Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3731
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: 45048
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:774 original size:45 final size:44
Alignment explanation
Indices: 674--916 Score: 197
Period size: 45 Copynumber: 5.5 Consensus size: 44
664 AATCCACTCT
* * * ** * * *
674 ACTGCAACTTCAAGGTGATAGGATTATTGGCTTTAATCTGCTCT
1 ACTGCAACTTCAAGGAGATAAGATTACTATCTTCAGTCTGCTCC
* * *
718 ACTGCAACTTCAAGGACATAAGATTCACCATCTTCAGTCTGCCCC
1 ACTGCAACTTCAAGGAGATAAGATT-ACTATCTTCAGTCTGCTCC
* * *
763 ACTGCAACTTCAGGGGGATAAGACTTGCTATCTTCAGTCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGA-TTACTATCTTCAGTCTGCTCC
* * * ** * *
808 ACTGCAACTTCAAGGAAATAGGATTATTGGCTTTAATCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGATTACTATCTTCAGTCTGCTCC
* ** * *
852 ACTGCAACTTCAGGGAGATAAGATT-C-GCCTTGA-TCTGCTCT
1 ACTGCAACTTCAAGGAGATAAGATTACTATCTTCAGTCTGCTCC
893 ACTGCAACTTC-AGAGAGATAAGAT
1 ACTGCAACTTCAAG-GAGATAAGAT
917 CTGTGACTTA
Statistics
Matches: 161, Mismatches: 35, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
40 1 0.01
41 28 0.17
42 5 0.03
44 59 0.37
45 66 0.41
46 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
ACTGCAACTTCAAGGAGATAAGATTACTATCTTCAGTCTGCTCC
Found at i:855 original size:89 final size:90
Alignment explanation
Indices: 710--874 Score: 224
Period size: 89 Copynumber: 1.8 Consensus size: 90
700 TTGGCTTTAA
* * * *
710 TCTGCTCTACTGCAACTTCAAGGACATAAGATTCACCATCTTCAGTCTGCCCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAAGGAAATAAGATTCACCAGCTTCAATCTGCCCCACTGCAACTTCA
*
775 GGGGGATAAGACTTGCTATCTTCAG
66 GGGAGATAAGACTTGCTATCTTCAG
* *** * *
800 TCTGCTCCACTGCAACTTCAAGGAAATAGGATT-ATTGGCTTTAATCTGCTCCACTGCAACTTCA
1 TCTGCTCCACTGCAACTTCAAGGAAATAAGATTCACCAGCTTCAATCTGCCCCACTGCAACTTCA
864 GGGAGATAAGA
66 GGGAGATAAGA
875 TTCGCCTTGA
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
89 34 0.53
90 30 0.47
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (90 bp):
TCTGCTCCACTGCAACTTCAAGGAAATAAGATTCACCAGCTTCAATCTGCCCCACTGCAACTTCA
GGGAGATAAGACTTGCTATCTTCAG
Found at i:857 original size:44 final size:44
Alignment explanation
Indices: 660--916 Score: 200
Period size: 44 Copynumber: 5.9 Consensus size: 44
650 CGTCTTGTTT
** * * * * *
660 CTTCAATCCACTCTACTGCAACTTCAAGGTGATAGGATTATTGG
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTACTAG
* * * * *
704 CTTTAATCTGCTCTACTGCAACTTCAAGGACATAAGATTCACCAT
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT-ACTAG
* * * * * *
749 CTTCAGTCTGCCCCACTGCAACTTCAGGGGGATAAGACTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TTACTAG
* * * * *
794 CTTCAGTCTGCTCCACTGCAACTTCAAGGAAATAGGATTATTGG
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTACTAG
* *
838 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-C--G
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTACTAG
* *
879 CCTT-GATCTGCTCTACTGCAACTTC-AGAGAGATAAGAT
1 -CTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGAT
917 CTGTGACTTA
Statistics
Matches: 172, Mismatches: 37, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
40 1 0.01
41 30 0.17
42 3 0.02
44 70 0.41
45 66 0.38
46 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTACTAG
Found at i:1014 original size:51 final size:50
Alignment explanation
Indices: 952--1817 Score: 720
Period size: 46 Copynumber: 17.9 Consensus size: 50
942 GCAATTCCAG
* * *
952 GGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAA
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAACGCCAA
* * * * *
1003 GGAAATAAGATTAGCTGTCTTCAGCTCTAA--TTT--ACTGCAACGCCAG
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAACGCCAA
* * * * * *
1049 GGAAATAAGATTTGCTACCTTCAGCATTAATCTGTTCCACTACAACACCAA
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAACGCCAA
* * * * *
1100 GGAAATAAGATTTGCTGTCTTCAGCTTTAATC--T--ATTGCAACGCCAG
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAACGCCAA
* * * *
1146 GGAAACAAGATTCACTGCCTTCAGCTTCAATC--T--ATTGCAACGCCAG
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAACGCCAA
*
1192 GGAAACAAG--TCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGGCAA
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAACGCCAA
* * * *
1241 GGAAATAAGATTCGTTGCCATCAGCTTTAATC--T--ATTGCAACG-CAA
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAACGCCAA
* * *
1286 GGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACACCGA
1 -GGAAACAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAACGCCAA
* * * * * *
1338 GGACATAAGATTTGCTGCCTTCAGCTTTAATC--T--ATTGCAACGCTAG
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAACGCCAA
*
1384 GGAAACAAGA-TCTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAATGCCAA
1 GGAAACAAGATTC-GCTGCCTTCAGCTTTAATCT-TTCCACTGCAACGCCAA
* *
1435 GGAAATAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTGCAACGCCAA
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAACGCCAA
* * * * * *
1486 GGAAATAAGATTCTCTGCCTTCAGCTTTAATC--T--ATTGCAATGCTAG
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAACGCCAA
* * * *
1532 GGAAACAAGATTCGCTGACTTTAGCTTTAATC--T--ATTGGAACGCC-A
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAACGCCAA
1577 GAGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAA
1 G-GAAACAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAACGCCAA
* * * * * *
1629 GGGAATAAGATTCACTGCCTTCAACTTTAATC--T--ATTGCAACGCCAG
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAACGCCAA
*
1675 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAA
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAACGCCAA
* * * *
1726 AGAAATAATATTCGCTGCCTTCAGGTTTAATCTATT--A---CAACGCC-A
1 GGAAACAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAACGCCAA
* * * *
1771 GTGAGACAAGATTTGCTGCCTTCATCTTTAATGTATTCCACTGCAAC
1 G-GAAACAAGATTCGCTGCCTTCAGCTTTAATCT-TTCCACTGCAAC
1818 ACCCGGGAAA
Statistics
Matches: 667, Mismatches: 104, Indels: 88
0.78 0.12 0.10
Matches are distributed among these distances:
44 19 0.03
45 6 0.01
46 314 0.47
47 1 0.00
48 9 0.01
49 26 0.04
51 286 0.43
52 6 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (50 bp):
GGAAACAAGATTCGCTGCCTTCAGCTTTAATCTTTCCACTGCAACGCCAA
Found at i:1060 original size:97 final size:100
Alignment explanation
Indices: 948--1758 Score: 613
Period size: 97 Copynumber: 8.4 Consensus size: 100
938 TATTGCAATT
* * *
948 CCAGGGAAACAAGATTTGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAAGGAAATAAGA
1 CCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAAGGAAACAAGA
* * *
1013 TTAGCTGTCTTCAGCTCTAA-T-TT-ACTGCAACG
66 TTCGCTGCCTTCAGCTTTAACTGTTCACTGCAACG
* * * *
1045 CCAGGGAAATAAGATTTGCTACCTTCAGCATTAATCTGTTCCACTACAACACCAAGGAAATAAGA
1 CCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAAGGAAACAAGA
* * * *
1110 TTTGCTGTCTTCAGCTTTAA-T-CT-ATTGCAACG
66 TTCGCTGCCTTCAGCTTTAACTGTTCACTGCAACG
* * * * * * *
1142 CCAGGGAAACAAGATTCACTGCCTTCAGCTTCAATC---T--ATTGCAACGCCAGGGAAACAAG-
1 CCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAAGGAAACAAGA
1201 -TCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACG
66 TTCGCTGCCTTCAGCTTTAA-CTGTT-CACTGCAACG
* * * * * * * *
1237 GCAAGGAAATAAGATTCGTTGCCATCAGCTTTAATCTATTGCA--AC-GCA--AGGGAAACAAGA
1 CCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAAGGAAACAAGA
* *
1297 TTTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACA
66 TTCGCTGCCTTCAGCTTTAA-CTGTT-CACTGCAACG
* * * * * * *
1334 CC-GAGGACATAAGATTTGCTGCCTTCAGCTTTAATC---T--ATTGCAACGCTAGGGAAACAAG
1 CCAG-GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAAGGAAACAAG
*
1393 A-TCTGCTGCCTTCAGCTTTAATCTGTTCCACTGCAATG
65 ATTC-GCTGCCTTCAGCTTTAA-CTGTT-CACTGCAACG
* * * * *
1431 CCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGA
1 CCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAAGGAAACAAGA
* * * *
1496 TTCTCTGCCTTCAGCTTTAA-T-CT-ATTGCAATG
66 TTCGCTGCCTTCAGCTTTAACTGTTCACTGCAACG
* * * * * ** *
1528 CTAGGGAAACAAGATTCGCTGACTTTAGCTTTAATC---T--ATTGGAACGCC-AGAGAAACAAG
1 CCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAAG-GAAACAAG
1587 ATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACG
65 ATTCGCTGCCTTCAGCTTTAA-CTGTT-CACTGCAACG
* * * * * *
1625 CCAAGGG-AATAAGATTCACTGCCTTCAACTTTAATC---T--ATTGCAACGCCAGGGAAACAAG
1 CC-AGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAAGGAAACAAG
*
1684 ATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACG
65 ATTCGCTGCCTTCAGCTTTAA-CTGTT-CACTGCAACG
** * *
1722 CCAAAGAAATAATATTCGCTGCCTTCAGGTTTAATCT
1 CCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCT
1759 ATTACAACGC
Statistics
Matches: 593, Mismatches: 85, Indels: 71
0.79 0.11 0.09
Matches are distributed among these distances:
90 17 0.03
91 2 0.00
92 55 0.09
93 1 0.00
94 5 0.01
95 50 0.08
96 3 0.01
97 412 0.69
98 7 0.01
99 1 0.00
100 3 0.01
102 35 0.06
103 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (100 bp):
CCAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACACCAAGGAAACAAGA
TTCGCTGCCTTCAGCTTTAACTGTTCACTGCAACG
Found at i:1759 original size:97 final size:97
Alignment explanation
Indices: 1036--1817 Score: 879
Period size: 97 Copynumber: 8.1 Consensus size: 97
1026 GCTCTAATTT
* * * * * * * *
1036 ACTGCAACGCCAGGGAAATAAGATTTGCTACCTTCAGCATTAATCTGTTCCACTACAACACCAAG
1 ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T--ATTGCAACGCCAGG
* * *
1101 GAAATAAGATTTGCTGTCTTCAGCTTTAATC---T--
61 GAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCC
* * * * *
1133 ATTGCAACGCCAGGGAAACAAGATTCACTGCCTTCAGCTTCAATCTATTGCAACGCCAGGGAAAC
1 ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAAC
1198 AAG--TCGCTGCCTTCAGCTTTAATCTGTTCC
66 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCC
* * * *
1228 ACTGCAACGGCAAGGAAATAAGATTCGTTGCCATCAGCTTTAATCTATTGCAACGCAAGGGAAAC
1 ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAAC
*
1293 AAGATTTGCTGCCTTCAGCTTTAATCTGTTCC
66 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCC
* * * * *
1325 ACTGCAACACCGAGGACATAAGATTTGCTGCCTTCAGCTTTAATCTATTGCAACGCTAGGGAAAC
1 ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAAC
1390 AAGA-TCTGCTGCCTTCAGCTTTAATCTGTTCC
66 AAGATTC-GCTGCCTTCAGCTTTAATCTGTTCC
* * * *
1422 ACTGCAATGCCAAGGAAATAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAG
1 ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T--ATTGCAACGCCAGG
* *
1487 GAAATAAGATTCTCTGCCTTCAGCTTTAATC---T--
61 GAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCC
* * * * * * * * *
1519 ATTGCAATGCTAGGGAAACAAGATTCGCTGACTTTAGCTTTAATCTATTGGAACGCCAGAGAAAC
1 ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAAC
1584 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCC
66 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCC
* * *
1616 ACTGCAACGCCAAGGGAATAAGATTCACTGCCTTCAACTTTAATCTATTGCAACGCCAGGGAAAC
1 ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAAC
1681 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCC
66 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCC
* * * * * * *
1713 ACTACAACGCCAAAGAAATAATATTCGCTGCCTTCAGGTTTAATCTATTACAACGCCAGTGAGAC
1 ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAAC
* * * *
1778 AAGATTTGCTGCCTTCATCTTTAATGTATTCC
66 AAGATTCGCTGCCTTCAGCTTTAATCTGTTCC
1810 ACTGCAAC
1 ACTGCAAC
1818 ACCCGGGAAA
Statistics
Matches: 582, Mismatches: 84, Indels: 38
0.83 0.12 0.05
Matches are distributed among these distances:
90 19 0.03
92 56 0.10
93 1 0.00
94 2 0.00
95 60 0.10
96 1 0.00
97 402 0.69
99 1 0.00
100 1 0.00
102 37 0.06
103 2 0.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (97 bp):
ACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAAC
AAGATTCGCTGCCTTCAGCTTTAATCTGTTCC
Found at i:3087 original size:14 final size:15
Alignment explanation
Indices: 3063--3098 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
3053 GCCTCTCTAT
3063 TTTTTACTTTTTTCA
1 TTTTTACTTTTTTCA
3078 TTTTTA-TTTTTTCA
1 TTTTTACTTTTTTCA
3092 TTTTTAC
1 TTTTTAC
3099 GACTCAAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTACTTTTTTCA
Found at i:9369 original size:13 final size:14
Alignment explanation
Indices: 9338--9372 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
9328 ATGAAACGAA
9338 TTAAAATAAATCAAT
1 TTAAAA-AAATCAAT
9353 TTAAAAAAATC-AT
1 TTAAAAAAATCAAT
9366 TTAAAAA
1 TTAAAAA
9373 TACATGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.45
14 5 0.25
15 6 0.30
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
TTAAAAAAATCAAT
Found at i:16300 original size:5 final size:5
Alignment explanation
Indices: 16290--16429 Score: 56
Period size: 5 Copynumber: 27.0 Consensus size: 5
16280 TTTGCCCTTC
** *
16290 TTTAT TTTAT TTTAT TTTA- TTTACT TAGCAT TTTA- -TTAA TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T T-TTAT TTTAT TTTAT TTTAT TTTAT
* * * *
16339 TGTA- TTTAT TTTAT TATTAT GCTTCAT TTAATT TTTAT TTTAT CTTAT
1 TTTAT TTTAT TTTAT T-TTAT --TTTAT TTTA-T TTTAT TTTAT TTTAT
* ** *
16387 TTATGAT ATTTA- GTTAT TTTAT TTGGT CTTAT TTTAT TCTTAT
1 TT-T-AT -TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT
16430 CCAGCCTGTT
Statistics
Matches: 100, Mismatches: 20, Indels: 29
0.67 0.13 0.19
Matches are distributed among these distances:
3 3 0.03
4 10 0.10
5 60 0.60
6 17 0.17
7 7 0.07
8 3 0.03
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (5 bp):
TTTAT
Found at i:16347 original size:14 final size:13
Alignment explanation
Indices: 16319--16354 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
16309 TTTACTTAGC
16319 ATTTTATTAATTT
1 ATTTTATTAATTT
*
16332 ATTTTATTGTATTT
1 ATTTTATT-AATTT
16346 ATTTTATTA
1 ATTTTATTA
16355 TTATGCTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
ATTTTATTAATTT
Found at i:16453 original size:27 final size:27
Alignment explanation
Indices: 16423--16514 Score: 76
Period size: 28 Copynumber: 3.3 Consensus size: 27
16413 TCTTATTTTA
16423 TTCTTATCCAGCCTGTTACATTTGGTT
1 TTCTTATCCAGCCTGTTACATTTGGTT
** * * * **
16450 TTCTTATTTGTATGACTATTACTTTTATTT
1 TTCTTA--TCCA-GCCTGTTACATTTGGTT
*
16480 TTAGTTATCCAGCCTGTTACATTTGGTT
1 TT-CTTATCCAGCCTGTTACATTTGGTT
16508 TTCTTAT
1 TTCTTAT
16515 TTGTATGACT
Statistics
Matches: 45, Mismatches: 16, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
27 10 0.22
28 14 0.31
29 4 0.09
30 14 0.31
31 3 0.07
ACGTcount: A:0.17, C:0.16, G:0.12, T:0.54
Consensus pattern (27 bp):
TTCTTATCCAGCCTGTTACATTTGGTT
Found at i:16490 original size:58 final size:58
Alignment explanation
Indices: 16426--16544 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
16416 TATTTTATTC
16426 TTATCCAGCCTGTTACATTTGGTTTTCTTATTTGTATGACTATTACTTTTATTTTTAG
1 TTATCCAGCCTGTTACATTTGGTTTTCTTATTTGTATGACTATTACTTTTATTTTTAG
16484 TTATCCAGCCTGTTACATTTGGTTTTCTTATTTGTATGACTATTACTTTTATTTTTAG
1 TTATCCAGCCTGTTACATTTGGTTTTCTTATTTGTATGACTATTACTTTTATTTTTAG
16542 TTA
1 TTA
16545 CTATAGTCTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.19, C:0.13, G:0.12, T:0.55
Consensus pattern (58 bp):
TTATCCAGCCTGTTACATTTGGTTTTCTTATTTGTATGACTATTACTTTTATTTTTAG
Found at i:21539 original size:25 final size:25
Alignment explanation
Indices: 21505--21555 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
21495 ATTACCACAT
21505 AGTCAAAATTACTTTTAATGTTATC
1 AGTCAAAATTACTTTTAATGTTATC
21530 AGTCAAAATTACTTTTAATGTTATC
1 AGTCAAAATTACTTTTAATGTTATC
21555 A
1 A
21556 TATCATGCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (25 bp):
AGTCAAAATTACTTTTAATGTTATC
Found at i:27355 original size:17 final size:17
Alignment explanation
Indices: 27315--27356 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
27305 TATAATTTAG
*
27315 ATGTAAAATATACTAAA
1 ATGTAAAATAAACTAAA
*
27332 ATATAAAATAAACTAGAA
1 ATGTAAAATAAACTA-AA
27350 A-GTAAAA
1 ATGTAAAA
27357 ATGGAGTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.24
Consensus pattern (17 bp):
ATGTAAAATAAACTAAA
Found at i:27497 original size:19 final size:17
Alignment explanation
Indices: 27467--27501 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
27457 ATAGATAAAT
27467 AAAAAATAAATATAATA
1 AAAAAATAAATATAATA
27484 AAAAAATTATAATATAAT
1 AAAAAA-TA-AATATAAT
27502 GAATTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATAAATATAATA
Found at i:27966 original size:39 final size:39
Alignment explanation
Indices: 27909--27983 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
27899 TAATTTGGCA
27909 GAAGTTTGTTTGGCAGTTAAACTGCATTATCATAATAAG
1 GAAGTTTGTTTGGCAGTTAAACTGCATTATCATAATAAG
* * *
27948 GAAGTTTGTTTGGTAGTTAAATTGTATTATCATAAT
1 GAAGTTTGTTTGGCAGTTAAACTGCATTATCATAAT
27984 TCGACAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (39 bp):
GAAGTTTGTTTGGCAGTTAAACTGCATTATCATAATAAG
Found at i:30809 original size:24 final size:24
Alignment explanation
Indices: 30781--30830 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
30771 AGGTCCTTAG
30781 TCATTCATTCTATCGGTTCCAAAA
1 TCATTCATTCTATCGGTTCCAAAA
* *
30805 TCATTCGTTCTATCGGTTCCCAAA
1 TCATTCATTCTATCGGTTCCAAAA
30829 TC
1 TC
30831 CTAACAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.28, G:0.10, T:0.38
Consensus pattern (24 bp):
TCATTCATTCTATCGGTTCCAAAA
Found at i:33688 original size:69 final size:69
Alignment explanation
Indices: 33540--34042 Score: 407
Period size: 69 Copynumber: 7.3 Consensus size: 69
33530 CATTTTTTTA
** * * * * *
33540 TGCGAACCTTGGTTTTACAGCTAGGAGCTTTGCTCTCGCTAGCTGTGCTAGAGGCCGTGGCTTTT
1 TGCGAACCTTAATTTTACAGCTGGGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTT
*
33605 TGCC
66 CGCC
* ** * * * * * *
33609 TGGGGTCCTTAATTTTACAGTTGGGAGCTTTGCCCTCGCTAACTGTGTTAGAGGTCATGGCACTT
1 TGCGAACCTTAATTTTACAGCTGGGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTT
*
33674 CACC
66 CGCC
* * * * * *
33678 TGCGAACCTTAGTTTTACAGATGGGAGCTTTGCTCTCACTAACTATGTTGCAGGTCGTGGCTCTT
1 TGCGAACCTTAATTTTACAGCTGGGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTT
33743 CGCC
66 CGCC
** ** * * * *****
33747 T-ATAGACCTTAATTTTACAATTGAGAGCTTCGCTCTTGCTAACTGTGCTGGAGGTTACACCTCT
1 TGCGA-ACCTTAATTTTACAGCTGGGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCT
*
33811 TTGCC
65 TCGCC
* * * * * * * *
33816 TGTGAACCTTAATTTTACAGTTGGGAACTTTGCTCTCGTTACCTATGCTGGAGGTTGTGCCTCTT
1 TGCGAACCTTAATTTTACAGCTGGGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTT
33881 CGCC
66 CGCC
* * * * ** *
33885 TGC-AACCCTTAATTTTATAGCTAGGAGATTTGCTCTCGTTAGTTGTGCTGGAGGTCGCGGCTCT
1 TGCGAA-CCTTAATTTTACAGCTGGGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCT
*
33949 TCACC
65 TCGCC
* * * * * ***
33954 TGCAAACCTTAATTTTACAACTGGGAGCTTTGCTCTTGCTAACTGTACTGAAGGTCGCAACTCTT
1 TGCGAACCTTAATTTTACAGCTGGGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTT
34019 CGCC
66 CGCC
**
34023 TGTAAACCTTAATTTTACAG
1 TGCGAACCTTAATTTTACAG
34043 GTAACATTTT
Statistics
Matches: 341, Mismatches: 89, Indels: 8
0.78 0.20 0.02
Matches are distributed among these distances:
68 3 0.01
69 335 0.98
70 3 0.01
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (69 bp):
TGCGAACCTTAATTTTACAGCTGGGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTCGTGGCTCTT
CGCC
Done.