Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_227
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: 123712
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:8175 original size:19 final size:19
Alignment explanation
Indices: 8127--8166 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
8117 AAAGTAAACC
8127 TCACCACAAAACCTCACAA
1 TCACCACAAAACCTCACAA
8146 TCACCACAAAACCTCACAA
1 TCACCACAAAACCTCACAA
8165 TC
1 TC
8167 TCTCGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.42, G:0.00, T:0.12
Consensus pattern (19 bp):
TCACCACAAAACCTCACAA
Found at i:14785 original size:13 final size:12
Alignment explanation
Indices: 14769--14888 Score: 72
Period size: 12 Copynumber: 10.0 Consensus size: 12
14759 TTTTTTCGCT
14769 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
14782 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
14796 TTTTCTTTTTC-
1 TTTTCTTTTTCA
* *
14807 TTTCACTTTTTTGA
1 TTT-TC-TTTTTCA
14821 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
14831 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
14844 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
14856 TTTTCTTTTT-G
1 TTTTCTTTTTCA
14867 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
14877 ATTTCTTTTTCA
1 TTTTCTTTTTCA
14889 ATCTCTTTCT
Statistics
Matches: 85, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 17 0.20
12 30 0.35
13 19 0.22
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:14798 original size:14 final size:14
Alignment explanation
Indices: 14769--14805 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
14759 TTTTTTCGCT
14769 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
14782 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
14796 TTTTCTTTTT
1 TTTTCTTTTT
14806 CTTTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:14805 original size:15 final size:15
Alignment explanation
Indices: 14769--14808 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
14759 TTTTTTCGCT
14769 TTTTCTTTTTC--AA
1 TTTTCTTTTTCTTAA
*
14782 TTTTC-TTTTCTTCA
1 TTTTCTTTTTCTTAA
14796 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
14809 TCACTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 5 0.22
13 5 0.22
14 6 0.26
15 7 0.30
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCTTTTTCTTAA
Found at i:14887 original size:6 final size:6
Alignment explanation
Indices: 14767--14874 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
14757 TCTTTTTTCG
* * **
14767 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTTTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
14818 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
14866 -GTTTT CTTT
1 CTTTTT CTTT
14875 CAATTTCTTT
Statistics
Matches: 76, Mismatches: 21, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
5 5 0.07
6 58 0.76
7 10 0.13
8 3 0.04
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:15933 original size:10 final size:11
Alignment explanation
Indices: 15918--15960 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
15908 TTTTGCTCAC
15918 CTTTTTTTTT-
1 CTTTTTTTTTG
15928 CTTTTTTTTTG
1 CTTTTTTTTTG
*
15939 ATTTTTTTTTG
1 CTTTTTTTTTG
*
15950 AATTTTTTTTT
1 -CTTTTTTTTT
15961 TGAATTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 10 0.33
11 10 0.33
12 10 0.33
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.84
Consensus pattern (11 bp):
CTTTTTTTTTG
Found at i:15945 original size:13 final size:11
Alignment explanation
Indices: 15919--15960 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
15909 TTTGCTCACC
*
15919 TTTTTTTTT-C
1 TTTTTTTTTGA
15929 TTTTTTTTTGA
1 TTTTTTTTTGA
15940 TTTTTTTTTGAA
1 TTTTTTTTTG-A
15952 TTTTTTTTT
1 TTTTTTTTT
15961 TGAATTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 9 0.31
11 10 0.34
12 10 0.34
ACGTcount: A:0.07, C:0.02, G:0.05, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:15961 original size:13 final size:13
Alignment explanation
Indices: 15929--15967 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
15919 TTTTTTTTTC
15929 TTTTTTTTTG-A-
1 TTTTTTTTTGAAT
15940 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
15953 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
15966 TT
1 TT
15968 CTTCTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 10 0.38
12 1 0.04
13 15 0.58
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:27491 original size:14 final size:14
Alignment explanation
Indices: 27444--27491 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
27434 GTACGAATGG
*
27444 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
27458 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
27472 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
27486 ATTGGT
1 AATGGT
27492 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:28797 original size:30 final size:30
Alignment explanation
Indices: 28712--28808 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
28702 TAAACTAAAA
* *
28712 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
28742 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
28772 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
28801 ATGAGCTA
1 -TGAGCTA
28809 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:36132 original size:20 final size:20
Alignment explanation
Indices: 36109--36155 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
36099 GGGTTAAGAT
*
36109 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
36129 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
36149 TGAGCTG
1 TGAGCTG
36156 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:40048 original size:20 final size:20
Alignment explanation
Indices: 40025--40071 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
40015 GGGTTAAGAT
*
40025 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
40045 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
40065 TGAGCTG
1 TGAGCTG
40072 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:41765 original size:18 final size:18
Alignment explanation
Indices: 41742--41817 Score: 58
Period size: 18 Copynumber: 4.6 Consensus size: 18
41732 TTGTCTTTTC
41742 TTTCTTTTTCAATCTCAA
1 TTTCTTTTTCAATCTCAA
* *
41760 TTTCTTTTTCGATTTC--
1 TTTCTTTTTCAATCTCAA
*
41776 TTTCTCTTT---T-TCACA
1 TTTCTTTTTCAATCTCA-A
*
41791 -TCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATCTCAA
41808 TTTCTTTTTC
1 TTTCTTTTTC
41818 CATGACACTC
Statistics
Matches: 44, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
12 2 0.05
13 1 0.02
14 6 0.14
16 8 0.18
17 2 0.05
18 25 0.57
ACGTcount: A:0.14, C:0.24, G:0.01, T:0.61
Consensus pattern (18 bp):
TTTCTTTTTCAATCTCAA
Found at i:50795 original size:581 final size:582
Alignment explanation
Indices: 49649--50813 Score: 2163
Period size: 581 Copynumber: 2.0 Consensus size: 582
49639 TGATACCAAA
* *
49649 TGATGTGATCCGGCTCGGTTGATGGAGTCGGGTTCACTTAAGATGCCCGATCGTCAACGAGAAGT
1 TGATGTGATCCGGCTCAGTTGATGGAGTCGGATTCACTT-AGATGCCCGATCGTCAACGAGAAGT
49714 TTGTTCAAATTTGTAGATAGATGGAGTTAGATGATTTTTTATAGCGGAAGTTGAGAAAATGGGTT
65 TTGTTCAAATTTGTAGATAGATGGAGTTAGATGATTTTTTATAGCGGAAGTTGAGAAAATGGGTT
49779 CAAAAGATGGTTTGAATAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTGTTTATAATTTA
130 CAAAAGATGGTTTGAATAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTGTTTATAATTTA
49844 ATAGTGAAAATGGAATGGAAAAATAGAACTCAAGCGAAGAACGATTCAATACTATATGAAGTATT
195 ATAGTGAAAATGGAATGGAAAAATAGAACTCAAGCGAAGAACGATTCAATACTATATGAAGTATT
*
49909 GCCCCGGGACTTATATTGCTCAAGGTGGATTAAATGGATTGTCGAAGATGGACCTTGACCCGTTA
260 GCCCCGGGACTTATATTGCTCAAGGTGGATTAAATGGATTGTCGAAGATGGACCTTGACCCATTA
*
49974 CCTATAGAGAGGTAGGAACCAAAGGTATAAAAAGGTGGATGAACGCCACACCAGGATGGTGATAA
325 CCTATAGAAAGGTAGGAACCAAAGGTATAAAAAGGTGGATGAACGCCACACCAGGATGGTGATAA
50039 GTTCAAGAAGTCGGGTTGACGCCACTAGCGAGCTAGATAAGTCAGAACGAGACTCGTACGAAATA
390 GTTCAAGAAGTCGGGTTGACGCCACTAGCGAGCTAGATAAGTCAGAACGAGACTCGTACGAAATA
50104 GGATAGGAGGAAACCTCACAATCAAGTTTTCAATAATCAAATTCTGTAACCTTTTACAATAAACA
455 GGATAGGAGGAAACCTCACAATCAAGTTTTCAATAATCAAATTCTGTAACCTTTTACAATAAACA
50169 AGTAAGCTATTTATAAGCCTAAAATGCCTATTGATATTCGGCATCTATGTTGTTCACACTAAC
520 AGTAAGCTATTTATAAGCCTAAAATGCCTATTGATATTCGGCATCTATGTTGTTCACACTAAC
* *
50232 TGATGTGATCCGGCTCAGTTGATTGAGTC-GATTCACTT-GATTGCCCGATCGTCGACGAGAAGT
1 TGATGTGATCCGGCTCAGTTGATGGAGTCGGATTCACTTAGA-TGCCCGATCGTCAACGAGAAGT
* *
50295 TTGTTCGATTTTGTAGATAGATGGAGTTAGATGATTTTTTATAGCGGAAGTTGAGAAAATGGGTT
65 TTGTTCAAATTTGTAGATAGATGGAGTTAGATGATTTTTTATAGCGGAAGTTGAGAAAATGGGTT
**
50360 CAAAAGATGGTTTGGGTAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTGTTTATAATTTA
130 CAAAAGATGGTTTGAATAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTGTTTATAATTTA
*
50425 ATAGTTAAAATGGAATGGAAAAATAGAACTCAAGCGAAGAACGATTCAATACTATATGAAGTATT
195 ATAGTGAAAATGGAATGGAAAAATAGAACTCAAGCGAAGAACGATTCAATACTATATGAAGTATT
* * *
50490 GCCCCGGGACTTATATTGCTTAAGGTGGGTTTAATGGATTGTCGAAGATGGACCTTGACCCATTA
260 GCCCCGGGACTTATATTGCTCAAGGTGGATTAAATGGATTGTCGAAGATGGACCTTGACCCATTA
50555 CCTATAGAAAGGTAGGAACCAAAGGTATAAAAAGGTGGATGAACGCCACACCAGGATGGTGATAA
325 CCTATAGAAAGGTAGGAACCAAAGGTATAAAAAGGTGGATGAACGCCACACCAGGATGGTGATAA
50620 GTTCAAGAAGTCGGGTTGACGCCACTAGCGAGCTAGATAAGTCAGAACGAGACTCGTACGAAATA
390 GTTCAAGAAGTCGGGTTGACGCCACTAGCGAGCTAGATAAGTCAGAACGAGACTCGTACGAAATA
50685 GGATAGGAGGAAACCTCACAATCAAGTTTTCAATAATCAAATTCTGTAACCTTTTACAATAAACA
455 GGATAGGAGGAAACCTCACAATCAAGTTTTCAATAATCAAATTCTGTAACCTTTTACAATAAACA
*
50750 AGTAATCTATTTATAAGCCTAAAATGCCTATTGATATTCGGCATCTATGTTGTTCACACTAAC
520 AGTAAGCTATTTATAAGCCTAAAATGCCTATTGATATTCGGCATCTATGTTGTTCACACTAAC
50813 T
1 T
50814 TAAATTCTGT
Statistics
Matches: 566, Mismatches: 15, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
580 2 0.00
581 529 0.93
582 8 0.01
583 27 0.05
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (582 bp):
TGATGTGATCCGGCTCAGTTGATGGAGTCGGATTCACTTAGATGCCCGATCGTCAACGAGAAGTT
TGTTCAAATTTGTAGATAGATGGAGTTAGATGATTTTTTATAGCGGAAGTTGAGAAAATGGGTTC
AAAAGATGGTTTGAATAGATGTTTGATAGGCTCGGTGAAATAAAGAAATATTGTTTATAATTTAA
TAGTGAAAATGGAATGGAAAAATAGAACTCAAGCGAAGAACGATTCAATACTATATGAAGTATTG
CCCCGGGACTTATATTGCTCAAGGTGGATTAAATGGATTGTCGAAGATGGACCTTGACCCATTAC
CTATAGAAAGGTAGGAACCAAAGGTATAAAAAGGTGGATGAACGCCACACCAGGATGGTGATAAG
TTCAAGAAGTCGGGTTGACGCCACTAGCGAGCTAGATAAGTCAGAACGAGACTCGTACGAAATAG
GATAGGAGGAAACCTCACAATCAAGTTTTCAATAATCAAATTCTGTAACCTTTTACAATAAACAA
GTAAGCTATTTATAAGCCTAAAATGCCTATTGATATTCGGCATCTATGTTGTTCACACTAAC
Found at i:51583 original size:20 final size:20
Alignment explanation
Indices: 51560--51605 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
51550 GGGTTAAGAT
*
51560 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
51580 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
51600 TGAGCT
1 TGAGCT
51606 AGAAACGAGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:54834 original size:48 final size:48
Alignment explanation
Indices: 54779--54884 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
54769 TTGTCTTTTC
*
54779 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
54827 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
54875 TTTCTTTTTC
1 TTTCTTTTTC
54885 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:57540 original size:20 final size:20
Alignment explanation
Indices: 57517--57563 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
57507 GGGTTAAGAT
*
57517 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
57537 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
57557 TGAGCTG
1 TGAGCTG
57564 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:58452 original size:20 final size:20
Alignment explanation
Indices: 58429--58475 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
58419 GGGTTAAGAT
*
58429 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
58449 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
58469 TGAGCTG
1 TGAGCTG
58476 GAAACAAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:70040 original size:10 final size:11
Alignment explanation
Indices: 70024--70054 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
70014 AAGAGTTCGA
70024 AAAAAAAATTG
1 AAAAAAAATTG
70035 AAAAAAAATTG
1 AAAAAAAATTG
70046 AAAAGAAAA
1 AAAA-AAAA
70055 AAAAATTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:70909 original size:15 final size:15
Alignment explanation
Indices: 70877--70910 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
70867 GTTCAACGAA
*
70877 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
70892 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
70907 GAGG
1 GAGG
70911 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:75188 original size:9 final size:9
Alignment explanation
Indices: 75174--75209 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
75164 CATAAATCAC
75174 TTTTTTTTA
1 TTTTTTTTA
75183 TTTTTTTTCGA
1 TTTTTTTT--A
75194 TTTTTTTTA
1 TTTTTTTTA
75203 TTTTTTT
1 TTTTTTT
75210 AAACTTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 16 0.64
11 9 0.36
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:75609 original size:13 final size:14
Alignment explanation
Indices: 75567--75609 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
75557 TAGAAAGAGG
* * *
75567 GGTACGAATGGAAT
1 GGTAGGAATGAAAA
75581 GGTAGGAATGAAAA
1 GGTAGGAATGAAAA
75595 GGTAGGAAT-AAAA
1 GGTAGGAATGAAAA
75608 GG
1 GG
75610 ATATGAACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.44, C:0.02, G:0.37, T:0.16
Consensus pattern (14 bp):
GGTAGGAATGAAAA
Found at i:79126 original size:12 final size:12
Alignment explanation
Indices: 79111--79139 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
79101 AAAGAGTTCG
79111 AAAAAAATTGAA
1 AAAAAAATTGAA
79123 AAAAAAATTGAA
1 AAAAAAATTGAA
79135 AAAAA
1 AAAAA
79140 GAAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:80233 original size:18 final size:18
Alignment explanation
Indices: 80195--80236 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
80185 AAATCGAAAG
* **
80195 AAAAGAAAAAGAGATTGA
1 AAAAGAAAAAGAAATCCA
80213 AAAAGAAAAAGAAATCCA
1 AAAAGAAAAAGAAATCCA
80231 AAAAGA
1 AAAAGA
80237 GAGTGAGGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCCA
Found at i:83878 original size:12 final size:13
Alignment explanation
Indices: 83861--83893 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
83851 CTATACAAGT
83861 TAAAAAAAAA-TC
1 TAAAAAAAAATTC
*
83873 TAAAAAAAAATTG
1 TAAAAAAAAATTC
83886 TAAAAAAA
1 TAAAAAAA
83894 TGATTTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (13 bp):
TAAAAAAAAATTC
Found at i:90930 original size:14 final size:14
Alignment explanation
Indices: 90913--90952 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
90903 CGAATGGAAT
*
90913 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
90927 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
90941 GATATGAACAAA
1 GGTAGGAACAAA
90953 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:95214 original size:14 final size:13
Alignment explanation
Indices: 95195--95234 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
95185 AAAGGAGAAG
95195 AAATTCAGAAAAAA
1 AAATTC-GAAAAAA
95209 AAATTC-AAAAAA
1 AAATTCGAAAAAA
95221 AAA-TCGAAAAAA
1 AAATTCGAAAAAA
95233 AA
1 AA
95235 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 17 0.68
14 6 0.24
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (13 bp):
AAATTCGAAAAAA
Found at i:95220 original size:12 final size:12
Alignment explanation
Indices: 95202--95261 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
95192 AAGAAATTCA
95202 GAAAAAAAAATTC
1 GAAAAAAAAA-TC
95215 -AAAAAAAAATC
1 GAAAAAAAAATC
*
95226 G-AAAAAAAA-G
1 GAAAAAAAAATC
95236 GAAAAAAAAAGT-
1 GAAAAAAAAA-TC
*
95248 GACAAAAAAATC
1 GAAAAAAAAATC
95260 GA
1 GA
95262 GTTAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 1 0.03
11 19 0.47
12 20 0.50
ACGTcount: A:0.73, C:0.07, G:0.12, T:0.08
Consensus pattern (12 bp):
GAAAAAAAAATC
Found at i:96226 original size:37 final size:37
Alignment explanation
Indices: 96175--96245 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
96165 CATTCTTGTA
96175 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
96212 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
96246 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:96245 original size:6 final size:6
Alignment explanation
Indices: 96185--96234 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
96175 AAGAGAAAAC
*
96185 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
96234 A
1 A
96235 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:96327 original size:11 final size:12
Alignment explanation
Indices: 96295--96325 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
96285 TTGAGAGAAC
96295 TTGAAAAAGCCT
1 TTGAAAAAGCCT
96307 TTGAAAAAGCCT
1 TTGAAAAAGCCT
96319 TTGAAAA
1 TTGAAAA
96326 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:96447 original size:6 final size:6
Alignment explanation
Indices: 96415--96522 Score: 67
Period size: 6 Copynumber: 17.7 Consensus size: 6
96405 AGAGAAATTG
* * ** *
96415 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * * *
96462 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
96513 AAAGAA AAAG
1 AAAGAA AAAG
96523 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 22, Indels: 11
0.69 0.20 0.10
Matches are distributed among these distances:
5 4 0.05
6 59 0.79
7 8 0.11
8 4 0.05
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:96502 original size:14 final size:13
Alignment explanation
Indices: 96483--96520 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
96473 AAAAGTGAGA
96483 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
96495 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
96510 GAAAAAGAAAA
1 GAAAAAGAAAA
96521 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:96557 original size:12 final size:12
Alignment explanation
Indices: 96526--96557 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
96516 GAAAAAGCGA
*
96526 AAAAAGAATTTG
1 AAAAAGAGTTTG
96538 AAAAAGAGTTTG
1 AAAAAGAGTTTG
96550 AAAAAGAG
1 AAAAAGAG
96558 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:104650 original size:48 final size:48
Alignment explanation
Indices: 104595--104700 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
104585 TTGTCTTTTC
*
104595 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
104643 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
104691 TTTCTTTTTC
1 TTTCTTTTTC
104701 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:105750 original size:22 final size:22
Alignment explanation
Indices: 105718--105785 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 22
105708 ACTCGCAATA
105718 CTTTTCACTTTTTTTGTTCTTTT
1 CTTTTCACTTTTTTT-TTCTTTT
105741 CTTTT-ACTTTTTTTTTCTTTT
1 CTTTTCACTTTTTTTTTCTTTT
*
105762 -TTTGCTCACTTCTTTTTTTTTTTT
1 CTTT--TCACTT-TTTTTTTCTTTT
105786 GAATTTCGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
20 3 0.08
21 7 0.17
22 10 0.25
23 9 0.22
24 11 0.28
ACGTcount: A:0.04, C:0.16, G:0.03, T:0.76
Consensus pattern (22 bp):
CTTTTCACTTTTTTTTTCTTTT
Found at i:105763 original size:23 final size:23
Alignment explanation
Indices: 105718--105778 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
105708 ACTCGCAATA
105718 CTTTTCACTTTTTTTGTTCTTTT
1 CTTTTCACTTTTTTTGTTCTTTT
105741 CTTTT-ACTTTTTTT-TTCTTTT
1 CTTTTCACTTTTTTTGTTCTTTT
105762 -TTTGCTCACTTCTTTTT
1 CTTT--TCACTT-TTTTT
105779 TTTTTTTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.09
21 7 0.21
22 10 0.29
23 9 0.26
24 5 0.15
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (23 bp):
CTTTTCACTTTTTTTGTTCTTTT
Found at i:105775 original size:32 final size:30
Alignment explanation
Indices: 105725--105785 Score: 77
Period size: 32 Copynumber: 2.0 Consensus size: 30
105715 ATACTTTTCA
* **
105725 CTTTTTTTGTTCTTTTCTTTTACTTTTTTTTT
1 CTTTTTTTGCTCACTTCTTTT--TTTTTTTTT
105757 CTTTTTTTGCTCACTTCTTTTTTTTTTTT
1 CTTTTTTTGCTCACTTCTTTTTTTTTTTT
105786 GAATTTCGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 8 0.31
32 18 0.69
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (30 bp):
CTTTTTTTGCTCACTTCTTTTTTTTTTTTT
Found at i:105886 original size:11 final size:11
Alignment explanation
Indices: 105870--105898 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
105860 CAACTCAAAA
105870 TTTTTTTTGA-
1 TTTTTTTTGAC
105880 TTTTTTTTGAC
1 TTTTTTTTGAC
105891 TTTTTTTT
1 TTTTTTTT
105899 TACATTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:114705 original size:23 final size:24
Alignment explanation
Indices: 114661--114712 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
114651 TGAGTGATAA
*
114661 AAAAAGAGAGAGTGATTCAAAA-G
1 AAAAAGAAAGAGTGATTCAAAATG
*
114684 AAAAAGAAACGAGTGA-TGAAAATG
1 AAAAAGAAA-GAGTGATTCAAAATG
114708 AAAAA
1 AAAAA
114713 AAGAATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.62, C:0.04, G:0.23, T:0.12
Consensus pattern (24 bp):
AAAAAGAAAGAGTGATTCAAAATG
Found at i:119322 original size:12 final size:12
Alignment explanation
Indices: 119305--119361 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
119295 TTGTAGATTC
119305 AAAAAAAAT-AA
1 AAAAAAAATGAA
119316 AAAAAAAATCG-A
1 AAAAAAAAT-GAA
*
119328 AAAAAAATTGAA
1 AAAAAAAATGAA
**
119340 AAAAAATTTGAA
1 AAAAAAAATGAA
119352 AAAAAAAATG
1 AAAAAAAATG
119362 CATACGGTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAATGAA
Done.