Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1987
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: 29417
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:5577 original size:43 final size:44
Alignment explanation
Indices: 5514--5718 Score: 145
Period size: 43 Copynumber: 4.7 Consensus size: 44
5504 TATCATCAAC
*
5514 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAAACT-AGAT
1 CTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAAAACTCAGAT
* * *** *
5557 CTTATCTTCACTGAGTAGGAGTGAAGCA-GATCAAATTTTGATGAAT
1 CTTATCTTCACTGAGTAGGAGTGGAGCAGGCT-AAAAACTCA-G-AT
* * ** ** * *
5603 CTTATCTCCAC---GTACCGGCAATGGAGCAGATTCCAATCATCAG-C
1 CTTATCTTCACTGAGTA--GG-AGTGGAGCAGGCTAAAAAC-TCAGAT
*
5647 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAAAAC-CAGAT
1 CTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAAAACTCAGAT
*
5690 CTTATCTTCACTGAGTAGGAGTGAAGCAG
1 CTTATCTTCACTGAGTAGGAGTGGAGCAG
5719 ATCGAATTTT
Statistics
Matches: 121, Mismatches: 28, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
42 5 0.04
43 60 0.50
44 24 0.20
45 5 0.04
46 22 0.18
47 5 0.04
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (44 bp):
CTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAAAACTCAGAT
Found at i:5690 original size:133 final size:135
Alignment explanation
Indices: 5505--6130 Score: 896
Period size: 135 Copynumber: 4.7 Consensus size: 135
5495 GATTACAGAT
* *
5505 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA-A-ACTAGATCTTATCTTCAC
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCAC
5568 TGAGTAGGAGTGAAGCAGATCAAATTTTGATG-AA-TCTTATCTCCACGTACCGGCAATGGAGCA
66 TGAGTAGGAGTGAAGCAGATCAAATTTTG--GCAAGTCTTATCTCCACGTACCGGCAATGGAGCA
5631 GATTCCA
129 GATTCCA
5638 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA-A-ACCAGATCTTATCTTCAC
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCAC
* *
5701 TGAGTAGGAGTGAAGCAGATCGAATTTTGATG-AA-TCTTATCTCCACGTACCGGCGATGGAGCA
66 TGAGTAGGAGTGAAGCAGATCAAATTTTG--GCAAGTCTTATCTCCACGTACCGGCAATGGAGCA
5764 GATTCCA
129 GATTCCA
*
5771 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAAGCTAAACATACCAGATCTTATCTTCAC
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCAC
* * *
5836 TGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGA
66 TGAGTAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCACGTACCGGCAATGGAGCAGA
**
5901 TTTTA
131 TTCCA
** * *
5906 GCCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGTAGGCTAAACATACCAGATCTTATCTTCAC
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCAC
* * *
5971 TGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGA
66 TGAGTAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCACGTACCGGCAATGGAGCAGA
**
6036 TTTTA
131 TTCCA
** * * *
6041 GCCA-CTATCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAACATA-CAGATCTTATCTTCG
1 ATCATC-AGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCA
*
6104 CTGATTAGGAGT-AGAGCAGATCAAATT
65 CTGAGTAGGAGTGA-AGCAGATCAAATT
6131 ACAGCAGACC
Statistics
Matches: 464, Mismatches: 23, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
133 174 0.38
134 41 0.09
135 249 0.54
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (135 bp):
ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCAC
TGAGTAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCACGTACCGGCAATGGAGCAGA
TTCCA
Found at i:5831 original size:45 final size:45
Alignment explanation
Indices: 5647--5987 Score: 161
Period size: 45 Copynumber: 7.6 Consensus size: 45
5637 AATCATCAGC
*
5647 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA-A-ACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAAGCTAAACATACCAGAT
* * * * *** **
5690 CTTATCTTCACTGAGTAGGAGTGAAGCAGATCGAATTTTGATGA-AT
1 CTTATCTTCACTGAGCAGGAGTGGAGCA-AGCTAAACAT-ACCAGAT
* * * * * * *
5736 CTTATCTCCAC-GTA-CCGGCGATGGAGCAGATTCCAATCAT--CAG-C
1 CTTATCTTCACTG-AGCAGGAG-TGGAGCA-A-GCTAAACATACCAGAT
5780 CTTATCTTCACTGAGCAGGAGTGGAGCAAGCTAAACATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAAGCTAAACATACCAGAT
* * ** **
5825 CTTATCTTCACTGAGCAGGAGTGAAGC-AGATCAAATTTTGGCA-AGT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAAGCT-AAA-CATACCAGA-T
* * * ** * * * *
5871 CTTATCTCCA-TGTATC-GGCAATGGAGCAGATTTTAGC-CACCAG-C
1 CTTATCTTCACTG-AGCAGG-AGTGGAGCA-AGCTAAACATACCAGAT
* *
5915 CTTATCTTCACTGAGCAGGAGTGGAGTAGGCTAAACATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAAGCTAAACATACCAGAT
*
5960 CTTATCTTCACTGAGCAGGAGTGAAGCA
1 CTTATCTTCACTGAGCAGGAGTGGAGCA
5988 GATCAAATTT
Statistics
Matches: 215, Mismatches: 58, Indels: 48
0.67 0.18 0.15
Matches are distributed among these distances:
42 6 0.03
43 30 0.14
44 51 0.24
45 75 0.35
46 42 0.20
47 9 0.04
48 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (45 bp):
CTTATCTTCACTGAGCAGGAGTGGAGCAAGCTAAACATACCAGAT
Found at i:7745 original size:14 final size:14
Alignment explanation
Indices: 7726--7758 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
7716 TTTATCATAC
7726 TTATTATATTTTAT
1 TTATTATATTTTAT
7740 TTATTATATTTTAT
1 TTATTATATTTTAT
7754 TTATT
1 TTATT
7759 TTTTCCTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTATATTTTAT
Found at i:13785 original size:30 final size:30
Alignment explanation
Indices: 13727--13788 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
13717 TTTAAGAAAT
* *
13727 TTACCATATTGTTCGTTCATGCGGTCTTTC
1 TTACCATATTGTTCGTTCATACGATCTTTC
*
13757 TTACCATATTGTTCGTTCATATGATCTTTC
1 TTACCATATTGTTCGTTCATACGATCTTTC
13787 TT
1 TT
13789 CACTTTTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (30 bp):
TTACCATATTGTTCGTTCATACGATCTTTC
Found at i:15793 original size:69 final size:70
Alignment explanation
Indices: 15661--15793 Score: 223
Period size: 69 Copynumber: 1.9 Consensus size: 70
15651 TAGTTTATTA
* * * *
15661 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTA
15726 CTTAG
66 CTTAG
15731 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
15794 GTTATGTCCT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
69 36 0.61
70 23 0.39
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:17643 original size:48 final size:48
Alignment explanation
Indices: 17571--17810 Score: 372
Period size: 48 Copynumber: 5.0 Consensus size: 48
17561 CACAAGATAA
17571 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
*
17619 GGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* * *
17667 GGATATGTATATGTGGTAAAGCCGAATGGCTTATGTGAAATATATATATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATGTATG
* *
17717 AGATATGTATATGTGGTAAACCCGAATGGCTAGTGTGAAATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* * * *
17765 AGATACGTATATGTGGTAAAGCCGAAGGGCTAGTGTGAAGTATGTA
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
17811 GGAGGTGTGG
Statistics
Matches: 178, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
48 133 0.75
49 4 0.02
50 41 0.23
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (48 bp):
AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:17760 original size:98 final size:97
Alignment explanation
Indices: 17571--17803 Score: 362
Period size: 98 Copynumber: 2.4 Consensus size: 97
17561 CACAAGATAA
* * *
17571 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AAATATGTATGGGATATGTATATGTGG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTTATGTGAAAATATATATGAGATATGTATATGTGG
*
17635 TAAAGCCGAATGGCTAATGTGAAATATGTATG
66 TAAACCCGAATGGCTAATGTGAAATATGTATG
*
17667 GGATATGTATATGTGGTAAAGCCGAATGGCTTATGTGAAATATATATATGAGATATGTATATGTG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTTATGTGAAA-ATATATATGAGATATGTATATGTG
*
17732 GTAAACCCGAATGGCTAGTGTGAAATATGTATG
65 GTAAACCCGAATGGCTAATGTGAAATATGTATG
* *
17765 AGATACGTATATGTGGTAAAGCCGAAGGGC-TAGTGTGAA
1 AGATATGTATATGTGGTAAAGCCGAATGGCTTA-TGTGAA
17804 GTATGTAGGA
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
96 35 0.28
97 4 0.03
98 86 0.69
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.30
Consensus pattern (97 bp):
AGATATGTATATGTGGTAAAGCCGAATGGCTTATGTGAAAATATATATGAGATATGTATATGTGG
TAAACCCGAATGGCTAATGTGAAATATGTATG
Found at i:17996 original size:37 final size:37
Alignment explanation
Indices: 17946--18060 Score: 160
Period size: 37 Copynumber: 3.1 Consensus size: 37
17936 ACATGAAACT
*
17946 TGGAAATATATTCCGGGTAAGACCCGATGACTACGTG
1 TGGAAAAATATTCCGGGTAAGACCCGATGACTACGTG
17983 TGGAAAAATATTCCGGGTAAGACCCGATGACTACGTG
1 TGGAAAAATATTCCGGGTAAGACCCGATGACTACGTG
* * * * *
18020 TGG-AGATTTTGTCCGGGTAAGACCCGATAACTTCGTG
1 TGGAAAAATAT-TCCGGGTAAGACCCGATGACTACGTG
18057 TGGA
1 TGGA
18061 GATTTCATCT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
36 4 0.06
37 66 0.94
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (37 bp):
TGGAAAAATATTCCGGGTAAGACCCGATGACTACGTG
Found at i:18943 original size:43 final size:43
Alignment explanation
Indices: 18882--18965 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
18872 GGGTGTTACA
18882 GCCTTTAGCGAGGCTTTTCCCACAAACACCGCTAAAGGTCATG
1 GCCTTTAGCGAGGCTTTTCCCACAAACACCGCTAAAGGTCATG
* *
18925 GCCTTTAGCG-GCGCTTTTCCCACAAACGCCGCTAAATGTCA
1 GCCTTTAGCGAG-GCTTTTCCCACAAACACCGCTAAAGGTCA
18966 CAAATTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (43 bp):
GCCTTTAGCGAGGCTTTTCCCACAAACACCGCTAAAGGTCATG
Found at i:19248 original size:19 final size:18
Alignment explanation
Indices: 19226--19266 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
19216 AATTAGAATC
19226 AAAACTAAAATAAATAATA
1 AAAACTAAAATAAAT-ATA
* *
19245 AAAACTAGATTAAATATA
1 AAAACTAAAATAAATATA
19263 AAAA
1 AAAA
19267 TATCAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAACTAAAATAAATATA
Found at i:19268 original size:31 final size:31
Alignment explanation
Indices: 19192--19265 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
19182 TCAAATTATC
*
19192 TTAAATATTAAAATAAAAATAAAAAATTAGAA
1 TTAAATA-TAAAATAAAAATAAAAAACTAGAA
*
19224 TCAAA-ACTAAAATAAATAAT-AAAAACTAG-A
1 TTAAATA-TAAAATAAA-AATAAAAAACTAGAA
19254 TTAAATATAAAA
1 TTAAATATAAAA
19266 ATATCAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.28
31 19 0.53
32 7 0.19
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.26
Consensus pattern (31 bp):
TTAAATATAAAATAAAAATAAAAAACTAGAA
Found at i:21736 original size:14 final size:14
Alignment explanation
Indices: 21700--21730 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21690 CCTATCAATC
*
21700 GAATCATATTTCAA
1 GAATCACATTTCAA
21714 GAATCACATTTCAA
1 GAATCACATTTCAA
21728 GAA
1 GAA
21731 ATACATGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (14 bp):
GAATCACATTTCAA
Found at i:24187 original size:7 final size:7
Alignment explanation
Indices: 24177--24277 Score: 64
Period size: 7 Copynumber: 14.4 Consensus size: 7
24167 CCATAAATAT
24177 TAAACCC
1 TAAACCC
24184 TAAACCC
1 TAAACCC
*
24191 TTAACCC
1 TAAACCC
*
24198 TTAACCC
1 TAAACCC
*
24205 TTAACCC
1 TAAACCC
*
24212 AAAACCC
1 TAAACCC
* *
24219 TTACACCT
1 -TAAACCC
24227 TAAACTCC
1 TAAAC-CC
24235 --AACCC
1 TAAACCC
24240 T-AACCC
1 TAAACCC
*
24246 ATAAACCT
1 -TAAACCC
* *
24254 TAAATCA
1 TAAACCC
*
24261 TAATCCC
1 TAAACCC
24268 TAAACCC
1 TAAACCC
24275 TAA
1 TAA
24278 TTCATCATAA
Statistics
Matches: 74, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
5 2 0.03
6 8 0.11
7 55 0.74
8 9 0.12
ACGTcount: A:0.40, C:0.39, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:24319 original size:7 final size:7
Alignment explanation
Indices: 24309--24403 Score: 55
Period size: 7 Copynumber: 13.0 Consensus size: 7
24299 CTAGTTAACT
24309 CTTAAAC
1 CTTAAAC
24316 CTTAAAC
1 CTTAAAC
*
24323 CCTAAAC
1 CTTAAAC
* * *
24330 CATATAT
1 CTTAAAC
24337 CTTAAAC
1 CTTAAAC
*
24344 CATAGTTAAC
1 C-T--TAAAC
*
24354 TCATAAAC
1 -CTTAAAC
24362 CTTAAAC
1 CTTAAAC
*
24369 CCTAAAC
1 CTTAAAC
* * *
24376 CATATAT
1 CTTAAAC
24383 CTTAAAC
1 CTTAAAC
*
24390 CATAAAC
1 CTTAAAC
24397 CTTAAAC
1 CTTAAAC
24404 TATAATGATA
Statistics
Matches: 64, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
7 54 0.84
8 5 0.08
10 4 0.06
11 1 0.02
ACGTcount: A:0.44, C:0.27, G:0.01, T:0.27
Consensus pattern (7 bp):
CTTAAAC
Found at i:24342 original size:21 final size:21
Alignment explanation
Indices: 24316--24397 Score: 92
Period size: 21 Copynumber: 3.7 Consensus size: 21
24306 ACTCTTAAAC
*
24316 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
* *
24337 CTTAAACCATAGTTAACTCATAAAC
1 CTTAAACCATA---AAC-CATATAT
*
24362 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
24383 CTTAAACCATAAACC
1 CTTAAACCATAAACC
24398 TTAAACTATA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 29 0.58
22 3 0.06
24 3 0.06
25 15 0.30
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.27
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:24355 original size:46 final size:46
Alignment explanation
Indices: 24300--24393 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
24290 CTTCAAATAC
*
24300 TAGTTAACTCTTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
24346 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
24392 TA
1 TA
24394 AACCTTAAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.30
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
Found at i:24408 original size:14 final size:14
Alignment explanation
Indices: 24309--24408 Score: 74
Period size: 14 Copynumber: 6.9 Consensus size: 14
24299 CTAGTTAACT
*
24309 CTTAAACCTTAAAC
1 CTTAAACCATAAAC
* * *
24323 CCTAAACCATATAT
1 CTTAAACCATAAAC
24337 CTTAAACCATAGTTAAC
1 CTTAAACCATA---AAC
* *
24354 TCATAAACCTTAAAC
1 -CTTAAACCATAAAC
* * *
24369 CCTAAACCATATAT
1 CTTAAACCATAAAC
24383 CTTAAACCATAAAC
1 CTTAAACCATAAAC
*
24397 CTTAAACTATAA
1 CTTAAACCATAA
24409 TGATAATTAA
Statistics
Matches: 65, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
14 52 0.80
15 3 0.05
17 1 0.02
18 9 0.14
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (14 bp):
CTTAAACCATAAAC
Found at i:24703 original size:82 final size:81
Alignment explanation
Indices: 24566--24725 Score: 209
Period size: 82 Copynumber: 2.0 Consensus size: 81
24556 TTATATAACT
24566 TTTAGCGACGTTTTACCAAAAGCGCCACTAATGCTCTGGTCTGTAGCGGCGTTTTACCAAAAGCG
1 TTTAGCGACGTTTTACCAAAAGCGCCACTAATGCTCTGGTCTGTAGCGGCGTTTTACCAAAA-CG
24631 CCACTAATGCTCTGGTC
65 CCACTAATGCTCTGGTC
* * * *
24648 TTTAGC-AGCGTTTTACCAAAAGCGCCGCT-ATGCTCT-GTTTTTAGCGGCGTTTTTTACTAAAA
1 TTTAGCGA-CGTTTTACCAAAAGCGCCACTAATGCTCTGGTCTGTAGCGGCG--TTTTACCAAAA
* *
24710 CGCCGCTATTGCTCTG
63 CGCCACTAATGCTCTG
24726 TTTGTGTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
80 11 0.16
81 22 0.32
82 36 0.52
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (81 bp):
TTTAGCGACGTTTTACCAAAAGCGCCACTAATGCTCTGGTCTGTAGCGGCGTTTTACCAAAACGC
CACTAATGCTCTGGTC
Found at i:24728 original size:41 final size:41
Alignment explanation
Indices: 24566--24700 Score: 211
Period size: 41 Copynumber: 3.3 Consensus size: 41
24556 TTATATAACT
*
24566 TTTAGCGACGTTTTACCAAAAGCGCCACTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCTCTGGTC
*
24607 TGTAGCGGCGTTTTACCAAAAGCGCCACTAATGCTCTGGTC
1 TTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCTCTGGTC
* * *
24648 TTTAGCAGCGTTTTACCAAAAGCGCCGCT-ATGCTCT-GTT
1 TTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCTCTGGTC
24687 TTTAGCGGCGTTTT
1 TTTAGCGGCGTTTT
24701 TTACTAAAAC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
39 15 0.17
40 7 0.08
41 65 0.75
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTACCAAAAGCGCCACTAATGCTCTGGTC
Done.