Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3683.1
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: 110682
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.29
Warning! 11614 characters in sequence are not A, C, G, or T
Found at i:1175 original size:71 final size:71
Alignment explanation
Indices: 1059--1200 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
1049 CTCCATCTAT
1059 CTACAAATTTGAACGAGCTTCTCGTCGACGATCGGGCATCTTAAGTGAACCCGACTCAATCAATC
1 CTACAAATTTGAACGAGCTTCTCGTCGACGATCGGGCATCTTAAGTGAACCCGACTCAATCAATC
1124 GGGCCG
66 GGGCCG
*
1130 CTACAAATTTGAACGAGCTTCTCGTCGACGATCGGGCATCTTAAGTGAACCTGACTCAATCAATC
1 CTACAAATTTGAACGAGCTTCTCGTCGACGATCGGGCATCTTAAGTGAACCCGACTCAATCAATC
1195 GGGCCG
66 GGGCCG
1201 GATCACATCA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (71 bp):
CTACAAATTTGAACGAGCTTCTCGTCGACGATCGGGCATCTTAAGTGAACCCGACTCAATCAATC
GGGCCG
Found at i:2943 original size:17 final size:19
Alignment explanation
Indices: 2907--2946 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
2897 AGCAGCCGAA
2907 AATTAATGTGTCTAAAATT
1 AATTAATGTGTCTAAAATT
*
2926 AATTAATTTG-CT-AAATT
1 AATTAATGTGTCTAAAATT
2943 AATT
1 AATT
2947 TTGTGTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (19 bp):
AATTAATGTGTCTAAAATT
Found at i:6580 original size:24 final size:25
Alignment explanation
Indices: 6527--6580 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
6517 AACAAATTCT
* *
6527 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
6552 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
6575 TTTTTT
1 TTTTTT
6581 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:13296 original size:20 final size:20
Alignment explanation
Indices: 13271--13316 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
13261 TGAGTTATTT
13271 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
*
13291 AAGTAAGAGAGTAAGTAAAG
1 AAGTAAGAGAGTAAGTAAAC
13311 AAGTAA
1 AAGTAA
13317 AGATCATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.57, C:0.04, G:0.24, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:18145 original size:21 final size:20
Alignment explanation
Indices: 18119--18173 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 20
18109 TTTTCAAGCT
18119 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
18140 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
18155 CTCTTTCAATTTCTTTTTC
1 CTCTTTCAATTTCTTTTTC
18174 TATCTCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:18237 original size:15 final size:15
Alignment explanation
Indices: 18214--18260 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
18204 TTTTGAAATC
18214 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
18229 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
18244 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
18260 T
1 T
18261 ATTATTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:20939 original size:10 final size:10
Alignment explanation
Indices: 20924--20961 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
20914 TTGGGTTAAG
20924 ATTGAGCTGA
1 ATTGAGCTGA
20934 ATTGAGCTCGA
1 ATTGAGCT-GA
20945 A-TGAGCTGA
1 ATTGAGCTGA
*
20954 CTTGAGCT
1 ATTGAGCT
20962 CAAGTGAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:23168 original size:56 final size:55
Alignment explanation
Indices: 23051--23168 Score: 150
Period size: 55 Copynumber: 2.1 Consensus size: 55
23041 TGCATGCTTT
* * * *
23051 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
* *
23105 CTTTAAATGCCGTTCTATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
23161 CATTAAAT
1 CATTAAAT
23169 CAGCAAGCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 3 0.06
55 28 0.52
56 23 0.43
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:23818 original size:20 final size:20
Alignment explanation
Indices: 23793--23847 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
23783 ACGAGTTAAA
* *
23793 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
23813 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
23833 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
23848 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:42328 original size:18 final size:19
Alignment explanation
Indices: 42288--42333 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
42278 TTGTCCAGAT
*
42288 TTTAAAC-AAATTAATTAA
1 TTTAAACTAAATTAACTAA
*
42306 CTTAAACTAAA-TAACTAA
1 TTTAAACTAAATTAACTAA
42324 TTT-AACTAAA
1 TTTAAACTAAA
42334 AACAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.29
18 14 0.58
19 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTAAACTAAATTAACTAA
Found at i:45357 original size:33 final size:33
Alignment explanation
Indices: 45320--45415 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 33
45310 TATGTAACTT
45320 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
1 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
*
45353 TCATGTTAGTTTAA--TT--AT--GTAAATT---
1 TCATGTTAG-TTAAGTTTGCATCATTAAATTAAG
*
45378 TCATGTTAGTAAAGTTTGCATCATTAAATTAAG
1 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
45411 TCATG
1 TCATG
45416 CATTAACTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 20
0.68 0.04 0.27
Matches are distributed among these distances:
24 3 0.06
25 9 0.18
26 2 0.04
28 8 0.16
30 8 0.16
32 2 0.04
33 14 0.28
34 4 0.08
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (33 bp):
TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
Found at i:47501 original size:46 final size:46
Alignment explanation
Indices: 47444--47537 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
47434 CAAAGAAAAG
*
47444 ACCTCGTCCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
* *
47490 ACCTCGACCCACTATCAAGGATGGTAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
47536 AC
1 AC
47538 GCCACACAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
Found at i:50874 original size:10 final size:10
Alignment explanation
Indices: 50859--50920 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
50849 TTTGAACCAT
*
50859 TACCAATTCG
1 TACCAATTCA
*
50869 TACCAAATACCA
1 TACC-AAT-TCA
*
50881 TACCATTTCA
1 TACCAATTCA
50891 TACCAATTCCA
1 TACCAATT-CA
* *
50902 TACCATTTCG
1 TACCAATTCA
50912 TACCAATTC
1 TACCAATTC
50921 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:50904 original size:21 final size:21
Alignment explanation
Indices: 50859--50921 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
50849 TTTGAACCAT
* *
50859 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
50881 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
50902 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
50922 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:52727 original size:10 final size:10
Alignment explanation
Indices: 52711--52768 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
52701 CAACTCCGAC
52711 CAGCTCAATT
1 CAGCTCAATT
* *
52721 GAGCTCATTT
1 CAGCTCAATT
52731 CAGCTCAA-T
1 CAGCTCAATT
52740 CGAGCTCAATT
1 C-AGCTCAATT
*
52751 TAGCTACAATT
1 CAGCT-CAATT
52762 CAGCTCA
1 CAGCTCA
52769 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:52734 original size:20 final size:20
Alignment explanation
Indices: 52711--52771 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
52701 CAACTCCGAC
52711 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
52731 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
52752 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
52772 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:61188 original size:9 final size:10
Alignment explanation
Indices: 61158--61191 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
61148 AGCTTATTAA
61158 GTTTAATATGT
1 GTTTAA-ATGT
61169 GTTTAAATGT
1 GTTTAAATGT
61179 GTTT-AATGT
1 GTTTAAATGT
61188 GTTT
1 GTTT
61192 TGATTGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 8 0.35
11 6 0.26
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.56
Consensus pattern (10 bp):
GTTTAAATGT
Found at i:61297 original size:55 final size:54
Alignment explanation
Indices: 61230--61354 Score: 198
Period size: 55 Copynumber: 2.3 Consensus size: 54
61220 TAAATTATGA
*
61230 ACAAGGGCTGTTACAAAGTGTTAAATGTGACT-ACTCAGTTGGAATCGGTTACAT
1 ACAAGGGTTGTTACAAAGTGTTAAATGTGACTAAC-CAGTTGGAATCGGTTACAT
61284 ACAAGGGGTTGTTACAAAGTGTTAAATGTGACTAACCAGTTGGAATCGGTTACAT
1 ACAA-GGGTTGTTACAAAGTGTTAAATGTGACTAACCAGTTGGAATCGGTTACAT
*
61339 ATAAAGGGTTGTTACA
1 A-CAAGGGTTGTTACA
61355 TCAATTAAAG
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
54 4 0.06
55 58 0.88
56 4 0.06
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (54 bp):
ACAAGGGTTGTTACAAAGTGTTAAATGTGACTAACCAGTTGGAATCGGTTACAT
Found at i:61432 original size:45 final size:44
Alignment explanation
Indices: 61340--61428 Score: 101
Period size: 45 Copynumber: 2.0 Consensus size: 44
61330 CGGTTACATA
**
61340 TAAAGGGTTGTTACATCAATTAAAGGAGGGCATTTTACATCATT
1 TAAAGGGTTGTTACATCAATTAAAGGAAAGCATTTTACATCATT
** *
61384 TAAAGGAGTTGTTATGTCATTTAAAGGAAAG-ATTTATACAT-ATT
1 TAAAGG-GTTGTTACATCAATTAAAGGAAAGCATTT-TACATCATT
61428 T
1 T
61429 TAAAATTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
44 14 0.37
45 24 0.63
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (44 bp):
TAAAGGGTTGTTACATCAATTAAAGGAAAGCATTTTACATCATT
Found at i:64278 original size:20 final size:20
Alignment explanation
Indices: 64227--64301 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
64217 CATGTGGTTC
64227 AGCTCACTCGAGCTCAAGTT
1 AGCTCACTCGAGCTCAAGTT
* *
64247 AGTTCATTCGAGCTCAAGTT
1 AGCTCACTCGAGCTCAAGTT
* *
64267 AGCTCACACGAGCTGAA-TT
1 AGCTCACTCGAGCTCAAGTT
*
64286 CAGCTCA-TTGAGCTCA
1 -AGCTCACTCGAGCTCA
64302 TTATTAGCTC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 8 0.18
20 37 0.82
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
AGCTCACTCGAGCTCAAGTT
Found at i:64311 original size:40 final size:40
Alignment explanation
Indices: 64227--64301 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
64217 CATGTGGTTC
* *
64227 AGCTCACTCGAGCTCAAGTTAGTTCATTCGAGCTCAAGTT
1 AGCTCACACGAGCTCAAGTTAGCTCATTCGAGCTCAAGTT
*
64267 AGCTCACACGAGCTGAA-TTCAGCTCATT-GAGCTCA
1 AGCTCACACGAGCTCAAGTT-AGCTCATTCGAGCTCA
64302 TTATTAGCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 9 0.29
40 22 0.71
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (40 bp):
AGCTCACACGAGCTCAAGTTAGCTCATTCGAGCTCAAGTT
Found at i:70537 original size:111 final size:111
Alignment explanation
Indices: 70392--70613 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
70382 AAGCACGTAT
**
70392 ATGGTGGAAAAACTTGCCTTGTTGACTATCAAGCACCCGAGCCCATATAAATGGAAATGGCTCAA
1 ATGGTGGAAAAACTTGCCTTGCCGACTATCAAGCACCCGAGCCCATATAAATGGAAATGGCTCAA
70457 CGAAGGGGTCAAATTAAAGGTTACCAAGCAAGCAATGATCACATTC
66 CGAAGGGGTCAAATTAAAGGTTACCAAGCAAGCAATGATCACATTC
* * *
70503 ATGGTGGAAAAACTTGCCTTGCCGACTATCAAGCACCCGAGCCCATATAAATTGTAATTGCTCAA
1 ATGGTGGAAAAACTTGCCTTGCCGACTATCAAGCACCCGAGCCCATATAAATGGAAATGGCTCAA
*
70568 CGAATGGGTCAAATTAAAGGTTACCAAGCAAGCAATGATCACATTC
66 CGAAGGGGTCAAATTAAAGGTTACCAAGCAAGCAATGATCACATTC
70614 TCCATTGGAA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (111 bp):
ATGGTGGAAAAACTTGCCTTGCCGACTATCAAGCACCCGAGCCCATATAAATGGAAATGGCTCAA
CGAAGGGGTCAAATTAAAGGTTACCAAGCAAGCAATGATCACATTC
Found at i:71478 original size:20 final size:20
Alignment explanation
Indices: 71455--71508 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
71445 AGTTTTTCCC
*
71455 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
71475 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
71495 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
71509 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:71490 original size:30 final size:30
Alignment explanation
Indices: 71455--71528 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
71445 AGTTTTTCCC
71455 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
71485 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
71515 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
71529 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:71518 original size:20 final size:20
Alignment explanation
Indices: 71455--71519 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
71445 AGTTTTTCCC
* * * *
71455 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
71475 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
71494 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
71515 AGCTC
1 AGCTC
71520 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:73236 original size:133 final size:132
Alignment explanation
Indices: 72975--73236 Score: 408
Period size: 133 Copynumber: 2.0 Consensus size: 132
72965 TTAACCTGGG
* *
72975 CCGGATCACATCATTTGGTATCAGAGCTACTAAAACGAGGAGTACCGATGTTCGTATCAAGCTCG
1 CCGGATCACATCATTTGGTATCAGAGCTACTAAAACGAGGAGCACCGACGTTCGTATCAAGCTCG
* *
73040 GAATAGGTTCGAAACGTGAAAAAAAAAATCAAAAAAAAAAGTTTGAGTTGTAATTTAAATTTTTT
66 CAATAGGTTCGAAACGTGAAAAAAAAAATCAAAAAAAAAAG-ATGAGTTGTAATTTAAATTTTTT
73105 TTT
130 TTT
*
73108 CCGGATCACATCATTTGGTATCAGAGCTACTAAAACGAGGAGCGCCGACGTTCGTAAT-AAGGC-
1 CCGGATCACATCATTTGGTATCAGAGCTACTAAAACGAGGAGCACCGACGTTCGT-ATCAA-GCT
73171 CGCAAGTAGGTTCGAAACGTG-AAAAAAAAATCAAAAAAAAAA-ATGAGTTGTAATTT-AATTTT
64 CGCAA-TAGGTTCGAAACGTGAAAAAAAAAATCAAAAAAAAAAGATGAGTTGTAATTTAAATTTT
73233 TTTT
128 TTTT
73237 CCCTTGTATT
Statistics
Matches: 121, Mismatches: 5, Indels: 9
0.90 0.04 0.07
Matches are distributed among these distances:
130 10 0.08
131 13 0.11
133 79 0.65
134 19 0.16
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (132 bp):
CCGGATCACATCATTTGGTATCAGAGCTACTAAAACGAGGAGCACCGACGTTCGTATCAAGCTCG
CAATAGGTTCGAAACGTGAAAAAAAAAATCAAAAAAAAAAGATGAGTTGTAATTTAAATTTTTTT
TT
Found at i:73290 original size:13 final size:13
Alignment explanation
Indices: 73272--73347 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 13
73262 TTGGAGTAAC
73272 AAAAAAAATCAAA
1 AAAAAAAATCAAA
*
73285 AAAAAAATTCGAAA
1 AAAAAAAATC-AAA
*
73299 AAAAAAATTGATTGAAA
1 AAAAAAA---A-TCAAA
*
73316 AAAAAAATTC-AA
1 AAAAAAAATCAAA
* *
73328 AAAAAAAGTGAAA
1 AAAAAAAATCAAA
73341 AAAAAAA
1 AAAAAAA
73348 TCGAGCAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
12 10 0.20
13 19 0.38
14 10 0.20
17 10 0.20
18 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAAAAAATCAAA
Found at i:73357 original size:16 final size:16
Alignment explanation
Indices: 73326--73379 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
73316 AAAAAAATTC
73326 AAAAAAAAAGT--G-A
1 AAAAAAAAAGTGAGCA
73339 AAAAAAAAA-TCGAGCA
1 AAAAAAAAAGT-GAGCA
73355 AAAAAAAAAGGTGAGCA
1 AAAAAAAAA-GTGAGCA
73372 AAAAAAAA
1 AAAAAAAA
73380 TCAAGTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.03
13 9 0.26
15 1 0.03
16 10 0.29
17 13 0.37
18 1 0.03
ACGTcount: A:0.74, C:0.06, G:0.15, T:0.06
Consensus pattern (16 bp):
AAAAAAAAAGTGAGCA
Found at i:73359 original size:25 final size:25
Alignment explanation
Indices: 73272--73348 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 25
73262 TTGGAGTAAC
*
73272 AAAAAAAA-TCAAAAAAAAAATTCGAA
1 AAAAAAAAGTGAAAAAAAAAATTC--A
73298 AAAAAAAATTGATTGAAAAAAAAAATTCA
1 AAAAAAAA--G--TGAAAAAAAAAATTCA
73327 AAAAAAAAGTGAAAAAAAAAAT
1 AAAAAAAAGTGAAAAAAAAAAT
73349 CGAGCAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
25 13 0.29
26 8 0.18
27 1 0.02
29 9 0.20
31 14 0.31
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.14
Consensus pattern (25 bp):
AAAAAAAAGTGAAAAAAAAAATTCA
Found at i:73359 original size:42 final size:43
Alignment explanation
Indices: 73272--73363 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 43
73262 TTGGAGTAAC
* *
73272 AAAAAAAATCAAAAAAAAAATTCGAAAAAAAAAATTGATTG-AAA
1 AAAAAAAATCAAAAAAAAAAGTCGAAAAAAAAAATCGA--GCAAA
*
73316 AAAAAAATTC-AAAAAAAAAGT-GAAAAAAAAAATCGAGCAAA
1 AAAAAAAATCAAAAAAAAAAGTCGAAAAAAAAAATCGAGCAAA
73357 AAAAAAA
1 AAAAAAA
73364 GGTGAGCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
40 1 0.02
41 10 0.23
42 14 0.32
43 10 0.23
44 9 0.20
ACGTcount: A:0.75, C:0.05, G:0.08, T:0.12
Consensus pattern (43 bp):
AAAAAAAATCAAAAAAAAAAGTCGAAAAAAAAAATCGAGCAAA
Found at i:74454 original size:17 final size:18
Alignment explanation
Indices: 74422--74455 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
74412 AAAAGAGAGT
*
74422 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
74440 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
74456 GGAGTGTTGT
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:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:76447 original size:20 final size:21
Alignment explanation
Indices: 76399--76448 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
76389 TATTGATGCT
*
76399 TTAGTGTGAACAACTTAAGTG
1 TTAGTGTGAACAAATTAAGTG
76420 TTAG-GTGAACAAGATT-A-TG
1 TTAGTGTGAACAA-ATTAAGTG
76439 TTAGTGTGAA
1 TTAGTGTGAA
76449 TACTATTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 14 0.54
21 6 0.23
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (21 bp):
TTAGTGTGAACAAATTAAGTG
Found at i:76974 original size:20 final size:19
Alignment explanation
Indices: 76949--76986 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
76939 AATTAGTTAT
76949 TTCAGCTCACCTGAGCTCAA
1 TTCAGCTCA-CTGAGCTCAA
*
76969 TTCAGCTCATTGAGCTCA
1 TTCAGCTCACTGAGCTCA
76987 TTATTAGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.29
Consensus pattern (19 bp):
TTCAGCTCACTGAGCTCAA
Found at i:79878 original size:22 final size:22
Alignment explanation
Indices: 79847--79888 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
79837 CCTTTTTGAA
79847 CCATTACCATTTCGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
*
79869 CCATTGCCATTTCGTACCAA
1 CCATTACCATTTCGTACCAA
79889 TTCCCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.33, G:0.07, T:0.31
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:83208 original size:33 final size:33
Alignment explanation
Indices: 83149--83223 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 33
83139 TTCTTGATTA
*
83149 CTTTCTTCACTCGTTTCTTTTGCAAACTCTTTTT
1 CTTT-TTCACTCGTTTCTTTTGCAAACTCTATTT
83183 CTTTTTCACTCGATTTCTTTT-CAAACTCTATTT
1 CTTTTTCACTCG-TTTCTTTTGCAAACTCTATTT
83216 CTTTTTCA
1 CTTTTTCA
83224 TTCTCAATCT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 27 0.69
34 12 0.31
ACGTcount: A:0.15, C:0.25, G:0.04, T:0.56
Consensus pattern (33 bp):
CTTTTTCACTCGTTTCTTTTGCAAACTCTATTT
Found at i:83215 original size:17 final size:17
Alignment explanation
Indices: 83162--83220 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
83152 TCTTCACTCG
*
83162 TTTCTTTTGCAAACTCTT
1 TTTCTTTT-CAAACTCTA
*
83180 TTTCTTTTTC--ACTCGA
1 TTTC-TTTTCAAACTCTA
83196 TTTCTTTTCAAACTCTA
1 TTTCTTTTCAAACTCTA
83213 TTTCTTTT
1 TTTCTTTT
83221 TCATTCTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 5 0.14
16 8 0.23
17 13 0.37
18 5 0.14
19 4 0.11
ACGTcount: A:0.15, C:0.22, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTCTTTTCAAACTCTA
Found at i:83223 original size:18 final size:18
Alignment explanation
Indices: 83162--83223 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
83152 TCTTCACTCG
* *
83162 TTTCTTTTGCAAACTCTT
1 TTTCTTTTTCAAACTCTA
*
83180 TTTCTTTTTC--ACTCGA
1 TTTCTTTTTCAAACTCTA
83196 TTTC-TTTTCAAACTCTA
1 TTTCTTTTTCAAACTCTA
83213 TTTCTTTTTCA
1 TTTCTTTTTCA
83224 TTCTCAATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 5 0.14
16 8 0.22
17 9 0.24
18 15 0.41
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTCTTTTTCAAACTCTA
Found at i:90444 original size:20 final size:19
Alignment explanation
Indices: 90421--90485 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
90411 AAGCTCAAAC
90421 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
90441 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
90461 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
90481 GAGCT
1 GAGCT
90486 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:93989 original size:54 final size:54
Alignment explanation
Indices: 93925--94033 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
93915 GAATTGAAAG
*
93925 TTTAAAGAAACTCATCTTTAGTTAAATAATTGAGTTGTTGAACATTTATTCAAC
1 TTTAAAGAAACTCATCTTTAGTTAAATAATTGAGTTGCTGAACATTTATTCAAC
93979 TTTAAAGAAACTCATCTTTAGTTAAATAATTGAGTTGCTGAACATTTATTCAAC
1 TTTAAAGAAACTCATCTTTAGTTAAATAATTGAGTTGCTGAACATTTATTCAAC
94033 T
1 T
94034 CATCTTTGTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (54 bp):
TTTAAAGAAACTCATCTTTAGTTAAATAATTGAGTTGCTGAACATTTATTCAAC
Found at i:103628 original size:11 final size:10
Alignment explanation
Indices: 103611--103638 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
103601 TTGATTTCAC
103611 ATTTTTTTGA
1 ATTTTTTTGA
103621 ATTTTTTTGA
1 ATTTTTTTGA
103631 ATTTTTTT
1 ATTTTTTT
103639 AAAATCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (10 bp):
ATTTTTTTGA
Found at i:103703 original size:14 final size:14
Alignment explanation
Indices: 103675--103715 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
103665 GAACACTTGA
103675 TTTCACAATTTTTT
1 TTTCACAATTTTTT
*
103689 TTTCA-AATTTCTT
1 TTTCACAATTTTTT
103702 TTTCTA-AATTTTTT
1 TTTC-ACAATTTTTT
103716 CAATTTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTCACAATTTTTT
Found at i:104045 original size:54 final size:54
Alignment explanation
Indices: 103979--104087 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
103969 GAACTGAAAT
*
103979 TTTAAAAAAACTCATCTTTAGTTAAATAATTGAGTTGCTGAACATTTATTCAAC
1 TTTAAAAAAACTCATCTTTAGTTAAATAATTGAGTTGCCGAACATTTATTCAAC
*
104033 TTTAAAGAAACTCATCTTTAGTTAAATAATTGAGTTGCCGAACATTTATTCAAC
1 TTTAAAAAAACTCATCTTTAGTTAAATAATTGAGTTGCCGAACATTTATTCAAC
104087 T
1 T
104088 CATCTTTGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.39
Consensus pattern (54 bp):
TTTAAAAAAACTCATCTTTAGTTAAATAATTGAGTTGCCGAACATTTATTCAAC
Done.