Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold885
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1053811
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 99868 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:969056 original size:106 final size:106
Alignment explanation
Indices: 968871--969296 Score: 816
Period size: 106 Copynumber: 4.0 Consensus size: 106
968861 AAAAACTTAT
* *
968871 GTTCTAACTATGGTGTAGACTTATGCAGGATATGTGGTCTTACGAAATAATTCAGTAAGAAATCA
1 GTTCTAACTACGGTGTAGACTAATGCAGGATATGTGGTCTTACGAAATAATTCAGTAAGAAATCA
968936 CGTATATTCTTTAAAGGAATGTTATTAAACTAATATTGGTG
66 CGTATATTCTTTAAAGGAATGTTATTAAACTAATATTGGTG
968977 GTTCTAACTACGGTGTAGACTAATGCAGGATATGTGGTCTTACGAAATAATTCAGTAAGAAATCA
1 GTTCTAACTACGGTGTAGACTAATGCAGGATATGTGGTCTTACGAAATAATTCAGTAAGAAATCA
969042 CGTATATTCTTTAAAGGAATGTTATTAAACTAATATTGGTG
66 CGTATATTCTTTAAAGGAATGTTATTAAACTAATATTGGTG
969083 GTTCTAACTACGGTGTAGACTAATGCAGGATATGTGGTCTTACGAAATAATTCAGTAAGAAATCA
1 GTTCTAACTACGGTGTAGACTAATGCAGGATATGTGGTCTTACGAAATAATTCAGTAAGAAATCA
969148 CGTATATTCTTTAAAGGAATGTTATTAAACTAATATTGGTG
66 CGTATATTCTTTAAAGGAATGTTATTAAACTAATATTGGTG
969189 GTTCTAACTACGGTGTAGACTAATGCAGGATATGTGGTCTTACGAAATAATTCAGTAAGAAATCA
1 GTTCTAACTACGGTGTAGACTAATGCAGGATATGTGGTCTTACGAAATAATTCAGTAAGAAATCA
* *
969254 CATTTATTCTTTAAAGGAATGTTATTAAACTAATATTGGTG
66 CGTATATTCTTTAAAGGAATGTTATTAAACTAATATTGGTG
969295 GT
1 GT
969297 CAAAATGAAG
Statistics
Matches: 316, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 316 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (106 bp):
GTTCTAACTACGGTGTAGACTAATGCAGGATATGTGGTCTTACGAAATAATTCAGTAAGAAATCA
CGTATATTCTTTAAAGGAATGTTATTAAACTAATATTGGTG
Found at i:976541 original size:38 final size:38
Alignment explanation
Indices: 976490--976646 Score: 314
Period size: 38 Copynumber: 4.1 Consensus size: 38
976480 TCTGACATGA
976490 AAATTGGTCTGCCATCATATCTAATGATGAACGTCAAC
1 AAATTGGTCTGCCATCATATCTAATGATGAACGTCAAC
976528 AAATTGGTCTGCCATCATATCTAATGATGAACGTCAAC
1 AAATTGGTCTGCCATCATATCTAATGATGAACGTCAAC
976566 AAATTGGTCTGCCATCATATCTAATGATGAACGTCAAC
1 AAATTGGTCTGCCATCATATCTAATGATGAACGTCAAC
976604 AAATTGGTCTGCCATCATATCTAATGATGAACGTCAAC
1 AAATTGGTCTGCCATCATATCTAATGATGAACGTCAAC
976642 AAATT
1 AAATT
976647 ACATATAAAT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 119 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (38 bp):
AAATTGGTCTGCCATCATATCTAATGATGAACGTCAAC
Found at i:977431 original size:63 final size:62
Alignment explanation
Indices: 977322--977657 Score: 347
Period size: 63 Copynumber: 5.4 Consensus size: 62
977312 TAGTCCCGGC
* * * *
977322 AGCTATAACAATATCAATGTAGCCTGCAGGGTAAGTCAAGTTAACAGGATAGATAACTCCTCT
1 AGCTATAACAATATCAATGTAGCTTG-AGAGTAAGTCAAGTAAACAGGATAGATAACTCCTGT
* *
977385 AACTATAACAATATCAATGTAGCTTGTAGAGTAAGTCAGGTAAACAGGATAGATAACTCCTGT
1 AGCTATAACAATATCAATGTAGCTTG-AGAGTAAGTCAAGTAAACAGGATAGATAACTCCTGT
* * * *
977448 AGCTATAACAATATCAAAGTAGCTTGAAGAGTAAGTAAAGTAAACAGGATAGGTAACTTCTGT
1 AGCTATAACAATATCAATGTAGCTTG-AGAGTAAGTCAAGTAAACAGGATAGATAACTCCTGT
* * * * *
977511 AGCTATAACAATATCAATGTA-CATGAGGAGTAAGTCAAGAAAACAGGGT-GA-AACTCATGA
1 AGCTATAACAATATCAATGTAGCTTGA-GAGTAAGTCAAGTAAACAGGATAGATAACTCCTGT
* * * * * * ** * ** *
977571 AGTTATAACAATATAAATGTAGTTTTTAGAGCAAGGCAAGTGTACAGAATTCACAACTCC-GAT
1 AGCTATAACAATATCAATGTAG-CTTGAGAGTAAGTCAAGTAAACAGGATAGATAACTCCTG-T
977634 AGCTATAACAATATCAATGTAGCT
1 AGCTATAACAATATCAATGTAGCT
977658 GAAGGCTTGA
Statistics
Matches: 226, Mismatches: 41, Indels: 13
0.81 0.15 0.05
Matches are distributed among these distances:
60 25 0.11
61 17 0.08
62 27 0.12
63 157 0.69
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (62 bp):
AGCTATAACAATATCAATGTAGCTTGAGAGTAAGTCAAGTAAACAGGATAGATAACTCCTGT
Found at i:977639 original size:186 final size:188
Alignment explanation
Indices: 977322--977661 Score: 422
Period size: 186 Copynumber: 1.8 Consensus size: 188
977312 TAGTCCCGGC
* ** * *
977322 AGCTATAACAATATCAATGTAGCCTGCAGGGTAAGTCAAGTTAACAGGATAGATAACTCCTCTAA
1 AGCTATAACAATATCAATGTAGCATGCAGGGTAAGTCAAGAAAACAGGATAGATAACTCATCGAA
* * * * * * *
977387 CTATAACAATATCAATGTAGCTTGTAGAGTAAGTCAGGTAAACAGGATAGATAACTCCTGTAGCT
66 CTATAACAATATAAATGTAGCTTGTAGAGCAAGGCAAGTAAACAGAATACACAACTCCTGTAGCT
977452 ATAACAATATCAAAGTAGCTTGAAGAGTAAGTAAAGTAAACAGGATAGGTAACTTCTGT
131 ATAACAATATCAAAGTAGC-TGAAGAGTAAGTAAAGTAAACAGGATAGGTAACTTCTGT
*
977511 AGCTATAACAATATCAATGTA-CATG-AGGAGTAAGTCAAGAAAACAGGGT-GA-AACTCAT-GA
1 AGCTATAACAATATCAATGTAGCATGCAGG-GTAAGTCAAGAAAACAGGATAGATAACTCATCGA
* * * ** *
977571 AGTTATAACAATATAAATGTAGTTTTTAGAGCAAGGCAAGTGTACAGAATTCACAACTCC-GATA
65 A-CTATAACAATATAAATGTAGCTTGTAGAGCAAGGCAAGTAAACAGAATACACAACTCCTG-TA
*
977635 GCTATAACAATATCAATGTAGCTGAAG
128 GCTATAACAATATCAAAGTAGCTGAAG
977662 GCTTGACTTC
Statistics
Matches: 128, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
185 8 0.06
186 74 0.58
187 5 0.04
188 20 0.16
189 21 0.16
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.25
Consensus pattern (188 bp):
AGCTATAACAATATCAATGTAGCATGCAGGGTAAGTCAAGAAAACAGGATAGATAACTCATCGAA
CTATAACAATATAAATGTAGCTTGTAGAGCAAGGCAAGTAAACAGAATACACAACTCCTGTAGCT
ATAACAATATCAAAGTAGCTGAAGAGTAAGTAAAGTAAACAGGATAGGTAACTTCTGT
Found at i:980151 original size:4 final size:4
Alignment explanation
Indices: 980142--980200 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
980132 TACAAATATN
980142 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
980190 TCTA TCTA TCT
1 TCTA TCTA TCT
980201 TACACTCACG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.24, C:0.25, G:0.00, T:0.51
Consensus pattern (4 bp):
TCTA
Found at i:982221 original size:17 final size:17
Alignment explanation
Indices: 982196--982252 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
982186 AGGGTATTAT
*
982196 TAATAAACGCTTCCTGA
1 TAATTAACGCTTCCTGA
*
982213 TAATTAACGCTTCATGA
1 TAATTAACGCTTCCTGA
982230 TAATTAACGCTTCCTGA
1 TAATTAACGCTTCCTGA
982247 TAATTA
1 TAATTA
982253 GTTTTTCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (17 bp):
TAATTAACGCTTCCTGA
Found at i:990676 original size:22 final size:22
Alignment explanation
Indices: 990619--990679 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
990609 CCTTTAAGCA
* *
990619 TCTTTAAGTGGCATTTACGCTC
1 TCTTTAAGTGGCCTTTACACTC
* *
990641 TCTTTACACT-GCCTTTACACTG
1 TCTTTA-AGTGGCCTTTACACTC
990663 TCTTTAAGTGGCCTTTA
1 TCTTTAAGTGGCCTTTA
990680 AGTCAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.43
Consensus pattern (22 bp):
TCTTTAAGTGGCCTTTACACTC
Found at i:991097 original size:2 final size:2
Alignment explanation
Indices: 991090--991120 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
991080 TCGGTGAAAA
991090 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
991121 GCGGTCTCTN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:991478 original size:167 final size:167
Alignment explanation
Indices: 991204--991510 Score: 411
Period size: 167 Copynumber: 1.8 Consensus size: 167
991194 CAACTTGAAC
* **
991204 CCCTGACCCAGGGGCCATGAATTTCGCAATTTAGGTAGAGGAGTTTGTGGACATCATAACCATGC
1 CCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGAGTCCGTGGACATCATAACCATGC
* *** * * * *
991269 ATTCAGTTTTTTCTCCACATGTGTCAGAGTAAAAAGGAAGATTTTCTAGGATTTAATACATTTTC
66 ACTCAGTTTTTTCAAAACATATATCAGAGTAAAAAGGAAGATTTTCTAAGATCTAATACATTTTC
991334 ACTATATGGCTAAATTGGCCTTGCCCTAGGGCCTAAA
131 ACTATATGGCTAAATTGGCCTTGCCCTAGGGCCTAAA
* * * *
991371 CCCTGCCCCGGGGGTCATGAATTTCACAATTTAGGTAGAGGAGTCCGTGGACATCTTAACCATGC
1 CCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGAGTCCGTGGACATCATAACCATGC
* ** *
991436 ACTCAGTTTTATT-AAAATATATATGGGAGTAGAGAA-GAAGATTTTCTAAGATCTAATACATTT
66 ACTCAGTTTT-TTCAAAACATATATCAGAGTA-AAAAGGAAGATTTTCTAAGATCTAATACATTT
991499 TCACTATATGGC
129 TCACTATATGGC
991511 CAAAGTGAAC
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
167 114 0.96
168 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (167 bp):
CCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGGAGTCCGTGGACATCATAACCATGC
ACTCAGTTTTTTCAAAACATATATCAGAGTAAAAAGGAAGATTTTCTAAGATCTAATACATTTTC
ACTATATGGCTAAATTGGCCTTGCCCTAGGGCCTAAA
Found at i:1009851 original size:20 final size:20
Alignment explanation
Indices: 1009826--1009864 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1009816 AAATAGAATA
1009826 GAATGCCGGTTCCGGTCACG
1 GAATGCCGGTTCCGGTCACG
1009846 GAATGCCGGTTCCGGTCAC
1 GAATGCCGGTTCCGGTCAC
1009865 ATAATGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (20 bp):
GAATGCCGGTTCCGGTCACG
Found at i:1009870 original size:20 final size:20
Alignment explanation
Indices: 1009825--1009870 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1009815 AAAATAGAAT
1009825 AGAATGCCGGTTCCGGTCAC
1 AGAATGCCGGTTCCGGTCAC
*
1009845 GGAATGCCGGTTCCGGTCAC
1 AGAATGCCGGTTCCGGTCAC
*
1009865 ATAATG
1 AGAATG
1009871 GATTAGTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (20 bp):
AGAATGCCGGTTCCGGTCAC
Found at i:1017174 original size:12 final size:12
Alignment explanation
Indices: 1017140--1017181 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
1017130 TAAAAAGTTT
*
1017140 ACAGACAGACGG
1 ACAGACAGATGG
1017152 ACAGACAGATGG
1 ACAGACAGATGG
*
1017164 ACAGACGGAT-G
1 ACAGACAGATGG
1017175 ACAGACA
1 ACAGACA
1017182 AAATGTGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 7 0.26
12 20 0.74
ACGTcount: A:0.43, C:0.21, G:0.31, T:0.05
Consensus pattern (12 bp):
ACAGACAGATGG
Found at i:1025830 original size:170 final size:169
Alignment explanation
Indices: 1025348--1026058 Score: 1005
Period size: 170 Copynumber: 4.2 Consensus size: 169
1025338 AAAGAATCAT
1025348 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTC-TATAT--ATTCCTATGTAAA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTTATATAAATTCCTATGTAAA
* *
1025410 ACTTTAAC-ACCCCTCCCCCCAATGTGGCCTCACCCTAC-CCCAAGGGATCATGATTTTCACAAC
66 AC-TT--CGA-----CCCCCCATTGTGGCCCCACCCTACACCC-AGGGATCATGATTTTCACAAC
* *
1025473 TTTGAATCTACACTACCTGAGGATACTTCCACATAAGTTTCAGCTTTC
122 TTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * * **
1025521 CTGACTGATAAGTTTCTGAGAAGAAGATTTTTAAATATAAACT-TTATAT--ATTCCTATGTAAA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTTATATAAATTCCTATGTAAA
* * *
1025583 ACTTCAACCCCCCAATTGTGGCCCCATCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATC
66 ACTTCGACCCCCC-ATTGTGGCCCCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAATC
1025648 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
130 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*
1025688 CTGGCTGATTAGTTTCTGTGAAGAAGATCTTTT-AAGATTTACTCTATATATAAATTCCTATGTA
1 CTGGCTGATTAGTTTCTGAGAAGAAGAT-TTTTAAAGATTTACTCT-TATATAAATTCCTATGTA
* *
1025752 AAACTTCGAGCCCCCATTGTGGCCCCACCCTACACCCAGGGATCATGAGTTTCACAACTTTGAAT
64 AAACTTCGACCCCCCATTGTGGCCCCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAAT
* *
1025817 CAACACTACCTGAGGATTCTTCCACACAAGTTTCAGCTTTC
129 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
1025858 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATAAATTCCTATGTAA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCT-TATATAAATTCCTATGTAA
* * *
1025923 AACTTCGAGCCCCCATTGTGGCCCCACCCTACATCCAGGGGTCATGATTTTCACAACTTTGAATC
65 AACTTCGACCCCCCATTGTGGCCCCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAATC
1025988 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTT-
130 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
1026027 CTGGCT--TTCTGGTTCTTGAGAAGAAGATTTTT
1 CTGGCTGATT-AGTTTC-TGAGAAGAAGATTTTT
1026059 GAAAAATTCT
Statistics
Matches: 495, Mismatches: 31, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
166 6 0.01
167 116 0.23
168 12 0.02
169 31 0.06
170 245 0.49
171 25 0.05
172 2 0.00
173 58 0.12
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (169 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTTATATAAATTCCTATGTAAA
ACTTCGACCCCCCATTGTGGCCCCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAATCT
ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
Found at i:1026018 original size:340 final size:334
Alignment explanation
Indices: 1025347--1026058 Score: 1008
Period size: 337 Copynumber: 2.1 Consensus size: 334
1025337 TAAAGAATCA
1025347 TCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC
1 TCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC
* *
1025412 TTTAACACCCCTCCCCCCAATGTGGCCTCACCCTACCCCAAGGGATCATGATTTTCACAACTTTG
66 TTT-ACA---C-CCCCCCAATGTGGCCCCACCCTACCCCAAGGGATCATGAGTTTCACAACTTTG
* *
1025477 AATCTACACTACCTGAGGATACTTCCACATAAGTTTCAGCTTTCCTGACTGATAAGTTTCTGAGA
126 AATCAACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTCCTGACTGATAAGTTTCTGAGA
*
1025542 AGAAGATTTTTAAATATAAACTTTATATATTCCTATGTAAAACTTCAACCCCCCAATTGTGGCCC
191 AGAAGATTTTTAAAGATAAACTTTATATATTCCTATGTAAAACTTCAACCCCCCAATTGTGGCCC
* *
1025607 CATCCTACCCCCAGGGATCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAC
256 CACCCTACACCCAGGGATCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAC
1025672 ACAAGTTTCAGCTT
321 ACAAGTTTCAGCTT
*
1025686 TCCTGGCTGATTAGTTTCTGTGAAGAAGATCTTTT-AAGATTTACTCTATATATAAATTCCTATG
1 T-CTGGCTGATTAGTTTCTGAGAAGAAGAT-TTTTAAAGATTTACTC--TATAT--ATTCCTATG
* *
1025750 TAAAAC-TT-CGA-GCCCCCATTGTGGCCCCACCCTACACCC-AGGGATCATGAGTTTCACAACT
60 TAAAACTTTAC-ACCCCCCCAATGTGGCCCCACCCTAC-CCCAAGGGATCATGAGTTTCACAACT
* * *
1025811 TTGAATCAACACTACCTGAGGATTCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTG
123 TTGAATCAACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTCCTGACTGATAAGTTTCTG
** * *
1025876 AGAAGAAGATTTTTAAAGATTTACTCTATATATAAATTCCTATGTAAAACTTCGAGCCCCC-ATT
188 AGAAGAAGATTTTTAAAGATAAACT-T-TATAT--ATTCCTATGTAAAACTTCAACCCCCCAATT
* *
1025940 GTGGCCCCACCCTACATCCAGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATG
249 GTGGCCCCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATG
1026005 CTTCCACACAAGTTTCAGCTT
314 CTTCCACACAAGTTTCAGCTT
* *
1026026 TCTGGCT--TTCTGGTTCTTGAGAAGAAGATTTTT
1 TCTGGCTGATT-AGTTTC-TGAGAAGAAGATTTTT
1026059 GAAAAATTCT
Statistics
Matches: 337, Mismatches: 22, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
337 126 0.37
338 12 0.04
339 23 0.07
340 124 0.37
341 29 0.09
342 6 0.02
343 2 0.01
344 15 0.04
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (334 bp):
TCTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC
TTTACACCCCCCCAATGTGGCCCCACCCTACCCCAAGGGATCATGAGTTTCACAACTTTGAATCA
ACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTCCTGACTGATAAGTTTCTGAGAAGAAG
ATTTTTAAAGATAAACTTTATATATTCCTATGTAAAACTTCAACCCCCCAATTGTGGCCCCACCC
TACACCCAGGGATCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAG
TTTCAGCTT
Found at i:1028896 original size:170 final size:170
Alignment explanation
Indices: 1028614--1028934 Score: 624
Period size: 170 Copynumber: 1.9 Consensus size: 170
1028604 TTGAAAATAA
1028614 TTGATAAATTCGATGTAATGTATTCTAAAGCATTGTTTTTCAAGGAAACTTATTTATGAATACCT
1 TTGATAAATTCGATGTAATGTATTCTAAAGCATTGTTTTTCAAGGAAACTTATTTATGAATACCT
* *
1028679 TGAAAATAGTCAGATTTTAAATGGTACGAACAATTTAAATATATTTTGTAGTCGTATGTATTCCT
66 TGAAAATAGTCAGATTTAAAATGGTACGAACAATTTAAATATATTTTGTAGTCGTATGTATTCAT
1028744 ACACCAGAGTTCAATATGGTCAATATGAAAATAATTCAAT
131 ACACCAGAGTTCAATATGGTCAATATGAAAATAATTCAAT
1028784 TTGATAAATTCGATGTAATGTATTCTAAAGCATTGTTTTTCAAGGAAACTTATTTATGAATACCT
1 TTGATAAATTCGATGTAATGTATTCTAAAGCATTGTTTTTCAAGGAAACTTATTTATGAATACCT
1028849 TGAAAATAGTCAGATTTAAAATGGTACGAACAATTTAAATATATTTTGTAGTCGTATGTATTCAT
66 TGAAAATAGTCAGATTTAAAATGGTACGAACAATTTAAATATATTTTGTAGTCGTATGTATTCAT
1028914 ACACCAGAGTTCAATATGGTC
131 ACACCAGAGTTCAATATGGTC
1028935 TTATTCAACT
Statistics
Matches: 149, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 149 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (170 bp):
TTGATAAATTCGATGTAATGTATTCTAAAGCATTGTTTTTCAAGGAAACTTATTTATGAATACCT
TGAAAATAGTCAGATTTAAAATGGTACGAACAATTTAAATATATTTTGTAGTCGTATGTATTCAT
ACACCAGAGTTCAATATGGTCAATATGAAAATAATTCAAT
Found at i:1031544 original size:17 final size:17
Alignment explanation
Indices: 1031522--1031556 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1031512 CCCAGGTTTC
*
1031522 ACTTCGGGAGATCAAGA
1 ACTTCGAGAGATCAAGA
1031539 ACTTCGAGAGATCAAGA
1 ACTTCGAGAGATCAAGA
1031556 A
1 A
1031557 TAAATTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (17 bp):
ACTTCGAGAGATCAAGA
Found at i:1032266 original size:42 final size:44
Alignment explanation
Indices: 1032182--1032267 Score: 140
Period size: 42 Copynumber: 2.0 Consensus size: 44
1032172 TTAGTTCAGG
*
1032182 CACCACAGCATAGGTCAAATACAGTAGCACTATAATGGGGCATA
1 CACCACAGCATAGGTCAAATACAGCAGCACTATAATGGGGCATA
*
1032226 CACCACAGCATAGGTC-AA-ACAGCAGCACTGTAATGGGGCATA
1 CACCACAGCATAGGTCAAATACAGCAGCACTATAATGGGGCATA
1032268 ATTAAATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 22 0.55
43 2 0.05
44 16 0.40
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (44 bp):
CACCACAGCATAGGTCAAATACAGCAGCACTATAATGGGGCATA
Found at i:1034447 original size:2 final size:2
Alignment explanation
Indices: 1034440--1034481 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1034430 ATAGCGGTAC
1034440 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1034482 GTACCTCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1035666 original size:25 final size:25
Alignment explanation
Indices: 1035638--1035694 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
1035628 CTTTCAGAAC
*
1035638 AGTACAGTACATTATAGCATAGTAT
1 AGTACAGTACATCATAGCATAGTAT
* *
1035663 AGTATAATACATCATAGCATAGTAT
1 AGTACAGTACATCATAGCATAGTAT
*
1035688 AATACAG
1 AGTACAG
1035695 CAAAGTAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (25 bp):
AGTACAGTACATCATAGCATAGTAT
Found at i:1035678 original size:20 final size:20
Alignment explanation
Indices: 1035655--1035693 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1035645 TACATTATAG
*
1035655 CATAGTATAGTATAATACAT
1 CATAGCATAGTATAATACAT
1035675 CATAGCATAGTATAATACA
1 CATAGCATAGTATAATACA
1035694 GCAAAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (20 bp):
CATAGCATAGTATAATACAT
Found at i:1041679 original size:14 final size:11
Alignment explanation
Indices: 1041650--1041685 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1041640 TTATCTTAGC
1041650 TTTATTATGAA
1 TTTATTATGAA
1041661 TTTATTATGAA
1 TTTATTATGAA
**
1041672 CGTATTATGAA
1 TTTATTATGAA
1041683 TTT
1 TTT
1041686 GATAATTATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.53
Consensus pattern (11 bp):
TTTATTATGAA
Found at i:1052658 original size:2 final size:2
Alignment explanation
Indices: 1052651--1052676 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1052641 TGACATATTA
1052651 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1052677 ATTTTTAGTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1053381 original size:2 final size:2
Alignment explanation
Indices: 1053376--1053425 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1053366 TGTATATATC
1053376 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1053418 CT CT CT CT
1 CT CT CT CT
1053426 GCATGTTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1053778 original size:2 final size:2
Alignment explanation
Indices: 1053771--1053810 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1053761 TATGCCTTGG
1053771 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1053811 G
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.