT
58488 TA
1 TA
58490 CTTATCCGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTAAT
Found at i:63159 original size:26 final size:26
Alignment explanation
Indices: 63129--63195 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
63119 GTTCAAGCCT
*
63129 TTTCGAGTTCAAGTTTCAATATTATA
1 TTTCGAGTTCGAGTTTCAATATTATA
*
63155 TTTCGAGTTCGAGTTTTAATATTATA
1 TTTCGAGTTCGAGTTTCAATATTATA
63181 TTTCGAGTTCGAGTT
1 TTTCGAGTTCGAGTT
63196 GAACTTGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.48
Consensus pattern (26 bp):
TTTCGAGTTCGAGTTTCAATATTATA
Found at i:63779 original size:30 final size:30
Alignment explanation
Indices: 63688--63779 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
63678 CAGTGTGATA
63688 GGAGGTCGCCAAGTGCTT-CGAACGACTTAT
1 GGAGGTCGCCAAGTG-TTCCGAACGACTTAT
* *
63718 GAAGGTCGCCAAGTGTTCCGAATGACTTAT
1 GGAGGTCGCCAAGTGTTCCGAACGACTTAT
* *
63748 GGAGGTCGTCAAGTGTTCCGAACGACCTAT
1 GGAGGTCGCCAAGTGTTCCGAACGACTTAT
63778 GG
1 GG
63780 TCGCTGTTGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 2 0.04
30 53 0.96
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (30 bp):
GGAGGTCGCCAAGTGTTCCGAACGACTTAT
Found at i:63895 original size:28 final size:29
Alignment explanation
Indices: 63862--63946 Score: 109
Period size: 29 Copynumber: 3.0 Consensus size: 29
63852 CCATGCACGG
*
63862 TAGGTCG-CTTGTGCTCCATGCGATCATA
1 TAGGTCGCCTTGTGCTCCATGCGACCATA
*
63890 TAGGTCGCCTTGTGCTTCATGCGACCATA
1 TAGGTCGCCTTGTGCTCCATGCGACCATA
* * **
63919 TAGGTCGTCGTGTGCTTTATGCGACCAT
1 TAGGTCGCCTTGTGCTCCATGCGACCAT
63947 GCGACCAAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 7 0.14
29 44 0.86
ACGTcount: A:0.16, C:0.25, G:0.26, T:0.33
Consensus pattern (29 bp):
TAGGTCGCCTTGTGCTCCATGCGACCATA
Found at i:64006 original size:12 final size:12
Alignment explanation
Indices: 63989--64018 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
63979 TCCCCTGCAT
63989 GCAGCATCAGCA
1 GCAGCATCAGCA
64001 GCAGCATCAGCA
1 GCAGCATCAGCA
64013 GCAGCA
1 GCAGCA
64019 ATTGTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.27, T:0.07
Consensus pattern (12 bp):
GCAGCATCAGCA
Found at i:64226 original size:50 final size:50
Alignment explanation
Indices: 64170--64269 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
64160 AGAAATGTAG
64170 AAAAAAGAAAGGGGGGCGAAAGAAAGGAAAGGAAGAAGAAATAGGCAAAC
1 AAAAAAGAAAGGGGGGCGAAAGAAAGGAAAGGAAGAAGAAATAGGCAAAC
64220 AAAAAAGAAAGGGGGGCGAAAGAAAGGAAAGGAAGAAGAAATAGGCAAAC
1 AAAAAAGAAAGGGGGGCGAAAGAAAGGAAAGGAAGAAGAAATAGGCAAAC
64270 CGATGAGGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.58, C:0.06, G:0.34, T:0.02
Consensus pattern (50 bp):
AAAAAAGAAAGGGGGGCGAAAGAAAGGAAAGGAAGAAGAAATAGGCAAAC
Found at i:64373 original size:46 final size:43
Alignment explanation
Indices: 64315--64466 Score: 198
Period size: 46 Copynumber: 3.3 Consensus size: 43
64305 AGTTTAAATT
64315 ATTAGTTTGTTAGTTTAAGTTATATTATATA-ACCAAAATATAGTTA
1 ATTAGTTTGTTAGTTTAAGTTATATTATATATA--AAAAT-TA-TTA
*
64361 ATTAATTTGTTAGTTTAAGTTATATTATATATAAAAATTTACTTA
1 ATTAGTTTGTTAGTTTAAGTTATATTATATATAAAAA-TTA-TTA
*
64406 ATTAGTTTGTTTGTTATAAGTTATATTATATATAAAAAATTATTCA
1 ATTAGTTTGTTAGTT-TAAGTTATATTATATAT-AAAAATTATT-A
64452 ATTAGTTTGTTAGTT
1 ATTAGTTTGTTAGTT
64467 ACGTAGTTTA
Statistics
Matches: 96, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
45 24 0.25
46 66 0.69
47 6 0.06
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (43 bp):
ATTAGTTTGTTAGTTTAAGTTATATTATATATAAAAATTATTA
Found at i:64597 original size:33 final size:32
Alignment explanation
Indices: 64521--64715 Score: 174
Period size: 33 Copynumber: 5.6 Consensus size: 32
64511 ATACAAAATT
*
64521 TAGTTAATTAGTTTAAGTTATATTATAATAAAAA
1 TAGTTTATTAGTTTAAGTTATA-TATAA-AAAAA
*
64555 TAGTTTATTAGCTTAAGTTATATCATAAAAAAA
1 TAGTTTATTAGTTTAAGTTATAT-ATAAAAAAA
* *
64588 TAGTGTATTAGTTTAAGTTATATTTAAAAAAAA
1 TAGTTTATTAGTTTAAGTTATATAT-AAAAAAA
64621 TAGTTTCTTAGTTTAAGTTTAAGTTATATTATATTAAAAAAAA
1 TAG--T-TTA--TT-AGTTTAAG-T-TA-TATA-TAAAAA-AA
* **
64664 TAGTTTATTAATTTAAGTTATATTATAAAAACG
1 TAGTTTATTAGTTTAAGTTATA-TATAAAAAAA
*
64697 TAGTTTATTAGTTGAAGTT
1 TAGTTTATTAGTTTAAGTT
64716 GAAGTTATAT
Statistics
Matches: 135, Mismatches: 12, Indels: 29
0.77 0.07 0.16
Matches are distributed among these distances:
32 1 0.01
33 54 0.40
34 32 0.24
35 5 0.04
36 3 0.02
37 7 0.05
38 4 0.03
39 8 0.06
40 4 0.03
41 3 0.02
42 8 0.06
43 6 0.04
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (32 bp):
TAGTTTATTAGTTTAAGTTATATATAAAAAAA
Found at i:64642 original size:39 final size:38
Alignment explanation
Indices: 64597--64750 Score: 149
Period size: 39 Copynumber: 4.0 Consensus size: 38
64587 ATAGTGTATT
64597 AGTTTAAGTTATATTTAAAAAAAATAGTTTCTTAGTTTA
1 AGTTTAAGTTATATTTAAAAAAAATAGTTT-TTAGTTTA
64636 AGTTTAAGTTATATTATATTAAAAAAAATAG--TTTA--TTA
1 AGTTTAAG-T-TA-TAT-TTAAAAAAAATAGTTTTTAGTTTA
** *
64674 A-TTTAAGTTATA-TTATAAAAACGTAGTTTATTAGTTGA
1 AGTTTAAGTTATATTTA-AAAAAAATAGTTT-TTAGTTTA
*
64712 AGTTGAAGTTATATTTAAAAAAAATTAGTTTGTTAGTTT
1 AGTTTAAGTTATATTTAAAAAAAA-TAGTTT-TTAGTTT
64751 GATAATTTTT
Statistics
Matches: 94, Mismatches: 8, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
32 3 0.03
33 8 0.09
34 2 0.02
35 3 0.03
36 4 0.04
37 6 0.06
38 7 0.07
39 23 0.24
40 19 0.20
41 3 0.03
42 3 0.03
43 13 0.14
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (38 bp):
AGTTTAAGTTATATTTAAAAAAAATAGTTTTTAGTTTA
Found at i:64668 original size:43 final size:40
Alignment explanation
Indices: 64597--64750 Score: 148
Period size: 40 Copynumber: 4.0 Consensus size: 40
64587 ATAGTGTATT
64597 AGTTTAAGTTATA-TT-TAAAAAAAATAGTTTCTTAGTTTA
1 AGTTTAAGTTATATTTATAAAAAAAATAGTTT-TTAGTTTA
64636 AGTTTAAGTTATATTATATTAAAAAAAATAG--TTTA--TTA
1 AGTTTAAGTTATATT-TA-TAAAAAAAATAGTTTTTAGTTTA
** *
64674 A-TTTAAGTTATA-TTAT-AAAAACGTAGTTTATTAGTTGA
1 AGTTTAAGTTATATTTATAAAAAAAATAGTTT-TTAGTTTA
* *
64712 AGTTGAAGTTATATTTA-AAAAAAATTAGTTTGTTAGTTT
1 AGTTTAAGTTATATTTATAAAAAAAATAGTTT-TTAGTTT
64751 GATAATTTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
33 8 0.08
34 1 0.01
35 3 0.03
36 4 0.04
37 11 0.12
38 7 0.07
39 23 0.24
40 24 0.25
41 2 0.02
43 12 0.13
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (40 bp):
AGTTTAAGTTATATTTATAAAAAAAATAGTTTTTAGTTTA
Found at i:64672 original size:109 final size:110
Alignment explanation
Indices: 64530--64750 Score: 288
Period size: 109 Copynumber: 2.0 Consensus size: 110
64520 TTAGTTAATT
* *
64530 AGTTTAAGTTATATTATAATAAAAATAGTTTATTAGCTTAAGTTATATCATAAAAAAATAGTGTA
1 AGTTTAAGTTATATTATAAAAAAAATAGTTTATTAACTTAAGTTATATCATAAAAAAATAGTGTA
64595 TTAG-T-TT-AAGTTATATTTAAAAAAAA-TAGTTTCTTAGTTTA
66 TTAGTTATTGAAGTTATATTTAAAAAAAATTAGTTTCTTAGTTTA
* * **
64636 AGTTTAAGTTATATTATATTAAAAAAAATAGTTTATTAATTTAAGTTATATTATAAAAACGTAGT
1 AGTTTAAGTTATA-T-TA-TAAAAAAAATAGTTTATTAACTTAAGTTATATCATAAAAAAATAGT
* *
64701 TTATTAGTTGAAGTTGAAGTTATATTTAAAAAAAATTAGTTTGTTAGTTT
63 GTATTAGTT--A-TTGAAGTTATATTTAAAAAAAATTAGTTTCTTAGTTT
64751 GATAATTTTT
Statistics
Matches: 97, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
106 13 0.13
107 1 0.01
108 2 0.02
109 46 0.47
110 1 0.01
114 2 0.02
115 19 0.20
116 13 0.13
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (110 bp):
AGTTTAAGTTATATTATAAAAAAAATAGTTTATTAACTTAAGTTATATCATAAAAAAATAGTGTA
TTAGTTATTGAAGTTATATTTAAAAAAAATTAGTTTCTTAGTTTA
Found at i:64673 original size:76 final size:75
Alignment explanation
Indices: 64572--64750 Score: 220
Period size: 76 Copynumber: 2.4 Consensus size: 75
64562 TTAGCTTAAG
* * *
64572 TTATATCATAAAAAAATAGTGTATTAGTTTAAGTTATATT-TAAAAAAAATAGTTTCTTAGTTTA
1 TTATAT-A-AAAAAAATAGTTTATTAGTTTAAGTTATATTAT-AAAAAAATAGTTTATTAGTTGA
*
64636 AGTTTAAGTTATA
63 AGTTGAAGTTATA
* **
64649 TTATATTAAAAAAAATAGTTTATTAATTTAAGTTATATTATAAAAACGTAGTTTATTAGTTGAAG
1 TTATA-TAAAAAAAATAGTTTATTAGTTTAAGTTATATTATAAAAAAATAGTTTATTAGTTGAAG
64714 TTGAAGTTATA
65 TTGAAGTTATA
* *
64725 TT-TA-AAAAAAATTAGTTTGTTAGTTT
1 TTATATAAAAAAAATAGTTTATTAGTTT
64751 GATAATTTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
73 19 0.21
75 2 0.02
76 61 0.68
77 7 0.08
78 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (75 bp):
TTATATAAAAAAAATAGTTTATTAGTTTAAGTTATATTATAAAAAAATAGTTTATTAGTTGAAGT
TGAAGTTATA
Found at i:67336 original size:25 final size:25
Alignment explanation
Indices: 67270--67339 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
67260 TTTTAACAGT
*
67270 AACTTAAATA-TATAAATTTTAATTTAA
1 AACTTAAATATTAT-AATATT-A-TTAA
67297 AA--TAAAT-TTA-AATATTATTAA
1 AACTTAAATATTATAATATTATTAA
67318 AACTTAAATATTATAATATTAT
1 AACTTAAATATTATAATATTAT
67340 ATATGTATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
21 6 0.16
22 1 0.03
23 10 0.27
24 3 0.08
25 15 0.41
27 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (25 bp):
AACTTAAATATTATAATATTATTAA
Found at i:67690 original size:16 final size:17
Alignment explanation
Indices: 67668--67708 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
67658 TTCGATTATT
*
67668 TATAAATAATAATAAGA
1 TATAAATAATAATAAAA
67685 TA-AAATAATAATAAAA
1 TATAAATAATAATAAAA
67701 TATAAATA
1 TATAAATA
67709 TTTCAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
TATAAATAATAATAAAA
Found at i:69174 original size:19 final size:19
Alignment explanation
Indices: 69150--69187 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
69140 ATTAGTGAGG
69150 CCAGGTGAGTACATGATAT
1 CCAGGTGAGTACATGATAT
69169 CCAGGTGAGTACATGATAT
1 CCAGGTGAGTACATGATAT
69188 TAAGTGTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (19 bp):
CCAGGTGAGTACATGATAT
Found at i:73436 original size:21 final size:21
Alignment explanation
Indices: 73412--73451 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
73402 TACTTACTCC
73412 CTCTCCCTTTCAATCTGCTCA
1 CTCTCCCTTTCAATCTGCTCA
73433 CTCTCCCTTTCAATCTGCT
1 CTCTCCCTTTCAATCTGCT
73452 ACCATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.42, G:0.05, T:0.40
Consensus pattern (21 bp):
CTCTCCCTTTCAATCTGCTCA
Found at i:73865 original size:29 final size:30
Alignment explanation
Indices: 73797--73878 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 30
73787 TGAAGGAAGG
*
73797 TCGCATGGAGCACACGACGCCCT-TCATGT
1 TCGCATGGAGCACACGACGACCTATCATGT
* *
73826 TCACATAGAGCACACGACGACCTAT-ATGGT
1 TCGCATGGAGCACACGACGACCTATCAT-GT
*
73856 T-GCATGGAGCACAAGACGACCTA
1 TCGCATGGAGCACACGACGACCTA
73879 GAGAAGAGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 41 0.91
30 4 0.09
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.18
Consensus pattern (30 bp):
TCGCATGGAGCACACGACGACCTATCATGT
Found at i:73972 original size:30 final size:30
Alignment explanation
Indices: 73938--73999 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
73928 GCAACAGTGA
* * *
73938 CCATAGGTCGTTCGGAGCACTTGGGGACCT
1 CCATAGGTCGTTCGAAGCACTTAGCGACCT
*
73968 CCATAGGTCGTTCGAAGTACTTAGCGACCT
1 CCATAGGTCGTTCGAAGCACTTAGCGACCT
73998 CC
1 CC
74000 TATCACATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.24
Consensus pattern (30 bp):
CCATAGGTCGTTCGAAGCACTTAGCGACCT
Found at i:74853 original size:18 final size:18
Alignment explanation
Indices: 74795--74865 Score: 63
Period size: 20 Copynumber: 3.8 Consensus size: 18
74785 TATTTTTAAA
74795 AAAAATTAAAA-ATCTAT
1 AAAAATTAAAATATCTAT
* * * *
74812 GAAAATTAAAAAATGTAAAC
1 AAAAATTAAAATATCT--AT
74832 AAAAATTAAAATATCTAT
1 AAAAATTAAAATATCTAT
74850 AAAAATACTAAAATAT
1 AAAAAT--TAAAATAT
74866 GACGAGTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
17 10 0.24
18 10 0.24
20 22 0.52
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAAATTAAAATATCTAT
Found at i:76266 original size:8 final size:8
Alignment explanation
Indices: 76253--76280 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
76243 GGTATCGGGC
76253 CGGGTAAT
1 CGGGTAAT
76261 CGGGTAAT
1 CGGGTAAT
76269 CGGGTAAT
1 CGGGTAAT
76277 CGGG
1 CGGG
76281 GCGGGGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.43, T:0.21
Consensus pattern (8 bp):
CGGGTAAT
Found at i:77942 original size:65 final size:65
Alignment explanation
Indices: 77873--77997 Score: 207
Period size: 65 Copynumber: 1.9 Consensus size: 65
77863 TACACTAGGG
*
77873 GTGCATCAGTACACAAAATGCATTCGATGTTTCAAA-ATATTCAAGAGTGCATCGATGCATGGCT
1 GTGCATCAGTACACAAAATGCATTCGAAGTTTCAAATA-ATTCAAGAGTGCATCGATGCATGGCT
77937 T
65 T
* *
77938 GTGCATCAGTACACAAAATGCATTCGAAGTTTCAATTAATTCAAGGGTGCATCGATGCAT
1 GTGCATCAGTACACAAAATGCATTCGAAGTTTCAAATAATTCAAGAGTGCATCGATGCAT
77998 TAAATGGTGC
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 55 0.98
66 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (65 bp):
GTGCATCAGTACACAAAATGCATTCGAAGTTTCAAATAATTCAAGAGTGCATCGATGCATGGCTT
Found at i:78424 original size:2 final size:2
Alignment explanation
Indices: 78417--78445 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
78407 AATCAACCAA
78417 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 A
78446 AGTTCAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80447 original size:23 final size:22
Alignment explanation
Indices: 80419--80498 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
80409 CACAGGAGAG
*
80419 TGCATCGATTCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* * *
80442 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
80463 TGTATCGATGCACATTCAAGGGA
1 TGCATCGATGCACATTCAA-GGA
80486 TGCATCGATGCAC
1 TGCATCGATGCAC
80499 TGTCTAGTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 29 0.63
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:80474 original size:21 final size:21
Alignment explanation
Indices: 80445--80517 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
80435 CAAGGAATGC
*
80445 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACCTTCATGGTGT
* * *
80466 ATCGATGCACATTCAAGGGATGC
1 ATCGATGCACCTTC-ATGG-TGT
*
80489 ATCGATGCA-CTGTC-TAGTGT
1 ATCGATGCACCT-TCATGGTGT
80509 ATCGATGCA
1 ATCGATGCA
80518 TAGTGCACAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
20 11 0.27
21 13 0.32
22 4 0.10
23 13 0.32
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (21 bp):
ATCGATGCACCTTCATGGTGT
Found at i:80477 original size:44 final size:43
Alignment explanation
Indices: 80417--80517 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 43
80407 TGCACAGGAG
* * *
80417 AGTGCATCGATTCACATTCAAGGAATGCATCGGTGCACCT-TCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGATGCA-CTGTC-T
* *
80461 GGTGTATCGATGCACATTCAAGGGATGCATCGATGCACTGTCT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGATGCACTGTCT
80504 AGTGTATCGATGCA
1 AGTGTATCGATGCA
80518 TAGTGCACAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 16 0.32
44 34 0.68
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (43 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGATGCACTGTCT
Found at i:88193 original size:18 final size:16
Alignment explanation
Indices: 88162--88196 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
88152 AAATAAACAA
88162 ATATTATTTATTATAT
1 ATATTATTTATTATAT
88178 ATATATATTTATT-TAT
1 ATAT-TATTTATTATAT
88194 ATA
1 ATA
88197 AATAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTATTTATTATAT
Found at i:89709 original size:3 final size:3
Alignment explanation
Indices: 89703--89775 Score: 114
Period size: 3 Copynumber: 24.7 Consensus size: 3
89693 ATTTATTATT
*
89703 TAA TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
89749 TAA TAA TAA TAA TAA TAA TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TA
89776 TAAGCAAATG
Statistics
Matches: 65, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
2 3 0.05
3 59 0.91
4 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:90310 original size:112 final size:112
Alignment explanation
Indices: 90100--90688 Score: 820
Period size: 113 Copynumber: 5.3 Consensus size: 112
90090 AGCATCAAAC
* * *
90100 AAAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-C-CTTCAGATGAGTTCTTCTTATTA
1 AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* *
90163 TGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTC-AGGCA
66 TGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCGA-GCA
* * * * * *
90210 AAAGGTTGATCAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTA
1 AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
90275 TGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCGAGCA
66 TGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCGAGCA
*
90322 AAAGTTTAAACAAGTTCTTCTCATTATGAACTTCTTCTT-C-CTTCAGATGAGTTCTTCTCATTA
1 AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* * *
90385 TGAACTCT-TCTGGAAATGCTGATCCATCGAA-TGATGAATTCAAGCA
66 TGAACTTTCTCTGGAAATGTTGATCCATC-AAGTGATGAATTCGAGCA
* *
90431 AAA-AGTTGAACAAGTTCTTCTCATTATTAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAGA-TTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCAT
* * *
90495 TATGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTCGAACA
64 TATGAACT-TTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCGAGCA
* *
90544 AAAGATTAAAAAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
* * *
90609 ATGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTCGAACA
65 ATGAACT-TTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCGAGCA
90657 AAAGATTAAACAAGTTCTTCTCATTATGAACT
1 AAAGATTAAACAAGTTCTTCTCATTATGAACT
90689 CTACCTGGAA
Statistics
Matches: 435, Mismatches: 32, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
109 68 0.16
110 66 0.15
111 2 0.00
112 129 0.30
113 169 0.39
114 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (112 bp):
AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCGAGCA
Found at i:90350 original size:222 final size:223
Alignment explanation
Indices: 90100--90688 Score: 848
Period size: 222 Copynumber: 2.6 Consensus size: 223
90090 AGCATCAAAC
* * *
90100 AAAGATTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTTCTTATTATG
1 AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTTCTCATTATG
* * * *
90165 AACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTGATCAAATTCTTC
66 AACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTC
* *
90230 TCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCTGGAAAT
131 TCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTAC-CTGGAAAT
*
90293 GTTGATCCATCAAGTGATGAATTCGAGCA
195 GTTGATCCATCAAGTGATGAATTCGAACA
*
90322 AAAGTTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTTCTCATTATG
1 AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTTCTCATTATG
* * * *
90387 AACTCT-TCTGGAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAAAGTTGAACAAGTTCTT
66 AACTTTCTCTGGAAATGTTGATCCATC-AAGTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTT
* *
90450 CTCATTATTAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAAT
130 CTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCTGGAAAT
*
90515 GTTGATCCATCAAGTGATGGATTCGAACA
195 GTTGATCCATCAAGTGATGAATTCGAACA
* *
90544 AAAGATTAAAAAAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTT-C--CTTCAGATGAGTTCTTCTCATT
* * * * *
90609 ATGAACTCTAC-CTGGAAATGTTGATCCATCAAGTGATGGATTC-GAACAAAAGATTAAACAAGT
63 ATGAACT-TTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAG-GCAAAAGGTTGAACAAGT
90672 TCTTCTCATTATGAACT
126 TCTTCTCATTATGAACT
90689 CTACCTGGAA
Statistics
Matches: 326, Mismatches: 31, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
221 67 0.21
222 168 0.52
223 3 0.01
225 31 0.10
226 57 0.17
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (223 bp):
AAAGATTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCAGATGAGTTCTTCTCATTATG
AACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAGTTCTTC
TCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCTGGAAATG
TTGATCCATCAAGTGATGAATTCGAACA
Found at i:90715 original size:73 final size:73
Alignment explanation
Indices: 90596--90761 Score: 314
Period size: 73 Copynumber: 2.3 Consensus size: 73
90586 TCTTCAGATG
*
90596 AGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGGATTCGAACAAAAG
1 AGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTCGAACAAAAG
90661 ATTAAACA
66 ATTAAACA
90669 AGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTCGAACAAAAG
1 AGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTCGAACAAAAG
*
90734 GTTAAACA
66 ATTAAACA
90742 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
90762 TCCTTTTCCT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 91 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTCGAACAAAAG
ATTAAACA
Found at i:94352 original size:114 final size:114
Alignment explanation
Indices: 94149--94373 Score: 387
Period size: 114 Copynumber: 2.0 Consensus size: 114
94139 AGAATATCAT
* * *
94149 CAAATTTATCTTTTAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
* *
94214 AAGAACACTTCCAGAAGATTCTATTGGATCTTCTTATTTCTACTATAAG
66 AAGAACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATAAG
94263 CAAATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
* *
94328 AAGAATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTAT
66 AAGAACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTAT
94374 GAGAACGTGG
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 104 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (114 bp):
CAAATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
AAGAACACTTCCAGAAGATGCTATTGGATCTCCTTATTTCTACTATAAG
Found at i:98444 original size:12 final size:12
Alignment explanation
Indices: 98429--98456 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
98419 ACAAACATAA
98429 AAATGCAAATGT
1 AAATGCAAATGT
98441 AAATGCAAATGT
1 AAATGCAAATGT
98453 AAAT
1 AAAT
98457 ATGTTAATGT
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:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:98455 original size:26 final size:26
Alignment explanation
Indices: 98397--98455 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
98387 AAATGTAATT
98397 ATGTAAAAATGAAAATGTAAATACAA
1 ATGTAAAAATGAAAATGTAAATACAA
** * *
98423 ACATAAAAATGCAAATGTAAATGCAA
1 ATGTAAAAATGAAAATGTAAATACAA
98449 ATGTAAA
1 ATGTAAA
98456 TATGTTAATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.59, C:0.07, G:0.12, T:0.22
Consensus pattern (26 bp):
ATGTAAAAATGAAAATGTAAATACAA
Found at i:98549 original size:7 final size:7
Alignment explanation
Indices: 98515--98556 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
98505 ATAAAAGTAT
98515 AAATGCA
1 AAATGCA
* *
98522 CAATGAA
1 AAATGCA
98529 AAATGCA
1 AAATGCA
98536 AAGATGCA
1 AA-ATGCA
98544 AAATGC-
1 AAATGCA
98550 AAATGCA
1 AAATGCA
98557 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:100077 original size:26 final size:28
Alignment explanation
Indices: 100048--100105 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
100038 AACATTAATA
*
100048 AAAATAAT-A-TACATATAAATATTATG
1 AAAATAATAAGTACATATAAAAATTATG
* *
100074 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAATAAGTACATATAAAAATTATG
100102 AAAA
1 AAAA
100106 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATAATAAGTACATATAAAAATTATG
Found at i:100150 original size:6 final size:7
Alignment explanation
Indices: 100131--100155 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
100121 TAAATATATG
100131 AATTTTT
1 AATTTTT
100138 AATTTTT
1 AATTTTT
100145 AATTTTT
1 AATTTTT
100152 AATT
1 AATT
100156 AATAGAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:100838 original size:15 final size:15
Alignment explanation
Indices: 100820--100860 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
100810 TTAATATTGA
100820 AAAATAATATATATT
1 AAAATAATATATATT
100835 AAAAT-ATGAT-TATT
1 AAAATAAT-ATATATT
100849 AAAAGTAATATA
1 AAAA-TAATATA
100861 GGATTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 10 0.45
15 10 0.45
16 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (15 bp):
AAAATAATATATATT
Found at i:100912 original size:2 final size:2
Alignment explanation
Indices: 100905--100944 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
100895 AAATATTATT
*
100905 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA T- TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
100945 AATAATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:100922 original size:15 final size:15
Alignment explanation
Indices: 100904--100944 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
100894 CAAATATTAT
100904 TTATATATATATATA
1 TTATATATATATATA
100919 TTATATATATATATA
1 TTATATATATATATA
*
100934 TTATATTTATA
1 TTATATATATA
100945 AATAATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATATATATATATA
Found at i:100939 original size:13 final size:13
Alignment explanation
Indices: 100907--100932 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
100897 ATATTATTTA
100907 TATATATATATAT
1 TATATATATATAT
100920 TATATATATATAT
1 TATATATATATAT
100933 ATTATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:102428 original size:3 final size:3
Alignment explanation
Indices: 102422--102496 Score: 141
Period size: 3 Copynumber: 24.7 Consensus size: 3
102412 ATTTATTATT
102422 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
102470 TAA TAA TAA TAAA TAA TAA TAA TAA TA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TA
102497 TAAGCAAATG
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:103391 original size:7 final size:7
Alignment explanation
Indices: 103381--103411 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
103371 ATAAAATGAA
103381 AAATTTT
1 AAATTTT
103388 AAATTTT
1 AAATTTT
103395 AAATTTT
1 AAATTTT
103402 AAATTTT
1 AAATTTT
103409 AAA
1 AAA
103412 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AAATTTT
Found at i:103498 original size:16 final size:15
Alignment explanation
Indices: 103465--103506 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
103455 TGTTAAATTT
103465 TAAAAGAAATAAAAAA
1 TAAAAGAAA-AAAAAA
*
103481 TAAAAGAAAAAAGTAA
1 TAAAAGAAAAAA-AAA
103497 TAAAA-AAAAA
1 TAAAAGAAAAA
103507 TTAAAGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (15 bp):
TAAAAGAAAAAAAAA
Found at i:103502 original size:57 final size:57
Alignment explanation
Indices: 103395--103503 Score: 141
Period size: 56 Copynumber: 1.9 Consensus size: 57
103385 TTTAAATTTT
* * * *
103395 AAATTTTAAATTTTAAAAAGAAAAATGAAATAAAATAAAATAAATAAAAAATGAAGA
1 AAATGTTAAATTTTAAAAAGAAAAATAAAATAAAAGAAAAAAAATAAAAAATGAAGA
103452 AAATGTTAAATTTT-AAAAGAAATAA-AAAATAAAAGAAAAAAGTAATAAAAAA
1 AAATGTTAAATTTTAAAAAGAAA-AATAAAATAAAAGAAAAAA--AATAAAAAA
103504 AAATTAAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
56 21 0.47
57 15 0.33
58 9 0.20
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (57 bp):
AAATGTTAAATTTTAAAAAGAAAAATAAAATAAAAGAAAAAAAATAAAAAATGAAGA
Found at i:106942 original size:33 final size:34
Alignment explanation
Indices: 106894--106986 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 34
106884 GGCATAATTC
*
106894 ATGCCAATAATGCACCCATATGCATTATTC-TTT
1 ATGCCGATAATGCACCCATATGCATTATTCTTTT
*
106927 ATGCTGATAATGCACCCATATGCATTATTCTTTT
1 ATGCCGATAATGCACCCATATGCATTATTCTTTT
*
106961 ATGCCGATGATGCACCCATATGCATT
1 ATGCCGATAATGCACCCATATGCATT
106987 TCAGCTAGGG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (34 bp):
ATGCCGATAATGCACCCATATGCATTATTCTTTT
Found at i:107091 original size:46 final size:46
Alignment explanation
Indices: 107039--107135 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
107029 ATTATTCTTT
*
107039 TATTCATTCATTTTAGAGTAGTTCATACTCTAAAATTCATTCATAA
1 TATTCATTCATTTTAGAGTAGTTCATACTCTAAAACTCATTCATAA
107085 TATTCATTCATTTTAGAGTAGTTCATACTCTAAAACTCATTCATAA
1 TATTCATTCATTTTAGAGTAGTTCATACTCTAAAACTCATTCATAA
107131 TATTC
1 TATTC
107136 TTTCCATACA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.43
Consensus pattern (46 bp):
TATTCATTCATTTTAGAGTAGTTCATACTCTAAAACTCATTCATAA
Found at i:109909 original size:17 final size:18
Alignment explanation
Indices: 109887--109923 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
109877 ATGCAAATGA
109887 AAAAAATGAAA-GAAAAC
1 AAAAAATGAAAGGAAAAC
109904 AAAAAATGAAAGGAAAAC
1 AAAAAATGAAAGGAAAAC
109922 AA
1 AA
109924 GTTAGTAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAAATGAAAGGAAAAC
Found at i:111791 original size:15 final size:14
Alignment explanation
Indices: 111773--111819 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
111763 ATCATATGAA
*
111773 ATGTGATAGAGAGCT
1 ATGTGATA-AGAACT
111788 ATGTGA-AAGAACT
1 ATGTGATAAGAACT
*
111801 ATGTGATATGAA-T
1 ATGTGATAAGAACT
111814 ATGTGA
1 ATGTGA
111820 ATGTATAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 18 0.62
14 5 0.17
15 6 0.21
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (14 bp):
ATGTGATAAGAACT
Found at i:112229 original size:2 final size:2
Alignment explanation
Indices: 112218--112254 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
112208 ATGTACATGA
112218 AT AT AT -T 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
112255 GAATATCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:117813 original size:5 final size:5
Alignment explanation
Indices: 117803--117834 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
117793 GGAAAATATT
117803 AAATA AAATA AAATA AAATA AAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
117835 ATGAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Done.