Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2637
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: 76479
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:2589 original size:13 final size:13
Alignment explanation
Indices: 2571--2595 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2561 ATTTGTCCAT
2571 GTATCGATACAAC
1 GTATCGATACAAC
2584 GTATCGATACAA
1 GTATCGATACAA
2596 AGCAACATGT
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:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAC
Found at i:3430 original size:253 final size:253
Alignment explanation
Indices: 2982--3490 Score: 950
Period size: 253 Copynumber: 2.0 Consensus size: 253
2972 AGGAAATTTC
2982 AAATTTTCAGTTTCGGGCAGCATATATGATCTTACCGAATTGTTCAAGCTTATAATCGATCATTC
1 AAATTTTCAGTTTCGGGCAGCATATATGATCTTACCGAATTGTTCAAGCTTATAATCGATCATTC
*
3047 TCTTGTATCAACATAGTTCAAAACCTGTAATCTGATATACATCTTCAAGAAACACATTAGAAAGT
66 TCTTGTATCAACATAGTTCAAAACCTGTAATCTGATACACATCTTCAAGAAACACATTAGAAAGT
*
3112 TCAAATATCAAAGTTTCGGTTTTTCTCCCCCTTAAACGATTATTTCCTCCTTTATAAAAAATTTT
131 TCAAATATCAAAGTTTCGATTTTTCTCCCCCTTAAACGATTATTTCCTCCTTTATAAAAAATTTT
*
3177 CCCTTTTAACAATTACCTTAAAATTTTGCCCC-TTTAATAATTATCTTCTCCTCCTTAA
196 CCCTTTTAACAATTACCTTAAAATTTT-CCCCATTTAATAATTATCTTCTCCCCCTTAA
*
3235 AAATTTTCA-TTTCCGGGTAGCATATATGATCTTACCGAATTGTTCAAGCTTATAATCGATCATT
1 AAATTTTCAGTTT-CGGGCAGCATATATGATCTTACCGAATTGTTCAAGCTTATAATCGATCATT
3299 CTCTTGTATCAACATAGTTCAAAACCTGTAATCTGATACACATCTTCAAGAAACACATTAGAAAG
65 CTCTTGTATCAACATAGTTCAAAACCTGTAATCTGATACACATCTTCAAGAAACACATTAGAAAG
3364 TTCAAATATCAAAGTTTCGATTTTTCTCCCCCTTAAACGATTATTTCCTCCTTTATAAAAAATTT
130 TTCAAATATCAAAGTTTCGATTTTTCTCCCCCTTAAACGATTATTTCCTCCTTTATAAAAAATTT
3429 TCCCTTTTAACAATTACCTTAAAATTTTCCCCATTTAATAATTATCTTCTCCCCCTTAA
195 TCCCTTTTAACAATTACCTTAAAATTTTCCCCATTTAATAATTATCTTCTCCCCCTTAA
3488 AAA
1 AAA
3491 ATTCTCCCCC
Statistics
Matches: 250, Mismatches: 4, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
252 7 0.03
253 243 0.97
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (253 bp):
AAATTTTCAGTTTCGGGCAGCATATATGATCTTACCGAATTGTTCAAGCTTATAATCGATCATTC
TCTTGTATCAACATAGTTCAAAACCTGTAATCTGATACACATCTTCAAGAAACACATTAGAAAGT
TCAAATATCAAAGTTTCGATTTTTCTCCCCCTTAAACGATTATTTCCTCCTTTATAAAAAATTTT
CCCTTTTAACAATTACCTTAAAATTTTCCCCATTTAATAATTATCTTCTCCCCCTTAA
Found at i:4757 original size:13 final size:13
Alignment explanation
Indices: 4739--4764 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4729 CAATTTGGTC
4739 ATGTATCGATACA
1 ATGTATCGATACA
4752 ATGTATCGATACA
1 ATGTATCGATACA
4765 TCTTGTATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4764 original size:34 final size:32
Alignment explanation
Indices: 4716--4784 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
4706 CGTTACAAGC
4716 CAATGTATCAATACAAT-TTGGTCATGTATCGATA
1 CAATGTATCAATAC-ATCTT-GT-ATGTATCGATA
*
4750 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCAATACATCTTGTATGTATCGATA
4782 CAA
1 CAA
4785 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 14 0.42
33 4 0.12
34 15 0.45
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (32 bp):
CAATGTATCAATACATCTTGTATGTATCGATA
Found at i:4882 original size:13 final size:13
Alignment explanation
Indices: 4864--4888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4854 TACAGTGGTC
4864 ATGTATCGATACA
1 ATGTATCGATACA
4877 ATGTATCGATAC
1 ATGTATCGATAC
4889 TGTGCATTAT
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:7371 original size:13 final size:13
Alignment explanation
Indices: 7341--7379 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
7331 TATAATTGCC
* *
7341 ATGTATCAATATA
1 ATGTATCGATACA
*
7354 GTGTATCGATACA
1 ATGTATCGATACA
7367 ATGTATCGATACA
1 ATGTATCGATACA
7380 GAGAATGCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11853 original size:79 final size:79
Alignment explanation
Indices: 11777--12280 Score: 595
Period size: 79 Copynumber: 6.4 Consensus size: 79
11767 AAAGGTGTTC
* * * * **
11777 TAGAAATAAAATCGAGGTTGGAGTATCCCCTTGGAAATAACAGGGTTGGATTATCCCTAATTAT-
1 TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATG
*** *
11841 AGAAAATTGGTGTTT
66 AG-AAATCAATATTT
* * * * *
11856 T-GAAAATAAAATC-AGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGTAGTATCCCCGATTG
1 TAG-AAATAAAACCGA-GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTA
11919 TGAGAAATCAATATTT
64 TGAGAAATCAATATTT
* * * * *
11935 TAGGAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCTCCGATTGTG
1 TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATG
12000 AGAAATCAATATTT
66 AGAAATCAATATTT
* * * * *
12014 TAGGAATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATG
1 TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATG
12079 AGAAATCAATATTT
66 AGAAATCAATATTT
* *
12093 TAGAAATAAAACCAAGGTTGGAGTATCCCCTCGGAAATAATGGGAG-TGGAGTATCCCCGATTAT
1 TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGGAAATAACGGG-GTTGGAGTATCCCCGATTAT
12157 GAGAAATCAATATTT
65 GAGAAATCAATATTT
* * * * *
12172 TAGGAATAAAGCCGGGGTTAGAGTATCCCCTCGGAAATAAC-GGGTTGGAGTATCCCCGATTGTG
1 TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATG
* * *
12236 AAAAATTAATGTTTT
66 AGAAATCAAT-ATTT
* *
12251 TAGAAATAAAATCGAAGTTGGAGTATCCCC
1 TAGAAATAAAACCGAGGTTGGAGTATCCCC
12281 GATTATAGAA
Statistics
Matches: 367, Mismatches: 50, Indels: 16
0.85 0.12 0.04
Matches are distributed among these distances:
77 1 0.00
78 30 0.08
79 332 0.90
80 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (79 bp):
TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATG
AGAAATCAATATTT
Found at i:11892 original size:26 final size:27
Alignment explanation
Indices: 11863--11914 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
11853 TTTTGAAAAT
11863 AAAAT-CAGGGTTGGAGTATCCCCGCG
1 AAAATACAGGGTTGGAGTATCCCCGCG
* *
11889 AAAATAACGGGGTTGTAGTATCCCCG
1 AAAAT-ACAGGGTTGGAGTATCCCCG
11915 ATTGTGAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
28 17 0.77
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (27 bp):
AAAATACAGGGTTGGAGTATCCCCGCG
Found at i:12211 original size:237 final size:237
Alignment explanation
Indices: 11777--12280 Score: 683
Period size: 237 Copynumber: 2.1 Consensus size: 237
11767 AAAGGTGTTC
* * * * *
11777 TAGAAATAAAATCGAGGTTGGAGTATCCCCTTGGAAATAACAGGGTTGGATTATCCCTAATTATA
1 TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATTATA
*** * * * *
11842 GAAAATTGGTGTTTTGAAAATAAAATCAGGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGTAG
66 GAAAATCAATATTTTGAAAATAAAACCAAGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAG
* *
11907 TATCCCCGATTGTGAGAAATCAATATTTTAGGAATAAAACCGGGGTTGGAGTATCCCCTCAGAAA
131 TATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAACCGGGGTTAGAGTATCCCCTCAGAAA
* *
11972 TAACGGGGTTGGAGTATCTCCGATTGTGAGAAATCAAT-ATTT
196 TAAC-GGGTTGGAGTATCCCCGATTGTGAAAAATCAATGATTT
* * * *
12014 TAGGAATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTAT-
1 TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATTATA
* * *
12078 GAGAAATCAATATTTT-AGAAATAAAACCAAGGTTGGAGTATCCCCTCGGAAATAATGGGAG-TG
66 GA-AAATCAATATTTTGA-AAATAAAACCAAGGTTGGAGTATCCCCGCGAAAATAACGGG-GTTG
* *
12141 GAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTAGAGTATCCCCTCGG
128 GAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAACCGGGGTTAGAGTATCCCCTCAG
* *
12206 AAATAACGGGTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTT
193 AAATAACGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGATTT
* *
12251 TAGAAATAAAATCGAAGTTGGAGTATCCCC
1 TAGAAATAAAACCGAGGTTGGAGTATCCCC
12281 GATTATAGAA
Statistics
Matches: 231, Mismatches: 32, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
236 33 0.14
237 197 0.85
238 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (237 bp):
TAGAAATAAAACCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCCAATTATA
GAAAATCAATATTTTGAAAATAAAACCAAGGTTGGAGTATCCCCGCGAAAATAACGGGGTTGGAG
TATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAACCGGGGTTAGAGTATCCCCTCAGAAA
TAACGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGATTT
Found at i:12394 original size:102 final size:103
Alignment explanation
Indices: 12213--12449 Score: 302
Period size: 102 Copynumber: 2.3 Consensus size: 103
12203 CGGAAATAAC
* * ** *
12213 GGGTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTTAGAAATAAAATCGAAGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTCGAGAAATAAAATCGAAGTTGGAATATC
*
12278 CCCGATTATAGAAAATTGGTATTTT-GAAAATAAAATC-G
66 CCCGATTATAGAAAATTAGTATTTTAG-AAATAAAA-CAG
* * * *
12316 GGGTTGGAGTATCCCCGATTTTGGAAAATTGGTGTTTCGA-AAATAAAATCGGAGTTGGAATATC
1 GGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTCGAGAAATAAAATCGAAGTTGGAATATC
* * *
12380 CCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACAG
66 CCCGATTATAGAAAATTAGTATTTTAGAAATAAAACAG
12418 GGGTTGGAGTA-CCCTCGATTATGAAAAATTGA
1 GGGTTGGAGTATCCC-CGATTATGAAAAATTGA
12450 GAAACTTAAC
Statistics
Matches: 116, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
101 4 0.03
102 77 0.66
103 35 0.30
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (103 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTCGAGAAATAAAATCGAAGTTGGAATATC
CCCGATTATAGAAAATTAGTATTTTAGAAATAAAACAG
Found at i:12446 original size:51 final size:52
Alignment explanation
Indices: 12213--12447 Score: 259
Period size: 51 Copynumber: 4.6 Consensus size: 52
12203 CGGAAATAAC
* *
12213 GGGTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTTAG-AAATAAAATCG
1 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTAGAAAATAAAATCG
** * *
12265 AAGTTGGAGTATCCCCGATTAT-AGAAAATTGGTATTTT-GAAAATAAAATCG
1 GGGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTAGAAAATAAAATCG
* * * *
12316 GGGTTGGAGTATCCCCGATTTTGGAAAATTGGTG-TTTCGAAAATAAAATCG
1 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAAATAAAATCG
* * * *
12367 GAGTTGGAATATCCCCGATTGTGGAAAATTAGTGTTTTAG-AAATAAAA-CAG
1 GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAAATAAAATC-G
12418 GGGTTGGAGTA-CCCTCGATTATGAAAAATT
1 GGGTTGGAGTATCCC-CGATTATGAAAAATT
12448 GAGAAACTTA
Statistics
Matches: 156, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
50 8 0.05
51 118 0.76
52 30 0.19
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (52 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAAATAAAATCG
Found at i:14787 original size:13 final size:13
Alignment explanation
Indices: 14771--14801 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
14761 ATACAATGAG
*
14771 CAATTTATCGATA
1 CAATGTATCGATA
14784 CAATGTATCGATA
1 CAATGTATCGATA
14797 CAATG
1 CAATG
14802 AGCAATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:14794 original size:33 final size:33
Alignment explanation
Indices: 14749--14823 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
14739 CGATACCTTG
*
14749 TAAAATGTATCGATACAATGAGCAATTTATCGA
1 TAAAATGTATCGATACAATGAGCAATGTATCGA
*
14782 TACAATGTATCGATACAATGAGCAATGTATCGA
1 TAAAATGTATCGATACAATGAGCAATGTATCGA
14815 TAAAATGTA
1 TAAAATGTA
14824 AAATGTATCG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (33 bp):
TAAAATGTATCGATACAATGAGCAATGTATCGA
Found at i:14807 original size:20 final size:19
Alignment explanation
Indices: 14732--14838 Score: 82
Period size: 20 Copynumber: 5.7 Consensus size: 19
14722 AAAATGCCTG
** *
14732 AATGTATCGATACCTTGTAA
1 AATGTATCGATACAATG-AC
14752 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
*
14772 AAT-T-T--AT-CGAT-AC
1 AATGTATCGATACAATGAC
14785 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
* *
14805 AATGTATCGATAAAATGTAA
1 AATGTATCGATACAATG-AC
14825 AATGTATCGATACA
1 AATGTATCGATACA
14839 TCTGGGTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
13 4 0.06
14 2 0.03
15 4 0.06
16 2 0.03
17 2 0.03
18 4 0.06
19 3 0.04
20 48 0.69
21 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:14895 original size:13 final size:13
Alignment explanation
Indices: 14877--14902 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14867 ACAAAGATCG
14877 ATGTATCGATACA
1 ATGTATCGATACA
14890 ATGTATCGATACA
1 ATGTATCGATACA
14903 TTTAATAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:16826 original size:13 final size:13
Alignment explanation
Indices: 16808--16832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16798 CATAAAGTGT
16808 TGTATCGATACAA
1 TGTATCGATACAA
16821 TGTATCGATACA
1 TGTATCGATACA
16833 TATTTTTTTG
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:16830 original size:33 final size:33
Alignment explanation
Indices: 16788--16854 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
16778 TTCAACGATT
16788 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
16821 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
16854 T
1 T
16855 TTAAGCTACT
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:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:16913 original size:13 final size:13
Alignment explanation
Indices: 16895--16919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16885 ATCACTTAAA
16895 TGTATCGATACAT
1 TGTATCGATACAT
16908 TGTATCGATACA
1 TGTATCGATACA
16920 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16971 original size:65 final size:67
Alignment explanation
Indices: 16894--17021 Score: 190
Period size: 69 Copynumber: 1.9 Consensus size: 67
16884 CATCACTTAA
**
16894 ATGTATCGATACA-T-TGTATCGATACACTGA-TCTTTGTATCGATACATGCAGGCAAATTTGCC
1 ATGTATCGATACATTATGTATCGATACACT-ATTCAATGTATCGATACATGCAGGCAAATTTGCC
16956 TGC
65 TGC
16959 ATGTATCGATACATTTTATGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 ATGTATCGATACA--TTATGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
17022 TCATATTTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
65 13 0.23
68 2 0.04
69 41 0.73
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (67 bp):
ATGTATCGATACATTATGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCT
GC
Found at i:16981 original size:17 final size:19
Alignment explanation
Indices: 16959--17009 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 19
16949 ATTTGCCTGC
*
16959 ATGTATCGATACAT-TT-T
1 ATGTATCGATACATATTCA
16976 ATGTATCGATACACTATTCA
1 ATGTATCGATACA-TATTCA
16996 ATGTATCGATACAT
1 ATGTATCGATACAT
17010 GCAGGCAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 13 0.43
18 1 0.03
19 3 0.10
20 13 0.43
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATATTCA
Found at i:21551 original size:13 final size:13
Alignment explanation
Indices: 21510--21558 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
21500 CGTTACAAGC
21510 CAATGTATCGATA
1 CAATGTATCGATA
*
21523 CAAT-T-T-GGT-
1 CAATGTATCGATA
21532 C-ATGTATCGATA
1 CAATGTATCGATA
21544 CAATGTATCGATA
1 CAATGTATCGATA
21557 CA
1 CA
21559 TCTTGTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 3 0.10
11 3 0.10
12 2 0.07
13 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:21553 original size:34 final size:32
Alignment explanation
Indices: 21510--21578 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
21500 CGTTACAAGC
21510 CAATGTATCGATACAAT-TTGGTCATGTATCGATA
1 CAATGTATCGATAC-ATCTT-GT-ATGTATCGATA
21544 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
21576 CAA
1 CAA
21579 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 14 0.41
33 4 0.12
34 16 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:21676 original size:13 final size:13
Alignment explanation
Indices: 21658--21682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21648 TATAGTGGTC
21658 ATGTATCGATACA
1 ATGTATCGATACA
21671 ATGTATCGATAC
1 ATGTATCGATAC
21683 TGTGCATTAT
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:22712 original size:15 final size:15
Alignment explanation
Indices: 22676--22705 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
22666 CGAGGGATGA
22676 ACCCCTCTTTGGTTT
1 ACCCCTCTTTGGTTT
22691 ACCCCTCTTTGGTTT
1 ACCCCTCTTTGGTTT
22706 CTCCCTCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.33, G:0.13, T:0.47
Consensus pattern (15 bp):
ACCCCTCTTTGGTTT
Found at i:23681 original size:13 final size:13
Alignment explanation
Indices: 23663--23704 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
23653 AAATAGTACC
23663 CAATGTATCGATA
1 CAATGTATCGATA
*
23676 CAATGTATCGAAA
1 CAATGTATCGATA
*
23689 CAATGTATCAATA
1 CAATGTATCGATA
23702 CAA
1 CAA
23705 GGAATGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:28348 original size:35 final size:35
Alignment explanation
Indices: 28307--28411 Score: 192
Period size: 35 Copynumber: 3.0 Consensus size: 35
28297 GACACTTGCC
*
28307 TTCTTCGGAGGTTCTTGTAAGTGTGCATATTTAAT
1 TTCTTCGGAGGTTCTTGTACGTGTGCATATTTAAT
*
28342 TTCTTCGGAGGTTCTTGTACGTGTGTATATTTAAT
1 TTCTTCGGAGGTTCTTGTACGTGTGCATATTTAAT
28377 TTCTTCGGAGGTTCTTGTACGTGTGCATATTTAAT
1 TTCTTCGGAGGTTCTTGTACGTGTGCATATTTAAT
28412 CTTCATTTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.18, C:0.12, G:0.23, T:0.47
Consensus pattern (35 bp):
TTCTTCGGAGGTTCTTGTACGTGTGCATATTTAAT
Found at i:29955 original size:13 final size:13
Alignment explanation
Indices: 29937--29967 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29927 ACATTTCTTC
29937 ATGTATCGATACA
1 ATGTATCGATACA
29950 ATGTATCGATACA
1 ATGTATCGATACA
*
29963 TTGTA
1 ATGTA
29968 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:29955 original size:33 final size:33
Alignment explanation
Indices: 29917--29983 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
29907 ATTACAAACT
29917 ATGTATCAATACATT-T-CTTCATGTATCGATACA
1 ATGTATCAATACATTGTAC--CATGTATCGATACA
*
29950 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCAATACATTGTACCATGTATCGATACA
29983 A
1 A
29984 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (33 bp):
ATGTATCAATACATTGTACCATGTATCGATACA
Found at i:30071 original size:13 final size:13
Alignment explanation
Indices: 30053--30079 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30043 TACAATGAAC
30053 ATGTATCGATACA
1 ATGTATCGATACA
30066 ATGTATCGATACA
1 ATGTATCGATACA
30079 A
1 A
30080 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:30094 original size:33 final size:32
Alignment explanation
Indices: 30034--30098 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
30024 TAATTTGTCC
*
30034 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
30066 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
30099 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:31776 original size:20 final size:20
Alignment explanation
Indices: 31753--31790 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31743 TCATGTATCG
31753 GTACAATGTATCGATACATT
1 GTACAATGTATCGATACATT
*
31773 GTACCATGTATCGATACA
1 GTACAATGTATCGATACA
31791 AATAGTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (20 bp):
GTACAATGTATCGATACATT
Found at i:31781 original size:33 final size:33
Alignment explanation
Indices: 31725--31791 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
31715 GTTACAAGCT
* *
31725 ATGTATCGATACAATTCTTCATGTATCGGTACA
1 ATGTATCGATACAATTCTCCATGTATCGATACA
*
31758 ATGTATCGATAC-ATTGTACCATGTATCGATACA
1 ATGTATCGATACAATTCT-CCATGTATCGATACA
31791 A
1 A
31792 ATAGTGATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
ATGTATCGATACAATTCTCCATGTATCGATACA
Found at i:31846 original size:21 final size:21
Alignment explanation
Indices: 31820--31896 Score: 122
Period size: 21 Copynumber: 3.8 Consensus size: 21
31810 CTGCCAGTTT
31820 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGTC
31841 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAATTTGTC
**
31862 CATGTATCGATACAA--TGAA
1 CATGTATCGATACAATTTGTC
31881 CATGTATCGATACAAT
1 CATGTATCGATACAAT
31897 GTATCAATAC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
19 17 0.32
21 36 0.68
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
CATGTATCGATACAATTTGTC
Found at i:31926 original size:33 final size:32
Alignment explanation
Indices: 31863--31927 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
31853 CAATTTGTCC
* *
31863 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCAATACAAAGAACATGTATCGATACA
* *
31895 ATGTATCAATACAAAGTAGCATGTATTGATACA
1 ATGTATCAATACAAAG-AACATGTATCGATACA
31928 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (32 bp):
ATGTATCAATACAAAGAACATGTATCGATACA
Found at i:34396 original size:13 final size:13
Alignment explanation
Indices: 34378--34419 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
34368 AAATAGTACC
34378 CAATGTATCGATA
1 CAATGTATCGATA
*
34391 CAATGTATCGAAA
1 CAATGTATCGATA
*
34404 CAATGTATCAATA
1 CAATGTATCGATA
34417 CAA
1 CAA
34420 GGAATGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:40697 original size:13 final size:13
Alignment explanation
Indices: 40679--40704 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40669 TACACACAAG
40679 ATGTATCGATACA
1 ATGTATCGATACA
40692 ATGTATCGATACA
1 ATGTATCGATACA
40705 TCCCAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:40721 original size:33 final size:32
Alignment explanation
Indices: 40661--40724 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
40651 CTTAACTGTT
*
40661 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
40693 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
40725 TTGTCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:47984 original size:13 final size:13
Alignment explanation
Indices: 47961--47999 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
47951 ACAGCATTCT
*
47961 CTGTATTGATACA
1 CTGTATCGATACA
*
47974 TTGTATCGATACA
1 CTGTATCGATACA
47987 CTGTATCGATACA
1 CTGTATCGATACA
48000 AGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:48463 original size:20 final size:21
Alignment explanation
Indices: 48423--48474 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
48413 CTCCTAGGCA
* *
48423 GCACCCACCAGGTCGCGACC-G
1 GCACCC-CCAGGTCACAACCGG
48444 GCACCCCCAGGTCACAACCGG
1 GCACCCCCAGGTCACAACCGG
48465 GCAGCCCCCA
1 GCA-CCCCCA
48475 CACTAGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 11 0.41
21 10 0.37
22 6 0.22
ACGTcount: A:0.21, C:0.50, G:0.25, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCACAACCGG
Found at i:50442 original size:20 final size:20
Alignment explanation
Indices: 50411--50467 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
50401 GTCAAAACCC
*
50411 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
50431 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
50451 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
50468 TGACCAAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:50557 original size:13 final size:13
Alignment explanation
Indices: 50539--50563 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50529 ACACACAGTA
50539 TGTATCGATACAT
1 TGTATCGATACAT
50552 TGTATCGATACA
1 TGTATCGATACA
50564 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:50560 original size:32 final size:33
Alignment explanation
Indices: 50519--50586 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
50509 GTAGCCAAAT
**
50519 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
50551 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
50584 TTG
1 TTG
50587 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:51366 original size:35 final size:35
Alignment explanation
Indices: 51320--51518 Score: 215
Period size: 35 Copynumber: 5.7 Consensus size: 35
51310 CTTTCACCTA
* *
51320 TTTTCATCATCATTTGACCATATCTGGTCAAGCTC
1 TTTTCATCATCATTTGACTATATCTGGTCAAACTC
* * * *
51355 TTTTCATCATCATTTGACCGA-ATATGGTCAAGCTT
1 TTTTCATCATCATTTGA-CTATATCTGGTCAAACTC
** *
51390 TTTTTGTCATCATTTGACTATATCAGGTCAAACTC
1 TTTTCATCATCATTTGACTATATCTGGTCAAACTC
* * *
51425 TTTTCATCATCCTTTGGCTATATCCGGTCAAACTC
1 TTTTCATCATCATTTGACTATATCTGGTCAAACTC
* *
51460 TTTTCATCATCCTTT-AGCTATATCTGGTCAAACTT
1 TTTTCATCATCATTTGA-CTATATCTGGTCAAACTC
*
51495 TTTTCATCATCGTTT-AGCTATATC
1 TTTTCATCATCATTTGA-CTATATC
51519 GGTTACCACC
Statistics
Matches: 142, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
34 2 0.01
35 138 0.97
36 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (35 bp):
TTTTCATCATCATTTGACTATATCTGGTCAAACTC
Found at i:51505 original size:105 final size:105
Alignment explanation
Indices: 51320--51518 Score: 249
Period size: 105 Copynumber: 1.9 Consensus size: 105
51310 CTTTCACCTA
* *
51320 TTTTCATCATCATTTGACCATATCTGGTCAAGCTCTTTTCATCATCATTTGACCGAATATGGTCA
1 TTTTCATCATCATTTGACCATATCCGGTCAAACTCTTTTCATCATCATTTGACCGAATATGGTCA
* **
51385 AGCTTTTTTTGTCATCATTT-GACTATATCAGGTCAAACTC
66 AACTTTTTTCATCATCATTTAG-CTATATCAGGTCAAACTC
* * * * * * *
51425 TTTTCATCATCCTTTGGCTATATCCGGTCAAACTCTTTTCATCATCCTTT-AGCTATATCTGGTC
1 TTTTCATCATCATTTGACCATATCCGGTCAAACTCTTTTCATCATCATTTGACCGA-ATATGGTC
*
51489 AAACTTTTTTCATCATCGTTTAGCTATATC
65 AAACTTTTTTCATCATCATTTAGCTATATC
51519 GGTTACCACC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
104 3 0.04
105 75 0.95
106 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (105 bp):
TTTTCATCATCATTTGACCATATCCGGTCAAACTCTTTTCATCATCATTTGACCGAATATGGTCA
AACTTTTTTCATCATCATTTAGCTATATCAGGTCAAACTC
Found at i:51896 original size:43 final size:43
Alignment explanation
Indices: 51755--51897 Score: 119
Period size: 43 Copynumber: 3.3 Consensus size: 43
51745 TCGGTTGACC
* * * * * *
51755 TTTTTATCCGTTGTTTCCCTATCAGCTTAGTCCTGAGTATATT
1 TTTTTATCCTTTGTTTACTTATCAACTTAGTCCCGAGTAAATT
* * * * * * * *
51798 CTTTCATCCTTTGTTAACTTATC-AGTTCAATCTCGA-TCAACT
1 TTTTTATCCTTTGTTTACTTATCAACTT-AGTCCCGAGTAAATT
* *
51840 TTTATATCCTTTGTTTACTTATCAACTTAGTCCCAAGTAAATT
1 TTTTTATCCTTTGTTTACTTATCAACTTAGTCCCGAGTAAATT
51883 TTTTTATCCTTTGTT
1 TTTTTATCCTTTGTT
51898 GACTAACGGT
Statistics
Matches: 72, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
42 29 0.40
43 43 0.60
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (43 bp):
TTTTTATCCTTTGTTTACTTATCAACTTAGTCCCGAGTAAATT
Found at i:52116 original size:43 final size:41
Alignment explanation
Indices: 51973--52125 Score: 128
Period size: 43 Copynumber: 3.6 Consensus size: 41
51963 CCCCAATCAA
* * * *
51973 CTTTTATATCTTTTGTTTACCTATCAACTTAGTCCTGAATAAAT
1 CTTTT-TATCTTTTGTTGACTTGTCAACTTAGT-CTG-GTAAAT
** * * * *
52017 CTTTTTATCTTTTGTTGACTTGTC-GGTTCAATCCCGGTCAAC
1 CTTTTTATCTTTTGTTGACTTGTCAACTT-AGT-CTGGTAAAT
* *
52059 CTTTTTATCCTTTGTTTACTTGTCAACTTAGTCTTAGGTAAAT
1 CTTTTTATCTTTTGTTGACTTGTCAACTTAGTC-T-GGTAAAT
52102 CTTTTTATCTTTTGTTGACTTGTC
1 CTTTTTATCTTTTGTTGACTTGTC
52126 GAGCCAATCC
Statistics
Matches: 85, Mismatches: 20, Indels: 9
0.75 0.18 0.08
Matches are distributed among these distances:
41 1 0.01
42 29 0.34
43 50 0.59
44 5 0.06
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (41 bp):
CTTTTTATCTTTTGTTGACTTGTCAACTTAGTCTGGTAAAT
Found at i:52191 original size:85 final size:85
Alignment explanation
Indices: 51932--52205 Score: 250
Period size: 85 Copynumber: 3.2 Consensus size: 85
51922 CTTTCTGATC
* * * * ** * * * * *
51932 CTTTCTATCCTTTGTTGGCTTATCGGTTTAACCCCAATCAACTTTTATATCTTTTGTTTACCTAT
1 CTTTTTATCTTTTGTTGACTTGTCGGTCCAATCCCAGTCAACCTTTATATCCTTTGTTTACCTGT
*
51997 CAACTTAGTCCTGAA-TAAAT
66 CAACTTAGTCC-CAAGTAAAT
* * * *
52017 CTTTTTATCTTTTGTTGACTTGTCGGTTCAATCCCGGTCAACCTTTTTATCCTTTGTTTACTTGT
1 CTTTTTATCTTTTGTTGACTTGTCGGTCCAATCCCAGTCAACCTTTATATCCTTTGTTTACCTGT
** *
52082 CAACTTAGTCTTAGGTAAAT
66 CAACTTAGTCCCAAGTAAAT
* * *
52102 CTTTTTATCTTTTGTTGACTTGTCGAG-CCAATCCTAGTGAA-CTTTGATCTCCTTTGTTTACCT
1 CTTTTTATCTTTTGTTGACTTGTCG-GTCCAATCCCAGTCAACCTTT-ATATCCTTTGTTTACCT
* *
52165 GTTAGCTTAGTCCCAAGT-AAT
64 GTCAACTTAGTCCCAAGTAAAT
* *
52186 CCTTTTCATCATTTGTTGAC
1 -CTTTTTATCTTTTGTTGAC
52206 CTAGCTACTT
Statistics
Matches: 155, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
84 8 0.05
85 146 0.94
86 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.46
Consensus pattern (85 bp):
CTTTTTATCTTTTGTTGACTTGTCGGTCCAATCCCAGTCAACCTTTATATCCTTTGTTTACCTGT
CAACTTAGTCCCAAGTAAAT
Found at i:53331 original size:13 final size:13
Alignment explanation
Indices: 53313--53337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53303 GCATAAGTGT
53313 TGTATCGATACAA
1 TGTATCGATACAA
53326 TGTATCGATACA
1 TGTATCGATACA
53338 GAGCTACCCT
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:57175 original size:168 final size:165
Alignment explanation
Indices: 56981--57369 Score: 471
Period size: 168 Copynumber: 2.3 Consensus size: 165
56971 TTTCATTGAC
* * *** *
56981 TTAAAACTTTTAAAATTCATCAAATATTATCATTTGACTCACATTAAATTTGTTTTGAAAAATTC
1 TTAAAATTTTTAAAATTCATCAAATATTATCATTTGACTCAAATTAAATCAATTTTAAAAAATTC
* * * *
57046 ATTTATTTTCATGAGTTTTAAATTTTTTCTTTGAAATT-TTTCTATTTTTTAAAAAACTC-AGTT
66 ATTCATTTTCATGAGTTTTAAATTTTTTATTTGAAATTCTCT-TA-TTTTCAAAAAA-TCGAG-T
57109 TTTCTATTCTATAAACT-TTTTCA-AGAAAATTTTCATCAAT
127 TTTCTATTCTATAAA-TATTTTCAGAG-AAATTTT-ATCAAT
* *
57149 TTTAAATTTTTAAAATTCATCAAATATTATCATTTGATTCAAATTAAATCAATTTTAAAAAATTC
1 TTAAAATTTTTAAAATTCATCAAATATTATCATTTGACTCAAATTAAATCAATTTTAAAAAATTC
*
57214 ATTCATTTTCATGAGTTTTTAATTTTTTATTTGAAATTCTCTTATTTTCAAAAAATCGAGTTTTC
66 ATTCATTTTCATGAGTTTTAAATTTTTTATTTGAAATTCTCTTATTTTCAAAAAATCGAGTTTTC
* * * *
57279 TATTCTATTAATATTTTCAGAGAGATTTTTTCAGT
131 TATTCTATAAATATTTTCAGAGAAATTTTATCAAT
* * * ** **
57314 TTAAAATTTTTAAAATTCATCTAATATTGTTATTAAACTCTCATTAAATCAATTTT
1 TTAAAATTTTTAAAATTCATCAAATATTATCATTTGACTCAAATTAAATCAATTTT
57370 GCAAAACTCA
Statistics
Matches: 191, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
165 52 0.27
166 29 0.15
167 14 0.07
168 94 0.49
169 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (165 bp):
TTAAAATTTTTAAAATTCATCAAATATTATCATTTGACTCAAATTAAATCAATTTTAAAAAATTC
ATTCATTTTCATGAGTTTTAAATTTTTTATTTGAAATTCTCTTATTTTCAAAAAATCGAGTTTTC
TATTCTATAAATATTTTCAGAGAAATTTTATCAAT
Found at i:58255 original size:13 final size:13
Alignment explanation
Indices: 58237--58262 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58227 CAATTTTTTG
58237 TGTATCGATACAT
1 TGTATCGATACAT
58250 TGTATCGATACAT
1 TGTATCGATACAT
58263 ACTTGCTGTA
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:68367 original size:21 final size:21
Alignment explanation
Indices: 68322--68368 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
68312 TAAAAAAATC
* *
68322 AAAATTATCAAAATTATCTTA
1 AAAATTATAAAAATTATCTAA
68343 AAAATTA-AAAAATTATCTCAA
1 AAAATTATAAAAATTATCT-AA
68364 AAAAT
1 AAAAT
68369 ATTAAAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTATAAAAATTATCTAA
Found at i:68892 original size:18 final size:17
Alignment explanation
Indices: 68869--68902 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
68859 CTGACATAAA
68869 TATATAAATATTAAAAAT
1 TATATAAA-ATTAAAAAT
*
68887 TATATATAATTAAAAA
1 TATATAAAATTAAAAA
68903 AATTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATATAAAATTAAAAAT
Found at i:69326 original size:24 final size:25
Alignment explanation
Indices: 69299--69352 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
69289 TAATGATACT
*
69299 ATATATTAT-ATTATT-AAAATATAA
1 ATAT-TTATGATTATTCAAAATAGAA
*
69323 ATATTTATGCTTATTCAAAATAGAA
1 ATATTTATGATTATTCAAAATAGAA
69348 ATATT
1 ATATT
69353 ATTTAAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 4 0.15
24 9 0.35
25 13 0.50
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (25 bp):
ATATTTATGATTATTCAAAATAGAA
Found at i:69377 original size:22 final size:21
Alignment explanation
Indices: 69347--69403 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 21
69337 TCAAAATAGA
*
69347 AATATTATTTAAGTAATTTTAT
1 AATAATATTTAA-TAATTTTAT
69369 AATAATATTTAAT-ATTTT-T
1 AATAATATTTAATAATTTTAT
*
69388 AA-AATTTTTAA-AATTT
1 AATAATATTTAATAATTT
69404 AAAACTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 12 0.38
19 3 0.09
20 5 0.16
21 1 0.03
22 11 0.34
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AATAATATTTAATAATTTTAT
Found at i:69394 original size:9 final size:9
Alignment explanation
Indices: 69361--69403 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
69351 TTATTTAAGT
69361 AATTTTATAA
1 AATTTT-TAA
*
69371 TAATATTTAA
1 -AATTTTTAA
*
69381 TATTTTTAA
1 AATTTTTAA
69390 AATTTTTAA
1 AATTTTTAA
69399 AATTT
1 AATTT
69404 AAAACTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 20 0.71
10 3 0.11
11 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTTTAA
Found at i:71431 original size:20 final size:20
Alignment explanation
Indices: 71393--71432 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
71383 ATATCATATT
* * *
71393 TTAAATTAATTTTACAAATA
1 TTAAATAAATTATAAAAATA
71413 TTAAATAAATTATAAAAATA
1 TTAAATAAATTATAAAAATA
71433 AAAATATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAATAAATTATAAAAATA
Found at i:71586 original size:22 final size:22
Alignment explanation
Indices: 71545--71586 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
71535 CATTTTATTA
**
71545 TAATTTAAATTATTTTTAAAAT
1 TAATTTAAATTATTAATAAAAT
71567 TAATTTAAATTATTAATAAA
1 TAATTTAAATTATTAATAAA
71587 TTATTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTTAAATTATTAATAAAAT
Found at i:72440 original size:3 final size:3
Alignment explanation
Indices: 72432--72464 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
72422 TCATAAAATA
72432 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
72465 GTGTTCTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:72725 original size:16 final size:18
Alignment explanation
Indices: 72692--72761 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 18
72682 TTCATAATAT
72692 TATTAAAATATTATTTTA
1 TATTAAAATATTATTTTA
*
72710 TATTAATAT-TTA-TTTA
1 TATTAAAATATTATTTTA
* * * *
72726 TTTTATAAT-TAAATTTA
1 TATTAAAATATTATTTTA
72743 -ATTAAAATATATATTTTA
1 TATTAAAATAT-TATTTTA
72761 T
1 T
72762 TTTTAATTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
16 18 0.46
17 8 0.21
18 13 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTAAAATATTATTTTA
Found at i:72726 original size:21 final size:21
Alignment explanation
Indices: 72702--72742 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
72692 TATTAAAATA
72702 TTATTTTAT-ATTAATATTTAT
1 TTATTTTATAATTAA-ATTTAT
72723 TTATTTTATAATTAAATTTA
1 TTATTTTATAATTAAATTTA
72743 ATTAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTTTATAATTAAATTTAT
Done.