Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold850
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: 46325
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:14547 original size:3 final size:3
Alignment explanation
Indices: 14539--14672 Score: 83
Period size: 3 Copynumber: 43.0 Consensus size: 3
14529 AAAGGAAAAT
** * *
14539 ATA ATA ATA ATA ATA ATA GCA ATA ATA CT- ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
14586 AGGT- ATA ATA ATA CATTA GATA GTA AAA AGGTA ATA ATA ATA ATA ATA
1 A--TA ATA ATA ATA -A-TA -ATA ATA ATA A--TA ATA ATA ATA ATA ATA
* * * * * *
14634 ATA ATG ATA ATA GTG GTA TTA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
14673 GAAAATATTA
Statistics
Matches: 102, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
2 2 0.02
3 90 0.88
4 4 0.04
5 6 0.06
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:14787 original size:15 final size:15
Alignment explanation
Indices: 14764--14796 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
14754 AATAGTATGT
14764 TAATAAAAATAATAC
1 TAATAAAAATAATAC
*
14779 TAATGAAAATAATAC
1 TAATAAAAATAATAC
14794 TAA
1 TAA
14797 CGGTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (15 bp):
TAATAAAAATAATAC
Found at i:14792 original size:3 final size:3
Alignment explanation
Indices: 14764--14837 Score: 51
Period size: 3 Copynumber: 24.7 Consensus size: 3
14754 AATAGTATGT
* * * ***
14764 TAA TAA AAA TAA TAC TAA TGAA -AA TAA TAC TAA CGG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
14809 TAA AAA TAA TAG TAA TAA TAT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
14838 TTAAAAAATT
Statistics
Matches: 51, Mismatches: 18, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:15946 original size:38 final size:37
Alignment explanation
Indices: 15896--15972 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 37
15886 GTTAAGTCTG
* *
15896 TTGGGTTTGGGTATTGGGTTTTCATGGATTTAGGGAT
1 TTGGGTTTGGGTATTGGGTTGTAATGGATTTAGGGAT
* *
15933 TTGGGTTTTGGGTATTTGGTTGTAATGGGTTTAGGGAT
1 TTGGG-TTTGGGTATTGGGTTGTAATGGATTTAGGGAT
15971 TT
1 TT
15973 TGGGAGGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
37 5 0.14
38 30 0.86
ACGTcount: A:0.13, C:0.01, G:0.38, T:0.48
Consensus pattern (37 bp):
TTGGGTTTGGGTATTGGGTTGTAATGGATTTAGGGAT
Found at i:16622 original size:64 final size:64
Alignment explanation
Indices: 16521--16646 Score: 216
Period size: 64 Copynumber: 2.0 Consensus size: 64
16511 AAAGAGTAAA
* ** *
16521 AAATTGAAAATACCTCAGTGTGTGACCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATAG
1 AAATTAAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATAG
16585 AAATTAAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGAT
1 AAATTAAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGAT
16647 TTTTTTGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (64 bp):
AAATTAAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATAG
Found at i:16860 original size:74 final size:75
Alignment explanation
Indices: 16585--16897 Score: 457
Period size: 75 Copynumber: 4.2 Consensus size: 75
16575 GAGTTGATAG
** *** *
16585 AAATTAAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTT
1 AAATTAAAAATACCTCAGCGCGTGATTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
16650 TTTGAAACAT
66 TTTGAAACAT
* * *
16660 AAACTAAAAATACCTCAGTGCGTGATTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
1 AAATTAAAAATACCTCAGCGCGTGATTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
16725 TTTGAAACAT
66 TTTGAAACAT
* * *
16735 AAATTGAAAATACCTCAGTGCGTGATTTGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
1 AAATTAAAAATACCTCAGCGCGTGATTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
16800 TTTGAAACAT
66 TTTGAAACAT
* * *
16810 AAATTGAAAATACCTCAGCGTGTGA-TTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
1 AAATTAAAAATACCTCAGCGCGTGATTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
16874 TTTGAAAAACAA
66 TTTG--AAACAT
16886 AAATTAAAAATA
1 AAATTAAAAATA
16898 TCAGGAAACA
Statistics
Matches: 219, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
74 41 0.19
75 162 0.74
76 16 0.07
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (75 bp):
AAATTAAAAATACCTCAGCGCGTGATTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TTTGAAACAT
Found at i:27115 original size:93 final size:93
Alignment explanation
Indices: 27006--27177 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
26996 CGCCCATAAG
* * ** *
27006 CGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
27071 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
* *
27099 CGAACTCAGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGATTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
27164 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
27178 TCAACCATCC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:27167 original size:46 final size:46
Alignment explanation
Indices: 26999--27172 Score: 158
Period size: 46 Copynumber: 3.8 Consensus size: 46
26989 TGTAACCCGC
* * ** *
26999 CCATAAGCGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
* * *
27045 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GA--AC-A-TTCGCAT
* * *
27095 --TTCA-CGAACTCAGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
* *
27138 CCATAAGTGAACTCGGATTCAACTCAACGAGTTCG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCG
27173 GATGCTCAAC
Statistics
Matches: 101, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 58 0.57
47 26 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
Found at i:29836 original size:29 final size:26
Alignment explanation
Indices: 29804--29856 Score: 61
Period size: 26 Copynumber: 1.9 Consensus size: 26
29794 ATGAAATACA
*
29804 AAAAGTAAATATAATATAATAATAATATT
1 AAAA-TAAA-ATAAT-TAAAAATAATATT
*
29833 AAAATAAAGTAATTAAAAATAATA
1 AAAATAAAATAATTAAAAATAATA
29857 CTATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 10 0.45
27 4 0.18
28 4 0.18
29 4 0.18
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (26 bp):
AAAATAAAATAATTAAAAATAATATT
Found at i:30023 original size:22 final size:21
Alignment explanation
Indices: 29998--30049 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
29988 AATAATAGTG
*
29998 ATAATAATGATAAATACAAATA
1 ATAATAATAATAAA-ACAAATA
*
30020 ATAATAATAATAAAACAGATA
1 ATAATAATAATAAAACAAATA
30041 ATAAATAAT
1 AT-AATAAT
30050 CAAAGGTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAATAATAATAAAACAAATA
Found at i:30044 original size:3 final size:3
Alignment explanation
Indices: 29900--30032 Score: 67
Period size: 3 Copynumber: 44.0 Consensus size: 3
29890 AAACGTACAC
* * * *
29900 TAA TAT TAA TAA TAA TAA TAA TATG TAT TAA -AA GGTAA -AA GAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA --TAA TAA TAA TAA
* * * * * * *
29946 TAG TAA TAA TAA T-T TAA AAA TGA TAA TAG TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
29993 TAG TGA TAA TAA TGA TAAA TACA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TA-A TAA TAA TAA TAA TAA TAA
30033 AACAGATAAT
Statistics
Matches: 95, Mismatches: 26, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
2 6 0.06
3 82 0.86
4 5 0.05
5 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.08, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:30221 original size:3 final size:3
Alignment explanation
Indices: 30213--30434 Score: 89
Period size: 3 Copynumber: 74.0 Consensus size: 3
30203 AAAGGAAAAT
* * * *
30213 ATA ATA ATA ATA ATA ATA ATA GTG ATA TTA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
30261 GAAA ATA TTA GTA CGTTA ATA ACA ATA ATA TATG TTA ATA ACA ATA ATA
1 -ATA ATA ATA ATA --ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
* * * * *
30310 A-C ATA A-A A-A ATA ATA AT- ATG GTA AAA ATA AGTA ATA AT- ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
* * * * ** *
30351 TTA ATA AAA ATA ATA GTA ATGA A-A ATA ATA CTA ACG GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * *
30396 ATA ATA GA-A ATA AAA ATA ATA GTA ATA ATA TTA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30435 TTAAAAAATA
Statistics
Matches: 157, Mismatches: 49, Indels: 26
0.68 0.21 0.11
Matches are distributed among these distances:
2 12 0.08
3 133 0.85
4 10 0.06
5 2 0.01
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:32447 original size:45 final size:45
Alignment explanation
Indices: 32371--32478 Score: 125
Period size: 45 Copynumber: 2.4 Consensus size: 45
32361 TTTCGCCTGT
32371 TAGGCTCG-AGGCCCG-ATATCAGTTCACCGGCATTATAGCCTAC
1 TAGGCTCGAAGGCCCGAATATCAGTTCACCGGCATTATAGCCTAC
** *
32414 TAGGCTCGAAGGCCCGAATAGT-A-TCTCACCGGCATTATAGTTTGC
1 TAGGCTCGAAGGCCCGAATA-TCAGT-TCACCGGCATTATAGCCTAC
* *
32459 TAAGCTCAAAGGCCCGAATA
1 TAGGCTCGAAGGCCCGAATA
32479 ATCAAGTCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
43 8 0.14
44 8 0.14
45 39 0.70
46 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (45 bp):
TAGGCTCGAAGGCCCGAATATCAGTTCACCGGCATTATAGCCTAC
Found at i:32883 original size:16 final size:16
Alignment explanation
Indices: 32843--32883 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
32833 ACACATCACC
*
32843 GGCACGAAACCTGCTA
1 GGCACGAAGCCTGCTA
32859 GGCACGAAGCCTGCTA
1 GGCACGAAGCCTGCTA
32875 GGCACGAAG
1 GGCACGAAG
32884 GCCCGAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.32, T:0.10
Consensus pattern (16 bp):
GGCACGAAGCCTGCTA
Found at i:32933 original size:38 final size:38
Alignment explanation
Indices: 32885--33008 Score: 185
Period size: 38 Copynumber: 3.3 Consensus size: 38
32875 GGCACGAAGG
* * * *
32885 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
32923 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
**
32961 CCCGGATATTTTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
32999 CCCTGATATA
1 CCCGGATATA
33009 CATCGAATAT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 78 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.23
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:38563 original size:30 final size:30
Alignment explanation
Indices: 38542--38606 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
38532 TTTGTTTGTA
38542 ATTGGG-CTGAGGGTATTGGGTTTGTGGGT
1 ATTGGGTCTGAGGGTATTGGGTTTGTGGGT
* *
38571 ATTGGGTTTGTGGGTATTGGGTTTGTGGGT
1 ATTGGGTCTGAGGGTATTGGGTTTGTGGGT
38601 ATTGGG
1 ATTGGG
38607 CCGGACAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.09, C:0.02, G:0.48, T:0.42
Consensus pattern (30 bp):
ATTGGGTCTGAGGGTATTGGGTTTGTGGGT
Found at i:38572 original size:15 final size:15
Alignment explanation
Indices: 38552--38606 Score: 110
Period size: 15 Copynumber: 3.7 Consensus size: 15
38542 ATTGGGCTGA
38552 GGGTATTGGGTTTGT
1 GGGTATTGGGTTTGT
38567 GGGTATTGGGTTTGT
1 GGGTATTGGGTTTGT
38582 GGGTATTGGGTTTGT
1 GGGTATTGGGTTTGT
38597 GGGTATTGGG
1 GGGTATTGGG
38607 CCGGACAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.07, C:0.00, G:0.49, T:0.44
Consensus pattern (15 bp):
GGGTATTGGGTTTGT
Found at i:38576 original size:7 final size:7
Alignment explanation
Indices: 38552--38606 Score: 56
Period size: 7 Copynumber: 7.4 Consensus size: 7
38542 ATTGGGCTGA
38552 GGGTATT
1 GGGTATT
*
38559 GGGTTTGT
1 GGGTAT-T
38567 GGGTATT
1 GGGTATT
*
38574 GGGTTTGT
1 GGGTAT-T
38582 GGGTATT
1 GGGTATT
*
38589 GGGTTTGT
1 GGGTAT-T
38597 GGGTATT
1 GGGTATT
38604 GGG
1 GGG
38607 CCGGACAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 21 0.54
8 18 0.46
ACGTcount: A:0.07, C:0.00, G:0.49, T:0.44
Consensus pattern (7 bp):
GGGTATT
Found at i:38584 original size:8 final size:8
Alignment explanation
Indices: 38558--38600 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
38548 CTGAGGGTAT
38558 TGGGTTTG
1 TGGGTTTG
*
38566 TGGGTAT-
1 TGGGTTTG
38573 TGGGTTTG
1 TGGGTTTG
*
38581 TGGGTAT-
1 TGGGTTTG
38588 TGGGTTTG
1 TGGGTTTG
38596 TGGGT
1 TGGGT
38601 ATTGGGCCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.05, C:0.00, G:0.49, T:0.47
Consensus pattern (8 bp):
TGGGTTTG
Found at i:38843 original size:41 final size:41
Alignment explanation
Indices: 38786--38972 Score: 160
Period size: 44 Copynumber: 4.4 Consensus size: 41
38776 AATCCATTGT
* *
38786 ACTTCAGGGAAATAAGACTTGATGCGATCTGCTCTACTGCA
1 ACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACTGCA
*** *
38827 ACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCTACTGCA
1 ACTTCAGAGAGATAAGA-CT-TGA-TGCGATCTGCTCTACTGCA
* * * * *
38871 ACTTCAGAGAGATAGGA-TTGGTTTCTTCTATCTGCTCCACTGCA
1 ACTTCAGAGAGATAAGACTT-G---ATGCGATCTGCTCTACTGCA
* * * *
38915 ACTTCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTA
1 ACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACTGCA
*
38956 ACCTCAGAGAGATAAGA
1 ACTTCAGAGAGATAAGA
38973 TCTTTTATTT
Statistics
Matches: 115, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
41 44 0.38
42 4 0.03
43 3 0.03
44 62 0.54
45 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (41 bp):
ACTTCAGAGAGATAAGACTTGATGCGATCTGCTCTACTGCA
Found at i:38872 original size:44 final size:44
Alignment explanation
Indices: 38816--39013 Score: 172
Period size: 44 Copynumber: 4.6 Consensus size: 44
38806 GATGCGATCT
38816 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCC
1 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCC
* * * *
38860 GCTCTACTGCAACTTCAGAGAGATAGGAT-TG-GTTTCTTCTATCT
1 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATT-TT-AATCC
* * *** *
38904 GCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGA-TGCGATCT
1 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCC
* * * * * *
38945 ACTCTGCTGTAACCTCAGAGAGATAAGATCTTTTATTTTAATCC
1 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCC
* * *
38989 GCTCCACTGTAACTTCAGGGAGATA
1 GCTCTACTGCAACTTCAGAGAGATA
39014 GGATAGTGTC
Statistics
Matches: 120, Mismatches: 27, Indels: 14
0.75 0.17 0.09
Matches are distributed among these distances:
41 26 0.22
42 5 0.04
43 7 0.06
44 82 0.68
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCC
Found at i:39082 original size:128 final size:127
Alignment explanation
Indices: 38789--39183 Score: 514
Period size: 129 Copynumber: 3.1 Consensus size: 127
38779 CCATTGTACT
* * * *
38789 TCAGGGAAATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTT
1 TCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCT-T-ATTT
* * * * * * * *
38854 TAATCCGCTCTACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTATCTGCTCCACTGCAA-C
64 TAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTAGTATCTTCGATCTGCTCCGCTGTAATC
*
38917 TTCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTAACCTCAGAGAGATAAGATCTTTTATT
1 -TCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATC--TTATT
*
38982 TTAATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TAGTGTCTTCGATCTGCTCCGCTGTAATC
63 TTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTAGTATCTTCGATCTGCTCCGCTGTAATC
* *
39046 TCAGGGAGATAAGACCTGATGCGGTCTACTCTGCTGTAACTTCAGAGAGATAAGATC---TTTTA
1 TCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTTATTTTA
* * * *
39108 ATCCGCTCCATTGTAA-TCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATC
66 ATCCGCTCCACTGTAACT-TCAGGGAGATAGGATTAGTATCTTCGATCTGCTCCGCTGTAATC
39170 TCAGGGAGATAAGA
1 TCAGGGAGATAAGA
39184 TCTTAAATTC
Statistics
Matches: 240, Mismatches: 21, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
122 1 0.00
123 33 0.14
124 40 0.17
128 76 0.32
129 88 0.37
130 1 0.00
131 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (127 bp):
TCAGGGAGATAAGACTTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTTATTTTA
ATCCGCTCCACTGTAACTTCAGGGAGATAGGATTAGTATCTTCGATCTGCTCCGCTGTAATC
Done.