Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008980.1 Corchorus capsularis cultivar CVL-1 contig09001, 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: 124535
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:848 original size:19 final size:17
Alignment explanation
Indices: 824--861 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
814 ACCTGAGTTC
824 TTCTTTCTTTTCTTCTCTT
1 TTCTTTCTTTT-TTCT-TT
843 TTCTTTCTTTTTTCTTT
1 TTCTTTCTTTTTTCTTT
860 TT
1 TT
862 TAGGTCTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 11 0.58
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTCTTTCTTTTTTCTTT
Found at i:851 original size:9 final size:9
Alignment explanation
Indices: 824--853 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
814 ACCTGAGTTC
824 TTCTTTCTT
1 TTCTTTCTT
833 TTCTTCTCTT
1 TTCTT-TCTT
843 TTCTTTCTT
1 TTCTTTCTT
852 TT
1 TT
854 TTCTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:2173 original size:20 final size:21
Alignment explanation
Indices: 2150--2193 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
2140 TTTGACAGCA
*
2150 AAACAAAAACGAAAC-AAAAC
1 AAACAAAAACAAAACAAAAAC
2170 AAACAAAAACAAAACAAAAAC
1 AAACAAAAACAAAACAAAAAC
2191 AAA
1 AAA
2194 AAACAGAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.80, C:0.18, G:0.02, T:0.00
Consensus pattern (21 bp):
AAACAAAAACAAAACAAAAAC
Found at i:2181 original size:15 final size:15
Alignment explanation
Indices: 2148--2193 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
2138 ATTTTGACAG
2148 CAAAACAAAAACGAAA
1 CAAAACAAAAAC-AAA
2164 CAAAACAAACAA-AAA
1 CAAAACAAA-AACAAA
2179 CAAAACAAAAACAAA
1 CAAAACAAAAACAAA
2194 AAACAGAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.07
15 15 0.54
16 9 0.32
17 2 0.07
ACGTcount: A:0.78, C:0.20, G:0.02, T:0.00
Consensus pattern (15 bp):
CAAAACAAAAACAAA
Found at i:2183 original size:5 final size:5
Alignment explanation
Indices: 2148--2194 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
2138 ATTTTGACAG
*
2148 CAAAA CAAAAA CGAAA CAAAA C-AAA CAAAAA CAAAA CAAAAA CAAAA
1 CAAAA C-AAAA CAAAA CAAAA CAAAA C-AAAA CAAAA C-AAAA CAAAA
2195 AACAGAAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
4 4 0.11
5 18 0.50
6 14 0.39
ACGTcount: A:0.79, C:0.19, G:0.02, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:2194 original size:11 final size:11
Alignment explanation
Indices: 2148--2194 Score: 71
Period size: 11 Copynumber: 4.5 Consensus size: 11
2138 ATTTTGACAG
2148 CAAAACAAAAA
1 CAAAACAAAAA
*
2159 CGAAAC-AAAA
1 CAAAACAAAAA
2169 C-AAACAAAAA
1 CAAAACAAAAA
2179 CAAAACAAAAA
1 CAAAACAAAAA
2190 CAAAA
1 CAAAA
2195 AACAGAAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
9 4 0.12
10 10 0.30
11 19 0.58
ACGTcount: A:0.79, C:0.19, G:0.02, T:0.00
Consensus pattern (11 bp):
CAAAACAAAAA
Found at i:2203 original size:6 final size:6
Alignment explanation
Indices: 2149--2195 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
2139 TTTTGACAGC
2149 AAAACA AAAACGA AACAA-A ACAAACA AAAAC- AAAACA AAAACA AAAA
1 AAAACA AAAAC-A AA-AACA A-AAACA AAAACA AAAACA AAAACA AAAA
2196 ACAGAAACGA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.14
6 23 0.64
7 6 0.17
8 2 0.06
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:5672 original size:18 final size:19
Alignment explanation
Indices: 5637--5673 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5627 AGAGTGTTCG
5637 ATTGAAGAGTCCGAGAGAAA
1 ATTGAAGAGT-CGAGAGAAA
5657 ATTGAAGAGT-GAGAGAA
1 ATTGAAGAGTCGAGAGAA
5674 TCAGTGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.32, T:0.16
Consensus pattern (19 bp):
ATTGAAGAGTCGAGAGAAA
Found at i:7105 original size:17 final size:17
Alignment explanation
Indices: 7085--7117 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
7075 AGGTGGACTT
7085 AAAATGACCAAAATGCA
1 AAAATGACCAAAATGCA
7102 AAAATGACCAAAATGC
1 AAAATGACCAAAATGC
7118 CCCTAGGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (17 bp):
AAAATGACCAAAATGCA
Found at i:7870 original size:36 final size:36
Alignment explanation
Indices: 7830--7903 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
7820 AGGGGCTTAT
7830 TTGGTCAAAATAAAAGTTTAAAGACTTATTTAACGG
1 TTGGTCAAAATAAAAGTTTAAAGACTTATTTAACGG
7866 TTGGTCAAAATAAAAGTTTAAAGACTTATTTAACGG
1 TTGGTCAAAATAAAAGTTTAAAGACTTATTTAACGG
7902 TT
1 TT
7904 CGGTGTAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (36 bp):
TTGGTCAAAATAAAAGTTTAAAGACTTATTTAACGG
Found at i:8307 original size:15 final size:14
Alignment explanation
Indices: 8287--8324 Score: 53
Period size: 12 Copynumber: 2.8 Consensus size: 14
8277 GTTCTGCTCT
8287 CAAATAAGTCATTCA
1 CAAATAAGTC-TTCA
8302 CAAATAAG--TTCA
1 CAAATAAGTCTTCA
8314 CAAATAAGTCT
1 CAAATAAGTCT
8325 GGTTTCAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.57
14 1 0.05
15 8 0.38
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.26
Consensus pattern (14 bp):
CAAATAAGTCTTCA
Found at i:14372 original size:62 final size:64
Alignment explanation
Indices: 14297--14427 Score: 212
Period size: 62 Copynumber: 2.1 Consensus size: 64
14287 ATTAAATTAA
* * *
14297 AAATTATGATAATTAGACTATTTTTTATGACGTTCTTATGAAATTTTGATAA-C-CTTCCTATG
1 AAATTATGATAATTACACTATTTTTTATGACGTCCTTATGAAATTTTGATAAGCAATTCCTATG
*
14359 AAATTATGATAATTACACTATTTTTTATGACGTCCTTGTGAAATTTTGATAAGCAATTCCTATG
1 AAATTATGATAATTACACTATTTTTTATGACGTCCTTATGAAATTTTGATAAGCAATTCCTATG
14423 AAATT
1 AAATT
14428 TCAATAACGA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 49 0.78
63 1 0.02
64 13 0.21
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (64 bp):
AAATTATGATAATTACACTATTTTTTATGACGTCCTTATGAAATTTTGATAAGCAATTCCTATG
Found at i:14495 original size:22 final size:22
Alignment explanation
Indices: 14470--14567 Score: 63
Period size: 22 Copynumber: 4.5 Consensus size: 22
14460 TTTTATAGTT
* * *
14470 TTTTTTTAACATTCTTATGAAA
1 TTTTGTTAACATCCCTATGAAA
*
14492 TTTTGTTAACCTCCCTATGAAA
1 TTTTGTTAACATCCCTATGAAA
* * *
14514 TTTTG-AAGACCTCACTATGAAA
1 TTTTGTTA-ACATCCCTATGAAA
* * * **
14536 TTTCGATAACTTCCAAATGAAA
1 TTTTGTTAACATCCCTATGAAA
*
14558 TTTTGATAAC
1 TTTTGTTAAC
14568 CAACACTATA
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
21 1 0.02
22 59 0.97
23 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TTTTGTTAACATCCCTATGAAA
Found at i:14614 original size:45 final size:45
Alignment explanation
Indices: 14485--14614 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 45
14475 TTAACATTCT
* * * * *
14485 TATGAAATTTTGTTAACCTCCCTATGAAATTTTGAAGACC-TCAC
1 TATGAAATTTCGATAACCTCCATATGAAATTTTGAAAACCAACAC
* * *
14529 TATGAAATTTCGATAACTTCCAAATGAAATTTTGATAACCAACAC
1 TATGAAATTTCGATAACCTCCATATGAAATTTTGAAAACCAACAC
* *
14574 TAT-AAGATGTT-GATAACCTCCATATGATATATTGAAAACCA
1 TATGAA-AT-TTCGATAACCTCCATATGAAATTTTGAAAACCA
14615 CGTTATGAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
44 35 0.50
45 33 0.47
46 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (45 bp):
TATGAAATTTCGATAACCTCCATATGAAATTTTGAAAACCAACAC
Found at i:14804 original size:22 final size:22
Alignment explanation
Indices: 14772--15006 Score: 112
Period size: 22 Copynumber: 10.9 Consensus size: 22
14762 CGAAGCCATG
* **
14772 AAAATTGTGATAACCTCGGTAT
1 AAAATTTTGATAACCTCCCTAT
*
14794 AAAATTTTGATAAATCTCCCTAT
1 AAAATTTTGAT-AACCTCCCTAT
14817 AAAATTTTGATAA-----CTA-
1 AAAATTTTGATAACCTCCCTAT
*
14833 CAAATTTTGATAACCTCCCTAT
1 AAAATTTTGATAACCTCCCTAT
* ** **
14855 GATTTTTTGATAACCTCATTAT
1 AAAATTTTGATAACCTCCCTAT
* * *
14877 GAAA-TTTGTTTAATCTCCCTAT
1 AAAATTTTG-ATAACCTCCCTAT
* * * *
14899 GAAATTTTGATCTACAT-ACTAT
1 AAAATTTTGAT-AACCTCCCTAT
* *
14921 GAAATTTTGATAACC-CTCTTAT
1 AAAATTTTGATAACCTC-CCTAT
* * **
14943 GAAATTTTGA-AAACTAAACTAT
1 AAAATTTTGATAACCT-CCCTAT
* *
14965 AAAATTTTGATAACCTTCATAT
1 AAAATTTTGATAACCTCCCTAT
* *
14987 GAAATTTTGATATCCTCCCT
1 AAAATTTTGATAACCTCCCT
15007 GAAATTTTGA
Statistics
Matches: 160, Mismatches: 38, Indels: 30
0.70 0.17 0.13
Matches are distributed among these distances:
16 12 0.08
17 3 0.02
21 12 0.08
22 104 0.65
23 29 0.18
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
AAAATTTTGATAACCTCCCTAT
Found at i:14863 original size:38 final size:39
Alignment explanation
Indices: 14795--14868 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
14785 CCTCGGTATA
*
14795 AAATTTTGATAAATCTCCCTATAAAATTTTGATAACTAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTAC
* **
14834 AAATTTTGAT-AACCTCCCTATGATTTTTTGATAAC
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAC
14869 CTCATTATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 21 0.68
39 10 0.32
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (39 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAACTAC
Found at i:14944 original size:44 final size:42
Alignment explanation
Indices: 14896--14997 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 42
14886 TTAATCTCCC
* *
14896 TATGAAATTTTGATCTACATACTATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATCTA-A-ACTATAAAATTTTGATAACCCTCA
* *
14940 TATGAAATTTTGAAAACTAAACTATAAAATTTTGATAACCTTCA
1 TATGAAATTTTG--ATCTAAACTATAAAATTTTGATAACCCTCA
14984 TATGAAATTTTGAT
1 TATGAAATTTTGAT
14998 ATCCTCCCTG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
42 1 0.02
44 45 0.88
45 1 0.02
46 4 0.08
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (42 bp):
TATGAAATTTTGATCTAAACTATAAAATTTTGATAACCCTCA
Found at i:15181 original size:2 final size:2
Alignment explanation
Indices: 15174--15248 Score: 62
Period size: 2 Copynumber: 42.5 Consensus size: 2
15164 CCGTTTAGTA
*
15174 AT AT AT AT A- AT -T AA AT AT AT AT -T AT AT AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
15211 AT CT A- AT AT AT AT A- AT -T AT AT AT AT A- AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15248 A
1 A
15249 ATTATTAAAC
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
1 10 0.17
2 49 0.83
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:15193 original size:12 final size:12
Alignment explanation
Indices: 15176--15252 Score: 69
Period size: 12 Copynumber: 6.9 Consensus size: 12
15166 GTTTAGTAAT
15176 ATATATAATTAA
1 ATATATAATTAA
*
15188 ATATAT-ATTAT
1 ATATATAATTAA
15199 ATATATAA-T-A
1 ATATATAATTAA
*
15209 ATATCTAA-T--
1 ATATATAATTAA
*
15218 ATATATAATTAT
1 ATATATAATTAA
15230 ATATATAA-TAA
1 ATATATAATTAA
15241 TATATATAATTA
1 -ATATATAATTA
15253 TTAAACGGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
9 7 0.13
10 9 0.17
11 13 0.24
12 23 0.43
13 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATATAATTAA
Found at i:15199 original size:21 final size:22
Alignment explanation
Indices: 15172--15253 Score: 105
Period size: 21 Copynumber: 3.7 Consensus size: 22
15162 AACCGTTTAG
15172 TAATATATATAATTA-AATATA
1 TAATATATATAATTATAATATA
* * *
15193 TATTATATAT-ATAATAATATC
1 TAATATATATAATTATAATATA
15214 TAATATATATAATTATATATATAA
1 TAATATATATAATTATA-ATAT-A
15238 TAATATATATAATTAT
1 TAATATATATAATTAT
15254 TAAACGGTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 3 0.06
21 23 0.45
22 5 0.10
23 4 0.08
24 16 0.31
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATATATATAATTATAATATA
Found at i:15217 original size:10 final size:10
Alignment explanation
Indices: 15172--15250 Score: 74
Period size: 10 Copynumber: 7.7 Consensus size: 10
15162 AACCGTTTAG
15172 TAAT-ATATA
1 TAATAATATA
15181 TAATTAAATATA
1 TAA-T-AATATA
*
15193 TATTATATATA
1 TAATA-ATATA
*
15204 TAATAATATC
1 TAATAATATA
15214 TAAT-ATATA
1 TAATAATATA
15223 TAATTATATATA
1 TAA-TA-ATATA
15235 TAATAATATA
1 TAATAATATA
15245 T-ATAAT
1 TAATAAT
15251 TATTAAACGG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
9 15 0.25
10 17 0.29
11 12 0.20
12 15 0.25
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (10 bp):
TAATAATATA
Found at i:15550 original size:22 final size:22
Alignment explanation
Indices: 15525--15644 Score: 100
Period size: 22 Copynumber: 5.5 Consensus size: 22
15515 TATCACATTT
* *
15525 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
15547 TGAAATTTTGATAACCTATCTA
1 TGAAATTTTGATAACCTCTCTA
* * ** *
15569 T-AAAATTTGTTGGCCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
15590 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
15612 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
15634 TGAAATTTTGA
1 TGAAATTTTGA
15645 AATTGGACAG
Statistics
Matches: 74, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
21 15 0.20
22 58 0.78
23 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:15619 original size:43 final size:43
Alignment explanation
Indices: 15500--15644 Score: 123
Period size: 44 Copynumber: 3.3 Consensus size: 43
15490 AGAAATACCA
* * * *
15500 CTATGAAATTTTGGTTATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATG-AAATTTGATAACCCCT
* * * **
15544 TTATGAAATTTTGATAA-C-CTATCTATAAAATTTGTTGGCCCCT
1 CTATGAAATTTTGATAATCAC-AT-TATGAAATTTGATAACCCCT
* * *
15587 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATG-AAATTTGATAACCCCT
*
15631 CTTTGAAATTTTGA
1 CTATGAAATTTTGA
15645 AATTGGACAG
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.01
43 34 0.44
44 42 0.54
45 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.43
Consensus pattern (43 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTGATAACCCCT
Found at i:15768 original size:37 final size:38
Alignment explanation
Indices: 15701--15797 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 38
15691 TATTTAAGCC
* * *
15701 TAAATAGGACGTTGGAGACGAAGACAAAAAG-CAAAAT
1 TAAATAGAACGTTGGAAACAAAGACAAAAAGACAAAAT
* *
15738 TAAATATAACGATTGGAAACAAAGAC-AAAAGATAAAAT
1 TAAATAGAACG-TTGGAAACAAAGACAAAAAGACAAAAT
*
15776 TAAATAGGACGTTGGAAACAAA
1 TAAATAGAACGTTGGAAACAAA
15798 AAGTCAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
37 25 0.49
38 26 0.51
ACGTcount: A:0.55, C:0.09, G:0.20, T:0.16
Consensus pattern (38 bp):
TAAATAGAACGTTGGAAACAAAGACAAAAAGACAAAAT
Found at i:18375 original size:150 final size:149
Alignment explanation
Indices: 18063--18359 Score: 463
Period size: 150 Copynumber: 2.0 Consensus size: 149
18053 GCTTAATCAG
*
18063 GTCTCA-GTTTGAGACCTTCCGTATGTAGCGTTTCCATTGGTAGACTCACCCACCAAACCCAAGT
1 GTCTCAGGTTTGAGACCTTCCGTATGTAGCGTCTCCATTGGTAGACTCACCCACCAAACCCAAGT
* * * *
18127 ACGCGACCCGGGTCAAATCCTAATTAGTCAGAGCAACTTGATACTGGATGGGAAACCAAAAAAAA
66 ACGCGACCCGGGTCAAATCCGAATTAGTCAGACCAACTTAATACCGGATGGGAAACC-AAAAAAA
*
18192 AAAATGTTTGCCTAGACTAA
130 AAAATGTTTGCCTAGACCAA
*
18212 GTCTCAGGTTTGAGACCTTGCGTATGTAGCGTCTCCATTGGTAGACTCACCCACCAAACCCAAGT
1 GTCTCAGGTTTGAGACCTTCCGTATGTAGCGTCTCCATTGGTAGACTCACCCACCAAACCCAAGT
* * * * *
18277 ACGCGACCTGGGTCGAATCCGGATTAGTCATACCAACTTAATACCGGATGGGAAAGC-AAAAAAA
66 ACGCGACCCGGGTCAAATCCGAATTAGTCAGACCAACTTAATACCGGATGGGAAACCAAAAAAAA
18341 AAATGTTTGCCTAGACCAA
131 AAATGTTTGCCTAGACCAA
18360 CAAGTTATTG
Statistics
Matches: 135, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
148 25 0.19
149 6 0.04
150 104 0.77
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (149 bp):
GTCTCAGGTTTGAGACCTTCCGTATGTAGCGTCTCCATTGGTAGACTCACCCACCAAACCCAAGT
ACGCGACCCGGGTCAAATCCGAATTAGTCAGACCAACTTAATACCGGATGGGAAACCAAAAAAAA
AAATGTTTGCCTAGACCAA
Found at i:18977 original size:13 final size:13
Alignment explanation
Indices: 18959--18983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18949 TTTGAAATTC
18959 AAATAATATTTAT
1 AAATAATATTTAT
18972 AAATAATATTTA
1 AAATAATATTTA
18984 CAAGTCATGT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:26892 original size:28 final size:28
Alignment explanation
Indices: 26839--26892 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
26829 AGGACTACCG
***
26839 AAAAGATTAAAATTTTGTTAACAAAAAA
1 AAAAGATTAAAATTTTAAAAACAAAAAA
*
26867 AAAAGATTAAAATTTTAAAAAGAAAA
1 AAAAGATTAAAATTTTAAAAACAAAA
26893 TACTTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (28 bp):
AAAAGATTAAAATTTTAAAAACAAAAAA
Found at i:30024 original size:1 final size:1
Alignment explanation
Indices: 30010--30052 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
30000 GCATGTATAA
* * * *
30010 CCCCCCTCCTCCCCCCCACCCCCCCCCCCCCCCCCCCCGCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
30053 TCCTCCTTCT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.02, C:0.91, G:0.02, T:0.05
Consensus pattern (1 bp):
C
Found at i:36777 original size:214 final size:210
Alignment explanation
Indices: 36272--36855 Score: 719
Period size: 214 Copynumber: 2.8 Consensus size: 210
36262 CTTTTTGTAA
* * * * * * * *
36272 AAATGACCTAAAAGTTTAGATATTTAATC-CCATCAAGAATAAAAAGTTAGGACATTTAAATAAT
1 AAATGACCAAAAAATCTAGTTATTTAATCACC-TCTAGAATCAAAAGTTAGGGCATTTAAGTAAT
** * * * * * * *
36336 TTACCAAGTAGGTAAAGACGAAAAAGATTACTTCTC-CAGCTCATCATTAATCCTGGTTAGGGAT
65 CGATCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTCA-CTCCTCATTAATCCGGGATAGGGAT
*** * * ** * ** * *
36400 CTTTTAGTAA-TTCCACCCAGCTCA-TCATTTATTCGAGGTAAGGATCTTTTAGTAATTCCACTA
129 CTTTTAGTAATTTCCATATA-TTTATTCAAATAAT-G-TTTATGGATCTTTTAGTAATTCAACTA
*
36463 CTCTATTAAAGTCATTTGAG
191 CTCTATTAAAGTAATTTGAG
36483 AAATGACCAAAAAATCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCATTTAAGTAATC
1 AAATGACCAAAAAATCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCATTTAAGTAATC
*
36548 GGTCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTCACTCCTCATTAATCCAGGG-TAGGGATC
66 GATCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTCACTCCTCATTAATCC-GGGATAGGGATC
* *
36612 TTTTAGTAATTTTCATATGTTTATTCAAATAATGTTTATGGATCTTTTAGTAATTCAACTACTCT
130 TTTTAGTAATTTCCATATATTTATTCAAATAATGTTTATGGATCTTTTAGTAATTCAACTACTCT
36677 ATTAAAGTAATTTGAG
195 ATTAAAGTAATTTGAG
36693 AAATGACCAAAAATTAAGTCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCATTTAAGT
1 AAATGACC-AAAA--AA-TCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCATTTAAGT
* * *
36758 AATCGATCAAGTGGGAAAAGACGAAAAAAATTAGTTCTCTCGCTCCTCATTAATCCGGGATAGGG
62 AATCGATCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTCACTCCTCATTAATCCGGGATAGGG
36823 ATCTTTTAGTAATTTCCATATATTTATTCAAAT
127 ATCTTTTAGTAATTTCCATATATTTATTCAAAT
36856 GATATGTAGT
Statistics
Matches: 325, Mismatches: 38, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
210 50 0.15
211 119 0.37
212 16 0.05
213 5 0.02
214 135 0.42
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (210 bp):
AAATGACCAAAAAATCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCATTTAAGTAATC
GATCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTCACTCCTCATTAATCCGGGATAGGGATCT
TTTAGTAATTTCCATATATTTATTCAAATAATGTTTATGGATCTTTTAGTAATTCAACTACTCTA
TTAAAGTAATTTGAG
Found at i:43285 original size:13 final size:13
Alignment explanation
Indices: 43267--43313 Score: 94
Period size: 13 Copynumber: 3.6 Consensus size: 13
43257 TCCCCCACGC
43267 AACGCAATTACCA
1 AACGCAATTACCA
43280 AACGCAATTACCA
1 AACGCAATTACCA
43293 AACGCAATTACCA
1 AACGCAATTACCA
43306 AACGCAAT
1 AACGCAAT
43314 AGAGGCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.47, C:0.30, G:0.09, T:0.15
Consensus pattern (13 bp):
AACGCAATTACCA
Found at i:53301 original size:29 final size:30
Alignment explanation
Indices: 53262--53338 Score: 138
Period size: 29 Copynumber: 2.6 Consensus size: 30
53252 GAGTAATATT
*
53262 AAAAGTTGGAATAAATGATATTTC-AAAAA
1 AAAAGTTGGAATAAATGATAATTCAAAAAA
53291 AAAAGTTGGAATAAATGATAATTCAAAAAA
1 AAAAGTTGGAATAAATGATAATTCAAAAAA
53321 AAAAGTTGGAATAAATGA
1 AAAAGTTGGAATAAATGA
53339 CGTGCATGTC
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 23 0.50
30 23 0.50
ACGTcount: A:0.57, C:0.03, G:0.16, T:0.25
Consensus pattern (30 bp):
AAAAGTTGGAATAAATGATAATTCAAAAAA
Found at i:55465 original size:22 final size:22
Alignment explanation
Indices: 55447--55569 Score: 72
Period size: 22 Copynumber: 5.6 Consensus size: 22
55437 TTAAGGTCTT
* *
55447 CAAAATTTCTTAAGGAGGTTAA
1 CAAAATTTCATAAGAAGGTTAA
55469 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATAAGAAGGTTAA
* **
55491 -AAGAACTTT-ATAAAAAGGTTCT
1 CAA-AA-TTTCATAAGAAGGTTAA
* * ** *
55513 CGAAATTCCAT-AGTATCGTTAT
1 CAAAATTTCATAAG-AAGGTTAA
* * * *
55535 TAAAATTTCATAGGAAGATTAT
1 CAAAATTTCATAAGAAGGTTAA
55557 CAAAATTTCATAA
1 CAAAATTTCATAA
55570 TGAGATCATA
Statistics
Matches: 75, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
21 5 0.07
22 65 0.87
23 5 0.07
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAAGAAGGTTAA
Found at i:55583 original size:22 final size:22
Alignment explanation
Indices: 55536--55583 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
55526 TATCGTTATT
* *
55536 AAAATTTCATAGGAAGATTATC
1 AAAATTTCATAGGAAGATCATA
*
55558 AAAATTTCATAATG-AGATCATA
1 AAAATTTCAT-AGGAAGATCATA
55580 AAAA
1 AAAA
55584 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAGGAAGATCATA
Found at i:63302 original size:22 final size:20
Alignment explanation
Indices: 63266--63405 Score: 91
Period size: 22 Copynumber: 6.4 Consensus size: 20
63256 GCCAAAGAGA
*
63266 TTATCAAAATGTCATAGCGAGG
1 TTAT-AAAATTTCATAG-GAGG
*
63288 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAG-GAGG
*
63310 TTAACAAAATTTCATTAGGAGG
1 TT-ATAAAATTTCA-TAGGAGG
*
63332 TTACTAATATTTCATAGGGAGG
1 TTA-TAAAATTTCATA-GGAGG
* * *
63354 TTATCAAAATTTTATAGTGTGA
1 TTAT-AAAATTTCATAG-GAGG
**
63376 TTATCAAAATTTCATATAAAGG
1 TTAT-AAAATTTCATA-GGAGG
63398 TTATAAAA
1 TTATAAAA
63406 GTCTCAATTT
Statistics
Matches: 94, Mismatches: 16, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
21 11 0.12
22 77 0.82
23 6 0.06
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (20 bp):
TTATAAAATTTCATAGGAGG
Found at i:63333 original size:44 final size:44
Alignment explanation
Indices: 63270--63370 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
63260 AAGAGATTAT
* * *
63270 CAAAATGTCATAGCGAGGTTA-TAAGAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGCGAGGTTACTAA-AATTTCATAGGGAGGTTAA
* *
63314 CAAAATTTCATTAG-GAGGTTACTAATATTTCATAGGGAGGTTAT
1 CAAAATTTCA-TAGCGAGGTTACTAAAATTTCATAGGGAGGTTAA
*
63358 CAAAATTTTATAG
1 CAAAATTTCATAG
63371 TGTGATTATC
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 3 0.06
44 40 0.82
45 6 0.12
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (44 bp):
CAAAATTTCATAGCGAGGTTACTAAAATTTCATAGGGAGGTTAA
Found at i:63399 original size:66 final size:66
Alignment explanation
Indices: 63277--63400 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 66
63267 TATCAAAATG
* *
63277 TCATAGCGAGGTTATAAGAATTTCATAGTGTGGTTAACAAAATTTCATTAGGAGGTTACTAATAT
1 TCATAGCGAGGTTATAAGAATTTCATAGTGTGATTAACAAAATTTCATTAGAAGGTTACTAATAT
63342 T
66 T
* * *
63343 TCATAGGGAGGTTATCAA-AATTTTATAGTGTGATTATCAAAATTTCATATA-AAGGTTA
1 TCATAGCGAGGTTAT-AAGAATTTCATAGTGTGATTAACAAAATTTCAT-TAGAAGGTTA
63401 TAAAAGTCTC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
66 47 0.92
67 4 0.08
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (66 bp):
TCATAGCGAGGTTATAAGAATTTCATAGTGTGATTAACAAAATTTCATTAGAAGGTTACTAATAT
T
Found at i:63480 original size:22 final size:22
Alignment explanation
Indices: 63411--63660 Score: 133
Period size: 22 Copynumber: 11.4 Consensus size: 22
63401 TAAAAGTCTC
* *
63411 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
63431 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
* *
63451 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
63473 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAGAG-T--GATTATCAA
**
63498 AATTT-ATAGAAAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
*
63519 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
* * * *
63541 AATTTCAAAGCGAGGTTATCAAA
1 AATTTCATAGAGTGATTATC-AA
* *
63564 AATTACATA-ATGTGATTATCAG
1 AATTTCATAGA-GTGATTATCAA
* * * *
63586 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* * * *
63608 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
63630 ATTTTCA-AAATGTGATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
63652 AATTTCATA
1 AATTTCATA
63661 ATGGTATTTT
Statistics
Matches: 176, Mismatches: 37, Indels: 31
0.72 0.15 0.13
Matches are distributed among these distances:
19 2 0.01
20 18 0.10
21 27 0.15
22 91 0.52
23 20 0.11
24 5 0.03
25 13 0.07
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:63584 original size:45 final size:45
Alignment explanation
Indices: 63489--63592 Score: 115
Period size: 45 Copynumber: 2.4 Consensus size: 45
63479 ATAGAGATCG
* * *
63489 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATGTT
** *
63533 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAAATTACATAATG-T
1 GATTATCAAAATTTCAAAGAAAGATTATC-AAAATTACATAATGTT
*
63577 GATTATCAGAATTTCA
1 GATTATCAAAATTTCA
63593 TAGAGGGGTC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
43 12 0.24
44 13 0.26
45 25 0.50
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (45 bp):
GATTATCAAAATTTCAAAGAAAGATTATCAAAATTACATAATGTT
Found at i:63609 original size:67 final size:66
Alignment explanation
Indices: 63510--63660 Score: 162
Period size: 67 Copynumber: 2.3 Consensus size: 66
63500 TTTATAGAAA
* ** * * * *
63510 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAAATTACATAA
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATC-AAAATTACAAAA
63574 TGT
64 TGT
* * * *
63577 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAATTTTCAAAATG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACAAAATG
63642 T
66 T
63643 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
63661 ATGGTATTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
65 1 0.01
66 27 0.39
67 40 0.57
68 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACAAAATG
T
Found at i:63783 original size:22 final size:22
Alignment explanation
Indices: 63728--63830 Score: 109
Period size: 22 Copynumber: 4.6 Consensus size: 22
63718 CAAGGGAGGT
*
63728 TTATCAAAATTTTATAG-GAAGA
1 TTATCAAAATTTCATAGCG-AGA
*
63750 TTTATCAAAATTTCATAGCGAGG
1 -TTATCAAAATTTCATAGCGAGA
* * *
63773 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGCGAGA
* * *
63795 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGCGAGA
63817 TTATCAAAATTTCA
1 TTATCAAAATTTCA
63831 GAGTGTGATT
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
22 52 0.73
23 18 0.25
24 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGA
Found at i:63805 original size:44 final size:42
Alignment explanation
Indices: 63751--64009 Score: 162
Period size: 44 Copynumber: 5.9 Consensus size: 42
63741 ATAGGAAGAT
*
63751 TTATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAG-GAGGTTATCA-AATTTCATAGTGTGG
* * * * *
63795 TTATCAAAATTTCAGAGTGTGATTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGGTTATC-AAATTTCATAGTGTGG
* * * **
63839 TTA-CTAACAA-TTCATATGGAGATTTTTAAATTTTCATAACGTGG
1 TTATC-AA-AATTTCATA-GGAGGTTATCAAA-TTTCATAGTGTGG
* * * *
63883 TTATCAATATATCATATGAAGGTTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATA-GGAGGTTATCAA-ATTTCATAGTG-TGG
* * * * *
63928 TCATCAAAATTTCATTGGGAAGTTATCGAAATTTCATATTGAGG
1 TTATCAAAATTTCA-TAGGAGGTTATC-AAATTTCATAGTGTGG
* * *
63972 TTTTCAAAATTTCTTAGGGAGGTTAACAAAATTTCATA
1 TTATCAAAATTTCATA-GGAGGTTATC-AAATTTCATA
64010 AGAAGGTTAA
Statistics
Matches: 165, Mismatches: 38, Indels: 24
0.73 0.17 0.11
Matches are distributed among these distances:
43 6 0.04
44 119 0.72
45 37 0.22
46 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (42 bp):
TTATCAAAATTTCATAGGAGGTTATCAAATTTCATAGTGTGG
Found at i:63852 original size:22 final size:22
Alignment explanation
Indices: 63751--63841 Score: 128
Period size: 22 Copynumber: 4.1 Consensus size: 22
63741 ATAGGAAGAT
* * * *
63751 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCAGAGTGTGA
* *
63773 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
63795 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
63817 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
63839 TTA
1 TTA
63842 CTAACAATTC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:63981 original size:22 final size:22
Alignment explanation
Indices: 63932--64024 Score: 78
Period size: 22 Copynumber: 4.2 Consensus size: 22
63922 TGTTGGTCAT
* * *
63932 CAAAATTTCATTGGGAAGTTAT
1 CAAAATTTCATAGGGAGGTTAA
* ** **
63954 CGAAATTTCATATTGAGGTTTT
1 CAAAATTTCATAGGGAGGTTAA
*
63976 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAGGGAGGTTAA
* *
63998 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATAGGGAGGTTAA
*
64020 AAAAA
1 CAAAA
64025 ATTTATAAAA
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGGGAGGTTAA
Found at i:64032 original size:22 final size:22
Alignment explanation
Indices: 63977--64032 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
63967 TGAGGTTTTC
* * * *
63977 AAAATTTCTTAGGGAGGTTAAC
1 AAAATTTCATAAGAAGGTTAAA
63999 AAAATTTCATAAGAAGGTTAAAA
1 AAAATTTCATAAGAAGGTT-AAA
64022 AAAATTT-ATAA
1 AAAATTTCATAA
64033 AAAGATTCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.30
Consensus pattern (22 bp):
AAAATTTCATAAGAAGGTTAAA
Found at i:65000 original size:22 final size:22
Alignment explanation
Indices: 64975--65016 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
64965 AAATGAAGTA
64975 TTCATACGAAATTATGATAACG
1 TTCATACGAAATTATGATAACG
**
64997 TTCATATTAAATTATGATAA
1 TTCATACGAAATTATGATAA
65017 TTACACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (22 bp):
TTCATACGAAATTATGATAACG
Found at i:65053 original size:22 final size:20
Alignment explanation
Indices: 65026--65133 Score: 69
Period size: 22 Copynumber: 5.2 Consensus size: 20
65016 ATTACACTAT
65026 TTTTGATAATGTCCTTATGAAA
1 TTTTGATAAT-TCC-TATGAAA
65048 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAA--TTCCTATGAAA
* * *
65070 TTATGATAATTAC-A--ATA
1 TTTTGATAATTCCTATGAAA
* **
65087 TTTTTATGACGTCCTTATGAAA
1 TTTTGAT-AATTCC-TATGAAA
65109 TTTTGATAACATTCCTATGAAA
1 TTTTGAT-A-ATTCCTATGAAA
65131 TTT
1 TTT
65134 CAATAACGAT
Statistics
Matches: 65, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
17 7 0.11
18 3 0.05
19 1 0.02
20 4 0.06
22 43 0.66
23 6 0.09
24 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (20 bp):
TTTTGATAATTCCTATGAAA
Found at i:65124 original size:61 final size:62
Alignment explanation
Indices: 64982--65132 Score: 223
Period size: 62 Copynumber: 2.5 Consensus size: 62
64972 GTATTCATAC
* * * * * *
64982 GAAATTATGATAACGTTCATATTAAATTATGATAATTACACTATTTTTGATAATGTCCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACAATATTTTTGATAACGTCCTTAT
* *
65044 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACAATATTTTT-ATGACGTCCTTAT
1 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACAATATTTTTGATAACGTCCTTAT
65105 GAAATTTTGATAACATTCCTATGAAATT
1 GAAATTTTGATAACATTCCTATGAAATT
65133 TCAATAACGA
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
61 38 0.47
62 43 0.53
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (62 bp):
GAAATTTTGATAACATTCCTATGAAATTATGATAATTACAATATTTTTGATAACGTCCTTAT
Found at i:65438 original size:23 final size:23
Alignment explanation
Indices: 65361--65623 Score: 144
Period size: 22 Copynumber: 11.9 Consensus size: 23
65351 AATTGTCAGT
* *
65361 AATCACACTCTGAAATTTTGAT-
1 AATCTCACTATGAAATTTTGATA
* *
65383 AATCACACTATGAAATTGTGAT-
1 AATCTCACTATGAAATTTTGATA
*
65405 AATCTCGCTATGAAATTTTGATA
1 AATCTCACTATGAAATTTTGATA
** * *
65428 AATCTTTCTATAAAATTCTGATA
1 AATCTCACTATGAAATTTTGATA
* *
65451 AATCTCCCTATAAAATTTTGAT-
1 AATCTCACTATGAAATTTTGATA
* *
65473 AACCTC-CTTATGAAATCTTGAT-
1 AATCTCAC-TATGAAATTTTGATA
65495 AA-CT-AC----AAATTTTGAT-
1 AATCTCACTATGAAATTTTGATA
* * **
65511 AACCTCCCTATGATTTTTTGAT-
1 AATCTCACTATGAAATTTTGATA
* * * *
65533 AACCTCATTATGAGATTTTG-TT
1 AATCTCACTATGAAATTTTGATA
*
65555 AATCTCCCTATGAAATTTTGATTTA
1 AATCTCACTATGAAATTTTGA--TA
*
65580 CATATAT-ACTATGAAATTTTGATA
1 -A-ATCTCACTATGAAATTTTGATA
* *
65604 ACTCTC-TTATGAAATTTTGA
1 AATCTCACTATGAAATTTTGA
65624 AAACTAAAAA
Statistics
Matches: 192, Mismatches: 33, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
18 1 0.01
21 5 0.03
22 113 0.59
23 39 0.20
24 2 0.01
25 1 0.01
26 15 0.08
27 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.41
Consensus pattern (23 bp):
AATCTCACTATGAAATTTTGATA
Found at i:65799 original size:22 final size:22
Alignment explanation
Indices: 65766--65887 Score: 93
Period size: 22 Copynumber: 5.5 Consensus size: 22
65756 GAAGTACCAC
65766 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGGTAATCAC-TT
* * *
65789 T-TGAAAATTTGATAATCTCTT
1 TATGAAATTTTGGTAATCACTT
* * *
65810 TATGAAATTTTGGTAACCGCTC
1 TATGAAATTTTGGTAATCACTT
* * * * * *
65832 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGGTAATCACTT
* *
65854 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGGTAATCACTT
*
65876 TATGTAATTTTG
1 TATGAAATTTTG
65888 ATAACCTTGC
Statistics
Matches: 78, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
21 3 0.04
22 74 0.95
23 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGGTAATCACTT
Found at i:65885 original size:44 final size:44
Alignment explanation
Indices: 65765--65893 Score: 134
Period size: 44 Copynumber: 2.9 Consensus size: 44
65755 AGAAGTACCA
* * * *
65765 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAATCTCT
1 CTATGAAATTTTGGTAATCACATTATGAAATTTTGATAACCCCT
* * * * * *
65809 TTATGAAATTTTGGTAACCGC-TCTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGGTAATCACAT-TATGAAATTTTGATAACCCCT
* *
65853 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACC
1 CTATGAAATTTTGGTAATCACATTATGAAATTTTGATAACC
65894 TTGCTTTGAA
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
43 1 0.02
44 63 0.97
45 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGGTAATCACATTATGAAATTTTGATAACCCCT
Found at i:72879 original size:11 final size:10
Alignment explanation
Indices: 72852--72877 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
72842 GGTTACGGAA
72852 TTTTTTCATT
1 TTTTTTCATT
72862 TTTTTTCATT
1 TTTTTTCATT
72872 TTTTTT
1 TTTTTT
72878 TCTTCAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:73439 original size:3 final size:3
Alignment explanation
Indices: 73431--73464 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
73421 CATAAAAAGG
73431 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
73465 AGACATAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:76266 original size:13 final size:13
Alignment explanation
Indices: 76248--76272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76238 TTATTAAGCT
76248 AATAATAATTATG
1 AATAATAATTATG
76261 AATAATAATTAT
1 AATAATAATTAT
76273 TATTATTCAA
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:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AATAATAATTATG
Found at i:80168 original size:44 final size:45
Alignment explanation
Indices: 80119--80211 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
80109 TGTCATTCTT
*
80119 TTAAGTTTTAA-CACCTATGAAAGATAAGTACTTCAGTACACAAA
1 TTAAGTTTTAAGCACCTATGAAAGATAAATACTTCAGTACACAAA
* *
80163 TTAAGTTTTAAGCACCTATGAAAGATAAATACTTCAGTATATAAA
1 TTAAGTTTTAAGCACCTATGAAAGATAAATACTTCAGTACACAAA
80208 TTAA
1 TTAA
80212 CACTTTTACA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 11 0.24
45 34 0.76
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (45 bp):
TTAAGTTTTAAGCACCTATGAAAGATAAATACTTCAGTACACAAA
Found at i:82077 original size:44 final size:44
Alignment explanation
Indices: 81994--82077 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
81984 ATTTAATTAG
* * *
81994 TGGTGATATTATATCACCATGTTTGGTGTAACAATGAAAATTCA
1 TGGTGATATTAGATCACCATGTTTGGTATAACAAGGAAAATTCA
*
82038 TGGTGATTTTAGATCACCATGTTTGGTATAA-ATAGGAAAA
1 TGGTGATATTAGATCACCATGTTTGGTATAACA-AGGAAAA
82078 AAAGAAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 34 0.97
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (44 bp):
TGGTGATATTAGATCACCATGTTTGGTATAACAAGGAAAATTCA
Found at i:82359 original size:18 final size:17
Alignment explanation
Indices: 82336--82389 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 17
82326 CCGACCGACT
82336 ATATTACTATATATAATA
1 ATATTA-TATATATAATA
82354 ATATTA-ATAT-TAATA
1 ATATTATATATATAATA
* *
82369 TTAATATATATATAAT-
1 ATATTATATATATAATA
82385 ATATT
1 ATATT
82390 CCTAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 9 0.30
16 11 0.37
17 4 0.13
18 6 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTATATATATAATA
Found at i:82381 original size:12 final size:13
Alignment explanation
Indices: 82346--82388 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
82336 ATATTACTAT
82346 ATATAATAATATTA
1 ATAT-ATAATATTA
82360 ATAT-TAATATTA
1 ATATATAATATTA
82372 ATATAT-ATA-TA
1 ATATATAATATTA
82383 ATATAT
1 ATATAT
82389 TCCTAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.29
12 15 0.54
13 1 0.04
14 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATAATATTA
Found at i:82468 original size:20 final size:22
Alignment explanation
Indices: 82445--82484 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
82435 TCTTTTTTCC
82445 TTTCTCTCT-CTTC-CTCTCGA
1 TTTCTCTCTCCTTCTCTCTCGA
*
82465 TTTCTTTCTCCTTCTCTCTC
1 TTTCTCTCTCCTTCTCTCTC
82485 CAATCTCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 4 0.24
22 5 0.29
ACGTcount: A:0.03, C:0.40, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTCTCTCTCCTTCTCTCTCGA
Found at i:85834 original size:97 final size:97
Alignment explanation
Indices: 85668--85861 Score: 370
Period size: 97 Copynumber: 2.0 Consensus size: 97
85658 GATCATATAG
* *
85668 ATGTTGTTGATCATATGGTCATTGATGATGGTGAAGAGAGCGCTATGGACTTGTTTTGGAAGCAT
1 ATGTTGTTGATCATATGGTCATGGATGATGGTGAAGAGAGCGCTATGGACTTGTTTTAGAAGCAT
85733 GAGGCAGAATCTGGAAAAGTCGAAAACAAGTC
66 GAGGCAGAATCTGGAAAAGTCGAAAACAAGTC
85765 ATGTTGTTGATCATATGGTCATGGATGATGGTGAAGAGAGCGCTATGGACTTGTTTTAGAAGCAT
1 ATGTTGTTGATCATATGGTCATGGATGATGGTGAAGAGAGCGCTATGGACTTGTTTTAGAAGCAT
85830 GAGGCAGAATCTGGAAAAGTCGAAAACAAGTC
66 GAGGCAGAATCTGGAAAAGTCGAAAACAAGTC
85862 TGAATTGGAC
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.27
Consensus pattern (97 bp):
ATGTTGTTGATCATATGGTCATGGATGATGGTGAAGAGAGCGCTATGGACTTGTTTTAGAAGCAT
GAGGCAGAATCTGGAAAAGTCGAAAACAAGTC
Found at i:87921 original size:37 final size:37
Alignment explanation
Indices: 87862--87932 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
87852 CTTGATCAAC
* ** * *
87862 ATACATGTCTTTTCGTATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAACAGACATAACCTTATGATCA
87899 ATACATGTCTTTCCAAACAGACATAACCTTATGA
1 ATACATGTCTTTCCAAACAGACATAACCTTATGA
87933 ATAATTATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (37 bp):
ATACATGTCTTTCCAAACAGACATAACCTTATGATCA
Found at i:91609 original size:2 final size:2
Alignment explanation
Indices: 91598--91631 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
91588 TCATAAATAA
91598 AT AT -T 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 AT AT AT A
91632 CACACACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91770 original size:26 final size:26
Alignment explanation
Indices: 91721--91770 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
91711 CTTAGTATTC
* *
91721 TTTTACTAGTAGCTTTTTTTTTTTCT
1 TTTTACTAGTAGCTTTTATATTTTCT
91747 TTTTACTAGTAGCTTTTATATTTT
1 TTTTACTAGTAGCTTTTATATTTT
91771 TAAAAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.16, C:0.10, G:0.08, T:0.66
Consensus pattern (26 bp):
TTTTACTAGTAGCTTTTATATTTTCT
Found at i:96080 original size:20 final size:20
Alignment explanation
Indices: 96057--96107 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
96047 ATTATTTGAT
96057 TAATTAATTAAATCTA-AATA
1 TAATTAATTAAAT-TATAATA
96077 TAATTAATTAAATTATAATA
1 TAATTAATTAAATTATAATA
96097 -AATTAATTAAA
1 TAATTAATTAAA
96108 ATTAACATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATTAATTAAATTATAATA
Found at i:96095 original size:15 final size:15
Alignment explanation
Indices: 96061--96112 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
96051 TTTGATTAAT
96061 TAATTAAATCTAAA-TA
1 TAATT-AAT-TAAATTA
96077 TAATTAATTAAATTA
1 TAATTAATTAAATTA
*
96092 TAATAAATT-AATTA
1 TAATTAATTAAATTA
*
96106 AAATTAA
1 TAATTAA
96113 CATGTAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 14 0.44
15 13 0.41
16 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTAATTAAATTA
Found at i:96616 original size:19 final size:19
Alignment explanation
Indices: 96592--96630 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
96582 ATAAGGGCCA
96592 AAATTAATAAATAATAATT
1 AAATTAATAAATAATAATT
96611 AAATTAATAAATAATAATT
1 AAATTAATAAATAATAATT
96630 A
1 A
96631 TTTTGGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTAATAAATAATAATT
Found at i:97904 original size:17 final size:17
Alignment explanation
Indices: 97882--97918 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
97872 GTTATCCAGC
97882 ACCTCATGCTACCTAGT
1 ACCTCATGCTACCTAGT
*
97899 ACCTCATGCTACCTGGT
1 ACCTCATGCTACCTAGT
97916 ACC
1 ACC
97919 ATGAGGGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.38, G:0.14, T:0.27
Consensus pattern (17 bp):
ACCTCATGCTACCTAGT
Found at i:99242 original size:134 final size:135
Alignment explanation
Indices: 99001--99267 Score: 367
Period size: 134 Copynumber: 2.0 Consensus size: 135
98991 AGAGAAAACA
**
99001 TCATGGCTCGGATTGGTCTCATCGATGAAAGACTTGGGGGGCAAGGACTCGGGGGGCAAAACCAA
1 TCATGGCTCGGATTGGTCTCATCGAAAAAAGACTTGGGGGGCAAGGACTCGGGGGGCAAAACCAA
* * * * * * * *
99066 CAACTGCTTGGTGCCCAACCTGGTCCTCTTCCCCTTCGACAAGTCAACCATCAGGTGAACAATCA
66 AAACTGCTTGGAGCCCAACCTGGCCCTCTTCCCCTTCAACAAGTCAACAATAAGATGAACAACCA
99131 ACAGG
131 ACAGG
* * * *
99136 TCATGGCTCAGG-TTGGTCTGATCGAAAAAAGACTTGTGGGG-AGGGGCTCGGGGGGCAAAACCA
1 TCATGGCTC-GGATTGGTCTCATCGAAAAAAGACTTGGGGGGCAAGGACTCGGGGGGCAAAACCA
* *
99199 AAAATTGCTTGGAGCCCAGCCTGGCCCTCTTCCCCTTCAACAAGTCAACAATAAGATGAACAACC
65 AAAACTGCTTGGAGCCCAACCTGGCCCTCTTCCCCTTCAACAAGTCAACAATAAGATGAACAACC
99264 AACA
130 AACA
99268 AGTTTCACCT
Statistics
Matches: 115, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
134 79 0.69
135 34 0.30
136 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19
Consensus pattern (135 bp):
TCATGGCTCGGATTGGTCTCATCGAAAAAAGACTTGGGGGGCAAGGACTCGGGGGGCAAAACCAA
AAACTGCTTGGAGCCCAACCTGGCCCTCTTCCCCTTCAACAAGTCAACAATAAGATGAACAACCA
ACAGG
Found at i:99439 original size:6 final size:6
Alignment explanation
Indices: 99428--99456 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
99418 TCGCATGAGG
99428 AATGGC AATGGC AATGGC AATGGC AATGG
1 AATGGC AATGGC AATGGC AATGGC AATGG
99457 TCATGGTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.17
Consensus pattern (6 bp):
AATGGC
Found at i:106575 original size:23 final size:22
Alignment explanation
Indices: 106549--106591 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
106539 AAAAAAACAA
*
106549 GCTCCGTGCTTATTTTCTCTTAG
1 GCTCCGTGCCT-TTTTCTCTTAG
*
106572 GCTCTGTGCCTTTTTCTCTT
1 GCTCCGTGCCTTTTTCTCTT
106592 GTTCATCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.05, C:0.28, G:0.16, T:0.51
Consensus pattern (22 bp):
GCTCCGTGCCTTTTTCTCTTAG
Found at i:120013 original size:31 final size:31
Alignment explanation
Indices: 119978--120040 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
119968 ATGTTTTTTG
*
119978 ATTGTACCCTTATTTTT-AAAATATATTTCTA
1 ATTGTACCCTT-TTTTTCAAAACATATTTCTA
**
120009 ATTGTATTCTTTTTTTCAAAACATATTTCTA
1 ATTGTACCCTTTTTTTCAAAACATATTTCTA
120040 A
1 A
120041 ATTGCCATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTGTACCCTTTTTTTCAAAACATATTTCTA
Found at i:120338 original size:21 final size:21
Alignment explanation
Indices: 120251--120346 Score: 70
Period size: 21 Copynumber: 4.4 Consensus size: 21
120241 TAAGAAGTAC
*
120251 CAAAATTTAATAGAAGGTTAT
1 CAAAATTTAATAGAAGATTAT
* *
120272 C-AAATCTCATAGAATGATTAT
1 CAAAATTTAATAGAA-GATTAT
* * *
120293 CGAAATTTCATAGAGATCAGGTTAT
1 CAAAATTT-A-ATAGA--AGATTAT
120318 CAAAATTT-ATAGGAAGATTAT
1 CAAAATTTAATA-GAAGATTAT
120339 CAAAATTT
1 CAAAATTT
120347 CATAATGTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
20 11 0.19
21 21 0.36
22 7 0.12
23 2 0.03
24 4 0.07
25 12 0.21
26 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (21 bp):
CAAAATTTAATAGAAGATTAT
Found at i:120404 original size:22 final size:22
Alignment explanation
Indices: 120333--120511 Score: 89
Period size: 22 Copynumber: 8.0 Consensus size: 22
120323 TTTATAGGAA
120333 GATTATCAAAATTTCATAATGTT
1 GATTATCAAAATTTCATAATG-T
* * *
120356 G-TTATCAAAATCT-A-AACGC
1 GATTATCAAAATTTCATAATGT
*
120375 GAGGTTATCAAAATTACATAATGT
1 GA--TTATCAAAATTTCATAATGT
* *
120399 GATTATCAGAATTTCATAGA-GG
1 GATTATCAAAATTTCATA-ATGT
* * * * *
120421 GGTCAACGTACAAAATTTTATAAAGA
1 GAT-TA--T-CAAAATTTCATAATGT
* * * *
120447 GGTTATCAAAATTTTATAAAGA
1 GATTATCAAAATTTCATAATGT
* *
120469 GATTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAATGT
120491 GATTA-CAAAAATTTCATAATG
1 GATTATC-AAAATTTCATAATG
120512 GTATTTCTGG
Statistics
Matches: 120, Mismatches: 24, Indels: 25
0.71 0.14 0.15
Matches are distributed among these distances:
19 1 0.01
20 3 0.03
21 2 0.02
22 87 0.73
23 5 0.04
24 5 0.04
25 3 0.03
26 14 0.12
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (22 bp):
GATTATCAAAATTTCATAATGT
Found at i:120756 original size:22 final size:22
Alignment explanation
Indices: 120731--120772 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
120721 TAAAATTTGT
*
120731 AGTTATCAAGATTTCATAAAAA
1 AGTTATCAAAATTTCATAAAAA
*
120753 AGTTATCAAAATTTTATAAA
1 AGTTATCAAAATTTCATAAA
120773 GAGGTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (22 bp):
AGTTATCAAAATTTCATAAAAA
Found at i:120805 original size:25 final size:25
Alignment explanation
Indices: 120756--120819 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
120746 ATAAAAAAGT
120756 TATCAAAATTTTATA-AAGAGGTTTA
1 TATCAAAATTTTATAGAAGA-GTTTA
120781 TATCAAAATTTTATAGGAAGA-TTTA
1 TATCAAAATTTTATA-GAAGAGTTTA
*
120806 T-T-AAAATTTCATAG
1 TATCAAAATTTTATAG
120820 CGAGGTTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 1 0.03
23 10 0.28
24 1 0.03
25 20 0.56
27 4 0.11
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (25 bp):
TATCAAAATTTTATAGAAGAGTTTA
Found at i:120835 original size:22 final size:22
Alignment explanation
Indices: 120810--120918 Score: 76
Period size: 22 Copynumber: 5.0 Consensus size: 22
120800 GATTTATTAA
*
120810 AATTTCATAGCGAGGTTATCAT
1 AATTTCATAGCGTGGTTATCAT
* * *
120832 AATTTCATAGTGTGATTATCAA
1 AATTTCATAGCGTGGTTATCAT
* * * *
120854 AATTTCAGAGTGTGGTTACTAAC
1 AATTTCATAGCGTGGTTA-TCAT
* * * *
120877 AA-TTCATAGGGAGGTTTTTAT
1 AATTTCATAGCGTGGTTATCAT
* *
120898 ATTTTCATAACGTGGTTATCA
1 AATTTCATAGCGTGGTTATCA
120919 ATATATAATA
Statistics
Matches: 65, Mismatches: 20, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
21 3 0.05
22 58 0.89
23 4 0.06
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
AATTTCATAGCGTGGTTATCAT
Found at i:121000 original size:22 final size:22
Alignment explanation
Indices: 120960--121016 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
120950 GTGTTGGTTA
**
120960 TCAAAATTTCATATTGAGGTGT
1 TCAAAATTTCATAGGGAGGTGT
*
120982 TCAAAATTTCTTAGGGAGGT-T
1 TCAAAATTTCATAGGGAGGTGT
*
121003 AACAAAATTTCATA
1 -TCAAAATTTCATA
121017 AGAAGGTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATAGGGAGGTGT
Found at i:121023 original size:22 final size:22
Alignment explanation
Indices: 120983--121039 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
120973 TTGAGGTGTT
* * *
120983 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAAGAAGGTTAA
121005 CAAAATTTCATAAGAAGGTTAA
1 CAAAATTTCATAAGAAGGTTAA
* *
121027 AAAAATTTTATAA
1 CAAAATTTCATAA
121040 AAAAGTTCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAAGAAGGTTAA
Found at i:121703 original size:19 final size:20
Alignment explanation
Indices: 121662--121703 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
121652 CCCTAACATG
* *
121662 TAATTATTTTATTTGATATA
1 TAATTAATTTATTTGATAGA
*
121682 TAATTAATTT-TTTGTTAGA
1 TAATTAATTTATTTGATAGA
121701 TAA
1 TAA
121704 ATGTAACCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
TAATTAATTTATTTGATAGA
Done.