Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007790.1 Hibiscus syriacus cultivar Beakdansim tig00110076_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: 2956777
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:1216173 original size:20 final size:20
Alignment explanation
Indices: 1216150--1216188 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1216140 AATATTTACA
*
1216150 TATTTT-TTATTAATTATTTT
1 TATTTTATT-TTAAGTATTTT
1216170 TATTTTATTTTAAGTATTT
1 TATTTTATTTTAAGTATTT
1216189 AAATTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TATTTTATTTTAAGTATTTT
Found at i:1217885 original size:30 final size:30
Alignment explanation
Indices: 1217825--1217886 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
1217815 TACATTTGCA
* * * *
1217825 TTTGCATTTTGTATTTTTCATATTTTCATT
1 TTTGCATTTTGCATTTTGCATAATTACATT
1217855 TTTGCA-TTTGCATATTTGCATAATTACATT
1 TTTGCATTTTGCAT-TTTGCATAATTACATT
1217885 TT
1 TT
1217887 ATTTCAAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (30 bp):
TTTGCATTTTGCATTTTGCATAATTACATT
Found at i:1221062 original size:32 final size:32
Alignment explanation
Indices: 1221026--1221087 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1221016 TCTGAAAATA
* *
1221026 AGAAGTATCTCTATGAGATGAGCATAACAACG
1 AGAAGTATCTCTATCAGATAAGCATAACAACG
1221058 AGAAGTATCTCTATCAGATAAGCATAACAA
1 AGAAGTATCTCTATCAGATAAGCATAACAA
1221088 TCATTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.23
Consensus pattern (32 bp):
AGAAGTATCTCTATCAGATAAGCATAACAACG
Found at i:1223563 original size:75 final size:75
Alignment explanation
Indices: 1223428--1223572 Score: 209
Period size: 75 Copynumber: 1.9 Consensus size: 75
1223418 ATAAATGAGC
* * * ** *
1223428 ATGCTGAAAACCCCTTTCAATCAGAATCAGGAATGTTGACGCATTTTGAACGTTTGTATCAGCAA
1 ATGCTGAAAACCCATTTCAATCAGAATCAGGAATGCTGACACATTTTGAACGTTCATATCAACAA
1223493 ATGTTGGGGT
66 ATGTTGGGGT
* *
1223503 ATGCTGAAAGCCCATTTCAATCATAATCAGGAATGCTGACACATTTTGAACGTTCATATCAACAA
1 ATGCTGAAAACCCATTTCAATCAGAATCAGGAATGCTGACACATTTTGAACGTTCATATCAACAA
*
1223568 TTGTT
66 ATGTT
1223573 AGGGCATATT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (75 bp):
ATGCTGAAAACCCATTTCAATCAGAATCAGGAATGCTGACACATTTTGAACGTTCATATCAACAA
ATGTTGGGGT
Found at i:1224887 original size:22 final size:19
Alignment explanation
Indices: 1224836--1224876 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
1224826 ATCTACATTC
1224836 TTCAAAGATGATAGATTTT
1 TTCAAAGATGATAGATTTT
*
1224855 CTCAAAGATGATAGATTCTT
1 TTCAAAGATGATAGATT-TT
1224875 TT
1 TT
1224877 TTCAAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (19 bp):
TTCAAAGATGATAGATTTT
Found at i:1225613 original size:45 final size:45
Alignment explanation
Indices: 1225547--1225763 Score: 407
Period size: 45 Copynumber: 4.8 Consensus size: 45
1225537 CTATTTCCAA
* * *
1225547 CATCTATAAGACCTGCAGTGCATGATGTTTCCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGT
1225592 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGT
1225637 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGT
1225682 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGT
1225727 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAC
1225764 TTCAGTGCAT
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 169 1.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.30
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAACCTTCGGGT
Found at i:1225771 original size:24 final size:24
Alignment explanation
Indices: 1225739--1225790 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1225729 TCTGTAAGCC
1225739 CTTCAGTGCATGATGTTTCCAAAA
1 CTTCAGTGCATGATGTTTCCAAAA
*
1225763 CTTCAGTGCATGATGTTTCCAAAC
1 CTTCAGTGCATGATGTTTCCAAAA
1225787 CTTC
1 CTTC
1225791 GGGTTATCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (24 bp):
CTTCAGTGCATGATGTTTCCAAAA
Found at i:1225806 original size:68 final size:69
Alignment explanation
Indices: 1225694--1225831 Score: 251
Period size: 68 Copynumber: 2.0 Consensus size: 69
1225684 TCTGTAAGCC
1225694 CTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
1 CTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
1225759 AAAA
66 AAAA
* *
1225763 CTTCAGTGCATGATGTTTCC-AAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGTTTTC
1 CTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
1225827 AAAA
66 AAAA
1225831 C
1 C
1225832 ATCTGTAAGC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 47 0.70
69 20 0.30
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (69 bp):
CTTCAGTGCATGATGTTTCCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
AAAA
Found at i:1225981 original size:3 final size:3
Alignment explanation
Indices: 1225967--1226029 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
1225957 TTTTCATTTC
* ** *
1225967 ATT ATC ATT ATT ATT AAA ATT ATT ATT ATT AAT ATT AATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT AT-T ATT
* *
1226014 TTT ATT TTT ATT ATT A
1 ATT ATT ATT ATT ATT A
1226030 AATAAATAAA
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1226599 original size:19 final size:20
Alignment explanation
Indices: 1226554--1226614 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
1226544 GGAAAAAGAG
*
1226554 AAGATAGAGAGCAATCCAAA
1 AAGACAGAGAGCAATCCAAA
*
1226574 AAGACAGAGAGCAACCCAAA
1 AAGACAGAGAGCAATCCAAA
1226594 AA-ACAGAGAGCAATCCAAA
1 AAGACAGAGAGCAATCCAAA
1226613 AA
1 AA
1226615 CAAAGACGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
19 18 0.47
20 20 0.53
ACGTcount: A:0.57, C:0.20, G:0.18, T:0.05
Consensus pattern (20 bp):
AAGACAGAGAGCAATCCAAA
Found at i:1227544 original size:17 final size:17
Alignment explanation
Indices: 1227524--1227587 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
1227514 TTTTTTATAA
1227524 ATAAATATTTTACTTTT
1 ATAAATATTTTACTTTT
*
1227541 ATAAATTATATATATTATTTTT
1 AT-AA--ATAT-T-TTACTTTT
1227563 AAATAAATATTTTACTTTT
1 --ATAAATATTTTACTTTT
1227582 ATAAAT
1 ATAAAT
1227588 TATATATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
17 8 0.21
18 2 0.05
19 7 0.18
20 5 0.13
21 5 0.13
22 7 0.18
23 2 0.05
24 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAAATATTTTACTTTT
Found at i:1227555 original size:24 final size:20
Alignment explanation
Indices: 1227509--1227602 Score: 102
Period size: 21 Copynumber: 4.6 Consensus size: 20
1227499 TCCATTTCTG
1227509 ATATTTT-TTTTATAAATAA
1 ATATTTTATTTTATAAATAA
*
1227528 ATATTTTACTTTTATAAATTAT
1 ATATTTTA-TTTTATAAA-TAA
*
1227550 ATATATTATTTT-TAAATAA
1 ATATTTTATTTTATAAATAA
*
1227569 ATATTTTACTTTTATAAATTAT
1 ATATTTTA-TTTTATAAA-TAA
*
1227591 ATATATTATTTT
1 ATATTTTATTTT
1227603 TTAATGTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
19 16 0.25
20 8 0.13
21 21 0.33
22 18 0.29
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTTTATTTTATAAATAA
Found at i:1227573 original size:41 final size:41
Alignment explanation
Indices: 1227516--1227603 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
1227506 CTGATATTTT
1227516 TTTTATAAATAAATATTTTACTTTTATAAATTATATATATTA
1 TTTT-TAAATAAATATTTTACTTTTATAAATTATATATATTA
1227558 TTTTTAAATAAATATTTTACTTTTATAAATTATATATATTA
1 TTTTTAAATAAATATTTTACTTTTATAAATTATATATATTA
1227599 TTTTT
1 TTTTT
1227604 TAATGTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 42 0.91
42 4 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (41 bp):
TTTTTAAATAAATATTTTACTTTTATAAATTATATATATTA
Found at i:1227628 original size:29 final size:31
Alignment explanation
Indices: 1227578--1227636 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
1227568 AATATTTTAC
1227578 TTTTATAAATTATATATATTATTTTTTAATG
1 TTTTATAAATTATATATATTATTTTTTAATG
* *
1227609 TTTTATTAA-TATTTAT-TTATTTTTTAAT
1 TTTTATAAATTATATATATTATTTTTTAAT
1227637 ATTAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
30 6 0.23
31 8 0.31
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (31 bp):
TTTTATAAATTATATATATTATTTTTTAATG
Found at i:1230389 original size:38 final size:37
Alignment explanation
Indices: 1230334--1230416 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
1230324 CATATTTGTT
*
1230334 GTGACAACTTTTTTTGTAACAATA-ATTATAACTTATA
1 GTGACAAATTTTTTTGTAACAATATATTATAA-TTATA
* ** *
1230371 GTTACAAATTTTGTTTGTAATTATATATTTTAATTATA
1 GTGACAAATTTT-TTTGTAACAATATATTATAATTATA
1230409 GTGACAAA
1 GTGACAAA
1230417 ATGTATAGTC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 10 0.26
38 22 0.58
39 6 0.16
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (37 bp):
GTGACAAATTTTTTTGTAACAATATATTATAATTATA
Found at i:1231035 original size:139 final size:138
Alignment explanation
Indices: 1230878--1231136 Score: 401
Period size: 139 Copynumber: 1.9 Consensus size: 138
1230868 TCACATCAAA
*
1230878 TAATAAAATTCAACTTTTTTGTAATAAATTATTTTTGTACTTATATATTTTAATCATTATGAAAA
1 TAATAAAATTCAACTTTTTTGTAATAAATTATTTTTGTACTTATATATTTTAATAATTATGAAAA
*
1230943 CGTATACTATCAGAACCATTTCTCCCTATTTTTTAGTGTCAAAAATGTTATATAGTAACAAAATA
66 CGTATACTATCAGAAACATTTCTCCCTATTTTTTAGTG-CAAAAATGTTATATAGTAACAAAATA
1231008 TATTGTAAT
130 TATTGTAAT
* * * **
1231017 TAATAAAATTTAAGTTTTTTGTAATTAATTATTTTTGTTGTTATATATTTTAATAATTATGAAAA
1 TAATAAAATTCAACTTTTTTGTAATAAATTATTTTTGTACTTATATATTTTAATAATTATGAAAA
* * * * *
1231082 CTTATACTATTAGAAATATTTCTTCCTATTTTTTGGTGCAAAAATGTTATATAGT
66 CGTATACTATCAGAAACATTTCTCCCTATTTTTTAGTGCAAAAATGTTATATAGT
1231137 GACACGTTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
138 17 0.16
139 91 0.84
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (138 bp):
TAATAAAATTCAACTTTTTTGTAATAAATTATTTTTGTACTTATATATTTTAATAATTATGAAAA
CGTATACTATCAGAAACATTTCTCCCTATTTTTTAGTGCAAAAATGTTATATAGTAACAAAATAT
ATTGTAAT
Found at i:1231246 original size:18 final size:19
Alignment explanation
Indices: 1231212--1231247 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1231202 TTTTAAATTA
*
1231212 ATAAAAGATTCATGTTTTT
1 ATAAAAAATTCATGTTTTT
1231231 ATAAAAAATT-ATGTTTT
1 ATAAAAAATTCATGTTTT
1231248 CAGATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (19 bp):
ATAAAAAATTCATGTTTTT
Found at i:1232000 original size:17 final size:17
Alignment explanation
Indices: 1231974--1232011 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1231964 CCTATATTTT
1231974 ATTTTAAA-GGAAATTG
1 ATTTTAAAGGGAAATTG
1231990 ATTTGTAAAGGGAAATTG
1 ATTT-TAAAGGGAAATTG
1232008 -TTTT
1 ATTTT
1232012 TGAGAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 7 0.35
18 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (17 bp):
ATTTTAAAGGGAAATTG
Found at i:1237618 original size:120 final size:115
Alignment explanation
Indices: 1237470--1237714 Score: 321
Period size: 118 Copynumber: 2.1 Consensus size: 115
1237460 CAGTTCTATC
1237470 ATCATAATCAGAATATACAAGCACACACAGTGCTATCATATCAGAATCATAATGTGCACACAAAG
1 ATCATAATCAGAATATACAAGCACACACAGTGCTATC--ATCAGAATCATAATGTGCACACAAAG
* * *
1237535 TGCAATCAGATCATAATATATATACTAGTGCACCCACTGGT-ACACCATAGTAT
64 TGCAATCACATCA-AA-ATATATACTAGTACACCCACTGGTAACACCACAGTAT
* * * *
1237588 ATCATAATCGGAACATATATAAGCACACACAGTGCTATCATCAGAATCTTGATGTGCACACAAAG
1 ATCATAATCAG-A-ATATACAAGCACACACAGTGCTATCATCAGAATCATAATGTGCACACAAAG
* * **
1237653 TGCAATCACATCAGAATATATACTAGTATACCTTCTGGTAACACCACAGTAT
64 TGCAATCACATCAAAATATATACTAGTACACCCACTGGTAACACCACAGTAT
*
1237705 ATCAGAATCA
1 ATCATAATCA
1237715 CTCCACCTCA
Statistics
Matches: 111, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
116 20 0.18
117 20 0.18
118 46 0.41
119 1 0.01
120 24 0.22
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (115 bp):
ATCATAATCAGAATATACAAGCACACACAGTGCTATCATCAGAATCATAATGTGCACACAAAGTG
CAATCACATCAAAATATATACTAGTACACCCACTGGTAACACCACAGTAT
Found at i:1239044 original size:19 final size:20
Alignment explanation
Indices: 1239020--1239064 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1239010 AAAATAATCA
* *
1239020 AATTTC-ACATTCTAACATC
1 AATTTCAACACTCAAACATC
*
1239039 AATTTCAACACTCAAACATT
1 AATTTCAACACTCAAACATC
1239059 AATTTC
1 AATTTC
1239065 TAGCATAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTCAACACTCAAACATC
Found at i:1239625 original size:16 final size:16
Alignment explanation
Indices: 1239601--1239634 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1239591 ATGATAGCAT
*
1239601 TTTTTGAATAGAACAA
1 TTTTCGAATAGAACAA
*
1239617 TTTTCGAATAGACCAA
1 TTTTCGAATAGAACAA
1239633 TT
1 TT
1239635 CCAAAGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
TTTTCGAATAGAACAA
Found at i:1239949 original size:25 final size:25
Alignment explanation
Indices: 1239921--1240003 Score: 157
Period size: 25 Copynumber: 3.3 Consensus size: 25
1239911 TTTACCCATG
*
1239921 CCATTTTCTAAAAATTTCAATATTT
1 CCATTTTCTAAAAATTTCAATCTTT
1239946 CCATTTTCTAAAAATTTCAATCTTT
1 CCATTTTCTAAAAATTTCAATCTTT
1239971 CCATTTTCTAAAAATTTCAATCTTT
1 CCATTTTCTAAAAATTTCAATCTTT
1239996 CCATTTTC
1 CCATTTTC
1240004 ATCCAACGGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.48
Consensus pattern (25 bp):
CCATTTTCTAAAAATTTCAATCTTT
Found at i:1255023 original size:33 final size:34
Alignment explanation
Indices: 1254986--1255049 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
1254976 AAATGAAAAT
*
1254986 GGATTTTGAAA-ATC-AAAATGAAATCTTGAAGAA
1 GGATTTAGAAATATCAAAAATGAAAT-TTGAAGAA
*
1255019 GGATTTAGAAATCTCAAAAATGAAATTTGAA
1 GGATTTAGAAATATCAAAAATGAAATTTGAA
1255050 AGTATTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 10 0.37
34 7 0.26
35 10 0.37
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.28
Consensus pattern (34 bp):
GGATTTAGAAATATCAAAAATGAAATTTGAAGAA
Found at i:1256144 original size:24 final size:24
Alignment explanation
Indices: 1256117--1256166 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1256107 GATGCTTGTG
1256117 CTAAAGGAAAACAAAAGCGAGTTT
1 CTAAAGGAAAACAAAAGCGAGTTT
1256141 CTAAAGGAAAACAAAAGCGAGTTT
1 CTAAAGGAAAACAAAAGCGAGTTT
1256165 CT
1 CT
1256167 TTTAAATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (24 bp):
CTAAAGGAAAACAAAAGCGAGTTT
Found at i:1264178 original size:17 final size:17
Alignment explanation
Indices: 1264143--1264186 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1264133 TTTTAACATT
*
1264143 TTGAATATTTTGGAATGA
1 TTGAAT-TTGTGGAATGA
*
1264161 TTGAATTTGTGGATTGA
1 TTGAATTTGTGGAATGA
*
1264178 TTGACTTTG
1 TTGAATTTG
1264187 AATTTGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (17 bp):
TTGAATTTGTGGAATGA
Found at i:1267909 original size:26 final size:25
Alignment explanation
Indices: 1267880--1267940 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
1267870 TTAAATTTTA
1267880 TTTTAATTTTAATTTTTAAAATATAT
1 TTTTAATTTTAATTTTTAAAATAT-T
* * *
1267906 TTTTACA-ATTAATTTTTTATATATT
1 TTTTA-ATTTTAATTTTTAAAATATT
*
1267931 TTTTACTTTT
1 TTTTAATTTT
1267941 TTAATTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
25 8 0.29
26 19 0.68
27 1 0.04
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTAATTTTAATTTTTAAAATATT
Found at i:1270010 original size:19 final size:19
Alignment explanation
Indices: 1269986--1270024 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1269976 TGATTACCCA
*
1269986 CGCAATTGATTTCCCTTTG
1 CGCAATTGATTTCCCCTTG
*
1270005 CGCAATTGCTTTCCCCTTG
1 CGCAATTGATTTCCCCTTG
1270024 C
1 C
1270025 AATTGAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.33, G:0.15, T:0.38
Consensus pattern (19 bp):
CGCAATTGATTTCCCCTTG
Found at i:1270028 original size:17 final size:18
Alignment explanation
Indices: 1269986--1270030 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
1269976 TGATTACCCA
*
1269986 CGCAATTGATTTCCCTTT
1 CGCAATTGATTTCCCCTT
*
1270004 GCGCAATTGCTTTCCCCTT
1 -CGCAATTGATTTCCCCTT
1270023 -GCAATTGA
1 CGCAATTGA
1270031 AACCCAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 7 0.30
19 16 0.70
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.38
Consensus pattern (18 bp):
CGCAATTGATTTCCCCTT
Found at i:1271032 original size:21 final size:20
Alignment explanation
Indices: 1271006--1271067 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 20
1270996 ATTTAAATTA
1271006 TTATAAAAATATATATTTAAT
1 TTATAAAAATATATATTT-AT
1271027 TTATAAAATCATATTAATATTTAT
1 TTATAAAA--ATA-T-ATATTTAT
1271051 TTA-AAATAATAT-TATTT
1 TTATAAA-AATATATATTT
1271068 TTAAATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
19 5 0.14
21 9 0.25
22 3 0.08
23 6 0.17
24 7 0.19
25 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATAAAAATATATATTTAT
Found at i:1271222 original size:27 final size:27
Alignment explanation
Indices: 1271191--1271260 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
1271181 AAAAAATTCA
* * *
1271191 AATAAATAATTAATAT-TTTTTCAAAT
1 AATAAATAAATAATATGATTTTAAAAT
1271217 ATATAAATAAATAATATGATTTTAAAAT
1 A-ATAAATAAATAATATGATTTTAAAAT
1271245 AATAAATTAAA-AATAT
1 AATAAA-TAAATAATAT
1271261 TATAATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 1 0.03
27 24 0.63
28 13 0.34
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (27 bp):
AATAAATAAATAATATGATTTTAAAAT
Found at i:1279626 original size:64 final size:63
Alignment explanation
Indices: 1279490--1279627 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 63
1279480 GCACTAAGAG
* * **
1279490 TGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGACTGG
1 TGCATCGATGCATCAAATGCATTCAATGTTTCAAAATAGCCAGAGTGCATCGATGCATGAC-AA
* *
1279554 TGCATCGATGCATCAAATGCATTCAATGTTTTCTTAAA-A-CTCTGAGTGCATCGATGCATGA-A
1 TGCATCGATGCATCAAATGCATTCAATG-TTTC-AAAATAGC-CAGAGTGCATCGATGCATGACA
1279616 A
63 A
1279617 TGCATTCGATG
1 TGCA-TCGATG
1279628 TTCAATTTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
63 4 0.06
64 33 0.52
65 24 0.38
66 3 0.05
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATCAAATGCATTCAATGTTTCAAAATAGCCAGAGTGCATCGATGCATGACAA
Found at i:1286632 original size:6 final size:6
Alignment explanation
Indices: 1286623--1286648 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1286613 CAATTCCATT
1286623 TCCTCG TCCTCG TCCTCG TCCTCG TC
1 TCCTCG TCCTCG TCCTCG TCCTCG TC
1286649 ATCTTCATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.15, T:0.35
Consensus pattern (6 bp):
TCCTCG
Found at i:1288215 original size:24 final size:27
Alignment explanation
Indices: 1288179--1288230 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
1288169 TTGTTTTTCC
* *
1288179 TTTTAAATTTTA-TTA-TGTTTTTGTT
1 TTTTAAATATTATTTAGTGTTATTGTT
1288204 TTTTAAA-ATTATTTAGTGTTATTGTT
1 TTTTAAATATTATTTAGTGTTATTGTT
1288230 T
1 T
1288231 ACTTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.13
25 10 0.43
26 10 0.43
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (27 bp):
TTTTAAATATTATTTAGTGTTATTGTT
Found at i:1288340 original size:28 final size:26
Alignment explanation
Indices: 1288273--1288345 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 26
1288263 GATTTAATAT
*
1288273 TTTTATCTTTTTTATTT-TATTTTATA
1 TTTT-TCTTTTTTATTTATATTTTACA
1288299 -TTTTCTTTGATTTATTTAATATTTTACA
1 TTTTTCTTT--TTTATTT-ATATTTTACA
1288327 TTTTTCTTCTTTTATTTAT
1 TTTTTCTT-TTTTATTTAT
1288346 TTTATTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
24 5 0.12
25 3 0.08
26 7 0.17
27 2 0.05
28 15 0.38
29 7 0.17
30 1 0.03
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.73
Consensus pattern (26 bp):
TTTTTCTTTTTTATTTATATTTTACA
Found at i:1288344 original size:32 final size:33
Alignment explanation
Indices: 1288301--1288390 Score: 119
Period size: 32 Copynumber: 2.7 Consensus size: 33
1288291 ATTTTATATT
*
1288301 TTCTTTGATTTATTTAATATTTTAC-ATTTTTC
1 TTCTTTTATTTATTTAATATTTTACTATTTTTC
* * *
1288333 TTCTTTTATTTATTTTATTTTTTACTTTTTTTC
1 TTCTTTTATTTATTTAATATTTTACTATTTTTC
1288366 TTCCTTTTGATTTATTTAATATTTT
1 TT-CTTTT-ATTTATTTAATATTTT
1288391 TTTCATTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
32 22 0.45
33 8 0.16
34 5 0.10
35 14 0.29
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (33 bp):
TTCTTTTATTTATTTAATATTTTACTATTTTTC
Found at i:1288414 original size:21 final size:23
Alignment explanation
Indices: 1288388--1288437 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
1288378 TATTTAATAT
1288388 TTTTTTCATTTTCTTA-TT-TTA
1 TTTTTTCATTTTCTTACTTATTA
*
1288409 TTTTTTCCTTTTCTTACTTATTA
1 TTTTTTCATTTTCTTACTTATTA
1288432 TTTTTT
1 TTTTTT
1288438 ATCTAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 15 0.58
22 2 0.08
23 9 0.35
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTTCATTTTCTTACTTATTA
Found at i:1288439 original size:59 final size:55
Alignment explanation
Indices: 1288264--1288450 Score: 144
Period size: 59 Copynumber: 3.2 Consensus size: 55
1288254 TACTTTTAAG
* * * * * **
1288264 ATTTAATATTTTTATCTTTTTTATTTTATTTTATATTTTCTT-TGATTTATTTAAT
1 ATTTAACATTTTTTTCTTTTTTATTTTATTTTTTCTTTTCTTCTTA-TTATTTTTT
* * * *
1288319 ATTTTACATTTTTCTTCTTTTATTTATTTTATTTTTTACTTTTTTTCTTCCTT-TTGATTT
1 ATTTAACATTTTT-TTC-TTT-TTTATTTTATTTTTT-CTTTTCTTCTT-ATTATT-TTTT
*
1288379 ATTTAATATTTTTTTCATTTTCTTATTTTATTTTTTCCTTTTCTTACTTATTATTTTTT
1 ATTTAACATTTTTTTC-TTTT-TTATTTTATTTTTT-CTTTTCTT-CTTATTATTTTTT
*
1288438 ATCTAACATTTTT
1 ATTTAACATTTTT
1288451 GACTTTTTAG
Statistics
Matches: 102, Mismatches: 20, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
55 11 0.11
56 2 0.02
57 3 0.03
58 15 0.15
59 51 0.50
60 20 0.20
ACGTcount: A:0.19, C:0.09, G:0.01, T:0.71
Consensus pattern (55 bp):
ATTTAACATTTTTTTCTTTTTTATTTTATTTTTTCTTTTCTTCTTATTATTTTTT
Found at i:1294053 original size:85 final size:85
Alignment explanation
Indices: 1293892--1294207 Score: 375
Period size: 85 Copynumber: 3.7 Consensus size: 85
1293882 TCCCAACCTA
* * * * *
1293892 TTACAGTATAGCTCAAGGCGAGAAGGGTTATCTGTCAA-C-AAACTTTCAAGTTTGATTACATTC
1 TTACAGCATAACTCAAGGCAAGAAGGGTTATCTGTCAACCAAAACCTTCAAGTTCGATTACATTC
*
1293955 AACTCAAGGACATATCAAAT
66 AGCTCAAGGACATATCAAAT
* ** * * * *
1293975 TTATAGCATAACTCAAGGTGAGAAGGGTTATTTGTCAACCAAAACCTTCGAGTTTGATTACATTT
1 TTACAGCATAACTCAAGGCAAGAAGGGTTATCTGTCAACCAAAACCTTCAAGTTCGATTACATTC
1294040 AGCTCAAGGACATATCAAAT
66 AGCTCAAGGACATATCAAAT
** * * * * * **
1294060 TTACAATATAACTCAAGGAAAGAATGGTTATTTGTCAACTAAAAACTTTGAGTTCGATTACATTC
1 TTACAGCATAACTCAAGGCAAGAAGGGTTATCTGTCAACCAAAACCTTCAAGTTCGATTACATTC
*
1294125 AGCTCAAGGACATATAAAAT
66 AGCTCAAGGACATATCAAAT
* * * *
1294145 TTACAGCATAACTCAAGCCAAAAAGAGTTATCTGCCAACCAAAACCTTCAAGTTCGATTACAT
1 TTACAGCATAACTCAAGGCAAGAAGGGTTATCTGTCAACCAAAACCTTCAAGTTCGATTACAT
1294208 ATAAAATTTA
Statistics
Matches: 197, Mismatches: 34, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
83 33 0.17
84 1 0.01
85 163 0.83
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (85 bp):
TTACAGCATAACTCAAGGCAAGAAGGGTTATCTGTCAACCAAAACCTTCAAGTTCGATTACATTC
AGCTCAAGGACATATCAAAT
Found at i:1294217 original size:70 final size:70
Alignment explanation
Indices: 1294134--1294277 Score: 225
Period size: 70 Copynumber: 2.1 Consensus size: 70
1294124 CAGCTCAAGG
*
1294134 ACATATAAAATTTACAGCATAACTCAAGCCAAAAAGAGTTATCTGCCAACCAAAACCTTCAAGTT
1 ACATATAAAATTTACAGCATAACTCAAGCCAAAAAGAGTTATCTGCCAACCAAAACCTTCAAGAT
1294199 CGATT
66 CGATT
* * * * * *
1294204 ACATATAAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGAT
1 ACATATAAAATTTACAGCATAACTCAAGCCAAAAAGAGTTATCTGCCAACCAAAACCTTCAAGAT
1294269 CGATT
66 CGATT
1294274 ACAT
1 ACAT
1294278 TCAGCTCAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (70 bp):
ACATATAAAATTTACAGCATAACTCAAGCCAAAAAGAGTTATCTGCCAACCAAAACCTTCAAGAT
CGATT
Found at i:1294344 original size:155 final size:155
Alignment explanation
Indices: 1294049--1294358 Score: 397
Period size: 155 Copynumber: 2.0 Consensus size: 155
1294039 TAGCTCAAGG
* * * * * * *
1294049 ACATATCAAATTTACAATATAACTCAAGGAAAGAATGGTTATTTGTCAACTAAAAACTTTGAGTT
1 ACATATAAAATTTACAACATAACTCAAGGAAAGAAGGGTTATCTGTCAACCAAAAACTTCGAGAT
* *
1294114 CGATTACATTCAGCTCAAGGACATATAAAATTTACAGCATAACTCAAGCCAAAAAGAGTTATCTG
66 CGATTACATTCAGCTCAAAGACATATAAAATTTACAACATAACTCAAGCCAAAAAGAGTTATCTG
*
1294179 CCAACCAAAACCT-TCAAGTTCGATT
131 CCAA-CAAAAACTATCAAGTTCGATT
* ** *
1294204 ACATATAAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGAT
1 ACATATAAAATTTACAACATAACTCAAGGAAAGAAGGGTTATCTGTCAACCAAAAACTTCGAGAT
* * * * * *
1294269 CGATTACATTCAGCTCAAAGACATATCAAATTTACAACATATCTCAAGGCGAGAAGGGTTATCTG
66 CGATTACATTCAGCTCAAAGACATATAAAATTTACAACATAACTCAAGCCAAAAAGAGTTATCTG
** *
1294334 TTAACAAAAACTATCGAGTTCGATT
131 CCAACAAAAACTATCAAGTTCGATT
1294359 CCATTCAGCT
Statistics
Matches: 131, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
154 7 0.05
155 124 0.95
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (155 bp):
ACATATAAAATTTACAACATAACTCAAGGAAAGAAGGGTTATCTGTCAACCAAAAACTTCGAGAT
CGATTACATTCAGCTCAAAGACATATAAAATTTACAACATAACTCAAGCCAAAAAGAGTTATCTG
CCAACAAAAACTATCAAGTTCGATT
Found at i:1294351 original size:85 final size:85
Alignment explanation
Indices: 1294204--1294382 Score: 252
Period size: 85 Copynumber: 2.1 Consensus size: 85
1294194 AAGTTCGATT
* * *
1294204 ACATATAAAATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGAT
1 ACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAAACTTCGAGAT
1294269 CGATTACATTCAGCTCAAAG
66 CGATTACATTCAGCTCAAAG
* * *
1294289 ACATATCAAATTTACAACATATCTCAAGGCGAGAAGGGTTATCTGTTAA-CAAAAACTATCGAGT
1 ACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAAACT-TCGAGA
* ** *
1294353 TCGATTCCATTCAGCTTGATG
65 TCGATTACATTCAGCTCAAAG
1294374 ACATATCAA
1 ACATATCAA
1294383 CCGCATGGTA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 7 0.08
85 76 0.92
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (85 bp):
ACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAAAACTTCGAGAT
CGATTACATTCAGCTCAAAG
Found at i:1294946 original size:5 final size:5
Alignment explanation
Indices: 1294936--1294960 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1294926 TTCCTCTGGA
1294936 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
1294961 ATATATAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:1295189 original size:26 final size:28
Alignment explanation
Indices: 1295147--1295201 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
1295137 TTGAATATAT
*
1295147 ATATATATATATAATATAATTTTTGAAA
1 ATATATATATATAATATAAGTTTTGAAA
1295175 ATATATATA-AT-ATATAAGTTTTGAAA
1 ATATATATATATAATATAAGTTTTGAAA
1295201 A
1 A
1295202 CATTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 15 0.58
27 2 0.08
28 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (28 bp):
ATATATATATATAATATAAGTTTTGAAA
Found at i:1295219 original size:69 final size:68
Alignment explanation
Indices: 1295096--1295298 Score: 162
Period size: 69 Copynumber: 2.9 Consensus size: 68
1295086 TTTGAAAATG
* ** *** *
1295096 ATTTTTGAAAATATATATATTATATAGTTTGCAAATGATTTTTGAATATATATATATATATATAA
1 ATTTTTGAAAATATATATAATATATAGTTTGCAAAACATTTAAAAAAATATATATA-ATATATAA
1295161 TATA
65 TATA
1295165 ATTTTTGAAAATATATATAATATATAAGTTTTG-AAAACATTTAAAAAAAT-TATATAATATATA
1 ATTTTTGAAAATATATATAATATAT-AG-TTTGCAAAACATTTAAAAAAATATATATAATATATA
* *
1295228 GTTTTGAA
64 -ATAT--A
* * *** *
1295236 ATCATTTTGAAAGCT-TATATAATATATAGTTT-TAAAACATTTTTGAAAATATATATTATATAT
1 AT--TTTTGAAA-ATATATATAATATATAGTTTGCAAAACATTTAAAAAAATATATATAATATAT
1295299 GTTTATTATT
Statistics
Matches: 110, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
68 7 0.06
69 32 0.29
70 13 0.12
71 24 0.22
72 13 0.12
73 20 0.18
74 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (68 bp):
ATTTTTGAAAATATATATAATATATAGTTTGCAAAACATTTAAAAAAATATATATAATATATAAT
ATA
Found at i:1295280 original size:36 final size:35
Alignment explanation
Indices: 1294962--1295302 Score: 184
Period size: 36 Copynumber: 9.5 Consensus size: 35
1294952 TTATTTTATA
* * *
1294962 TATATAGTATA-ATTTTTGAAAATATTTTTGAAAA-
1 TATATAATATATAGTTTTGAAAACA-TTTTGAAAAT
*
1294996 -ATATAATATATAATTGTTTAGAAAACGATTTTTGAAAA-
1 TATATAATATAT-A--GTTTTGAAAAC-A-TTTTGAAAAT
* ** * *
1295034 CATATAATATACT-GTTTAAAAAATCATTTTTTAAAAA
1 TATATAATATA-TAGTTTTGAAAA-CA-TTTTGAAAAT
* * *
1295071 TATATATTATATAGCTTTGAAAATGATTTTTGAAAAT
1 TATATAATATATAGTTTTGAAAA-CA-TTTTGAAAAT
* ** *
1295108 ATATATATTATATAG-TTTGCAAATGATTTTTGAATA-
1 -TATATAATATATAGTTTTG-AAAACA-TTTTGAAAAT
** * *
1295144 TATATATATATATA-TAAT-ATAA-TTTTTGAAAAT
1 TATATA-ATATATAGTTTTGAAAACATTTTGAAAAT
**
1295177 ATATATAATATATAAGTTTTGAAAACATTTAAAAAAAT
1 -TATATAATATAT-AGTTTTGAAAACATTT-TGAAAAT
* *
1295215 TATATAATATATAGTTTTGAAATCATTTTGAAAGCT
1 TATATAATATATAGTTTTGAAAACATTTTGAAA-AT
1295251 TATATAATATATAGTTTT-AAAACATTTTTGAAAA-
1 TATATAATATATAGTTTTGAAAACA-TTTTGAAAAT
*
1295285 TATATATTATATATGTTT
1 TATATAATATATA-GTTT
1295303 ATTATTATTA
Statistics
Matches: 247, Mismatches: 36, Indels: 47
0.75 0.11 0.14
Matches are distributed among these distances:
32 8 0.03
33 15 0.06
34 21 0.09
35 21 0.09
36 72 0.29
37 66 0.27
38 33 0.13
39 10 0.04
40 1 0.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (35 bp):
TATATAATATATAGTTTTGAAAACATTTTGAAAAT
Found at i:1295309 original size:3 final size:3
Alignment explanation
Indices: 1295301--1295354 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
1295291 TTATATATGT
* *
1295301 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTG TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1295347 TT- TTA TTA
1 TTA TTA TTA
1295355 ATGTTTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.91
4 2 0.04
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1296870 original size:15 final size:15
Alignment explanation
Indices: 1296850--1296879 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1296840 ATTATATAAC
1296850 TTAAATACAAAATGT
1 TTAAATACAAAATGT
1296865 TTAAATACAAAATGT
1 TTAAATACAAAATGT
1296880 GGTGAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
TTAAATACAAAATGT
Found at i:1299427 original size:20 final size:20
Alignment explanation
Indices: 1299389--1299428 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1299379 TTTCAAATAT
* *
1299389 ATATAGTTTTTTAAGATACA
1 ATATAGTTTTTGAAAATACA
1299409 ATATAGTTTTTGAAAATACA
1 ATATAGTTTTTGAAAATACA
1299429 TTTTTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (20 bp):
ATATAGTTTTTGAAAATACA
Found at i:1299469 original size:36 final size:35
Alignment explanation
Indices: 1299429--1299567 Score: 149
Period size: 37 Copynumber: 3.8 Consensus size: 35
1299419 TGAAAATACA
1299429 TTTTTGAAAACATA-AT-ATATAGTTTTAAAAAAACGG
1 TTTTTGAAAACATATATAATATAGTTTT---AAAACGG
**
1299465 TTTTTGAAAACATATATAATATAGTTTTTGAAAACATA
1 TTTTTGAAAACATATATAATATAG-TTTT-AAAAC-GG
*
1299503 TTTTTGAAAACGTATA-ATATATAGTTGTTAAAACGG
1 TTTTTGAAAACATATATA-ATATAGTT-TTAAAACGG
1299539 TTTTTTGAAAACATATATAATATAGTTTT
1 -TTTTTGAAAACATATATAATATAGTTTT
1299568 TGAAAACATA
Statistics
Matches: 88, Mismatches: 7, Indels: 16
0.79 0.06 0.14
Matches are distributed among these distances:
36 16 0.18
37 38 0.43
38 30 0.34
39 4 0.05
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (35 bp):
TTTTTGAAAACATATATAATATAGTTTTAAAACGG
Found at i:1299491 original size:74 final size:74
Alignment explanation
Indices: 1299408--1299575 Score: 261
Period size: 74 Copynumber: 2.3 Consensus size: 74
1299398 TTTAAGATAC
*
1299408 AATATAGTTTTTGAAAATACATTTTTGAAAAC-ATAATATATAGTT-TTAAAAAAACGG-TTTTT
1 AATATAGTTTTTGAAAACACATTTTTGAAAACGATAATATATAGTTGTT---AAAACGGTTTTTT
1299470 GAAAACATATAT
63 GAAAACATATAT
*
1299482 AATATAGTTTTTGAAAACATATTTTTGAAAACGTATAATATATAGTTGTTAAAACGGTTTTTTGA
1 AATATAGTTTTTGAAAACACATTTTTGAAAACG-ATAATATATAGTTGTTAAAACGGTTTTTTGA
1299547 AAACATATAT
65 AAACATATAT
1299557 AATATAGTTTTTGAAAACA
1 AATATAGTTTTTGAAAACA
1299576 TATACATATA
Statistics
Matches: 88, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
74 37 0.42
75 36 0.41
76 13 0.15
77 2 0.02
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (74 bp):
AATATAGTTTTTGAAAACACATTTTTGAAAACGATAATATATAGTTGTTAAAACGGTTTTTTGAA
AACATATAT
Found at i:1299507 original size:38 final size:38
Alignment explanation
Indices: 1299408--1299578 Score: 192
Period size: 38 Copynumber: 4.6 Consensus size: 38
1299398 TTTAAGATAC
* *
1299408 AATATAGTTTTTGAAAATACATTTTTGAAAACATA-AT
1 AATATAGTTTTTGAAAACATATTTTTGAAAACATATAT
* * **
1299445 -ATATAG-TTTTAAAAAAACGGTTTTTGAAAACATATAT
1 AATATAGTTTTTGAAAACA-TATTTTTGAAAACATATAT
*
1299482 AATATAGTTTTTGAAAACATATTTTTGAAAACGTATA-
1 AATATAGTTTTTGAAAACATATTTTTGAAAACATATAT
* *
1299519 ATATATAGTTGTT-AAAACGGT-TTTTTGAAAACATATAT
1 A-ATATAGTTTTTGAAAAC-ATATTTTTGAAAACATATAT
1299557 AATATAGTTTTTGAAAACATAT
1 AATATAGTTTTTGAAAACATAT
1299579 ACATATAGTT
Statistics
Matches: 111, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
35 9 0.08
36 20 0.18
37 34 0.31
38 39 0.35
39 9 0.08
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (38 bp):
AATATAGTTTTTGAAAACATATTTTTGAAAACATATAT
Found at i:1299572 original size:75 final size:72
Alignment explanation
Indices: 1299408--1299578 Score: 263
Period size: 75 Copynumber: 2.3 Consensus size: 72
1299398 TTTAAGATAC
* *
1299408 AATATAGTTTTTGAAAATACATTTTTGAAAACATAATATATAGTTTTAAAAAAACGGTTTTTGAA
1 AATATAGTTTTTGAAAACATATTTTTGAAAACATAATATATAGTTTT--AAAAACGGTTTTTGAA
1299473 AACATATAT
64 AACATATAT
1299482 AATATAGTTTTTGAAAACATATTTTTGAAAACGTATAATATATAGTTGTT-AAAACGGTTTTTTG
1 AATATAGTTTTTGAAAACATATTTTTGAAAAC--ATAATATATAGTT-TTAAAAACGG-TTTTTG
1299546 AAAACATATAT
62 AAAACATATAT
1299557 AATATAGTTTTTGAAAACATAT
1 AATATAGTTTTTGAAAACATAT
1299579 ACATATAGTT
Statistics
Matches: 91, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
74 37 0.41
75 39 0.43
76 13 0.14
77 2 0.02
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (72 bp):
AATATAGTTTTTGAAAACATATTTTTGAAAACATAATATATAGTTTTAAAAACGGTTTTTGAAAA
CATATAT
Found at i:1299584 original size:23 final size:24
Alignment explanation
Indices: 1299540--1299596 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
1299530 TTAAAACGGT
1299540 TTTTTGAAAACATATATAATATAG
1 TTTTTGAAAACATATATAATATAG
*
1299564 TTTTTGAAAACATATA-CATATAG
1 TTTTTGAAAACATATATAATATAG
*
1299587 TTTTTAAAAA
1 TTTTTGAAAA
1299597 ATGATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (24 bp):
TTTTTGAAAACATATATAATATAG
Found at i:1299619 original size:62 final size:61
Alignment explanation
Indices: 1299503--1299624 Score: 149
Period size: 62 Copynumber: 2.0 Consensus size: 61
1299493 TGAAAACATA
* * *
1299503 TTTTTGAAAACGTATAATATATAGTTGTTAAAACGGTTTTTTGAAAACATATATAATATAG
1 TTTTTGAAAACATATAACATATAGTTGTTAAAACGATTTTTTGAAAACATATATAATATAG
* * *
1299564 TTTTTGAAAACATAT-ACATATAGTTTTTAAAAAATGATTTTTTGAAATCGA-ATATAATATA
1 TTTTTGAAAACATATAACATATAGTTGTT--AAAACGATTTTTTGAAAAC-ATATATAATATA
1299625 TAATCTTTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
60 11 0.21
61 14 0.27
62 26 0.50
63 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.42
Consensus pattern (61 bp):
TTTTTGAAAACATATAACATATAGTTGTTAAAACGATTTTTTGAAAACATATATAATATAG
Found at i:1299735 original size:23 final size:24
Alignment explanation
Indices: 1299688--1299759 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 24
1299678 CTTTAATACA
* * *
1299688 TATATTTTATATTTCTTTTTCTTTT
1 TATATATT-TATTTATTTTTATTTT
1299713 TATATATTTATTT-TTTTTATTTT
1 TATATATTTATTTATTTTTATTTT
* *
1299736 TATTTATTTATTTATTTTCATTTT
1 TATATATTTATTTATTTTTATTTT
1299760 GGTTTAGGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 21 0.50
24 14 0.33
25 7 0.17
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.76
Consensus pattern (24 bp):
TATATATTTATTTATTTTTATTTT
Found at i:1300898 original size:16 final size:17
Alignment explanation
Indices: 1300879--1300911 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1300869 ATTTTATTCC
1300879 TTTTATTTAC-TTATTT
1 TTTTATTTACTTTATTT
1300895 TTTTATTTACTTTATTT
1 TTTTATTTACTTTATTT
1300912 CGATCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTACTTTATTT
Found at i:1315517 original size:7 final size:6
Alignment explanation
Indices: 1315481--1315530 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
1315471 TTATTTTTCC
* *
1315481 TTTA-T TTTATT TTTATT CTTATT CTTATTT TTTATT TCTTA-T TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTATT T-TTATT TTTATT
1315529 TT
1 TT
1315531 GTAGATAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 7 0.18
6 24 0.62
7 8 0.21
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:1315519 original size:20 final size:18
Alignment explanation
Indices: 1315482--1315530 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1315472 TATTTTTCCT
1315482 TTATTTTA-TTTTTATTC
1 TTATTTTATTTTTTATTC
1315499 TTATTCTTATTTTTTATTTC
1 TTATT-TTATTTTTTA-TTC
1315519 TTATTTTATTTT
1 TTATTTTATTTT
1315531 GTAGATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.17
18 3 0.10
19 13 0.45
20 8 0.28
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
TTATTTTATTTTTTATTC
Found at i:1315655 original size:14 final size:15
Alignment explanation
Indices: 1315632--1315661 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1315622 TTAGGGAATA
1315632 TATT-CTTTTTTATT
1 TATTCCTTTTTTATT
1315646 TATTCCTTTTTTATT
1 TATTCCTTTTTTATT
1315661 T
1 T
1315662 TCTTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTCCTTTTTTATT
Found at i:1321606 original size:200 final size:200
Alignment explanation
Indices: 1321262--1322040 Score: 812
Period size: 200 Copynumber: 3.9 Consensus size: 200
1321252 AACCATTCAC
* * * * * * * *
1321262 AGCATAGCTCAAGACGAGAAGGGCTATCAATCAAAAAAACTTTTGAGTTCAATTTCATTCAACTT
1 AGCATAGCTCAAGGCAAGAAGGGCTATCTATCAAAAAAACTTTTAAGTTCGATTCCATTCAGCTC
* * * * * * * * *
1321327 GAGGGCGTATCAGCTGTATGGTAGCAACTAGGAACTACTTTCCTGTTAAATTTTGAACCGAGGTC
66 GAGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTTAAACTGAGGTC
* * * *
1321392 TTTAAGTGAAGAAGAATACCTATGTTGGCTGCGATTTAGCAACAATGAACTACATCCCAACCTAA
131 TTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTAGCAACAATGAACTACATCACAACCTAA
1321457 TTTAT
196 TTTAT
*
1321462 AGCATAGCTCAAGGCAAGAAGGGCTATCTATCAATAAAAACTTTTAAGTTCGATTACATTCAGCT
1 AGCATAGCTCAAGGCAAGAAGGGCTATCTATCAA-AAAAACTTTTAAGTTCGATTCCATTCAGCT
* * * * *
1321527 CGAGGG-TTATCAACTGCATAGTAGCAGTGAGGAACTACTTTTCAGTTGAAGTTTAAACTGAGGT
65 CGAGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTTAAACTGAGGT
* * * * *
1321591 CTTTTAGTCAAGAAGAAGACCTATATTGGCTACGATTTAGCAACAATGATCTATATCTCAACCTA
130 CTTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTAGCAACAATGAACTACATCACAACCTA
1321656 ATTTAT
195 ATTTAT
* * * *
1321662 AGCATAGCTCAAGGCAAGAAGGACTATCTGTCAAAGAAAACTTTTCAAGTTTGATTCCGTTCAGC
1 AGCATAGCTCAAGGCAAGAAGGGCTATCTATCAAA-AAAACTTTT-AAGTTCGATTCCATTCAGC
* * ** * *
1321727 TCGAGGGCGCATTAACCACATGGTAGCAGCGAGGAACTACTTTTTGGTTGAATTTTGAA-TCGAG
64 TCGAGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTTAAACT-GAG
* * * **
1321791 GTCTTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATATAGCAACAAGGAAATATC-TCACAGT
128 GTCTTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTAGCAACAATGAACTA-CATCACAAC
*
1321855 CTAATTTAC
192 CTAATTTAT
* * * * ** * * * * * * *
1321864 AACATAGCTTAAGTCGAGAAAAGTTGTATGTCAACAAAAACTTTCAAGTTCGATTCCATTTAGTT
1 AGCATAGCTCAAGGCAAGAAGGGCTATCTATCAA-AAAAACTTTTAAGTTCGATTCCATTCAGCT
* * * * *
1321929 CGAGGGTGTATCAACTGTATGGTAGCAGCGAGGAACTACTTTTCGGTTGAA-TTTAAAATCAAAG
65 CGAGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTTAAACT-GAGG
* * * * *
1321993 TCTTTAAGCCAATAAGAAGACCAAGGTTGACTACGATTT-GACAACAAT
129 TCTTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTAG-CAACAAT
1322041 AAGCCAATTT
Statistics
Matches: 482, Mismatches: 88, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
199 1 0.00
200 186 0.39
201 158 0.33
202 136 0.28
203 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (200 bp):
AGCATAGCTCAAGGCAAGAAGGGCTATCTATCAAAAAAACTTTTAAGTTCGATTCCATTCAGCTC
GAGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTTAAACTGAGGTC
TTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTAGCAACAATGAACTACATCACAACCTAA
TTTAT
Found at i:1322012 original size:201 final size:199
Alignment explanation
Indices: 1321262--1322040 Score: 778
Period size: 201 Copynumber: 3.9 Consensus size: 199
1321252 AACCATTCAC
* * * ** ** * * * *
1321262 AGCATAGCTCAAGACGAGAAGGGCTATCAATCAAAAAAACTTTTGAGTTCAATTTCATTCAACTT
1 AGCATAGCTCAAGGCAAGAAAGGCTATCTGTCAAAAAAACTTTCAAGTTCGATTCCATTCAGCTC
* * * * * * * ** *
1321327 GAGGGCGTATCAGCTGTATGGTAGCAACTAGGAACTACTTTCCTGTTAAATTTTGAACCGAGGTC
66 GAGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTAAAATCGAGGTC
* * * * *
1321392 TTTAAGTGAAGAAGAATACCTATGTTGGCTGCGATTTAGCAACAATGAACTA-CATCCCAACCTA
131 TTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTAGCAACAATGAAATATC-TCAC-ACCTA
1321456 ATTTAT
194 ATTTAT
* * * *
1321462 AGCATAGCTCAAGGCAAGAAGGGCTATCTATCAATAAAAACTTTTAAGTTCGATTACATTCAGCT
1 AGCATAGCTCAAGGCAAGAAAGGCTATCTGTCAA-AAAAACTTTCAAGTTCGATTCCATTCAGCT
* * * * *
1321527 CGAGGG-TTATCAACTGCATAGTAGCAGTGAGGAACTACTTTTCAGTTGAAGTTTAAACT-GAGG
65 CGAGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAA-TTTAAAATCGAGG
* * *
1321590 TCTTTTAGTCAAGAAGAAGACCTATATTGGCTACGATTTAGCAACAATGATCTATATCTCA-ACC
129 TCTTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTAGCAACAATGA--AATATCTCACACC
1321654 TAATTTAT
192 TAATTTAT
* *
1321662 AGCATAGCTCAAGGCAAG-AAGGACTATCTGTCAAAGAAAACTTTTCAAGTTTGATTCCGTTCAG
1 AGCATAGCTCAAGGCAAGAAAGG-CTATCTGTCAAA-AAAAC-TTTCAAGTTCGATTCCATTCAG
* * ** * **
1321726 CTCGAGGGCGCATTAACCACATGGTAGCAGCGAGGAACTACTTTTTGGTTGAATTTTGAATCGAG
63 CTCGAGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTAAAATCGAG
* * *
1321791 GTCTTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATATAGCAACAAGGAAATATCTCACAGTC
128 GTCTTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTAGCAACAATGAAATATCTCACA-CC
*
1321856 TAATTTAC
192 TAATTTAT
* * * * * * * * * *
1321864 AACATAGCTTAAGTCGAGAAAAGTTGTATGTCAACAAAAACTTTCAAGTTCGATTCCATTTAGTT
1 AGCATAGCTCAAGGCAAGAAAGGCTATCTGTCAA-AAAAACTTTCAAGTTCGATTCCATTCAGCT
* * * *
1321929 CGAGGGTGTATCAACTGTATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTAAAATCAAAGT
65 CGAGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTAAAATCGAGGT
* * * * *
1321994 CTTTAAGCCAATAAGAAGACCAAGGTTGACTACGATTT-GACAACAAT
130 CTTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTAG-CAACAAT
1322041 AAGCCAATTT
Statistics
Matches: 479, Mismatches: 85, Indels: 29
0.81 0.14 0.05
Matches are distributed among these distances:
199 4 0.01
200 167 0.35
201 179 0.37
202 124 0.26
203 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (199 bp):
AGCATAGCTCAAGGCAAGAAAGGCTATCTGTCAAAAAAACTTTCAAGTTCGATTCCATTCAGCTC
GAGGGCGTATCAACTGCATGGTAGCAGCGAGGAACTACTTTTCGGTTGAATTTAAAATCGAGGTC
TTTAAGTCAAGAAGAAGACCTATGTTGGCTACGATTTAGCAACAATGAAATATCTCACACCTAAT
TTAT
Found at i:1322779 original size:20 final size:20
Alignment explanation
Indices: 1322754--1322793 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1322744 TATACAATAT
*
1322754 ATATAGTTTTTGAAGATACA
1 ATATAGTTTTTGAAAATACA
1322774 ATATAGTTTTTGAAAATACA
1 ATATAGTTTTTGAAAATACA
1322794 TTTTTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (20 bp):
ATATAGTTTTTGAAAATACA
Found at i:1322872 original size:14 final size:14
Alignment explanation
Indices: 1322853--1322880 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1322843 ATATAATATA
1322853 GTTTTTGAAAACAT
1 GTTTTTGAAAACAT
1322867 GTTTTTGAAAACAT
1 GTTTTTGAAAACAT
1322881 ATAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
GTTTTTGAAAACAT
Found at i:1322879 original size:38 final size:37
Alignment explanation
Indices: 1322773--1322902 Score: 140
Period size: 38 Copynumber: 3.5 Consensus size: 37
1322763 TTGAAGATAC
*
1322773 AATATAGTTTTTGAAAATACATTTTTGAAAACATA-AT
1 AATATAGTTTTTGAAAACA-ATTTTTGAAAACATATAT
* * **
1322810 -ACATACTTTTAAAAAAACAATTTTTGAAAACATATAT
1 AATATAGTTTT-TGAAAACAATTTTTGAAAACATATAT
*
1322847 AATATAGTTTTTGAAAACATGTTTTTGAAAACATATA-
1 AATATAGTTTTTGAAAACA-ATTTTTGAAAACATATAT
*
1322884 ATATGTAGTTTTTGAAAAC
1 A-ATATAGTTTTTGAAAAC
1322903 GTATATAATA
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
36 23 0.30
37 14 0.18
38 40 0.52
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.39
Consensus pattern (37 bp):
AATATAGTTTTTGAAAACAATTTTTGAAAACATATAT
Found at i:1322894 original size:24 final size:22
Alignment explanation
Indices: 1322867--1322930 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 22
1322857 TTGAAAACAT
1322867 GTTTTTGAAAACATATAATATGTA
1 GTTTTTGAAAACATATAATA--TA
1322891 GTTTTTGAAAACGTATATAATATA
1 GTTTTTGAAAAC--ATATAATATA
1322915 GTTTTTGAAAACATAT
1 GTTTTTGAAAACATAT
1322931 TTTTGAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.11
24 26 0.68
26 8 0.21
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (22 bp):
GTTTTTGAAAACATATAATATA
Found at i:1322908 original size:62 final size:62
Alignment explanation
Indices: 1322830--1322964 Score: 227
Period size: 62 Copynumber: 2.2 Consensus size: 62
1322820 AAAAAAACAA
* * *
1322830 TTTTTGAAAACATATATAATATAGTTTTTGAAAACATGTTTTTGAAAACATATAATATGTAG
1 TTTTTGAAAACGTATATAATATAGTTTTTGAAAACATATTTTTGAAAACATATAATATATAG
*
1322892 TTTTTGAAAACGTATATAATATAGTTTTTGAAAACATATTTTTGAAAACGTATAATATATAG
1 TTTTTGAAAACGTATATAATATAGTTTTTGAAAACATATTTTTGAAAACATATAATATATAG
1322954 TTTTT-AAAACG
1 TTTTTGAAAACG
1322965 GTTTTGTGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
61 6 0.09
62 63 0.91
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.42
Consensus pattern (62 bp):
TTTTTGAAAACGTATATAATATAGTTTTTGAAAACATATTTTTGAAAACATATAATATATAG
Found at i:1322934 original size:38 final size:39
Alignment explanation
Indices: 1322892--1323065 Score: 209
Period size: 38 Copynumber: 4.6 Consensus size: 39
1322882 TAATATGTAG
1322892 TTTTTGAAAACGTATATAATATAGTTTTTGAAAACATA-
1 TTTTTGAAAACGTATATAATATAGTTTTTGAAAACATAT
**
1322930 TTTTTGAAAACGTATA-ATATATAGTTTTT-AAAAC-GGT
1 TTTTTGAAAACGTATATA-ATATAGTTTTTGAAAACATAT
* **
1322967 TTTGTGAAAATATATATAATATAGTTTTTGAAAACATAT
1 TTTTTGAAAACGTATATAATATAGTTTTTGAAAACATAT
* *
1323006 TTTTTGAATA--TATATATATATAGTTTTAGAAAACA-AT
1 TTTTTGAAAACGTATATA-ATATAGTTTTTGAAAACATAT
*
1323043 TTTTTAAAAACGTATATAATATA
1 TTTTTGAAAACGTATATAATATA
1323066 TATAATCTTT
Statistics
Matches: 116, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
37 46 0.40
38 55 0.47
39 15 0.13
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (39 bp):
TTTTTGAAAACGTATATAATATAGTTTTTGAAAACATAT
Found at i:1322976 original size:75 final size:75
Alignment explanation
Indices: 1322890--1323065 Score: 232
Period size: 75 Copynumber: 2.3 Consensus size: 75
1322880 TATAATATGT
1322890 AGTTTTTGAAAACGTATATAATATAGTTTTTGAAAACATA-TTTTTGAAAACGTATA-ATATATA
1 AGTTTTTGAAAACGTATATAATATAGTTTTTGAAAACATATTTTTTGAAAA--TATATATATATA
*
1322953 GTTTT-TAAAAC
64 GTTTTAGAAAAC
* ** *
1322964 GGTTTTGTGAAAATATATATAATATAGTTTTTGAAAACATATTTTTTGAATATATATATATATAG
1 AGTTTT-TGAAAACGTATATAATATAGTTTTTGAAAACATATTTTTTGAAAATATATATATATAG
1323029 TTTTAGAAAAC
65 TTTTAGAAAAC
* *
1323040 AATTTTTTAAAAACGTATATAATATA
1 -AGTTTTTGAAAACGTATATAATATA
1323066 TATAATCTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
74 9 0.10
75 44 0.51
76 30 0.34
77 4 0.05
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (75 bp):
AGTTTTTGAAAACGTATATAATATAGTTTTTGAAAACATATTTTTTGAAAATATATATATATAGT
TTTAGAAAAC
Found at i:1323172 original size:19 final size:19
Alignment explanation
Indices: 1323137--1323187 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1323127 ATACATATAT
* *
1323137 TTTATATTT-TATAATTTA
1 TTTATATTTATTTTATTTA
1323155 TTTATATTTATTTTATTTA
1 TTTATATTTATTTTATTTA
1323174 TTTAT-TTTCATTTT
1 TTTATATTT-ATTTT
1323188 GGTTTTGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATATTTATTTTATTTA
Found at i:1327351 original size:20 final size:20
Alignment explanation
Indices: 1327326--1327373 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1327316 ATTTACAGCT
1327326 TCCAACGGATCCAAATCATC
1 TCCAACGGATCCAAATCATC
* *
1327346 TCCAACAGCTCCAAATCATC
1 TCCAACGGATCCAAATCATC
1327366 TCCAACGG
1 TCCAACGG
1327374 CCAACAACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.38, G:0.10, T:0.19
Consensus pattern (20 bp):
TCCAACGGATCCAAATCATC
Found at i:1332646 original size:16 final size:17
Alignment explanation
Indices: 1332620--1332651 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1332610 TCTTCTGAAT
1332620 AAATGTATGTGAATTAG
1 AAATGTATGTGAATTAG
1332637 AAAT-TATGTGAATTA
1 AAATGTATGTGAATTA
1332652 AGGATTATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AAATGTATGTGAATTAG
Found at i:1341479 original size:20 final size:20
Alignment explanation
Indices: 1341441--1341486 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1341431 TTAAAGAAGA
*
1341441 AAAAAGAAGGAGAAAAAAAG
1 AAAAAGAAAGAGAAAAAAAG
*
1341461 AAAAAGAAAGAAAATAAAATAG
1 AAAAAGAAAGAGAA-AAAA-AG
1341483 AAAA
1 AAAA
1341487 TAAAAAGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 4 0.18
22 6 0.27
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (20 bp):
AAAAAGAAAGAGAAAAAAAG
Found at i:1341878 original size:21 final size:22
Alignment explanation
Indices: 1341838--1341878 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
1341828 ATTTATTAAT
1341838 AAATTCTAAGTTTATCTTTTTG
1 AAATTCTAAGTTTATCTTTTTG
1341860 AAATTC-AA-TTTATTCTTTT
1 AAATTCTAAGTTTA-TCTTTT
1341879 ATAAACATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (22 bp):
AAATTCTAAGTTTATCTTTTTG
Found at i:1342594 original size:122 final size:123
Alignment explanation
Indices: 1342370--1342702 Score: 521
Period size: 122 Copynumber: 2.7 Consensus size: 123
1342360 CACTCGATGG
* *
1342370 ATCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATATGAGAAGGAAGAAAAAGTTCATA
1 ATCAACATTGCCAGATAGAGTTCATAATGAGAAGAAATCATCTGAGAAGGAAGAAAAAGTTCATA
* * *
1342435 ATGAGAAGAAATTGTTCAACCTTTTGCTCGACTCTATCACAGAATGAGATAAATCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAAATCAGC
*
1342493 A-CTAATATTGCCAGATAGAGTTCATAATGAGAAGAAATCATCTGAGAAGGAA-AAAAAGTTCAT
1 ATC-AACATTGCCAGATAGAGTTCATAATGAGAAGAAATCATCTGAGAAGGAAGAAAAAGTTCAT
*
1342556 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATATATCAGC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAAATCAGC
* * *
1342615 ATCAACATTTCCAGATAGAGTTCATAATGAGAA-AAACTCATCTGA-AGGGGAAGAAGAAGTTCA
1 ATCAACATTGCCAGATAGAGTTCATAATGAGAAGAAA-TCATCTGAGA-AGGAAGAAAAAGTTCA
1342678 TAATGAGAAGAACTTGTTCAACCTT
64 TAATGAGAAGAACTTGTTCAACCTT
1342703 GCCTTAATTA
Statistics
Matches: 194, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
121 4 0.02
122 108 0.56
123 82 0.42
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (123 bp):
ATCAACATTGCCAGATAGAGTTCATAATGAGAAGAAATCATCTGAGAAGGAAGAAAAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAAAAGGAGATAAATCAGC
Found at i:1342926 original size:39 final size:39
Alignment explanation
Indices: 1342881--1342985 Score: 174
Period size: 39 Copynumber: 2.7 Consensus size: 39
1342871 TGTCATTCCT
1342881 AGTGGAAGAGTTCATAATGAGAAGAAATAGTCCCAAAGA
1 AGTGGAAGAGTTCATAATGAGAAGAAATAGTCCCAAAGA
*
1342920 AGTGGAAGAGTTCATAATGAGAAGAACTAGTCCCAAAGA
1 AGTGGAAGAGTTCATAATGAGAAGAAATAGTCCCAAAGA
**
1342959 AGAAGAAGAAGTTCATAATGAGAAGAA
1 AGTGGAAG-AGTTCATAATGAGAAGAA
1342986 CTTGTTCAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
39 44 0.71
40 18 0.29
ACGTcount: A:0.48, C:0.10, G:0.26, T:0.17
Consensus pattern (39 bp):
AGTGGAAGAGTTCATAATGAGAAGAAATAGTCCCAAAGA
Found at i:1342982 original size:20 final size:19
Alignment explanation
Indices: 1342885--1342985 Score: 57
Period size: 20 Copynumber: 5.2 Consensus size: 19
1342875 ATTCCTAGTG
1342885 GAAGAGTTCATAATGAGAA
1 GAAGAGTTCATAATGAGAA
* * **
1342904 GAAATAGTCCCA-AA-GAAGTG
1 G-AAGAGT-TCATAATG-AGAA
1342924 GAAGAGTTCATAATGAGAA
1 GAAGAGTTCATAATGAGAA
* *
1342943 GAACTAGTCCCA-AA-GAAGAA
1 GAA-GAGT-TCATAATG-AGAA
1342963 GAAGAAGTTCATAATGAGAA
1 GAAG-AGTTCATAATGAGAA
1342983 GAA
1 GAA
1342986 CTTGTTCAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 21
0.64 0.13 0.23
Matches are distributed among these distances:
18 2 0.03
19 17 0.29
20 35 0.59
21 5 0.08
ACGTcount: A:0.49, C:0.10, G:0.25, T:0.17
Consensus pattern (19 bp):
GAAGAGTTCATAATGAGAA
Found at i:1342992 original size:20 final size:20
Alignment explanation
Indices: 1342928--1342993 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
1342918 GAAGTGGAAG
1342928 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
1342948 AGTCCCA-AA-GAAGAAGAAGA
1 AGT-TCATAATG-AGAAGAACT
1342968 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
1342988 TGTTCA
1 AGTTCA
1342994 ACATTTCCAT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 3 0.09
20 29 0.83
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:1353746 original size:37 final size:36
Alignment explanation
Indices: 1353705--1353812 Score: 153
Period size: 37 Copynumber: 2.9 Consensus size: 36
1353695 AACATAACGT
*
1353705 TAGAGTTTTACTAGGATTCAAATTCTTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAATTC-TAAAAATATGA
*
1353742 TAGAGTTTTACTATGATTCAAAATTCTAAAAATTTGA
1 TAGAGTTTTACTATGATTC-AAATTCTAAAAATATGA
* *
1353779 TAGAGTTTTACTTTGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTATGATTCAAA-TTCTAAAAATA
1353813 AGATCCATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 3 0.05
37 55 0.86
38 6 0.09
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (36 bp):
TAGAGTTTTACTATGATTCAAATTCTAAAAATATGA
Found at i:1354542 original size:10 final size:9
Alignment explanation
Indices: 1354512--1354606 Score: 50
Period size: 10 Copynumber: 9.7 Consensus size: 9
1354502 ATTATTAGTA
1354512 TTATTATTAT
1 TTATT-TTAT
1354522 TCTATTTTAT
1 T-TATTTTAT
1354532 TTATTTCTAT
1 TTATTT-TAT
1354542 TTACCTTTTTAT
1 TTA---TTTTAT
*
1354554 TT-TTATTCT
1 TTATT-TTAT
1354563 TTATCTTTAT
1 TTAT-TTTAT
1354573 TT-TTTTAT
1 TTATTTTAT
* *
1354581 CTTCTTTACAT
1 -TTATTT-TAT
*
1354592 TTGTTTTAT
1 TTATTTTAT
1354601 TTATTT
1 TTATTT
1354607 GTGTTTTCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
8 7 0.10
9 20 0.29
10 26 0.38
11 7 0.10
12 5 0.07
13 3 0.04
ACGTcount: A:0.18, C:0.09, G:0.01, T:0.72
Consensus pattern (9 bp):
TTATTTTAT
Found at i:1354598 original size:23 final size:24
Alignment explanation
Indices: 1354548--1354604 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
1354538 CTATTTACCT
* *
1354548 TTTTATTTTTATTCTTTATCTTTA
1 TTTTATTTATCTTCTTTATCTTTA
*
1354572 TTTT-TTTATCTTCTTTA-CATTTG
1 TTTTATTTATCTTCTTTATC-TTTA
1354595 TTTTATTTAT
1 TTTTATTTAT
1354605 TTGTGTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 1 0.04
23 18 0.64
24 9 0.32
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTTATTTATCTTCTTTATCTTTA
Found at i:1357671 original size:24 final size:24
Alignment explanation
Indices: 1357641--1357686 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1357631 CAAAAAGAAA
* *
1357641 AAAGAGAAAATACAAAGAAAAAGT
1 AAAGAGAAAATAAAAACAAAAAGT
1357665 AAAGAGAAAATAAAAACAAAAA
1 AAAGAGAAAATAAAAACAAAAA
1357687 CAAAGGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (24 bp):
AAAGAGAAAATAAAAACAAAAAGT
Found at i:1359285 original size:43 final size:43
Alignment explanation
Indices: 1359231--1359333 Score: 143
Period size: 43 Copynumber: 2.4 Consensus size: 43
1359221 ACGAAGGGGT
* *
1359231 CATCCATGATTTCAACTCCACGATGGAGGATATCGTACCCACG
1 CATCCACGATTTCAACTCCACGATGGAGGATATCGTACCCACA
* * *
1359274 GATCCACGATTTCAACTCCACGATGGTGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGATGGAGGATATCGTACCCACA
* *
1359317 CAACCACGATTTGAACT
1 CATCCACGATTTCAACT
1359334 TCACAACGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGATGGAGGATATCGTACCCACA
Found at i:1359733 original size:124 final size:124
Alignment explanation
Indices: 1359495--1359735 Score: 304
Period size: 124 Copynumber: 1.9 Consensus size: 124
1359485 TAGTACAAGC
* * * *
1359495 TTGGATTTCAACTTCACGACAAAGGATGTTCAAGTCAAGGCTCAACTTCACGACGAATGGGCCGT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAATGGGCCAT
** * * *
1359560 CCACGGTTTCAACTTCACGACGAAAGGAATTGTGCACACAAGCATCATTCATATTTATA
66 CCACAATTTCAACTTCACGACGAAAGGAATCGTACACACAAGCAACATTCATATTTATA
* * * * *
1359619 TTGGATTTCAACTTCACGTCGAATGATATCCAATTCAAGGCTCAACTTCATAACGAA-GGTGCCA
1 TTGGATTTCAACTTCACGACAAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAATGG-GCCA
* * * *
1359683 TCCACAATTTGAACTTCACGACGAAGGGAATCGTACCCACTAGCAACATTCAT
65 TCCACAATTTCAACTTCACGACGAAAGGAATCGTACACACAAGCAACATTCAT
1359736 CTTCAGGAAC
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
123 2 0.02
124 96 0.98
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGACAAAGGATATCCAAGTCAAGGCTCAACTTCACAACGAATGGGCCAT
CCACAATTTCAACTTCACGACGAAAGGAATCGTACACACAAGCAACATTCATATTTATA
Found at i:1359847 original size:37 final size:35
Alignment explanation
Indices: 1359803--1359961 Score: 194
Period size: 36 Copynumber: 4.4 Consensus size: 35
1359793 TGTCGTTTCG
1359803 CTTGAGACTAATTTACTC-AAAACAAAGTTTTGTCTCT
1 CTTGAGAC-AATTT-CTCTAAAACAAA-TTTTGTCTCT
1359840 CTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCT
1 CTTGAGACAATTTCTC-TAAAACAAATTTTGTCTCT
* * * *
1359876 CTTGAGACAGTTTCTCTTGAAACAAATTTTTTGTCT
1 CTTGAGACAATTTCTC-TAAAACAAATTTTGTCTCT
* *
1359912 CTTGAGACAGTTTCCCTTAAAACAAATTTTGTCTCT
1 CTTGAGACAATTTCTC-TAAAACAAATTTTGTCTCT
*
1359948 CTTGAGACAGTTTC
1 CTTGAGACAATTTC
1359962 CCTTGAAACA
Statistics
Matches: 112, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
35 3 0.03
36 93 0.83
37 16 0.14
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (35 bp):
CTTGAGACAATTTCTCTAAAACAAATTTTGTCTCT
Found at i:1359870 original size:36 final size:36
Alignment explanation
Indices: 1359821--1359973 Score: 234
Period size: 36 Copynumber: 4.2 Consensus size: 36
1359811 TAATTTACTC
*
1359821 AAAACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
1359858 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * * *
1359894 GAAACAAATTTTTTGTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
1359930 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
1359966 GAAACAAA
1 AAAACAAA
1359974 ATCTTTGAAT
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
36 99 0.93
37 8 0.07
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.39
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:1360023 original size:101 final size:103
Alignment explanation
Indices: 1359886--1360075 Score: 278
Period size: 102 Copynumber: 1.9 Consensus size: 103
1359876 CTTGAGACAG
* * *
1359886 TTTCTCTTGAAACAAATTTTTTGTCTCTTGAGACAGTTTCCCTT-AAAAC-AAATTTTGTCTCTC
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTT-CCTTCAAAACTAAATTTTGTCTCTC
*
1359949 TTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTGT
65 TTGAGACAGTTTCCCTTAAAACAAAATCTTTGAATTTGT
* ** *
1359988 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTCGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCTTCAAAACTAAATTTTGTCTCTCT
1360052 TGAGACAGTTTCCCTTAAAACAAA
66 TGAGACAGTTTCCCTTAAAACAAA
1360076 GTTTTATCTC
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 3 0.04
101 34 0.44
102 41 0.53
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (103 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCTTCAAAACTAAATTTTGTCTCTCT
TGAGACAGTTTCCCTTAAAACAAAATCTTTGAATTTGT
Found at i:1360054 original size:37 final size:36
Alignment explanation
Indices: 1359996--1360110 Score: 124
Period size: 37 Copynumber: 3.1 Consensus size: 36
1359986 GTTTTCCTTG
* *
1359996 AAACAAA-TTTTGTCTCCCTTGAGACAGTTTCTTTCG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTT-A
* * *
1360032 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTA
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTT-CTTTA
* * *
1360069 AAACAAAGTTTTATCTCTCTTGAGACAATTTCTCTTG
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCT-TTA
1360106 AAACA
1 AAACA
1360111 CCAATCTTTG
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
36 6 0.09
37 56 0.86
38 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (36 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTA
Found at i:1360577 original size:14 final size:14
Alignment explanation
Indices: 1360558--1360596 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1360548 TAATGGGGAG
1360558 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
1360572 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
1360586 GAATCTCTGCA
1 TAATCCCTGCA
1360597 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:1365493 original size:37 final size:37
Alignment explanation
Indices: 1365452--1365526 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
1365442 AACATAACGT
*
1365452 TAGAGTTTTATTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
*
1365489 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1365526 T
1 T
1365527 CCATAAGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:1366071 original size:21 final size:21
Alignment explanation
Indices: 1366002--1366071 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
1365992 TTTATTTGCA
*
1366002 TATTCATTATATTTTTTATCT-
1 TATT-ATTATATTTTTTCTCTC
* *
1366023 TATT-TTAT-TTAATTTCCCTAC
1 TATTATTATATT-TTTTCTCT-C
*
1366044 CATTATTATATTTTTTCTCTC
1 TATTATTATATTTTTTCTCTC
1366065 TATTATT
1 TATTATT
1366072 TATCTATACA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
18 2 0.05
19 9 0.24
21 14 0.38
22 10 0.27
23 2 0.05
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTATTATATTTTTTCTCTC
Found at i:1366272 original size:10 final size:9
Alignment explanation
Indices: 1366198--1366274 Score: 52
Period size: 10 Copynumber: 8.0 Consensus size: 9
1366188 ACCCTTCTAT
1366198 TTTTATTTTA
1 TTTTA-TTTA
1366208 TTTTA-TTA
1 TTTTATTTA
*
1366216 CTCTTTACTTA
1 -T-TTTATTTA
1366227 TTGTT-TTTA
1 TT-TTATTTA
1366236 TTATTA-TTA
1 TT-TTATTTA
1366245 TTATTATTCTA
1 TT-TTATT-TA
1366256 TTTTATTTA
1 TTTTATTTA
1366265 TTTCTATTTA
1 TTT-TATTTA
1366275 CCTTTTTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
8 3 0.05
9 23 0.40
10 24 0.42
11 7 0.12
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.70
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1366458 original size:25 final size:25
Alignment explanation
Indices: 1366416--1366472 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
1366406 CGTATTCATT
*
1366416 TTTATCTTCACTC-TTTTTTTTATTCC
1 TTTAT-TTCACTCGTTTTTTATATT-C
*
1366442 TTTATTTCAGTCGTTTTTTATATTC
1 TTTATTTCACTCGTTTTTTATATTC
1366467 TTTATT
1 TTTATT
1366473 CTATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.14, C:0.16, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTATTTCACTCGTTTTTTATATTC
Found at i:1368143 original size:3 final size:3
Alignment explanation
Indices: 1368135--1368232 Score: 196
Period size: 3 Copynumber: 32.7 Consensus size: 3
1368125 AAGTGTTTTG
1368135 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
1368183 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
1368231 TA
1 TA
1368233 TAAGGTAATG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1369466 original size:2 final size:2
Alignment explanation
Indices: 1369459--1369490 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1369449 TCCTAAAATA
1369459 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
1369491 GTATGTATGT
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):
AT
Found at i:1375810 original size:81 final size:81
Alignment explanation
Indices: 1375673--1375826 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
1375663 CTTGTATAAC
* ** *
1375673 CGGCTCGGTAGCTTCCTTCTCTACACCTCTGTGAGAGCTTTTCGATCCGCCATTTCGTGTGCGAA
1 CGGCTCAGTAGCTTCCCACTCTACACCTCGGTGAGAGCTTTTCGATCCGCCATTTCGTGTGCGAA
1375738 CCATTCTCGGTACAAT
66 CCATTCTCGGTACAAT
* * * *
1375754 CGGCTCAGTAGCTTCCCACTCTACACTTCGGTGAGAGCTTGTT-GCTCTGCCGTTTCGTGTGCGA
1 CGGCTCAGTAGCTTCCCACTCTACACCTCGGTGAGAGCTT-TTCGATCCGCCATTTCGTGTGCGA
1375818 ACCATTCTC
65 ACCATTCTC
1375827 TATAACTCGC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 62 0.97
82 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.22, T:0.32
Consensus pattern (81 bp):
CGGCTCAGTAGCTTCCCACTCTACACCTCGGTGAGAGCTTTTCGATCCGCCATTTCGTGTGCGAA
CCATTCTCGGTACAAT
Found at i:1376000 original size:55 final size:55
Alignment explanation
Indices: 1375939--1376183 Score: 312
Period size: 55 Copynumber: 4.5 Consensus size: 55
1375929 TTCTTGAATT
* *
1375939 AATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTATAGCTAAA
1 AATGATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGTAGCTAAA
* * *
1375994 AGTGATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAA
1 AATGATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGTAGCTAAA
* * * * * * *
1376049 AATGACTGAGCACCTATGTGCTTC-AGCCAGGAGCTCACACCTCTGTGTAGCTAAG
1 AATGATTGAGCACCTCTGTGCTTCAATCGA-GAACTGACACCTCTGTGTAGCTAAA
* * * *
1376104 ACTGATTGAGCACCTCTGTGCCTCAACCGAGAACTGACACCTCTGTGTAGTTAAA
1 AATGATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGTAGCTAAA
* *
1376159 AATGACTAAGCACCTCTGTGCTTCA
1 AATGATTGAGCACCTCTGTGCTTCA
1376184 GTCTAAAATC
Statistics
Matches: 159, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
54 3 0.02
55 153 0.96
56 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (55 bp):
AATGATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGTAGCTAAA
Found at i:1376039 original size:27 final size:27
Alignment explanation
Indices: 1375949--1376041 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 27
1375939 AATGATTGAG
*
1375949 CACCTCTGTGCTTCAATCGAGAGCTGA
1 CACCTCTGTGCTTCAATCGAGAACTGA
** * *
1375976 CACCTCTGTATAGC-T-AAAAGTG-ATTGA
1 CACCTCTG--T-GCTTCAATCGAGAACTGA
1376003 GCACCTCTGTGCTTCAATCGAGAACTGA
1 -CACCTCTGTGCTTCAATCGAGAACTGA
1376031 CACCTCTGTGC
1 CACCTCTGTGC
1376042 AGTTAAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 26 0.52
28 16 0.32
29 2 0.04
30 2 0.04
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (27 bp):
CACCTCTGTGCTTCAATCGAGAACTGA
Found at i:1376059 original size:110 final size:111
Alignment explanation
Indices: 1375939--1376183 Score: 368
Period size: 110 Copynumber: 2.2 Consensus size: 111
1375929 TTCTTGAATT
* * * * *
1375939 AATGATTGAGCACCTCTGTGCTTCAATCGA-GAGCTGACACCTCTGTATAGCTAAAAGTGATTGA
1 AATGACTGAGCACCTCTGTGCTTCAAGCCAGGAGCTCACACCTCTGTATAGCTAAAACTGATTGA
* *
1376003 GCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAA
66 GCACCTCTGTGCCTCAACCGAGAACTGACACCTCTGTGCAGTTAAA
* * *
1376049 AATGACTGAGCACCTATGTGCTTC-AGCCAGGAGCTCACACCTCTGTGTAGCTAAGACTGATTGA
1 AATGACTGAGCACCTCTGTGCTTCAAGCCAGGAGCTCACACCTCTGTATAGCTAAAACTGATTGA
*
1376113 GCACCTCTGTGCCTCAACCGAGAACTGACACCTCTGTGTAGTTAAA
66 GCACCTCTGTGCCTCAACCGAGAACTGACACCTCTGTGCAGTTAAA
*
1376159 AATGACTAAGCACCTCTGTGCTTCA
1 AATGACTGAGCACCTCTGTGCTTCA
1376184 GTCTAAAATC
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
109 3 0.03
110 117 0.98
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (111 bp):
AATGACTGAGCACCTCTGTGCTTCAAGCCAGGAGCTCACACCTCTGTATAGCTAAAACTGATTGA
GCACCTCTGTGCCTCAACCGAGAACTGACACCTCTGTGCAGTTAAA
Found at i:1377468 original size:16 final size:16
Alignment explanation
Indices: 1377449--1377489 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1377439 AATAATTTTT
1377449 TAATATTATAATCATA
1 TAATATTATAATCATA
* *
1377465 TAATATTATATTTATA
1 TAATATTATAATCATA
*
1377481 TAAAATTAT
1 TAATATTAT
1377490 TATACTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATATTATAATCATA
Found at i:1381502 original size:20 final size:20
Alignment explanation
Indices: 1381477--1381526 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1381467 TCACCCTGAA
1381477 TATCGATACTGTAAGGGCAT
1 TATCGATACTGTAAGGGCAT
1381497 TATCGATACTGTAAGGGCAT
1 TATCGATACTGTAAGGGCAT
1381517 TATCGATACT
1 TATCGATACT
1381527 ATTGGAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (20 bp):
TATCGATACTGTAAGGGCAT
Found at i:1382839 original size:22 final size:22
Alignment explanation
Indices: 1382804--1382845 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1382794 GACCACACGG
**
1382804 CCACTGCCTCTGCTGCCACCAT
1 CCACTGCCGATGCTGCCACCAT
*
1382826 CCACTGCCGATGCTTCCACC
1 CCACTGCCGATGCTGCCACC
1382846 GTCAGGTGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.50, G:0.14, T:0.21
Consensus pattern (22 bp):
CCACTGCCGATGCTGCCACCAT
Found at i:1383780 original size:30 final size:28
Alignment explanation
Indices: 1383743--1383826 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 28
1383733 TAGAGCTTTT
1383743 AATTTTAATATTTTATATTTTAATCACTG
1 AATTTTAATATTTTATATTTTAATCA-TG
*
1383772 ATATTTTAATTACTTTTAT-TTTT-ACCATG
1 A-ATTTTAA-TA-TTTTATATTTTAATCATG
* *
1383801 AATTTTATATATTTTACAATTTAATC
1 AATTTTA-ATATTTTATATTTTAATC
1383827 CTATAATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
27 5 0.11
28 11 0.24
29 7 0.16
30 10 0.22
31 6 0.13
32 6 0.13
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.56
Consensus pattern (28 bp):
AATTTTAATATTTTATATTTTAATCATG
Found at i:1383791 original size:15 final size:15
Alignment explanation
Indices: 1383738--1383793 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
1383728 CAAATTAGAG
1383738 CTTTTAATTTTAA-TA
1 CTTTT-ATTTTAATTA
* *
1383753 TTTTATATTTTAATCA
1 CTTT-TATTTTAATTA
**
1383769 CTGATATTTTAATTA
1 CTTTTATTTTAATTA
1383784 CTTTTATTTT
1 CTTTTATTTT
1383794 TACCATGAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 28 0.90
16 3 0.10
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (15 bp):
CTTTTATTTTAATTA
Found at i:1386498 original size:43 final size:42
Alignment explanation
Indices: 1386437--1386518 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 42
1386427 TGTCTTTGGA
*
1386437 GAAGTTAGAAGTGAAAGTTATCTCCTATATGTAAAGTTTTATT
1 GAAGTTAGAAGTGAAAGTTATC-CATATATGTAAAGTTTTATT
*
1386480 GAAGTTAGGAA-TGAAAGTTATCCATGTATGTAAAGTTTT
1 GAAGTTA-GAAGTGAAAGTTATCCATATATGTAAAGTTTT
1386519 GTATGATGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 15 0.42
43 18 0.50
44 3 0.08
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (42 bp):
GAAGTTAGAAGTGAAAGTTATCCATATATGTAAAGTTTTATT
Found at i:1386629 original size:6 final size:7
Alignment explanation
Indices: 1386599--1386634 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
1386589 TTCATACATA
1386599 TTTGCAT
1 TTTGCAT
1386606 TTTGCAT
1 TTTGCAT
1386613 CTTTGCAT
1 -TTTGCAT
1386621 TTT-CAT
1 TTTGCAT
1386627 TTTGCAT
1 TTTGCAT
1386634 T
1 T
1386635 CATACTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.22
7 14 0.52
8 7 0.26
ACGTcount: A:0.14, C:0.17, G:0.11, T:0.58
Consensus pattern (7 bp):
TTTGCAT
Found at i:1387058 original size:42 final size:42
Alignment explanation
Indices: 1386997--1387080 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
1386987 AGAGATGATT
* * * *
1386997 GATCAAGTAAAAAAGTTCCAAGGTGATTCAAATGAACAAATG
1 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
*
1387039 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAGCAAATG
1 GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
1387081 ACAAAACTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.19
Consensus pattern (42 bp):
GATCAAGCAAAAAAATTCCAAGATGATTCAAAAGAACAAATG
Found at i:1392806 original size:29 final size:28
Alignment explanation
Indices: 1392774--1392906 Score: 142
Period size: 27 Copynumber: 4.7 Consensus size: 28
1392764 TTTTTTTAAA
* *
1392774 TAATTACCAAAATAGCACCATTTTCGAAT
1 TAATTCCCAAAATAACACCA-TTTCGAAT
* * **
1392803 TAATTCCCAAAATAGCACCGTTTTTTAAAT
1 TAATTCCCAAAATAACACC--ATTTCGAAT
*
1392833 TAATTCCCAAAATAACACTATTTCGAAT
1 TAATTCCCAAAATAACACCATTTCGAAT
*
1392861 T-ATTCCCAAAATAACATCATTTCGAAT
1 TAATTCCCAAAATAACACCATTTCGAAT
* *
1392888 TAATTGCTAAAATAACACC
1 TAATTCCCAAAATAACACC
1392907 CAGTCAACGG
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
27 25 0.29
28 21 0.24
29 18 0.21
30 23 0.26
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.32
Consensus pattern (28 bp):
TAATTCCCAAAATAACACCATTTCGAAT
Found at i:1392836 original size:30 final size:29
Alignment explanation
Indices: 1392765--1392873 Score: 116
Period size: 30 Copynumber: 3.8 Consensus size: 29
1392755 ATATCACCTT
*
1392765 TTTTTTAAA-TAATTACCAAAATAGCACC
1 TTTTTTAAATTAATTCCCAAAATAGCACC
* **
1392793 ATTTTCGAATTAATTCCCAAAATAGCACC
1 TTTTTTAAATTAATTCCCAAAATAGCACC
*
1392822 GTTTTTTAAATTAATTCCCAAAATAACA-C
1 -TTTTTTAAATTAATTCCCAAAATAGCACC
* **
1392851 TATTTCGAATT-ATTCCCAAAATA
1 TTTTTTAAATTAATTCCCAAAATA
1392874 ACATCATTTC
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
27 12 0.18
28 14 0.21
29 19 0.28
30 23 0.34
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (29 bp):
TTTTTTAAATTAATTCCCAAAATAGCACC
Found at i:1392860 original size:58 final size:57
Alignment explanation
Indices: 1392765--1392873 Score: 166
Period size: 58 Copynumber: 1.9 Consensus size: 57
1392755 ATATCACCTT
*
1392765 TTTTTTAAATAATTACCAAAATAGCACCATTTTCGAATTAATTCCCAAAATAGCACCG
1 TTTTTTAAATAATTACCAAAATAACACCATTTTCGAATT-ATTCCCAAAATAGCACCG
* *
1392823 TTTTTTAAATTAATTCCCAAAATAACACTA-TTTCGAATTATTCCCAAAATA
1 TTTTTTAAA-TAATTACCAAAATAACACCATTTTCGAATTATTCCCAAAATA
1392874 ACATCATTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
57 12 0.26
58 18 0.38
59 17 0.36
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (57 bp):
TTTTTTAAATAATTACCAAAATAACACCATTTTCGAATTATTCCCAAAATAGCACCG
Found at i:1399716 original size:208 final size:208
Alignment explanation
Indices: 1399284--1399701 Score: 836
Period size: 208 Copynumber: 2.0 Consensus size: 208
1399274 AACATATCAG
1399284 AAATATACAGTAAATAAGATATCAGGTACACAATATTCCTATATATATTTGAAACATTACTAATG
1 AAATATACAGTAAATAAGATATCAGGTACACAATATTCCTATATATATTTGAAACATTACTAATG
1399349 TAACACTGTCGGGAAACACACCTGTAACAGTCTGAGAAATCAGATACGGAAGCTTATTACTGGGT
66 TAACACTGTCGGGAAACACACCTGTAACAGTCTGAGAAATCAGATACGGAAGCTTATTACTGGGT
1399414 TTGTCGATCACGCTCTGCTACAACGCTAGATCATACGAATTGAAAAAATCCATATTGGAATCCTA
131 TTGTCGATCACGCTCTGCTACAACGCTAGATCATACGAATTGAAAAAATCCATATTGGAATCCTA
1399479 ATATAAATAATCT
196 ATATAAATAATCT
1399492 AAATATACAGTAAATAAGATATCAGGTACACAATATTCCTATATATATTTGAAACATTACTAATG
1 AAATATACAGTAAATAAGATATCAGGTACACAATATTCCTATATATATTTGAAACATTACTAATG
1399557 TAACACTGTCGGGAAACACACCTGTAACAGTCTGAGAAATCAGATACGGAAGCTTATTACTGGGT
66 TAACACTGTCGGGAAACACACCTGTAACAGTCTGAGAAATCAGATACGGAAGCTTATTACTGGGT
1399622 TTGTCGATCACGCTCTGCTACAACGCTAGATCATACGAATTGAAAAAATCCATATTGGAATCCTA
131 TTGTCGATCACGCTCTGCTACAACGCTAGATCATACGAATTGAAAAAATCCATATTGGAATCCTA
1399687 ATATAAATAATCT
196 ATATAAATAATCT
1399700 AA
1 AA
1399702 CTATTATTTA
Statistics
Matches: 210, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
208 210 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (208 bp):
AAATATACAGTAAATAAGATATCAGGTACACAATATTCCTATATATATTTGAAACATTACTAATG
TAACACTGTCGGGAAACACACCTGTAACAGTCTGAGAAATCAGATACGGAAGCTTATTACTGGGT
TTGTCGATCACGCTCTGCTACAACGCTAGATCATACGAATTGAAAAAATCCATATTGGAATCCTA
ATATAAATAATCT
Found at i:1400251 original size:30 final size:30
Alignment explanation
Indices: 1400216--1400314 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 30
1400206 GCATTTTTCA
* * *
1400216 AAAATATCACCTTTTTTTAAAATAATTACC
1 AAAATAACACCTGTTTTCAAAATAATTACC
* * * *
1400246 AAAATAGCA-CAGTTTTCAAATTAATTCCC
1 AAAATAACACCTGTTTTCAAAATAATTACC
* * * *
1400275 AAAATAACACCT-ATTTCGAATTAATTCCC
1 AAAATAACACCTGTTTTCAAAATAATTACC
1400304 AAAATAACACC
1 AAAATAACACC
1400315 CATTTTGAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
29 49 0.84
30 9 0.16
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAATAACACCTGTTTTCAAAATAATTACC
Found at i:1400270 original size:29 final size:28
Alignment explanation
Indices: 1400229--1400338 Score: 105
Period size: 29 Copynumber: 3.8 Consensus size: 28
1400219 ATATCACCTT
* * * *
1400229 TTTTTAAAATAATTACCAAAATAGCACA
1 TTTTCAAATTAATTCCCAAAATAACACA
*
1400257 GTTTTCAAATTAATTCCCAAAATAACACC
1 -TTTTCAAATTAATTCCCAAAATAACACA
*
1400286 TATTTCGAATTAATTCCCAAAATAACACCCA
1 T-TTTCAAATTAATTCCCAAAATAACA--CA
* *
1400317 TTTT-GAATTAATTCCTAAAATA
1 TTTTCAAATTAATTCCCAAAATA
1400339 GCACCCGGTC
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.01
29 64 0.91
30 3 0.04
31 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.34
Consensus pattern (28 bp):
TTTTCAAATTAATTCCCAAAATAACACA
Found at i:1400343 original size:29 final size:29
Alignment explanation
Indices: 1400259--1400344 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
1400249 ATAGCACAGT
* *
1400259 TTTCAAATTAATTCCCAAAATAACACCTA
1 TTTCGAATTAATTCCCAAAATAACACCCA
1400288 TTTCGAATTAATTCCCAAAATAACACCCA
1 TTTCGAATTAATTCCCAAAATAACACCCA
* * *
1400317 TTTTGAATTAATTCCTAAAATAGCACCC
1 TTTCGAATTAATTCCCAAAATAACACCC
1400345 GGTCAACGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.31
Consensus pattern (29 bp):
TTTCGAATTAATTCCCAAAATAACACCCA
Found at i:1401443 original size:52 final size:51
Alignment explanation
Indices: 1401370--1401559 Score: 202
Period size: 54 Copynumber: 3.6 Consensus size: 51
1401360 CACTGGAAAT
* * * *
1401370 GATGAATGTGTTATCTAATGTTTTACGAACATCTATGCAGAAACTAGCCAAA
1 GATGAATGTGTTGTCAAATGTTTTACGAACATCTATGTAGAAAC-AGCAAAA
* ** * *
1401422 GATAAATGTGTTGTCAAATGTTTTACGAACATCTGGGTAAAAGCCACAGGAAAA
1 GATGAATGTGTTGTCAAATGTTTTACGAACATCTATGTAGAA---ACAGCAAAA
*
1401476 AATGAATGTGTTGTCAAATGTTTTACGAACATCTATGTAGAAAACA-CAAGAAA
1 GATGAATGTGTTGTCAAATGTTTTACGAACATCTATGTAG-AAACAGC-A-AAA
*
1401529 GGATGAATGTGTTGTCAAATGTTTTATGAAC
1 -GATGAATGTGTTGTCAAATGTTTTACGAAC
1401560 TAGTGATTAT
Statistics
Matches: 114, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
52 39 0.34
53 3 0.03
54 68 0.60
55 4 0.04
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (51 bp):
GATGAATGTGTTGTCAAATGTTTTACGAACATCTATGTAGAAACAGCAAAA
Found at i:1402503 original size:83 final size:83
Alignment explanation
Indices: 1402358--1402547 Score: 317
Period size: 83 Copynumber: 2.3 Consensus size: 83
1402348 CTAAAGAGGA
*
1402358 AGAAGAAGTTCATAATGATAAGAACTTGTACAACCTTTTGCTCGACTCTATCACAGAAGGAGATA
1 AGAAG-AGTTCATAATGAGAAGAACTTGTACAACCTTTTGCTCGACTCTATCACAGAAGGAGATA
**
1402423 GATCAGTATCAACATTTCC
65 GATCAACATCAACATTTCC
* *
1402442 AGAGGAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAG
1 AGAAGAGTTCATAATGAGAAGAACTTGTACAACCTTTTGCTCGACTCTATCACAGAAGGAGATAG
1402507 ATCAACATCAACATTTCC
66 ATCAACATCAACATTTCC
*
1402525 AGAAGAGTTCATAATGTGAAGAA
1 AGAAGAGTTCATAATGAGAAGAA
1402548 TTCATCTGAA
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
83 95 0.96
84 4 0.04
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (83 bp):
AGAAGAGTTCATAATGAGAAGAACTTGTACAACCTTTTGCTCGACTCTATCACAGAAGGAGATAG
ATCAACATCAACATTTCC
Found at i:1404221 original size:16 final size:16
Alignment explanation
Indices: 1404200--1404231 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1404190 ACTTAAATTT
1404200 AATGAATTAATCTAAA
1 AATGAATTAATCTAAA
1404216 AATGAATTAATCTAAA
1 AATGAATTAATCTAAA
1404232 TCTAAAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31
Consensus pattern (16 bp):
AATGAATTAATCTAAA
Found at i:1405310 original size:13 final size:13
Alignment explanation
Indices: 1405292--1405317 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1405282 TTTCGTCAAA
1405292 CTCAAATGGAGAT
1 CTCAAATGGAGAT
1405305 CTCAAATGGAGAT
1 CTCAAATGGAGAT
1405318 TATGAGATCT
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:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CTCAAATGGAGAT
Found at i:1407342 original size:21 final size:22
Alignment explanation
Indices: 1407304--1407345 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1407294 CTATAACATG
*
1407304 GGGTATCAGGTACCCCTTCATA
1 GGGTATCAGGTACACCTTCATA
1407326 GGGTATC-GGTACACCTTCAT
1 GGGTATCAGGTACACCTTCAT
1407346 TAAATTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (22 bp):
GGGTATCAGGTACACCTTCATA
Found at i:1418539 original size:36 final size:36
Alignment explanation
Indices: 1418489--1418560 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
1418479 TGCAACCAGG
* *
1418489 GTGTATGGATACACTGCATAGTGTATCGGTACACTA
1 GTGTACGGAAACACTGCATAGTGTATCGGTACACTA
* * *
1418525 GTGTACGGAAACACTTCATGGTGTATCGGTGCACTA
1 GTGTACGGAAACACTGCATAGTGTATCGGTACACTA
1418561 ATTACGTTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (36 bp):
GTGTACGGAAACACTGCATAGTGTATCGGTACACTA
Found at i:1420849 original size:17 final size:18
Alignment explanation
Indices: 1420816--1420853 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1420806 AAATGTATAT
1420816 AAAAATAAATAATAAATA
1 AAAAATAAATAATAAATA
1420834 AAAAATAAGA-AA-AAATA
1 AAAAATAA-ATAATAAATA
1420851 AAA
1 AAA
1420854 TTCTTAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 10 0.53
19 1 0.05
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (18 bp):
AAAAATAAATAATAAATA
Done.