Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003549.1 Hibiscus syriacus cultivar Beakdansim tig00007488_pilon, 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: 82635
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4353 original size:20 final size:20
Alignment explanation
Indices: 4328--4389 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
4318 TTTTGGTGCA
4328 GAGGGAATCGATCCCCCCCT
1 GAGGGAATCGATCCCCCCCT
* *
4348 GAGGGAACCGATTCCCCCCACA
1 GAGGGAATCGA-TCCCCCC-CT
*
4370 G-GGGAATCGATACCCCCCT
1 GAGGGAATCGATCCCCCCCT
4389 G
1 G
4390 GGGTTCTGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.06
20 16 0.46
21 15 0.43
22 2 0.06
ACGTcount: A:0.23, C:0.39, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAATCGATCCCCCCCT
Found at i:8879 original size:20 final size:20
Alignment explanation
Indices: 8854--8907 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
8844 AATAGTTTCT
8854 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
8874 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
8894 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
8908 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:9159 original size:20 final size:21
Alignment explanation
Indices: 9134--9182 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
9124 TCTGAGAGAT
9134 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* **
9154 GGAGATGGGGACGGATTTCGTT
1 GGAGAT-GAGACGGATTTCGCC
9176 GGAGATG
1 GGAGATG
9183 GGTGAGAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.22, C:0.12, G:0.43, T:0.22
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:9168 original size:22 final size:22
Alignment explanation
Indices: 9141--9184 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9131 GATGGAGATA
9141 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
**
9163 GACGGATTTCGTTGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
9185 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:9397 original size:20 final size:20
Alignment explanation
Indices: 9372--9465 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
9362 GATTATGTAT
9372 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
9392 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
** *** * *
9412 TATCTTGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
9433 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
9453 TATCGCATTGCGA
1 TATCGCGTTGCGA
9466 TTTTCCCAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 46 0.79
21 12 0.21
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:9443 original size:21 final size:21
Alignment explanation
Indices: 9419--9510 Score: 59
Period size: 20 Copynumber: 4.5 Consensus size: 21
9409 AAGTATCTTG
* *
9419 TTGCGATTTTTTATTATCGCA
1 TTGCGATTTTTCAGTATCGCA
**
9440 TTGCGA-TAGTCAGTATCGCA
1 TTGCGATTTTTCAGTATCGCA
* * *
9460 TTGCGATTTTCCCAAT-TCGCG
1 TTGCGATTTT-TCAGTATCGCA
9481 TTGCGATTTACTT-A-T-TCGCA
1 TTGCGATTT--TTCAGTATCGCA
9501 TTGCGATTTT
1 TTGCGATTTT
9511 CCCAATTCGC
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
18 1 0.02
20 30 0.54
21 21 0.38
22 3 0.05
23 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (21 bp):
TTGCGATTTTTCAGTATCGCA
Found at i:9464 original size:41 final size:41
Alignment explanation
Indices: 9392--9469 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
9382 CGAAAGTCAG
* ***
9392 TATCGCGTTGCGAAAGTAAGTATCTTGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
9433 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
9470 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:9466 original size:20 final size:20
Alignment explanation
Indices: 9352--9466 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
9342 CGCTTTGAAA
*
9352 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
9373 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
9393 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
*** ** * *
9413 ATCTTGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
9434 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
9454 ATCGCATTGCGAT
1 ATCGCATTGCGAT
9467 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.66
21 23 0.31
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:9485 original size:41 final size:41
Alignment explanation
Indices: 9455--9547 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
9445 ATAGTCAGTA
* *
9455 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
9496 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
9537 TCGCATTGCGA
1 TCGCATTGCGA
9548 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:9520 original size:21 final size:20
Alignment explanation
Indices: 9455--9547 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
9445 ATAGTCAGTA
*
9455 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
9476 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
9496 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
9517 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
9537 TCGCATTGCGA
1 TCGCATTGCGA
9548 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:9581 original size:21 final size:21
Alignment explanation
Indices: 9556--9607 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
9546 GAATTGGGAA
9556 AATCGCAACGATACTGTAGAC
1 AATCGCAACGATACTGTAGAC
*
9577 CATCGCAACGATACTGTAGAC
1 AATCGCAACGATACTGTAGAC
9598 AATCGCAACG
1 AATCGCAACG
9608 CGATTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (21 bp):
AATCGCAACGATACTGTAGAC
Found at i:12962 original size:26 final size:26
Alignment explanation
Indices: 12926--12977 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12916 CTTATGATGC
12926 ACACCTTACGTGTAAAATTTGAACTT
1 ACACCTTACGTGTAAAATTTGAACTT
12952 ACACCTTACGTGTAAAATTTGAACTT
1 ACACCTTACGTGTAAAATTTGAACTT
12978 GTTCTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (26 bp):
ACACCTTACGTGTAAAATTTGAACTT
Found at i:21958 original size:2 final size:2
Alignment explanation
Indices: 21951--21980 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21941 AGAAGAAATA
*
21951 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21981 GAAGGGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:22301 original size:2 final size:2
Alignment explanation
Indices: 22294--22328 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22284 AAAGAATTTA
22294 AT AT AT 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
22329 ATTTAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28783 original size:182 final size:182
Alignment explanation
Indices: 28477--29975 Score: 2380
Period size: 182 Copynumber: 8.2 Consensus size: 182
28467 TGGTAAAAAT
** * * *
28477 ATGATAAAACCGGTAAACCGCTACCGAATATTTTGAAAGTATCGATAAATTAATATAAGTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
*
28542 CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTATACAAATG
66 CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
* * * *
28607 TATCGATCCATAACAATATAACAGGTAATAATATGACAAAACCGGTGTC-ATT
131 TATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGA-A
** *
28659 ATGATAAAACCGGTAAACCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCAA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
*
28724 CATTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
66 CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
*
28789 TATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACATGTCTCGAA
131 TATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
* * *
28841 ATGATAAAAGCGGTAAAAAACTACCGGATATATTGAAAGTGTTGATAAATTAATATAAGTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
* * * *
28906 TACTTTTG-ATATTTAAAAGAGAATAAGTTATAGCACCTAAAAAGTGTCGATATTTTATACAAAT
66 CACTTTTGTA-ATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAAT
*
28970 GTATCGATCCATATCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
130 GTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
* *
29023 ATGATAAAACCGGTAAAAAGATACCAGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
29088 CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
66 CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
* *
29153 TATCGATCCATAACAATATAACAGGTAATAATATGACAAAACAAGTCTCGAA
131 TATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
* *
29205 ATGATAAAACCGGTAAAAAGATATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
* *
29270 CATTTTTGTAATTTAAAAGAGAATAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
66 CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
* *
29335 TATCGATCCATAGCAATATAACATGTAATAATATGATAAAACAGGTCTCGAA
131 TATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
* *
29387 ATGATAAAACCGGTAAAAAGCTATCGGATATATTGAAAGTGTCGATAAATTAATATAATTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
* * *
29452 CACTTTT-TATATTTAAAAGAAAAGAAGTTATAGTGCCTAAAAAGTGTCGATATTTTATACAAAT
66 CACTTTTGTA-ATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAAT
* *
29516 GTATCGATCCATAGCATTATAACAGGTAATAATATGACAAAACATGTCTCGAA
130 GTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
* * *
29569 ATGATAAAACCGGTAAAAAGCTATCGGATATATTGAAAATGTCGATAAATTAATATAATTATCGA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
*
29634 CACTTTT-TATATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATATTTTATACAAAT
66 CACTTTTGTA-ATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAAT
*
29698 GTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAATAGGTCTCGAA
130 GTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
*
29751 ATGATAAAACCGGTAAAAA-CTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCAA
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
* *
29815 CACTTTCGTAATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTGTCGATACTTTATGA-AAAT
66 CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT-ACAAAT
* * * * * *
29879 GTACCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGTATCGAA
130 GTATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
* ** * *
29932 ATGACAAAACCGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCG
1 ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCG
29976 GTACTTTAAT
Statistics
Matches: 1231, Mismatches: 79, Indels: 14
0.93 0.06 0.01
Matches are distributed among these distances:
181 162 0.13
182 1067 0.87
183 2 0.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (182 bp):
ATGATAAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGA
CACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATACAAATG
TATCGATCCATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAA
Found at i:31802 original size:22 final size:22
Alignment explanation
Indices: 31751--31806 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
31741 AATGTTTTTG
*
31751 TTTTTTTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
31774 TAGTTATTATATAAAATGAT-TAA
1 T-TTTATTATATAAAATGATGT-A
31797 TTTTATTATA
1 TTTTATTATA
31807 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 3 0.11
24 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:32478 original size:18 final size:18
Alignment explanation
Indices: 32455--32493 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
32445 GAGAAAATTT
32455 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
32473 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
32491 GAA
1 GAA
32494 ATGAGGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:32817 original size:17 final size:17
Alignment explanation
Indices: 32795--32830 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
32785 TTTAAATATT
32795 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
32812 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
32829 TC
1 TC
32831 CTAATGATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (17 bp):
TCATGAAAAGATATTAA
Found at i:34655 original size:198 final size:197
Alignment explanation
Indices: 34155--35063 Score: 1383
Period size: 198 Copynumber: 4.6 Consensus size: 197
34145 CATTCCAAGT
** *
34155 ATACTTTGTGTCCAGAATGATTTCCTTACCAA-GTGCATGGA-AATGTGTTGATACATTTATAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-CCATAATGTGTCGATACATTTATAAA
* *
34218 AAGTATTGATCCAAAATATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
64 AAGTATCGATCCAAAA-ACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
* * *
34283 CGGTCTAAATATACCAGTTTATGAGAAAACATGTGTACATAAAGTATCGACACTTGTTT-AATTT
128 CGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTT-TTTGAATTT
*
34347 GTGTCA
192 GTGTCG
* * * *
34353 ATCCCGTACTTTGTGTTCATAATGATTTCCTTACCAAGGTCACCATAATGTTTCGATACCTTTAT
1 A-----TACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACATTTAT
34418 AAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
61 AAAAAGTATCGAT-CCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
* *
34483 AACCGGTCTAAATACACCGGTTTATGAGAAAAAAGGTGTACATGAAGTATCGACACTTTTTGAAT
125 AACCGGTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAAT
*
34548 TTATGTCG
190 TTGTGTCG
* *
34556 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTGACCATAATGTGTCGATACCTTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACATTTATAAAAA
34621 GTATCGATTCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
66 GTATCGA-TCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
* * *
34686 GTCTAAATACACCGGTTTATGAGAAAATAGGTGTACATGAAGTATCGACACGTTTTGAATTTGTG
130 GTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAATTTGTG
34751 TCG
195 TCG
* * *
34754 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGATCACCACAATGTGTCAATACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACATTTATAAAAA
*
34819 GTATCGATCCAAAAAACATTGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
66 GTATCGATCC-AAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
* * * ** *
34884 GTCTAAATAAACCAGTTTATGAGAAAACAGATGTACATTAAGTATTAACACTTTTTTAATTTGTG
130 GTCTAAATACACCAGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAATTTGTG
34949 TCG
195 TCG
* *
34952 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTGTAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACATTTATAAAAA
35017 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGT
66 GTATCGATCC-AAAAACATCGAGACCCATAATTATAATGTAATAGGT
35064 CATTTTGCAA
Statistics
Matches: 658, Mismatches: 42, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
197 3 0.00
198 476 0.72
199 1 0.00
202 4 0.01
203 166 0.25
204 8 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (197 bp):
ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTCGATACATTTATAAAAA
GTATCGATCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCGG
TCTAAATACACCAGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTGAATTTGTGT
CG
Found at i:35475 original size:15 final size:15
Alignment explanation
Indices: 35455--35504 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
35445 AGAATCGGGG
*
35455 CTCTTCTCAACCCAT
1 CTCTTCTCAACCCAA
*
35470 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAA
35485 CTCTTCTCAACCCAA
1 CTCTTCTCAACCCAA
35500 CTCTT
1 CTCTT
35505 ATGAGGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.20, C:0.48, G:0.00, T:0.32
Consensus pattern (15 bp):
CTCTTCTCAACCCAA
Found at i:36679 original size:12 final size:12
Alignment explanation
Indices: 36632--36681 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
36622 CAAGCGGTCA
*
36632 ATGAAGATGACG
1 ATGAAGATGATG
*
36644 ATGAAGATGAAG
1 ATGAAGATGATG
*
36656 ATGAAGAAGATG
1 ATGAAGATGATG
*
36668 ATGATGATGATG
1 ATGAAGATGATG
36680 AT
1 AT
36682 CCAAATAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.44, C:0.02, G:0.32, T:0.22
Consensus pattern (12 bp):
ATGAAGATGATG
Found at i:36681 original size:6 final size:6
Alignment explanation
Indices: 36632--36677 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
36622 CAAGCGGTCA
* * * *
36632 ATGAAG ATGACG ATGAAG ATGAAG ATGAAG AAGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
36678 TGATCCAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.46, C:0.02, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:38053 original size:24 final size:24
Alignment explanation
Indices: 38002--38054 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
37992 TTTCATTTAT
* * *
38002 AATTAGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATGTA
38026 AATTTGAGTTTGAATTTAAATGTA
1 AATTTGAGTTTGAATTTAAATGTA
38050 AATTT
1 AATTT
38055 TGCTCCACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATGTA
Found at i:38947 original size:200 final size:199
Alignment explanation
Indices: 38415--39288 Score: 1028
Period size: 200 Copynumber: 4.4 Consensus size: 199
38405 AATGAATTTG
* * * *
38415 CTTTATTCATTTGTGTCGATACATGT-TGTCCAGAATGTA-TTTCCAAACCAAGTGCACGAACAA
1 CTTTATACATTTGTGTCGATAC-TTTATGTCCATAATGTATTTTCCAAA-CAAGTTCACGAA-AA
* * * *
38478 AGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAAT
63 AGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAAT
* * * *
38543 AGGTAAAATAACAATGTAACCAATCTAAATATACTGGTT-TATGAGAAAAGAGGTATACATAAAG
128 AGGTAAAATAACAATGTAACCAATCTAAATATACCGGTTAT-TAAGAAAAAAGGTATACATAATG
38607 TATCGACA
192 TATCGACA
*
38615 CTTTATACATTTGTGTCGATACTTTGTGTCCATAATGTATTTTCCAACCAAAACAAGTTCAC-AA
1 CTTTATACATTTGTGTCGATACTTTATGTCCATAATGTATTTT----CC-AAACAAGTTCACGAA
* * * * * * *
38679 ATAAGTGTCGACACATTTATATCAAGTGTCGATCCCAAAAATATTGAAACCCGTAACTATAATGT
61 A-AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGT
* * ** * ** * * * * *
38744 AATAAGTCACTTTACAATGTAACCGGTTTAAATTTATCGGTT-TTATGAGAAAATAGGTCTACA-
125 AATAGGTAAAATAACAATGTAACCAATCTAAATATACCGGTTATTA--AGAAAAAAGGTATACAT
38807 ATATGTATCGACA
188 A-ATGTATCGACA
* * * *
38820 CTTTATTCATTTGTGTCGATACATGT-TGTCCAGAATGTA-TTTCCAAACCAAGTGCACGAAAAA
1 CTTTATACATTTGTGTCGATAC-TTTATGTCCATAATGTATTTTCCAAA-CAAGTTCACGAAAAA
* *
38883 GTGTCGATACATTTATAACAAGTGTCGATCCTAAAAATATCGAAACACATAATTATAATGTAATA
64 GTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATA
** * *
38948 GGTAAAATAACAATGTAACCGGTCTAAATATACCGATTATTAAAAAAGAAAGGTATACATAATGT
129 GGTAAAATAACAATGTAACCAATCTAAATATACCGGTTATTAAGAAA-AAAGGTATACATAATGT
*
39013 ATCGATA
193 ATCGACA
* ** *
39020 CTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCATGAAAAAGT
1 CTTTATACATTTGTGTCGATACTTTATGTCCATAATGTATTTTCCAAACAAGTTCACGAAAAAGT
* *
39085 GTTGATACATTTATAACAAGTGTCGATCTCAAAAACATCGAAACACATAATTATAATGTAATAGG
66 GTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGG
* * *
39150 TAACATAACAATGTAACCAATCTAAACATACCAGTTATTAA-AAAAAAGGTATACATAATGTATC
131 TAAAATAACAATGTAACCAATCTAAATATACCGGTTATTAAGAAAAAAGGTATACATAATGTATC
*
39214 GATA
196 GACA
* * **
39218 CTTTATACACTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGT
1 CTTTATACATTTGTGTCGATACTTTATGTCCATAATGTATTTTCCAAACAAGTTCACGAAAAAGT
39283 GTCGAT
66 GTCGAT
39289 CCTAAAAACA
Statistics
Matches: 582, Mismatches: 73, Indels: 40
0.84 0.11 0.06
Matches are distributed among these distances:
198 92 0.16
199 14 0.02
200 292 0.50
201 18 0.03
203 2 0.00
204 92 0.16
205 67 0.12
206 5 0.01
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (199 bp):
CTTTATACATTTGTGTCGATACTTTATGTCCATAATGTATTTTCCAAACAAGTTCACGAAAAAGT
GTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAATGTAATAGG
TAAAATAACAATGTAACCAATCTAAATATACCGGTTATTAAGAAAAAAGGTATACATAATGTATC
GACA
Found at i:39027 original size:22 final size:21
Alignment explanation
Indices: 39001--39046 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
38991 AAAAGAAAGG
*
39001 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
39023 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
39044 TAT
1 TAT
39047 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:42342 original size:198 final size:198
Alignment explanation
Indices: 41829--42344 Score: 493
Period size: 198 Copynumber: 2.6 Consensus size: 198
41819 ATTAGATTTT
* * *
41829 GTGTCGATACATTTATAACAAGTATCGATCC-C-AAA-ATCAAAGAGACCGATAATTATAATGTA
1 GTGTCGATACATTTGTAAAAAGTATCGATCCTCGAAACATC-AA-A-ACCGATAATCATAATGTA
* * * * * *
41891 ATAGGTAAATTTCCAATGTAATCG-GTAGAAATATACCGGGTTCATGAGAGAATAGGTC-A-ATA
63 ACAGGTAATTTTACAATGTAATCGATTA-AAATATACC-GGTTAATGAGAAAATAGGTCTACAT-
* * * * * * *
41953 TAGAGTATCGACACTTTTTTAATTTGTGTCGATATATTTTTCCAAAATGAATGGCAAACGAGGTG
125 TA-TGTATCAACACTCTTTAAATATGTGTCGATATATTTTTCCAAAATGAAAGACAAACGAGGTG
*
42018 TACGCATAAA
189 CACGCATAAA
* * *
42028 GTGTCGATACATTTGTAAAAAGTATCGATCCTCGAAACATCAAAATCGATAATTATTATGTAACA
1 GTGTCGATACATTTGTAAAAAGTATCGATCCTCGAAACATCAAAACCGATAATCATAATGTAACA
* * *
42093 GGTAATTTTACAATGTAATCGGTTAAAATATACCGGTTAATTAGCAAATAGGTCTACATTATGTA
66 GGTAATTTTACAATGTAATCGATTAAAATATACCGGTTAATGAGAAAATAGGTCTACATTATGTA
* *
42158 TCAACACTCTTTAAATATGTGTCGATACT-TTTTTCTAAAAT-AAAGCACAAACGAGTTGCACGC
131 TCAACACTCTTTAAATATGTGTCGATA-TATTTTTCCAAAATGAAAG-ACAAACGAGGTGCACGC
42221 ATAAA
194 ATAAA
* **
42226 GTGTCGATACA-TT-TAAAATTGTATCGATCC-CGAAAACATTGAAACCGAT-ATACATAATGTA
1 GTGTCGATACATTTGTAAAA-AGTATCGATCCTCG-AAACATCAAAACCGATAAT-CATAATGTA
* * * * * *
42287 ATAGGTTAA-TTTATAATGTAA-CTGATTTAAATTTACCGCTTTTATGAGAAAATAGGTC
63 ACAGG-TAATTTTACAATGTAATC-GATTAAAATATACCG-GTTAATGAGAAAATAGGTC
42345 AATATAAGCG
Statistics
Matches: 266, Mismatches: 37, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
196 10 0.04
197 62 0.23
198 101 0.38
199 79 0.30
200 6 0.02
201 5 0.02
202 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (198 bp):
GTGTCGATACATTTGTAAAAAGTATCGATCCTCGAAACATCAAAACCGATAATCATAATGTAACA
GGTAATTTTACAATGTAATCGATTAAAATATACCGGTTAATGAGAAAATAGGTCTACATTATGTA
TCAACACTCTTTAAATATGTGTCGATATATTTTTCCAAAATGAAAGACAAACGAGGTGCACGCAT
AAA
Found at i:42448 original size:23 final size:23
Alignment explanation
Indices: 42422--42480 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
42412 CGGTTAAATG
*
42422 CCTATTTTATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
* *
42445 CCTATTACATTATATAAGTGCTA
1 CCTATTATATTATATAAGCGCTA
*
42468 CCTAATATATTAT
1 CCTATTATATTAT
42481 TGTGCTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (23 bp):
CCTATTATATTATATAAGCGCTA
Found at i:42453 original size:87 final size:87
Alignment explanation
Indices: 42346--42508 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
42336 AAATAGGTCA
* *
42346 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
42411 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
42433 ATATAAGCGCTACCTATTACATTATATAAGTGCTACCTAATATATTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
42498 CCGGTTAAATG
66 CCGGTTAAATG
42509 ATATAATATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:43168 original size:2 final size:2
Alignment explanation
Indices: 43161--43190 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43151 GTAATTTTAG
43161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43191 TAATAAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48045 original size:16 final size:16
Alignment explanation
Indices: 47980--48046 Score: 107
Period size: 16 Copynumber: 4.2 Consensus size: 16
47970 ATGATCAAAC
*
47980 GTTGAATGATTTAAAC
1 GTTGAATGATTTAAAT
*
47996 GTTAAATGATTTAAAT
1 GTTGAATGATTTAAAT
48012 GTTGAATGATTTAAAT
1 GTTGAATGATTTAAAT
*
48028 GTTGAATGATTTAGAT
1 GTTGAATGATTTAAAT
48044 GTT
1 GTT
48047 TTATATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.43
Consensus pattern (16 bp):
GTTGAATGATTTAAAT
Found at i:48075 original size:24 final size:22
Alignment explanation
Indices: 48032--48075 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
48022 TTAAATGTTG
**
48032 AATGATTTAGATGTTTTATATA
1 AATGATTTAGATGTGATATATA
48054 AATGAATTATAGATGTGATATA
1 AATG-ATT-TAGATGTGATATA
48076 CTGTTTGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 3 0.17
24 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (22 bp):
AATGATTTAGATGTGATATATA
Found at i:48362 original size:18 final size:19
Alignment explanation
Indices: 48328--48367 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
48318 CCTTTCGCTA
*
48328 AAAATACCATTTAAATATC
1 AAAATACCATATAAATATC
48347 AAAATA-CATATAAATATC
1 AAAATACCATATAAATATC
48365 AAA
1 AAA
48368 CATTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATACCATATAAATATC
Found at i:49144 original size:24 final size:24
Alignment explanation
Indices: 49117--49165 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
49107 TTGAGTAATG
49117 TCAGAGGTTCGAATCCTGACATTA
1 TCAGAGGTTCGAATCCTGACATTA
49141 TCAGAGGTTCGAATCCTGACATTA
1 TCAGAGGTTCGAATCCTGACATTA
49165 T
1 T
49166 GAATGAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (24 bp):
TCAGAGGTTCGAATCCTGACATTA
Found at i:55457 original size:18 final size:18
Alignment explanation
Indices: 55434--55480 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
55424 ATATAGAGTA
55434 GTATCAGTACCCCTTTGG
1 GTATCAGTACCCCTTTGG
55452 GTATCAGTACCCCTTTGG
1 GTATCAGTACCCCTTTGG
*
55470 GTATCGGTACC
1 GTATCAGTACC
55481 AATTTTGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (18 bp):
GTATCAGTACCCCTTTGG
Found at i:61273 original size:11 final size:11
Alignment explanation
Indices: 61249--61280 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
61239 AATTTTTTTC
61249 ATTATAAA--A
1 ATTATAAATTA
61258 ATTATAAATTA
1 ATTATAAATTA
61269 ATTATAAATTA
1 ATTATAAATTA
61280 A
1 A
61281 ATTTATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 8 0.38
11 13 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTATAAATTA
Found at i:62089 original size:2 final size:2
Alignment explanation
Indices: 62082--62114 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
62072 TTTGATACAA
62082 AT AT 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 A
62115 ATCTTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62901 original size:2 final size:2
Alignment explanation
Indices: 62894--62921 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
62884 TATAAAATCA
62894 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62922 TGATTAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64709 original size:25 final size:25
Alignment explanation
Indices: 64639--64709 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
64629 ATGAATAAGA
* *
64639 TAATAAAAAAATAATAATG--AAAG
1 TAATAATAAAATAATATTGCAAAAG
*
64662 TAATAATTTAAAT-ATATAT-CAAAAG
1 TAATAA-TAAAATAATAT-TGCAAAAG
64687 TAATAATAAAATAATATTGCAAA
1 TAATAATAAAATAATATTGCAAA
64710 TAAATAATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
23 9 0.24
24 11 0.29
25 18 0.47
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.30
Consensus pattern (25 bp):
TAATAATAAAATAATATTGCAAAAG
Found at i:66744 original size:3 final size:3
Alignment explanation
Indices: 66738--66774 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
66728 ATAATATATT
66738 TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
66775 AAGTAAACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:67041 original size:44 final size:45
Alignment explanation
Indices: 66928--67066 Score: 183
Period size: 45 Copynumber: 3.1 Consensus size: 45
66918 GAAGTCCTAT
* * *
66928 CATCTTGCACTGTAGGTCTTAAAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
** *
66973 CATCATTTACTGAAGG-CATTACAGATGACCCGAAGTTTTTGAAAA
1 CATCATGCACTGAAGGTC-TTACAGATGACCCGAAGGTTTTGAAAA
*
67018 CATCATGCACTG-AGGTCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
*
67062 TATCA
1 CATCA
67067 AAAATCTCCT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
44 33 0.41
45 48 0.59
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (45 bp):
CATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
Found at i:67245 original size:76 final size:76
Alignment explanation
Indices: 67001--67366 Score: 521
Period size: 75 Copynumber: 4.9 Consensus size: 76
66991 TTACAGATGA
*
67001 CCCGAA-G-TTTTTGAAAACATCATGCACTG-AGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
*
67063 ATCAAAAATCT
66 ATCAAAAAGCT
* * * ** * *
67074 CCTGAAGACTTTTTGAAAACATCCTGCACTATAGGTCTTATGGATGACCTG-AGGTTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
67138 ATCAAAAAGCT
66 ATCAAAAAGCT
* * *
67149 TCCGAAGGCTTTTTGAAAACATCCTGCAATGTAGGTCTTACAGATGACCCGAAGGCTTTAAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
67214 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
67225 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATG-TCCGAAGGTTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
*
67289 ATCATAAAGCT
66 ATCAAAAAGCT
* * *
67300 -CCGAAGGCTTTTTTAAAACATCCTGCATTGTAGGTCTTACAGATGA-CCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
67363 ATCA
66 ATCA
67367 TGCACTGAAG
Statistics
Matches: 259, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
73 5 0.02
74 62 0.24
75 110 0.42
76 82 0.32
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAAT
ATCAAAAAGCT
Found at i:67313 original size:151 final size:151
Alignment explanation
Indices: 67008--67366 Score: 555
Period size: 151 Copynumber: 2.4 Consensus size: 151
66998 TGACCCGAAG
* * *
67008 TTTTTGAAAACATCATGCACTG-AGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAT
1 TTTTTGAAAACATCCTGCAATGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAG
* **
67072 CTCCTGAAGACTTTTTGAAAACATCCTGCACTATAGGTCTTATGGATGACCTGAGGTTTTGAAAA
66 CTCCCGAAGACTTTTTGAAAACATCCTGCACTATAGGTCTTACAGATGACCTGAGGTTTTGAAAA
67137 TATCAAAAAGCTTCCGAAGGC
131 TATCAAAAAGCTTCCGAAGGC
*
67158 TTTTTGAAAACATCCTGCAATGTAGGTCTTACAGATGACCCGAAGGCTTTAAAAATATCAAAAAG
1 TTTTTGAAAACATCCTGCAATGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAG
* * *
67223 CTCCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGTCC-GAAGGTTTTGAAA
66 CTCCCGAAGACTTTTTGAAAACATCCTGCACTATAGGTCTTACAGATGACCTG-AGGTTTTGAAA
*
67287 ATATCATAAAGC-TCCGAAGGC
130 ATATCAAAAAGCTTCCGAAGGC
* * *
67308 TTTTTTAAAACATCCTGCATTGTAGGTCTTACAGATGA-CCGAAGGCTTTGAAAACATCA
1 TTTTTGAAAACATCCTGCAATGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCA
67367 TGCACTGAAG
Statistics
Matches: 192, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
149 19 0.10
150 66 0.34
151 107 0.56
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (151 bp):
TTTTTGAAAACATCCTGCAATGTAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAG
CTCCCGAAGACTTTTTGAAAACATCCTGCACTATAGGTCTTACAGATGACCTGAGGTTTTGAAAA
TATCAAAAAGCTTCCGAAGGC
Found at i:67383 original size:44 final size:45
Alignment explanation
Indices: 67300--67388 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 45
67290 TCATAAAGCT
* * * * *
67300 CCGAAGGCTTTTTTAAAACATCCTGCATTGTAGGTCTTACAGATGA
1 CCGAAGGC-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
67346 CCGAAGGC-TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 CCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
67389 TGGGAAATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 30 0.79
46 8 0.21
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (45 bp):
CCGAAGGCTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:69748 original size:118 final size:118
Alignment explanation
Indices: 69604--70021 Score: 719
Period size: 118 Copynumber: 3.5 Consensus size: 118
69594 CTGAATTGGA
* *
69604 CCTTCAAAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCGAGATTCCCCAATATTTG
1 CCTTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTG
* *
69669 CTTCTTGCTAATATGAGCTTTCAAAAATACCCAAATATTCATACTGGCGTGGG
66 CTTCTTGCTAATATGAGCTTTCAAAAATGCCCAAATATTCATACTGACGTGGG
* * *
69722 CCTTCAAAATGCCTCTCATGAATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTG
1 CCTTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTG
*
69787 CTTCTTGCTAATATGAGCTTTCAAAAATGCTCAAATATTCATACTGACGTGGG
66 CTTCTTGCTAATATGAGCTTTCAAAAATGCCCAAATATTCATACTGACGTGGG
*
69840 CCTTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCAAGATGCCCCAATATTTG
1 CCTTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTG
* *
69905 CTTCTTGATAATATGAGCTTTCAAAAATGCCCAAATATTCATACCGACGTGGG
66 CTTCTTGCTAATATGAGCTTTCAAAAATGCCCAAATATTCATACTGACGTGGG
* *
69958 CCTTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGAGCTTTCGAGATGCCCCAACATTT
1 CCTTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTT
70022 TAAACTGTAA
Statistics
Matches: 282, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 282 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (118 bp):
CCTTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGGCTTTCGAGATGCCCCAATATTTG
CTTCTTGCTAATATGAGCTTTCAAAAATGCCCAAATATTCATACTGACGTGGG
Found at i:70815 original size:34 final size:32
Alignment explanation
Indices: 70753--70822 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
70743 ACCTTACAAC
* * *
70753 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
*
70785 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
70819 TCCC
1 TCCC
70823 ATTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:71785 original size:21 final size:21
Alignment explanation
Indices: 71760--71801 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
71750 CCGTTAGACA
71760 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
71781 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
71802 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:74540 original size:21 final size:21
Alignment explanation
Indices: 74515--74556 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
74505 CCGTTAGACA
74515 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
74536 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
74557 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:78206 original size:14 final size:14
Alignment explanation
Indices: 78144--78225 Score: 51
Period size: 14 Copynumber: 5.7 Consensus size: 14
78134 AATGTAATGT
*
78144 AAATGCAAAAATGC
1 AAATGCAAATATGC
* *
78158 ATAAATGCAAAAAT-A
1 --AAATGCAAATATGC
*
78173 AGAATGCAAACTGTGC
1 A-AATGCAAA-TATGC
78189 -AATGCAAATATGC
1 AAATGCAAATATGC
* **
78202 AAATGAAAATATAA
1 AAATGCAAATATGC
78216 AAATGCAAAT
1 AAATGCAAAT
78226 GCAAACATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
13 5 0.09
14 35 0.66
15 1 0.02
16 12 0.23
ACGTcount: A:0.56, C:0.11, G:0.13, T:0.20
Consensus pattern (14 bp):
AAATGCAAATATGC
Found at i:78223 original size:20 final size:20
Alignment explanation
Indices: 78198--78238 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
78188 CAATGCAAAT
*
78198 ATGCAAATGAAAATATAAAA
1 ATGCAAATGAAAACATAAAA
*
78218 ATGCAAATGCAAACATAAAA
1 ATGCAAATGAAAACATAAAA
78238 A
1 A
78239 ATGAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (20 bp):
ATGCAAATGAAAACATAAAA
Found at i:81147 original size:2 final size:2
Alignment explanation
Indices: 81140--81167 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
81130 CTAAGGAAAA
81140 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81168 TTAGGGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.