Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2423
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: 45041
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:406 original size:10 final size:10
Alignment explanation
Indices: 377--579 Score: 69
Period size: 10 Copynumber: 21.1 Consensus size: 10
367 AACCCTGCTC
377 TTATATAAAAA
1 TTATA-AAAAA
*
388 TTGTAAAAAAA
1 TTAT-AAAAAA
*
399 TTGT--AAAA
1 TTATAAAAAA
*
407 TTATTTAAAAA
1 TTA-TAAAAAA
418 TTAATAAAAAA
1 TT-ATAAAAAA
429 TTA-AAAAAA
1 TTATAAAAAA
438 -T-T-AAAAA
1 TTATAAAAAA
*
445 TTAT-TAAAA
1 TTATAAAAAA
454 -TATATAAAAA
1 TTATA-AAAAA
* **
464 TTGTAAAATT
1 TTATAAAAAA
474 TTATAAAAAA
1 TTATAAAAAA
* **
484 TTGTAAAATT
1 TTATAAAAAA
494 TTATAAAAAA
1 TTATAAAAAA
504 GTT-T-AAAAA
1 -TTATAAAAAA
* *
513 TTTTAAAATA
1 TTATAAAAAA
*
523 -TAT-AGAAA
1 TTATAAAAAA
531 -TAT--AAAA
1 TTATAAAAAA
* *
538 TTTTATAAAA
1 TTATAAAAAA
*
548 TCATAAGAAAA
1 TTATAA-AAAA
*
559 TTATACAAAA
1 TTATAAAAAA
569 TGTA-AAAAAA
1 T-TATAAAAAA
579 T
1 T
580 AAATTTGTAA
Statistics
Matches: 144, Mismatches: 29, Indels: 39
0.68 0.14 0.18
Matches are distributed among these distances:
7 8 0.06
8 21 0.15
9 20 0.14
10 52 0.36
11 41 0.28
12 2 0.01
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:435 original size:19 final size:20
Alignment explanation
Indices: 412--514 Score: 76
Period size: 20 Copynumber: 5.4 Consensus size: 20
402 TAAAATTATT
412 TAAAAATTAATAAAAAA-T-
1 TAAAAATTAATAAAAAATTG
* *
430 TAAAAA--AATTAAAAATTA
1 TAAAAATTAATAAAAAATTG
*
448 TTAAAA-T-ATATAAAAATTG
1 TAAAAATTAATA-AAAAATTG
* *
467 TAAAATTTTATAAAAAATTG
1 TAAAAATTAATAAAAAATTG
* *
487 TAAAATTTTATAAAAAAGTT-
1 TAAAAATTAATAAAAAA-TTG
507 TAAAAATT
1 TAAAAATT
515 TTAAAATATA
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
16 8 0.11
17 1 0.01
18 13 0.18
19 11 0.15
20 33 0.46
21 5 0.07
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
TAAAAATTAATAAAAAATTG
Found at i:452 original size:27 final size:27
Alignment explanation
Indices: 411--485 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
401 GTAAAATTAT
*
411 TTAAAAATTAATAAAAAATTAAAAAAA
1 TTAAAAATTATTAAAAAATTAAAAAAA
* *
438 TTAAAAATTATTAAAATA-TATAAAAA
1 TTAAAAATTATTAAAAAATTAAAAAAA
* *
464 TTGTAAAATTTTATAAAAAATT
1 TT-AAAAATTAT-TAAAAAATT
486 GTAAAATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 9 0.23
27 23 0.59
28 6 0.15
29 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (27 bp):
TTAAAAATTATTAAAAAATTAAAAAAA
Found at i:482 original size:20 final size:20
Alignment explanation
Indices: 454--517 Score: 94
Period size: 20 Copynumber: 3.1 Consensus size: 20
444 ATTATTAAAA
454 TATATAAAAATTGTAAAATTT
1 TATA-AAAAATTGTAAAATTT
475 TATAAAAAATTGTAAAATTT
1 TATAAAAAATTGTAAAATTT
495 TATAAAAAAGTT-TAAAAATTT
1 TATAAAAAA-TTGT-AAAATTT
516 TA
1 TA
518 AAATATATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TATAAAAAATTGTAAAATTT
Found at i:556 original size:27 final size:26
Alignment explanation
Indices: 507--557 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
497 TAAAAAAGTT
507 TAAAAATTTTAAAATATATAGAAATA
1 TAAAAATTTTAAAATATATAGAAATA
*
533 TAAAATTTTATAAAATCATA-AGAAA
1 TAAAAATTT-TAAAAT-ATATAGAAA
558 ATTATACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 11 0.50
28 3 0.14
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
TAAAAATTTTAAAATATATAGAAATA
Found at i:809 original size:19 final size:19
Alignment explanation
Indices: 787--847 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
777 TTTTGATGGA
787 TTTTATATATTTTTATGAT
1 TTTTATATATTTTTATGAT
* * *
806 TTTTATAAAATTTTATAAT
1 TTTTATATATTTTTATGAT
* *
825 TTTT-TTTATTTTTGACGAT
1 TTTTATATATTTTT-ATGAT
844 TTTT
1 TTTT
848 CTAAAAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
18 6 0.18
19 27 0.82
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTATATATTTTTATGAT
Found at i:1066 original size:87 final size:88
Alignment explanation
Indices: 958--1117 Score: 279
Period size: 88 Copynumber: 1.8 Consensus size: 88
948 TAAGAGCAGG
*
958 GGCTTAATTGCTTTTTTG-AAAAAAATTTAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACC
1 GGCTTAATTGCTTTTTTGAAAAAAAAATTAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACC
1022 CAATTGAGTGGGAAAAAACTAAA
66 CAATTGAGTGGGAAAAAACTAAA
*
1045 GGCTTAATTG-TTTCTTTGAAAAAAAAATTAAGGTCTTTTTGATGCATTATGAAAGTTCAAGTAC
1 GGCTTAATTGCTTT-TTTGAAAAAAAAATTAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTAC
1109 CCAATTGAG
65 CCAATTGAG
1118 CAGAAAAAGT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
86 3 0.04
87 14 0.20
88 52 0.75
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (88 bp):
GGCTTAATTGCTTTTTTGAAAAAAAAATTAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACC
CAATTGAGTGGGAAAAAACTAAA
Found at i:3502 original size:18 final size:20
Alignment explanation
Indices: 3481--3517 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3471 TATTTTGTTT
3481 TATTT-ATTTCTA-AACCCA
1 TATTTCATTTCTACAACCCA
*
3499 TATTTCTTTTCTACAACCC
1 TATTTCATTTCTACAACCC
3518 CAATTATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTTCATTTCTACAACCCA
Found at i:9773 original size:28 final size:29
Alignment explanation
Indices: 9711--9773 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
9701 ATTTCCCTCA
*
9711 TTTTCTCTCACTTTATTTATATTTGAAAT
1 TTTTATCTCACTTTATTTATATTTGAAAT
* **
9740 TCTTATCT-ACTTTCATTTA-ATTTTTAAT
1 TTTTATCTCACTTT-ATTTATATTTGAAAT
9768 TTTTAT
1 TTTTAT
9774 AATTTTGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.24, C:0.13, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTATCTCACTTTATTTATATTTGAAAT
Found at i:14697 original size:72 final size:72
Alignment explanation
Indices: 14594--14834 Score: 401
Period size: 72 Copynumber: 3.3 Consensus size: 72
14584 GAATTGACAA
* *
14594 TGGAATTTGTCCACTCAATTGGTTCATCGGCAAGTGTAAATGAGTGAGATGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGGCAAGTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
14659 ATGATCT
66 ATGATCT
* *
14666 TGGAATTTTTCCACTCAATTGGTTCACCGGCAACTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGGCAAGTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
14731 ATGATCT
66 ATGATCT
* *** *
14738 TGGAATTTGTCCGCTCAATTGGTTCACCAATAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGGCAAGTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
14803 ATGATCT
66 ATGATCT
14810 TGGAATTTGTCCACTCAATTGGTTC
1 TGGAATTTGTCCACTCAATTGGTTC
14835 CCCAATGATC
Statistics
Matches: 157, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 157 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (72 bp):
TGGAATTTGTCCACTCAATTGGTTCACCGGCAAGTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
ATGATCT
Found at i:14834 original size:36 final size:36
Alignment explanation
Indices: 14722--14942 Score: 161
Period size: 36 Copynumber: 6.1 Consensus size: 36
14712 AGTTGCAAGA
*
14722 GGTTCCCCAATGATCTTGGAATTTGTCCGCTCAATT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
* * * ** * * **
14758 GGTTCACCAATAAGTC-T-AAATGAGT-GAGTTGCAAGA
1 GGTTCCCCAATGA-TCTTGGAATTTGTCCA-CT-CAATT
14794 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
14830 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
* ** * * **
14866 GGTTCACCGACAA-G-TC-T-AAATGAGT-GAGTTGCAAGA
1 GGTTC-CC--CAATGATCTTGGAATTTGTCCA-CT-CAATT
14902 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
14938 GGTTC
1 GGTTC
14943 ACCGACAAGT
Statistics
Matches: 136, Mismatches: 33, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
33 3 0.02
34 2 0.01
35 18 0.13
36 89 0.65
37 18 0.13
38 3 0.02
39 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (36 bp):
GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
Found at i:14857 original size:108 final size:108
Alignment explanation
Indices: 14722--14942 Score: 415
Period size: 108 Copynumber: 2.0 Consensus size: 108
14712 AGTTGCAAGA
* *
14722 GGTTCCCCAATGATCTTGGAATTTGTCCGCTCAATTGGTTCACCAATAAGTCTAAATGAGTGAGT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCAACAAGTCTAAATGAGTGAGT
14787 TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
66 TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
*
14830 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCAACAAGTCTAAATGAGTGAGT
14895 TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
66 TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
14938 GGTTC
1 GGTTC
14943 ACCGACAAGT
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 110 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (108 bp):
GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCAACAAGTCTAAATGAGTGAGT
TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
Found at i:14947 original size:72 final size:72
Alignment explanation
Indices: 14830--15217 Score: 577
Period size: 72 Copynumber: 5.3 Consensus size: 72
14820 CCACTCAATT
14830 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
14895 TGCAAGA
66 TGCAAGA
14902 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAG--TAAATGAGTGAGT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
14965 TGCAAGA
66 TGCAAGA
* * *
14972 TGTTCCCCAATGATCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAATCTAA
1 -G---------GTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAA
15037 ATGAGTGAGTTGCAAGA
56 ATGAGTGAGTTGCAAGA
15054 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTC-CACGACAAGTCTAAATGAGTGAG
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCAC-CGACAAGTCTAAATGAGTGAG
*
15118 TTGAAAGA
65 TTGCAAGA
* **
15126 GGTTCCCCAATAATCTTGGAATTTGTCCACTCAATTGGTTCTGCGACAAGTCTAAATGAGTGAGT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
15191 TGCAAGA
66 TGCAAGA
*
15198 GGTT-CCCAGTGATCTTGGAA
1 GGTTCCCCAATGATCTTGGAA
15218 CCGGTCCTGA
Statistics
Matches: 290, Mismatches: 12, Indels: 29
0.88 0.04 0.09
Matches are distributed among these distances:
70 20 0.07
71 15 0.05
72 188 0.65
80 46 0.16
81 1 0.00
82 20 0.07
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (72 bp):
GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
TGCAAGA
Found at i:15078 original size:152 final size:150
Alignment explanation
Indices: 14833--15217 Score: 594
Period size: 152 Copynumber: 2.6 Consensus size: 150
14823 CTCAATTGGT
*
14833 TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGC
1 TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAGTCTAAATGAGTGAGTTGC
14898 AAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTT-CACCGACAAG-TAAATGAGT
66 AAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCCA-CGACAAGCTAAATGAGT
* *
14961 GAGTTGCAAGATGTTCCCCAATGA
130 GAGTTGAAAGAGGTTCCCC-A--A
*
14985 TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAATCTAAATGAGTGAGTTGC
1 TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAGTCTAAATGAGTGAGTTGC
15050 AAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCCACGACAAGTCTAAATGAGT
66 AAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCCACGACAAG-CTAAATGAGT
15115 GAGTTGAAAGAGGTTCCCCAA
130 GAGTTGAAAGAGGTTCCCCAA
15136 T-----A--ATCTTGGAATTTGTCCACTCAATTGGTTC-TGCGACAAGTCTAAATGAGTGAGTTG
1 TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCAT-CGACAAGTCTAAATGAGTGAGTTG
*
15193 CAAGAGGTT-CCCAGTGATCTTGGAA
65 CAAGAGGTTCCCCAATGATCTTGGAA
15218 CCGGTCCTGA
Statistics
Matches: 223, Mismatches: 6, Indels: 17
0.91 0.02 0.07
Matches are distributed among these distances:
143 16 0.07
144 61 0.27
146 1 0.00
151 2 0.01
152 114 0.51
153 3 0.01
154 26 0.12
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (150 bp):
TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAGTCTAAATGAGTGAGTTGC
AAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCCACGACAAGCTAAATGAGTG
AGTTGAAAGAGGTTCCCCAA
Found at i:24279 original size:18 final size:20
Alignment explanation
Indices: 24258--24294 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
24248 TATTTTGTTT
24258 TATTT-ATTTCTA-AACTCA
1 TATTTCATTTCTATAACTCA
*
24276 TATTTCTTTTCTATAACTC
1 TATTTCATTTCTATAACTC
24295 CAATTATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTCATTTCTATAACTCA
Found at i:25136 original size:3 final size:3
Alignment explanation
Indices: 25130--25165 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
25120 TGTATTGTTG
25130 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25166 ACACCACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:29225 original size:30 final size:29
Alignment explanation
Indices: 29191--29337 Score: 129
Period size: 30 Copynumber: 4.9 Consensus size: 29
29181 AAAAAATTTA
* *
29191 AAAATTGTATTTTGACCTCTGAACTTTTCT
1 AAAATTATATTTTGACC-CTAAACTTTTCT
* *
29221 AAAATT-TCATTTTGACCCTTAAATTTTTAT
1 AAAATTAT-ATTTTGACCC-TAAACTTTTCT
* *
29251 AAAATTATATTTTAACCCTTAATA-TTTTTT
1 AAAATTATATTTTGACCC-TAA-ACTTTTCT
29281 AAAATTATATTTTGACCCTAAAC-TTTCT
1 AAAATTATATTTTGACCCTAAACTTTTCT
* * *
29309 CAAAATTACATTTTTGCCCCAAAACTTTT
1 -AAAATTATA-TTTTGACCCTAAACTTTT
29338 GCTACATTTA
Statistics
Matches: 99, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
28 5 0.05
29 13 0.13
30 76 0.77
31 5 0.05
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.46
Consensus pattern (29 bp):
AAAATTATATTTTGACCCTAAACTTTTCT
Found at i:29256 original size:60 final size:59
Alignment explanation
Indices: 29187--29322 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 59
29177 TTAAAAAAAA
* * *
29187 TTTAAAAATTGTATTTTGACCTCTGAA-CTTTTCTAAAATT-TCATTTTGACCCTTAAATT
1 TTTAAAAATTATATTTTAACC-CTGAATATTTTCTAAAATTAT-ATTTTGACCCTTAAATT
* *
29246 TTTATAAAATTATATTTTAACCCTTAATATTTTTTAAAATTATATTTTGACCC-TAAACTT
1 TTTA-AAAATTATATTTTAACCCTGAATATTTTCTAAAATTATATTTTGACCCTTAAA-TT
* * *
29306 TCTCAAAATTACATTTT
1 TTTAAAAATTATATTTT
29323 TGCCCCAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
59 24 0.37
60 40 0.62
61 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.49
Consensus pattern (59 bp):
TTTAAAAATTATATTTTAACCCTGAATATTTTCTAAAATTATATTTTGACCCTTAAATT
Found at i:29542 original size:9 final size:9
Alignment explanation
Indices: 29525--29561 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
29515 TGAGTTTTCG
29525 AATTCGAAT
1 AATTCGAAT
*
29534 AACTCGAAT
1 AATTCGAAT
29543 AATTCGAAT
1 AATTCGAAT
29552 AATTCGAAT
1 AATTCGAAT
29561 A
1 A
29562 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:29809 original size:30 final size:31
Alignment explanation
Indices: 29775--29834 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
29765 AAACCTTTTA
*
29775 TTTTCTCCC-AAAATTTTTACT-CCCTCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCCTCCCAC
*
29805 TTTTCCCCTAAAACTTTTATTCCCCTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCCTCCCA
29835 TCTATCCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 15 0.58
31 8 0.31
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCCTCCCAC
Found at i:30466 original size:5 final size:5
Alignment explanation
Indices: 30456--30481 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30446 GAACAAATAT
30456 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
30482 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:32265 original size:61 final size:61
Alignment explanation
Indices: 32199--32318 Score: 152
Period size: 61 Copynumber: 2.0 Consensus size: 61
32189 TTTGTGAGAT
* * *
32199 TAATGAGAATTTTC-AAAATTTAAGAGTGCTTAATTAAAATTTTCAAAAAAATTAAAAGGTA
1 TAATGAAAATTTTCAAAAATTT-AGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGGTA
* * * * *
32260 TAATGAAAATTTTCAAAAATTTTGAGGGCCTAATTGAAATTTTCTAAAAATTTTAAAGG
1 TAATGAAAATTTTCAAAAATTTAGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGG
32319 AAAAAACAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
61 43 0.86
62 7 0.14
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (61 bp):
TAATGAAAATTTTCAAAAATTTAGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGGTA
Found at i:32330 original size:61 final size:61
Alignment explanation
Indices: 32206--32331 Score: 137
Period size: 61 Copynumber: 2.1 Consensus size: 61
32196 GATTAATGAG
* * * * **
32206 AATTTTCAAAATTTAAGAGTGCTTAATTAAAATTTTCAAAAAAATTAAAAGGTATAATGAA
1 AATTTTCAAAATTTAAGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGGAAAAAACAA
* * * * *
32267 AATTTTCAAAAATTT-TGAGGGCCTAATTGAAATTTTCTAAAAATTTTAAAGGAAAAAACAA
1 AATTTTC-AAAATTTAAGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGGAAAAAACAA
32328 AATT
1 AATT
32332 CTTCGATTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 46 0.87
62 7 0.13
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.34
Consensus pattern (61 bp):
AATTTTCAAAATTTAAGAGGGCCTAATTAAAATTTTCAAAAAAATTAAAAGGAAAAAACAA
Found at i:33747 original size:21 final size:21
Alignment explanation
Indices: 33708--33748 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33698 AATTAAGCTC
* * *
33708 TCAATGTTTATATATTATGTG
1 TCAATGTTAATAGAATATGTG
33729 TCAATGTTAATAGAATATGT
1 TCAATGTTAATAGAATATGT
33749 AATTGTTGCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (21 bp):
TCAATGTTAATAGAATATGTG
Found at i:36004 original size:50 final size:50
Alignment explanation
Indices: 35927--36047 Score: 172
Period size: 50 Copynumber: 2.4 Consensus size: 50
35917 TACAAATTTA
* * * *
35927 ACTATCAATTGTTTATTGACTATACTTTTAACTCCAC-AAAAAGGGCTAAG
1 ACTATCAATTGTCTATTGACTACAC-TTTAACTCCACAAAAAAAGACTAAG
*
35977 ACTATCAATTGTCTATTGACTACACTTTAACTCGACAAAAAAAGACTAAG
1 ACTATCAATTGTCTATTGACTACACTTTAACTCCACAAAAAAAGACTAAG
*
36027 ACTATCAGTTGTCTATTGACT
1 ACTATCAATTGTCTATTGACT
36048 TCACACTTGC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 10 0.16
50 54 0.84
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (50 bp):
ACTATCAATTGTCTATTGACTACACTTTAACTCCACAAAAAAAGACTAAG
Found at i:37968 original size:88 final size:85
Alignment explanation
Indices: 37821--38009 Score: 265
Period size: 88 Copynumber: 2.2 Consensus size: 85
37811 TAAGAGTAGG
37821 GGCTTAATTGCTTTTTTG-AAAAAAATAAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACCC
1 GGCTTAATTGCTTTTTTGAAAAAAAATAAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACCC
*
37885 AATTGAGTGGGAAAAAAATAGA
66 AATTGAG-CGGAAAAAAA-AGA
* ** *
37907 GGCTTAATTG-TTTCTTTGAAAAAAAATTTAAGGTTTTTTTTATGCATTATGAAAGTTCAAGTAC
1 GGCTTAATTGCTTT-TTTGAAAAAAAA-TAAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTAC
*
37971 CCAATTGAGCGGAAAAAAAAGG
64 CCAATTGAGCGGAAAAAAAAGA
*
37993 GGTTTAATTGCTTTTTT
1 GGCTTAATTGCTTTTTT
38010 TGAAGAAGTG
Statistics
Matches: 92, Mismatches: 7, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
85 3 0.03
86 28 0.30
87 19 0.21
88 42 0.46
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (85 bp):
GGCTTAATTGCTTTTTTGAAAAAAAATAAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACCC
AATTGAGCGGAAAAAAAAGA
Found at i:38032 original size:88 final size:87
Alignment explanation
Indices: 37821--38075 Score: 252
Period size: 86 Copynumber: 3.0 Consensus size: 87
37811 TAAGAGTAGG
***
37821 GGCTTAATTGCTTT-TTTGAAAAAAA-TAAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACC
1 GGCTTAATTG-TTTCTTTGAAAAAAATTAAAGATTTTTTTGATGCATTATGAAAGTTCAAGTACC
*
37884 CAATTGAGTGGGAAAAAAATAGA
65 CAATTGAGTCGGAAAAAAATAGA
* * *
37907 GGCTTAATTGTTTCTTTGAAAAAAAATTTAAGGTTTTTTTTATGCATTATGAAAGTTCAAGTACC
1 GGCTTAATTGTTTCTTTG-AAAAAAATTAAAGATTTTTTTGATGCATTATGAAAGTTCAAGTACC
*
37972 CAATTGAG-CGGAAAAAAA-AGG
65 CAATTGAGTCGGAAAAAAATAGA
* * * * * * * * * *
37993 GGTTTAATTGCTTTTTTTG-AAGAAGTGTAAAGATATTTTTGATACATTTTAAAAGTTTAAGTGC
1 GGCTTAATTG-TTTCTTTGAAAAAAAT-TAAAGATTTTTTTGATGCATTATGAAAGTTCAAGTAC
* *
38057 TCAATTGAGT-AGAAAAAAA
64 CCAATTGAGTCGGAAAAAAA
38076 GGACTTAAAT
Statistics
Matches: 142, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
85 8 0.06
86 69 0.49
87 23 0.16
88 42 0.30
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (87 bp):
GGCTTAATTGTTTCTTTGAAAAAAATTAAAGATTTTTTTGATGCATTATGAAAGTTCAAGTACCC
AATTGAGTCGGAAAAAAATAGA
Found at i:42347 original size:54 final size:54
Alignment explanation
Indices: 42265--42373 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
42255 TTAAAATTGG
* *
42265 ATGCTTTTTCTTTTAGCAAAATCTTGTATTTCATAAAAACGTTTATACTTTTAT
1 ATGCTTTTTCTTTTAGCAAAATCTTGTATTTCATAAAAACGTGTATACTTATAT
* *
42319 ATGCTTTTTCTTTTAGCAAGATCTTGTATTTCATAAAAATGTGTATACTTATAT
1 ATGCTTTTTCTTTTAGCAAAATCTTGTATTTCATAAAAACGTGTATACTTATAT
42373 A
1 A
42374 AATTCACGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (54 bp):
ATGCTTTTTCTTTTAGCAAAATCTTGTATTTCATAAAAACGTGTATACTTATAT
Found at i:43242 original size:14 final size:15
Alignment explanation
Indices: 43223--43251 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43213 TAATAAAAAT
43223 AAAAA-TATTTTTAA
1 AAAAATTATTTTTAA
43237 AAAAATTATTTTTAA
1 AAAAATTATTTTTAA
43252 CCCTTTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAAATTATTTTTAA
Found at i:43865 original size:50 final size:52
Alignment explanation
Indices: 43781--43903 Score: 135
Period size: 57 Copynumber: 2.3 Consensus size: 52
43771 AGTTTGGTCC
*
43781 CAATTGTCTATTGACTATAAATTTAACTCCAC-AAAAAG-GGCTAAGACTAT
1 CAATTGTCTATTGACTATAAATTTAACTCCACAAAAAAGAGACTAAGACTAT
* * *
43831 CAATTGTCTATTGACTA-CACTTTAACTCAGACAAAAAAAGACAAAGACTAAGACTAT
1 CAATTGTCTATTGACTATAAATTTAACTC-CAC-AAAAAAG----AGACTAAGACTAT
43888 CAATTGTCTATTGACT
1 CAATTGTCTATTGACT
43904 TCACACTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
49 9 0.15
50 19 0.31
52 6 0.10
57 27 0.44
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (52 bp):
CAATTGTCTATTGACTATAAATTTAACTCCACAAAAAAGAGACTAAGACTAT
Done.