Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009622.1 Hibiscus syriacus cultivar Beakdansim tig00117011_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: 790348
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 4
Found at i:281234 original size:20 final size:20
Alignment explanation
Indices: 281204--281246 Score: 72
Period size: 18 Copynumber: 2.2 Consensus size: 20
281194 AGAGAAAAAG
281204 AAAAGAAAAAAAAAG--GAA
1 AAAAGAAAAAAAAAGAAGAA
281222 AAAAGAAAAAAAAAGAAGAA
1 AAAAGAAAAAAAAAGAAGAA
281242 AAAAG
1 AAAAG
281247 GGGGGTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 15 0.65
20 8 0.35
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAAGAAGAA
Found at i:281243 original size:11 final size:10
Alignment explanation
Indices: 281196--281246 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
281186 ATGCTTGAAG
281196 AGAAAAAGAAA
1 AGAAAAA-AAA
281207 AGAAAAAAAA
1 AGAAAAAAAA
*
281217 AG--GAAAAA
1 AGAAAAAAAA
281225 AGAAAAAAAA
1 AGAAAAAAAA
*
281235 AGAAGAAAAA
1 AGAAAAAAAA
281245 AG
1 AG
281247 GGGGGTCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 7 0.20
10 21 0.60
11 7 0.20
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:281585 original size:16 final size:16
Alignment explanation
Indices: 281564--281603 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
281554 TACAATTTCT
281564 ATTTATTTCAAG-TTCA
1 ATTTATTT-AAGATTCA
*
281580 ATTTATTTGAGATTCA
1 ATTTATTTAAGATTCA
281596 ATTTATTT
1 ATTTATTT
281604 TCGAAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (16 bp):
ATTTATTTAAGATTCA
Found at i:282565 original size:83 final size:83
Alignment explanation
Indices: 282425--282927 Score: 862
Period size: 83 Copynumber: 6.0 Consensus size: 83
282415 AGAAGACTCA
* *
282425 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACAAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATT
282490 TGAAAGATGAATGTGCTC
66 TGAAAGATGAATGTGCTC
* * * *
282508 ATAGCATCTTCTGGAAGTGTACTTTGAGTTATCTGATCTAGTTTGGCAGAACCAATCATTGAAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATT
282573 TGAAAGATGAATGTGCTC
66 TGAAAGATGAATGTGCTC
* *
282591 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATT
282656 TGAAAGATGAATGTGCTC
66 TGAAAGATGAATGTGCTC
*
282674 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATT
282739 TGAAAGATGAATGTGCTC
66 TGAAAGATGAATGTGCTC
*
282757 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATT
*
282822 TGAAAGATGAATGTGCCC
66 TGAAAGATGAATGTGCTC
* *
282840 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCGATCATTGAAT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAAT
* *
282905 TTAAAAGATGAATTTGCTC
65 TTGAAAGATGAATGTGCTC
282924 ATAG
1 ATAG
282928 TAGAAATAAG
Statistics
Matches: 405, Mismatches: 14, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
83 326 0.80
84 79 0.20
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACCAATCATTGAATT
TGAAAGATGAATGTGCTC
Found at i:284068 original size:113 final size:115
Alignment explanation
Indices: 283714--284168 Score: 516
Period size: 113 Copynumber: 4.0 Consensus size: 115
283704 TAGCAAAGAT
** * ***
283714 TTAAATCCATCATTCAATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAA-C-TCATCT
1 TTAAATCCATCATTTGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACCGTCATCT
*
283777 GAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTTAACCCTTTTGC
66 GAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CCTTTTGC
* * * ***
283828 TTGAATTCATCATTTGATGGATCAGCAGCACCA-AGGAGAGTTCATAATGAGAAGAACTCGTCAT
1 TTAAATCCATCATTTGATGGATCAACATTTCCAGA-GAGAGTTCATAATGAGAAGAAC-CGTCAT
* * * * *
283892 CTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGC
64 CTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
* * * *
283944 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA-C-TCATCT
1 TTAAATCCATCATTTGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACCGTCATCT
* * * *
284007 GAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 GAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
* * *
284057 TTAAATTCATCATTTGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCAT
1 TTAAATCCATCATTTGATGGATCAACATTTCCAGAG-AGAGTTCATAATGAGAAGAAC-CGTCAT
* *
284121 CT---GAA-GAAGAAGAAGTTCATAATAAGAAGAGCTTGTTCAACTTTTTGC
64 CTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
284169 ATAATTCTAT
Statistics
Matches: 288, Mismatches: 44, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
112 38 0.13
113 101 0.35
114 44 0.15
115 1 0.00
116 60 0.21
117 44 0.15
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (115 bp):
TTAAATCCATCATTTGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACCGTCATCT
GAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
Found at i:284287 original size:84 final size:82
Alignment explanation
Indices: 284133--284316 Score: 208
Period size: 84 Copynumber: 2.2 Consensus size: 82
284123 GAAGAAGAAG
* * * * * *
284133 AAGTTCATAATAAGAAGAGCTTGTTCAACTTTTTGCATAATTCTATCACAGAAGGAGATAGATTA
1 AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAAAAAGATCA
*
284198 GCATCAGCCTTTCCAG-AGA
66 ACATCAGCC---CCAGTAGA
* * * * *
284217 AAGTTCATAATGAGAAGAGCTTATTTAACCTTTTGGATGACTCTATCACAGAAGGAAAAAGGTCA
1 AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAAAAAGATCA
* *
284282 ACATCATCCCCAGTGGA
66 ACATCAGCCCCAGTAGA
284299 AAGTTCATAATAAGAAGA
1 AAGTTCATAATAAGAAGA
284317 ACTCATCTGA
Statistics
Matches: 84, Mismatches: 15, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
81 4 0.05
82 19 0.23
84 61 0.73
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (82 bp):
AAGTTCATAATAAGAAGAGCTTATTCAACCTTTTGCATAACTCTATCACAGAAGGAAAAAGATCA
ACATCAGCCCCAGTAGA
Found at i:284490 original size:3 final size:3
Alignment explanation
Indices: 284482--284565 Score: 123
Period size: 3 Copynumber: 28.0 Consensus size: 3
284472 CCATATTGAT
* * * *
284482 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TAA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
284530 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
284566 AATATATTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:286012 original size:16 final size:16
Alignment explanation
Indices: 285991--286041 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
285981 ATATAATGAA
285991 TAATAATTTATTTTTT
1 TAATAATTTATTTTTT
*
286007 TAATAAATTA--TTTT
1 TAATAATTTATTTTTT
*
286021 AAAT-ATTTATTTTTT
1 TAATAATTTATTTTTT
286036 TCAATA
1 T-AATA
286042 TCGAAGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
13 4 0.15
14 7 0.26
15 4 0.15
16 12 0.44
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATAATTTATTTTTT
Found at i:293051 original size:23 final size:25
Alignment explanation
Indices: 293000--293056 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
292990 CAAGGAATGT
* *
293000 GTCACAAGAACAGTGAAAAAACGTA
1 GTCACAAAAACAGAGAAAAAACGTA
293025 -TCACAAAAACAGAG-AAAAACG-A
1 GTCACAAAAACAGAGAAAAAACGTA
293047 GTCACAAAAA
1 GTCACAAAAA
293057 TAAATATTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 1 0.03
23 16 0.55
24 12 0.41
ACGTcount: A:0.58, C:0.18, G:0.16, T:0.09
Consensus pattern (25 bp):
GTCACAAAAACAGAGAAAAAACGTA
Found at i:293993 original size:21 final size:21
Alignment explanation
Indices: 293969--294011 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
293959 ATGCTTTTAA
*
293969 ATAATTTTATTTTTATTTTTT
1 ATAATTTTATTTTTATATTTT
293990 ATAATTTTATTTTTATATTTT
1 ATAATTTTATTTTTATATTTT
294011 A
1 A
294012 AAAATTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
ATAATTTTATTTTTATATTTT
Found at i:294011 original size:13 final size:14
Alignment explanation
Indices: 293973--294011 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
293963 TTTTAAATAA
293973 TTTTAT-TTTTATT
1 TTTTATATTTTATT
293986 TTTTATAATTTTA-T
1 TTTTAT-ATTTTATT
294000 TTTTATATTTTA
1 TTTTATATTTTA
294012 AAAATTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 7 0.29
15 5 0.21
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATATTTTATT
Found at i:299554 original size:22 final size:21
Alignment explanation
Indices: 299529--299571 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
299519 TATTTAAAAC
*
299529 AAGAGATTTAAATATATAATCT
1 AAGAGATATAAAT-TATAATCT
*
299551 AAGAGATATAAATTATTATCT
1 AAGAGATATAAATTATAATCT
299572 TAAAGCTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (21 bp):
AAGAGATATAAATTATAATCT
Found at i:300905 original size:26 final size:25
Alignment explanation
Indices: 300849--300905 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
300839 AATGAATATG
*
300849 ATTATAAAATTTTAAGAAATGATAA
1 ATTATAAAATTTTAAGAAATAATAA
300874 ATTTATAAAATTTTAGAAGAAA-AATAA
1 A-TTATAAAATTTT--AAGAAATAATAA
300901 ATTAT
1 ATTAT
300906 TAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 1 0.04
26 16 0.57
27 5 0.18
28 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (25 bp):
ATTATAAAATTTTAAGAAATAATAA
Found at i:302492 original size:17 final size:17
Alignment explanation
Indices: 302470--302514 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
302460 GCTAGTTTGT
302470 TCAATGAACTAGT-TAAA
1 TCAATGAACTAGTGT-AA
*
302487 TGAATGAACTAGTGTAA
1 TCAATGAACTAGTGTAA
302504 TCAATGAACTA
1 TCAATGAACTA
302515 ACTTTATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 24 0.96
18 1 0.04
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (17 bp):
TCAATGAACTAGTGTAA
Found at i:302595 original size:34 final size:34
Alignment explanation
Indices: 302506--302583 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
302496 TAGTGTAATC
* * *
302506 AATGAACTAACTTTATTAGATGGA-CTAAATGCATG
1 AATGAACTAGC-TTATTAAAT-GATCTAAATGCATA
*
302541 AATGAAGTAGCTTATTAAATGATCTAAATGCATA
1 AATGAACTAGCTTATTAAATGATCTAAATGCATA
302575 AATGAACTA
1 AATGAACTA
302584 CTTCCATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 2 0.05
34 26 0.70
35 9 0.24
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (34 bp):
AATGAACTAGCTTATTAAATGATCTAAATGCATA
Found at i:309325 original size:20 final size:20
Alignment explanation
Indices: 309300--309350 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
309290 ATCAGCATCG
309300 ATACCGAAGGGGGAGTATCA
1 ATACCGAAGGGGGAGTATCA
* **
309320 ATACCGAAAGGGGAGTATTG
1 ATACCGAAGGGGGAGTATCA
309340 ATACCGAAGGG
1 ATACCGAAGGG
309351 AAGGTATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.14, G:0.35, T:0.16
Consensus pattern (20 bp):
ATACCGAAGGGGGAGTATCA
Found at i:309357 original size:20 final size:20
Alignment explanation
Indices: 309299--309364 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
309289 AATCAGCATC
* * *
309299 GATACCGAAGGGGGAGTATC
1 GATACCGAAAGGGAAGTATT
* *
309319 AATACCGAAAGGGGAGTATT
1 GATACCGAAAGGGAAGTATT
309339 GATACCG-AAGGGAAGGTATT
1 GATACCGAAAGGGAA-GTATT
309359 GATACC
1 GATACC
309365 ATTTTGAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.15
20 34 0.85
ACGTcount: A:0.35, C:0.14, G:0.33, T:0.18
Consensus pattern (20 bp):
GATACCGAAAGGGAAGTATT
Found at i:309457 original size:19 final size:19
Alignment explanation
Indices: 309388--309466 Score: 106
Period size: 19 Copynumber: 4.2 Consensus size: 19
309378 ATGAAAAATG
*
309388 GTATCGATGCCACA-TCATA
1 GTATCGATGCCATAGT-ATA
*
309407 GTATCGATGCCATAGCATA
1 GTATCGATGCCATAGTATA
309426 GTATCGATGCCATAGTATA
1 GTATCGATGCCATAGTATA
* *
309445 GTATCGGTACCATAGTATA
1 GTATCGATGCCATAGTATA
309464 GTA
1 GTA
309467 GTATCGATAC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (19 bp):
GTATCGATGCCATAGTATA
Found at i:309910 original size:55 final size:55
Alignment explanation
Indices: 309821--309979 Score: 257
Period size: 55 Copynumber: 2.9 Consensus size: 55
309811 CTATGTGTAC
*
309821 TACAGGCACTGTGTATGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTGTGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
*
309876 TACATGCACTGTGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
1 TACAGGCACTGTGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
* * * *
309931 TACAGGCACTATATGTGC-AACCCACGGAATTCATCATGAGTTGATGAAT
1 TACAGGCACTGTGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAAT
309980 TACTATATAG
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
54 29 0.30
55 68 0.70
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (55 bp):
TACAGGCACTGTGTGTGCAAATCCATGGAATTCATCATGAGTTGATGAATAACCG
Found at i:310767 original size:82 final size:83
Alignment explanation
Indices: 310594--310767 Score: 228
Period size: 82 Copynumber: 2.1 Consensus size: 83
310584 AAATCAATCT
* * *
310594 TCATTGCATGCCTCCTTGTTATGACGTGAGTAACCTTCAAAAATATAATAAATAAGGCCTTGAAT
1 TCATTGCATGCCTCCTTGTTATGACGTGAATAACCTTCAAAAAGATAATAAATAAGGCCTCGAAT
* * *
310659 GCAAGGTTTGAATGCTTG
66 ACAAGGTTTAAAGGCTTG
* * *
310677 -CTATTGCATGTCTCCTTGTTA-GAACGTGAATAGCCTTC-AAAAGATGATAAATAAGGCCTCGA
1 TC-ATTGCATGCCTCCTTGTTATG-ACGTGAATAACCTTCAAAAAGATAATAAATAAGGCCTCGA
310739 ATACAAGGTTTAAAGGCTTG
64 ATACAAGGTTTAAAGGCTTG
310759 TCATTGCAT
1 TCATTGCAT
310768 ATTTCAAGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
82 47 0.59
83 32 0.41
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (83 bp):
TCATTGCATGCCTCCTTGTTATGACGTGAATAACCTTCAAAAAGATAATAAATAAGGCCTCGAAT
ACAAGGTTTAAAGGCTTG
Found at i:311043 original size:17 final size:17
Alignment explanation
Indices: 311023--311061 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
311013 GTTTGTTCAG
*
311023 TGAACTAGT-TAAATGAA
1 TGAACTAGTGT-AATCAA
311040 TGAACTAGTGTAATCAA
1 TGAACTAGTGTAATCAA
311057 TGAAC
1 TGAAC
311062 CAACTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.44, C:0.10, G:0.18, T:0.28
Consensus pattern (17 bp):
TGAACTAGTGTAATCAA
Found at i:312118 original size:2 final size:2
Alignment explanation
Indices: 312113--312140 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
312103 ATATATATAT
312113 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
312141 TTGGGTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:314198 original size:2 final size:2
Alignment explanation
Indices: 314191--314249 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
314181 TGCCTGCTAA
314191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
314233 AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT A
314250 ATCATGGCTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:314461 original size:21 final size:20
Alignment explanation
Indices: 314375--314532 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
314365 AAATGACCAA
**
314375 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
314394 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
314414 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
314434 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
314455 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
314476 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
314496 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
314517 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
314533 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:314523 original size:20 final size:20
Alignment explanation
Indices: 314499--314808 Score: 343
Period size: 20 Copynumber: 15.5 Consensus size: 20
314489 CGATTTTCCA
** *
314499 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
314519 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
314539 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
314559 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
314579 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
314599 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
314619 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
314639 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
314659 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
314679 AAATCGCAACGCTAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
314699 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
314719 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
314739 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
314759 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
314779 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
314799 AAATCACAAC
1 AAATCGCAAC
314809 ACTGAAATTT
Statistics
Matches: 254, Mismatches: 34, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
20 253 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:315530 original size:24 final size:24
Alignment explanation
Indices: 315491--315537 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
315481 AAATTTGGTC
315491 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
315515 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
315538 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:317468 original size:33 final size:33
Alignment explanation
Indices: 317417--317704 Score: 201
Period size: 33 Copynumber: 8.2 Consensus size: 33
317407 CGGAAATTAC
* *
317417 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
*
317450 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * *
317484 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
*
317523 AAT-GCGAA-ATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAAGAAAATCGCAATGCGAAATGAA
317555 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C---AA-GAAAATCGCAATGCGAAATGAA
* * *
317594 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
*
317633 AAT-GCGAA-ATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAAGAAAATCGCAATGCGAAATGAA
* * *
317665 AATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
317698 AATCGCA
1 AATCGCA
317705 TTGTGATTCT
Statistics
Matches: 208, Mismatches: 23, Indels: 48
0.75 0.08 0.17
Matches are distributed among these distances:
31 2 0.01
32 16 0.08
33 81 0.39
34 17 0.08
36 1 0.00
38 28 0.13
39 61 0.29
40 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:317500 original size:19 final size:19
Alignment explanation
Indices: 317431--317704 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
317421 GCAACGAGAG
317431 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
317450 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
317464 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
317484 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
317503 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
317517 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
317536 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
317555 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
317575 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
317594 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
317613 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
317627 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
317646 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
317665 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
317679 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
317698 AATCGCA
1 AATCGCA
317705 TTGTGATTCT
Statistics
Matches: 224, Mismatches: 9, Indels: 44
0.81 0.03 0.16
Matches are distributed among these distances:
14 40 0.18
15 5 0.02
16 7 0.03
17 7 0.03
18 3 0.01
19 129 0.58
20 33 0.15
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:317554 original size:52 final size:52
Alignment explanation
Indices: 317431--317704 Score: 440
Period size: 52 Copynumber: 5.1 Consensus size: 52
317421 GCAACGAGAG
* * *
317431 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
317484 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
317536 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAA
317594 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
317646 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
317698 AATCGCA
1 AATCGCA
317705 TTGTGATTCT
Statistics
Matches: 209, Mismatches: 6, Indels: 13
0.92 0.03 0.06
Matches are distributed among these distances:
52 114 0.55
53 42 0.20
54 1 0.00
55 2 0.01
56 1 0.00
57 1 0.00
58 48 0.23
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:317759 original size:19 final size:19
Alignment explanation
Indices: 317719--317816 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
317709 GATTCTCCCG
317719 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
317739 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
317758 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
317772 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
317791 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
317810 TTGCGAT
1 TTGCGAT
317817 AGTCAATTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 35 0.50
20 15 0.21
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:317767 original size:53 final size:52
Alignment explanation
Indices: 317700--317816 Score: 198
Period size: 53 Copynumber: 2.2 Consensus size: 52
317690 GAAATTAAAA
*
317700 TCGCATTGTGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
* *
317753 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTTATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
317805 TCGCATTGCGAT
1 TCGCATTGCGAT
317817 AGTCAATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 29 0.48
53 32 0.52
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:317942 original size:14 final size:14
Alignment explanation
Indices: 317923--317959 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
317913 CATCAATTAC
317923 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
317937 ACAAATCATCTTTT
1 ACAAATCAACTTTT
317951 ACAAATCAA
1 ACAAATCAA
317960 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:319959 original size:14 final size:14
Alignment explanation
Indices: 319940--319996 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
319930 GCGAAATGAA
*
319940 AATCGCAACGACAG
1 AATCGCAACGAAAG
319954 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
319971 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
319987 AATCGCAACG
1 AATCGCAACG
319997 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:319967 original size:33 final size:33
Alignment explanation
Indices: 319921--320013 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
319911 GCGAAACCAA
*
319921 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
319954 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
319987 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
320014 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:319978 original size:19 final size:19
Alignment explanation
Indices: 319884--320018 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
319874 TAGTTTACTT
* *
319884 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
319904 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
319923 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
319942 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
319956 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
319975 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
319989 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
320008 TCGCAATGCGA
1 TCGCAACGCGA
320019 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:320036 original size:19 final size:19
Alignment explanation
Indices: 320014--320142 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
320004 AAAATCGCAA
320014 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
320033 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
320047 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
320066 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
320080 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
320099 TGCGATGTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
320118 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
320138 TGCGA
1 TGCGA
320143 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 46 0.52
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:320056 original size:33 final size:33
Alignment explanation
Indices: 320014--320104 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
320004 AAAATCGCAA
320014 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
320047 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
320080 TGCGATTTTCATTTCGCGTTGCGAT
1 TGCGATTTTGGTTTCGCGTTGCGAT
320105 GTTGGTTTCG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:320306 original size:93 final size:93
Alignment explanation
Indices: 320190--320565 Score: 736
Period size: 93 Copynumber: 4.1 Consensus size: 93
320180 ATGGATTGTA
320190 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
320254 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
320282 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
320347 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
320375 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
320440 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
320468 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
320533 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
320561 TTACT
1 TTACT
320566 AAGCAATCTA
Statistics
Matches: 282, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 278 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:322290 original size:14 final size:14
Alignment explanation
Indices: 322271--322360 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
322261 TTGAAATGAA
322271 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
322285 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
322304 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
322318 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
322337 AATCGCAACGAGAG
1 AATCGCAACGAGAG
322351 AATCGCAACG
1 AATCGCAACG
322361 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:322303 original size:33 final size:33
Alignment explanation
Indices: 322263--322377 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
322253 TCTTTTGGTT
322263 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
322296 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
322329 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
322362 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
322378 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:322309 original size:19 final size:19
Alignment explanation
Indices: 322285--322382 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
322275 GCAACGAGAG
322285 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
322304 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
322318 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
322337 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
322351 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
322370 AATCGCAATGCGA
1 AATCGCAACGCGA
322383 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:322413 original size:14 final size:14
Alignment explanation
Indices: 322394--322450 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
322384 TTTGGTTTCG
322394 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
322408 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
322427 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
322441 CGTTGCGATT
1 CGTTGCGATT
322451 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:322426 original size:33 final size:33
Alignment explanation
Indices: 322378--322458 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
322368 AAAATCGCAA
**
322378 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
322411 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
322444 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
322459 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:322483 original size:23 final size:21
Alignment explanation
Indices: 322435--322490 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
322425 CGCGTTGCGA
322435 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
322456 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
322477 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
322491 CTCTTCTGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.11, C:0.23, G:0.16, T:0.50
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:322612 original size:33 final size:33
Alignment explanation
Indices: 322570--322640 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
322560 AATACTAACT
*
322570 TGAAAATCGCAACGAGAGAATAGCAACGCAAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCAAAA
* * *
322603 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCAAAA
322636 TGAAA
1 TGAAA
322641 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCAAAA
Found at i:322874 original size:22 final size:22
Alignment explanation
Indices: 322822--322876 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
322812 TGGTTGTGAG
**
322822 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
322844 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
322866 GGATTTCTTCG
1 GGATTTCTTCG
322877 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:323048 original size:20 final size:20
Alignment explanation
Indices: 323023--323176 Score: 159
Period size: 20 Copynumber: 7.7 Consensus size: 20
323013 CTTTAAATAT
323023 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
323043 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
323065 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
323084 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
323104 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
323124 CGCGTTACGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
323144 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
323164 CGCGTTGCGATTT
1 CGCGTTGCGATTT
323177 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.83
21 15 0.14
22 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:323150 original size:40 final size:40
Alignment explanation
Indices: 323022--323176 Score: 177
Period size: 40 Copynumber: 3.9 Consensus size: 40
323012 GCTTTAAATA
*
323022 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
323063 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* * *
323103 ACACGTTGCGATTTACGGATACGCGTTACGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
323143 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
323177 TGGAAAATCG
Statistics
Matches: 94, Mismatches: 18, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
40 64 0.68
41 30 0.32
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:323193 original size:21 final size:21
Alignment explanation
Indices: 323143--323262 Score: 93
Period size: 21 Copynumber: 5.8 Consensus size: 21
323133 ATTTATGTGT
* * *
323143 TCGCGTTGCGATTTT-CATAT
1 TCGCATTGCGATTTTGCAAAA
* *
323163 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGCAAAA
* * * **
323184 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGCAAAA
323205 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGCAA-AA
*
323226 TCGCGTTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGCAA-AA
*
323247 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
323263 GAAACTGATT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.20
21 66 0.80
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTGCAAAA
Found at i:323236 original size:42 final size:42
Alignment explanation
Indices: 323143--323262 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
323133 ATTTATGTGT
* *
323143 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTTTGCAAAA
**
323184 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTTTGCAA-AA
* * *
323226 TCGCGTTGCG-ATTTTCAAGAATCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTTC-ATATTCGCATTGCGATTTTG
323263 GAAACTGATT
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
40 1 0.02
41 15 0.24
42 44 0.70
43 3 0.05
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTTTGCAAAA
Found at i:323506 original size:2 final size:2
Alignment explanation
Indices: 323499--323548 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
323489 ACAACTAACA
323499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
323541 AT AT AT AT
1 AT AT AT AT
323549 CTTTCGTCAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:339000 original size:2 final size:2
Alignment explanation
Indices: 338993--339113 Score: 90
Period size: 2 Copynumber: 67.0 Consensus size: 2
338983 AACTAAAGTA
*
338993 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T TT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
339032 AT AA AT A- AT AT GAT -T AT AT -T AT AT -T AT A- AT -T TT AT A-
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
339068 AT AT A- AT AT -T A- AT AT AT AT AT AT AT AT AT AT -T AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
339106 TT AT AT AT
1 AT AT AT AT
339114 GATTTATAAT
Statistics
Matches: 98, Mismatches: 6, Indels: 30
0.73 0.04 0.22
Matches are distributed among these distances:
1 14 0.14
2 82 0.84
3 2 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:339066 original size:13 final size:14
Alignment explanation
Indices: 338991--339111 Score: 67
Period size: 13 Copynumber: 8.9 Consensus size: 14
338981 AAAACTAAAG
*
338991 TAATATATATA-TA
1 TAATATTTATATTA
*
339004 T-ATATATATATATA
1 TAATATTTATAT-TA
339018 TAATATTT-TA-TA
1 TAATATTTATATTA
* * *
339030 TAATAAATAATATGA
1 TAAT-ATTTATATTA
*
339045 TTATA-TTATATTA
1 TAATATTTATATTA
*
339058 TAAT-TTTATAATA
1 TAATATTTATATTA
*
339071 TAATATTAATATATA
1 TAATATTTATAT-TA
*
339086 TATATATATATATTA
1 TA-ATATTTATATTA
*
339101 T-ATTTTTATAT
1 TAATATTTATAT
339112 ATGATTTATA
Statistics
Matches: 83, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
12 15 0.18
13 31 0.37
14 13 0.16
15 16 0.19
16 8 0.10
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (14 bp):
TAATATTTATATTA
Found at i:339544 original size:22 final size:23
Alignment explanation
Indices: 339500--339544 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
339490 AGGTTTATGG
*
339500 TTTGTTTGGGATTTTAGGATTTT
1 TTTGTTTGGGAATTTAGGATTTT
*
339523 TTTG-TTGGGAATTT-GGGTTTT
1 TTTGTTTGGGAATTTAGGATTTT
339544 T
1 T
339545 AGGATTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 9 0.45
23 4 0.20
ACGTcount: A:0.11, C:0.00, G:0.29, T:0.60
Consensus pattern (23 bp):
TTTGTTTGGGAATTTAGGATTTT
Found at i:345303 original size:103 final size:103
Alignment explanation
Indices: 345120--345337 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
345110 TAATTTCCAT
*
345120 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
345185 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AACCTCACACATGTTCCAAAGAATACATATATGTCCCA
*
345223 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
345288 AACCTCACACGTGTTCCAAAGAATACATATATGTCCTA
66 AACCTCACACATGTTCCAAAGAATACATATATGTCCCA
345326 AAGGACCACATA
1 AAGGACCACATA
345338 GACCCTTTAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
AACCTCACACATGTTCCAAAGAATACATATATGTCCCA
Found at i:349592 original size:21 final size:21
Alignment explanation
Indices: 349562--349612 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
349552 CGCTTCGAAA
* * *
349562 ACAAGTCCCAGCAGCCATCTG
1 ACAAGCCCCAGCAACCATCCG
349583 ACAAGCCCCAGCAACCATCCG
1 ACAAGCCCCAGCAACCATCCG
349604 ACAAGCCCC
1 ACAAGCCCC
349613 GGAATGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.45, G:0.16, T:0.08
Consensus pattern (21 bp):
ACAAGCCCCAGCAACCATCCG
Found at i:351342 original size:23 final size:23
Alignment explanation
Indices: 351316--351368 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
351306 ATTGCATCTA
351316 AGTGCCACATAGAATTGCACCGG
1 AGTGCCACATAGAATTGCACCGG
* * * *
351339 AGTGCCGCGTAGAATTGTACCGT
1 AGTGCCACATAGAATTGCACCGG
351362 AGTGCCA
1 AGTGCCA
351369 TATAATAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (23 bp):
AGTGCCACATAGAATTGCACCGG
Found at i:356033 original size:3 final size:3
Alignment explanation
Indices: 356025--356052 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
356015 CTCCTCACTC
356025 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
356053 GAGCAGATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:357163 original size:17 final size:20
Alignment explanation
Indices: 357127--357164 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
357117 GAAATAATTT
357127 TTATTATATACTAAATAAAA
1 TTATTATATACTAAATAAAA
357147 TTATTA-ATA-TAAA-AAAA
1 TTATTATATACTAAATAAAA
357164 T
1 T
357165 CAGTATTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 4 0.22
19 3 0.17
20 6 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
TTATTATATACTAAATAAAA
Found at i:359036 original size:14 final size:14
Alignment explanation
Indices: 359013--359068 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
359003 CGTTCGTGAA
359013 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
* *
359027 CGTTCAGTTAT-AT
1 CGTTCGGTTATGTT
*
359040 --TT-GTTTATGTT
1 CGTTCGGTTATGTT
359051 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
359065 CGTT
1 CGTT
359069 TATGTTCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
10 4 0.12
11 3 0.09
13 3 0.09
14 22 0.69
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:359085 original size:38 final size:38
Alignment explanation
Indices: 359013--359088 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
359003 CGTTCGTGAA
* **
359013 CGTTCGGTTATGTTCGTTCAGTTATATTTGTTTATGTT
1 CGTTCGGTTATGTTCGTTCAGTTACATTCATTTATGTT
*
359051 CGTTCGGTTATGTTCGTTTATGTT-CATTCATTTATGTT
1 CGTTCGGTTATGTTCGTTCA-GTTACATTCATTTATGTT
359089 TAACCCAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 30 0.91
39 3 0.09
ACGTcount: A:0.13, C:0.12, G:0.20, T:0.55
Consensus pattern (38 bp):
CGTTCGGTTATGTTCGTTCAGTTACATTCATTTATGTT
Found at i:359086 original size:24 final size:24
Alignment explanation
Indices: 359014--359088 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
359004 GTTCGTGAAC
*
359014 GTTCGGTTATGTTCGTTCAGTTAT
1 GTTCGTTTATGTTCGTTCAGTTAT
* * *
359038 ATTTGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCAGTTAT
* *
359062 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCAGTTAT
359086 GTT
1 GTT
359089 TAACCCAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCAGTTAT
Found at i:360099 original size:16 final size:16
Alignment explanation
Indices: 360078--360128 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
360068 GTCTCCAACG
360078 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
360094 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
360110 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
360124 TTTAT
1 TTTAT
360129 TAAATGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.15
15 2 0.06
16 26 0.79
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:360211 original size:16 final size:16
Alignment explanation
Indices: 360190--360222 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
360180 AAAAAAATTT
360190 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
360206 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
360222 T
1 T
360223 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:364076 original size:6 final size:6
Alignment explanation
Indices: 364065--364106 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
364055 ATGCATGCGC
*
364065 GCGTGT GCGTGT GCGTGT GCGTGT GCGTGT GCGTGT GTGTGT
1 GCGTGT GCGTGT GCGTGT GCGTGT GCGTGT GCGTGT GCGTGT
364107 CATATTCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.14, G:0.50, T:0.36
Consensus pattern (6 bp):
GCGTGT
Found at i:372812 original size:23 final size:23
Alignment explanation
Indices: 372786--372854 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
372776 CACCACAGCT
*
372786 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
372809 CGTAGAATTGCACCGGAGTACCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
372832 CGTAGAATTGCACTGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
372855 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:373033 original size:103 final size:104
Alignment explanation
Indices: 372854--373074 Score: 358
Period size: 103 Copynumber: 2.1 Consensus size: 104
372844 CTGTAGTGCC
* *
372854 ATATA-ATAATGT-CCATAAGGAACACATATCATTCCTTAAGAATCATATACATATACTAGGGAT
1 ATATATAT-ATGTCCCATAAGGAACACATATCATTCCTTAAGAATCATATACATATACCAAGGAT
*
372917 CAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
65 CAAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAAA
* *
372957 ATATATATATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATC
1 ATATATATATGTCCCATAAGGAACACATATCATTCCTTAAGAATCATATACATATACCAAGGATC
373021 AAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAAA
66 AAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAAA
*
373060 ATACATATATGTCCC
1 ATATATATATGTCCC
373075 GAATGACTGC
Statistics
Matches: 110, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
103 105 0.95
104 5 0.05
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (104 bp):
ATATATATATGTCCCATAAGGAACACATATCATTCCTTAAGAATCATATACATATACCAAGGATC
AAGTATGTGTCTCACCAGACTTCACACATGTTCCAAAAA
Found at i:374479 original size:20 final size:20
Alignment explanation
Indices: 374438--374513 Score: 107
Period size: 20 Copynumber: 3.7 Consensus size: 20
374428 TTTGCTTGAG
*
374438 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATT-CCC-TTGAAT
*
374460 GGGTATCGATTCCCTTGAAT
1 GGGTACCGATTCCCTTGAAT
374480 GGGTACCGATTCCCTTGAAT
1 GGGTACCGATTCCCTTGAAT
*
374500 CGGTACCGATTCCC
1 GGGTACCGATTCCC
374514 CTTGCCCATA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 38 0.73
21 3 0.06
22 11 0.21
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (20 bp):
GGGTACCGATTCCCTTGAAT
Found at i:376213 original size:16 final size:16
Alignment explanation
Indices: 376174--376216 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
376164 AGCATCAGTT
*
376174 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
376190 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
376207 CTTATCAATC
1 CTTATCAATC
376217 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:378976 original size:23 final size:23
Alignment explanation
Indices: 378950--379018 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
378940 CACCACAGCT
*
378950 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
378973 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
378996 CATAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
379019 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:379150 original size:103 final size:103
Alignment explanation
Indices: 379034--379241 Score: 335
Period size: 103 Copynumber: 2.0 Consensus size: 103
379024 TAATGTCCAT
* * * * *
379034 AAGGACCATATATCATTCCTTAATAATTATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
379099 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
379137 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
379202 GACTTTACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
379240 AA
1 AA
379242 TGACTGCGTA
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:380643 original size:22 final size:21
Alignment explanation
Indices: 380618--380679 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
380608 TTCGCTTGAG
*
380618 GGGTATTGATTCCCCATTGAAT
1 GGGTACTGATTCCCC-TTGAAT
*
380640 GGGTACTGAAT-CCCTTGAAT
1 GGGTACTGATTCCCCTTGAAT
*
380660 GGGTACCGATT-CCCTTGAAT
1 GGGTACTGATTCCCCTTGAAT
380680 CGATATCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 24 0.67
21 3 0.08
22 9 0.25
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (21 bp):
GGGTACTGATTCCCCTTGAAT
Found at i:385530 original size:34 final size:34
Alignment explanation
Indices: 385481--385565 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
385471 GACGCAAAAT
* *
385481 AAAATTTGTATAGAATTTTTTACTTAGATAATAG
1 AAAATTTGTTTAGAATTCTTTACTTAGATAATAG
* * *
385515 AAATTTTTTTTAGAATTCTTTACTTAGATGATAG
1 AAAATTTGTTTAGAATTCTTTACTTAGATAATAG
385549 AAAATTTGTTTAGAATT
1 AAAATTTGTTTAGAATT
385566 GAGCGATGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.47
Consensus pattern (34 bp):
AAAATTTGTTTAGAATTCTTTACTTAGATAATAG
Found at i:391413 original size:23 final size:23
Alignment explanation
Indices: 391379--391448 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
391369 GAGTCGAGGG
*
391379 TTCTACGCGGTCCTTCAGGATAA
1 TTCTACGCGGTCCTTCGGGATAA
* * *
391402 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGATAA
*
391425 TTCTACGCGGTCTTTCGGGATAA
1 TTCTACGCGGTCCTTCGGGATAA
391448 T
1 T
391449 ATTATGTGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.34
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGATAA
Found at i:391431 original size:46 final size:46
Alignment explanation
Indices: 391379--391471 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
391369 GAGTCGAGGG
*
391379 TTCTACGCGGTCCTTCAGGATAAT-TCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCAGGATAATAT-TACGTGGTCCTTAGGGACAT
* * * *
391425 TTCTACGCGGTCTTTCGGGATAATATTATGTGGTCCTTATGGACAT
1 TTCTACGCGGTCCTTCAGGATAATATTACGTGGTCCTTAGGGACAT
391471 T
1 T
391472 CTATGTGGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
46 40 0.98
47 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.37
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCAGGATAATATTACGTGGTCCTTAGGGACAT
Found at i:394387 original size:18 final size:18
Alignment explanation
Indices: 394366--394402 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
394356 GATCAACACC
394366 ATTTAGCACCTCAAACTT
1 ATTTAGCACCTCAAACTT
* *
394384 ATTTAGTACCTTAAACTT
1 ATTTAGCACCTCAAACTT
394402 A
1 A
394403 CACTTAGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (18 bp):
ATTTAGCACCTCAAACTT
Found at i:395153 original size:2 final size:2
Alignment explanation
Indices: 395146--395177 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
395136 AATAATTCAT
395146 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
395178 AAATAACCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:396581 original size:20 final size:20
Alignment explanation
Indices: 396556--396600 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
396546 CAAAACGGTT
396556 AGTTTATACTAAACGCATTA
1 AGTTTATACTAAACGCATTA
396576 AGTTTATACTAAACGCATTA
1 AGTTTATACTAAACGCATTA
396596 AGTTT
1 AGTTT
396601 CTAACAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (20 bp):
AGTTTATACTAAACGCATTA
Found at i:397678 original size:47 final size:47
Alignment explanation
Indices: 397609--397699 Score: 182
Period size: 47 Copynumber: 1.9 Consensus size: 47
397599 CGTAGCCTAT
397609 AGTTTGTGTGTCATAACTCACAATCTAAAATAGTTTTCTTCATTTTC
1 AGTTTGTGTGTCATAACTCACAATCTAAAATAGTTTTCTTCATTTTC
397656 AGTTTGTGTGTCATAACTCACAATCTAAAATAGTTTTCTTCATT
1 AGTTTGTGTGTCATAACTCACAATCTAAAATAGTTTTCTTCATT
397700 CAGTTTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (47 bp):
AGTTTGTGTGTCATAACTCACAATCTAAAATAGTTTTCTTCATTTTC
Found at i:402482 original size:16 final size:16
Alignment explanation
Indices: 402461--402499 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
402451 GGTATTACCC
* *
402461 GACCTGTTTTCAACTT
1 GACCTGTTATCAACCT
*
402477 GACCTGTTATGAACCT
1 GACCTGTTATCAACCT
402493 GACCTGT
1 GACCTGT
402500 AATTAACTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:402674 original size:18 final size:17
Alignment explanation
Indices: 402647--402739 Score: 87
Period size: 18 Copynumber: 5.1 Consensus size: 17
402637 TACTTTTTGA
402647 AATTTAATTTTTATATT
1 AATTTAATTTTTATATT
*
402664 AATTATAATTTGTATATTATA
1 AATT-TAATTT-T-TA-TATT
*
402685 AATTTGATTTTTATATT
1 AATTTAATTTTTATATT
402702 AATTCTAATTCTTTATATT
1 AATT-TAATT-TTTATATT
* *
402721 ATTTATAATTCTTATATT
1 AATT-TAATTTTTATATT
402739 A
1 A
402740 TAATTTTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
17 11 0.17
18 20 0.32
19 18 0.29
20 7 0.11
21 7 0.11
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.59
Consensus pattern (17 bp):
AATTTAATTTTTATATT
Found at i:402689 original size:38 final size:39
Alignment explanation
Indices: 402646--402722 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
402636 TTACTTTTTG
402646 AAATTTAATTTTTATATTAATTATAATT-TGTATATTAT
1 AAATTTAATTTTTATATTAATTATAATTCTGTATATTAT
* * *
402684 AAATTTGATTTTTATATTAATTCTAATTCTTTATATTAT
1 AAATTTAATTTTTATATTAATTATAATTCTGTATATTAT
402723 TTATAATTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 26 0.74
39 9 0.26
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (39 bp):
AAATTTAATTTTTATATTAATTATAATTCTGTATATTAT
Found at i:402699 original size:20 final size:20
Alignment explanation
Indices: 402646--402754 Score: 69
Period size: 18 Copynumber: 5.8 Consensus size: 20
402636 TTACTTTTTG
402646 AAATTTAATTTTTATA-T-T
1 AAATTTAATTTTTATATTAT
*
402664 -AATTATAATTTGTATATTAT
1 AAATT-TAATTTTTATATTAT
*
402684 AAATTTGATTTTTATA-T-T
1 AAATTTAATTTTTATATTAT
402702 -AATTCTAATTCTTTATATTAT
1 AAATT-TAATT-TTTATATTAT
*
402723 ---TTATAATTCTTATATTAT
1 AAATT-TAATTTTTATATTAT
*
402741 -AATTT-TTTTTTATA
1 AAATTTAATTTTTATA
402755 ATCACTAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
17 8 0.11
18 31 0.42
19 16 0.22
20 13 0.18
21 5 0.07
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (20 bp):
AAATTTAATTTTTATATTAT
Found at i:402727 original size:57 final size:53
Alignment explanation
Indices: 402647--402754 Score: 146
Period size: 57 Copynumber: 2.0 Consensus size: 53
402637 TACTTTTTGA
402647 AATTTAATTTTTATATTAATTATAATT-TGTATATTATAAATTTGATTTTTATATT
1 AATTTAATTTTTATATTAATTATAATTCT-TATATTAT-AATTT-ATTTTTATATT
* *
402702 AATTCTAATTCTTTATATTATTTATAATTCTTATATTATAATTTTTTTTTATA
1 AATT-TAATT-TTTATATTAATTATAATTCTTATATTATAATTTATTTTTATA
402755 ATCACTAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
55 12 0.25
56 10 0.21
57 25 0.52
58 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (53 bp):
AATTTAATTTTTATATTAATTATAATTCTTATATTATAATTTATTTTTATATT
Found at i:403359 original size:23 final size:22
Alignment explanation
Indices: 403329--403383 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 22
403319 GCAGCAACTG
403329 GCAAGCATCAATGTAC-CAATTCA
1 GCAAGCATC-AT-TACACAATTCA
403352 GCAAGCATCATTACATCAATTCA
1 GCAAGCATCATTACA-CAATTCA
403375 GCAAGCATC
1 GCAAGCATC
403384 CTACATTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.10
22 2 0.07
23 25 0.83
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (22 bp):
GCAAGCATCATTACACAATTCA
Found at i:406133 original size:61 final size:60
Alignment explanation
Indices: 406057--406193 Score: 159
Period size: 61 Copynumber: 2.2 Consensus size: 60
406047 TCTTACTTTT
* * * *
406057 AAATTTATTCGATTTAGTACAAATTTAATGATGTA-ATATATTAATTTAAGCTTCATATTTC
1 AAATTTGTTCAATTTAATACAAATTTAATG-T-TACATATATTAATTTAAGCTTCATATTTA
* * * * *
406118 AAATTTTTTTAATTTAATCCAAATTTAATGTTACTTTTTATTAATTTAAGCTTCATATTTA
1 AAATTTGTTCAATTTAATACAAATTTAATGTTAC-ATATATTAATTTAAGCTTCATATTTA
406179 AAATTTGTTCAATTT
1 AAATTTGTTCAATTT
406194 GATCCTTATA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 2 0.03
60 1 0.02
61 61 0.95
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (60 bp):
AAATTTGTTCAATTTAATACAAATTTAATGTTACATATATTAATTTAAGCTTCATATTTA
Found at i:406266 original size:10 final size:8
Alignment explanation
Indices: 406237--406265 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
406227 TATATATGTT
406237 TATATTAA
1 TATATTAA
406245 TATATTAA
1 TATATTAA
406253 TATATTAA
1 TATATTAA
406261 TATAT
1 TATAT
406266 AGTTTATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TATATTAA
Found at i:406296 original size:18 final size:18
Alignment explanation
Indices: 406227--406489 Score: 106
Period size: 18 Copynumber: 14.9 Consensus size: 18
406217 TTTCAATTAA
406227 TATATATGTTTATAT-TA-
1 TATATA-GTTTATATATAC
* *
406244 -ATATA-TTAATATATTAA
1 TATATAGTTTATATA-TAC
*
406261 TATATAGTTTATACATAC
1 TATATAGTTTATATATAC
406279 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
406297 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
* *
406312 TTTATAGTTTGTATATAC
1 TATATAGTTTATATATAC
* * *
406330 CATATACTATATAGGTTATA-
1 TATATAGTTTATA---TATAC
* * ** *
406350 TGTACTAATGAACTATATAA
1 TATA-TAGTTTA-TATATAC
406370 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
406388 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
406403 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
** *
406421 TA-AT-GAACTATATATAA
1 TATATAG-TTTATATATAC
*
406438 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* * **
406456 GATATAGTCTATATATGT
1 TATATAGTTTATATATAC
406474 TATATAGTTTATATAT
1 TATATAGTTTATATAT
406490 GCTAATAAAC
Statistics
Matches: 178, Mismatches: 44, Indels: 47
0.66 0.16 0.17
Matches are distributed among these distances:
14 8 0.04
15 15 0.08
16 14 0.08
17 17 0.10
18 93 0.52
19 16 0.09
20 5 0.03
21 8 0.04
22 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.46
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:406320 original size:33 final size:33
Alignment explanation
Indices: 406279--406517 Score: 244
Period size: 33 Copynumber: 7.3 Consensus size: 33
406269 TTATACATAC
406279 TATATAGTTTATATATACTAATGAACTATATAA
1 TATATAGTTTATATATACTAATGAACTATATAA
* * *
406312 TTTATAGTTTGTATATAC-------C-ATATAC
1 TATATAGTTTATATATACTAATGAACTATATAA
* *
406337 TATATAGGTTATATGTACTAATGAACTATATAA
1 TATATAGTTTATATATACTAATGAACTATATAA
406370 TATATAGTTTATATATACTAATGAACTATATAA
1 TATATAGTTTATATATACTAATGAACTATATAA
406403 TATATAGTTTATATATACTAATGAACTATATATAA
1 TATATAGTTTATATATACTAATGAAC--TATATAA
* * * *
406438 TGTATAGTTTATATATACGATAT-AGTCTATATATGT
1 TATATAGTTTATATATACTA-ATGA-ACTATATA--A
* * *
406474 TATATAGTTTATATATGCTAATAAACTATATAT
1 TATATAGTTTATATATACTAATGAACTATATAA
*
406507 TGTATAGTTTA
1 TATATAGTTTA
406518 GGGTTTAGTA
Statistics
Matches: 172, Mismatches: 19, Indels: 30
0.78 0.09 0.14
Matches are distributed among these distances:
25 19 0.11
26 1 0.01
32 1 0.01
33 89 0.52
34 6 0.03
35 35 0.20
36 21 0.12
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (33 bp):
TATATAGTTTATATATACTAATGAACTATATAA
Found at i:406349 original size:58 final size:58
Alignment explanation
Indices: 406275--406479 Score: 221
Period size: 58 Copynumber: 3.3 Consensus size: 58
406265 TAGTTTATAC
* * *
406275 ATACTATATAGTTTATATATACTAATGAACTATATAATTTATAGTTTGTATATACCAT
1 ATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACCAT
*
406333 ATACTATATAGGTTATATGTACTAATGAACTATATAATATATAGTTTATATATACTAATGAACTA
1 ATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATAC-------C-A
406398 T
58 T
* * * *
406399 ATAATATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATACGAT
1 ATACTATATAGGTTATATATACTAATGAAC--TATATAATATATAGTTTATATATACCAT
*
406459 ATAGTCTATATATGTTATATA
1 ATA--CTATATAGGTTATATA
406480 GTTTATATAT
Statistics
Matches: 123, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
58 51 0.41
60 5 0.04
62 13 0.11
65 1 0.01
66 29 0.24
68 24 0.20
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.43
Consensus pattern (58 bp):
ATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACCAT
Found at i:406401 original size:17 final size:17
Alignment explanation
Indices: 406379--406436 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
406369 ATATATAGTT
406379 TATATATACTAATGAAC
1 TATATATACTAATGAAC
**
406396 TATATA-A-TATAT-AGTT
1 TATATATACTA-ATGA-AC
406412 TATATATACTAATGAAC
1 TATATATACTAATGAAC
406429 TATATATA
1 TATATATA
406437 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAC
Found at i:406571 original size:34 final size:36
Alignment explanation
Indices: 406533--406599 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 36
406523 TAGTATTTTT
*
406533 ATATATAGTTCATATGTA-AAT-TATACTATATAGC
1 ATATATAGTTCATATATATAATATATACTATATAGC
* *
406567 ATATATAGTTTATATATATAATATATAGTATAT
1 ATATATAGTTCATATATATAATATATACTATAT
406600 GAATATAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 16 0.57
35 3 0.11
36 9 0.32
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (36 bp):
ATATATAGTTCATATATATAATATATACTATATAGC
Found at i:406605 original size:20 final size:20
Alignment explanation
Indices: 406567--406624 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
406557 ACTATATAGC
*
406567 ATATATAGTTTATATATATA
1 ATATATAGTATATATATATA
406587 ATATATAGTATATGA-ATATA
1 ATATATAGTATAT-ATATATA
406607 A-ACTATAGTATATATATA
1 ATA-TATAGTATATATATA
406625 GGTCATATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 2 0.06
20 31 0.91
21 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (20 bp):
ATATATAGTATATATATATA
Found at i:406643 original size:51 final size:52
Alignment explanation
Indices: 406588--406711 Score: 169
Period size: 55 Copynumber: 2.3 Consensus size: 52
406578 ATATATATAA
*
406588 TATATAGTATATGAATATAAACTATAG-TATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATAGATATATATATAGGTCATATGTAAAC
* *
406639 TATATAGTATATAAATGTCAACTATAGTATATATATATATAGGTCATATGTAAAC
1 TATATAGTATATAAATATAAACTATAG---ATATATATATAGGTCATATGTAAAC
* *
406694 TATATAGTTTATATATAT
1 TATATAGTATATAAATAT
406712 TGTTCATATG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
51 24 0.38
55 39 0.62
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (52 bp):
TATATAGTATATAAATATAAACTATAGATATATATATAGGTCATATGTAAAC
Found at i:406656 original size:22 final size:22
Alignment explanation
Indices: 406631--406673 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
406621 TATAGGTCAT
406631 ATGTAAACTATA-TAGTATATAA
1 ATGTAAACTATAGTA-TATATAA
*
406653 ATGTCAACTATAGTATATATA
1 ATGTAAACTATAGTATATATA
406674 TATATAGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
ATGTAAACTATAGTATATATAA
Found at i:406707 original size:20 final size:20
Alignment explanation
Indices: 406674--406810 Score: 73
Period size: 20 Copynumber: 7.2 Consensus size: 20
406664 AGTATATATA
* *
406674 TATATAGGTCATATGTAAAC
1 TATATAGTTTATATGTAAAC
406694 TATATAGTTTATA--T--A-
1 TATATAGTTTATATGTAAAC
*
406709 TAT-T-GTTCATATGTAAAC
1 TATATAGTTTATATGTAAAC
* * *
406727 --TATAGTTCATATGCAAATAT
1 TATATAGTTTATATG-TAA-AC
*
406747 TAACTATAGTTTATATGCAAAC
1 T-A-TATAGTTTATATGTAAAC
*
406769 --TATAG-TTAGTATATAAAC
1 TATATAGTTTA-TATGTAAAC
406787 TATATAGTTTATATGTAAAC
1 TATATAGTTTATATGTAAAC
406807 TATA
1 TATA
406811 GTTCATATAT
Statistics
Matches: 89, Mismatches: 11, Indels: 34
0.66 0.08 0.25
Matches are distributed among these distances:
13 6 0.07
14 1 0.01
15 4 0.04
16 2 0.02
17 5 0.06
18 22 0.25
19 2 0.02
20 29 0.33
21 3 0.03
22 1 0.01
23 2 0.02
24 12 0.13
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (20 bp):
TATATAGTTTATATGTAAAC
Found at i:406736 original size:18 final size:18
Alignment explanation
Indices: 406713--406823 Score: 89
Period size: 18 Copynumber: 5.7 Consensus size: 18
406703 TATATATATT
406713 GTTCATATGTAAACTATA
1 GTTCATATGTAAACTATA
406731 GTTCATATGCAAATATTAACTATA
1 GTTCATATG----TA--AACTATA
* *
406755 GTTTATATGCAAACTATA
1 GTTCATATGTAAACTATA
*
406773 GTT-AGTATATAAACTATATA
1 GTTCA-TATGTAAAC--TATA
*
406793 GTTTATATGTAAACTATA
1 GTTCATATGTAAACTATA
*
406811 GTTCATATATAAA
1 GTTCATATGTAAA
406824 TATCAACCTT
Statistics
Matches: 76, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
17 1 0.01
18 41 0.54
20 16 0.21
21 1 0.01
22 2 0.03
24 15 0.20
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (18 bp):
GTTCATATGTAAACTATA
Found at i:406875 original size:18 final size:18
Alignment explanation
Indices: 406854--406935 Score: 80
Period size: 18 Copynumber: 4.7 Consensus size: 18
406844 TATTTATATA
*
406854 TATAGTTCATATGTAAAC
1 TATAGTTCATATATAAAC
* *
406872 TATAGTTTATATATATAC
1 TATAGTTCATATATAAAC
* *
406890 TATAGTTCATATATATAG
1 TATAGTTCATATATAAAC
*
406908 TATA--T-AAATATAAAC
1 TATAGTTCATATATAAAC
*
406923 TATAGTTTATATA
1 TATAGTTCATATA
406936 AATAGTATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
15 11 0.21
16 1 0.02
17 1 0.02
18 39 0.75
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (18 bp):
TATAGTTCATATATAAAC
Found at i:406919 original size:33 final size:32
Alignment explanation
Indices: 406882--406951 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
406872 TATAGTTTAT
* *
406882 ATATATACTATAGTTCATATATATAGTATATAA
1 ATATAAACTATAGTTCATATAAATAGTATA-AA
*
406915 ATATAAACTATAGTTTATATAAATAGTATAAA
1 ATATAAACTATAGTTCATATAAATAGTATAAA
406947 ATATA
1 ATATA
406952 GTATATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 7 0.21
33 27 0.79
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (32 bp):
ATATAAACTATAGTTCATATAAATAGTATAAA
Found at i:406923 original size:51 final size:49
Alignment explanation
Indices: 406836--406973 Score: 148
Period size: 51 Copynumber: 2.9 Consensus size: 49
406826 TCAACCTTAG
*
406836 TATATAC-ATATTTATATATATAGT-TCAT--ATGTAAACTATAGTTTATA
1 TATATACTATA-TTATATATATAGTAT-ATAAATATAAACTATAGTTTATA
406883 TATATACTATAGTTCATATATATAGTATATAAATATAAACTATAGTTTATA
1 TATATACTATA-TT-ATATATATAGTATATAAATATAAACTATAGTTTATA
* * *
406934 TAAATAGTATA--A-A-ATATAGTATATAAATATAAATTATAGT
1 TATATACTATATTATATATATAGTATATAAATATAAACTATAGT
406974 ATGTAGTTTA
Statistics
Matches: 81, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
45 26 0.32
46 1 0.01
47 8 0.10
48 5 0.06
49 13 0.16
50 1 0.01
51 27 0.33
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (49 bp):
TATATACTATATTATATATATAGTATATAAATATAAACTATAGTTTATA
Found at i:406926 original size:20 final size:20
Alignment explanation
Indices: 406902--406975 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
406892 TAGTTCATAT
406902 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
406922 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
406947 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
406967 TTATAGTAT
1 ATATAGTAT
406976 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:406951 original size:25 final size:23
Alignment explanation
Indices: 406902--406962 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
406892 TAGTTCATAT
406902 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
406922 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
406947 ATATAGTATATAAATA
1 ATATAGTATATAAATA
406963 TAAATTATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.15
22 5 0.15
23 12 0.35
24 1 0.03
25 11 0.32
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATAGTATATAAATAGTATAAA
Found at i:406954 original size:12 final size:13
Alignment explanation
Indices: 406915--406964 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
406905 TAGTATATAA
406915 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
406929 TTATATAA-ATAGT
1 ATATA-AATATAGT
406942 ATA-AAATATAGT
1 ATATAAATATAGT
406954 ATATAAATATA
1 ATATAAATATA
406965 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:406963 original size:29 final size:29
Alignment explanation
Indices: 406931--406999 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
406921 ACTATAGTTT
406931 ATATAAATAGTATAAAATATAG-TATATAA
1 ATATAAATA-TATAAAATATAGTTATATAA
** *
406960 ATATAAAT-TATAGTATGTAGTTTATATAA
1 ATATAAATATATAAAATATAG-TTATATAA
406989 ATATAAATATA
1 ATATAAATATA
407000 AACCCTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
29 23 0.68
30 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
ATATAAATATATAAAATATAGTTATATAA
Found at i:407056 original size:22 final size:24
Alignment explanation
Indices: 407022--407080 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
407012 TAAAGCATAA
*
407022 TATATATATATAAACTATATAGTT
1 TATATATATATAAACTATATAATT
407046 TATAT-TA-ATAAACTATATAATT
1 TATATATATATAAACTATATAATT
*
407068 TATACAATATATA
1 TATA-TATATATA
407081 TTATTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 18 0.60
23 2 0.07
24 7 0.23
25 3 0.10
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (24 bp):
TATATATATATAAACTATATAATT
Found at i:407221 original size:20 final size:20
Alignment explanation
Indices: 407192--407303 Score: 97
Period size: 20 Copynumber: 5.5 Consensus size: 20
407182 AAACTATATT
407192 GTAT-TATAGTTTATAAATG
1 GTATATATAGTTTATAAATG
407211 GTATATATAGTTTATATTTTATACATG
1 GTATATATAG-TT-TA---TA-A-ATG
*
407238 GTATATATAGTTTAT--ATA
1 GTATATATAGTTTATAAATG
* *
407256 GTAT-TCTAGTTTATATATG
1 GTATATATAGTTTATAAATG
*
407275 GTATATATAGTTTATACATG
1 GTATATATAGTTTATAAATG
407295 GTATATATA
1 GTATATATA
407304 TATATATATA
Statistics
Matches: 77, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
17 9 0.12
18 6 0.08
19 10 0.13
20 27 0.35
21 2 0.03
22 3 0.04
25 4 0.05
26 3 0.04
27 13 0.17
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (20 bp):
GTATATATAGTTTATAAATG
Found at i:407226 original size:9 final size:9
Alignment explanation
Indices: 407214--407290 Score: 52
Period size: 9 Copynumber: 8.4 Consensus size: 9
407204 ATAAATGGTA
407214 TATATAGTT
1 TATATAGTT
407223 TATAT--TT
1 TATATAGTT
* *
407230 TATACATGGTA
1 TAT--ATAGTT
407241 TATATAGTT
1 TATATAGTT
*
407250 TATATAGTA
1 TATATAGTT
*
407259 T-TCTAGTT
1 TATATAGTT
*
407267 TATATATGGTA
1 TATATA--GTT
407278 TATATAGTT
1 TATATAGTT
407287 TATA
1 TATA
407291 CATGGTATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
7 5 0.10
8 6 0.12
9 29 0.56
11 12 0.23
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.52
Consensus pattern (9 bp):
TATATAGTT
Found at i:407227 original size:37 final size:37
Alignment explanation
Indices: 407186--407290 Score: 104
Period size: 37 Copynumber: 3.1 Consensus size: 37
407176 ATATATAAAC
407186 TATATTGTATTATAGTTTATAAATGGTATATATAG--
1 TATATTGTATTATAGTTTATAAATGGTATATATAGTT
*
407221 ----TT-TA-TAT--TTTATACATGGTATATATAGTT
1 TATATTGTATTATAGTTTATAAATGGTATATATAGTT
* * *
407250 TATATAGTATTCTAGTTTATATATGGTATATATAGTT
1 TATATTGTATTATAGTTTATAAATGGTATATATAGTT
407287 TATA
1 TATA
407291 CATGGTATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
27 19 0.34
29 3 0.05
30 2 0.04
31 2 0.04
33 1 0.02
34 2 0.04
35 2 0.04
37 25 0.45
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.51
Consensus pattern (37 bp):
TATATTGTATTATAGTTTATAAATGGTATATATAGTT
Found at i:407231 original size:27 final size:27
Alignment explanation
Indices: 407186--407254 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
407176 ATATATAAAC
* *
407186 TATATTGTATTATAGTTTATAAATGGTA
1 TATATAGT-TTATATTTTATAAATGGTA
*
407214 TATATAGTTTATATTTTATACATGGTA
1 TATATAGTTTATATTTTATAAATGGTA
407241 TATATAGTTTATAT
1 TATATAGTTTATAT
407255 AGTATTCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 31 0.82
28 7 0.18
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (27 bp):
TATATAGTTTATATTTTATAAATGGTA
Found at i:407301 original size:2 final size:2
Alignment explanation
Indices: 407296--407334 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
407286 TTATACATGG
*
407296 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
407335 TAGTTGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:407308 original size:37 final size:37
Alignment explanation
Indices: 407214--407321 Score: 105
Period size: 37 Copynumber: 2.9 Consensus size: 37
407204 ATAAATGGTA
* * *
407214 TATATAGT-TTATATTTTATACATGGTATATATAGTT
1 TATATAGTATTATAGTATATATATGGTATATATAGTT
* *
407250 TATATAGTATTCTAGTTTATATATGGTATATATAGTT
1 TATATAGTATTATAGTATATATATGGTATATATAGTT
* *
407287 TATACATGGTATATATA-TATATATAT-ATATATATA
1 TAT--ATAGTAT-TATAGTATATATATGGTATATATA
407322 TATATATCTA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
36 8 0.13
37 28 0.46
38 8 0.13
39 14 0.23
40 3 0.05
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.50
Consensus pattern (37 bp):
TATATAGTATTATAGTATATATATGGTATATATAGTT
Found at i:407318 original size:64 final size:63
Alignment explanation
Indices: 407176--407327 Score: 164
Period size: 64 Copynumber: 2.4 Consensus size: 63
407166 TCAATAGTTC
* * ** *
407176 ATATATAAACTATATTGTATTATAGTTTATAAATGGTATATATAGTTTATATTTTATACATGGT
1 ATATATATA-TATATAGTATTATAGTTTATAAATGGTATATATAGTTTATATGGTATACATGAT
* * * *
407240 ATATATAGTTTATATAGTATTCTAGTTTATATATGGTATATATAGTTTATACATGGTATATAT-A
1 ATATATA-TATATATAGTATTATAGTTTATAAATGGTATATATAGTTTAT--ATGGTATACATGA
407304 T
63 T
407305 ATATATATATATATA-TATATATA
1 ATATATATATATATAGTAT-TATA
407328 TCTATATTAG
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
63 3 0.04
64 54 0.74
65 8 0.11
66 8 0.11
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.49
Consensus pattern (63 bp):
ATATATATATATATAGTATTATAGTTTATAAATGGTATATATAGTTTATATGGTATACATGAT
Found at i:407720 original size:210 final size:213
Alignment explanation
Indices: 407354--408171 Score: 1199
Period size: 210 Copynumber: 3.8 Consensus size: 213
407344 TAATTTTTTT
* * *
407354 CTCA-ACTTATTACTTATTTCTATTTATT-AATTGGTCCATAAGTTTTTAAATGAGTATAATTTA
1 CTCATACTTATTACTTATTTCTATTT-TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTA
* * *
407417 GTACATTTTTGTATTAATTTTAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-T-T-TAT
65 GTACTTTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATATGTGT
* *
407479 GTTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTTCTCCAACTTT
130 GTTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTT
**
407544 TATTTGCACCTGAAATTGA
195 TATTTGCATATGAAATTGA
407563 CTCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAG
1 CTCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAG
* *
407628 TACTTTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTTGATTTGATCCCT-T-T-TGCG
66 TACTTTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATATGTGTG
407690 TTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
131 TTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
407755 ATTTGCATATGAAATTGA
196 ATTTGCATATGAAATTGA
* * * * *
407773 CCCATACTTATTACTTATTTATA-TTTTAAATTGACTCATAACTTTTTAAATGGTTATAATTTAG
1 CTCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAG
* *
407837 TACTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGT
66 TACTTTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-AT--ATGT
* * *
407902 GTGTTGTTTAATTTATTTAAATTTTTATTTATAATTTCATATTTTTTCAATTTAGTCCTCCAAAT
128 GTGTTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAAT
407967 TTTATTTGCATATGAAATTGA
193 TTTATTTGCATATGAAATTGA
* * * *
407988 -TCCAGACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAACTTTTTAAATGTGTATAATTT
1 CT-CATACTTATTACTTATTTCTA-TTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTT
* * *
408052 AGTAC-TTTTTGTATTAATTTCAACCTTACAATTTAAAATTGTTTCGATTTGATCCCTCATCAAT
64 AGTACTTTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT-AT--AT
* *
408116 GTGTGTTGTTTAATTTATTTAAATTTTTATTTTTAATTTCATATTTGTTCAATTTA
126 GTGTGTTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
408172 ATTAATAAAT
Statistics
Matches: 560, Mismatches: 38, Indels: 15
0.91 0.06 0.02
Matches are distributed among these distances:
209 97 0.17
210 211 0.38
211 1 0.00
214 1 0.00
215 101 0.18
216 110 0.20
217 39 0.07
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (213 bp):
CTCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAG
TACTTTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCTATATGTGTG
TTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
ATTTGCATATGAAATTGA
Found at i:415757 original size:13 final size:13
Alignment explanation
Indices: 415739--415768 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
415729 TAACCGACCC
415739 GACCCGACACGTT
1 GACCCGACACGTT
*
415752 GACCCGACCCGTT
1 GACCCGACACGTT
415765 GACC
1 GACC
415769 GGCGTTGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACACGTT
Found at i:418243 original size:24 final size:24
Alignment explanation
Indices: 418216--418307 Score: 132
Period size: 24 Copynumber: 3.8 Consensus size: 24
418206 TTCGATTTGA
418216 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
418240 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
* * *
418264 ATTCTAATTTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
418288 ATTCTGATCTGATACTTGAC
1 ATTCTGATCTGATACTTGAC
418308 CTAATTTCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.02
24 57 0.97
25 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:418268 original size:48 final size:47
Alignment explanation
Indices: 418215--418331 Score: 146
Period size: 48 Copynumber: 2.4 Consensus size: 47
418205 TTTCGATTTG
*
418215 AATTCTGATCTGATACTTGACATGGATTCTGATCTGATA-TCTGACAT
1 AATTCTGATATGATACTTGACATGGATTCTGATCTGATACT-TGACAT
* * * *
418262 AGATTCTAATTTGATACTTGACTTGGATTCTGATCTGATACTTGACCT
1 A-ATTCTGATATGATACTTGACATGGATTCTGATCTGATACTTGACAT
*
418310 AATTTCTGATATGGTACTTGAC
1 AA-TTCTGATATGATACTTGAC
418332 CTGATTTATG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
47 2 0.03
48 57 0.95
49 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.40
Consensus pattern (47 bp):
AATTCTGATATGATACTTGACATGGATTCTGATCTGATACTTGACAT
Found at i:418316 original size:24 final size:23
Alignment explanation
Indices: 418216--418337 Score: 120
Period size: 24 Copynumber: 5.1 Consensus size: 23
418206 TTCGATTTGA
418216 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACAT-G
418240 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACAT-G
* * *
418264 ATTCTAATTTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACAT-G
* *
418288 ATTCTGATCTGATACTTGACCTA
1 ATTCTGATCTGATACTTGACATG
* * *
418311 ATTTCTGATATGGTACTTGACCTG
1 A-TTCTGATCTGATACTTGACATG
418335 ATT
1 ATT
418338 TATGTTTTGA
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
23 4 0.05
24 78 0.94
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (23 bp):
ATTCTGATCTGATACTTGACATG
Found at i:422689 original size:24 final size:24
Alignment explanation
Indices: 422646--422737 Score: 114
Period size: 24 Copynumber: 3.8 Consensus size: 24
422636 TTCGATTTGA
* *
422646 ATTCTAATATGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
422670 ATTATGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
* *
422694 ATTCTAATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
422718 ATTCTGATCTGGTACTTGAC
1 ATTCTGATCTGATACTTGAC
422738 CTAATTTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:427441 original size:45 final size:45
Alignment explanation
Indices: 427390--427480 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
427380 AAGCTGTACC
427390 TCCGTAATGCAATACAACCCAAAATCAGTATTTCAAAAATACTAT
1 TCCGTAATGCAATACAACCCAAAATCAGTATTTCAAAAATACTAT
427435 TCCGTAATGCAATACAACCCAAAATCAGTATTTCAAAAATACTAT
1 TCCGTAATGCAATACAACCCAAAATCAGTATTTCAAAAATACTAT
427480 T
1 T
427481 TATGCAGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (45 bp):
TCCGTAATGCAATACAACCCAAAATCAGTATTTCAAAAATACTAT
Found at i:428296 original size:29 final size:29
Alignment explanation
Indices: 428215--428321 Score: 126
Period size: 29 Copynumber: 3.6 Consensus size: 29
428205 CCCATTTGAA
*
428215 AATTCCCACAATGTCACATTTTTT-AAAAT
1 AATTCCCAGAATGTCAC-TTTTTTCAAAAT
*
428244 AATTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAGAATGTCACTTTTTTCAAAAT
* *
428273 ATTTCCCAGAATGTCACTTTTTTCACAAAAA
1 AATTCCCAGAATGTCACTTTTTT--CAAAAT
* *
428304 AAATCCTAGAATGTCACT
1 AATTCCCAGAATGTCACT
428322 GGGTCGAGTC
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 5 0.07
29 42 0.63
31 20 0.30
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (29 bp):
AATTCCCAGAATGTCACTTTTTTCAAAAT
Done.