Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_24 ID=scaffold_24-JGI_221_v2.0
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: 80187
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.27
Warning! 16207 characters in sequence are not A, C, G, or T
Found at i:8676 original size:20 final size:20
Alignment explanation
Indices: 8651--8694 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
8641 ACAATATTTA
* *
8651 ATGTGGGAGTGGTTTGTTTG
1 ATGTGGGAGTGATTTGGTTG
8671 ATGTGGGAGTGATTTGGTTG
1 ATGTGGGAGTGATTTGGTTG
8691 ATGT
1 ATGT
8695 TTAGGCTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (20 bp):
ATGTGGGAGTGATTTGGTTG
Found at i:11590 original size:42 final size:42
Alignment explanation
Indices: 11539--11635 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
11529 ACGGCCAAAC
* * *
11539 CACATGCCCGTG-CGCATGGCCGTGTGTCACACACGGCTGAGA
1 CACACGCCCGTGTCGC-TGCCCGTATGTCACACACGGCTGAGA
* * *
11581 TACACGCCCGTGTCTCTGCCCGTATGTCACACATGGCTGAGA
1 CACACGCCCGTGTCGCTGCCCGTATGTCACACACGGCTGAGA
*
11623 CACATGCCCGTGT
1 CACACGCCCGTGT
11636 GGACAAAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.19, C:0.34, G:0.27, T:0.21
Consensus pattern (42 bp):
CACACGCCCGTGTCGCTGCCCGTATGTCACACACGGCTGAGA
Found at i:15273 original size:21 final size:20
Alignment explanation
Indices: 15236--15276 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
15226 CTCTTAGGTT
15236 TTTAAAAAATATGTATTTTA
1 TTTAAAAAATATGTATTTTA
* *
15256 TTTATAAAAGTATTTATTTTA
1 TTTA-AAAAATATGTATTTTA
15277 ATAAATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTAAAAAATATGTATTTTA
Found at i:16186 original size:2 final size:2
Alignment explanation
Indices: 16179--16204 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16169 AGTATACTCC
16179 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
16205 GGGAGATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18859 original size:38 final size:38
Alignment explanation
Indices: 18779--18852 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
18769 GTTATTGCTG
* ** * * *
18779 CTACTGCTTTTGTTTTATTGATTGCATGTTCAGCATAC
1 CTACTGCTTCTGTTAAACTGATTGCATGATAAGCATAC
18817 CTACTGCTTCTGTTAAACTGATTGCATGATAAGCAT
1 CTACTGCTTCTGTTAAACTGATTGCATGATAAGCAT
18853 GACTACTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (38 bp):
CTACTGCTTCTGTTAAACTGATTGCATGATAAGCATAC
Found at i:20754 original size:17 final size:17
Alignment explanation
Indices: 20718--20751 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20708 ATAAAAAATA
*
20718 AAAGTCCATTTACAATT
1 AAAGTCCAATTACAATT
20735 AAAGTCCAAATTACAAT
1 AAAGTCC-AATTACAAT
20752 AAACCCGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (17 bp):
AAAGTCCAATTACAATT
Found at i:21860 original size:21 final size:22
Alignment explanation
Indices: 21784--21860 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
21774 AGTCCTTCTG
* * *
21784 TTATTATTTTATTTTATTATGTA
1 TTATTATTTTAATTT-TCATATA
*
21807 ATATTATTTTAAGTTTTTCATATA
1 TTATTATTTTAA--TTTTCATATA
21831 TTA-TATTTTAA-TTTCATA-A
1 TTATTATTTTAATTTTCATATA
21850 TGTATTATTTT
1 T-TATTATTTT
21861 GTTTTTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.04
20 9 0.20
21 6 0.13
23 18 0.40
24 7 0.16
25 3 0.07
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.64
Consensus pattern (22 bp):
TTATTATTTTAATTTTCATATA
Found at i:22177 original size:12 final size:12
Alignment explanation
Indices: 22156--22188 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
22146 TTGTTTTAAC
*
22156 TATTACATATAT
1 TATTATATATAT
22168 TATTATATATAT
1 TATTATATATAT
22180 TATT-TATAT
1 TATTATATAT
22189 TGAGTGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATATATAT
Found at i:25510 original size:20 final size:20
Alignment explanation
Indices: 25487--25527 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
25477 ATGTTTAATA
*
25487 TGGGAGTGGTTTGTTTGATG
1 TGGGAGTGGTTTGGTTGATG
25507 TGGGAGTGGTTTGGTTGATG
1 TGGGAGTGGTTTGGTTGATG
25527 T
1 T
25528 TTAGGCTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.46, T:0.44
Consensus pattern (20 bp):
TGGGAGTGGTTTGGTTGATG
Found at i:30408 original size:3 final size:3
Alignment explanation
Indices: 30402--30440 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
30392 ATTAATCTTG
30402 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
30441 GGTATTAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30776 original size:17 final size:17
Alignment explanation
Indices: 30756--30788 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30746 TATAACTTAT
30756 TTATATATATATGTATG
1 TTATATATATATGTATG
*
30773 TTATATCTATATGTAT
1 TTATATATATATGTAT
30789 ATATGCATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (17 bp):
TTATATATATATGTATG
Found at i:30987 original size:35 final size:33
Alignment explanation
Indices: 30910--30987 Score: 77
Period size: 35 Copynumber: 2.2 Consensus size: 33
30900 AATATACCCC
* *
30910 TTTTTTACATACATAGTTTTTATATTTTATGAT
1 TTTTATACATACATAGTTTTTATATTTTATGAA
*
30943 TTGTATATACATACATATTTTTTCATATATTTTAT-AA
1 TT-T-TATACATACATA-GTTTT--TATATTTTATGAA
30980 TTTTATAC
1 TTTTATAC
30988 TTCATAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
33 2 0.05
34 1 0.03
35 16 0.43
36 5 0.14
37 3 0.08
38 10 0.27
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.58
Consensus pattern (33 bp):
TTTTATACATACATAGTTTTTATATTTTATGAA
Found at i:33264 original size:45 final size:43
Alignment explanation
Indices: 33161--33322 Score: 134
Period size: 44 Copynumber: 3.7 Consensus size: 43
33151 TTTTAATCCT
* * **
33161 CTCCACTGCAACTTCAAGGAGATAGGATTATTGC-C-TTTAACCTG
1 CTCCACTGCAACTTC-AGGAGATAAGA--CTTGCTCATTTAGTCTG
* **
33205 CTCCATTGCAACTTCAGGGAGATAAGGTTTGC-CATCTTCAGTCTG
1 CTCCACTGCAACTTCA-GGAGATAAGACTTGCTCAT-TT-AGTCTG
* *
33250 C-CTCACTGCAACTTCAAGAGGATAAGACTTGCTTATTTAGTCTG
1 CTC-CACTGCAACTTCAGGA-GATAAGACTTGCTCATTTAGTCTG
33294 CTCCACTGCAACTTCAAGGAGATAAGACT
1 CTCCACTGCAACTTC-AGGAGATAAGACT
33323 AGATGGGATC
Statistics
Matches: 97, Mismatches: 12, Indels: 18
0.76 0.09 0.14
Matches are distributed among these distances:
42 5 0.05
43 2 0.02
44 55 0.57
45 33 0.34
46 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGAGATAAGACTTGCTCATTTAGTCTG
Found at i:34230 original size:25 final size:27
Alignment explanation
Indices: 34202--34257 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 27
34192 AAGTGTCTTG
34202 AAAGAAAAAAGTATTT-AAGAA-CAAC
1 AAAGAAAAAAGTATTTAAAGAACCAAC
*
34227 AAAGAATAAAGTATTTACAAGAACCAAC
1 AAAGAAAAAAGTATTTA-AAGAACCAAC
34255 AAA
1 AAA
34258 CTCGGTACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 15 0.56
27 5 0.19
28 7 0.26
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (27 bp):
AAAGAAAAAAGTATTTAAAGAACCAAC
Found at i:41579 original size:24 final size:24
Alignment explanation
Indices: 41550--41595 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41540 ATCACTTTTT
*
41550 GCTGCTCATTCATTTACTTTTGAA
1 GCTGCTCATGCATTTACTTTTGAA
* *
41574 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTACTTTTG
41596 GAACTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTACTTTTGAA
Found at i:51232 original size:30 final size:30
Alignment explanation
Indices: 51196--51256 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
51186 TTGAGTTATG
51196 AGATATGAGAATGTTTGACTGAATGATATA
1 AGATATGAGAATGTTTGACTGAATGATATA
51226 AGATATGAGAATGTTTGACTGAATGATATA
1 AGATATGAGAATGTTTGACTGAATGATATA
51256 A
1 A
51257 TGTGTTGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (30 bp):
AGATATGAGAATGTTTGACTGAATGATATA
Found at i:57001 original size:15 final size:15
Alignment explanation
Indices: 56981--57030 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
56971 AAATAAATAC
56981 TGAATGATAAACAAT
1 TGAATGATAAACAAT
*
56996 TGAATGGAGGAAAC---
1 TGAAT-GA-TAAACAAT
57010 TGAATGATAAACAAT
1 TGAATGATAAACAAT
57025 TGAATG
1 TGAATG
57031 GAGGAAGCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
12 4 0.14
13 2 0.07
14 5 0.18
15 11 0.39
16 2 0.07
17 4 0.14
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.24
Consensus pattern (15 bp):
TGAATGATAAACAAT
Found at i:57011 original size:29 final size:29
Alignment explanation
Indices: 56979--57036 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
56969 TGAAATAAAT
56979 ACTGAATGATAAACAATTGAATGGAGGAA
1 ACTGAATGATAAACAATTGAATGGAGGAA
57008 ACTGAATGATAAACAATTGAATGGAGGAA
1 ACTGAATGATAAACAATTGAATGGAGGAA
57037 GCGGAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.07, G:0.24, T:0.21
Consensus pattern (29 bp):
ACTGAATGATAAACAATTGAATGGAGGAA
Found at i:59444 original size:53 final size:53
Alignment explanation
Indices: 59369--59631 Score: 303
Period size: 53 Copynumber: 4.9 Consensus size: 53
59359 GACATTTAAG
* * * * *
59369 GACCATATCATGTAAGATCGTAACTGGTGAGTTATGACATCATAAGGGAAGGA
1 GACCATATCATGTAAAACCGTAACTGGTGGGTTATGACATCATATGGGAAGAA
* * * *
59422 GACAATATCATGTAAAACCGTAACTAGTGGGTTATGGCATCATATGGAAAGAA
1 GACCATATCATGTAAAACCGTAACTGGTGGGTTATGACATCATATGGGAAGAA
* * * * * *
59475 TACCATATCGTGTAAGATCGTAATTGGTGGGTTATGACATCATATGAGAAGAA
1 GACCATATCATGTAAAACCGTAACTGGTGGGTTATGACATCATATGGGAAGAA
* * * *
59528 AACCATATCATGTAAAACCATAACTTGTGGGTTATGGCATCATATGGGAAGAA
1 GACCATATCATGTAAAACCGTAACTGGTGGGTTATGACATCATATGGGAAGAA
* * *
59581 GCCCATATCATGTAAAACCATAATTGGTGGGTTATGGA-ATCATATGAGGAA
1 GACCATATCATGTAAAACCGTAACTGGTGGGTTAT-GACATCATATG-GGAA
59632 ATTTAATTTT
Statistics
Matches: 175, Mismatches: 33, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
53 170 0.97
54 5 0.03
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (53 bp):
GACCATATCATGTAAAACCGTAACTGGTGGGTTATGACATCATATGGGAAGAA
Found at i:59558 original size:106 final size:106
Alignment explanation
Indices: 59369--59628 Score: 360
Period size: 106 Copynumber: 2.5 Consensus size: 106
59359 GACATTTAAG
* * * * * *
59369 GACCATATCATGTAAGATCGTAACTGGTGAGTTATGACATCATAAGGGAAGGAGACAATATCATG
1 GACCATATCATGTAAGATCGTAATTGGTGGGTTATGACATCATATGAGAAGAAAACAATATCATG
*
59434 TAAAACCGTAACTAGTGGGTTATGGCATCATATGGAAAGAA
66 TAAAACCATAACTAGTGGGTTATGGCATCATATGGAAAGAA
* * *
59475 TACCATATCGTGTAAGATCGTAATTGGTGGGTTATGACATCATATGAGAAGAAAACCATATCATG
1 GACCATATCATGTAAGATCGTAATTGGTGGGTTATGACATCATATGAGAAGAAAACAATATCATG
* *
59540 TAAAACCATAACTTGTGGGTTATGGCATCATATGGGAAGAA
66 TAAAACCATAACTAGTGGGTTATGGCATCATATGGAAAGAA
* * * *
59581 GCCCATATCATGTAAAACCATAATTGGTGGGTTATGGA-ATCATATGAG
1 GACCATATCATGTAAGATCGTAATTGGTGGGTTAT-GACATCATATGAG
59629 GAAATTTAAT
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
106 133 0.99
107 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.27
Consensus pattern (106 bp):
GACCATATCATGTAAGATCGTAATTGGTGGGTTATGACATCATATGAGAAGAAAACAATATCATG
TAAAACCATAACTAGTGGGTTATGGCATCATATGGAAAGAA
Found at i:62685 original size:41 final size:40
Alignment explanation
Indices: 62622--62894 Score: 285
Period size: 41 Copynumber: 6.6 Consensus size: 40
62612 ATTTGAATGT
* * * *
62622 AAGGGGTTGCTAAGTGCAGATTCCTCGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGAT-TAA
* * *
62663 AAGGGGTTGCTATGTGCTGATTCCTCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
* * *
62703 AAGGTGGTTGCTAAGTGCCGATTCCACCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-T-TAA
* * * *
62747 AAGGGGTTGCTATGTGCTGATTCCCGGAATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
* *
62787 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-T-TAA
* * *
62831 AAGGGGTTGCTATGTGTTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
62871 AAGGTGGTTGCTAAGTGCTGATTC
1 AAGG-GGTTGCTAAGTGCTGATTC
62895 GACCGGGATC
Statistics
Matches: 192, Mismatches: 31, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
40 15 0.08
41 90 0.47
42 39 0.20
43 38 0.20
44 10 0.05
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
Found at i:62765 original size:84 final size:83
Alignment explanation
Indices: 62662--62899 Score: 413
Period size: 84 Copynumber: 2.8 Consensus size: 83
62652 CATTGATCAA
*
62662 AAAGGGGTTGCTATGTGCTGATTCCTCGTATCATTGATTATAAGGTGGTTGCTAAGTGCCGATTC
1 AAAGGGGTTGCTATGTGCTGATTCC-CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
62727 CACCGTATCCTTGATTGTG
65 CACCGTATCCTTGATTGTG
*
62746 AAAGGGGTTGCTATGTGCTGATTCCCGGAATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCC-GTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
62811 CACCGTATCCTTGATTGTG
65 CACCGTATCCTTGATTGTG
*
62830 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATT-CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
*
62895 GACCG
65 CACCG
62900 GGATCCTTTG
Statistics
Matches: 147, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
83 1 0.01
84 143 0.97
85 3 0.02
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (83 bp):
AAAGGGGTTGCTATGTGCTGATTCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCC
ACCGTATCCTTGATTGTG
Found at i:62880 original size:125 final size:124
Alignment explanation
Indices: 62621--62942 Score: 341
Period size: 125 Copynumber: 2.6 Consensus size: 124
62611 TATTTGAATG
* * *
62621 TAAGGGGTTGCTAAGTGCAGATTCCTC-GAATCATTGATCAAAAAGG-GGTTGCTATGTGCTGAT
1 TAAGGGGTTGCTAAGTGCTGATTCC-CGGAATCATTGAT-AATAAGGTGGTTGCTAAGTGCTGAT
* * *
62684 TCC-TCGTATCATTGATTATAAGGTGGTTGCTAAGTGCCGATTCCACCGTATCCTTGATTG
64 TCCACCGTATCATTGATTATAAGGTGGTTGCTAAGTGCCGATTCCACCGTATCATTGATTA
* *
62744 TGAAAGGGGTTGCTATGTGCTGATTCCCGGAATCATTGATTATAAGGTGGTTGCTAAGTGCTGAT
1 T--AAGGGGTTGCTAAGTGCTGATTCCCGGAATCATTGATAATAAGGTGGTTGCTAAGTGCTGAT
* * * **
62809 TCCACCGTATCCTTGATTGTGAAAGG-GGTTGCTATGTGTTGATTCC-CCGTATCATTGATTA
64 TCCACCGTATCATTGATTAT--AAGGTGGTTGCTAAGTGCCGATTCCACCGTATCATTGATTA
* * * * *
62870 TAAGGTGGTTGCTAAGTGCTGATTCGACCGGGATCCTTTGA-ACATGAGATGGTTGCTAAGTGTT
1 TAAGG-GGTTGCTAAGTGCTGATTC--CCGGAAT-CATTGATA-ATAAGGTGGTTGCTAAGTGCT
62934 GATTCCACC
61 GATTCCACC
62943 ATATAATGGT
Statistics
Matches: 167, Mismatches: 20, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
123 1 0.01
124 10 0.06
125 70 0.42
126 27 0.16
127 23 0.14
128 36 0.22
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (124 bp):
TAAGGGGTTGCTAAGTGCTGATTCCCGGAATCATTGATAATAAGGTGGTTGCTAAGTGCTGATTC
CACCGTATCATTGATTATAAGGTGGTTGCTAAGTGCCGATTCCACCGTATCATTGATTA
Found at i:64091 original size:15 final size:16
Alignment explanation
Indices: 64058--64094 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
64048 GAAATAGGAA
64058 ATTTTTAAGTTAGGGGT
1 ATTTTTAAGTTA-GGGT
64075 ATTTTTAAGTT-GGGT
1 ATTTTTAAGTTAGGGT
64090 ATTTT
1 ATTTT
64095 GGTAATTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (16 bp):
ATTTTTAAGTTAGGGT
Found at i:73733 original size:29 final size:28
Alignment explanation
Indices: 73622--73750 Score: 132
Period size: 28 Copynumber: 4.5 Consensus size: 28
73612 TGGCTATATT
* **
73622 TATTAAAGGAAGTCTTTATGAAGATCTC
1 TATTAAAGGAAGCCTTTATGGCGATCTC
* * * *
73650 TGTTAAAGGAAGCCTTTGTGCCTATCTC
1 TATTAAAGGAAGCCTTTATGGCGATCTC
* * **
73678 TGTTAAAGGAAGCCTTTGTGGTTATCTC
1 TATTAAAGGAAGCCTTTATGGCGATCTC
73706 TATTAAAAGGAAGCCTTTATGGCGATCTC
1 TATT-AAAGGAAGCCTTTATGGCGATCTC
73735 TATTAAAAAGGAAGCC
1 TATT--AAAGGAAGCC
73751 ATTGTTGCAG
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
28 51 0.59
29 25 0.29
30 11 0.13
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (28 bp):
TATTAAAGGAAGCCTTTATGGCGATCTC
Done.