Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1920
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: 35524
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Found at i:944 original size:3 final size:3
Alignment explanation
Indices: 938--963 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
928 AATAAGTAGG
938 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
964 GGACTAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2609 original size:85 final size:83
Alignment explanation
Indices: 2425--2619 Score: 309
Period size: 83 Copynumber: 2.3 Consensus size: 83
2415 CTCAGTCTAT
* * * * *
2425 TCCACTGTAATCTCAGGGAAATAAGACCTGACACGATCTACTCTGCTTAACTTCAGAGAGATAAG
1 TCCACTGTAATCTCAGGGAGATAGGATCTGAAACGATCTACTCTACTTAACTTCAGAGAGATAAG
2490 ATCCTTCATTTAATCCGC
66 ATCCTTCATTTAATCCGC
2508 TCCACTGTAATCTCAGGGAGATAGGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAGATAGGATCTGAAACGATCTACTCTACT-TAACTTCAGAGAGATAA
*
2573 GATCCTTCGTTTTAATCCGC
65 GATCCTTC-ATTTAATCCGC
*
2593 TCCACTGTAATATCAGGGAGATAGGAT
1 TCCACTGTAATCTCAGGGAGATAGGAT
2620 ACTATCTTAT
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
83 42 0.41
84 25 0.24
85 36 0.35
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (83 bp):
TCCACTGTAATCTCAGGGAGATAGGATCTGAAACGATCTACTCTACTTAACTTCAGAGAGATAAG
ATCCTTCATTTAATCCGC
Found at i:2673 original size:127 final size:128
Alignment explanation
Indices: 2499--2793 Score: 531
Period size: 127 Copynumber: 2.3 Consensus size: 128
2489 GATCCTTCAT
* * *
2499 TTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATCTGAAACGATCTACTCTACTGTAACTTCA
1 TTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCA
2564 GAGAGATAAGATCCTTCGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGA-TACTATC
66 GAGAGATAAGATCCTTCGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTATC
2626 TT-ATCTGCTCCGCTGTAATCTCAGGGAAGATAAGATCTGAAACGATCTACTCTACTGTAACTTC
1 TTAATCTGCTCCGCTGTAATCTCAGGG-AGATAAGATCTGAAACGATCTACTCTACTGTAACTTC
2690 AGAGAGATAAGATCCTTCGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTATC
65 AGAGAGATAAGATCCTTCGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTATC
2754 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTG
1 TT-AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTG
2794 CCATCTTCAA
Statistics
Matches: 161, Mismatches: 3, Indels: 6
0.95 0.02 0.04
Matches are distributed among these distances:
126 22 0.14
127 94 0.58
128 9 0.06
129 12 0.07
130 24 0.15
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (128 bp):
TTAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCA
GAGAGATAAGATCCTTCGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTATC
Found at i:2766 original size:44 final size:41
Alignment explanation
Indices: 2347--2956 Score: 233
Period size: 44 Copynumber: 14.4 Consensus size: 41
2337 TTTGCAGAAC
* * *
2347 TTCAGGGAGATAGGAT-TATTGGCTTCAATCTGCTCCGCTATAA
1 TTCAGGGAGATAAGATCTA-T--CTTCAATCTGCTCCACTGTAA
* **
2390 TCTCAGGGAGATAAGATCTGAAAT-TCTCAGTCTATTCCACTGTAA
1 T-TCAGGGAGATAAGATCT---ATCT-TCAATCTGCTCCACTGTAA
* * * * * **
2435 TCTCAGGGAAATAAGACCTGA-C-ACGATCTACTCTGCT-TAA
1 T-TCAGGGAGATAAGATCT-ATCTTCAATCTGCTCCACTGTAA
* * *
2475 CTTCAGAGAGATAAGATCCT-TCATTTAATCCGCTCCACTGTAA
1 -TTCAGGGAGATAAGAT-CTATC-TTCAATCTGCTCCACTGTAA
* ** * * *
2518 TCTCAGGGAGATAGGATCTGA--AACGATCTACTCTACTGTAA
1 T-TCAGGGAGATAAGATCT-ATCTTCAATCTGCTCCACTGTAA
* * *
2559 CTTCAGAGAGATAAGATCCT-TCGTTTTAATCCGCTCCACTGTAA
1 -TTCAGGGAGATAAGAT-CTATC--TTCAATCTGCTCCACTGTAA
* *
2603 TATCAGGGAGATAGGATACTATCTT--ATCTGCTCCGCTGTAA
1 T-TCAGGGAGATAAGAT-CTATCTTCAATCTGCTCCACTGTAA
** * * *
2644 TCTCAGGGAAGATAAGATCTGA--AACGATCTACTCTACTGTAA
1 T-TCAGGG-AGATAAGATCT-ATCTTCAATCTGCTCCACTGTAA
* * *
2686 CTTCAGAGAGATAAGATCCT-TCGTTTTAATCCGCTCCACTGTAA
1 -TTCAGGGAGATAAGAT-CTATC--TTCAATCTGCTCCACTGTAA
* *
2730 TATCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAA
1 T-TCAGGGAGATAAGA-T-CTATCTTCAATCTGCTCCACTGTAA
*
2774 TCTCAGGGAGATAAGATCTGCCATCTTCAATGTGC-CCAC--T--
1 T-TCAGGGAGATAAGATCT---ATCTTCAATCTGCTCCACTGTAA
** * * *
2814 TT--GGGAGATAAGATCTGA--AACGATCTACTCTACTGTAA
1 TTCAGGGAGATAAGATCT-ATCTTCAATCTGCTCCACTGTAA
* * **
2852 CTTCAGAGAGATAAGATCTTTAT-TTTAATCCACTCCACTGTAA
1 -TTCAGGGAGATAAGATC--TATCTTCAATCTGCTCCACTGTAA
* *
2895 TCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAA
1 T-TCAGGGAGATAAGA-T-CTATCTTCAATCTGCTCCACTGTAA
2939 TTCAGGGAGATAAGATCT
1 TTCAGGGAGATAAGATCT
2957 GAAATTCTTT
Statistics
Matches: 418, Mismatches: 94, Indels: 112
0.67 0.15 0.18
Matches are distributed among these distances:
33 5 0.01
34 3 0.01
35 1 0.00
36 1 0.00
37 14 0.03
39 3 0.01
40 17 0.04
41 84 0.20
42 49 0.12
43 66 0.16
44 121 0.29
45 50 0.12
46 2 0.00
47 1 0.00
48 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (41 bp):
TTCAGGGAGATAAGATCTATCTTCAATCTGCTCCACTGTAA
Found at i:2906 original size:43 final size:45
Alignment explanation
Indices: 2840--2956 Score: 118
Period size: 43 Copynumber: 2.7 Consensus size: 45
2830 GAAACGATCT
* * * * *
2840 ACTCTACTGTAA-CTTCAGAGAGATAAGATCT-TTA-TTTTAATCC
1 ACTCCACTGTAATC-TCAGGGAGATAAGATCTACTAGCTTCAATCC
* *
2883 ACTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCAATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCTACTAGCTTCAATCC
*
2927 GCTCCACTGTAAT-TCAGGGAGATAAGATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCT
2957 GAAATTCTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.02
43 40 0.66
44 20 0.33
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (45 bp):
ACTCCACTGTAATCTCAGGGAGATAAGATCTACTAGCTTCAATCC
Found at i:2927 original size:165 final size:165
Alignment explanation
Indices: 2653--2957 Score: 540
Period size: 165 Copynumber: 1.8 Consensus size: 165
2643 ATCTCAGGGA
*
2653 AGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCGTTTTAATCC
1 AGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCC
* * *
2718 GCTCCACTGTAATATCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGA
66 ACTCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAAT-TCAGGGA
2783 GATAAGATCTGCCATCTTCAATGTGCCCACTTTGGG
130 GATAAGATCTGCCATCTTCAATGTGCCCACTTTGGG
*
2819 AGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTTTATTTTAATCC
1 AGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCC
*
2883 ACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATTCAGGGAG
66 ACTCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATTCAGGGAG
2948 ATAAGATCTG
131 ATAAGATCTG
2958 AAATTCTTTG
Statistics
Matches: 133, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
164 18 0.14
165 65 0.49
166 50 0.38
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (165 bp):
AGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCC
ACTCCACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATTCAGGGAG
ATAAGATCTGCCATCTTCAATGTGCCCACTTTGGG
Found at i:2995 original size:166 final size:166
Alignment explanation
Indices: 2657--2997 Score: 479
Period size: 165 Copynumber: 2.1 Consensus size: 166
2647 CAGGGAAGAT
* *
2657 AAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCGTTTTAATCCGCTC
1 AAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCACTC
* *
2722 CACTGTAATATCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATA
66 CACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATA
** * ** * *
2787 AGATCTGCCATCTTCAATGTGCCCACTTTGGGAGAT
131 AGATCTGAAATCTTCAATCTGCCCACCGTCGGAGAC
*
2823 AAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTTTATTTTAATCCACTC
1 AAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCACTC
*
2887 CACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAAT-TCAGGGAGATA
66 CACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATA
** * * * *
2951 AGATCTGAAATTCTTTGATCTGCTTCGCCGTCGTAGGC
131 AGATCTGAAA-TCTTCAATCTGC-CCACCGTCGGAGAC
2989 AAGATCTGA
1 AAGATCTGA
2998 TGTCTTTATT
Statistics
Matches: 154, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
164 19 0.12
165 74 0.48
166 61 0.40
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (166 bp):
AAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCACTC
CACTGTAATATCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATA
AGATCTGAAATCTTCAATCTGCCCACCGTCGGAGAC
Found at i:6749 original size:44 final size:43
Alignment explanation
Indices: 6695--7310 Score: 238
Period size: 44 Copynumber: 14.4 Consensus size: 43
6685 AGAATTTCAG
*
6695 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGATAG-A
* * ** * *
6739 ATCCTATCTCCCTGAGATTACAGTGGAGTGGATT-AAAATAAAGG
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGAT--AGA
* * * * * **
6783 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG--TTTCAG-
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGAT-AGA
* *
6824 ATCTTATCTCCC----A--A-AGTGGAGCACATTGAAGATGGCA
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGATAG-A
* *
6861 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTA
1 -ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGATAG-A
* * * * *
6906 ATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAACGA-AGG
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATT-GAA-GATAGA
* * * * * **
6950 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG--TTTCAG-
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGAT-AGA
* * *
6991 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGATAGTA
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGATAG-A
* * * * *
7035 ATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAACGA-AGG
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATT-GAA-GATAGA
* * * * * **
7079 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCG--TTTCAG-
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGAT-AGA
* * * * *
7120 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATGAAGG
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGAT--AGA
* * ** * * *
7164 ATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCG-TG-TCAG-
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGAT-AGA
* * * ** *
7205 GTCTTATTTCCCTGAGATTACAGTGGAATAGACTGAAGAATTTCAG-
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAG-A--T-AGA
* * * *
7251 ATCTTATCTCCCTGAGATTATAGCGGAGCAGATTGAAGCCA-ATA
1 ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAG--ATAGA
*
7295 ATCCTATCTCCCTGAA
1 ATCTTATCTCCCTGAA
7311 GTTGCTGCAA
Statistics
Matches: 415, Mismatches: 118, Indels: 78
0.68 0.19 0.13
Matches are distributed among these distances:
34 10 0.02
35 2 0.00
36 1 0.00
38 12 0.03
41 89 0.21
42 13 0.03
43 9 0.02
44 209 0.50
45 30 0.07
46 39 0.09
47 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGATAGA
Found at i:6968 original size:167 final size:167
Alignment explanation
Indices: 6692--7002 Score: 559
Period size: 167 Copynumber: 1.9 Consensus size: 167
6682 CAAAGAATTT
* *
6692 CAGATCTTATCTCCCTGAAATTACAGTGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGAT
1 CAGATCTTATCTCCCTGAAATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGAT
* *
6757 TACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTTC
66 TACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTTC
6822 AGATCTTATCTCCCAAAGTGGAGCACATTGAAGATGG
131 AGATCTTATCTCCCAAAGTGGAGCACATTGAAGATGG
* *
6859 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGATAT
1 CAGATCTTATCTCCCTGAAATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGAT
*
6924 TACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTTC
66 TACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTTC
6989 AGATCTTATCTCCC
131 AGATCTTATCTCCC
7003 TGAGATTACA
Statistics
Matches: 137, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
167 137 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (167 bp):
CAGATCTTATCTCCCTGAAATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGAT
TACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTTC
AGATCTTATCTCCCAAAGTGGAGCACATTGAAGATGG
Found at i:7124 original size:85 final size:85
Alignment explanation
Indices: 7035--7231 Score: 331
Period size: 85 Copynumber: 2.3 Consensus size: 85
7025 AAAGATAGTA
*
7035 ATCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTAC
* *
7100 AGTAGAGTAGATCGTTTCAG
66 AGCAGAGTAGATCGTGTCAG
*
7120 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATGAAGGATCTTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTAC
7185 AGCAGAGTAGATCGTGTCAG
66 AGCAGAGTAGATCGTGTCAG
* * *
7205 GTCTTATTTCCCTGAGATTACAGTGGA
1 ATCCTATCTCCCTGAGATTACAGTGGA
7232 ATAGACTGAA
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 105 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (85 bp):
ATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTAC
AGCAGAGTAGATCGTGTCAG
Found at i:7173 original size:129 final size:129
Alignment explanation
Indices: 6859--7156 Score: 560
Period size: 129 Copynumber: 2.3 Consensus size: 129
6849 TTGAAGATGG
*
6859 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGATAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGATAGTAATCCTATCTCCCTGATAT
6924 TACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTT
66 TACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTT
6988 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGATAGTAATCCTATCTCCCTGATAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGATAGTAATCCTATCTCCCTGATAT
7053 TACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTT
66 TACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTT
* * *
7117 CAGATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAA
7157 ATGAAGGATC
Statistics
Matches: 165, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 165 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (129 bp):
CAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGATAGTAATCCTATCTCCCTGATAT
TACAGTGGAGCGGATTAAAACGAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTTT
Found at i:7288 original size:46 final size:46
Alignment explanation
Indices: 7201--7288 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
7191 GTAGATCGTG
* * * *
7201 TCAGGTCTTATTTCCCTGAGATTACAGTGGAATAGACTGAAGAATT
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAACAGACTGAAGAATT
* * *
7247 TCAGATCTTATCTCCCTGAGATTATAGCGGAGCAGATTGAAG
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAACAGACTGAAG
7289 CCAATAATCC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 35 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (46 bp):
TCAGATCTTATCTCCCTGAGATTACAGCGGAACAGACTGAAGAATT
Found at i:8723 original size:3 final size:3
Alignment explanation
Indices: 8715--8743 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
8705 GATTTACTCC
8715 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
8744 CCTACTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:9011 original size:22 final size:23
Alignment explanation
Indices: 8963--9016 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
8953 AAATATACTT
*
8963 TATATATTTTGTTAATTTATATA
1 TATATATATTGTTAATTTATATA
* * *
8986 TATATATATT-TTAGTTTATGTC
1 TATATATATTGTTAATTTATATA
9008 TATATATAT
1 TATATATAT
9017 CTTTTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (23 bp):
TATATATATTGTTAATTTATATA
Found at i:23752 original size:3 final size:3
Alignment explanation
Indices: 23744--23775 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
23734 GATTTAGTCC
23744 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
23776 CCTACTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:24042 original size:24 final size:23
Alignment explanation
Indices: 23991--24047 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
23981 AAATATACTT
*
23991 TATATATTTTGTTAATTTATATA
1 TATATATTTTGTTAATGTATATA
* *
24014 TATATATTTTAGTTTATGTCTATA
1 TATATATTTT-GTTAATGTATATA
*
24038 TATATCTTTT
1 TATATATTTT
24048 TATATTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (23 bp):
TATATATTTTGTTAATGTATATA
Done.