Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009261.1 Hibiscus syriacus cultivar Beakdansim tig00112912_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: 923215
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:754681 original size:83 final size:82
Alignment explanation
Indices: 754433--754707 Score: 244
Period size: 83 Copynumber: 3.4 Consensus size: 82
754423 TATTATTGCG
* * ** *
754433 TTTGTAAAAAAATGTCGTTAAAATACTACTCTATTACGGTATTT-TTGAAAAAAATGCCACTACA
1 TTTGTATAAAAACGTCACTAAAATACTACTCTGTTACGGTATTTGTTG-AAAAAATGCCACTACA
* * *
754497 GATGAATCTAATTGTGGTA
65 GATGAAACT-ATTGTAGCA
* * * * *
754516 TTTATATAAAAACGCCGCTAAAATACTACTCTGTT---G--TTTGTTGAAAAAATACCACTACAT
1 TTTGTATAAAAACGTCACTAAAATACTACTCTGTTACGGTATTTGTTGAAAAAATGCCACTACAG
754576 ATGAATACTA-T-TACGACA
66 ATGAA-ACTATTGTA-G-CA
* * * *
754594 TTTGTATAAAAACGTCACTAAAGTACTACTCTGTTACGGTATTTGTTGAAAAAATGTCATTATAG
1 TTTGTATAAAAACGTCACTAAAATACTACTCTGTTACGGTATTTGTTGAAAAAATGCCACTACAG
* *
754659 ATGAACCCTATTGTAGCG
66 ATGAA-ACTATTGTAGCA
* *
754677 TTTGTTTAAAAACG-CACTAAAGTACTACTCT
1 TTTGTATAAAAACGTCACTAAAATACTACTCT
754708 ATTGCGGCGT
Statistics
Matches: 157, Mismatches: 24, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
76 1 0.01
77 2 0.01
78 56 0.36
79 5 0.03
80 1 0.01
81 1 0.01
82 17 0.11
83 70 0.45
84 2 0.01
85 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (82 bp):
TTTGTATAAAAACGTCACTAAAATACTACTCTGTTACGGTATTTGTTGAAAAAATGCCACTACAG
ATGAAACTATTGTAGCA
Found at i:763133 original size:25 final size:25
Alignment explanation
Indices: 763095--763146 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
763085 AGATTGCATC
*
763095 TTTGGCAAACAAAATAAAGCCAGTT
1 TTTGGCAAACAAAAGAAAGCCAGTT
*
763120 TTTGGCAAATAAAAGAAAGCCAGTT
1 TTTGGCAAACAAAAGAAAGCCAGTT
763145 TT
1 TT
763147 GCAAAGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (25 bp):
TTTGGCAAACAAAAGAAAGCCAGTT
Found at i:774657 original size:81 final size:81
Alignment explanation
Indices: 774512--774816 Score: 463
Period size: 81 Copynumber: 3.8 Consensus size: 81
774502 ACTTGCATGA
* *
774512 CATTAATATTTTACTCAAAGGTATTTAACA---CATCTAACTGGCATAATTAACACCTTTCTGTC
1 CATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGTC
* * * *
774574 AAATGTATAGCTAAGC
66 AAATGCACAACTAGGC
* *
774590 CATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGAGACTTTTCTGTC
1 CATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGTC
774655 AAATGCACAACTAGGC
66 AAATGCACAACTAGGC
* * * *
774671 CATTAATCTTTTACTCAAAGGTATTTAACCTTTCATATAACTGGCATAATTGACATCTTTCTATC
1 CATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGTC
*
774736 AAATGCACAATTAGGC
66 AAATGCACAACTAGGC
*
774752 CATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAATTGGCATAATTGACACCTTTCTGTC
1 CATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGTC
774817 TACTCAAAGG
Statistics
Matches: 204, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
78 29 0.14
81 175 0.86
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (81 bp):
CATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTCTGTC
AAATGCACAACTAGGC
Found at i:775154 original size:54 final size:55
Alignment explanation
Indices: 775096--775217 Score: 169
Period size: 54 Copynumber: 2.2 Consensus size: 55
775086 TGTACGTGGG
775096 TTGCACACATA-TTACCAATATCG-AAACTCATAAACTTATTATGAATTTATTA-TT
1 TTGCACACATAGTTACC-ATA-CGAAAACTCATAAACTTATTATGAATTTATTAGTT
* * * *
775150 TTGCACACAAAGTTTCCATACGAAAATTCATAAACTTATTATGAATTTCTTAGTT
1 TTGCACACATAGTTACCATACGAAAACTCATAAACTTATTATGAATTTATTAGTT
775205 TTGCACACATAGT
1 TTGCACACATAGT
775218 GTCATTTGGT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
53 2 0.03
54 40 0.67
55 18 0.30
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (55 bp):
TTGCACACATAGTTACCATACGAAAACTCATAAACTTATTATGAATTTATTAGTT
Found at i:775957 original size:19 final size:20
Alignment explanation
Indices: 775903--775949 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
775893 TTAGCTTCTT
775903 AAAACATCTAAAATCTCCTA
1 AAAACATCTAAAATCTCCTA
775923 AAAACATCTAAAATCTCAC-A
1 AAAACATCTAAAATCTC-CTA
775943 AAAACAT
1 AAAACAT
775950 TCAAATCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAACATCTAAAATCTCCTA
Found at i:779542 original size:32 final size:31
Alignment explanation
Indices: 779505--779581 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
779495 CGAGGCCATG
* **
779505 GGGCCTACCTAAGAACCCATCTTAGGGCCGTA
1 GGGCCTACCTAAGAA-CAATCCCAGGGCCGTA
** *
779537 GGGCCTACCCGAGAATAATCCCAGGGCCGTA
1 GGGCCTACCTAAGAACAATCCCAGGGCCGTA
*
779568 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
779582 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCCCAGGGCCGTA
Found at i:784346 original size:32 final size:31
Alignment explanation
Indices: 784310--784386 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
784300 TGGGGTAATG
* *
784310 GGGCCAACCTAAGAACACATCTTAGGGCCACA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCACA
** * *
784342 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCACA
*
784373 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
784387 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.31, C:0.31, G:0.25, T:0.13
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCACA
Found at i:793937 original size:81 final size:81
Alignment explanation
Indices: 793784--794442 Score: 926
Period size: 81 Copynumber: 8.1 Consensus size: 81
793774 AACCTTTAGA
* * * * * * * * *
793784 CTTTTACCCAAAGGCATATAGCATTTCATCTAACTTGCATGATTGACAC-CTTCATGTTAAATGC
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTC-TGTCAAATGC
* *
793848 ATAGCTAGGCTATTAAT
65 ACAGCTAGGCCATTAAT
* * * * *
793865 ATTTTACTCAAATGTATTTAACCTTTCATCTAACTGGTATAAATGACACATTTCTGTCAAATCCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCA
* *
793930 TAACTAGGCCATT-AT
66 CAGCTAGGCCATTAAT
* * *
793945 CTTTTACTCAAAGATATTTAACATTTCATCTAACTGGCATAATTGACATATTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCA
794010 CAGCTAGGCCATTAAT
66 CAGCTAGGCCATTAAT
* *
794026 CTTTTACTCAAAGAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACATATTTCTGTCAAA
1 CTTTTACTC----AAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAA
* *
794091 TGCACAGCTAGACCATTAGT
62 TGCACAGCTAGGCCATTAAT
*
794111 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCA
794176 CAGCTAGGCCATTAAT
66 CAGCTAGGCCATTAAT
* * *
794192 CTTTTACTCAAAGGTATTTAATCTTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCA
* * *
794257 TAACTAGTCCATTAAT
66 CAGCTAGGCCATTAAT
*
794273 CTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACATTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCA
*
794338 CAACTAGGCCATTAAT
66 CAGCTAGGCCATTAAT
* * *
794354 ATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGACACATTTCTATCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCA
794419 CAGCTAGGCCATTAAT
66 CAGCTAGGCCATTAAT
794435 CTTTTACT
1 CTTTTACT
794443 TTGGAATAGT
Statistics
Matches: 519, Mismatches: 53, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
80 70 0.13
81 370 0.71
82 3 0.01
85 76 0.15
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (81 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCA
CAGCTAGGCCATTAAT
Found at i:794984 original size:22 final size:19
Alignment explanation
Indices: 794958--795011 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 19
794948 TACCCCTACC
794958 ATGGTATTGATACTACTATACT
1 ATGGTATTGATACT-CTAT--T
**
794980 ATGGTAACGATACTCTATT
1 ATGGTATTGATACTCTATT
*
794999 ACGGTATTGATAC
1 ATGGTATTGATAC
795012 CATTTTTGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 11 0.41
21 4 0.15
22 12 0.44
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (19 bp):
ATGGTATTGATACTCTATT
Found at i:795010 original size:19 final size:21
Alignment explanation
Indices: 794960--795011 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
794950 CCCCTACCAT
*
794960 GGTATTGATACTACTATACTAT
1 GGTATTGATACTACTATA-TAC
**
794982 GGTAACGATACT-CTAT-TAC
1 GGTATTGATACTACTATATAC
795001 GGTATTGATAC
1 GGTATTGATAC
795012 CATTTTTGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 11 0.44
21 4 0.16
22 10 0.40
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (21 bp):
GGTATTGATACTACTATATAC
Found at i:797459 original size:20 final size:20
Alignment explanation
Indices: 797436--797473 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
797426 AATTGTCACA
* *
797436 GTTCATCCAGTATTGATATT
1 GTTCATACAATATTGATATT
797456 GTTCATACAATATTGATA
1 GTTCATACAATATTGATA
797474 CTCTAACCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
GTTCATACAATATTGATATT
Found at i:799953 original size:20 final size:20
Alignment explanation
Indices: 799930--800043 Score: 70
Period size: 20 Copynumber: 5.6 Consensus size: 20
799920 TGCATGCTAA
799930 CATGTGTGCATGTACGTGTG
1 CATGTGTGCATGTACGTGTG
* * *
799950 CATGTGTACATGTATGTATG
1 CATGTGTGCATGTACGTGTG
* **
799970 CATGTGTGTATGCGCGTGTG
1 CATGTGTGCATGTACGTGTG
* **
799990 CTCGTGTGTGCATGCGTACGCATG
1 --CATGTGTGCAT--GTACGTGTG
* *
800014 TATGTGTG-A-GTATGTGTG
1 CATGTGTGCATGTACGTGTG
*
800032 CATGAGTGCATG
1 CATGTGTGCATG
800044 AATGTATACA
Statistics
Matches: 66, Mismatches: 22, Indels: 12
0.66 0.22 0.12
Matches are distributed among these distances:
18 12 0.18
19 1 0.02
20 32 0.48
21 1 0.02
22 15 0.23
24 5 0.08
ACGTcount: A:0.17, C:0.14, G:0.34, T:0.35
Consensus pattern (20 bp):
CATGTGTGCATGTACGTGTG
Found at i:800056 original size:8 final size:8
Alignment explanation
Indices: 800045--800088 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
800035 GAGTGCATGA
*
800045 ATGTATAC
1 ATGTATCC
800053 ATGTATCC
1 ATGTATCC
800061 ATGTATCC
1 ATGTATCC
800069 ATGTATCC
1 ATGTATCC
*
800077 ATGTATGC
1 ATGTATCC
800085 ATGT
1 ATGT
800089 GAATGTGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (8 bp):
ATGTATCC
Found at i:803280 original size:35 final size:35
Alignment explanation
Indices: 803229--803333 Score: 174
Period size: 35 Copynumber: 3.0 Consensus size: 35
803219 CTATAACTAA
* * *
803229 TAATATAATAACAATTAAGATAAGAAAGCATATTT
1 TAATATAATAATAATTAAAATAACAAAGCATATTT
803264 TAATATAATAATAATTAAAATAACAAAGCATATTT
1 TAATATAATAATAATTAAAATAACAAAGCATATTT
*
803299 TAATATAATAATAACTAAAATAACAAAGCATATTT
1 TAATATAATAATAATTAAAATAACAAAGCATATTT
803334 AAAAAACCTC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (35 bp):
TAATATAATAATAATTAAAATAACAAAGCATATTT
Found at i:803592 original size:71 final size:71
Alignment explanation
Indices: 803470--803840 Score: 354
Period size: 71 Copynumber: 5.2 Consensus size: 71
803460 AATGAGGGTG
* * * * *
803470 CTCTATGACTGAGGCTCGAGATTGCGTTCGACTTCCTGCATGGTTGCAGGTTCGTCTAGTAACGG
1 CTCTATGACTGAGGCTCGGGGTTGCGTTCGACTTCCTCCATGGTTGAAGGTTCGTCTACTAACGG
803535 GGTGTC
66 GGTGTC
* * * ** * * * *
803541 ATCTATGACTAAGGATCGGGGTTGTATTCGACTTTCTCTATGGTTGAAGGTTCGTCTACTAATGA
1 CTCTATGACTGAGGCTCGGGGTTGCGTTCGACTTCCTCCATGGTTGAAGGTTCGTCTACTAACGG
*
803606 GTTGT-
66 GGTGTC
* * * * * *
803611 CTGCCATGAATGAGGCTCGGGGTTGCGTTTGACTTCCTCTATGGTTTAGGGTTTC-TCTA-TCAA
1 CT-CTATGACTGAGGCTCGGGGTTGCGTTCGACTTCCTCCATGGTTGAAGG-TTCGTCTACT-AA
*
803674 C-GAGTGTC
63 CGGGGTGTC
* * * * * * *
803682 CTCTATGACTGAGGCTCAGGGTTGTGTTTGACTTTCTCCATGGCTAAAGGCTCGTCTACTAACGG
1 CTCTATGACTGAGGCTCGGGGTTGCGTTCGACTTCCTCCATGGTTGAAGGTTCGTCTACTAACGG
*
803747 GGTATC
66 GGTGTC
* * * * * *
803753 CTCCATGACTGAGGCTCGGGGTTGCGTTCAACTTCCTCCATGATTGATGGTTCGCCTACTAACGA
1 CTCTATGACTGAGGCTCGGGGTTGCGTTCGACTTCCTCCATGGTTGAAGGTTCGTCTACTAACGG
*
803818 GTTGTC
66 GGTGTC
803824 CTCTATGACTGAGGCTC
1 CTCTATGACTGAGGCTC
803841 ATGAATTTCC
Statistics
Matches: 235, Mismatches: 58, Indels: 14
0.77 0.19 0.05
Matches are distributed among these distances:
69 2 0.01
70 51 0.22
71 179 0.76
72 3 0.01
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (71 bp):
CTCTATGACTGAGGCTCGGGGTTGCGTTCGACTTCCTCCATGGTTGAAGGTTCGTCTACTAACGG
GGTGTC
Found at i:803715 original size:141 final size:141
Alignment explanation
Indices: 803474--803841 Score: 375
Period size: 141 Copynumber: 2.6 Consensus size: 141
803464 AGGGTGCTCT
* * * * * * * * *
803474 ATGACTGAGGCTCGAGATTGCGTTCGACTTCCTGCATGGTTGCA-GGTTCGTCTAGTAACGGGGT
1 ATGAATGAGGCTCGGGGTTGCGTTCAACTTCCTCCATGATTG-AGGGTTCGCCTACTAAC-GAGT
* * * * * * * *
803538 GTCATCTATGACTAAGGATCGGGGTTGTATTCGACTTTCTCTATGGTTGAAGGTTCGTCTACTAA
64 GTCCTCTATGACTGAGGCTCAGGGTTGTATTCGACTTTCTCCATGGCTAAAGGCTCGTCTACTAA
* * *
803603 TGAGTTGT-CTGCC
129 CGAGGTATCCT-CC
** * * * *
803616 ATGAATGAGGCTCGGGGTTGCGTTTGACTTCCTCTATGGTTTAGGGTTTC-TCTA-TCAACGAGT
1 ATGAATGAGGCTCGGGGTTGCGTTCAACTTCCTCCATGATTGAGGG-TTCGCCTACT-AACGAGT
* *
803679 GTCCTCTATGACTGAGGCTCAGGGTTGTGTTTGACTTTCTCCATGGCTAAAGGCTCGTCTACTAA
64 GTCCTCTATGACTGAGGCTCAGGGTTGTATTCGACTTTCTCCATGGCTAAAGGCTCGTCTACTAA
*
803744 CGGGGTATCCTCC
129 CGAGGTATCCTCC
* *
803757 ATGACTGAGGCTCGGGGTTGCGTTCAACTTCCTCCATGATTGATGGTTCGCCTACTAACGAGTTG
1 ATGAATGAGGCTCGGGGTTGCGTTCAACTTCCTCCATGATTGAGGGTTCGCCTACTAACGAG-TG
803822 TCCTCTATGACTGAGGCTCA
65 TCCTCTATGACTGAGGCTCA
803842 TGAATTTCCT
Statistics
Matches: 189, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
140 3 0.02
141 114 0.60
142 69 0.37
143 3 0.02
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.33
Consensus pattern (141 bp):
ATGAATGAGGCTCGGGGTTGCGTTCAACTTCCTCCATGATTGAGGGTTCGCCTACTAACGAGTGT
CCTCTATGACTGAGGCTCAGGGTTGTATTCGACTTTCTCCATGGCTAAAGGCTCGTCTACTAACG
AGGTATCCTCC
Found at i:804727 original size:3 final size:3
Alignment explanation
Indices: 804719--804744 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
804709 TATTTTCCCT
804719 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
804745 GTTTTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:808439 original size:36 final size:36
Alignment explanation
Indices: 808392--808463 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
808382 TAGGTTAATT
808392 TCATAGTTTAATAGCTATGAACATGCACACATTATG
1 TCATAGTTTAATAGCTATGAACATGCACACATTATG
808428 TCATAGTTTAATAGCTATGAACATGCACACATTATG
1 TCATAGTTTAATAGCTATGAACATGCACACATTATG
808464 GTTTTTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (36 bp):
TCATAGTTTAATAGCTATGAACATGCACACATTATG
Found at i:808768 original size:22 final size:23
Alignment explanation
Indices: 808727--808778 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
808717 GAGTCGATGG
** *
808727 TTTCATAGGTCCTTCGGGACATA
1 TTTCATAGGTCCTTAAGGACAAA
808750 -TTCATAGGTCCTTAAGGACAAA
1 TTTCATAGGTCCTTAAGGACAAA
808772 TTTCATA
1 TTTCATA
808779 TGCCACTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (23 bp):
TTTCATAGGTCCTTAAGGACAAA
Found at i:817201 original size:100 final size:98
Alignment explanation
Indices: 817091--817381 Score: 345
Period size: 100 Copynumber: 2.9 Consensus size: 98
817081 ATCGCAAATT
* * *
817091 AGGTGGACCGACATTTCCAGAAGAGTTCATAATGATAAGAACTCGCCCCAAAGGAGAAAGTTC-A
1 AGGTGGACCGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGCCCCAAAGAAGAAAGTTCAA
817155 -GAG-AGAACTTATTCCTTTCAAATCCAACGCATAAAG
66 TGAGAAGAACTTATTCCTTTCAAAT-C-ACG---AAAG
* * ** *
817191 AGGTGGACCGATATTTTCAAAAGAGTTCATAATGAGAAGAACTCATCTCAAAGAAGAAAGTTCAT
1 AGGTGGACCGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGCCCCAAAGAAGAAAGTTC--
*
817256 AATGAGAAGAACTTATTCCTTTCAAATCACGAAGG
64 AATGAGAAGAACTTATTCCTTTCAAATCACGAAAG
* * ** *
817291 AGGTGGACCGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGCTCTAAATTAGAAGGTTCAT
1 AGGTGGACCGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGCCCCAAAGAAGAAAGTTC--
*
817356 AATGAGAAGAACTTGTTCCTTTCAAA
64 AATGAGAAGAACTTATTCCTTTCAAA
817382 CACATCGCAA
Statistics
Matches: 166, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
100 138 0.83
103 4 0.02
104 4 0.02
105 20 0.12
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (98 bp):
AGGTGGACCGACATTTCCAAAAGAGTTCATAATGAGAAGAACTCGCCCCAAAGAAGAAAGTTCAA
TGAGAAGAACTTATTCCTTTCAAATCACGAAAG
Found at i:817486 original size:36 final size:37
Alignment explanation
Indices: 817435--817513 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
817425 GTTTATAACA
817435 AGAAG-AACTCATCTCGAGGAG-AAAAGTTCATAATG
1 AGAAGAAACTCATCTCGAGGAGAAAAAGTTCATAATG
*
817470 AGAAGAAACTCGTCTCGAGGAGAAAAAGTTCATAATG
1 AGAAGAAACTCATCTCGAGGAGAAAAAGTTCATAATG
817507 AGAAGAA
1 AGAAGAA
817514 CTTGTTCATT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 5 0.12
36 15 0.37
37 21 0.51
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.18
Consensus pattern (37 bp):
AGAAGAAACTCATCTCGAGGAGAAAAAGTTCATAATG
Found at i:821032 original size:16 final size:16
Alignment explanation
Indices: 820999--821053 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
820989 TTTCTACACA
*
820999 AACTTTT-CTAACAACT
1 AACTTTTACTAAC-TCT
821015 AACTTTTACTAACTCT
1 AACTTTTACTAACTCT
*
821031 AAC--TTACTAATTTCT
1 AACTTTTACTAA-CTCT
821046 AACTTTTA
1 AACTTTTA
821054 ACCACTAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 7 0.21
15 6 0.18
16 12 0.36
17 8 0.24
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.44
Consensus pattern (16 bp):
AACTTTTACTAACTCT
Found at i:824821 original size:17 final size:16
Alignment explanation
Indices: 824781--824826 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
824771 TTAATCCTTA
824781 TATAACTAATA-ATAAC
1 TATAA-TAATATATAAC
824797 -ATAA-AATATATAAC
1 TATAATAATATATAAC
824811 TTATAATAATATATAA
1 -TATAATAATATATAA
824827 ACCCAAACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.15
14 5 0.19
15 4 0.15
16 4 0.15
17 9 0.35
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (16 bp):
TATAATAATATATAAC
Found at i:826638 original size:13 final size:13
Alignment explanation
Indices: 826620--826682 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
826610 CCCCATTTTA
826620 TTTCTTTTTTCTT
1 TTTCTTTTTTCTT
*
826633 TTTCTTTTTTGTGT
1 TTTCTTTTTTCT-T
826647 TTGTCTTTATTTCTT
1 TT-TCTTT-TTTCTT
*
826662 TTCCTCTTTTT-TT
1 TTTCT-TTTTTCTT
*
826675 TCTCTTTT
1 TTTCTTTT
826683 CCTTTTTTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 3 0.07
13 16 0.39
14 8 0.20
15 10 0.24
16 4 0.10
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.78
Consensus pattern (13 bp):
TTTCTTTTTTCTT
Found at i:835501 original size:14 final size:14
Alignment explanation
Indices: 835482--835510 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
835472 ATAACTAATA
835482 ACTTATCCTTATAT
1 ACTTATCCTTATAT
835496 ACTTATCCTTATAT
1 ACTTATCCTTATAT
835510 A
1 A
835511 ACTATAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (14 bp):
ACTTATCCTTATAT
Found at i:835555 original size:10 final size:10
Alignment explanation
Indices: 835514--835548 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
835504 TTATATAACT
*
835514 ATAACATATA
1 ATAACTTATA
835524 ATAACTTATA
1 ATAACTTATA
835534 TATAACTTATA
1 -ATAACTTATA
835545 ATAA
1 ATAA
835549 TATATAAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (10 bp):
ATAACTTATA
Found at i:835649 original size:2 final size:2
Alignment explanation
Indices: 835642--835674 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
835632 TTTTATATTT
835642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
835675 TATTTTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:835909 original size:21 final size:21
Alignment explanation
Indices: 835883--835932 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
835873 TCTTCCAAGT
835883 TATTTTTGTTTTATCTTATCC
1 TATTTTTGTTTTATCTTATCC
* * *
835904 TATTTTTATTTTATTTTATCT
1 TATTTTTGTTTTATCTTATCC
*
835925 TAGTTTTG
1 TATTTTTG
835933 ATATTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.16, C:0.08, G:0.06, T:0.70
Consensus pattern (21 bp):
TATTTTTGTTTTATCTTATCC
Found at i:838111 original size:12 final size:13
Alignment explanation
Indices: 838088--838116 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
838078 AAAGTTTTGA
838088 GAAAAATAAAATG
1 GAAAAATAAAATG
838101 GAAAAAT-AAATG
1 GAAAAATAAAATG
838113 GAAA
1 GAAA
838117 GGGATAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAAAATAAAATG
Found at i:844419 original size:3 final size:3
Alignment explanation
Indices: 844397--844505 Score: 163
Period size: 3 Copynumber: 37.0 Consensus size: 3
844387 GAATATTTCA
844397 TAT TA- TAT GTAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
844441 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
844488 TAGT TAT TAT TA- TAT TAT
1 TA-T TAT TAT TAT TAT TAT
844506 ATAATTATAT
Statistics
Matches: 99, Mismatches: 1, Indels: 12
0.88 0.01 0.11
Matches are distributed among these distances:
2 8 0.08
3 86 0.87
4 5 0.05
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:844516 original size:2 final size:2
Alignment explanation
Indices: 844498--844660 Score: 96
Period size: 2 Copynumber: 83.5 Consensus size: 2
844488 TAGTTATTAT
*
844498 TA TA T- TA TA TA -A T- TA TA TA GTA TA TG T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
844537 TA GTA TA TG T- TA TA TA TA TA GTA TT TG TA TT TA TA TA TA GTA
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * *
844579 TA TA T- TA TA TA -A TA TT TA TA T- TT TA TA TA TA GTA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
844619 T- TA TA TA TA TA TA GTA TT TA TA TA T- TA T- TA GTA TA TT TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
844660 T
1 T
844661 TGTATTTATT
Statistics
Matches: 127, Mismatches: 16, Indels: 36
0.71 0.09 0.20
Matches are distributed among these distances:
1 11 0.09
2 102 0.80
3 14 0.11
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (2 bp):
TA
Found at i:844527 original size:22 final size:21
Alignment explanation
Indices: 844502--844685 Score: 111
Period size: 19 Copynumber: 9.5 Consensus size: 21
844492 TATTATTATA
844502 TTATATAATTATATAGTATATG
1 TTATAT-ATTATATAGTATATG
844524 TTATATATATATATAGTATATG
1 TTATATAT-TATATAGTATATG
*
844546 -T-TATA-TATATAGTATTTG
1 TTATATATTATATAGTATATG
* *
844564 -TATTTA-TATATAGTATATA
1 TTATATATTATATAGTATATG
*
844583 TTATATA--ATAT-TTATAT-
1 TTATATATTATATAGTATATG
* *
844600 TT-TATA-TATAGTA-TTTATA
1 TTATATATTATA-TAGTATATG
844619 TTATATA-TATATAG--TAT-
1 TTATATATTATATAGTATATG
844636 TTATATATTAT-TAGTATAT-
1 TTATATATTATATAGTATATG
* * *
844655 TTATAT-TGTATTTATTATATA
1 TTATATAT-TATATAGTATATG
844676 TTAT-TATTAT
1 TTATATATTAT
844686 TATTTAGTAC
Statistics
Matches: 138, Mismatches: 8, Indels: 34
0.77 0.04 0.19
Matches are distributed among these distances:
16 4 0.03
17 15 0.11
18 30 0.22
19 34 0.25
20 28 0.20
21 8 0.06
22 19 0.14
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (21 bp):
TTATATATTATATAGTATATG
Found at i:845980 original size:14 final size:14
Alignment explanation
Indices: 845961--845987 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
845951 TTTAATCTTT
845961 TTTATTCTATTTTA
1 TTTATTCTATTTTA
845975 TTTATTCTATTTT
1 TTTATTCTATTTT
845988 TATAAATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTCTATTTTA
Found at i:846217 original size:177 final size:181
Alignment explanation
Indices: 845994--846334 Score: 591
Period size: 182 Copynumber: 1.9 Consensus size: 181
845984 TTTTTATAAA
*
845994 TTGGTACCCTTACTCATTTGTTGTTTTGCAATATTTATTTATTTACTTAATATTAA-T-T-TTTT
1 TTGGTACCCTGACTCATTTGTTGTTTTGCAATATTTATTTATTTACTTAATATTAATTCTATTTT
*
846056 TT-AAAATGAATCCTTCTAAATCCCAAAAATTCATCAAAGGTAAGTAATTTGGATCGAATATTTA
66 TTAAAAAAGAATCCTTCTAAATCCCAAAAATTCATCAAAGGTAAGTAATTTGGATCGAATATTTA
*
846120 AATTTTCATCTAAATTTAAAATTTCTCAATTAAGACAACTGAGTAATTGTG
131 AAATTTCATCTAAATTTAAAATTTCTCAATTAAGACAACTGAGTAATTGTG
846171 TTGGTACCCTGACTCATTTGTTGTTTTGCAATATTTATTTATTTACTTAATATTAATTCTATTTT
1 TTGGTACCCTGACTCATTTGTTGTTTTGCAATATTTATTTATTTACTTAATATTAATTCTATTTT
*
846236 TTAAAAAAAGAATCCTTTTAAATCCCAAAAATTCATCAAAGGTAAGTAATTTGGATCGAATATTT
66 TT-AAAAAAGAATCCTTCTAAATCCCAAAAATTCATCAAAGGTAAGTAATTTGGATCGAATATTT
* *
846301 AAAATTTCATCTAAATTTTAAATTTCTCATTTAA
130 AAAATTTCATCTAAATTTAAAATTTCTCAATTAA
846335 AAGGGTAGTA
Statistics
Matches: 153, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
177 55 0.36
178 1 0.01
179 1 0.01
180 6 0.04
182 90 0.59
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (181 bp):
TTGGTACCCTGACTCATTTGTTGTTTTGCAATATTTATTTATTTACTTAATATTAATTCTATTTT
TTAAAAAAGAATCCTTCTAAATCCCAAAAATTCATCAAAGGTAAGTAATTTGGATCGAATATTTA
AAATTTCATCTAAATTTAAAATTTCTCAATTAAGACAACTGAGTAATTGTG
Found at i:848530 original size:26 final size:25
Alignment explanation
Indices: 848500--848571 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 25
848490 TTTGAAGTAG
*
848500 ACAAAAATGAATTGGAAGAAAAATT
1 ACAAAAAGGAATTGGAAGAAAAATT
* *
848525 AGCAAAAAGGAATTTGAAG---TA-T
1 A-CAAAAAGGAATTGGAAGAAAAATT
848547 ACAAAAAGGAATTGGAAGAAAAATT
1 ACAAAAAGGAATTGGAAGAAAAATT
848572 GAAGAAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
21 16 0.43
22 2 0.05
23 1 0.03
24 1 0.03
25 2 0.05
26 15 0.41
ACGTcount: A:0.57, C:0.04, G:0.19, T:0.19
Consensus pattern (25 bp):
ACAAAAAGGAATTGGAAGAAAAATT
Found at i:848551 original size:21 final size:21
Alignment explanation
Indices: 848479--848564 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 21
848469 CTGGAGATAG
* *
848479 CAAAGAAGGAATTTGAAGTAGA
1 CAAA-AAGGAATTGGAAGTATA
* *
848501 CAAAAATGAATTGGAAGAAAAATTA
1 CAAAAAGGAATTGGAAG---TA-TA
*
848526 GCAAAAAGGAATTTGAAGTATA
1 -CAAAAAGGAATTGGAAGTATA
848548 CAAAAAGGAATTGGAAG
1 CAAAAAGGAATTGGAAG
848565 AAAAATTGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
21 27 0.53
22 6 0.12
23 1 0.02
24 1 0.02
25 1 0.02
26 15 0.29
ACGTcount: A:0.53, C:0.05, G:0.23, T:0.19
Consensus pattern (21 bp):
CAAAAAGGAATTGGAAGTATA
Found at i:848551 original size:47 final size:48
Alignment explanation
Indices: 848476--848571 Score: 167
Period size: 47 Copynumber: 2.0 Consensus size: 48
848466 GAACTGGAGA
*
848476 TAGCAAAGAAGGAATTTGAAGTAGACAAAAATGAATTGGAAGAAAAAT
1 TAGCAAAGAAGGAATTTGAAGTAGACAAAAAGGAATTGGAAGAAAAAT
*
848524 TAGCAAA-AAGGAATTTGAAGTATACAAAAAGGAATTGGAAGAAAAAT
1 TAGCAAAGAAGGAATTTGAAGTAGACAAAAAGGAATTGGAAGAAAAAT
848571 T
1 T
848572 GAAGAAATTG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 39 0.85
48 7 0.15
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (48 bp):
TAGCAAAGAAGGAATTTGAAGTAGACAAAAAGGAATTGGAAGAAAAAT
Found at i:856184 original size:243 final size:243
Alignment explanation
Indices: 855762--856226 Score: 560
Period size: 243 Copynumber: 1.9 Consensus size: 243
855752 CAAGACAAAG
855762 GAGTCATCCACAACATAGCTCAACTCAACAGAGAGGAACTATTTTCAAACCAAGGTCTGCAAGTC
1 GAGTCATCCACAACATAGCTCAACTCAACAGAGAGGAACTATTTTCAAACCAAGGTCTGCAAGTC
* * * * * * *
855827 AAATTTAAACTTCACGACGAAGGATATTGAATTAGAAGAATACCCAAAATCGACTGTGATTTAGC
66 AAATATAAACTTCACAAAGAAGGATATAGAATTAGAAGAAAACCCAAAATCGACTGCGATTAAGC
* * * * * * * *
855892 TTAACTCAACAACGAAGAGTTATTTCCAACCTAAATTTTAAGTTAGATTTTAACTTCAGGATGAA
131 TTAACTCAACAACGAAGAGCTATTCCCAACCCAAATTTCAAGCTAGATTTCAACTTCAGAAAGAA
* *
855957 GGATTTCAAGCTCGAGTCATCCAAGATCGAATTAAATTCATGATGAAT
196 GGATATCAAGCTCAAGTCATCCAAGATCGAATTAAATTCATGATGAAT
** * * * * *
856005 GAGTCATCCACAACATATTTTAACTCAACA-A-CGGACATGTATTTTCTAACCAAGGTCTTCAAG
1 GAGTCATCCACAACATAGCTCAACTCAACAGAGAGGA-A-CTATTTTCAAACCAAGGTCTGCAAG
* * * *
856068 TCAAATATCAACTTCTCAAATAAGGATATCAG-GTTAGAAGAAAACCCAAAATCGACTGCGATTA
64 TCAAATATAAACTTCACAAAGAAGGATAT-AGAATTAGAAGAAAACCCAAAATCGACTGCGATTA
* * * *
856132 AGCTT-ACTCAACAACGAGGAGCTACTTCCCAACCCAGATTTCGAGCTAGATTTCAACTTCATAA
128 AGCTTAACTCAACAACGAAGAGCTA-TTCCCAACCCAAATTTCAAGCTAGATTTCAACTTCAGAA
* *
856196 AGAATGATATCATGCTCAAGTCATCCAAGAT
192 AGAAGGATATCAAGCTCAAGTCATCCAAGAT
856227 TGACTTAACT
Statistics
Matches: 184, Mismatches: 34, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
241 3 0.02
242 19 0.10
243 161 0.88
244 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (243 bp):
GAGTCATCCACAACATAGCTCAACTCAACAGAGAGGAACTATTTTCAAACCAAGGTCTGCAAGTC
AAATATAAACTTCACAAAGAAGGATATAGAATTAGAAGAAAACCCAAAATCGACTGCGATTAAGC
TTAACTCAACAACGAAGAGCTATTCCCAACCCAAATTTCAAGCTAGATTTCAACTTCAGAAAGAA
GGATATCAAGCTCAAGTCATCCAAGATCGAATTAAATTCATGATGAAT
Found at i:856872 original size:9 final size:9
Alignment explanation
Indices: 856858--856962 Score: 53
Period size: 9 Copynumber: 11.9 Consensus size: 9
856848 GAAAATTTCA
856858 TATTATATG
1 TATTATATG
856867 TATTATAT-
1 TATTATATG
856875 TATTATTAT-
1 TATTA-TATG
856884 TATTAT-TG
1 TATTATATG
856892 TTATTATA--
1 -TATTATATG
*
856900 TATTATATA
1 TATTATATG
* *
856909 T-TTAGCATA
1 TATTA-TATG
856918 TATTATATAG
1 TATTATAT-G
* **
856928 TAGTAGGTG
1 TATTATATG
856937 TTATTATATG
1 -TATTATATG
*
856947 TATTAT-TA
1 TATTATATG
856955 TATTATAT
1 TATTATAT
856963 AATATTTTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
7 8 0.11
8 16 0.21
9 37 0.49
10 14 0.19
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.56
Consensus pattern (9 bp):
TATTATATG
Found at i:856880 original size:3 final size:3
Alignment explanation
Indices: 856858--856910 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
856848 GAAAATTTCA
*
856858 TAT TA- TAT GTAT TA- TAT TAT TAT TAT TAT TAT TGT TAT TAT ATAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
856903 TAT ATAT T
1 TAT -TAT T
856911 TAGCATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
2 4 0.09
3 30 0.70
4 9 0.21
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:856896 original size:26 final size:26
Alignment explanation
Indices: 856858--857057 Score: 103
Period size: 25 Copynumber: 7.5 Consensus size: 26
856848 GAAAATTTCA
856858 TATTATATGTATTATATTATTAT-TAT
1 TATTATATGTATTATA-TATTATATAT
856884 TATTAT-TGTTATTATATATTATATA-
1 TATTATATG-TATTATATATTATATAT
* * * *
856909 T-TTAGCATATATTATATAGTAGTAGGTGT
1 TATTA-TATGTATTATATATTA-TA--TAT
*
856938 TATTATATGTATTATTATATTATATAA
1 TATTATATGTATTA-TATATTATATAT
* * *
856965 TATT-T-TATAGTATATGTTATATA-
1 TATTATATGTATTATATATTATATAT
* * *
856988 TATAATATTTACATTATATATTATATAG
1 TATTATATGT--ATTATATATTATATAT
* *
857016 TATTTATATTTTATTAGTATATTTATATTT
1 TA-TTATA-TGTATTA-TATA-TTATATAT
857046 TATT-TAT-TATTA
1 TATTATATGTATTA
857058 GCATTATTTA
Statistics
Matches: 136, Mismatches: 19, Indels: 38
0.70 0.10 0.20
Matches are distributed among these distances:
23 3 0.02
24 14 0.10
25 27 0.20
26 24 0.18
27 19 0.14
28 9 0.07
29 20 0.15
30 20 0.15
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.57
Consensus pattern (26 bp):
TATTATATGTATTATATATTATATAT
Found at i:856905 original size:7 final size:7
Alignment explanation
Indices: 856857--857057 Score: 75
Period size: 7 Copynumber: 27.9 Consensus size: 7
856847 TGAAAATTTC
856857 ATATTAT
1 ATATTAT
856864 ATGTATTAT
1 A--TATTAT
856873 ATTATTAT
1 A-TATTAT
856881 -TATTAT
1 ATATTAT
*
856887 -TATTGT
1 ATATTAT
856893 -TATTAT
1 ATATTAT
856899 ATATTAT
1 ATATTAT
856906 ATATTTAGCAT
1 ATA-TT---AT
856917 ATATTAT
1 ATATTAT
*
856924 ATAGTAGT
1 ATATTA-T
*
856932 AGGTGTTATT
1 A--TATTA-T
856942 ATATGTAT
1 ATAT-TAT
856950 -TATTAT
1 ATATTAT
856956 AT-TATAT
1 ATAT-TAT
*
856963 AATATTTT
1 -ATATTAT
*
856971 ATAGTAT
1 ATATTAT
*
856978 ATGTTAT
1 ATATTAT
856985 ATA-TAT
1 ATATTAT
856991 AATATT-T
1 -ATATTAT
*
856998 ACATTAT
1 ATATTAT
857005 ATATTAT
1 ATATTAT
*
857012 ATAGTATTT
1 ATA-T-TAT
857021 ATATT-T
1 ATATTAT
857027 -TATTAGT
1 ATATTA-T
857034 ATATT-T
1 ATATTAT
*
857040 ATATTTT
1 ATATTAT
857047 AT-TTAT
1 ATATTAT
857053 -TATTA
1 ATATTA
857058 GCATTATTTA
Statistics
Matches: 151, Mismatches: 18, Indels: 51
0.69 0.08 0.23
Matches are distributed among these distances:
5 5 0.03
6 40 0.26
7 55 0.36
8 24 0.16
9 15 0.10
10 7 0.05
11 5 0.03
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:856972 original size:17 final size:17
Alignment explanation
Indices: 856857--857057 Score: 64
Period size: 17 Copynumber: 11.5 Consensus size: 17
856847 TGAAAATTTC
*
856857 ATATTATATGTATTATAT
1 ATATTAT-TATATTATAT
856875 -TATTATTATTATTAT-T
1 ATATTATTA-TATTATAT
*
856891 GTTATTA-TATATTATAT
1 -ATATTATTATATTATAT
*
856908 AT-TTAGCATATATTATAT
1 ATATTA--TTATATTATAT
*
856926 AGTAGTAGGTGT-TATTATAT
1 A-TATTA--T-TATATTATAT
*
856946 GTATTATTATATTATAT
1 ATATTATTATATTATAT
*
856963 AATATT-TTATAGTATAT
1 -ATATTATTATATTATAT
* * *
856980 GT-TATATATATAATATTT
1 ATAT-TAT-TATATTATAT
*
856998 ACATTA-TATATTATAT
1 ATATTATTATATTATAT
*
857014 AGTA-T-TTATATTTTAT
1 A-TATTATTATATTATAT
*
857030 -TAGTATATTTATATTTTAT
1 ATA-T-TA-TTATATTATAT
*
857049 TTATTATTA
1 ATATTATTA
857058 GCATTATTTA
Statistics
Matches: 141, Mismatches: 18, Indels: 49
0.68 0.09 0.24
Matches are distributed among these distances:
14 2 0.01
15 4 0.03
16 31 0.22
17 40 0.28
18 32 0.23
19 18 0.13
20 13 0.09
21 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (17 bp):
ATATTATTATATTATAT
Found at i:856983 original size:44 final size:43
Alignment explanation
Indices: 856858--857007 Score: 103
Period size: 44 Copynumber: 3.3 Consensus size: 43
856848 GAAAATTTCA
* *
856858 TATTATATGTATTATATTATTATTATTATTAT-TGTTATTATA-TAT
1 TATTATAT-TA-TATAATATT-TTA-TAGTATATGTTATTATATTAT
* *
856903 TA-TATATT-TAGCATATATTATATAGTAGTAGGTGTTATTATATGTAT
1 TATTATATTATA-TA-ATATTTTATAGTA-TA--TGTTATTATAT-TAT
*
856950 TATTATATTATATAATATTTTATAGTATATGTTA-TATATATAA
1 TATTATATTATATAATATTTTATAGTATATGTTATTATAT-TAT
*
856993 TATTTACATTATATA
1 TA-TTATATTATATA
857008 TTATATAGTA
Statistics
Matches: 85, Mismatches: 9, Indels: 23
0.73 0.08 0.20
Matches are distributed among these distances:
41 6 0.07
42 4 0.05
43 14 0.16
44 21 0.25
45 12 0.14
46 2 0.02
47 17 0.20
48 7 0.08
49 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (43 bp):
TATTATATTATATAATATTTTATAGTATATGTTATTATATTAT
Found at i:860165 original size:16 final size:16
Alignment explanation
Indices: 860144--860187 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
860134 AGTAATCCAT
860144 TAACCCATTAAAGTCC
1 TAACCCATTAAAGTCC
860160 TAACCCATTAAAGTCC
1 TAACCCATTAAAGTCC
*
860176 TAACCCAATAAA
1 TAACCCATTAAA
860188 AATTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.43, C:0.30, G:0.05, T:0.23
Consensus pattern (16 bp):
TAACCCATTAAAGTCC
Found at i:863891 original size:21 final size:21
Alignment explanation
Indices: 863866--863916 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
863856 TGTTGACTTT
863866 GGTCAGA-GTTGACCATTGACC
1 GGTCAGACGTTGA-CATTGACC
*
863887 GGTCAGACCGTTGACTTTGACC
1 GGTCAGA-CGTTGACATTGACC
*
863909 GTTCAGAC
1 GGTCAGAC
863917 CATTGACTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 13 0.50
23 5 0.19
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (21 bp):
GGTCAGACGTTGACATTGACC
Found at i:863909 original size:22 final size:23
Alignment explanation
Indices: 863881--863930 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
863871 GAGTTGACCA
*
863881 TTGACCGGTCAGACCGTTGACT-
1 TTGACCGGTCAGACCATTGACTG
*
863903 TTGACCGTTCAGACCATTGACTG
1 TTGACCGGTCAGACCATTGACTG
863926 TTGAC
1 TTGAC
863931 TTTGATCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (23 bp):
TTGACCGGTCAGACCATTGACTG
Found at i:864837 original size:27 final size:27
Alignment explanation
Indices: 864808--864860 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
864798 TGGATTTATA
*
864808 AAAATGTC-ATAAAGTGTAAAATGACC
1 AAAATGCCGATAAAGTGTAAAATGACC
*
864834 AAAATGCCGCTAAAGTGTAAAATGACC
1 AAAATGCCGATAAAGTGTAAAATGACC
864861 TAAAGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (27 bp):
AAAATGCCGATAAAGTGTAAAATGACC
Found at i:868507 original size:22 final size:22
Alignment explanation
Indices: 868475--868516 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
868465 GAGTTTACCG
*
868475 TTGACCGGTCAGACCGTTGACT
1 TTGACCAGTCAGACCGTTGACT
868497 TTGACCAGTCAGACCGTTGA
1 TTGACCAGTCAGACCGTTGA
868517 TCGTTAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
TTGACCAGTCAGACCGTTGACT
Found at i:874007 original size:20 final size:20
Alignment explanation
Indices: 873979--874018 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
873969 CGGTTGCTGC
873979 ACAACGAGTTTCAAAACTTT
1 ACAACGAGTTTCAAAACTTT
* *
873999 ACAAGGAGTTTCGAAACTTT
1 ACAACGAGTTTCAAAACTTT
874019 GGCAAAGTAT
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:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
ACAACGAGTTTCAAAACTTT
Found at i:874045 original size:20 final size:20
Alignment explanation
Indices: 874011--874056 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
874001 AAGGAGTTTC
*
874011 GAAACT-TTGGCAAAGTATG
1 GAAACTCTTGGAAAAGTATG
*
874030 GAAACTCTTGGAAAAGTATT
1 GAAACTCTTGGAAAAGTATG
874050 GAAACTC
1 GAAACTC
874057 CAAAACACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (20 bp):
GAAACTCTTGGAAAAGTATG
Found at i:878433 original size:22 final size:22
Alignment explanation
Indices: 878386--878460 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
878376 GTTCAATATT
*
878386 CGTCCCAAAGGACCACT--AT-
1 CGTCCCGAAGGACCACTAGATA
*
878405 -GTCCCGAAGGATCACTAGATA
1 CGTCCCGAAGGACCACTAGATA
*
878426 CGTCCCGAAGGACCACTGGATA
1 CGTCCCGAAGGACCACTAGATA
* *
878448 CATCCTGAAGGAC
1 CGTCCCGAAGGAC
878461 TAATATACCC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
18 14 0.30
20 2 0.04
22 30 0.65
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.16
Consensus pattern (22 bp):
CGTCCCGAAGGACCACTAGATA
Found at i:879897 original size:64 final size:65
Alignment explanation
Indices: 879821--879962 Score: 164
Period size: 66 Copynumber: 2.2 Consensus size: 65
879811 TCGATGCACT
* ** * * *
879821 TGCATCGGTGCATAAATCTTATTCGATGTT-TGT-ATTTTAA-GCAGGTTCATCGATGCACTCTT
1 TGCATCGATGCATAAATCGAATTCGATGTTATGTAATTTAAATG-A-GTGCATCGATGCACTCCT
879883 TA
64 TA
* *
879885 TGCATCGATGCATAAATGGAATTCGATGTTAATTTAATTTAAATGAGTGCATCGATGCACTCCTT
1 TGCATCGATGCATAAATCGAATTCGATGTT-ATGTAATTTAAATGAGTGCATCGATGCACTCCTT
879950 A
65 A
879951 TGCATCGATGCA
1 TGCATCGATGCA
879963 CCTTCAACAA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
64 26 0.39
66 32 0.48
67 7 0.11
68 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (65 bp):
TGCATCGATGCATAAATCGAATTCGATGTTATGTAATTTAAATGAGTGCATCGATGCACTCCTTA
Found at i:881154 original size:12 final size:12
Alignment explanation
Indices: 881137--881173 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
881127 TATTGACATT
881137 TCTTTATCTTCA
1 TCTTTATCTTCA
881149 TCTTTATCTTCA
1 TCTTTATCTTCA
881161 TCTTTATCTTCA
1 TCTTTATCTTCA
881173 T
1 T
881174 TATTTGAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTTTATCTTCA
Found at i:881278 original size:21 final size:20
Alignment explanation
Indices: 881222--881285 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
881212 ACACCAATCT
881222 TTTTTCTTTTTCTTCTTC-TC
1 TTTTTCTTTTT-TTCTTCATC
* *
881242 TATTTCCTTATTTTCTTCATC
1 T-TTTTCTTTTTTTCTTCATC
*
881263 TTTCTTCTTTTTTTCTTCTTC
1 TTT-TTCTTTTTTTCTTCATC
881284 TT
1 TT
881286 CCTTTACCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 9 0.25
21 27 0.75
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTCTTTTTTTCTTCATC
Found at i:881290 original size:18 final size:19
Alignment explanation
Indices: 881244--881290 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
881234 TTCTTCTCTA
*
881244 TTTCCTTATTTTCTTCATC
1 TTTCCTTTTTTTCTTCATC
*
881263 TTTCTTCTTTTTTTCTTCTTC
1 TTTC--CTTTTTTTCTTCATC
881284 -TTCCTTT
1 TTTCCTTT
881291 ACCATCATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 3 0.12
21 13 0.54
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTCCTTTTTTTCTTCATC
Found at i:889321 original size:46 final size:45
Alignment explanation
Indices: 889236--889333 Score: 108
Period size: 46 Copynumber: 2.2 Consensus size: 45
889226 TAACTCTTAG
* * *
889236 AAAATATTAAAAATATATATGATAATTTTAAATAAATTAAAATATT
1 AAAAAATTAAAAAAATATATAATAATTTTAAATAAATTAAAA-ATT
* **
889282 AAAAAATTAAAAAAATATA-AATATTTTTATAATTTATTAAAAATT
1 AAAAAATTAAAAAAATATATAATAATTTTA-AATAAATTAAAAATT
*
889327 ATAAAAT
1 AAAAAAT
889334 AATTGAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
45 17 0.39
46 27 0.61
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (45 bp):
AAAAAATTAAAAAAATATATAATAATTTTAAATAAATTAAAAATT
Found at i:889323 original size:29 final size:30
Alignment explanation
Indices: 889291--889366 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
889281 TAAAAAATTA
* *
889291 AAAAAATATAAATATTTTTATAA-TTTATT
1 AAAAAATATAAATATTTTGAAAATTTTATT
* *
889320 AAAAATTATAAA-ATAATTGAAAATTTTATT
1 AAAAAATATAAATAT-TTTGAAAATTTTATT
889350 AAAAAATATAAAATATT
1 AAAAAATAT-AAATATT
889367 CAAAAATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.05
29 16 0.43
30 14 0.38
31 3 0.08
32 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
AAAAAATATAAATATTTTGAAAATTTTATT
Found at i:889373 original size:30 final size:30
Alignment explanation
Indices: 889314--889373 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
889304 ATTTTTATAA
* *
889314 TTTATTAAAAATTATAAAATAATTGAAAAT
1 TTTATTAAAAAATATAAAATAATTAAAAAT
889344 TTTATTAAAAAATATAAAAT-ATTCAAAAAT
1 TTTATTAAAAAATATAAAATAATT-AAAAAT
889374 ATTTCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTATTAAAAAATATAAAATAATTAAAAAT
Found at i:893330 original size:17 final size:17
Alignment explanation
Indices: 893308--893344 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
893298 TTTGTATTTC
893308 CATAATGAATCCAAAAA
1 CATAATGAATCCAAAAA
893325 CATAATGAATCCAAAAA
1 CATAATGAATCCAAAAA
893342 CAT
1 CAT
893345 TCATTTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.19, G:0.05, T:0.19
Consensus pattern (17 bp):
CATAATGAATCCAAAAA
Found at i:893928 original size:17 final size:17
Alignment explanation
Indices: 893902--893949 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
893892 TGAAAAACAT
*
893902 AAAATATGACTTTTCAA
1 AAAATTTGACTTTTCAA
893919 AAAATTTGACTTTTCAA
1 AAAATTTGACTTTTCAA
893936 AAAATTTGACTTTT
1 AAAATTTGACTTTT
893950 TGGTCAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (17 bp):
AAAATTTGACTTTTCAA
Found at i:897491 original size:27 final size:27
Alignment explanation
Indices: 897453--897506 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
897443 AGGTTATGAG
897453 ATTAAAAATTTAATCATATCCTAGTAA
1 ATTAAAAATTTAATCATATCCTAGTAA
*
897480 ATTAAAATTTTAATCATATCCTAGTAA
1 ATTAAAAATTTAATCATATCCTAGTAA
897507 GCATATTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (27 bp):
ATTAAAAATTTAATCATATCCTAGTAA
Found at i:899474 original size:16 final size:16
Alignment explanation
Indices: 899453--899485 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
899443 GAGTCTTTGA
*
899453 ACATATATTTTCTTGT
1 ACATATATTTTATTGT
899469 ACATATATTTTATTGT
1 ACATATATTTTATTGT
899485 A
1 A
899486 TTTACCCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (16 bp):
ACATATATTTTATTGT
Found at i:899513 original size:2 final size:2
Alignment explanation
Indices: 899506--899560 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
899496 TGTATCAAAA
899506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
899548 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
899561 ACCTAATTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:905724 original size:34 final size:34
Alignment explanation
Indices: 905681--905750 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
905671 ATATCTTATA
*
905681 GTCGAGGGATTAGATGTGTCTACAAGGTATATGT
1 GTCGAGGGATCAGATGTGTCTACAAGGTATATGT
* * *
905715 GTCGAGGGATCGGCTGTGTCTACAAGGTATGTGT
1 GTCGAGGGATCAGATGTGTCTACAAGGTATATGT
905749 GT
1 GT
905751 TGTCAATGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.31
Consensus pattern (34 bp):
GTCGAGGGATCAGATGTGTCTACAAGGTATATGT
Found at i:906531 original size:21 final size:21
Alignment explanation
Indices: 906505--906579 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
906495 ATTCTGACTA
906505 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
906526 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* ** *
906547 TCGCAATGCGATAGTCCAAAA
1 TCGCATTGCGATTTTCCAAAT
906568 TCGCATTGCGAT
1 TCGCATTGCGAT
906580 AGCACTGTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:906597 original size:21 final size:21
Alignment explanation
Indices: 906573--906726 Score: 213
Period size: 21 Copynumber: 7.4 Consensus size: 21
906563 CAAAATCGCA
906573 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
* *
906594 TTGCGATATCATTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
906615 TTGCGATAGCACTGTTTA-CG
1 TTGCGATAGCACTGTTCACCG
906635 TTGCGATAGCACTGTTCA-CG
1 TTGCGATAGCACTGTTCACCG
* * *
906655 ATGCGATAGTACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
* *
906676 TTACGATAGCACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
*
906697 TTGCGATAGCACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
906718 TTGCGATAG
1 TTGCGATAG
906727 TGATCAAAAT
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
20 37 0.31
21 82 0.69
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:906670 original size:82 final size:83
Alignment explanation
Indices: 906574--906726 Score: 227
Period size: 82 Copynumber: 1.9 Consensus size: 83
906564 AAAATCGCAT
* * * * * * *
906574 TGCGATAGCACTGTTCACCGTTGCGATATCATTGTTCACCGTTGCGATAGCACTGTTTA-CGTTG
1 TGCGATAGCACTGTTCACCATTACGATAGCACTGTTCACCATTGCGATAGCACTGTTCACCATTG
906638 CGATAGCACTGTTCACGA
66 CGATAGCACTGTTCACGA
*
906656 TGCGATAGTACTGTTCACCATTACGATAGCACTGTTCACCATTGCGATAGCACTGTTCACCATTG
1 TGCGATAGCACTGTTCACCATTACGATAGCACTGTTCACCATTGCGATAGCACTGTTCACCATTG
906721 CGATAG
66 CGATAG
906727 TGATCAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
82 52 0.84
83 10 0.16
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.31
Consensus pattern (83 bp):
TGCGATAGCACTGTTCACCATTACGATAGCACTGTTCACCATTGCGATAGCACTGTTCACCATTG
CGATAGCACTGTTCACGA
Found at i:912644 original size:48 final size:46
Alignment explanation
Indices: 912576--912691 Score: 133
Period size: 46 Copynumber: 2.5 Consensus size: 46
912566 ATTATACTTA
* * *
912576 TAGCACGTGTCTGACATCTGTGTGACGGTGGTGCTACTGTATGATACT
1 TAGCACGTGTATGACATC--TGTGACAGTGGTGCTACTATATGATACT
* * *
912624 TAGCACGTGTATGTCGTCTGTGACAGTGGTGCTACTATATGGTACT
1 TAGCACGTGTATGACATCTGTGACAGTGGTGCTACTATATGATACT
* * *
912670 TAGCACATGTCTGACATTTGTG
1 TAGCACGTGTATGACATCTGTG
912692 TGATAGTAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 42 0.74
48 15 0.26
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (46 bp):
TAGCACGTGTATGACATCTGTGACAGTGGTGCTACTATATGATACT
Found at i:912931 original size:27 final size:27
Alignment explanation
Indices: 912896--912985 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 27
912886 ACGAAATGAA
*
912896 AAAGTGAAT-AGTATATGATATGAAATG
1 AAAGTGAATGA-TACATGATATGAAATG
*
912923 AAAGTGAATGATACATGCTATGAAATG
1 AAAGTGAATGATACATGATATGAAATG
* *
912950 AATTAAATGAATGATACATGCTATGAAAT-
1 -A--AAGTGAATGATACATGATATGAAATG
912979 AAA-TGAA
1 AAAGTGAA
912986 ATGAATGGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
25 4 0.07
26 2 0.04
27 23 0.41
28 3 0.05
30 24 0.43
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (27 bp):
AAAGTGAATGATACATGATATGAAATG
Found at i:912963 original size:30 final size:30
Alignment explanation
Indices: 912909--913011 Score: 136
Period size: 30 Copynumber: 3.4 Consensus size: 30
912899 GTGAATAGTA
*
912909 TATGATATGAAATGAAAGTGAATGATACATGC
1 TATGAAATG-AATGAAA-TGAATGATACATGC
*
912941 TATGAAATGAATTAAATGAATGATACATGC
1 TATGAAATGAATGAAATGAATGATACATGC
* *
912971 TATGAAATAAATGAAATGAATGGA-AGATGC
1 TATGAAATGAATGAAATGAAT-GATACATGC
913001 TATGAAATGAA
1 TATGAAATGAA
913012 CAAAGTGAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
30 48 0.75
31 8 0.12
32 8 0.12
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (30 bp):
TATGAAATGAATGAAATGAATGATACATGC
Found at i:913028 original size:60 final size:62
Alignment explanation
Indices: 912909--913042 Score: 152
Period size: 60 Copynumber: 2.2 Consensus size: 62
912899 GTGAATAGTA
* * *
912909 TATGATATGAAATGAAAGTGAATGATACATGCTATGAAATGAATTAAATGAATGATACATGC
1 TATGAAATGAAATGAAAGTGAATGATACATGCTATGAAATGAATCAAATGAAAGATACATGC
* *
912971 TATGAAAT-AAATGAAA-TGAATGGA-AGATGCTATGAAATGAA-CAAAGTGAAAGGTACATG-
1 TATGAAATGAAATGAAAGTGAAT-GATACATGCTATGAAATGAATCAAA-TGAAAGATACATGC
* *
913030 TTTGATATGAAAT
1 TATGAAATGAAAT
913043 AAAAATGTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
59 9 0.15
60 36 0.58
61 10 0.16
62 7 0.11
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (62 bp):
TATGAAATGAAATGAAAGTGAATGATACATGCTATGAAATGAATCAAATGAAAGATACATGC
Found at i:922003 original size:32 final size:32
Alignment explanation
Indices: 921966--922036 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
921956 GGAGAAGAAT
921966 AAGTGTTTAATGTTTTACATGATAAATTGAAG
1 AAGTGTTTAATGTTTTACATGATAAATTGAAG
921998 AAGTGTTTAATGTTTTACATGATAAATTGAAG
1 AAGTGTTTAATGTTTTACATGATAAATTGAAG
922030 AAGTGTT
1 AAGTGTT
922037 AAAGTAAGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.41
Consensus pattern (32 bp):
AAGTGTTTAATGTTTTACATGATAAATTGAAG
Found at i:922279 original size:22 final size:22
Alignment explanation
Indices: 922251--922293 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
922241 TCATTTTTTG
922251 ATCCTTACTTAAGTGTAAAATA
1 ATCCTTACTTAAGTGTAAAATA
922273 ATCCTTACTTAAGTGTAAAAT
1 ATCCTTACTTAAGTGTAAAAT
922294 TAAGTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (22 bp):
ATCCTTACTTAAGTGTAAAATA
Done.