Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_399
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: 79344
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1856 original size:10 final size:10
Alignment explanation
Indices: 1841--1921 Score: 53
Period size: 8 Copynumber: 9.3 Consensus size: 10
1831 TTATTGATTA
1841 ATATATATAT
1 ATATATATAT
*
1851 ATATATTTA-
1 ATATATATAT
1860 ATA-AT-TA-
1 ATATATATAT
1867 AGTATAT-TAT
1 A-TATATATAT
1877 AT-TATAT-T
1 ATATATATAT
1885 ATAT-TATAT
1 ATATATATAT
1894 -TATAT-TAT
1 ATATATATAT
1902 AT-TATAT-T
1 ATATATATAT
1910 ATAT-TATAT
1 ATATATATAT
1919 ATA
1 ATA
1922 AAAGAAACAA
Statistics
Matches: 59, Mismatches: 1, Indels: 23
0.71 0.01 0.28
Matches are distributed among these distances:
7 3 0.05
8 28 0.47
9 19 0.32
10 9 0.15
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (10 bp):
ATATATATAT
Found at i:1879 original size:5 final size:5
Alignment explanation
Indices: 1869--1918 Score: 100
Period size: 5 Copynumber: 10.0 Consensus size: 5
1859 AATAATTAAG
1869 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1919 ATAAAAGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:3062 original size:6 final size:6
Alignment explanation
Indices: 3043--3073 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3033 GTGTGTCGAA
*
3043 TACTGT TACCGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
3074 TCAGATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:3889 original size:18 final size:17
Alignment explanation
Indices: 3850--3909 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 17
3840 CGAAATTTAT
*
3850 AAAAAAAAGAAATAAAA
1 AAAAAAAAGAAATAATA
3867 GAAAAGAAAAGAAATAATA
1 -AAAA-AAAAGAAATAATA
3886 AAAATAAAA-ATAATAATA
1 AAAA-AAAAGA-AATAATA
3904 ATAAAA
1 A-AAAA
3910 TTGGAATACT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 1 0.03
18 21 0.57
19 15 0.41
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (17 bp):
AAAAAAAAGAAATAATA
Found at i:3898 original size:15 final size:15
Alignment explanation
Indices: 3878--3909 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3868 AAAAGAAAAG
3878 AAATAATAAAAATAA
1 AAATAATAAAAATAA
*
3893 AAATAATAATAATAA
1 AAATAATAAAAATAA
3908 AA
1 AA
3910 TTGGAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AAATAATAAAAATAA
Found at i:4181 original size:47 final size:46
Alignment explanation
Indices: 4127--4291 Score: 158
Period size: 47 Copynumber: 3.5 Consensus size: 46
4117 GTGCCGATGC
*
4127 CATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTAATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTATCATAGTATGGCCAATG
* * *
4174 CATGTCCCAGACATGTCTTACACTAGCCCTCGTC-TAG-AT-GCCGATG
1 CATGTCCCAGACATGTCTTACACT-G-GCT-ATCATAGTATGGCCAATG
* * * * *
4220 CCATGTCCCAGACATGGTCTTACTCTAGCTCTCATAATGTGGCCGAA-G
1 -CATGTCCCAGACAT-GTCTTACACTGGCTATCATAGTATGGCC-AATG
4268 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
4292 AGCGCACAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
45 2 0.02
46 28 0.29
47 46 0.47
48 18 0.19
49 3 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTATCATAGTATGGCCAATG
Found at i:4279 original size:94 final size:94
Alignment explanation
Indices: 4118--4294 Score: 284
Period size: 94 Copynumber: 1.9 Consensus size: 94
4108 CTCATCTCTG
* * *
4118 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATAGTATGGCTAATGCATGTCCCA
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATAATATGGCGAATGCATGTCCCA
4183 GACATGTCTTACACTAGCCCTCGTCTAGA
66 GACATGTCTTACACTAGCCCTCGTCTAGA
* * *
4212 TGCCGATGCCATGTCCCAGACATGGTCTTACTCTAGCTCTCATAATGTGGCCGAA-GCATGTCCC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATAATATGG-CGAATGCATGTCCC
4276 AGACATGTCTTACACTAGC
65 AGACATGTCTTACACTAGC
4295 GCACAAATCA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
94 73 0.96
95 3 0.04
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (94 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATAATATGGCGAATGCATGTCCCA
GACATGTCTTACACTAGCCCTCGTCTAGA
Found at i:21743 original size:27 final size:27
Alignment explanation
Indices: 21712--21799 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
21702 CATCCACATG
21712 ACAGACTTCACCACAAAGGTGCATTTA
1 ACAGACTTCACCACAAAGGTGCATTTA
* * * *
21739 ACAGAATT-AGCCACAAGGGCTCACATATA
1 ACAGACTTCA-CCACAAAGG-T-GCATTTA
* * *
21768 ACATACTTCACCACAAAGGCGCATTTG
1 ACAGACTTCACCACAAAGGTGCATTTA
21795 ACAGA
1 ACAGA
21800 ATTAGCCACA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
26 1 0.02
27 23 0.51
28 1 0.02
29 19 0.42
30 1 0.02
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (27 bp):
ACAGACTTCACCACAAAGGTGCATTTA
Found at i:21776 original size:56 final size:56
Alignment explanation
Indices: 21716--21832 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 56
21706 CACATGACAG
*
21716 ACTTCACCACAAAGGTGCATTTAACAGAATTAGCCACAAGGGCTCACATATAACAT
1 ACTTCACCACAAAGGCGCATTTAACAGAATTAGCCACAAGGGCTCACATATAACAT
* *
21772 ACTTCACCACAAAGGCGCATTTGACAGAATTAGCCACAAGGGCTCACATATATCAT
1 ACTTCACCACAAAGGCGCATTTAACAGAATTAGCCACAAGGGCTCACATATAACAT
21828 ACTTC
1 ACTTC
21833 CCTACTAAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (56 bp):
ACTTCACCACAAAGGCGCATTTAACAGAATTAGCCACAAGGGCTCACATATAACAT
Found at i:21781 original size:29 final size:30
Alignment explanation
Indices: 21747--21832 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 30
21737 TAACAGAATT
21747 AGCCACAAGGGCTCACATATAACATACTTC
1 AGCCACAAGGGCTCACATATAACATACTTC
* * * * * *
21777 A-CCACAAAGG--CGCATTTGACAGAATT-
1 AGCCACAAGGGCTCACATATAACATACTTC
*
21803 AGCCACAAGGGCTCACATATATCATACTTC
1 AGCCACAAGGGCTCACATATAACATACTTC
21833 CCTACTAAGA
Statistics
Matches: 39, Mismatches: 13, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
26 1 0.03
27 19 0.49
29 18 0.46
30 1 0.03
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (30 bp):
AGCCACAAGGGCTCACATATAACATACTTC
Found at i:21810 original size:27 final size:27
Alignment explanation
Indices: 21722--21810 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
21712 ACAGACTTCA
*
21722 CCACAAAGGTGCATTTAACAGAATTAG
1 CCACAAAGGCGCATTTAACAGAATTAG
* * * * *
21749 CCACAAGGGCTCACATATAACATACTTCA-
1 CCACAAAGG--CGCATTTAACAGAATT-AG
*
21778 CCACAAAGGCGCATTTGACAGAATTAG
1 CCACAAAGGCGCATTTAACAGAATTAG
21805 CCACAA
1 CCACAA
21811 GGGCTCACAT
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
26 1 0.02
27 25 0.54
29 19 0.41
30 1 0.02
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (27 bp):
CCACAAAGGCGCATTTAACAGAATTAG
Found at i:25341 original size:10 final size:10
Alignment explanation
Indices: 25309--25342 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
25299 CGTTTTATCC
25309 CTTTTTGGCT
1 CTTTTTGGCT
25319 CATTTTTGGCT
1 C-TTTTTGGCT
*
25330 CTTTTTGACT
1 CTTTTTGGCT
25340 CTT
1 CTT
25343 GGTGCTCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.06, C:0.21, G:0.15, T:0.59
Consensus pattern (10 bp):
CTTTTTGGCT
Found at i:30038 original size:38 final size:38
Alignment explanation
Indices: 29994--30070 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
29984 AAGCAATATA
29994 TGTCTATAGGCCTTTAGCACACTACCCGCAATATTTTT
1 TGTCTATAGGCCTTTAGCACACTACCCGCAATATTTTT
30032 TGTCTATAGGCCTTTAGCACACTACCCGCAATATTTTT
1 TGTCTATAGGCCTTTAGCACACTACCCGCAATATTTTT
30070 T
1 T
30071 TTCTCTTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (38 bp):
TGTCTATAGGCCTTTAGCACACTACCCGCAATATTTTT
Found at i:34753 original size:20 final size:20
Alignment explanation
Indices: 34724--34768 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
34714 AGCACATGTA
* *
34724 TTCATAAAATTTTATAATTT
1 TTCATAAAATTTTACAACTT
*
34744 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
34764 TTCAT
1 TTCAT
34769 TTTAGCCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:35841 original size:15 final size:16
Alignment explanation
Indices: 35813--35842 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35803 ACATATCATT
35813 TATTTCATTATACCAA
1 TATTTCATTATACCAA
35829 TATTTCA-TATACCA
1 TATTTCATTATACCA
35843 TAGTTCCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.20, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTTCATTATACCAA
Found at i:37789 original size:30 final size:30
Alignment explanation
Indices: 37755--37815 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
37745 TCCTTAACTC
37755 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
37785 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
37815 A
1 A
37816 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:39519 original size:22 final size:21
Alignment explanation
Indices: 39492--39534 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39482 ATATTATATT
*
39492 ATAATAAATAAATAAAAGAAAA
1 ATAATAAA-AAATAAAACAAAA
*
39514 ATAATAAAAAATGAAACAAAA
1 ATAATAAAAAATAAAACAAAA
39535 CATAGAAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (21 bp):
ATAATAAAAAATAAAACAAAA
Found at i:39617 original size:37 final size:36
Alignment explanation
Indices: 39567--39640 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 36
39557 GAAAAAAAGG
39567 AAAGAAAAAAGGAGAATTAGGGTTTTAATGGTTCAA
1 AAAGAAAAAAGGAGAATTAGGGTTTTAATGGTTCAA
39603 AAAGAAAAAAAGGAGAATTAGGGTTTTAATGGTTCAA
1 AAAG-AAAAAAGGAGAATTAGGGTTTTAATGGTTCAA
39640 A
1 A
39641 GCTCAATTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 4 0.11
37 33 0.89
ACGTcount: A:0.49, C:0.03, G:0.24, T:0.24
Consensus pattern (36 bp):
AAAGAAAAAAGGAGAATTAGGGTTTTAATGGTTCAA
Found at i:42034 original size:47 final size:47
Alignment explanation
Indices: 41969--42245 Score: 213
Period size: 47 Copynumber: 5.6 Consensus size: 47
41959 GCATTGGCAC
* *
41969 TAAGACAAGGATACCATGTAAGACCATGTTTGGAATATGGCATTTGG
1 TAAGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *** *
42016 TAAGATAAGGATATCATGTAAGACCATGCCAAGG--CATGGCATTGATAAGTTCTA
1 TAAGATAAGGATACCATGTAAGACCATG-TTTGGAACATGGCATT--T--G----G
*
42070 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *** * *
42117 TAAGATAAGGATATCATGTAAGACCATGCCAAGG--TATGGCA-TTGA
1 TAAGATAAGGATACCATGTAAGACCATG-TTTGGAACATGGCATTTGG
42162 TAAGTTCTATAAGACAATGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAG----ATAAG-----GATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
42218 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGATAAGGATACCATGTAAGACCATG
42246 CCAAGGCATG
Statistics
Matches: 179, Mismatches: 27, Indels: 48
0.70 0.11 0.19
Matches are distributed among these distances:
45 7 0.04
46 14 0.08
47 70 0.39
48 5 0.03
49 5 0.03
50 1 0.01
51 1 0.01
52 5 0.03
53 5 0.03
54 44 0.25
55 15 0.08
56 7 0.04
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (47 bp):
TAAGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:42095 original size:101 final size:101
Alignment explanation
Indices: 41969--42516 Score: 663
Period size: 101 Copynumber: 5.3 Consensus size: 101
41959 GCATTGGCAC
*
41969 TAAGACAAGGATACCATGTAAGACCATGTTTGGAATATGGCATTTGGTAAGATAAGGATATCATG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATG
42034 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
66 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
42070 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATG
*
42135 TAAGACCATGCCAAGGTATGGCATTGATAAGTTCTA
66 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
*
42171 TAAGACAATGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATG
42236 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
66 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
* * * * *** ** *
42272 TAAGGCAAGGAAATCATGGAAGACCATGTCAAG-ACATGGCATTGATGAGTTATTATAAGGCAAA
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATT--TG-G-TAAGATAAGG-ATA
* * *
42336 GGTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGCTC-A
61 --T--CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
* *** ** *
42380 TAAGGCAAGGATACCATGTAAGACCATGTCAAG-ACATGGCATTGATGAGTTACTATAAGGCAAA
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATT--TG-G-TAAGATAAGG-ATA
*
42444 GGTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTC-A
61 --T--CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
* **
42488 TAAGGCAAGGATACCACATAAGACCATGT
1 TAAGACAAGGATACCATGTAAGACCATGT
42517 CAAGACATGG
Statistics
Matches: 412, Mismatches: 26, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
100 10 0.02
101 223 0.54
102 2 0.00
103 1 0.00
104 8 0.02
105 2 0.00
107 1 0.00
108 130 0.32
109 35 0.08
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (101 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATATCATG
TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
Found at i:42416 original size:108 final size:108
Alignment explanation
Indices: 42232--42528 Score: 504
Period size: 108 Copynumber: 2.7 Consensus size: 108
42222 ATAAGGATAT
* * * *
42232 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGGAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTC-ATAAGGCAAGGATACCATGTAAGACC
*
42297 ATGTCAAGACATGGCATTGATGAGTTATTATAAGGCAAAGGTCC
65 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
* *
42341 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGCTCATAAGGCAAGGATACCATGTAAGACCA
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGCAAGGATACCATGTAAGACCA
42406 TGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
66 TGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
**
42449 CATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGCAAGGATACCACATAAGACCA
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGCAAGGATACCATGTAAGACCA
42514 TGTCAAGACATGGCA
66 TGTCAAGACATGGCA
42529 ATGGTAAGTT
Statistics
Matches: 177, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
108 142 0.80
109 35 0.20
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (108 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGCAAGGATACCATGTAAGACCA
TGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
Found at i:42534 original size:53 final size:53
Alignment explanation
Indices: 42022--42540 Score: 426
Period size: 55 Copynumber: 9.9 Consensus size: 53
42012 TTGGTAAGAT
* * *
42022 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGAC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTC-ATAAGGC
**** *
42076 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAG---AT-----
1 AAGGATACCATGTAAGACCATGCCAAG-ACATGGCA-TTGATAAGTTCATAAGGC
* ** *
42123 AAGGATATCATGTAAGACCATGCCAAGGTATGGCATTGATAAGTTCTATAAGAC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTC-ATAAGGC
* **** *
42177 AATGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAG---AT-----
1 AAGGATACCATGTAAGACCATGCCAAG-ACATGGCA-TTGATAAGTTCATAAGGC
* *
42224 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTC-ATAAGGC
* * * * * *
42278 AAGGAAATCATGGAAGACCATGTCAAGACATGGCATTGATGAGTTATTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAG-T-TCATAAGGC
* * * * *
42333 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGCTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGC
* *
42386 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-C-ATAAGGC
* * *
42441 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGC
** * * *
42494 AAGGATACCACATAAGACCATGTCAAGACATGGCAATGGTAAGTTCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCA
42541 AAAAGGAAAA
Statistics
Matches: 372, Mismatches: 63, Indels: 61
0.75 0.13 0.12
Matches are distributed among these distances:
45 14 0.04
46 13 0.03
47 43 0.12
49 4 0.01
52 12 0.03
53 86 0.23
54 83 0.22
55 94 0.25
56 23 0.06
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGC
Found at i:58915 original size:40 final size:40
Alignment explanation
Indices: 58850--58943 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
58840 GACTATGCTC
*
58850 GGCACTAAGTGTGCGGTTCGAAATAGCTCCTGCTATA-AA
1 GGCACTAAGTGTGCGGTTCGAAATAGCTCCGGCTATATAA
* * *
58889 TGGCACTAAGTGTGCGTGTT-GGAATAGCTTCGGCTATATGA
1 -GGCACTAAGTGTGCG-GTTCGAAATAGCTCCGGCTATATAA
58930 GGCACTAAGTGTGC
1 GGCACTAAGTGTGC
58944 AATACCGAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 44 0.92
41 4 0.08
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (40 bp):
GGCACTAAGTGTGCGGTTCGAAATAGCTCCGGCTATATAA
Found at i:59628 original size:24 final size:24
Alignment explanation
Indices: 59601--59698 Score: 151
Period size: 24 Copynumber: 4.0 Consensus size: 24
59591 AAGGCTGTCA
59601 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
*
59625 GGAGAGGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
59649 GGAGAGGATTTAGGAGCTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
*
59673 GGAGAAGATTTAGGAGTTGATCAAG
1 GGAGAAGATTTAGGAGCTGAT-AAG
59698 G
1 G
59699 AGTAGGAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
24 65 0.96
25 3 0.04
ACGTcount: A:0.36, C:0.04, G:0.39, T:0.21
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:61393 original size:33 final size:34
Alignment explanation
Indices: 61316--61396 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
61306 TATAGGCCAT
*
61316 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
* * **
61350 AATGTAATCTGAA-AA-GGGCTCTGGCCCAGTATC
1 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGT-TC
61383 ACTGTTATCTGAAT
1 ACTGTTATCTGAAT
61397 GGGCTTAAGC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 13 0.34
33 14 0.37
34 11 0.29
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (34 bp):
ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTC
Found at i:61401 original size:32 final size:31
Alignment explanation
Indices: 61316--61401 Score: 73
Period size: 32 Copynumber: 2.6 Consensus size: 31
61306 TATAGGCCAT
*
61316 ACTGTTATCTGAATAAGGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAAT---GGGCTAAGGCCCAGTTC
* * * **
61350 AATGTAATCTGAAAAGGGCTCTGGCCCAGTATC
1 ACTGTTATCTG-AATGGGCTAAGGCCCAGT-TC
61383 ACTGTTATCTGAATGGGCT
1 ACTGTTATCTGAATGGGCT
61402 TAAGCCCGAT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
32 20 0.49
33 10 0.24
34 9 0.22
35 2 0.05
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (31 bp):
ACTGTTATCTGAATGGGCTAAGGCCCAGTTC
Found at i:70215 original size:15 final size:16
Alignment explanation
Indices: 70186--70215 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
70176 CAAACATGCT
70186 TTAACACATTATCAAA
1 TTAACACATTATCAAA
70202 TTAACACA-TATCAA
1 TTAACACATTATCAA
70216 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:72133 original size:28 final size:29
Alignment explanation
Indices: 72101--72157 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
72091 TCCTCTTAAA
* *
72101 TAACAACTAATATCTCAA-ATTCATCAAT
1 TAACAACTAAAATCACAAGATTCATCAAT
* *
72129 TAACATCTAAAATCACAAGGTTCATCAAT
1 TAACAACTAAAATCACAAGATTCATCAAT
72158 GACAGCATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.30
Consensus pattern (29 bp):
TAACAACTAAAATCACAAGATTCATCAAT
Found at i:73519 original size:18 final size:19
Alignment explanation
Indices: 73488--73526 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
73478 AATAGATAAT
*
73488 AAAATGAAATGAAAGTAAA
1 AAAATGAAATGAAAGGAAA
*
73507 AAAATTAAA-GAAAGGAAA
1 AAAATGAAATGAAAGGAAA
73525 AA
1 AA
73527 TAAAAACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAATGAAATGAAAGGAAA
Done.