Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4342.1
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: 66123
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1038 original size:85 final size:85
Alignment explanation
Indices: 895--1158 Score: 501
Period size: 85 Copynumber: 3.1 Consensus size: 85
885 GGCCGGCCAT
*
895 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAGGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
960 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
980 GAGCATGGGTGGACAGGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAGGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1045 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
1065 GAGCATGGGTGGACAGGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAGGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
*
1130 GTAAGGATTAACAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
1150 GGGCATGGG
1 GAGCATGGG
1159 CAATAAAATA
Statistics
Matches: 176, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 176 1.00
ACGTcount: A:0.37, C:0.09, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAGGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:3398 original size:47 final size:47
Alignment explanation
Indices: 3347--4387 Score: 1938
Period size: 47 Copynumber: 22.1 Consensus size: 47
3337 TTAGGATTTT
*
3347 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3394 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
***
3441 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
3492 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3539 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3586 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3633 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3680 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3727 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3774 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3821 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3868 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3915 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
3962 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
4009 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
4056 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
4103 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
4150 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
4197 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
4244 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
4291 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
** * * *
4338 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
4385 ATG
1 ATG
4388 CGAAACGTGT
Statistics
Matches: 976, Mismatches: 14, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
47 931 0.95
49 2 0.00
51 43 0.04
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
Found at i:4450 original size:46 final size:46
Alignment explanation
Indices: 4361--4451 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
4351 GAACATGAAT
* * * *
4361 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
* * *
4407 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTACGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATG
4452 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.25
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
Found at i:4704 original size:37 final size:37
Alignment explanation
Indices: 4596--4704 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
4586 GGAAATATAT
*
4596 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
4633 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
4670 TCCGGGTAAGACCCGATAACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
4705 CGTCTGAGCT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:6575 original size:27 final size:27
Alignment explanation
Indices: 6531--6620 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
6521 GTTACAATTA
* *
6531 TTTTTCCCTTATGTGGTAAAATGACTG
1 TTTTGCCCTTATATGGTAAAATGACTG
* * *
6558 TTGTGCCCTTATACGGTAAAATGACTA
1 TTTTGCCCTTATATGGTAAAATGACTG
* *
6585 TTTTGCCCTTGTATGGTAATATGACTG
1 TTTTGCCCTTATATGGTAAAATGACTG
6612 TTTTGCCCT
1 TTTTGCCCT
6621 ATGTGATGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (27 bp):
TTTTGCCCTTATATGGTAAAATGACTG
Found at i:6963 original size:18 final size:18
Alignment explanation
Indices: 6940--7002 Score: 81
Period size: 18 Copynumber: 3.5 Consensus size: 18
6930 GACTTGTATT
*
6940 CTGTTACTGCATTGATTA
1 CTGTTACTGCACTGATTA
6958 CTGTTACTGCACTGATTA
1 CTGTTACTGCACTGATTA
* * *
6976 CTGCTGCTGCACTGTTTA
1 CTGTTACTGCACTGATTA
*
6994 TTGTTACTG
1 CTGTTACTG
7003 TATTGGGCCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (18 bp):
CTGTTACTGCACTGATTA
Found at i:11314 original size:40 final size:40
Alignment explanation
Indices: 11283--11413 Score: 210
Period size: 40 Copynumber: 3.3 Consensus size: 40
11273 GGACTAAGAT
11283 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* * *
11323 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
*
11363 CCGAAGGCATTTGTGCGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATT-AATTCCGGGTTAAGTC
11403 CCGAAGGCATT
1 CCGAAGGCATT
11414 GTATGAGTTA
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 82 0.99
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
Found at i:11434 original size:39 final size:38
Alignment explanation
Indices: 11231--11450 Score: 167
Period size: 40 Copynumber: 5.6 Consensus size: 38
11221 TGAATGCTGT
* * * *
11231 CCGGGCTAAGTCCCGAAGGC-TCTGTGCTAAGTGACTATAT
1 CCGGGTTAAGTCCCGAAGGCAT-TGTGC-GAGTTACTA-AA
** * *
11271 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAATT
1 CCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
11311 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAA-A
*
11351 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-AAA
**
11390 TCCGGGTTAAGTCCCGAAGGCATTGTATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTA-AA
* *
11430 CCGGGCTATGTCCCGAAGGCA
1 CCGGGTTAAGTCCCGAAGGCA
11451 CTTGAACGAG
Statistics
Matches: 151, Mismatches: 18, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
39 33 0.22
40 110 0.73
41 7 0.05
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:14911 original size:47 final size:45
Alignment explanation
Indices: 14840--15057 Score: 169
Period size: 46 Copynumber: 4.6 Consensus size: 45
14830 GGGTTATTGT
* *
14840 GAGCTAGTGTAAGACCTGTCTGGGACATGCATCGGCCATATTATGA-
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAT-TGA-GAC
*
14886 GAGCCAGTGTAAGAACATGTCTGGGACATGGCATCGG-CATTGAGAC
1 GAGCTAGTGTAAG-ACATGTCTGGGACAT-GCATCGGCCATTGAGAC
* *
14932 GAGGGCTAGTGTAAGACATGTTTGGGACATGCATCGGCC-TCGAGAC
1 GA--GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTGAGAC
* * **
14978 ATAAG-TCAGTGTAAGACATGTCTGGGA-ATGGTATCGGCACAGATATGCTA-
1 --GAGCT-AGTGTAAGACATGTCTGGGACAT-GCATCGGC-C--AT-TGAGAC
*
15028 GAGCTTGTGTAAGACCATGTCTGGGACATG
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG
15058 GCATTGACAC
Statistics
Matches: 140, Mismatches: 14, Indels: 33
0.75 0.07 0.18
Matches are distributed among these distances:
45 5 0.04
46 56 0.40
47 33 0.24
48 28 0.20
49 13 0.09
50 3 0.02
51 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTGAGAC
Found at i:22105 original size:46 final size:46
Alignment explanation
Indices: 22050--22507 Score: 799
Period size: 46 Copynumber: 9.8 Consensus size: 46
22040 GGTTGAGCAT
*
22050 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
22096 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
22142 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
22188 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
22234 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
22280 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
22326 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATAACTAGGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG---AAC---GC
* * *
22378 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
1 --CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
22426 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
22472 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
22508 GCGGGTTACA
Statistics
Matches: 397, Mismatches: 7, Indels: 16
0.95 0.02 0.04
Matches are distributed among these distances:
46 349 0.88
48 1 0.00
49 3 0.01
51 2 0.01
52 2 0.01
54 40 0.10
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:23313 original size:41 final size:41
Alignment explanation
Indices: 23253--23331 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
23243 AAATTGAAGT
*
23253 TTAATGAGTCTATTTTCATGTGGATTGAACAAAACAGGAGC
1 TTAATGAGTCTATTCTCATGTGGATTGAACAAAACAGGAGC
*
23294 TTAATGAGTCTATTCTCATGTGGATTGAACAAATCAGG
1 TTAATGAGTCTATTCTCATGTGGATTGAACAAAACAGG
23332 CATATAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (41 bp):
TTAATGAGTCTATTCTCATGTGGATTGAACAAAACAGGAGC
Found at i:26907 original size:39 final size:39
Alignment explanation
Indices: 26862--26940 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
26852 CTGCGGTGGT
*
26862 ATTTGCTTCGAAGATTTGGCGATATTATTTGTATGGTGA
1 ATTTGCTTCGAAGATTTGGCGACATTATTTGTATGGTGA
*
26901 ATTTGCTTTGAAGATTTGGCGACATTATTTGTATGGTGA
1 ATTTGCTTCGAAGATTTGGCGACATTATTTGTATGGTGA
26940 A
1 A
26941 AAGTGCCGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.24, C:0.08, G:0.25, T:0.43
Consensus pattern (39 bp):
ATTTGCTTCGAAGATTTGGCGACATTATTTGTATGGTGA
Found at i:28678 original size:34 final size:34
Alignment explanation
Indices: 28635--28701 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
28625 ATTTTCGAGA
*
28635 ACGAAAATCCTTAAAGGGGGGGAGAGTTGTAATG
1 ACGAAAATCCTTAAAAGGGGGGAGAGTTGTAATG
28669 ACGAAAATCCTTAAAAGGGGGGAGAGTTGTAAT
1 ACGAAAATCCTTAAAAGGGGGGAGAGTTGTAAT
28702 ATCCTGAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.09, G:0.33, T:0.21
Consensus pattern (34 bp):
ACGAAAATCCTTAAAAGGGGGGAGAGTTGTAATG
Found at i:29577 original size:46 final size:46
Alignment explanation
Indices: 29522--29628 Score: 205
Period size: 46 Copynumber: 2.3 Consensus size: 46
29512 GGTTGAGCAT
*
29522 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
29568 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
29614 CCGAGCTCGTTGAGT
1 CCGAGCTCGTTGAGT
29629 GTAACTAGGC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:35828 original size:23 final size:23
Alignment explanation
Indices: 35796--35841 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
35786 CATTCATTGA
35796 TCTTTAGCCATCCCTCACCACCC
1 TCTTTAGCCATCCCTCACCACCC
*
35819 TCTTTGGCCATCCCTCACCACCC
1 TCTTTAGCCATCCCTCACCACCC
35842 CAAACTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.52, G:0.07, T:0.26
Consensus pattern (23 bp):
TCTTTAGCCATCCCTCACCACCC
Found at i:37764 original size:23 final size:23
Alignment explanation
Indices: 37738--37782 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
37728 TTATATTAAA
37738 ATTAAAAATAAAATATAAATATG
1 ATTAAAAATAAAATATAAATATG
*
37761 ATTAAAAATAAAATATATATAT
1 ATTAAAAATAAAATATAAATAT
37783 TTAGTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
ATTAAAAATAAAATATAAATATG
Found at i:43007 original size:71 final size:71
Alignment explanation
Indices: 42923--43206 Score: 559
Period size: 71 Copynumber: 4.0 Consensus size: 71
42913 ACTATTTCAT
42923 TTGATTGTTCATATTTCTTAATTAAAATGCAAACGATTTCTAGACATAGAAGACTGTTTGTATAC
1 TTGATTGTTCATATTTCTTAATTAAAATGCAAACGATTTCTAGACATAGAAGACTGTTTGTATAC
42988 TTATAA
66 TTATAA
42994 TTGATTGTTCATATTTCTTAATTAAAATGCAAACGATTTCTAGACATAGAAGACTGTTTGTATAC
1 TTGATTGTTCATATTTCTTAATTAAAATGCAAACGATTTCTAGACATAGAAGACTGTTTGTATAC
43059 TTATAA
66 TTATAA
43065 TTGATTGTTCATATTTCTTAATTAAAATGCAAACGATTTCTAGACATAGAAGACTGTTTGTATAC
1 TTGATTGTTCATATTTCTTAATTAAAATGCAAACGATTTCTAGACATAGAAGACTGTTTGTATAC
43130 TTATAA
66 TTATAA
*
43136 TTGATTGTTCATATTTCTTAATTAAAATGCAAACGATTTCTAGACATAGAAGACTGTTCGTATAC
1 TTGATTGTTCATATTTCTTAATTAAAATGCAAACGATTTCTAGACATAGAAGACTGTTTGTATAC
43201 TTATAA
66 TTATAA
43207 ACTGATTCTA
Statistics
Matches: 212, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 212 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (71 bp):
TTGATTGTTCATATTTCTTAATTAAAATGCAAACGATTTCTAGACATAGAAGACTGTTTGTATAC
TTATAA
Found at i:43750 original size:23 final size:25
Alignment explanation
Indices: 43724--43770 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
43714 TATCATTCAT
*
43724 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
43747 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
43771 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:44119 original size:46 final size:46
Alignment explanation
Indices: 44031--44334 Score: 327
Period size: 46 Copynumber: 7.0 Consensus size: 46
44021 TTTGACGTGA
* * * * * * *
44031 TGCCATAGTGTCTTTCAACTATGGCCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
44077 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
44123 TGCCATGGTATCTTTCAACCATAGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
44169 TGCCATGGTATCTTCCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
44215 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
44253 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
44291 TGCCATGGTATCTTTTAACTATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
44335 AGAGCACACT
Statistics
Matches: 229, Mismatches: 20, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
38 69 0.30
39 1 0.00
40 3 0.01
41 1 0.00
43 1 0.00
44 3 0.01
45 5 0.02
46 146 0.64
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:44261 original size:38 final size:38
Alignment explanation
Indices: 44210--44323 Score: 210
Period size: 38 Copynumber: 3.0 Consensus size: 38
44200 CATTTCATAT
44210 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
44248 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
* *
44286 CAGGTTGCCATGGTATCTTTTAACTATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
44324 TTTCATATCA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 74 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:46488 original size:27 final size:27
Alignment explanation
Indices: 46456--46535 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
46446 TTTCTTTATA
46456 TATTAATAAAATAATAATAAAATATCT
1 TATTAATAAAATAATAATAAAATATCT
* *
46483 TATTAA-AGTATTAATAA-AATAATAT-T
1 TATTAATA-AAATAATAATAA-AATATCT
* *
46509 TATCTAATTAAATAATTATAAAATATC
1 TAT-TAATAAAATAATAATAAAATATC
46536 AAAATATCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
26 7 0.17
27 32 0.78
28 2 0.05
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (27 bp):
TATTAATAAAATAATAATAAAATATCT
Found at i:46489 original size:24 final size:24
Alignment explanation
Indices: 46453--46508 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
46443 TTCTTTCTTT
46453 ATATATTAATAAAATAATAATAAA
1 ATATATTAATAAAATAATAATAAA
* * * *
46477 ATATCTTATTAAAGTATTAATAAA
1 ATATATTAATAAAATAATAATAAA
46501 ATAATATT
1 AT-ATATT
46509 TATCTAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
ATATATTAATAAAATAATAATAAA
Found at i:54075 original size:21 final size:21
Alignment explanation
Indices: 54051--54120 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
54041 GGGTGTCGAC
54051 CACGGCCTGGCCATTGACCCA
1 CACGGCCTGGCCATTGACCCA
54072 CACGGCCTGGCCATTGACCCA
1 CACGGCCTGGCCATTGACCCA
* * *
54093 TACGGCCTGACCATTAACCCA
1 CACGGCCTGGCCATTGACCCA
54114 CACGGCC
1 CACGGCC
54121 GTGTGCAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.14
Consensus pattern (21 bp):
CACGGCCTGGCCATTGACCCA
Found at i:55040 original size:13 final size:13
Alignment explanation
Indices: 55022--55050 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
55012 TTTAGTTCAG
55022 TTAGTTAATTAGT
1 TTAGTTAATTAGT
55035 TTAGTTAATTAGT
1 TTAGTTAATTAGT
55048 TTA
1 TTA
55051 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:57187 original size:118 final size:118
Alignment explanation
Indices: 56979--57213 Score: 434
Period size: 118 Copynumber: 2.0 Consensus size: 118
56969 GGCCTTATTA
* *
56979 CATTTAAAAACCCAAAACTTCAAACGTAAATAAAAGGATGTCCAGTTCACCAGAAGAAAATCAAA
1 CATTTAAAAACCCAAAACTTCAAACGTAAATAAAAAGATGTCCAATTCACCAGAAGAAAATCAAA
*
57044 CTTTCAGAACGGGTGGCCACTCCGAATTCCCTCACAGCTCCAATCCCACTATG
66 CTTTCAGAACGGGTGGCCACTCCGAATTCCCTCACAGCTCCAAGCCCACTATG
57097 CATTTAAAAACCCAAAACTTCAAACGTAAATAAAAAGATGTCCAATTCACCAGAAGAAAATCAAA
1 CATTTAAAAACCCAAAACTTCAAACGTAAATAAAAAGATGTCCAATTCACCAGAAGAAAATCAAA
*
57162 CTTTCAGAACGGGTGGCCACTCCGAATTCCCTCACAGCTCCAAGCTCACTAT
66 CTTTCAGAACGGGTGGCCACTCCGAATTCCCTCACAGCTCCAAGCCCACTAT
57214 AGTTGGGGAT
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (118 bp):
CATTTAAAAACCCAAAACTTCAAACGTAAATAAAAAGATGTCCAATTCACCAGAAGAAAATCAAA
CTTTCAGAACGGGTGGCCACTCCGAATTCCCTCACAGCTCCAAGCCCACTATG
Found at i:57566 original size:27 final size:26
Alignment explanation
Indices: 57518--57577 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
57508 GCGAGGCTGC
*
57518 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
*
57545 CAGATATTGTGGC-AGAGCCACCAGAA
1 CAGATATTGTGACGA-AGCCACCAGAA
*
57571 CAAATAT
1 CAGATAT
57578 AGATATATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:57666 original size:27 final size:26
Alignment explanation
Indices: 57618--57748 Score: 131
Period size: 27 Copynumber: 4.9 Consensus size: 26
57608 GCAAGGCTGC
* *
57618 CAGATATTGTGAC-GAAGTCACCAGAT
1 CAGATATTGTGGCAG-AGCCACCAGAT
57644 ACAGATATTGTGGCAGAGCCACCAGAT
1 -CAGATATTGTGGCAGAGCCACCAGAT
*
57671 CAGATAATTGTGGCATAGCCACCAGGA-
1 CAGAT-ATTGTGGCAGAGCCACCA-GAT
**
57698 CAGATATATGTGGCAGAGCTGCCAGAT
1 CAGATAT-TGTGGCAGAGCCACCAGAT
* *
57725 CAAATAATTGTGGCATAGCCACCA
1 CAGAT-ATTGTGGCAGAGCCACCA
57749 AGACGCTTCC
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
26 9 0.10
27 74 0.84
28 5 0.06
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAT
Found at i:57710 original size:54 final size:53
Alignment explanation
Indices: 57644--57748 Score: 174
Period size: 54 Copynumber: 2.0 Consensus size: 53
57634 GTCACCAGAT
*
57644 ACAGATATTGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGG
1 ACAGATATTGTGGCAGAGCCACCAGATCAAATAATTGTGGCATAGCCACCAGG
**
57697 ACAGATATATGTGGCAGAGCTGCCAGATCAAATAATTGTGGCATAGCCACCA
1 ACAGATAT-TGTGGCAGAGCCACCAGATCAAATAATTGTGGCATAGCCACCA
57749 AGACGCTTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 8 0.17
54 40 0.83
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (53 bp):
ACAGATATTGTGGCAGAGCCACCAGATCAAATAATTGTGGCATAGCCACCAGG
Done.