Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000109.1 Hibiscus syriacus cultivar Beakdansim tig00000193_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: 69422
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:501 original size:41 final size:41
Alignment explanation
Indices: 429--506 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
419 TTCCAAGGAT
*
429 TTTTTGCTCAAAGGATCGATCCCCTAGAAAAATGATCGATC
1 TTTTTGCTCAAAGGATCGATCCCCTAGAAAAAGGATCGATC
* **
470 TTTTTG-TCCAAATGATCGATCCCCTTTAAAAAGGATC
1 TTTTTGCT-CAAAGGATCGATCCCCTAGAAAAAGGATC
507 ATTCCTTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.03
41 31 0.97
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (41 bp):
TTTTTGCTCAAAGGATCGATCCCCTAGAAAAAGGATCGATC
Found at i:6595 original size:20 final size:21
Alignment explanation
Indices: 6570--6609 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
6560 GGTAAAAAAT
*
6570 TACCTAAAAC-TTATTATTTC
1 TACCTAAAACATTAATATTTC
6590 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
6610 TTTAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:7621 original size:22 final size:22
Alignment explanation
Indices: 7585--7635 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
7575 CACAACATAA
* *
7585 ATTTGATTAATAAT-ATACTTT
1 ATTTTATTAATAATAAGACTTT
*
7606 ATTTTATTAAATAATAAGATTTT
1 ATTTTATT-AATAATAAGACTTT
7629 ATTTTAT
1 ATTTTAT
7636 ATATCATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
22 6 0.24
23 12 0.48
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTTTATTAATAATAAGACTTT
Found at i:10750 original size:2 final size:2
Alignment explanation
Indices: 10743--10769 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10733 GCAGCTTAAG
10743 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
10770 GCATACATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:21946 original size:21 final size:21
Alignment explanation
Indices: 21922--21969 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
21912 GTTATGAAAC
*
21922 TATGAACTTTGAA-CATGTGAA
1 TATGAACTTCGAATCA-GTGAA
21943 TATGAACTTCGAATCAGTGAA
1 TATGAACTTCGAATCAGTGAA
*
21964 TGTGAA
1 TATGAA
21970 TATACTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (21 bp):
TATGAACTTCGAATCAGTGAA
Found at i:25689 original size:23 final size:23
Alignment explanation
Indices: 25658--25705 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
25648 TCACCACAGC
*
25658 CCGCGTAGAAATGCACCAAAGTG
1 CCGCATAGAAATGCACCAAAGTG
25681 CCGCATAGAAATGCACCAAAGTG
1 CCGCATAGAAATGCACCAAAGTG
25704 CC
1 CC
25706 ATATAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.29, G:0.23, T:0.12
Consensus pattern (23 bp):
CCGCATAGAAATGCACCAAAGTG
Found at i:25806 original size:21 final size:19
Alignment explanation
Indices: 25748--25806 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 19
25738 CTCCTTAAGG
* *
25748 ACCATATATATTCCAAAGG
1 ACCATATATGTTCCAAAGA
*
25767 ACCAAATATGTGTCTCAAAGA
1 ACCATATATGT-TC-CAAAGA
25788 ACCGCATATATGTTCCAAA
1 A-C-CATATATGTTCCAAA
25807 AGATTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 9 0.28
20 2 0.06
21 10 0.31
22 3 0.09
23 8 0.25
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (19 bp):
ACCATATATGTTCCAAAGA
Found at i:26048 original size:22 final size:22
Alignment explanation
Indices: 26009--26050 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
25999 TATTGTAATG
*
26009 CATATCATATGAGTTCATGTCA
1 CATATCATATCAGTTCATGTCA
26031 CATATCATATCA-TATCATGT
1 CATATCATATCAGT-TCATGT
26051 AATGTAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (22 bp):
CATATCATATCAGTTCATGTCA
Found at i:26536 original size:20 final size:21
Alignment explanation
Indices: 26511--26565 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
26501 TATTTCCAAA
*
26511 ATGGTATCGATACCT-GCCTT
1 ATGGTATCGATACCTACCCTT
*
26531 ATGGTACCGATA-CTACCCTT
1 ATGGTATCGATACCTACCCTT
26551 -TCGGTATCGATACCT
1 AT-GGTATCGATACCT
26566 CATGAAGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.10
20 24 0.83
21 2 0.07
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (21 bp):
ATGGTATCGATACCTACCCTT
Found at i:30585 original size:2 final size:2
Alignment explanation
Indices: 30578--30611 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
30568 AAAAATCGAT
30578 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30612 TAGGTTCGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:32926 original size:215 final size:215
Alignment explanation
Indices: 32552--33034 Score: 776
Period size: 215 Copynumber: 2.3 Consensus size: 215
32542 ATTTAAAAAT
*
32552 TAAATTGAACAAATATGAAATTACAAA-AAAAA-TTAAATAAATTAATCAACACACATTGACGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGACGAG
32615 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATTATAC
* * * * *
32680 CCATTTAAAAAGTTATGGGCCAATTAAAAATATAAATAAGTAATAAGTA-CGGATCAATTTCATA
131 CCATTTAAAAAGTTATGAGCCAATTAAAAATAGAAATAAGTAATAAGTATAGG-TCAATTTAAAA
* *
32744 TGCAAATAAATTTTAGAGGAC
195 TGAAAATAAAATTTAGAGGAC
*
32765 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGACGAG
* *
32830 GGATCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAAT-ACAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATTATAC
* *
32894 TCATTTAAAAAGTTATGAGCCAATTAAAAAATAGAAATAAGTAATAAGTATAGGTCGATTTAAAA
131 CCATTTAAAAAGTTATGAGCCAATT-AAAAATAGAAATAAGTAATAAGTATAGGTCAATTTAAAA
* *
32959 TGAAAATAAAATTTGGAGGAT
195 TGAAAATAAAATTTAGAGGAC
*
32980 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
33035 AAAGGATTAA
Statistics
Matches: 250, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
213 27 0.11
214 48 0.19
215 173 0.69
216 2 0.01
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (215 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGACGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAAAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGAGCCAATTAAAAATAGAAATAAGTAATAAGTATAGGTCAATTTAAAAT
GAAAATAAAATTTAGAGGAC
Found at i:33197 original size:2 final size:2
Alignment explanation
Indices: 33123--33179 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
33113 TAATACATAC
*
33123 AT AT AT AC AT AT 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 AT AT AT AT AT AT
33165 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
33180 AACTAGATAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33255 original size:22 final size:21
Alignment explanation
Indices: 33201--33256 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
33191 TTATATAAAG
*
33201 AGTTTAT-ATATAAAGTATAT
1 AGTTTATAATATAAACTATAT
33221 -GTATTATATATATAAACTATAT
1 AGT-TTATA-ATATAAACTATAT
33243 AGTTTATCAATATA
1 AGTTTAT-AATATA
33257 TTATGTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 2 0.07
20 4 0.13
22 21 0.70
23 3 0.10
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (21 bp):
AGTTTATAATATAAACTATAT
Found at i:33396 original size:33 final size:32
Alignment explanation
Indices: 33348--33412 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
33338 TTCATATGTT
*
33348 AACTATAGTTCATATATATAGTATATAAATATA
1 AACTATAGTTCATATAAATAGTATA-AAATATA
* *
33381 AACTATATTTTATATAAATAGTATAAAATATA
1 AACTATAGTTCATATAAATAGTATAAAATATA
33413 GTATATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.40
Consensus pattern (32 bp):
AACTATAGTTCATATAAATAGTATAAAATATA
Found at i:33415 original size:12 final size:13
Alignment explanation
Indices: 33376--33425 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
33366 TAGTATATAA
*
33376 ATATAAACTATATT
1 ATATAAA-TATAGT
*
33390 TTATATAA-ATAGT
1 ATATA-AATATAGT
33403 ATA-AAATATAGT
1 ATATAAATATAGT
33415 ATATAAATATA
1 ATATAAATATA
33426 AATTATAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
11 2 0.07
12 9 0.30
13 13 0.43
14 4 0.13
15 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:33445 original size:20 final size:20
Alignment explanation
Indices: 33363--33436 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
33353 TAGTTCATAT
33363 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
**
33383 CTATATTTTATATAAATAGTATAAA
1 --ATATAGTATAT-AA-A-TATAAA
33408 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
33428 TTATAGTAT
1 ATATAGTAT
33437 GTAGTTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 14 0.32
21 1 0.02
22 11 0.25
23 11 0.25
24 1 0.02
25 6 0.14
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:33499 original size:19 final size:20
Alignment explanation
Indices: 33475--33547 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 20
33465 CTAAACCATA
33475 TATATA-TATATATATAAAC
1 TATATAGTATATATATAAAC
* *
33494 TATATAGTTTATAT-TAATC
1 TATATAGTATATATATAAAC
* * *
33513 TATATAGTTTACATATGAAC
1 TATATAGTATATATATAAAC
33533 TATATA-TATACTATA
1 TATATAGTATA-TATA
33548 GTTGATATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 26 0.59
20 18 0.41
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (20 bp):
TATATAGTATATATATAAAC
Found at i:33576 original size:18 final size:18
Alignment explanation
Indices: 33515--33617 Score: 70
Period size: 18 Copynumber: 5.7 Consensus size: 18
33505 TATTAATCTA
*
33515 TATAGTTTACATATGAAC
1 TATAGTTTATATATGAAC
* **
33533 TATA-TATATACTAT-AGT
1 TATAGTTTATA-TATGAAC
33550 TGATA-TTTATATATGAAC
1 T-ATAGTTTATATATGAAC
* *
33568 TATAGTTTACATATAAAC
1 TATAGTTTATATATGAAC
33586 TATATAGTTTATATA-GTAAC
1 --TATAGTTTATATATG-AAC
*
33606 TATAGTTGATAT
1 TATAGTTTATAT
33618 TTACATATGA
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
17 12 0.18
18 39 0.59
20 15 0.23
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.44
Consensus pattern (18 bp):
TATAGTTTATATATGAAC
Found at i:33608 original size:62 final size:62
Alignment explanation
Indices: 33533--33653 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 62
33523 ACATATGAAC
*
33533 TATATATATACTATAGTTGATATTTATATATGAACTATAGTTTACATATAAACTATATAGTT
1 TATATATATACTATAGTTGATATTTACATATGAACTATAGTTTACATATAAACTATATAGTT
* *
33595 TATATAGTA-ACTATAGTTGATATTTACATATGAACTATATTTTACATATTAACTATATA
1 TATATA-TATACTATAGTTGATATTTACATATGAACTATAGTTTACATATAAACTATATA
33654 TATAAACTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 53 0.96
63 2 0.04
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (62 bp):
TATATATATACTATAGTTGATATTTACATATGAACTATAGTTTACATATAAACTATATAGTT
Found at i:33640 original size:18 final size:18
Alignment explanation
Indices: 33515--33652 Score: 68
Period size: 18 Copynumber: 7.3 Consensus size: 18
33505 TATTAATCTA
*
33515 TATAGTTTACATATGAAC
1 TATATTTTACATATGAAC
* **
33533 TATATATATAC-TAT-AGT
1 TATAT-TTTACATATGAAC
*
33550 TGATA-TTTATATATGAAC
1 T-ATATTTTACATATGAAC
* *
33568 TATAGTTTACATATAAAC
1 TATATTTTACATATGAAC
*
33586 TATATAGTTTATATA-GTAAC
1 TATAT--TTTACATATG-AAC
33606 TATAGTTGATATTTACATATGAAC
1 --TA--T-AT-TTTACATATGAAC
*
33630 TATATTTTACATATTAAC
1 TATATTTTACATATGAAC
33648 TATAT
1 TATAT
33653 ATATAAACTA
Statistics
Matches: 90, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
16 3 0.03
17 8 0.09
18 44 0.49
19 6 0.07
20 11 0.12
22 4 0.04
24 11 0.12
25 3 0.03
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (18 bp):
TATATTTTACATATGAAC
Found at i:33723 original size:96 final size:99
Alignment explanation
Indices: 33565--33782 Score: 270
Period size: 96 Copynumber: 2.2 Consensus size: 99
33555 TTTATATATG
* * *
33565 AACTATAGTTTACATATAAACTATATAGT-T-TATATAGTAACTATAGTTGATATTTACATATGA
1 AACTATAGTTTACATATAAACTCTCT-CTCTCTATATAGTAACTATAGTTGATATTTACATATGA
* *
33628 ACTATATTTTACATATT-AACTATATA-TATAAACT
65 ACTACAGTTTACAT-TTAAACTATATATTATAAACT
* *
33662 -A-TATAGTTTACATGTAAACTCTCTCTCTCTATATA-TATACTATAGTTGATATTTATATATGA
1 AACTATAGTTTACATATAAACTCTCTCTCTCTATATAGTA-ACTATAGTTGATATTTACATATGA
*
33724 ACTACAGTTTACATTTAAACTATATATTTTATATACT
65 ACTACAGTTTACATTTAAACTATATA--TTATAAACT
33761 AACTATAGTTTACATATAAACT
1 AACTATAGTTTACATATAAACT
33783 ATAGTTGATA
Statistics
Matches: 103, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
94 1 0.01
95 25 0.24
96 51 0.50
99 7 0.07
100 1 0.01
101 18 0.17
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.43
Consensus pattern (99 bp):
AACTATAGTTTACATATAAACTCTCTCTCTCTATATAGTAACTATAGTTGATATTTACATATGAA
CTACAGTTTACATTTAAACTATATATTATAAACT
Found at i:33772 original size:18 final size:18
Alignment explanation
Indices: 33713--33793 Score: 65
Period size: 18 Copynumber: 4.4 Consensus size: 18
33703 ATAGTTGATA
* *
33713 TTTATATATGAACTACAG
1 TTTATATATAAACTATAG
* *
33731 TTTACATTTAAACTATA-
1 TTTATATATAAACTATAG
*
33748 TATTTTATATACTAACTATAG
1 T-TTATATATA--AACTATAG
*
33769 TTTACATATAAACTATAG
1 TTTATATATAAACTATAG
*
33787 TTGATAT
1 TTTATAT
33794 TTACATATGA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
17 1 0.02
18 32 0.67
20 14 0.29
21 1 0.02
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTATATATAAACTATAG
Found at i:33808 original size:42 final size:42
Alignment explanation
Indices: 33694--33827 Score: 179
Period size: 42 Copynumber: 3.3 Consensus size: 42
33684 CTCTCTCTAT
* *
33694 ATATATACTATAGTTGATATTTATATATGAACTACAGTTTAC
1 ATATAAACTATAGTTGATATTTATATATGAACTATAGTTTAC
*
33736 ATTTAAACTATA--T-AT-TTTATATACT-AACTATAGTTTAC
1 ATATAAACTATAGTTGATATTTATATA-TGAACTATAGTTTAC
*
33774 ATATAAACTATAGTTGATATTTACATATGAACTATAGTTTAC
1 ATATAAACTATAGTTGATATTTATATATGAACTATAGTTTAC
*
33816 ATATTAACTATA
1 ATATAAACTATA
33828 TATATAAACT
Statistics
Matches: 80, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
38 31 0.39
39 3 0.04
40 2 0.03
41 3 0.04
42 41 0.51
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (42 bp):
ATATAAACTATAGTTGATATTTATATATGAACTATAGTTTAC
Found at i:33816 original size:18 final size:18
Alignment explanation
Indices: 33793--33827 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33783 ATAGTTGATA
*
33793 TTTACATATGAACTATAG
1 TTTACATATAAACTATAG
*
33811 TTTACATATTAACTATA
1 TTTACATATAAACTATA
33828 TATATAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTACATATAAACTATAG
Found at i:33838 original size:31 final size:32
Alignment explanation
Indices: 33798--33866 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
33788 TGATATTTAC
*
33798 ATATGAAC-TATAGTTTACATATTAAC-TATAT
1 ATATAAACATATAGTTTACATA-TAACATATAT
*
33829 ATATAAACTATATAGTTTACATATGACATATAT
1 ATATAAAC-ATATAGTTTACATATAACATATAT
33862 ATATA
1 ATATA
33867 GTTTATTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 7 0.21
32 3 0.09
33 23 0.70
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.41
Consensus pattern (32 bp):
ATATAAACATATAGTTTACATATAACATATAT
Found at i:33899 original size:2 final size:2
Alignment explanation
Indices: 33894--33984 Score: 60
Period size: 2 Copynumber: 43.0 Consensus size: 2
33884 ATAAACTATT
* * *
33894 TA TA TA -A TA TA TA CTA TA TA TA TA AA CA TA CTA TA GTT TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA -TA TA TA
* *
33936 TT TA TA TA CTA TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
33978 TA GTA TA
1 TA -TA TA
33985 ATTTACATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
1 2 0.03
2 57 0.80
3 12 0.17
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:33927 original size:44 final size:42
Alignment explanation
Indices: 33879--33972 Score: 118
Period size: 44 Copynumber: 2.2 Consensus size: 42
33869 TTATTAGTGA
33879 ACTATATAAACTATTTATATAATATATACTATATATATAAACAT
1 ACTATATAAA-TATTTATATAATATATACTATATATATAAAC-T
** * *
33923 ACTATAGTTTATATTTATATACTATATATTATATATATAAACT
1 ACTATA-TAAATATTTATATAATATATACTATATATATAAACT
33966 A-TATATA
1 ACTATATA
33973 CTATATAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 1 0.02
42 4 0.09
43 2 0.05
44 35 0.80
45 2 0.05
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (42 bp):
ACTATATAAATATTTATATAATATATACTATATATATAAACT
Found at i:33928 original size:22 final size:21
Alignment explanation
Indices: 33900--34031 Score: 97
Period size: 22 Copynumber: 5.9 Consensus size: 21
33890 TATTTATATA
33900 ATATATACTATATATATAAAC
1 ATATATACTATATATATAAAC
* * *
33921 ATACTATAGTTTATATTTATATAC
1 ATA-TATA--CTATATATATAAAC
*
33945 -TATATATTATATATATAAAC
1 ATATATACTATATATATAAAC
33965 TATATATACTATATAGTATAATTTAC
1 -ATATATACTATATA-TATAA---AC
*
33991 ATATGA-ACTATATATAAAAACC
1 ATAT-ATACTATATATATAAA-C
*
34013 ATATAAACTATATACTATA
1 ATATATACTATATA-TATA
34032 GTTGATATTT
Statistics
Matches: 90, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
20 12 0.13
21 5 0.06
22 33 0.37
23 10 0.11
24 15 0.17
25 12 0.13
26 3 0.03
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATATACTATATATATAAAC
Found at i:33944 original size:20 final size:20
Alignment explanation
Indices: 33881--33984 Score: 87
Period size: 20 Copynumber: 5.4 Consensus size: 20
33871 ATTAGTGAAC
* *
33881 TATATAAACTATTTA-TATA
1 TATATATACTATATATTATA
33900 -ATATATACTATATA-TATA
1 TATATATACTATATATTATA
*
33918 -A-ACATACTATAGT-TTATA
1 TATATATACTATA-TATTATA
*
33936 TTTATATACTATATATTATA
1 TATATATACTATATATTATA
*
33956 TATATAAACTATATA-TACTA
1 TATATATACTATATATTA-TA
33976 TATAGTATA
1 TATA-TATA
33985 ATTTACATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
17 9 0.13
18 22 0.31
19 3 0.04
20 33 0.47
21 3 0.04
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (20 bp):
TATATATACTATATATTATA
Found at i:34001 original size:34 final size:36
Alignment explanation
Indices: 33882--34006 Score: 112
Period size: 34 Copynumber: 3.4 Consensus size: 36
33872 TTAGTGAACT
* *
33882 ATATAAACTATTTATATAATATATACTATATATATAAAC
1 ATATAAACTA--TATATACTATATACTATATAT-TATAC
* * * * *
33921 ATACTATAGTTTATAT-TTATATACTATATATTATAT
1 ATA-TAAACTATATATACTATATACTATATATTATAC
*
33957 ATATAAACTATATATACTATATAGTATA-ATT-TAC
1 ATATAAACTATATATACTATATACTATATATTATAC
*
33991 ATATGAACTATATATA
1 ATATAAACTATATATA
34007 AAAACCATAT
Statistics
Matches: 71, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
34 17 0.24
35 12 0.17
36 16 0.23
37 14 0.20
38 5 0.07
39 3 0.04
40 4 0.06
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (36 bp):
ATATAAACTATATATACTATATACTATATATTATAC
Found at i:34111 original size:18 final size:18
Alignment explanation
Indices: 34067--34306 Score: 103
Period size: 18 Copynumber: 13.2 Consensus size: 18
34057 TAATTTATAC
34067 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
* *
34085 TATGGTATATATAAATTA
1 TATAGTATATATAAACTA
**
34103 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
34119 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
**
34136 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
*
34152 T-TAGTATATATAACCTA
1 TATAGTATATATAAACTA
34169 TATAGTATATGGTATATACAAGCTA
1 TATAG--TA---TATATA-AA-CTA
* *
34194 TATATTATATAGTGCATTACTA
1 TATAGTATATA-T--A-AACTA
* *
34216 TATA-TA-ACCTATATAGTA
1 TATAGTATA--TATAAACTA
* *
34234 TATGGTATATACAAACTA
1 TATAGTATATATAAACTA
**
34252 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
34268 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
34285 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
34303 TATA
1 TATA
34307 TTGAAAAGTT
Statistics
Matches: 168, Mismatches: 25, Indels: 58
0.67 0.10 0.23
Matches are distributed among these distances:
15 13 0.08
16 23 0.14
17 24 0.14
18 66 0.39
19 3 0.02
20 8 0.05
21 4 0.02
22 9 0.05
23 10 0.06
24 1 0.01
25 7 0.04
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:34172 original size:33 final size:33
Alignment explanation
Indices: 34089--34295 Score: 203
Period size: 33 Copynumber: 6.8 Consensus size: 33
34079 AAACTATATG
*
34089 GTATATATAAATTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
34122 GTATATATAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
* *
34155 GTATATATAACCTATATAGTATAT-G-------
1 GTATATATAAACTATATATTATATAGTTCATTA
* * *
34180 GTATATACAAGCTATATATTATATAGTGCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
* * *
34213 CTATATATAACCTATATAGTATAT-G-------
1 GTATATATAAACTATATATTATATAGTTCATTA
*
34238 GTATATACAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
*
34271 GTATATATAAACTATATAGTATATA
1 GTATATATAAACTATATATTATATA
34296 TAAACTATAT
Statistics
Matches: 142, Mismatches: 16, Indels: 32
0.75 0.08 0.17
Matches are distributed among these distances:
25 41 0.29
26 2 0.01
32 2 0.01
33 97 0.68
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (33 bp):
GTATATATAAACTATATATTATATAGTTCATTA
Found at i:34175 original size:51 final size:51
Alignment explanation
Indices: 34067--34340 Score: 259
Period size: 58 Copynumber: 5.1 Consensus size: 51
34057 TAATTTATAC
** ** **
34067 TATAGTATATATAAACTATATGGTATATA-TAAATTA-TATATTATATAGTTCA
1 TATAGTATATATAAACTATATATTATATAGTTCATTAGTATA-TATA-ACCT-A
34119 T-TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTA
1 TATAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTA
* *
34169 TATAGTATATGGTATATACAAGCTATATATTATATAGTGCATTACTATATATAACCTA
1 TATAG--TA---TATATA-AA-CTATATATTATATAGTTCATTAGTATATATAACCTA
*
34227 TATAGTATATGGTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTA
1 TATAG--TA---TATAT--AAACTATATATTATATAGTTCATTAGTATATATAACCTA
*
34285 TATAGTATATATAAACTATATATTGA-AAAGTTCATTAGTATATTATAACCTA
1 TATAGTATATATAAACTATATATT-ATATAGTTCATTAGTATA-TATAACCTA
34337 TATA
1 TATA
34341 TTAATTTATT
Statistics
Matches: 195, Mismatches: 13, Indels: 28
0.83 0.06 0.12
Matches are distributed among these distances:
50 2 0.01
51 57 0.29
52 23 0.12
53 11 0.06
56 8 0.04
57 2 0.01
58 89 0.46
59 2 0.01
60 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (51 bp):
TATAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTA
Found at i:34184 original size:58 final size:58
Alignment explanation
Indices: 34122--34340 Score: 310
Period size: 58 Copynumber: 3.9 Consensus size: 58
34112 TAGTTCATTA
*
34122 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
* * *
34180 GTATATACAAGCTATATATTATATAGTGCATTACTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
*
34238 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAG--TA--
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
*
34292 -TATAT--AAACTATATATTGA-AAAGTTCATTAGTATATTATAACCTATATA
1 GTATATACAAACTATATATT-ATATAGTTCATTAGTATA-TATAACCTATATA
34341 TTAATTTATT
Statistics
Matches: 149, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
51 27 0.18
52 13 0.09
53 5 0.03
56 2 0.01
58 102 0.68
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (58 bp):
GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
Found at i:34194 original size:25 final size:25
Alignment explanation
Indices: 34155--34203 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
34145 TAGTTCATTA
*
34155 GTATATATAACCTATATAGTATATG
1 GTATATACAACCTATATAGTATATG
* *
34180 GTATATACAAGCTATATATTATAT
1 GTATATACAACCTATATAGTATAT
34204 AGTGCATTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (25 bp):
GTATATACAACCTATATAGTATATG
Found at i:34252 original size:25 final size:25
Alignment explanation
Indices: 34214--34261 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
34204 AGTGCATTAC
* *
34214 TATATATAACCTATATAGTATATGG
1 TATATACAAACTATATAGTATATGG
*
34239 TATATACAAACTATATATTATAT
1 TATATACAAACTATATAGTATAT
34262 AGTTCATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (25 bp):
TATATACAAACTATATAGTATATGG
Found at i:34481 original size:61 final size:61
Alignment explanation
Indices: 34400--34529 Score: 190
Period size: 61 Copynumber: 2.1 Consensus size: 61
34390 TATAATGATC
* * * *
34400 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGTAAT-ATTAAATTTGGACT
1 AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATTG-AATCATTAAATCTGGACT
* *
34461 AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATATATTGCATCATTAAATCTGGACT
1 AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATTGAATCATTAAATCTGGACT
34522 AAATTGAA
1 AAATTGAA
34530 CAAATTCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
60 2 0.03
61 60 0.97
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (61 bp):
AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATTGAATCATTAAATCTGGACT
Found at i:34671 original size:18 final size:17
Alignment explanation
Indices: 34650--34683 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34640 TTTTCAGCAT
34650 TTTCCTTAGTTTTTCTCA
1 TTTCCTTA-TTTTTCTCA
*
34668 TTTCGTTATTTTTCTC
1 TTTCCTTATTTTTCTC
34684 TCTCTAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.09, C:0.21, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTCCTTATTTTTCTCA
Found at i:34705 original size:18 final size:20
Alignment explanation
Indices: 34682--34726 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
34672 GTTATTTTTC
*
34682 TCTCTCTAACT-CTCTG-AT
1 TCTCTCTAAATCCTCTGCAT
34700 TCTCTC-AAATCCTCTGCAT
1 TCTCTCTAAATCCTCTGCAT
34719 TCTCTCTA
1 TCTCTCTA
34727 GAAAATTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 11 0.48
19 8 0.35
20 1 0.04
ACGTcount: A:0.18, C:0.36, G:0.04, T:0.42
Consensus pattern (20 bp):
TCTCTCTAAATCCTCTGCAT
Found at i:34991 original size:123 final size:122
Alignment explanation
Indices: 34741--35115 Score: 520
Period size: 123 Copynumber: 3.0 Consensus size: 122
34731 ATTAACCGTG
*
34741 TTCATTTTTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACCAAA
1 TTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACC-AAACCAAA
* *
34806 ACATTTTCGTGTTTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCTTCCGTGTTC
65 CCA-TTTCGTG-TTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCATCCGTGTTC
* *
34866 TTCATTTGTTCGTCCCAGTTCTTCCCCAAAA-CCTTATTTGATCTTCAAAAACACCTAAACACAA
1 TTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACC-AAAC-CAA
* * * *
34930 ACCATTTCGTGTTTTTTTCGATCAAACACCCAAATTTTCTTCGGTGTTCATCTGTGTTC
64 ACCATTTCGTGTTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCATCCGTGTTC
* * * *
34989 TTCATTTGTTCATCCCAATTCTTCCCCAAAACCCTCATTTAATATTCAAAAACACCGAACCCAAA
1 TTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACC-AAACCAAA
* * *
35054 CCATTTCGTGTTGTTTTCTATCAAACACCCACAA-ATTCATCCATTGTTCATCCGTGTTC
65 CCATTTCGTGTTTTTTTCGATCAAACACCCA-AATATTCATCC-GTGTTCATCCGTGTTC
35113 TTC
1 TTC
35116 CCTAAATCCT
Statistics
Matches: 222, Mismatches: 24, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
123 110 0.50
124 77 0.35
125 35 0.16
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.37
Consensus pattern (122 bp):
TTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAACCAAAC
CATTTCGTGTTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCATCCGTGTTC
Found at i:35268 original size:6 final size:6
Alignment explanation
Indices: 35250--35375 Score: 79
Period size: 6 Copynumber: 21.2 Consensus size: 6
35240 AATCCAAACA
* * *
35250 CTAACC C-AGACC CTAACC C-AGACC CAAACC TTAA-T CTATACC CTAACC
1 CTAACC CTA-ACC CTAACC CTA-ACC CTAACC CTAACC CTA-ACC CTAACC
*
35298 CTAACC CTAACC CTAACC TTAACC C-ATACC C-ATACC C-ATACC CTAACC
1 CTAACC CTAACC CTAACC CTAACC CTA-ACC CTA-ACC CTA-ACC CTAACC
* *
35346 CTAA-C CTGAACC C-AACC CGAACC CAAACC C
1 CTAACC CT-AACC CTAACC CTAACC CTAACC C
35376 AGGTATTTCT
Statistics
Matches: 101, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
5 13 0.13
6 80 0.79
7 8 0.08
ACGTcount: A:0.35, C:0.47, G:0.03, T:0.15
Consensus pattern (6 bp):
CTAACC
Found at i:35316 original size:36 final size:36
Alignment explanation
Indices: 35253--35363 Score: 122
Period size: 36 Copynumber: 3.1 Consensus size: 36
35243 CCAAACACTA
* * * *
35253 ACCCAGACCCTAACCC-AGACCCAAACCTTAATCTAT
1 ACCCATACCCTAACCCTA-ACCCTAACCTTAACCCAT
35289 ACCC-TAACCCTAACCCTAACCCTAACCTTAACCCAT
1 ACCCAT-ACCCTAACCCTAACCCTAACCTTAACCCAT
*
35325 ACCCATACCC-ATACCCTAACCCTAACCTGAACCCA-
1 ACCCATACCCTA-ACCCTAACCCTAACCTTAACCCAT
35360 ACCC
1 ACCC
35364 GAACCCAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
35 5 0.08
36 59 0.89
37 2 0.03
ACGTcount: A:0.34, C:0.47, G:0.03, T:0.16
Consensus pattern (36 bp):
ACCCATACCCTAACCCTAACCCTAACCTTAACCCAT
Found at i:35538 original size:2 final size:2
Alignment explanation
Indices: 35531--35601 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
35521 TATATGCTTG
35531 AT AT AT AT AT AT 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 AT AT AT AT AT AT
35573 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 A
35602 CTGGTTTATT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35638 original size:31 final size:31
Alignment explanation
Indices: 35597--35686 Score: 137
Period size: 31 Copynumber: 2.9 Consensus size: 31
35587 ATATATATAT
35597 ATATACTGGTTTATTGTTGTTGATGTAAATG
1 ATATACTGGTTTATTGTTGTTGATGTAAATG
* *
35628 ATGTACTGGTTTATTGCTGTTGATGTAAATG
1 ATATACTGGTTTATTGTTGTTGATGTAAATG
* *
35659 ATATACTGATTTATTGTTG-TAATGTAAA
1 ATATACTGGTTTATTGTTGTTGATGTAAA
35687 CTAACCATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 8 0.15
31 45 0.85
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (31 bp):
ATATACTGGTTTATTGTTGTTGATGTAAATG
Found at i:38062 original size:20 final size:20
Alignment explanation
Indices: 38024--38103 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
38014 AATACTTAGA
* * *
38024 GCTTGATTCTGTTTTATATT
1 GCTTGCTTCTATTTGATATT
*
38044 GTTTGCTTCTATTTGATATT
1 GCTTGCTTCTATTTGATATT
38064 GCTTGCTTCTATTTGATATT
1 GCTTGCTTCTATTTGATATT
*
38084 GCTTGCTTCTACTTGATATT
1 GCTTGCTTCTATTTGATATT
38104 TGTAAGGGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.15, C:0.14, G:0.15, T:0.56
Consensus pattern (20 bp):
GCTTGCTTCTATTTGATATT
Found at i:38981 original size:51 final size:48
Alignment explanation
Indices: 38925--39053 Score: 168
Period size: 51 Copynumber: 2.6 Consensus size: 48
38915 AATATAAAAC
*
38925 TAAATTTCAAAAAGTAATCATATTAATTTGATTATCATAATAATTTATGA
1 TAAATTTCAAAAAGTAATCATATTAATTTAATTATCAT-A-AATTTATGA
*
38975 TAAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAATTTATTA
1 T-AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAATTTATGA
* * *
39024 TAAATTTAAAATAACATAATTATATTAATT
1 TAAATTTCAAA-AA-GTAATCATATTAATT
39054 GTAACTTCAC
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
48 9 0.13
49 11 0.15
50 15 0.21
51 36 0.51
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (48 bp):
TAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAATTTATGA
Found at i:49362 original size:9 final size:9
Alignment explanation
Indices: 49348--49383 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
49338 TAAAATAAAC
49348 AATATTAAT
1 AATATTAAT
49357 AATATTAAT
1 AATATTAAT
49366 AATA-TAAT
1 AATATTAAT
*
49374 AATAATAAT
1 AATATTAAT
49383 A
1 A
49384 TAATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AATATTAAT
Found at i:49374 original size:14 final size:14
Alignment explanation
Indices: 49355--49392 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
49345 AACAATATTA
49355 ATAATATTAATAAT
1 ATAATATTAATAAT
*
49369 ATAATAATAATAAT
1 ATAATATTAATAAT
49383 ATAATTATTA
1 ATAA-TATTA
49393 TATCCCGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATATTAATAAT
Found at i:55458 original size:19 final size:19
Alignment explanation
Indices: 55434--55472 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
55424 ATGCCAAGAG
55434 TCGACGGTTCTATGCGGTC
1 TCGACGGTTCTATGCGGTC
55453 TCGACGGTTCTATGCGGTC
1 TCGACGGTTCTATGCGGTC
55472 T
1 T
55473 TTCGAGACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.26, G:0.31, T:0.33
Consensus pattern (19 bp):
TCGACGGTTCTATGCGGTC
Found at i:55487 original size:21 final size:21
Alignment explanation
Indices: 55463--55556 Score: 104
Period size: 21 Copynumber: 4.5 Consensus size: 21
55453 TCGACGGTTC
*
55463 TATGCGGTCTTTCGAGACATA
1 TATGTGGTCTTTCGAGACATA
*
55484 TATGTGATCCTTT-G-GACATA
1 TATGTGGT-CTTTCGAGACATA
*
55504 TATGTGTTCTTTCGAGACATA
1 TATGTGGTCTTTCGAGACATA
* *
55525 TATTTGGTCATTTGGA-ACATA
1 TATGTGGTC-TTTCGAGACATA
55546 TATGTGGTCTT
1 TATGTGGTCTT
55557 ACAAGACAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.06
20 16 0.26
21 33 0.53
22 9 0.15
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (21 bp):
TATGTGGTCTTTCGAGACATA
Found at i:55527 original size:41 final size:42
Alignment explanation
Indices: 55463--55556 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 42
55453 TCGACGGTTC
* *
55463 TATGCGGTCTTTCGAGACATATATGTGATCCTTTGG-ACATA
1 TATGTGGTCTTTCGAGACATATATGTGATCATTTGGAACATA
* * *
55504 TATGTGTTCTTTCGAGACATATATTTGGTCATTTGGAACATA
1 TATGTGGTCTTTCGAGACATATATGTGATCATTTGGAACATA
55546 TATGTGGTCTT
1 TATGTGGTCTT
55557 ACAAGACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 31 0.67
42 15 0.33
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (42 bp):
TATGTGGTCTTTCGAGACATATATGTGATCATTTGGAACATA
Found at i:55658 original size:23 final size:23
Alignment explanation
Indices: 55611--55665 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
55601 ATTCGGGACA
* *
55611 TTCTATGTGGCACTTCAATGTAT
1 TTCTACGTGGCACTTCAATGCAT
**
55634 TTCTACGTGGCACTTCGGTGCAT
1 TTCTACGTGGCACTTCAATGCAT
*
55657 TTATACGTG
1 TTCTACGTG
55666 TTGTGGTGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (23 bp):
TTCTACGTGGCACTTCAATGCAT
Found at i:57512 original size:19 final size:20
Alignment explanation
Indices: 57475--57513 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
57465 CAGATTGCCC
57475 AGAGGGAACCGATTCCCCCA
1 AGAGGGAACCGATTCCCCCA
*
57495 AGAGGGTACCGATTCCCCC
1 AGAGGGAACCGATTCCCCC
57514 TTGAATGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.36, G:0.26, T:0.13
Consensus pattern (20 bp):
AGAGGGAACCGATTCCCCCA
Found at i:63307 original size:22 final size:20
Alignment explanation
Indices: 63277--63334 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
63267 TGGTGCAGGA
* *
63277 GGAATCGATACCCCTTTGAAGG
1 GGAACCGATACCCC-CTGAA-G
* *
63299 GGAACCGATTCCCCCTGGAG
1 GGAACCGATACCCCCTGAAG
63319 GGAACCGATACCCCCT
1 GGAACCGATACCCCCT
63335 ACGGGGTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 16 0.52
21 3 0.10
22 12 0.39
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (20 bp):
GGAACCGATACCCCCTGAAG
Done.