Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2312_ERROPOS37353+
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: 165851
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7364 original size:21 final size:21
Alignment explanation
Indices: 7312--7366 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
7302 TTCAAAACAA
7312 AATTAACTTA-TT-AATTATT
1 AATTAACTTATTTAAATTATT
*
7331 AATTAA-TAAATTTAAATTATT
1 AATTAACT-TATTTAAATTATT
7352 AATTAACTTATTTAA
1 AATTAACTTATTTAA
7367 GTATGAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 7 0.23
20 2 0.07
21 19 0.63
22 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTAACTTATTTAAATTATT
Found at i:7436 original size:14 final size:14
Alignment explanation
Indices: 7417--7446 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7407 TTGAACTCAA
7417 AATTTAAATAATTT
1 AATTTAAATAATTT
*
7431 AATTTAATTAATTT
1 AATTTAAATAATTT
7445 AA
1 AA
7447 AATTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAAATAATTT
Found at i:9542 original size:7 final size:7
Alignment explanation
Indices: 9530--9558 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
9520 TTCTTCTGCT
9530 TTTTAAA
1 TTTTAAA
9537 TTTTAAA
1 TTTTAAA
9544 TTTTAAA
1 TTTTAAA
9551 TTTTAAA
1 TTTTAAA
9558 T
1 T
9559 ATAATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:9667 original size:15 final size:14
Alignment explanation
Indices: 9649--9695 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
9639 AATCACATTA
9649 TAATAAACTTGAA-TT
1 TAATAAA-TT-AATTT
9664 TAATAAATTAATTT
1 TAATAAATTAATTT
*
9678 TAATAATATTAATAT
1 TAATAA-ATTAATTT
9693 TAA
1 TAA
9696 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 2 0.07
14 10 0.34
15 17 0.59
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (14 bp):
TAATAAATTAATTT
Found at i:17773 original size:40 final size:40
Alignment explanation
Indices: 17729--17980 Score: 346
Period size: 40 Copynumber: 6.3 Consensus size: 40
17719 GACTTAAGGT
*
17729 CCGCAGGCTTTGTGCTGGAATTGTATCTGGGCTTAAAGAC
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
* * *
17769 CCGCAGGCTATATGCTGGAATTATATCCGGGCTTAAAGAC
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
* **
17809 CCGCAGGCTTTGTGCTGGAATTGTATCCGGACTT-AAGGT
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
17848 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
* * * *
17888 CCACAGGCTTCGTGCTGGAATTGTATCTGAGCTTAAAGAC
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
* * * *
17928 CCGCAGGCTTCGTGCTGGAATTGTATTCAGACTT-AAGAC
1 CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
*
17967 CCGTAGGCTTTGTG
1 CCGCAGGCTTTGTG
17981 AATTCGGGGT
Statistics
Matches: 186, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
39 53 0.28
40 133 0.72
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (40 bp):
CCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGAC
Found at i:17864 original size:79 final size:79
Alignment explanation
Indices: 17711--17980 Score: 328
Period size: 79 Copynumber: 3.4 Consensus size: 79
17701 ATATTTGATG
** * *
17711 TATATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCTGGGCTTAAAGACCCGCAGG
1 TATATCCGGACTTAAGACCCGCAGGCTTTGTGCTGGAATTGTATCCGGACTTAAAGACCCGCAGG
* *
17776 CTATATGCTGGAAT
66 CTTTGTGCTGGAAT
* **
17790 TATATCCGGGCTTAAAGACCCGCAGGCTTTGTGCTGGAATTGTATCCGGACTT-AAGGTCCGCAG
1 TATATCCGGACTT-AAGACCCGCAGGCTTTGTGCTGGAATTGTATCCGGACTTAAAGACCCGCAG
17854 GCTTTGTGCTGGAAT
65 GCTTTGTGCTGGAAT
* * * * *
17869 TGTATCCGGGCTTAAAGACCCACAGGCTTCGTGCTGGAATTGTAT-CTGAGCTTAAAGACCCGCA
1 TATATCCGGACTT-AAGACCCGCAGGCTTTGTGCTGGAATTGTATCCGGA-CTTAAAGACCCGCA
*
17933 GGCTTCGTGCTGGAAT
64 GGCTTTGTGCTGGAAT
* * * *
17949 TGTATTCAGACTTAAGACCCGTAGGCTTTGTG
1 TATATCCGGACTTAAGACCCGCAGGCTTTGTG
17981 AATTCGGGGT
Statistics
Matches: 166, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
78 3 0.02
79 95 0.57
80 68 0.41
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (79 bp):
TATATCCGGACTTAAGACCCGCAGGCTTTGTGCTGGAATTGTATCCGGACTTAAAGACCCGCAGG
CTTTGTGCTGGAAT
Found at i:17924 original size:119 final size:119
Alignment explanation
Indices: 17713--17980 Score: 412
Period size: 119 Copynumber: 2.3 Consensus size: 119
17703 ATTTGATGTA
* *
17713 TATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCTGGGCTTAAAGACCCGCAGGCT
1 TATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
* *
17778 ATATGCTGGAATTATATCCGGGCTTAAAGACCCGCAGGCTTTGTGCTGGAATTG
66 ATATGCTGGAATTATATCCGAGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
17832 TATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
1 TATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
* * *
17897 -TCGTGCTGGAATTGTATCTGAGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
66 AT-ATGCTGGAATTATATCCGAGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
* * ** *
17951 TATTCAGACTTAAGACCCGTAGGCTTTGTG
1 TATCCGGACTTAAGGTCCGCAGGCTTTGTG
17981 AATTCGGGGT
Statistics
Matches: 136, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
118 1 0.01
119 135 0.99
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (119 bp):
TATCCGGACTTAAGGTCCGCAGGCTTTGTGCTGGAATTGTATCCGGGCTTAAAGACCCACAGGCT
ATATGCTGGAATTATATCCGAGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
Found at i:19706 original size:53 final size:53
Alignment explanation
Indices: 19573--19729 Score: 190
Period size: 53 Copynumber: 2.9 Consensus size: 53
19563 GTTACATTTC
* * * *
19573 TAAGGCAAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACCA
1 TAAGGCAAGG-TACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTA-CA
* * * *
19628 TAAGGTAAAGGTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTT-CA
1 TAAGG-CAAGGTACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTACA
*
19681 TAAGGCAAGGCTACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG
1 TAAGGCAAGG-TACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
19730 CAAAAGGATA
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
52 4 0.05
53 41 0.47
55 38 0.44
56 4 0.05
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (53 bp):
TAAGGCAAGGTACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTACA
Found at i:19765 original size:46 final size:46
Alignment explanation
Indices: 19687--19775 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
19677 TTCATAAGGC
* * *
19687 AAGGCTACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGCAA
1 AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAGCAA
*
19733 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAG
19776 GTACCCGTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (46 bp):
AAGGATACCACGTAAGACCATGACAAGACATGGCAATGGTAAGCAA
Found at i:22961 original size:46 final size:47
Alignment explanation
Indices: 22871--23062 Score: 199
Period size: 46 Copynumber: 4.0 Consensus size: 47
22861 GAAATGTGAT
* * *
22871 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATATGTGC
1 TTCCGTATAAGACCATATCTGGGATATGGCATC-G-G---TGTGATATGTGC
22923 TTCCGTATAAGACCATATC-GGGATATGGCATCGGTGTGATATGTGC
1 TTCCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGC
* * *
22969 TACTGTATAAGACCATATCTGGGATATGGCATCAGTGTGATATGTG-
1 TTCCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGC
* * ** * *
23015 ATCCGTGTAAGACCATGGCTGGGCTATGGCCTCGGTATGTGATATGTG
1 TTCCGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG
23063 ACTATGTGCA
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
46 55 0.45
47 25 0.20
48 11 0.09
49 1 0.01
50 1 0.01
51 11 0.09
52 18 0.15
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (47 bp):
TTCCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGC
Found at i:34318 original size:56 final size:50
Alignment explanation
Indices: 34081--34329 Score: 327
Period size: 50 Copynumber: 4.8 Consensus size: 50
34071 GATAATAACA
* ** * *
34081 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
34132 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
34182 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
34232 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
*
34287 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
34330 TTACCCAAAT
Statistics
Matches: 175, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
50 96 0.55
51 33 0.19
53 3 0.02
54 1 0.01
55 2 0.01
56 40 0.23
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:34445 original size:13 final size:13
Alignment explanation
Indices: 34424--34454 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
34414 GCTTAGATCA
*
34424 TCATCAAATAAAT
1 TCATAAAATAAAT
34437 TCATAAAATAAAT
1 TCATAAAATAAAT
34450 TCATA
1 TCATA
34455 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:34702 original size:30 final size:30
Alignment explanation
Indices: 34667--34724 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
34657 CCTCGACTCT
*
34667 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
34697 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
34725 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:38935 original size:104 final size:104
Alignment explanation
Indices: 38755--39021 Score: 464
Period size: 104 Copynumber: 2.6 Consensus size: 104
38745 TTGTATATAA
** *
38755 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
38819 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
38859 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
38924 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
38963 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
39022 ATAACGGTTA
Statistics
Matches: 155, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
104 154 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:46411 original size:104 final size:103
Alignment explanation
Indices: 46232--46497 Score: 453
Period size: 104 Copynumber: 2.6 Consensus size: 103
46222 TTGTATATAA
** *
46232 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATGGTGGTGCTATGTGCG-TGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGAT-ATCCACCATATCTT
46296 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
46335 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCGATATCCACCATATCTT
46400 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
46439 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCGATATCCACCA
46498 ATAACGGTTA
Statistics
Matches: 154, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
103 28 0.18
104 125 0.81
105 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.30
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGATATCCACCATATCTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:49154 original size:21 final size:21
Alignment explanation
Indices: 49130--49171 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49120 TCATCAGATA
* *
49130 TACACCTTGAGGCATCGGGGG
1 TACAACTTGAGGAATCGGGGG
*
49151 TACAAGTTGAGGAATCGGGGG
1 TACAACTTGAGGAATCGGGGG
49172 AGGTGGGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.40, T:0.19
Consensus pattern (21 bp):
TACAACTTGAGGAATCGGGGG
Found at i:51434 original size:30 final size:30
Alignment explanation
Indices: 51400--51459 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
51390 ATTTAATACG
*
51400 AACTTTGGTAAAATTACAATTTTGCCCCTA
1 AACTTTGGCAAAATTACAATTTTGCCCCTA
* * *
51430 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACAATTTTGCCCCTA
51460 GACTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACAATTTTGCCCCTA
Found at i:54188 original size:22 final size:22
Alignment explanation
Indices: 54154--54195 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54144 ATAGCTAAAG
54154 TTAAATTTAAAATATAAAAAAA
1 TTAAATTTAAAATATAAAAAAA
*
54176 TTAAATATT-AAATATTAAAA
1 TTAAAT-TTAAAATATAAAAA
54196 TTATGAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAATTTAAAATATAAAAAAA
Found at i:65669 original size:33 final size:34
Alignment explanation
Indices: 65597--65672 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
65587 ATGTTTAAAT
* *
65597 GTAAGACCATACCTGGGTTATGGCATTTCAGTGAA
1 GTAAGACCATAACTGAGTTATGGCA-TTCAGTGAA
65632 --AAGACCATAACTGAGTTATGGCA-TC-GTGAA
1 GTAAGACCATAACTGAGTTATGGCATTCAGTGAA
65662 CGTAAGACCAT
1 -GTAAGACCAT
65673 GGTTGGACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
30 5 0.14
31 2 0.06
33 29 0.81
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (34 bp):
GTAAGACCATAACTGAGTTATGGCATTCAGTGAA
Found at i:65770 original size:103 final size:96
Alignment explanation
Indices: 65577--65826 Score: 241
Period size: 103 Copynumber: 2.5 Consensus size: 96
65567 ACCATGTTTA
* * * *
65577 GACCATGGCAATGTTTAAATGTAAGACCATACCTGGGTTATGGCATTTCAGTGAAAAGACCATAA
1 GACCATGGCAAT-ATT-CATGTAAGACCATAGCTGGGCTATGGCA--TCAGTGAAAAGACCATAA
**
65642 CTGAGTTATGGCATCGTGAACGTAAGACCATGGTTG
62 CTGAGTTATGGCATCG-GAACGTAAGACCATGGCAG
*
65678 GACCATGGCAATAAATATTCATGTAAGACCATAGCTGGGCTATGGCATCATGATGATAAGACCAT
1 GACCATGGC----AATATTCATGTAAGACCATAGCTGGGCTATGGCATCA-G-TGAAAAGACCAT
* **
65743 AACTGGGTTATGGCACTAC-GAGTGTAAGACCATGGCAG
60 AACTGAGTTATGGCA-T-CGGAACGTAAGACCATGGCAG
* * * * *
65781 GGCCATGGCAATATTCGTGTAAGACTATAGTTGGACTATGGCATCA
1 GACCATGGCAATATTCATGTAAGACCATAGCTGGGCTATGGCATCA
65827 AGTAAACGAT
Statistics
Matches: 126, Mismatches: 15, Indels: 18
0.79 0.09 0.11
Matches are distributed among these distances:
99 33 0.26
101 12 0.10
102 1 0.01
103 73 0.58
104 3 0.02
105 4 0.03
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (96 bp):
GACCATGGCAATATTCATGTAAGACCATAGCTGGGCTATGGCATCAGTGAAAAGACCATAACTGA
GTTATGGCATCGGAACGTAAGACCATGGCAG
Found at i:65771 original size:33 final size:32
Alignment explanation
Indices: 65698--65775 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
65688 ATAAATATTC
* *
65698 ATGTAAGACCATAGCTGGGCTATGGCATCATG
1 ATGTAAGACCATAACTGGGCTATGGCATCACG
*
65730 ATGATAAGACCATAACTGGGTTATGGCA-CTACG
1 ATG-TAAGACCATAACTGGGCTATGGCATC-ACG
65763 AGTGTAAGACCAT
1 A-TGTAAGACCAT
65776 GGCAGGGCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
32 4 0.10
33 34 0.85
34 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (32 bp):
ATGTAAGACCATAACTGGGCTATGGCATCACG
Found at i:68058 original size:63 final size:61
Alignment explanation
Indices: 67973--68092 Score: 186
Period size: 63 Copynumber: 1.9 Consensus size: 61
67963 TCAAAATCAG
* *
67973 TGTGTAATTATTTGTCAGGTATCAGTCACTCTTTGTATATATGTATTGATGCTTCTTATACCA
1 TGTGTAATTATTTGTCAAGTATCAGTCACTCTTTG--TATATCTATTGATGCTTCTTATACCA
* *
68036 TGTGTAGTTATTTTTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCTTAT
1 TGTGTAATTATTTGTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCTTAT
68093 CATTTGGCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 21 0.40
63 32 0.60
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (61 bp):
TGTGTAATTATTTGTCAAGTATCAGTCACTCTTTGTATATCTATTGATGCTTCTTATACCA
Found at i:69181 original size:23 final size:23
Alignment explanation
Indices: 69155--69227 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
69145 TGCTGTTATG
*
69155 GGTGTTGTTTTGGTGTTGTAATA
1 GGTGCTGTTTTGGTGTTGTAATA
**
69178 GGTGCTGTCATGGTGTTGTAATA
1 GGTGCTGTTTTGGTGTTGTAATA
* * * * *
69201 GCTACTGGTTTGGTGGTGTTATA
1 GGTGCTGTTTTGGTGTTGTAATA
69224 GGTG
1 GGTG
69228 TCATTTTGTT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.14, C:0.05, G:0.37, T:0.44
Consensus pattern (23 bp):
GGTGCTGTTTTGGTGTTGTAATA
Found at i:90414 original size:24 final size:24
Alignment explanation
Indices: 90387--90445 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
90377 CCCATCAGCT
*
90387 CCTCCTCCTTCTACCA-CTCCATCC
1 CCTCCTCCTTCTACCACCT-CATCA
* *
90411 CCTCCTCCTCCTTCCACCTCATCA
1 CCTCCTCCTTCTACCACCTCATCA
*
90435 CCTCCGCCTTC
1 CCTCCTCCTTC
90446 ATCCTCTGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.10, C:0.59, G:0.02, T:0.29
Consensus pattern (24 bp):
CCTCCTCCTTCTACCACCTCATCA
Found at i:90596 original size:36 final size:36
Alignment explanation
Indices: 90519--90598 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
90509 CCCTCCGCCG
* * * *
90519 CCGCCACCGAGGAGTCCCGGTACTGCATCTCCACCA
1 CCGCCTCCGAGGAATCCCGGGACTCCATCTCCACCA
* * *
90555 CCGCCTCCGAGGAATTCCGGGACTCCATCTCCTCCT
1 CCGCCTCCGAGGAATCCCGGGACTCCATCTCCACCA
90591 CCGCCTCC
1 CCGCCTCC
90599 TTCTGATTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.15, C:0.47, G:0.20, T:0.17
Consensus pattern (36 bp):
CCGCCTCCGAGGAATCCCGGGACTCCATCTCCACCA
Found at i:103027 original size:14 final size:14
Alignment explanation
Indices: 103008--103036 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
102998 GAGCTCTAAG
103008 TAAGTCCTTTTTTC
1 TAAGTCCTTTTTTC
103022 TAAGTCCTTTTTTC
1 TAAGTCCTTTTTTC
103036 T
1 T
103037 TTTTAATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.59
Consensus pattern (14 bp):
TAAGTCCTTTTTTC
Found at i:122474 original size:53 final size:53
Alignment explanation
Indices: 122393--122543 Score: 205
Period size: 53 Copynumber: 2.8 Consensus size: 53
122383 CTTACACGGT
* *
122393 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
122448 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** * *
122501 TCACATTGCACCGATGCCATAGCCCAGCTATAGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
122544 GCACACTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:129572 original size:53 final size:53
Alignment explanation
Indices: 129491--129641 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
129481 CTTACACGGT
* *
129491 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
129546 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
129599 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
129642 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:162460 original size:1 final size:1
Alignment explanation
Indices: 162454--162482 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
162444 TTTGCTTCCT
162454 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
162483 CTTTGGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:163928 original size:42 final size:40
Alignment explanation
Indices: 163882--164079 Score: 127
Period size: 42 Copynumber: 4.9 Consensus size: 40
163872 TTCCTTCCCT
163882 GATTACAGCGGAGCAGATCAAAGAGTAATCCTATCTCCTTGA
1 GATTACAGCGGAGCAGATCAAAGAG--ATCCTATCTCCTTGA
** * * *
163924 GATTACAATGGAGCGGATTAAAG-GATCTTATCT-CTCTGA
1 GATTACAGCGGAGCAGATCAAAGAGATCCTATCTCCT-TGA
** * ** * *
163963 -AGTTACAGTAGAGAAGATCACATCAGATCTTATCTCCCTGA
1 GA-TTACAGCGGAGCAGATCA-AAGAGATCCTATCTCCTTGA
*
164004 GATTACAGCGGAGCAGAT-AAGATAGTAATCCTATCTCCTTGA
1 GATTACAGCGGAGCAGATCAA-AGAG--ATCCTATCTCCTTGA
** * * *
164046 GATTACAATGGAGCGGATTAAAG-GATCTTATCTC
1 GATTACAGCGGAGCAGATCAAAGAGATCCTATCTC
164080 TCTGAAGTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 23
0.72 0.15 0.14
Matches are distributed among these distances:
38 3 0.02
39 34 0.28
40 4 0.03
41 28 0.23
42 50 0.41
43 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (40 bp):
GATTACAGCGGAGCAGATCAAAGAGATCCTATCTCCTTGA
Found at i:164082 original size:122 final size:118
Alignment explanation
Indices: 163882--164138 Score: 417
Period size: 122 Copynumber: 2.1 Consensus size: 118
163872 TTCCTTCCCT
163882 GATTACAGCGGAGCAGATCAAAGAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG
1 GATTACAGCGGAGCAGATCAAAGAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG
163947 GATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGATCTTATCTCCCTGA
66 GATCTTATCTCTCTGAAGTTACAGT-GAGAAGAT---ATCAGATCTTATCTCCCTGA
*
164004 GATTACAGCGGAGCAGAT-AAGATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAA
1 GATTACAGCGGAGCAGATCAA-AGAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAA
* *
164068 GGATCTTATCTCTCTGAAGTTACAGTGAGTAGATATCAGGTCTTATCTCCCTGA
65 GGATCTTATCTCTCTGAAGTTACAGTGAGAAGATATCAGATCTTATCTCCCTGA
* *
164122 GATTACAGTGGAACAGA
1 GATTACAGCGGAGCAGA
164139 CCGAAGAAAT
Statistics
Matches: 129, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
118 34 0.26
121 9 0.07
122 86 0.67
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (118 bp):
GATTACAGCGGAGCAGATCAAAGAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG
GATCTTATCTCTCTGAAGTTACAGTGAGAAGATATCAGATCTTATCTCCCTGA
Found at i:164201 original size:165 final size:176
Alignment explanation
Indices: 163986--164365 Score: 452
Period size: 165 Copynumber: 2.2 Consensus size: 176
163976 AAGATCACAT
*
163986 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATAAGATAGTAATCCTATCTCCTTG-AGATT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATAAGATAGTAATCCTATCTCCCTGAAG-TT
164050 ACAATGGA-GCGGA-T-TAAAGGATCTTATCTCTCTGAAGTTAC-AGT-GAGTAGAT-A-TCAGG
65 ACAATGGAGGCGGATTATAAAGGATCTTATCTCTCTGAAGTTACAAGTAGAGTAGATCATTCAGG
164108 TCTTATC-TCCCTGAGATTAC-AGTGGAAC-AGACCG-AAGAAATTG
130 TCTTATCGTCCCTGAGATTACAAGTGGAACTAGACCGAAAGAAATTG
* *
164151 CAGATCTTGTCTCGCCTGAGGTTACAGC-G-GCAGATCGAAGATA-TAATCCTATCTCCCTGAAG
1 CAGATCTTATCTC-CCTGAGATTACAGCGGAGCAGAT--AAGATAGTAATCCTATCTCCCTGAAG
* *
164213 TTACAGTGGAGGCGGATTAAAATAAAGGATCTTATCTCTCTGACGTTACAAGTAGAGTAGATGCA
63 TTACAATGGAGGCGGATT---ATAAAGGATCTTATCTCTCTGAAGTTACAAGTAGAGTAGAT-CA
* * * *
164278 TTCAGGTCTTATCGTCTCTGAGGTTACAAGTGGAGCTAGACCGAAAGAATTTG
124 TTCAGGTCTTATCGTCCCTGAGATTACAAGTGGAACTAGACCGAAAGAAATTG
* * *
164331 CAGATCTT-TCCCCCTGAAAGTTA-AGTGGAGCAGAT
1 CAGATCTTATCTCCCTGAGA-TTACAGCGGAGCAGAT
164366 TGCAAGCCAG
Statistics
Matches: 180, Mismatches: 13, Indels: 29
0.81 0.06 0.13
Matches are distributed among these distances:
164 6 0.03
165 37 0.21
166 26 0.14
167 1 0.01
171 26 0.14
172 3 0.02
173 8 0.04
175 1 0.01
176 12 0.07
177 11 0.06
178 14 0.08
179 13 0.07
180 22 0.12
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (176 bp):
CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATAAGATAGTAATCCTATCTCCCTGAAGTTA
CAATGGAGGCGGATTATAAAGGATCTTATCTCTCTGAAGTTACAAGTAGAGTAGATCATTCAGGT
CTTATCGTCCCTGAGATTACAAGTGGAACTAGACCGAAAGAAATTG
Found at i:164624 original size:194 final size:188
Alignment explanation
Indices: 164317--164680 Score: 453
Period size: 194 Copynumber: 1.9 Consensus size: 188
164307 GTGGAGCTAG
* *
164317 ACCGAAAGAATTTGCAGATCTTTCCCCCTGAAAGTTAAGTGGAGCAGATTGCAAGCCAGGAAGAT
1 ACCGAAAGAATTGGCAGATCTTTCCACCTGAAAGTTAAGTGGAGCAGATTG-AAGCCAGGAAGAT
*
164382 CTTATTTCCCCGAGATTACAGCGGAGACAGATCGAAGACCTTCCTATCTCCCTGAAGTTACAGTG
65 CTTATCTCCCCGAGATTACAGCGGAGACAGATCGAAGACCTTCCTATCT-CCTGAAGTTACAGTG
164447 G-AGTGGGGTTTTAAAATAAAGGATACTTAT-TCTCTGAGGTTACAGTGGGAGTAGACCAAAAAA
129 GAAGT-GGG---T--AATAAAGGAT-CTTATCTCTCTGAGGTTACAGTGGGAGTAGACCAAAAAA
164510 AT
187 AT
164512 ACCG-AAGAATTGGCAGATCTTAT-CACCTG-AAGTTACAGTGGAAGCAGATTG-AGCCA-G-AG
1 ACCGAAAGAATTGGCAGATCTT-TCCACCTGAAAGTTA-AGTGG-AGCAGATTGAAGCCAGGAAG
164571 A-CTTATCTCGCGCCGAGATTACAGCGGAG-CAAGATCGACAG-CACTATCCTATCTCCTGAAGT
63 ATCTTATCTC-C-CCGAGATTACAGCGGAGAC-AGATCGA-AGAC-CT-TCCTATCTCCTGAAGT
164633 TACAGTGGAAAGTGGGTAATAAAGGATCTTATCTCTCTGAGGTTACAG
122 TACAGTGG-AAGTGGGTAATAAAGGATCTTATCTCTCTGAGGTTACAG
164681 CGAGGTAGGA
Statistics
Matches: 154, Mismatches: 3, Indels: 30
0.82 0.02 0.16
Matches are distributed among these distances:
188 5 0.03
189 25 0.16
190 7 0.05
191 6 0.04
192 26 0.17
193 31 0.20
194 37 0.24
195 17 0.11
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (188 bp):
ACCGAAAGAATTGGCAGATCTTTCCACCTGAAAGTTAAGTGGAGCAGATTGAAGCCAGGAAGATC
TTATCTCCCCGAGATTACAGCGGAGACAGATCGAAGACCTTCCTATCTCCTGAAGTTACAGTGGA
AGTGGGTAATAAAGGATCTTATCTCTCTGAGGTTACAGTGGGAGTAGACCAAAAAAAT
Done.