Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015121.1 Kokia drynarioides strain JFW-HI SEQ_130165, 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: 186149
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:985 original size:57 final size:55
Alignment explanation
Indices: 851--1160 Score: 169
Period size: 57 Copynumber: 5.4 Consensus size: 55
841 AAGGTCCCTA
* * * *
851 AACTATCCAAAAATTACATTTTTACCCCTAAACTTTCC-AAATTCCATTTTGACC-C
1 AACTTTCC-AAAATTACATTTTTACCCTTGAACTTTCCAAAATTACATTTT-ACCTC
*
906 AAAC-TTCCTAAAAATTACATTTTTACCCTTGAACTTTCCAAAATTTCATTTTACCTC
1 -AACTTTCC--AAAATTACATTTTTACCCTTGAACTTTCCAAAATTACATTTTACCTC
*
963 TAAGCTTTCCAAAATT-CTATTTTTGA-CCTTG-ATTTTCCAAAAATTACATTTTTTACCCTC
1 -AA-CTTTCCAAAATTAC-ATTTTT-ACCCTTGAACTTTCC-AAAATTACA--TTTTA-CCTC
* *
1023 GAACTTTCCAAAATTCCATTTTTTATCCC--G-A-TTTCCCAAAATTACCATTTTACCCCC
1 -AACTTTCCAAAATTACA-TTTTTA-CCCTTGAACTTT-CCAAAATTA-CATTTTA-CCTC
* * * * *
1080 AATCTTCCCAAAATTCCATTTTTGACCC-T-AATTTTTCCAAAAATGATCATTTTACCCTG
1 AA-CTTTCCAAAATTACATTTTT-ACCCTTGAA-CTTTCC-AAAATTA-CATTTTA-CCTC
*
1139 AAC-TTCCAAAATTTCCATTTTT
1 AACTTTCCAAAA-TTACATTTTT
1161 TTACACCGAT
Statistics
Matches: 214, Mismatches: 15, Indels: 48
0.77 0.05 0.17
Matches are distributed among these distances:
55 3 0.01
56 51 0.24
57 71 0.33
58 25 0.12
59 50 0.23
60 12 0.06
61 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (55 bp):
AACTTTCCAAAATTACATTTTTACCCTTGAACTTTCCAAAATTACATTTTACCTC
Found at i:1160 original size:28 final size:27
Alignment explanation
Indices: 846--1160 Score: 155
Period size: 28 Copynumber: 11.0 Consensus size: 27
836 CCCTAAAGGT
* *
846 CCCTAAACTATCCAAAAATTACATTTTTA
1 CCCTGAACT-TCC-AAAATTCCATTTTTA
* *
875 CCCCTAAACTTTCC-AAATTCCATTTTGA
1 -CCCTGAAC-TTCCAAAATTCCATTTTTA
* *
903 CCC-AAACTTCCTAAAAATTACATTTTTA
1 CCCTGAACTTCC--AAAATTCCATTTTTA
*
931 CCCTTGAACTTTCCAAAATTTCA-TTTTA
1 CCC-TGAAC-TTCCAAAATTCCATTTTTA
*
959 CCTCT-AAGCTTTCCAAAATTCTATTTTTGA
1 CC-CTGAA-C-TTCCAAAATTCCATTTTT-A
* ** *
989 CCTTGATTTTCCAAAAATTACATTTTTTA
1 CCCTGAACTTCC-AAAATTCCA-TTTTTA
1018 CCCTCGAACTTTCCAAAATTCCATTTTTTA
1 CCCT-GAAC-TTCCAAAATTCCA-TTTTTA
*
1048 TCCC-G-ATTTCCCAAAATTACCA-TTTTA
1 -CCCTGAACTT-CCAAAATT-CCATTTTTA
**
1075 CCCCCAATCTTCCCAAAATTCCATTTTTGA
1 CCCTGAA-CTT-CCAAAATTCCATTTTT-A
*
1105 CCCT-AATTTTTCCAAAAATGAT-CA-TTTTA
1 CCCTGAA--CTTCC-AAAAT--TCCATTTTTA
1134 CCCTGAACTTCCAAAATTTCCATTTTT
1 CCCTGAACTTCCAAAA-TTCCATTTTT
1161 TTACACCGAT
Statistics
Matches: 230, Mismatches: 23, Indels: 66
0.72 0.07 0.21
Matches are distributed among these distances:
25 4 0.02
26 8 0.03
27 18 0.08
28 74 0.32
29 53 0.23
30 58 0.25
31 14 0.06
32 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.03, T:0.39
Consensus pattern (27 bp):
CCCTGAACTTCCAAAATTCCATTTTTA
Found at i:1161 original size:59 final size:58
Alignment explanation
Indices: 916--1255 Score: 229
Period size: 59 Copynumber: 5.8 Consensus size: 58
906 AAACTTCCTA
* *
916 AAAATTACATTTTT-ACCCTTGAACTTTCC-AAAATT-TCATTTTACCTCT-AAGCTTTCC
1 AAAATTCCATTTTTGACCC-TG-ATTTTCCAAAAATTATCATTTTACC-CTGAAGCTTTCC
* *
973 AAAATTCTATTTTTGACCTTGATTTTCCAAAAATTA-CATTTTTTACCCTCGAA-CTTTCC
1 AAAATTCCATTTTTGACCCTGATTTTCCAAAAATTATCA--TTTTACCCT-GAAGCTTTCC
* * * ** * *
1032 AAAATTCCATTTTTTATCCC-GA-TTTCCCAAAATTACCATTTTACCCCCAATCTTCCC
1 AAAATTCCATTTTTGA-CCCTGATTTTCCAAAAATTATCATTTTACCCTGAAGCTTTCC
* *
1089 AAAATTCCATTTTTGACCCTAATTTTTCCAAAAATGATCATTTTACCCTGAA-C-TTCC
1 AAAATTCCATTTTTGACCCTGA-TTTTCCAAAAATTATCATTTTACCCTGAAGCTTTCC
* * * * * * *
1146 AAAATTTCCATTTTTTTACACC-GATTCTTCCAAAAAGTACCATTTTACCATCG--GATGTCTA
1 AAAA-TTCCA-TTTTTGAC-CCTGATT-TTCCAAAAATTATCATTTTACCCT-GAAGCTTTC-C
* * * * *
1207 AAAATTCCGTTTTTGACCCCCGACTTTCCTAAAATTACCATTTTACCCT
1 AAAATTCCATTTTTGA-CCCTGATTTTCCAAAAATTATCATTTTACCCT
1256 CGAGTGACCA
Statistics
Matches: 226, Mismatches: 34, Indels: 44
0.74 0.11 0.14
Matches are distributed among these distances:
56 11 0.05
57 58 0.26
58 25 0.11
59 111 0.49
60 17 0.08
61 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.39
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCCTGATTTTCCAAAAATTATCATTTTACCCTGAAGCTTTCC
Found at i:1695 original size:97 final size:98
Alignment explanation
Indices: 1497--1695 Score: 253
Period size: 97 Copynumber: 2.0 Consensus size: 98
1487 TTCATGAAAA
* * * *
1497 CTTTAAAATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGC
1 CTTTAAAATCGAGGCAATATTCTTTTATCTCGAGTTCTGAAAATTTGTACCTAAACTTACTAGGC
*
1562 ACGATTTTTCTTCAAATCGAAATAATCGAATAC
66 ACGATTTTTCTTCAAATCGAAATAATCGAACAC
*
1595 CTTT-AAATCGAGGCAATGTT-TATTTATCTCTGA-TTCTGAAAATTTGTACCTAAACTTACTAG
1 CTTTAAAATCGAGGCAATATTCT-TTTATCTC-GAGTTCTGAAAATTTGTACCTAAACTTACTAG
** * *
1657 GTGCGATTTTT-TTCAAATCGAGATATTCGAACATC
64 GCACGATTTTTCTTCAAATCGAAATAATCGAACA-C
1692 CTTT
1 CTTT
1696 TTTGAAGTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
96 20 0.23
97 62 0.70
98 6 0.07
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.40
Consensus pattern (98 bp):
CTTTAAAATCGAGGCAATATTCTTTTATCTCGAGTTCTGAAAATTTGTACCTAAACTTACTAGGC
ACGATTTTTCTTCAAATCGAAATAATCGAACAC
Found at i:2380 original size:87 final size:89
Alignment explanation
Indices: 2280--2455 Score: 225
Period size: 87 Copynumber: 2.0 Consensus size: 89
2270 GTAAAAAATT
** * * *
2280 TTCAAACTTTTTCAAAAAAAACAATTAAGTTTTTA-TTTT-TTTTA-ATTCACTTGGGTATTTGA
1 TTCAAACTTTTTCAAAAAAAACAATTAAGTCCTTATTTTTATTTTACACTCAATTGGGTACTTGA
*
2342 ACTTTTAAAATACATCAAAAAGGCC
66 AC-TGTAAAATACATCAAAAAGGCC
* *
2367 TTCAAA-TTATTTCAAAAAAAGCAATTAAGTCCTTATTTTTATTTTACACTGAATTGGGTACTTG
1 TTCAAACTT-TTTCAAAAAAAACAATTAAGTCCTTATTTTTATTTTACACTCAATTGGGTACTTG
*
2431 AACTGTCAAATACATCAAAAAGGCC
65 AACTGTAAAATACATCAAAAAGGCC
2456 CTTTAACCGT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
86 2 0.03
87 29 0.38
88 4 0.05
89 25 0.33
90 16 0.21
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (89 bp):
TTCAAACTTTTTCAAAAAAAACAATTAAGTCCTTATTTTTATTTTACACTCAATTGGGTACTTGA
ACTGTAAAATACATCAAAAAGGCC
Found at i:2600 original size:10 final size:10
Alignment explanation
Indices: 2575--2651 Score: 50
Period size: 10 Copynumber: 7.7 Consensus size: 10
2565 AAAAAATAAA
*
2575 AATAAAAATC
1 AATAAAAATT
2585 AATAAAAATT
1 AATAAAAATT
* **
2595 ATTAAATCTT
1 AATAAAAATT
2605 AATAAAAATAT
1 AATAAAAAT-T
*
2616 AAAAAATAATT
1 AATAAA-AATT
** *
2627 TTTTAAAATT
1 AATAAAAATT
2637 AA-AAAAATT
1 AATAAAAATT
2646 -ATAAAA
1 AATAAAA
2652 TGCATCAAAA
Statistics
Matches: 49, Mismatches: 15, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
8 1 0.02
9 10 0.20
10 26 0.53
11 9 0.18
12 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (10 bp):
AATAAAAATT
Found at i:2885 original size:90 final size:90
Alignment explanation
Indices: 2745--2983 Score: 256
Period size: 89 Copynumber: 2.6 Consensus size: 90
2735 TTAGGGACAA
* * *
2745 TTCAAGTACCCAATTGAGTG-CAA-AAAAGTAAGGGCTTAATTGCTTCTTTTTTTGAAAAAGTTT
1 TTCAAGTACCCAATTGAGTGAAAATAAAAG-CAGGGCTTAATT-ATT-TTTTTTTGAAAAAGTTT
*
2808 AAGGGTC-TTTTTGATACATTTTGAAAG
63 AAGGGTCTTTTTTGATACATATTGAAAG
*
2835 TTCAAGTACCCAATTGAGTGAAAAATAAAAGCAGTGGCTT-A--ATTTTTTTTTGAAAAAGTTTG
1 TTCAAGTACCCAATTGAGTG-AAAATAAAAGCAG-GGCTTAATTATTTTTTTTTGAAAAAGTTTA
* *
2897 AGGGTCTTTTTTTATGCATATTGAAAG
64 AGGGTCTTTTTTGATACATATTGAAAG
* * * * * *
2924 TTTAAGTACCTAATTGAATGCAAAATAAAAACAGAGGGTTAATTACTTTTTTTTGAAAAA
1 TTCAAGTACCCAATTGAGTG-AAAATAAAAGCAG-GGCTTAATTATTTTTTTTTGAAAAA
2984 ATTTGAAGAT
Statistics
Matches: 126, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
88 23 0.18
89 52 0.41
90 21 0.17
92 20 0.16
93 10 0.08
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (90 bp):
TTCAAGTACCCAATTGAGTGAAAATAAAAGCAGGGCTTAATTATTTTTTTTTGAAAAAGTTTAAG
GGTCTTTTTTGATACATATTGAAAG
Found at i:2901 original size:88 final size:91
Alignment explanation
Indices: 2791--2989 Score: 260
Period size: 89 Copynumber: 2.2 Consensus size: 91
2781 TAATTGCTTC
* * *
2791 TTTTTTTGAAAAAGTTTAAGGGTC-TTTTTGATACATTTTGAAAGTTCAAGTACCCAATTGAGTG
1 TTTTTTTGAAAAAGTTTGAGGGTCTTTTTTGATACATATTGAAAGTTCAAGTACCCAATTGAATG
* *
2855 AAAAATAAAAGCAGTGGCTTAA-T-T
66 AAAAATAAAAACAGAGGCTTAATTAT
* * * *
2879 TTTTTTTGAAAAAGTTTGAGGGTCTTTTTTTATGCATATTGAAAGTTTAAGTACCTAATTGAATG
1 TTTTTTTGAAAAAGTTTGAGGGTCTTTTTTGATACATATTGAAAGTTCAAGTACCCAATTGAATG
* *
2944 CAAAATAAAAACAGAGGGTTAATTACT
66 AAAAATAAAAACAGAGGCTTAATTA-T
*
2971 TTTTTTTGAAAAAATTTGA
1 TTTTTTTGAAAAAGTTTGA
2990 AGATTTTTTA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
88 23 0.24
89 52 0.55
90 1 0.01
92 19 0.20
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.40
Consensus pattern (91 bp):
TTTTTTTGAAAAAGTTTGAGGGTCTTTTTTGATACATATTGAAAGTTCAAGTACCCAATTGAATG
AAAAATAAAAACAGAGGCTTAATTAT
Found at i:4792 original size:20 final size:20
Alignment explanation
Indices: 4755--4793 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4745 GGGTGTATGA
* *
4755 TTTATCTTACTTTAAAATTC
1 TTTATCTAAATTTAAAATTC
*
4775 TTTATCTAAATTTTAAATT
1 TTTATCTAAATTTAAAATT
4794 TGTCAAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATCTAAATTTAAAATTC
Found at i:5841 original size:150 final size:146
Alignment explanation
Indices: 5687--6514 Score: 943
Period size: 150 Copynumber: 5.6 Consensus size: 146
5677 CTTCTTCTTC
* * ** *
5687 TTTTTTTTTTTTAAAAAAATCAAAAGTGTTCATTTGATTAAACAAAAATCACTACTTTACTTAAA
1 TTTTTTATTTTT-AAAAAAT-AAAACT-TTC-TTTTTTTAAA-AAAAATCACTATTTTACTTAAA
* * *
5752 AATCCAAACTTTTATTTTGAAATAGTTAAAATAAATCAAAATTTTGTTAAAAATTTAAA-TTTT-
61 AATCCAAACTTTTATTTCGAAATAATTAAAA-AAATCAAAACTTTGTTAAAAATTTAAACTTTTC
5815 TTTAAAATAACTAAAAAACAGA
125 TTTAAAATAACTAAAAAACAGA
* * ** *
5837 -TTTTTATTTTTTAAAAATCTAAACTTTCTCTTTTTTTAAAGGAAATCATTATTTTACTTAAAAA
1 TTTTTTATTTTTAAAAAAT-AAAAC-TT-TCTTTTTTTAAAAAAAATCACTATTTTACTTAAAAA
* * * *
5901 TTCAAATTTTTATTTCAAAATAATTAAAAAAAATCAAAACTTTGTTAAAATTTTAAACTTTTTCT
63 TCCAAACTTTTATTTCGAAATAATT-AAAAAAATCAAAACTTTGTTAAAAATTTAAAC-TTTTCT
*
5966 TTAAAATAACTAAAAAA-TG-
126 TTAAAATAACTAAAAAACAGA
* * *
5985 TATTTTTATTTTTATAAAATATAAACTTTCTCTTTTTTAAAGAAAAGT-ACTATTTTAATTAAAA
1 T-TTTTTATTTTTAAAAAATA-AAACTTTCT-TTTTTTAAA-AAAAATCACTATTTTACTTAAAA
6049 ATCCAAACTTTTATTTCGAAATAATTTAAAAAAATCAAAAACTTTGTTAAAAATTTAAACTTTTT
62 ATCCAAACTTTTATTTCGAAATAA-TTAAAAAAATC-AAAACTTTGTTAAAAATTTAAAC-TTTT
6114 CTTTAAAATAACTAAAAAAACAGA
124 CTTTAAAATAACT-AAAAAACAGA
*
6138 -TTTTTA-TTTTAAAATATAAAA-TTTCTCTTTTTT-AAAAAAATCACTA-TTTACTTAAAAATC
1 TTTTTTATTTTTAAAAAATAAAACTTTCT-TTTTTTAAAAAAAATCACTATTTTACTTAAAAATC
* * *
6198 CAAACTTTTATTTCGTAATAATTAAGAAAAATCAAAATTTTATTAAAAATTTAAACTTTTTCTTT
65 CAAACTTTTATTTCGAAATAATTAA-AAAAATCAAAACTTTGTTAAAAATTTAAAC-TTTTCTTT
*
6263 AAAATAACT-AAAAACACA
128 AAAATAACTAAAAAACAGA
* *
6281 TATTTTTATTTTT-AAAAATATAAACTTTCTCTTTTTTTAAAGAAAATCACTATTTTACCTAAAA
1 T-TTTTTATTTTTAAAAAATA-AAAC-TT-TCTTTTTTTAAAAAAAATCACTATTTTACTTAAAA
* *
6345 ATCCAAACTTTTATTTCGAAATAGTT-AAAAAATCAAAACTTTATTAAAAATTTAAACTTTTTCT
62 ATCCAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTTTGTTAAAAATTTAAAC-TTTTCT
6409 TTAAAATAACTAAAAAACAGA
126 TTAAAATAACTAAAAAACAGA
* * *
6430 -TTTTTATTTTT-AAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTGCTTAAAAAA
1 TTTTTTATTTTTAAAAAAT-AAAACTTTCT-TTTTTTAAAAAAAATCACTATTTTACTT--AAAA
*
6493 AT-TAAAGCTTTTATTTCGAAAT
62 ATCCAAA-CTTTTATTTCGAAAT
6515 TGTTTTAAAA
Statistics
Matches: 595, Mismatches: 50, Indels: 68
0.83 0.07 0.10
Matches are distributed among these distances:
143 8 0.01
145 58 0.10
146 80 0.13
147 95 0.16
148 114 0.19
149 100 0.17
150 127 0.21
151 12 0.02
152 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (146 bp):
TTTTTTATTTTTAAAAAATAAAACTTTCTTTTTTTAAAAAAAATCACTATTTTACTTAAAAATCC
AAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTCTTTAAA
ATAACTAAAAAACAGA
Found at i:5957 original size:147 final size:147
Alignment explanation
Indices: 5731--6514 Score: 1104
Period size: 147 Copynumber: 5.3 Consensus size: 147
5721 TGATTAAACA
* * * * *
5731 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTTGAAATAGTTAAAATAAATCAAAATTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
*
5796 TGTTAAAAATTTAAA-TTTT-TTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAAATCTAA
66 TGTTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAAACAGATTTTTA-TTTTTAAAAATATAA
5859 ACTTTCTCTTTTTTTAAAG
130 ACTTTCTC-TTTTTTAAAG
* * * * *
5878 GAAATCATTATTTTACTTAAAAATTCAAATTTTTATTTCAAAATAATTAAAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
* *
5943 TGTTAAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAA-TGTATTTTTATTTTTATAAAATAT
66 TGTTAAAAATTTAAAC-TTTTCTTTAAAATAACTAAAAAACAG-ATTTTTATTTTTA-AAAATAT
6007 AAACTTTCTCTTTTTTAAAG
128 AAACTTTCTCTTTTTTAAAG
* *
6027 AAAAGT-ACTATTTTAATTAAAAATCCAAACTTTTATTTCGAAATAATTTAAAAAAATCAAAAAC
1 AAAA-TCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAAATC-AAAAC
6091 TTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAACAGATTTTTA-TTTT-AAAATA
64 TTTGTTAAAAATTTAAAC-TTTTCTTTAAAATAACT-AAAAAACAGATTTTTATTTTTAAAAATA
*
6154 TAAAATTTCTCTTTTTTAAA-
127 TAAACTTTCTCTTTTTTAAAG
* * *
6174 AAAATCACTA-TTTACTTAAAAATCCAAACTTTTATTTCGTAATAATTAAGAAAAATCAAAATTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
* *
6238 TATTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAACACATATTTTTATTTTTAAAAATATA
66 TGTTAAAAATTTAAAC-TTTTCTTTAAAATAACTAAAAA-ACAGATTTTTATTTTTAAAAATATA
6303 AACTTTCTCTTTTTTTAAAG
129 AACTTTCTC-TTTTTTAAAG
* *
6323 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTT--AAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
* *
6386 TATTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATCTAA
66 TGTTAAAAATTTAAAC-TTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
6451 ACTTTCTCTTTTTTAAAG
130 ACTTTCTCTTTTTTAAAG
* *
6469 AAAATCACTATTTTGCTTAAAAAAAT-TAAAGCTTTTATTTCGAAAT
1 AAAATCACTATTTTACTT--AAAAATCCAAA-CTTTTATTTCGAAAT
6515 TGTTTTAAAA
Statistics
Matches: 577, Mismatches: 41, Indels: 37
0.88 0.06 0.06
Matches are distributed among these distances:
144 5 0.01
145 49 0.08
146 74 0.13
147 128 0.22
148 107 0.19
149 80 0.14
150 120 0.21
151 13 0.02
152 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (147 bp):
AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAATTAAAAAAAATCAAAACTT
TGTTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAA
CTTTCTCTTTTTTAAAG
Found at i:6359 original size:296 final size:296
Alignment explanation
Indices: 5731--6491 Score: 1173
Period size: 296 Copynumber: 2.6 Consensus size: 296
5721 TGATTAAACA
* * *
5731 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTTGAAATAGTTAAAATAAATCAAAATTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAA-AAATCAAAACTT
5796 TGTTAAAAATTTAAA--TTTT-TTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAAATCTA
65 TGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTA-TTTTTAAAAATCTA
* * * *
5858 AACTTTCTCTTTTTTTAAAGGAAATCATTATTTTACTTAAAAATTCAAATTTTTATTTCAAAATA
129 AACTTTCTC-TTTTTTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCAAAATA
* * **
5923 ATTAAAAAAAATCAAAACTTTGTTAAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAATGTAT
193 ATTAAAAAAAATCAAAACTTTATTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATAT
5988 TTTTATTTTTATAAAATATAAACTTTCTCTTTTTTAAAG
258 TTTTATTTTTATAAAATATAAACTTTCTCTTTTTTAAAG
* *
6027 AAAAGT-ACTATTTTAATTAAAAATCCAAACTTTTATTTCGAAATAATTTAAAAAAATCAAAAAC
1 AAAA-TCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAAT-AGTTAAAAAAATC-AAAAC
*
6091 TTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAACAGATTTTTA-TTTT-AAAATA
63 TTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAACAGATTTTTATTTTTAAAAATC
* **
6154 TAAAATTTCTCTTTTTTAAA-AAAATCACTA-TTTACTTAAAAATCCAAACTTTTATTTCGTAAT
127 TAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCAAAAT
* *
6217 AATTAAGAAAAATCAAAATTTTATTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAACACAT
192 AATTAAAAAAAATCAAAACTTTATTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAA-ACAT
6282 ATTTTTATTTTTA-AAAATATAAACTTTCTCTTTTTTTAAAG
256 ATTTTTATTTTTATAAAATATAAACTTTCTC-TTTTTTAAAG
*
6323 AAAATCACTATTTTACCTAAAAATCCAAACTTTTATTTCGAAATAGTT-AAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
*
6387 ATTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATCTAAA
66 GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATCTAAA
*
6452 CTTTCTCTTTTTTAAAGAAAATCACTATTTTGCTTAAAAA
131 CTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAA
6492 AATTAAAGCT
Statistics
Matches: 425, Mismatches: 26, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
292 16 0.04
293 44 0.10
294 32 0.08
295 116 0.27
296 128 0.30
297 38 0.09
298 15 0.04
299 8 0.02
300 12 0.03
301 16 0.04
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (296 bp):
AAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATCTAAA
CTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCAAAATAATT
AAAAAAAATCAAAACTTTATTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTT
TATTTTTATAAAATATAAACTTTCTCTTTTTTAAAG
Found at i:7047 original size:3 final size:3
Alignment explanation
Indices: 7039--7069 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
7029 NNNNNNNNNN
7039 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
7070 GTGATGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17640 original size:31 final size:30
Alignment explanation
Indices: 17573--17656 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
17563 GTTTTATGTC
*
17573 TCATTTTATTAAATTATTTAAAACAATTTA
1 TCATTATATTAAATTATTTAAAACAATTTA
*
17603 TCATTATATTAAATTATTTAAATATAATTTA
1 TCATTATATTAAATTATTTAAA-ACAATTTA
* *
17634 TTATTATATTTAAAAT-TTTAAAA
1 TCATTATA-TTAAATTATTTAAAA
17657 TATTTAATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.46
31 20 0.42
32 6 0.12
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (30 bp):
TCATTATATTAAATTATTTAAAACAATTTA
Found at i:18489 original size:99 final size:99
Alignment explanation
Indices: 18318--18514 Score: 394
Period size: 99 Copynumber: 2.0 Consensus size: 99
18308 AAAAAATATC
18318 TTCGTTGAAGTCTTTGATATAAGAACTAGAGGATTTAAAGTCTCACAATAAGAACCGTTTCATCT
1 TTCGTTGAAGTCTTTGATATAAGAACTAGAGGATTTAAAGTCTCACAATAAGAACCGTTTCATCT
18383 TTCTGACATTTCTGTAAGTTTGAAAGCTAGGGTA
66 TTCTGACATTTCTGTAAGTTTGAAAGCTAGGGTA
18417 TTCGTTGAAGTCTTTGATATAAGAACTAGAGGATTTAAAGTCTCACAATAAGAACCGTTTCATCT
1 TTCGTTGAAGTCTTTGATATAAGAACTAGAGGATTTAAAGTCTCACAATAAGAACCGTTTCATCT
18482 TTCTGACATTTCTGTAAGTTTGAAAGCTAGGGT
66 TTCTGACATTTCTGTAAGTTTGAAAGCTAGGGT
18515 GTATCTGATA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (99 bp):
TTCGTTGAAGTCTTTGATATAAGAACTAGAGGATTTAAAGTCTCACAATAAGAACCGTTTCATCT
TTCTGACATTTCTGTAAGTTTGAAAGCTAGGGTA
Found at i:21397 original size:31 final size:27
Alignment explanation
Indices: 21361--21435 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 27
21351 AACATGTTAG
21361 GAAAGGAAAGCCTTCGTGACAAGCTCTGAAT
1 GAAAGGAAAGCCTTCGTGACAAG---TG-AT
* *
21392 GAAAGG-AAGCCTTTGTGGCAAGTGAT
1 GAAAGGAAAGCCTTCGTGACAAGTGAT
21418 GAAAGGAAATGCCTTCGT
1 GAAAGGAAA-GCCTTCGT
21436 AGCAAACTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 8 0.21
27 4 0.10
28 7 0.18
30 14 0.36
31 6 0.15
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.21
Consensus pattern (27 bp):
GAAAGGAAAGCCTTCGTGACAAGTGAT
Found at i:22714 original size:25 final size:24
Alignment explanation
Indices: 22679--22765 Score: 95
Period size: 25 Copynumber: 3.5 Consensus size: 24
22669 GCCCAAGTAG
* *
22679 AATATCGCTCTTTCGAGCCAGACA
1 AATATCACTCTTTCGAGCTAGACA
*
22703 AAGTATCACTCTTTTGAGCTAGACA
1 AA-TATCACTCTTTCGAGCTAGACA
22728 GAATATCACTC-TTCTGAGCTAGACAA
1 -AATATCACTCTTTC-GAGCTAGAC-A
*
22754 AATATCGCTCTT
1 AATATCACTCTT
22766 ACAACTCTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
24 4 0.08
25 45 0.85
26 4 0.08
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (24 bp):
AATATCACTCTTTCGAGCTAGACA
Found at i:28632 original size:25 final size:25
Alignment explanation
Indices: 28555--28679 Score: 133
Period size: 25 Copynumber: 5.0 Consensus size: 25
28545 TTATCTCATA
* *
28555 CGAGCCCAGATAGAATATCTCTCTTT
1 CGAG-CCAGACAGAATATCGCTCTTT
* * * *
28581 CAAGCCAAACAGAGTATCACTCTTT
1 CGAGCCAGACAGAATATCGCTCTTT
*
28606 CGAGCCAGACAAAATATCGCTCTTT
1 CGAGCCAGACAGAATATCGCTCTTT
* * *
28631 CGATCCAGATAGAATATTGCTCTTT
1 CGAGCCAGACAGAATATCGCTCTTT
* *
28656 TGAGCTAGACAGAATATCGCTCTT
1 CGAGCCAGACAGAATATCGCTCTT
28680 ACAAGTCAAA
Statistics
Matches: 80, Mismatches: 19, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
25 77 0.96
26 3 0.04
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (25 bp):
CGAGCCAGACAGAATATCGCTCTTT
Found at i:35027 original size:69 final size:69
Alignment explanation
Indices: 34871--35039 Score: 211
Period size: 68 Copynumber: 2.5 Consensus size: 69
34861 AACCAATTTT
* *
34871 TTCACTACTTTCATTAAAAAGTTAATTTTAAT-TCCACATTGACTAAAAATACTCTTATAGCTCA
1 TTCACTATTTTTATTAAAAAGTTAATTTTAATCTCCACATTGACTAAAAATACTCTTATAGCTCA
34935 CTCC
66 CTCC
** * *
34939 TTCGTTATTTTTATTAAAAAGTTAATTTTAATCT-CACATTGACTAGAAAATGCT-TTCATAGTT
1 TTCACTATTTTTATTAAAAAGTTAATTTTAATCTCCACATTGACTA-AAAATACTCTT-ATAGCT
*
35002 CACTTC
64 CACTCC
* *
35008 TTCACTATTTTTACTAAAAA-TTAACTTTAATC
1 TTCACTATTTTTATTAAAAAGTTAATTTTAATC
35040 CCTTAAAAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
68 52 0.60
69 35 0.40
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (69 bp):
TTCACTATTTTTATTAAAAAGTTAATTTTAATCTCCACATTGACTAAAAATACTCTTATAGCTCA
CTCC
Found at i:35048 original size:21 final size:22
Alignment explanation
Indices: 35022--35063 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35012 CTATTTTTAC
35022 TAAAAA-TTAACTTTAATCCCT
1 TAAAAAGTTAACTTTAATCCCT
*
35043 TAAAAAGTTAATTTTAATCCC
1 TAAAAAGTTAACTTTAATCCC
35064 ACATTGACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAAAAGTTAACTTTAATCCCT
Found at i:35153 original size:94 final size:94
Alignment explanation
Indices: 35042--35282 Score: 315
Period size: 94 Copynumber: 2.6 Consensus size: 94
35032 CTTTAATCCC
*
35042 TTAAAAAGTTAATTTTAATCCCACATTGACTAGAGAATACTCTCAT-GCTCACACTTACCATATA
1 TTAAAAAGTTAATTTTAATCTCACATTGACTAGAGAATACTCTCATAGCTCACACTTACCATATA
* ** *
35106 CATAAGTGTCAATTTCTTCAATATTTTCA
66 AATAAGTAACAAATTCTTCAATATTTTCA
* * * * *
35135 TTAAAGAAGTTAATTTTAA-CATCACATTGACTAGAGAATGCTCCCATATCTCACATTTACCTTA
1 TTAAA-AAGTTAATTTTAATC-TCACATTGACTAGAGAATACTCTCATAGCTCACACTTACCATA
*
35199 TAAATAAGTAACAAATTCTTCACTATTTTCA
64 TAAATAAGTAACAAATTCTTCAATATTTTCA
* * * *
35230 TTAAAAAGTTAATTTTAATCTCACGTTGACTAAAAAATACTCTTATAGCTCAC
1 TTAAAAAGTTAATTTTAATCTCACATTGACTAGAGAATACTCTCATAGCTCAC
35283 TTCTTCACTA
Statistics
Matches: 126, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
93 6 0.05
94 75 0.60
95 45 0.36
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (94 bp):
TTAAAAAGTTAATTTTAATCTCACATTGACTAGAGAATACTCTCATAGCTCACACTTACCATATA
AATAAGTAACAAATTCTTCAATATTTTCA
Found at i:43517 original size:13 final size:12
Alignment explanation
Indices: 43489--43529 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
43479 ATATTTAATA
43489 ATTTTATACATT
1 ATTTTATACATT
*
43501 -TTTTATATAGTT
1 ATTTTATACA-TT
43513 ATTTTAT-CATT
1 ATTTTATACATT
43524 ATTTTA
1 ATTTTA
43530 ATATTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 16 0.64
12 3 0.12
13 6 0.24
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (12 bp):
ATTTTATACATT
Found at i:43528 original size:24 final size:23
Alignment explanation
Indices: 43489--43537 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
43479 ATATTTAATA
43489 ATTTTATACATTTTTTATATAGTT
1 ATTTTATACATTTTTTA-ATAGTT
*
43513 ATTTTAT-CATTATTTTAATATTT
1 ATTTTATACATT-TTTTAATAGTT
43536 AT
1 AT
43538 ATTAGAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (23 bp):
ATTTTATACATTTTTTAATAGTT
Found at i:50123 original size:15 final size:16
Alignment explanation
Indices: 50103--50136 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
50093 AATATTTTAA
50103 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
50118 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
50134 AAA
1 AAA
50137 ATTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:50436 original size:2 final size:2
Alignment explanation
Indices: 50429--50460 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
50419 TTTCTCCCTT
50429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50461 ATCCTCTTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58366 original size:79 final size:79
Alignment explanation
Indices: 58164--58352 Score: 306
Period size: 79 Copynumber: 2.4 Consensus size: 79
58154 TTTAACTGAT
*
58164 TAGAGCTGGACTCACATTTGCGGTTTATCTGCTAGGCATTGGGTGCCAGGATTTGACGAACATCG
1 TAGAGCTGGGCTCACATTTGCGGTTTATCTGCTAGGCATTGGGTGCCAGGATTTGACGAACATCG
58229 TTGGTTAATCCAAC
66 TTGGTTAATCCAAC
* * * * * * *
58243 TAGAGGTGAGCTCACATTTGCAGTTTTTCTGCTAGGCATTGGGTGTCAGGATTTGACGGACATTG
1 TAGAGCTGGGCTCACATTTGCGGTTTATCTGCTAGGCATTGGGTGCCAGGATTTGACGAACATCG
58308 TTGGTTAATCCAAC
66 TTGGTTAATCCAAC
58322 TAGAGCTGGGCTCACATTTGCGGTTTATCTG
1 TAGAGCTGGGCTCACATTTGCGGTTTATCTG
58353 TTACGTACTG
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 98 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (79 bp):
TAGAGCTGGGCTCACATTTGCGGTTTATCTGCTAGGCATTGGGTGCCAGGATTTGACGAACATCG
TTGGTTAATCCAAC
Found at i:64077 original size:24 final size:24
Alignment explanation
Indices: 64059--64213 Score: 231
Period size: 24 Copynumber: 6.5 Consensus size: 24
64049 TTTAGCCCAC
* * *
64059 ACGAGCCTAGAATGATTAGCTCCT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
64083 ATGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
64107 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
64131 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
64155 ACGA-CCCTAGAATGGTTAGGTCTT
1 ACGAGCCC-AGAATGGTTAGCTCTT
* *
64179 ACGAGCCCAAAATGGTTAGGTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
64203 ACGAGCCCAGA
1 ACGAGCCCAGA
64214 CAGAGTTTAA
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
23 3 0.02
24 115 0.95
25 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.25
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:69112 original size:24 final size:24
Alignment explanation
Indices: 69051--69113 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
69041 TAAAGTAATA
* * * *
69051 AGAGTTTGACTCAAACAAATGAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
69075 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
69099 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
69114 GAATATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:72483 original size:118 final size:122
Alignment explanation
Indices: 72274--72540 Score: 398
Period size: 118 Copynumber: 2.2 Consensus size: 122
72264 GTATCTTCCT
* *
72274 TGTACCTCACCAAGAAGATGGGATTTGAAGCTTCACTCACATTTGAGCTTCACCTCATTATTTTG
1 TGTACCTCACCAGGAAGATGAGATTTGAAGCTTCACTCACATTTGAGCTTCACCTCATTATTTTG
* * * *
72339 GTTTACTTCTTTGTATCTCACTAGGAAGATGAA-A-TTG-T-TTCGACCCACTTCTC
66 GTCTACTTCTCTGTATCTCACCAGGAAGAAGAACACTTGTTGTTCGACCCACTTCTC
*
72392 TGTACCTCACCAGGAAGATGAGATTTGAAGCTTCACTCACATTTGAGTTTCACCTCATTATTTTG
1 TGTACCTCACCAGGAAGATGAGATTTGAAGCTTCACTCACATTTGAGCTTCACCTCATTATTTTG
*
72457 GTCTACTTCTCTGTATCTCACCAGGAAGAAGAACACTTTGTTGTTTGACCCACTTCTC
66 GTCTACTTCTCTGTATCTCACCAGGAAGAAGAACAC-TTGTTGTTCGACCCACTTCTC
* * *
72515 TATATCTCACTAGGAAGATGAGATTT
1 TGTACCTCACCAGGAAGATGAGATTT
72541 TAAAGTTTCA
Statistics
Matches: 133, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
118 91 0.68
119 1 0.01
121 3 0.02
122 1 0.01
123 37 0.28
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (122 bp):
TGTACCTCACCAGGAAGATGAGATTTGAAGCTTCACTCACATTTGAGCTTCACCTCATTATTTTG
GTCTACTTCTCTGTATCTCACCAGGAAGAAGAACACTTGTTGTTCGACCCACTTCTC
Found at i:85631 original size:2 final size:2
Alignment explanation
Indices: 85626--85653 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
85616 TAAAAGTACA
85626 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
85654 GGAGATGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88700 original size:32 final size:32
Alignment explanation
Indices: 88659--88729 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
88649 TTGTAGTGTT
88659 TATTTTTGGTGGTGACAACATGGATATTTGTG
1 TATTTTTGGTGGTGACAACATGGATATTTGTG
* *
88691 TATTTTTGGTGGTGACAGCATGGTTATTTGTG
1 TATTTTTGGTGGTGACAACATGGATATTTGTG
88723 TATTTTT
1 TATTTTT
88730 CAGTTTAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.18, C:0.06, G:0.27, T:0.49
Consensus pattern (32 bp):
TATTTTTGGTGGTGACAACATGGATATTTGTG
Found at i:98095 original size:59 final size:60
Alignment explanation
Indices: 98026--98150 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 60
98016 AATATTTAAT
* * * *
98026 AAATTTAAGTATCAAATTGAATCTAAAAAAAATTTAGGTACCAAATTAGGAAAAA-TATC
1 AAATTCAAGTATCAAATTGAATCTAAAAAAAATTTAAGTACAAAATTAAGAAAAAGTATC
* ** * *
98085 AAATTCAAGTATTAAATTGGGTCTAAAAAAAGTTTAAGTACAAAATTAAGAAAAAGTGTC
1 AAATTCAAGTATCAAATTGAATCTAAAAAAAATTTAAGTACAAAATTAAGAAAAAGTATC
98145 AAATTC
1 AAATTC
98151 GGATAACAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
59 47 0.84
60 9 0.16
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (60 bp):
AAATTCAAGTATCAAATTGAATCTAAAAAAAATTTAAGTACAAAATTAAGAAAAAGTATC
Found at i:98488 original size:15 final size:15
Alignment explanation
Indices: 98465--98495 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
98455 AATTTTAAAA
*
98465 TATTTTTTTAATATT
1 TATTCTTTTAATATT
98480 TATTCTTTTAATATT
1 TATTCTTTTAATATT
98495 T
1 T
98496 TTGTAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTCTTTTAATATT
Found at i:98570 original size:33 final size:32
Alignment explanation
Indices: 98499--98574 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
98489 AATATTTTTG
98499 TAAAATAAAAATATGTAAAAATTAAAAAATAA
1 TAAAATAAAAATATGTAAAAATTAAAAAATAA
*
98531 TAAAATAAAAATATTTTGTAAAAA-T-AAAAATGA
1 TAAAATAAAAATA---TGTAAAAATTAAAAAATAA
*
98564 TGAAATAAAAA
1 TAAAATAAAAA
98575 GTTAAAAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 13 0.33
33 17 0.44
34 1 0.03
35 8 0.21
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (32 bp):
TAAAATAAAAATATGTAAAAATTAAAAAATAA
Found at i:99999 original size:2 final size:2
Alignment explanation
Indices: 99992--100020 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
99982 AAATCATTAA
99992 AT 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 A
100021 AATTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:100054 original size:22 final size:23
Alignment explanation
Indices: 100019--100061 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
100009 TATATATATA
*
100019 TAAATTTTAATTCAATCGTTTTT
1 TAAATTTTAATTCAATAGTTTTT
*
100042 TAAA-TTTAGTTCAATAGTTT
1 TAAATTTTAATTCAATAGTTT
100062 CATACTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (23 bp):
TAAATTTTAATTCAATAGTTTTT
Found at i:105098 original size:3 final size:3
Alignment explanation
Indices: 105090--105158 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
105080 TAGTACCCTT
105090 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
105138 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
105159 TATTTTATGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:115753 original size:30 final size:30
Alignment explanation
Indices: 115719--115775 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
115709 TTTTAATTTT
115719 TTTAAAAATATTTAT-T-TTATTTATTTAATA
1 TTTAAAAAT-TTTATATATT-TTTATTTAATA
*
115749 TTTAATAATTTTATATATTTTTATTTA
1 TTTAAAAATTTTATATATTTTTATTTA
115776 TTGATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.21
30 17 0.71
31 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTAAAAATTTTATATATTTTTATTTAATA
Found at i:115782 original size:23 final size:24
Alignment explanation
Indices: 115727--115789 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 24
115717 TTTTTAAAAA
* *
115727 TATTTATTTTATTTATTTAATATT
1 TATTAATTTTATATATTTAATATT
* *
115751 TAATAATTTTATATATTT-TTATT
1 TATTAATTTTATATATTTAATATT
* *
115774 TATTGATTTTTTATAT
1 TATTAATTTTATATAT
115790 AATATTAAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 17 0.53
24 15 0.47
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TATTAATTTTATATATTTAATATT
Found at i:117174 original size:108 final size:108
Alignment explanation
Indices: 117035--117236 Score: 359
Period size: 108 Copynumber: 1.9 Consensus size: 108
117025 TAACTGTCCC
117035 TACCCCTAACTTGACTGCTTCGTAACATGCGAGGCCCTCTACTTCGAAAGCAAACCCAACACCCT
1 TACCCCTAACTTGACTGCTTCGTAACATGCGAGGCCCTCTACTTCGAAAGCAAACCCAACACCCT
* *
117100 CGTGTAGGACAAACTTTTCTGCTAGAACCTAACTGTTCATCCT
66 CGTGTAGGAAAAACTTTTATGCTAGAACCTAACTGTTCATCCT
* * *
117143 TACCCCTAACTTGACTGCTTCGTAACATGCGAGGGCCTCTACTTCGAAAGCAGAGCCAACACCCT
1 TACCCCTAACTTGACTGCTTCGTAACATGCGAGGCCCTCTACTTCGAAAGCAAACCCAACACCCT
117208 CGTGTAGGAAAAACTTTTATGCTAGAACC
66 CGTGTAGGAAAAACTTTTATGCTAGAACC
117237 CTTCCAGATG
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 89 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.25
Consensus pattern (108 bp):
TACCCCTAACTTGACTGCTTCGTAACATGCGAGGCCCTCTACTTCGAAAGCAAACCCAACACCCT
CGTGTAGGAAAAACTTTTATGCTAGAACCTAACTGTTCATCCT
Found at i:130510 original size:16 final size:16
Alignment explanation
Indices: 130489--130519 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
130479 GAAATTTTAG
*
130489 TGTTAAAGGACTAAAA
1 TGTTAAAGGAATAAAA
130505 TGTTAAAGGAATAAA
1 TGTTAAAGGAATAAA
130520 TTTGTAAGGA
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:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (16 bp):
TGTTAAAGGAATAAAA
Found at i:131262 original size:61 final size:60
Alignment explanation
Indices: 131108--131299 Score: 197
Period size: 61 Copynumber: 3.2 Consensus size: 60
131098 ATGTCATTGT
* * * **
131108 AGTATTACATGGAAATGAATCCAATTATGGATTAAAGGTCCGATAACTTTGTGTGATTGTG
1 AGTATTAAAT-GAAATGAATCCAATTATGGATTAAAGGTCCGATGACTTTGTGTCATCATG
* * ** *
131169 AGTATTAAATGCAATTAATCCAATTACAGATTAAAAGATCCGATGACTTTGTGTCATCATG
1 AGTATTAAATGAAATGAATCCAATTATGGATT-AAAGGTCCGATGACTTTGTGTCATCATG
** * * * *
131230 AGTATTAAATGAAATGAATATTAA-TATGGATTATAGGTCCGATGACTCTATGTCAACATG
1 AGTATTAAATGAAATGAAT-CCAATTATGGATTAAAGGTCCGATGACTTTGTGTCATCATG
*
131290 AGTATCAAAT
1 AGTATTAAAT
131300 ACGAACTCAA
Statistics
Matches: 107, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
60 50 0.47
61 55 0.51
62 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (60 bp):
AGTATTAAATGAAATGAATCCAATTATGGATTAAAGGTCCGATGACTTTGTGTCATCATG
Found at i:135802 original size:16 final size:16
Alignment explanation
Indices: 135781--135811 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
135771 GAAATTTTAG
*
135781 TGTTAAAGGACTAAAA
1 TGTTAAAGGAATAAAA
135797 TGTTAAAGGAATAAA
1 TGTTAAAGGAATAAA
135812 TTTGTAAGGA
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:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (16 bp):
TGTTAAAGGAATAAAA
Found at i:136499 original size:60 final size:60
Alignment explanation
Indices: 136380--136526 Score: 195
Period size: 60 Copynumber: 2.4 Consensus size: 60
136370 GTTGCGGATT
* * * * *
136380 CTCTATGTCATTGTGAGTATTACATGGAAATGAATCCTATTATGGATTAAAGGTCCGATGA
1 CTCTGTGTCATCGTGAGTATTAAAT-GAAATGAATCCTAATATGAATTAAAGGTCCGATGA
* * *
136441 CTTTGTGTCATCGTGAGTATTAAATGAAATGAATCCTAATATGAATTATAGGTTCGATGA
1 CTCTGTGTCATCGTGAGTATTAAATGAAATGAATCCTAATATGAATTAAAGGTCCGATGA
* *
136501 CTCTGTGTCATCATGAGTATCAAATG
1 CTCTGTGTCATCGTGAGTATTAAATG
136527 CGAATTGAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
60 54 0.72
61 21 0.28
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.35
Consensus pattern (60 bp):
CTCTGTGTCATCGTGAGTATTAAATGAAATGAATCCTAATATGAATTAAAGGTCCGATGA
Found at i:138402 original size:29 final size:29
Alignment explanation
Indices: 138363--138421 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
138353 TATTAATTAT
*
138363 TTAAACTAATTAATTATATTATAAAAATA
1 TTAAACTAATTAATAATATTATAAAAATA
*
138392 TTAAATTAATTAATAATATTATAAAAATA
1 TTAAACTAATTAATAATATTATAAAAATA
138421 T
1 T
138422 AGACATCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TTAAACTAATTAATAATATTATAAAAATA
Found at i:142944 original size:71 final size:71
Alignment explanation
Indices: 142823--142986 Score: 195
Period size: 71 Copynumber: 2.3 Consensus size: 71
142813 TAGCGCGAGC
* * * * * * *
142823 TCAAAGCTCCCAGCTATCATCTTAAGGCTCATTGATTCAATATCGCAGCCTTTAGAATAA-TTAG
1 TCAAAGCTCCCAGCTGTAATCTCAAGGCTCACTGATTCAATATCACAGCCTGTAAAATAATTTA-
*
142887 TGAGAGT
65 CGAGAGT
* * *
142894 TCAAAGCTCCCAACTGTAATCTCAAGGCTCGCTGATTCAATATCATAGCCTGTAAAATAATTTAC
1 TCAAAGCTCCCAGCTGTAATCTCAAGGCTCACTGATTCAATATCACAGCCTGTAAAATAATTTAC
142959 GAGAGT
66 GAGAGT
* *
142965 TTAAAGCTCCCAGTTGTAATCT
1 TCAAAGCTCCCAGCTGTAATCT
142987 TAGATCTCGC
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
71 75 0.96
72 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (71 bp):
TCAAAGCTCCCAGCTGTAATCTCAAGGCTCACTGATTCAATATCACAGCCTGTAAAATAATTTAC
GAGAGT
Found at i:143084 original size:58 final size:58
Alignment explanation
Indices: 142992--143107 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
142982 AATCTTAGAT
* *
142992 CTCGCGGATTCATTTTCCCAACTGATGATGTTAGAAAATTGT-CTTAAGTTTAAAACAG
1 CTCGCGGATTCATATTCCCAACTGATGATGTTAGAAAATT-TCCTCAAGTTTAAAACAG
* * *
143050 CTCGCGGATTCATATTCCCAGCTGATGATTTTAGAAGATTTCCTCAAGTTTAAAACAG
1 CTCGCGGATTCATATTCCCAACTGATGATGTTAGAAAATTTCCTCAAGTTTAAAACAG
143108 TTCGTAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
57 1 0.02
58 51 0.98
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (58 bp):
CTCGCGGATTCATATTCCCAACTGATGATGTTAGAAAATTTCCTCAAGTTTAAAACAG
Found at i:145952 original size:37 final size:37
Alignment explanation
Indices: 145851--146034 Score: 169
Period size: 37 Copynumber: 5.0 Consensus size: 37
145841 AACATTCATT
*
145851 CTTGAA-TCACCGACACAAAAGCCTGCTAGACACATAG
1 CTTGAATTCACCGACAC-AAAGCCTGCTAGGCACATAG
* * * * *
145888 -TCCG-ATTACACTGGCACGAAGCTTGCTAGGCACATAG
1 CT-TGAATT-CACCGACACAAAGCCTGCTAGGCACATAG
*
145925 CTTGAATTCACCGACACAAAGCCTGCTAGGTACATAG
1 CTTGAATTCACCGACACAAAGCCTGCTAGGCACATAG
* * * *
145962 CTTGAATTCACCAACATAAAGCGTGCTAGGCACATAA
1 CTTGAATTCACCGACACAAAGCCTGCTAGGCACATAG
** * *
145999 CCCGAATAT-ATCAACACAAAGCCTGCTAGGCACATA
1 CTTGAAT-TCACCGACACAAAGCCTGCTAGGCACATA
146035 ACCCAAATTT
Statistics
Matches: 119, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
36 2 0.02
37 105 0.88
38 12 0.10
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.20
Consensus pattern (37 bp):
CTTGAATTCACCGACACAAAGCCTGCTAGGCACATAG
Found at i:153028 original size:37 final size:37
Alignment explanation
Indices: 152942--153127 Score: 173
Period size: 37 Copynumber: 5.0 Consensus size: 37
152932 AACATTCATT
* *
152942 CTTGAA-TCACCGACACAAAAGCCTGCTAGACACATAG
1 CTTGAATTCACTGACAC-AAAGCCTGCTAGGCACATAG
* * * *
152979 TCTT--ATTACACTGGCACGAAGCTTGCTTGGCACATAG
1 -CTTGAATT-CACTGACACAAAGCCTGCTAGGCACATAG
153016 CTTGAATTCACTGACACAAAGCCTGCTAGGCACATAG
1 CTTGAATTCACTGACACAAAGCCTGCTAGGCACATAG
** * *
153053 CTTGAATTCACCAACATAAAGCGTGCTAGGCACATAG
1 CTTGAATTCACTGACACAAAGCCTGCTAGGCACATAG
** * * *
153090 CCCGAATACA-TCGGCACAAAGCCTGTTAGGCACATAG
1 CTTGAATTCACT-GACACAAAGCCTGCTAGGCACATAG
153127 C
1 C
153128 CTGCTAGGCA
Statistics
Matches: 120, Mismatches: 23, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
36 4 0.03
37 103 0.86
38 13 0.11
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.21
Consensus pattern (37 bp):
CTTGAATTCACTGACACAAAGCCTGCTAGGCACATAG
Found at i:153123 original size:16 final size:16
Alignment explanation
Indices: 153102--153146 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
153092 CGAATACATC
*
153102 GGCACAAAGCCTGTTA
1 GGCACAAAGCCTGCTA
*
153118 GGCACATAGCCTGCTA
1 GGCACAAAGCCTGCTA
*
153134 GGCACACAGCCTG
1 GGCACAAAGCCTG
153147 AATTTCTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.16
Consensus pattern (16 bp):
GGCACAAAGCCTGCTA
Found at i:155110 original size:114 final size:115
Alignment explanation
Indices: 154909--155137 Score: 406
Period size: 114 Copynumber: 2.0 Consensus size: 115
154899 AAGAGGAAGC
* * *
154909 AAAAAGCTATCCTAGATGGTTTCACTCAACCTATGTGGTCCCTCAGGAATGGAAAATTCGTACAT
1 AAAAAGCTATCCTAAATGGTTTCACTCAACCTATGTGGTCCCTCAGGAATGGAAAAGTCGTACAC
154974 AAAATGGGGGATTTATATCCCTCGCACGGTTAAGGCTCGTCGCATTTCCT
66 AAAATGGGGGATTTATATCCCTCGCACGGTTAAGGCTCGTCGCATTTCCT
155024 AAAAAGCTATCCTAAATGGTTTCACTCAACCTATGT-GTCCCTCAGGAATGGAAAAGTCGTACAC
1 AAAAAGCTATCCTAAATGGTTTCACTCAACCTATGTGGTCCCTCAGGAATGGAAAAGTCGTACAC
* *
155088 AAAATGGGGGATTTATATCCCTCGCACGGTTAGGGCTCGTCGTATTTCCT
66 AAAATGGGGGATTTATATCCCTCGCACGGTTAAGGCTCGTCGCATTTCCT
155138 CTATTTTCGT
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
114 74 0.68
115 35 0.32
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (115 bp):
AAAAAGCTATCCTAAATGGTTTCACTCAACCTATGTGGTCCCTCAGGAATGGAAAAGTCGTACAC
AAAATGGGGGATTTATATCCCTCGCACGGTTAAGGCTCGTCGCATTTCCT
Found at i:162558 original size:16 final size:16
Alignment explanation
Indices: 162539--162575 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
162529 AATTATCATA
*
162539 TTAGGTTAAATTGCAT
1 TTAGGATAAATTGCAT
162555 TTAGGGATAAATTGCAT
1 TTA-GGATAAATTGCAT
162572 TTAG
1 TTAG
162576 ATATATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (16 bp):
TTAGGATAAATTGCAT
Found at i:164395 original size:8 final size:8
Alignment explanation
Indices: 164378--164437 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
164368 TATTACTATC
*
164378 ATTATATT
1 ATTATTTT
164386 ATTATTTT
1 ATTATTTT
*
164394 ATT-TATT
1 ATTATTTT
*
164401 ACTA-TTT
1 ATTATTTT
164408 ATTATTTT
1 ATTATTTT
*
164416 ATTATGTT
1 ATTATTTT
164424 ATTAATTGTT
1 ATT-ATT-TT
164434 ATTA
1 ATTA
164438 ATTGTATTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
7 10 0.24
8 23 0.56
9 3 0.07
10 5 0.12
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (8 bp):
ATTATTTT
Found at i:164418 original size:30 final size:29
Alignment explanation
Indices: 164367--164426 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
164357 TTTATTACCA
*
164367 TTATTACTATCATTATATTATTATTTTAT
1 TTATTACTATCATTATATTATTATGTTAT
* *
164396 TTATTACTATTTATTATTTTATTATGTTAT
1 TTATTACTA-TCATTATATTATTATGTTAT
164426 T
1 T
164427 AATTGTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (29 bp):
TTATTACTATCATTATATTATTATGTTAT
Found at i:164420 original size:38 final size:40
Alignment explanation
Indices: 164346--164436 Score: 107
Period size: 38 Copynumber: 2.3 Consensus size: 40
164336 ATTATTCTTA
*
164346 ATTAATTGATATTTATTACCATTATTACTATCATTATATT
1 ATTAATTGTTATTTATTACCATTATTACTATCATTATATT
* * * *
164386 ATT-ATT-TTATTTATTACTATTTATTA-TTTTATTATGTT
1 ATTAATTGTTATTTATTACCA-TTATTACTATCATTATATT
164424 ATTAATTGTTATT
1 ATTAATTGTTATT
164437 AATTGTATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
38 23 0.53
39 12 0.28
40 8 0.19
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.60
Consensus pattern (40 bp):
ATTAATTGTTATTTATTACCATTATTACTATCATTATATT
Found at i:183294 original size:29 final size:28
Alignment explanation
Indices: 183262--183316 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
183252 ACATTATCAA
183262 ATTT-TAAATATAAAAAATTATTATTATAC
1 ATTTATAAATA-AAAAAATTATT-TTATAC
**
183291 ATTTATTCATAAAAAAATTATTTTAT
1 ATTTATAAATAAAAAAATTATTTTAT
183317 GGACACTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.17
29 15 0.65
30 4 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTATAAATAAAAAAATTATTTTATAC
Done.