Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold750
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: 55300
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Found at i:9311 original size:10 final size:10
Alignment explanation
Indices: 9296--9322 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9286 ATGTATCAAG
9296 CAAAAACAAA
1 CAAAAACAAA
9306 CAAAAACAAA
1 CAAAAACAAA
9316 CAAAAAC
1 CAAAAAC
9323 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:13520 original size:52 final size:51
Alignment explanation
Indices: 13442--13591 Score: 246
Period size: 52 Copynumber: 2.9 Consensus size: 51
13432 CGAAATATGA
13442 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
*
13494 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
13546 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACAT
13592 TTAAGTGATG
Statistics
Matches: 92, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.96
53 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:13672 original size:13 final size:13
Alignment explanation
Indices: 13654--13678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13644 CAAAAAAATA
13654 TGTATCGATACAT
1 TGTATCGATACAT
13667 TGTATCGATACA
1 TGTATCGATACA
13679 ACACTTTATG
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:13677 original size:33 final size:33
Alignment explanation
Indices: 13632--13698 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
13622 AGTAGCTTAA
*
13632 ATTGTATTGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
13665 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
13698 A
1 A
13699 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:18457 original size:14 final size:14
Alignment explanation
Indices: 18438--18469 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
18428 GTAAATTTCA
*
18438 TTATATAATTATTT
1 TTATATAATTAATT
18452 TTATATAATTAATT
1 TTATATAATTAATT
18466 TTAT
1 TTAT
18470 TTATTATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATATAATTAATT
Found at i:22155 original size:1 final size:1
Alignment explanation
Indices: 22149--22263 Score: 68
Period size: 1 Copynumber: 115.0 Consensus size: 1
22139 GGCGTCCTCC
* ** * ** ** * *
22149 AAAAAAAAAAAAAAAAAAACAAAAAAAATGAAAAAACAAAAAAAAATGATGATAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
22214 AACAAAAGAAAAAAAAACAAAAACAATAAAAAAACAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22264 GGGGGTCCGG
Statistics
Matches: 81, Mismatches: 33, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.84, C:0.08, G:0.03, T:0.04
Consensus pattern (1 bp):
A
Found at i:22175 original size:21 final size:21
Alignment explanation
Indices: 22149--22263 Score: 97
Period size: 21 Copynumber: 5.2 Consensus size: 21
22139 GGCGTCCTCC
22149 AAAAAAAAAAAAAAAAAAACA
1 AAAAAAAAAAAAAAAAAAACA
22170 AAAAAAATGAAAAAACAAAAAA-A
1 AAAAAAA--AAAAAA-AAAAAACA
* *
22193 AATGATGATAAAAAACAAAAAAACA
1 AA--A--AAAAAAAAAAAAAAAACA
* *
22218 AAAGAAAAAAAAACAAAAACA
1 AAAAAAAAAAAAAAAAAAACA
* * *
22239 ATAAAAAAACAAACAAAAACA
1 AAAAAAAAAAAAAAAAAAACA
22260 AAAA
1 AAAA
22264 GGGGGTCCGG
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
21 42 0.55
23 10 0.13
24 12 0.16
25 9 0.12
27 3 0.04
ACGTcount: A:0.84, C:0.08, G:0.03, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAAAAACA
Found at i:23762 original size:30 final size:29
Alignment explanation
Indices: 23707--24156 Score: 261
Period size: 30 Copynumber: 15.3 Consensus size: 29
23697 TCACCCTTCA
*
23707 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
*
23736 AAAGCCCACAAGTCAATGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
***
23765 GAAAGCCCACAAGTCAGTGGCA--ACCTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
* ** *
23793 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTTC
* * * *
23823 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
* * * *
23852 AAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTG
1 AAAGCCCACAAGTCAGTGGCA-----TTT-TTTTC
* * * * * *
23887 TAAGCTCACAACTCTA-TAGCACTCTTTTC
1 AAAGCCCACAAGTC-AGTGGCATTTTTTTC
* ***
23916 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
*
23943 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
*** *
23973 AAAAGCCCACAAGTCAGTGGCA-ACCTTTA
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
* *** *
24002 AAAGCCCACAAGTTAGTGGCACCCTGTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
* *
24031 AAAAGCCCACAAGTCAATGGCATATTTTTTA
1 -AAAGCCCACAAGTCAGTGGCAT-TTTTTTC
*** *
24062 AAAGCCCACAAGTCAGTGGCA-ACCTTTA
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
***
24090 AAAGCCCACAAGTCAGTGGCA--ACCTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
* ** *
24117 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTTC
24147 AAAGCCCACA
1 AAAGCCCACA
24157 CAAGTCGATG
Statistics
Matches: 334, Mismatches: 66, Indels: 41
0.76 0.15 0.09
Matches are distributed among these distances:
26 1 0.00
27 63 0.19
28 48 0.14
29 62 0.19
30 137 0.41
31 3 0.01
34 2 0.01
35 18 0.05
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTTC
Found at i:23808 original size:27 final size:27
Alignment explanation
Indices: 23766--23818 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
23756 ATTTTTTTCG
*
23766 AAAGCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
*
23793 AAAGCCCACAAATCAGTGGCACCCTT
1 AAAGCCCACAAATCAGTGGCAACCTT
23819 TTCCGAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:24021 original size:88 final size:87
Alignment explanation
Indices: 23916--24156 Score: 369
Period size: 88 Copynumber: 2.8 Consensus size: 87
23906 CACTCTTTTC
23916 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCC-TTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
23981 ACAAGTCAGTGGCAACCTTTAAA
65 ACAAGTCAGTGGCAACCTTTAAA
* *
24004 AGCCCACAAGTTAGTGGCACCCTGTTCAAAAGCCCACAAGTCAATGGCATATTTTTTAAAAGCCC
1 AGCCCACAAGTTAGTGGCACCCT-TTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
24069 ACAAGTCAGTGGCAACCTTTAAA
65 ACAAGTCAGTGGCAACCTTTAAA
* * * *** *
24092 AGCCCACAAGTCAGTGGCAACC-TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCA
1 AGCCCACAAGTTAGTGGCACCCTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCA
24155 CA
66 CA
24157 CAAGTCGATG
Statistics
Matches: 141, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
85 33 0.23
86 3 0.02
87 1 0.01
88 104 0.74
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (87 bp):
AGCCCACAAGTTAGTGGCACCCTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCCA
CAAGTCAGTGGCAACCTTTAAA
Found at i:24032 original size:58 final size:58
Alignment explanation
Indices: 23916--24156 Score: 299
Period size: 58 Copynumber: 4.1 Consensus size: 58
23906 CACTCTTTTC
* * ***
23916 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAA
1 AGCCCACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
* *
23976 AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTTAGTGGCACCCTGTTCAAA
1 AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
* ** *
24034 AGCCCACAAGTCAATGGCATATTTTTTAAAAGCCCACAAGTCAGTGGCAACC-TTT-AAA
1 AGCCCACAAGTCAGTGGCA-A-CCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
* * *
24092 AGCCCACAAGTCAGTGGCAACC-TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCAA
1 AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
24149 AGCCCACA
1 AGCCCACA
24157 CAAGTCGATG
Statistics
Matches: 157, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
55 24 0.15
56 3 0.02
57 11 0.07
58 67 0.43
59 6 0.04
60 46 0.29
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (58 bp):
AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
Found at i:24239 original size:49 final size:49
Alignment explanation
Indices: 24177--24428 Score: 290
Period size: 49 Copynumber: 5.0 Consensus size: 49
24167 GCAACCCTTC
* *
24177 TAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
24226 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
24275 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTT
* * * *
24327 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * * * *
24382 TAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCATCTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTTATC
24429 ACTTTTCTCA
Statistics
Matches: 176, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
49 89 0.51
50 3 0.02
51 2 0.01
52 39 0.22
53 2 0.01
54 2 0.01
55 38 0.22
56 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:24408 original size:107 final size:99
Alignment explanation
Indices: 24172--24425 Score: 305
Period size: 107 Copynumber: 2.5 Consensus size: 99
24162 CGATGGCAAC
*
24172 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACC-TTTATCTTTAAGTCCAAT
1 CCTT-TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTATCTTTAAGTCCAAT
* *
24236 ATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
65 ATAGCTGGCCTTGAATCAGCACATTGACACCTTCA
* *
24271 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTT--ATCTTTAAGTCCAA
*
24336 TGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCA
64 TATAGCTGGCCTTGAATCAGCACATTGACA-CC----T-TCA
* * * * *
24378 TCTTTAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCATCTTT
1 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTT
24426 ATCACTTTTC
Statistics
Matches: 133, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
98 39 0.29
99 7 0.05
101 40 0.30
102 2 0.02
106 2 0.02
107 43 0.32
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.34
Consensus pattern (99 bp):
CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTATCTTTAAGTCCAATA
TAGCTGGCCTTGAATCAGCACATTGACACCTTCA
Found at i:24760 original size:33 final size:33
Alignment explanation
Indices: 24723--24789 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
24713 TTCAACGATT
24723 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
24756 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
24789 T
1 T
24790 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:24761 original size:13 final size:13
Alignment explanation
Indices: 24743--24767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24733 CATAAAATGT
24743 TGTATCGATACAA
1 TGTATCGATACAA
24756 TGTATCGATACA
1 TGTATCGATACA
24768 TATTTTTTTG
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:24848 original size:13 final size:13
Alignment explanation
Indices: 24830--24854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24820 ATTACTCAAA
24830 TGTATCGATACAT
1 TGTATCGATACAT
24843 TGTATCGATACA
1 TGTATCGATACA
24855 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:29081 original size:10 final size:10
Alignment explanation
Indices: 29066--29092 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29056 TGCTAACTAA
29066 GTTTTTGTTT
1 GTTTTTGTTT
29076 GTTTTTGTTT
1 GTTTTTGTTT
29086 GTTTTTG
1 GTTTTTG
29093 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:38793 original size:1 final size:1
Alignment explanation
Indices: 38787--38898 Score: 71
Period size: 1 Copynumber: 112.0 Consensus size: 1
38777 GGCGTCCTCC
* ** * ** ** * *
38787 AAAAAAAAAAAAAAAAACAAAAAAAATGAAAAAACAAAAAAAATGATGAAAAAAAACAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
38852 AAAAGAAAAAAAAACAAAAACAATAAAAAAACAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38899 GGGGGTCCGG
Statistics
Matches: 80, Mismatches: 31, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.85, C:0.08, G:0.04, T:0.04
Consensus pattern (1 bp):
A
Found at i:38810 original size:17 final size:17
Alignment explanation
Indices: 38788--38898 Score: 89
Period size: 17 Copynumber: 6.3 Consensus size: 17
38778 GCGTCCTCCA
38788 AAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAC
**
38805 AAAAAAAATGAAAAAAC
1 AAAAAAAAAAAAAAAAC
**
38822 AAAAAAAATGATGAAAAA-
1 AAAAAAAA--AAAAAAAAC
* * *
38840 AAACAAAAAAACAAAAG
1 AAAAAAAAAAAAAAAAC
*
38857 AAAAAAAAACAAAAACAAT
1 AAAAAAAAA-AAAAA-AAC
*
38876 AAAAAAACAAACAAAAAC
1 AAAAAAA-AAAAAAAAAC
38894 AAAAA
1 AAAAA
38899 GGGGGTCCGG
Statistics
Matches: 74, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
16 5 0.07
17 31 0.42
18 18 0.24
19 18 0.24
20 2 0.03
ACGTcount: A:0.85, C:0.08, G:0.04, T:0.04
Consensus pattern (17 bp):
AAAAAAAAAAAAAAAAC
Found at i:38893 original size:21 final size:20
Alignment explanation
Indices: 38786--38895 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
38776 CGGCGTCCTC
38786 CAAAAA-AA-AAAAAAAAAA
1 CAAAAACAATAAAAAAAAAA
* *
38804 CAAAAAAAATGAAAAAACAAA
1 CAAAAACAAT-AAAAAAAAAA
**
38825 -AAAAATGATGAAAAAAAACAA
1 CAAAAACAAT-AAAAAAAA-AA
*
38846 -AAAAACAAAAGAAAAAAAAA
1 CAAAAACAATA-AAAAAAAAA
38866 CAAAAACAATAAAAAAACAAA
1 CAAAAACAATAAAAAAA-AAA
38887 CAAAAACAA
1 CAAAAACAA
38896 AAAGGGGGTC
Statistics
Matches: 77, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
18 6 0.08
19 2 0.03
20 24 0.31
21 45 0.58
ACGTcount: A:0.84, C:0.09, G:0.04, T:0.04
Consensus pattern (20 bp):
CAAAAACAATAAAAAAAAAA
Found at i:40396 original size:30 final size:29
Alignment explanation
Indices: 40341--40790 Score: 270
Period size: 30 Copynumber: 15.3 Consensus size: 29
40331 TCACCCTTCA
*
40341 AAAGTCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
40370 AAAGCCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
***
40399 GAAAGCCCACAAGTCAGTGGCA--ACCTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
* ** *
40427 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTTC
* * * *
40457 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
* * * *
40486 AAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTG
1 AAAGCCCACAAGTCAGTGGCA-----TTT-TTTTC
* * * * * *
40521 TAAGCTCACAACTCTA-TAGCACTCTTTTC
1 AAAGCCCACAAGTC-AGTGGCATTTTTTTC
* ***
40550 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
*
40577 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
*** *
40607 AAAAGCCCACAAGTCAGTGGCA-ACCTTTA
1 -AAAGCCCACAAGTCAGTGGCATTTTTTTC
* *** *
40636 AAAGCCCACAAGTTAGTGGCACCCTGTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
* *
40665 AAAAGCCCACAAGTCAATGGCATATTTTTTA
1 -AAAGCCCACAAGTCAGTGGCAT-TTTTTTC
*** *
40696 AAAGCCCACAAGTCAGTGGCA-ACCTTTA
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
***
40724 AAAGCCCACAAGTCAGTGGCA--ACCTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTC
* ** *
40751 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTTC
40781 AAAGCCCACA
1 AAAGCCCACA
40791 CAAGTCGATG
Statistics
Matches: 336, Mismatches: 64, Indels: 41
0.76 0.15 0.09
Matches are distributed among these distances:
26 1 0.00
27 63 0.19
28 48 0.14
29 63 0.19
30 138 0.41
31 3 0.01
34 2 0.01
35 18 0.05
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTTC
Found at i:40655 original size:88 final size:88
Alignment explanation
Indices: 40337--40790 Score: 388
Period size: 88 Copynumber: 5.2 Consensus size: 88
40327 TTCATCACCC
* *** * *** *
40337 TTCAAAAGTCCACAAGTCAGTGGCATTTTTTTCAAAGCCCACAAGTCAGTGGCATTTTTTTCGAA
1 TTCAAAAGCCCACAAGTCAGTGGCA-ACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
**
40402 AGCCCACAAGTCAGTGGCA-A-CC
65 AGCCCACAAGTCAGTGGCATATTT
* * ** * * *
40424 TTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGGCA-TCTTTTCCA
1 TTCAAAAGCCCACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTCAGTGGCACCCTTTTCAA
* * * *
40487 AAGTCCACAACTCCGTGGCACTCTTT
64 AAGCCCACAAGTCAGTGGCA-TATTT
** * * * ** *
40513 TTCTTTTGTAAGCTCACAACTCTA-TAGC-ACTCTTT-TCAGCCCACAAGTTAGTGGCACCCTTT
1 TTC----AAAAGCCCACAAGTC-AGTGGCAAC-CTTTAAAAGCCCACAAGTCAGTGGCACCCTTT
40575 TCAAAAGCCCACAAGTCAGTGGCATATTT
60 TCAAAAGCCCACAAGTCAGTGGCATATTT
* *
40604 TTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTTAGTGGCACCCTGTTCAAAA
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAA
*
40669 GCCCACAAGTCAATGGCATATTT
66 GCCCACAAGTCAGTGGCATATTT
* *
40692 TTTAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCAACC--TTC-AAA
1 TTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAA
* ***
40754 GCCCACAAATCAGTGGCACCCTT
66 GCCCACAAGTCAGTGGCATATTT
*
40777 TTCCAAAGCCCACA
1 TTCAAAAGCCCACA
40791 CAAGTCGATG
Statistics
Matches: 302, Mismatches: 49, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
85 33 0.11
86 50 0.17
87 41 0.14
88 107 0.35
89 3 0.01
91 24 0.08
92 24 0.08
93 4 0.01
94 15 0.05
95 1 0.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (88 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAA
GCCCACAAGTCAGTGGCATATTT
Found at i:40666 original size:58 final size:58
Alignment explanation
Indices: 40550--40790 Score: 299
Period size: 58 Copynumber: 4.1 Consensus size: 58
40540 CACTCTTTTC
* * ***
40550 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAA
1 AGCCCACAAGTCAGTGGCAACC-TTT-AAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
* *
40610 AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTTAGTGGCACCCTGTTCAAA
1 AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
* ** *
40668 AGCCCACAAGTCAATGGCATATTTTTTAAAAGCCCACAAGTCAGTGGCAACC-TTT-AAA
1 AGCCCACAAGTCAGTGGCA-A-CCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
* * *
40726 AGCCCACAAGTCAGTGGCAACC-TTCAAAGCCCACAAATCAGTGGCACCCTTTTCCAA
1 AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
40783 AGCCCACA
1 AGCCCACA
40791 CAAGTCGATG
Statistics
Matches: 157, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
55 24 0.15
56 3 0.02
57 11 0.07
58 67 0.43
59 6 0.04
60 46 0.29
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (58 bp):
AGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCACCCTTTTCAAA
Found at i:40873 original size:49 final size:49
Alignment explanation
Indices: 40811--41062 Score: 290
Period size: 49 Copynumber: 5.0 Consensus size: 49
40801 GCAACCCTTC
* *
40811 TAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
40860 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
40909 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTT
* * * *
40961 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * * * *
41016 TAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCATCTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTTATC
41063 ACTTTTCTCA
Statistics
Matches: 176, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
49 89 0.51
50 3 0.02
51 2 0.01
52 39 0.22
53 2 0.01
54 2 0.01
55 38 0.22
56 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:41042 original size:107 final size:99
Alignment explanation
Indices: 40806--41059 Score: 305
Period size: 107 Copynumber: 2.5 Consensus size: 99
40796 CGATGGCAAC
*
40806 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACC-TTTATCTTTAAGTCCAAT
1 CCTT-TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTATCTTTAAGTCCAAT
* *
40870 ATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
65 ATAGCTGGCCTTGAATCAGCACATTGACACCTTCA
* *
40905 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTT--ATCTTTAAGTCCAA
*
40970 TGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCA
64 TATAGCTGGCCTTGAATCAGCACATTGACA-CC----T-TCA
* * * * *
41012 TCTTTAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCATCTTT
1 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTT
41060 ATCACTTTTC
Statistics
Matches: 133, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
98 39 0.29
99 7 0.05
101 40 0.30
102 2 0.02
106 2 0.02
107 43 0.32
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.34
Consensus pattern (99 bp):
CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTATCTTTAAGTCCAATA
TAGCTGGCCTTGAATCAGCACATTGACACCTTCA
Found at i:41907 original size:33 final size:33
Alignment explanation
Indices: 41870--41936 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
41860 TTCAACGATT
41870 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
41903 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
41936 T
1 T
41937 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:41908 original size:13 final size:13
Alignment explanation
Indices: 41890--41914 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41880 CATAAAATGT
41890 TGTATCGATACAA
1 TGTATCGATACAA
41903 TGTATCGATACA
1 TGTATCGATACA
41915 TATTTTTTTG
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:41995 original size:13 final size:13
Alignment explanation
Indices: 41977--42001 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41967 ATTACTCAAA
41977 TGTATCGATACAT
1 TGTATCGATACAT
41990 TGTATCGATACA
1 TGTATCGATACA
42002 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:46230 original size:10 final size:10
Alignment explanation
Indices: 46215--46241 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
46205 TGCTAACTAA
46215 GTTTTTGTTT
1 GTTTTTGTTT
46225 GTTTTTGTTT
1 GTTTTTGTTT
46235 GTTTTTG
1 GTTTTTG
46242 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Done.