Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2418
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: 62262
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:4611 original size:20 final size:20
Alignment explanation
Indices: 4588--4659 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
4578 CACACCCAGA
*
4588 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCAT
*
4608 TGTATCGATACA-TATTCAT
1 TGTATCGATACATTATGCAT
* *
4627 TGTATCGATACATGA-ACAAT
1 TGTATCGATACATTATGC-AT
4647 TGTATCGATACAT
1 TGTATCGATACAT
4660 GAAATTGGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.39
20 28 0.61
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTATGCAT
Found at i:8707 original size:34 final size:34
Alignment explanation
Indices: 8664--8733 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
8654 CATGTTGTTT
*
8664 TTAGTGATTCTAACTCCTCCGAAAGGAAGGTATC
1 TTAGTGATTCTAACTCCTCCGAAAAGAAGGTATC
* *
8698 TTAGTGATTCTAACTCCTCTGAAAATAAGGTATC
1 TTAGTGATTCTAACTCCTCCGAAAAGAAGGTATC
8732 TT
1 TT
8734 TTGTTGACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (34 bp):
TTAGTGATTCTAACTCCTCCGAAAAGAAGGTATC
Found at i:10950 original size:13 final size:13
Alignment explanation
Indices: 10914--10950 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
10904 ACATTCCTTA
*
10914 TATCGATACAATG
1 TATCGATACATTG
10927 TATCGATACATTG
1 TATCGATACATTG
10940 TATCGATACAT
1 TATCGATACAT
10951 GGGTTACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:16734 original size:3 final size:3
Alignment explanation
Indices: 16726--16793 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
16716 TAGTTGAGTT
* * *
16726 TTA TTA TTA TTA TTA TTA TTC TTA TTA TTA TTA TCA TTA TTA TTC TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16774 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
16794 TTAAACAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:17212 original size:22 final size:22
Alignment explanation
Indices: 17160--17213 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
17150 ACCTAACACA
17160 TTACCTAACACACATAATATAC
1 TTACCTAACACACATAATATAC
* * * **
17182 TCACTTAACACACCTAATATGT
1 TTACCTAACACACATAATATAC
17204 TTACCTAACA
1 TTACCTAACA
17214 TACCACCTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.28, G:0.02, T:0.30
Consensus pattern (22 bp):
TTACCTAACACACATAATATAC
Found at i:17858 original size:16 final size:16
Alignment explanation
Indices: 17837--17868 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17827 TGAAACAAAT
*
17837 TTAAAATAATTTAAAA
1 TTAAAATAATCTAAAA
17853 TTAAAATAATCTAAAA
1 TTAAAATAATCTAAAA
17869 ATGTAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAATAATCTAAAA
Found at i:20808 original size:50 final size:51
Alignment explanation
Indices: 20754--20882 Score: 131
Period size: 53 Copynumber: 2.5 Consensus size: 51
20744 GATTCATGTG
*
20754 TTTATATTATATTTATATATTTTA-TTACATTATAATCATATTTAAA-ATAT-
1 TTTATATTATATTTATATATTTTATTTACATTATAA-AAT-TTTAAATATATA
* * *
20804 TTTATATAAT-TTTAATATATTAATAATTTATATTATAAAATTTTAAATATATA
1 TTTATATTATATTT-ATATATT--TTATTTACATTATAAAATTTTAAATATATA
20857 TTTATATTATATCTTATCATATTTTA
1 TTTATATTATAT-TTAT-ATATTTTA
20883 ATTTTATATA
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
49 3 0.05
50 16 0.25
51 6 0.09
52 8 0.12
53 21 0.33
54 3 0.05
55 7 0.11
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (51 bp):
TTTATATTATATTTATATATTTTATTTACATTATAAAATTTTAAATATATA
Found at i:20840 original size:18 final size:19
Alignment explanation
Indices: 20754--20840 Score: 56
Period size: 18 Copynumber: 4.6 Consensus size: 19
20744 GATTCATGTG
*
20754 TTTATATTATATTTATATA
1 TTTATATTATATTAATATA
*
20773 TTT-TATTACATTATAATCATA
1 TTTATATTATA-T-TAAT-ATA
* * *
20794 TTTAAAATAT-TTTATATAA
1 TTTATATTATATTAATAT-A
*
20813 TTT-TAATATATTAATA-A
1 TTTATATTATATTAATATA
20830 TTTATATTATA
1 TTTATATTATA
20841 AAATTTTAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
17 4 0.08
18 19 0.37
19 16 0.31
20 4 0.08
21 6 0.12
22 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTATATTATATTAATATA
Found at i:20893 original size:15 final size:16
Alignment explanation
Indices: 20851--20914 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 16
20841 AAATTTTAAA
20851 TATATATTTATATTATATCT
1 TATATATTTATA--AT-T-T
20871 TATCATATTT-TAATTT
1 TAT-ATATTTATAATTT
*
20887 TATATATATTATAATTA
1 TATATAT-TTATAATTT
20904 TATA-ATTTATA
1 TATATATTTATA
20915 TTTAAAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
15 9 0.22
16 8 0.20
17 10 0.25
18 2 0.05
20 5 0.12
21 6 0.15
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATATTTATAATTT
Found at i:20901 original size:17 final size:17
Alignment explanation
Indices: 20808--20907 Score: 59
Period size: 17 Copynumber: 5.7 Consensus size: 17
20798 AAATATTTTA
20808 TATAATTTTA-ATATAT
1 TATAATTTTATATATAT
20824 TAATAA-TTTATAT-TA-
1 T-ATAATTTTATATATAT
*
20839 TAAAATTTTAAATATATATT
1 TATAATTTT--ATATATA-T
20859 TATATTATATCTTATCATAT-T
1 TATA--AT-T-TTAT-ATATAT
20880 T-TAATTTTATATATAT
1 TATAATTTTATATATAT
*
20896 TATAATTATATA
1 TATAATTTTATA
20908 ATTTATATTT
Statistics
Matches: 66, Mismatches: 3, Indels: 29
0.67 0.03 0.30
Matches are distributed among these distances:
14 3 0.05
15 8 0.12
16 13 0.20
17 20 0.30
18 4 0.06
20 5 0.08
21 2 0.03
22 4 0.06
23 5 0.08
24 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TATAATTTTATATATAT
Found at i:21582 original size:3 final size:3
Alignment explanation
Indices: 21574--21604 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
21564 TATGTTTCCT
21574 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
21605 ATCTTGTACG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25356 original size:139 final size:139
Alignment explanation
Indices: 25106--25381 Score: 543
Period size: 139 Copynumber: 2.0 Consensus size: 139
25096 AGCTGATGCA
25106 TAGTACTTGTTGCTATTTTAGATAAGTTAGATGTCAAAGGCATGTTAAACAAAACCCATATGTCT
1 TAGTACTTGTTGCTATTTTAGATAAGTTAGATGTCAAAGGCATGTTAAACAAAACCCATATGTCT
25171 TGCTCTTGCTTATTTGCTTCTCTACTTGAATTGACCAAATGCACAGTTGGATTAAACTGATTGGT
66 TGCTCTTGCTTATTTGCTTCTCTACTTGAATTGACCAAATGCACAGTTGGATTAAACTGATTGGT
25236 TTACACCAG
131 TTACACCAG
*
25245 TAGTACTTGTTGCTATTTTAGATGAGTTAGATGTCAAAGGCATGTTAAACAAAACCCATATGTCT
1 TAGTACTTGTTGCTATTTTAGATAAGTTAGATGTCAAAGGCATGTTAAACAAAACCCATATGTCT
25310 TGCTCTTGCTTATTTGCTTCTCTACTTGAATTGACCAAATGCACAGTTGGATTAAACTGATTGGT
66 TGCTCTTGCTTATTTGCTTCTCTACTTGAATTGACCAAATGCACAGTTGGATTAAACTGATTGGT
25375 TTACACC
131 TTACACC
25382 GATTTTACTG
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (139 bp):
TAGTACTTGTTGCTATTTTAGATAAGTTAGATGTCAAAGGCATGTTAAACAAAACCCATATGTCT
TGCTCTTGCTTATTTGCTTCTCTACTTGAATTGACCAAATGCACAGTTGGATTAAACTGATTGGT
TTACACCAG
Found at i:29509 original size:22 final size:22
Alignment explanation
Indices: 29476--29532 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
29466 CAAATTTGAA
* * *
29476 AGAACAAAGAGAGATGAAAAATG
1 AGAAAAAAGAGA-ATAAAAAAAG
29499 -GAAAAAAGAGAATAAAAAAAG
1 AGAAAAAAGAGAATAAAAAAAG
*
29520 AGAGAAAAGAGAA
1 AGAAAAAAGAGAA
29533 GGCATTCTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 8 0.28
22 21 0.72
ACGTcount: A:0.68, C:0.02, G:0.25, T:0.05
Consensus pattern (22 bp):
AGAAAAAAGAGAATAAAAAAAG
Found at i:30251 original size:58 final size:57
Alignment explanation
Indices: 30189--30341 Score: 200
Period size: 58 Copynumber: 2.6 Consensus size: 57
30179 TAATCTATGA
* *
30189 TCATTTTAGATGATTTCATCATTTTAAGGCCATTTAGGTTATTTTACATAACCTAAGG
1 TCATTTTAGA-AATTTCATCATTTTAAGGCCATTTAGGTTATTTTACATAACCAAAGG
* * *
30247 TCATTTTAGAAAATTTCATCATTTT-AGGACCATTTAAGTTATTTTACATAATCAAATG
1 TCATTTTAG-AAATTTCATCATTTTAAGG-CCATTTAGGTTATTTTACATAACCAAAGG
* *
30305 TCATTTTAGAAAATTCTATCATTTTAAGGCTATTTAG
1 TCATTTTAGAAATTTC-ATCATTTTAAGGCCATTTAG
30342 ACATTTTATA
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
57 9 0.11
58 70 0.84
59 4 0.05
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (57 bp):
TCATTTTAGAAATTTCATCATTTTAAGGCCATTTAGGTTATTTTACATAACCAAAGG
Found at i:34278 original size:28 final size:28
Alignment explanation
Indices: 34164--35088 Score: 1230
Period size: 28 Copynumber: 32.5 Consensus size: 28
34154 CACTAACTTA
* *
34164 TGTGGGCTTTGAAAAGAGTTGCCACCGACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * *
34194 CGTGTGGGCTTTGAAAAGAGTTACCACT-AGTT
1 --TGTGGGCTTTG-AAAG-GGTGCCACTGA-CT
**
34226 TGTGGGCTTTGAAAAGAATGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
34255 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
34283 TGTGGG-TTCTGAAATGATGCCACTGACT
1 TGTGGGCTT-TGAAAGGGTGCCACTGACT
*
34311 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
34340 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
34368 TGCATGGGCTTTGAATGGGTGCCACTGACT
1 TG--TGGGCTTTGAAAGGGTGCCACTGACT
*
34398 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
34426 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
34454 TGTGGGCTTTGAAAAAAGTGCCACTGACC
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
34483 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
34511 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
34539 TGTGGGCTTTGAAA-GGTGCCAATGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
34566 TGCGTGGGCTTTGAATA-AGTGCCACTGACT
1 T--GTGGGCTTTGAA-AGGGTGCCACTGACT
34596 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
34624 TATGGGCTTTGAAAGGATGCTACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
34652 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
34680 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
34708 TGTGAGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
34736 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
34764 TGCGTGGGCATT-AAATGGGTGCCACTAACT
1 T--GTGGGCTTTGAAA-GGGTGCCACTGACT
*
34794 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
34822 TGCGTGGGCATTGAATGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
34852 TGTAGGCTTTGATATGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
34880 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
34908 TTTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
34936 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
34964 TATGGGCTTTGAAATGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
34992 TGTGGGCTATAAAAGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
35020 TGTGGGTTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
35048 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
35076 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
35089 GAGATGAACG
Statistics
Matches: 794, Mismatches: 81, Indels: 40
0.87 0.09 0.04
Matches are distributed among these distances:
27 16 0.02
28 559 0.70
29 88 0.11
30 105 0.13
31 1 0.00
32 25 0.03
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:34863 original size:256 final size:254
Alignment explanation
Indices: 34164--35088 Score: 1290
Period size: 256 Copynumber: 3.6 Consensus size: 254
34154 CACTAACTTA
* * * *
34164 TGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTTACCACT-AGTTTG
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAG-G-TGCCACTGA-CTTG
**
34228 TGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG-TTC
59 TGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT-
* *
34292 TGAAATGATGCCACTGACTT--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
122 TGAAAGGATGCCACTGACTTGCGTGGGCTTTG-AATGAGTGCCACTGACTTGTGGGCTTTGAAAG
* *
34355 GGTGCCACTGACTTGCATGGGCTTTGAATGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCA
186 GGTGCCACTGACTT--ATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
34420 CTGACT
249 CTGACT
* *
34426 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAAAGTGCCACTGACCTGTGGGCT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAAGGTGCCACTGACTTGTGGGCT
34491 TTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGG-
65 TTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
34555 TGCCAATGACTTGCGTGGGCTTTGAATAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
130 TGCCACTGACTTGCGTGGGCTTTGAATGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* * *
34620 GACTTATGGGCTTTGAAAGGATGCTACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACT
195 GACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* *
34680 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
* * *
34745 TGAAAGGGTGCCACTAACTTGCGTGGGCATT-AAATGGGTGCCACTAACTTGTGGGCTTTGAAAG
66 TGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * * *
34809 GATGCCACTGACTTGCGTGGGCATTGAATGGGTGCCACTGACTTGTAGGCTTTGATATGATGCCA
128 GATGCCACTGACTTGCGTGGGCTTTGAATGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* *
34874 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTTTGGGCTTTGAAAGGGTGCCACTGACT
193 CTGACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
34936 TGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAATGATGCCACTGACTTGTGGGCTA
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
* * * * *
35001 TAAAAGGGTACCACTGACTTGTGGGTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGT
66 TGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAT
35066 GCCACTGACTT--GTGGGCTTTGAA
131 GCCACTGACTTGCGTGGGCTTTGAA
35089 GAGATGAACG
Statistics
Matches: 600, Mismatches: 53, Indels: 30
0.88 0.08 0.04
Matches are distributed among these distances:
252 11 0.02
253 43 0.07
254 137 0.23
255 51 0.09
256 286 0.48
257 29 0.05
258 13 0.02
259 4 0.01
260 11 0.02
261 4 0.01
262 11 0.02
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (254 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
TGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAT
GCCACTGACTTGCGTGGGCTTTGAATGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTG
ACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:41024 original size:48 final size:49
Alignment explanation
Indices: 40908--41031 Score: 155
Period size: 48 Copynumber: 2.5 Consensus size: 49
40898 ACAATGTATC
*
40908 GATACATGAATA-GTGATTGAACAGTGATTTTATCGATACATGAATAAAGT
1 GATACGTGAATAGGT-A-TGAACAGTGATTTTATCGATACATGAATAAAGT
* * *
40958 GATACGTGAACAGTTATGAACAGTGATTTTTATCGATACAT-AA-ATAGT
1 GATACGTGAATAGGTATGAACAGTGA-TTTTATCGATACATGAATAAAGT
*
41006 GATACGTGAATAGGTATGAATAGTGA
1 GATACGTGAATAGGTATGAACAGTGA
41032 AAAGTGAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
48 27 0.42
49 12 0.18
50 25 0.38
51 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (49 bp):
GATACGTGAATAGGTATGAACAGTGATTTTATCGATACATGAATAAAGT
Found at i:41155 original size:13 final size:13
Alignment explanation
Indices: 41137--41161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41127 TACCAATGCT
41137 ATGTATCGATACA
1 ATGTATCGATACA
41150 ATGTATCGATAC
1 ATGTATCGATAC
41162 TTAGCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:45972 original size:19 final size:19
Alignment explanation
Indices: 45948--45986 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
45938 AAATAATGGG
*
45948 AATGAATAGCAAGAAAAAA
1 AATGAACAGCAAGAAAAAA
* *
45967 AATGAACATCAATAAAAAA
1 AATGAACAGCAAGAAAAAA
45986 A
1 A
45987 GAATGGCCCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.10, T:0.13
Consensus pattern (19 bp):
AATGAACAGCAAGAAAAAA
Found at i:49530 original size:19 final size:19
Alignment explanation
Indices: 49506--49573 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
49496 AATTCAACAA
49506 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
49525 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
49540 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
49557 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
49574 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:49545 original size:13 final size:13
Alignment explanation
Indices: 49527--49551 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49517 ACATAAGTTT
49527 TGTATCGATACAA
1 TGTATCGATACAA
49540 TGTATCGATACA
1 TGTATCGATACA
49552 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:49549 original size:32 final size:32
Alignment explanation
Indices: 49508--49570 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
49498 TTCAACAATT
*
49508 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
49540 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
49571 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:49631 original size:13 final size:13
Alignment explanation
Indices: 49613--49638 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49603 CATTTTTCTG
49613 TGTATCGATACAT
1 TGTATCGATACAT
49626 TGTATCGATACAT
1 TGTATCGATACAT
49639 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:49635 original size:33 final size:33
Alignment explanation
Indices: 49593--49659 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
49583 GCCAAGGAAA
***
49593 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
49626 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
49659 T
1 T
49660 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:52077 original size:51 final size:52
Alignment explanation
Indices: 52000--52123 Score: 162
Period size: 51 Copynumber: 2.4 Consensus size: 52
51990 CAATTCTCCG
* * * *
52000 CAATCGGGGATATTTCATCTCCGATTTTATTTTC-AAAACACTAA-TTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACAAATTTTTC-A
*
52051 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAAAACACAAATTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC--AAAAACACAAATTTTTCA
52105 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
52124 CCCGTTAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 30 0.48
54 28 0.44
55 5 0.08
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACAAATTTTTCA
Found at i:52113 original size:54 final size:51
Alignment explanation
Indices: 52000--52123 Score: 160
Period size: 54 Copynumber: 2.4 Consensus size: 51
51990 CAATTCTCCG
* * * *
52000 CAATCGGGGATATTTCATCTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTTCTA
*
52051 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAAAACACAAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC---AAAACACAAATTTTCT-A
52105 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
52124 CCCGTTAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 30 0.48
53 1 0.02
54 32 0.51
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTTCTA
Found at i:52351 original size:53 final size:52
Alignment explanation
Indices: 52134--52359 Score: 226
Period size: 52 Copynumber: 4.3 Consensus size: 52
52124 CCCGTTAATC
* * * *** * *
52134 ATCGGGGATACTCCAACCCCTACTTTA-TTCTTAAAATATTGA-TTTCTCATA
1 ATCGGGGATACTCCAACCCCGATTTTATTTC-TAAAACACCAATTTTTTCACA
* * *
52185 ATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTCCACA
1 ATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTTCACA
* * *
52237 ATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACAGCAATTTTCCTT--TA
1 ATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTT--TTCACA
* * *
52289 ATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCACA
1 ATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACACCAATTTTTTCACA
*
52342 ATCGAGGATACTCCAACC
1 ATCGGGGATACTCCAACC
52360 TCGTTATTTC
Statistics
Matches: 144, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
51 35 0.24
52 79 0.55
53 29 0.20
54 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (52 bp):
ATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTTTCACA
Found at i:52521 original size:79 final size:79
Alignment explanation
Indices: 52370--52576 Score: 218
Period size: 79 Copynumber: 2.6 Consensus size: 79
52360 TCGTTATTTC
* * ** * *
52370 ATCGGGGATACTCAAACCTCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT
* *
52435 ATTGATTTCTCATA
66 ATCGATTTCTCACA
* * * * * *
52449 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTCC-TAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT
52513 CATCGATTTCTCACA
66 -ATCGATTTCTCACA
* * * * * *
52528 ATCGGGGATACTCCAGCCCTGTCATTTTCAAGGGGACACCCCAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
52577 TTATTATCTC
Statistics
Matches: 105, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 3 0.03
79 102 0.97
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT
ATCGATTTCTCACA
Done.