Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1051
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: 83277
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1826 original size:28 final size:27
Alignment explanation
Indices: 1774--1833 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
1764 TTTTAAACTA
*
1774 ATAATTATTTATTTTAAATAAAATAAC
1 ATAATTATTTATCTTAAATAAAATAAC
**
1801 ATAATATATTTATCTTAAATTTAATAAC
1 ATAAT-TATTTATCTTAAATAAAATAAC
1829 -TAATT
1 ATAATT
1834 GAATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 9 0.31
28 19 0.66
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAATTATTTATCTTAAATAAAATAAC
Found at i:10091 original size:19 final size:19
Alignment explanation
Indices: 10051--10093 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
10041 AACTTATTAT
*
10051 TTAAAATATATTGTTTTTA
1 TTAAAATATATTGTTTTAA
*
10070 TTAATATATATT-TTTATAA
1 TTAAAATATATTGTTT-TAA
10089 TTAAA
1 TTAAA
10094 TTAAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTAAAATATATTGTTTTAA
Found at i:12951 original size:27 final size:26
Alignment explanation
Indices: 12904--12957 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 26
12894 TCTGTTTGGC
12904 TCTTCTATTTGCAATGATATTTAATG
1 TCTTCTATTTGCAATGATATTTAATG
12930 TCTTCTATTTTGCAAT-ACTATTTAATG
1 TCTTCTA-TTTGCAATGA-TATTTAATG
12957 T
1 T
12958 AAACGTCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (26 bp):
TCTTCTATTTGCAATGATATTTAATG
Found at i:18905 original size:2 final size:2
Alignment explanation
Indices: 18898--18923 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18888 TTAAAAAGAT
18898 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
18924 AAGGTATAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20604 original size:16 final size:16
Alignment explanation
Indices: 20585--20641 Score: 59
Period size: 12 Copynumber: 3.7 Consensus size: 16
20575 GTAATAAATC
20585 TTATTTTTATAATAAA
1 TTATTTTTATAATAAA
20601 TTA---TT-TAATAAA
1 TTATTTTTATAATAAA
20613 TTGATTTTATATAATAAA
1 TT-ATTTT-TATAATAAA
*
20631 TTAATTTTATA
1 TTATTTTTATA
20642 TCTTTTTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
12 9 0.26
13 3 0.09
16 8 0.24
17 5 0.15
18 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TTATTTTTATAATAAA
Found at i:20610 original size:30 final size:30
Alignment explanation
Indices: 20576--20633 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
20566 GATTAATTTG
*
20576 TAATAAATCTTATTTT-TATAATAAATTATT
1 TAATAAAT-TGATTTTATATAATAAATTATT
20606 TAATAAATTGATTTTATATAATAAATTA
1 TAATAAATTGATTTTATATAATAAATTA
20634 ATTTTATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
TAATAAATTGATTTTATATAATAAATTATT
Found at i:20627 original size:18 final size:18
Alignment explanation
Indices: 20601--20642 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
20591 TTATAATAAA
* *
20601 TTATTTAATAAATTGATT
1 TTATATAATAAATTAATT
20619 TTATATAATAAATTAATT
1 TTATATAATAAATTAATT
20637 TTATAT
1 TTATAT
20643 CTTTTTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TTATATAATAAATTAATT
Found at i:27118 original size:14 final size:15
Alignment explanation
Indices: 27085--27122 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
27075 TTGGATCCTC
*
27085 ATTTTTTTTCTTTTT
1 ATTTATTTTCTTTTT
*
27100 GTTTATTTTC-TTTT
1 ATTTATTTTCTTTTT
27114 ATTTATTTT
1 ATTTATTTT
27123 ATTATTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.11, C:0.05, G:0.03, T:0.82
Consensus pattern (15 bp):
ATTTATTTTCTTTTT
Found at i:28960 original size:13 final size:13
Alignment explanation
Indices: 28942--28995 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
28932 ATTTTTTCTT
28942 TTTGTTTATTTTA
1 TTTGTTTATTTTA
*
28955 TTTGTTTATTTTCT
1 TTTGTTTATTTT-A
*
28969 TTTATTTATTTTA
1 TTTGTTTATTTTA
28982 TTAT-TTTATTTTA
1 TT-TGTTTATTTTA
28995 T
1 T
28996 ATTCTGAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 24 0.67
14 12 0.33
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.78
Consensus pattern (13 bp):
TTTGTTTATTTTA
Found at i:28966 original size:22 final size:22
Alignment explanation
Indices: 28946--28995 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
28936 TTTCTTTTTG
28946 TTTATTTTATTTGT-TTATTTTCT
1 TTTA-TTTATTT-TATTATTTTCT
*
28969 TTTATTTATTTTATTATTTTAT
1 TTTATTTATTTTATTATTTTCT
28991 TTTAT
1 TTTAT
28996 ATTCTGAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.80
23 4 0.16
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTATTTATTTTATTATTTTCT
Found at i:28977 original size:27 final size:28
Alignment explanation
Indices: 28935--28993 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 28
28925 GTCCTAAATT
*
28935 TTTTCTTTTTGTTTATTTTATT-TGTTTA
1 TTTTCTTTTTATTTATTTTATTAT-TTTA
28963 TTTTC-TTTTATTTATTTTATTATTTTA
1 TTTTCTTTTTATTTATTTTATTATTTTA
28990 TTTT
1 TTTT
28994 ATATTCTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (28 bp):
TTTTCTTTTTATTTATTTTATTATTTTA
Found at i:31447 original size:39 final size:39
Alignment explanation
Indices: 31393--31474 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
31383 AGTCCAATTA
* *
31393 TTATTATTATTATAACTTGTTGGTAATGGATAATCAGAT
1 TTATTATTATTATAACTTGTTAGCAATGGATAATCAGAT
31432 TTATTATTATTATAACTTGTTAGCAATGGATAATCAGAT
1 TTATTATTATTATAACTTGTTAGCAATGGATAATCAGAT
31471 TTAT
1 TTAT
31475 CCTAGCATAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (39 bp):
TTATTATTATTATAACTTGTTAGCAATGGATAATCAGAT
Found at i:32170 original size:20 final size:19
Alignment explanation
Indices: 32145--32182 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
32135 AATTCAATCT
32145 CTTTTTTTATTTAAATTTAG
1 CTTTTTTT-TTTAAATTTAG
*
32165 CTTTTTTTTTTTAATTTA
1 CTTTTTTTTTTAAATTTA
32183 TTTAAGTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (19 bp):
CTTTTTTTTTTAAATTTAG
Found at i:32360 original size:30 final size:30
Alignment explanation
Indices: 32324--32412 Score: 169
Period size: 30 Copynumber: 3.0 Consensus size: 30
32314 GACTAATCGT
*
32324 TTAGTGCCTTGCCCGGAAATTAAATGACCA
1 TTAGTGCCTTGCCTGGAAATTAAATGACCA
32354 TTAGTGCCTTGCCTGGAAATTAAATGACCA
1 TTAGTGCCTTGCCTGGAAATTAAATGACCA
32384 TTAGTGCCTTGCCTGGAAATTAAATGACC
1 TTAGTGCCTTGCCTGGAAATTAAATGACC
32413 GGATTAAGTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (30 bp):
TTAGTGCCTTGCCTGGAAATTAAATGACCA
Found at i:32846 original size:79 final size:79
Alignment explanation
Indices: 32715--32873 Score: 318
Period size: 79 Copynumber: 2.0 Consensus size: 79
32705 TTCATATATA
32715 TTATATATTCTGTTAATTGGAAAACTCTTTGGTAGTGGAAAACCATTAAGCTATTTCTACAAGCA
1 TTATATATTCTGTTAATTGGAAAACTCTTTGGTAGTGGAAAACCATTAAGCTATTTCTACAAGCA
32780 TGTTTGAAGTTTAT
66 TGTTTGAAGTTTAT
32794 TTATATATTCTGTTAATTGGAAAACTCTTTGGTAGTGGAAAACCATTAAGCTATTTCTACAAGCA
1 TTATATATTCTGTTAATTGGAAAACTCTTTGGTAGTGGAAAACCATTAAGCTATTTCTACAAGCA
32859 TGTTTGAAGTTTAT
66 TGTTTGAAGTTTAT
32873 T
1 T
32874 GTACTCCTTG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (79 bp):
TTATATATTCTGTTAATTGGAAAACTCTTTGGTAGTGGAAAACCATTAAGCTATTTCTACAAGCA
TGTTTGAAGTTTAT
Found at i:33326 original size:24 final size:24
Alignment explanation
Indices: 33272--33319 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
33262 ACCTTCCTCA
33272 GCAGGTTTTGTAACCAGGTTGGAG
1 GCAGGTTTTGTAACCAGGTTGGAG
33296 GCAGGTTTTGTAACCAGGTTGGAG
1 GCAGGTTTTGTAACCAGGTTGGAG
33320 AGAGGTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.38, T:0.29
Consensus pattern (24 bp):
GCAGGTTTTGTAACCAGGTTGGAG
Found at i:34450 original size:10 final size:12
Alignment explanation
Indices: 34423--34448 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34413 CAAGAGAAGA
34423 TATAAAAAATGT
1 TATAAAAAATGT
34435 TATAAAAAATGT
1 TATAAAAAATGT
34447 TA
1 TA
34449 AATGTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (12 bp):
TATAAAAAATGT
Found at i:39667 original size:13 final size:13
Alignment explanation
Indices: 39649--39676 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39639 TAAAAGTCCC
39649 AAGTTATGATAGG
1 AAGTTATGATAGG
39662 AAGTTATGATAGG
1 AAGTTATGATAGG
39675 AA
1 AA
39677 TATTTACGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (13 bp):
AAGTTATGATAGG
Found at i:41239 original size:92 final size:93
Alignment explanation
Indices: 41124--41292 Score: 259
Period size: 92 Copynumber: 1.8 Consensus size: 93
41114 GGATAAGAGG
* * *
41124 GTAACCAAGTTACCACGCAACAAAATCTTTAAGGCATATAAATGAGTAACCAAGTTACCATGCAT
1 GTAACCAAGTTACCACACAACAAAATCCTTAAGGCATATAAACGAGTAACCAAGTTACCATGCAT
*
41189 A-ATGCTACGGAACTACAAGGCGGTGAA
66 ACATGCGACGGAACTACAAGGCGGTGAA
* * * *
41216 GTAAGCAAGTTATCACACAACAAAATCCTTAGGGCATATAAGCGAGTAACCAAGTTACCATGCAT
1 GTAACCAAGTTACCACACAACAAAATCCTTAAGGCATATAAACGAGTAACCAAGTTACCATGCAT
41281 ACATGCGACGGA
66 ACATGCGACGGA
41293 GTTACAAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
92 59 0.87
93 9 0.13
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (93 bp):
GTAACCAAGTTACCACACAACAAAATCCTTAAGGCATATAAACGAGTAACCAAGTTACCATGCAT
ACATGCGACGGAACTACAAGGCGGTGAA
Found at i:47546 original size:13 final size:13
Alignment explanation
Indices: 47528--47553 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47518 ACAAAGATCC
47528 ATGTATCGATACA
1 ATGTATCGATACA
47541 ATGTATCGATACA
1 ATGTATCGATACA
47554 TTTCGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:47565 original size:20 final size:20
Alignment explanation
Indices: 47540--47577 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
47530 GTATCGATAC
47540 AATGTATCGATACATTTCGT
1 AATGTATCGATACATTTCGT
47560 AATGTATCGATACATTTC
1 AATGTATCGATACATTTC
47578 CTTGGTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTCGT
Found at i:48257 original size:27 final size:27
Alignment explanation
Indices: 48194--48257 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
48184 ACGAGTCCTA
* *
48194 ATTTTTTTTCTTTTTGTTTATTTTATT
1 ATTTTTTTTCTTTTTATTCATTTTATT
48221 -TGTTTCTTTTC-TTTTATTCATTTTATT
1 AT-TTT-TTTTCTTTTTATTCATTTTATT
48248 ATTTTATTTT
1 ATTTT-TTTT
48258 ATATTTTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.03
27 24 0.77
28 6 0.19
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.78
Consensus pattern (27 bp):
ATTTTTTTTCTTTTTATTCATTTTATT
Found at i:50723 original size:39 final size:39
Alignment explanation
Indices: 50669--50750 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
50659 AGTCCAATTA
* *
50669 TTATTATTATTATAACTTGTTGGTAATGGATAATCAGAT
1 TTATTATTATTATAACTTGTTAGCAATGGATAATCAGAT
50708 TTATTATTATTATAACTTGTTAGCAATGGATAATCAGAT
1 TTATTATTATTATAACTTGTTAGCAATGGATAATCAGAT
50747 TTAT
1 TTAT
50751 CCTAGCATAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (39 bp):
TTATTATTATTATAACTTGTTAGCAATGGATAATCAGAT
Found at i:54926 original size:13 final size:12
Alignment explanation
Indices: 54874--54931 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 12
54864 ACGAGTCCTA
54874 ATTTTTT-TTTT
1 ATTTTTTCTTTT
54885 ATTTGTTTCTTTT
1 ATTT-TTTCTTTT
*
54898 CTTTTATTCATTTT
1 ATTTT-TTC-TTTT
54912 ATTATTTTCTTTT
1 ATT-TTTTCTTTT
54925 ATATTTT
1 AT-TTTT
54932 GAAGGTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 4 0.10
12 4 0.10
13 19 0.49
14 10 0.26
15 2 0.05
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.78
Consensus pattern (12 bp):
ATTTTTTCTTTT
Found at i:55470 original size:3 final size:3
Alignment explanation
Indices: 55456--55507 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
55446 TATTAAAGAT
55456 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55502 TAA TAA
1 TAA TAA
55508 AAAATATATT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:57601 original size:97 final size:97
Alignment explanation
Indices: 57432--57628 Score: 315
Period size: 97 Copynumber: 2.0 Consensus size: 97
57422 ATCCTAATAT
*
57432 TTAGGACATTTTTCAATTAGAATGAATGTCCTTATCAAGTGCAAGTCTTGTAGTTGTTTATTTAA
1 TTAGGACATTTTTCAATTAAAATGAATGTCC-T-TCAAGTGCAAGTCTTGTAGTTGTTTATTTAA
*
57497 TAAAAAAGGCTTATGTTTTTTTTTTAAAATTGAAA
64 TAAAAAAGGCTCAT-TTTTTTTTTTAAAATTGAAA
*
57532 TTAGGACATTTTTCAATTAAAATGAATGTCC-TCAAGTGCAAGTCTTGTAGTTGTTTATTTCATA
1 TTAGGACATTTTTCAATTAAAATGAATGTCCTTCAAGTGCAAGTCTTGTAGTTGTTTATTTAATA
**
57596 AAAAAGGCTCATTTTTTTTTTTTGAATTGAAA
66 AAAAAGGCTCATTTTTTTTTTTAAAATTGAAA
57628 T
1 T
57629 CTTTAAATTA
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
96 19 0.21
97 43 0.47
100 30 0.33
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (97 bp):
TTAGGACATTTTTCAATTAAAATGAATGTCCTTCAAGTGCAAGTCTTGTAGTTGTTTATTTAATA
AAAAAGGCTCATTTTTTTTTTTAAAATTGAAA
Found at i:57860 original size:23 final size:23
Alignment explanation
Indices: 57830--57875 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
57820 TAACCTTGGG
57830 ATTGATAATTTTGCGGTAACTTT
1 ATTGATAATTTTGCGGTAACTTT
*
57853 ATTGATAATTTTGGGGTAACTTT
1 ATTGATAATTTTGCGGTAACTTT
57876 TGTTAGAGCA
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:0.26, C:0.07, G:0.20, T:0.48
Consensus pattern (23 bp):
ATTGATAATTTTGCGGTAACTTT
Found at i:58200 original size:34 final size:34
Alignment explanation
Indices: 58154--58371 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
58144 GTAAAAACCA
*
58154 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
58188 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
58222 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
58256 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
58289 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
58323 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
58356 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
58372 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:58268 original size:68 final size:67
Alignment explanation
Indices: 58152--58371 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
58142 TGGTAAAAAC
* * *
58152 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
58217 AT
66 AT
* * *
58219 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
58284 AAT
65 AAT
* * * * * *
58287 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
58352 AT
66 AT
58354 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
58372 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:62464 original size:19 final size:19
Alignment explanation
Indices: 62437--62499 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
62427 TCACGTGTAC
* *
62437 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
62456 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
62475 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
62494 AGTACC
1 AGTACC
62500 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:62850 original size:34 final size:34
Alignment explanation
Indices: 62804--63020 Score: 280
Period size: 34 Copynumber: 6.4 Consensus size: 34
62794 GTAAAAACCA
*
62804 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
62838 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
62872 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
62906 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
62939 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
62973 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
63006 CCATTTAATCAACAA
1 CCATTTAATCAACAA
63021 CTTTATTAAT
Statistics
Matches: 161, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 44 0.27
34 115 0.71
35 2 0.01
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:62918 original size:68 final size:67
Alignment explanation
Indices: 62802--63020 Score: 321
Period size: 67 Copynumber: 3.3 Consensus size: 67
62792 TGGTAAAAAC
* * *
62802 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
62867 AT
66 AT
* * *
62869 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
62934 AAT
65 AAT
* * * * * *
62937 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
63002 AT
66 AT
63004 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
63021 CTTTATTAAT
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:63495 original size:21 final size:21
Alignment explanation
Indices: 63470--63514 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
63460 TAGAGCACCA
63470 CTTAGTTAACAG-TTACCACAT
1 CTTAGTTAACAGATT-CCACAT
*
63491 CTTAGTTAGCAGATTCCACAT
1 CTTAGTTAACAGATTCCACAT
63512 CTT
1 CTT
63515 TAATCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (21 bp):
CTTAGTTAACAGATTCCACAT
Found at i:69028 original size:15 final size:15
Alignment explanation
Indices: 69010--69040 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
69000 AAAGAAAAAA
*
69010 CTTGATGATTGGAGC
1 CTTGATGATTAGAGC
69025 CTTGATGATTAGAGC
1 CTTGATGATTAGAGC
69040 C
1 C
69041 ACTTTGCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (15 bp):
CTTGATGATTAGAGC
Found at i:69907 original size:19 final size:19
Alignment explanation
Indices: 69883--69950 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
69873 AATTCAAAAA
69883 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
69902 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
69917 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
69934 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
69951 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:69921 original size:32 final size:32
Alignment explanation
Indices: 69885--69947 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
69875 TTCAAAAATT
*
69885 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
69917 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
69948 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:69922 original size:13 final size:13
Alignment explanation
Indices: 69904--69928 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69894 ACATAAGTTT
69904 TGTATCGATACAA
1 TGTATCGATACAA
69917 TGTATCGATACA
1 TGTATCGATACA
69929 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:70008 original size:13 final size:13
Alignment explanation
Indices: 69990--70015 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69980 CATTTTTCTG
69990 TGTATCGATACAT
1 TGTATCGATACAT
70003 TGTATCGATACAT
1 TGTATCGATACAT
70016 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:70012 original size:33 final size:33
Alignment explanation
Indices: 69970--70036 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
69960 GCCAAGGAAA
***
69970 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
70003 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
70036 T
1 T
70037 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:72675 original size:52 final size:52
Alignment explanation
Indices: 72546--72715 Score: 175
Period size: 52 Copynumber: 3.3 Consensus size: 52
72536 TTATTTCCGA
** * *
72546 GGGGATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTCCAAAACACCAATTTTTCCACAATC
* * **
72598 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATTTCCAAAACACCAATTTTTCC-ACAATC
* * *
72650 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTCT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTCC-AAAACACCAATTTTTCCACAATC
* *
72702 GAGGATGCTCCAAC
1 GGGGATACTCCAAC
72716 CTCGTTATTT
Statistics
Matches: 96, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
51 9 0.09
52 72 0.75
53 12 0.12
54 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACTCCGGTTTTATTTCCAAAACACCAATTTTTCCACAATC
Found at i:72960 original size:80 final size:76
Alignment explanation
Indices: 72729--72963 Score: 209
Period size: 80 Copynumber: 2.9 Consensus size: 76
72719 GTTATTTCAT
* * * * *
72729 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCCGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTC-AAGGGATACTCCAA-CCCCGTTTTATT-CCAAAACAT
* *
72794 TGATTTCTCATAAT
63 TGATTTCTCACAAC
* * * * * *
72808 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTTCTAATCA
1 CGGGGATACTCCAACCCCGTTATTTTC-AAGGGATACTCCAACCCCG---TTTTATTCCAAAACA
*
72873 TCGATTTCTCACAAC
62 TTGATTTCTCACAAC
* * *
72888 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCTGTTATTATCTCCAAAACAT
1 CGGGGATACTCCAACCCCGTTATTTTCAAGGG-ATACTCCAACCCCGTT-TTAT-TCCAAAACAT
*
72953 TAAATTTCTCA
63 T-GATTTCTCA
72964 TCGGGAAATA
Statistics
Matches: 124, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
77 2 0.02
78 7 0.06
79 50 0.40
80 60 0.48
81 5 0.04
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (76 bp):
CGGGGATACTCCAACCCCGTTATTTTCAAGGGATACTCCAACCCCGTTTTATTCCAAAACATTGA
TTTCTCACAAC
Found at i:74238 original size:2 final size:2
Alignment explanation
Indices: 74231--74255 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
74221 GTTTGGCTTA
74231 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
74256 CACGCACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78167 original size:2 final size:2
Alignment explanation
Indices: 78160--78198 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
78150 ATTTGCAGTG
* *
78160 TA TA TA TA TA GA TA GA TA TA TA TA TA TA TA GTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
78199 AATGACTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (2 bp):
TA
Found at i:78731 original size:21 final size:21
Alignment explanation
Indices: 78696--78751 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
78686 ATTCTTATAA
* *
78696 TTTTAAAATATAATTTTATTAT
1 TTTTAAAA-AAAATTATATTAT
*
78718 TTTTAAAAAAAATTATCTTAT
1 TTTTAAAAAAAATTATATTAT
* *
78739 ATTTAACAAAAAT
1 TTTTAAAAAAAAT
78752 AAATATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTAAAAAAAATTATATTAT
Done.