Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014084.1 Kokia drynarioides strain JFW-HI SEQ_129115, whole genome shotgun sequence
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: 123658
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:31 original size:13 final size:13
Alignment explanation
Indices: 15--48 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5 TTAATATTTA
15 AAATTAAAAGCCC
1 AAATTAAAAGCCC
*
28 AAATTAAAAGTCC
1 AAATTAAAAGCCC
*
41 AAAATAAA
1 AAATTAAA
49 TACAAAGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (13 bp):
AAATTAAAAGCCC
Found at i:699 original size:9 final size:9
Alignment explanation
Indices: 682--753 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
672 TCAAAATGTC
*
682 ATTAATAAT
1 ATTATTAAT
691 ATTATTAATT
1 ATTATTAA-T
701 ATTATGGTAAT
1 ATTAT--TAAT
712 A--A-TAAT
1 ATTATTAAT
*
718 ATTATTATT
1 ATTATTAAT
*
727 ATTACTAAT
1 ATTATTAAT
*
736 ATTGTTAAT
1 ATTATTAAT
*
745 AATATTAAT
1 ATTATTAAT
754 GACAATAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
6 5 0.10
8 1 0.02
9 32 0.65
10 6 0.12
11 2 0.04
12 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (9 bp):
ATTATTAAT
Found at i:699 original size:12 final size:12
Alignment explanation
Indices: 682--805 Score: 78
Period size: 12 Copynumber: 10.6 Consensus size: 12
672 TCAAAATGTC
682 ATTAATAATATT
1 ATTAATAATATT
694 ATTAAT--TATT
1 ATTAATAATATT
*
704 ATGGTAATAATAAT
1 AT--TAATAATATT
718 ATT-AT--TATT
1 ATTAATAATATT
*
727 ATTACTAATATT
1 ATTAATAATATT
*
739 GTTAATAATATT
1 ATTAATAATATT
* * * *
751 AATGACAATAAT
1 ATTAATAATATT
* *
763 AATAATAACATT
1 ATTAATAATATT
* *
775 AATAATAACATT
1 ATTAATAATATT
*
787 AATAATAATATT
1 ATTAATAATATT
*
799 AATAATA
1 ATTAATA
806 GCATTAATTA
Statistics
Matches: 90, Mismatches: 15, Indels: 14
0.76 0.13 0.12
Matches are distributed among these distances:
9 6 0.07
10 7 0.08
11 2 0.02
12 70 0.78
14 5 0.06
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (12 bp):
ATTAATAATATT
Found at i:735 original size:24 final size:26
Alignment explanation
Indices: 684--736 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
674 AAAATGTCAT
*
684 TAATAATATTATTAATTATTATGGTAA
1 TAATAATATTATTAATTATTA-GCTAA
711 TAATAATATTATT-ATTATTA-CTAA
1 TAATAATATTATTAATTATTAGCTAA
735 TA
1 TA
737 TTGTTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 5 0.20
26 7 0.28
27 13 0.52
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (26 bp):
TAATAATATTATTAATTATTAGCTAA
Found at i:747 original size:3 final size:3
Alignment explanation
Indices: 741--805 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
731 CTAATATTGT
* * * * * * *
741 TAA TAA TAT TAA TGA CAA TAA TAA TAA TAA CAT TAA TAA TAA CAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
789 TAA TAA TAT TAA TAA TA
1 TAA TAA TAA TAA TAA TA
806 GCATTAATTA
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:804 original size:24 final size:24
Alignment explanation
Indices: 741--813 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
731 CTAATATTGT
* * * *
741 TAATAATATTAATGACAATAATAA
1 TAATAATATTAATAATAACATTAA
*
765 TAATAACATTAATAATAACATTAA
1 TAATAATATTAATAATAACATTAA
*
789 TAATAATATTAATAATAGCATTAA
1 TAATAATATTAATAATAACATTAA
813 T
1 T
814 TAAAAATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (24 bp):
TAATAATATTAATAATAACATTAA
Found at i:811 original size:12 final size:12
Alignment explanation
Indices: 762--813 Score: 86
Period size: 12 Copynumber: 4.3 Consensus size: 12
752 ATGACAATAA
762 TAATAATAACAT
1 TAATAATAACAT
774 TAATAATAACAT
1 TAATAATAACAT
*
786 TAATAATAATAT
1 TAATAATAACAT
*
798 TAATAATAGCAT
1 TAATAATAACAT
810 TAAT
1 TAAT
814 TAAAAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (12 bp):
TAATAATAACAT
Found at i:1960 original size:29 final size:29
Alignment explanation
Indices: 1867--2127 Score: 196
Period size: 29 Copynumber: 8.8 Consensus size: 29
1857 GAGGTCCCTA
*
1867 AACTGTCCGAAAATTACCATTTTACCCATCG
1 AACT-TCCAAAAATTACCATTTTACCC-TCG
* * * **
1898 AACTTCTACAAA-TCCCATTTTTAACCCTAA
1 AACTTCCAAAAATTACCA-TTTT-ACCCTCG
*
1928 AACTTCCAAAAATTACCATTTCACCCTCG
1 AACTTCCAAAAATTACCATTTTACCCTCG
1957 AACTTCCAAAAA-T-CCATTTTTGACCC-CG
1 AACTTCCAAAAATTACCA-TTTT-ACCCTCG
**
1985 AAACTTCCAAAAATTACCATTTTACCCTAA
1 -AACTTCCAAAAATTACCATTTTACCCTCG
* * *
2015 AACTTCCAAGAA-TCCCATTTTTTA-CCTCAA
1 AACTTCCAAAAATTACCA--TTTTACCCTC-G
2045 AACTTCCAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATTACCATTTTACCCTCG
* * *
2074 AACTTCCAAGAA-TCCCATTTTTGA-CTTCG
1 AACTTCCAAAAATTACCA-TTTT-ACCCTCG
**
2103 AAACTTTAAAAAATTACCATTTTAC
1 -AACTTCCAAAAATTACCATTTTAC
2128 TCCCGAATGT
Statistics
Matches: 183, Mismatches: 28, Indels: 39
0.73 0.11 0.16
Matches are distributed among these distances:
27 3 0.02
28 14 0.08
29 80 0.44
30 63 0.34
31 23 0.13
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATTACCATTTTACCCTCG
Found at i:2048 original size:117 final size:119
Alignment explanation
Indices: 1866--2127 Score: 370
Period size: 117 Copynumber: 2.2 Consensus size: 119
1856 AGAGGTCCCT
* ** *
1866 AAACTGTCCGAAAATTACCATTTTACCCATCGAACTTCTACAAATCCCATTTTTAACCCTAAAAC
1 AAACT-TCCAAAAATTACCATTTTACCCATAAAACTTCCACAAATCCCATTTTTAACCCTAAAAC
1931 TTCCAAAAATTACCATTTCACCCTCGAACTTCCAAAAAT-CCATTTTTGACCCCG
65 TTCCAAAAATTACCATTTCACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
*
1985 AAACTTCCAAAAATTACCATTTTACCC-TAAAACTTCCA-AGAATCCCATTTTTTA-CCTCAAAA
1 AAACTTCCAAAAATTACCATTTTACCCATAAAACTTCCACA-AATCCCATTTTTAACCCT-AAAA
* * **
2047 CTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAGAATCCCATTTTTGACTTCG
64 CTTCCAAAAATTACCATTTCACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
**
2103 AAACTTTAAAAAATTACCATTTTAC
1 AAACTTCCAAAAATTACCATTTTAC
2128 TCCCGAATGT
Statistics
Matches: 129, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
116 4 0.03
117 63 0.49
118 57 0.44
119 5 0.04
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (119 bp):
AAACTTCCAAAAATTACCATTTTACCCATAAAACTTCCACAAATCCCATTTTTAACCCTAAAACT
TCCAAAAATTACCATTTCACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:2062 original size:59 final size:59
Alignment explanation
Indices: 1866--2191 Score: 353
Period size: 59 Copynumber: 5.5 Consensus size: 59
1856 AGAGGTCCCT
* * *
1866 AAACTGTCCGAAAATTACCATTTTACCCATCGAACTTCTACA-AATCCCATTTTTAACC-CTA
1 AAACT-TCCAAAAATTACCATTTTACCC-TCGAACTTCCA-AGAATCCCATTTTTGACCTC-A
* * * *
1927 AAACTTCCAAAAATTACCATTTCACCCTCGAACTTCCAAAAAT-CCATTTTTGACCCCG
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAGAATCCCATTTTTGACCTCA
** *
1985 AAACTTCCAAAAATTACCATTTTACCCTAAAACTTCCAAGAATCCCATTTTTTACCTCA
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAGAATCCCATTTTTGACCTCA
* *
2044 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAGAATCCCATTTTTGACTTCG
1 AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAGAATCCCATTTTTGACCTCA
** * * * * *
2103 AAACTTTAAAAAATTACCATTTTACTCC-CGAATGTTCGAAGACT-CCATTTTCGACCTCG
1 AAACTTCCAAAAATTACCATTTTAC-CCTCGAA-CTTCCAAGAATCCCATTTTTGACCTCA
*
2162 AAAC-TCTC-AAAATTACCCTTTTACCC-CGAA
1 AAACTTC-CAAAAATTACCATTTTACCCTCGAA
2192 TATTCCCAAA
Statistics
Matches: 232, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
57 6 0.03
58 67 0.29
59 124 0.53
60 30 0.13
61 5 0.02
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAGAATCCCATTTTTGACCTCA
Found at i:2210 original size:118 final size:116
Alignment explanation
Indices: 1876--2191 Score: 331
Period size: 117 Copynumber: 2.7 Consensus size: 116
1866 AAACTGTCCG
* * **
1876 AAAATTACCATTTTA-CCCATCGAACTTCTACA-AATCCCATTTTTAACC-CTAAAACTTCCAAA
1 AAAATTACCATTTTACCCCA--AAACTTCCA-AGAATCCCATTTTCGACCTC-AAAACTTCCAAA
* *
1938 AATTACCATTTCACCCTCGAACTTCCAAAAATCCATTTTTGACCCCGAAACTTCCA
62 AATTACCATTTTACCCTCGAACTTCC-AAAATCCATTTTTGACCCCGAAACTTCAA
* **
1994 AAAATTACCATTTTACCCTAAAACTTCCAAGAATCCCATTTTTTACCTCAAAACTTCCAAAAATT
1 AAAATTACCATTTTACCCCAAAACTTCCAAGAATCCCATTTTCGACCTCAAAACTTCCAAAAATT
** *
2059 ACCATTTTACCCTCGAACTTCCAAGAATCCCATTTTTGACTTCGAAACTTTAA
66 ACCATTTTACCCTCGAACTTCCAA-AAT-CCATTTTTGACCCCGAAACTTCAA
* ** * * *
2112 AAAATTACCATTTTACTCCCGAATGTTCGAAGACT-CCATTTTCGACCTCGAAAC-TCTC-AAAA
1 AAAATTACCATTTTAC-CCCAAAACTTCCAAGAATCCCATTTTCGACCTCAAAACTTC-CAAAAA
*
2174 TTACCCTTTTACCC-CGAA
64 TTACCATTTTACCCTCGAA
2192 TATTCCCAAA
Statistics
Matches: 172, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
116 7 0.04
117 81 0.47
118 69 0.40
119 15 0.09
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.31
Consensus pattern (116 bp):
AAAATTACCATTTTACCCCAAAACTTCCAAGAATCCCATTTTCGACCTCAAAACTTCCAAAAATT
ACCATTTTACCCTCGAACTTCCAAAATCCATTTTTGACCCCGAAACTTCAA
Found at i:2596 original size:97 final size:96
Alignment explanation
Indices: 2453--2645 Score: 230
Period size: 97 Copynumber: 2.0 Consensus size: 96
2443 AAACTTTAAA
* * * * *
2453 AATCGAGGCAATGTTCTTTTATTTCGAGTTTTGAAAATTCGTGCCTTAACTCACTAGGCGTAATT
1 AATCGAGGCAATGTTCTCTTATTTCGAGTTCTGAAAATTCGCGCCTTAACTCACTAGGCGCAA-C
* *
2518 TTTTCTTCAAATCGAAATAATCGAATACCCTT
65 CTTTCTTCAAATAGAAATAATCGAATACCCTT
* *
2550 AATCGAGGCAATGTT-TCCTTATCTTCGA-TTCTGAAATATT-GCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATGTTCT-CTTAT-TTCGAGTTCTGAAA-ATTCGCGCCTTAACTCACTAGGCGCA
* *
2612 ACCTTTCTTCAAATAGAGATAATCGAATATCCTT
63 ACCTTTCTTCAAATAGAAATAATCGAATACCCTT
2646 TTGCAAAAAT
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
96 29 0.35
97 45 0.55
98 8 0.10
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATGTTCTCTTATTTCGAGTTCTGAAAATTCGCGCCTTAACTCACTAGGCGCAACC
TTTCTTCAAATAGAAATAATCGAATACCCTT
Found at i:13529 original size:27 final size:28
Alignment explanation
Indices: 13493--13550 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 28
13483 AATTTTCAAC
*
13493 TAATGATTGTTTCCTTTGATCCTCTTTT
1 TAATGATTGTTTCCTTTGATCCTCTTCT
13521 TAAT-ATTGTTTCCTTTGATCCTCTTCT
1 TAATGATTGTTTCCTTTGATCCTCTTCT
13548 TAA
1 TAA
13551 ATACGACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.17, C:0.19, G:0.09, T:0.55
Consensus pattern (28 bp):
TAATGATTGTTTCCTTTGATCCTCTTCT
Found at i:14500 original size:203 final size:204
Alignment explanation
Indices: 14055--14815 Score: 1047
Period size: 203 Copynumber: 3.7 Consensus size: 204
14045 CATCTTCCTG
* *
14055 ATCAAACCCACGCTCAAAGTGAGCAAAATCTTCGAACCCCAGCTTCTTGAGAAGACACTGAGAAG
1 ATCAAACCCACGCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGAGAAGACACTGAGAAG
*
14120 CAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTC
66 CAGGTCGAAGCAATAAAAGGTTAACTTCCTGATGAGATACTGAGGAGTGAACCAAATTC-TCTTC
* * *
14185 CTGATGAGCTACAGAGAGACGGATTAAGACAAACGATGCGGTCATCTTCCTGATGAGATACTGAG
130 CTGATGAGATACA-AGAGAAGGATTAAGACAAACGACGCGGTCATCTTCCTGATGAGATACTGAG
14250 AAGAAGACCAA
194 AAGAAGACCAA
* * * *
14261 ATCAAACCCACGCTCAAAACGAGCAAAATGTTCGAACCCCAACTTCCTGAGAAGACACTAAGAAG
1 ATCAAACCCACGCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGAGAAGACACTGAGAAG
*
14326 CAGGTCGAAGCAATAAAAGGTTAACTTCCTGATGAGATACTGAGAAGTGAACCAAA-T-TCTTCC
66 CAGGTCGAAGCAATAAAAGGTTAACTTCCTGATGAGATACTGAGGAGTGAACCAAATTCTCTTCC
*
14389 TGATGAGATACAAAGAGAAGGATTAAGACAAACGACGCGGTCATCTTCCTGATGAGATACTCAGA
131 TGATGAGATAC-AAGAGAAGGATTAAGACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGA
14454 AGAAGACCAA
195 AGAAGACCAA
* * * *
14464 ATCAAAACCATGCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTAAGAAGATACTGAGAAG
1 ATCAAACCCACGCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGAGAAGACACTGAGAAG
*
14529 TAGGTCGAAGCAATAAAAGGTTAACTTCCTGATGAGATACTGAGGAGTGAACCAAATTCATCTTC
66 CAGGTCGAAGCAATAAAAGGTTAACTTCCTGATGAGATACTGAGGAGTGAACCAAATTC-TCTTC
* *
14594 CTGATGAGATAC-AGAGAAGCAGATTGAGACAAACGACGCGGTCATCTTCCTGATAAGATACTGA
130 CTGATGAGATACAAGAGAAG--GATTAAGACAAACGACGCGGTCATCTTCCTGATGAGATACTGA
14658 GAAGAAGACCAA
193 GAAGAAGACCAA
* * * * * * * * *
14670 GTCAAACCCACGCGC-GA-TGAAC-GAACCTTCAAACCCCAGCTTCCTGATG-AGATACTGAGAA
1 ATCAAACCCACGCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGA-GAAGACACTGAGAA
* * * * * *
14731 GCAGGTCGAAGCAATAAAACGGTTAGCTTCCTGATGAAATAC-GGGGAAATAAACCAAAATTATC
65 GCAGGTCGAAGCAATAAAA-GGTTAACTTCCTGATGAGATACTGAGG-AGTGAACC-AAATTCTC
*
14795 TTCCTAATGA-A-ACAAGAGAAG
127 TTCCTGATGAGATACAAGAGAAG
14816 TGGATCAAAA
Statistics
Matches: 500, Mismatches: 44, Indels: 25
0.88 0.08 0.04
Matches are distributed among these distances:
202 2 0.00
203 248 0.50
204 50 0.10
205 7 0.01
206 193 0.39
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (204 bp):
ATCAAACCCACGCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGAGAAGACACTGAGAAG
CAGGTCGAAGCAATAAAAGGTTAACTTCCTGATGAGATACTGAGGAGTGAACCAAATTCTCTTCC
TGATGAGATACAAGAGAAGGATTAAGACAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAA
GAAGACCAA
Found at i:15254 original size:6 final size:6
Alignment explanation
Indices: 15233--15317 Score: 75
Period size: 6 Copynumber: 14.2 Consensus size: 6
15223 TTTAAATTGG
** * **
15233 TTTAAA TTTATT TTTAAA TTTAAA TTTATA -TTAAA TTTAAA TTTATCTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA
**
15282 TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
15318 GGATTTAAAA
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
5 7 0.11
6 50 0.82
8 4 0.07
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:15268 original size:17 final size:18
Alignment explanation
Indices: 15233--15314 Score: 105
Period size: 17 Copynumber: 4.6 Consensus size: 18
15223 TTTAAATTGG
15233 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTTAAA
*
15251 TTTAAATTTA-TATTAAA
1 TTTAAATTTATTTTTAAA
15268 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTA--TTTTTAAA
**
15288 TTTAAATTT-GCTTTAAA
1 TTTAAATTTATTTTTAAA
15305 TTTAAATTTA
1 TTTAAATTTA
15315 AATGGATTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
17 31 0.55
18 10 0.18
20 15 0.27
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:15291 original size:37 final size:35
Alignment explanation
Indices: 15233--15314 Score: 121
Period size: 37 Copynumber: 2.3 Consensus size: 35
15223 TTTAAATTGG
15233 TTTAAATTTATTTTTAAATTTAAATTT-ATATTAAA
1 TTTAAATTTATTTTTAAATTTAAATTTGAT-TTAAA
*
15268 TTTAAATTTATCTTTTTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTA--TTTTTAAATTTAAATTTGATTTAAA
15305 TTTAAATTTA
1 TTTAAATTTA
15315 AATGGATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 10 0.23
37 32 0.74
38 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (35 bp):
TTTAAATTTATTTTTAAATTTAAATTTGATTTAAA
Found at i:15356 original size:13 final size:13
Alignment explanation
Indices: 15340--15373 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
15330 TTAATATTTA
15340 AAATTAAAAGCCC
1 AAATTAAAAGCCC
*
15353 AAATTAAAAGTCC
1 AAATTAAAAGCCC
*
15366 AAAATAAA
1 AAATTAAA
15374 TACAAAGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (13 bp):
AAATTAAAAGCCC
Found at i:18049 original size:16 final size:16
Alignment explanation
Indices: 18028--18071 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
18018 CGATAGTCAC
18028 AATTGTTCTAAATACA-
1 AATTGTTCTAAATA-AT
*
18044 AATTGTTCCAAATAAT
1 AATTGTTCTAAATAAT
*
18060 GATTGTTCTAAA
1 AATTGTTCTAAA
18072 CAAAACTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (16 bp):
AATTGTTCTAAATAAT
Found at i:20230 original size:20 final size:20
Alignment explanation
Indices: 20192--20244 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
20182 AATGAGAGAG
20192 AGTAAAAGTTTTGGAAAAAA
1 AGTAAAAGTTTTGGAAAAAA
20212 AGTAGAAAGTTTTGGAAAAAA
1 AGTA-AAAGTTTTGGAAAAAA
20233 A-TAAAAAGTTTT
1 AGT-AAAAGTTTT
20245 AAAGGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (20 bp):
AGTAAAAGTTTTGGAAAAAA
Found at i:30155 original size:21 final size:22
Alignment explanation
Indices: 30113--30156 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
30103 CTTCTCTATA
* **
30113 TTTTTTGTCTTTTCTTTTTTAT
1 TTTTTTGTCTGTTCTTCATTAT
30135 TTTTTTGT-TGTTCTTCATTAT
1 TTTTTTGTCTGTTCTTCATTAT
30156 T
1 T
30157 CTATTTTGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (22 bp):
TTTTTTGTCTGTTCTTCATTAT
Found at i:31037 original size:13 final size:14
Alignment explanation
Indices: 31019--31048 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
31009 GATTTAAGAT
31019 TTATTTAAT-TTTA
1 TTATTTAATATTTA
31032 TTATTTAATATTTA
1 TTATTTAATATTTA
31046 TTA
1 TTA
31049 AAAGTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTAATATTTA
Found at i:32118 original size:22 final size:21
Alignment explanation
Indices: 32090--32133 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
32080 ATTATTTTCA
32090 TATAATTTTCAGTTATTATTAT
1 TATAATTTTCAGTTA-TATTAT
* *
32112 TATAATTTTTATTTATATTAT
1 TATAATTTTCAGTTATATTAT
32133 T
1 T
32134 TTTAATTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TATAATTTTCAGTTATATTAT
Found at i:32497 original size:20 final size:20
Alignment explanation
Indices: 32472--32518 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
32462 AAATCTCGAA
32472 CTCAAACCCTAAACTCAAAC
1 CTCAAACCCTAAACTCAAAC
*
32492 CTCAAACCCTAAACTTAAAC
1 CTCAAACCCTAAACTCAAAC
32512 CTCAAAC
1 CTCAAAC
32519 ATTGAACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (20 bp):
CTCAAACCCTAAACTCAAAC
Found at i:32544 original size:21 final size:21
Alignment explanation
Indices: 32488--32538 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
32478 CCCTAAACTC
** *
32488 AAACCTCAAACCCT-AAACTT
1 AAACCTCAAACATTGAACCTT
32508 AAACCTCAAACATTGAACCTT
1 AAACCTCAAACATTGAACCTT
*
32529 AAACTTCAAA
1 AAACCTCAAA
32539 GCTTGATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (21 bp):
AAACCTCAAACATTGAACCTT
Found at i:32592 original size:20 final size:20
Alignment explanation
Indices: 32553--32606 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
32543 GATCTTGATC
* **
32553 CCCAAACCTCAAACTTCAAA
1 CCCAAACCTTAAACCCCAAA
32573 CCCTAAA-CTTAAACCCCAAA
1 CCC-AAACCTTAAACCCCAAA
32593 CCCAAACCTTAAAC
1 CCCAAACCTTAAAC
32607 TAAAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 23 0.79
21 3 0.10
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (20 bp):
CCCAAACCTTAAACCCCAAA
Found at i:35824 original size:19 final size:20
Alignment explanation
Indices: 35800--35838 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
35790 TGCATTGCTT
35800 TCTTGTGGCT-TTTCATTTC
1 TCTTGTGGCTCTTTCATTTC
* *
35819 TCTTGTTGCTCTTTCCTTTC
1 TCTTGTGGCTCTTTCATTTC
35839 GAGTTCTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.03, C:0.26, G:0.13, T:0.59
Consensus pattern (20 bp):
TCTTGTGGCTCTTTCATTTC
Found at i:37820 original size:24 final size:24
Alignment explanation
Indices: 37784--37857 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
37774 AGAAATAATA
37784 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
37808 TTTTAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
37832 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
37856 TT
1 TT
37858 CGAGTCAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.58
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:40121 original size:52 final size:52
Alignment explanation
Indices: 40052--40276 Score: 310
Period size: 52 Copynumber: 4.3 Consensus size: 52
40042 AGGTCTAATT
* * * *
40052 ACTATGTGTCATAGTGAGTATATGAATCATTTACGGGTTATGAGGTCCAATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
* *
40104 ACTATGTGTCATCGTGAGTATAT-AATCCTTTATGGATTATGAGGTTCGATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
* *
40155 ACTATGTGTCATCGTGAGTATCTAAATCCTTTACGGATTATGAGGTCCGATG
1 ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
* * *
40207 ACTACGTGTCATCGTGAGTA-AGTGAATCCTTTACGGATTGTGAGGTTCGATG
1 ACTATGTGTCATCGTGAGTATA-TGAATCCTTTACGGATTATGAGGTCCGATG
* *
40259 ACTATGTTTCATAGTGAG
1 ACTATGTGTCATCGTGAG
40277 AATCAAATGC
Statistics
Matches: 154, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
51 45 0.29
52 109 0.71
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (52 bp):
ACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
Found at i:42092 original size:24 final size:24
Alignment explanation
Indices: 42008--42082 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
41998 AGAAATATTC
42008 TTTCAATTAAACTATGTTTATTTG
1 TTTCAATTAAACTATGTTTATTTG
* * *
42032 TTTCAATTACACTCTATTTATTTG
1 TTTCAATTAAACTATGTTTATTTG
*
42056 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTATGTTTATTTG
42080 TTT
1 TTT
42083 GAGTCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTATGTTTATTTG
Found at i:46078 original size:80 final size:80
Alignment explanation
Indices: 45993--46152 Score: 286
Period size: 80 Copynumber: 2.0 Consensus size: 80
45983 TTTACACGAT
45993 TATATATATATATATATATATCATAT-TCATTTCATACACTTTATGTAAAAGCTTGTATTTTAGT
1 TATATATATATATATATATATCAT-TGTCATTTCATACACTTTATGTAAAAGCTTGTATTTTAGT
*
46057 GGTATTGAAAACGGTG
65 GATATTGAAAACGGTG
46073 TATATATATATATATATATATCATTGTCATTTCATACACTTTATGTAAAAGCTTGTATTTTAGTG
1 TATATATATATATATATATATCATTGTCATTTCATACACTTTATGTAAAAGCTTGTATTTTAGTG
*
46138 ATGTTGAAAACGGTG
66 ATATTGAAAACGGTG
46153 ATTTCAAGAC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
79 1 0.01
80 76 0.99
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (80 bp):
TATATATATATATATATATATCATTGTCATTTCATACACTTTATGTAAAAGCTTGTATTTTAGTG
ATATTGAAAACGGTG
Found at i:48410 original size:21 final size:20
Alignment explanation
Indices: 48372--48410 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
48362 TATGTGTTGA
*
48372 TTTTGGTAAGTTTTGATGAG
1 TTTTGGTAAGTTTGGATGAG
*
48392 TTTTGAGTAGGTTTGGATG
1 TTTTG-GTAAGTTTGGATG
48411 TTGATCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (20 bp):
TTTTGGTAAGTTTGGATGAG
Found at i:48980 original size:348 final size:348
Alignment explanation
Indices: 48343--49040 Score: 1207
Period size: 348 Copynumber: 2.0 Consensus size: 348
48333 TATTGGTTAA
*
48343 GCACTTAGGATGTATGAAATATGTGTTGATTTTGGTAAGTTTTGATGAGTTTTGAGTAGGTTTGG
1 GCACTTAGGACGTATGAAATATGTGTTGATTTTGGTAAGTTTTGATGAGTTTTGAGTAGGTTTGG
*
48408 ATGTTGATCTAATGTGACTTGTGACACAAGTGTACTAAGAATAGGTAACTTTTTGAAAAAGGGAC
66 ATATTGATCTAATGTGACTTGTGACACAAGTGTACTAAGAATAGGTAACTTTTTGAAAAAGGGAC
* * * **
48473 ATTTGGTACACACGGGCTGATACATGGCTTGACACACGATTGTGTGCCATACACGGGTATATGGC
131 ATTTGGTACACACGGGCTGATACAAGGCCTGACACACAACCGTGTGCCATACACGGGTATATGGC
* * * * *
48538 ACGACCATGTGGTCTGTGTGATTTAGGTTTCAATTGACAGATGCTATCATAGTTTGTTACACGGT
196 ACAACCATGTGGTCTGTGTGACTTAGGTTTCAATTGACACATACTATCAGAGTTTGTTACACGGT
48603 CTAGAGACACAATTGTGTGCCTCCTCCTACATGGTTTTAGCCCTTGCGTACGACTAGACGACACG
261 CTAGAGACACAATTGTGTGCCTCCTCCTACATGGTTTTAGCCCTTGCGTACGACTAGACGACACG
* *
48668 GCCATGCCCTATAGCTTCAGACG
326 ACCATGCCCTATAGCTTCACACG
*
48691 GCACTTAGGACGTATGAAATATGTGTTGATTTTGGTATGTTTTGATGAGTTTTGAGTAGGTTTGG
1 GCACTTAGGACGTATGAAATATGTGTTGATTTTGGTAAGTTTTGATGAGTTTTGAGTAGGTTTGG
*
48756 ATATTGGTCTAATGTGACTTGTGACACAAGTGTACTAAGAATAGGTAACTTTTTGAAAAAGGGAC
66 ATATTGATCTAATGTGACTTGTGACACAAGTGTACTAAGAATAGGTAACTTTTTGAAAAAGGGAC
48821 ATTTGGTACACACGGGCTGATACAAGGCCTGACACACAACCGTGTGCCATACACGGGTATATGGC
131 ATTTGGTACACACGGGCTGATACAAGGCCTGACACACAACCGTGTGCCATACACGGGTATATGGC
* *
48886 ACAACCATGTGGTCTGTGTGACTTAGGTTTCAATTGACACATACTGTCAGAGTTTGTTACATGGT
196 ACAACCATGTGGTCTGTGTGACTTAGGTTTCAATTGACACATACTATCAGAGTTTGTTACACGGT
* * *
48951 TTAGAGACACAATTGTGTGCCTCCTCCTACGTGGTTTTAGCCCTTGCGTACGACTGGACGACACG
261 CTAGAGACACAATTGTGTGCCTCCTCCTACATGGTTTTAGCCCTTGCGTACGACTAGACGACACG
49016 ACCATGCCCTATAGCTTCACACG
326 ACCATGCCCTATAGCTTCACACG
49039 GC
1 GC
49041 CTAGCCACAC
Statistics
Matches: 329, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
348 329 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (348 bp):
GCACTTAGGACGTATGAAATATGTGTTGATTTTGGTAAGTTTTGATGAGTTTTGAGTAGGTTTGG
ATATTGATCTAATGTGACTTGTGACACAAGTGTACTAAGAATAGGTAACTTTTTGAAAAAGGGAC
ATTTGGTACACACGGGCTGATACAAGGCCTGACACACAACCGTGTGCCATACACGGGTATATGGC
ACAACCATGTGGTCTGTGTGACTTAGGTTTCAATTGACACATACTATCAGAGTTTGTTACACGGT
CTAGAGACACAATTGTGTGCCTCCTCCTACATGGTTTTAGCCCTTGCGTACGACTAGACGACACG
ACCATGCCCTATAGCTTCACACG
Found at i:59470 original size:15 final size:15
Alignment explanation
Indices: 59418--59467 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
59408 AATAATATTT
59418 AAAATTAAGTATTGA
1 AAAATTAAGTATTGA
* *
59433 AAAAATAAGTGTTGA
1 AAAATTAAGTATTGA
59448 AAAATTAAGTATT-A
1 AAAATTAAGTATTGA
59462 AAAATT
1 AAAATT
59468 TAATTACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 7 0.23
15 24 0.77
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (15 bp):
AAAATTAAGTATTGA
Found at i:59779 original size:2 final size:2
Alignment explanation
Indices: 59772--59802 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
59762 GTATGAGGTT
59772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59803 TATTTACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73073 original size:44 final size:43
Alignment explanation
Indices: 73019--73104 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 43
73009 TATTTTTTAT
73019 TTTCCACTTAAACTCTGATTAGTGTAAGTTATTTTAATATTAG
1 TTTCCACTTAAACTCTGATTAGTGTAAGTTATTTTAATATTAG
* *
73062 TTTCTCACTTAAACTCTGATTATTGTAGGTTATTTTAATATTA
1 TTTC-CACTTAAACTCTGATTAGTGTAAGTTATTTTAATATTA
73105 TTTGACCTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 4 0.10
44 36 0.90
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (43 bp):
TTTCCACTTAAACTCTGATTAGTGTAAGTTATTTTAATATTAG
Found at i:77036 original size:50 final size:50
Alignment explanation
Indices: 76977--77076 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
76967 AAATATTAAG
76977 TATGATCTTTTGTCAGAACGTTTCTAATTGAATAAGAAATGCAGAAAGTA
1 TATGATCTTTTGTCAGAACGTTTCTAATTGAATAAGAAATGCAGAAAGTA
77027 TATGATCTTTTGTCAGAACGTTTCTAATTGAATAAGAAATGCAGAAAGTA
1 TATGATCTTTTGTCAGAACGTTTCTAATTGAATAAGAAATGCAGAAAGTA
77077 ATCACCTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (50 bp):
TATGATCTTTTGTCAGAACGTTTCTAATTGAATAAGAAATGCAGAAAGTA
Found at i:78145 original size:31 final size:32
Alignment explanation
Indices: 78083--78162 Score: 144
Period size: 31 Copynumber: 2.5 Consensus size: 32
78073 TTATAGAATT
*
78083 AAAATACCTACTCACTTATATTCAAAAAAAAA
1 AAAATAGCTACTCACTTATATTCAAAAAAAAA
78115 AAAATAGCTACTCACTTATATTC-AAAAAAAA
1 AAAATAGCTACTCACTTATATTCAAAAAAAAA
78146 AAAATAGCTACTCACTT
1 AAAATAGCTACTCACTT
78163 GCAAGAGTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 25 0.53
32 22 0.47
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.26
Consensus pattern (32 bp):
AAAATAGCTACTCACTTATATTCAAAAAAAAA
Found at i:89399 original size:16 final size:16
Alignment explanation
Indices: 89380--89429 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
89370 TAAATTTTTT
89380 ATATAAAAAATTAAAA
1 ATATAAAAAATTAAAA
* * *
89396 ATATAATACATCAAAA
1 ATATAAAAAATTAAAA
89412 ATACTAAAAACATTAAAA
1 ATA-TAAAAA-ATTAAAA
89430 TAAATGTGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 16 0.62
17 4 0.15
18 6 0.23
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (16 bp):
ATATAAAAAATTAAAA
Found at i:90103 original size:22 final size:22
Alignment explanation
Indices: 90077--90138 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
90067 ATATCTAAAT
*
90077 AATAACAATAAAATAGTAATAA
1 AATAACAATAAAATAGTAAAAA
* * * *
90099 TATAATAGTGAAATAGTAAAAA
1 AATAACAATAAAATAGTAAAAA
* *
90121 AACAACAAGAAAATAGTA
1 AATAACAATAAAATAGTA
90139 GATTTTTTTG
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.65, C:0.05, G:0.10, T:0.21
Consensus pattern (22 bp):
AATAACAATAAAATAGTAAAAA
Found at i:91698 original size:22 final size:24
Alignment explanation
Indices: 91651--91699 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
91641 ATATGGGTGG
*
91651 AAAATATTTATATATTAAATTTATT
1 AAAATATTTATATA-TAAATTAATT
91676 AAAAT-TTTATATA-AAATTAATT
1 AAAATATTTATATATAAATTAATT
91698 AA
1 AA
91700 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 10 0.43
24 8 0.35
25 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAATATTTATATATAAATTAATT
Found at i:92391 original size:19 final size:19
Alignment explanation
Indices: 92369--92405 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
92359 TTCTTTCTTT
* *
92369 TTTTTTTTTTTTGAAATGA
1 TTTTTATTTTCTGAAATGA
92388 TTTTTATTTTCTGAAATG
1 TTTTTATTTTCTGAAATG
92406 TGTATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTTATTTTCTGAAATGA
Found at i:93252 original size:20 final size:20
Alignment explanation
Indices: 93227--93272 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
93217 ACCAAATAAA
* *
93227 AAATATATTATTAATATACG
1 AAATATATTATCAATATACC
* *
93247 AAATATGTTGTCAATATACC
1 AAATATATTATCAATATACC
93267 AAATAT
1 AAATAT
93273 TAACTCAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.37
Consensus pattern (20 bp):
AAATATATTATCAATATACC
Found at i:94474 original size:3 final size:3
Alignment explanation
Indices: 94460--94519 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
94450 GCATTAAATA
* * *
94460 AAT AAT ATT AAT AAT AAT CAT AAT AAT AA- ATAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
*
94505 AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT
94520 TTTAATAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
2 1 0.02
3 45 0.96
4 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:95797 original size:29 final size:28
Alignment explanation
Indices: 95657--95980 Score: 235
Period size: 29 Copynumber: 11.2 Consensus size: 28
95647 CCAAAATCAT
**
95657 ATTTTGACCCCTAAACTTCACAAAAATTTT
1 ATTTT-ACCCCTAAACTTC-CAAAAATTAC
* *
95687 ATTTTGACCCCTAAACTTTCCAAAAAATAT
1 ATTTT-ACCCCTAAAC-TTCCAAAAATTAC
* * * *
95717 ATTTTAACCCTTGAATTTTC-AAAATTAC
1 ATTTT-ACCCCTAAACTTCCAAAAATTAC
* *
95745 ATCTTTTCCCCCAAACTTCCAAAAATTAC
1 AT-TTTACCCCTAAACTTCCAAAAATTAC
**
95774 CGTTTACCCCTAAACTTCCAAAAATTATC
1 ATTTTACCCCTAAACTTCCAAAAATTA-C
*
95803 ATTTTACCCCT-AACTTTTCAAAAATTAC
1 ATTTTACCCCTAAAC-TTCCAAAAATTAC
*
95831 ATTTTGCCCCTAAACTTCCAAAAATTAC
1 ATTTTACCCCTAAACTTCCAAAAATTAC
* *
95859 ATTTTTGACCTC-GAACATTCCAAAAATTACC
1 A-TTTT-ACCCCTAAAC-TTCCAAAAATTA-C
**
95890 ATTTTACCCCCGAA-TGTCCAAAAATTACC
1 ATTTTACCCCTAAACT-TCCAAAAATTA-C
* * *
95919 GTTTTACCCCCGAACCTT-CAAAAATTACC
1 ATTTTA-CCCCTAAACTTCCAAAAATTA-C
** * * *
95948 ATTTTACCCCCGAGCATCCAAAAATCAC
1 ATTTTACCCCTAAACTTCCAAAAATTAC
95976 ATTTT
1 ATTTT
95981 TGACTCCGTT
Statistics
Matches: 241, Mismatches: 38, Indels: 32
0.77 0.12 0.10
Matches are distributed among these distances:
28 80 0.33
29 91 0.38
30 64 0.27
31 6 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
ATTTTACCCCTAAACTTCCAAAAATTAC
Found at i:95944 original size:58 final size:58
Alignment explanation
Indices: 95737--95980 Score: 223
Period size: 57 Copynumber: 4.2 Consensus size: 58
95727 TTGAATTTTC
* * * * *
95737 AAAATTA-CATCTTTTCCCCCAAACTTCCAAAAATTACC-GTTTACCCCTAAACTTCCA
1 AAAATTACCAT-TTTACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCA
* * * * * *
95794 AAAATTATCATTTTACCCCTAACTTTTCAAAAATTA-CATTTTGCCCCTAAACTTCCA
1 AAAATTACCATTTTACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCA
* * *
95851 AAAATTA-CATTTTTGACCTCGAACATTCCAAAAATTACCATTTTACCCCCGAA-TGTCCA
1 AAAATTACCA-TTTT-ACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAACT-TCCA
* * * *
95910 AAAATTACCGTTTTACCCCCGAACCTT-CAAAAATTACCATTTTACCCCCGAGCATCCA
1 AAAATTACCATTTTA-CCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCA
*
95968 AAAATCA-CATTTT
1 AAAATTACCATTTT
95981 TGACTCCGTT
Statistics
Matches: 157, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
56 3 0.02
57 60 0.38
58 57 0.36
59 36 0.23
60 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCGAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCA
Found at i:101349 original size:2 final size:2
Alignment explanation
Indices: 101342--101380 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
101332 AAAAGTACCT
101342 TA TA TA TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
101381 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:102943 original size:16 final size:16
Alignment explanation
Indices: 102922--102952 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
102912 ATAATGGGGA
*
102922 AGAAAATAAGGGGAAC
1 AGAAAATAAAGGGAAC
102938 AGAAAATAAAGGGAA
1 AGAAAATAAAGGGAA
102953 GATGAATAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.29, T:0.06
Consensus pattern (16 bp):
AGAAAATAAAGGGAAC
Found at i:103050 original size:29 final size:27
Alignment explanation
Indices: 103000--103109 Score: 122
Period size: 29 Copynumber: 4.1 Consensus size: 27
102990 GGGATGATGA
103000 TTATATTTTAAAATAATTTTAATAAAT
1 TTATATTTTAAAATAATTTTAATAAAT
103027 TTATATTTTAAAA-AATAATTT--TAAA-
1 TTATATTTTAAAATAAT--TTTAATAAAT
* *
103052 TTA-ATTTTAAAATAATTTGAATAATT
1 TTATATTTTAAAATAATTTTAATAAAT
*
103078 TTATATTTTAAAAAATAATTTTAATAATT
1 TTATATTTT--AAAATAATTTTAATAAAT
103107 TTA
1 TTA
103110 AAATCATTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.03
24 9 0.13
25 9 0.13
26 10 0.14
27 18 0.25
28 3 0.04
29 20 0.28
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
TTATATTTTAAAATAATTTTAATAAAT
Found at i:103081 original size:51 final size:49
Alignment explanation
Indices: 102999--103122 Score: 187
Period size: 51 Copynumber: 2.5 Consensus size: 49
102989 CGGGATGATG
102999 ATTATATTTTAAAATAATTTTAATAAATTTATATTTTAAAAAATAATTTTAA
1 ATTA-ATTTTAAAATAA-TTTAATAAATTTATATTTTAAAAAATAATTTT-A
*
103051 ATTAATTTTAAAATAATTTGAATAATTTTATATTTTAAAAAATAATTTTA
1 ATTAATTTTAAAATAATTT-AATAAATTTATATTTTAAAAAATAATTTTA
*
103101 A-TAATTTTAAAATCATTTAATA
1 ATTAATTTTAAAATAATTTAATA
103123 TGGCATATAA
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
48 4 0.06
49 16 0.23
50 5 0.07
51 40 0.58
52 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (49 bp):
ATTAATTTTAAAATAATTTAATAAATTTATATTTTAAAAAATAATTTTA
Found at i:103094 original size:20 final size:22
Alignment explanation
Indices: 103071--103112 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
103061 AAATAATTTG
103071 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
103091 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
103113 TCATTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:103113 original size:20 final size:20
Alignment explanation
Indices: 103040--103122 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 20
103030 TATTTTAAAA
*
103040 AATAATTTTAAATTAATTTT
1 AATAATTTTAAAATAATTTT
*
103060 AA-AATAATTT-GAATAATTTT
1 AATAAT--TTTAAAATAATTTT
103080 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
103100 AATAATTTTAAAATCA-TTT
1 AATAATTTTAAAATAATTTT
103119 AATA
1 AATA
103123 TGGCATATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
17 3 0.06
19 13 0.25
20 25 0.49
21 5 0.10
22 5 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:114286 original size:2 final size:2
Alignment explanation
Indices: 114274--114306 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
114264 AATTAAGAAA
*
114274 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
114307 CATGACAGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:114999 original size:23 final size:23
Alignment explanation
Indices: 114908--114994 Score: 138
Period size: 23 Copynumber: 3.7 Consensus size: 23
114898 AAGGTGTTGG
* *
114908 ACAGAGTTTGAATCAAACAAATAA
1 ACAGAGTTT-AATGAAACAATTAA
114932 ACAGAGTTTAATGAAACAATTAA
1 ACAGAGTTTAATGAAACAATTAA
114955 ACAGAGTTTAATGAAACAATTAA
1 ACAGAGTTTAATGAAACAATTAA
114978 ACAGAGTTTAACTGAAA
1 ACAGAGTTTAA-TGAAA
114995 GATTATTTCT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
23 46 0.77
24 14 0.23
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (23 bp):
ACAGAGTTTAATGAAACAATTAA
Found at i:116983 original size:24 final size:24
Alignment explanation
Indices: 116922--116984 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
116912 TAGACTAATA
* * *
116922 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
116946 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
116970 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
116985 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:121511 original size:12 final size:12
Alignment explanation
Indices: 121494--121523 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
121484 GGGGTTATGC
121494 CTTGTCTGATTT
1 CTTGTCTGATTT
121506 CTTGTCTGATTT
1 CTTGTCTGATTT
121518 CTTGTC
1 CTTGTC
121524 GGATGATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.20, G:0.17, T:0.57
Consensus pattern (12 bp):
CTTGTCTGATTT
Found at i:123175 original size:15 final size:15
Alignment explanation
Indices: 123157--123216 Score: 77
Period size: 15 Copynumber: 4.0 Consensus size: 15
123147 TGGCTTGTCA
123157 TCTTTTGATTTTTCG
1 TCTTTTGATTTTTCG
*
123172 TCTTTGGATTTGTT-G
1 TCTTTTGATTT-TTCG
* *
123187 TCTTTTGATTTGTCA
1 TCTTTTGATTTTTCG
123202 TCTTTTGATTTTTCG
1 TCTTTTGATTTTTCG
123217 CCATTGACGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 1 0.03
15 34 0.92
16 2 0.05
ACGTcount: A:0.08, C:0.12, G:0.17, T:0.63
Consensus pattern (15 bp):
TCTTTTGATTTTTCG
Done.