Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1723
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: 76629
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1974 original size:24 final size:24
Alignment explanation
Indices: 1942--1991 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1932 GCATCCATGG
1942 TTGGTAACCATTAAATTGTTAGTT
1 TTGGTAACCATTAAATTGTTAGTT
1966 TTGGTAACCATTAAATTGTTAGTT
1 TTGGTAACCATTAAATTGTTAGTT
1990 TT
1 TT
1992 CTTTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (24 bp):
TTGGTAACCATTAAATTGTTAGTT
Found at i:3092 original size:3 final size:3
Alignment explanation
Indices: 3084--3132 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
3074 AAACACACAC
* * *
3084 ACA ACA ACA GCA GCA ACA ACA ACA ACA ACA ACA ACA ACA ATA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
3132 A
1 A
3133 ACAATAAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.63, C:0.31, G:0.04, T:0.02
Consensus pattern (3 bp):
ACA
Found at i:9573 original size:29 final size:29
Alignment explanation
Indices: 9531--9590 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
9521 GAGTTAGATT
9531 AATAAGGGTTGCAAAATGTAATTTTGGTA
1 AATAAGGGTTGCAAAATGTAATTTTGGTA
9560 AATAAGGGTTGCAAAATGTAATTTTGGTA
1 AATAAGGGTTGCAAAATGTAATTTTGGTA
9589 AA
1 AA
9591 CAAGATGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (29 bp):
AATAAGGGTTGCAAAATGTAATTTTGGTA
Found at i:19078 original size:18 final size:17
Alignment explanation
Indices: 19036--19078 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
19026 TTTCTCTTTC
*
19036 TTTATTCTTTTCGATTA
1 TTTATTTTTTTCGATTA
*
19053 TTTCATTTTTTTCGATCTG
1 TTT-ATTTTTTTCGAT-TA
19072 TTTATTT
1 TTTATTT
19079 ATAAAAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.14, C:0.12, G:0.07, T:0.67
Consensus pattern (17 bp):
TTTATTTTTTTCGATTA
Found at i:19745 original size:21 final size:22
Alignment explanation
Indices: 19708--19751 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
19698 TATTATATAA
19708 TTTATATTAAATTATTT-CTAT
1 TTTATATTAAATTATTTCCTAT
*
19729 TTTATA-TATATTGATTTCCTAT
1 TTTATATTAAATT-ATTTCCTAT
19751 T
1 T
19752 ATTGTAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTATATTAAATTATTTCCTAT
Found at i:22956 original size:202 final size:199
Alignment explanation
Indices: 22587--23189 Score: 839
Period size: 202 Copynumber: 3.0 Consensus size: 199
22577 AATACACCAC
* * ** *
22587 AAAGGCTTAGCAGATTACGCCACACAGACCATCATACAAAATCACGTGTTTATTGTCTTAGTAAA
1 AAAGGCTTAGTAGATTACGCCACACAG-CCATCATACAAAATCACGTGTTTACTGT-TCCG-GAA
* * **
22652 CTTTCATAAAAGGCGCTATGGGTATCTCCCTCATAGACTTATACATATTTTCATGTTGTGATCTG
63 CTTTCACAAAAGGCGCTATGGGTATCTCCCTCATGGACTTATACATATTTTCATGTCATGATCTG
* * * * **
22717 CCAATCTGGTTTACATGCTACCGAAGCCATCACCATGAATATTCATACAATCATATCTTGTCATG
128 CTAGTCCGATTTACATATTACCGAAGCCATCACCATGAATATTCATACAATCATATCTTGTCATG
22782 GGTCCCA
193 GGTCCCA
* * * * *
22789 GAAGGTTTAGTAGATAACGCCACAGATGCCATCATACAAAATCACATGTTTACTGTTCCGGCAGA
1 AAAGGCTTAGTAGATTACGCCACACA-GCCATCATACAAAATCACGTGTTTACTGTTCCGG-A-A
*
22854 CTTTCACAAAAGGCGCTATGGGTATCTCCCTCATGGACTTATACATATTTTCATGTCATAATCTG
63 CTTTCACAAAAGGCGCTATGGGTATCTCCCTCATGGACTTATACATATTTTCATGTCATGATCTG
* * *
22919 CTAGTCCGATTTACATATTACCGAAACCATTACCATGAATATTCATACAGTCATATCTTGTCATG
128 CTAGTCCGATTTACATATTACCGAAGCCATCACCATGAATATTCATACAATCATATCTTGTCATG
*
22984 AGTCCCA
193 GGTCCCA
* *
22991 AAAAGCTTAGTAGATTACGCCACATAGGCCATCATACAAAATCACGTGTTTACTGTTCCAGTGAA
1 AAAGGCTTAGTAGATTACGCCACACA-GCCATCATACAAAATCACGTGTTTACTGTTCC-G-GAA
* *
23056 CTTTCACAAAAGGCGCTATGGGTATCTCCCTCATGGACTTATACATATTTTCATGTCTTGATCTA
63 CTTTCACAAAAGGCGCTATGGGTATCTCCCTCATGGACTTATACATATTTTCATGTCATGATCTG
*
23121 CTAGTCC-AGTTTACATATTACCGAAGCTATCACCATGAATATTCATACAATCATATCTTGTCAT
128 CTAGTCCGA-TTTACATATTACCGAAGCCATCACCATGAATATTCATACAATCATATCTTGTCAT
23185 GGGTC
192 GGGTC
23190 TCAACCACAT
Statistics
Matches: 355, Mismatches: 40, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
201 4 0.01
202 347 0.98
203 3 0.01
204 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (199 bp):
AAAGGCTTAGTAGATTACGCCACACAGCCATCATACAAAATCACGTGTTTACTGTTCCGGAACTT
TCACAAAAGGCGCTATGGGTATCTCCCTCATGGACTTATACATATTTTCATGTCATGATCTGCTA
GTCCGATTTACATATTACCGAAGCCATCACCATGAATATTCATACAATCATATCTTGTCATGGGT
CCCA
Found at i:25382 original size:20 final size:20
Alignment explanation
Indices: 25344--25383 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25334 ACAACCCAAC
*
25344 AACCAGGATTGGGTCTCACT
1 AACCAGGATTGGATCTCACT
*
25364 AACCAGGATTGGATTTCACT
1 AACCAGGATTGGATCTCACT
25384 TGTAAGAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.28
Consensus pattern (20 bp):
AACCAGGATTGGATCTCACT
Found at i:27457 original size:101 final size:102
Alignment explanation
Indices: 27251--27496 Score: 386
Period size: 101 Copynumber: 2.4 Consensus size: 102
27241 AATTCATCCT
* * * *
27251 TTACATTCGTAGTGCCATAACCCAGTTATGATTTTATCATCAGAATGCCATAGCCCAAGCTATGA
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTATTATCATCAGAATGCCATAGCCCAAGCTATGA
* *
27316 TCTTACATATAAACATTGCTATGGTCCAACCATGGTC
66 TCTTACATATAAACAATGCCATGGTCCAACCATGGTC
*
27353 TTACGTTCATAGTGCCATAACCCAGTTATGGTATTATCATTAGAATGCCATAGCCC-AGCTATGA
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTATTATCATCAGAATGCCATAGCCCAAGCTATGA
27417 TCTTACATATAAACAATGCCATGGTCCAACCATGGTC
66 TCTTACATATAAACAATGCCATGGTCCAACCATGGTC
* * *
27454 TTACGTTCATAATGCCATAACCTAGTTATGGTCTTATCCATCA
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTATTAT-CATCA
27497 ATTCATCATT
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
101 77 0.58
102 55 0.42
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (102 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTATTATCATCAGAATGCCATAGCCCAAGCTATGA
TCTTACATATAAACAATGCCATGGTCCAACCATGGTC
Found at i:36046 original size:14 final size:14
Alignment explanation
Indices: 36027--36053 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36017 AACAACATGA
36027 ATGATAATATATAC
1 ATGATAATATATAC
36041 ATGATAATATATA
1 ATGATAATATATA
36054 TAAAAAGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (14 bp):
ATGATAATATATAC
Found at i:38014 original size:66 final size:66
Alignment explanation
Indices: 37876--38059 Score: 196
Period size: 66 Copynumber: 2.8 Consensus size: 66
37866 CTAGTGAGTT
* * *
37876 TACTGACTTGGGTCACACGGCCAAGCCACATG-TCCGTGTGCTAGGCCGTGTGAAAAATAATGAG
1 TACTGACTTGTGTCACATGGCCAAGCCACACGCT-CGTGTGCTAGGCCGTGTGAAAAATAATGAG
37940 CA
65 CA
* * * * * * *
37942 TTCTGACTTGTGACACATGGCTAAGCCACACGCTCGTGTGCTAGGTCGTGTGAAAACTGGA-GGG
1 TACTGACTTGTGTCACATGGCCAAGCCACACGCTCGTGTGCTAGGCCGTGTGAAAAAT-AATGAG
*
38006 TA
65 CA
* *
38008 TACTGACTTGTGTCACATGGCCAA-CCACACAACT-GTGTGTTAGGCCGTGTGA
1 TACTGACTTGTGTCACATGGCCAAGCCACAC-GCTCGTGTGCTAGGCCGTGTGA
38060 GGCTACTGAC
Statistics
Matches: 98, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
65 22 0.22
66 74 0.76
67 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (66 bp):
TACTGACTTGTGTCACATGGCCAAGCCACACGCTCGTGTGCTAGGCCGTGTGAAAAATAATGAGC
A
Found at i:45190 original size:26 final size:26
Alignment explanation
Indices: 45159--45211 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
45149 CCCATTTTTT
* * *
45159 AATAAACATTAAAAAATTATTTTAAA
1 AATAAAAAATAAAAAAATATTTTAAA
45185 AATAAAAAATAAAAAAATATTTTAAA
1 AATAAAAAATAAAAAAATATTTTAAA
45211 A
1 A
45212 GTATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (26 bp):
AATAAAAAATAAAAAAATATTTTAAA
Found at i:55460 original size:10 final size:10
Alignment explanation
Indices: 55445--55493 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
55435 TCCAAGCTTG
55445 TTATAATTAA
1 TTATAATTAA
55455 TTATAATTAA
1 TTATAATTAA
*
55465 -AACT-ATTAA
1 TTA-TAATTAA
55474 -TATAATTAA
1 TTATAATTAA
55483 TTATAACTTAA
1 TTATAA-TTAA
55494 AAAATATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 1 0.03
9 12 0.36
10 16 0.48
11 4 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (10 bp):
TTATAATTAA
Found at i:59689 original size:14 final size:14
Alignment explanation
Indices: 59670--59697 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59660 GCGGATATTG
59670 ATCACTTATATTTA
1 ATCACTTATATTTA
59684 ATCACTTATATTTA
1 ATCACTTATATTTA
59698 CATTAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (14 bp):
ATCACTTATATTTA
Found at i:64740 original size:21 final size:20
Alignment explanation
Indices: 64715--64756 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
64705 AATTTAAAAT
64715 ATTTA-TTTATTTTAGTAGAAA
1 ATTTAGTTTATTTT--TAGAAA
64736 ATTTAGTTTATTTTTAGAAA
1 ATTTAGTTTATTTTTAGAAA
64756 A
1 A
64757 GCTGACGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (20 bp):
ATTTAGTTTATTTTTAGAAA
Found at i:66343 original size:3 final size:3
Alignment explanation
Indices: 66322--66369 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
66312 AAGCATAAAC
* * *
66322 TAA TAA AAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
66370 CATTGGAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:66482 original size:23 final size:23
Alignment explanation
Indices: 66464--66517 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
66454 TGTATACACG
66464 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATATATACTAA
* *
66487 TACATAATAATAATA-ATAGTAA
1 TACATAATAAAAATATATACTAA
66509 TAC-TAATAA
1 TACATAATAA
66518 TACTAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (23 bp):
TACATAATAAAAATATATACTAA
Found at i:66498 original size:3 final size:3
Alignment explanation
Indices: 66467--66532 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
66457 ATACACGTAC
* * * *
66467 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
66514 ATA ATA CTA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA A
66533 CAAGGATATT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:68525 original size:126 final size:126
Alignment explanation
Indices: 68344--68588 Score: 350
Period size: 126 Copynumber: 1.9 Consensus size: 126
68334 GACCCGAGGC
*
68344 TCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCC
1 TCAACCCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCC
*
68409 CCGAGGCTCAACTCACCTCTAGCAATATGAGCTGA-TTTTGAAAAAGTAGAAATTAAAAGGT
66 CCGAGGCTCAACTCACCTCTAGCAATATGAGCTGATTTTTGAAAAA-CAGAAATTAAAAGGT
** * ** * * *
68470 TCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAA-GTAGAATTTGAAAATACCTCGGCGTGC
1 TCAACCCACCTCTCGCAATATGAGTTGA-AATTAAAACACAAAAATTGAAAATACCTCAGCGTGC
* *
68534 CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
65 CCCGAGGCTCAACTCACCTCTAGCAATATGAGCTGATTTTTGAAAAACAGAAATT
68589 GAAATTACCT
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
126 90 0.86
127 15 0.14
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (126 bp):
TCAACCCACCTCTCGCAATATGAGTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCC
CCGAGGCTCAACTCACCTCTAGCAATATGAGCTGATTTTTGAAAAACAGAAATTAAAAGGT
Found at i:68559 original size:72 final size:73
Alignment explanation
Indices: 68470--69156 Score: 805
Period size: 74 Copynumber: 9.4 Consensus size: 73
68460 ATTAAAAGGT
* ** * * * *
68470 TCAACCCACCTCTCGCAATATGAGTTGATTTTTG-AAAGTAGAATTTGAAAATACCTCGGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGT
*
68534 CCCGAGGC
66 CCTGAGGC
68542 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGT
68607 CCTGAGGC
66 CCTGAGGC
*
68615 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGGAATTGAAAATA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC----A--G---A--AATTGAAATTA
* *
68680 CCTCAACGTGTCTTGAGGC
55 CCTCAGCGTGTCCTGAGGC
* * **
68699 TCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCTCAATGT
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTT-TTGAAAAACAGAAATTGAAATTACCTCAGCGT
*
68764 GTCTTGAGGC
64 GTCCTGAGGC
*
68774 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-ACAACAGAAATTGAAATTACCTCAGCGT
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTGAAATTACCTCAGCGT
68838 GTCCTGAGGC
64 GTCCTGAGGC
* *
68848 TCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATTGAAATTACCTCAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGT
68912 CCTGAGGC
66 CCTGAGGC
** *
68920 TCAACTCATTTCTCGCAATATGAGTTGATTTTTTTG-ACAACAGAAATTGAAATTACCTCAGCGT
1 TCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTGAAATTACCTCAGCGT
68984 GTCCTGAGGC
64 GTCCTGAGGC
* *
68994 TCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATTGAAATTACCTCAGC--GT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGT
69056 --T-AGGC
66 CCTGAGGC
* * * * * * *
69061 TCAACTCA--TCTCGCAATATGAG-TCA-ATTT--AAAACATAAACT-AAAATACCTCGGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGT
*
69119 CCCGAGGC
66 CCTGAGGC
*
69127 TCAACTCACTTCTCGCAATATGAGTTGATT
1 TCAACTCACCTCTCGCAATATGAGTTGATT
69157 AAAAATACCT
Statistics
Matches: 543, Mismatches: 43, Indels: 60
0.84 0.07 0.09
Matches are distributed among these distances:
61 11 0.02
62 10 0.02
63 1 0.00
64 5 0.01
65 13 0.02
66 12 0.02
67 12 0.02
68 15 0.03
69 2 0.00
70 2 0.00
71 10 0.02
72 118 0.22
73 71 0.13
74 120 0.22
75 65 0.12
76 4 0.01
77 2 0.00
79 1 0.00
80 1 0.00
82 2 0.00
84 55 0.10
85 3 0.01
86 8 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (73 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGT
CCTGAGGC
Found at i:68866 original size:74 final size:73
Alignment explanation
Indices: 68470--69156 Score: 782
Period size: 72 Copynumber: 9.4 Consensus size: 73
68460 ATTAAAAGGT
* ** * * * *
68470 TCAACCCACCTCTCGCAATATGAGTTGA-TTTTTGAAAGTAGAATTTGAAAATACCTCGGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGT
*
68534 CCCGAGGC
66 CCTGAGGC
68542 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAATTACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAACAGAAATTGAAATTACCTCAGCGTG
68606 TCCTGAGGC
65 TCCTGAGGC
*
68615 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACATAAATTGAACAGGAATTGAAAAT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAAC----A--G---A--AATTGAAATT
* *
68679 ACCTCAACGTGTCTTGAGGC
54 ACCTCAGCGTGTCCTGAGGC
* **
68699 TCAACTCACCTCTCGCAATATGAGTTGATTTTCTTGAAAAGCAGAAATTGAAAATACCTCAATGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTT-TTGAAAA-CAGAAATTGAAATTACCTCAGCGT
*
68764 GTCTTGAGGC
64 GTCCTGAGGC
*
68774 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
68839 TCCTGAGGC
65 TCCTGAGGC
* *
68848 TCAACTCACCTCTAGCAATATGAGTTGA--TTTTGAAAAACAAAAATTGAAATTACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAACAGAAATTGAAATTACCTCAGCGTG
68911 TCCTGAGGC
65 TCCTGAGGC
** *
68920 TCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTG
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
68985 TCCTGAGGC
65 TCCTGAGGC
* *
68994 TCAACTCACCTCTAGCAATATGAGTTGA--TTTTGAAAAACAAAAATTGAAATTACCTCAGC--G
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAACAGAAATTGAAATTACCTCAGCGTG
69055 T--T-AGGC
65 TCCTGAGGC
* * * * * * *
69061 TCAACTCA--TCTCGCAATATGAG-TCA--ATTT-AAAACATAAACT-AAAATACCTCGGCGTGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGT
*
69119 CCCGAGGC
66 CCTGAGGC
*
69127 TCAACTCACTTCTCGCAATATGAGTTGATT
1 TCAACTCACCTCTCGCAATATGAGTTGATT
69157 AAAAATACCT
Statistics
Matches: 544, Mismatches: 40, Indels: 63
0.84 0.06 0.10
Matches are distributed among these distances:
61 11 0.02
62 10 0.02
63 1 0.00
64 5 0.01
65 13 0.02
66 12 0.02
67 12 0.02
68 15 0.03
69 2 0.00
70 2 0.00
71 10 0.02
72 118 0.22
73 71 0.13
74 118 0.22
75 68 0.12
76 4 0.01
77 2 0.00
79 1 0.00
80 1 0.00
82 2 0.00
84 55 0.10
85 7 0.01
86 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (73 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGT
CCTGAGGC
Found at i:68950 original size:146 final size:143
Alignment explanation
Indices: 68663--69156 Score: 648
Period size: 146 Copynumber: 3.5 Consensus size: 143
68653 ACATAAATTG
* * * *
68663 AACAGGAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-
* * * **
68728 TTTCTTGAAAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAAT
65 -TT-TTGAAAAACAAAAATTGAAATTACCTCAGCGTGTC-TGAGGCTCAACTCA--TCTCGCAAT
68793 ATGAGTTGATTTTTTTGAC
125 ATGAGTTGATTTTTTTGAC
*
68812 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGAT
68877 TTTGAAAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATG
66 TTTGAAAAACAAAAATTGAAATTACCTCAGCGTGT-CTGAGGCTCAACTCA--TCTCGCAATATG
68942 AGTTGATTTTTTTGAC
128 AGTTGATTTTTTTGAC
*
68958 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGAT
69023 TTTGAAAAACAAAAATTGAAATTACCTCAGC--GT-T-AGGCTCAACTCATCTCGCAATATGAG-
66 TTTGAAAAACAAAAATTGAAATTACCTCAGCGTGTCTGAGGCTCAACTCATCTCGCAATATGAGT
* * *
69083 TCA---ATTT-AA
131 TGATTTTTTTGAC
* * * * * * *
69092 AACATAAACT-AAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGAT
69156 T
66 T
69157 AAAAATACCT
Statistics
Matches: 321, Mismatches: 23, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
133 49 0.15
134 9 0.03
135 3 0.01
138 2 0.01
139 14 0.04
141 12 0.04
142 1 0.00
144 2 0.01
146 167 0.52
147 3 0.01
149 59 0.18
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (143 bp):
AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGAT
TTTGAAAAACAAAAATTGAAATTACCTCAGCGTGTCTGAGGCTCAACTCATCTCGCAATATGAGT
TGATTTTTTTGAC
Done.