Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2065
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: 52098
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:9017 original size:26 final size:26
Alignment explanation
Indices: 8964--9017 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
8954 CATTTTTTTT
*
8964 TTTTTTTAACAAAACAAAATCTTAGA
1 TTTTTTTAACAAAACAAAATATTAGA
** * *
8990 TTTTTTTAATGAAATAAAATATTGGA
1 TTTTTTTAACAAAACAAAATATTAGA
9016 TT
1 TT
9018 GCTTTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (26 bp):
TTTTTTTAACAAAACAAAATATTAGA
Found at i:12789 original size:13 final size:13
Alignment explanation
Indices: 12771--12795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12761 CATAAAGTGT
12771 TGTATCGATACAA
1 TGTATCGATACAA
12784 TGTATCGATACA
1 TGTATCGATACA
12796 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12808 original size:19 final size:19
Alignment explanation
Indices: 12749--12814 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
12739 ATTTCAACGA
12749 TTTT-TATCGATACATAAAG
1 TTTTGTATCGATACAT-AAG
*
12768 TGTTGTATCGATAC--AA-
1 TTTTGTATCGATACATAAG
12784 ---TGTATCGATACATAAG
1 TTTTGTATCGATACATAAG
12800 TTTTGTATCGATACA
1 TTTTGTATCGATACA
12815 ATGTAAGCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 15 0.38
20 9 0.23
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (19 bp):
TTTTGTATCGATACATAAG
Found at i:12811 original size:32 final size:33
Alignment explanation
Indices: 12753--12819 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
12743 CAACGATTTT
12753 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACATAAAGTGTTGTATCGATACAATG
*
12786 TATCGATACAT-AAGTTTTGTATCGATACAATG
1 TATCGATACATAAAGTGTTGTATCGATACAATG
12818 TA
1 TA
12820 AGCTACTGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (33 bp):
TATCGATACATAAAGTGTTGTATCGATACAATG
Found at i:12875 original size:13 final size:13
Alignment explanation
Indices: 12857--12881 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12847 ATTACTCAAA
12857 TGTATCGATACAT
1 TGTATCGATACAT
12870 TGTATCGATACA
1 TGTATCGATACA
12882 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12934 original size:52 final size:52
Alignment explanation
Indices: 12890--13018 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
12880 CACTGATCTT
*
12890 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
12942 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
12994 TGTATCAATACAAGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
13019 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:14255 original size:21 final size:19
Alignment explanation
Indices: 14229--14271 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
14219 AATCCATGAA
*
14229 TCATGCATTTTGAGCTATGCT
1 TCATGCATTTAGAGC-ATG-T
14250 TCATGCATTTAGAGCATGT
1 TCATGCATTTAGAGCATGT
14269 TCA
1 TCA
14272 ACACCTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 3 0.14
21 14 0.67
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (19 bp):
TCATGCATTTAGAGCATGT
Found at i:16099 original size:326 final size:326
Alignment explanation
Indices: 15506--16153 Score: 1269
Period size: 326 Copynumber: 2.0 Consensus size: 326
15496 TTTATTCATC
15506 GGGGACACTCCAACCCCATTCCTCCGAGGGGACACTCCAACCCCGTTTTCAACCAAAAATTAAAT
1 GGGGACACTCCAACCCCATTCCTCCGAGGGGACACTCCAACCCCGTTTTCAACCAAAAATTAAAT
15571 TCCTTTTTCTCTCTCAAATTTCGAGTCAAACTCGTTTTCGAACTTCAATTAATCAGAGAATCCGG
66 TCCTTTTTCTCTCTCAAATTTCGAGTCAAACTCGTTTTCGAACTTCAATTAATCAGAGAATCCGG
15636 ACAAATCTCTCAGTTGTCAATTCGATTATCTCAAGATAATCGGTGGCAATTATGAGATACATTAC
131 ACAAATCTCTCAGTTGTCAATTCGATTATCTCAAGATAATCGGTGGCAATTATGAGATACATTAC
15701 GATTTTTACGTTTTGTTTCTTCTTCCTTGTTTAACCCAGGTAATTCATTTGCATGGAATATCATA
196 GATTTTTACGTTTTGTTTCTTCTTCCTTGTTTAACCCAGGTAATTCATTTGCATGGAATATCATA
*
15766 TGCTTCTATTGCCTTGTTAGCATGCTTCCTCCTTATTAATCTTGATGGCACTCATACTTTAATCT
261 TGCTTCTATTGCCTTGTTAGCATGCTTCCTCCTTATCAATCTTGATGGCACTCATACTTTAATCT
15831 T
326 T
15832 GGGGACACTCCAACCCCATTCCTCCGAGGGGACACTCCAACCCCGTTTTCAACCAAAAATTAAAT
1 GGGGACACTCCAACCCCATTCCTCCGAGGGGACACTCCAACCCCGTTTTCAACCAAAAATTAAAT
*
15897 TCCTTTTTCTCTCTCAAATTTCGAGTCAAACTCGTTTTCGAACTTCAATTAATTAGAGAATCCGG
66 TCCTTTTTCTCTCTCAAATTTCGAGTCAAACTCGTTTTCGAACTTCAATTAATCAGAGAATCCGG
*
15962 ACAAATCTCTCAGTTGTCAATTTGATTATCTCAAGATAATCGGTGGCAATTATGAGATACATTAC
131 ACAAATCTCTCAGTTGTCAATTCGATTATCTCAAGATAATCGGTGGCAATTATGAGATACATTAC
16027 GATTTTTACGTTTTGTTTCTTCTTCCTTGTTTAACCCAGGTAATTCATTTGCATGGAATATCATA
196 GATTTTTACGTTTTGTTTCTTCTTCCTTGTTTAACCCAGGTAATTCATTTGCATGGAATATCATA
16092 TGCTTCTATTGCCTTGTTAGCATGCTTCCTCCTTATCAATCTTGATGGCACTCATACTTTAA
261 TGCTTCTATTGCCTTGTTAGCATGCTTCCTCCTTATCAATCTTGATGGCACTCATACTTTAA
16154 AATTGGTTTA
Statistics
Matches: 319, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
326 319 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (326 bp):
GGGGACACTCCAACCCCATTCCTCCGAGGGGACACTCCAACCCCGTTTTCAACCAAAAATTAAAT
TCCTTTTTCTCTCTCAAATTTCGAGTCAAACTCGTTTTCGAACTTCAATTAATCAGAGAATCCGG
ACAAATCTCTCAGTTGTCAATTCGATTATCTCAAGATAATCGGTGGCAATTATGAGATACATTAC
GATTTTTACGTTTTGTTTCTTCTTCCTTGTTTAACCCAGGTAATTCATTTGCATGGAATATCATA
TGCTTCTATTGCCTTGTTAGCATGCTTCCTCCTTATCAATCTTGATGGCACTCATACTTTAATCT
T
Found at i:20485 original size:83 final size:82
Alignment explanation
Indices: 20347--20508 Score: 288
Period size: 83 Copynumber: 2.0 Consensus size: 82
20337 TCGAGAATAT
* *
20347 GTATGGTTGAGATTATTGGTTCACATGTTCAAAAAGAATATAATCTTTCAACAATTAAAGGGAGT
1 GTATGGTTGAGATTATTGGTTCACATGTTCAAAAAAAATATAATCTTTCAACAATTAAAAGGAGT
20412 CCAACAATTTTATATAC
66 CCAACAATTTTATATAC
*
20429 GTATGGTTGAGATTATTGGTTTCACATGTTCAAAAAAAATATAATCTTTCAACAATTAAAATGAG
1 GTATGGTTGAGATTATTGG-TTCACATGTTCAAAAAAAATATAATCTTTCAACAATTAAAAGGAG
20494 TCCAACAATTTTATA
65 TCCAACAATTTTATA
20509 CGAGGGTAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 19 0.25
83 57 0.75
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (82 bp):
GTATGGTTGAGATTATTGGTTCACATGTTCAAAAAAAATATAATCTTTCAACAATTAAAAGGAGT
CCAACAATTTTATATAC
Found at i:25292 original size:15 final size:15
Alignment explanation
Indices: 25272--25302 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25262 TAAAAATGTC
*
25272 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
25287 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
25302 C
1 C
25303 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:27351 original size:13 final size:13
Alignment explanation
Indices: 27333--27370 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
27323 CATTTTTCTT
27333 TGTATCGATACAA
1 TGTATCGATACAA
*
27346 TGTATCGATACAC
1 TGTATCGATACAA
27359 TGTATCGATACA
1 TGTATCGATACA
27371 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:29893 original size:20 final size:20
Alignment explanation
Indices: 29848--29899 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
29838 GTAGCCAAAC
**
29848 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
29868 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
29887 TTGTATCGATACA
1 TTGTATCGATACA
29900 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:31404 original size:21 final size:22
Alignment explanation
Indices: 31374--31423 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
31364 ATGTAAAAAG
*
31374 TTAAAATTAAATT-ATTTTAAT
1 TTAAAATTAAATTGATTTAAAT
*
31395 TTAAATTTAAATTGATTTAAAT
1 TTAAAATTAAATTGATTTAAAT
31417 TTAAAAT
1 TTAAAAT
31424 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAAAATTAAATTGATTTAAAT
Found at i:31412 original size:16 final size:16
Alignment explanation
Indices: 31390--31441 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
31380 TTAAATTATT
31390 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
*
31406 TTGATTTAAATTTAAA
1 TTAATTTAAATTTAAA
* *
31422 ATAATTTAAAATTAAA
1 TTAATTTAAATTTAAA
31438 TTAA
1 TTAA
31442 ATATAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:31450 original size:32 final size:32
Alignment explanation
Indices: 31391--31451 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
31381 TAAATTATTT
* * *
31391 TAATTTAAATTTAAATTGATTTAAATTTAAAA
1 TAATTTAAAATTAAATTAATATAAATTTAAAA
31423 TAATTTAAAATTAAATTAA-ATATAATTTA
1 TAATTTAAAATTAAATTAATATA-AATTTA
31452 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.08
32 23 0.92
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (32 bp):
TAATTTAAAATTAAATTAATATAAATTTAAAA
Found at i:31918 original size:15 final size:15
Alignment explanation
Indices: 31898--31938 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
31888 AATTACATTT
*
31898 AATAAAATAATAAAA
1 AATAAAAAAATAAAA
*
31913 ATTAAAAAAATAAAA
1 AATAAAAAAATAAAA
31928 AATAAAAAAAT
1 AATAAAAAAAT
31939 TAACAGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAAAAAAATAAAA
Found at i:31920 original size:7 final size:7
Alignment explanation
Indices: 31898--31936 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
31888 AATTACATTT
31898 AATAAAA
1 AATAAAA
31905 TAATAAAA
1 -AATAAAA
*
31913 ATTAAAAA
1 AAT-AAAA
31921 AATAAAA
1 AATAAAA
31928 AATAAAA
1 AATAAAA
31935 AA
1 AA
31937 ATTAACAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 15 0.54
8 13 0.46
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AATAAAA
Found at i:31937 original size:8 final size:8
Alignment explanation
Indices: 31901--31938 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
31891 TACATTTAAT
31901 AAAATAATA
1 AAAATAA-A
31910 AAAATTAAA
1 AAAA-TAAA
31919 AAAAT-AA
1 AAAATAAA
31926 AAAATAAA
1 AAAATAAA
31934 AAAAT
1 AAAAT
31939 TAACAGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.26
8 8 0.30
9 9 0.33
10 3 0.11
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAATAAA
Found at i:38528 original size:19 final size:20
Alignment explanation
Indices: 38504--38546 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
38494 ATACTCTCTC
*
38504 TCTCTTTCCTTCTTCT-TTT
1 TCTCTTTACTTCTTCTATTT
*
38523 TCTCTTTAGTTCTTCTATTT
1 TCTCTTTACTTCTTCTATTT
38543 TCTC
1 TCTC
38547 CCGATTCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.05, C:0.28, G:0.02, T:0.65
Consensus pattern (20 bp):
TCTCTTTACTTCTTCTATTT
Found at i:42869 original size:2 final size:2
Alignment explanation
Indices: 42862--42892 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
42852 AATAAATGAA
*
42862 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42893 AAACAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:42909 original size:26 final size:26
Alignment explanation
Indices: 42880--42931 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
42870 ATATATATAT
42880 ATATATAAATATAAAACAAGAAATCA
1 ATATATAAATATAAAACAAGAAATCA
*
42906 ATATATAAATATAAAGCAAGAAATCA
1 ATATATAAATATAAAACAAGAAATCA
42932 TGTGAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.23
Consensus pattern (26 bp):
ATATATAAATATAAAACAAGAAATCA
Found at i:43914 original size:20 final size:21
Alignment explanation
Indices: 43881--43920 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
43871 ATTAATCAAA
*
43881 TGAACTTGACTTTCTAAGCTT
1 TGAACTTGACTTTCAAAGCTT
*
43902 TGAA-TTGATTTTCAAAGCT
1 TGAACTTGACTTTCAAAGCT
43921 CATGTAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (21 bp):
TGAACTTGACTTTCAAAGCTT
Found at i:47045 original size:50 final size:50
Alignment explanation
Indices: 46986--47162 Score: 282
Period size: 50 Copynumber: 3.5 Consensus size: 50
46976 TTGATATAGA
* *
46986 GTCAACAATTATGGTCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTAGTGAAGAATC
* * * *
47036 GTCAACAATTATGACCACCTCCTTCTATTATCAAAAGTTAGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTAGTGAAGAATC
*
47086 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTTGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTAGTGAAGAATC
*
47136 GTCAACAATTATGGTCACCTCCCTCTA
1 GTCAACAATTATGGCCACCTCCCTCTA
47163 GGGCCTTAGC
Statistics
Matches: 115, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 115 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTAGTGAAGAATC
Found at i:50145 original size:20 final size:20
Alignment explanation
Indices: 50122--50160 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
50112 ATACTAAAAC
50122 ATTTTATAAA-AATTTTTGAT
1 ATTTTA-AAAGAATTTTTGAT
*
50142 ATTTTAAAAGGATTTTTGA
1 ATTTTAAAAGAATTTTTGA
50161 ACATGCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
ATTTTAAAAGAATTTTTGAT
Found at i:51609 original size:52 final size:51
Alignment explanation
Indices: 51531--51678 Score: 233
Period size: 51 Copynumber: 2.9 Consensus size: 51
51521 CGAACTATGA
*
51531 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTAGGC
* *
51583 AAATTTGCCTGCATGTATCGATACATTTATAATGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTAGGC
**
51634 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
51679 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 48 0.55
52 40 0.45
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTAGGC
Found at i:51685 original size:13 final size:13
Alignment explanation
Indices: 51667--51691 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51657 CAAAGATCAG
51667 TGTATCGATACAA
1 TGTATCGATACAA
51680 TGTATCGATACA
1 TGTATCGATACA
51692 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:51773 original size:13 final size:13
Alignment explanation
Indices: 51755--51779 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51745 AAAAAAAATA
51755 TGTATCGATACAT
1 TGTATCGATACAT
51768 TGTATCGATACA
1 TGTATCGATACA
51780 ATACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:52066 original size:50 final size:51
Alignment explanation
Indices: 51985--52098 Score: 142
Period size: 50 Copynumber: 2.2 Consensus size: 51
51975 ACAATCTAAA
*
51985 AACCATTTGACAATAAAAGGAGGTGACCATAATTGTTGACGA-TT-CTTCACC
1 AACC-TTTGACAATAAAAGGAGGTGACCATAA-TGTTAACGATTTGCTTCACC
* * ** *
52036 AACCTTTGACAATATAGGGAGGTGGTCATAATGTTAACGATTTGTTTCACC
1 AACCTTTGACAATAAAAGGAGGTGACCATAATGTTAACGATTTGCTTCACC
52087 AACCTTTGACAA
1 AACCTTTGACAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
49 8 0.15
50 25 0.45
51 22 0.40
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (51 bp):
AACCTTTGACAATAAAAGGAGGTGACCATAATGTTAACGATTTGCTTCACC
Done.