Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold279
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: 97020
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1458 original size:40 final size:40
Alignment explanation
Indices: 1403--1671 Score: 450
Period size: 40 Copynumber: 6.8 Consensus size: 40
1393 TGAGCATTGG
1403 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1443 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1483 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
*
1523 GATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
1563 AATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGAT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* *
1603 GATATATCC-GGCTAAGACCCGAAGGCAATTATGCAAGTT
1 AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
* * *
1642 GATATGTCCGGGTTAAGACCCGAAGGCAAT
1 AATATATCCGGGCTAAGACCCGAAGGCAAT
1672 GTGTTTGCGG
Statistics
Matches: 216, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 35 0.16
40 181 0.84
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (40 bp):
AATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTT
Found at i:3901 original size:93 final size:93
Alignment explanation
Indices: 3789--3960 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
3779 CGCCCATAAG
* *
3789 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3854 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
3882 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3947 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
3961 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:3957 original size:46 final size:46
Alignment explanation
Indices: 3782--3957 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
3772 TGTAACCCGC
* * *
3782 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
3828 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
3878 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
3921 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
3958 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:11408 original size:93 final size:93
Alignment explanation
Indices: 11296--11467 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
11286 CGCCCATAAG
*
11296 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTCCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATCCGCATCCATAAGTGAACTCGGACTCAACTC
11360 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
* *
11389 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATCCGCATCCATAAGTGAACTCGGACTCAACTCA
11454 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
11468 TCAATCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATCCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:11464 original size:46 final size:46
Alignment explanation
Indices: 11289--11464 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
11279 TGTAACCCGC
* * *
11289 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTCCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
11335 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
11385 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
11428 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
11465 TGCTCAATCA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:20345 original size:31 final size:31
Alignment explanation
Indices: 20307--20369 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
20297 GTTATTATGA
20307 AATTAATGCTTCGATATGGTATAAAATGTAT
1 AATTAATGCTTCGATATGGTATAAAATGTAT
20338 AATTAATGCTTCGATATGGTATAAAATGTAT
1 AATTAATGCTTCGATATGGTATAAAATGTAT
20369 A
1 A
20370 CTTGTGTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (31 bp):
AATTAATGCTTCGATATGGTATAAAATGTAT
Found at i:32185 original size:40 final size:40
Alignment explanation
Indices: 32134--32530 Score: 668
Period size: 40 Copynumber: 9.9 Consensus size: 40
32124 ATAACCGCAA
* * * *
32134 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
32174 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
32214 GCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
32254 GCATAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
32294 GCACAAATGCCTTCGGGTTTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
32334 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
32374 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
32414 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
32454 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
32494 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAA
32531 ATGCTCATGC
Statistics
Matches: 339, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 339 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:38114 original size:40 final size:41
Alignment explanation
Indices: 37970--38107 Score: 183
Period size: 40 Copynumber: 3.4 Consensus size: 41
37960 TGGATATTCG
* *
37970 GAAGGCATTTGTGTGAGTTACTA-ATTCCGGGCTAAGTCCC
1 GAAGGCATTTGTGCGAGTTACTATAATCCGGGCTAAGTCCC
* *
38010 GAAGGCATTTGTGCGAGTTACCA-AATTCGGGCTAAGTCCC
1 GAAGGCATTTGTGCGAGTTACTATAATCCGGGCTAAGTCCC
* * *
38050 GAAGGCATTGGTGCGAGTTACTATAA-CCGGGCTATGTCCA
1 GAAGGCATTTGTGCGAGTTACTATAATCCGGGCTAAGTCCC
*
38090 GAAGGCATTTGAGCGAGT
1 GAAGGCATTTGTGCGAGT
38108 AGCTATATTC
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 84 0.98
41 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (41 bp):
GAAGGCATTTGTGCGAGTTACTATAATCCGGGCTAAGTCCC
Found at i:51257 original size:34 final size:34
Alignment explanation
Indices: 51219--51286 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
51209 AGATTATGAT
51219 GTAATGAGCTTACCTATATTTAATCGATGATTCC
1 GTAATGAGCTTACCTATATTTAATCGATGATTCC
51253 GTAATGAGCTTACCTATATTTAATCGATGATTCC
1 GTAATGAGCTTACCTATATTTAATCGATGATTCC
51287 ACGATGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (34 bp):
GTAATGAGCTTACCTATATTTAATCGATGATTCC
Found at i:59471 original size:80 final size:80
Alignment explanation
Indices: 59334--59497 Score: 303
Period size: 80 Copynumber: 2.1 Consensus size: 80
59324 ACTCATGCAC
59334 GTTA-GTTTATAATGGTAGATCAATTGTTGATGTCTATTTTGATAGCTAATGAGTGTATTTGTGC
1 GTTACGTTTATAATGGTAGATCAATTGTTGATGTCTATTTTGATAGCTAATGAGTGTATTTGTGC
59398 ATGAAGTATTGTAAG
66 ATGAAGTATTGTAAG
*
59413 GTTACGTTTATAATGGTAGATCAATTGTTGATGTCTATTTTGATAGCTAATGAGTGTATTTGTGT
1 GTTACGTTTATAATGGTAGATCAATTGTTGATGTCTATTTTGATAGCTAATGAGTGTATTTGTGC
59478 ATGAAGTATTGTAAG
66 ATGAAGTATTGTAAG
*
59493 CTTAC
1 GTTAC
59498 TACATGATAA
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
79 4 0.05
80 78 0.95
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.43
Consensus pattern (80 bp):
GTTACGTTTATAATGGTAGATCAATTGTTGATGTCTATTTTGATAGCTAATGAGTGTATTTGTGC
ATGAAGTATTGTAAG
Found at i:59938 original size:23 final size:23
Alignment explanation
Indices: 59905--59983 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
59895 TAATGTTTTA
* *
59905 TAAAGCTTTTGTGGCTTATTCTG
1 TAAAGCCTTTGTGGCATATTCTG
*
59928 TAAAGCCTTTGTGGCGTATTCTG
1 TAAAGCCTTTGTGGCATATTCTG
* * *
59951 TAAAGCCTGTCTGGCATATTTTG
1 TAAAGCCTTTGTGGCATATTCTG
59974 TAAAGCCTTT
1 TAAAGCCTTT
59984 ATGGTGTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (23 bp):
TAAAGCCTTTGTGGCATATTCTG
Found at i:59993 original size:23 final size:23
Alignment explanation
Indices: 59905--59995 Score: 101
Period size: 23 Copynumber: 4.0 Consensus size: 23
59895 TAATGTTTTA
* * *
59905 TAAAGCTTTTGTGGCTTATTCTG
1 TAAAGCCTTTATGGCGTATTCTG
*
59928 TAAAGCCTTTGTGGCGTATTCTG
1 TAAAGCCTTTATGGCGTATTCTG
* * * *
59951 TAAAGCCTGTCTGGCATATTTTG
1 TAAAGCCTTTATGGCGTATTCTG
*
59974 TAAAGCCTTTATGGTGTATTCT
1 TAAAGCCTTTATGGCGTATTCT
59996 ATGATGCTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (23 bp):
TAAAGCCTTTATGGCGTATTCTG
Found at i:60528 original size:24 final size:24
Alignment explanation
Indices: 60497--60545 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
60487 TGTGATATGG
60497 GTTGATTTAAGACATGATTTGACT
1 GTTGATTTAAGACATGATTTGACT
60521 GTTGATTTAAGACATGATTTGACT
1 GTTGATTTAAGACATGATTTGACT
60545 G
1 G
60546 GTAATCTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (24 bp):
GTTGATTTAAGACATGATTTGACT
Found at i:61749 original size:20 final size:20
Alignment explanation
Indices: 61704--61749 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
61694 AAATACTAAC
*
61704 TATATTTTATAAAATAAAAA
1 TATATTTTATAAAAAAAAAA
61724 TA-ATTTT-TAATAAAAAAAA
1 TATATTTTATAA-AAAAAAAA
61743 TATATTT
1 TATATTT
61750 GTAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 3 0.13
19 14 0.61
20 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATTTTATAAAAAAAAAA
Found at i:62503 original size:15 final size:16
Alignment explanation
Indices: 62478--62510 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
62468 GGAGCAAATG
*
62478 TATTATAATTTGACTT
1 TATTATAATTTAACTT
62494 TATT-TAATTTAACTT
1 TATTATAATTTAACTT
62509 TA
1 TA
62511 AGTTTTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
TATTATAATTTAACTT
Found at i:66637 original size:81 final size:80
Alignment explanation
Indices: 66488--66646 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 80
66478 TTTTTAGAAG
* * * *
66488 ATAGGTTAAAAAGAATTTTGTATTTGTCGAAAGGAAAAAGATTAGAGGAGATTGAAATAGCAGCA
1 ATAGGTTAAAAACAACTTTGTATTTGTAGAAAGGAAAAAGATTAGAGGAGATTGAAATAGCAACA
66553 TACAAAAGAAATAAT
66 TACAAAAGAAATAAT
* *
66568 ATAGGTTTAAAACAACTTTGTATTTGTAGAAAGGAAAAAGATTTAGAGGAGATTGAAATAGCAAT
1 ATAGGTTAAAAACAACTTTGTATTTGTAGAAAGGAAAAAGA-TTAGAGGAGATTGAAATAGCAAC
66633 ATACAAAAGAAATA
65 ATACAAAAGAAATA
66647 TATGTTCATC
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 37 0.51
81 35 0.49
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.26
Consensus pattern (80 bp):
ATAGGTTAAAAACAACTTTGTATTTGTAGAAAGGAAAAAGATTAGAGGAGATTGAAATAGCAACA
TACAAAAGAAATAAT
Found at i:66673 original size:81 final size:79
Alignment explanation
Indices: 66508--66654 Score: 208
Period size: 81 Copynumber: 1.9 Consensus size: 79
66498 AAGAATTTTG
* *
66508 TATTTGTCGAAAGGAAAAAGATTAGAGGAGATTGAAATAGCAGCATACAAAAGAAATAATATAGG
1 TATTTGTAGAAAGGAAAAAGATTAGAGGAGATTGAAATAGCAACATACAAAAGAAATAATATA-G
* **
66573 TTTAAAACAACTTTG
65 TTCAAAACAACTTAC
*
66588 TATTTGTAGAAAGGAAAAAGATTTAGAGGAGATTGAAATAGCAATATACAAAAGAAAT-ATAT-G
1 TATTTGTAGAAAGGAAAAAGA-TTAGAGGAGATTGAAATAGCAACATACAAAAGAAATAATATAG
66651 TTCA
65 TTCA
66655 TCATCTATCT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
78 4 0.06
80 24 0.39
81 34 0.55
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (79 bp):
TATTTGTAGAAAGGAAAAAGATTAGAGGAGATTGAAATAGCAACATACAAAAGAAATAATATAGT
TCAAAACAACTTAC
Found at i:66723 original size:20 final size:21
Alignment explanation
Indices: 66698--66740 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
66688 TCAAGTTTAA
66698 ATATTT-AATTTT-ATTAAAAT
1 ATATTTAAATTTTCA-TAAAAT
66718 ATATTTAAATTTTCATAAAAT
1 ATATTTAAATTTTCATAAAAT
66739 AT
1 AT
66741 CCTTTCATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 14 0.67
22 1 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTTAAATTTTCATAAAAT
Found at i:67898 original size:14 final size:15
Alignment explanation
Indices: 67871--67899 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
67861 TAATACCTCT
67871 AGTTTTCATATTAAA
1 AGTTTTCATATTAAA
67886 AGTTTTC-TATTAAA
1 AGTTTTCATATTAAA
67900 TAATCTAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
AGTTTTCATATTAAA
Found at i:72214 original size:17 final size:19
Alignment explanation
Indices: 72194--72231 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
72184 TTTTATATAA
72194 AAAATAA-AATTATT-CTT
1 AAAATAATAATTATTGCTT
*
72211 AAAATAATACTTATTGCTT
1 AAAATAATAATTATTGCTT
72230 AA
1 AA
72232 TAAAAACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 6 0.33
19 5 0.28
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAATAATAATTATTGCTT
Found at i:85732 original size:27 final size:26
Alignment explanation
Indices: 85676--85733 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
85666 CGCACGAATG
*
85676 AAATTTAATTTAAATAAAAATATTTTT
1 AAATTTAATTTAAATAAAAATA-TTAT
*
85703 AAATTTAAATTTAATTATAAAATA-TAT
1 AAATTT-AATTTAAATA-AAAATATTAT
85730 AAAT
1 AAAT
85734 AAAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.44
28 9 0.33
29 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATTTAATTTAAATAAAAATATTAT
Found at i:85745 original size:7 final size:7
Alignment explanation
Indices: 85718--85750 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
85708 TAAATTTAAT
85718 TATAAAA
1 TATAAAA
85725 TATATAAA
1 TATA-AAA
85733 TA-AAAA
1 TATAAAA
85739 TATAAAA
1 TATAAAA
85746 TATAA
1 TATAA
85751 TTTTAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.21
7 14 0.58
8 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TATAAAA
Found at i:86599 original size:14 final size:14
Alignment explanation
Indices: 86582--86627 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
86572 TAATATAATT
*
86582 GTTGGAATGTGACC
1 GTTGGAATATGACC
*
86596 GTTGCAATATGACC
1 GTTGGAATATGACC
* *
86610 ATTAGAATATGACC
1 GTTGGAATATGACC
86624 GTTG
1 GTTG
86628 CTTCCTCGAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (14 bp):
GTTGGAATATGACC
Found at i:88295 original size:93 final size:95
Alignment explanation
Indices: 88123--88314 Score: 334
Period size: 93 Copynumber: 2.0 Consensus size: 95
88113 AGCTTAAGAT
88123 ATAAAGAAAATTGTTAGTCCAATGATAAATAGAAAAAAAAAATAAAGAACAAGAAACTAACATAA
1 ATAAAGAAAATTGTTAGTCCAATGATAAATAG--AAAAAAAATAAAGAACAAGAAACTAACATAA
*
88188 AACTCCAAAGTATCTCAAAATACTAAGTTAAC
64 AACTCCAAAGTATCTCAAAATACAAAGTTAAC
88220 ATAAAGAAAATTGTTAGTCCAATGATAAATAG-AAAAAAA-AAAGAACAAGAAACTAACATAAAA
1 ATAAAGAAAATTGTTAGTCCAATGATAAATAGAAAAAAAATAAAGAACAAGAAACTAACATAAAA
*
88283 CTCTAAAGTATCTCAAAATACAAAGTTAAC
66 CTCCAAAGTATCTCAAAATACAAAGTTAAC
88313 AT
1 AT
88315 TTAGTGCAAC
Statistics
Matches: 93, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
93 54 0.58
94 7 0.08
97 32 0.34
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (95 bp):
ATAAAGAAAATTGTTAGTCCAATGATAAATAGAAAAAAAATAAAGAACAAGAAACTAACATAAAA
CTCCAAAGTATCTCAAAATACAAAGTTAAC
Found at i:88790 original size:15 final size:15
Alignment explanation
Indices: 88770--88798 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
88760 AGATGTTTGA
88770 ATATATATGAGAGAG
1 ATATATATGAGAGAG
88785 ATATATATGAGAGA
1 ATATATATGAGAGA
88799 TAGGTTCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (15 bp):
ATATATATGAGAGAG
Found at i:94150 original size:29 final size:29
Alignment explanation
Indices: 94117--94190 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
94107 GTTGTGAGAT
* *
94117 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
94146 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
94175 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
94191 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:95894 original size:40 final size:40
Alignment explanation
Indices: 95863--96114 Score: 253
Period size: 40 Copynumber: 6.3 Consensus size: 40
95853 GGACTAAGAT
95863 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
*
95903 CCGAAGGCATTTGTGCGAAATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
* *
95943 CCGAAGGCCTTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
* * ** *
95983 CCGAAGGCATTCGTGCGAGTTGTTAAA-TCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCC
* * ** * *
96023 CCGAAGGCATTCGTGCGAGTTGTTAAA-TCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCC
* * * * * *
96063 CCGAAGGCA-TTGTGTGAGTTACTAAA-ACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
96102 CCGAAGGCATTTG
1 CCGAAGGCATTTG
96115 AACGAGGAGC
Statistics
Matches: 192, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 32 0.17
40 157 0.82
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
Found at i:95947 original size:80 final size:79
Alignment explanation
Indices: 95810--96078 Score: 274
Period size: 80 Copynumber: 3.4 Consensus size: 79
95800 TTGAATGCTG
* * * ** **
95810 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGA-ATATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAAATGACA-A-ATCCGGGTTAAGCCCCGAAGGCAT
95873 TTGTGCGAGATACAAA
64 TTGTGCGAGATACAAA
* *
95889 TTCCGGGTTAAGCCCCGAAGGCATTTGTGCGAAAT-ACAAATTCCGGGTTAAGCCCCGAAGGCCT
1 -TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAAATGACAAA-TCCGGGTTAAGCCCCGAAGGCAT
95953 TTGTGCGAGATACTAAA
64 TTGTGCGAGATAC-AAA
* ** ** * *
95970 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAAATGACAAATCCGGGTTAAGCCCCGAAGGCATTT
* **
96035 GTGCGAGTTGTTAAA
66 GTGCGAGAT-ACAAA
*
96050 TCCGGGTTATGTCCCGAAGGCATTGTGTG
1 TCCGGGTTAAGTCCCGAAGGCATT-TGTG
96079 AGTTACTAAA
Statistics
Matches: 159, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
79 1 0.01
80 138 0.87
81 20 0.13
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAAATGACAAATCCGGGTTAAGCCCCGAAGGCATTT
GTGCGAGATACAAA
Found at i:96026 original size:120 final size:119
Alignment explanation
Indices: 95863--96112 Score: 297
Period size: 120 Copynumber: 2.1 Consensus size: 119
95853 GGACTAAGAT
* *
95863 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTTGTGCGAAAT-ACA
1 CCGAAGGCATTCGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAAATGACA
* * *
95927 AATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
66 AA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTC
* ** * ** **
95983 CCGAAGGCATTCGTGCGAGTTGTTAAA-TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTT
1 CCGAAGGCATTCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAAATGAC
* * * * *
96047 AAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTC
65 AAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTC
96102 CCGAAGGCATT
1 CCGAAGGCATT
96113 TGAACGAGGA
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
119 37 0.34
120 67 0.61
121 6 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
CCGAAGGCATTCGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAAATGACA
AATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTC
Found at i:96132 original size:79 final size:80
Alignment explanation
Indices: 95890--96147 Score: 227
Period size: 80 Copynumber: 3.2 Consensus size: 80
95880 AGATACAAAT
* * ** * * * *
95890 TCCGGGTTAAGCCCCGAAGGCATTTGTGCGAAATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATT
* ** *
95954 TGTGCGA-GATACTAAA
65 CGAACGAGGA-GCTAAA
** * *
95970 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** ** *
96035 GTGCGAGTTGTTAAA
66 GAACGAGGAGCTAAA
* * * *
96050 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
96114 GAACGAGGAGCTATA
66 GAACGAGGAGCTAAA
*
96129 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
96148 TACGTGATTT
Statistics
Matches: 147, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
78 14 0.10
79 45 0.31
80 85 0.58
81 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGAGCTAAA
Done.