Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011639.1 Corchorus capsularis cultivar CVL-1 contig11660, 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: 67578
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:11437 original size:18 final size:18
Alignment explanation
Indices: 11416--11451 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11406 AAAAGAAAGA
11416 AAAAAAAGGAAGGGACGG
1 AAAAAAAGGAAGGGACGG
11434 AAAAAAAGGAAGGGACGG
1 AAAAAAAGGAAGGGACGG
11452 TAGCGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.39, T:0.00
Consensus pattern (18 bp):
AAAAAAAGGAAGGGACGG
Found at i:19750 original size:7 final size:7
Alignment explanation
Indices: 19738--19798 Score: 50
Period size: 7 Copynumber: 7.9 Consensus size: 7
19728 TTCGGGTTAT
19738 TCGGGTC
1 TCGGGTC
19745 TCGGGTC
1 TCGGGTC
*
19752 ATTCGGGTT
1 --TCGGGTC
19761 TCGGGTC
1 TCGGGTC
*
19768 ATTCGAGTC
1 --TCGGGTC
19777 TCGGGTC
1 TCGGGTC
19784 TACCGGGTC
1 T--CGGGTC
19793 TCGGGT
1 TCGGGT
19799 TGGGCGGGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
7 25 0.57
9 19 0.43
ACGTcount: A:0.07, C:0.25, G:0.38, T:0.31
Consensus pattern (7 bp):
TCGGGTC
Found at i:19750 original size:16 final size:16
Alignment explanation
Indices: 19725--19799 Score: 82
Period size: 16 Copynumber: 4.8 Consensus size: 16
19715 CGGGTCATCT
19725 GGGT-TCGGGTTATTC
1 GGGTCTCGGGTTATTC
*
19740 GGGTCTCGGGTCATTC
1 GGGTCTCGGGTTATTC
* *
19756 GGGTTTCGGGTCATTC
1 GGGTCTCGGGTTATTC
* *
19772 GAGTCTCGGGTCTA-CC
1 GGGTCTCGGGT-TATTC
19788 GGGTCTCGGGTT
1 GGGTCTCGGGTT
19800 GGGCGGGTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
15 5 0.10
16 45 0.88
17 1 0.02
ACGTcount: A:0.07, C:0.21, G:0.39, T:0.33
Consensus pattern (16 bp):
GGGTCTCGGGTTATTC
Found at i:19791 original size:32 final size:32
Alignment explanation
Indices: 19714--19798 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
19704 TGTAGTTTTT
* * *
19714 TCGGGTCATCTGGG-TTCGGGTTATTCGGGTC
1 TCGGGTCATCCGGGTTTCGGGTCATTCGAGTC
*
19745 TCGGGTCATTCGGGTTTCGGGTCATTCGAGTC
1 TCGGGTCATCCGGGTTTCGGGTCATTCGAGTC
*
19777 TCGGGTC-TACCGGGTCTCGGGT
1 TCGGGTCAT-CCGGGTTTCGGGT
19799 TGGGCGGGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 13 0.28
32 33 0.72
ACGTcount: A:0.07, C:0.22, G:0.38, T:0.33
Consensus pattern (32 bp):
TCGGGTCATCCGGGTTTCGGGTCATTCGAGTC
Found at i:20269 original size:21 final size:20
Alignment explanation
Indices: 20244--20295 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
20234 TAGCCAATTT
20244 ATAATAGGTAAAATCATAACA
1 ATAATA-GTAAAATCATAACA
*
20265 ATAATTAGTAAAATTATAACA
1 ATAA-TAGTAAAATCATAACA
20286 ATAATA-TAAA
1 ATAATAGTAAA
20296 TTGTATTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 2 0.07
21 21 0.72
22 2 0.07
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (20 bp):
ATAATAGTAAAATCATAACA
Found at i:20425 original size:16 final size:16
Alignment explanation
Indices: 20400--20452 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
20390 GTTAATGTCC
*
20400 CGGGTTATTCGGGTTT
1 CGGGTCATTCGGGTTT
*
20416 CGGGTCATTCGGGTCT
1 CGGGTCATTCGGGTTT
*
20432 CGGGTCA-TCTGGGTTG
1 CGGGTCATTC-GGGTTT
20448 CGGGT
1 CGGGT
20453 TCGTCTGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 2 0.06
16 30 0.94
ACGTcount: A:0.06, C:0.19, G:0.42, T:0.34
Consensus pattern (16 bp):
CGGGTCATTCGGGTTT
Found at i:20553 original size:9 final size:9
Alignment explanation
Indices: 20522--20555 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
20512 GGACGGGTTA
20522 CGGGTTCGGG
1 CGGGTT-GGG
*
20532 CGGATTGGG
1 CGGGTTGGG
20541 CGGGTTGGG
1 CGGGTTGGG
20550 CGGGTT
1 CGGGTT
20556 ATCAGGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.03, C:0.15, G:0.59, T:0.24
Consensus pattern (9 bp):
CGGGTTGGG
Found at i:21807 original size:20 final size:20
Alignment explanation
Indices: 21782--21822 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
21772 CTATCTATCT
21782 ATACTATATATAAAAGTACG
1 ATACTATATATAAAAGTACG
21802 ATACTATATATAAAAGTACG
1 ATACTATATATAAAAGTACG
21822 A
1 A
21823 GTTTTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (20 bp):
ATACTATATATAAAAGTACG
Found at i:23252 original size:38 final size:38
Alignment explanation
Indices: 23201--23277 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
23191 GATCCCCTTT
23201 ACATTTAATGCTAATCTGCTTTACTTGCAAGCAAAGTA
1 ACATTTAATGCTAATCTGCTTTACTTGCAAGCAAAGTA
*
23239 ACATTTAATGCTAATCTGTTTTACTTGCAAGCAAAGTA
1 ACATTTAATGCTAATCTGCTTTACTTGCAAGCAAAGTA
23277 A
1 A
23278 AATCTAACGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (38 bp):
ACATTTAATGCTAATCTGCTTTACTTGCAAGCAAAGTA
Found at i:23339 original size:21 final size:18
Alignment explanation
Indices: 23320--23356 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
23310 CCAGGTAATC
23320 TCCTTGATTCTCTCATTAA
1 TCCTTGATTCTCTC-TTAA
*
23339 TGCTTGATTCTCTCTTAA
1 TCCTTGATTCTCTCTTAA
23357 ACCAAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49
Consensus pattern (18 bp):
TCCTTGATTCTCTCTTAA
Found at i:25832 original size:38 final size:38
Alignment explanation
Indices: 25781--25857 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
25771 CCGTTAGATT
25781 TTACTTTGCTTGCAAGTAAAGCAGATTAGCATTAAATG
1 TTACTTTGCTTGCAAGTAAAGCAGATTAGCATTAAATG
25819 TTACTTTGCTTGCAAGTAAAGCAGATTAGCATTAAATG
1 TTACTTTGCTTGCAAGTAAAGCAGATTAGCATTAAATG
25857 T
1 T
25858 AAAGGGGATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (38 bp):
TTACTTTGCTTGCAAGTAAAGCAGATTAGCATTAAATG
Found at i:26900 original size:30 final size:30
Alignment explanation
Indices: 26774--27250 Score: 578
Period size: 30 Copynumber: 15.6 Consensus size: 30
26764 AGTCTCCAAA
* *
26774 TGACACCAGAAGTTGTCATGATAAATCT-CCAT
1 TGACACCAGAAGTTGTCATGAT---TTTACAAT
* *
26806 TGACACCAGAAGTTGTCAATGGTGTTACAAT
1 TGACACCAGAAGTTGTC-ATGATTTTACAAT
* * * *
26837 TGACACAAGAAGTTGTCAATAATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATTTTACAAT
* *
26868 TGACACCAGAAGTTGTCATGATTTTGCAAA
1 TGACACCAGAAGTTGTCATGATTTTACAAT
*
26898 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* *
26928 TGACACCATAAGTTGTCATGATCTTACAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* * *
26958 TGACACCAGAAGTTGTCAATAATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATTTTACAAT
*
26989 TGACACCAGAAGTTGTCATAATTTTACAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* * *
27019 TGACACCAGAAGTTGTCAATAATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATTTTACAAT
* * *
27050 TGACACCAGAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* *
27080 TGACACCAGAAGTTATCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
*
27110 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
*
27140 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
* *
27170 TGACACCAAAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTACAAT
** *
27200 TGACACTTGAAGATGTCATGATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGATTTTA--CAAT
27232 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
27251 ATACACCATG
Statistics
Matches: 398, Mismatches: 41, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
30 256 0.64
31 101 0.25
32 37 0.09
33 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATTTTACAAT
Found at i:27083 original size:182 final size:181
Alignment explanation
Indices: 26774--27250 Score: 654
Period size: 182 Copynumber: 2.6 Consensus size: 181
26764 AGTCTCCAAA
* * *
26774 TGACACCAGAAGTTGTCATGATAAATC-TCCATTGACACCAGAAGTTGTCAATGGTGTTACAATT
1 TGACACCAGAAGTTGTCA--AT-AATCTTCAATTGACACCAGAAGTTGTC-ATGATTTTACAATT
* *
26838 GACACAAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGATTTTGCAAATGACA
62 GACACAAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGATCTTACAAATGACA
* *
26903 CCAGAAGTTGTCATGATTTTGCAATTGACACCATAAGTTGTCATGATCTTACAAT
127 CCAGAAGTTATCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTACAAT
* *
26958 TGACACCAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATAATTTTACAATTGAC
1 TGACACCAGAAGTTGTCAATAATCTT-CAATTGACACCAGAAGTTGTCATGATTTTACAATTGAC
* *
27023 ACCAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGGTCTTACAAATGACACCA
65 ACAAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGATCTTACAAATGACACCA
* *
27088 GAAGTTATCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAAT
130 GAAGTTATCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTACAAT
* * * *
27140 TGACACCAGAAGTTGTC-ATGATTTTGCAATTGACACCAAAAGTTGTCATGATTTTGCAATTGAC
1 TGACACCAGAAGTTGTCAATAATCTT-CAATTGACACCAGAAGTTGTCATGATTTTACAATTGAC
** * * * *
27204 ACTTGAAGATGTC-ATGATTTTATTCAATTGACACCAGAAGTTGTCAT
65 ACAAGAAGTTGTCAATAATCTTA--CAAATGACACCAGAAGTTGTCAT
27251 ATACACCATG
Statistics
Matches: 263, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
180 7 0.03
181 54 0.21
182 165 0.63
183 19 0.07
184 18 0.07
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (181 bp):
TGACACCAGAAGTTGTCAATAATCTTCAATTGACACCAGAAGTTGTCATGATTTTACAATTGACA
CAAGAAGTTGTCAATAATCTTACAAATGACACCAGAAGTTGTCATGATCTTACAAATGACACCAG
AAGTTATCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTACAAT
Found at i:28084 original size:30 final size:30
Alignment explanation
Indices: 28048--28104 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28038 TACTCTTAGC
28048 TTCACTAATTTACAAA-ATCCTAACCGTACA
1 TTCACTAATTTA-AAAGATCCTAACCGTACA
*
28078 TTCACTAATTTAAAAGATCCTAGCCGT
1 TTCACTAATTTAAAAGATCCTAACCGT
28105 TGGTCATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (30 bp):
TTCACTAATTTAAAAGATCCTAACCGTACA
Found at i:28290 original size:16 final size:16
Alignment explanation
Indices: 28269--28300 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28259 CTTGATTTCA
*
28269 TTTCTCGATTTCCTCT
1 TTTCTCGATTCCCTCT
28285 TTTCTCGATTCCCTCT
1 TTTCTCGATTCCCTCT
28301 CCTGTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.34, G:0.06, T:0.53
Consensus pattern (16 bp):
TTTCTCGATTCCCTCT
Found at i:28420 original size:29 final size:29
Alignment explanation
Indices: 28364--28420 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
28354 AAACACTACG
* *
28364 AAGTTTGTAAGAATTCAGGGCAAGAAAAC
1 AAGTTTGTAAGAATTCAGGGAAAAAAAAC
28393 AAGTTTGTAAGAAATT-AGGGAAAAAAAA
1 AAGTTTGTAAG-AATTCAGGGAAAAAAAA
28421 AAGAAATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (29 bp):
AAGTTTGTAAGAATTCAGGGAAAAAAAAC
Found at i:35463 original size:18 final size:15
Alignment explanation
Indices: 35440--35478 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
35430 ACTAGTACTC
35440 ACAAAAGTAATGGTAATA
1 ACAAAAG-AAT-GTAA-A
35458 ACAAAAGAATGTAAA
1 ACAAAAGAATGTAAA
35473 ACAAAA
1 ACAAAA
35479 TTACCTGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 4 0.19
17 3 0.14
18 7 0.33
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15
Consensus pattern (15 bp):
ACAAAAGAATGTAAA
Found at i:44358 original size:6 final size:6
Alignment explanation
Indices: 44349--44386 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
44339 AGTTCAACTA
44349 TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TC
1 TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TCCAAT TC
44387 TCAGTTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCAAT
Found at i:44879 original size:29 final size:28
Alignment explanation
Indices: 44812--44887 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
44802 AAACTTACAC
44812 AAAATGGCCAAATAAACCCCTGAACTCTA
1 AAAAT-GCCAAATAAACCCCTGAACTCTA
** *
44841 ATTGCA-GCCAAATAAGCCCCTGAACTCTTA
1 A--AAATGCCAAATAAACCCCTGAACTC-TA
*
44871 AAAATGCCAAACAAACC
1 AAAATGCCAAATAAACC
44888 ATTTTCTGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
28 1 0.03
29 31 0.86
30 3 0.08
31 1 0.03
ACGTcount: A:0.43, C:0.29, G:0.11, T:0.17
Consensus pattern (28 bp):
AAAATGCCAAATAAACCCCTGAACTCTA
Found at i:49345 original size:18 final size:17
Alignment explanation
Indices: 49318--49352 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
49308 AAGAATCTTT
*
49318 TTATAAATTTTTTTAAC
1 TTATAAATTTTGTTAAC
49335 TTATGAAATTTTGTTAAC
1 TTAT-AAATTTTGTTAAC
49353 CTCCTTAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (17 bp):
TTATAAATTTTGTTAAC
Found at i:49459 original size:22 final size:22
Alignment explanation
Indices: 49336--49873 Score: 169
Period size: 22 Copynumber: 24.9 Consensus size: 22
49326 TTTTTTAACT
* *
49336 TATGAAATTTTGTTAACCTCCT
1 TATGAAATTTTGATAACCTCCA
* * *
49358 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTCCA
*
49380 TATGAAATTTTGATAACTTTCCA
1 TATGAAATTTTGATAAC-CTCCA
**
49403 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
* *
49424 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
* * * * **
49447 TATGATATATTGATAATCACGT
1 TATGAAATTTTGATAACCTCCA
* * *
49469 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
*
49491 TAT-TAATTGTT-AGTAA--TCACA
1 TATGAAATT-TTGA-TAACCTC-CA
* *
49512 CTTTAAAATTTTGATAATCACT-C-
1 -TATGAAATTTTGATAA-C-CTCCA
* *
49535 TATGAAATTGTGATAATCTCGC-
1 TATGAAATTTTGATAACCTC-CA
* *
49557 TATGAAATTTTGACAAATCTTCCCA
1 TATGAAATTTTGA-TAA-CCT-CCA
*
49582 TA--AAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCA
* * * * *
49603 TATAAAATTTTGTTAACTTTCT
1 TATGAAATTTTGATAACCTCCA
*
49625 TATGAAATCTTGATAA----C-
1 TATGAAATTTTGATAACCTCCA
* * *
49642 TA-CAAATTTT-ATAAGCTCCC
1 TATGAAATTTTGATAACCTCCA
* **
49662 TGTGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* * *
49683 TTATGAAATTTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTCCA
* * *
49706 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
**
49728 TATGAAATTTTGATAACC-CTGT
1 TATGAAATTTTGATAACCTC-CA
* **
49750 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
*
49771 CTATGAAATTTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTCCA
* *
49794 TATGAAATTTGGATATCCTCC-
1 TATGAAATTTTGATAACCTCCA
* * *
49815 -CTG-AATTTTGATATCCTCCC
1 TATGAAATTTTGATAACCTCCA
*
49835 TA--AAATTTTGATTA-CTCCA
1 TATGAAATTTTGATAACCTCCA
* * *
49854 TAATAAAAGTTTAATAACCT
1 T-ATGAAATTTTGATAACCT
49874 TTCTAATTTG
Statistics
Matches: 374, Mismatches: 96, Indels: 91
0.67 0.17 0.16
Matches are distributed among these distances:
15 4 0.01
16 6 0.02
17 2 0.01
18 1 0.00
19 21 0.06
20 17 0.05
21 24 0.06
22 233 0.62
23 59 0.16
24 3 0.01
25 3 0.01
26 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:49587 original size:23 final size:23
Alignment explanation
Indices: 49556--49614 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
49546 GATAATCTCG
* *
49556 CTATGAAATTTTGACAAATCTTCC
1 CTATAAAATTTTGACAAA-CCTCC
*
49580 C-ATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGACAAACCTCC
49602 CTATAAAATTTTG
1 CTATAAAATTTTG
49615 TTAACTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.16
23 25 0.81
24 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (23 bp):
CTATAAAATTTTGACAAACCTCC
Found at i:49827 original size:19 final size:20
Alignment explanation
Indices: 49798--49846 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
49788 CCTTCATATG
*
49798 AAATTTGGATATCCTCCCT-
1 AAATTTTGATATCCTCCCTA
*
49817 GAATTTTGATATCCTCCCTA
1 AAATTTTGATATCCTCCCTA
49837 AAATTTTGAT
1 AAATTTTGAT
49847 TACTCCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (20 bp):
AAATTTTGATATCCTCCCTA
Found at i:50159 original size:21 final size:21
Alignment explanation
Indices: 49952--50236 Score: 103
Period size: 22 Copynumber: 12.8 Consensus size: 21
49942 AGTCACATTT
* *
49952 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCT-TCTA
* *
49974 TGAAATATTGATAACCTTTTTA
1 TGAAATTTTGATAACC-TTCTA
* * * *
49996 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGAT-AACCTTCTA
* * *
50018 TGAAATTCTGATAATCACAT-TG
1 TGAAATTTTGATAA-C-CTTCTA
* * *
50040 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCT-TCTA
*
50062 TGAAATTTTGATAATCTTC-A
1 TGAAATTTTGATAACCTTCTA
*
50082 TGTAAATTTTGATAATCCGATTTTTA
1 TG-AAATTTTGATAA-CC---TTCTA
*
50108 TGAAATTTCGATAATCAC-TCTA
1 TGAAATTTTGATAA-C-CTTCTA
*
50130 TGAGA-TTTGATAACCTTCTA
1 TGAAATTTTGATAACCTTCTA
* * * *
50150 TCAAATTTTGGTACTCCTTATGAAA
1 TGAAATTTTGATA-ACCTTCT---A
*
50175 TTGAGACTTTT-ATAACCTTCATA
1 -TGA-AATTTTGATAACCTTC-TA
* **
50198 TGAAATTTTAATAACCACACTA
1 TGAAATTTTGATAACC-TTCTA
*
50220 TAAAATTTTGATAACCT
1 TGAAATTTTGATAACCT
50237 CCCACTGAAA
Statistics
Matches: 194, Mismatches: 45, Indels: 49
0.67 0.16 0.17
Matches are distributed among these distances:
19 1 0.01
20 11 0.06
21 33 0.17
22 107 0.55
23 8 0.04
25 20 0.10
26 9 0.05
27 5 0.03
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (21 bp):
TGAAATTTTGATAACCTTCTA
Found at i:50510 original size:66 final size:65
Alignment explanation
Indices: 50356--50563 Score: 222
Period size: 66 Copynumber: 3.1 Consensus size: 65
50346 TTGTGATAAT
* ** * *
50356 TAACCACCCTATGAAATTTCAATAACCAACCT-AAGAAATTTTAATAACCTGACCCTATAAAATT
1 TAACCACACTATGAAATTTTGATAACC-TCCTCATGAAATTTTAATAACC--A-CCTATAAAATT
50420 TTGG
62 TTGG
* * *
50424 TAACCACACTATGAAATTTTGGTAACCTCACT-ATGAAATTTTAGTAACCACACTATGAAATTTT
1 TAACCACACTATGAAATTTTGATAACCTC-CTCATGAAATTTTAATAACCAC-CTATAAAATTTT
50488 GG
64 GG
* * * *
50490 TAACCACACTATGTAATTTTGATAACCTCCTCATGGAATTATAATAACCATCTTATAAAATTTTG
1 TAACCACACTATGAAATTTTGATAACCTCCTCATGAAATTTTAATAACCA-CCTATAAAATTTTG
*
50555 A
65 G
50556 TAACCACA
1 TAACCACA
50564 TAGAGACAAG
Statistics
Matches: 120, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
65 3 0.03
66 75 0.62
67 2 0.02
68 40 0.33
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (65 bp):
TAACCACACTATGAAATTTTGATAACCTCCTCATGAAATTTTAATAACCACCTATAAAATTTTGG
Found at i:50529 original size:22 final size:22
Alignment explanation
Indices: 50356--50563 Score: 172
Period size: 22 Copynumber: 9.4 Consensus size: 22
50346 TTGTGATAAT
* **
50356 TAACCACCCTATGAAATTTCAA
1 TAACCACACTATGAAATTTTGA
* *
50378 TAACCA-ACCTAAGAAATTTTAA
1 TAACCACA-CTATGAAATTTTGA
* * *
50400 TAACCTGACCCTATAAAATTTTGG
1 TAACC--ACACTATGAAATTTTGA
*
50424 TAACCACACTATGAAATTTTGG
1 TAACCACACTATGAAATTTTGA
*
50446 TAACCTCACTATGAAATTTT-A
1 TAACCACACTATGAAATTTTGA
*
50467 GTAACCACACTATGAAATTTTGG
1 -TAACCACACTATGAAATTTTGA
*
50490 TAACCACACTATGTAATTTTGA
1 TAACCACACTATGAAATTTTGA
* * * *
50512 TAACCTC-CTCATGGAATTATAA
1 TAACCACACT-ATGAAATTTTGA
* *
50534 TAACCATC-TTATAAAATTTTGA
1 TAACCA-CACTATGAAATTTTGA
50556 TAACCACA
1 TAACCACA
50564 TAGAGACAAG
Statistics
Matches: 151, Mismatches: 26, Indels: 18
0.77 0.13 0.09
Matches are distributed among these distances:
21 3 0.02
22 130 0.86
23 2 0.01
24 16 0.11
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (22 bp):
TAACCACACTATGAAATTTTGA
Found at i:50770 original size:19 final size:20
Alignment explanation
Indices: 50739--50776 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
50729 TATTAACATT
50739 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
50758 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
50777 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:52302 original size:15 final size:16
Alignment explanation
Indices: 52277--52310 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
52267 TAATATACGT
*
52277 ATTATATAATGTAATA
1 ATTATATAATGGAATA
52293 ATTA-ATAATGGAATA
1 ATTATATAATGGAATA
52308 ATT
1 ATT
52311 TATGATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (16 bp):
ATTATATAATGGAATA
Found at i:52568 original size:22 final size:22
Alignment explanation
Indices: 52526--52569 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
52516 TATTCATATG
* *
52526 AAATTATGATAATCTCTCTATT
1 AAATTACGATAATCTCACTATT
52548 AAATTACGATAAT-TACACTATT
1 AAATTACGATAATCT-CACTATT
52570 TTTTATGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (22 bp):
AAATTACGATAATCTCACTATT
Found at i:52696 original size:22 final size:22
Alignment explanation
Indices: 52637--52714 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 22
52627 AATAATAATA
* ** *
52637 TTATGAAATTTCGAGAACCTTT
1 TTATGAAATTTTGTTAACCTTC
* *
52659 TTAT-AATTTTTTTTAACCTTC
1 TTATGAAATTTTGTTAACCTTC
*
52680 TTATGAAATTTTGTTAACCTCC
1 TTATGAAATTTTGTTAACCTTC
* *
52702 CTAAGAAATTTTG
1 TTATGAAATTTTG
52715 AAGACCTCAA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 15 0.34
22 29 0.66
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.47
Consensus pattern (22 bp):
TTATGAAATTTTGTTAACCTTC
Found at i:52885 original size:22 final size:22
Alignment explanation
Indices: 52860--52986 Score: 78
Period size: 23 Copynumber: 5.6 Consensus size: 22
52850 AATCACACTC
*
52860 TGAAATTTTAATAATCATCCTA
1 TGAAATTTTAATAATCTTCCTA
* * *
52882 TGAAA-TTGAGATAACCTTGCTA
1 TGAAATTTTA-ATAATCTTCCTA
*
52904 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTAAT-AATCTTCCTA
* * * *
52927 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTAAT-AATCTTCCTA
* * *
52950 TAAAATTTTTGATAA-CTTTCTTA
1 TGAAA-TTTTAATAATC-TTCCTA
*
52973 TGAAATCTTAATAA
1 TGAAATTTTAATAA
52987 CTACAAATTT
Statistics
Matches: 84, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.04
22 29 0.35
23 45 0.54
24 7 0.08
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (22 bp):
TGAAATTTTAATAATCTTCCTA
Found at i:52932 original size:23 final size:23
Alignment explanation
Indices: 52877--52964 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
52867 TTAATAATCA
* **
52877 TCCTATGAAATTGAGAT-AACCT
1 TCCTATAAAATTTTGATAAACCT
* * *
52899 TGCTATGAAATTTTGATAAATCT
1 TCCTATAAAATTTTGATAAACCT
52922 TCCTATAAAATTTTGATAAACCT
1 TCCTATAAAATTTTGATAAACCT
*
52945 CCCTATAAAATTTTTGATAA
1 TCCTATAAAA-TTTTGATAA
52965 CTTTCTTATG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 14 0.25
23 33 0.59
24 9 0.16
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (23 bp):
TCCTATAAAATTTTGATAAACCT
Found at i:52940 original size:45 final size:46
Alignment explanation
Indices: 52860--52964 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 46
52850 AATCACACTC
* * **
52860 TGAAATTTTAAT-AATCATCCTATGAAATTGAGAT-AACCTTGCTA
1 TGAAATTTTGATAAATCATCCTATAAAATTGAGATAAACCTCCCTA
* **
52904 TGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGATAAATCATCCTATAAAATTGAGATAAACCTCCCTA
*
52950 TAAAATTTTTGATAA
1 TGAAA-TTTTGATAA
52965 CTTTCTTATG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 11 0.22
45 18 0.36
46 12 0.24
47 9 0.18
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (46 bp):
TGAAATTTTGATAAATCATCCTATAAAATTGAGATAAACCTCCCTA
Found at i:53041 original size:22 final size:22
Alignment explanation
Indices: 52681--53173 Score: 189
Period size: 22 Copynumber: 22.6 Consensus size: 22
52671 TTAACCTTCT
* *
52681 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
52703 TAAGAAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTCAC
** *
52725 TATGAAATTTTGATAAATTCCC
1 TATGAAATTTTGATAACCTCAC
* **
52747 AATGAAATTTTGATAACGAACAC
1 TATGAAATTTTGATAAC-CTCAC
* *
52770 TATGAGATGTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
* * * * **
52792 TATGATATATCGATAACCACGT
1 TATGAAATTTTGATAACCTCAC
* * * *
52814 TTTGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
52835 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* * *
52858 TCTGAAATTTTAATAATCATC-C
1 TATGAAATTTTGATAA-CCTCAC
** **
52880 TATGAAATTGAGATAACCTTGC
1 TATGAAATTTTGATAACCTCAC
*
52902 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCTCAC
* *
52925 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
* * *
52948 TATAAAATTTTTGATAACTTTC-T
1 TATGAAA-TTTTGATAAC-CTCAC
* *
52971 TATGAAATCTTAATAA-CT-AC
1 TATGAAATTTTGATAACCTCAC
*
52991 ----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** *
53009 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* ** *
53031 TATGAAATTTTGTTAATGTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
53053 TATGAAATCTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
**
53075 TATGAAATTTTGATAACCT-TT
1 TATGAAATTTTGATAACCTCAC
* *
53096 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
*
53118 TTTGAAATTTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
* *
53140 TATGGAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
*
53161 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
53174 TACTCCATAG
Statistics
Matches: 343, Mismatches: 97, Indels: 64
0.68 0.19 0.13
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
20 16 0.05
21 26 0.08
22 208 0.61
23 68 0.20
24 12 0.03
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:53386 original size:14 final size:14
Alignment explanation
Indices: 53369--53395 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53359 AACCTTGTTT
53369 TGAAATTTTGATAC
1 TGAAATTTTGATAC
53383 TGAAATTTTGATA
1 TGAAATTTTGATA
53396 AGCTTCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
TGAAATTTTGATAC
Found at i:53597 original size:22 final size:22
Alignment explanation
Indices: 53515--53637 Score: 70
Period size: 22 Copynumber: 5.5 Consensus size: 22
53505 ATAAGCTTAA
* * *
53515 TATGAAATTTTGATAATCACAC
1 TATGAAATTTTGTTAACCTCAC
* * *
53537 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGTTAACCTCAC
* * * *
53559 CATCAACTATTAG-TAACCTC-C
1 TATGAAAT-TTTGTTAACCTCAC
*
53580 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGTTAACCTCAC
* * *
53603 TATGAAATTCTTATAAACCTCGC
1 TATGAAATT-TTGTTAACCTCAC
*
53626 TATGACATTTTG
1 TATGAAATTTTG
53638 ATAATCTCTT
Statistics
Matches: 77, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
21 4 0.05
22 51 0.66
23 22 0.29
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGTTAACCTCAC
Found at i:53738 original size:24 final size:22
Alignment explanation
Indices: 53677--53858 Score: 99
Period size: 22 Copynumber: 8.3 Consensus size: 22
53667 TTGTGATAAT
* *
53677 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
53699 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
**
53721 TAA-CATGATCCTATGAAATTTTGG
1 TAACCA--A-CCTATGAAATTTTAA
*
53745 TAACC-ACACTATGAAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* **
53767 TATTCC-A--TATGAAATTTTGG
1 TA-ACCAACCTATGAAATTTTAA
* * *
53787 TAACC-GCACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* *
53809 TAACC-TCCTCATGAAATTGTAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
53831 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
53853 TAACCA
1 TAACCA
53859 CATAGAGACA
Statistics
Matches: 129, Mismatches: 20, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
19 2 0.02
20 14 0.11
21 5 0.04
22 85 0.66
23 7 0.05
24 15 0.12
25 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:53749 original size:46 final size:41
Alignment explanation
Indices: 53684--53806 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
53674 AATTAACCAC
***
53684 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACATGAT
1 CCTATGAAATTTTGGTAACCACA-CTAAGAAATTTTAAT---AT--T
* *
53730 CCTATGAAATTTTGGTAACCACACTATGAAATTTTGATATT
1 CCTATGAAATTTTGGTAACCACACTAAGAAATTTTAATATT
* * *
53771 CCATATGAAATTTTGGTAACCGCACTATGGAATTTT
1 CC-TATGAAATTTTGGTAACCACACTAAGAAATTTT
53807 GATAACCTCC
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
41 3 0.04
42 31 0.46
43 2 0.03
46 31 0.46
47 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (41 bp):
CCTATGAAATTTTGGTAACCACACTAAGAAATTTTAATATT
Found at i:55129 original size:38 final size:37
Alignment explanation
Indices: 55087--55168 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 37
55077 GATGTTTGAG
55087 ACAAAAACAAAATG-CAAAATTAAATACAACGATTGGAA
1 ACAAAAACAAAA-GACAAAATTAAATACAACG-TTGGAA
* ** *
55125 ACAAAGACAAAAGACAAAATTAAATAGGATGTTGGAA
1 ACAAAAACAAAAGACAAAATTAAATACAACGTTGGAA
55162 ACAAAAA
1 ACAAAAA
55169 GCCAAATTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 13 0.34
38 25 0.66
ACGTcount: A:0.61, C:0.11, G:0.13, T:0.15
Consensus pattern (37 bp):
ACAAAAACAAAAGACAAAATTAAATACAACGTTGGAA
Found at i:55347 original size:31 final size:32
Alignment explanation
Indices: 55289--55348 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
55279 TGATAATTTA
55289 GAAATATGTTTTAAAAAAAAAGAGTACAATTG
1 GAAATATGTTTTAAAAAAAAAGAGTACAATTG
*
55321 GAAATATGTTTTAAAAATAAAG-GTACAA
1 GAAATATGTTTTAAAAAAAAAGAGTACAA
55349 GCGGAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.28
Consensus pattern (32 bp):
GAAATATGTTTTAAAAAAAAAGAGTACAATTG
Found at i:55355 original size:31 final size:32
Alignment explanation
Indices: 55289--55355 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
55279 TGATAATTTA
**
55289 GAAATATGTTTTAAAAAAAAAGAGTACAATTG
1 GAAATATGTTTTAAAAAAAAAGAGTACAAGCG
*
55321 GAAATATGTTTTAAAAATAAAG-GTACAAGCG
1 GAAATATGTTTTAAAAAAAAAGAGTACAAGCG
55352 GAAA
1 GAAA
55356 ACATAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.52, C:0.04, G:0.18, T:0.25
Consensus pattern (32 bp):
GAAATATGTTTTAAAAAAAAAGAGTACAAGCG
Found at i:55737 original size:91 final size:92
Alignment explanation
Indices: 55612--55795 Score: 325
Period size: 91 Copynumber: 2.0 Consensus size: 92
55602 TTTTTTAAAA
*
55612 AAAAAAACTGCCCATTTAAAAAAAATTATGTCAAAAAGGAAAACTATCATTAACTACCCTCTTTA
1 AAAAAAACTACCCATTTAAAAAAAATTATGTCAAAAAGGAAAACTATCATTAACTACCCTCTTTA
*
55677 ATATTATTTTATTATATTTTCACACTT
66 ATACTATTTTATTATATTTTCACACTT
*
55704 AAAAAAACTACCCATTT-AAAAAAATTATGTCAAAAAGGAAAACTATCATTAACTACCCTTTTTA
1 AAAAAAACTACCCATTTAAAAAAAATTATGTCAAAAAGGAAAACTATCATTAACTACCCTCTTTA
*
55768 ATACTATTTTATTGTATTTTCACACTT
66 ATACTATTTTATTATATTTTCACACTT
55795 A
1 A
55796 CATAGTAGTG
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 72 0.82
92 16 0.18
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.36
Consensus pattern (92 bp):
AAAAAAACTACCCATTTAAAAAAAATTATGTCAAAAAGGAAAACTATCATTAACTACCCTCTTTA
ATACTATTTTATTATATTTTCACACTT
Found at i:55844 original size:2 final size:2
Alignment explanation
Indices: 55837--55874 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
55827 TTATTATTAT
55837 TA TA TA TA TA TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55875 GTAGTAGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:58740 original size:110 final size:110
Alignment explanation
Indices: 58541--58800 Score: 452
Period size: 110 Copynumber: 2.4 Consensus size: 110
58531 TCTTCAATTA
58541 AATTAAATCTAATATCTTTATAATTACTTTATTTTTACC-AAAAAATTTGGATATACTAAAATTT
1 AATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAAATTTGGATATACTAAAATTT
58605 TTTCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTT
66 TTTCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTT
*
58650 AATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAAATTTGGATATATTAAAATTT
1 AATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAAATTTGGATATACTAAAATTT
58715 TTTCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTT
66 TTTCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTT
* **
58760 AATTAAAT-TCAATATTTTATATAATTTTTTTATTTTTACCA
1 AATTAAATCT-AATATCTT-TATAATTACTTTATTTTTACCA
58801 TTTTAATTTA
Statistics
Matches: 144, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
109 40 0.28
110 84 0.58
111 20 0.14
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (110 bp):
AATTAAATCTAATATCTTTATAATTACTTTATTTTTACCAAAAAAATTTGGATATACTAAAATTT
TTTCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTT
Found at i:62837 original size:29 final size:29
Alignment explanation
Indices: 62791--62851 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
62781 ATTTTGAGTA
* *
62791 AACTTATTAACTATTCTATTAACATCCCT
1 AACTTATTAACTACTCTATTAAAATCCCT
* *
62820 AACTTGTTAACTACTCTATTAAAATGCCT
1 AACTTATTAACTACTCTATTAAAATCCCT
62849 AAC
1 AAC
62852 CTTACAAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
AACTTATTAACTACTCTATTAAAATCCCT
Found at i:66081 original size:266 final size:266
Alignment explanation
Indices: 65602--66089 Score: 757
Period size: 266 Copynumber: 1.8 Consensus size: 266
65592 TCAAAACACT
* * *
65602 CCAACCAATTCTTATATATGGTTTCAATGTAAGTAATTTCATTGTTACCGATGCGAGTGATAAGC
1 CCAACCAATTCTTATATATGGTATCAATGTAAGTAATTTCATTGTTACCGATGCAAGTGAAAAGC
*
65667 AAACCTAAACCATCACCAATCTGAATGGCATCAGTGCCATCATAATAATAGGAAAGAGAAAGATC
66 AAACCTAAACCATCACCAATCTGAATGGCATCAGTGCCATCATAATAATAGGAAAGAGAAACATC
* * * *
65732 CTTCAAGTCAGATACAACATGATAAGAAGCCCAAAAATCCATACACAAATTTTTACCATGGTTAG
131 ATTCAAGTCAGATACAACATGATAAGAAGCCCAAAAATCCACACACAAAGTTTTACCAAGGTTAG
65797 AGTTGTCATCCTTCATATCAAAACACTACTGTATATATTATAACATACACAACAACAATAAGTTA
196 AGTTGTCATCCTTCATATCAAAACACTACTGTATATATTATAACATACACAACAACAATAAGTTA
65862 TCTTTC
261 TCTTTC
* *
65868 CCAATCAATTCTTATATATGGTATCAGTGTAAGTAATTTCATTGTTACC-ATTGCAAGTGAAAAG
1 CCAACCAATTCTTATATATGGTATCAATGTAAGTAATTTCATTGTTACCGA-TGCAAGTGAAAAG
* * *
65932 CAAACTTAAGA-CATCACCAATTTGAATGGCATCTGTGCCATCATAATAATAGGAAAGAGAAACA
65 CAAACCTAA-ACCATCACCAATCTGAATGGCATCAGTGCCATCATAATAATAGGAAAGAGAAACA
* * * * * *
65996 TCATTCATGTCAGATACAACATTA-AGAGAAGCCCCATAATCCACACACCAAGTTTTGCCAAGGT
129 TCATTCAAGTCAGATACAACATGATA-AGAAGCCCAAAAATCCACACACAAAGTTTTACCAAGGT
66060 TAGAGTTGTCATCCTTCATATCAAAACACT
193 TAGAGTTGTCATCCTTCATATCAAAACACT
66090 CTAATCAATT
Statistics
Matches: 200, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
265 2 0.01
266 197 0.99
267 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.28
Consensus pattern (266 bp):
CCAACCAATTCTTATATATGGTATCAATGTAAGTAATTTCATTGTTACCGATGCAAGTGAAAAGC
AAACCTAAACCATCACCAATCTGAATGGCATCAGTGCCATCATAATAATAGGAAAGAGAAACATC
ATTCAAGTCAGATACAACATGATAAGAAGCCCAAAAATCCACACACAAAGTTTTACCAAGGTTAG
AGTTGTCATCCTTCATATCAAAACACTACTGTATATATTATAACATACACAACAACAATAAGTTA
TCTTTC
Found at i:66256 original size:222 final size:222
Alignment explanation
Indices: 65870--66311 Score: 719
Period size: 222 Copynumber: 2.0 Consensus size: 222
65860 TATCTTTCCC
*
65870 AATCAATTCTTATATATGGTATCAGTGTAAGTAATTTCATTGTTACCATTGCAAGTGAAAAGCAA
1 AATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTGTTACCATTGCAAGTGAAAAGCAA
* *
65935 ACTTAAGACATCACCAATTTGAATGGCATCTGTGCCATCATAATAATAGGAAAGAGAAACATCAT
66 ACTTAAGACATCACCAATTTCAATGGCATATGTGCCATCATAATAATAGGAAAGAGAAACATCAT
* * *
66000 TCATGTCAGATACAACATTAAGAGAAGCCCCATAATCCACACACCAAGTTTTGCCAAGGTTAGAG
131 TCATGTCAAATACAACATGAAGAGAAGCCCCATAATCCACACACCAAGTTTTGACAAGGTTAGAG
66065 TTGTCATCCTTCATATCAAAACACTCT
196 TTGTCATCCTTCATATCAAAACACTCT
* *
66092 AATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTGTTACCGA-TGCGAGTGATAAGCA
1 AATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTGTTACC-ATTGCAAGTGAAAAGCA
* *
66156 ATCTTAA-ACCATCACCAATTTCAATGGCATATGTGCCATCATAATAATAGGAAAGAGAAAGATC
65 AACTTAAGA-CATCACCAATTTCAATGGCATATGTGCCATCATAATAATAGGAAAGAGAAACATC
* * *
66220 CTTCATGTCAAATACAACATGATA-AGAAGCCCCATAATCCATACACCAAGTTTTGACATGGTTA
129 ATTCATGTCAAATACAACATGA-AGAGAAGCCCCATAATCCACACACCAAGTTTTGACAAGGTTA
66284 GAGTTGTCATCCTTCATATCAAAACACT
193 GAGTTGTCATCCTTCATATCAAAACACT
66312 GATATGTATA
Statistics
Matches: 204, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
221 1 0.00
222 201 0.99
223 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (222 bp):
AATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTGTTACCATTGCAAGTGAAAAGCAA
ACTTAAGACATCACCAATTTCAATGGCATATGTGCCATCATAATAATAGGAAAGAGAAACATCAT
TCATGTCAAATACAACATGAAGAGAAGCCCCATAATCCACACACCAAGTTTTGACAAGGTTAGAG
TTGTCATCCTTCATATCAAAACACTCT
Found at i:66501 original size:488 final size:488
Alignment explanation
Indices: 65585--66577 Score: 1455
Period size: 488 Copynumber: 2.0 Consensus size: 488
65575 TCCACCTCTA
* *
65585 CTTCATATCAAAACACTCCAACCAATTCTTATATATGGTTTCAATGTAAGTAATTTCATTGTTAC
1 CTTCATATCAAAACACTCCAACCAATTCTTATATATGGTATCAATGCAAGTAATTTCATTGTTAC
*
65650 CGATGCGAGTGATAAGCAAACCTAAACCATCACCAATCTGAATGGCATCAGTGCCATCATAATAA
66 CGATGCGAGTGATAAGCAAACCTAAACCATCACCAATCTCAATGGCATCAGTGCCATCATAATAA
*
65715 TAGGAAAGAGAAAGATCCTTCAAGTCAGATACAACATGATAAGAAGCCCAAAAATCCATACACAA
131 TAGGAAAGAGAAAGATCCTTCAAGTCAAATACAACATGATAAGAAGCCCAAAAATCCATACACAA
* *
65780 ATTTTTACCATGGTTAGAGTTGTCATCCTTCATATCAAAACACTACTGTATATATTATAACATAC
196 ATTTTGACCATGGTTAGAGTTGTCATCCTTCATATCAAAACACTACTATATATATTATAACATAC
* * *
65845 ACAACAACAATAAGTTATCTTTCCCAATCAATTCTTATATATGGTATCAGTGTAAGTAATTTCAT
261 ACAACAACAATAAGTTATCCTTCCAAATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCAT
* * *
65910 TGTTACCATTGCAAGTGAAAAGCAAACTTAAGACATCACCAATTTGAATGGCATCTGTGCCATCA
326 TATTACCATTGCAAGTGAAAAGAAAACTTAAGACATCACCAATTTGAATGACATCTGTGCCATCA
*
65975 TAATAATAGGAAAGAGAAACATCATTCATGTCAGATACAACATTA-AGAGAAGCCCCATAATCCA
391 TAATAATAGGAAAGAGAAACATCATTCATGTCAGATACAACATGATA-AGAAGCCCCATAATCCA
66039 CACACCAAGTTTTGCCAAGGTTAGAGTTGTCATC
455 CACACCAAGTTTTGCCAAGGTTAGAGTTGTCATC
* * *
66073 CTTCATATCAAAACACTCTAATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTGTTAC
1 CTTCATATCAAAACACTCCAACCAATTCTTATATATGGTATCAATGCAAGTAATTTCATTGTTAC
* * *
66138 CGATGCGAGTGATAAGCAATCTTAAACCATCACCAATTTCAATGGCAT-ATGTGCCATCATAATA
66 CGATGCGAGTGATAAGCAAACCTAAACCATCACCAATCTCAATGGCATCA-GTGCCATCATAATA
* * *
66202 ATAGGAAAGAGAAAGATCCTTCATGTCAAATACAACATGATAAGAAGCCCCATAATCCATACACC
130 ATAGGAAAGAGAAAGATCCTTCAAGTCAAATACAACATGATAAGAAGCCCAAAAATCCATACA-C
* * *
66267 AAGTTTTGA-CATGGTTAGAGTTGTCATCCTTCATATCAAAACACTGA-TATGTATATTATACCA
194 AAATTTTGACCATGGTTAGAGTTGTCATCCTTCATATCAAAACACT-ACTATATATATTATAACA
* *
66330 -AGTACAACATA-AGA-AAGTTTTCCTTCCAAATCAATTCTTATATATGGTATCAGTGCAAGTAA
258 TA-CACAACA-ACA-ATAAGTTATCCTTCCAAATCAATTCTTATATATGGTATCAGTGCAAGTAA
* * * ** *
66392 TTTCATTATTACCCA-TGCGAGTGATAAGAAAACTTAA-ACCATTATTAATTTGAATGACATTTG
320 TTTCATTATTA-CCATTGCAAGTGAAAAGAAAACTTAAGA-CATCACCAATTTGAATGACATCTG
* * * *
66455 TGCCATCATAATCATAGGAATGAGAAAGATCATTTATGTCAGATACAACATGATAAGAAGCCCCA
383 TGCCATCATAATAATAGGAAAGAGAAACATCATTCATGTCAGATACAACATGATAAGAAGCCCCA
* * * *
66520 TAATCCATACACCAAGTTTTGTCATGGTTTGAGTTGTCATC
448 TAATCCACACACCAAGTTTTGCCAAGGTTAGAGTTGTCATC
* *
66561 CTTTATTTCAAAACACT
1 CTTCATATCAAAACACT
66578 ACTGTGTATA
Statistics
Matches: 453, Mismatches: 43, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
487 3 0.01
488 435 0.96
489 15 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.30
Consensus pattern (488 bp):
CTTCATATCAAAACACTCCAACCAATTCTTATATATGGTATCAATGCAAGTAATTTCATTGTTAC
CGATGCGAGTGATAAGCAAACCTAAACCATCACCAATCTCAATGGCATCAGTGCCATCATAATAA
TAGGAAAGAGAAAGATCCTTCAAGTCAAATACAACATGATAAGAAGCCCAAAAATCCATACACAA
ATTTTGACCATGGTTAGAGTTGTCATCCTTCATATCAAAACACTACTATATATATTATAACATAC
ACAACAACAATAAGTTATCCTTCCAAATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCAT
TATTACCATTGCAAGTGAAAAGAAAACTTAAGACATCACCAATTTGAATGACATCTGTGCCATCA
TAATAATAGGAAAGAGAAACATCATTCATGTCAGATACAACATGATAAGAAGCCCCATAATCCAC
ACACCAAGTTTTGCCAAGGTTAGAGTTGTCATC
Found at i:66574 original size:266 final size:267
Alignment explanation
Indices: 66092--66844 Score: 1152
Period size: 266 Copynumber: 2.8 Consensus size: 267
66082 AAAACACTCT
*
66092 AATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTGTTACCGATGCGAGTGATAAGCAA
1 AATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCGATGCGAGTGATAAGCAA
* *
66157 TCTTAAACCATCACCAATTTCAATGGCATATGTGCCATCATAATAATAGGAAAGAGAAAGATCCT
66 ACTTAAACCATCACCAATTTGAATGGCATATGTGCCATCATAATAATAGGAAAGAGAAAGATCCT
*
66222 TCATGTCAAATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGACATGGTTAGAG
131 TCATGTCAGATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGACATGGTTAGAG
* * **
66287 TTGTCATCCTTCATATCAAAACACTGA-TATGTATATTATACCAAGTACAACATAAGAAAGTTTT
196 TTGTCATCCTTCATATCAAAACACTGACTATGTATATTATACCAAATACAACAGAAGAAAGTCAT
66351 CCTTCCA-
261 -CTTCCAC
* *
66358 AATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCCATGCGAGTGATAAGAAA
1 AATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCGATGCGAGTGATAAGCAA
* ** * * * * *
66423 ACTTAAACCATTATTAATTTGAATGACATTTGTGCCATCATAATCATAGGAATGAGAAAGATCAT
66 ACTTAAACCATCACCAATTTGAATGGCATATGTGCCATCATAATAATAGGAAAGAGAAAGATCCT
* * *
66488 TTATGTCAGATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGTCATGGTTTGAG
131 TCATGTCAGATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGACATGGTTAGAG
* * * *
66553 TTGTCATCCTTTATTTCAAAACACT-ACTGTGTATATTATACCAAATACAACAGAAGTAAGTCAT
196 TTGTCATCCTTCATATCAAAACACTGACTATGTATATTATACCAAATACAACAGAAGAAAGTCAT
*
66617 CTTTCAC
261 CTTCCAC
* *
66624 AATCAATACTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCGATGCAAGTGATAAGCAA
1 AATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCGATGCGAGTGATAAGCAA
* * *
66689 ACTTAAACCATCACCAATTTGAATGGCATCTATGCCATCATAATAATAGGAAAGAGAAACATCCT
66 ACTTAAACCATCACCAATTTGAATGGCATATGTGCCATCATAATAATAGGAAAGAGAAAGATCCT
* * * * *
66754 TCATGTCAGATACAACTTGATAAGAAGCCGCATAATCGATGCACCAAGTTTTGCCATGGTTAGAG
131 TCATGTCAGATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGACATGGTTAGAG
66819 TTGTCATCCTTCATATCAAAACACTG
196 TTGTCATCCTTCATATCAAAACACTG
66845 CATACTTCAT
Statistics
Matches: 435, Mismatches: 49, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
265 6 0.01
266 429 0.99
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (267 bp):
AATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCGATGCGAGTGATAAGCAA
ACTTAAACCATCACCAATTTGAATGGCATATGTGCCATCATAATAATAGGAAAGAGAAAGATCCT
TCATGTCAGATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGACATGGTTAGAG
TTGTCATCCTTCATATCAAAACACTGACTATGTATATTATACCAAATACAACAGAAGAAAGTCAT
CTTCCAC
Found at i:66926 original size:97 final size:97
Alignment explanation
Indices: 66752--66942 Score: 285
Period size: 97 Copynumber: 2.0 Consensus size: 97
66742 GAGAAACATC
* * * *
66752 CTTCATGTCAGATACAACTTGATAAGAAGCCGCATAATCGATGCACCAAGTTTTGCCATGGTTAG
1 CTTCATGTCAGATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTTAG
*
66817 AGTTGTCATCCTTCATATCAAAACACTGCATA
66 AGTTATCATCCTTCATATCAAAACACTGCATA
* *
66849 CTTCATGTCAGATACAACATGATGAGGAA-CCCCATAATCCATACACCGAGTTTTGCCATGGTTA
1 CTTCATGTCAGATACAACATGAT-AAGAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTTA
* *
66913 GAGTTATCGTCCTTCATATCAAAACTCTGC
65 GAGTTATCATCCTTCATATCAAAACACTGC
66943 GTGTATATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
97 80 0.95
98 4 0.05
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (97 bp):
CTTCATGTCAGATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTTAG
AGTTATCATCCTTCATATCAAAACACTGCATA
Found at i:67163 original size:362 final size:363
Alignment explanation
Indices: 66490--67196 Score: 1062
Period size: 362 Copynumber: 2.0 Consensus size: 363
66480 AAGATCATTT
* *
66490 ATGTCAGATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGTCATGGTTTGAGTT
1 ATGTCAGATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTTAGAGTT
* * *
66555 GTCATCCTTTATTTCAAAACACTACTGTGTATATTATACCAAATACAACAGAAGTAAGTCATCTT
66 ATCATCCTTCATATCAAAACACTACTGTGTATATTATACCAAATACAACAGAAGTAAGTCATCTT
*
66620 TCACAATCAATACTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCGATGCAAGTGATAA
131 TCACAATCAATACTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCAATGCAAGTGATAA
*
66685 GCAAACTTAAACCATCACCAATTTGAATGGCATCTATGCCATCATAATAATAGGAAAGAGAAACA
196 GCAAACTTAAACCATCACCAATTTGAATGGAATCTATGCCATCATAATAATAGGAAAGAGAAACA
* * * * * *
66750 TCCTTCATGTCAGATACAACTTGATAAGAAGCCGCATAATCGATGCACCAAGTTTTGCCATGGTT
261 TCCTTCATGTCAGATACAACATGATAAGAAGCCCCACAATCCATACACCAAGATTTGCCATGGTT
*
66815 AGAGTTGTCATCCTTCATATCAAAACACTGCATACTTC
326 AGACTTGTCATCCTTCATATCAAAACACTGCATACTTC
* *
66853 ATGTCAGATACAACATGATGAGGAA-CCCCATAATCCATACACCGAGTTTTGCCATGGTTAGAGT
1 ATGTCAGATACAACATGAT-AAGAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTTAGAGT
* * * *
66917 TATCGTCCTTCATATCAAAACTCTGC-GTGTATATTATACCAAATACAACAGAAGTAAGTTATCT
65 TATCATCCTTCATATCAAAACACTACTGTGTATATTATACCAAATACAACAGAAGTAAGTCATCT
* * * *
66981 TTCCCAATCAATTCTTATATATTGTATCAGTGCAAGTAATTTCATTGTTACCAATG-AGAGTGAT
130 TTCACAATCAATACTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCAATGCA-AGTGAT
* * * *
67045 AAGCAAACGTT-AGCCATCACCAATTTGAATGGAATCTGTGCCATCATAATCATAGGAATGAGAA
194 AAGCAAAC-TTAAACCATCACCAATTTGAATGGAATCTATGCCATCATAATAATAGGAAAGAGAA
* * *
67109 AGATCCTTTATGTCAGATACAACATGATGAGAAGCCCCACAATCCATACACCAAGATTTGCCATG
258 ACATCCTTCATGTCAGATACAACATGATAAGAAGCCCCACAATCCATACACCAAGATTTGCCATG
* *
67174 GTTTGACTTGTCATCCTTTATAT
323 GTTAGACTTGTCATCCTTCATAT
67197 TTAAACATTG
Statistics
Matches: 308, Mismatches: 33, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
361 1 0.00
362 226 0.73
363 77 0.25
364 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (363 bp):
ATGTCAGATACAACATGATAAGAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTTAGAGTT
ATCATCCTTCATATCAAAACACTACTGTGTATATTATACCAAATACAACAGAAGTAAGTCATCTT
TCACAATCAATACTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCAATGCAAGTGATAA
GCAAACTTAAACCATCACCAATTTGAATGGAATCTATGCCATCATAATAATAGGAAAGAGAAACA
TCCTTCATGTCAGATACAACATGATAAGAAGCCCCACAATCCATACACCAAGATTTGCCATGGTT
AGACTTGTCATCCTTCATATCAAAACACTGCATACTTC
Found at i:67387 original size:264 final size:263
Alignment explanation
Indices: 66853--67578 Score: 980
Period size: 264 Copynumber: 2.7 Consensus size: 263
66843 TGCATACTTC
*
66853 ATGTCAGATACAACATGATGAGGAA-CCCCATAATCCATACACCGAGTTTTGCCATGGTTAGAGT
1 ATGTCAGATACAACATGATGA-GAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTTAGAGT
* * * *
66917 TATCGTCCTTCATATCAAAAC-TCTGCGTGTATATTATACCAAATACAACAGAAGTAAGTTATCT
65 TATCATCCTTAATATCAAAACAT-TGTGTGTATATTATATCAAATACAACAGAAGTAAGTTATCT
* *
66981 TTCCCAATCAATTCTTATATATTGTATCAGTGCAAGTAATTTCATTGTTACCAATGA-GAGTGAT
129 TTCCCAATCAATTCTTATATA-TG-GTCAGTGCAAGTAATTTCATTGTTACCCAT-ACGAGTGAT
* * *
67045 AAGCAAACGTTAGCCATCACCAATTTGAATGGAATCTGTGCCATCATAATCATAGGAATGAGAAA
191 AAGCAAACGTTAGCCATCACCAATTTGAATGGAATCTGTGACATCATAATAATAGGAAAGAGAAA
* *
67110 GATCCTTT
256 CATCCTAT
* * * *
67118 ATGTCAGATACAACATGATGAGAAGCCCCACAATCCATACACCAAGATTTGCCATGGTTTGACTT
1 ATGTCAGATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTTAGAGTT
* * ** * *
67183 GTCATCCTTTATATTTAAACATTGTTGTGTATAATATATCAAATACAACAGAAGTATGTTATCTT
66 ATCATCCTTAATATCAAAACATTG-TGTGTATATTATATCAAATACAACAGAAGTAAGTTATCTT
*
67248 TCCCAATCAATTCATATATATGGT-AGTGCAAGTAATTTCATTGTTACCCGATACGAGTGATAAG
130 TCCCAATCAATTCTTATATATGGTCAGTGCAAGTAATTTCATTGTTACCC-ATACGAGTGATAAG
* *
67312 CAAAC-TTAAGTCATCACCAATTTGGAT-GACATCTGTGACATCATAATAATAGGAAAGAGAAAC
194 CAAACGTT-AGCCATCACCAATTTGAATGGA-ATCTGTGACATCATAATAATAGGAAAGAGAAAC
67375 ATCCTAT
257 ATCCTAT
*
67382 ATGTCAGATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTAAGAGTT
1 ATGTCAGATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTTAGAGTT
* * * * *
67447 CTCATCCTTAATATCAAAACACTGATGTATATATTAT-TCTAAATACAACAGAGGTAACTTATCT
66 ATCATCCTTAATATCAAAACATTG-TGTGTATATTATATC-AAATACAACAGAAGTAAGTTATCT
* * *
67511 TTCCTAATCAATTCTTATATATGGTATCAGTGCAAGTAATTTCATTATTACCCATGCGAGTGATA
129 TTCCCAATCAATTCTTATATATGG--TCAGTGCAAGTAATTTCATTGTTACCCATACGAGTGATA
67576 AGC
192 AGC
Statistics
Matches: 406, Mismatches: 44, Indels: 21
0.86 0.09 0.04
Matches are distributed among these distances:
263 31 0.08
264 205 0.50
265 75 0.18
266 71 0.17
267 24 0.06
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (263 bp):
ATGTCAGATACAACATGATGAGAAGCCCCATAATCCATACACCAAGTTTTGCCATGGTTAGAGTT
ATCATCCTTAATATCAAAACATTGTGTGTATATTATATCAAATACAACAGAAGTAAGTTATCTTT
CCCAATCAATTCTTATATATGGTCAGTGCAAGTAATTTCATTGTTACCCATACGAGTGATAAGCA
AACGTTAGCCATCACCAATTTGAATGGAATCTGTGACATCATAATAATAGGAAAGAGAAACATCC
TAT
Done.