Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold216
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: 469096
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 3
Found at i:273011 original size:16 final size:17
Alignment explanation
Indices: 272980--273017 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
272970 GATGCAAATA
* *
272980 ATGATGTTATTGATGTT
1 ATGATGTCATTGATGTC
272997 ATGATGTCA-TGATGTC
1 ATGATGTCATTGATGTC
273013 ATGAT
1 ATGAT
273018 TACAGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGATGTCATTGATGTC
Found at i:274198 original size:13 final size:12
Alignment explanation
Indices: 274180--274210 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
274170 TTTTTATGTG
274180 TTTTTTGTTTTT
1 TTTTTTGTTTTT
274192 TTGTTTTGTTTTT
1 TT-TTTTGTTTTT
274205 TTTTTT
1 TTTTTT
274211 ACTTTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:274216 original size:18 final size:18
Alignment explanation
Indices: 274181--274235 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
274171 TTTTATGTGT
**
274181 TTTTTGTTTTTTTGTTTTG
1 TTTTT-TTTTTTACTTTTG
274200 TTTTTTTTTTTACTTTTG
1 TTTTTTTTTTTACTTTTG
* * *
274218 TTTGTGTGTTTACTTTTG
1 TTTTTTTTTTTACTTTTG
274236 ACTTTTTCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.04, C:0.04, G:0.15, T:0.78
Consensus pattern (18 bp):
TTTTTTTTTTTACTTTTG
Found at i:281285 original size:19 final size:19
Alignment explanation
Indices: 281261--281310 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
281251 AGCGATACAT
281261 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
281280 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
281299 TGTGTCGATACA
1 TGTATCGATACA
281311 TTGTATTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:291866 original size:27 final size:27
Alignment explanation
Indices: 291835--291905 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
291825 GGTTGAAAAC
*
291835 GGGGTTGGAATGTTCCCTCAGAGGAAT
1 GGGGTTGGAATGTCCCCTCAGAGGAAT
* *
291862 GGGGTTGGAGTGTCCCCTCGGAGGAAT
1 GGGGTTGGAATGTCCCCTCAGAGGAAT
*
291889 GGGGTTGGAGTGTCCCC
1 GGGGTTGGAATGTCCCC
291906 GATGATGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.15, C:0.18, G:0.42, T:0.24
Consensus pattern (27 bp):
GGGGTTGGAATGTCCCCTCAGAGGAAT
Found at i:294106 original size:20 final size:20
Alignment explanation
Indices: 294081--294118 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
294071 ATGTATCGAT
294081 ATAATATATCGATACATTGA
1 ATAATATATCGATACATTGA
294101 ATAATATATCGATACATT
1 ATAATATATCGATACATT
294119 TCCTTGGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (20 bp):
ATAATATATCGATACATTGA
Found at i:296278 original size:96 final size:96
Alignment explanation
Indices: 296152--296387 Score: 436
Period size: 96 Copynumber: 2.4 Consensus size: 96
296142 TTTGATTGAA
*
296152 AAAAACGGGGTTGGAGTATCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTAA
1 AAAAACGGGGTTGGAGTATCCCTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGACAATTTAA
296217 GAGAGAATAAGATTTGAATCTTAACAAGTTT
66 GAGAGAATAAGATTTGAATCTTAACAAGTTT
*
296248 AAAAGCGGGGTTGGAGTATCCCTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGACAATTTAA
1 AAAAACGGGGTTGGAGTATCCCTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGACAATTTAA
296313 GAGAGAATAAGATTTGAATCTTAACAAGTTT
66 GAGAGAATAAGATTTGAATCTTAACAAGTTT
*
296344 AAAAACGGGGTTGGAGTATTCCCTCGGAAGAATAGGGTTGGAGT
1 AAAAACGGGGTTGGAGTA-TCCCTCGGAGGAATAGGGTTGGAGT
296388 ATCTCCAATG
Statistics
Matches: 135, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
96 111 0.82
97 24 0.18
ACGTcount: A:0.32, C:0.12, G:0.31, T:0.25
Consensus pattern (96 bp):
AAAAACGGGGTTGGAGTATCCCTCGGAGGAATAGGGTTGGAGTGTCCCCGATGATGACAATTTAA
GAGAGAATAAGATTTGAATCTTAACAAGTTT
Found at i:302794 original size:52 final size:52
Alignment explanation
Indices: 302594--302774 Score: 317
Period size: 52 Copynumber: 3.5 Consensus size: 52
302584 CAAAATATGA
* *
302594 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
302646 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
302698 AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
*
302750 AAATTTACCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
302775 AAGATCAGTG
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 122 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:302801 original size:13 final size:13
Alignment explanation
Indices: 302783--302807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
302773 CAAAGATCAG
302783 TGTATCGATACAA
1 TGTATCGATACAA
302796 TGTATCGATACA
1 TGTATCGATACA
302808 TTTAAGCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:302874 original size:19 final size:18
Alignment explanation
Indices: 302850--302947 Score: 72
Period size: 19 Copynumber: 5.8 Consensus size: 18
302840 TAGCTTAAAT
302850 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
302869 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
302882 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
302901 TGTATCGATGC--A--T-
1 TGTATCGATACAAACTTA
302914 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
*
302934 TGTATCAATACAAA
1 TGTATCGATACAAA
302948 TCGTTGAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 26
0.68 0.03 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.37
20 12 0.19
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:302887 original size:13 final size:13
Alignment explanation
Indices: 302869--302925 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
302859 ACAAAACTTA
302869 TGTATCGATACAT
1 TGTATCGATACAT
302882 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
*
302900 ATGTATCGATGCAT
1 -TGTATCGATACAT
302914 TGTATCGATACA
1 TGTATCGATACA
302926 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 5 0.14
18 1 0.03
19 9 0.25
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:302889 original size:32 final size:32
Alignment explanation
Indices: 302848--302945 Score: 160
Period size: 32 Copynumber: 3.0 Consensus size: 32
302838 AGTAGCTTAA
*
302848 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
302880 ATTGTATCGATACAACACTTATGTATCGATGC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
302912 ATTGTATCGATACAACACTTTATGTATCAATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
302945 A
1 A
302946 AATCGTTGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 48 0.79
33 13 0.21
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:314064 original size:13 final size:13
Alignment explanation
Indices: 314046--314073 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
314036 CATTATTCAA
314046 TGTATCGATACAT
1 TGTATCGATACAT
314059 TGTATCGATACAT
1 TGTATCGATACAT
314072 TG
1 TG
314074 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:314068 original size:33 final size:33
Alignment explanation
Indices: 314026--314091 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
314016 GCCAAGGAAA
314026 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
314059 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
314092 CTAGAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:321150 original size:8 final size:8
Alignment explanation
Indices: 321139--321178 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
321129 AGTCAAAAGT
*
321139 AAAAACAC
1 AAAAAAAC
321147 AAAAAAAC
1 AAAAAAAC
*
321155 AAAAAAAA
1 AAAAAAAC
321163 AACAAAAAC
1 AA-AAAAAC
321172 AAAAAAA
1 AAAAAAA
321179 ACACACAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 21 0.75
9 7 0.25
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:321159 original size:17 final size:17
Alignment explanation
Indices: 321149--321189 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 17
321139 AAAAACACAA
321149 AAAAACAAAAAAAAAAC
1 AAAAACAAAAAAAAAAC
321166 AAAAACAAAAAAAACACAC
1 AAAAACAAAAAAAA-A-AC
321185 AAAAA
1 AAAAA
321190 AAAGAGTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 14 0.64
18 1 0.05
19 7 0.32
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAAAAAAAC
Found at i:321161 original size:11 final size:11
Alignment explanation
Indices: 321147--321176 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
321137 GTAAAAACAC
321147 AAAAAAACAAA
1 AAAAAAACAAA
321158 AAAAAAACAAA
1 AAAAAAACAAA
321169 AACAAAAA
1 AA-AAAAA
321177 AAACACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:321190 original size:11 final size:9
Alignment explanation
Indices: 321139--321181 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
321129 AGTCAAAAGT
321139 AAAAACACAA
1 AAAAACA-AA
321149 AAAAACAAA
1 AAAAACAAA
*
321158 AAAAA-AAC
1 AAAAACAAA
321166 AAAAACAAA
1 AAAAACAAA
321175 AAAAACA
1 AAAAACA
321182 CACAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 7 0.23
9 16 0.53
10 7 0.23
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAACAAA
Found at i:321192 original size:17 final size:17
Alignment explanation
Indices: 321139--321192 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 17
321129 AGTCAAAAGT
321139 AAAAACACA-AAAAAACA
1 AAAAACACACAAAAAA-A
* *
321156 AAAAAAAAACAAAAACAAA
1 AAAAACACAC-AAAA-AAA
321175 AAAAACACACAAAAAAA
1 AAAAACACACAAAAAAA
321192 A
1 A
321193 GAGTGCAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 11 0.37
18 4 0.13
19 13 0.43
20 2 0.07
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAACACACAAAAAAA
Found at i:322489 original size:30 final size:30
Alignment explanation
Indices: 322454--323002 Score: 557
Period size: 30 Copynumber: 17.8 Consensus size: 30
322444 TCTTCAAATC
* *
322454 TCTCTTCTCAAAGTACACGACTTAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* * *
322484 TCTCTTCTCAAAGTCCACAATTCAGTAGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
*
322514 TCTCTTTTCTTCAAAGTCCACGACTTAGTGGCA
1 TCTC--TTC-TCAAAGTCCACGACTCAGTGGCA
* *
322547 TCT-TGTCCCAAAGTCCACGACTCAATGGCAA
1 TCTCT-TCTCAAAGTCCACGACTCAGTGGC-A
* * *
322578 TCTTTTCTCAAAGTCCACAACTCAGTTGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* * * * *
322608 TATCTTTTCTAAGCCCACGACTTAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* *
322638 TTCTTTTCTTCCAAGTCCACGACTCAGTGGCA
1 -TCTCTTC-TCAAAGTCCACGACTCAGTGGCA
*
322670 TCTCTTTTCTCAAAGTCCACAACTCAGTGGCA
1 TCTC--TTCTCAAAGTCCACGACTCAGTGGCA
* * *
322702 TCTTTTTTCTCAAAGTTCACAACTCAGTGGCA
1 TC--TCTTCTCAAAGTCCACGACTCAGTGGCA
* * *
322734 TCTCTCTTCCCAAAGTCCATGACTTAGTGGCA
1 --TCTCTTCTCAAAGTCCACGACTCAGTGGCA
322766 TCGT-TTCCTCAAAGTCCACGACTCAGTGGCA
1 TC-TCTT-CTCAAAGTCCACGACTCAGTGGCA
*
322797 TCTCTTCCCAAAGTCCACGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
* * *
322827 TCTTTTCTTCAAAGTCCATGACTTAGTGGCAA
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGC-A
*
322859 TCTCTTCTCAAAGTCCACGACTCAATGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
*
322889 TCT-TGTCTCAAAGTCCATGACTCAGTGGCA
1 TCTCT-TCTCAAAGTCCACGACTCAGTGGCA
* * * *
322919 TCTTTTCTTCAAAGTCCACAACTTAGTGGCG
1 TCTCTTC-TCAAAGTCCACGACTCAGTGGCA
*
322950 TTTCTTCTCAAAGTCCACGACTCAGTGGCA
1 TCTCTTCTCAAAGTCCACGACTCAGTGGCA
*
322980 TCTATT-TCCAAAGTCCACGACTC
1 TCTCTTCT-CAAAGTCCACGACTC
323003 TGTGCCACCT
Statistics
Matches: 430, Mismatches: 66, Indels: 46
0.79 0.12 0.08
Matches are distributed among these distances:
29 2 0.00
30 177 0.41
31 122 0.28
32 101 0.23
33 25 0.06
34 3 0.01
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (30 bp):
TCTCTTCTCAAAGTCCACGACTCAGTGGCA
Found at i:322626 original size:61 final size:60
Alignment explanation
Indices: 322458--323002 Score: 572
Period size: 61 Copynumber: 8.8 Consensus size: 60
322448 CAAATCTCTC
* * * * * *
322458 TTCTCAAAGTACACGACTTAGTGGCATCTCTTCTCAAAGTCCACAATTCAGTAGCATCTCTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTCTTTTCAAAGTCCACGACTCAGTGGCA--TCTT
* ** *
322520 TTCTTCAAAGTCCACGACTTAGTGGCATCT-TGTCCCAAAGTCCACGACTCAATGGCAATCTT
1 TTC-TCAAAGTCCACGACTCAGTGGCATCTCT-TTTCAAAGTCCACGACTCAGTGGC-ATCTT
* * * * * *
322582 TTCTCAAAGTCCACAACTCAGTTGCATATCTTTTCTAAGCCCACGACTTAGTGGCATTCTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTCTTTTCAAAGTCCACGACTCAGTGGCA-TCTT
* *
322643 TTCTTCCAAGTCCACGACTCAGTGGCATCTCTTTTCTCAAAGTCCACAACTCAGTGGCATCTTTT
1 TTC-TCAAAGTCCACGACTCAGTGGCATCTC-TTT-TCAAAGTCCACGACTCAGTGGCATC--TT
* * * * *
322708 TTCTCAAAGTTCACAACTCAGTGGCATCTCTCTTCCCAAAGTCCATGACTTAGTGGCATCGTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTCT-TT-TCAAAGTCCACGACTCAGTGGCATC-TT
* **
322771 TCCTCAAAGTCCACGACTCAGTGGCATCTCTTCCCAAAGTCCACGACTCAGTGGCATCTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTCTTTTCAAAGTCCACGACTCAGTGGCATCTT
* * * *
322831 TTCTTCAAAGTCCATGACTTAGTGGCAATCTCTTCTCAAAGTCCACGACTCAATGGCATCTT
1 TTC-TCAAAGTCCACGACTCAGTGGC-ATCTCTTTTCAAAGTCCACGACTCAGTGGCATCTT
* * * * * *
322893 GTCTCAAAGTCCATGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTTAGTGGCGT-TT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTCTT-TTCAAAGTCCACGACTCAGTGGCATCTT
* *
322953 CTTCTCAAAGTCCACGACTCAGTGGCATCTATTTCCAAAGTCCACGACTC
1 -TTCTCAAAGTCCACGACTCAGTGGCATCTCTTTTCAAAGTCCACGACTC
323003 TGTGCCACCT
Statistics
Matches: 411, Mismatches: 57, Indels: 32
0.82 0.11 0.06
Matches are distributed among these distances:
60 27 0.07
61 160 0.39
62 71 0.17
63 80 0.19
64 68 0.17
65 5 0.01
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (60 bp):
TTCTCAAAGTCCACGACTCAGTGGCATCTCTTTTCAAAGTCCACGACTCAGTGGCATCTT
Found at i:322869 original size:92 final size:91
Alignment explanation
Indices: 322461--323002 Score: 608
Period size: 92 Copynumber: 5.8 Consensus size: 91
322451 ATCTCTCTTC
* * *
322461 TCAAAGTACACGACTTAGTGGCATCTCTTCTCAAAGTCCACAATTCAGTAGCATCTCTTTTCTTC
1 TCAAAGTCCACGACTTAGTGGCATCTCTTCTCAAAGTCCACAACTCAGTGGCATCTC--TTC-TC
* *
322526 AAAGTCCACGACTTAGTGGCATCTTGTC-
63 AAAGTCCACGACTCAGTGGCATCTTTTCT
* * * * * * * *
322554 CCAAAGTCCACGACTCAATGGCAATCTTTTCTCAAAGTCCACAACTCAGTTGCATATCTTTTCTA
1 TCAAAGTCCACGACTTAGTGGC-ATCTCTTCTCAAAGTCCACAACTCAGTGGCATCTCTTCTCAA
* *
322619 AGCCCACGACTTAGTGGCATTCTTTTCT
65 AGTCCACGACTCAGTGGCA-TCTTTTCT
* * *
322647 TCCAAGTCCACGACTCAGTGGCATCTCTTTTCTCAAAGTCCACAACTCAGTGGCATCTTTTTTCT
1 TCAAAGTCCACGACTTAGTGGCATCTC--TTCTCAAAGTCCACAACTCAGTGGCATC--TCTTCT
* *
322712 CAAAGTTCACAACTCAGTGGCATCTCTCTTC-
62 CAAAGTCCACGACTCAGTGGCATCT-T-TTCT
* * * *
322743 CCAAAGTCCATGACTTAGTGGCATCGT-TTCCTCAAAGTCCACGACTCAGTGGCATCTCTTCCCA
1 TCAAAGTCCACGACTTAGTGGCATC-TCTT-CTCAAAGTCCACAACTCAGTGGCATCTCTTCTCA
322807 AAGTCCACGACTCAGTGGCATCTTTTCT
64 AAGTCCACGACTCAGTGGCATCTTTTCT
* * *
322835 TCAAAGTCCATGACTTAGTGGCAATCTCTTCTCAAAGTCCACGACTCAATGGCATCT-TGTCTCA
1 TCAAAGTCCACGACTTAGTGGC-ATCTCTTCTCAAAGTCCACAACTCAGTGGCATCTCT-TCTCA
*
322899 AAGTCCATGACTCAGTGGCATCTTTTCT
64 AAGTCCACGACTCAGTGGCATCTTTTCT
* * * * *
322927 TCAAAGTCCACAACTTAGTGGCGTTTCTTCTCAAAGTCCACGACTCAGTGGCATCTATT-TCCAA
1 TCAAAGTCCACGACTTAGTGGCATCTCTTCTCAAAGTCCACAACTCAGTGGCATCTCTTCT-CAA
322991 AGTCCACGACTC
65 AGTCCACGACTC
323003 TGTGCCACCT
Statistics
Matches: 388, Mismatches: 44, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
90 1 0.00
91 71 0.18
92 113 0.29
93 69 0.18
94 59 0.15
95 28 0.07
96 43 0.11
97 4 0.01
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (91 bp):
TCAAAGTCCACGACTTAGTGGCATCTCTTCTCAAAGTCCACAACTCAGTGGCATCTCTTCTCAAA
GTCCACGACTCAGTGGCATCTTTTCT
Found at i:323122 original size:34 final size:32
Alignment explanation
Indices: 323079--323682 Score: 369
Period size: 34 Copynumber: 19.3 Consensus size: 32
323069 TCTGTGGCAC
*
323079 CCTTTTAAGTCCATAACTCCGTGGCAATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGC-A-CTTTTT
*
323113 CCTTTTAAGTCCACAACTCCGTGGTAC-----
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTT
323140 CCTTTTAAGTCCACAACTCCGTGGCAATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGC-A-CTTTTT
*
323174 CCTTTTAAGTCCACAACTCCGTGGCACCTTATT
1 CCTTTTAAGTCCACAACTCCGTGGCA-CTTTTT
* ** ** *
323207 CTTTTTAAAACCCACAACTTTGTGGTACTCTTTTT
1 CCTTTT-AAGTCCACAACTCCGTGG--CACTTTTT
* *
323242 TCTTTTAAGTCCACAACTCCGTGGCACCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCA-CTTTTT
* * *
323275 CTTTTTAAAGCCCACAACTCTGTGGCAC-----
1 CCTTTT-AAGTCCACAACTCCGTGGCACTTTTT
* * *
323303 CCTTTTAAGTCTACAATTCTGTGGCA-----T
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTT
* * *
323330 CCTTTTAAGTCCATAACTCCGCGTGC-CTTTGT
1 CCTTTTAAGTCCACAACTCCGTG-GCACTTTTT
* * *
323362 --TTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA--CTTTTT
* * *
323394 CCTTTTAAGCCCACAACTTCGTGGCACCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCA-CTTTTT
* * *
323427 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTCT
1 CCTTTT-AAGTCCACAACTCCGTGGCACT-TTT-T
* *
323462 CTTTTTAAGTCCACAACTCCATGGCAC-----
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTT
*
323489 CCTTTTAAGTCCACAACTTCGTGGCAC-----
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTT
**
323516 CCTTTTAAGTCCACAACTCCGTAACACCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA-CTTTTT
* * * *
323549 --TTTAAAGCCCATAACTCCATGGCACTCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA--CTTTTT
323581 CCTTTTAAGTCCACAACTCCGTGGCAC-----
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTT
*
323608 CCTTTTAAGTCCACAACTCCGTGGCACCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTT
* * ** *
323640 CTTTTTAAGTCCACGACTTTGTGGCACCCTTTTC
1 CCTTTTAAGTCCACAACTCCGTGGCA--CTTTTT
323674 CCTTTTAAG
1 CCTTTTAAG
323683 CCCATACCTC
Statistics
Matches: 452, Mismatches: 75, Indels: 86
0.74 0.12 0.14
Matches are distributed among these distances:
27 133 0.29
28 9 0.02
29 3 0.01
30 16 0.04
31 18 0.04
32 37 0.08
33 34 0.08
34 185 0.41
35 16 0.04
36 1 0.00
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (32 bp):
CCTTTTAAGTCCACAACTCCGTGGCACTTTTT
Found at i:323186 original size:342 final size:339
Alignment explanation
Indices: 322457--323172 Score: 724
Period size: 342 Copynumber: 2.1 Consensus size: 339
322447 TCAAATCTCT
* * * * * * *
322457 CTTCTCAAAGTACACGACTTAGTGGCATCTCTTC-TCAAAGTCCA-CAATTCAGTAGC-ATCTCT
1 CTTC-CAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTT-AGTGGCAATCTC-
* *
322519 TTTCTTCAAAGTCCACGACTTAGTGGCATCTTGTCCCAAAGTCCACGACTCAATGGCAATCTTTT
63 -TTC-TCAAAGTCCACGACTCAATGGCATCTTGTCCCAAAGTCCACGACTCAATGGCAATCTTTT
* * * *
322584 CTCAAAGTCCACAACTCAGTTGCATATCTTTTCTAAGCCCACGACTTAGTGGCATTCTTTTCTTC
126 CTCAAAGTCCACAACTCAGTGGCATATCTTCTCAAAGCCCACGACTCAGTGGCATTCTTTTC-TC
* * * *
322649 CAAGTCCACGACTCAGTGGCATCTCTTTTCTCAAAGTCCACAACTCAGTGGCATCTTTTTTCTCA
190 AAAGTCCACGACTCAGTGCCATCTCTTTTCTCAAAGCCCACAACTCAGTAGCATCTTTTTTCTCA
* *
322714 AAGTTCACAACTCAGTGGCATCTCTCTTCCCAAAGTCCATGACTTAGTGGCATCGTTTCCTCAAA
255 AAGTTCACAACTCAGTGGCATCTCTCTT-CCAAAGTCCATAACTCAGTGGCATCGTTTCCTCAAA
* *
322779 GTCCACGACTCAGTGGCATCT
319 GTCCACAACTCAGTGGCATCC
*
322800 CTTCCCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTTAGTGGCAATCTCTT
1 CTT-CCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTTAGTGGCAATCTCTT
* * *
322865 CTCAAAGTCCACGACTCAATGGCATCTTGTCTCAAAGTCCATGACTCAGTGGC-ATCTTTTCTTC
65 CTCAAAGTCCACGACTCAATGGCATCTTGTCCCAAAGTCCACGACTCAATGGCAATCTTTTC-TC
* * * *
322929 AAAGTCCACAACTTAGTGGCGTTTCTTCTCAAAGTCCACGACTCAGTGGCA-TCTATTTC-CAAA
129 AAAGTCCACAACTCAGTGGCATATCTTCTCAAAGCCCACGACTCAGTGGCATTCT-TTTCTCAAA
* * * *
322992 GTCCACGACTCTGTGCCACCT-TTTTCTTTTTC-AAGCCCAGAACTCTGTAGCA-CTATTTTTCC
193 GTCCACGACTCAGTGCCATCTCTTTTC----TCAAAGCCCACAACTCAGTAGCATCT-TTTTT-C
* * ** * *
323054 TTCAAAGTTCATAACTCTGTGGCA-C-C-CTT-TTAAGTCCATAACTCCGTGGCAATCTTTTTCC
252 -TCAAAGTTCACAACTCAGTGGCATCTCTCTTCCAAAGTCCATAACTCAGTGGC-ATC-GTTTCC
** * *
323115 TTTTAAGTCCACAACTCCGTGGTA-CC
314 -TCAAAGTCCACAACTCAGTGGCATCC
** *
323141 CTT-TTAAGTCCACAACTCCGTGGCAATCTTTT
1 CTTCCAAAGTCCACAACTCAGTGGC-ATCTTTT
323173 TCCTTTTAAG
Statistics
Matches: 311, Mismatches: 45, Indels: 37
0.79 0.11 0.09
Matches are distributed among these distances:
339 38 0.12
340 31 0.10
341 25 0.08
342 136 0.44
343 36 0.12
344 37 0.12
345 8 0.03
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (339 bp):
CTTCCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTTAGTGGCAATCTCTTC
TCAAAGTCCACGACTCAATGGCATCTTGTCCCAAAGTCCACGACTCAATGGCAATCTTTTCTCAA
AGTCCACAACTCAGTGGCATATCTTCTCAAAGCCCACGACTCAGTGGCATTCTTTTCTCAAAGTC
CACGACTCAGTGCCATCTCTTTTCTCAAAGCCCACAACTCAGTAGCATCTTTTTTCTCAAAGTTC
ACAACTCAGTGGCATCTCTCTTCCAAAGTCCATAACTCAGTGGCATCGTTTCCTCAAAGTCCACA
ACTCAGTGGCATCC
Found at i:323224 original size:68 final size:67
Alignment explanation
Indices: 322990--323682 Score: 314
Period size: 61 Copynumber: 11.0 Consensus size: 67
322980 TCTATTTCCA
* * * * * * * * *
322990 AAGTCCACGACTCTGTGCCACCTTTTTCTTTTTCAAGCCCAGAACTCTGTAGCACTATTTTTCCT
1 AAGTCCACAACTCCGTGGCACC-TTTTCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTCCT
**
323055 TCA
65 TTT
* * * * *
323058 AAGTTCATAACTCTGTGGCACC----C-TTTT-AAGTCCATAACTCCGTGGCAATCTTTTTCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTCCTT
323117 TT
66 TT
* *
323119 AAGTCCACAACTCCGTGGTACC----C-TTTT-AAGTCCACAACTCCGTGGCAATCTTTTTCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTCCTT
323178 TT
66 TT
* ** * * *
323180 AAGTCCACAACTCCGTGGCACCTTATTCTTTTTAAAACCCACAACTTTGTGGTACTCTTTTTTCT
1 AAGTCCACAACTCCGTGGCACCTT-TTCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTCCT
323245 TTT
65 TTT
*
323248 AAGTCCACAACTCCGTGGCACCTTGTTCTTTTTAAAGCCCACAACTCTGTGGC-A-C-----CCT
1 AAGTCCACAACTCCGTGGCACCTT-TTCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTCCT
323306 TTT
65 TTT
* * * * * * * *
323309 AAGTCTACAATTCTGTGGCA-----TCCTTTT-AAGTCCATAACTCCGCGTGC---CTTTGT--T
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTTAAAGCCCACAACTCCGTG-GCAATCTTTTTCCT
*
323363 TTA
65 TTT
* * * * * * *
323366 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT-AAGCCCACAACTTCGTGGC-ACCTTGTTCT
1 AAGTCCACAACTCCGTGGCAC-C-TTTTCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTCC
323429 TTTT
64 TTTT
* * * *
323433 AAAGCCCACAACTCTGTGGCACTCTTTCTCTTTTT-AAGTCCACAACTCCATGGC-A-C-----C
1 -AAGTCCACAACTCCGTGGCAC-CTTT-TCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTC
323490 CTTTT
63 CTTTT
* * ** *
323495 AAGTCCACAACTTCGTGGCACC----C-TTTT-AAGTCCACAACTCCGTAAC-ACCTTTTT--TT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTCCTT
*
323551 TA
66 TT
* * * * *
323553 AAGCCCATAACTCCATGGCACTCTTTTTCCTTTT-AAGTCCACAACTCCGTGGC-A-C-----CC
1 AAGTCCACAACTCCGTGGCAC-C-TTTTCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTCC
323610 TTTT
64 TTTT
* * ** ** *
323614 AAGTCCACAACTCCGTGGCACCTTTTCTTTTT-AAGTCCACGACTTTGTGGCACCCTTTTCCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTCCTT
323678 TT
66 TT
323680 AAG
1 AAG
323683 CCCATACCTC
Statistics
Matches: 500, Mismatches: 77, Indels: 98
0.74 0.11 0.15
Matches are distributed among these distances:
54 35 0.07
55 10 0.02
57 20 0.04
58 20 0.04
59 26 0.05
60 2 0.00
61 165 0.33
62 9 0.02
63 3 0.01
64 22 0.04
65 26 0.05
66 11 0.02
67 11 0.02
68 140 0.28
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (67 bp):
AAGTCCACAACTCCGTGGCACCTTTTCTTTTTAAAGCCCACAACTCCGTGGCAATCTTTTTCCTT
TT
Found at i:323454 original size:186 final size:180
Alignment explanation
Indices: 323113--323672 Score: 628
Period size: 186 Copynumber: 3.0 Consensus size: 180
323103 CAATCTTTTT
* * *
323113 CCTTTTAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCCGTGGCAATCTTTTTCCTT
1 CCTTTTAAGTCCACAA-TTCGTGGCACCCTTTTAAGTCCACAACTCCGAGGC---CTTTTT--TT
* * * * * * * *
323178 TTAAGTCCACAACTCCGTGGCAC-CTTATTCTTTTTAAAACCCACAACTTTGTGGTACTCTTTTT
60 TAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT-AAGCCCACAACTTCGTGGCAC-CTTTTC
*
323242 TCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCTTTTTAAAGCCCACAACTCTGTGGCAC
123 T-TTTTAAGTCCACAACTCCGTGGCACCTT-TTCTTTTT-AAGTCCACAACTCTGTGGCAC
* * * * *
323303 CCTTTTAAGTCTACAATTCTGTGGCATCCTTTTAAGTCCATAACTCCGCGTGCCTTTGTTTTAAA
1 CCTTTTAAGTCCACAATTC-GTGGCACCCTTTTAAGTCCACAACTCCGAG-GCCTTTTTTTTAAA
*
323368 GCCCACAACTCTGTGGCACTCTTTTTCCTTTTAAGCCCACAACTTCGTGGCACCTTGTTCTTTTT
64 GCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTTCGTGGCACCTT-TTCTTTTT
* * **
323433 AAAGCCCACAACTCTGTGGCACTCTTTCTCTTTTTAAGTCCACAACTCCATGGCAC
128 -AAGTCCACAACTCCGTGGCAC-CTTT-TCTTTTTAAGTCCACAACTCTGTGGCAC
**
323489 CCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCCGTAACACCTTTTTTTTAA
1 CCTTTTAAGTCCACAA-TTCGTGGCACCCTTTTAAGTCCACAACTCCG--AGGCCTTTTTTTTAA
* * * *
323554 AGCCCATAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC----C-TTTT
63 AGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTTCGTGGCACCTTTTCTTTTT
* *
323614 AAGTCCACAACTCCGTGGCACCTTTTCTTTTTAAGTCCACGACTTTGTGGCAC
128 AAGTCCACAACTCCGTGGCACCTTTTCTTTTTAAGTCCACAACTCTGTGGCAC
323667 CCTTTT
1 CCTTTT
323673 CCCTTTTAAG
Statistics
Matches: 321, Mismatches: 39, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
178 30 0.09
179 4 0.01
180 19 0.06
181 4 0.01
182 1 0.00
185 7 0.02
186 122 0.38
187 84 0.26
188 5 0.02
189 2 0.01
190 41 0.13
191 2 0.01
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.36
Consensus pattern (180 bp):
CCTTTTAAGTCCACAATTCGTGGCACCCTTTTAAGTCCACAACTCCGAGGCCTTTTTTTTAAAGC
CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTTCGTGGCACCTTTTCTTTTTAAG
TCCACAACTCCGTGGCACCTTTTCTTTTTAAGTCCACAACTCTGTGGCAC
Found at i:323572 original size:119 final size:121
Alignment explanation
Indices: 323394--323639 Score: 363
Period size: 119 Copynumber: 2.0 Consensus size: 121
323384 CACTCTTTTT
* ** **
323394 CCTTTTAAGCCCACAACTTCGTGGCACCTTGTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTT
1 CCTTTTAAGCCCACAACTCCGTAACACCTTGTTCTTTTTAAAGCCCACAACTCCATGGCACTCTT
* *
323459 TCTCTTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTTCGTGGCA
66 TCTCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCA
* *
323515 CCCTTTTAAGTCCACAACTCCGTAACACC-T-TT-TTTTTAAAGCCCATAACTCCATGGCACTCT
1 -CCTTTTAAGCCCACAACTCCGTAACACCTTGTTCTTTTTAAAGCCCACAACTCCATGGCACTCT
* *
323577 TTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA
65 TTCTCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCA
323634 CCTTTT
1 CCTTTT
323640 CTTTTTAAGT
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
118 6 0.05
119 80 0.71
120 2 0.02
121 1 0.01
122 24 0.21
ACGTcount: A:0.22, C:0.33, G:0.12, T:0.33
Consensus pattern (121 bp):
CCTTTTAAGCCCACAACTCCGTAACACCTTGTTCTTTTTAAAGCCCACAACTCCATGGCACTCTT
TCTCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCA
Found at i:323705 original size:35 final size:34
Alignment explanation
Indices: 323666--323733 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
323656 CTTTGTGGCA
* *
323666 CCCTTTTCCCTTTTAAGCCCATACCTCCATGACAT
1 CCCTTTTCCC-TATAAGCCCATAACTCCATGACAT
* * *
323701 CCCTTTTTCCTATAAGTCCATAACTCCGTGACA
1 CCCTTTTCCCTATAAGCCCATAACTCCATGACA
323734 CCTTTAAGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 19 0.68
35 9 0.32
ACGTcount: A:0.22, C:0.37, G:0.07, T:0.34
Consensus pattern (34 bp):
CCCTTTTCCCTATAAGCCCATAACTCCATGACAT
Found at i:323894 original size:87 final size:87
Alignment explanation
Indices: 323738--324724 Score: 1052
Period size: 87 Copynumber: 11.0 Consensus size: 87
323728 GTGACACCTT
* * * *
323738 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGTACCTTGTCTTTAAGACCAATGTCGCTA
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
*
323803 GCCTTAAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * * *
323825 TACGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTTGCTG
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
323890 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * * *
323912 TAAGTCTAATATCGCTGGCCGTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCACTG
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
323977 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * * * *
323999 TAAGTCTAATATCGTTGGTCGTGAATTAGCATATTGGCACCTTATCTTTAAGACCCATGTCGCTG
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
324064 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * *
324086 TCTTCATCTTTGAGTCCAATATCGTTGGCCTTGAATTAGCATATTGGC-TCTTCATCTTTAAAAC
1 ---T-A------AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGAC
*
324150 CAATGTCGTTGGCCTTGAATCAGCACATTGGCA
55 CAATGTCGCTGGCCTTGAATCAGCACATTGGCA
* * * * ** *
324183 CAAGCCCAATATCGCTAGCCTTGAATCAGCATATTAGCATATTCATCTTTAA-ATCCAATATCGC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGA-CCAATGTCGC
*
324247 TGGCCTTGAATCAGCATATTGGCA
64 TGGCCTTGAATCAGCACATTGGCA
* * *
324271 CCTTTACCATCTTGAGTCTAATATCGCTAGCCTTGAATCAACATATTGGCACCTTATCTTTAAGA
1 ----T---A-----AGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGA
** *
324336 CCAATGTCATTGGCCTTGAATCAGCACATTAGCA
54 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
* * * * * * *
324370 CAAGCCCAATATCGCTAGCCTTGAATTAGCATATTGGCACTTTGTCTCTAAGACCAATGTCGCTG
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
*
324435 GCCTTGAATAAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* *
324457 CAAGTCCAATATCGCTGGCCTTGAATCAGCATAGTGGCACCTTTATCTTTAAGACCAATGTCGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTATCTTTAAGACCAATGTCGCT
* * *
324522 AGCCTTTAATCAGCACATTGACGCCTT
65 GGCCTTGAATCAGCACATTG--G-C-A
*
324549 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCA-C----CTTTAAGACCAATGTCGCTG
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
324609 GCCTTGAATCAGCACATTGGCA
66 GCCTTGAATCAGCACATTGGCA
* * * *
324631 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTTACCATCTTGAGTCCAAT
1 ----TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-ACCTTATC-T-TTAAGACCAAT
* *
324696 ATCGCTGGCCTTGAATCAGCATATTGGCA
59 GTCGCTGGCCTTGAATCAGCACATTGGCA
324725 CCTTGTCTTT
Statistics
Matches: 772, Mismatches: 85, Indels: 79
0.82 0.09 0.08
Matches are distributed among these distances:
83 1 0.00
84 1 0.00
86 74 0.10
87 383 0.50
88 81 0.10
90 2 0.00
91 3 0.00
92 38 0.05
93 2 0.00
94 36 0.05
95 1 0.00
96 3 0.00
97 74 0.10
99 37 0.05
100 36 0.05
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (87 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTG
GCCTTGAATCAGCACATTGGCA
Found at i:323940 original size:39 final size:39
Alignment explanation
Indices: 323886--324037 Score: 124
Period size: 39 Copynumber: 3.7 Consensus size: 39
323876 GACCAATGTT
*
323886 GCTGGCCTTGAATCAGCACATTGGCATAAGTCTAATATC
1 GCTGGCCGTGAATCAGCACATTGGCATAAGTCTAATATC
* * * *
323925 GCTGGCCGTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTC
1 GCTGGCCGTGAATCAGCACATTGGCA---------TAAGTCTAATATC
* *
323973 ACTGGCCTTGAATCAGCACATTGGCATAAGTCTAATATC
1 GCTGGCCGTGAATCAGCACATTGGCATAAGTCTAATATC
* * * *
324012 GTTGGTCGTGAATTAGCATATTGGCA
1 GCTGGCCGTGAATCAGCACATTGGCA
324038 CCTTATCTTT
Statistics
Matches: 87, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
39 54 0.62
48 33 0.38
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (39 bp):
GCTGGCCGTGAATCAGCACATTGGCATAAGTCTAATATC
Found at i:324116 original size:49 final size:49
Alignment explanation
Indices: 323999--325059 Score: 767
Period size: 49 Copynumber: 22.8 Consensus size: 49
323989 CACATTGGCA
* * * * *
323999 TAAGTCTAATATCGTTGGTCGTGAATTAGCATATTGGCACCTT-ATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
324047 TAAGACCCATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
324096 TGAGTCCAATATCGTTGGCCTTGAATTAGCATATTGGC-TCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
** * * *
324144 TAAAACCAATGTCGTTGGCCTTGAATCAGCACATTGG------CA-C--
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * **
324184 -AAGCCCAATATCGCTAGCCTTGAATCAGCATATTAGCATATTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
324232 TAAATCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATC-T
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT--CATCTT
* * * *
324283 TGAGTCTAATATCGCTAGCCTTGAATCAACATATTGGCACCTT-ATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * ** * *
324331 TAAGACCAATGTCATTGGCCTTGAATCAGCACATT---A---GCA-C--
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * ** *
324371 -AAGCCCAATATCGCTAGCCTTGAATTAGCATATTGGCA-CTTTGTCTC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
324418 TAAGACCAATGTCGCTGGCCTTGAATAAGCACATTGG------CA-C--
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
324458 -AAGTCCAATATCGCTGGCCTTGAATCAGCATAGTGGCACCTTTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * * *
324506 TAAGACCAATGTCGCTAGCCTTTAATCAGCACATT-G-A-C-GC--CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
324549 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCA----C--CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
324592 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
324635 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAACTTTACCATC-T
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-ACCTT--CATCTT
* *
324686 TGAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
324734 TAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGG------CA-C--
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
324774 -AAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
** * * * * *
324822 TAAAACCGATGTCGTTGGCCTTAAATCAACATATTGGCACCTTAACCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT---CATCTT
* *** * * *
324874 TAAGTCCAATGTCGCCAACCTTGAATCAGCACATTAGCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
324923 TAAATCCGATATCGCTGGCCTTGAATCAGCATAGTAGCACCTTTATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * *
324972 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
325021 TAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCA
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
325060 TTTTTAACAT
Statistics
Matches: 802, Mismatches: 150, Indels: 121
0.75 0.14 0.11
Matches are distributed among these distances:
39 118 0.15
42 5 0.01
43 115 0.14
44 2 0.00
45 8 0.01
46 4 0.00
47 6 0.01
48 166 0.21
49 252 0.31
50 9 0.01
51 75 0.09
52 42 0.05
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:324564 original size:43 final size:43
Alignment explanation
Indices: 324503--324815 Score: 310
Period size: 43 Copynumber: 7.1 Consensus size: 43
324493 GCACCTTTAT
* * * *
324503 CTTTAAGACCAATGTCGCTAGCCTTTAATCAGCACATTGACGC
1 CTTTAAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCAC
* *
324546 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCAC
* *
324589 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCAC
* * * *
324632 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAA
1 CTTTAAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCAC
* *
324675 CTTTACCATCTTGAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC
1 CTTTA--A----GA--CCAATATCGCTAGCCTTGAATCAGCACATTGGCA-C
* * *
324727 TTGTCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCA-
1 ----CTTTAAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCAC
* *
324773 C---AAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCAC
324813 CTT
1 CTT
324816 CATCTTTAAA
Statistics
Matches: 230, Mismatches: 24, Indels: 33
0.80 0.08 0.11
Matches are distributed among these distances:
39 33 0.14
40 1 0.00
42 1 0.00
43 120 0.52
45 1 0.00
48 31 0.13
49 1 0.00
50 2 0.01
51 34 0.15
54 1 0.00
56 5 0.02
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (43 bp):
CTTTAAGACCAATATCGCTAGCCTTGAATCAGCACATTGGCAC
Found at i:325800 original size:16 final size:16
Alignment explanation
Indices: 325779--325827 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
325769 GAAAAAATCA
325779 ATAAATGTATCAATAC
1 ATAAATGTATCAATAC
325795 ATAAATGTATCAATAC
1 ATAAATGTATCAATAC
*
325811 ATAAATGTATCGATAC
1 ATAAATGTATCAATAC
325827 A
1 A
325828 ATGTATCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (16 bp):
ATAAATGTATCAATAC
Found at i:325832 original size:13 final size:13
Alignment explanation
Indices: 325814--325841 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
325804 TCAATACATA
325814 AATGTATCGATAC
1 AATGTATCGATAC
325827 AATGTATCGATAC
1 AATGTATCGATAC
325840 AA
1 AA
325842 AGTTGCCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:325908 original size:13 final size:13
Alignment explanation
Indices: 325890--325915 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
325880 TTATTCAATA
325890 TATCGATACATTG
1 TATCGATACATTG
325903 TATCGATACATTG
1 TATCGATACATTG
325916 ATCTTTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:325964 original size:51 final size:51
Alignment explanation
Indices: 325901--326035 Score: 227
Period size: 51 Copynumber: 2.6 Consensus size: 51
325891 ATCGATACAT
325901 TGTATCGATACATTGATCTTTGTATCGATACATCTGAAAATTTTACCCAGA
1 TGTATCGATACATTGATCTTTGTATCGATACATCTGAAAATTTTACCCAGA
*
325952 TGTATCGATACATTGATCTTTGTATCGATACATCTGGAAATTTTACCCAGA
1 TGTATCGATACATTGATCTTTGTATCGATACATCTGAAAATTTTACCCAGA
**
326003 TGTATCGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCTTTGTATCGATACAT
326036 GTAGGCAAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
50 1 0.01
51 79 0.99
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (51 bp):
TGTATCGATACATTGATCTTTGTATCGATACATCTGAAAATTTTACCCAGA
Found at i:334750 original size:20 final size:20
Alignment explanation
Indices: 334696--334751 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
334686 AAAAAGACAG
* * *
334696 AATGTATCGATACAATCATA
1 AATGTATCGATACATTAAAA
*
334716 CATGTATCGATACATTAAAA
1 AATGTATCGATACATTAAAA
334736 AATGTATCGATACATT
1 AATGTATCGATACATT
334752 TGGGTAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Found at i:334780 original size:71 final size:72
Alignment explanation
Indices: 334645--334822 Score: 182
Period size: 71 Copynumber: 2.5 Consensus size: 72
334635 TTTTAACTAG
* * * * *
334645 ATGTACCGATACATTGAAAAATATATC-ATTACATCTGGAAAAAAAAGACAGAATGTATCGATAC
1 ATGTATCGATACATTAAAAAATGTATCGA-TACATTTGGAAAAAAAAGACAGAATGTATCAATAC
*
334709 AATCATA-C
65 AATCA-AGA
** *
334717 ATGTATCGATACATTAAAAAATGTATCGATACATTTGG-GTAAAAAGATAGAATGTATCAATACA
1 ATGTATCGATACATTAAAAAATGTATCGATACATTTGGAAAAAAAAGACAGAATGTATCAATACA
* *
334781 TTGAAGA
66 ATCAAGA
* * * *
334788 ATGTATCGATACAGTCATACATGTATCGATACATT
1 ATGTATCGATACATTAAAAAATGTATCGATACATT
334823 GAAAAATGAT
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
70 1 0.01
71 55 0.62
72 32 0.36
73 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.29
Consensus pattern (72 bp):
ATGTATCGATACATTAAAAAATGTATCGATACATTTGGAAAAAAAAGACAGAATGTATCAATACA
ATCAAGA
Found at i:342343 original size:15 final size:14
Alignment explanation
Indices: 342317--342373 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
342307 AATTTATTAA
342317 AAAATTAATAATTT
1 AAAATTAATAATTT
342331 AAAATTAATTAATTT
1 AAAATTAA-TAATTT
* *
342346 GAATATAGAATAATTT
1 -AAAAT-TAATAATTT
*
342362 AAATTTAA-AATT
1 AAAATTAATAATT
342374 ATTTAAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.11
14 10 0.29
15 9 0.26
16 10 0.29
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (14 bp):
AAAATTAATAATTT
Found at i:342377 original size:16 final size:16
Alignment explanation
Indices: 342358--342429 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
342348 ATATAGAATA
*
342358 ATTTAAATTTAAAATT
1 ATTTAAATTTAAAATG
* *
342374 ATTTAAAATCAAAATG
1 ATTTAAATTTAAAATG
* *
342390 ATTCAAAATTAAAATG
1 ATTTAAATTTAAAATG
* * *
342406 ATTCAAATATAAAAATA
1 ATTTAAAT-TTAAAATG
342423 ATTTAAA
1 ATTTAAA
342430 ATTTTTAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
16 34 0.74
17 12 0.26
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTTAAATTTAAAATG
Found at i:342399 original size:33 final size:34
Alignment explanation
Indices: 342354--342433 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 34
342344 TTGAATATAG
* * * *
342354 AATAATT-TAAATTTAAAATTATTTAAA-ATCAA
1 AATAATTCAAAATTTAAAATGATTCAAATATAAA
*
342386 AATGATTCAAAA-TTAAAATGATTCAAATATAAA
1 AATAATTCAAAATTTAAAATGATTCAAATATAAA
*
342419 AATAATTTAAAATTT
1 AATAATTCAAAATTT
342434 TTAAAATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 19 0.50
33 17 0.45
34 2 0.05
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (34 bp):
AATAATTCAAAATTTAAAATGATTCAAATATAAA
Found at i:342595 original size:15 final size:16
Alignment explanation
Indices: 342562--342596 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
342552 TTTTTAAAAA
342562 ATTTAACTATAAAAGT
1 ATTTAACTATAAAAGT
*
342578 ATTTAA-TATAAAATT
1 ATTTAACTATAAAAGT
342593 ATTT
1 ATTT
342597 TTAATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
ATTTAACTATAAAAGT
Found at i:342795 original size:13 final size:13
Alignment explanation
Indices: 342776--342809 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
342766 ATAATTGATT
342776 ATGATAAATATTA
1 ATGATAAATATTA
*
342789 ATTATAAATATTA
1 ATGATAAATATTA
342802 ATGATAAA
1 ATGATAAA
342810 AAAATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (13 bp):
ATGATAAATATTA
Found at i:343940 original size:13 final size:13
Alignment explanation
Indices: 343922--343967 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
343912 TTTAATGATT
343922 TTTATTATTAATA
1 TTTATTATTAATA
343935 TTTATTA-TAATTA
1 TTTATTATTAA-TA
* *
343948 ATTA-TAATAATA
1 TTTATTATTAATA
343960 TTTATTAT
1 TTTATTAT
343968 ATTTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:343942 original size:16 final size:17
Alignment explanation
Indices: 343904--343949 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
343894 ATGAGATTAC
343904 TATTATTATTTAATGATT
1 TATTATTA-TTAATGATT
343922 T-TTATTATTAAT-ATT
1 TATTATTATTAATGATT
*
343937 TATTATAATTAAT
1 TATTATTATTAAT
343950 TATAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 6 0.23
18 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTATTATTAATGATT
Found at i:344679 original size:20 final size:20
Alignment explanation
Indices: 344654--344694 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
344644 AATAACGTTA
344654 TAATTTTTATTT-AATAATTT
1 TAATTTTT-TTTCAATAATTT
*
344674 TAATTTTTTTTCATTAATTT
1 TAATTTTTTTTCAATAATTT
344694 T
1 T
344695 TATAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TAATTTTTTTTCAATAATTT
Found at i:344715 original size:16 final size:15
Alignment explanation
Indices: 344690--344720 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
344680 TTTTTCATTA
344690 ATTTTTATAATTAAT
1 ATTTTTATAATTAAT
344705 ATTTATTATAATTAAT
1 ATTT-TTATAATTAAT
344721 TAAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTATAATTAAT
Found at i:346931 original size:17 final size:17
Alignment explanation
Indices: 346909--346968 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
346899 TCTTATAAAT
346909 TTTTTTATAAATATATA
1 TTTTTTATAAATATATA
346926 TTTTTTA-AAAT-TAT-
1 TTTTTTATAAATATATA
* *
346940 TTATTTAAAAAAATATATA
1 TT-TTT-TATAAATATATA
346959 TTTTTT-TAAA
1 TTTTTTATAAA
346969 AATTAATGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
14 2 0.06
15 6 0.17
16 8 0.23
17 11 0.31
18 6 0.17
19 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTTATAAATATATA
Found at i:347183 original size:19 final size:19
Alignment explanation
Indices: 347161--347221 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
347151 ATATATTTTT
*
347161 AAAATTATTTTTTATTTAAA
1 AAAATTATTTTTT-TTAAAA
347181 AAAATTATTTATTTTT-AAA
1 AAAATTATTT-TTTTTAAAA
* *
347200 AAAACTATTTTTTTCAAAA
1 AAAATTATTTTTTTTAAAA
347219 AAA
1 AAA
347222 TCTAATACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.11
19 18 0.49
20 12 0.32
21 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATTATTTTTTTTAAAA
Found at i:347186 original size:20 final size:19
Alignment explanation
Indices: 347161--347222 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 19
347151 ATATATTTTT
347161 AAAATTATTTTTTATTTAAA
1 AAAATTATTTTTT-TTTAAA
*
347181 AAAATTATTTATTTTTAAA
1 AAAATTATTTTTTTTTAAA
* *
347200 AAAACTA-TTTTTTTCAAA
1 AAAATTATTTTTTTTTAAA
347218 AAAAT
1 AAAAT
347223 CTAATACTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 13 0.35
19 12 0.32
20 12 0.32
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATTATTTTTTTTTAAA
Found at i:347289 original size:19 final size:20
Alignment explanation
Indices: 347255--347301 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
347245 AATTACCAAC
* *
347255 TTATAAAATATTTATTTTTA
1 TTATAATATATTTATTATTA
347275 TTATAATAT-TTTATTATTA
1 TTATAATATATTTATTATTA
347294 TTATAATA
1 TTATAATA
347302 ATAAAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATAATATATTTATTATTA
Found at i:348595 original size:2 final size:2
Alignment explanation
Indices: 348588--348614 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
348578 CTCTATTATC
348588 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
348615 TTGAGGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:351470 original size:65 final size:64
Alignment explanation
Indices: 351395--351525 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 64
351385 CTTATCATTG
351395 TTGAGATATGGGAATTTTCTTCCTTTTATCTAAAATGTCTGTGTCCTTTAGCTTTATCTTTTGGT
1 TTGAGATATGGGAATTTTCTTCCTTTTATCTAAAATGTC-GTGTCCTTTAGCTTTATCTTTTGGT
351460 TTGAGATATGGGAATTTTCTTCCTTTTATCTAAAATGTCGTGTCCTTTAGCTTTATCTTTTGGT
1 TTGAGATATGGGAATTTTCTTCCTTTTATCTAAAATGTCGTGTCCTTTAGCTTTATCTTTTGGT
351524 TT
1 TT
351526 TGTTTTCTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
64 27 0.41
65 39 0.59
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (64 bp):
TTGAGATATGGGAATTTTCTTCCTTTTATCTAAAATGTCGTGTCCTTTAGCTTTATCTTTTGGT
Found at i:354598 original size:215 final size:213
Alignment explanation
Indices: 354203--354796 Score: 961
Period size: 215 Copynumber: 2.8 Consensus size: 213
354193 TGTGGTTAAT
* ** *
354203 AAATAACCCAGTGTTTCATGAAAATACAAAACCT-AAGGTACCCAAAACATTTAATAATCATAAT
1 AAATAACCCAGTGTTTGATGAAAACGCAAAACCTGAA-GTACCCAAAACATTTAATAATCACAAT
* *
354267 TAAGCCCATAGAACATACAAAATTAACAAAACGACTCTTTAAATGACTTGGTTGTTTGTGATGTT
65 TAAGCCCATAGAACATACAAAATTAACAAAACAACTCTTTAAATGACTTGATTGTTTGTGATGTT
* *
354332 GTTGCACATCAGGCAGCTTTTAGATGTATTTGTTATCCAAGGCAGCTTGTGATTGTTTCAATGCA
130 GTTGCACATCAGGCAGCTTTTAGATGTATTTATTATCCAAGGCAGCTTGTGATTGCTTCAATGCA
354397 TGACCATTTTGAACTTATC
195 TGACCATTTTGAACTTATC
354416 AAATAACCCAGTGTTTGATGAAAACGCAAAACCTGAAGTACCCAAAACATTTAATAATCACAATT
1 AAATAACCCAGTGTTTGATGAAAACGCAAAACCTGAAGTACCCAAAACATTTAATAATCACAATT
* * *
354481 AAGCCTATAGAACAGTACAAACTTAACAAAACAACTCTTTAAACTGACTTGACTGTTTGTGATGT
66 AAGCCCATAGAACA-TACAAAATTAACAAAACAACTCTTTAAA-TGACTTGATTGTTTGTGATGT
354546 TGTTGCACATCAGGCAGCTTTTAGATGTATTTATTATCCAAGGCAGCTTGTGATTGCTTCAATGC
129 TGTTGCACATCAGGCAGCTTTTAGATGTATTTATTATCCAAGGCAGCTTGTGATTGCTTCAATGC
354611 ATGACCATTTTGAACTTATC
194 ATGACCATTTTGAACTTATC
* *
354631 ----AA---AGTGTTCGATGAAAACGCAAAACCTGAGGTACCCAAAACATTTAATAATCACAATT
1 AAATAACCCAGTGTTTGATGAAAACGCAAAACCTGAAGTACCCAAAACATTTAATAATCACAATT
*
354689 AAGCCCATAGAACATACAAAATTAACAAAAGAACTCTTTAAATGACTTGATTGTTTGTGATGTTG
66 AAGCCCATAGAACATACAAAATTAACAAAACAACTCTTTAAATGACTTGATTGTTTGTGATGTTG
* *
354754 TTGCATATCAGGCAGCTTTTAGATGTGTTTATTATCCAAGGCA
131 TTGCACATCAGGCAGCTTTTAGATGTATTTATTATCCAAGGCA
354797 CCCAGTGTTT
Statistics
Matches: 359, Mismatches: 19, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
206 63 0.18
207 26 0.07
208 67 0.19
211 2 0.01
213 71 0.20
214 28 0.08
215 102 0.28
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (213 bp):
AAATAACCCAGTGTTTGATGAAAACGCAAAACCTGAAGTACCCAAAACATTTAATAATCACAATT
AAGCCCATAGAACATACAAAATTAACAAAACAACTCTTTAAATGACTTGATTGTTTGTGATGTTG
TTGCACATCAGGCAGCTTTTAGATGTATTTATTATCCAAGGCAGCTTGTGATTGCTTCAATGCAT
GACCATTTTGAACTTATC
Found at i:354916 original size:167 final size:167
Alignment explanation
Indices: 354633--354962 Score: 590
Period size: 167 Copynumber: 2.0 Consensus size: 167
354623 AACTTATCAA
354633 AGTGTTCGATGAAAACGCAAAACCTGAGGTACCCAAAACATTTAATAATCACAATTAAGCCCATA
1 AGTGTTCGATGAAAACGCAAAACCTGAGGTACCCAAAACATTTAATAATCACAATTAAGCCCATA
* *
354698 GAACATACAAAATTAACAAAAGAACTCTTTAAATGACTTGATTGTTTGTGATGTTGTTGCATATC
66 GAACATACAAAATTAACAAAACAACTCTTTAAATGACTTGATTGTTTGTGATGTTGTTGCACATC
*
354763 AGGCAGCTTTTAGATGTGTTTATTATCCAAGGCACCC
131 AGGCAGCTTTTAGATGTATTTATTATCCAAGGCACCC
* *
354800 AGTGTTTGATGAAAATGCAAAACCTGAGGTACCCAAAACATTTAATAATCACAATTAAGCCCATA
1 AGTGTTCGATGAAAACGCAAAACCTGAGGTACCCAAAACATTTAATAATCACAATTAAGCCCATA
*
354865 GAACATACAAAATTAACAAAACAACT-TTCTAAATGACTTGATTGTTTGTGATGTTTTTGCACAT
66 GAACATACAAAATTAACAAAACAACTCTT-TAAATGACTTGATTGTTTGTGATGTTGTTGCACAT
354929 CAGGCAGCTTTTAGATGTATTTATTATCCAAGGC
130 CAGGCAGCTTTTAGATGTATTTATTATCCAAGGC
354963 TGCTAGTGAT
Statistics
Matches: 156, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
166 2 0.01
167 154 0.99
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (167 bp):
AGTGTTCGATGAAAACGCAAAACCTGAGGTACCCAAAACATTTAATAATCACAATTAAGCCCATA
GAACATACAAAATTAACAAAACAACTCTTTAAATGACTTGATTGTTTGTGATGTTGTTGCACATC
AGGCAGCTTTTAGATGTATTTATTATCCAAGGCACCC
Found at i:358510 original size:15 final size:15
Alignment explanation
Indices: 358490--358521 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
358480 TTATAGAACA
358490 TTTAATTTATTTATT
1 TTTAATTTATTTATT
*
358505 TTTAATTTTTTTATT
1 TTTAATTTATTTATT
358520 TT
1 TT
358522 CTCTTATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTAATTTATTTATT
Found at i:359479 original size:17 final size:16
Alignment explanation
Indices: 359457--359508 Score: 79
Period size: 17 Copynumber: 3.2 Consensus size: 16
359447 CTATGTTATT
359457 ATTAAAAAAATTTAAAA
1 ATTAAAAAAATTT-AAA
359474 ATTAAAAAAA-TTAAA
1 ATTAAAAAAATTTAAA
359489 ATTAAAAAAATTTGAAA
1 ATTAAAAAAATTT-AAA
359506 ATT
1 ATT
359509 TATATTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.39
16 4 0.12
17 16 0.48
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
ATTAAAAAAATTTAAA
Found at i:359482 original size:9 final size:9
Alignment explanation
Indices: 359457--359500 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
359447 CTATGTTATT
359457 ATTAAAAAA
1 ATTAAAAAA
*
359466 ATT-TAAAA
1 ATTAAAAAA
359474 ATTAAAAAA
1 ATTAAAAAA
359483 ATT---AAA
1 ATTAAAAAA
359489 ATTAAAAAA
1 ATTAAAAAA
359498 ATT
1 ATT
359501 TGAAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
6 6 0.21
8 7 0.24
9 16 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:359489 original size:15 final size:16
Alignment explanation
Indices: 359457--359500 Score: 72
Period size: 15 Copynumber: 2.8 Consensus size: 16
359447 CTATGTTATT
359457 ATTAAAAAAATTTAAAA
1 ATTAAAAAAA-TTAAAA
359474 ATTAAAAAAATT-AAA
1 ATTAAAAAAATTAAAA
359489 ATTAAAAAAATT
1 ATTAAAAAAATT
359501 TGAAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.56
16 2 0.07
17 10 0.37
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAAAATTAAAA
Found at i:359580 original size:7 final size:7
Alignment explanation
Indices: 359526--359626 Score: 60
Period size: 8 Copynumber: 13.6 Consensus size: 7
359516 ATTTTTTTTG
359526 AAAATTCA
1 AAAATT-A
359534 AAAATATA
1 AAAAT-TA
359542 AAAATTCA
1 AAAATT-A
*
359550 AAAAAT-
1 AAAATTA
** *
359556 AATTTTT
1 AAAATTA
359563 AAAATTCA
1 AAAATT-A
359571 AAAATTA
1 AAAATTA
*
359578 AAAATCTC
1 AAAAT-TA
359586 AAAATTA
1 AAAATTA
*
359593 AAGATATA
1 AAAAT-TA
*
359601 TAAAATAA
1 -AAAATTA
*
359609 AAAATTT
1 AAAATTA
359616 AAAATTA
1 AAAATTA
359623 AAAA
1 AAAA
359627 AAAATCAATG
Statistics
Matches: 71, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
6 3 0.04
7 31 0.44
8 32 0.45
9 5 0.07
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.29
Consensus pattern (7 bp):
AAAATTA
Found at i:359605 original size:16 final size:15
Alignment explanation
Indices: 359526--359627 Score: 59
Period size: 15 Copynumber: 6.8 Consensus size: 15
359516 ATTTTTTTTG
*
359526 AAAATTCAAAAATAT
1 AAAATTAAAAAATAT
*
359541 AAAAATTCAAAAA-AT
1 -AAAATTAAAAAATAT
** * *
359556 AATTTTTAAAATTCA-
1 AAAATTAAAAAAT-AT
*
359571 AAAATT-AAAAATCT
1 AAAATTAAAAAATAT
*
359585 CAAAATTAAAGATATAT
1 -AAAATTAAA-AAATAT
*
359602 AAAA-TAAAAAATTT
1 AAAATTAAAAAATAT
359616 AAAATTAAAAAA
1 AAAATTAAAAAA
359628 AAATCAATGG
Statistics
Matches: 67, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 21 0.31
15 23 0.34
16 19 0.28
17 4 0.06
ACGTcount: A:0.66, C:0.05, G:0.01, T:0.28
Consensus pattern (15 bp):
AAAATTAAAAAATAT
Found at i:361455 original size:3 final size:3
Alignment explanation
Indices: 361447--361492 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
361437 GTTTCTGAGA
* * *
361447 TAT TAT TAT TAT TAT TGT TGT TGT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
361493 TGCAATCGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:365278 original size:34 final size:33
Alignment explanation
Indices: 365235--365326 Score: 127
Period size: 30 Copynumber: 2.8 Consensus size: 33
365225 AGTAAAAAAA
365235 AGTGATAATAAAGCTTTTTTTTTTAATTATTTTT
1 AGTGATAATAAAG-TTTTTTTTTTAATTATTTTT
*
365269 AGTGATAAT--AG-TCTTTTTTTAATTATTTTT
1 AGTGATAATAAAGTTTTTTTTTTAATTATTTTT
*
365299 AGTGATAATAAAATCTTTTTTTTTAATT
1 AGTGATAATAAAGT-TTTTTTTTTAATT
365327 TTACCATGCA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
30 27 0.53
32 3 0.06
34 21 0.41
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (33 bp):
AGTGATAATAAAGTTTTTTTTTTAATTATTTTT
Found at i:366274 original size:2 final size:2
Alignment explanation
Indices: 366267--366310 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
366257 GTCTCTGTGG
* *
366267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT CT 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
366309 AT
1 AT
366311 GATGTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:367588 original size:6 final size:6
Alignment explanation
Indices: 367577--367644 Score: 58
Period size: 6 Copynumber: 12.3 Consensus size: 6
367567 TAAATTTAGA
** *
367577 TAAATT TAAA-T TAAA-T TATTTT TAAATT TAAA-T T-ATTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
367621 TAAA-T T-ATTT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
367645 TTTCGATTCG
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
4 2 0.04
5 16 0.33
6 31 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TAAATT
Found at i:367622 original size:22 final size:22
Alignment explanation
Indices: 367577--367644 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
367567 TAAATTTAGA
**
367577 TAAATTTAAATTAAATTATTTT
1 TAAATTTAAATTAAATTAAATT
**
367599 TAAATTTAAATTATTTTAAATT
1 TAAATTTAAATTAAATTAAATT
**
367621 TAAA-TTATTTTAAATTTAAATT
1 TAAATTTAAATTAAA-TTAAATT
367643 TA
1 TA
367645 TTTCGATTCG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 6 0.16
22 31 0.84
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAAATTTAAATTAAATTAAATT
Found at i:367642 original size:16 final size:16
Alignment explanation
Indices: 367567--367647 Score: 110
Period size: 16 Copynumber: 5.0 Consensus size: 16
367557 CTCAAACAAA
* * *
367567 TAAATTTAGATAAATT
1 TAAATTTAAATTATTT
367583 TAAA-TTAAATTATTTT
1 TAAATTTAAATTA-TTT
367599 TAAATTTAAATTATTT
1 TAAATTTAAATTATTT
367615 TAAATTTAAATTATTT
1 TAAATTTAAATTATTT
367631 TAAATTTAAATTTATTT
1 TAAATTTAAA-TTATTT
367648 CGATTCGAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
15 6 0.10
16 39 0.66
17 14 0.24
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (16 bp):
TAAATTTAAATTATTT
Found at i:368972 original size:25 final size:25
Alignment explanation
Indices: 368910--368972 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 25
368900 TTTCTTTTTT
* *
368910 TTTTAAGTAAAATTGTAAGTAGTTTT
1 TTTTAAGTAAAATAGTAAGTAG-TTA
*
368936 TTTTAAAG-AAAATAGTTAATTA-TTA
1 TTTT-AAGTAAAATAG-TAAGTAGTTA
368961 TTTTAAGTAAAA
1 TTTTAAGTAAAA
368973 ATACACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 3 0.10
25 10 0.32
26 10 0.32
27 8 0.26
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (25 bp):
TTTTAAGTAAAATAGTAAGTAGTTA
Found at i:370480 original size:19 final size:17
Alignment explanation
Indices: 370426--370486 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 17
370416 AAGAAATTAC
370426 TAAAATT-AAAATTTTA
1 TAAAATTAAAAATTTTA
370442 -AAAATTAATAAATATTTA
1 TAAAATTAA-AAAT-TTTA
370460 TATAAATATAAAAATTTTA
1 TA-AAAT-TAAAAATTTTA
370479 TAATAATT
1 TAA-AATT
370487 TCATTTATAG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
15 6 0.16
16 1 0.03
17 4 0.11
18 6 0.16
19 10 0.26
20 8 0.21
21 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTAAAAATTTTA
Found at i:370740 original size:15 final size:14
Alignment explanation
Indices: 370707--370746 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
370697 AAATGCATCG
370707 AAAT-TTATATAAT
1 AAATATTATATAAT
*
370720 AAATATTATATATT
1 AAATATTATATAAT
370734 AAA-A-TATATAAT
1 AAATATTATATAAT
370746 A
1 A
370747 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 5 0.21
14 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATATTATATAAT
Found at i:373254 original size:32 final size:33
Alignment explanation
Indices: 373216--373285 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
373206 ATTTTATCAT
*
373216 AAAATATAAAAAT-ATTAATATCTTAATAG-ATA
1 AAAATATAAAAATAAATAATAT-TTAATAGAATA
** *
373248 AAAATATTTAAATAAATATTATTTAATAGAATA
1 AAAATATAAAAATAAATAATATTTAATAGAATA
373281 AAAAT
1 AAAAT
373286 TATATTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (33 bp):
AAAATATAAAAATAAATAATATTTAATAGAATA
Found at i:373631 original size:18 final size:19
Alignment explanation
Indices: 373589--373632 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
373579 TAATACATAC
373589 TATTTTTAAGTAATGTTTGA
1 TATTTTTAAGTAA-GTTTGA
373609 TATTTTTAAGATAA-TTT-A
1 TATTTTTAAG-TAAGTTTGA
373627 TATTTT
1 TATTTT
373633 ATATCATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.30
19 3 0.13
20 10 0.43
21 3 0.13
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (19 bp):
TATTTTTAAGTAAGTTTGA
Found at i:374459 original size:23 final size:23
Alignment explanation
Indices: 374433--374505 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
374423 TTCAAATTAA
374433 TATTTAATAATTAAAAATATTTT
1 TATTTAATAATTAAAAATATTTT
*
374456 TATTTAAATTTAATTAAAAA-ATTTA
1 TATTT-AA--TAATTAAAAATATTTT
** *
374481 TAAATATTAATATAAAAATATTTT
1 TATTTAATAAT-TAAAAATATTTT
374505 T
1 T
374506 TAATTTTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 4 0.10
23 11 0.28
24 8 0.20
25 7 0.17
26 10 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTTAATAATTAAAAATATTTT
Found at i:375496 original size:42 final size:42
Alignment explanation
Indices: 375415--375506 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
375405 CCTGCGACAT
* * * * *
375415 TTGATGCTGTGTTTATGATATTTGTTGCCTGGTGAGCGGCGC
1 TTGATACTGTGTCTATGACATTTGTTGCATGCTGAGCGGCGC
* *
375457 TTGATACTGTGTCTATGACATTTGTTGCAAT-CTGGGCGGCGT
1 TTGATACTGTGTCTATGACATTTGTTGC-ATGCTGAGCGGCGC
375499 TTGATACT
1 TTGATACT
375507 TTGTTTAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.40
Consensus pattern (42 bp):
TTGATACTGTGTCTATGACATTTGTTGCATGCTGAGCGGCGC
Found at i:379648 original size:22 final size:22
Alignment explanation
Indices: 379623--379683 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
379613 TATATTTATT
379623 TAAATTTAATTATATAAAAATA
1 TAAATTTAATTATATAAAAATA
**
379645 TAAAAAT-ATTAATATAAAAATA
1 TAAATTTAATT-ATATAAAAATA
* *
379667 -ATATTTTAATAATATAA
1 TA-AATTTAATTATATAA
379684 TCAACAGTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
21 4 0.13
22 24 0.80
23 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTTAATTATATAAAAATA
Found at i:382548 original size:18 final size:18
Alignment explanation
Indices: 382522--382556 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
382512 TTCAAATAAT
382522 TTAAAATTTTTTAAATTA
1 TTAAAATTTTTTAAATTA
*
382540 TTAATATTTTTTAAATT
1 TTAAAATTTTTTAAATT
382557 TTGATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAAATTTTTTAAATTA
Found at i:382972 original size:2 final size:2
Alignment explanation
Indices: 382965--382989 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
382955 TTAACATTAC
382965 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 A
382990 AATACTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:387577 original size:20 final size:19
Alignment explanation
Indices: 387531--387587 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
387521 TTGTATCGAA
* *
387531 ACATTTTATCGATACATGT
1 ACATTGTATCGATACATGG
*
387550 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
387569 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
387588 AACTGGCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:391905 original size:20 final size:20
Alignment explanation
Indices: 391880--391917 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
391870 AAAATTTTTC
*
391880 AGAATGTATTGATACATTGA
1 AGAATGTATCGATACATTGA
391900 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
391918 TGAAAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:394488 original size:19 final size:19
Alignment explanation
Indices: 394445--394516 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
394435 CACACCCAGA
*
394445 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
394465 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
394484 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
394504 TGTATCGATACAT
1 TGTATCGATACAT
394517 AAAACTAGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
19 17 0.36
20 29 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:394580 original size:13 final size:13
Alignment explanation
Indices: 394562--394592 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
394552 CGATACATGG
394562 TACATTATATCGA
1 TACATTATATCGA
*
394575 TACATTGTATCGA
1 TACATTATATCGA
394588 TACAT
1 TACAT
394593 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTATATCGA
Found at i:394588 original size:33 final size:33
Alignment explanation
Indices: 394546--394613 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
394536 CTACCACTGT
*
394546 TTGTATCGATACATGGT-ACATTATATCGATACA
1 TTGTATCGATACATGATGA-ATTATATCGATACA
*
394579 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTATATCGATACA
394612 TT
1 TT
394614 ACTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTATATCGATACA
Found at i:398140 original size:29 final size:29
Alignment explanation
Indices: 398098--398160 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
398088 CTAACACTTT
398098 TGCTACAATTTTATATAAACTACCCACTA
1 TGCTACAATTTTATATAAACTACCCACTA
398127 TGCTACAATTTTATATAAACTACCCACTA
1 TGCTACAATTTTATATAAACTACCCACTA
*
398156 AGCTA
1 TGCTA
398161 ATCAGGCGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (29 bp):
TGCTACAATTTTATATAAACTACCCACTA
Found at i:407374 original size:23 final size:23
Alignment explanation
Indices: 407348--407397 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
407338 ATTCTTTAAA
*
407348 TAATATTATAAATTTTTTTAT-AT
1 TAATATT-TAAATATTTTTATAAT
*
407371 TAATATTTATATATTTTTATAAT
1 TAATATTTAAATATTTTTATAAT
407394 TAAT
1 TAAT
407398 TTAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TAATATTTAAATATTTTTATAAT
Found at i:411984 original size:39 final size:40
Alignment explanation
Indices: 411941--412036 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
411931 ATTTTTGTGG
* ** **
411941 TTGGCATAGCCGCCCAATTGTTTATTT-ATTTTTCATGGA
1 TTGGCATAGCCGCCCAACTGCATATTTAAAATTTCATGGA
* * *
411980 TTGGCATAGTCACCCAACTGCATATTTAAAATTTCGTGGA
1 TTGGCATAGCCGCCCAACTGCATATTTAAAATTTCATGGA
412020 TTGGCATAGCCGCCCAA
1 TTGGCATAGCCGCCCAA
412037 ATTCTAACAA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
39 22 0.48
40 24 0.52
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (40 bp):
TTGGCATAGCCGCCCAACTGCATATTTAAAATTTCATGGA
Found at i:415942 original size:16 final size:16
Alignment explanation
Indices: 415923--415962 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
415913 TTGTGTTCAG
415923 GTTATTTTGAGTTTAA
1 GTTATTTTGAGTTTAA
* * *
415939 GTTATGTCGGGTTTAA
1 GTTATTTTGAGTTTAA
415955 GTTATTTT
1 GTTATTTT
415963 AGATTTGAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.55
Consensus pattern (16 bp):
GTTATTTTGAGTTTAA
Found at i:416353 original size:17 final size:18
Alignment explanation
Indices: 416331--416367 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
416321 CATATTATTA
416331 TTAAAAAAATTT-AAAAT
1 TTAAAAAAATTTGAAAAT
416348 TT-AAAAAATTTGAAAAT
1 TTAAAAAAATTTGAAAAT
416365 TTA
1 TTA
416368 TATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TTAAAAAAATTTGAAAAT
Found at i:416413 original size:8 final size:8
Alignment explanation
Indices: 416400--416457 Score: 66
Period size: 8 Copynumber: 7.4 Consensus size: 8
416390 TATAATTTTT
416400 AAAATTAA
1 AAAATTAA
416408 AAAATTAA
1 AAAATTAA
* *
416416 AAAACT-C
1 AAAATTAA
416423 AAAATTAA
1 AAAATTAA
*
416431 AAAATATAT
1 AAAAT-TAA
416440 AAAA-TAA
1 AAAATTAA
416447 AAAATTAA
1 AAAATTAA
416455 AAA
1 AAA
416458 TAAAAAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
7 11 0.27
8 24 0.59
9 6 0.15
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAATTAA
Found at i:416443 original size:24 final size:23
Alignment explanation
Indices: 416400--416465 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
416390 TATAATTTTT
*
416400 AAAATTAAAAAATTAAAAAACT-C
1 AAAATTAAAAAATTAAAAAA-TAA
*
416423 AAAATTAAAAAATATATAAAATAA
1 AAAATTAAAAAAT-TAAAAAATAA
*
416447 AAAATT-AAAAATAAAAAAA
1 AAAATTAAAAAATTAAAAAA
416466 ATCAATGGCG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 5 0.14
23 20 0.54
24 12 0.32
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (23 bp):
AAAATTAAAAAATTAAAAAATAA
Found at i:416448 original size:15 final size:14
Alignment explanation
Indices: 416400--416464 Score: 67
Period size: 16 Copynumber: 4.3 Consensus size: 14
416390 TATAATTTTT
416400 AAAATTAAAAAATTAA
1 AAAATT-AAAAA-TAA
* *
416416 AAAACTCAAAATTAA
1 AAAA-TTAAAAATAA
416431 AAAATATATAAAATAA
1 AAAAT-TA-AAAATAA
416447 AAAATTAAAAATAA
1 AAAATTAAAAATAA
416461 AAAA
1 AAAA
416465 AATCAATGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
14 12 0.29
15 10 0.24
16 19 0.45
17 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATTAAAAATAA
Found at i:416464 original size:7 final size:7
Alignment explanation
Indices: 416400--416464 Score: 58
Period size: 7 Copynumber: 8.7 Consensus size: 7
416390 TATAATTTTT
*
416400 AAAATTA
1 AAAAATA
416407 AAAAATTA
1 AAAAA-TA
*
416415 AAAAACTC
1 AAAAA-TA
*
416423 AAAATTA
1 AAAAATA
416430 AAAAATA
1 AAAAATA
416437 TATAAAATA
1 -A-AAAATA
*
416446 AAAAATT
1 AAAAATA
416453 AAAAATA
1 AAAAATA
416460 AAAAA
1 AAAAA
416465 AATCAATGGC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
7 27 0.57
8 14 0.30
9 6 0.13
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (7 bp):
AAAAATA
Found at i:424236 original size:17 final size:17
Alignment explanation
Indices: 424199--424236 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
424189 CTTTCTTAGC
*
424199 ATTTTTTAAATATAATT
1 ATTTTTTAAATATAATA
424216 ATTTTTTAAAATATAA-A
1 ATTTTTT-AAATATAATA
424233 ATTT
1 ATTT
424237 ATGATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTTTAAATATAATA
Found at i:424481 original size:2 final size:2
Alignment explanation
Indices: 424474--424500 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
424464 TAATAAACTA
424474 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 A
424501 ATGAATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:429533 original size:23 final size:23
Alignment explanation
Indices: 429507--429556 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
429497 ATTCTTTAAA
*
429507 TAATATTATAAATTTTTTTAT-AT
1 TAATATT-TAAATATTTTTATAAT
*
429530 TAATATTTATATATTTTTATAAT
1 TAATATTTAAATATTTTTATAAT
429553 TAAT
1 TAAT
429557 TTAATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TAATATTTAAATATTTTTATAAT
Found at i:434998 original size:21 final size:21
Alignment explanation
Indices: 434963--435019 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
434953 TTTAAGGTAG
*
434963 TAGTAG-TTCTTTTAAAAGAA
1 TAGTAGTTTTTTTTAAAAGAA
* *
434983 TAGTAGTTTTTTTTAAGAGAG
1 TAGTAGTTTTTTTTAAAAGAA
*
435004 TA--AGTTTTATTTAAAA
1 TAGTAGTTTTTTTTAAAA
435020 ATAGTATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 12 0.39
20 6 0.19
21 13 0.42
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.46
Consensus pattern (21 bp):
TAGTAGTTTTTTTTAAAAGAA
Found at i:435000 original size:19 final size:19
Alignment explanation
Indices: 434963--435025 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
434953 TTTAAGGTAG
**
434963 TAGTAGTTCTTTTAAAAGAA
1 TAGTAGTT-TTTTTTAAGAA
434983 TAGTAGTTTTTTTTAAG-A
1 TAGTAGTTTTTTTTAAGAA
* * *
435001 GAGTAAGTTTTATTTAAAAA
1 TAGT-AGTTTTTTTTAAGAA
435021 TAGTA
1 TAGTA
435026 TAATTAGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 4 0.11
19 19 0.54
20 12 0.34
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.44
Consensus pattern (19 bp):
TAGTAGTTTTTTTTAAGAA
Found at i:437482 original size:39 final size:40
Alignment explanation
Indices: 437439--437534 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
437429 ATTTTTGTGG
* ** **
437439 TTGGCATAGCCGCCCAATTGTTTATTT-ATTTTTCATGGA
1 TTGGCATAGCCGCCCAACTGCATATTTAAAATTTCATGGA
* * *
437478 TTGGCATAGTCACCCAACTGCATATTTAAAATTTCGTGGA
1 TTGGCATAGCCGCCCAACTGCATATTTAAAATTTCATGGA
437518 TTGGCATAGCCGCCCAA
1 TTGGCATAGCCGCCCAA
437535 ATTCTAACAA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
39 22 0.48
40 24 0.52
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (40 bp):
TTGGCATAGCCGCCCAACTGCATATTTAAAATTTCATGGA
Found at i:441439 original size:16 final size:16
Alignment explanation
Indices: 441420--441459 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
441410 TTGTGTTCAG
441420 GTTATTTTGAGTTTAA
1 GTTATTTTGAGTTTAA
* * *
441436 GTTATGTCGGGTTTAA
1 GTTATTTTGAGTTTAA
441452 GTTATTTT
1 GTTATTTT
441460 AGATTTGAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.55
Consensus pattern (16 bp):
GTTATTTTGAGTTTAA
Found at i:441853 original size:17 final size:18
Alignment explanation
Indices: 441831--441867 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
441821 CATATTATTA
441831 TTAAAAAAATTT-AAAAT
1 TTAAAAAAATTTGAAAAT
441848 TT-AAAAAATTTGAAAAT
1 TTAAAAAAATTTGAAAAT
441865 TTA
1 TTA
441868 TATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TTAAAAAAATTTGAAAAT
Found at i:441913 original size:8 final size:8
Alignment explanation
Indices: 441900--441957 Score: 66
Period size: 8 Copynumber: 7.4 Consensus size: 8
441890 TATAATTTTT
441900 AAAATTAA
1 AAAATTAA
441908 AAAATTAA
1 AAAATTAA
* *
441916 AAAACT-C
1 AAAATTAA
441923 AAAATTAA
1 AAAATTAA
*
441931 AAAATATAT
1 AAAAT-TAA
441940 AAAA-TAA
1 AAAATTAA
441947 AAAATTAA
1 AAAATTAA
441955 AAA
1 AAA
441958 TAAAAAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
7 11 0.27
8 24 0.59
9 6 0.15
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAATTAA
Found at i:441943 original size:24 final size:23
Alignment explanation
Indices: 441900--441965 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
441890 TATAATTTTT
*
441900 AAAATTAAAAAATTAAAAAACT-C
1 AAAATTAAAAAATTAAAAAA-TAA
*
441923 AAAATTAAAAAATATATAAAATAA
1 AAAATTAAAAAAT-TAAAAAATAA
*
441947 AAAATT-AAAAATAAAAAAA
1 AAAATTAAAAAATTAAAAAA
441966 ATCAATGGCG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 5 0.14
23 20 0.54
24 12 0.32
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (23 bp):
AAAATTAAAAAATTAAAAAATAA
Found at i:441948 original size:15 final size:14
Alignment explanation
Indices: 441900--441964 Score: 67
Period size: 16 Copynumber: 4.3 Consensus size: 14
441890 TATAATTTTT
441900 AAAATTAAAAAATTAA
1 AAAATT-AAAAA-TAA
* *
441916 AAAACTCAAAATTAA
1 AAAA-TTAAAAATAA
441931 AAAATATATAAAATAA
1 AAAAT-TA-AAAATAA
441947 AAAATTAAAAATAA
1 AAAATTAAAAATAA
441961 AAAA
1 AAAA
441965 AATCAATGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
14 12 0.29
15 10 0.24
16 19 0.45
17 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATTAAAAATAA
Found at i:441964 original size:7 final size:7
Alignment explanation
Indices: 441900--441964 Score: 58
Period size: 7 Copynumber: 8.7 Consensus size: 7
441890 TATAATTTTT
*
441900 AAAATTA
1 AAAAATA
441907 AAAAATTA
1 AAAAA-TA
*
441915 AAAAACTC
1 AAAAA-TA
*
441923 AAAATTA
1 AAAAATA
441930 AAAAATA
1 AAAAATA
441937 TATAAAATA
1 -A-AAAATA
*
441946 AAAAATT
1 AAAAATA
441953 AAAAATA
1 AAAAATA
441960 AAAAA
1 AAAAA
441965 AATCAATGGC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
7 27 0.57
8 14 0.30
9 6 0.13
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (7 bp):
AAAAATA
Found at i:454962 original size:22 final size:23
Alignment explanation
Indices: 454937--454984 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
454927 CATTCTTTAA
454937 AATATTATAAAT-TTTTTAT-ATT
1 AATATT-TAAATATTTTTATAATT
*
454959 AATATTTATATATTTTTATAATT
1 AATATTTAAATATTTTTATAATT
454982 AAT
1 AAT
454985 TTAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 13 0.57
23 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AATATTTAAATATTTTTATAATT
Found at i:454973 original size:23 final size:22
Alignment explanation
Indices: 454937--454984 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
454927 CATTCTTTAA
454937 AATATTATAAATTTTT-TATATT
1 AATATTATAAATTTTTATA-ATT
*
454959 AATATTTATATATTTTTATAATT
1 AATA-TTATAAATTTTTATAATT
454982 AAT
1 AAT
454985 TTAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 17 0.74
24 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATATTATAAATTTTTATAATT
Found at i:460395 original size:21 final size:21
Alignment explanation
Indices: 460360--460416 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
460350 TTTAAGGTAG
*
460360 TAGTAG-TTCTTTTAAAAGAA
1 TAGTAGTTTTTTTTAAAAGAA
* *
460380 TAGTAGTTTTTTTTAAGAGAG
1 TAGTAGTTTTTTTTAAAAGAA
*
460401 TA--AGTTTTATTTAAAA
1 TAGTAGTTTTTTTTAAAA
460417 ATAGTATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 12 0.39
20 6 0.19
21 13 0.42
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.46
Consensus pattern (21 bp):
TAGTAGTTTTTTTTAAAAGAA
Found at i:460397 original size:19 final size:19
Alignment explanation
Indices: 460360--460422 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
460350 TTTAAGGTAG
**
460360 TAGTAGTTCTTTTAAAAGAA
1 TAGTAGTT-TTTTTTAAGAA
460380 TAGTAGTTTTTTTTAAG-A
1 TAGTAGTTTTTTTTAAGAA
* * *
460398 GAGTAAGTTTTATTTAAAAA
1 TAGT-AGTTTTTTTTAAGAA
460418 TAGTA
1 TAGTA
460423 TAATTAGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 4 0.11
19 19 0.54
20 12 0.34
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.44
Consensus pattern (19 bp):
TAGTAGTTTTTTTTAAGAA
Found at i:467237 original size:16 final size:17
Alignment explanation
Indices: 467216--467247 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
467206 TATATTATTA
467216 AAAAAATTT-AAAATTT
1 AAAAAATTTGAAAATTT
467232 AAAAAATTTGAAAATT
1 AAAAAATTTGAAAATT
467248 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAAATTTGAAAATTT
Found at i:467281 original size:19 final size:18
Alignment explanation
Indices: 467212--467291 Score: 55
Period size: 17 Copynumber: 4.6 Consensus size: 18
467202 TTCATATATT
*
467212 ATTAAAAAA-ATTT-AAA
1 ATTAAAAAATTTTTGAAA
467228 ATTTAAAAAA--TTTGAAA
1 A-TTAAAAAATTTTTGAAA
* **
467245 ATT-ATATTTTTTTGAAA
1 ATTAAAAAATTTTTGAAA
467262 ATTCAAAATAATTTTT-AAA
1 ATT-AAAA-AATTTTTGAAA
467281 ATTAAAAAATT
1 ATTAAAAAATT
467292 AAAACAACTC
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
15 2 0.04
16 6 0.12
17 26 0.51
18 4 0.08
19 8 0.16
20 5 0.10
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAAAAATTTTTGAAA
Found at i:467291 original size:8 final size:8
Alignment explanation
Indices: 467278--467346 Score: 54
Period size: 8 Copynumber: 8.6 Consensus size: 8
467268 AATAATTTTT
467278 AAAATTAA
1 AAAATTAA
467286 AAAATTAA
1 AAAATTAA
* *
467294 AACAACT-C
1 AA-AATTAA
467302 AAAATTAAA
1 AAAATT-AA
*
467311 AAATATTAT
1 AAA-ATTAA
467320 AAAA-TAA
1 AAAATTAA
467327 AAAATT-A
1 AAAATTAA
*
467334 AAAATAAA
1 AAAATTAA
467342 AAAAT
1 AAAAT
467347 CAATGGCGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
7 15 0.31
8 20 0.42
9 10 0.21
10 3 0.06
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATTAA
Found at i:467333 original size:15 final size:14
Alignment explanation
Indices: 467309--467344 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 14
467299 CTCAAAATTA
467309 AAAAATATTATAAAAT
1 AAAAA-ATTA-AAAAT
467325 AAAAAATTAAAAAT
1 AAAAAATTAAAAAT
467339 AAAAAA
1 AAAAAA
467345 ATCAATGGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.55
15 4 0.20
16 5 0.25
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAAATTAAAAAT
Done.