Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013368.1 Kokia drynarioides strain JFW-HI SEQ_128391, 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: 267042
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 27 characters in sequence are not A, C, G, or T
Found at i:355 original size:205 final size:204
Alignment explanation
Indices: 1--769 Score: 1085
Period size: 205 Copynumber: 3.8 Consensus size: 204
*
1 TGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATT
1 TGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATT
* * * *
66 CGTCTTCCTGATGAGATAC-GAAGAAGCGAATTGAAAAAAACAACGCGGCCATCTTCCTGATGAG
66 CGTCTTCCTGATGAGATACAG-AGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAG
*
130 ATACTGAGAAGAAGACCAAATCAAACCTACGCTCGATGTGAGCAAATCTTCGAACCACAGCTTCT
130 ATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACC-CAGCTTCT
195 TGATGAGACAC
194 TGATGAGACAC
* * * *
206 TAAGAAGCAGGTCAAAGCAATAAAAGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATT
1 TGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATT
* * *
271 TGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAGCAAACGATGCAGTCATCTTCCTGATGAGA
66 CGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGA
336 TACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCTT
131 TACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAA-CCCAGCTTCTT
401 GATGAGACAC
195 GATGAGACAC
* *
411 TGAGAAGCAGGTCGAAGCAAAAAAAGGTTAGCTTCCTAATGAAATACTGAGAAGTGGACCAAATT
1 TGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATT
* *
476 CGTCTTCCTGATGAGATATAGAG-AGATGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAG
66 CGTCTTCCTGATGAGATACAGAGAAG-CGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAG
* *
540 ATACTGAGAAGAAGACCAAATCAAACCCACGGTCGATGTGAGCAAATCTTCGAATCCCAGCTTCC
130 ATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAA-CCCAGCTTCT
* *
605 TGATGAAATAC
194 TGATGAGACAC
* * *
616 TGAGAAGCAGGTTGAAGTAATAAAATGGTTAGCTTCCTGATGAAATAC-GAGGAAGTGAACCAAA
1 TGAGAAGCAGGTCGAAGCAATAAAA-GGTTAGCTTCCTGATGAAATACTGA-GAAGTGGACCAAA
** * * * * * ** ** ****
680 ACCATCTTCCTGATGAAACACAGAAAAGTGAATCAAAACAAGTGATATGGTCATCTTCCTGATGA
64 TTCGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGA
* *
745 GATACTGAGAAGAAGGCCAAGTCAA
129 GATACTGAGAAGAAGACCAAATCAA
770 TGAAACCAGA
Statistics
Matches: 509, Mismatches: 49, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
204 2 0.00
205 399 0.78
206 106 0.21
207 2 0.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (204 bp):
TGAGAAGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAAATACTGAGAAGTGGACCAAATT
CGTCTTCCTGATGAGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCATCTTCCTGATGAGA
TACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCAGCTTCTTG
ATGAGACAC
Found at i:709 original size:37 final size:37
Alignment explanation
Indices: 648--718 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
638 AAATGGTTAG
* *
648 CTTCCTGATGAAATACGAGGAAGTGAACCAAAACCAT
1 CTTCCTGATGAAACACGAGAAAGTGAACCAAAACCAT
*
685 CTTCCTGATGAAACAC-AGAAAAGTGAATCAAAAC
1 CTTCCTGATGAAACACGAG-AAAGTGAACCAAAAC
719 AAGTGATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 2 0.07
37 28 0.93
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (37 bp):
CTTCCTGATGAAACACGAGAAAGTGAACCAAAACCAT
Found at i:1105 original size:6 final size:6
Alignment explanation
Indices: 1091--1152 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
1081 TTTAAATTTT
* * **
1091 TTTAAA TTTAGA TTT-AT TTTAAA TTTGGA TTTAAA -TT-AA TCTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
1137 TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
1153 TTATAAAGTC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
4 2 0.05
5 5 0.11
6 34 0.77
7 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:1112 original size:17 final size:17
Alignment explanation
Indices: 1081--1123 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1071 CTGGGCCCCT
*
1081 TTTAAATTT-TTTTAAA
1 TTTAGATTTATTTTAAA
1097 TTTAGATTTATTTTAAA
1 TTTAGATTTATTTTAAA
*
1114 TTTGGATTTA
1 TTTAGATTTA
1124 AATTAATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (17 bp):
TTTAGATTTATTTTAAA
Found at i:1123 original size:23 final size:23
Alignment explanation
Indices: 1091--1159 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1081 TTTAAATTTT
*
1091 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTAAATTTATTTTAAA
** * *
1114 TTTGGATTTAAATTAATCTTAAA
1 TTTAAATTTAAATTTATTTTAAA
*
1137 TTTAAATTTAAATTTATTATAAA
1 TTTAAATTTAAATTTATTTTAAA
1160 GTCCAATTAC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (23 bp):
TTTAAATTTAAATTTATTTTAAA
Found at i:1129 original size:17 final size:17
Alignment explanation
Indices: 1092--1152 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
1082 TTAAATTTTT
**
1092 TTAAATTTAGATTTATT
1 TTAAATTTAGATTTAAA
*
1109 TTAAATTTGGATTTAAA
1 TTAAATTTAGATTTAAA
*
1126 TT-AATCTTAAATTTAAA
1 TTAAAT-TTAGATTTAAA
1143 TTTAAATTTA
1 -TTAAATTTA
1153 TTATAAAGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 3 0.08
17 25 0.69
18 5 0.14
19 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (17 bp):
TTAAATTTAGATTTAAA
Found at i:1141 original size:12 final size:11
Alignment explanation
Indices: 1095--1152 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
1085 AATTTTTTTA
*
1095 AATTTAGATTT
1 AATTTAAATTT
*
1106 ATTTTAAATTT
1 AATTTAAATTT
*
1117 GGATTTAAA-TT
1 -AATTTAAATTT
1128 AATCTTAAATTT
1 AAT-TTAAATTT
1140 AAATTTAAATTT
1 -AATTTAAATTT
1152 A
1 A
1153 TTATAAAGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
10 2 0.05
11 17 0.45
12 16 0.42
13 3 0.08
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:1176 original size:14 final size:15
Alignment explanation
Indices: 1157--1185 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1147 AATTTATTAT
1157 AAAGTCC-AATTACA
1 AAAGTCCAAATTACA
1171 AAAGTCCAAATTACA
1 AAAGTCCAAATTACA
1186 TGTCTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAGTCCAAATTACA
Found at i:1894 original size:3 final size:3
Alignment explanation
Indices: 1815--1880 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
1805 AATAAGGCTT
** * * *
1815 TAA TAA TAA TAA TGG TAA TAA TAA TAA TAA AAA TAA TAT TAC TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1862 TCAT TAA TAA TAT TAA TAA
1 T-AA TAA TAA TAA TAA TAA
1881 CGGCAATAAT
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
2 2 0.04
3 45 0.94
4 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2956 original size:29 final size:29
Alignment explanation
Indices: 2924--3291 Score: 266
Period size: 29 Copynumber: 12.7 Consensus size: 29
2914 TAAACTGTCA
*
2924 AAAAATTACATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCC
*
2953 -AAAATTCCATTTTTGA--CGCGAAACTTCC
1 AAAAATTCCATTTTT-ACCCTCG-AACTTCC
*
2981 AAAAATTTCA-TTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCC
*
3009 AAAAATTCCATTTTTGACCC-CAAAACTTCC
1 AAAAATTCCATTTTT-ACCCTC-GAACTTCC
* * * *
3039 AAAAAATCTATTTTTACCCCCAAACTT-C
1 AAAAATTCCATTTTTACCCTCGAACTTCC
* *
3067 AAAAATTCCAGTTTTGACCCT-AAAGCTTCC
1 AAAAATTCCA-TTTTTACCCTCGAA-CTTCC
* *
3097 AAAAATTCAAATTTTACCCTCGAGACTTCC
1 AAAAATTCCATTTTTACCCTCGA-ACTTCC
*
3127 AAAAATTCCATTTTTACCCTCGAACCT-C
1 AAAAATTCCATTTTTACCCTCGAACTTCC
3155 AAAAATTTCCATTTTTGA-CCTCGAAACGTT-C
1 AAAAA-TTCCATTTTT-ACCCTCG-AAC-TTCC
* *
3186 AAAAATTACCA-TTTTGCCC-CGGA-TGTCC
1 AAAAATT-CCATTTTTACCCTCGAACT-TCC
*
3214 AAAAACTT-CATTTTTGA-CCTCAAAAC-TCTC
1 AAAAA-TTCCATTTTT-ACCCTC-GAACTTC-C
* * * *
3244 -AAAACTCCCTTTTTACCCTCAAACGTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCC
*
3272 AAAAATTTCATTTTTGACCC
1 AAAAATTCCATTTTT-ACCC
3292 CGAGAATCCA
Statistics
Matches: 275, Mismatches: 30, Indels: 67
0.74 0.08 0.18
Matches are distributed among these distances:
26 1 0.00
27 7 0.03
28 78 0.28
29 98 0.36
30 80 0.29
31 11 0.04
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCTCGAACTTCC
Found at i:3038 original size:30 final size:29
Alignment explanation
Indices: 2915--3292 Score: 259
Period size: 30 Copynumber: 13.0 Consensus size: 29
2905 GGATTTCCCT
* *
2915 AAACTGTCAAAAAATTACATTTTT-ACCCTC
1 AAACT-TCCAAAAATTCCATTTTTGACCC-C
* * *
2945 GAACTTCC-AAAATTCCATTTTTGACGCG
1 AAACTTCCAAAAATTCCATTTTTGACCCC
*
2973 AAACTTCCAAAAATTTCA-TTTT-ACCCTC
1 AAACTTCCAAAAATTCCATTTTTGACCC-C
*
3001 GAACTTCCAAAAATTCCATTTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
* *
3030 AAAACTTCCAAAAAATCTATTTTT-ACCCCC
1 -AAACTTCCAAAAATTCCATTTTTGA-CCCC
* *
3060 AAACTT-CAAAAATTCCAGTTTTGACCCT
1 AAACTTCCAAAAATTCCATTTTTGACCCC
* *
3088 AAAGCTTCCAAAAATTCAAATTTT-ACCCTC
1 AAA-CTTCCAAAAATTCCATTTTTGACCC-C
*
3118 GAGACTTCCAAAAATTCCATTTTT-ACCCTC
1 -AAACTTCCAAAAATTCCATTTTTGACCC-C
* * *
3148 GAACCT-CAAAAATTTCCATTTTTGACCTCG
1 AAACTTCCAAAAA-TTCCATTTTTGACC-CC
3178 AAACGTT-CAAAAATTACCA-TTTTG-CCCC
1 AAAC-TTCCAAAAATT-CCATTTTTGACCCC
** *
3206 GGA-TGTCCAAAAACTT-CATTTTTGACCTCA
1 AAACT-TCCAAAAA-TTCCATTTTTGACC-CC
* *
3236 AAAC-TCTC-AAAACTCCCTTTTT-ACCCTC
1 AAACTTC-CAAAAATTCCATTTTTGACCC-C
* *
3264 AAACGTCCAAAAATTTCATTTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
3293 GAGAATCCAA
Statistics
Matches: 276, Mismatches: 42, Indels: 61
0.73 0.11 0.16
Matches are distributed among these distances:
26 1 0.00
27 7 0.03
28 87 0.32
29 78 0.28
30 90 0.33
31 13 0.05
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTGACCCC
Found at i:3301 original size:29 final size:28
Alignment explanation
Indices: 2924--3313 Score: 166
Period size: 28 Copynumber: 13.5 Consensus size: 28
2914 TAAACTGTCA
* *
2924 AAAAATTACATTTTT-ACCCTCGAACTTCC
1 AAAAATTCCATTTTTGACCC-CGAA-ATCC
*
2953 -AAAATTCCATTTTTGA-CGCGAAACTTCC
1 AAAAATTCCATTTTTGACCCCGAAA--TCC
* *
2981 AAAAATTTCA-TTTT-ACCCTCGAACTTCC
1 AAAAATTCCATTTTTGACCC-CGAA-ATCC
*
3009 AAAAATTCCATTTTTGACCCCAAAACTTCC
1 AAAAATTCCATTTTTGACCCCGAAA--TCC
* * * *
3039 AAAAAATCTATTTTT-ACCCCCAAACTTC
1 AAAAATTCCATTTTTGACCCCGAAA-TCC
* *
3067 AAAAATTCCAGTTTTGA-CCCTAAAGCTTCC
1 AAAAATTCCATTTTTGACCCCGAAA---TCC
* * *
3097 AAAAATTCAAATTTT-ACCCTCGAGACTTCC
1 AAAAATTCCATTTTTGACCC-CGA-A-ATCC
*
3127 AAAAATTCCATTTTT-ACCCTCG-AACCTC
1 AAAAATTCCATTTTTGACCC-CGAAATC-C
* *
3155 AAAAATTTCCATTTTTGACCTCGAAACGTTC
1 AAAAA-TTCCATTTTTGACCCCGAAA--TCC
**
3186 AAAAATTACCA-TTTTG-CCCCGGATGTCC
1 AAAAATT-CCATTTTTGACCCC-GAAATCC
* *
3214 AAAAACTT-CATTTTTGACCTCAAAACTCTC
1 AAAAA-TTCCATTTTTGACCCCGAAA-TC-C
* *
3244 -AAAACTCCCTTTTT-ACCCTC-AAACGTCC
1 AAAAATTCCATTTTTGACCC-CGAAA--TCC
*
3272 AAAAATTTCATTTTTGACCCCGAGAATCC
1 AAAAATTCCATTTTTGACCCCGA-AATCC
3301 -AAAATTACCATTT
1 AAAAATT-CCATTT
3314 CGCCCCCGAG
Statistics
Matches: 275, Mismatches: 47, Indels: 78
0.69 0.12 0.19
Matches are distributed among these distances:
27 8 0.03
28 88 0.32
29 85 0.31
30 80 0.29
31 13 0.05
32 1 0.00
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (28 bp):
AAAAATTCCATTTTTGACCCCGAAATCC
Found at i:6238 original size:17 final size:17
Alignment explanation
Indices: 6216--6249 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6206 CTAAGGATTT
6216 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
6233 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
6250 GTATTAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:7917 original size:16 final size:15
Alignment explanation
Indices: 7896--7925 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7886 CCTTTTGCGA
*
7896 TTTTTCCTTCTTTAT
1 TTTTTTCTTCTTTAT
7911 TTTTTTCTTCTTTAT
1 TTTTTTCTTCTTTAT
7926 ACAAACTCCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTCTTCTTTAT
Found at i:11829 original size:33 final size:33
Alignment explanation
Indices: 11787--11854 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
11777 CATTTATATA
11787 CATAATCTACAACAAGAATTATATAAGTATTTC
1 CATAATCTACAACAAGAATTATATAAGTATTTC
11820 CATAATCTACAACAAGAATTATATAAGTATTTC
1 CATAATCTACAACAAGAATTATATAAGTATTTC
11853 CA
1 CA
11855 GATGAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (33 bp):
CATAATCTACAACAAGAATTATATAAGTATTTC
Found at i:16561 original size:17 final size:17
Alignment explanation
Indices: 16539--16572 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16529 CTAAGAATTT
16539 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
16556 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
16573 GTATTAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:29076 original size:342 final size:342
Alignment explanation
Indices: 28451--29135 Score: 1129
Period size: 342 Copynumber: 2.0 Consensus size: 342
28441 TTTCATTACA
* *
28451 AACATCTCCCTCGAGAGTTTTGGGCTGAAGCTATGCAGTGTGCATGCGACATAATAAATCGCTTA
1 AACATCTCCCTCGAGAGTTTTGGGCTGAAGCTACGCAGTGTGCATGCCACATAATAAATCGCTTA
*
28516 CCACCTTGGCCATGTAAAGAGAAGTCCCCACTTGAAATTTCATATAATATCAAGCCAAATGAAAA
66 CCACCTTGGCCAGGTAAAGAGAAGTCCCCACTTGAAATTTCATATAATATCAAGCCAAATGAAAA
*
28581 TTATTTTCAGCTATTTGGTTCAATTTGTTATGTACATGTTCCAAAATCTAACAGAACCAAACTTG
131 TTATTTTCAGCTATTTGGTTCAATTTGTTATGTACATGTTCCAAAATCTAACAGAAACAAACTTG
*
28646 ACCCAAAAGCGAAGAAGAGCATTCTTGTTGGATATAATCCTTGTAGGAAAGGGTGGAGATGTATA
196 ACCCAAAAGCGAAGAAGAGCATTCTTGTTGGATATAATCCTTGTAGGAAACGGTGGAGATGTATA
*
28711 GATCCAAAAACAAAGAAGTTTGTCACTTCTAGAGACATTGCTTTTGATGAAGTGTCATCTTATTT
261 GATCCAAAAACAAAGAAGTTTGTCACTTCTACAGACATTGCTTTTGATGAAGTGTCATCTTATTT
*
28776 ACCAGAAGCTGGACATG
326 ACCAGAAGCTAGACATG
*
28793 AACATCTCCCTCGAGAGTTTTGGGCTGAAGCTACGTAGTGTGCATGCCACATAATAAATCGCTTA
1 AACATCTCCCTCGAGAGTTTTGGGCTGAAGCTACGCAGTGTGCATGCCACATAATAAATCGCTTA
* * *
28858 CCTCCTTGGCCAGGTAACA-AGAAGTCCCCACTTGAAATTTTATATAATATCAAGCCAAATGTAA
66 CCACCTTGGCCAGGTAA-AGAGAAGTCCCCACTTGAAATTTCATATAATATCAAGCCAAATGAAA
* *
28922 ATTATTTTCAGGTATTTGGTTTAATTTGTTATGTACATGTTCCAAAATCTAACAGAAACAAACTT
130 ATTATTTTCAGCTATTTGGTTCAATTTGTTATGTACATGTTCCAAAATCTAACAGAAACAAACTT
* * * * *
28987 GACCTAAAAGCGAAGAAGTGCATTTTTGTTGGCTATAATCCTTGTAGGAAACGGTGGAGATGTTT
195 GACCCAAAAGCGAAGAAGAGCATTCTTGTTGGATATAATCCTTGTAGGAAACGGTGGAGATGTAT
* * * * **
29052 GGATCTAGAAACAAAGAAGTTTGTCACTTTTACAGATGTTGCTTTTGATGAAGTGTCATCTTATT
260 AGATCCAAAAACAAAGAAGTTTGTCACTTCTACAGACATTGCTTTTGATGAAGTGTCATCTTATT
*
29117 TGCCAGAAGCTAGACATG
325 TACCAGAAGCTAGACATG
29135 A
1 A
29136 TGATGAGCAA
Statistics
Matches: 317, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
342 316 1.00
343 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (342 bp):
AACATCTCCCTCGAGAGTTTTGGGCTGAAGCTACGCAGTGTGCATGCCACATAATAAATCGCTTA
CCACCTTGGCCAGGTAAAGAGAAGTCCCCACTTGAAATTTCATATAATATCAAGCCAAATGAAAA
TTATTTTCAGCTATTTGGTTCAATTTGTTATGTACATGTTCCAAAATCTAACAGAAACAAACTTG
ACCCAAAAGCGAAGAAGAGCATTCTTGTTGGATATAATCCTTGTAGGAAACGGTGGAGATGTATA
GATCCAAAAACAAAGAAGTTTGTCACTTCTACAGACATTGCTTTTGATGAAGTGTCATCTTATTT
ACCAGAAGCTAGACATG
Found at i:32583 original size:18 final size:18
Alignment explanation
Indices: 32541--32584 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
32531 AATATTTAAA
*
32541 AATATTTTTATACTTTTT
1 AATATTTTAATACTTTTT
*
32559 AAAATTTTAATACTTTTT
1 AATATTTTAATACTTTTT
*
32577 GATATTTT
1 AATATTTT
32585 TATATAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (18 bp):
AATATTTTAATACTTTTT
Found at i:37503 original size:21 final size:20
Alignment explanation
Indices: 37479--37517 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
37469 GAACTAAGAT
*
37479 TTCTATCGATACAACTCTAGG
1 TTCTATCAATACAA-TCTAGG
37500 TTCTATCAATACAATCTA
1 TTCTATCAATACAATCTA
37518 AACTTCTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (20 bp):
TTCTATCAATACAATCTAGG
Found at i:39354 original size:21 final size:20
Alignment explanation
Indices: 39327--39378 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
39317 TTTATTTATA
*
39327 TTAATTTAGTCATTTTTAATTT
1 TTAATTTAAT-ATTTTT-ATTT
*
39349 TTATTTTAATATTTTTATTT
1 TTAATTTAATATTTTTATTT
39369 TTAATTTAAT
1 TTAATTTAAT
39379 GTTTCTATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 13 0.48
21 6 0.22
22 8 0.30
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTAATTTAATATTTTTATTT
Found at i:39387 original size:20 final size:20
Alignment explanation
Indices: 39345--39387 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
39335 GTCATTTTTA
* *
39345 ATTTTTATTTTAATATTTTT
1 ATTTTTAATTTAATATTTCT
*
39365 ATTTTTAATTTAATGTTTCT
1 ATTTTTAATTTAATATTTCT
39385 ATT
1 ATT
39388 CTATTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTTTAATTTAATATTTCT
Found at i:43528 original size:42 final size:43
Alignment explanation
Indices: 43471--43660 Score: 212
Period size: 42 Copynumber: 4.5 Consensus size: 43
43461 TTATGCTCTA
* * * *
43471 TCGAGTCATAAGTCTTCCTTTAATTATATTCTCATTCTCATCC
1 TCGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
*
43514 T-GAGACATGAGTCTTCCTTTAATCATAATCTCATTCTC-TTC
1 TCGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
43555 TCGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCAT-C
1 TCGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
* * * * * *
43597 TCAAGGCATGAGTCTTCCATTT-ATACA-AATTGTCGTGCTCAACC
1 TCGAGACATGAGTCTTCC-TTTAAT-CATAA-TCTCATTCTCATCC
43641 -CGAGACATGAGTCTTCCTTT
1 TCGAGACATGAGTCTTCCTTT
43661 TTATACATCA
Statistics
Matches: 128, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
41 3 0.02
42 94 0.73
43 30 0.23
44 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (43 bp):
TCGAGACATGAGTCTTCCTTTAATCATAATCTCATTCTCATCC
Found at i:52341 original size:17 final size:16
Alignment explanation
Indices: 52308--52341 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
52298 CTTGAAACCC
*
52308 TAAATATTAACCATTA
1 TAAATATTAAACATTA
52324 TAAATATCTAAACATTA
1 TAAATAT-TAAACATTA
52341 T
1 T
52342 TCTAATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATTAAACATTA
Found at i:56951 original size:2 final size:2
Alignment explanation
Indices: 56944--56983 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
56934 ATAGTCCATA
56944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56984 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56988 original size:2 final size:2
Alignment explanation
Indices: 56983--57014 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56973 TATATATATA
56983 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
57015 ATAATAGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:66104 original size:43 final size:43
Alignment explanation
Indices: 66043--66130 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
66033 GTCTGTTAAG
66043 AAAGGCTCTCTATGGGTTGTAACAAGCTCCCAAAGCATGGTAC
1 AAAGGCTCTCTATGGGTTGTAACAAGCTCCCAAAGCATGGTAC
66086 AAAGGCTCTCTATGGGTTGTAACAAGCTCCCAAAGCATGGTAC
1 AAAGGCTCTCTATGGGTTGTAACAAGCTCCCAAAGCATGGTAC
66129 AA
1 AA
66131 TAAGATAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (43 bp):
AAAGGCTCTCTATGGGTTGTAACAAGCTCCCAAAGCATGGTAC
Found at i:66114 original size:21 final size:21
Alignment explanation
Indices: 66047--66114 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
66037 GTTAAGAAAG
66047 GCTCTCTATGGGTTGTAACAA
1 GCTCTCTATGGGTTGTAACAA
* * * ** *
66068 GCTCCCAAAGCATGGT-ACAAA
1 GCTCTCTATGGGTTGTAAC-AA
66089 GGCTCTCTATGGGTTGTAACAA
1 -GCTCTCTATGGGTTGTAACAA
66111 GCTC
1 GCTC
66115 CCAAAGCATG
Statistics
Matches: 32, Mismatches: 12, Indels: 6
0.64 0.24 0.12
Matches are distributed among these distances:
20 2 0.06
21 16 0.50
22 12 0.38
23 2 0.06
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (21 bp):
GCTCTCTATGGGTTGTAACAA
Found at i:77314 original size:18 final size:18
Alignment explanation
Indices: 77279--77336 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
77269 AATAATTTTC
*
77279 AAAA-TTCTAAATACTTAT
1 AAAATTTCTAAA-AATTAT
*
77297 AAAATTTCTAAAATTTAT
1 AAAATTTCTAAAAATTAT
* * *
77315 ATATTTTTTAAAAATTAT
1 AAAATTTCTAAAAATTAT
77333 AAAA
1 AAAA
77337 ATTTTGAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 25 0.78
19 7 0.22
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTTCTAAAAATTAT
Found at i:77341 original size:18 final size:18
Alignment explanation
Indices: 77279--77347 Score: 50
Period size: 18 Copynumber: 3.7 Consensus size: 18
77269 AATAATTTTC
* *
77279 AAAATTCTAAATACTTAT-
1 AAAATTTTAAA-AATTATA
*
77297 AAAATTTCTAAAATTTATA
1 AAAATTT-TAAAAATTATA
* **
77316 TATTTTTTAAAAATTATA
1 AAAATTTTAAAAATTATA
77334 AAAATTTTGAAAAA
1 AAAATTTT-AAAAA
77348 AAAAATTCTA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
18 26 0.67
19 13 0.33
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (18 bp):
AAAATTTTAAAAATTATA
Found at i:78592 original size:22 final size:22
Alignment explanation
Indices: 78566--78621 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
78556 ATATTTAAAC
78566 AATAATAAAAAAAT-AGTAGTAA
1 AATAATAAAAAAATGA-TAGTAA
* *
78588 TATAATAATAAAATGATAGTAA
1 AATAATAAAAAAATGATAGTAA
*
78610 AATAATGAAAAA
1 AATAATAAAAAA
78622 CAGTAAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (22 bp):
AATAATAAAAAAATGATAGTAA
Found at i:86947 original size:19 final size:18
Alignment explanation
Indices: 86925--86962 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
86915 CAAAAAAAGG
86925 AGAAAAAGAGAAAAAAGAA
1 AGAAAAA-AGAAAAAAGAA
*
86944 AGAAAAAATAAAAAAGAA
1 AGAAAAAAGAAAAAAGAA
86962 A
1 A
86963 ATAGAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (18 bp):
AGAAAAAAGAAAAAAGAA
Found at i:86962 original size:25 final size:26
Alignment explanation
Indices: 86927--86976 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
86917 AAAAAAGGAG
86927 AAAAAGAGAAAAAAGAAAGAAAAAAT
1 AAAAAGAGAAAAAAGAAAGAAAAAAT
* *
86953 AAAAA-AGAAAATAGAAGGAAAAAA
1 AAAAAGAGAAAAAAGAAAGAAAAAA
86977 ATGAGAGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (26 bp):
AAAAAGAGAAAAAAGAAAGAAAAAAT
Found at i:87435 original size:112 final size:113
Alignment explanation
Indices: 87290--87506 Score: 337
Period size: 112 Copynumber: 1.9 Consensus size: 113
87280 ATGTCTGTCA
*
87290 TTTTTAAATCTTTTCATTCATACGAACTTTGCCTCTAATAAAATTCAATTTTATCCACCTTACAA
1 TTTTTAAATCTTTTCATTCACACGAACTTTGCCTCTAATAAAATTCAATTTTATCCACCTTACAA
* *
87355 CTCTATTCAAGCATGTTTGCATTAAAATAACGGTTAGTGGACCAATGG
66 CACTATTCAAGCATGTTTGCACTAAAATAACGGTTAGTGGACCAATGG
* * *
87403 TTTTT-AATCTTTTCATTCACACGAGCTTTGCCTCTAATAAAATTTAATTTTATCCACTTTACAA
1 TTTTTAAATCTTTTCATTCACACGAACTTTGCCTCTAATAAAATTCAATTTTATCCACCTTACAA
* * * *
87467 CACTATTCAAGTATTTTTGCACTGAAATGACGGTTAGTGG
66 CACTATTCAAGCATGTTTGCACTAAAATAACGGTTAGTGG
87507 CCTAACGGTA
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
112 89 0.95
113 5 0.05
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (113 bp):
TTTTTAAATCTTTTCATTCACACGAACTTTGCCTCTAATAAAATTCAATTTTATCCACCTTACAA
CACTATTCAAGCATGTTTGCACTAAAATAACGGTTAGTGGACCAATGG
Found at i:88015 original size:49 final size:49
Alignment explanation
Indices: 87943--88927 Score: 752
Period size: 49 Copynumber: 20.1 Consensus size: 49
87933 TTAAACCATG
* * * * *
87943 TACCCTAAAGATGTAGAGGGAAAGATTGAAGCCATAATAGTGAATCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* *
87992 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGTAATGGCGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* *
88041 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCTGTAATGACGAATCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* * * *
88090 TACCTTAGAGATATAGAGGGAAAGATTGAAGCCGCT-ATGGTGAATCTT-
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCG-TAATGGCGAATCTTA
* * * * * *
88138 TAAACCTAGAGATGTTGAGGGAAAGACTGAAGTCGCAACT-GCAAATCTTA
1 T-ACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAA-TGGCGAATCTTA
* ** * * * * *
88188 TACCCTTGAGACATGGAGGGAAAGGTTGAAGTCGTAACGACGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
** * * * * * *
88237 TATGCTAGAGATGTGAAGGGAAAGATTGAACCCATAACGGTGAATCTTG
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* * * * ** * *
88286 TACCTTAGAGATAT-AATGGGAAAGAATGAAGCCACAATGACGAATCTTG
1 TACCCTAGAGATGTGGA-GGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* * * * * *
88335 TACCTTAGAGATGT-GATGGAAAAGATTGAAG-CGACAACGGTGAATCTCA
1 TACCCTAGAGATGTGGA-GGGAAAGATTGAAGCCG-TAATGGCGAATCTTA
* * * * * * *
88384 TACCCTAGAGATGTGGTGGGAAAGGTTTAAGCCGCAACGAC-AAACTTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATC-TTA
* * * * * * *
88433 TACCTTAGAGATGT-GATGGGAAAGATTTAA-CTCGCAACGGTGAATCCTG
1 TACCCTAGAGATGTGGA-GGGAAAGATTGAAGC-CGTAATGGCGAATCTTA
* * * * * ** *
88482 TACCCTAGATATATAGAGGGAAAGGTTGAAGCCGCAATGATGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* * * * *
88531 TACCCTAGAGATGTGGAGGGAAAGGTTGAATCCATAATGGTGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* * * *
88580 TACCTTAGAGATGT-GATGGGAAAGATTGAAGTCGTAACGACGAATCTTA
1 TACCCTAGAGATGTGGA-GGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* * * * *
88629 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGTAAAGACAAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* *** ** * *
88678 TACCTTAGAGATGTATTGGGAAAGATTGAATTCGTAACGG-TAATCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* * * * * *
88726 TACACTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* * * * *
88775 TACCTTAAAGATGT-GATGGGAAATATTGAAGCCGCAATGGCGAATCTTG
1 TACCCTAGAGATGTGGA-GGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* * * * *
88824 TACCCTAAAGATATGGAGGGAAAGGTTGAAGCCGAAATGGCGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
* * * ** *
88873 TACCATAGTGATGTGAAGGGAAAGATTGAAGCCACAATGGTGAATCTTA
1 TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
88922 TACCCT
1 TACCCT
88928 GAAGATGAAG
Statistics
Matches: 744, Mismatches: 171, Indels: 42
0.78 0.18 0.04
Matches are distributed among these distances:
48 49 0.07
49 679 0.91
50 16 0.02
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (49 bp):
TACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGTAATGGCGAATCTTA
Found at i:90116 original size:19 final size:19
Alignment explanation
Indices: 90083--90122 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
90073 GTTGGTTAAA
*
90083 AAAGTCAACAGTCAATGTC
1 AAAGTCAACAGTCAAGGTC
90102 AAAGTCAAC-GATCAAGGTC
1 AAAGTCAACAG-TCAAGGTC
90121 AA
1 AA
90123 TGGGTCGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.17
Consensus pattern (19 bp):
AAAGTCAACAGTCAAGGTC
Found at i:100648 original size:14 final size:14
Alignment explanation
Indices: 100629--100674 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
100619 TTAAATAAAA
100629 ATAATATAAAATTT
1 ATAATATAAAATTT
*
100643 ATAATATATAACTTTT
1 ATAATATA-AA-ATTT
100659 ATAA-A-AAAATTT
1 ATAATATAAAATTT
100671 ATAA
1 ATAA
100675 AGTGTCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 7 0.25
13 2 0.07
14 9 0.32
15 3 0.11
16 7 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATATAAAATTT
Found at i:119709 original size:32 final size:33
Alignment explanation
Indices: 119668--119746 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
119658 ATCTAGAAGG
*
119668 GCATTAATTTCAAGGAAGAAATTAGGC-AAAAA
1 GCATTAATTTCAAGGAAGAAATTAAGCAAAAAA
* *
119700 GCATTAATTTCTACGAAGAAATTAAGCAAAAAA
1 GCATTAATTTCAAGGAAGAAATTAAGCAAAAAA
119733 GCATTAATTTCAAG
1 GCATTAATTTCAAG
119747 ATAAAAGATG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 24 0.59
33 17 0.41
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.25
Consensus pattern (33 bp):
GCATTAATTTCAAGGAAGAAATTAAGCAAAAAA
Found at i:125462 original size:17 final size:16
Alignment explanation
Indices: 125436--125492 Score: 71
Period size: 17 Copynumber: 3.5 Consensus size: 16
125426 GCCCCCTTTT
125436 TTTAATTTATTTTAAA
1 TTTAATTTATTTTAAA
125452 TTTAGATTTATTTTAAA
1 TTTA-ATTTATTTTAAA
* *
125469 -TAAATTTAATTTTAAT
1 TTTAATTT-ATTTTAAA
125485 TTTAATTT
1 TTTAATTT
125493 CAAAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 4 0.11
16 13 0.37
17 18 0.51
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTAATTTATTTTAAA
Found at i:125472 original size:21 final size:22
Alignment explanation
Indices: 125448--125489 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
125438 TAATTTATTT
125448 TAAATTTAGA-TTT-ATTTTAAA
1 TAAATTTA-ATTTTAATTTTAAA
125469 TAAATTTAATTTTAATTTTAA
1 TAAATTTAATTTTAATTTTAA
125490 TTTCAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 11 0.58
22 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TAAATTTAATTTTAATTTTAAA
Found at i:127273 original size:19 final size:19
Alignment explanation
Indices: 127249--127285 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
127239 ATTGTCATCG
127249 TCGCACACTGTCGTTACTA
1 TCGCACACTGTCGTTACTA
* *
127268 TCGCACGCTGTTGTTACT
1 TCGCACACTGTCGTTACT
127286 GCCATACCAT
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:0.16, C:0.30, G:0.19, T:0.35
Consensus pattern (19 bp):
TCGCACACTGTCGTTACTA
Found at i:130375 original size:19 final size:19
Alignment explanation
Indices: 130339--130376 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
130329 ATAGCTTATT
*
130339 TTATATTTATTTGAACATA
1 TTATATTTATTTAAACATA
130358 TTATATTT-TTTAAGACATA
1 TTATATTTATTTAA-ACATA
130377 AAGTGGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (19 bp):
TTATATTTATTTAAACATA
Found at i:130476 original size:23 final size:22
Alignment explanation
Indices: 130450--130493 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
130440 AAAATATTTC
130450 ATTAAATAACTTGGGTTGAATTA
1 ATTAAATAACTTGGGTT-AATTA
* *
130473 ATTAATTAAGTTGGGTTAATT
1 ATTAAATAACTTGGGTTAATT
130494 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.43
Consensus pattern (22 bp):
ATTAAATAACTTGGGTTAATTA
Found at i:137429 original size:23 final size:23
Alignment explanation
Indices: 137399--137444 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
137389 TGAACTGGCG
137399 GGGAAATTTCTACAAAAGTTTTT
1 GGGAAATTTCTACAAAAGTTTTT
137422 GGGAAATTTCTACAAAAGTTTTT
1 GGGAAATTTCTACAAAAGTTTTT
137445 CCTTATGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (23 bp):
GGGAAATTTCTACAAAAGTTTTT
Found at i:139213 original size:20 final size:21
Alignment explanation
Indices: 139172--139215 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
139162 ATTTTGATTC
139172 TAAAATATTTAAAAAGAATTA
1 TAAAATATTTAAAAAGAATTA
*
139193 TAAAA-ATTATAAAAA-AGTTA
1 TAAAATATT-TAAAAAGAATTA
139213 TAA
1 TAA
139216 TGAATCTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
TAAAATATTTAAAAAGAATTA
Found at i:142603 original size:17 final size:17
Alignment explanation
Indices: 142582--142635 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
142572 TCAAACCTTT
*
142582 AAACCCAAACCCAAACT
1 AAACCCAAACCCAAACC
142599 AAA-CCAAACCCAAACC
1 AAACCCAAACCCAAACC
* *
142615 AAAACCAAAACCAAACC
1 AAACCCAAACCCAAACC
142632 AAAC
1 AAAC
142636 TCAATTGAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 15 0.45
17 18 0.55
ACGTcount: A:0.59, C:0.39, G:0.00, T:0.02
Consensus pattern (17 bp):
AAACCCAAACCCAAACC
Found at i:142607 original size:5 final size:5
Alignment explanation
Indices: 142586--142635 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 5
142576 ACCTTTAAAC
*
142586 CCAAA CCCAAA CTAAA CCAAA CCCAAA CCAAAA CCAAAA CCAAA CCAAA
1 CCAAA -CCAAA CCAAA CCAAA -CCAAA CC-AAA CC-AAA CCAAA CCAAA
142635 C
1 C
142636 TCAATTGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 19 0.47
6 21 0.52
ACGTcount: A:0.58, C:0.40, G:0.00, T:0.02
Consensus pattern (5 bp):
CCAAA
Found at i:142613 original size:11 final size:11
Alignment explanation
Indices: 142582--142635 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
142572 TCAAACCTTT
142582 AAACCCAAACCC
1 AAACCCAAA-CC
*
142594 AAA-CTAAACC
1 AAACCCAAACC
142604 AAACCCAAACC
1 AAACCCAAACC
*
142615 AAAACCAAAACC
1 -AAACCCAAACC
142627 AAA-CCAAAC
1 AAACCCAAAC
142636 TCAATTGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 10 0.28
11 13 0.36
12 13 0.36
ACGTcount: A:0.59, C:0.39, G:0.00, T:0.02
Consensus pattern (11 bp):
AAACCCAAACC
Found at i:142730 original size:13 final size:13
Alignment explanation
Indices: 142712--142764 Score: 72
Period size: 13 Copynumber: 4.0 Consensus size: 13
142702 GTCGTTGATC
142712 GATCGTTGACTTT
1 GATCGTTGACTTT
*
142725 GATCGTTGACCGTT
1 GATCGTTGA-CTTT
142739 GATCGTTGACTTT
1 GATCGTTGACTTT
142752 GA-CTGTTGACTTT
1 GATC-GTTGACTTT
142765 TTTGAAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 1 0.03
13 23 0.64
14 12 0.33
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (13 bp):
GATCGTTGACTTT
Found at i:142742 original size:14 final size:14
Alignment explanation
Indices: 142712--142748 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
142702 GTCGTTGATC
*
142712 GATCGTTGA-CTTT
1 GATCGTTGACCGTT
142725 GATCGTTGACCGTT
1 GATCGTTGACCGTT
142739 GATCGTTGAC
1 GATCGTTGAC
142749 TTTGACTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.38
Consensus pattern (14 bp):
GATCGTTGACCGTT
Found at i:144239 original size:2 final size:2
Alignment explanation
Indices: 144232--144261 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
144222 TTTATATTAC
144232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
144262 GATTTATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:149093 original size:14 final size:14
Alignment explanation
Indices: 149074--149108 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
149064 TGGTCCAGGT
149074 AAATTTCGAGGGTG
1 AAATTTCGAGGGTG
*
149088 AAATTTCGATGGTG
1 AAATTTCGAGGGTG
149102 AAATTTC
1 AAATTTC
149109 TTCTAAGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (14 bp):
AAATTTCGAGGGTG
Found at i:149832 original size:5 final size:5
Alignment explanation
Indices: 149812--149886 Score: 60
Period size: 5 Copynumber: 14.0 Consensus size: 5
149802 TCAAACCTTT
* ** * *
149812 AAACC TAAACCC AAACC AAACC AAACC AAACC CAATT GAACC AAGTCC
1 AAACC -AAA-CC AAACC AAACC AAACC AAACC AAACC AAACC AA-ACC
149860 AAACCC AAACCC AAACC AAACC AAACC
1 AAA-CC AAA-CC AAACC AAACC AAACC
149887 CAATTGAACC
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
5 34 0.60
6 21 0.37
7 2 0.04
ACGTcount: A:0.52, C:0.40, G:0.03, T:0.05
Consensus pattern (5 bp):
AAACC
Found at i:149880 original size:43 final size:42
Alignment explanation
Indices: 149818--149901 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 42
149808 CTTTAAACCT
149818 AAACCCAAACCAAACCAAACCAAACCCAATTGAACCAAGTCC
1 AAACCCAAACCAAACCAAACCAAACCCAATTGAACCAAGTCC
149860 AAACCCAAACCCAAACCAAACCAAACCCAATTGAACCAAGTC
1 AAACCCAAA-CCAAACCAAACCAAACCCAATTGAACCAAGTC
149902 AGACCGTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 9 0.22
43 32 0.78
ACGTcount: A:0.50, C:0.38, G:0.05, T:0.07
Consensus pattern (42 bp):
AAACCCAAACCAAACCAAACCAAACCCAATTGAACCAAGTCC
Found at i:149889 original size:6 final size:6
Alignment explanation
Indices: 149812--149889 Score: 58
Period size: 6 Copynumber: 13.3 Consensus size: 6
149802 TCAAACCTTT
* * **
149812 AAACCT AAACCC AAA-CC AAA-CC AAA-CC AAACCC AATTGAACC AAGTCC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AA---ACCC AAACCC
149860 AAACCC AAACCC AAA-CC AAA-CC AAACCC AA
1 AAACCC AAACCC AAACCC AAACCC AAACCC AA
149890 TTGAACCAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
5 25 0.41
6 31 0.51
9 5 0.08
ACGTcount: A:0.53, C:0.40, G:0.03, T:0.05
Consensus pattern (6 bp):
AAACCC
Found at i:166453 original size:52 final size:53
Alignment explanation
Indices: 166375--166561 Score: 258
Period size: 52 Copynumber: 3.6 Consensus size: 53
166365 TAAATGAAAA
166375 GAGGTCC-GATGGCTATGTGTCATCATGAGTATATGAATCCTTTACGGATTAT
1 GAGGTCCTGATGGCTATGTGTCATCATGAGTATATGAATCCTTTACGGATTAT
* * *
166427 GAGGTTC-GATGCCTATGTATCATCATGAGTATATGAATCCTTTACAGG-TTAT
1 GAGGTCCTGATGGCTATGTGTCATCATGAGTATATGAATCCTTTAC-GGATTAT
* * **
166479 GAGGT-CTGATAGCTATGTGTCATCGTGAGTATATGAATCCTTTATAGATTAT
1 GAGGTCCTGATGGCTATGTGTCATCATGAGTATATGAATCCTTTACGGATTAT
*
166531 GAGGTCCTG-TGGCTATGTGTCACCATGAGTA
1 GAGGTCCTGATGGCTATGTGTCATCATGAGTA
166562 CACGAATGAA
Statistics
Matches: 119, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
51 2 0.02
52 112 0.94
53 5 0.04
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (53 bp):
GAGGTCCTGATGGCTATGTGTCATCATGAGTATATGAATCCTTTACGGATTAT
Found at i:168238 original size:35 final size:35
Alignment explanation
Indices: 168197--168265 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
168187 ACCTAGATTC
*
168197 TAAGAGATTGCTTGCAAGTCAAGTTAAACAAAATT
1 TAAGAGATTGCTTGCAAGTCAACTTAAACAAAATT
* *
168232 TAAGAGATTGCTTGCAATTCAACTTAAATAAAAT
1 TAAGAGATTGCTTGCAAGTCAACTTAAACAAAAT
168266 ATATTATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (35 bp):
TAAGAGATTGCTTGCAAGTCAACTTAAACAAAATT
Found at i:169653 original size:105 final size:105
Alignment explanation
Indices: 169529--169723 Score: 239
Period size: 105 Copynumber: 1.9 Consensus size: 105
169519 AACTTTTTTT
* * * * * * * * * * *
169529 TTGCAAAGGGCATCTATCAATGTATTATACGTCACAACATTAGGATCATTGCCTTTCT-TTGTCA
1 TTGCAAAGCGCATCGATCAATATAATAAACCTAACAACATTAGGATCAATGCCTTGCTAAT-ACA
*
169593 TTCTACCAATAATATCTTTAGCTTCAAAAACCATCTCGTCC
65 TTCTACCAACAATATCTTTAGCTTCAAAAACCATCTCGTCC
*
169634 TTGCAAAGCGCATCGATCAATATAATAAACCTAACAACATTAGGCTCAATGCCTTGCTAATACAT
1 TTGCAAAGCGCATCGATCAATATAATAAACCTAACAACATTAGGATCAATGCCTTGCTAATACAT
* *
169699 TGTCCCAACAATATCTTTAGCTTCA
66 TCTACCAACAATATCTTTAGCTTCA
169724 GAAATCAACC
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
105 73 0.99
106 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (105 bp):
TTGCAAAGCGCATCGATCAATATAATAAACCTAACAACATTAGGATCAATGCCTTGCTAATACAT
TCTACCAACAATATCTTTAGCTTCAAAAACCATCTCGTCC
Found at i:169963 original size:105 final size:105
Alignment explanation
Indices: 169795--170194 Score: 437
Period size: 105 Copynumber: 3.8 Consensus size: 105
169785 CTTATAGTGT
* ** * ** * ** * * * *
169795 CAACAATAACTTCAACTTTAGAAACCAAACCTTTCTTGCAAAGCATATCAATGAGTATACTATAC
1 CAACAATATCTTCGGCTTTAAAAACCATTCCCTTCTTGCAAAGCGCATCGATCAATATACTATAT
* ** * *
169860 GTGACAACATTAGGCTCGATGTCTTGCGTTGTCATTTTGC
66 GTGACAACATCAGGCTTAATGCCTTGCTTTGTCATTTTGC
* ** * * *
169900 CAACAAAATCTTTAGCTTCAAAAACC-TT-CTTGGTCTTGCAAAGCGCATCGATCAATATGCTAT
1 CAACAATATCTTCGGCTTTAAAAACCATTCCCT--TCTTGCAAAGCGCATCGATCAATATACTAT
* *
169963 ATGTGACAACATCACGCTTAATACCTTGCTTTGTCATTGTT-C
64 ATGTGACAACATCAGGCTTAATGCCTTGCTTTGTCATT-TTGC
* * *
170005 CAACGATATCTTCGGCTTTAAAAACCATTCCCTTCTTGCAAAGCGCATAGATCAATATATTATAT
1 CAACAATATCTTCGGCTTTAAAAACCATTCCCTTCTTGCAAAGCGCATCGATCAATATACTATAT
* *
170070 GTGACAACATTAGGCTTAATGCCTTGCTTTGTCATTGTGC
66 GTGACAACATCAGGCTTAATGCCTTGCTTTGTCATTTTGC
* * *
170110 CAACAATATCTTCGGCTTTAGAAACCATTCCCTTCTTGCAAAGTGCATCAATCAATATACTATAT
1 CAACAATATCTTCGGCTTTAAAAACCATTCCCTTCTTGCAAAGCGCATCGATCAATATACTATAT
*
170175 GTAACAACATCAGGCTTAAT
66 GTGACAACATCAGGCTTAAT
170195 TCATTACTTT
Statistics
Matches: 246, Mismatches: 43, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
103 3 0.01
104 1 0.00
105 236 0.96
106 4 0.02
107 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (105 bp):
CAACAATATCTTCGGCTTTAAAAACCATTCCCTTCTTGCAAAGCGCATCGATCAATATACTATAT
GTGACAACATCAGGCTTAATGCCTTGCTTTGTCATTTTGC
Found at i:178065 original size:14 final size:14
Alignment explanation
Indices: 178046--178076 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
178036 CTTACATCGC
178046 AAACAAAATAAAAT
1 AAACAAAATAAAAT
*
178060 AAACAAAATACAAT
1 AAACAAAATAAAAT
178074 AAA
1 AAA
178077 AACCCAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (14 bp):
AAACAAAATAAAAT
Found at i:186250 original size:40 final size:40
Alignment explanation
Indices: 186180--186268 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
186170 AAGTCAACGA
** ** *
186180 TCAATGGGTTGAGTCAACGATTTTGAGTCAATGGGTCGGG
1 TCAATGGGTCAAGTCAACGATTCAGAGTCAACGGGTCGGG
**
186220 TCAATGGGTCAAGTCAACGAGTTCAG-GTCAACGGGTTTGG
1 TCAATGGGTCAAGTCAACGA-TTCAGAGTCAACGGGTCGGG
186260 TCAATGGGT
1 TCAATGGGT
186269 TCACTTGGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 38 0.93
41 3 0.07
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.28
Consensus pattern (40 bp):
TCAATGGGTCAAGTCAACGATTCAGAGTCAACGGGTCGGG
Found at i:186270 original size:27 final size:27
Alignment explanation
Indices: 186180--186271 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 27
186170 AAGTCAACGA
* **
186180 TCAATGGGTTGA-GTCAACGATTTTGAG
1 TCAATGGGTTCAGGTCAACGGGTTTG-G
* * ***
186207 TCAATGGG-TCGGGTCAATGGGTCAAG
1 TCAATGGGTTCAGGTCAACGGGTTTGG
* *
186233 TCAACGAGTTCAGGTCAACGGGTTTGG
1 TCAATGGGTTCAGGTCAACGGGTTTGG
186260 TCAATGGGTTCA
1 TCAATGGGTTCA
186272 CTTGGTTTGA
Statistics
Matches: 46, Mismatches: 17, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
26 8 0.17
27 38 0.83
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (27 bp):
TCAATGGGTTCAGGTCAACGGGTTTGG
Found at i:187550 original size:2 final size:2
Alignment explanation
Indices: 187543--187589 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
187533 TAGTAACAAA
187543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
187585 AT AT A
1 AT AT A
187590 AAGAATTAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:190325 original size:21 final size:20
Alignment explanation
Indices: 190292--190333 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
190282 TTATAAAGGT
190292 TAAAAATGTAATAATATGTTA
1 TAAAAATGTAAT-ATATGTTA
*
190313 TAAAAAT-TCAATATATTTTA
1 TAAAAATGT-AATATATGTTA
190333 T
1 T
190334 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (20 bp):
TAAAAATGTAATATATGTTA
Found at i:197883 original size:23 final size:23
Alignment explanation
Indices: 197857--197903 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
197847 ACCAGATTCT
*
197857 ATCAGAAACGAAAAATTCAAAAG
1 ATCAAAAACGAAAAATTCAAAAG
*
197880 ATCAAAAACGAAAAGTTCAAAAG
1 ATCAAAAACGAAAAATTCAAAAG
197903 A
1 A
197904 AGAACAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13
Consensus pattern (23 bp):
ATCAAAAACGAAAAATTCAAAAG
Found at i:211738 original size:34 final size:34
Alignment explanation
Indices: 211699--211766 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
211689 ACCAAATGAT
211699 GTAAGGGAATACCTTGAGATACTGAAAACGAATA
1 GTAAGGGAATACCTTGAGATACTGAAAACGAATA
*
211733 GTAAGGGAATACCTTGAGATACTGAAAACTAATA
1 GTAAGGGAATACCTTGAGATACTGAAAACGAATA
211767 TATTCAGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (34 bp):
GTAAGGGAATACCTTGAGATACTGAAAACGAATA
Found at i:212044 original size:62 final size:61
Alignment explanation
Indices: 211943--212066 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 61
211933 GAGTTTGGAC
* *
211943 ATCATAAAAAAAACATTCAAAGTTTTTGAGTTTACCGAGTTTAAACAATTATAAAGTGTGT
1 ATCACAAAAAAAACATTCAAAGTTTTTGAGTTTACCGAGTTTAAACAATCATAAAGTGTGT
* *
212004 ATCACAAAAAAAATATTCAAAGTTTTTTGAGTTTATCGAGTTTAAACAATCATAAAGTGTGT
1 ATCACAAAAAAAACATTCAAAG-TTTTTGAGTTTACCGAGTTTAAACAATCATAAAGTGTGT
212066 A
1 A
212067 AATATTAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
61 20 0.34
62 38 0.66
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (61 bp):
ATCACAAAAAAAACATTCAAAGTTTTTGAGTTTACCGAGTTTAAACAATCATAAAGTGTGT
Found at i:212411 original size:25 final size:24
Alignment explanation
Indices: 212376--212423 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
212366 GGTGACAAAA
*
212376 ATAATATTTATTTTTAATATTAAT
1 ATAATATTTATCTTTAATATTAAT
212400 ATAATAATTTATCTTTAATATTAA
1 ATAAT-ATTTATCTTTAATATTAA
212424 CTGTGGGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATAATATTTATCTTTAATATTAAT
Found at i:213330 original size:109 final size:112
Alignment explanation
Indices: 213180--213395 Score: 289
Period size: 109 Copynumber: 1.9 Consensus size: 112
213170 CAACGAACAT
* * *
213180 TTATCGATTTTAAATAGGATGTTCAATTACTTAGGTTCAAAG-AAAAAACT-ATACCCATCACGT
1 TTATCGATTTTAAATAGGATCTTCAATTACTTAGGTTCAAAGAAAAAAAATCATACCCAACACGT
* * *
213243 TA-AGACACAATTTTTTG-AGTCCCTAAAATAACAGAACATTCATCAC
66 TAGAG-CACAATTTCTCGAAGTCCCTAAAATAAAAGAACATTCATCAC
*
213289 TTATCGATTTTAAATAGGATACTT-AATTATTTAGGTTCAAAGAAAAAAAAATCATACCCAACAC
1 TTATCGATTTTAAATAGGAT-CTTCAATTACTTAGGTTCAAAG-AAAAAAAATCATACCCAACAC
* *
213353 GTTAGAGCACAATTTCTCGAATTCCTTAAAATAAAAGAACATT
64 GTTAGAGCACAATTTCTCGAAGTCCCTAAAATAAAAGAACATT
213396 GCCTTGATTT
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
109 37 0.40
110 2 0.02
111 7 0.08
112 24 0.26
113 22 0.24
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (112 bp):
TTATCGATTTTAAATAGGATCTTCAATTACTTAGGTTCAAAGAAAAAAAATCATACCCAACACGT
TAGAGCACAATTTCTCGAAGTCCCTAAAATAAAAGAACATTCATCAC
Found at i:215370 original size:46 final size:45
Alignment explanation
Indices: 215302--215944 Score: 680
Period size: 45 Copynumber: 14.1 Consensus size: 45
215292 ACTTTTGTGA
* * *
215302 GATGGTAGCTTCAATCTACCCCT-TTGGATTTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTT-GA-TTAGGGGTAAAAGATTG
* * * *
215348 GATGGTGGCTTCAATCTGCCCCTCTAGATTTGGGATATAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * * * * *
215393 GATGCAGTGACTTCAATCT-CCTCCTCTAGATTTGGGATATAAGACTG
1 GATG--GTGGCTTCAATCTGCC-CCTCTTGATTAGGGGTAAAAGATTG
* * *
215440 GACGCGGTGACTTCAATATGCCCCTCTTGATTAGGGGTAAAAGATTG
1 GA--TGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * *
215487 GATGGTGACTTCAATCTACCCCTCTTAATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * * *
215532 GATGGTGGTTTCAATCTGTCCTTCTTGACTTAGGGGTAAAAGATTA
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
* * * * *
215578 AATGGTAGTTTCAATCTACCCCTCTTGACTTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
* * *
215624 GATGGTGACTTCAATATGTCCCTCTTGACTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
*
215670 GATGGTGGCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * * *
215715 GATGGTGACTTCAATCTGCCCCTCTTAACTTAGGGGT-AAATATTC
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
* *
215760 GATGGTGGCTTTAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTG
* * * * * *
215806 GATTGTAGTTTCAATGTACCCCTCTTGATTAAGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * * *
215851 GATGGTAGCTTCAATTTACCCCTCTTGATTAGGGGTAAAAGATTA
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* * * **
215896 GATGCTAGTTTCAATCAACCCCTCTTGATTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
215941 GATG
1 GATG
215945 AGGTGATGTA
Statistics
Matches: 512, Mismatches: 75, Indels: 21
0.84 0.12 0.03
Matches are distributed among these distances:
45 258 0.50
46 178 0.35
47 73 0.14
48 2 0.00
49 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (45 bp):
GATGGTGGCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTG
Found at i:215583 original size:91 final size:90
Alignment explanation
Indices: 215302--215944 Score: 634
Period size: 91 Copynumber: 7.0 Consensus size: 90
215292 ACTTTTGTGA
* *
215302 GATGGT-AGCTTCAATCTACCCCT-TTGGATTTAAGGGTAAAAGATTGGATGGTGGCTTCAATCT
1 GATGGTGA-CTTCAATCTACCCCTCTT--AATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCT
* * * *
215365 GCCCCTCTAGATTTGGGATATAAGATTG
63 GCCCCTCTTGATTAGGGGTAAAAGATTG
* * * * * *
215393 GATGCAGTGACTTCAATCT-CCTCCTC-TAGATTTGGGATATAAGACTGGACGCGGTGACTTCAA
1 GATG--GTGACTTCAATCTACC-CCTCTTA-ATTAGGGGTAAAAGATTGGA--TGGTGGCTTCAA
*
215456 TATGCCCCTCTTGATTAGGGGTAAAAGATTG
60 TCTGCCCCTCTTGATTAGGGGTAAAAGATTG
* *
215487 GATGGTGACTTCAATCTACCCCTCTTAATTAGGGGTAAAAGATTGGATGGTGGTTTCAATCTGTC
1 GATGGTGACTTCAATCTACCCCTCTTAATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* *
215552 CTTCTTGACTTAGGGGTAAAAGATTA
66 CCTCTTGA-TTAGGGGTAAAAGATTG
* * * * * *
215578 AATGGT-AGTTTCAATCTACCCCTCTTGACTTAAGGGTAAAAGATTGGATGGTGACTTCAATATG
1 GATGGTGA-CTTCAATCTACCCCTCTT-AATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG
*
215642 TCCCTCTTGACTTAGGGGTAAAAGATTG
64 CCCCTCTTGA-TTAGGGGTAAAAGATTG
* * * * *
215670 GATGGTGGCTTCAATCTGCCCCTCTTGATTAAGGGTAAAAGATTGGATGGTGACTTCAATCTGCC
1 GATGGTGACTTCAATCTACCCCTCTTAATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
* * *
215735 CCTCTTAACTTAGGGGT-AAATATTC
66 CCTCTTGA-TTAGGGGTAAAAGATTG
* * * * * * * * * *
215760 GATGGTGGCTTTAATCTGCCCCTCTTGACTTAGAGGTAAAAGATTGGATTGTAGTTTCAATGTAC
1 GATGGTGACTTCAATCTACCCCTCTT-AATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGC
*
215825 CCCTCTTGATTAAGGGTAAAAGATTG
65 CCCTCTTGATTAGGGGTAAAAGATTG
* * * * * * **
215851 GATGGT-AGCTTCAATTTACCCCTCTTGATTAGGGGTAAAAGATTAGATGCTAGTTTCAATCAAC
1 GATGGTGA-CTTCAATCTACCCCTCTTAATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGC
215915 CCCTCTTGATTAGGGGTAAAAGATTG
65 CCCTCTTGATTAGGGGTAAAAGATTG
215941 GATG
1 GATG
215945 AGGTGATGTA
Statistics
Matches: 463, Mismatches: 72, Indels: 35
0.81 0.13 0.06
Matches are distributed among these distances:
90 118 0.25
91 157 0.34
92 128 0.28
93 19 0.04
94 41 0.09
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (90 bp):
GATGGTGACTTCAATCTACCCCTCTTAATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTGCC
CCTCTTGATTAGGGGTAAAAGATTG
Found at i:218547 original size:28 final size:29
Alignment explanation
Indices: 218487--218541 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
218477 TGAATAGAAC
* * *
218487 ATTTCGTCAATTTGGACAAGAATAAATAT
1 ATTTCGTCAAATTGAACAAGAACAAATAT
218516 ATTT-GTCAAATTGAACAAGAACAAAT
1 ATTTCGTCAAATTGAACAAGAACAAAT
218542 GAATTTAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (29 bp):
ATTTCGTCAAATTGAACAAGAACAAATAT
Found at i:220840 original size:14 final size:15
Alignment explanation
Indices: 220814--220845 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
220804 GTCTGATAGG
220814 TTGTCGCCATTTTCC
1 TTGTCGCCATTTTCC
220829 TTGTCG-CATTTTCC
1 TTGTCGCCATTTTCC
220843 TTG
1 TTG
220846 ACCACATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.06, C:0.28, G:0.16, T:0.50
Consensus pattern (15 bp):
TTGTCGCCATTTTCC
Found at i:222928 original size:94 final size:93
Alignment explanation
Indices: 222767--222956 Score: 362
Period size: 94 Copynumber: 2.0 Consensus size: 93
222757 GTGGAAGGAC
222767 GTGGGGATAAATATCCCAAATTCTGAAAACACGTTGACCCTGGTGGGTTGGATCCGGGTCGGTGC
1 GTGGGGATAAATATCCCAAATTCTGAAAACACGTTGACCCTGGTGGGTTGGATCCGGGTCGGTGC
222832 CGGTTGGTGTGAAACGACGTCGTTTTGG
66 CGGTTGGTGTGAAACGACGTCGTTTTGG
*
222860 NGTGGGGATAAATATCCCAAATTTTGAAAACACGTTGACCCTGGTGGGTTGGATCCGGGTCGGTG
1 -GTGGGGATAAATATCCCAAATTCTGAAAACACGTTGACCCTGGTGGGTTGGATCCGGGTCGGTG
222925 CCGGTTGGTGTGAAACGACGTCGTTTTGG
65 CCGGTTGGTGTGAAACGACGTCGTTTTGG
222954 GTG
1 GTG
222957 TTAAAATCCA
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 3 0.03
94 92 0.97
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.27
Consensus pattern (93 bp):
GTGGGGATAAATATCCCAAATTCTGAAAACACGTTGACCCTGGTGGGTTGGATCCGGGTCGGTGC
CGGTTGGTGTGAAACGACGTCGTTTTGG
Found at i:224307 original size:24 final size:24
Alignment explanation
Indices: 224256--224307 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
224246 TTCGTAAGTC
* *
224256 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
224280 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
224304 AAAT
1 AAAT
224308 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:227667 original size:19 final size:19
Alignment explanation
Indices: 227643--227737 Score: 127
Period size: 19 Copynumber: 5.0 Consensus size: 19
227633 GATCAACAAA
227643 ACTGGCTCGTAAGAGCAAT
1 ACTGGCTCGTAAGAGCAAT
* *
227662 ACTGGCTCGTAGGAGCAAC
1 ACTGGCTCGTAAGAGCAAT
*
227681 ACTGGCTAGTAAGAGCAAT
1 ACTGGCTCGTAAGAGCAAT
* * *
227700 ATTGGCTCGTTAGAGCGAT
1 ACTGGCTCGTAAGAGCAAT
*
227719 ACTGGCTCGTAGGAGCAAT
1 ACTGGCTCGTAAGAGCAAT
227738 TTACTAACTA
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 63 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.22
Consensus pattern (19 bp):
ACTGGCTCGTAAGAGCAAT
Found at i:233413 original size:17 final size:18
Alignment explanation
Indices: 233381--233414 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
233371 GTTTATTGTG
*
233381 TTTAATTGCTTGTTTATA
1 TTTAATTGCATGTTTATA
233399 TTTAATT-CATGTTTAT
1 TTTAATTGCATGTTTAT
233415 GTTCTTATAG
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:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (18 bp):
TTTAATTGCATGTTTATA
Found at i:250703 original size:40 final size:40
Alignment explanation
Indices: 250647--250725 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
250637 ACATTTTTAA
** * *
250647 GGGTTTGTTGTGACATAGACAAGCTACGTTGCGACGAAGG
1 GGGTTTGTTGCAACATAGACAACCTACGTTGCAACGAAGG
* *
250687 GGGTTTGTTGCAACATAGACATCCTATGTTGCAACGAAG
1 GGGTTTGTTGCAACATAGACAACCTACGTTGCAACGAAG
250726 AAAGCAGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (40 bp):
GGGTTTGTTGCAACATAGACAACCTACGTTGCAACGAAGG
Found at i:258038 original size:50 final size:49
Alignment explanation
Indices: 257963--258057 Score: 172
Period size: 50 Copynumber: 1.9 Consensus size: 49
257953 TCACACTACT
*
257963 GCGCGAAATTATGCGCATCCCGAAACAAATTGGGCTAATAGAATCTGGA
1 GCGCGAAATTATGCGCATCCCGAAACAAATTGGGCCAATAGAATCTGGA
258012 NGCGCGAAATTATGCGCATCCCGAAACAAATTGGGCCAATAGAATC
1 -GCGCGAAATTATGCGCATCCCGAAACAAATTGGGCCAATAGAATC
258058 CGGATTGTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.19
Consensus pattern (49 bp):
GCGCGAAATTATGCGCATCCCGAAACAAATTGGGCCAATAGAATCTGGA
Found at i:260668 original size:23 final size:22
Alignment explanation
Indices: 260633--260675 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
260623 AAATATTTCA
*
260633 TTAAATAATTTGGGTTGAATTAT
1 TTAAATAAATTGGGTT-AATTAT
*
260656 TTAATTAAATTGGGTTAATT
1 TTAAATAAATTGGGTTAATT
260676 TTATTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (22 bp):
TTAAATAAATTGGGTTAATTAT
Done.