Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1785
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: 18532
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2697 original size:15 final size:16
Alignment explanation
Indices: 2667--2700 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2657 CTTGTTATTG
2667 TATATAATTGATTTTT
1 TATATAATTGATTTTT
*
2683 TATAT-ATTTATTTTT
1 TATATAATTGATTTTT
2698 TAT
1 TAT
2701 TTTTGCTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TATATAATTGATTTTT
Found at i:8585 original size:11 final size:11
Alignment explanation
Indices: 8569--8651 Score: 57
Period size: 12 Copynumber: 7.4 Consensus size: 11
8559 GTGGAGGCAA
8569 AAAAAAAAGAC
1 AAAAAAAAGAC
8580 AAAAAAAAAGA-
1 -AAAAAAAAGAC
*
8591 AAAAAAAAGTAA
1 AAAAAAAAG-AC
*
8603 AAAAAAAACGAG
1 AAAAAAAA-GAC
8615 AAAATAAAA-AGC
1 AAAA-AAAAGA-C
8627 AAAAAAAA-ACC
1 AAAAAAAAGA-C
*
8638 AAATAAAAGA-
1 AAAAAAAAGAC
8648 AAAA
1 AAAA
8652 CCTCTATTGG
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
10 12 0.20
11 15 0.25
12 28 0.47
13 5 0.08
ACGTcount: A:0.82, C:0.06, G:0.08, T:0.04
Consensus pattern (11 bp):
AAAAAAAAGAC
Found at i:8585 original size:12 final size:11
Alignment explanation
Indices: 8567--8635 Score: 77
Period size: 12 Copynumber: 5.8 Consensus size: 11
8557 CAGTGGAGGC
8567 AAAAAAAAAAG
1 AAAAAAAAAAG
8578 ACAAAAAAAAAG
1 A-AAAAAAAAAG
8590 -AAAAAAAAAG
1 AAAAAAAAAAG
8600 TAAAAAAAAAACG
1 -AAAAAAAAAA-G
8613 AGAAAATAAAAAG
1 A-AAAA-AAAAAG
8626 CAAAAAAAAA
1 -AAAAAAAAA
8636 CCAAATAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.20
11 1 0.02
12 24 0.47
13 10 0.20
14 6 0.12
ACGTcount: A:0.84, C:0.04, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:8595 original size:25 final size:25
Alignment explanation
Indices: 8567--8635 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 25
8557 CAGTGGAGGC
8567 AAAAAAAAAAGACAAAAAAAAAGAA
1 AAAAAAAAAAGACAAAAAAAAAGAA
** * *
8592 AAAAAAAGTA-A-AAAAAAAACGAG
1 AAAAAAAAAAGACAAAAAAAAAGAA
*
8615 AAAATAAAAAG-CAAAAAAAAA
1 AAAAAAAAAAGACAAAAAAAAA
8636 CCAAATAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
23 17 0.50
24 9 0.26
25 8 0.24
ACGTcount: A:0.84, C:0.04, G:0.09, T:0.03
Consensus pattern (25 bp):
AAAAAAAAAAGACAAAAAAAAAGAA
Found at i:8636 original size:25 final size:22
Alignment explanation
Indices: 8568--8636 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 22
8558 AGTGGAGGCA
8568 AAAAAAAAAGACAAAAAAAA-AG
1 AAAAAAAAAGA-AAAAAAAACAG
8590 AAAAAAAAAGTAAAAAAAAAACGAG
1 AAAAAAAAAG--AAAAAAAAAC-AG
8615 AAAATAAAAAGCAAAAAAAAAC
1 AAAA-AAAAAG-AAAAAAAAAC
8637 CAAATAAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 10 0.24
23 8 0.20
24 1 0.02
25 16 0.39
26 6 0.15
ACGTcount: A:0.83, C:0.06, G:0.09, T:0.03
Consensus pattern (22 bp):
AAAAAAAAAGAAAAAAAAACAG
Found at i:9098 original size:20 final size:20
Alignment explanation
Indices: 9061--9098 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9051 TTCACTTGAA
*
9061 AAAAAAAGAAAAGAAAAATG
1 AAAAAAAGAAAAAAAAAATG
*
9081 AAAAAATGAAAAAAAAAA
1 AAAAAAAGAAAAAAAAAA
9099 GAGGAGAGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAAAATG
Found at i:9574 original size:104 final size:105
Alignment explanation
Indices: 9410--9601 Score: 269
Period size: 104 Copynumber: 1.8 Consensus size: 105
9400 TTTGTATTCT
* * *
9410 AGCAACATTTGCTATCTTGATTAATTTGTTCATTTAGAGCTTTGCTCTCAGCAAATTTTCATCTT
1 AGCAAAATTTGCTATCTTG---AATTTGTTCATTTAGAGCTTTGCTCTCAACAAAATTTCATCTT
*
9475 ATCCGTTGTGATAATCTTTTTCATCTTATTCATCTCGTATCTC
63 ATCCATTGTGATAATCTTTTTCATCTTATTCATCTCGTATCTC
** * *
9518 AGCAAAATTTGCTATCTTG-ATTTGTTTGTTTAGAGCTTTGCTCTCAACAAAATTTCATTTTGTC
1 AGCAAAATTTGCTATCTTGAATTTGTTCATTTAGAGCTTTGCTCTCAACAAAATTTCATCTTATC
*
9582 CATTTTGATAATCTTTTTCA
66 CATTGTGATAATCTTTTTCA
9602 AGCATTTTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
104 57 0.76
108 18 0.24
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.47
Consensus pattern (105 bp):
AGCAAAATTTGCTATCTTGAATTTGTTCATTTAGAGCTTTGCTCTCAACAAAATTTCATCTTATC
CATTGTGATAATCTTTTTCATCTTATTCATCTCGTATCTC
Found at i:10361 original size:132 final size:132
Alignment explanation
Indices: 10200--11254 Score: 1722
Period size: 132 Copynumber: 8.0 Consensus size: 132
10190 TAACAGGTCC
* *
10200 TGTC-TCCCTATATTGGTAGG-G-AGTGGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCG
1 TGTCTTCCC-ATATTGGT-GGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCG
* *
10262 TGAAGTAGATCGGAGGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAG
64 TGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAG
10327 ATCT
129 ATCT
*
10331 TGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* *
10396 AAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGAT
66 AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGAT
10461 CT
131 CT
*
10463 TGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
*
10528 AAGTAGATCGAAGGTAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGAT
66 AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGAT
10593 CT
131 CT
*
10595 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* * * *
10660 AAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAGGAGGTGGATCCAAGATGCAGAT
66 AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGAT
10725 CT
131 CT
*
10727 TGTCTTCCCATGTTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
10792 AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGAT
66 AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGAT
10857 CT
131 CT
*
10859 TGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* * * * *
10924 AAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAGGAGGTGGATCCAATATGCAGAT
66 AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGAT
10989 CT
131 CT
*
10991 TGTCTT-CCATGTTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* *
11055 AAGTAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGAT
66 AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGAT
11120 CT
131 CT
* * *
11122 TGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATATTGTCTTCATGTATGGGCGTG
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* * ** * * **
11187 AAGTAGATCGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCA
66 AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATA-TTGGTAG-GAAGTGGATCAAAGAT-GCA
11252 GAT
128 GAT
11255 TTTACCTCCC
Statistics
Matches: 871, Mismatches: 46, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
130 2 0.00
131 138 0.16
132 706 0.81
133 6 0.01
134 13 0.01
135 6 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (132 bp):
TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGAT
CT
Found at i:11223 original size:44 final size:45
Alignment explanation
Indices: 10055--11254 Score: 931
Period size: 44 Copynumber: 27.3 Consensus size: 45
10045 GGTTGAAGTC
* * *
10055 AAGAAAGCAGATCTTGTCTTCATGTATT-GGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * * * *** * *
10099 AGGATAGCAGGTCCTATCTTCCTATATTGATAG-GAAGTGGATCC
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* *
10143 AAGAT-GCAGATCTTGTCTTCATGTATT-GGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * * * ** * *
10186 AAGATAACAGGTCCTGTCTCCCTATATTGGTAG-GGAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * * *
10230 AAGAAAGCAAATCTTGTCTTCATGTATT-GGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * * * ** * *
10274 GAGGTAGCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCA
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* *
10318 AAGAT-GCAGATCTTGTCTTCCCATATTGGTG-GCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-GCGTGAAGTAGATCG
* * * *
10362 CAGAAAGCAGATCTTGTCTTCATGTATT-GGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * * ** *
10406 AAGGTAGCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* *
10450 AAGAT-GCAGATCTTGTCTTCCCATATTGGTG-GCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-GCGTGAAGTAGATCG
* * * *
10494 CAGAAAGCAGATCTTGTCTTCATGTATT-GGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * * ** * *
10538 AAGGTAGCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCA
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * *
10582 AAGAT-GCAGATCTTGTCTTCCCATACTGGTG-GCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-GCGTGAAGTAGATCG
* * *
10626 AAGAAAGCAGATCTTGTCTTCATGTATT-GGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * * *** * * *
10670 AAGATAGCAGGTCCTATCTTCCTATATTGATAG-GAGGTGGATCC
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * *
10714 AAGAT-GCAGATCTTGTCTTCCCATGTTGGTG-GCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-GCGTGAAGTAGATCG
* * *
10758 AAGAAAGCAGATCTTGTCTTCATGTATT-GGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * ** * *
10802 AAGATAGCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCA
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * *
10846 AAGAT-GCAGATCTTGTCTTCCCATACTGGTG-GCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-GCGTGAAGTAGATCG
* * *
10890 AAGAAAGCAGATCTTGTCTTCATGTATT-GGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * * *** * * *
10934 AAGATAGCAGGTCCTATCTTCCTATATTGATAG-GAGGTGGATCC
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * *
10978 AATAT-GCAGATCTTGTCTTCC-ATGTTGGTG-GCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-GCGTGAAGTAGATCG
* * *
11021 AAGAAAGCAGATCTTGTCTTCATGTATT-GGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * * ** *
11065 AAGATAGCAGGTCCTATCTTCCTATATTGGTAG-GAAGTGGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* *
11109 AAGAT-GCAGATCTTGTCTTCCCATATTGGTG-GCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGG-GCGTGAAGTAGATCG
* * * * *
11153 CAGAAAGCAGATATTGTCTTCATGTA-TGGGCGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
* * * * * * *
11197 AAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCA
1 AAGATAGCAGATCTTGTCTTCCTATATTGGGC-GTGAAGTAGATCG
*
11243 AAGATGGCAGAT
1 AAGATAGCAGAT
11255 TTTACCTCCC
Statistics
Matches: 884, Mismatches: 229, Indels: 84
0.74 0.19 0.07
Matches are distributed among these distances:
42 7 0.01
43 190 0.21
44 536 0.61
45 130 0.15
46 21 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (45 bp):
AAGATAGCAGATCTTGTCTTCCTATATTGGGCGTGAAGTAGATCG
Found at i:11601 original size:192 final size:190
Alignment explanation
Indices: 11237--11668 Score: 740
Period size: 192 Copynumber: 2.3 Consensus size: 190
11227 GCAGCGAAGC
* * *
11237 AGATCAAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAGCCAATAACTCTAT
*
11302 CTCCCTGCATTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCATGTGACTA
66 CTCCCTGCATTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCA-CTGACTA
* *
11367 CAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGCATTTGGCAGTGGAATAGATTGA
130 CAGTAGAGTACATTGAAGCCAATAACTCTATCTCCCTGCATTTGGCAGTGGAATAGATTGA
11428 AGATCAAAGATGGCAGATTTTACCTCCATGTGACTACAGTGGAGTACATTGAAGCCAATAACTCT
1 AGATCAAAGATGGCAGATTTTACCTCC-T-TGACTACAGTGGAGTACATTGAAGCCAATAACTCT
*
11493 ATCTCCTTGCATTTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCC-CTGAC
64 ATCTCCCTGCA-TTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCACTGAC
11557 TACAGTAGAGTACATTGAAGCCAATAACTCTATCTCCCTGCATTTGGCAGTGGAATAGATTGA
128 TACAGTAGAGTACATTGAAGCCAATAACTCTATCTCCCTGCATTTGGCAGTGGAATAGATTGA
* *
11620 AGATCAAAGATGGCAAATTTTACCTCCTTGATTACAGTGGAGTACATTG
1 AGATCAAAGATGGCAGATTTTACCTCCTTGACTACAGTGGAGTACATTG
11669 GAGCTGATAG
Statistics
Matches: 229, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
190 20 0.09
191 28 0.12
192 91 0.40
193 43 0.19
194 47 0.21
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (190 bp):
AGATCAAAGATGGCAGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAGCCAATAACTCTAT
CTCCCTGCATTGGCAGTGGAATAGATTGAAGATCAAAGATGGCAGATTTTACCTCCACTGACTAC
AGTAGAGTACATTGAAGCCAATAACTCTATCTCCCTGCATTTGGCAGTGGAATAGATTGA
Found at i:11684 original size:95 final size:95
Alignment explanation
Indices: 11237--11689 Score: 746
Period size: 97 Copynumber: 4.7 Consensus size: 95
11227 GCAGCGAAGC
* *
11237 AGATCAAAGATGGCAGATTTTACCTCCCTGACCACAGTGGAGTACATTGAAGCCGATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
11302 CTCCCTGCA-TTGGCAGTGGAATAGATTGA
66 CTCCCTGCATTTGGCAGTGGAATAGATTGA
11331 AGATCAAAGATGGCAGATTTTACCTCCATGTGACTACAGTGGAGTACATTGAAGCCGATAACTCT
1 AGATCAAAGATGGCAGATTTTACCTCC-T-TGACTACAGTGGAGTACATTGAAGCCGATAACTCT
11396 ATCTCCCTGCATTTGGCAGTGGAATAGATTGA
64 ATCTCCCTGCATTTGGCAGTGGAATAGATTGA
*
11428 AGATCAAAGATGGCAGATTTTACCTCCATGTGACTACAGTGGAGTACATTGAAGCCAATAACTCT
1 AGATCAAAGATGGCAGATTTTACCTCC-T-TGACTACAGTGGAGTACATTGAAGCCGATAACTCT
*
11493 ATCTCCTTGCATTTGGCAGTGGAATAGATTGA
64 ATCTCCCTGCATTTGGCAGTGGAATAGATTGA
* * *
11525 AGATCAAAGATGGCAGATTTTACCTCCCTGACTACAGTAGAGTACATTGAAGCCAATAACTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
11590 CTCCCTGCATTTGGCAGTGGAATAGATTGA
66 CTCCCTGCATTTGGCAGTGGAATAGATTGA
* * * * **
11620 AGATCAAAGATGGCAAATTTTACCTCCTTGATTACAGTGGAGTACATTGGAGCTGATAGTTCTAT
1 AGATCAAAGATGGCAGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
11685 CTCCC
66 CTCCC
11690 GGGCAAGAAA
Statistics
Matches: 340, Mismatches: 16, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
94 27 0.08
95 126 0.37
96 45 0.13
97 142 0.42
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (95 bp):
AGATCAAAGATGGCAGATTTTACCTCCTTGACTACAGTGGAGTACATTGAAGCCGATAACTCTAT
CTCCCTGCATTTGGCAGTGGAATAGATTGA
Found at i:11750 original size:44 final size:45
Alignment explanation
Indices: 11700--12130 Score: 335
Period size: 44 Copynumber: 9.8 Consensus size: 45
11690 GGGCAAGAAA
* * * *
11700 TAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAG-GAAA
1 TAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAG
* * * *
11744 TGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAG
1 TAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAG
* * * ** * *
11788 TAGATCGCAGAAAGAAGATCTTGTCTTTATGTATTGG-CGTGAAG
1 TAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAG
* * *
11832 TAGATCGAAGGTAGCAGATCATATCTTCCTATATTGGTAG-GAAG
1 TAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAG
* * * * *
11876 TGGATCGAAGAT-GTAGATCTTGTCTTCCCATATTGGTGGCGAAG
1 TAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAG
* * * *** *
11920 TAGATCGCAGAAAGCAGATCTTGTATTCAGGTATTGG-CGTGAAG
1 TAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAG
* * * *
11964 TAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAG-GAAG
1 TAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAG
* * * * * *
12008 TGGATCCAAGATA-CAGATCCTGTCTTCCCATACTGGTGGTGAAG
1 TAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAG
* * *
12052 TAGATCGAAGAAAGCAGATCTTGTC--CCTGTATTTGGCAGTGGAA-
1 TAGATCGAAGATAGCAGATCTTGTCTTCCTATA-TTGGTAGT-GAAG
* * * * *
12096 TAGATTGAGGATTGCAGATCTTGCCTTCCTGTATT
1 TAGATCGAAGATAGCAGATCTTGTCTTCCTATATT
12131 TGGCAGCGAA
Statistics
Matches: 298, Mismatches: 77, Indels: 23
0.75 0.19 0.06
Matches are distributed among these distances:
43 68 0.23
44 169 0.57
45 55 0.18
46 6 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (45 bp):
TAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGTAGTGAAG
Found at i:11881 original size:132 final size:132
Alignment explanation
Indices: 11700--12076 Score: 601
Period size: 132 Copynumber: 2.9 Consensus size: 132
11690 GGGCAAGAAA
* *
11700 TAGATCGAAGATAGCTGATCCTATCTTCCTATATTGGTAGGAAATGGATCGAAGATGCAGATCTT
1 TAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTT
* * *
11765 GTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGAAGATCTTGTCTTTATGTATTGGCGTGA
66 GTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCAGGTATTGGCGTGA
11830 AG
131 AG
* * *
11832 TAGATCGAAGGTAGCAGATCATATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGTAGATCTT
1 TAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTT
*
11897 GTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTATTCAGGTATTGGCGTGA
66 GTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCAGGTATTGGCGTGA
11962 AG
131 AG
* * * * *
11964 TAGATCGAAGATAGCAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGATCCT
1 TAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTT
* * *
12029 GTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTC
66 GTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTC
12077 CCTGTATTTG
Statistics
Matches: 224, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 224 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (132 bp):
TAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTT
GTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCAGGTATTGGCGTGA
AG
Found at i:14602 original size:15 final size:15
Alignment explanation
Indices: 14582--14615 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
14572 TTTACTTTTG
* *
14582 TTATTTTTGCTCGTA
1 TTATTTTTACTCGCA
14597 TTATTTTTACTCGCA
1 TTATTTTTACTCGCA
14612 TTAT
1 TTAT
14616 CGTAATTGTT
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:0.18, C:0.15, G:0.09, T:0.59
Consensus pattern (15 bp):
TTATTTTTACTCGCA
Done.