Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009183.1 Hibiscus syriacus cultivar Beakdansim tig00112754_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: 103613
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1448 original size:26 final size:26
Alignment explanation
Indices: 1404--1457 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
1394 GATTACTTAT
*
1404 GCCCCTACATGCTGCCCTGGGCCATC
1 GCCCCTACATACTGCCCTGGGCCATC
* *
1430 GCCCCTACATACTGTCCTGGGCCGTC
1 GCCCCTACATACTGCCCTGGGCCATC
1456 GC
1 GC
1458 TCATCTGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.11, C:0.44, G:0.24, T:0.20
Consensus pattern (26 bp):
GCCCCTACATACTGCCCTGGGCCATC
Found at i:11301 original size:19 final size:19
Alignment explanation
Indices: 11274--11310 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11264 ATGACCAACA
*
11274 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
11293 AAATTGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
11311 CAGTATTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:11418 original size:41 final size:41
Alignment explanation
Indices: 11336--11430 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
11326 GTTTACAGAT
* * * * *
11336 TCGCAACGCGATTTTGACTATTGTATTGCGATTTTCTAAAA
1 TCGCAACGCGATTCTGACTATCGCATTGCGATATACTAAAA
*
11377 TCGCAACGCGATTCTGACTATCGCGTTGCGATAATAC-AAAA
1 TCGCAACGCGATTCTGACTATCGCATTGCGAT-ATACTAAAA
* *
11418 TCGTAATGCGATT
1 TCGCAACGCGATT
11431 TTCAAAGCGC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCATTGCGATATACTAAAA
Found at i:11610 original size:20 final size:20
Alignment explanation
Indices: 11585--11630 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
11575 ATCCGTCCCC
*
11585 ATCTCCGACGAAATCCGTCT
1 ATCTCCGACGAAATCCATCT
* *
11605 ATCTCCGGCGAAATTCATCT
1 ATCTCCGACGAAATCCATCT
11625 ATCTCC
1 ATCTCC
11631 ATCTCTCAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.28
Consensus pattern (20 bp):
ATCTCCGACGAAATCCATCT
Found at i:12023 original size:19 final size:19
Alignment explanation
Indices: 12001--12140 Score: 96
Period size: 20 Copynumber: 7.4 Consensus size: 19
11991 AAATCGCAAC
12001 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
12020 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
12039 GCGATTATC--TT---GTT
1 GCGATTTTCATTTCGCGTT
**
12053 GCGATAGTCAAATTT-GCGTT
1 GCGATTTTC--ATTTCGCGTT
** *
12073 GCGATAGTCATTTTCGTGTT
1 GCGATTTTCA-TTTCGCGTT
* *
12093 GCGATTTTCATTTTTGTGTT
1 GCGATTTTCA-TTTCGCGTT
*
12113 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCA-TTTCGCGTT
12133 GCGATTTT
1 GCGATTTT
12141 AAGTTTCAGA
Statistics
Matches: 104, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.10
17 2 0.02
18 3 0.03
19 28 0.27
20 61 0.59
ACGTcount: A:0.14, C:0.15, G:0.23, T:0.49
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:12093 original size:20 final size:20
Alignment explanation
Indices: 12049--12137 Score: 99
Period size: 20 Copynumber: 4.5 Consensus size: 20
12039 GCGATTATCT
*
12049 TGTTGCGATAGTCAAATTT-G
1 TGTTGCGATAGTC-ATTTTCG
*
12069 CGTTGCGATAGTCATTTTCG
1 TGTTGCGATAGTCATTTTCG
** *
12089 TGTTGCGATTTTCATTTTTG
1 TGTTGCGATAGTCATTTTCG
**
12109 TGTTGCGATTTTCATTTTCG
1 TGTTGCGATAGTCATTTTCG
12129 TGTTGCGAT
1 TGTTGCGAT
12138 TTTAAGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.07
20 57 0.93
ACGTcount: A:0.15, C:0.13, G:0.24, T:0.48
Consensus pattern (20 bp):
TGTTGCGATAGTCATTTTCG
Found at i:12147 original size:20 final size:20
Alignment explanation
Indices: 12070--12140 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
12060 TCAAATTTGC
**
12070 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
12090 GTTGCGATTTTCATTTTTGT
1 GTTGCGATTTTCATTTTCGT
12110 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
12130 GTTGCGATTTT
1 GTTGCGATTTT
12141 AAGTTTCAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.11, C:0.13, G:0.23, T:0.54
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:13720 original size:21 final size:21
Alignment explanation
Indices: 13696--13751 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
13686 TGGTGCATGG
* * *
13696 CGTGATGAGGTATCTACTTTA
1 CGTGATGAGGTAGCGACTCTA
*
13717 CGTGGTGAGGTAGCGACTCTA
1 CGTGATGAGGTAGCGACTCTA
13738 CGTGA-GATGGTAGC
1 CGTGATGA-GGTAGC
13752 ATCGTTGTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.21, C:0.16, G:0.34, T:0.29
Consensus pattern (21 bp):
CGTGATGAGGTAGCGACTCTA
Found at i:14096 original size:33 final size:34
Alignment explanation
Indices: 14044--14114 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
14034 TTTGACTATT
* *
14044 GCAACGGGATAATCGCAATGCG-AAATAAAAATC
1 GCAACGGGAAAATCACAATGCGAAAATAAAAATC
* *
14077 GCAACGTGAAAATCACAATGCGAAAATGAAAATC
1 GCAACGGGAAAATCACAATGCGAAAATAAAAATC
14111 GCAA
1 GCAA
14115 TGCGAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 19 0.58
34 14 0.42
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (34 bp):
GCAACGGGAAAATCACAATGCGAAAATAAAAATC
Found at i:14106 original size:20 final size:20
Alignment explanation
Indices: 14083--14120 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14073 AATCGCAACG
14083 TGAAAATCACAATGCGAAAA
1 TGAAAATCACAATGCGAAAA
*
14103 TGAAAATCGCAATGCGAA
1 TGAAAATCACAATGCGAA
14121 TTTAGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.16
Consensus pattern (20 bp):
TGAAAATCACAATGCGAAAA
Found at i:14137 original size:19 final size:19
Alignment explanation
Indices: 14115--14178 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
14105 AAAATCGCAA
*
14115 TGCGAATTTAGTTTCGCGT
1 TGCGATTTTAGTTTCGCGT
*
14134 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAGTTTCGCGT
*
14153 TGCGATTTTTA-TTTCGCAT
1 TGCGA-TTTTAGTTTCGCGT
14172 TGCGATT
1 TGCGATT
14179 ATCCCGTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 2 0.05
19 34 0.85
20 4 0.10
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTAGTTTCGCGT
Found at i:14239 original size:20 final size:20
Alignment explanation
Indices: 14183--14251 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
14173 GCGATTATCC
*
14183 CGTTGCGATAGTCAAATTCC-
1 CGTTGCGATAGTC-ATTTCCA
* *
14203 TGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCA
* *
14223 CGTTGCGATAGTTATTTTCA
1 CGTTGCGATAGTCATTTCCA
14243 CGTTGCGAT
1 CGTTGCGAT
14252 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.12
20 37 0.88
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCA
Found at i:14261 original size:20 final size:20
Alignment explanation
Indices: 14238--14282 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
14228 CGATAGTTAT
14238 TTTCACGTTGCGATTTTAAG
1 TTTCACGTTGCGATTTTAAG
**
14258 TTTCGTGTTGCGATTTTAAG
1 TTTCACGTTGCGATTTTAAG
14278 TTTCA
1 TTTCA
14283 GAAACTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.13, G:0.20, T:0.49
Consensus pattern (20 bp):
TTTCACGTTGCGATTTTAAG
Found at i:14832 original size:42 final size:42
Alignment explanation
Indices: 14768--14883 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
14758 CTGTCATCGT
* * *
14768 TCAAGAGG-CCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGTCC-CTCCCACCGTTCAAGAGGCCCATATCATCCC
* **
14810 TCAAGA-GTCTCCTCCCACCGTTCAAGAGGCCCATGTCATCGT
1 TCAAGAGGTC-CCTCCCACCGTTCAAGAGGCCCATATCATCCC
* *
14852 TGAAGAGGTCCCTCCCACCATTCAAGA-GCCCA
1 TCAAGAGGTCCCTCCCACCGTTCAAGAGGCCCA
14884 ATTCACACGG
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
41 6 0.10
42 53 0.84
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAAGAGGTCCCTCCCACCGTTCAAGAGGCCCATATCATCCC
Found at i:14852 original size:21 final size:20
Alignment explanation
Indices: 14757--14864 Score: 74
Period size: 21 Copynumber: 5.2 Consensus size: 20
14747 GCCCGACTCA
14757 CCTGTCATCGTTCAAGAGGC
1 CCTGTCATCGTTCAAGAGGC
*
14777 CTCT-CCTATCGTTCAAGAGGCC
1 C-CTGTC-ATCGTTCAAGAGG-C
* ** *
14799 CCTATCATCCCTCAAGAGTC
1 CCTGTCATCGTTCAAGAGGC
** *
14819 TCCTCCCACCGTTCAAGAGGC
1 -CCTGTCATCGTTCAAGAGGC
*
14840 CCATGTCATCGTTGAAGAGGTC
1 CC-TGTCATCGTTCAAGAGG-C
14862 CCT
1 CCT
14865 CCCACCATTC
Statistics
Matches: 66, Mismatches: 15, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
20 5 0.08
21 55 0.83
22 6 0.09
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.25
Consensus pattern (20 bp):
CCTGTCATCGTTCAAGAGGC
Found at i:14878 original size:21 final size:21
Alignment explanation
Indices: 14765--14879 Score: 67
Period size: 21 Copynumber: 5.5 Consensus size: 21
14755 CACCTGTCAT
* *
14765 CGTTCAAGAGG-CCTCTCCTAT
1 CGTTCAAGAGGTCC-CTCCCAC
* **
14786 CGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGTCCCTCCCA-C
*
14808 C-CTCAAGA-GTCTCCTCCCAC
1 CGTTCAAGAGGTC-CCTCCCAC
** *
14828 CGTTCAAGAGG-CCCATGTCAT
1 CGTTCAAGAGGTCCC-TCCCAC
*
14849 CGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGTCCCTCCCAC
*
14870 CATTCAAGAG
1 CGTTCAAGAG
14880 CCCAATTCAC
Statistics
Matches: 69, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
20 6 0.09
21 56 0.81
22 7 0.10
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGTCCCTCCCAC
Found at i:16271 original size:14 final size:14
Alignment explanation
Indices: 16252--16288 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
16242 GCTTGTTTAA
*
16252 TTGATTTGTAAAGG
1 TTGATTTGTAAAAG
16266 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
16280 TTGATTTGT
1 TTGATTTGT
16289 TTAATTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:16433 original size:20 final size:20
Alignment explanation
Indices: 16408--16461 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
16398 AGGTACACTT
*
16408 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
16428 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
16448 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
16462 TCAATTTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:16533 original size:20 final size:20
Alignment explanation
Indices: 16504--16620 Score: 171
Period size: 20 Copynumber: 5.8 Consensus size: 20
16494 GCGATTTTCT
* *
16504 CGTTGTGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
16524 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
16544 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
16564 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
16584 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
16604 TGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
16621 GAATGTGTAA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:16814 original size:18 final size:18
Alignment explanation
Indices: 16791--16825 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16781 AAGCCGGTTG
*
16791 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
16809 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
16826 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:18884 original size:14 final size:14
Alignment explanation
Indices: 18865--18901 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
18855 TCCCGTGGCA
18865 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
18879 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
18893 TTCTTCTTC
1 TT-TTCTTC
18902 TTATTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:19125 original size:24 final size:24
Alignment explanation
Indices: 19091--19144 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
19081 CTGAAACATC
19091 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
19115 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
19139 ATCAAA
1 ATCAAA
19145 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:19990 original size:20 final size:20
Alignment explanation
Indices: 19965--20072 Score: 146
Period size: 20 Copynumber: 5.3 Consensus size: 20
19955 GAAATTCAGT
19965 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
**
19985 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
*
20006 GTTGCGATAGTCAGAATCGT
1 GTTGCGATAGTCAGAATCGC
*
20026 GTTGCGATAGTCAGAATCGT
1 GTTGCGATAGTCAGAATCGC
*
20046 GTTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAGAATCGC
20066 GTTGCGA
1 GTTGCGA
20073 ATCTGGAAAC
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
19 2 0.03
20 59 0.76
21 15 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.31
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:20094 original size:60 final size:60
Alignment explanation
Indices: 19963--20113 Score: 159
Period size: 60 Copynumber: 2.5 Consensus size: 60
19953 TTGAAATTCA
* ** *
19963 GTGTTGCGATAGTCAGAATCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATC
1 GTGTTGCGATAGTCAGAATCGTGTTGCGA-TATGTAAAATCGCGTTGCGATAGTCAGAAAC
*
20024 GTGTTGCGATAGTCAGAATCGTGTTGCGATA-GTCAAAATCGCGTTGCGA-A-TCTGGAAAC
1 GTGTTGCGATAGTCAGAATCGTGTTGCGATATGT-AAAATCGCGTTGCGATAGTC-AGAAAC
*
20083 -TGATTTGCGATACT-AGAGATCGTGTTGCGAT
1 GTG--TTGCGATAGTCAGA-ATCGTGTTGCGAT
20114 TTAGAGATCG
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
58 4 0.05
59 10 0.13
60 37 0.47
61 28 0.35
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (60 bp):
GTGTTGCGATAGTCAGAATCGTGTTGCGATATGTAAAATCGCGTTGCGATAGTCAGAAAC
Found at i:20120 original size:19 final size:19
Alignment explanation
Indices: 20096--20134 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
20086 TTTGCGATAC
**
20096 TAGAGATCGTGTTGCGATT
1 TAGAGATCGCATTGCGATT
20115 TAGAGATCGCATTGCGATT
1 TAGAGATCGCATTGCGATT
20134 T
1 T
20135 TGTTGGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (19 bp):
TAGAGATCGCATTGCGATT
Found at i:31909 original size:3 final size:3
Alignment explanation
Indices: 31901--31930 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31891 TTGCGAATTG
31901 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
31931 GAAACAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:36702 original size:20 final size:20
Alignment explanation
Indices: 36677--36716 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
36667 AGATTGTGCA
36677 GGGGGTA-CAGATTCCCCCTT
1 GGGGGTATC-GATTCCCCCTT
36697 GGGGGTATCGATTCCCCCTT
1 GGGGGTATCGATTCCCCCTT
36717 AAAGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTT
Found at i:36850 original size:59 final size:59
Alignment explanation
Indices: 36779--36897 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
36769 TTTAGGCTTC
36779 TGATAATTGTTTTGAAATGTTATATTTATATAGATATTAAGCCTAAACAAGTTTCGGAA
1 TGATAATTGTTTTGAAATGTTATATTTATATAGATATTAAGCCTAAACAAGTTTCGGAA
*
36838 TGATAATTGTTTTGAAATGTTATATTTATATAGATATTGAGCCTAAACAAGTTTCGGAA
1 TGATAATTGTTTTGAAATGTTATATTTATATAGATATTAAGCCTAAACAAGTTTCGGAA
36897 T
1 T
36898 AATTAAAGGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (59 bp):
TGATAATTGTTTTGAAATGTTATATTTATATAGATATTAAGCCTAAACAAGTTTCGGAA
Found at i:37613 original size:21 final size:21
Alignment explanation
Indices: 37579--37635 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
37569 GGGTTTCATA
* *
37579 GGTCATTCGGGACAATACAGT
1 GGTCCTTCGAGACAATACAGT
*
37600 GGTCCTTCTAGACAATACAGT
1 GGTCCTTCGAGACAATACAGT
37621 GGTCCTTCGAGACAA
1 GGTCCTTCGAGACAA
37636 ATTTCATATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
GGTCCTTCGAGACAATACAGT
Found at i:40116 original size:2 final size:2
Alignment explanation
Indices: 40109--40136 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40099 TTGACTGGAA
40109 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
40137 GGATAGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41627 original size:4 final size:4
Alignment explanation
Indices: 41618--41646 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
41608 GGAATAATGG
41618 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
41647 GATTGAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:41629 original size:16 final size:16
Alignment explanation
Indices: 41600--41646 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
41590 TGACTTTGAA
**
41600 GGAATAAAGGAATAAT
1 GGAATAAATAAATAAT
41616 GGAATAAATAAATAAAT
1 GGAATAAATAAAT-AAT
*
41633 -AAATAAATAAATAA
1 GGAATAAATAAATAA
41647 GATTGAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 2 0.07
16 22 0.81
17 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (16 bp):
GGAATAAATAAATAAT
Found at i:43632 original size:18 final size:17
Alignment explanation
Indices: 43605--43638 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
43595 TGATAGAAGA
*
43605 GAAAGAACAAGTGATAT
1 GAAAGAACAAATGATAT
43622 GAAATGAACAAATGATA
1 GAAA-GAACAAATGATA
43639 ATGCCCATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.18
Consensus pattern (17 bp):
GAAAGAACAAATGATAT
Found at i:44433 original size:20 final size:20
Alignment explanation
Indices: 44408--44453 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
44398 TGAAAACTAT
44408 GATTTTTATAAATTTATACG
1 GATTTTTATAAATTTATACG
44428 GATTTTTATAAATTTATACG
1 GATTTTTATAAATTTATACG
*
44448 TATTTT
1 GATTTT
44454 GCAGAAGTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (20 bp):
GATTTTTATAAATTTATACG
Found at i:44516 original size:22 final size:21
Alignment explanation
Indices: 44477--44517 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
44467 AGCAGTACTA
*
44477 TAGCAGGGTATCGATTCCCTG
1 TAGCAGGGGATCGATTCCCTG
*
44498 TAGCAGGGGGATCGGTTCCC
1 TAGCA-GGGGATCGATTCCC
44518 CTATTACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.17, C:0.24, G:0.34, T:0.24
Consensus pattern (21 bp):
TAGCAGGGGATCGATTCCCTG
Found at i:46612 original size:23 final size:23
Alignment explanation
Indices: 46577--46632 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
46567 AATTTCTTTC
46577 TTTTTTTAATTTT-TTATATCAAG
1 TTTTTTTAATTTTATT-TATCAAG
** * *
46600 TTTTTTTTCTTTTATTTTTTAAG
1 TTTTTTTAATTTTATTTATCAAG
46623 TTTTTTTAAT
1 TTTTTTTAAT
46633 GATTTTACCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 24 0.92
24 2 0.08
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTTTTTAATTTTATTTATCAAG
Found at i:49801 original size:27 final size:28
Alignment explanation
Indices: 49764--49837 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 28
49754 AACAAGTAAA
*
49764 AAAATATAAAAACATAAAATATAA-GA-T
1 AAAATATAAAAAAATAAAATA-AATGAGT
49791 -AAATATAAAAATAGAT-AAATAAATGAGT
1 AAAATATAAAAA-A-ATAAAATAAATGAGT
49819 AAAATATAAAAAAATAAAA
1 AAAATATAAAAAAATAAAA
49838 GCATATATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
26 13 0.32
27 9 0.22
28 7 0.17
29 11 0.28
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (28 bp):
AAAATATAAAAAAATAAAATAAATGAGT
Found at i:49808 original size:16 final size:16
Alignment explanation
Indices: 49763--49811 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
49753 AAACAAGTAA
* * *
49763 AAAAATATAAAAACAT
1 AAAAATAGATAAATAT
49779 AAAATATAAGATAAATAT
1 AAAA-AT-AGATAAATAT
49797 AAAAATAGATAAATA
1 AAAAATAGATAAATA
49812 AATGAGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 13 0.46
17 4 0.14
18 11 0.39
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (16 bp):
AAAAATAGATAAATAT
Found at i:49976 original size:33 final size:31
Alignment explanation
Indices: 49918--50010 Score: 87
Period size: 33 Copynumber: 2.9 Consensus size: 31
49908 GAAATATATA
* *
49918 AATATATATATATAATAACACTAATAAAAAAC
1 AATATACATATATAATAA-AATAATAAAAAAC
* **
49950 ATATATACATATATAATAAAATTAATAGAAAGT
1 A-ATATACATATATAATAAAA-TAATAAAAAAC
* *
49983 AATATGCATATATAACAAGAATAATAAA
1 AATATACATATATAATAA-AATAATAAA
50011 GTAGGAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
32 23 0.46
33 27 0.54
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.29
Consensus pattern (31 bp):
AATATACATATATAATAAAATAATAAAAAAC
Found at i:50419 original size:37 final size:36
Alignment explanation
Indices: 50376--50477 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
50366 ATAGTATAAC
50376 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
* *
50413 TTTATCCTATTTTTAGAAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
50447 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
50478 TAGGACGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
34 32 0.54
37 27 0.46
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:51212 original size:100 final size:104
Alignment explanation
Indices: 51025--51259 Score: 334
Period size: 100 Copynumber: 2.3 Consensus size: 104
51015 CATTGTTCCA
* * **
51025 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGGAA-C-GGAAATTGTTTGTTGACAAC
* *
51090 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
51131 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCT-GAA-TGAAA-T-TTTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGGAACGGAAATTGTTTGTTGACAACCA
* *
51192 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
51231 AGTCCAATATCCTTCGTTGTGAAGTTGAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAA
51260 CTTGCGTTGT
Statistics
Matches: 119, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
100 77 0.65
101 1 0.01
102 4 0.03
105 3 0.03
106 34 0.29
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (104 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGGAACGGAAATTGTTTGTTGACAACCA
GCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
Found at i:51259 original size:43 final size:43
Alignment explanation
Indices: 51198--51302 Score: 201
Period size: 43 Copynumber: 2.4 Consensus size: 43
51188 AGCAGCGGTC
*
51198 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
51241 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
51284 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTTGTGAAGTTGAA
51303 ATTGGCTCTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (43 bp):
CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:51398 original size:148 final size:143
Alignment explanation
Indices: 51100--51407 Score: 499
Period size: 148 Copynumber: 2.1 Consensus size: 143
51090 CAGCCGTCCC
*
51100 TTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGA
1 TTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGA
*
51165 ATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 ATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
*
51230 GAGTCCAATATCC
131 GAGTCCAATATCA
* *
51243 TTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG
1 TTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGA
* *
51308 CTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATT
66 ATCTGA-A-T--GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATT
*
51373 GTCTGGAGTCTAATATCA
126 GTCTGGAGTCCAATATCA
51391 TTCGTTGTGAAGTTGAA
1 TTCGTTGTGAAGTTGAA
51408 ATTGGCTCTG
Statistics
Matches: 152, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
143 67 0.44
144 1 0.01
145 1 0.01
147 5 0.03
148 78 0.51
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (143 bp):
TTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGA
ATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
GAGTCCAATATCA
Found at i:51423 original size:105 final size:105
Alignment explanation
Indices: 51241--51899 Score: 1120
Period size: 105 Copynumber: 6.3 Consensus size: 105
51231 AGTCCAATAT
* *
51241 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* *
51306 GGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTC
* * * *
51346 CCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCTAATATCATTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* * *
51411 GGCTCTGAGATTGGGAAGTTGTTATTGACAAGCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTC
51451 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
51516 GGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTC
*
51556 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
51621 GGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTC
*
51661 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCATTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
51726 GGCTCTGAAATTGAGAAGTTGTTGTTGACAGGCAGCGGTC
66 GGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTC
*
51766 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
* **
51831 GGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGTTGTC
66 GGCTCTGAAATTGAGAAGTTG-TTGTTGACAAGCAGCGGTC
* *
51872 CCTTCGTTGTGAAGTTGAACTTGTGTTG
1 CCTTCGTCGTGAAGTTGAACTTGCGTTG
51900 CCTCGAGTGC
Statistics
Matches: 531, Mismatches: 22, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 490 0.92
106 41 0.08
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (105 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGTC
Found at i:52676 original size:67 final size:66
Alignment explanation
Indices: 52541--52698 Score: 203
Period size: 68 Copynumber: 2.4 Consensus size: 66
52531 AAGATATCTG
* * **
52541 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
52606 TT
65 TT
* *
52608 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGAA-AAAATT-TGTTTTAGGGGAAATAAATTCAAAG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGA-AACAAAATTATGTTTTAAGGGAAATAAATTCAAAG
*
52671 GTT
64 ATT
*
52674 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
52699 ATAGACGAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 30 0.38
69 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:52725 original size:36 final size:35
Alignment explanation
Indices: 52674--52896 Score: 165
Period size: 36 Copynumber: 6.4 Consensus size: 35
52664 TTCAAAGGTT
* *
52674 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
52710 TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
52745 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
52783 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
52812 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
52847 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
52884 TTGTTTCAAGAGA
1 TTGTTTCAAGAGA
52897 GACAAAATTT
Statistics
Matches: 148, Mismatches: 24, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
28 2 0.01
29 17 0.11
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 7 0.05
36 82 0.55
37 32 0.22
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:52769 original size:37 final size:36
Alignment explanation
Indices: 52685--52796 Score: 120
Period size: 37 Copynumber: 3.1 Consensus size: 36
52675 TGTTTCAAGG
* * *
52685 GAAACTGTCTCAAGATAGACGAAAATTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACGAAAATTGTTCCAAAA
*
52721 GAAACTATCTCAAGAGAGAC-AAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACGAAAA-TT-GTTCCAAAA
* * * *
52758 GAAACTGTCTCAAGGGAGACGGAATTTGTTTC-AAA
1 GAAACTGTCTCAAGAGAGACGAAAATTGTTCCAAAA
52793 GAAA
1 GAAA
52797 ACATATTCAA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
35 11 0.17
36 24 0.38
37 27 0.42
38 2 0.03
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACGAAAATTGTTCCAAAA
Found at i:52784 original size:138 final size:138
Alignment explanation
Indices: 52622--52878 Score: 354
Period size: 138 Copynumber: 1.9 Consensus size: 138
52612 TTTCAAGAGT
* ** * * *
52622 AACTGTCTCAAGGGAGAAAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGAAAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
52687 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGT
52751 TCCAAAAGA
130 TCCAAAAGA
*** * *
52760 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGAAAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * *
52825 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGAC
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTATCTCAAGAGAGAC
52879 GAAATTTGTT
Statistics
Matches: 102, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
137 4 0.04
138 98 0.96
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (138 bp):
AACTGTCTCAAGGGAGAAAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTT
CCAAAAGA
Found at i:52892 original size:21 final size:21
Alignment explanation
Indices: 52868--52914 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
52858 GGAAACTGTC
* *
52868 TCAAGATAGACGAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
52889 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
52910 TCAAG
1 TCAAG
52915 GGAAACTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:52989 original size:35 final size:35
Alignment explanation
Indices: 52889--52989 Score: 89
Period size: 35 Copynumber: 2.9 Consensus size: 35
52879 GAAATTTGTT
* * *
52889 TCAAGAGAGACAAAAT-TTGTTTCAAGGGAAACTGTC
1 TCAAGAGAGAC-AAATCTTGTTTTAA-GAAAACGGTC
* * * *
52925 TCAAGAGAGACAAAAC-TCTTATAGTGAAAACGGTC
1 TCAAGAGAGACAAATCTTGTTTTA-AGAAAACGGTC
*
52960 TCAAGCGAGACAAATCTTGTTTTAAGAAAA
1 TCAAGAGAGACAAATCTTGTTTTAAGAAAA
52990 ACAATCATGA
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
35 34 0.68
36 16 0.32
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (35 bp):
TCAAGAGAGACAAATCTTGTTTTAAGAAAACGGTC
Found at i:53446 original size:18 final size:18
Alignment explanation
Indices: 53419--53454 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53409 TGTTGAATCC
* *
53419 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
53437 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
53455 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:53896 original size:22 final size:22
Alignment explanation
Indices: 53870--53918 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
53860 TTGTGTTTGG
* *
53870 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
53892 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
53914 TCAAA
1 TCAAA
53919 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:53925 original size:22 final size:22
Alignment explanation
Indices: 53882--53925 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
53872 AAAGGTTTGG
* * *
53882 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
53904 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
53926 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:54576 original size:8 final size:7
Alignment explanation
Indices: 54564--54634 Score: 61
Period size: 8 Copynumber: 9.1 Consensus size: 7
54554 TGATTTTTGC
54564 TCTTTTT
1 TCTTTTT
54571 TCCTTTTGT
1 T-CTTTT-T
*
54580 TCTTGTT
1 TCTTTTT
54587 TCTCTTTT
1 TCT-TTTT
54595 TCTTTGTT
1 TCTTT-TT
*
54603 TTTTTTT
1 TCTTTTT
54610 TGCTTTTT
1 T-CTTTTT
54618 TGCTTCTTT
1 T-CTT-TTT
54627 TCTTTTT
1 TCTTTTT
54634 T
1 T
54635 GTTCTTGATT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
7 14 0.26
8 34 0.63
9 6 0.11
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:54577 original size:16 final size:17
Alignment explanation
Indices: 54558--54613 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
54548 TCTTTTTGAT
*
54558 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
54574 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* * *
54591 TTTTTCT-TTGTTTTTT
1 TTTTGCTCTTGTTTCTC
54607 TTTTGCT
1 TTTTGCT
54614 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 26 0.81
17 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:54631 original size:16 final size:16
Alignment explanation
Indices: 54589--54640 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
54579 TTCTTGTTTC
*
54589 TCTTTTTCTTTGTTT-T
1 TCTTTTGCTTT-TTTGT
*
54605 TTTTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
54622 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
54637 TCTT
1 TCTT
54641 GATTGGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.26
16 17 0.55
17 6 0.19
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:57864 original size:16 final size:18
Alignment explanation
Indices: 57832--57866 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
57822 ATATAAAAAC
57832 ATAAAATATATGATAAAT
1 ATAAAATATATGATAAAT
57850 ATAAAA-ATA-GATAAAT
1 ATAAAATATATGATAAAT
57866 A
1 A
57867 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAAAATATATGATAAAT
Found at i:57891 original size:17 final size:17
Alignment explanation
Indices: 57799--57927 Score: 55
Period size: 19 Copynumber: 6.8 Consensus size: 17
57789 TAATGCAAAT
*
57799 AAATAAATAAAACAAGTA
1 AAATATATAAAA-AAGTA
*
57817 AAAGAATATAAAAACA-TA
1 AAA-TATATAAAAA-AGTA
*
57835 AAATATATGATAAATA-TAA
1 AAATATAT-A-AAAAAGT-A
*
57854 AAATAGATAAATAAATGAGTA
1 AAATATAT-AA-AAA--AGTA
57875 AAATATATAAAAAAGTAA
1 AAATATATAAAAAAGT-A
* *
57893 AAGCATATATATATAAGTA
1 AA--ATATATAAAAAAGTA
57912 AAATAATAATAAAAAA
1 AAAT-AT-ATAAAAAA
57928 AAGAAAATCA
Statistics
Matches: 85, Mismatches: 12, Indels: 27
0.69 0.10 0.22
Matches are distributed among these distances:
17 9 0.11
18 18 0.21
19 34 0.40
20 14 0.16
21 9 0.11
22 1 0.01
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (17 bp):
AAATATATAAAAAAGTA
Found at i:57902 original size:20 final size:20
Alignment explanation
Indices: 57876--57927 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
57866 AAATGAGTAA
57876 AATATATAAAAAAGTAAAAG
1 AATATATAAAAAAGTAAAAG
* * * *
57896 CATATATATATAAGTAAAAT
1 AATATATAAAAAAGTAAAAG
57916 AATA-ATAAAAAA
1 AATATATAAAAAA
57928 AAGAAAATCA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
AATATATAAAAAAGTAAAAG
Found at i:58482 original size:37 final size:36
Alignment explanation
Indices: 58439--58540 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
58429 ATAGTATAAC
58439 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
58476 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
58510 TCTATCCTATTTTTAGGAGTTTAAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
58541 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:60344 original size:20 final size:20
Alignment explanation
Indices: 60319--60374 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
60309 TTAAATTATT
60319 TAAATAATACTTTTTTAAGC
1 TAAATAATACTTTTTTAAGC
*
60339 TAAATACTAC-TTTTTAAGC
1 TAAATAATACTTTTTTAAGC
*
60358 TAAATAATACTTATTTA
1 TAAATAATACTTTTTTA
60375 TTGATAAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.45
Consensus pattern (20 bp):
TAAATAATACTTTTTTAAGC
Found at i:65621 original size:29 final size:29
Alignment explanation
Indices: 65588--65648 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
65578 TTGGAGTGAA
* *
65588 AGGATTAGGGATTTGTGTATCATAGATTT
1 AGGATTAGAGATTTGTGTATAATAGATTT
*
65617 AGGATTAGAGATTTGTGTATAATATATTT
1 AGGATTAGAGATTTGTGTATAATAGATTT
65646 AGG
1 AGG
65649 GATTTGAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.41
Consensus pattern (29 bp):
AGGATTAGAGATTTGTGTATAATAGATTT
Found at i:66053 original size:21 final size:21
Alignment explanation
Indices: 66029--66068 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
66019 ATAATTTGAG
66029 TATTTATTT-TTCAATTAAACC
1 TATTT-TTTATTCAATTAAACC
*
66050 TATTTTTTATTTAATTAAA
1 TATTTTTTATTCAATTAAA
66069 ATAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTTTATTCAATTAAACC
Found at i:69339 original size:36 final size:36
Alignment explanation
Indices: 69291--69363 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
69281 AATTTTAGCA
*
69291 TATCTCAATCAACATGTTAACTGCCAACTCAAATTG
1 TATCTCAATCAACAAGTTAACTGCCAACTCAAATTG
* * *
69327 TATCT-AAGTCAACAAGTTAACTTCTAACTCAGATTG
1 TATCTCAA-TCAACAAGTTAACTGCCAACTCAAATTG
69363 T
1 T
69364 CGTCAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (36 bp):
TATCTCAATCAACAAGTTAACTGCCAACTCAAATTG
Found at i:70409 original size:17 final size:18
Alignment explanation
Indices: 70387--70420 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
70377 TTAGCCGGTC
70387 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
70404 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
70421 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:71324 original size:21 final size:21
Alignment explanation
Indices: 71300--71349 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
71290 TGCATTTCGG
71300 GTTGCGATAGTTGAAAATCGC
1 GTTGCGATAGTTGAAAATCGC
71321 GTTGCGATAGTTGAAAATCGC
1 GTTGCGATAGTTGAAAATCGC
71342 GTTGCGAT
1 GTTGCGAT
71350 TTTCCATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (21 bp):
GTTGCGATAGTTGAAAATCGC
Found at i:71363 original size:20 final size:20
Alignment explanation
Indices: 71338--71430 Score: 134
Period size: 20 Copynumber: 4.6 Consensus size: 20
71328 TAGTTGAAAA
71338 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
71358 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
71379 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
71399 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
71419 TCGCGTTGCGAT
1 TCGCGTTGCGAT
71431 AGTCTACAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.06
20 44 0.69
21 12 0.19
22 4 0.06
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:71365 original size:41 final size:41
Alignment explanation
Indices: 71317--71410 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
71307 TAGTTGAAAA
71317 TCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCT-AAAATCGCGTTGCGATTTTCCATT
* *
71358 TCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTTTCCATT
71399 TCGCGTTGCGAT
1 TCGCGTTGCGAT
71411 TTTCCATTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 49 0.98
42 1 0.02
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTTTCCATT
Found at i:71450 original size:22 final size:22
Alignment explanation
Indices: 71422--71474 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
71412 TTCCATTTCG
71422 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
71444 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
71466 CGTTGCGAT
1 CGTTGCGAT
71475 TTTCCAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:71587 original size:6 final size:6
Alignment explanation
Indices: 71576--71652 Score: 140
Period size: 6 Copynumber: 13.2 Consensus size: 6
71566 CACGTATTAT
71576 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
71624 CACGAC CACGAC CACGAC C-CGAC C-CGAC C
1 CACGAC CACGAC CACGAC CACGAC CACGAC C
71653 CGAGACGAGA
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.14
6 61 0.86
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:78044 original size:38 final size:36
Alignment explanation
Indices: 77988--78062 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 36
77978 TTTAGAAAAT
*
77988 ATTTATATATTTTATTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTATTTT-AAAAAATTAAAAT-ATAAA
*
78026 ATTTATATAATTTT-TTTTACAAAATTAAAATATAAA
1 ATTTATAT-ATTTTATTTTAAAAAATTAAAATATAAA
78062 A
1 A
78063 AGGTTTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 6 0.18
37 11 0.32
38 12 0.35
39 5 0.15
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTATTTTAAAAAATTAAAATATAAA
Found at i:82253 original size:20 final size:20
Alignment explanation
Indices: 82230--82281 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
82220 AACGCGATCC
82230 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
82250 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
82270 CCAAAATCGCAA
1 CCAGAATCGCAA
82282 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:82362 original size:20 final size:20
Alignment explanation
Indices: 82337--82530 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
82327 GATTTTCCAT
* *
82337 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
82357 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
82377 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
82397 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
82417 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
82437 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
82457 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
82477 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
82498 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
82518 AATCGCAACGCGA
1 AATCGCAACGCGA
82531 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:82382 original size:40 final size:39
Alignment explanation
Indices: 82333--82530 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
82323 TTGCGATTTT
* ** *
82333 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
82371 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
82412 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
82452 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
82491 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
82531 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:82420 original size:60 final size:60
Alignment explanation
Indices: 82337--82529 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
82327 GATTTTCCAT
* ** * *
82337 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
82397 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
82457 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
82518 AATCGCAACGCG
1 AATCGCAACGCG
82530 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:82950 original size:33 final size:33
Alignment explanation
Indices: 82911--82981 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
82901 TTCACTTAGA
*
82911 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
82944 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
82977 TTTCA
1 TTTCA
82982 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:83120 original size:14 final size:14
Alignment explanation
Indices: 83101--83155 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
83091 AGAATGACTG
83101 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
83115 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
83134 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
83148 TCGCAACG
1 TCGCAACG
83156 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:83138 original size:33 final size:33
Alignment explanation
Indices: 83101--83171 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
83091 AGAATGACTG
**
83101 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
83134 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
83167 TCGCA
1 TCGCA
83172 TTGCGATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:83219 original size:33 final size:33
Alignment explanation
Indices: 83172--83285 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
83162 CAAAATCGCA
* *
83172 TTGCGA-TTTCATTTCGCGTTACGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
83204 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
83237 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
83270 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
83286 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 6 0.08
33 69 0.92
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:83226 original size:19 final size:18
Alignment explanation
Indices: 83167--83263 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
83157 GAAACCAAAA
*
83167 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
* *
83185 TCGCGTTACGA-TTC-TG
1 TCGCGTTGCGATTTCATT
83201 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
83218 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
* *
83232 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATT
83251 TCGCGTTGCGATT
1 TCGCGTTGCGATT
83264 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
14 17 0.27
15 1 0.02
16 7 0.11
17 8 0.13
18 9 0.15
19 20 0.32
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:83240 original size:14 final size:14
Alignment explanation
Indices: 83221--83277 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
83211 TTTCATTTCG
83221 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
83235 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
83252 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
83268 CGTTGCGATT
1 CGTTGCGATT
83278 TTCATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
15 1 0.03
16 5 0.13
17 5 0.13
18 1 0.03
19 8 0.21
ACGTcount: A:0.09, C:0.26, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:85297 original size:92 final size:93
Alignment explanation
Indices: 84984--85362 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
84974 TAGATTGCTT
*
84984 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
85049 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
85077 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
85142 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
85170 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
85234 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
85262 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTC-TTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
85326 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
85354 AGTAAATTT
1 AGTAAATTT
85363 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
91 16 0.06
92 114 0.40
93 154 0.54
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:85297 original size:185 final size:185
Alignment explanation
Indices: 84984--85364 Score: 737
Period size: 185 Copynumber: 2.1 Consensus size: 185
84974 TAGATTGCTT
84984 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
85049 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
85114 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTC-TTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
85170 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
85234 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
85299 GTGTATTCTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
85354 AGTAAATTTAT
1 AGTAAATTTAT
85365 CCATTCAAGT
Statistics
Matches: 193, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 57 0.30
185 75 0.39
186 61 0.32
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:85446 original size:19 final size:19
Alignment explanation
Indices: 85406--85534 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
85396 TAGTTTACTT
* *
85406 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
85426 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
85445 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
85464 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
85478 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
85497 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
85511 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
85530 TCGCA
1 TCGCA
85535 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:85480 original size:33 final size:32
Alignment explanation
Indices: 85442--85534 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
85432 CGCGAAACCA
**
85442 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
85474 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
85507 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
85535 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:85532 original size:52 final size:52
Alignment explanation
Indices: 85406--85534 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
85396 TAGTTTACTT
* **
85406 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
*** *
85458 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
85511 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
85535 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
51 3 0.05
52 47 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:85552 original size:19 final size:19
Alignment explanation
Indices: 85530--85664 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
85520 GAAACCAAAA
*
85530 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
85549 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
85565 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
85582 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
85598 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
85615 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
85634 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
85654 TCGTGTTGCGA
1 TCGCGTTGCGA
85665 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:85571 original size:14 final size:14
Alignment explanation
Indices: 85552--85608 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
85542 TTTCATTTCG
85552 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
85566 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
85583 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
85599 CGTTGCGATT
1 CGTTGCGATT
85609 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:85577 original size:33 final size:33
Alignment explanation
Indices: 85535--85627 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
85525 CAAAATCGCA
*
85535 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
85568 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
85601 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
85628 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:87587 original size:14 final size:14
Alignment explanation
Indices: 87568--87603 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
87558 ATTGTTTAAT
87568 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
87582 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
87596 TGATTTGT
1 TGATTTGT
87604 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:87726 original size:19 final size:19
Alignment explanation
Indices: 87710--87811 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
87700 AAAAATGACT
87710 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
87729 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
87748 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
87762 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
87781 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
87801 ATCGCAATGCG
1 ATCGCAATGCG
87812 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:87864 original size:19 final size:19
Alignment explanation
Indices: 87840--88112 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
87830 GATTATCTCG
87840 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87859 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87878 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
87892 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87911 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87930 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
87949 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
87967 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
87986 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
88000 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
88019 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
88038 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
88052 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
88072 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
88086 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
88105 TTGCGATT
1 TTGCGATT
88113 GTATTTTCCG
Statistics
Matches: 224, Mismatches: 8, Indels: 44
0.81 0.03 0.16
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 20 0.09
18 21 0.09
19 118 0.53
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:87880 original size:52 final size:52
Alignment explanation
Indices: 87818--88084 Score: 428
Period size: 52 Copynumber: 5.0 Consensus size: 52
87808 TGCGTTTATA
*
87818 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
87870 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
87922 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
87978 ATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
88030 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
88083 AT
1 AT
88085 GTTGGGATTT
Statistics
Matches: 202, Mismatches: 6, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
51 6 0.03
52 122 0.60
53 21 0.10
54 6 0.03
55 5 0.02
56 36 0.18
57 6 0.03
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:87975 original size:108 final size:102
Alignment explanation
Indices: 87840--88079 Score: 167
Period size: 108 Copynumber: 2.3 Consensus size: 102
87830 GATTATCTCG
87840 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
87902 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
87949 TTGCGA-TTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * * * *
88010 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
88052 TTGCGATTTTCATTTCCGCATTGCGATT
1 TTGCGATTTTCATTT-CGCATTGCGATT
88080 TTCATGTTGG
Statistics
Matches: 118, Mismatches: 7, Indels: 18
0.83 0.05 0.13
Matches are distributed among these distances:
101 7 0.06
102 4 0.03
103 13 0.11
104 9 0.08
105 10 0.08
106 2 0.02
108 67 0.57
109 6 0.05
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (102 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:88075 original size:34 final size:33
Alignment explanation
Indices: 87818--88112 Score: 155
Period size: 33 Copynumber: 8.5 Consensus size: 33
87808 TGCGTTTATA
*
87818 ATTTCGCATTGCGATTATC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCAT-GTTGCGATTTTC
*
87851 ATTTCGCATTGCGATTTTCAT-TT-CGCATTGCGATTC
1 ATTTCGCATTGCGATTCTCATGTTGCG-ATT----TTC
*
87887 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCA--T-G--TTGCGATTTTC
*
87922 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCA--T-G--TTGCGATTTTC
* * *
87959 ATTTCGCATTGCGATTTTAAT-TT-CGCA-TTGC
1 ATTTCGCATTGCGATTCTCATGTTGCG-ATTTTC
* *
87990 GA-TTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 -ATTTC-G-CATTGCGATTCTCA--T-G--TTGCGATTTTC
88030 ATTTCGCATTGCGATTCTC-TCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCAT-GTTGCGATTTTC
* *
88063 ATTTCCGCATTGCGATTTTCATGTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTCATGTTGCGATTTTC
*
88097 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
88113 GTATTTTCCG
Statistics
Matches: 220, Mismatches: 11, Indels: 62
0.75 0.04 0.21
Matches are distributed among these distances:
30 2 0.01
31 11 0.05
32 7 0.03
33 68 0.31
34 30 0.14
35 15 0.07
36 8 0.04
37 23 0.10
38 36 0.16
39 10 0.05
40 10 0.05
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCATGTTGCGATTTTC
Found at i:90621 original size:24 final size:24
Alignment explanation
Indices: 90587--90633 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
90577 CTGAAACATC
90587 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
90611 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
90634 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:91344 original size:20 final size:20
Alignment explanation
Indices: 91316--91684 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
91306 AAATTTAAGT
* * * *
91316 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
91336 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
91356 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
91376 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
91396 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91416 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
91436 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
91456 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91476 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91496 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
91516 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
91536 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
91556 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
91576 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
91596 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
91616 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
91636 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
91656 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
91676 GTTGCGATT
1 GTTGCGATT
91685 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:96964 original size:25 final size:25
Alignment explanation
Indices: 96932--96979 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
96922 TTTCTATACG
96932 ATTTTTT-AATAATAAAAGTTTTCT
1 ATTTTTTAAATAATAAAAGTTTTCT
*
96956 ATTTCTTTAAATAATAAAATTTTT
1 ATTT-TTTAAATAATAAAAGTTTT
96980 AGAGGGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 3 0.14
26 14 0.67
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTTTTTAAATAATAAAAGTTTTCT
Found at i:99458 original size:31 final size:32
Alignment explanation
Indices: 99414--99480 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
99404 CTATTTAAAA
*
99414 TTTTAAAAATTTTGGA-GGTTTAAATTATATT
1 TTTTAAAAATTTTGAATGGTTTAAATTATATT
** **
99445 TTTTAAATTTTTTGAATGGTTTAGTTTATATT
1 TTTTAAAAATTTTGAATGGTTTAAATTATATT
99477 TTTT
1 TTTT
99481 TTCTTCAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (32 bp):
TTTTAAAAATTTTGAATGGTTTAAATTATATT
Found at i:102297 original size:13 final size:13
Alignment explanation
Indices: 102279--102342 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 13
102269 AATAGCACCA
102279 GTCAACGGGTCGG
1 GTCAACGGGTCGG
102292 GTCAACGGGTCGG
1 GTCAACGGGTCGG
*
102305 GT---CGGGTCAACG
1 GTCAACGGGTC--GG
102317 GT---CGGGTCGG
1 GTCAACGGGTCGG
102327 GTCAACGGGTCGG
1 GTCAACGGGTCGG
102340 GTC
1 GTC
102343 GTGACCGGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
10 9 0.20
12 9 0.20
13 26 0.59
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:102307 original size:18 final size:18
Alignment explanation
Indices: 102284--102343 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
102274 CACCAGTCAA
102284 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
102302 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
102319 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
102337 CGGGTCG
1 CGGGTCG
102344 TGACCGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.41
18 24 0.59
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:102366 original size:10 final size:10
Alignment explanation
Indices: 102346--102397 Score: 63
Period size: 9 Copynumber: 5.3 Consensus size: 10
102336 TCGGGTCGTG
102346 ACCGGTC-AA
1 ACCGGTCAAA
102355 ACCGGTCAAA
1 ACCGGTCAAA
102365 ACCGGTTCAAA
1 ACCGG-TCAAA
*
102376 ACCGGT-TAA
1 ACCGGTCAAA
*
102385 ACCGATCAAA
1 ACCGGTCAAA
102395 ACC
1 ACC
102398 AGTTTCGAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 14 0.38
10 13 0.35
11 10 0.27
ACGTcount: A:0.38, C:0.31, G:0.17, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:102376 original size:11 final size:11
Alignment explanation
Indices: 102353--102382 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
102343 GTGACCGGTC
102353 AAACCGG-TCA
1 AAACCGGTTCA
102363 AAACCGGTTCA
1 AAACCGGTTCA
102374 AAACCGGTT
1 AAACCGGTT
102383 AAACCGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.17
Consensus pattern (11 bp):
AAACCGGTTCA
Done.