Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2820
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: 51359
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:3217 original size:17 final size:17
Alignment explanation
Indices: 3195--3228 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3185 TCCACCTAAT
*
3195 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
3212 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
3229 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:7848 original size:17 final size:17
Alignment explanation
Indices: 7826--7859 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7816 ATCCACTAAT
*
7826 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
7843 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
7860 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:9127 original size:44 final size:44
Alignment explanation
Indices: 9064--9181 Score: 193
Period size: 44 Copynumber: 2.7 Consensus size: 44
9054 ATGATCACAG
9064 ACACAGATTTGAGAATATGGAAGCAAAAAAGGAAATGACCAGAA
1 ACACAGATTTGAGAATATGGAAGCAAAAAAGGAAATGACCAGAA
**
9108 ACACAGATTTGAGAATATGGAAGCAAAAAAGGAAATGATGAGAA
1 ACACAGATTTGAGAATATGGAAGCAAAAAAGGAAATGACCAGAA
*
9152 ACACAGGTTTGAGAACT-TGGAAGCAAAAAA
1 ACACAGATTTGAGAA-TATGGAAGCAAAAAA
9182 CACATTGGAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
44 69 0.99
45 1 0.01
ACGTcount: A:0.51, C:0.10, G:0.24, T:0.15
Consensus pattern (44 bp):
ACACAGATTTGAGAATATGGAAGCAAAAAAGGAAATGACCAGAA
Found at i:11723 original size:24 final size:23
Alignment explanation
Indices: 11691--11735 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
11681 AATTTATAAG
11691 ATTTTTAAAAATTAAAAATTATT
1 ATTTTTAAAAATTAAAAATTATT
* *
11714 ATTTTATAAATATTGAAAATTA
1 ATTTT-TAAAAATTAAAAATTA
11736 AATTCATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTTTAAAAATTAAAAATTATT
Found at i:14669 original size:23 final size:24
Alignment explanation
Indices: 14618--14669 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
14608 TATATTATTT
* *
14618 ATTAAAGGTTATTTTAGTGTTATA
1 ATTAAAGGTTAATATAGTGTTATA
14642 A-TAAATGGTTAATATA-TGTTA-A
1 ATTAAA-GGTTAATATAGTGTTATA
14664 ATTAAA
1 ATTAAA
14670 ACTTGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 2 0.08
23 13 0.54
24 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (24 bp):
ATTAAAGGTTAATATAGTGTTATA
Found at i:16846 original size:15 final size:15
Alignment explanation
Indices: 16826--16859 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16816 GATTTTTTTG
* *
16826 TTATTTTTGCTCGTA
1 TTATTTTTACTCGCA
16841 TTATTTTTACTCGCA
1 TTATTTTTACTCGCA
16856 TTAT
1 TTAT
16860 CGTAATTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.59
Consensus pattern (15 bp):
TTATTTTTACTCGCA
Found at i:18862 original size:62 final size:62
Alignment explanation
Indices: 18765--18885 Score: 242
Period size: 62 Copynumber: 2.0 Consensus size: 62
18755 CTTTTTTTTT
18765 TGCATTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAATA
1 TGCATTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAATA
18827 TGCATTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAA
1 TGCATTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAA
18886 GTACGTCGAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.32
Consensus pattern (62 bp):
TGCATTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAATA
Found at i:20197 original size:17 final size:17
Alignment explanation
Indices: 20158--20213 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 17
20148 AGTAGAGGCC
20158 AAAAAAAAGAACAAAAA
1 AAAAAAAAGAACAAAAA
20175 ACAAAAAAA-AACAAAAGTA
1 A-AAAAAAAGAACAAAA--A
20194 AAAAACAAGAGAA-AAAAA
1 AAAAA-AA-AGAACAAAAA
20212 AA
1 AA
20214 CTCTACCGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
17 8 0.24
18 14 0.42
19 4 0.12
20 5 0.15
21 2 0.06
ACGTcount: A:0.84, C:0.07, G:0.07, T:0.02
Consensus pattern (17 bp):
AAAAAAAAGAACAAAAA
Found at i:20211 original size:13 final size:13
Alignment explanation
Indices: 20158--20211 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
20148 AGTAGAGGCC
20158 AAAA-AAAAGAACA
1 AAAACAAAAGAA-A
*
20171 AAAA-ACAA-AAA
1 AAAACAAAAGAAA
*
20182 AAAACAAAAGTAA
1 AAAACAAAAGAAA
*
20195 AAAACAAGAGAAA
1 AAAACAAAAGAAA
20208 AAAA
1 AAAA
20212 AACTCTACCG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 24 0.71
ACGTcount: A:0.83, C:0.07, G:0.07, T:0.02
Consensus pattern (13 bp):
AAAACAAAAGAAA
Found at i:20662 original size:7 final size:7
Alignment explanation
Indices: 20643--20713 Score: 56
Period size: 7 Copynumber: 9.9 Consensus size: 7
20633 TACTTCACTT
20643 GAAAAAA
1 GAAAAAA
20650 -ACAAAAA
1 GA-AAAAA
20657 GAAAAAGA
1 GAAAAA-A
20665 GAAAAAA
1 GAAAAAA
*
20672 -ATGAAAA
1 GA-AAAAA
*
20679 GAGAAAA
1 GAAAAAA
20686 GAAAAAAA
1 G-AAAAAA
* *
20694 GAAGAAC
1 GAAAAAA
20701 GAAAAAA
1 GAAAAAA
20708 GAAAAA
1 GAAAAA
20714 GGAGAGGCCA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
6 2 0.04
7 35 0.67
8 15 0.29
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (7 bp):
GAAAAAA
Found at i:20671 original size:22 final size:21
Alignment explanation
Indices: 20643--20713 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 21
20633 TACTTCACTT
20643 GAAAAAAACAAAAAGAAAAAGA
1 GAAAAAAACAAAAAGAAAAA-A
** *
20665 GAAAAAAATGAAAAGAGAAAA
1 GAAAAAAACAAAAAGAAAAAA
* *
20686 GAAAAAAAGAAGAACGAAAAAA
1 GAAAAAAACAA-AAAGAAAAAA
20708 GAAAAA
1 GAAAAA
20714 GGAGAGGCCA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 10 0.24
22 31 0.76
ACGTcount: A:0.79, C:0.03, G:0.17, T:0.01
Consensus pattern (21 bp):
GAAAAAAACAAAAAGAAAAAA
Found at i:21984 original size:100 final size:100
Alignment explanation
Indices: 21808--22620 Score: 968
Period size: 100 Copynumber: 8.2 Consensus size: 100
21798 TCAAACGTTT
* * * * * *
21808 TTCTCTGGCAATGCAGTGGGA-CAGATTAAAGCTACGACAGCGAATCTTGCTTCCTCGACATTGC
1 TTCTCTGGCAGTACAGT-GGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGC
*
21872 AATTAAAGAGATTGAAGCCACAACGGTGAATCTCAC
65 AATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * * * * *
21908 TTCTCTGGCAGTACAGTGCAGCAGATTAAAGCTACGACGGTAAATCTTGCTTCCCTGATATTGCA
1 TTCTCTGGCAGTACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA
*** *
21973 ATTTAAA-AGATTGAAGTTGCAACGGCGAATCTTAC
66 A-TTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * *
22008 TT-TATTGGC-GATGCAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGATATTG
1 TTCT-CTGGCAG-TACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTG
* * *
22071 CAAGTAAAGAGATTGAAGCCACAACAGTGAATCTCAC
64 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * * * * *
22108 TTCTCTGGCAGTACAGTGCAGCAGATTAAAGCTACGACGGCGAATCTTGCTTCCCTGATATTGCA
1 TTCTCTGGCAGTACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA
* ** * *
22173 ATTTAAA-AGATTGAAGCCGCAACAACGACTCTTAC
66 A-TTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * *
22208 TT-TCTTGGC-GATGCAGTGGATCAGATTAAAGCTACAATGGTGAATCTTGCTTCCCCGGCATTG
1 TTCTC-TGGCAG-TACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTG
22271 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
64 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * * * * *
22308 TTCTCTGGCAGTATAGTGCAGCAGATTAAAGCTACGACGGTGAATCTTGCTTCCCTGATATTGCA
1 TTCTCTGGCAGTACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA
** * *
22373 ATTTAAA-AGATTGAAGCTGCAACGGCAAATCTTAC
66 A-TTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
* * * *
22408 TT-TCTTGGC-GATGCAGTGGATCAGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTG
1 TTCTC-TGGCAG-TACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTG
22471 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
64 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
*
22508 TTCTCTGGCAGTACAGTGGATCAGATTGAAGCTACAACGGTGAATCTTG-TTCCCCGACATTGCA
1 TTCTCTGGCAGTACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA
22572 ATTAAAGAGATTG-AGCCACAACGGCGAATCTCAC
66 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
*
22606 TTCTCTAGCAG-ACAG
1 TTCTCTGGCAGTACAG
22621 AACCACAGAT
Statistics
Matches: 608, Mismatches: 86, Indels: 41
0.83 0.12 0.06
Matches are distributed among these distances:
97 4 0.01
98 31 0.05
99 52 0.09
100 499 0.82
101 22 0.04
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (100 bp):
TTCTCTGGCAGTACAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGCA
ATTAAAGAGATTGAAGCCACAACGGCGAATCTCAC
Found at i:22161 original size:200 final size:200
Alignment explanation
Indices: 21807--22607 Score: 1241
Period size: 200 Copynumber: 4.0 Consensus size: 200
21797 ATCAAACGTT
* * * *
21807 TTTCTCTGGCAATGCAGTGGGA-CAGATTAAAGCTACGACAGCGAATCTTGCTTCCTCGACATTG
1 TTTCT-TGGCGATGCAGT-GGATCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTG
*
21871 CAATTAAAGAGATTGAAGCCACAACGGTGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTA
64 CAATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTA
* **
21936 AAGCTACGACGGTAAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGTTGCAACGGCGA
129 AAGCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACGGCGA
22001 ATCTTAC
194 ATCTTAC
* * *
22008 TTTATTGGCGATGCAGTGGATCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGATATTGCA
1 TTTCTTGGCGATGCAGTGGATCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
* * *
22073 AGTAAAGAGATTGAAGCCACAACAGTGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTAAA
66 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTAAA
* ** *
22138 GCTACGACGGCGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACAACGACT
131 GCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAAT
22203 CTTAC
196 CTTAC
* * *
22208 TTTCTTGGCGATGCAGTGGATCAGATTAAAGCTACAATGGTGAATCTTGCTTCCCCGGCATTGCA
1 TTTCTTGGCGATGCAGTGGATCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
*
22273 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTATAGTGCAGCAGATTAAA
66 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTAAA
* *
22338 GCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCTGCAACGGCAAAT
131 GCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAAT
22403 CTTAC
196 CTTAC
* *
22408 TTTCTTGGCGATGCAGTGGATCAGATTGAAGCTACAATGGCGAATCTTGCTTCCCCGACATTGCA
1 TTTCTTGGCGATGCAGTGGATCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
* * *
22473 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGGATCAGATTGAA
66 ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTAAA
* * * *
22538 GCTACAACGGTGAATCTTG-TTCCCCGACATTGCAA-TTAAAGAGATTG-AGCCACAACGGCGAA
131 GCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAA-AGATTGAAGCCGCAACGGCGAA
*
22600 TCTCAC
195 TCTTAC
22606 TT
1 TT
22608 CTCTAGCAGA
Statistics
Matches: 554, Mismatches: 44, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
198 24 0.04
199 23 0.04
200 503 0.91
201 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (200 bp):
TTTCTTGGCGATGCAGTGGATCAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCA
ATTAAAGAGATTGAAGCCACAACGGCGAATCTCACTTCTCTGGCAGTACAGTGCAGCAGATTAAA
GCTACGACGGTGAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTGAAGCCGCAACGGCGAAT
CTTAC
Found at i:22867 original size:84 final size:84
Alignment explanation
Indices: 22626--23292 Score: 1031
Period size: 84 Copynumber: 7.9 Consensus size: 84
22616 GACAGAACCA
*
22626 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTTTCTCCCTAAGCAGT-G
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
22690 TGGAGCAGACGAAATAAAC
66 TGGAGCAGACGAAAGAAAC
* * * *
22709 CAG-TCTTATCTCCCTAAGCAGTAATGGAGCAGA-CGAAAGAAACAAGTTTTATCTCCCTAAGCA
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAGTCTTATCTCCCTAAGCA
*
22772 GTAGTGGAGCAGACAAAAGAAAC
62 GTAGTGGAGCAGACGAAAGAAAC
* * *
22795 TAGATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCACATTAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
22860 TGGAGCAGACAAAAGAAAC
66 TGGAGCAGACGAAAGAAAC
22879 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
22944 TGGAGTAGACGAAAGAAAC
66 TGGAGCAGACGAAAGAAAC
*
22963 CAGATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
23028 T-GAGGCAGACGAAAGAAAC
66 TGGA-GCAGACGAAAGAAAC
23047 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
23112 T-GAGGCAGACGAAAGAAAC
66 TGGA-GCAGACGAAAGAAAC
23131 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
*
23196 TGGAGTAGACGAAAGAAAC
66 TGGAGCAGACGAAAGAAAC
* * * *
23215 CGGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCTAAGC
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCTAAGC
23279 AGTAGTGGAGCAGA
61 AGTAGTGGAGCAGA
23293 TCACATCAAC
Statistics
Matches: 542, Mismatches: 28, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
81 1 0.00
82 29 0.05
83 6 0.01
84 398 0.73
85 25 0.05
86 21 0.04
87 32 0.06
88 30 0.06
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (84 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
TGGAGCAGACGAAAGAAAC
Found at i:23307 original size:84 final size:82
Alignment explanation
Indices: 22629--23416 Score: 898
Period size: 84 Copynumber: 9.4 Consensus size: 82
22619 AGAACCACAG
* *
22629 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTTTCTCCCTAAGCAGT-GTGG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGTGG
*
22693 AGCAGACGAAATAAACC
66 AGCAGACGAAAGAAACC
* * *
22710 AGTCTTATCTCCCTAAGCAGTAATGGAGCAGA-CGAAAGAAACAAGTTTTATCTCCCTAAGCAGT
1 A-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CAACAAGTCTTATCTCCCTAAGCAGT
* *
22774 AGTGGAGCAGACAAAAGAAACTAG
61 AGTGGAGCAGACGAAAGAAAC--C
* **
22798 ATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCACATTAAGTCTTATCTCCCTAAGCAGTAGTGG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGTGG
*
22863 AGCAGACAAAAGAAACC
66 AGCAGACGAAAGAAACC
*
22880 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGT
*
22945 GGAGTAGACGAAAGAAACC
64 GGAGCAGACGAAAGAAACC
* *
22964 AGATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGT
23029 -GAGGCAGACGAAAGAAACC
64 GGA-GCAGACGAAAGAAACC
*
23048 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGT
23113 -GAGGCAGACGAAAGAAACC
64 GGA-GCAGACGAAAGAAACC
*
23132 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGT
*
23197 GGAGTAGACGAAAGAAACC
64 GGAGCAGACGAAAGAAACC
* *
23216 GGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACCAGATCTTATCTCCCTAAGCA
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CAACAAG-TCTTATCTCCCTAAGCA
* **
23280 GTAGTGGAGCAGATC-ACATCAA-C
59 GTAGTGGAGCAGA-CGAAAGAAACC
** * * * *
23303 -TCTTATCTCCCTAAAAAGTAGTGGAACAGA-CAAAAGAAACCAGATCTTATCTCCTTAAGCAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CAACAAG-TCTTATCTCCCTAAGCAGT
* * **
23366 AGTAGAGCAGATCG-CACCAA--
61 AGTGGAGCAGA-CGAAAGAAACC
*
23386 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
23417 CGAAAAAAAC
Statistics
Matches: 645, Mismatches: 41, Indels: 39
0.89 0.06 0.05
Matches are distributed among these distances:
81 2 0.00
82 29 0.04
83 3 0.00
84 498 0.77
85 25 0.04
86 19 0.03
87 33 0.05
88 35 0.05
89 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (82 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACAACAAGTCTTATCTCCCTAAGCAGTAGTGG
AGCAGACGAAAGAAACC
Found at i:23309 original size:168 final size:168
Alignment explanation
Indices: 22629--23424 Score: 993
Period size: 168 Copynumber: 4.7 Consensus size: 168
22619 AGAACCACAG
*
22629 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTTTCTCCCTAAGCAGT-GTGG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGG
* * *
22693 AGCAGACGAAATAAACCAG-TCTTATCTCCCTAAGCAGTAATGGAGCAGACGAAAGAAACAAGTT
66 AGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAA-AAACAAGTC
* *
22757 TTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACTAG
130 TTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAAC--C
* *
22798 ATCTTATCTCCCTAAGCAGTAGTAGAGCAGATCACATTAAGTCTTATCTCCCTAAGCAGTAGTGG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGG
* * *
22863 AGCAGACAAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---ACATCAAGTC
66 AGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAAAACAAGTC
*
22925 TTATCTCCCTAAGCAGTAGTGGAGTAGACGAAAGAAACC
130 TTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
*
22964 AGATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
* *
23029 -GAGGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---ACATCAA
64 GGA-GCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAAAACAA
23090 GTCTTATCTCCCTAAGCAGTAGT-GAGGCAGACGAAAGAAACC
127 GTCTTATCTCCCTAAGCAGTAGTGGA-GCAGACGAAAGAAACC
23132 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
1 --ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT
* * *
23197 GGAGTAGACGAAAGAAACCGGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCAG
64 GGAGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAA-AAACAAG
* **
23262 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAA-C
128 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACC
** * * * * *
23303 -TCTTATCTCCCTAAAAAGTAGTGGAACAGA-CAAAAGAAACCAGATCTTATCTCCTTAAGCAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC---A-CATCAAG-TCTTATCTCCCTAAGCAGT
* *
23366 AGTAGAGCAGATC----G-CACCA-AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAA
61 AGTGGAGCAGA-CGAAAGAAACCAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAA
23425 ACCAATCTCA
Statistics
Matches: 568, Mismatches: 37, Indels: 46
0.87 0.06 0.07
Matches are distributed among these distances:
167 10 0.02
168 373 0.66
169 61 0.11
170 23 0.04
171 38 0.07
172 59 0.10
173 4 0.01
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (168 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGG
AGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAAAACAAGTCT
TATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACC
Found at i:23309 original size:252 final size:252
Alignment explanation
Indices: 22626--23416 Score: 1067
Period size: 252 Copynumber: 3.1 Consensus size: 252
22616 GACAGAACCA
*
22626 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTTTCTCCCTAAGCAGT-G
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
* * *
22690 TGGAGCAGACGAAATAAACCAG-TCTTATCTCCCTAAGCAGTAATGGAGCAGACGAAAGAAACAA
66 TGGAGTAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACAA
*
22754 GTTTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACTAGATCTTATCTCCCTAAGCAGTA
131 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAAC---ATCTTATCTCCCTAAGCAGTA
* *
22819 GTAGAGCAGATCACATTAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAAC
193 GTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAAC
22879 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
* * *
22944 TGGAGTAGACGAAAGAAACCAGATCTTATCTTCCTAAGCAGTAGTGGAGCAGATC---A-CATCA
66 TGGAGTAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CGAAAGAAACA
*
23005 AGTCTTATCTCCCTAAGCAGTAGT-GAGGCAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAG
130 AGTCTTATCTCCCTAAGCAGTAGTGGA-GCAGACAAAAGAAA-C--ATCTTATCTCCCTAAGCAG
*
23069 TAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGT-GAGGCAGACGAAAGAAAC
191 TAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGA-GCAGACAAAAGAAAC
23131 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
* *
23196 TGGAGTAGACGAAAGAAACCGGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACCA
66 TGGAGTAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACAA
* ** **
23261 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-ACATCAAC-TCTTATCTCCCTAAAAAGTAG
131 G-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAAGAAACATCTTATCTCCCTAAGCAGTAG
* * * * * * *
23324 TGGAACAGA-CAAAAGAAACCAGATCTTATCTCCTTAAGCAGTAGTAGAGCAGATC----G-CAC
194 TGGAGCAGATC---A-CATCAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA-CAAAAGAAAC
23383 CA-AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGA
1 CAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
23417 CGAAAAAAAC
Statistics
Matches: 489, Mismatches: 28, Indels: 43
0.87 0.05 0.08
Matches are distributed among these distances:
251 7 0.01
252 293 0.60
253 65 0.13
254 23 0.05
255 37 0.08
256 58 0.12
257 6 0.01
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (252 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAG
TGGAGTAGACGAAAGAAACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGACGAAAGAAACAA
GTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAACATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCACATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAAAAGAAAC
Found at i:25102 original size:22 final size:22
Alignment explanation
Indices: 25055--25124 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
25045 ATATATTTTT
* *
25055 TTATATTTCATATTCTCTACATA
1 TTATAATTCATATACT-TACATA
*
25078 TATATATACTT-ATATATTTACATA
1 T-TATA-A-TTCATATACTTACATA
*
25102 TTTTAATTCATATACTTACATA
1 TTATAATTCATATACTTACATA
25124 T
1 T
25125 GTATGTACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
21 2 0.05
22 14 0.37
23 4 0.11
24 11 0.29
25 5 0.13
26 2 0.05
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATAATTCATATACTTACATA
Found at i:25533 original size:15 final size:15
Alignment explanation
Indices: 25513--25546 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25503 ATTTTTTTTG
* *
25513 TTATTTTTGCTCGTA
1 TTATTTTTACTCGCA
25528 TTATTTTTACTCGCA
1 TTATTTTTACTCGCA
25543 TTAT
1 TTAT
25547 CGTAATTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.59
Consensus pattern (15 bp):
TTATTTTTACTCGCA
Found at i:44608 original size:16 final size:16
Alignment explanation
Indices: 44587--44621 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
44577 TTCTTCAAAT
44587 ACTGCTTCTGAGACAA
1 ACTGCTTCTGAGACAA
44603 ACTGCTTCTGAGACAA
1 ACTGCTTCTGAGACAA
44619 ACT
1 ACT
44622 AACTCTGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (16 bp):
ACTGCTTCTGAGACAA
Found at i:48655 original size:22 final size:23
Alignment explanation
Indices: 48630--48679 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
48620 CGTGGAACTC
48630 TCCACA-TTTTGAACAATTGTCT
1 TCCACAGTTTTGAACAATTGTCT
*
48652 TCCATATGTTTTGAACAATTGTCT
1 TCCACA-GTTTTGAACAATTGTCT
48676 TCCA
1 TCCA
48680 TATTCTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.20
24 20 0.80
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (23 bp):
TCCACAGTTTTGAACAATTGTCT
Found at i:48663 original size:24 final size:24
Alignment explanation
Indices: 48636--48682 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
48626 ACTCTCCACA
48636 TTTTGAACAATTGTCTTCCATATG
1 TTTTGAACAATTGTCTTCCATATG
48660 TTTTGAACAATTGTCTTCCATAT
1 TTTTGAACAATTGTCTTCCATAT
48683 TCTAACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (24 bp):
TTTTGAACAATTGTCTTCCATATG
Done.