Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007968.1 Hibiscus syriacus cultivar Beakdansim tig00110403_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: 1361854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:580289 original size:61 final size:61
Alignment explanation
Indices: 580214--580340 Score: 209
Period size: 61 Copynumber: 2.1 Consensus size: 61
580204 ATTTTAGATA
* * * *
580214 ATCGCAATGCGATAATACGTGATCGTAACGCGATTTTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
*
580275 ATCGCAACGTGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
580336 ATCGC
1 ATCGC
580341 GTTGCGATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (61 bp):
ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
Found at i:580361 original size:61 final size:61
Alignment explanation
Indices: 580214--580370 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
580204 ATTTTAGATA
* *** * * *
580214 ATCGCAATGCGATAATACGTGATCGTAACGCGATTTTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
* ***
580275 ATCGCAACGTGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
*** * * *
580336 ATCGCGTTGCGATATTATAAAATCGCAATGCGATT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATT
580371 TTCAAAGCAC
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 81 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (61 bp):
ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
Found at i:580535 original size:22 final size:22
Alignment explanation
Indices: 580503--580582 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
580493 TCACTCTCTA
*
580503 CGGCGACATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
* *
580525 CGACGAAATCCGTCCCTATCTC
1 CGGCGAAATCCGTCCCCATCTC
580547 CGGCGAAATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTC
580569 CGGCGAAATCCGTC
1 CGGCGAAATCCGTC
580583 TATCTCCATC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.19
Consensus pattern (22 bp):
CGGCGAAATCCGTCCCCATCTC
Found at i:580985 original size:18 final size:20
Alignment explanation
Indices: 580962--581009 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
580952 GCGATTATCT
*
580962 CGTTGCGATAG-C-CATTCG
1 CGTTGCGATAGTCAAATTCG
580980 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
581000 CGTTGCGATA
1 CGTTGCGATA
581010 ATCATTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 11 0.41
19 1 0.04
20 15 0.56
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:581041 original size:20 final size:20
Alignment explanation
Indices: 581016--581059 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
581006 GATAATCATT
581016 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
581036 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
581056 TTTC
1 TTTC
581060 AGAAACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:583033 original size:20 final size:20
Alignment explanation
Indices: 582913--583186 Score: 163
Period size: 20 Copynumber: 14.6 Consensus size: 20
582903 AGAAGAATAG
* *
582913 TCGCAACACGAAAATGATTA
1 TCGCAACGCGAAAATGACTA
* **
582933 TCGCAACACGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
582953 TCGCAACGCG-AAATGACTA
1 TCGCAACGCGAAAATGACTA
*
582972 TCGCAACG-G--GAT-A--A
1 TCGCAACGCGAAAATGACTA
*
582986 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
583006 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
583026 TCGCAACG-G--GAT-A--A
1 TCGCAACGCGAAAATGACTA
* * *
583040 TCTCAATGTGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
583060 TCGCAATGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
583080 TCGTAAACG-G--GAT-A--A
1 TCG-CAACGCGAAAATGACTA
* **
583095 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGACTA
* **
583115 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGACTA
* **
583135 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGACTA
* **
583155 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGACTA
583175 TCGCAACGCGAA
1 TCGCAACGCGAA
583187 TTTAGTTTCG
Statistics
Matches: 211, Mismatches: 24, Indels: 38
0.77 0.09 0.14
Matches are distributed among these distances:
14 18 0.09
15 7 0.03
16 2 0.01
17 11 0.05
18 6 0.03
19 16 0.08
20 148 0.70
21 3 0.01
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:583047 original size:54 final size:54
Alignment explanation
Indices: 582947--583186 Score: 284
Period size: 54 Copynumber: 4.3 Consensus size: 54
582937 AACACGAATT
582947 TGACTATCGCAACGCG-AAATGACTATCGCAACGGGATAATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAAAATGACTATCGCAACGGGATAATCGCAATGCGAAAA
* *
583000 TGACTATCGCAACGCGAAAATGACTATCGCAACGGGATAATCTCAATGTGAAAA
1 TGACTATCGCAACGCGAAAATGACTATCGCAACGGGATAATCGCAATGCGAAAA
* * *
583054 TGACTATCGCAATGCGGAAATGACTATCGTAAACGGGATAATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAAAATGACTATCG-CAACGGGATAATCGCAATGCGAAAA
** * ** * *
583109 TGAAAATCGCAATGCGAAAATGAAAATCGCAATGCGAAAATGAAAATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAAAATGACTATCGCAA--CG----GGATAATCGCAATGCGAAAA
**
583169 TGAAAATCGCAACGCGAA
1 TGACTATCGCAACGCGAA
583187 TTTAGTTTCG
Statistics
Matches: 163, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
53 16 0.10
54 64 0.39
55 46 0.28
56 2 0.01
60 35 0.21
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (54 bp):
TGACTATCGCAACGCGAAAATGACTATCGCAACGGGATAATCGCAATGCGAAAA
Found at i:583204 original size:19 final size:19
Alignment explanation
Indices: 583182--583223 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
583172 AAATCGCAAC
583182 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* *
583201 GCGATTTTGGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
583220 GCGA
1 GCGA
583224 TAATCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.17, G:0.31, T:0.40
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:583254 original size:20 final size:20
Alignment explanation
Indices: 583231--583274 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
583221 CGATAATCAT
*
583231 TTTCGTGTTGTAATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
*
583251 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCAATTTTAAG
583271 TTTC
1 TTTC
583275 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCAATTTTAAG
Found at i:583847 original size:21 final size:21
Alignment explanation
Indices: 583756--583859 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 21
583746 GACTCACCTG
*
583756 TCATCGTTCAAGAGGCCTCTCA
1 TCATCGTTCAAGAGGCCCCT-A
583778 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
** * *
583798 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* * *
583819 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTA
* *
583840 TCATCGTTGAAGAGGTCCCT
1 TCATCGTTCAAGAGGCCCCT
583860 CCCAACATTC
Statistics
Matches: 66, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
20 2 0.03
21 63 0.95
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:583853 original size:42 final size:42
Alignment explanation
Indices: 583752--583863 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 42
583742 GCCCGACTCA
* * ** *
583752 CCTGTCATCGTTCAAGAGGCCTCTCATATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
* **
583794 CCTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
*
583836 CCTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CCTGTCATCGTTCAAGA-GTCCCCTCCCA
583864 ACATTCTAGA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 55 0.96
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:585264 original size:30 final size:30
Alignment explanation
Indices: 585230--585354 Score: 132
Period size: 30 Copynumber: 4.2 Consensus size: 30
585220 ATAAGAGTTG
585230 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
*
585260 ATTTGTTTAAATGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
** * * * *
585290 ATTTGTGCTTGTTTAAT-TGATTAA-AAGT-TG
1 ATTTGT--TTAATTGATGTG-TAAATAATTCTT
585320 ATTTGTTT-ATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
585349 ATTTGT
1 ATTTGT
585355 GCTTGTTTAA
Statistics
Matches: 76, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
27 7 0.09
28 7 0.09
29 7 0.09
30 42 0.55
31 5 0.07
32 8 0.11
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:585344 original size:59 final size:62
Alignment explanation
Indices: 585260--585388 Score: 219
Period size: 59 Copynumber: 2.1 Consensus size: 62
585250 AATAATTCTT
585260 ATTTGTTTAAATGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATT-AAA-AGTTG
1 ATTTGTTTAAATGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTGAAAGAGTTG
*
585320 ATTTGTTT-ATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTGAAATGAGTTG
1 ATTTGTTTAAATGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTGAAA-GAGTTG
585382 ATTTGTT
1 ATTTGTT
585389 GATTTTAATC
Statistics
Matches: 65, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
59 42 0.65
60 11 0.17
62 12 0.18
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (62 bp):
ATTTGTTTAAATGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATTGAAAGAGTTG
Found at i:585470 original size:20 final size:20
Alignment explanation
Indices: 585445--585774 Score: 237
Period size: 20 Copynumber: 17.9 Consensus size: 20
585435 TGCAATTTCT
*
585445 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
585465 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
585485 CGTTGCGATAGTC--ATTCG
1 CGTTGCGATAGTCAAATTCG
*
585503 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
585522 CGTTGCGAT--T---A-TCT
1 CGTTGCGATAGTCAAATTCG
585536 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
585556 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
585576 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
**
585596 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
585616 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* **
585630 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
**
585650 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
585670 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* **
585684 CTTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
585704 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* * *
585718 CGTTACGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
585738 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
585758 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
585775 GAAAGTGTAA
Statistics
Matches: 251, Mismatches: 34, Indels: 50
0.75 0.10 0.15
Matches are distributed among these distances:
14 41 0.16
16 4 0.02
17 1 0.00
18 21 0.08
19 15 0.06
20 169 0.67
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:585561 original size:34 final size:34
Alignment explanation
Indices: 585465--585774 Score: 178
Period size: 34 Copynumber: 8.5 Consensus size: 34
585455 GTCAAATTCC
*
585465 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T-A-TCG
* *
585503 CGTTGCGATAGTC-ATTTCGCGTTGCGATTATCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTATCG
585536 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCG--A-TT--A-TCG
*
585576 CGTTGCGATAGTCATATTCGCGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T-A---TCG
* ** * *
585616 CATTGCGATTA-TCCCATT-GCGATAGTC-ATTTTCG
1 CGTTGCGA-TAGTCAAATTCGCG-TTG-CGATTATCG
** * *
585650 CGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTATCG
* ** * *
585684 CTTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTATCG
* * *
585718 CGTTACGATATTCAAATTCACGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCG--A-T--TA-TCG
585758 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
585775 GAAAGTGTAA
Statistics
Matches: 218, Mismatches: 31, Indels: 44
0.74 0.11 0.15
Matches are distributed among these distances:
33 18 0.08
34 87 0.40
35 3 0.01
36 2 0.01
37 18 0.08
38 15 0.07
39 7 0.03
40 65 0.30
41 3 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTATCG
Found at i:585564 original size:53 final size:52
Alignment explanation
Indices: 585485--585584 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 52
585475 ATCAAATTCG
* *
585485 CGTTGCGATAGTCATTCGCGTTGCGATAG-TCATTTCGCGTTGCGATTATCT
1 CGTTGCGATAGTCATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATTATCT
585536 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTTAAATTCGCGTTGCGAT
1 CGTTGCGATAGTC--ATTCGCGTTGCGATAGTTAAATTCGCGTTGCGAT
585585 AGTCATATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 13 0.30
53 16 0.36
54 15 0.34
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (52 bp):
CGTTGCGATAGTCATTCGCGTTGCGATAGTTAAATTCGCGTTGCGATTATCT
Found at i:585636 original size:54 final size:54
Alignment explanation
Indices: 585578--585712 Score: 243
Period size: 54 Copynumber: 2.5 Consensus size: 54
585568 TAAATTCGCG
*
585578 TTGCGATAGTCATATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
1 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
*
585632 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCT
1 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
*
585686 TTGCGATAGTCATTTTCGCATTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
585713 TATCCCGTTA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (54 bp):
TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCA
Found at i:588249 original size:24 final size:24
Alignment explanation
Indices: 588215--588268 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
588205 CTGAAACATC
588215 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
588239 ATCAAAGTCCGGGTATTGACCATG
1 ATCAAAATCCGAGTATTGACCAAG
588263 ATCAAA
1 ATCAAA
588269 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:589115 original size:20 final size:20
Alignment explanation
Indices: 589087--589193 Score: 144
Period size: 20 Copynumber: 5.3 Consensus size: 20
589077 AATTCAGTGA
589087 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
* *
589107 TGAGATAGTCAGAATCTCGT
1 TGCGATAGTCAGAATCGCGT
589127 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
** *
589147 TGCGATCACGT-ATTATCGCAT
1 TGCGAT-A-GTCAGAATCGCGT
589168 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
589188 TGCGAT
1 TGCGAT
589194 CACGTATTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 56 0.76
21 14 0.19
22 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:589170 original size:21 final size:21
Alignment explanation
Indices: 589140--589214 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
589130 GATAGTCAGA
589140 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCACGTATT
* **
589161 ATCGCATTGCGAT-A-GTCAGA
1 ATCGCGTTGCGATCACGT-ATT
589181 ATCGCGTTGCGATCACGTATT
1 ATCGCGTTGCGATCACGTATT
*
589202 ATTGCGTTGCGAT
1 ATCGCGTTGCGAT
589215 TTACATATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 2 0.05
20 14 0.32
21 26 0.59
22 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (21 bp):
ATCGCGTTGCGATCACGTATT
Found at i:589183 original size:41 final size:41
Alignment explanation
Indices: 589087--589214 Score: 179
Period size: 41 Copynumber: 3.1 Consensus size: 41
589077 AATTCAGTGA
* ** *
589087 TGCGATAGTCAGAATCGCGTTGAGAT-A-GTCAGAATCTCGT
1 TGCGATAGTCAGAATCGCGTTGCGATCACGT-ATTATCGCGT
*
589127 TGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCAT
1 TGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
*
589168 TGCGATAGTCAGAATCGCGTTGCGATCACGTATTATTGCGT
1 TGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
589209 TGCGAT
1 TGCGAT
589215 TTACATATTC
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
40 25 0.32
41 52 0.66
42 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (41 bp):
TGCGATAGTCAGAATCGCGTTGCGATCACGTATTATCGCGT
Found at i:589333 original size:20 final size:19
Alignment explanation
Indices: 589309--589355 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
589299 TGGAAACTGA
*
589309 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
589329 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
589348 ATTGCGAT
1 ATTGCGAT
589356 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:589345 original size:19 final size:19
Alignment explanation
Indices: 589321--589357 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
589311 TGCGATAATG
*
589321 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
589340 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
589358 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:590114 original size:17 final size:16
Alignment explanation
Indices: 590088--590119 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
590078 AGAAAAAAAG
590088 AATTAGAAAAGTATTA
1 AATTAGAAAAGTATTA
590104 AATTGAGAAAAGTATT
1 AATT-AGAAAAGTATT
590120 GTCCCTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (16 bp):
AATTAGAAAAGTATTA
Found at i:590397 original size:38 final size:39
Alignment explanation
Indices: 590301--590398 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 39
590291 TTTTGAACGA
* * **
590301 GTACTAAAACGAAACAAAAACTAAAGTTTTTAATGGTGTG
1 GTACT-AAATGAAACAAAAACTAAAGTTTTTAACGACGTG
* * *
590341 GTAATAAATGAAATAAAAACTGAAGTTTTTAACGACG-G
1 GTACTAAATGAAACAAAAACTAAAGTTTTTAACGACGTG
590379 GTACTAAATGAAACAAAAAC
1 GTACTAAATGAAACAAAAAC
590399 AACTAAACCT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 19 0.39
39 26 0.53
40 4 0.08
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.24
Consensus pattern (39 bp):
GTACTAAATGAAACAAAAACTAAAGTTTTTAACGACGTG
Found at i:590882 original size:28 final size:25
Alignment explanation
Indices: 590868--590915 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
590858 TTATTATAAC
*
590868 TTAATTTAAA-TATATTTTAATT-T
1 TTAATTTAAATTATATTTTTATTAT
590891 TTAATTTAAATTATATATTTTATTA
1 TTAATTTAAATTATAT-TTTTATTA
590916 AAATATTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 5 0.24
25 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTAATTTAAATTATATTTTTATTAT
Found at i:592320 original size:46 final size:48
Alignment explanation
Indices: 592252--592346 Score: 167
Period size: 46 Copynumber: 2.0 Consensus size: 48
592242 TTTTATTATT
592252 ATTTAGTATAAAAATAATTTAAAATATAAAATTAAACCC-ATGGTAAC
1 ATTTAGTATAAAAATAATTTAAAATATAAAATTAAACCCAATGGTAAC
592299 ATTTAGTAT-AAAATAATTTAAAATATAAAATTAAACCCAAATGGTAAC
1 ATTTAGTATAAAAATAATTTAAAATATAAAATTAAACCC-AATGGTAAC
592347 CGTCTATTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
46 29 0.63
47 9 0.20
48 8 0.17
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (48 bp):
ATTTAGTATAAAAATAATTTAAAATATAAAATTAAACCCAATGGTAAC
Found at i:601814 original size:42 final size:42
Alignment explanation
Indices: 601700--602160 Score: 266
Period size: 42 Copynumber: 11.1 Consensus size: 42
601690 AAACTAAAGT
* *
601700 AAAAGATGGGATTG-AAAAATTA-GAGTCCTCAATTATAAA-CTAA
1 AAAAG-TGAGATTGAAAAAATTAGGAG--CTCAATTATAAAGGT-A
* * *
601743 AAAAATGAGATT---AAAATTAGGGGCCCAATTATAAAGGTA
1 AAAAGTGAGATTGAAAAAATTAGGAGCTCAATTATAAAGGTA
* *
601782 GAAAGTGAGATTGAAAAAATTAGGAGCTCAATTATAAATGTA
1 AAAAGTGAGATTGAAAAAATTAGGAGCTCAATTATAAAGGTA
* * * *
601824 TAAAGTGAGATTAAAAAAATTA-GAGGCCTTAATTTTAAAGGTA
1 AAAAGTGAGATTGAAAAAATTAGGA-G-CTCAATTATAAAGGTA
** * *
601867 AAAAGTGAGACCGAAAAAATTAGGGAACTAAATTATATAA-GT-
1 AAAAGTGAGATTGAAAAAATTA-GGAGCTCAATTATA-AAGGTA
* *
601909 AAAAGTTGGGATTG--AAAATTA-GACGCCTCAATTAT-AACGTA
1 AAAAG-TGAGATTGAAAAAATTAGGA-G-CTCAATTATAAAGGTA
* *
601950 AAAAATGAGATT--AAAATTTAGGAGGCTCAATTATAAAGGTA
1 AAAAGTGAGATTGAAAAAATTAGGA-GCTCAATTATAAAGGTA
* ** * * *
601991 GAAAGTGAGATTGAAAATTTTAGGAGTTCATTTATAAATGTA
1 AAAAGTGAGATTGAAAAAATTAGGAGCTCAATTATAAAGGTA
* * * * *
602033 TAAAGTGGGATTGAAAAACTTA-AAGTCGTCAATTATAAATGTAAA
1 AAAAGTGAGATTGAAAAAATTAGGAG-C-TCAATTATAAAGGT--A
* * * *
602078 AAAAATGAGATTGAAAAAATTA-AAG---GA-TA-AAAAGTA
1 AAAAGTGAGATTGAAAAAATTAGGAGCTCAATTATAAAGGTA
* * *
602114 AAAAGT-AGAATTAAAAAAATTAGGGACCTCAATTATAAAGATA
1 AAAAGTGAG-ATTGAAAAAATTA-GGAGCTCAATTATAAAGGTA
602157 AAAA
1 AAAA
602161 TAAAATTAAA
Statistics
Matches: 328, Mismatches: 58, Indels: 64
0.73 0.13 0.14
Matches are distributed among these distances:
35 2 0.01
36 18 0.05
38 6 0.02
39 28 0.09
40 32 0.10
41 44 0.13
42 90 0.27
43 82 0.25
44 2 0.01
45 24 0.07
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.26
Consensus pattern (42 bp):
AAAAGTGAGATTGAAAAAATTAGGAGCTCAATTATAAAGGTA
Found at i:602079 original size:209 final size:209
Alignment explanation
Indices: 601696--602079 Score: 569
Period size: 209 Copynumber: 1.8 Consensus size: 209
601686 GCTTAAACTA
601696 AAGTAAAAGATGGGATTGAAAAATTAGAGTCCTCAATTATAAACTAAAAAAATGAGATTAAAATT
1 AAGTAAAAGATGGGATTGAAAAATTAGAGTCCTCAATTATAAACTAAAAAAATGAGATTAAAATT
601761 AGGGGCCCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAGGAGCTCAATTATAAATGTATA
66 AGGGGCCCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAGGAGCTCAATTATAAATGTATA
* * *
601826 AAGTGAGATTAAAAAAATTAGAGGCCTTAATTTTAAAGGTAAAAAGTGAGACCGAAAAAATTAGG
131 AAGTGAGATTAAAAAAATTAAAGGCCTCAATTATAAAGGTAAAAAGTGAGACCGAAAAAATTAGG
601891 GAACTAAATTATAT
196 GAACTAAATTATAT
*
601905 AAGTAAAAGTTGGGATTG-AAAATTAGACG-CCTCAATTAT-AACGT-AAAAAATGAGATTAAAA
1 AAGTAAAAGATGGGATTGAAAAATTAGA-GTCCTCAATTATAAAC-TAAAAAAATGAGATTAAAA
* ** * *
601966 TTTAGGAGGCTCAATTATAAAGGTAGAAAGTGAGATTGAAAATTTTAGGAGTTCATTTATAAATG
64 -TTAGG-GGCCCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAGGAGCTCAATTATAAATG
* * * * * *
602031 TATAAAGTGGGATTGAAAAACTTAAAGTCGTCAATTATAAATGTAAAAA
127 TATAAAGTGAGATTAAAAAAATTAAAGGCCTCAATTATAAAGGTAAAAA
602080 AAATGAGATT
Statistics
Matches: 156, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
207 20 0.13
208 25 0.16
209 111 0.71
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (209 bp):
AAGTAAAAGATGGGATTGAAAAATTAGAGTCCTCAATTATAAACTAAAAAAATGAGATTAAAATT
AGGGGCCCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAGGAGCTCAATTATAAATGTATA
AAGTGAGATTAAAAAAATTAAAGGCCTCAATTATAAAGGTAAAAAGTGAGACCGAAAAAATTAGG
GAACTAAATTATAT
Found at i:602173 original size:43 final size:43
Alignment explanation
Indices: 602108--602214 Score: 116
Period size: 43 Copynumber: 2.6 Consensus size: 43
602098 TAAAGGATAA
* **
602108 AAAG-TAAAAAGTAGAATT-AAAAAAATT-AGGGACCTCAATTAT
1 AAAGATAAAAA-TAAAATTAAAAAAAATTAAAAGA-CTCAATTAT
*
602150 AAAGATAAAAATAAAATTAAAAAAAATTAAAAGATTCAATTAT
1 AAAGATAAAAATAAAATTAAAAAAAATTAAAAGACTCAATTAT
*
602193 AAA-ATAAAAATATAA-TAAAAAA
1 AAAGATAAAAATAAAATTAAAAAA
602215 TTAGAAAAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
41 7 0.12
42 21 0.37
43 26 0.46
44 3 0.05
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.23
Consensus pattern (43 bp):
AAAGATAAAAATAAAATTAAAAAAAATTAAAAGACTCAATTAT
Found at i:602545 original size:39 final size:39
Alignment explanation
Indices: 602452--602547 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 39
602442 GAAAATGTAT
* **
602452 TAAAATGAAACAAAAACTAAAGTTTTTAATGGTGTGATAC
1 TAAAATGAAACAAAAACTAAAGTTTTTAACGACGT-ATAC
*
602492 TAAAATGAAACAAAAACTGAAGTTTTTAACGACG-ATTAC
1 TAAAATGAAACAAAAACTAAAGTTTTTAACGACGTA-TAC
*
602531 TAAAATGAACCAAAAAC
1 TAAAATGAAACAAAAAC
602548 AACTAAACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 1 0.02
39 19 0.38
40 30 0.60
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.25
Consensus pattern (39 bp):
TAAAATGAAACAAAAACTAAAGTTTTTAACGACGTATAC
Found at i:603007 original size:24 final size:25
Alignment explanation
Indices: 602975--603023 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
602965 ATATTTTATA
*
602975 TATATTAATTT-TTAAAAATATTTT
1 TATACTAATTTATTAAAAATATTTT
* *
602999 TATACTAATTTATTGAATATATTTT
1 TATACTAATTTATTAAAAATATTTT
603024 ATTATTAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TATACTAATTTATTAAAAATATTTT
Found at i:604799 original size:6 final size:6
Alignment explanation
Indices: 604788--604816 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
604778 AATGTAATGA
604788 AATAAT AATAAT AATAAT AATAA- AATAAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT
604817 TTGTAGTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATAAT
Found at i:604802 original size:9 final size:9
Alignment explanation
Indices: 604788--604816 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
604778 AATGTAATGA
604788 AATAATAAT
1 AATAATAAT
604797 AATAATAAT
1 AATAATAAT
604806 AATAA-AAT
1 AATAATAAT
604814 AAT
1 AAT
604817 TTGTAGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AATAATAAT
Found at i:604808 original size:23 final size:25
Alignment explanation
Indices: 604763--604816 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
604753 TTTTTTATAT
*
604763 ATAATAATATATAAAAATGTAATGAA
1 ATAATAATATATAAAAA-GTAATAAA
*
604789 ATAATAATA-ATAATAA-TAATAAA
1 ATAATAATATATAAAAAGTAATAAA
604812 ATAAT
1 ATAAT
604817 TTGTAGTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
25 6 0.23
26 9 0.35
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (25 bp):
ATAATAATATATAAAAAGTAATAAA
Found at i:608152 original size:18 final size:19
Alignment explanation
Indices: 608129--608169 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
608119 TGTGATATTC
608129 GGGTCGGGTTTAGGGTTT-
1 GGGTCGGGTTTAGGGTTTA
608147 GGGTCGGGTTTAGGGTTTA
1 GGGTCGGGTTTAGGGTTTA
608166 GGGT
1 GGGT
608170 TTTTTAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.07, C:0.05, G:0.51, T:0.37
Consensus pattern (19 bp):
GGGTCGGGTTTAGGGTTTA
Found at i:608667 original size:17 final size:18
Alignment explanation
Indices: 608645--608692 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
608635 GTTTCAGATT
*
608645 CAGATTCTAATTCC-TGA
1 CAGATTCTAATTCCTTCA
608662 CAGATT-TCAATTCCTTCA
1 CAGATTCT-AATTCCTTCA
*
608680 CAGATTCAAATTC
1 CAGATTCTAATTC
608693 TCTCATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 1 0.04
17 12 0.46
18 13 0.50
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (18 bp):
CAGATTCTAATTCCTTCA
Found at i:608692 original size:18 final size:16
Alignment explanation
Indices: 608645--608688 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
608635 GTTTCAGATT
*
608645 CAGATTCTAATTCCTGA
1 CAGATTC-AATTCCTCA
608662 CAGATTTCAATTCCTTCA
1 CAGA-TTCAATTCC-TCA
608680 CAGATTCAA
1 CAGATTCAA
608689 ATTCTCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (16 bp):
CAGATTCAATTCCTCA
Found at i:610525 original size:21 final size:21
Alignment explanation
Indices: 610499--610569 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
610489 TTTGCAGAAG
*
610499 AATCGCAACAAGAGAAATGAA
1 AATCGCAACGAGAGAAATGAA
* *
610520 AATCGCAACGCGA-AAATGAC
1 AATCGCAACGAGAGAAATGAA
*
610540 TATCTGCAACGAGAGAAATGAA
1 AATC-GCAACGAGAGAAATGAA
610562 AATCGCAA
1 AATCGCAA
610570 TGATAAAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 9 0.22
21 23 0.56
22 9 0.22
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (21 bp):
AATCGCAACGAGAGAAATGAA
Found at i:610592 original size:33 final size:33
Alignment explanation
Indices: 610554--610634 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
610544 TGCAACGAGA
* *
610554 GAAATGAAAATCGCAATGATAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAAAATCGCAACGC
*
610587 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAAAATCGCAACGC
**
610620 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
610635 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAAAATCGCAACGC
Found at i:610598 original size:19 final size:19
Alignment explanation
Indices: 610512--610604 Score: 79
Period size: 19 Copynumber: 4.9 Consensus size: 19
610502 CGCAACAAGA
610512 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
610531 GAAAATGACTATCTGCAACGAGA
1 G-AAATGAAAATC-GCAAC--GC
*
610554 GAAATGAAAATCGCAA--T
1 GAAATGAAAATCGCAACGC
610571 G--AT-AAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
610587 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
610605 AGAGAATCGC
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
14 10 0.17
15 2 0.03
16 1 0.02
17 1 0.02
18 2 0.03
19 13 0.22
20 9 0.16
21 9 0.16
22 9 0.16
23 2 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:610710 original size:20 final size:19
Alignment explanation
Indices: 610630--610742 Score: 119
Period size: 19 Copynumber: 6.1 Consensus size: 19
610620 GAAACCAAAA
*
610630 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
610649 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
610668 TCGTGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
610682 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
610701 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
610721 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
610741 TC
1 TC
610743 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 9 0.12
16 3 0.04
17 3 0.04
19 31 0.40
20 30 0.39
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:612748 original size:93 final size:94
Alignment explanation
Indices: 612438--612816 Score: 602
Period size: 94 Copynumber: 4.1 Consensus size: 94
612428 TAGATTGCTT
* *
612438 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
*
612503 ATTTATCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
* *
612532 AGTAAATTTATTCGGTTGCTGCCAATTCTTCTAAACTGTTTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
612597 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
* * *
612626 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACGGTGTATTCTTTAACACTGTGAA-ATAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
612690 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
* * **
612719 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACCCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
* *
612784 ATTTGTC-TTTGTTTTGTCTATTGGTTGG
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
612812 AGTAA
1 AGTAA
612817 TGCAATCCAT
Statistics
Matches: 267, Mismatches: 16, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
92 20 0.07
93 71 0.27
94 176 0.66
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
Found at i:612765 original size:187 final size:187
Alignment explanation
Indices: 612438--612816 Score: 600
Period size: 187 Copynumber: 2.0 Consensus size: 187
612428 TAGATTGCTT
* * *
612438 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACGGTGTATTCTTTAACACTATGAAGATAGT
*
612503 ATTTATCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTTCTAAAC
66 ATTTATCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
* * *
612568 TGTTTATTCTTTAACACTATGAAGTTAGTATTTGTCTTTTGTTTTGTCTTTTGGTTGA
131 TGTGTATTCTTTAACACCATGAAGTTAGTATTTGTC-TTTGTTTTGTCTATTGGTTGA
* *
612626 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACGGTGTATTCTTTAACACTGTGAA-ATAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACGGTGTATTCTTTAACACTATGAAGATAGT
* *
612690 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAA
66 ATTTATCTTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAA
* * *
612754 CTGTGTATTCTTTAATACCCTGAAGTTAGTATTTGTCTTTGTTTTGTCTATTGGTTGG
130 CTGTGTATTCTTTAACACCATGAAGTTAGTATTTGTCTTTGTTTTGTCTATTGGTTGA
612812 AGTAA
1 AGTAA
612817 TGCAATCCAT
Statistics
Matches: 176, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
186 44 0.25
187 77 0.44
188 55 0.31
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (187 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACGGTGTATTCTTTAACACTATGAAGATAGT
ATTTATCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
TGTGTATTCTTTAACACCATGAAGTTAGTATTTGTCTTTGTTTTGTCTATTGGTTGA
Found at i:613178 original size:39 final size:39
Alignment explanation
Indices: 613129--613225 Score: 126
Period size: 39 Copynumber: 2.5 Consensus size: 39
613119 TTGAATGGGT
*
613129 AATAAAATGAAACAAAAACT-AAATTTTTAATGGCATGA-A
1 AATAAAATGAAACAAAAACTGAAATTTTTAA-AG-ATGAGA
* *
613168 AATAAAATGAAACAAAAACTGAAGTTTTTAAAGATGAGT
1 AATAAAATGAAACAAAAACTGAAATTTTTAAAGATGAGA
*
613207 ACTAAAATGAAACAAAAAC
1 AATAAAATGAAACAAAAAC
613226 AACTAAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
38 4 0.08
39 39 0.75
40 9 0.17
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.23
Consensus pattern (39 bp):
AATAAAATGAAACAAAAACTGAAATTTTTAAAGATGAGA
Found at i:613740 original size:42 final size:41
Alignment explanation
Indices: 613694--613824 Score: 129
Period size: 42 Copynumber: 3.1 Consensus size: 41
613684 GAAAATGATT
**
613694 AAAATAGGGGCTTAAACTATTAAA-GTAAAAAGTTTGATTAAA
1 AAAATA-GGGCTTAAACTA-TAAAGGTAAAAAGTGAGATTAAA
* *
613736 AAAATTAGGGCTTCAATTATAAAGGTAAAAAGTGAGATTAAA
1 AAAA-TAGGGCTTAAACTATAAAGGTAAAAAGTGAGATTAAA
* * * * *
613778 AAAATTAGGAGCCTCAATTTTAAAGGTAAAACGTGAGATTAAA
1 AAAA-TAGG-GCTTAAACTATAAAGGTAAAAAGTGAGATTAAA
613821 AAAA
1 AAAA
613825 ATTAGGGGTC
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
41 4 0.05
42 39 0.49
43 36 0.46
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (41 bp):
AAAATAGGGCTTAAACTATAAAGGTAAAAAGTGAGATTAAA
Found at i:613781 original size:43 final size:41
Alignment explanation
Indices: 613714--614154 Score: 282
Period size: 43 Copynumber: 10.7 Consensus size: 41
613704 CTTAAACTAT
**
613714 TAAA-GTAAAAAGTTTGATTAAAAAAATTAGGGCTTCAATTA
1 TAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGC-TCAATTA
*
613755 TAAAGGTAAAAAGTGAGATTAAAAAAATTAGGAGCCTCAATTT
1 TAAAGGTAAAAAGTGAGATTAAAAAAATTAGG-G-CTCAATTA
* * *
613798 TAAAGGTAAAACGTGAGATTAAAAAAAATTAGGGGTCTCAGTTT
1 TAAAGGTAAAAAGTGAGATT-AAAAAAATTA-GGG-CTCAATTA
* *
613842 TAAAGGT--AAA-T--G----AAAAAATTAAGGAACTAAATTA
1 TAAAGGTAAAAAGTGAGATTAAAAAAATT-AGG-GCTCAATTA
*
613876 TATAA-GT-AAAAGATGAGATTAAAAAAATTAGAGACATCAATTA
1 TA-AAGGTAAAAAG-TGAGATTAAAAAAATTAG-GGC-TCAATTA
613919 TAAAGGTAAACAA-TGAGATT-AAAAAATTAGGGGCTCAATTA
1 TAAAGGTAAA-AAGTGAGATTAAAAAAATTA-GGGCTCAATTA
*
613960 TAAAGGT-AAAAGTGAGATTGAAAAAAA-TATGAGCTCAATTA
1 TAAAGGTAAAAAGTGAGATT-AAAAAAATTA-GGGCTCAATTA
* * * *
614001 TAAAGGTACAAAGT-AGGATTGAAAAACTTAGAGTCGTCAATTA
1 TAAAGGTAAAAAGTGA-GATTAAAAAAATTAG-GGC-TCAATTA
* * * *
614044 TAAATGTAAAAAAATGATATTGAAAAAATTAAGGG----A-TA
1 TAAAGGT-AAAAAGTGAGATTAAAAAAATT-AGGGCTCAATTA
*
614082 -AAAAGTAAAAAGT-AGAATTAAAAAAATTAGGGACCTCAATTA
1 TAAAGGTAAAAAGTGAG-ATTAAAAAAATTAGGG--CTCAATTA
* * * *
614124 TAAAGATAAAAAATAAAATTGAAAAAAATTA
1 TAAAGGTAAAAAGTGAGATT-AAAAAAATTA
614155 AAAGATTAAA
Statistics
Matches: 321, Mismatches: 34, Indels: 87
0.73 0.08 0.20
Matches are distributed among these distances:
34 19 0.06
35 11 0.03
36 17 0.05
37 6 0.02
38 2 0.01
39 5 0.02
40 9 0.03
41 46 0.14
42 64 0.20
43 79 0.25
44 56 0.17
45 7 0.02
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.25
Consensus pattern (41 bp):
TAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGCTCAATTA
Found at i:613843 original size:44 final size:43
Alignment explanation
Indices: 613713--613851 Score: 183
Period size: 44 Copynumber: 3.3 Consensus size: 43
613703 GCTTAAACTA
** *
613713 TTAAA-GTAAAAAGTTTGATTAAAAAAATTAGGGCT-TCAATT
1 TTAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGGTCTCAATT
* * *
613754 ATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGAGCCTCAATT
1 TTAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGGTCTCAATT
* *
613797 TTAAAGGTAAAACGTGAGATTAAAAAAAATTAGGGGTCTCAGTT
1 TTAAAGGTAAAAAGTGAGATT-AAAAAAATTAGGGGTCTCAATT
613841 TTAAAGGTAAA
1 TTAAAGGTAAA
613852 TGAAAAAATT
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
41 4 0.05
42 25 0.30
43 25 0.30
44 30 0.36
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (43 bp):
TTAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGGTCTCAATT
Found at i:613885 original size:121 final size:118
Alignment explanation
Indices: 613750--613969 Score: 304
Period size: 121 Copynumber: 1.8 Consensus size: 118
613740 TTAGGGCTTC
* * *
613750 AATTATAAAGGTAAAA-AGTGAGATTAAAAAAATTAG-GAGCCTCAATTTTAAAGGTAAA-ACGT
1 AATTATAAAGGTAAAAGA-TGAGATTAAAAAAATTAGAGA-CATCAATTATAAAGGTAAACA-AT
* *
613812 GAGATTAAAAAAAATTAGGGGTCTCAGTTTTAAAGGTAAATGAAAAAATTAAGGAACTA
63 GAGATT--AAAAAATTAGGGG-CTCAATTATAAAGGTAAATGAAAAAATTAAGGAACTA
613871 AATTATATAA-GTAAAAGATGAGATTAAAAAAATTAGAGACATCAATTATAAAGGTAAACAATGA
1 AATTATA-AAGGTAAAAGATGAGATTAAAAAAATTAGAGACATCAATTATAAAGGTAAACAATGA
613935 GATTAAAAAATTAGGGGCTCAATTATAAAGGTAAA
65 GATTAAAAAATTAGGGGCTCAATTATAAAGGTAAA
613970 AGTGAGATTG
Statistics
Matches: 90, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
118 16 0.18
119 13 0.14
121 55 0.61
122 6 0.07
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.25
Consensus pattern (118 bp):
AATTATAAAGGTAAAAGATGAGATTAAAAAAATTAGAGACATCAATTATAAAGGTAAACAATGAG
ATTAAAAAATTAGGGGCTCAATTATAAAGGTAAATGAAAAAATTAAGGAACTA
Found at i:614156 original size:23 final size:21
Alignment explanation
Indices: 614119--614182 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 21
614109 TAGGGACCTC
* *
614119 AATTATAAAGATAAAAAATAA
1 AATTAAAAAAATAAAAAATAA
* *
614140 AATTGAAAAAAATTAAAAGATTA
1 AATT-AAAAAAA-TAAAAAATAA
*
614163 AATTATAAAAATAAAAAATA
1 AATTAAAAAAATAAAAAATA
614183 TAAGGAACCT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 11 0.32
22 11 0.32
23 12 0.35
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (21 bp):
AATTAAAAAAATAAAAAATAA
Found at i:614171 original size:31 final size:30
Alignment explanation
Indices: 614119--614180 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
614109 TAGGGACCTC
*
614119 AATTATAAAGATAAAAAATAAAATTGAAAAA
1 AATTATAAAGATAAAAAATAAAAAT-AAAAA
**
614150 AATTA-AAAGATTAAATTATAAAAATAAAAA
1 AATTATAAAGA-TAAAAAATAAAAATAAAAA
614180 A
1 A
614181 TATAAGGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (30 bp):
AATTATAAAGATAAAAAATAAAAATAAAAA
Found at i:615122 original size:41 final size:40
Alignment explanation
Indices: 615075--615176 Score: 145
Period size: 40 Copynumber: 2.5 Consensus size: 40
615065 AATTTTGAAC
**
615075 GAGTACTAAAATGAAACAAAAAACTAAAGTTTTTAATTGTAT
1 GAGTACTAAAATGAAACAAAAAACTAAAGTTTTTAA--CAAT
*
615117 G-GTACTAAAATGAAAC-AAAAACTGAAGTTTTTAACAAT
1 GAGTACTAAAATGAAACAAAAAACTAAAGTTTTTAACAAT
615155 GAGTACTAAAATGAAACAAAAA
1 GAGTACTAAAATGAAACAAAAA
615177 CAATTAAACT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
38 3 0.05
39 15 0.27
40 21 0.38
41 15 0.27
42 1 0.02
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (40 bp):
GAGTACTAAAATGAAACAAAAAACTAAAGTTTTTAACAAT
Found at i:615172 original size:39 final size:40
Alignment explanation
Indices: 615075--615177 Score: 147
Period size: 39 Copynumber: 2.6 Consensus size: 40
615065 AATTTTGAAC
**
615075 GAGTACTAAAATGAAACAAAAAACTAAAGTTTTTAATTGTAT
1 GAGTACTAAAATGAAAC-AAAAACTAAAGTTTTTAA-TCAAT
*
615117 G-GTACTAAAATGAAACAAAAACTGAAGTTTTTAA-CAAT
1 GAGTACTAAAATGAAACAAAAACTAAAGTTTTTAATCAAT
615155 GAGTACTAAAATGAAACAAAAAC
1 GAGTACTAAAATGAAACAAAAAC
615178 AATTAAACTT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
38 3 0.05
39 21 0.37
40 17 0.30
41 15 0.26
42 1 0.02
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (40 bp):
GAGTACTAAAATGAAACAAAAACTAAAGTTTTTAATCAAT
Found at i:618408 original size:29 final size:29
Alignment explanation
Indices: 618376--618432 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
618366 ATTTTACCAT
*
618376 TTTTTCCTATTTTACTTAATATACTTTTA
1 TTTTTCCTATTTTACTTAATAAACTTTTA
**
618405 TTTTTTTTATTTTACTTAATAAACTTTT
1 TTTTTCCTATTTTACTTAATAAACTTTT
618433 GAATTACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTTCCTATTTTACTTAATAAACTTTTA
Found at i:619652 original size:43 final size:43
Alignment explanation
Indices: 619605--619907 Score: 241
Period size: 43 Copynumber: 7.1 Consensus size: 43
619595 AAAAATGATT
*
619605 AAAA-TAGGGGCTTAAACTATTAAA-GTAAAAAAGTTTA-ATTAAA
1 AAAATTAGGGGCTTAAACTA-TAAAGGT-AAAAAG-TGAGATTAAA
* *
619648 AAAATTA-GGGCTTCAATTATAAAGGTAAAAAGTGAGATTAAA
1 AAAATTAGGGGCTTAAACTATAAAGGTAAAAAGTGAGATTAAA
* * * *
619690 AAAATTAGGGGCCTCAATTTTAAAGGTAAAAAGTGAGATTAAAA
1 AAAATTAGGGGCTTAAACTATAAAGGTAAAAAGTGAGATT-AAA
* ** * * *
619734 AAAATTAGGGG-TCTCAGTTTTAAAGGAAAAAAGTGAGATTGAA
1 AAAATTAGGGGCT-TAAACTATAAAGGTAAAAAGTGAGATTAAA
* * *
619777 AAAATTAGGGAAC-TAAATTATATAA-GT-AGAAGATGAGATTAAA
1 AAAATTAGGG-GCTTAAACTATA-AAGGTAAAAAG-TGAGATTAAA
* * * * *
619820 AAAATTAGAGGCATCAATTATAAAGGTAAAAAATGAGATT-AA
1 AAAATTAGGGGCTTAAACTATAAAGGTAAAAAGTGAGATTAAA
* * *
619862 AAAATTAGGGGC-TCAATTATAAAGGT-AAAAGTGAGATTGAA
1 AAAATTAGGGGCTTAAACTATAAAGGTAAAAAGTGAGATTAAA
619903 AAAAT
1 AAAAT
619908 ATGAGCTCAA
Statistics
Matches: 223, Mismatches: 23, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
40 11 0.05
41 23 0.10
42 43 0.19
43 100 0.45
44 46 0.21
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.25
Consensus pattern (43 bp):
AAAATTAGGGGCTTAAACTATAAAGGTAAAAAGTGAGATTAAA
Found at i:619765 original size:130 final size:126
Alignment explanation
Indices: 619625--619994 Score: 346
Period size: 130 Copynumber: 2.9 Consensus size: 126
619615 CTTAAACTAT
* * *
619625 TAAAGTAAAAAAGTTTA-ATTAAAAAAATTAGGG-CTTCAATTATA-AAGGTAAAA-AGTGAGAT
1 TAAAGGAAAAAAG-TGAGATTAAAAAAATTAGGGAC-TAAATTATATAA-GTAAAAGA-TGAGAT
* * * * *
619686 TAAAAAAATTAGGGGCCTCAATTTTAAAGGTAAAAAGTGAGATTAAAAAAAATTAGGGGTCTCAG
62 TAAAAAAATTAGAGGCATCAATTATAAAGGTAAAAAATGAGATT--AAAAAATTAGGGG-CTCAA
*
619751 TTT
124 TTA
* *
619754 TAAAGGAAAAAAGTGAGATTGAAAAAATTAGGGAACTAAATTATATAAGTAGAAGATGAGATTAA
1 TAAAGGAAAAAAGTGAGATTAAAAAAATTAGGG-ACTAAATTATATAAGTAAAAGATGAGATTAA
619819 AAAAATTAGAGGCATCAATTATAAAGGTAAAAAATGAGATTAAAAAATTAGGGGCTCAATTA
65 AAAAATTAGAGGCATCAATTATAAAGGTAAAAAATGAGATTAAAAAATTAGGGGCTCAATTA
* * * * *
619881 TAAAGG-TAAAAGTGAGATTGAAAAAA-TA-TGAGCTCAATTATA-AAGGT-ACA-ATGTAGGAT
1 TAAAGGAAAAAAGTGAGATTAAAAAAATTAGGGA-CTAAATTATATAA-GTAAAAGATG-A-GAT
* * * * * *
619940 TGAAAAATTTAGAGTCGTCAATTATAAATGTAAAAAAATGAAATTGAAAAAATTA
62 TAAAAAAATTAGAGGCATCAATTATAAAGGT-AAAAAATGAGATT-AAAAAATTA
619995 AGGGATAAAA
Statistics
Matches: 208, Mismatches: 22, Indels: 25
0.82 0.09 0.10
Matches are distributed among these distances:
122 3 0.01
123 5 0.02
124 41 0.20
125 14 0.07
126 28 0.13
127 12 0.06
128 15 0.07
129 27 0.13
130 59 0.28
131 4 0.02
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.26
Consensus pattern (126 bp):
TAAAGGAAAAAAGTGAGATTAAAAAAATTAGGGACTAAATTATATAAGTAAAAGATGAGATTAAA
AAAATTAGAGGCATCAATTATAAAGGTAAAAAATGAGATTAAAAAATTAGGGGCTCAATTA
Found at i:619786 original size:87 final size:83
Alignment explanation
Indices: 619642--619926 Score: 330
Period size: 87 Copynumber: 3.4 Consensus size: 83
619632 AAAAAGTTTA
* *
619642 ATTAAAAAAATTAGGGCT-TCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGGGGCCTCA
1 ATTAAAAAAATTAGGGGTCTCAATTATAAAGGAAAAAAGTGAGATT-AAAAAATTAGGGG-CTCA
*
619706 ATTTTAAAGGTAAAAAGTGAG
64 ATTATAAAGGT-AAAAGTGAG
* * * *
619727 ATTAAAAAAAATTAGGGGTCTCAGTTTTAAAGGAAAAAAGTGAGATTGAAAAAATTAGGGAACTA
1 ATT-AAAAAAATTAGGGGTCTCAATTATAAAGGAAAAAAGTGAGATT-AAAAAATTAGGG-GCTC
*
619792 AATTATATAA-GTAGAAGATGAG
63 AATTATA-AAGGTAAAAG-TGAG
*
619814 ATTAAAAAAATTAGAGG-CATCAATTATAAAGGTAAAAAA-TGAGATTAAAAAATTAGGGGCTCA
1 ATTAAAAAAATTAGGGGTC-TCAATTATAAAGG-AAAAAAGTGAGATTAAAAAATTAGGGGCTCA
619877 ATTATAAAGGTAAAAGTGAG
64 ATTATAAAGGTAAAAGTGAG
* * *
619897 ATTGAAAAAA-TATGAG-CTCAATTATAAAGG
1 ATTAAAAAAATTAGGGGTCTCAATTATAAAGG
619927 TACAATGTAG
Statistics
Matches: 173, Mismatches: 19, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
81 13 0.08
82 4 0.02
83 15 0.09
84 15 0.09
85 16 0.09
86 49 0.28
87 59 0.34
88 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (83 bp):
ATTAAAAAAATTAGGGGTCTCAATTATAAAGGAAAAAAGTGAGATTAAAAAATTAGGGGCTCAAT
TATAAAGGTAAAAGTGAG
Found at i:619941 original size:41 final size:41
Alignment explanation
Indices: 619646--619973 Score: 171
Period size: 43 Copynumber: 7.8 Consensus size: 41
619636 AGTTTAATTA
* *
619646 AAAAAATTAGG-GCTTCAATTATAAAGGTAAAAAGT-GAGATTA
1 AAAAAATTAGGAGC-TCAATTATAAAGGT-AAATGTAG-GATTG
* * * *
619688 AAAAAATTAGGGGCCTCAATTTTAAAGGTAAAAAGT-GAGATTAA
1 AAAAAATTAGGAG-CTCAATTATAAAGGT-AAATGTAG-GATT-G
* * * * *
619732 AAAAAATTAGGGGTCTCAGTTTTAAAGGAAAAAAGT-GAGATTG
1 AAAAAATTAGGAG-CTCAATTATAAAGG-TAAATGTAG-GATTG
* * *
619775 AAAAAATTAGGGAACTAAATTATATAA-GTAGAA-G-ATGAGATTA
1 AAAAAATTA-GGAGCTCAATTATA-AAGGTA-AATGTA-G-GATTG
619818 AAAAAATTA-GAGGCATCAATTATAAAGGTAAAAAATG-A-GATT-
1 AAAAAATTAGGA-GC-TCAATTATAAAGGT---AAATGTAGGATTG
* *
619860 AAAAAATTAGGGGCTCAATTATAAAGGTAAAAGT-GAGATTG
1 AAAAAATTAGGAGCTCAATTATAAAGGTAAATGTAG-GATTG
*
619901 AAAAAA-TATGAGCTCAATTATAAAGGTACAATGTAGGATTG
1 AAAAAATTAGGAGCTCAATTATAAAGGTA-AATGTAGGATTG
* *
619942 AAAAATTTA-GAGTCGTCAATTATAAATGTAAA
1 AAAAAATTAGGAG-C-TCAATTATAAAGGTAAA
619974 AAAATGAAAT
Statistics
Matches: 239, Mismatches: 21, Indels: 52
0.77 0.07 0.17
Matches are distributed among these distances:
38 4 0.02
40 24 0.10
41 39 0.16
42 33 0.14
43 90 0.38
44 44 0.18
45 2 0.01
46 3 0.01
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.26
Consensus pattern (41 bp):
AAAAAATTAGGAGCTCAATTATAAAGGTAAATGTAGGATTG
Found at i:620047 original size:44 final size:43
Alignment explanation
Indices: 619999--620124 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 43
619989 AAATTAAGGG
* *
619999 ATAAAAAGTAAAAAGTATAATTAAAAAAATTAGGAACCTCAATT
1 ATAAAAA-TAAAAAATATAATTAAAAAAATTAGGAACCTAAATT
* * * **
620043 ATAAAGATAAAAAATAAAATTGAAAAAAATTA-AAAGATTAAATT
1 ATAAAAATAAAAAATATAATT-AAAAAAATTAGGAA-CCTAAATT
620087 ATAAAAATAAAAAATATAA-T-AAAAAATTAAGGAACCTA
1 ATAAAAATAAAAAATATAATTAAAAAAATT-AGGAACCTA
620125 TAAAATATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
41 8 0.12
42 3 0.05
43 17 0.26
44 38 0.58
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.24
Consensus pattern (43 bp):
ATAAAAATAAAAAATATAATTAAAAAAATTAGGAACCTAAATT
Found at i:620076 original size:23 final size:21
Alignment explanation
Indices: 620039--620112 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
620029 TAGGAACCTC
* *
620039 AATTATAAAGATAAAAAATAA
1 AATTAAAAAAATAAAAAATAA
* *
620060 AATTGAAAAAAATTAAAAGATTA
1 AATT-AAAAAAA-TAAAAAATAA
* *
620083 AATTATAAAAATAAAAAATAT
1 AATTAAAAAAATAAAAAATAA
620104 AA-TAAAAAA
1 AATTAAAAAA
620113 TTAAGGAACC
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
20 6 0.14
21 13 0.31
22 11 0.26
23 12 0.29
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (21 bp):
AATTAAAAAAATAAAAAATAA
Found at i:620091 original size:31 final size:30
Alignment explanation
Indices: 620039--620109 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
620029 TAGGAACCTC
*
620039 AATTATAAAGATAAAAAATAAAATTGAAAAA
1 AATTATAAAGATAAAAAATAAAAAT-AAAAA
**
620070 AATTA-AAAGATTAAATTATAAAAATAAAAA
1 AATTATAAAGA-TAAAAAATAAAAATAAAAA
*
620100 ATATAATAAA
1 A-ATTATAAA
620110 AAATTAAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
30 11 0.33
31 19 0.58
32 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.25
Consensus pattern (30 bp):
AATTATAAAGATAAAAAATAAAAATAAAAA
Found at i:620907 original size:15 final size:15
Alignment explanation
Indices: 620887--620925 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
620877 GATAATGTCC
620887 AAGTCTTCTTAGCCA
1 AAGTCTTCTTAGCCA
620902 AAGTCTTCTTAGCCA
1 AAGTCTTCTTAGCCA
620917 AAGTCTTCT
1 AAGTCTTCT
620926 AACCCACCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (15 bp):
AAGTCTTCTTAGCCA
Found at i:622024 original size:22 final size:23
Alignment explanation
Indices: 621983--622025 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
621973 TTTTATATAT
621983 AATAATATATAAAAATGCAATGA
1 AATAATATATAAAAATGCAATGA
622006 AATAATA-ATAATAAA-GCAAT
1 AATAATATATAA-AAATGCAAT
622026 TTGTAGTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.26
Consensus pattern (23 bp):
AATAATATATAAAAATGCAATGA
Found at i:622299 original size:12 final size:12
Alignment explanation
Indices: 622281--622322 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
622271 ATTCTTGCAA
622281 GCCTTGCCATAT
1 GCCTTGCCATAT
*
622293 TCCTTGCCATAT
1 GCCTTGCCATAT
*
622305 GCCTTGCAATAT
1 GCCTTGCCATAT
622317 GCCTTG
1 GCCTTG
622323 GAAAACTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.36
Consensus pattern (12 bp):
GCCTTGCCATAT
Found at i:626724 original size:20 final size:19
Alignment explanation
Indices: 626692--626729 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
626682 TCAATATTTT
626692 TTTTATTATTATTTTGTTA
1 TTTTATTATTATTTTGTTA
*
626711 TTTTATTTTATATTTTGTT
1 TTTTATTAT-TATTTTGTT
626730 TTATCTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTATTATTATTTTGTTA
Found at i:626763 original size:20 final size:18
Alignment explanation
Indices: 626738--626803 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 18
626728 TTTTATCTCA
*
626738 TTTTTTCTTTTTTGATTT
1 TTTTTTTTTTTTTGATTT
626756 GTTTTTTTTGGTTTTTGATTT
1 -TTTTTTTT--TTTTTGATTT
626777 TTTTCTTTTTCTTTTGATTT
1 TTTT-TTTTT-TTTTGATTT
626797 TATTTTT
1 T-TTTTT
626804 ATGTTTTTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 8 0.20
20 16 0.39
21 17 0.41
ACGTcount: A:0.06, C:0.05, G:0.09, T:0.80
Consensus pattern (18 bp):
TTTTTTTTTTTTTGATTT
Found at i:626764 original size:21 final size:21
Alignment explanation
Indices: 626738--626791 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
626728 TTTTATCTCA
626738 TTTTTTCTTTTTTGATTTGTT
1 TTTTTTCTTTTTTGATTTGTT
** *
626759 TTTTTTGGTTTTTGATTTTTT
1 TTTTTTCTTTTTTGATTTGTT
626780 TCTTTTTCTTTT
1 T-TTTTTCTTTT
626792 GATTTTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.04, C:0.06, G:0.09, T:0.81
Consensus pattern (21 bp):
TTTTTTCTTTTTTGATTTGTT
Found at i:626801 original size:25 final size:24
Alignment explanation
Indices: 626768--626824 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
626758 TTTTTTTGGT
*
626768 TTTTGATTTTTTTCTTTTTCTTTTGA
1 TTTT-ATTTTTATCTTTTTC-TTTGA
*
626794 TTTTATTTTTATGTTTTTCTTTGA
1 TTTTATTTTTATCTTTTTCTTTGA
626818 -TTTATTT
1 TTTTATTT
626825 AACATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 7 0.24
24 5 0.17
25 13 0.45
26 4 0.14
ACGTcount: A:0.11, C:0.05, G:0.07, T:0.77
Consensus pattern (24 bp):
TTTTATTTTTATCTTTTTCTTTGA
Found at i:629225 original size:36 final size:36
Alignment explanation
Indices: 629184--629254 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
629174 GTTATGTTTC
629184 GATTTTATTTTGATTCTTGTTGTTAAAAAAATTAAT
1 GATTTTATTTTGATTCTTGTTGTTAAAAAAATTAAT
629220 GATTTTATTTTGATTCTTGTTGTTAAAAAAATTAA
1 GATTTTATTTTGATTCTTGTTGTTAAAAAAATTAA
629255 CATAATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (36 bp):
GATTTTATTTTGATTCTTGTTGTTAAAAAAATTAAT
Found at i:629264 original size:36 final size:36
Alignment explanation
Indices: 629188--629264 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 36
629178 TGTTTCGATT
* *
629188 TTATTTTGATTCTTGTTGTTAAAAAAATTAATGATT
1 TTATTTTGATTCTTGTTGTTAAAAAAATTAATCATA
629224 TTATTTTGATTCTTGTTGTTAAAAAAATTAA-CATAA
1 TTATTTTGATTCTTGTTGTTAAAAAAATTAATCAT-A
629260 TTATT
1 TTATT
629265 GATGTGACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 2 0.05
36 36 0.95
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (36 bp):
TTATTTTGATTCTTGTTGTTAAAAAAATTAATCATA
Found at i:630819 original size:43 final size:42
Alignment explanation
Indices: 630771--631026 Score: 247
Period size: 42 Copynumber: 6.1 Consensus size: 42
630761 TTAGGGATTA
* ** *
630771 GTAAAAAGTGAGATTAAAAAAATTATGTTCCTCAATTTTAAAG
1 GTAAAAAGTGAGATTGAAAAAATTA-GGGCCTCAATTATAAAG
* * *
630814 GTAAAAAGTGAGATT-AAAATATTAGGGGCCTCAATTTTAAAA
1 GTAAAAAGTGAGATTGAAAAAATTA-GGGCCTCAATTATAAAG
* * *
630856 GTAAAAAGTGAGACTGAAAAAATTAGGGAACTAAATTATATAA-
1 GTAAAAAGTGAGATTGAAAAAATTAGGG-CCTCAATTATA-AAG
* *
630899 GT-AAAAGAT-AGGAATGAAAAAATT-GAGGTCTCAATTATAAAG
1 GTAAAAAG-TGA-GATTGAAAAAATTAG-GGCCTCAATTATAAAG
* *
630941 GTAAAAAATGAGATT-AAAAAATTAGGGGCTCAATTATAAAG
1 GTAAAAAGTGAGATTGAAAAAATTAGGGCCTCAATTATAAAG
* *
630982 GTAGAAAGTGAGATTGAAAAAATTAAGAG-CTCAATTATAAAG
1 GTAAAAAGTGAGATTGAAAAAATT-AGGGCCTCAATTATAAAG
631024 GTA
1 GTA
631027 TATGTAGACA
Statistics
Matches: 182, Mismatches: 19, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
41 38 0.21
42 86 0.47
43 56 0.31
44 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.26
Consensus pattern (42 bp):
GTAAAAAGTGAGATTGAAAAAATTAGGGCCTCAATTATAAAG
Found at i:631221 original size:37 final size:38
Alignment explanation
Indices: 631147--631403 Score: 255
Period size: 39 Copynumber: 6.9 Consensus size: 38
631137 TTTTGACAAA
* * * *
631147 ATATAATATATAATTTTCACAAAACGATTTTCGAAAATTT
1 ATATAATATATAGTTTTTA-AAAAC-ATTTTTGAAAAATT
* * * *
631187 ATATATTGTATAGTTTTTGAAAATA-TTTTG-AAAATAT
1 ATATAATATATAGTTTTTAAAAACATTTTTGAAAAAT-T
*
631224 ATATAATATATAGTTTTTAAAAACATTTTTGAAAACTT
1 ATATAATATATAGTTTTTAAAAACATTTTTGAAAAATT
* * *
631262 ATATAATATATACTTTTAAAAAACATTTTTAAAAAAATT
1 ATATAATATATAGTTTTTAAAAACATTTTT-GAAAAATT
631301 ATATAATATATAGTTTTTAAAAAACATTTTTGAAAAATT
1 ATATAATATATAGTTTTT-AAAAACATTTTTGAAAAATT
* *
631340 ATATAATATATAG-TTTTGAAAAC-TTTTT-TAAAA-T
1 ATATAATATATAGTTTTTAAAAACATTTTTGAAAAATT
* *
631374 ATAT--TATATAG--TTAAAAAATATTTTTGAAA
1 ATATAATATATAGTTTTTAAAAACATTTTTGAAA
631404 TATATGTTAT
Statistics
Matches: 184, Mismatches: 26, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
31 6 0.03
32 12 0.07
33 2 0.01
34 5 0.03
35 4 0.02
36 9 0.05
37 31 0.17
38 39 0.21
39 50 0.27
40 26 0.14
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (38 bp):
ATATAATATATAGTTTTTAAAAACATTTTTGAAAAATT
Found at i:631375 original size:25 final size:25
Alignment explanation
Indices: 631314--631376 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
631304 TAATATATAG
* * *
631314 TTTTTAAAAAACATTTTTGAAAAAT
1 TTTTTAAAATATAGTTTTGAAAAAT
* * * *
631339 TATATAATATATAGTTTTGAAAACT
1 TTTTTAAAATATAGTTTTGAAAAAT
631364 TTTTTAAAATATA
1 TTTTTAAAATATA
631377 TTATATAGTT
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (25 bp):
TTTTTAAAATATAGTTTTGAAAAAT
Found at i:631445 original size:2 final size:2
Alignment explanation
Indices: 631440--631481 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
631430 TTTTTTTAAA
631440 AT AT AT AT AT -T AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
631482 GTATTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:638287 original size:18 final size:17
Alignment explanation
Indices: 638237--638285 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
638227 AAGTGTGATA
638237 TTCGGGTCGGGTTTAGGG
1 TTCGGGTC-GGTTTAGGG
*
638255 TTTGGGTCAGGTTTAGGG
1 TTCGGGTC-GGTTTAGGG
*
638273 TTCGAGTCGGTTT
1 TTCGGGTCGGTTT
638286 TAAAGTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.08, C:0.10, G:0.43, T:0.39
Consensus pattern (17 bp):
TTCGGGTCGGTTTAGGG
Found at i:638798 original size:17 final size:18
Alignment explanation
Indices: 638776--638823 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
638766 GTTTCAGATT
*
638776 CAGATTCCAATTCC-TGA
1 CAGATTCCAATTCCTTCA
638793 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
*
638811 CAGATTCAAATTC
1 CAGATTCCAATTC
638824 TCTCATAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.31
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:641939 original size:3 final size:3
Alignment explanation
Indices: 641931--641963 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
641921 TTGTAATTAG
641931 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
641964 AATCAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:650523 original size:65 final size:66
Alignment explanation
Indices: 650404--650534 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 66
650394 TTCTTTAATT
*
650404 GATCAAGTTTGGCATCCATGGCTCTACTTCGCGTGTGATAAGGATTGGAGTTTTTACTTGCCAGA
1 GATCAAGCTTGGCATCCATGGCTCTACTTCGCGTGTGATAAGGATTGGAGTTTTTACTTGCCAGA
650469 A
66 A
650470 GATCAAGCTTGGCATCCATGGCTCTAC-TCGCGTGTGATAAGGATTGGAGTTTTTACTTGCCAGA
1 GATCAAGCTTGGCATCCATGGCTCTACTTCGCGTGTGATAAGGATTGGAGTTTTTACTTGCCAGA
650534 A
66 A
650535 TCGTCTGTCA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
65 38 0.59
66 26 0.41
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (66 bp):
GATCAAGCTTGGCATCCATGGCTCTACTTCGCGTGTGATAAGGATTGGAGTTTTTACTTGCCAGA
A
Found at i:656962 original size:3 final size:3
Alignment explanation
Indices: 656954--656985 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
656944 TTGTAATTAG
656954 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
656986 AAAAATCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:668044 original size:16 final size:16
Alignment explanation
Indices: 668023--668089 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
668013 GTCTCTAACG
668023 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
668039 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
668055 TTTATGTTCATGTTCG
1 TTTATGTTCGTGTTCA
668071 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
668085 TTTAT
1 TTTAT
668090 TAAATGAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:668062 original size:32 final size:32
Alignment explanation
Indices: 668021--668081 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
668011 GGGTCTCTAA
*
668021 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCATGTTCATTTATGTTCGTGTT
*
668053 CGTTTATGTTCATGTTCGTTTATGTTCGT
1 CGTTTATGTTCATGTTCATTTATGTTCGT
668082 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.10, C:0.13, G:0.21, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCATGTTCATTTATGTTCGTGTT
Found at i:680002 original size:13 final size:13
Alignment explanation
Indices: 679984--680008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
679974 AAAACCTATA
679984 ATTATAATAATTT
1 ATTATAATAATTT
679997 ATTATAATAATT
1 ATTATAATAATT
680009 AAAATATGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTATAATAATTT
Found at i:685212 original size:219 final size:221
Alignment explanation
Indices: 684833--685273 Score: 868
Period size: 219 Copynumber: 2.0 Consensus size: 221
684823 CATTCTCGGT
684833 GGGTTTGGGTTTAGGGTTCTGGAGGGAGCGAAAGGGTTAGGACTTGGCTTATCGGCATCGAGTGA
1 GGGTTTGGGTTTAGGGTTCTGGAGGGAGCGAAAGGGTTAGGACTTGGCTTATCGGCATCGAGTGA
684898 TAGTCGGGGAAAATCGTCGTGCTCGTGACCGGAAGACGATGAAGAAGAAAGGGATAATCTCGATG
66 TAGTCGGGGAAAATCGTCGTGCTCGTGACCGGAAGACGATGAAGAAGAAAGGGATAATCTCGATG
684963 CGGATATGGCGACCGATTTAGAATCTGAGCTTTTCAACAGTGGAAGGCTCAATGAA-ACTCTAAG
131 CGGATATGGCGACCGATTTAGAATCTGAGCTTTTCAACAGTGGAAGGCTCAATGAAGACTCTAAG
685027 GAAGAAGAAGATTTCGAG-TTCTATG
196 GAAGAAGAAGATTTCGAGCTTCTATG
685052 GGGTTTGGGTTTAGGGTTCTGGAGGGAGCGAAAGGGTTAGGACTTGGCTTATCGGCATCGAGTGA
1 GGGTTTGGGTTTAGGGTTCTGGAGGGAGCGAAAGGGTTAGGACTTGGCTTATCGGCATCGAGTGA
685117 TAGTCGGGGAAAATCGTCGTGCTCGTGACCGGAAGACGATGAAGAAGAAAGGGATAATCTCGATG
66 TAGTCGGGGAAAATCGTCGTGCTCGTGACCGGAAGACGATGAAGAAGAAAGGGATAATCTCGATG
685182 CGGATATGGCGACCGATTTAGAATCTGAGCTTTTCAACAGTGGAAGGCTCAATGAAGACTCTAAG
131 CGGATATGGCGACCGATTTAGAATCTGAGCTTTTCAACAGTGGAAGGCTCAATGAAGACTCTAAG
685247 GAAGAAGAAGATTTCGAGCTTCTATG
196 GAAGAAGAAGATTTCGAGCTTCTATG
685273 G
1 G
685274 AGGAAATGCT
Statistics
Matches: 220, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
219 186 0.85
220 26 0.12
221 8 0.04
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (221 bp):
GGGTTTGGGTTTAGGGTTCTGGAGGGAGCGAAAGGGTTAGGACTTGGCTTATCGGCATCGAGTGA
TAGTCGGGGAAAATCGTCGTGCTCGTGACCGGAAGACGATGAAGAAGAAAGGGATAATCTCGATG
CGGATATGGCGACCGATTTAGAATCTGAGCTTTTCAACAGTGGAAGGCTCAATGAAGACTCTAAG
GAAGAAGAAGATTTCGAGCTTCTATG
Found at i:687899 original size:72 final size:73
Alignment explanation
Indices: 687814--687959 Score: 267
Period size: 74 Copynumber: 2.0 Consensus size: 73
687804 CTGTCGTAAA
*
687814 ATTTTTAAC-AAAAAAAAAACGAGTCTGGAACATATGAATAGTAAGATTATAATTTGATAACTTT
1 ATTTTTAACAAAAAAAAAAACGAGTCTGAAACATATGAATAGTAAGATTATAATTTGATAACTTT
687878 TAATAGTC
66 TAATAGTC
687886 ATTTTTAACAAAAAAAAAAAACGAGTCTGAAACATATGAATAGTAAGATTATAATTTGATAACTT
1 ATTTTTAAC-AAAAAAAAAAACGAGTCTGAAACATATGAATAGTAAGATTATAATTTGATAACTT
687951 TTAATAGTC
65 TTAATAGTC
687960 TATGGACTCA
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
72 9 0.13
74 62 0.87
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (73 bp):
ATTTTTAACAAAAAAAAAAACGAGTCTGAAACATATGAATAGTAAGATTATAATTTGATAACTTT
TAATAGTC
Found at i:697537 original size:71 final size:72
Alignment explanation
Indices: 697454--697599 Score: 258
Period size: 74 Copynumber: 2.0 Consensus size: 72
697444 CTGTCGTAAA
*
697454 ATTTTTAAC-AAAAAAAAACGAGTCTGGAACATATGAATAGTAAGATTATAATTTGATAACTTTT
1 ATTTTTAACAAAAAAAAAACGAGTCTAGAACATATGAATAGTAAGATTATAATTTGATAACTTTT
697518 AATAGTC
66 AATAGTC
697525 ATTTTTAACAAAAAAAAAAAACGAGTCTAGAACATATGAATAGTAAGATTATAATTTGATAACTT
1 ATTTTTAAC--AAAAAAAAAACGAGTCTAGAACATATGAATAGTAAGATTATAATTTGATAACTT
697590 TTAATAGTC
64 TTAATAGTC
697599 A
1 A
697600 ATGGACTCAA
Statistics
Matches: 71, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
71 9 0.13
74 62 0.87
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (72 bp):
ATTTTTAACAAAAAAAAAACGAGTCTAGAACATATGAATAGTAAGATTATAATTTGATAACTTTT
AATAGTC
Found at i:703639 original size:20 final size:22
Alignment explanation
Indices: 703616--703657 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
703606 CCAAATAACA
*
703616 TATTTAATAA-AA-AAATATTT
1 TATTCAATAACAATAAATATTT
703636 TATTCAATAACAATAAATATTT
1 TATTCAATAACAATAAATATTT
703658 GATTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTCAATAACAATAAATATTT
Found at i:703673 original size:23 final size:21
Alignment explanation
Indices: 703621--703673 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
703611 TAACATATTT
* *
703621 AATAAAA-AAATATTTTATTC
1 AATAAAATAAATATTTGATTA
703641 AATAACAATAAATATTTGATTAA
1 AATAA-AATAAATATTTGATT-A
703664 AATAATAATA
1 AATAA-AATA
703674 TATAAGGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 2 0.07
22 11 0.41
23 9 0.33
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (21 bp):
AATAAAATAAATATTTGATTA
Found at i:711810 original size:24 final size:24
Alignment explanation
Indices: 711778--711886 Score: 139
Period size: 24 Copynumber: 4.6 Consensus size: 24
711768 CATTTAAATG
*
711778 ATAAACGAACACAAATGAACGATC
1 ATAAACGAACACAAATGAACGAAC
* ** *
711802 ATAAACGAACAGATGTAAACGAAC
1 ATAAACGAACACAAATGAACGAAC
*
711826 ATAAACGAATAC-AATGAACGAAC
1 ATAAACGAACACAAATGAACGAAC
*
711849 GTAAACGAACACAAATGAACGAAC
1 ATAAACGAACACAAATGAACGAAC
*
711873 GTAAACGAACACAA
1 ATAAACGAACACAA
711887 TAAATGAACT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
23 18 0.25
24 54 0.75
ACGTcount: A:0.55, C:0.19, G:0.15, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAAATGAACGAAC
Found at i:711854 original size:47 final size:47
Alignment explanation
Indices: 711778--711887 Score: 139
Period size: 47 Copynumber: 2.3 Consensus size: 47
711768 CATTTAAATG
* * **
711778 ATAAACGAACACAAATGAACGATCATAAACGAACAGATGTAAACGAAC
1 ATAAACGAACAC-AATGAACGAACATAAACGAACACAAATAAACGAAC
* * *
711826 ATAAACGAATACAATGAACGAACGTAAACGAACACAAATGAACGAAC
1 ATAAACGAACACAATGAACGAACATAAACGAACACAAATAAACGAAC
*
711873 GTAAACGAACACAAT
1 ATAAACGAACACAAT
711888 AAATGAACTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 42 0.79
48 11 0.21
ACGTcount: A:0.55, C:0.19, G:0.15, T:0.12
Consensus pattern (47 bp):
ATAAACGAACACAATGAACGAACATAAACGAACACAAATAAACGAAC
Found at i:711912 original size:47 final size:47
Alignment explanation
Indices: 711778--711914 Score: 130
Period size: 47 Copynumber: 2.9 Consensus size: 47
711768 CATTTAAATG
* * * * ** *
711778 ATAAACGAACACAAATGAACGATCATAAACGAACAGATGTAAACGAAC
1 ATAAACGAACAC-AATAAACGAACGTAAACGAACACAAATGAACGAAC
* *
711826 ATAAACGAATACAATGAACGAACGTAAACGAACACAAATGAACGAAC
1 ATAAACGAACACAATAAACGAACGTAAACGAACACAAATGAACGAAC
* * * ** *
711873 GTAAACGAACACAATAAATGAACTTAAATTAACATAAATGAA
1 ATAAACGAACACAATAAACGAACGTAAACGAACACAAATGAA
711915 AATATTTTTT
Statistics
Matches: 74, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
47 63 0.85
48 11 0.15
ACGTcount: A:0.55, C:0.17, G:0.13, T:0.15
Consensus pattern (47 bp):
ATAAACGAACACAATAAACGAACGTAAACGAACACAAATGAACGAAC
Found at i:712121 original size:14 final size:14
Alignment explanation
Indices: 712082--712122 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
712072 TGGGCTAAAC
* *
712082 ATAAATGAACACAA
1 ATAAACGAACATAA
712096 ATAAACGAACATAA
1 ATAAACGAACATAA
*
712110 ATGAACGAACATA
1 ATAAACGAACATA
712123 TTACCGAACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.61, C:0.15, G:0.10, T:0.15
Consensus pattern (14 bp):
ATAAACGAACATAA
Found at i:723720 original size:13 final size:12
Alignment explanation
Indices: 723697--723736 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
723687 GGCACCGATT
723697 TTTTATTATTAA
1 TTTTATTATTAA
723709 TTTTATTGATTAA
1 TTTTATT-ATTAA
*
723722 TTTAATTTATTAA
1 TTTTA-TTATTAA
723735 TT
1 TT
723737 AATTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 7 0.28
13 16 0.64
14 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
TTTTATTATTAA
Found at i:723732 original size:17 final size:17
Alignment explanation
Indices: 723705--723746 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
723695 TTTTTTATTA
*
723705 TTAATTTTATTGATTAAT
1 TTAA-TTTATTAATTAAT
723723 TTAATTTATTAATTAAT
1 TTAATTTATTAATTAAT
723740 TTAATTT
1 TTAATTT
723747 TTTTATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTAATTTATTAATTAAT
Found at i:730135 original size:177 final size:177
Alignment explanation
Indices: 729839--730193 Score: 694
Period size: 177 Copynumber: 2.0 Consensus size: 177
729829 ATAGGATTAT
729839 TAATCCTGAGGAATGGTGAGGTCGAGGGAGCTTCGTCGAAGGCAGCAGTCGACGGGAGTTTAGGG
1 TAATCCTGAGGAATGGTGAGGTCGAGGGAGCTTCGTCGAAGGCAGCAGTCGACGGGAGTTTAGGG
729904 TTGAAATGAGAGTTTTCAAAGTTTTGGGTTATTTCAAAACTTTTTTTTTTGTTTTTTAAAATATA
66 TTGAAATGAGAGTTTTCAAAGTTTTGGGTTATTTCAAAACTTTTTTTTTTGTTTTTTAAAATATA
729969 ATTTCAATTTTTTTAATTTTAAATAAAATTTTAAAACTACCTGAATG
131 ATTTCAATTTTTTTAATTTTAAATAAAATTTTAAAACTACCTGAATG
730016 TAATCCTGAGGAATGGTGAGGTCGAGGGAGCTTCGTCGAAGGCAGCAGTCGACGGGAGTTTAGGG
1 TAATCCTGAGGAATGGTGAGGTCGAGGGAGCTTCGTCGAAGGCAGCAGTCGACGGGAGTTTA-GG
730081 GTTGAAATGAGAGTTTTCAAAGTTTTGGGTTATTTCAAAAC-TTTTTTTTTGTTTTTTAAAATAT
65 GTTGAAATGAGAGTTTTCAAAGTTTTGGGTTATTTCAAAACTTTTTTTTTTGTTTTTTAAAATAT
730145 AATTTCAATTTTTTTAATTTTAAATAAAATTTTAAAACTACCTGAATG
130 AATTTCAATTTTTTTAATTTTAAATAAAATTTTAAAACTACCTGAATG
730193 T
1 T
730194 GACACGTGAC
Statistics
Matches: 177, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
177 134 0.76
178 43 0.24
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.39
Consensus pattern (177 bp):
TAATCCTGAGGAATGGTGAGGTCGAGGGAGCTTCGTCGAAGGCAGCAGTCGACGGGAGTTTAGGG
TTGAAATGAGAGTTTTCAAAGTTTTGGGTTATTTCAAAACTTTTTTTTTTGTTTTTTAAAATATA
ATTTCAATTTTTTTAATTTTAAATAAAATTTTAAAACTACCTGAATG
Found at i:733660 original size:29 final size:29
Alignment explanation
Indices: 733588--733660 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
733578 GAATTTTAAA
* * *
733588 AAAAATGATCGAAAATATTATTAGACGTT
1 AAAAATGACCGAAAAAATTATTAGACGCT
* **
733617 AAAAATAACAAAAAAAATTATTAGACGCT
1 AAAAATGACCGAAAAAATTATTAGACGCT
733646 AAAAATGACCGAAAA
1 AAAAATGACCGAAAA
733661 TATAAAAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.58, C:0.10, G:0.11, T:0.22
Consensus pattern (29 bp):
AAAAATGACCGAAAAAATTATTAGACGCT
Found at i:738680 original size:53 final size:53
Alignment explanation
Indices: 738600--738705 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
738590 TTTTAATTTG
738600 TTCTACTCGAACACAAAAAAAAATATAGGAAGTTCCATTACTCTTGGCGATTC
1 TTCTACTCGAACACAAAAAAAAATATAGGAAGTTCCATTACTCTTGGCGATTC
738653 TTCTACTCGAACACAAAAAAAAATATAGGAAGTTCCATTACTCTTGGCGATTC
1 TTCTACTCGAACACAAAAAAAAATATAGGAAGTTCCATTACTCTTGGCGATTC
738706 ATGATCTCCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (53 bp):
TTCTACTCGAACACAAAAAAAAATATAGGAAGTTCCATTACTCTTGGCGATTC
Found at i:741465 original size:2 final size:2
Alignment explanation
Indices: 741458--741494 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
741448 AGATCCTAAC
741458 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
741495 AGTAGATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:747387 original size:19 final size:20
Alignment explanation
Indices: 747355--747393 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
747345 AAATATTTAG
* *
747355 AATTAAATATTTTTTATAAT
1 AATTAAATAATTTTAATAAT
747375 AATT-AATAATTTTAATAAT
1 AATTAAATAATTTTAATAAT
747394 GGTATGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTAAATAATTTTAATAAT
Found at i:748950 original size:21 final size:21
Alignment explanation
Indices: 748912--748952 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
748902 GGATATATGA
* * *
748912 TTTTTAAATTACATTTAAATT
1 TTTTTAAATAAAAGTTAAATT
748933 TTTTTAAATAAAAGTTAAAT
1 TTTTTAAATAAAAGTTAAAT
748953 GTTTAAATCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTTTAAATAAAAGTTAAATT
Found at i:751221 original size:29 final size:29
Alignment explanation
Indices: 751175--751239 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
751165 GAACATAATG
*
751175 AATAGTCGAGTGACCAATTTGTAACTTTT
1 AATAGTCGAGTAACCAATTTGTAACTTTT
*
751204 AATAGTCGAGTAATCAATTTGTAACTTTT
1 AATAGTCGAGTAACCAATTTGTAACTTTT
751233 AATAGTC
1 AATAGTC
751240 AAATGACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (29 bp):
AATAGTCGAGTAACCAATTTGTAACTTTT
Found at i:751439 original size:48 final size:48
Alignment explanation
Indices: 751383--751479 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
751373 TAAGTTATTA
*
751383 ACATAATATATAACAATGAGAATAAGATGAGATTATATATAAATTAGG
1 ACATAATATATAACAATGAGAATAAGATAAGATTATATATAAATTAGG
*
751431 ACATAATATATGACAATGAGAATAAGATAAGATTATATATAAATTAGG
1 ACATAATATATAACAATGAGAATAAGATAAGATTATATATAAATTAGG
751479 A
1 A
751480 AGTTTATTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (48 bp):
ACATAATATATAACAATGAGAATAAGATAAGATTATATATAAATTAGG
Found at i:753070 original size:11 final size:11
Alignment explanation
Indices: 753054--753088 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
753044 TCATTGGGAA
753054 GAAAGGAAACG
1 GAAAGGAAACG
753065 GAAAGGAAACG
1 GAAAGGAAACG
*
753076 GAAAAG-AACG
1 GAAAGGAAACG
753086 GAA
1 GAA
753089 TTGATGGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 7 0.30
11 16 0.70
ACGTcount: A:0.57, C:0.09, G:0.34, T:0.00
Consensus pattern (11 bp):
GAAAGGAAACG
Found at i:754430 original size:43 final size:40
Alignment explanation
Indices: 754340--754435 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 40
754330 AGTTCGTTTA
* *
754340 TGTTCGTTTATTT-ATTAAATGAACGAACATAAACAAGAT
1 TGTTCGTTCATTTAATTAAATGAACGAACACAAACAAGAT
* *
754379 T-TTGCGTTCGTTTAATTAAATGAACGAACACAAACAAAGGGCT
1 TGTT-CGTTCATTTAATTAAATGAACGAACACAAAC-AA--GAT
754422 TGTTCGTTCATTTA
1 TGTTCGTTCATTTA
754436 CGTTCGTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
38 2 0.04
39 8 0.17
40 20 0.43
41 2 0.04
43 12 0.26
44 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (40 bp):
TGTTCGTTCATTTAATTAAATGAACGAACACAAACAAGAT
Found at i:754479 original size:46 final size:46
Alignment explanation
Indices: 754422--754534 Score: 208
Period size: 46 Copynumber: 2.5 Consensus size: 46
754412 ACAAAGGGCT
*
754422 TGTTCGTTCATTTACGTTCGTGAACGTTCGGTTATATGTTCGTTAA
1 TGTTTGTTCATTTACGTTCGTGAACGTTCGGTTATATGTTCGTTAA
754468 TGTTTGTTCATTTACGTTCGTGAACGTTCGGTTATATGTTCGTTAA
1 TGTTTGTTCATTTACGTTCGTGAACGTTCGGTTATATGTTCGTTAA
*
754514 TGTTTGTTCATTTATGTTCGT
1 TGTTTGTTCATTTACGTTCGT
754535 TCATTTATGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.16, C:0.13, G:0.21, T:0.50
Consensus pattern (46 bp):
TGTTTGTTCATTTACGTTCGTGAACGTTCGGTTATATGTTCGTTAA
Found at i:754530 original size:14 final size:14
Alignment explanation
Indices: 754513--754547 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
754503 ATGTTCGTTA
*
754513 ATGTTTGTTCATTT
1 ATGTTCGTTCATTT
754527 ATGTTCGTTCATTT
1 ATGTTCGTTCATTT
754541 ATGTTCG
1 ATGTTCG
754548 AACAGAGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.57
Consensus pattern (14 bp):
ATGTTCGTTCATTT
Found at i:754534 original size:24 final size:24
Alignment explanation
Indices: 754456--754535 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
754446 CGTTCGGTTA
754456 TATGTTCGTTAATGTTTGTTCATT
1 TATGTTCGTTAATGTTTGTTCATT
* * * *
754480 TACGTTCGTGAACGTTCGGTT-A--
1 TATGTTCGTTAATGTT-TGTTCATT
754502 TATGTTCGTTAATGTTTGTTCATT
1 TATGTTCGTTAATGTTTGTTCATT
754526 TATGTTCGTT
1 TATGTTCGTT
754536 CATTTATGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
21 3 0.07
22 14 0.32
24 24 0.55
25 3 0.07
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.53
Consensus pattern (24 bp):
TATGTTCGTTAATGTTTGTTCATT
Found at i:754845 original size:14 final size:14
Alignment explanation
Indices: 754826--754866 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
754816 CATTTATTAT
754826 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
754840 GTTCGTTT--G-T-
1 GTTCGTTTACGTTC
754850 GTTCGTTTACGTTC
1 GTTCGTTTACGTTC
754864 GTT
1 GTT
754867 TATCATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 8 0.35
11 1 0.04
12 2 0.09
13 1 0.04
14 11 0.48
ACGTcount: A:0.05, C:0.17, G:0.24, T:0.54
Consensus pattern (14 bp):
GTTCGTTTACGTTC
Found at i:756098 original size:16 final size:16
Alignment explanation
Indices: 756077--756111 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
756067 GTTATCTCGG
756077 TCCTTCCCTGTGGCCA
1 TCCTTCCCTGTGGCCA
756093 TCCTTCCCTGTGGCCA
1 TCCTTCCCTGTGGCCA
756109 TCC
1 TCC
756112 ATTGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.06, C:0.46, G:0.17, T:0.31
Consensus pattern (16 bp):
TCCTTCCCTGTGGCCA
Found at i:758630 original size:229 final size:228
Alignment explanation
Indices: 758225--758673 Score: 808
Period size: 229 Copynumber: 2.0 Consensus size: 228
758215 GTAAATTATC
* * *
758225 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
758290 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
758355 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
758420 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTTCAAAAAAGTATA
*
758453 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
758518 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
758583 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
758648 GAAACATAAATTACATAACTTTCAAA
195 GAAACATAAATTACATAACTTTCAAA
758674 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
228 36 0.17
229 175 0.83
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTCAAAAAAGTATA
Found at i:758762 original size:20 final size:19
Alignment explanation
Indices: 758739--758784 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
758729 CGATATACCA
758739 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
758759 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
758779 GGTAAA
1 GGTAAA
758785 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:758929 original size:20 final size:19
Alignment explanation
Indices: 758906--758952 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
758896 CGATATAACA
758906 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
758926 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
758946 GGTAAAA
1 GGTAAAA
758953 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:758954 original size:17 final size:19
Alignment explanation
Indices: 758915--758957 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
758905 AGGTAAAAAT
758915 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
758935 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
758952 ATGATA
1 ATGATA
758958 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:761870 original size:23 final size:23
Alignment explanation
Indices: 761839--761902 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
761829 ATAGGTAAAC
*
761839 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
761862 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
761885 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
761903 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:761909 original size:23 final size:23
Alignment explanation
Indices: 761839--761911 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
761829 ATAGGTAAAC
* **
761839 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
761862 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
761885 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
761908 ATAT
1 ATAT
761912 TGTAAAGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:762335 original size:23 final size:23
Alignment explanation
Indices: 762264--762336 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
762254 ATAGGTAAAC
* * *
762264 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTCGTT
762287 ATATAATGTAATAGGTA-TCGTAT
1 ATATAATGTAATAGGTAGTCGT-T
*
762310 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTCGTT
762333 ATAT
1 ATAT
762337 TGTAAAGTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.05
23 39 0.89
24 3 0.07
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTCGTT
Found at i:762768 original size:428 final size:415
Alignment explanation
Indices: 761760--762605 Score: 1282
Period size: 425 Copynumber: 2.0 Consensus size: 415
761750 AAAAATTGAA
* *
761760 ACATAAATTACATAAGTTTTAAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCA
1 ACATAAATTACAT-A-TTTT--AAAAAAGTATCGATCCTTTATATAAAAAGTATGGACAATTTCA
* * * * *
761825 ATAT-ATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTTTATAT
62 ATATAATAGGTAAACATATGA-GTAACAGGTAGCACTTATAAAATGTAATA-GTAGCGTATATAT
* *
761889 AATGTAATAGGTAGTGGTTATATTGTAAAGTTTCTATCCTTTTATAAAAGTGTCCATACTTTTTT
125 AATGTAATAGGTACTAGTTATATTGTAAAGTTTCTATCCTTTTATAAAAGTGTCCATACTTTTTT
761954 CACTGTGGAAAACATTAATTTAATATTAATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTA
190 CACTGTGGAAAACATTAATTTAATATTAATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTA
762019 TAGGCGTCTAATGATTATTTTTTACGTTACGGTATATATATTATTAATTAAAAATTCTAAATAAT
255 TAGGCGTCTAATGATTATTTTTTACGTTACGGTATATATATTATTAATTAAAAATTCTAAATAAT
762084 ATTTTATAAAATATAAAAACAATCAAATAATTTTTTCTGCAAATGAAATTATTAAATCAATATTG
320 ATTTTATAAAATATAAAAACAATCAAATAATTTTTTCTGCAAATGAAATTATTAAATCAATATTG
*
762149 TAGGTGGAAAACATGAAACACTGTTAAAAAAATTG
385 TAGGTGCAAAACATGAAACACTGTT---AAAA-TG
* *
762184 AAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCA
1 --ACATAAATTACAT-A-TTTTAAAAAAGTATCGATCCTTTATATAAAAAGTATGGACAATTTCA
* * * *
762249 ATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGTAATAGGTATCGTATATAT
62 ATATAATAGGTAAACATATGA-GTAACAGGTAGCACTTATAAAATGTAATA-GTAGCGTATATAT
* *
762314 AATGTAATAGGTAGTGGTTATATTGTAAAGTTTCTATCCTTTTTATAAAAGTGTCCATACTTTTT
125 AATGTAATAGGTACTAGTTATATTGTAAAGTTTCTATCC-TTTTATAAAAGTGTCCATACTTTTT
762379 TCACTGTGGAAAACATTAATTTAATATTAATTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
189 TCACTGTGGAAAACATTAATTTAATATTAA-TTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
762444 TATAGGCGTCTAATGATTA-TTTTTACGTTACGGTATATATTATTATTAAATTAAAAATTCTAAA
253 TATAGGCGTCTAATGATTATTTTTTACGTTACGGTATATA-TATTATT-AATTAAAAATTCTAAA
* * *
762508 TAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAAT
316 TAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTCTGCAAATGAAATTATTAAATCAAT
**
762573 ATTGTAGGTGCATTCACATGAAACACTGTTAAA
381 ATTGTAGGTGCA-AAACATGAAACACTGTTAAA
762606 GTATCGATCC
Statistics
Matches: 407, Mismatches: 7, Indels: 12
0.96 0.02 0.03
Matches are distributed among these distances:
424 47 0.12
425 98 0.24
426 98 0.24
427 60 0.15
428 89 0.22
429 15 0.04
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (415 bp):
ACATAAATTACATATTTTAAAAAAGTATCGATCCTTTATATAAAAAGTATGGACAATTTCAATAT
AATAGGTAAACATATGAGTAACAGGTAGCACTTATAAAATGTAATAGTAGCGTATATATAATGTA
ATAGGTACTAGTTATATTGTAAAGTTTCTATCCTTTTATAAAAGTGTCCATACTTTTTTCACTGT
GGAAAACATTAATTTAATATTAATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
TCTAATGATTATTTTTTACGTTACGGTATATATATTATTAATTAAAAATTCTAAATAATATTTTA
TAAAATATAAAAACAATCAAATAATTTTTTCTGCAAATGAAATTATTAAATCAATATTGTAGGTG
CAAAACATGAAACACTGTTAAAATG
Found at i:770080 original size:13 final size:13
Alignment explanation
Indices: 770064--770093 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
770054 TTTTTTTTGT
770064 AATTTTAGGATCA
1 AATTTTAGGATCA
770077 AATTTTAGGATCA
1 AATTTTAGGATCA
770090 AATT
1 AATT
770094 ATAAAGGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (13 bp):
AATTTTAGGATCA
Found at i:775079 original size:19 final size:19
Alignment explanation
Indices: 775055--775091 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
775045 ATATTATTAA
775055 AATTTAAAATATAATTTTT
1 AATTTAAAATATAATTTTT
*
775074 AATTTAAAATATTATTTT
1 AATTTAAAATATAATTTT
775092 ATCAAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTTAAAATATAATTTTT
Found at i:777574 original size:33 final size:33
Alignment explanation
Indices: 777537--777602 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
777527 TGGAATTCTG
777537 ATTCCCATTTCTATTTGATTTTGATGTTTACTT
1 ATTCCCATTTCTATTTGATTTTGATGTTTACTT
777570 ATTCCCATTTCTATTTGATTTTGATGTTTACTT
1 ATTCCCATTTCTATTTGATTTTGATGTTTACTT
777603 TTTCATATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.58
Consensus pattern (33 bp):
ATTCCCATTTCTATTTGATTTTGATGTTTACTT
Found at i:779492 original size:16 final size:15
Alignment explanation
Indices: 779471--779501 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
779461 ACACAAATAA
779471 TAATAAAATCGAAATT
1 TAATAAAATC-AAATT
779487 TAATAAAATCAAATT
1 TAATAAAATCAAATT
779502 ATATATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (15 bp):
TAATAAAATCAAATT
Done.