Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold89
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: 1412700
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 51868 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1367154 original size:44 final size:44
Alignment explanation
Indices: 1367093--1367202 Score: 150
Period size: 44 Copynumber: 2.5 Consensus size: 44
1367083 GATTTGCTCT
* *
1367093 CTGCAACTTCAGAGAGATAAGATCT-ATGGTTTTAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGAT-TAATGGCTTTAATCTGCTCCA
* * * *
1367137 CTGCAACTTCAGGGAGATAGGATTAATTGCTTTCATCTGCTCCG
1 CTGCAACTTCAGGGAGATAAGATTAATGGCTTTAATCTGCTCCA
1367181 CTGCAACTTCAGGGAGATAAGA
1 CTGCAACTTCAGGGAGATAAGA
1367203 CTTGCCATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 1 0.02
44 57 0.98
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGATTAATGGCTTTAATCTGCTCCA
Found at i:1379630 original size:36 final size:37
Alignment explanation
Indices: 1379574--1379650 Score: 140
Period size: 36 Copynumber: 2.1 Consensus size: 37
1379564 GAAAATATGT
1379574 GTATGCATATATTAAAACTTGTATATATAAGTATACA
1 GTATGCATATATTAAAACTTGTATATATAAGTATACA
1379611 GTATGCATAT-TTAAAACTTGTATATATAAGTATACA
1 GTATGCATATATTAAAACTTGTATATATAAGTATACA
1379647 -TATG
1 GTATG
1379651 TAAAAAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 4 0.10
36 26 0.65
37 10 0.25
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.39
Consensus pattern (37 bp):
GTATGCATATATTAAAACTTGTATATATAAGTATACA
Found at i:1380054 original size:3 final size:3
Alignment explanation
Indices: 1380046--1380100 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
1380036 ATATGTAGGT
* *
1380046 ATA ATA ATA ATA ATA ATA ATA TATA AT- ATA ATA ATG ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
*
1380091 ATA TTA ATA A
1 ATA ATA ATA A
1380101 AAAACTTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1380068 original size:30 final size:27
Alignment explanation
Indices: 1380045--1380099 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1380035 TATATGTAGG
*
1380045 TATAATAATAATAATAATAATATATAA
1 TATAATAATAATAATAACAATATATAA
*
1380072 TATAATAATGATAATAACAATAT-TAA
1 TATAATAATAATAATAACAATATATAA
1380098 TA
1 TA
1380100 AAAAACTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
TATAATAATAATAATAACAATATATAA
Found at i:1380784 original size:17 final size:18
Alignment explanation
Indices: 1380762--1380807 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1380752 CACCTTCAAA
*
1380762 CTTTTACTTTTTTG-ATT
1 CTTTTACTTTTGTGTATT
* *
1380779 CTTTTACTTTCGTGTTTT
1 CTTTTACTTTTGTGTATT
1380797 CTTTTACTTTT
1 CTTTTACTTTT
1380808 CAATACAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.09, C:0.15, G:0.07, T:0.70
Consensus pattern (18 bp):
CTTTTACTTTTGTGTATT
Found at i:1382858 original size:21 final size:21
Alignment explanation
Indices: 1382832--1382874 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1382822 GTGAGATTCT
*
1382832 AACTTTTTATTGATTAAACTA
1 AACTTTTTATTCATTAAACTA
1382853 AACTTTTTATTCATTAAACTA
1 AACTTTTTATTCATTAAACTA
1382874 A
1 A
1382875 GTGAGTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (21 bp):
AACTTTTTATTCATTAAACTA
Found at i:1385231 original size:32 final size:32
Alignment explanation
Indices: 1385175--1385254 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
1385165 ATAAGTATAT
* *
1385175 TAATATGATTGGCACAAAGACATCAGTAGTAG
1 TAATATGATTGGCACAAAGACATCAATAGAAG
* * * *
1385207 TAATATGATCGGCAGAACGGCATCAATAGAAG
1 TAATATGATTGGCACAAAGACATCAATAGAAG
*
1385239 TGATATGATTGGCACA
1 TAATATGATTGGCACA
1385255 CAGCCTGTAG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (32 bp):
TAATATGATTGGCACAAAGACATCAATAGAAG
Found at i:1385335 original size:26 final size:26
Alignment explanation
Indices: 1385303--1385353 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1385293 TCAGTAGCAT
1385303 CGTAGCAAAGCTGCCAGCAACAGTAC
1 CGTAGCAAAGCTGCCAGCAACAGTAC
*
1385329 CGTAGCAAAGCTGCCAGTAACAGTA
1 CGTAGCAAAGCTGCCAGCAACAGTA
1385354 TATGTCGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (26 bp):
CGTAGCAAAGCTGCCAGCAACAGTAC
Found at i:1385372 original size:27 final size:26
Alignment explanation
Indices: 1385342--1385406 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
1385332 AGCAAAGCTG
*
1385342 CCAGTAACAGTATATGTCGCCA-AGCCA
1 CCAGTAACAGTAT-TGT-GACAGAGCCA
1385369 CCAGTAACAGTGATTGTGACAGAGCCA
1 CCAGTAACAGT-ATTGTGACAGAGCCA
1385396 CCAGT-ACAGTA
1 CCAGTAACAGTA
1385407 CTTCGTCCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 8 0.23
27 24 0.69
28 2 0.06
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (26 bp):
CCAGTAACAGTATTGTGACAGAGCCA
Found at i:1385501 original size:24 final size:24
Alignment explanation
Indices: 1385469--1385527 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1385459 GCCATGATCA
*
1385469 AAATTAGTCATA-CAATTCACAGAC
1 AAATCAGTCATACCAA-TCACAGAC
1385493 AAATCAGTCATACCAATCACAGAC
1 AAATCAGTCATACCAATCACAGAC
1385517 AAATCAGTCAT
1 AAATCAGTCAT
1385528 TTACATCTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.22
Consensus pattern (24 bp):
AAATCAGTCATACCAATCACAGAC
Found at i:1385541 original size:24 final size:24
Alignment explanation
Indices: 1385485--1385578 Score: 93
Period size: 24 Copynumber: 3.9 Consensus size: 24
1385475 GTCATACAAT
*
1385485 TCACAGACAAATCAGTCA--TACCAA
1 TCACAGACAAATCAATCATTTA-C-A
*
1385509 TCACAGACAAATCAGTCATTTACA
1 TCACAGACAAATCAATCATTTACA
* * * *
1385533 TCTCGGACAAATAAATCACTTACA
1 TCACAGACAAATCAATCATTTACA
*
1385557 TCACAGATAAATCAATCATTTA
1 TCACAGACAAATCAATCATTTA
1385579 ACCTCGAGGG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
24 55 0.95
25 1 0.02
26 2 0.03
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.24
Consensus pattern (24 bp):
TCACAGACAAATCAATCATTTACA
Found at i:1385740 original size:27 final size:27
Alignment explanation
Indices: 1385644--1385740 Score: 124
Period size: 27 Copynumber: 3.6 Consensus size: 27
1385634 TAACAGAGGT
1385644 ATTACAATCATTTTAC-CTACAGGGGC
1 ATTACAATCATTTTACACTACAGGGGC
* ** *
1385670 ATCACGGTCATTTTACCCTACAGGGGC
1 ATTACAATCATTTTACACTACAGGGGC
* *
1385697 ATTACAATCATTTTACATTACAGGGGA
1 ATTACAATCATTTTACACTACAGGGGC
*
1385724 ATTACGATCATTTTACA
1 ATTACAATCATTTTACA
1385741 AATATTAAGG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
26 13 0.22
27 47 0.78
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (27 bp):
ATTACAATCATTTTACACTACAGGGGC
Found at i:1386910 original size:133 final size:133
Alignment explanation
Indices: 1386672--1386938 Score: 534
Period size: 133 Copynumber: 2.0 Consensus size: 133
1386662 ACAACATTAT
1386672 CTATTAAGCATCAATATCAATAACAAAGGTTAAACAATTACTATCCTAAGGAAAACACACGGCCA
1 CTATTAAGCATCAATATCAATAACAAAGGTTAAACAATTACTATCCTAAGGAAAACACACGGCCA
1386737 ACAAGAGAACTAGACATTCAGCCAGTATTTGAAAGCACATAACAACTTGCCCCTAACAATCAGCC
66 ACAAGAGAACTAGACATTCAGCCAGTATTTGAAAGCACATAACAACTTGCCCCTAACAATCAGCC
1386802 AAC
131 AAC
1386805 CTATTAAGCATCAATATCAATAACAAAGGTTAAACAATTACTATCCTAAGGAAAACACACGGCCA
1 CTATTAAGCATCAATATCAATAACAAAGGTTAAACAATTACTATCCTAAGGAAAACACACGGCCA
1386870 ACAAGAGAACTAGACATTCAGCCAGTATTTGAAAGCACATAACAACTTGCCCCTAACAATCAGCC
66 ACAAGAGAACTAGACATTCAGCCAGTATTTGAAAGCACATAACAACTTGCCCCTAACAATCAGCC
1386935 AAC
131 AAC
1386938 C
1 C
1386939 AAATGAATTA
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 134 1.00
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.19
Consensus pattern (133 bp):
CTATTAAGCATCAATATCAATAACAAAGGTTAAACAATTACTATCCTAAGGAAAACACACGGCCA
ACAAGAGAACTAGACATTCAGCCAGTATTTGAAAGCACATAACAACTTGCCCCTAACAATCAGCC
AAC
Found at i:1387874 original size:16 final size:15
Alignment explanation
Indices: 1387841--1387878 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1387831 ATGATGTGTA
1387841 AATATAA-TATAAAT
1 AATATAATTATAAAT
*
1387855 AATATAATTAATATAT
1 AATATAATT-ATAAAT
1387871 AATATAAT
1 AATATAAT
1387879 AAGTGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 1 0.05
16 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAATTATAAAT
Found at i:1394768 original size:32 final size:32
Alignment explanation
Indices: 1394718--1394856 Score: 147
Period size: 32 Copynumber: 4.4 Consensus size: 32
1394708 AACCACTACT
* *
1394718 AGCCATAAGTA-TAGTAATATGATTGGCACAA
1 AGCCATCAGTAGTAGTAATATGATCGGCACAA
*
1394749 AGCCATCAGTAGTGGTAATATGATCGGCACAA
1 AGCCATCAGTAGTAGTAATATGATCGGCACAA
* * *
1394781 AGCCATCAGTAGAAGTGATATGATCGGCACAC
1 AGCCATCAGTAGTAGTAATATGATCGGCACAA
*** *
1394813 AGCCTAT-AGTAACGGTAATATGATCGGCATAA
1 AGCC-ATCAGTAGTAGTAATATGATCGGCACAA
* *
1394845 AACCATTAGTAG
1 AGCCATCAGTAG
1394857 CATCGCAGCA
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
31 12 0.13
32 76 0.84
33 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (32 bp):
AGCCATCAGTAGTAGTAATATGATCGGCACAA
Found at i:1394830 original size:64 final size:64
Alignment explanation
Indices: 1394734--1394856 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 64
1394724 AAGTATAGTA
* ** *
1394734 ATATGATTGGCACAAAGCCATCAGTAGTGGTAATATGATCGGCACAAAGCCATCAGTAGAAGTG
1 ATATGATCGGCACAAAGCCATCAGTAACGGTAATATGATCGGCACAAAACCATCAGTAGAAGTG
* * *
1394798 ATATGATCGGCACACAGCCTAT-AGTAACGGTAATATGATCGGCATAAAACCATTAGTAG
1 ATATGATCGGCACAAAGCC-ATCAGTAACGGTAATATGATCGGCACAAAACCATCAGTAG
1394857 CATCGCAGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 49 0.96
65 2 0.04
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (64 bp):
ATATGATCGGCACAAAGCCATCAGTAACGGTAATATGATCGGCACAAAACCATCAGTAGAAGTG
Found at i:1394929 original size:27 final size:26
Alignment explanation
Indices: 1394863--1394963 Score: 96
Period size: 27 Copynumber: 3.8 Consensus size: 26
1394853 GTAGCATCGC
* * **
1394863 AGCAAAGCTGCCAGCAACAGTACCGT
1 AGCAAAGCTACCAGTAACAGTATTGT
* *
1394889 AGCAAAGTTGCCAGTAACAGTATATGT
1 AGCAAAGCTACCAGTAACAGTAT-TGT
1394916 AGCAAAGCTACCAGTAACAGTGATTGT
1 AGCAAAGCTACCAGTAACAGT-ATTGT
* * *
1394943 GGCAGAGCCACCAGT-ACAGTA
1 AGCAAAGCTACCAGTAACAGTA
1394964 CTTCCTCCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.02
26 25 0.39
27 36 0.56
28 2 0.03
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.18
Consensus pattern (26 bp):
AGCAAAGCTACCAGTAACAGTATTGT
Found at i:1395111 original size:24 final size:24
Alignment explanation
Indices: 1395026--1395108 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
1395016 GCCATGCACA
*
1395026 AAATCAGTCATACAATTCACAGAC
1 AAATCAGTCATACAAATCACAGAC
*
1395050 AAATCAGTCATACCAATCACAGAC
1 AAATCAGTCATACAAATCACAGAC
* **
1395074 AAATTAGTCATTTAAATCACAGAC
1 AAATCAGTCATACAAATCACAGAC
1395098 AAATCAGTCAT
1 AAATCAGTCAT
1395109 TTACATCTCG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (24 bp):
AAATCAGTCATACAAATCACAGAC
Found at i:1395122 original size:24 final size:24
Alignment explanation
Indices: 1395026--1395125 Score: 110
Period size: 24 Copynumber: 4.2 Consensus size: 24
1395016 GCCATGCACA
** *
1395026 AAATCAGTCATACAATTCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
***
1395050 AAATCAGTCATACCAATCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
*
1395074 AAATTAGTCATTTAAATCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
* * *
1395098 AAATCAGTCATTTACATCTCGGAC
1 AAATCAGTCATTTAAATCACAGAC
1395122 AAAT
1 AAAT
1395126 TAATCGTCGC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.24
Consensus pattern (24 bp):
AAATCAGTCATTTAAATCACAGAC
Found at i:1395727 original size:19 final size:20
Alignment explanation
Indices: 1395700--1395737 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1395690 CACGCGAGCC
*
1395700 CATTCGACCCAA-AACGGTA
1 CATTAGACCCAATAACGGTA
*
1395719 CATTAGACCTAATAACGGT
1 CATTAGACCCAATAACGGT
1395738 CAAGTCTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (20 bp):
CATTAGACCCAATAACGGTA
Found at i:1399246 original size:17 final size:17
Alignment explanation
Indices: 1399216--1399265 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
1399206 ATAAAAAGTC
**
1399216 AAAGATATAAGTATCAG
1 AAAGATATGGGTATCAG
*
1399233 AAAGTTATGGGTATCAG
1 AAAGATATGGGTATCAG
1399250 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
1399266 AAATCTGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:1406010 original size:17 final size:17
Alignment explanation
Indices: 1405988--1406020 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1405978 GCCCGGTCCA
1405988 ATAAAAGCAA-AAAATAG
1 ATAAAA-CAATAAAATAG
1406005 ATAAAACAATAAAATA
1 ATAAAACAATAAAATA
1406021 AAAGCAGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (17 bp):
ATAAAACAATAAAATAG
Found at i:1407236 original size:14 final size:14
Alignment explanation
Indices: 1407217--1407247 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1407207 ATAATTATTA
1407217 TTATATATATAGTT
1 TTATATATATAGTT
*
1407231 TTATATATATATTT
1 TTATATATATAGTT
1407245 TTA
1 TTA
1407248 CTAAAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
TTATATATATAGTT
Found at i:1407926 original size:44 final size:44
Alignment explanation
Indices: 1407877--1408193 Score: 181
Period size: 44 Copynumber: 7.2 Consensus size: 44
1407867 TATCTTGGAA
*
1407877 AGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGG
1 AGATAAGATTCGCCATCTTCAATCTACTCCACTACTGCTTAGGG
* * * * *
1407921 AGATAAGA-TCTACAATCTTCAACCTTCTCCACTACTGCTCAGGG
1 AGATAAGATTC-GCCATCTTCAATCTACTCCACTACTGCTTAGGG
* * **** * *
1407965 AGACAAGGCTT-GGTGGC-TCAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGCCATCTTC-AATCTAC-T-CCACTACTGCTTAGG-G
*
1408009 AGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGG
1 AGATAAGATTCGCCATCTTCAATCTACTCCACTACTGCTTAGGG
* * * * *
1408053 AGATAAGA-TCTACAATCTTCAACCTTCTCCACTACTGCTCAGGG
1 AGATAAGATTC-GCCATCTTCAATCTACTCCACTACTGCTTAGGG
* * **** * *
1408097 AGACAAGGCTT-GGTGGC-TCAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCGCCATCTTC-AATCTAC-T-CCACTACTGCTTAGG-G
*
1408141 AGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTTAGGG
1 AGATAAGATTCGCCATCTTCAATCTACTCCACTACTGCTTAGGG
1408185 AGATAAGAT
1 AGATAAGAT
1408194 CTACAATCTT
Statistics
Matches: 197, Mismatches: 52, Indels: 48
0.66 0.18 0.16
Matches are distributed among these distances:
42 12 0.06
43 22 0.11
44 135 0.69
45 14 0.07
46 14 0.07
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
AGATAAGATTCGCCATCTTCAATCTACTCCACTACTGCTTAGGG
Found at i:1408089 original size:132 final size:132
Alignment explanation
Indices: 1407852--1408243 Score: 766
Period size: 132 Copynumber: 3.0 Consensus size: 132
1407842 NNNNNNNNNN
1407852 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
1407917 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAGGCTTGGTGGC
66 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAGGCTTGGTGGC
1407982 TC
131 TC
1407984 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
1408049 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAGGCTTGGTGGC
66 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAGGCTTGGTGGC
1408114 TC
131 TC
1408116 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
1 AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
**
1408181 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCACCGCTGCTCAGGGAGACAAGGCTTGGTG
66 AGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAGGCTTGGTG
1408244 TTTCACCGAT
Statistics
Matches: 258, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 258 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (132 bp):
AAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCATCTTCGATCTACTCCACTACTGCTT
AGGGAGATAAGATCTACAATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAGGCTTGGTGGC
TC
Found at i:1408203 original size:44 final size:44
Alignment explanation
Indices: 1407891--1408231 Score: 170
Period size: 44 Copynumber: 7.8 Consensus size: 44
1407881 AAGATTCGCC
*
1407891 ATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTACA
* * * * * **
1407935 ATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAG-GCT-TG
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTACA
* * * * *
1407977 GTGGC-TCAAATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGAT-TCGCC
1 AT--CTTC-AATCTAC-T-CCACTACTGCTTAGG-GAGATAAGATCT-ACA
*
1408023 ATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTACA
* * * * * **
1408067 ATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAG-GCT-TG
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTACA
* * * * *
1408109 GTGGC-TCAAATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGAT-TCGCC
1 AT--CTTC-AATCTAC-T-CCACTACTGCTTAGG-GAGATAAGATCT-ACA
*
1408155 ATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTACA
* * ** *
1408199 ATCTTCAACCTTCTCCACCGCTGCTCAGGGAGA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGA
1408232 CAAGGCTTGG
Statistics
Matches: 217, Mismatches: 52, Indels: 56
0.67 0.16 0.17
Matches are distributed among these distances:
42 14 0.06
43 16 0.07
44 159 0.73
45 14 0.06
46 14 0.06
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (44 bp):
ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTACA
Done.