Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2478
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: 72442
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1140 original size:40 final size:37
Alignment explanation
Indices: 1002--1142 Score: 129
Period size: 35 Copynumber: 3.9 Consensus size: 37
992 TAGTAACCCA
1002 TTGTATCGATTACAATG-T-ATCGATACAAAG--AATG
1 TTGTATCGA-TACAATGTTGATCGATACAAAGAAAATG
* * * *
1036 TTGGATCG-TACACT-TTGTATCGATACAACG-AATTG
1 TTGTATCGATACAATGTTG-ATCGATACAAAGAAAATG
1071 TTGTATCGATACAATGTTG-TCGATACAAAGAAAATG
1 TTGTATCGATACAATGTTGATCGATACAAAGAAAATG
1107 TTTGTCATCGATACAAT-TATCGATCGATACAAAGAA
1 -TTGT-ATCGATACAATGT-T-GATCGATACAAAGAA
1143 TTTTGTATCG
Statistics
Matches: 87, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
32 6 0.07
34 18 0.21
35 20 0.23
36 9 0.10
37 8 0.09
38 12 0.14
39 1 0.01
40 13 0.15
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (37 bp):
TTGTATCGATACAATGTTGATCGATACAAAGAAAATG
Found at i:5023 original size:21 final size:20
Alignment explanation
Indices: 4985--5027 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
4975 GAATCATGCA
4985 AATTCTTGTTTTTCTTAGCT
1 AATTCTTGTTTTTCTTAGCT
5005 AATTCATT-TTTTTCATTAGCT
1 AATTC-TTGTTTTTC-TTAGCT
5026 AA
1 AA
5028 CTTTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (20 bp):
AATTCTTGTTTTTCTTAGCT
Found at i:5959 original size:20 final size:20
Alignment explanation
Indices: 5936--6009 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
5926 ACAATTCAAA
5936 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
5956 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
5977 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
5997 GTATCGATACATG
1 GTATCGATACATG
6010 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:5980 original size:21 final size:21
Alignment explanation
Indices: 5954--6029 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
5944 ACATGTTGCA
5954 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
5975 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
5995 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
6016 ATGTATCGATACAT
1 ATGTATCGATACAT
6030 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:5987 original size:41 final size:41
Alignment explanation
Indices: 5936--6029 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
5926 ACAATTCAAA
5936 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
5977 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
6018 GTATCGATACAT
1 GTATCGATACAT
6030 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:6086 original size:13 final size:13
Alignment explanation
Indices: 6068--6093 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6058 TACAGCAAGT
6068 ATGTATCGATACA
1 ATGTATCGATACA
6081 ATGTATCGATACA
1 ATGTATCGATACA
6094 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:8333 original size:21 final size:21
Alignment explanation
Indices: 8300--8344 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
8290 TTGCAAGTTG
*
8300 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
8322 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
8342 AAA
1 AAA
8345 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:10168 original size:15 final size:15
Alignment explanation
Indices: 10148--10178 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10138 TAAAAATGTC
*
10148 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
10163 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
10178 C
1 C
10179 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:12263 original size:20 final size:21
Alignment explanation
Indices: 12194--12271 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
12184 AATGTCCAAA
*
12194 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
12214 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
12239 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
12259 TTGTATCGATACA
1 ATGTATCGATACA
12272 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 30 0.64
24 3 0.06
25 14 0.30
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:12278 original size:13 final size:13
Alignment explanation
Indices: 12260--12297 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
12250 CATTTTTCTT
12260 TGTATCGATACAA
1 TGTATCGATACAA
*
12273 TGTATCGATACAC
1 TGTATCGATACAA
12286 TGTATCGATACA
1 TGTATCGATACA
12298 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:14778 original size:20 final size:20
Alignment explanation
Indices: 14755--14828 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
14745 ACAATTCAAA
14755 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
14775 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
14796 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
14816 GTATCGATACATG
1 GTATCGATACATG
14829 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:14799 original size:21 final size:21
Alignment explanation
Indices: 14773--14848 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
14763 ACATGTTGCA
14773 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
14794 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
14814 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
14835 ATGTATCGATACAT
1 ATGTATCGATACAT
14849 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:14806 original size:41 final size:41
Alignment explanation
Indices: 14755--14848 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
14745 ACAATTCAAA
14755 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
14796 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
14837 GTATCGATACAT
1 GTATCGATACAT
14849 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:14905 original size:13 final size:13
Alignment explanation
Indices: 14887--14912 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14877 TACAGCAAGT
14887 ATGTATCGATACA
1 ATGTATCGATACA
14900 ATGTATCGATACA
1 ATGTATCGATACA
14913 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:17300 original size:33 final size:33
Alignment explanation
Indices: 17261--17324 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
17251 CGTTACAAGT
* *
17261 AATGTATCGATACAAT-TCATCATGTATCGATAC
1 AATGTATCAATACAATGT-ACCATGTATCGATAC
*
17294 AATGTATCAATGCAATGTACCATGTATCGAT
1 AATGTATCAATACAATGTACCATGTATCGAT
17325 GCAAACAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (33 bp):
AATGTATCAATACAATGTACCATGTATCGATAC
Found at i:17382 original size:20 final size:20
Alignment explanation
Indices: 17357--17411 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
17347 CTGTTAGTTT
**
17357 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
17377 CATGTATCAATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
17396 CATGTATAGATACAAT
1 CATGTATCGATACAAT
17412 GTATCGATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:23614 original size:16 final size:16
Alignment explanation
Indices: 23593--23623 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
23583 ACCTATGCTC
23593 TTGATGCTACAAATAA
1 TTGATGCTACAAATAA
23609 TTGATGCTACAAATA
1 TTGATGCTACAAATA
23624 CAATGAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (16 bp):
TTGATGCTACAAATAA
Found at i:25250 original size:23 final size:23
Alignment explanation
Indices: 25213--25261 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
25203 GTGACTCAAT
*
25213 TTTAAGATAATTTTAATTTTATA
1 TTTAAGATAAATTTAATTTTATA
* *
25236 TTTAAGTTAAATTTAATTTTGTA
1 TTTAAGATAAATTTAATTTTATA
25259 TTT
1 TTT
25262 TTAGTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (23 bp):
TTTAAGATAAATTTAATTTTATA
Found at i:25427 original size:7 final size:7
Alignment explanation
Indices: 25415--25442 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
25405 GTGCATTGCG
25415 ATTATTA
1 ATTATTA
25422 ATTATTA
1 ATTATTA
25429 ATTATTA
1 ATTATTA
25436 ATTATTA
1 ATTATTA
25443 TTGGCTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTATTA
Found at i:25575 original size:16 final size:16
Alignment explanation
Indices: 25556--25592 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
25546 TTTTTAATTT
*
25556 TTTTTCTTTTTTTTTC
1 TTTTTCTTTTTTTTTA
25572 TTTTTCTTTTTTTTTA
1 TTTTTCTTTTTTTTTA
25588 TTTTT
1 TTTTT
25593 TTATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTA
Found at i:27136 original size:402 final size:393
Alignment explanation
Indices: 26363--27163 Score: 1062
Period size: 402 Copynumber: 2.0 Consensus size: 393
26353 GAAATTAGGT
* *
26363 TATTAATGAAATATCAAATATTTGTTTTTTTTCTAAATGTATTAAATTTGAAAATCATTTAACTA
1 TATTAATGAAATATCAAATATTTGATTATTTTCTAAATGTATTAAATTTGAAAATCATTTAACTA
*
26428 AAATATAGGAATTAAATGCACATGTTTAATATTAAGTAATGTTAATTAAAGTAAATTAATAAAAA
66 AAATATAGGAATTAAATGCACATGTTTAATATAAAGTAATGTTAATTAAAGTAAATTAATAAAAA
** ** * *
26493 TAAATATACTATTTAATTAAATTTCAAGTATCAAATATTTAATTATTCTCTTAATGAATTCAATT
131 TAAATATACTATTTAATTAAATGACAAAAATCAAATATTTAATTACTCTCTTAATAAATTCAATT
* * *
26558 TGAAATATCAAGGGGTTAAAACGTAAGAATTTAATGCATATGTTTAATATTATTAATGTATATTA
196 TGAAATATCAAGAGGCTAAAACGTAAGAATTTAATGCATACG-TTAATA-TATTAATGTATATTA
* * *
26623 AGCTAAATCAATTGAAAATAATTATATTATTTAATTAAATACCAAATATGAGTTTATTACATGTA
259 AGCTAAATCAATTGAAAATAATTATATTATATAATTAAATACCAAAAATAAGTTTATTACATGTA
*
26688 AGCACATACGTTATCTTTTCAAATTTTGTCAAAATTTTTA-TTTTTTTAATTA-TGATTTATGTA
324 AGCACAAACGTTATCTTTTCAAATTTTGTCAAAATTTTTATTTTTTTTAATTACT-ATTTATGTA
*
26751 ATCAAA
388 ATAAAA
26757 TATTAATGAAATATCAAATATTTGATTATTTTCTAAAACTGATAAATTTGAAATTTGAAATATCA
1 TATTAATGAAATATCAAATATTTGATTATTTTCT-AAA-TG-T--A-TT-AAATTTGAAA-ATCA
* * *
26822 TTTAACTAAAATATAGGAATTAAATGCACGTGTTTAATATAAAGTAATGTTAATTCATGTAAATT
58 TTTAACTAAAATATAGGAATTAAATGCACATGTTTAATATAAAGTAATGTTAATTAAAGTAAATT
* *
26887 AATAAAAATAATTATGCTA-TTAATTAAATGACAAAAATCAAATATTTAATTACTCT-TTAAATA
123 AATAAAAATAAATATACTATTTAATTAAATGACAAAAATCAAATATTTAATTACTCTCTT-AATA
* *
26950 AATTCAATTTGAAATATCAA-ATGCTAAAACGTAAGAATTTAATGCATACG-T-CTA-ATTAATG
187 AATTCAATTTGAAATATCAAGAGGCTAAAACGTAAGAATTTAATGCATACGTTAATATATTAATG
* * * **
27011 TGTATTAAGGTAAATTAA-TGAAAATAATTATATTATATAATTAAAAATATTAAAAATAAGTTTA
252 TATATTAAGCTAAATCAATTGAAAATAATTATATTATATAATT--AAATACCAAAAATAAGTTTA
* * * *
27075 TTATATGTGATCACAAACGTTATGTTTTCAAATTTTGTCAAAATTTTTATTCTCTTTTTTTTTAA
315 TTACATGTAAGCACAAACGTTATCTTTTCAAATTTTGTCAAAATTTTTA------TTTTTTTTAA
27140 TTACTATTTATGTAATAAAA
374 TTACTATTTATGTAATAAAA
27160 TATT
1 TATT
27164 TTAACTTTTA
Statistics
Matches: 355, Mismatches: 33, Indels: 29
0.85 0.08 0.07
Matches are distributed among these distances:
394 55 0.15
395 25 0.07
396 62 0.17
397 3 0.01
398 1 0.00
399 1 0.00
400 30 0.08
401 65 0.18
402 82 0.23
403 30 0.08
404 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (393 bp):
TATTAATGAAATATCAAATATTTGATTATTTTCTAAATGTATTAAATTTGAAAATCATTTAACTA
AAATATAGGAATTAAATGCACATGTTTAATATAAAGTAATGTTAATTAAAGTAAATTAATAAAAA
TAAATATACTATTTAATTAAATGACAAAAATCAAATATTTAATTACTCTCTTAATAAATTCAATT
TGAAATATCAAGAGGCTAAAACGTAAGAATTTAATGCATACGTTAATATATTAATGTATATTAAG
CTAAATCAATTGAAAATAATTATATTATATAATTAAATACCAAAAATAAGTTTATTACATGTAAG
CACAAACGTTATCTTTTCAAATTTTGTCAAAATTTTTATTTTTTTTAATTACTATTTATGTAATA
AAA
Found at i:28253 original size:1 final size:1
Alignment explanation
Indices: 28220--28244 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
28210 GATTCACCTG
28220 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
28245 GAGGAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30333 original size:20 final size:20
Alignment explanation
Indices: 30308--30428 Score: 80
Period size: 20 Copynumber: 5.5 Consensus size: 20
30298 TTTCACCTAG
30308 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
*
30328 ATGTATCAATACATTCTGTCTTTTACCCA
1 ATGTATCGATACA-----T-TTTT---CA
* *
30357 GATGTATCGACACATTCTTCA
1 -ATGTATCGATACATTTTTCA
* * *
30378 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
30398 ATGTTTCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
30418 ATGTATCGATA
1 ATGTATCGATA
30429 TATTCTGTCT
Statistics
Matches: 76, Mismatches: 15, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
20 52 0.68
21 2 0.03
24 3 0.04
25 2 0.03
26 4 0.05
29 2 0.03
30 11 0.14
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:30433 original size:20 final size:20
Alignment explanation
Indices: 30358--30434 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
30348 TTTTACCCAG
*
30358 ATGTATCGACACATTCTTCA
1 ATGTATCGATACATTCTTCA
* *
30378 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
30398 ATGTTTCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
30418 ATGTATCGATATATTCT
1 ATGTATCGATACATTCT
30435 GTCTTTTTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:30479 original size:91 final size:90
Alignment explanation
Indices: 30308--30485 Score: 275
Period size: 91 Copynumber: 2.0 Consensus size: 90
30298 TTTCACCTAG
* *
30308 ATGTATCGATACATTTTTCAATGTATCAATACATTCTGTCTTTTACCCAGATGTATCGACACATT
1 ATGTATCGATACATTCTTCAATGTATCAATACATTCTGTCTTTTACCCAGATCTATCGACACATT
30373 CTTCAATGTATCGATACATGTATGA
66 CTTCAATGTATCGATACATGTATGA
* * * * *
30398 ATGTTTCGATACATTCTTCAATGTATCGATATATTCTGTCTTTTTACCCAGATCTATCGATATAT
1 ATGTATCGATACATTCTTCAATGTATCAATACATTCTGTC-TTTTACCCAGATCTATCGACACAT
*
30463 TTTTCAATGTATCGATACATGTA
65 TCTTCAATGTATCGATACATGTA
30486 GTTAAAATTA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 36 0.46
91 43 0.54
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.42
Consensus pattern (90 bp):
ATGTATCGATACATTCTTCAATGTATCAATACATTCTGTCTTTTACCCAGATCTATCGACACATT
CTTCAATGTATCGATACATGTATGA
Found at i:36509 original size:18 final size:18
Alignment explanation
Indices: 36450--36502 Score: 79
Period size: 20 Copynumber: 2.8 Consensus size: 18
36440 TTTTATTATC
36450 TAATTATTATGACAATTA
1 TAATTATTATGACAATTA
*
36468 TAACATTATAATGACAATTA
1 T-A-ATTATTATGACAATTA
36488 TAATTATTATGACAA
1 TAATTATTATGACAA
36503 ATTTAATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 13 0.42
19 2 0.06
20 16 0.52
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (18 bp):
TAATTATTATGACAATTA
Found at i:37066 original size:18 final size:18
Alignment explanation
Indices: 37040--37074 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37030 TGGAATGAAA
*
37040 ATTTGGATTTTTATTTTT
1 ATTTGGATTTTGATTTTT
*
37058 ATTTTGATTTTGATTTT
1 ATTTGGATTTTGATTTT
37075 GTGATAGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.71
Consensus pattern (18 bp):
ATTTGGATTTTGATTTTT
Found at i:40597 original size:26 final size:25
Alignment explanation
Indices: 40560--40612 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
40550 ATTTTTCTGA
*
40560 TTTTTAAAATTTT-TCATTTTTTATT
1 TTTTTAAAATTTTAT-ATTTTATATT
*
40585 TTTTTAATTATTTTATATTTTATATT
1 TTTTTAA-AATTTTATATTTTATATT
40611 TT
1 TT
40613 ATGATAGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 16 0.67
27 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTTAAAATTTTATATTTTATATT
Found at i:44581 original size:24 final size:24
Alignment explanation
Indices: 44546--44631 Score: 79
Period size: 24 Copynumber: 3.6 Consensus size: 24
44536 CAAATAAATA
44546 TAATATATATTAAAAATATTATTT
1 TAATATATATTAAAAATATTATTT
44570 TAATCATA-ATTAAAAATATTATATT
1 TAAT-ATATATTAAAAATATTAT-TT
* **
44595 ATAATTTATA-T-ATTATATTATTT
1 -TAATATATATTAAAAATATTATTT
* *
44618 TTATATTTATTAAA
1 TAATATATATTAAA
44632 TGTGTTTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
22 6 0.12
23 3 0.06
24 27 0.55
25 8 0.16
26 5 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATATATATTAAAAATATTATTT
Found at i:44609 original size:19 final size:18
Alignment explanation
Indices: 44585--44627 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
44575 ATAATTAAAA
44585 ATATTATATTATAATTTAT
1 ATATTATATTAT-ATTTAT
*
44604 ATATTATATTATTTTTAT
1 ATATTATATTATATTTAT
44622 AT-TTAT
1 ATATTAT
44628 TAAATGTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.17
18 7 0.30
19 12 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTATATTATATTTAT
Found at i:45036 original size:13 final size:13
Alignment explanation
Indices: 45018--45042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45008 TATTAAAATT
45018 TATTAAAAATAAC
1 TATTAAAAATAAC
45031 TATTAAAAATAA
1 TATTAAAAATAA
45043 TTTAATCATT
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
TATTAAAAATAAC
Found at i:45143 original size:70 final size:70
Alignment explanation
Indices: 45069--45280 Score: 397
Period size: 70 Copynumber: 3.0 Consensus size: 70
45059 TAATCATATC
45069 TTTCTAATGTTTTAAAAAAAATCATGCCTATAAAAATATTTTACTTTTCCACAGCATGTTTTAAC
1 TTTCTAATGTTTTAAAAAAAATCATGCCTATAAAAATATTTTACTTTTCCACAGCATGTTTTAAC
45134 AAGTA
66 AAGTA
45139 TTTCTAATGTTTTAAAAAAAATCATGCCTATAAAAATATTTTACTTTTCCACAGCATGTTTTAAC
1 TTTCTAATGTTTTAAAAAAAATCATGCCTATAAAAATATTTTACTTTTCCACAGCATGTTTTAAC
45204 AAGTA
66 AAGTA
* * *
45209 TTTCTAATGTTTTTAAAAAAATCATGTCTATAAAAATATTTTACTTTCCCACAGCATGTTTTAAC
1 TTTCTAATGTTTTAAAAAAAATCATGCCTATAAAAATATTTTACTTTTCCACAGCATGTTTTAAC
45274 AAGTA
66 AAGTA
45279 TT
1 TT
45281 CAAGAATATC
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 139 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (70 bp):
TTTCTAATGTTTTAAAAAAAATCATGCCTATAAAAATATTTTACTTTTCCACAGCATGTTTTAAC
AAGTA
Found at i:45433 original size:12 final size:12
Alignment explanation
Indices: 45409--45446 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
45399 TGTTATTTTA
45409 AAAATACATAAAT
1 AAAATA-ATAAAT
45422 AAATATAA-AAAT
1 AAA-ATAATAAAT
45434 AAAATAATAAAT
1 AAAATAATAAAT
45446 A
1 A
45447 TAAAATGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.17
12 12 0.52
13 4 0.17
14 3 0.13
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:48864 original size:13 final size:13
Alignment explanation
Indices: 48848--48872 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48838 CCCCCCCCCC
48848 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
48861 CAAAAAAAAAAA
1 CAAAAAAAAAAA
48873 CCACCTTCCT
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:49735 original size:49 final size:49
Alignment explanation
Indices: 49676--49772 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
49666 AAAGGCTAAG
*
49676 TTTTGTGTGTTCAAGCTGATTGGGGATTAGGAAAAGATCACTTGAATTA
1 TTTTCTGTGTTCAAGCTGATTGGGGATTAGGAAAAGATCACTTGAATTA
*
49725 TTTTCTGTGTTTAAGCTGATTGGGGATTAGGAAAAGATCACTTGAATT
1 TTTTCTGTGTTCAAGCTGATTGGGGATTAGGAAAAGATCACTTGAATT
49773 GTTTAGGAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (49 bp):
TTTTCTGTGTTCAAGCTGATTGGGGATTAGGAAAAGATCACTTGAATTA
Found at i:51289 original size:35 final size:35
Alignment explanation
Indices: 51250--51357 Score: 103
Period size: 35 Copynumber: 3.1 Consensus size: 35
51240 GTTTAAACTC
51250 ATTCTACTCATAATACTACTAATTATTTTATGAGA
1 ATTCTACTCATAATACTACTAATTATTTTATGAGA
* * * * * * * **
51285 ATTCT-TTCATAGTGTCTAATAATAAGTTTA-AACTC
1 ATTCTACTCATAAT-ACTACTAATTATTTTATGA-GA
51320 ATTCTACTCATAATACTACTAATTATTTTATGAGA
1 ATTCTACTCATAATACTACTAATTATTTTATGAGA
51355 ATT
1 ATT
51358 TTTTGTTACA
Statistics
Matches: 51, Mismatches: 18, Indels: 8
0.66 0.23 0.10
Matches are distributed among these distances:
34 7 0.14
35 37 0.73
36 7 0.14
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (35 bp):
ATTCTACTCATAATACTACTAATTATTTTATGAGA
Found at i:51297 original size:70 final size:70
Alignment explanation
Indices: 51216--51357 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
51206 AATGTTGGGT
51216 TTCTTTCATAGTGTCTAATAATAAGTTTAAACTCATTCTACTCATAATACTACTAATTATTTTAT
1 TTCTTTCATAGTGTCTAATAATAAGTTTAAACTCATTCTACTCATAATACTACTAATTATTTTAT
51281 GAGAA
66 GAGAA
51286 TTCTTTCATAGTGTCTAATAATAAGTTTAAACTCATTCTACTCATAATACTACTAATTATTTTAT
1 TTCTTTCATAGTGTCTAATAATAAGTTTAAACTCATTCTACTCATAATACTACTAATTATTTTAT
51351 GAGAA
66 GAGAA
51356 TT
1 TT
51358 TTTTGTTACA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (70 bp):
TTCTTTCATAGTGTCTAATAATAAGTTTAAACTCATTCTACTCATAATACTACTAATTATTTTAT
GAGAA
Found at i:52977 original size:78 final size:77
Alignment explanation
Indices: 52895--53147 Score: 244
Period size: 78 Copynumber: 3.3 Consensus size: 77
52885 TTATTAGTGT
* * *
52895 CATTTAAGTAATATTACATTAATACTGAGTCTTTAGGTTCATGTGAGAACTTTCATGTTCATGCA
1 CATTTAGGTAATATTACATTAATACTGAGTCTTTAGGCTCATGTGAGAACTTTCATGTTCATACA
* *
52960 TGTCCATTATAAG
66 TGTCTATTA-AGG
* * ** *
52973 CATTTAGGTAATATTATATGAA-ACCAAGTCTTAAGGCT-ATGT-AGGAACTTTCATG-TCAATA
1 CATTTAGGTAATATTACATTAATACTGAGTCTTTAGGCTCATGTGA-GAACTTTCATGTTC-ATA
*
53034 CATATCTATTAAGG
64 CATGTCTATTAAGG
* * * * * * * * *
53048 TTATTTAGGTAATATTGCATTAATAATGAGTCCTTAGGGTCATGTGGGAACTTTTATATTAATAC
1 -CATTTAGGTAATATTACATTAATACTGAGTCTTTAGGCTCATGTGAGAACTTTCATGTTCATAC
53113 ATGTCTATTAAGG
65 ATGTCTATTAAGG
* *
53126 TATTTAGGTGATATTACATTAA
1 CATTTAGGTAATATTACATTAA
53148 AATCGAGTCT
Statistics
Matches: 140, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
75 5 0.04
76 44 0.31
77 42 0.30
78 48 0.34
79 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (77 bp):
CATTTAGGTAATATTACATTAATACTGAGTCTTTAGGCTCATGTGAGAACTTTCATGTTCATACA
TGTCTATTAAGG
Found at i:53192 original size:77 final size:78
Alignment explanation
Indices: 52879--53209 Score: 238
Period size: 78 Copynumber: 4.3 Consensus size: 78
52869 TCATATTGAA
* * * * *
52879 ACATGTTTATT-AGTGTCATTTAAGTAATATTACATTAATACTGAGT-CTTTAGGTTCATGTGAG
1 ACATGTCTATTAAG-GT-ATTTAGGTAATATTACATTAATAATGAGTCCTTAAGG-TCATGTGGG
52942 AAC-TTTCATGTTC-AT
63 AACTTTTCATG-TCAAT
* * * * * * *** *
52957 GCATGTCCATTATAAGCATTTAGGTAATATTATATGAA-ACCAAGT-CTTAAGG-CTATGTAGGA
1 ACATGTCTATTA-AGGTATTTAGGTAATATTACATTAATAATGAGTCCTTAAGGTC-ATGTGGGA
53019 AC-TTTCATGTCAAT
64 ACTTTTCATGTCAAT
* * *
53033 ACATATCTATTAAGGTTATTTAGGTAATATTGCATTAATAATGAGTCCTTAGGGTCATGTGGGAA
1 ACATGTCTATTAAGG-TATTTAGGTAATATTACATTAATAATGAGTCCTTAAGGTCATGTGGGAA
* *
53098 CTTTT-ATATTAAT
65 CTTTTCATGTCAAT
* *
53111 ACATGTCTATTAAGGTATTTAGGTGATATTACATTAA-AATCGAGT-CTATAAGGTCAT-TTGGA
1 ACATGTCTATTAAGGTATTTAGGTAATATTACATTAATAAT-GAGTCCT-TAAGGTCATGTGGGA
* *
53173 TA-TTTTCATGTCGAC
64 -ACTTTTCATGTCAAT
* *
53188 ACATGTCTTTTAGAGTTATTTA
1 ACATGTCTATTA-AGGTATTTA
53210 CATAACATCA
Statistics
Matches: 200, Mismatches: 39, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
75 5 0.03
76 57 0.28
77 63 0.31
78 69 0.34
79 5 0.03
80 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (78 bp):
ACATGTCTATTAAGGTATTTAGGTAATATTACATTAATAATGAGTCCTTAAGGTCATGTGGGAAC
TTTTCATGTCAAT
Found at i:54834 original size:20 final size:20
Alignment explanation
Indices: 54806--54847 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
54796 TGCATTCTGC
*
54806 TAAGGAAATGTATTGATACA
1 TAAGGAAATGTATCGATACA
*
54826 TAAGTAAATGTATCGATACA
1 TAAGGAAATGTATCGATACA
54846 TA
1 TA
54848 TGTATCGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (20 bp):
TAAGGAAATGTATCGATACA
Found at i:54852 original size:14 final size:14
Alignment explanation
Indices: 54833--54860 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54823 ACATAAGTAA
54833 ATGTATCGATACAT
1 ATGTATCGATACAT
54847 ATGTATCGATACAT
1 ATGTATCGATACAT
54861 GCTTACAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
ATGTATCGATACAT
Found at i:56768 original size:20 final size:20
Alignment explanation
Indices: 56743--56780 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
56733 AAATGGTTGT
*
56743 AATTGTATCGATATATTATG
1 AATTGTATCGATACATTATG
56763 AATTGTATCGATACATTA
1 AATTGTATCGATACATTA
56781 AGTCCAACGG
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:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (20 bp):
AATTGTATCGATACATTATG
Found at i:57978 original size:3 final size:3
Alignment explanation
Indices: 57972--58017 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
57962 CAAGTTGTTG
57972 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
58018 TAATTAACCA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:58430 original size:29 final size:28
Alignment explanation
Indices: 58398--58457 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
58388 GCACTTTAGG
*
58398 TAGAAATTCTTTAGAATAGA-TACTTTTGA
1 TAGAAATTCCTT--AATAGAGTACTTTTGA
*
58427 TAGAGATTCCTTAATAGAGGTACTTTTGA
1 TAGAAATTCCTTAATAGA-GTACTTTTGA
58456 TA
1 TA
58458 AAGGTACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.22
29 21 0.78
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (28 bp):
TAGAAATTCCTTAATAGAGTACTTTTGA
Found at i:58470 original size:14 final size:15
Alignment explanation
Indices: 58444--58473 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
58434 TCCTTAATAG
58444 AGGTACTTTTGATAA
1 AGGTACTTTTGATAA
58459 AGGTAC-TTTGATAA
1 AGGTACTTTTGATAA
58473 A
1 A
58474 AATATTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (15 bp):
AGGTACTTTTGATAA
Found at i:60520 original size:20 final size:20
Alignment explanation
Indices: 60497--60571 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
60487 AAATATCGAG
60497 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
60517 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
60537 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
60557 ATGTATCGATACATT
1 ATGTATCGATACATT
60572 CTGTCTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:63013 original size:19 final size:19
Alignment explanation
Indices: 62989--63055 Score: 125
Period size: 19 Copynumber: 3.5 Consensus size: 19
62979 AAACCGTAAA
62989 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
63008 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
63027 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
63046 TGTATCGATA
1 TGTATCGATA
63056 TAATGTATCG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:63108 original size:21 final size:21
Alignment explanation
Indices: 63082--63123 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
63072 AGCTACTGCC
63082 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
63103 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
63124 GTATCGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:63128 original size:13 final size:13
Alignment explanation
Indices: 63110--63135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63100 ATTAAGGAAA
63110 TGTATCGATACAT
1 TGTATCGATACAT
63123 TGTATCGATACAT
1 TGTATCGATACAT
63136 CGATCTTTGT
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):
TGTATCGATACAT
Found at i:65701 original size:103 final size:101
Alignment explanation
Indices: 65479--65708 Score: 284
Period size: 103 Copynumber: 2.2 Consensus size: 101
65469 GTTTCTCAAT
* *** *
65479 TTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTTGAAACACCAATTTTTCACAATTGGG
1 TTTTCACAATCGGGGATACTCCAACGCCGATTTTATTTCAAAAACACCAATTTTTCACAATCGGG
*
65544 GATACTCTAACCCCAGTTTTATTTTCAAAACACCAA
66 GATACTCCAACCCCAGTTTTATTTTCAAAACACCAA
* *
65580 TTTTCTATAATCGAGGATACTCCAACGCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCG
1 TTTTC-ACAATCGGGGATACTCCAACGCCGATTTTATTT-CAAAAACACCAATTTTTCACAATCG
* ***
65645 GGGATACTCCAACCCC-GATTTTA-TTTCTAAAATATTGA
64 GGGATACTCCAACCCCAG-TTTTATTTTC-AAAACACCAA
*
65683 TTTCTCACAATTGGGGATACTCCAAC
1 TTT-TCACAATCGGGGATACTCCAAC
65709 CCCGTTATTT
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
101 5 0.05
102 35 0.32
103 67 0.61
104 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (101 bp):
TTTTCACAATCGGGGATACTCCAACGCCGATTTTATTTCAAAAACACCAATTTTTCACAATCGGG
GATACTCCAACCCCAGTTTTATTTTCAAAACACCAA
Found at i:65711 original size:51 final size:51
Alignment explanation
Indices: 65475--65712 Score: 284
Period size: 51 Copynumber: 4.6 Consensus size: 51
65465 TTAAGTTTCT
* * *
65475 CAATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTTGAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
* *
65526 CAATTTTTCACAATTGGGGATACTCTAACCCC-AGTTTTATTT-TCAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGA-TTTTATTTCT-AAAACAC
* * * *
65577 CAA-TTTTCTATAATCGAGGATACTCCAACGCCGATTTTATTTCCAAAAACAC
1 CAATTTTTC-ACAATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACAC
* *
65629 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAATAT
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
** * *
65680 TGATTTCTCACAATTGGGGATACTCCAACCCCG
1 CAATTTTTCACAATCGGGGATACTCCAACCCCG
65713 TTATTTCTGA
Statistics
Matches: 160, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
50 7 0.04
51 107 0.67
52 41 0.26
53 5 0.03
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (51 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACAC
Found at i:65779 original size:79 final size:79
Alignment explanation
Indices: 65644--65827 Score: 298
Period size: 79 Copynumber: 2.3 Consensus size: 79
65634 TTTCACAATC
* *
65644 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATTGATTTCTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTCCTAAAATATTGATTTCTCACAATTGGGGATACTCCAAA
**
65709 CCCGTTATTTCTGA
66 CCCGTTATTTCCAA
*
65723 GGGGATACTCCAACCCCGGTTTTATTCCTAAAATATTGATTTCTCACAA-TGAGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTCCTAAAATATTGATTTCTCACAATTG-GGGATACTCCAA
*
65787 ACCTGTTATTTCCAA
65 ACCCGTTATTTCCAA
65802 GGGGATACTCCAACCCCGATTTTATT
1 GGGGATACTCCAACCCCGATTTTATT
65828 TCCAGAACAC
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
78 2 0.02
79 95 0.98
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTCCTAAAATATTGATTTCTCACAATTGGGGATACTCCAAA
CCCGTTATTTCCAA
Found at i:67995 original size:22 final size:21
Alignment explanation
Indices: 67965--68009 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
67955 TGGATGAAGA
**
67965 TTTTTGAATTTTTTTAAAATT
1 TTTTTGAATGGTTTTAAAATT
*
67986 TTTTTAGAATGGTTTTAATATT
1 TTTTT-GAATGGTTTTAAAATT
68008 TT
1 TT
68010 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTTTGAATGGTTTTAAAATT
Found at i:68055 original size:19 final size:19
Alignment explanation
Indices: 68010--68057 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
68000 TTAATATTTT
68010 ATTTTTTAAAGGTTTTTAA
1 ATTTTTTAAAGGTTTTTAA
***
68029 AAAATTTAAAGGTTTTTAA
1 ATTTTTTAAAGGTTTTTAA
*
68048 TTTTTTTAAA
1 ATTTTTTAAA
68058 AATTGTTTGG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
ATTTTTTAAAGGTTTTTAA
Found at i:68492 original size:13 final size:13
Alignment explanation
Indices: 68474--68499 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
68464 TACAGCAAGT
68474 ATGTATCGATACA
1 ATGTATCGATACA
68487 ATGTATCGATACA
1 ATGTATCGATACA
68500 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:70748 original size:21 final size:21
Alignment explanation
Indices: 70715--70759 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
70705 TTGCAAGTTG
*
70715 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
70737 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
70757 AAA
1 AAA
70760 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Done.