Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold563
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: 45632
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:2601 original size:21 final size:21
Alignment explanation
Indices: 2577--2621 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2567 GTCCCAGTTG
*
2577 GCATTGTAGGCATTTTTTTGA
1 GCATTCTAGGCATTTTTTTGA
*
2598 GCATTCTAGGCATTTTTTTTA
1 GCATTCTAGGCATTTTTTTGA
2619 GCA
1 GCA
2622 CTAAACACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (21 bp):
GCATTCTAGGCATTTTTTTGA
Found at i:3120 original size:24 final size:24
Alignment explanation
Indices: 3088--3133 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3078 GAATCAGCAA
*
3088 ACACACACATATCTGCACATATTG
1 ACACACACATATATGCACATATTG
3112 ACACACACATATATGCACATAT
1 ACACACACATATATGCACATAT
3134 AGACTACTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (24 bp):
ACACACACATATATGCACATATTG
Found at i:3424 original size:39 final size:39
Alignment explanation
Indices: 3381--3463 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
3371 AAATTCTACT
*
3381 GAAATTTAATTATGTGTCAAGCTTAATAATTGCAATTTA
1 GAAATTTAATTATGTGTCAAGCTTAAGAATTGCAATTTA
*
3420 GAAATTTGATTATGTGTCAAGCTTAAGAATTGCAATTTA
1 GAAATTTAATTATGTGTCAAGCTTAAGAATTGCAATTTA
3459 GAAAT
1 GAAAT
3464 GTTATCAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (39 bp):
GAAATTTAATTATGTGTCAAGCTTAAGAATTGCAATTTA
Found at i:4361 original size:174 final size:174
Alignment explanation
Indices: 4071--4488 Score: 836
Period size: 174 Copynumber: 2.4 Consensus size: 174
4061 ATCTTTTAAG
4071 GTAACTTTTATTTTATTTACTTAAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAGAG
1 GTAACTTTTATTTTATTTACTTAAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAGAG
4136 AAACATGAAATTATACCTGTCAATTTGTTATTGCCAAGATAAAGCTGTCGAAGAGAAGTCAAGTT
66 AAACATGAAATTATACCTGTCAATTTGTTATTGCCAAGATAAAGCTGTCGAAGAGAAGTCAAGTT
4201 TTCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCA
131 TTCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCA
4245 GTAACTTTTATTTTATTTACTTAAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAGAG
1 GTAACTTTTATTTTATTTACTTAAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAGAG
4310 AAACATGAAATTATACCTGTCAATTTGTTATTGCCAAGATAAAGCTGTCGAAGAGAAGTCAAGTT
66 AAACATGAAATTATACCTGTCAATTTGTTATTGCCAAGATAAAGCTGTCGAAGAGAAGTCAAGTT
4375 TTCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCA
131 TTCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCA
4419 GTAACTTTTATTTTATTTACTTAAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAGAG
1 GTAACTTTTATTTTATTTACTTAAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAGAG
4484 AAACA
66 AAACA
4489 GAGGAGAATT
Statistics
Matches: 244, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 244 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (174 bp):
GTAACTTTTATTTTATTTACTTAAAAAAGATTGCATAAATTTAATAACAAAAAGGAGAATAAGAG
AAACATGAAATTATACCTGTCAATTTGTTATTGCCAAGATAAAGCTGTCGAAGAGAAGTCAAGTT
TTCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCA
Found at i:8154 original size:945 final size:945
Alignment explanation
Indices: 6324--8211 Score: 3652
Period size: 945 Copynumber: 2.0 Consensus size: 945
6314 ATAGAAAGTT
* *
6324 GACATCAATGAGTCTCTCGACTCCACAAGTTTTTGCGGCAAAATAAAAACTAACAATATTTAAGC
1 GACATCAATCAGTCTCTCAACTCCACAAGTTTTTGCGGCAAAATAAAAACTAACAATATTTAAGC
*
6389 ACATGAAATGCAATGAAAACAAACAACAGTTCTGAAGAAACAAAGTAAATGCAACCTCAAAAAAG
66 ACATGAAATGCAATGAAAACAAACAACAGTTCTCAAGAAACAAAGTAAATGCAACCTCAAAAAAG
6454 TTTGGTTCTGCTAGCACTGAACTTAGTGGTTATTGTTTAAAGTCCCGCTTCACTACTTAAAACAA
131 TTTGGTTCTGCTAGCACTGAACTTAGTGGTTATTGTTTAAAGTCCCGCTTCACTACTTAAAACAA
6519 CTGTTGATGGAAATTAGATCAAAATGAATGAAACAATAACCAGGAATTGTTTACCTTTGAAATGG
196 CTGTTGATGGAAATTAGATCAAAATGAATGAAACAATAACCAGGAATTGTTTACCTTTGAAATGG
6584 TTGAGACCAAGACCCAACGTCTTGAGCAAAGTCAAATTTCCAATTTCTGTAGGTATACTTCCCTC
261 TTGAGACCAAGACCCAACGTCTTGAGCAAAGTCAAATTTCCAATTTCTGTAGGTATACTTCCCTC
6649 CAAGGAGTTGTTAAACAATGATAAAAACTTCAGCTCTTTGCACTTGAATAAACTATTTGGAATTC
326 CAAGGAGTTGTTAAACAATGATAAAAACTTCAGCTCTTTGCACTTGAATAAACTATTTGGAATTC
*
6714 TACCGGAAATTTGATTCCCACCCAAGCTCAACCTTTCTAGTTTTGACAAATTGCCTAGAGTAGAT
391 TACCGGAAATTTGATTCCCACCCAAGCTCAACATTTCTAGTTTTGACAAATTGCCTAGAGTAGAT
6779 GGGATAACACCAATGAAGTTGTTAAGGTACAGAGACAATCTTCGAAGTTTACTGAAGCAACCAAA
456 GGGATAACACCAATGAAGTTGTTAAGGTACAGAGACAATCTTCGAAGTTTACTGAAGCAACCAAA
* *
6844 CCATGGTGGGATTTCTCCATTGAAGCTATTGTTACCTAAGTCCAAATAATTCATCCGACGCAAAT
521 CCATGATGGGATTTCTCCATTGAAGCTATTGTTACCAAAGTCCAAATAATTCATCCGACGCAAAT
*
6909 TAGTTAACTCAATGGGTAAAGAGCCTTGGAAACTATTTTGATGAATATCGAGCCAAGCAAGGAAA
586 TAGTTAACTCAATGGGTAAAGAGCCTTGAAAACTATTTTGATGAATATCGAGCCAAGCAAGGAAA
6974 GATAGATTTCCCAATTGAGAAGAAATGGTGCCTGTGAGATCCATGCTTGACAAATTCAGAGCAGT
651 GATAGATTTCCCAATTGAGAAGAAATGGTGCCTGTGAGATCCATGCTTGACAAATTCAGAGCAGT
*
7039 GACTCTATAGTGTTTAGATCCACATGTGACACCAATCCAGCTACAAACGGAGATAGAAGTAGTCC
716 GACTCTATAGTGTTTAGATCCACATGTGACACCAATCCAGCTACAAACGGAGATAGAAGTAGACC
7104 AATTGGTTGTCAAGAAATTGTGAGGATCATGAATTATATGAGATTTGAGTGCTAGAAGAGCAGAT
781 AATTGGTTGTCAAGAAATTGTGAGGATCATGAATTATATGAGATTTGAGTGCTAGAAGAGCAGAT
7169 TGATCAACGGTGATGCTAGAATATTTTGCAGATAAAATAACCCCAAAGGTTGCAAATAGCAGCCC
846 TGATCAACGGTGATGCTAGAATATTTTGCAGATAAAATAACCCCAAAGGTTGCAAATAGCAGCCC
7234 AAACATAAACGGAGGGAGGAAGCTTGGTTTTTCGG
911 AAACATAAACGGAGGGAGGAAGCTTGGTTTTTCGG
*
7269 GACATCAATCAGTCTCTCAACTCCACAAGTTTTTGC-GCAAAAATAAAAACTAACAATATTTAAT
1 GACATCAATCAGTCTCTCAACTCCACAAGTTTTTGCGGC-AAAATAAAAACTAACAATATTTAAG
7333 CACATGAAATGCAATGAAAACAAACAACAGTTCTCAAGAAACAAAGTAAATGCAACCTCAAAAAA
65 CACATGAAATGCAATGAAAACAAACAACAGTTCTCAAGAAACAAAGTAAATGCAACCTCAAAAAA
7398 GTTTGGTTCTGCTAGCACTGAACTTAGTGGTTATTGTTTAAAGTCCCGCTTCACTACTTAAAACA
130 GTTTGGTTCTGCTAGCACTGAACTTAGTGGTTATTGTTTAAAGTCCCGCTTCACTACTTAAAACA
7463 ACTGTTGATGGAAATTAGATCAAAATGAATGAAACAATAACCAGGAATTGTTTACCTTTGAAATG
195 ACTGTTGATGGAAATTAGATCAAAATGAATGAAACAATAACCAGGAATTGTTTACCTTTGAAATG
7528 GTTGAGACCAAGACCCAACGTCTTGAGCAAAGTCAAATTTCCAATTTCTGTAGGTATACTTCCCT
260 GTTGAGACCAAGACCCAACGTCTTGAGCAAAGTCAAATTTCCAATTTCTGTAGGTATACTTCCCT
7593 CCAAGGAGTTGTTAAACAATGATAAAAACTTCAGCTCTTTGCACTTGAATAAACTATTTGGAATT
325 CCAAGGAGTTGTTAAACAATGATAAAAACTTCAGCTCTTTGCACTTGAATAAACTATTTGGAATT
7658 CTACCGGAAATTTGATTCCCACCCAAGCTCAACATTTCTAGTTTTGACAAATTGCCTAGAGTAGA
390 CTACCGGAAATTTGATTCCCACCCAAGCTCAACATTTCTAGTTTTGACAAATTGCCTAGAGTAGA
7723 TGGGATAACACCAATGAAGTTGTTAAGGTACAGAGACAATCTTCGAAGTTTACTGAAGCAACCAA
455 TGGGATAACACCAATGAAGTTGTTAAGGTACAGAGACAATCTTCGAAGTTTACTGAAGCAACCAA
*
7788 ACCATGATGGGATTTCTCCATTGAAGCTATTGTTACCAAAGTCCAAATATTTCATCCGACGCAAA
520 ACCATGATGGGATTTCTCCATTGAAGCTATTGTTACCAAAGTCCAAATAATTCATCCGACGCAAA
7853 TTAGTTAACTCAATGGGTAAAGAGCCTTGAAAACTATTTTGATGAATATCGAGCCAAGCAAGGAA
585 TTAGTTAACTCAATGGGTAAAGAGCCTTGAAAACTATTTTGATGAATATCGAGCCAAGCAAGGAA
7918 AGATAGATTTCCCAATTGAGAAGAAATGGTGCCTGTGAGATCCATGCTTGACAAATTCAGAGCAG
650 AGATAGATTTCCCAATTGAGAAGAAATGGTGCCTGTGAGATCCATGCTTGACAAATTCAGAGCAG
*
7983 TGACTCTATAGTGTTTAGATCCACATGTGACACCAATCCAGCTACAAACGGAGGTAGAAGTAGAC
715 TGACTCTATAGTGTTTAGATCCACATGTGACACCAATCCAGCTACAAACGGAGATAGAAGTAGAC
*
8048 CAATTGGTTGTCAAGAAATTGTGAGGATCATGAGTTATATGAGATTTGAGTGCTAGAAGAGCAGA
780 CAATTGGTTGTCAAGAAATTGTGAGGATCATGAATTATATGAGATTTGAGTGCTAGAAGAGCAGA
8113 TTGATCAACGGTGATGCTAGAATATTTTGCAGATAAAATAACCCCAAAGGTTGCAAATAGCAGCC
845 TTGATCAACGGTGATGCTAGAATATTTTGCAGATAAAATAACCCCAAAGGTTGCAAATAGCAGCC
8178 CAAACATAAACGGAGGGAGGAAGCTTGGTTTTTC
910 CAAACATAAACGGAGGGAGGAAGCTTGGTTTTTC
8212 CATAAGGTTG
Statistics
Matches: 930, Mismatches: 12, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
944 2 0.00
945 928 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (945 bp):
GACATCAATCAGTCTCTCAACTCCACAAGTTTTTGCGGCAAAATAAAAACTAACAATATTTAAGC
ACATGAAATGCAATGAAAACAAACAACAGTTCTCAAGAAACAAAGTAAATGCAACCTCAAAAAAG
TTTGGTTCTGCTAGCACTGAACTTAGTGGTTATTGTTTAAAGTCCCGCTTCACTACTTAAAACAA
CTGTTGATGGAAATTAGATCAAAATGAATGAAACAATAACCAGGAATTGTTTACCTTTGAAATGG
TTGAGACCAAGACCCAACGTCTTGAGCAAAGTCAAATTTCCAATTTCTGTAGGTATACTTCCCTC
CAAGGAGTTGTTAAACAATGATAAAAACTTCAGCTCTTTGCACTTGAATAAACTATTTGGAATTC
TACCGGAAATTTGATTCCCACCCAAGCTCAACATTTCTAGTTTTGACAAATTGCCTAGAGTAGAT
GGGATAACACCAATGAAGTTGTTAAGGTACAGAGACAATCTTCGAAGTTTACTGAAGCAACCAAA
CCATGATGGGATTTCTCCATTGAAGCTATTGTTACCAAAGTCCAAATAATTCATCCGACGCAAAT
TAGTTAACTCAATGGGTAAAGAGCCTTGAAAACTATTTTGATGAATATCGAGCCAAGCAAGGAAA
GATAGATTTCCCAATTGAGAAGAAATGGTGCCTGTGAGATCCATGCTTGACAAATTCAGAGCAGT
GACTCTATAGTGTTTAGATCCACATGTGACACCAATCCAGCTACAAACGGAGATAGAAGTAGACC
AATTGGTTGTCAAGAAATTGTGAGGATCATGAATTATATGAGATTTGAGTGCTAGAAGAGCAGAT
TGATCAACGGTGATGCTAGAATATTTTGCAGATAAAATAACCCCAAAGGTTGCAAATAGCAGCCC
AAACATAAACGGAGGGAGGAAGCTTGGTTTTTCGG
Found at i:15143 original size:16 final size:16
Alignment explanation
Indices: 15124--15166 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
15114 ATATTTCAAA
*
15124 AAAAAGAAAGAAGAAG
1 AAAAAGAAAGAAAAAG
15140 -AAAAGAAAAGAAAAAG
1 AAAAAG-AAAGAAAAAG
15156 AAAAATGAAAG
1 AAAAA-GAAAG
15167 GCCAAGGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 8 0.35
18 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:16617 original size:51 final size:51
Alignment explanation
Indices: 16541--16639 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
16531 GAGCGGACTG
*
16541 AAGGTAGCGAATCTTATTTCCCTGGCTTTGCAGTGGAACAGATTAAAGCTA
1 AAGGTAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTA
* * *
16592 AAGGTAGTGAATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAG
1 AAGGTAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAG
16640 TTGAAGTGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (51 bp):
AAGGTAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTA
Found at i:16733 original size:123 final size:123
Alignment explanation
Indices: 16538--16891 Score: 566
Period size: 123 Copynumber: 2.9 Consensus size: 123
16528 GTGGAGCGGA
** * * *
16538 CTGAAGGTAGCGAATCTTATTTCCCTGGCTTTGCAGTGGAACAGATTAAAGCTAAAGGTAGTGAA
1 CTGAAGGCGGCGAATCCTATCTCCTTGGCTTTGCAGTGGAACAGATTAAAGCTAAAGGTAGTGAA
*
16603 TCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGTTGAAGTGGAGCGGATTAAAG
66 TCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAG
* *
16661 CTGAAGGGGGCGAATCCTATCTCCTTGGCTTTGTAGTGGAACAGATTAAAGCTAAAGGTAG-GAA
1 CTGAAGGCGGCGAATCCTATCTCCTTGGCTTTGCAGTGGAACAGATTAAAGCTAAAGGTAGTG-A
*
16725 ATCTTGTTTCCCTAGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAG
65 ATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAG
* *
16784 CTGAAGGCGGCGAATCCTATCTCCTTGGCGTTACAGTGGAACAGATTAAAGCTAAAGGTAGTGAA
1 CTGAAGGCGGCGAATCCTATCTCCTTGGCTTTGCAGTGGAACAGATTAAAGCTAAAGGTAGTGAA
* * *
16849 TCTTGTTTCCCTGGCATTGCAGCGGAGTATATTAAAGCTGAAG
66 TCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTGAAG
16892 GCAACGAATT
Statistics
Matches: 213, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
122 1 0.00
123 211 0.99
124 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (123 bp):
CTGAAGGCGGCGAATCCTATCTCCTTGGCTTTGCAGTGGAACAGATTAAAGCTAAAGGTAGTGAA
TCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGCGGATTAAAG
Found at i:16772 original size:21 final size:21
Alignment explanation
Indices: 16746--16789 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
16736 CTAGCATTGC
*
16746 AGTGGAATAGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
* *
16767 AGTGGAGCGGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
16788 AG
1 AG
16790 GCGGCGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.20
Consensus pattern (21 bp):
AGTGGAACAGATTAAAGCTGA
Found at i:18873 original size:18 final size:18
Alignment explanation
Indices: 18835--18879 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
18825 TTTAATGGTG
* *
18835 TTATCATTATTTTTACCA
1 TTATTATTATTTTTAACA
*
18853 TTATTATTATTTTTAATA
1 TTATTATTATTTTTAACA
*
18871 TTACTATTA
1 TTATTATTA
18880 CTATTATTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATTATTTTTAACA
Found at i:19026 original size:2 final size:2
Alignment explanation
Indices: 19019--19123 Score: 58
Period size: 2 Copynumber: 54.5 Consensus size: 2
19009 TGTACACGTG
*
19019 TA TA TA TA TA TA T- TT TA TA TA -A CT- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
** ** * * * * *
19059 TA TA CG TA CC CA TA TA TA TA TA TA TT TA TA T- TT TA TC TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
19100 TA TC TA CA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19124 TTTCATGAAT
Statistics
Matches: 77, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
1 5 0.06
2 72 0.94
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19143 original size:35 final size:34
Alignment explanation
Indices: 19072--19145 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 34
19062 ACGTACCCAT
*
19072 ATATATATATATTTATATTTTATCTACATATCTAC
1 ATATATATATATTTATATTTTATATACATA-CTAC
19107 ATATATATATA-TTATATTTTCATGAATACATA-TAC
1 ATATATATATATTTATATTTT-AT--ATACATACTAC
19142 ATAT
1 ATAT
19146 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
34 9 0.26
35 20 0.57
37 6 0.17
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (34 bp):
ATATATATATATTTATATTTTATATACATACTAC
Found at i:19860 original size:13 final size:13
Alignment explanation
Indices: 19842--19867 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19832 CCTTAACGTA
19842 TTGGGCTGCGATT
1 TTGGGCTGCGATT
19855 TTGGGCTGCGATT
1 TTGGGCTGCGATT
19868 CTTCAACTGA
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:0.08, C:0.15, G:0.38, T:0.38
Consensus pattern (13 bp):
TTGGGCTGCGATT
Found at i:22567 original size:1 final size:1
Alignment explanation
Indices: 22561--22588 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
22551 AATGAGATAC
22561 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
22589 CATTTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26197 original size:5 final size:5
Alignment explanation
Indices: 26189--26219 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
26179 TATTTAGTTT
26189 ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA A
26220 AACATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:33321 original size:31 final size:31
Alignment explanation
Indices: 33262--33321 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
33252 TTATCTCTAT
* **
33262 CGTTTTAGATCATTTCTATTTTGGTCACTTA
1 CGTTTTAGAGCATTTCTATTTTACTCACTTA
*
33293 CGTTTTAGAGCATTTTTATTTTACTCACT
1 CGTTTTAGAGCATTTCTATTTTACTCACT
33322 CTTCATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.52
Consensus pattern (31 bp):
CGTTTTAGAGCATTTCTATTTTACTCACTTA
Found at i:33768 original size:25 final size:26
Alignment explanation
Indices: 33740--33810 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
33730 GAAACTATAT
*
33740 AAATATATATTTTAAAATATA-AAGG
1 AAATATAAATTTTAAAATATATAAGG
* * *
33765 AAATTATAAATTATAAAA-ATATATGT
1 AAA-TATAAATTTTAAAATATATAAGG
*
33791 AAATAAAAATTTTAAAATAT
1 AAATATAAATTTTAAAATAT
33811 TACAAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
25 18 0.49
26 19 0.51
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (26 bp):
AAATATAAATTTTAAAATATATAAGG
Found at i:39431 original size:23 final size:23
Alignment explanation
Indices: 39403--39521 Score: 139
Period size: 23 Copynumber: 5.2 Consensus size: 23
39393 GTTATTGATT
* *
39403 AGTGGTAACTTCGGCTACATTTC
1 AGTGGTAGCTTCGGCTACATATC
* * *
39426 AATGGTAGCTACAGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
* *
39449 AGTGGTAGCTTCGGCTACATTTT
1 AGTGGTAGCTTCGGCTACATATC
* * *
39472 AGTGGTATCTACGTCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
*
39495 AGTGGTAGCTTCGGCTACATATT
1 AGTGGTAGCTTCGGCTACATATC
39518 AGTG
1 AGTG
39522 TGACACTTAT
Statistics
Matches: 77, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 77 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACATATC
Found at i:39470 original size:46 final size:46
Alignment explanation
Indices: 39403--39514 Score: 172
Period size: 46 Copynumber: 2.4 Consensus size: 46
39393 GTTATTGATT
*
39403 AGTGGTAACTTCGGCTACATTTCAATGGTAGCTACAG-CTACATATC
1 AGTGGTAGCTTCGGCTACATTTCAATGGTAGCTAC-GTCTACATATC
* * *
39449 AGTGGTAGCTTCGGCTACATTTTAGTGGTATCTACGTCTACATATC
1 AGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGTCTACATATC
39495 AGTGGTAGCTTCGGCTACAT
1 AGTGGTAGCTTCGGCTACAT
39515 ATTAGTGTGA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 1 0.02
46 60 0.98
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (46 bp):
AGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGTCTACATATC
Found at i:40537 original size:31 final size:30
Alignment explanation
Indices: 40502--40569 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
40492 ATTTAAAGGA
* *
40502 GAGTGATCAAAATAGAAACAATCTAAAGTGT
1 GAGTGACCAAAATAGAAACAATATAAA-TGT
*
40533 GAGTGACCAAAATAGAAATAATATAAATGT
1 GAGTGACCAAAATAGAAACAATATAAATGT
*
40563 AAGTGAC
1 GAGTGAC
40570 TAAATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.22
Consensus pattern (30 bp):
GAGTGACCAAAATAGAAACAATATAAATGT
Found at i:40582 original size:30 final size:31
Alignment explanation
Indices: 40503--40582 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
40493 TTTAAAGGAG
* * * * *
40503 AGTGATCAAAATAGAAACAATCTAAAGTGTG
1 AGTGACCAAAATAAAAATAATATAAAGTGTA
*
40534 AGTGACCAAAATAGAAATAATATAAA-TGTA
1 AGTGACCAAAATAAAAATAATATAAAGTGTA
* *
40564 AGTGACTAAATTAAAAATA
1 AGTGACCAAAATAAAAATA
40583 TTCATAGTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 19 0.45
31 23 0.55
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (31 bp):
AGTGACCAAAATAAAAATAATATAAAGTGTA
Done.