Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397271.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_89.0, 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: 4184555
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 83639 characters in sequence are not A, C, G, or T
File 5 of 11
Found at i:1416115 original size:21 final size:21
Alignment explanation
Indices: 1416067--1416120 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1416057 TACTAAAATT
*
1416067 CTAATAAAAAAAAATCTCAAA
1 CTAATAAAATAAAATCTCAAA
*
1416088 CTAAATAAAATAAAATC-CTAAG
1 CT-AATAAAATAAAATCTC-AAA
1416110 CTAATAAAATA
1 CTAATAAAATA
1416121 CTAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.63, C:0.13, G:0.02, T:0.22
Consensus pattern (21 bp):
CTAATAAAATAAAATCTCAAA
Found at i:1421016 original size:37 final size:37
Alignment explanation
Indices: 1420966--1421042 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
1420956 CTTATATATT
*
1420966 TATGAACCCTGCTACACATATTGCTTTACTATAGAAA
1 TATGAACCCTGCTACACATATGGCTTTACTATAGAAA
*
1421003 TATGAACCCTGCTATACATATGGCTTTACTATAGAAA
1 TATGAACCCTGCTACACATATGGCTTTACTATAGAAA
1421040 TAT
1 TAT
1421043 TTTTTGAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (37 bp):
TATGAACCCTGCTACACATATGGCTTTACTATAGAAA
Found at i:1433034 original size:16 final size:16
Alignment explanation
Indices: 1433003--1433040 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1432993 AAGGAAGAAA
1433003 AAAAGAAGAAAGGAAG
1 AAAAGAAGAAAGGAAG
*
1433019 CAAAGCAAGAAA-GAAG
1 AAAAG-AAGAAAGGAAG
1433035 AAAAGA
1 AAAAGA
1433041 GGAAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 12 0.63
17 6 0.32
ACGTcount: A:0.68, C:0.05, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAAGAAGAAAGGAAG
Found at i:1434288 original size:27 final size:25
Alignment explanation
Indices: 1434256--1434305 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
1434246 ACATGGCTGG
*
1434256 GGTCATAGTTTGTAATATATGTGGCAA
1 GGTCATAGGTTG--ATATATGTGGCAA
*
1434283 GGTCATGGGTTGATATATGTGGC
1 GGTCATAGGTTGATATATGTGGC
1434306 TAGGCCTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
27 10 0.48
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (25 bp):
GGTCATAGGTTGATATATGTGGCAA
Found at i:1441002 original size:18 final size:19
Alignment explanation
Indices: 1440968--1441013 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
1440958 TCAAACAACT
1440968 AAATTGAAATTATACAAA-A
1 AAATT-AAATTATACAAACA
1440987 AAATTAAATGTA-ACAAACTA
1 AAATTAAAT-TATACAAAC-A
1441007 AAATTAA
1 AAATTAA
1441014 GACTAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 9 0.38
19 7 0.29
20 8 0.33
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (19 bp):
AAATTAAATTATACAAACA
Found at i:1441548 original size:34 final size:33
Alignment explanation
Indices: 1441486--1441572 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
1441476 AAAAGAAATT
* *
1441486 AAAATAAAATATATAATATAAAAAATTATATTAAA
1 AAAATAAAA-ATAAAATATAAAAAATTATAAT-AA
* *
1441521 AAAATAAAAATAAAATATATAAGATTATAATAA
1 AAAATAAAAATAAAATATAAAAAATTATAATAA
* *
1441554 GAAATGAAAATAAAATATA
1 AAAATAAAAATAAAATATA
1441573 CGACATAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 19 0.41
34 18 0.39
35 9 0.20
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (33 bp):
AAAATAAAAATAAAATATAAAAAATTATAATAA
Found at i:1443667 original size:14 final size:14
Alignment explanation
Indices: 1443648--1443676 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1443638 TTGTTGGTGC
1443648 TAGGGTGCTCACCT
1 TAGGGTGCTCACCT
1443662 TAGGGTGCTCACCT
1 TAGGGTGCTCACCT
1443676 T
1 T
1443677 GAGAGACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.31
Consensus pattern (14 bp):
TAGGGTGCTCACCT
Found at i:1447650 original size:42 final size:42
Alignment explanation
Indices: 1447581--1447673 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
1447571 TAGAGCCAAT
* *
1447581 CACAAAACAATCATGGGAAATGGAGACCTTCTCAATCCACTC
1 CACAAAACAAGCATAGGAAATGGAGACCTTCTCAATCCACTC
* * *
1447623 CACAACACAAGCATAGG-AATGTGAGACCTTTTCAATCCACTTT
1 CACAAAACAAGCATAGGAAATG-GAGACCTTCTCAATCCAC-TC
1447666 CACAAAAC
1 CACAAAAC
1447674 TCATATGCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
41 4 0.09
42 31 0.72
43 8 0.19
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.20
Consensus pattern (42 bp):
CACAAAACAAGCATAGGAAATGGAGACCTTCTCAATCCACTC
Found at i:1449679 original size:18 final size:19
Alignment explanation
Indices: 1449656--1449695 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1449646 CAGGTGGAGG
1449656 ATTTTG-AAATAAAATAAT
1 ATTTTGTAAATAAAATAAT
*
1449674 ATTTTGTTAATAAAATAAT
1 ATTTTGTAAATAAAATAAT
1449693 ATT
1 ATT
1449696 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTTGTAAATAAAATAAT
Found at i:1450596 original size:56 final size:56
Alignment explanation
Indices: 1450493--1450611 Score: 130
Period size: 56 Copynumber: 2.1 Consensus size: 56
1450483 GGTTGGCCAA
* * *** * *
1450493 GTGGTCAAATGAAAACAAAGGAAAATTGGTGCACGTGTTGTGGTTGGTTTCAAAGG
1 GTGGCCAAATGAAAACAAAAGAAAATTGGTGCACGAAATGTGATTGGTTCCAAAGG
* * * *
1450549 GTGGCCAAATGAACACAAAAGAAAATTTGTGCATGAAATGTGATTGGTTCCAATGG
1 GTGGCCAAATGAAAACAAAAGAAAATTGGTGCACGAAATGTGATTGGTTCCAAAGG
*
1450605 GAGGCCA
1 GTGGCCA
1450612 TATAACTACT
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.24
Consensus pattern (56 bp):
GTGGCCAAATGAAAACAAAAGAAAATTGGTGCACGAAATGTGATTGGTTCCAAAGG
Found at i:1457346 original size:15 final size:15
Alignment explanation
Indices: 1457326--1457362 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1457316 AAGCACTTTA
1457326 TGAAATGGATTTTCT
1 TGAAATGGATTTTCT
1457341 TGAAATGGATTTTCT
1 TGAAATGGATTTTCT
1457356 TGAAATG
1 TGAAATG
1457363 AAGTTTGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (15 bp):
TGAAATGGATTTTCT
Found at i:1457726 original size:29 final size:28
Alignment explanation
Indices: 1457670--1457763 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 28
1457660 ATCAAGCAAT
* * *
1457670 AACCCATGATTTTTAATGGGTTTAACCATA
1 AACCCATG-GTTTTAATGGG-TTCACCACA
*
1457700 AACCCATGGTTTTCAATGAGTTCACCACA
1 AACCCATGGTTTT-AATGGGTTCACCACA
* *
1457729 AACCAATGGCTTTTAATGGGGTCACCACA
1 AACCCATGG-TTTTAATGGGTTCACCACA
1457758 AACCCA
1 AACCCA
1457764 CGCAATGGCT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 37 0.69
30 17 0.31
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (28 bp):
AACCCATGGTTTTAATGGGTTCACCACA
Found at i:1465030 original size:29 final size:29
Alignment explanation
Indices: 1464971--1465036 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
1464961 TTAATGGGTT
* * *
1464971 ACCCATGGTTTTCAATGGGCTAACTACAA
1 ACCCATGGATTTCAATGGGCTAACCAAAA
* * *
1465000 ACCTATGGATTTCAATGGGTTCACCAAAA
1 ACCCATGGATTTCAATGGGCTAACCAAAA
1465029 ACCCATGG
1 ACCCATGG
1465037 TTTTTAACGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (29 bp):
ACCCATGGATTTCAATGGGCTAACCAAAA
Found at i:1471486 original size:15 final size:15
Alignment explanation
Indices: 1471466--1471500 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1471456 TTGAAACTGG
*
1471466 TATTTTTTTTTTAGT
1 TATTTTTGTTTTAGT
*
1471481 TATTTTTGTTTTATT
1 TATTTTTGTTTTAGT
1471496 TATTT
1 TATTT
1471501 ATATTTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (15 bp):
TATTTTTGTTTTAGT
Found at i:1471497 original size:19 final size:20
Alignment explanation
Indices: 1471470--1471507 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1471460 AACTGGTATT
*
1471470 TTTTTTTTAGTTAT-TTTTG
1 TTTTATTTAGTTATATTTTG
*
1471489 TTTTATTTATTTATATTTT
1 TTTTATTTAGTTATATTTT
1471508 TACATTAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTATTTAGTTATATTTTG
Found at i:1477340 original size:21 final size:21
Alignment explanation
Indices: 1477314--1477372 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
1477304 GTTCATACAA
1477314 TTCATGACAAAGAATGACACC
1 TTCATGACAAAGAATGACACC
*
1477335 TTCATGGA-AAA-AACTAACACC
1 TTCAT-GACAAAGAA-TGACACC
*
1477356 TACATGACAAAGAATGA
1 TTCATGACAAAGAATGA
1477373 TGCCACTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 4 0.13
21 23 0.74
22 4 0.13
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.19
Consensus pattern (21 bp):
TTCATGACAAAGAATGACACC
Found at i:1480509 original size:17 final size:17
Alignment explanation
Indices: 1480487--1480536 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
1480477 AATTATTTCT
1480487 TAGCTTTCAAAAATATC
1 TAGCTTTCAAAAATATC
1480504 TAGCTTTCAAAAATATC
1 TAGCTTTCAAAAATATC
*
1480521 TAACTTTTCAAAAATA
1 TAGC-TTTCAAAAATA
1480537 ACCCAATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 20 0.65
18 11 0.35
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (17 bp):
TAGCTTTCAAAAATATC
Found at i:1480923 original size:20 final size:20
Alignment explanation
Indices: 1480895--1480935 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1480885 TGTAAATACC
*
1480895 TAGGGATGTATCGAA-ACATT
1 TAGGAATGTATC-AATACATT
1480915 TAGGAATGTATCAATACATT
1 TAGGAATGTATCAATACATT
1480935 T
1 T
1480936 GCATAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
TAGGAATGTATCAATACATT
Found at i:1496212 original size:27 final size:25
Alignment explanation
Indices: 1496152--1496211 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
1496142 GTGGTTGAAA
**
1496152 CCACATATATCAACTTGTGGCCTAG
1 CCACATATATCAACCAGTGGCCTAG
*
1496177 CCACATATATCAACCAGTGGCCTTG
1 CCACATATATCAACCAGTGGCCTAG
1496202 CCACATATAT
1 CCACATATAT
1496212 AAATCACAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (25 bp):
CCACATATATCAACCAGTGGCCTAG
Found at i:1497697 original size:23 final size:23
Alignment explanation
Indices: 1497654--1497697 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1497644 TTTTCTTCTT
*
1497654 TCTTCTCTCTCTTTTTTCTTTCC
1 TCTTCTCTCTCTTTTTCCTTTCC
*
1497677 TCTTTTCTC-CTTTCTTCCTTT
1 TCTTCTCTCTCTTT-TTCCTTT
1497698 TTTTGCTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (23 bp):
TCTTCTCTCTCTTTTTCCTTTCC
Found at i:1504052 original size:14 final size:14
Alignment explanation
Indices: 1504035--1504061 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1504025 GCTGTAGCAC
1504035 TGGAGAAGTAGCGT
1 TGGAGAAGTAGCGT
1504049 TGGAGAAGTAGCG
1 TGGAGAAGTAGCG
1504062 CCACAGCGTT
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:0.30, C:0.07, G:0.44, T:0.19
Consensus pattern (14 bp):
TGGAGAAGTAGCGT
Found at i:1509907 original size:21 final size:21
Alignment explanation
Indices: 1509882--1509922 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1509872 TCCAAGCCCT
*
1509882 TTTTC-TTCTTTCTCTTTTCTC
1 TTTTCTTTC-TTCTCCTTTCTC
1509903 TTTTCTTTCTTCTCCTTTCT
1 TTTTCTTTCTTCTCCTTTCT
1509923 GTCCTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTCTTTCTTCTCCTTTCTC
Found at i:1522622 original size:3 final size:3
Alignment explanation
Indices: 1522614--1522639 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1522604 TGGCTGTGGC
1522614 TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TG
1522640 AAGGTGGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
TGT
Found at i:1526576 original size:35 final size:35
Alignment explanation
Indices: 1526537--1526630 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 35
1526527 TAGAAAAAGG
* *
1526537 CATTTGTAAAGGTTGTACTTGCTCCCATGAAATGA
1 CATTTGTAAAGGTTGTACTTACTCCAATGAAATGA
* * * *
1526572 CATTTGTAAGGGTTGTGCTTACTCTAATGAAATGG
1 CATTTGTAAAGGTTGTACTTACTCCAATGAAATGA
* * * *
1526607 CATTTTTGAGGGTTGTGCTTACTC
1 CATTTGTAAAGGTTGTACTTACTC
1526631 ATATAAAAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (35 bp):
CATTTGTAAAGGTTGTACTTACTCCAATGAAATGA
Found at i:1526644 original size:35 final size:34
Alignment explanation
Indices: 1526580--1526682 Score: 122
Period size: 35 Copynumber: 3.0 Consensus size: 34
1526570 GACATTTGTA
*
1526580 AGGGTTGTGCTTACTC-TAATGAAATGGCATTTTTG
1 AGGGTTGTGCTTACTCAT-AT-AAAAGGCATTTTTG
*
1526615 AGGGTTGTGCTTACTCATATAAAAAGGCA-TTGTG
1 AGGGTTGTGCTTACTCATAT-AAAAGGCATTTTTG
1526649 AGGGTTGTGCTTGAACTCAT-TAAAAGGCATTTTT
1 AGGGTTGTGCTT--ACTCATATAAAAGGCATTTTT
1526683 CCCTTGGTGG
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
34 24 0.40
35 29 0.48
36 7 0.12
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (34 bp):
AGGGTTGTGCTTACTCATATAAAAGGCATTTTTG
Found at i:1545264 original size:22 final size:23
Alignment explanation
Indices: 1545237--1545308 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
1545227 CACTTTTTCT
1545237 TTTCTTCG-TTC-TCCTCTCTCCC
1 TTTCTTCGTTTCTTCCTCTCT-CC
*
1545259 TTTCTTCGTTTCTTCCTTTCTCC
1 TTTCTTCGTTTCTTCCTCTCTCC
1545282 TTTCTTTC-TTTCTT--TCT-TCC
1 TTTC-TTCGTTTCTTCCTCTCTCC
1545302 TTTCTTC
1 TTTCTTC
1545309 CTTTGTTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
19 3 0.07
20 7 0.16
21 2 0.04
22 8 0.18
23 15 0.33
24 10 0.22
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.61
Consensus pattern (23 bp):
TTTCTTCGTTTCTTCCTCTCTCC
Found at i:1545272 original size:8 final size:8
Alignment explanation
Indices: 1545223--1545312 Score: 62
Period size: 8 Copynumber: 11.1 Consensus size: 8
1545213 TTAGGCCGAA
1545223 TCTTCACTT
1 TCTTC-CTT
*
1545232 T-TTCTTT
1 TCTTCCTT
*
1545239 TCTT-CGT
1 TCTTCCTT
*
1545246 TC-TCCTC
1 TCTTCCTT
*
1545253 TCTCCCTT
1 TCTTCCTT
*
1545261 TCTTCGTT
1 TCTTCCTT
1545269 TCTTCCTT
1 TCTTCCTT
1545277 TC-TCCTT
1 TCTTCCTT
1545284 TCTTTCTTTCTT
1 TC-TTC---CTT
1545296 TCTTCCTT
1 TCTTCCTT
1545304 TCTTCCTT
1 TCTTCCTT
1545312 T
1 T
1545313 GTTTCCTAGT
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
6 1 0.02
7 16 0.25
8 35 0.56
9 3 0.05
11 3 0.05
12 5 0.08
ACGTcount: A:0.01, C:0.34, G:0.02, T:0.62
Consensus pattern (8 bp):
TCTTCCTT
Found at i:1545290 original size:4 final size:4
Alignment explanation
Indices: 1545258--1545317 Score: 52
Period size: 4 Copynumber: 15.2 Consensus size: 4
1545248 TCCTCTCTCC
* * *
1545258 CTTT C-TT CGTTT CTTC CTTT C-TC CTTT CTTT CTTT CTTT CTTC CTTT
1 CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
* *
1545305 CTTC CTTT GTTT C
1 CTTT CTTT CTTT C
1545318 CTAGTCGAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
3 5 0.12
4 35 0.81
5 3 0.07
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:1545304 original size:20 final size:19
Alignment explanation
Indices: 1545267--1545317 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1545257 CCTTTCTTCG
*
1545267 TTTCTTCCTTTCTCCTTTC
1 TTTCTTTCTTTCTCCTTTC
1545286 TTTCTTTCTTTCTTCCTTTC
1 TTTCTTTCTTTC-TCCTTTC
* *
1545306 TTCCTTTGTTTC
1 TTTCTTTCTTTC
1545318 CTAGTCGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTCTTTCTTTCTCCTTTC
Found at i:1546909 original size:35 final size:35
Alignment explanation
Indices: 1546865--1547046 Score: 166
Period size: 35 Copynumber: 5.2 Consensus size: 35
1546855 GATTCATTAA
* *
1546865 ATTGTGCCTAATTCATTAAATTATTTAATTAAGTC
1 ATTGGGCCTAATTCATTAAATTATTTAATTAAGTT
* * ***
1546900 ATTGGGCCTAATTAATTGAATTAAACAATTAAGTT
1 ATTGGGCCTAATTCATTAAATTATTTAATTAAGTT
* * * * * * *
1546935 ATTAGTCTTAATTGATAAAATTTGTTTAATCAAGTT
1 ATTGGGCCTAATTCATTAAA-TTATTTAATTAAGTT
* *
1546971 ATTGGGCCTAATTCATTAAATTGTTTAATTAAATT
1 ATTGGGCCTAATTCATTAAATTATTTAATTAAGTT
* ***
1547006 ATTAGGCCTAATTCATTAAATTAAACAATTAAGTT
1 ATTGGGCCTAATTCATTAAATTATTTAATTAAGTT
*
1547041 AATGGG
1 ATTGGG
1547047 GCTTCTTAAG
Statistics
Matches: 113, Mismatches: 33, Indels: 2
0.76 0.22 0.01
Matches are distributed among these distances:
35 88 0.78
36 25 0.22
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (35 bp):
ATTGGGCCTAATTCATTAAATTATTTAATTAAGTT
Found at i:1547018 original size:71 final size:71
Alignment explanation
Indices: 1546870--1547027 Score: 183
Period size: 71 Copynumber: 2.2 Consensus size: 71
1546860 ATTAAATTGT
* * *
1546870 GCCTAATTCATTAAA-TTATTTAATTAAGTCATTGGGCCTAATTAATTGAATTAAACAATTAAGT
1 GCCTAATTCATTAAATTTATTTAATCAAGTCATTGGGCCTAATTAATTAAATTAAACAATTAAAT
1546934 TATTAG
66 TATTAG
* * * * * * * ****
1546940 TCTTAATTGATAAAATTTGTTTAATCAAGTTATTGGGCCTAATTCATTAAATTGTTTAATTAAAT
1 GCCTAATTCATTAAATTTATTTAATCAAGTCATTGGGCCTAATTAATTAAATTAAACAATTAAAT
1547005 TATTAG
66 TATTAG
1547011 GCCTAATTCATTAAATT
1 GCCTAATTCATTAAATT
1547028 AAACAATTAA
Statistics
Matches: 69, Mismatches: 18, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
70 11 0.16
71 58 0.84
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (71 bp):
GCCTAATTCATTAAATTTATTTAATCAAGTCATTGGGCCTAATTAATTAAATTAAACAATTAAAT
TATTAG
Found at i:1551365 original size:105 final size:105
Alignment explanation
Indices: 1551200--1551391 Score: 303
Period size: 105 Copynumber: 1.8 Consensus size: 105
1551190 TTTCAACCTC
* * * *
1551200 AAGCTTTATAGCTCACACTTTGGTTGTAATGTTACTATTGTACTTGGTCGCAAGCTTTATCGCTC
1 AAGCTTCATAGCTCACACTTTGGTTGTAATGTTACTATTGCACTTGATCACAAGCTTTATCGCTC
*
1551265 ATTCTTTGACCATATAATTCATTATTCATGGTTCGGCCAT
66 ATTCCTTGACCATATAATTCATTATTCATGGTTCGGCCAT
** * *
1551305 AAGCTTCATAGCTCTTACTTTGGTTGTAATGTTATTGTTGCACTTGATCACAAGCTTTATCGCTC
1 AAGCTTCATAGCTCACACTTTGGTTGTAATGTTACTATTGCACTTGATCACAAGCTTTATCGCTC
1551370 ATTCCTTGACCATATAATTCAT
66 ATTCCTTGACCATATAATTCAT
1551392 CACTTATATT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 78 1.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.41
Consensus pattern (105 bp):
AAGCTTCATAGCTCACACTTTGGTTGTAATGTTACTATTGCACTTGATCACAAGCTTTATCGCTC
ATTCCTTGACCATATAATTCATTATTCATGGTTCGGCCAT
Found at i:1551414 original size:105 final size:105
Alignment explanation
Indices: 1551183--1551415 Score: 288
Period size: 105 Copynumber: 2.2 Consensus size: 105
1551173 AAAAACAAAA
* * * * * *
1551183 ATTCATATTTCAACCTCAAGCTTTATAGCTCACACTTTGGTTGTAATGTTACTATTGTACTTGGT
1 ATTCATAGTTCAGCCACAAGCTTCATAGCTCACACTTTGGTTGTAATGTTACTATTGCACTTGAT
* * *
1551248 CGCAAGCTTTATCGCTCATTCTTTGACCATATAATTCATT
66 CACAAGCTTTATCGCTCATTCCTTGACCATATAATTCATC
* * * ** * *
1551288 ATTCATGGTTCGGCCATAAGCTTCATAGCTCTTACTTTGGTTGTAATGTTATTGTTGCACTTGAT
1 ATTCATAGTTCAGCCACAAGCTTCATAGCTCACACTTTGGTTGTAATGTTACTATTGCACTTGAT
1551353 CACAAGCTTTATCGCTCATTCCTTGACCATATAATTCATC
66 CACAAGCTTTATCGCTCATTCCTTGACCATATAATTCATC
* *
1551393 ACTT-ATATTTCAGCTACAAGCTT
1 A-TTCATAGTTCAGCCACAAGCTT
1551416 TAACAATTTG
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
105 104 0.98
106 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.41
Consensus pattern (105 bp):
ATTCATAGTTCAGCCACAAGCTTCATAGCTCACACTTTGGTTGTAATGTTACTATTGCACTTGAT
CACAAGCTTTATCGCTCATTCCTTGACCATATAATTCATC
Found at i:1553190 original size:52 final size:53
Alignment explanation
Indices: 1553133--1553250 Score: 163
Period size: 52 Copynumber: 2.3 Consensus size: 53
1553123 ACGCTAATAT
* *
1553133 GGACATTTC-AAGTGCAGAATGCCCAAA-AGCATTCCAAGTCTGTAATACCCAA
1 GGACATTTCTAAGTGCAGAACGCCCAAAGA-CATTCCAAGTATGTAATACCCAA
* *
1553185 GGACA-TTCTAAGTGCATAACGCCCAAGGACATTCCAAGTATGTAATACCCAA
1 GGACATTTCTAAGTGCAGAACGCCCAAAGACATTCCAAGTATGTAATACCCAA
1553237 GGACA-TTCTAAGTG
1 GGACATTTCTAAGTG
1553251 TGTAACAAGC
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
51 3 0.05
52 56 0.93
53 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (53 bp):
GGACATTTCTAAGTGCAGAACGCCCAAAGACATTCCAAGTATGTAATACCCAA
Found at i:1553191 original size:26 final size:26
Alignment explanation
Indices: 1553162--1553255 Score: 109
Period size: 26 Copynumber: 3.6 Consensus size: 26
1553152 TGCCCAAAAG
1553162 CATTCCAAGTCTGTAATACCCAAGGA
1 CATTCCAAGTCTGTAATACCCAAGGA
* * **
1553188 CATTCTAAGTGC-ATAACGCCCAAGGA
1 CATTCCAAGT-CTGTAATACCCAAGGA
*
1553214 CATTCCAAGTATGTAATACCCAAGGA
1 CATTCCAAGTCTGTAATACCCAAGGA
* *
1553240 CATTCTAAGTGTGTAA
1 CATTCCAAGTCTGTAA
1553256 CAAGCACAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
26 54 0.98
27 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (26 bp):
CATTCCAAGTCTGTAATACCCAAGGA
Found at i:1553425 original size:24 final size:25
Alignment explanation
Indices: 1553387--1553436 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1553377 CCAAGTGTGT
*
1553387 AACACCTAGAAATGTT-CTAAGTGC
1 AACACCTAGAAATGTTCCTAACTGC
**
1553411 AACACCTAGTGATGTTCCTAACTGC
1 AACACCTAGAAATGTTCCTAACTGC
1553436 A
1 A
1553437 TAAGCATAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (25 bp):
AACACCTAGAAATGTTCCTAACTGC
Found at i:1553550 original size:26 final size:26
Alignment explanation
Indices: 1553481--1553550 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
1553471 AAAGATATTC
*
1553481 CCAAGTGTGTAACGCATAGGGACATT
1 CCAAGTGTGTAACGCCTAGGGACATT
*
1553507 CCAAGTGCGTAACGCCTAGGGACATT
1 CCAAGTGTGTAACGCCTAGGGACATT
*
1553533 CCAAGTGTGTAACACCTA
1 CCAAGTGTGTAACGCCTA
1553551 CTGATGTTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (26 bp):
CCAAGTGTGTAACGCCTAGGGACATT
Found at i:1573249 original size:2 final size:2
Alignment explanation
Indices: 1573242--1573285 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
1573232 AAGTAGGAGT
*
1573242 TA TA TA TA TA TA TA TA TA TA TA TT TA TGA TA T- TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
1573283 TA T
1 TA T
1573286 TCAAAGTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1576288 original size:35 final size:35
Alignment explanation
Indices: 1576219--1576291 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
1576209 AAAGTTATCT
*
1576219 ATGTAAGGGGAAGAACTCCTGATAAAATAGGTTGA
1 ATGTAAGGGGAAGAACTCCTGATAAAATAAGTTGA
* ** *
1576254 ATGTAAGGGGAAGAACTCTTGATGTAGTAAGTTGA
1 ATGTAAGGGGAAGAACTCCTGATAAAATAAGTTGA
1576289 ATG
1 ATG
1576292 CAGAGAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (35 bp):
ATGTAAGGGGAAGAACTCCTGATAAAATAAGTTGA
Found at i:1578071 original size:30 final size:31
Alignment explanation
Indices: 1578037--1578103 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1578027 ATGGGTGAAG
1578037 TTGTAA-TTATG-AACAAGTTGAAGGATCAAA
1 TTGTAATTTATGAAAC-AGTTGAAGGATCAAA
*
1578067 TTGTAATTTATGAAACATTTGAAGGATCAAA
1 TTGTAATTTATGAAACAGTTGAAGGATCAAA
1578098 TTGTAA
1 TTGTAA
1578104 AGATAAAAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 6 0.18
31 25 0.74
32 3 0.09
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (31 bp):
TTGTAATTTATGAAACAGTTGAAGGATCAAA
Found at i:1580386 original size:2 final size:2
Alignment explanation
Indices: 1580379--1580411 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1580369 TTACGTAACC
1580379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1580412 GAAATATGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1580856 original size:25 final size:25
Alignment explanation
Indices: 1580827--1580886 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
1580817 CGGTCTGTGA
**
1580827 TTATACGTGGCAAAGCCATGAGTTG
1 TTATACGTGGCAAAGCCACAAGTTG
* *
1580852 TTATATGTGGCAAGGCCACAAGTTG
1 TTATACGTGGCAAAGCCACAAGTTG
*
1580877 ATATACGTGG
1 TTATACGTGG
1580887 TTACAACCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (25 bp):
TTATACGTGGCAAAGCCACAAGTTG
Found at i:1582433 original size:355 final size:353
Alignment explanation
Indices: 1582023--1582702 Score: 972
Period size: 354 Copynumber: 1.9 Consensus size: 353
1582013 ATATATATAC
* * *
1582023 TTTAAATGTAAACATATTTACTTTCTATTTTGTATTAACATTACAAAATTATAACTTATAAAATT
1 TTTAAATATAAACATATTTACTTTCTATTTTGTACTAACATTACAAAATTATAACTCATAAAATT
* **
1582088 ATTAATTATAATATATATAATTTTGTTTATAT-AAGCTTATAA-TATATAAATTTAAAGAGATGT
66 ATTAATTACAATATATATAATTTTGTTTATATAAAG-TTATAACT-TATAAATTTAAAG-GAAAT
* * * * * * *
1582151 TTTGAGATTAGAGTAGT-TCTAAAACGTAGTTATTTTTTTTAATTTTATGTAATTAAGGACAAAC
128 TGTGAGATTAGAATAATGT-TAAAACCTAGTTATTTTTTTTAATTTCATATAATTAAAGACAAAC
* * * *
1582215 TCGTATAATTAATTAAATTAATTCATGAAACTATGATTATTAATTAACTTATAATGTCGTTTAAT
192 TCATATAATTAATTAAATTAATTAATAAAACTATGATTATTAATTAACTTATAACGTC-TTTAAT
* * *
1582280 ATGTACTTTATATATATT-AGATTCATTTATAAGGAATATAATTACTATTATATATATTAAAATA
256 ATATACTTTATATACATTGAG-TTCATTTATAAGAAATATAATTACTATTATATATATTAAAATA
1582344 CTTTTAATTTATGTGTGTATATATATATGTGTAT
320 CTTTTAATTTATGTGTGTATATATATATGTGTAT
* * * *
1582378 TTTAAATATAAACATATTTACTTTTTATTTTGTGCTAATATTATAAAATTATAACTCATAAAATT
1 TTTAAATATAAACATATTTACTTTCTATTTTGTACTAACATTACAAAATTATAACTCATAAAATT
* *
1582443 ATTAGTTACAATATATATACTTTTGTTTATATAAAGTTATAACTTATAAATTTAAAGGAAATTGT
66 ATTAATTACAATATATATAATTTTGTTTATATAAAGTTATAACTTATAAATTTAAAGGAAATTGT
* *
1582508 GAGATTAGAATAATGTTGAAACCTAGTTATTTTTTTTAATTTCATATAATTAAAGATAAACTCAT
131 GAGATTAGAATAATGTTAAAACCTAGTTATTTTTTTTAATTTCATATAATTAAAGACAAACTCAT
* * * * *
1582573 ATAGTTAATTAAATTAATTAATAAAATTATGATTATTAATTGACTTGTAACGTCTTTTATATATA
196 ATAATTAATTAAATTAATTAATAAAACTATGATTATTAATTAACTTATAACGTCTTTAATATATA
*
1582638 CTTTATATACATTGAGTTCATTTATAAGAAATATAATTACTATTATATATATTAAAATATTTTTA
261 CTTTATATACATTGAGTTCATTTATAAGAAATATAATTACTATTATATATATTAAAATACTTTTA
1582703 GTATATATAC
Statistics
Matches: 287, Mismatches: 34, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
353 68 0.24
354 108 0.38
355 107 0.37
356 4 0.01
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (353 bp):
TTTAAATATAAACATATTTACTTTCTATTTTGTACTAACATTACAAAATTATAACTCATAAAATT
ATTAATTACAATATATATAATTTTGTTTATATAAAGTTATAACTTATAAATTTAAAGGAAATTGT
GAGATTAGAATAATGTTAAAACCTAGTTATTTTTTTTAATTTCATATAATTAAAGACAAACTCAT
ATAATTAATTAAATTAATTAATAAAACTATGATTATTAATTAACTTATAACGTCTTTAATATATA
CTTTATATACATTGAGTTCATTTATAAGAAATATAATTACTATTATATATATTAAAATACTTTTA
ATTTATGTGTGTATATATATATGTGTAT
Found at i:1595249 original size:2 final size:2
Alignment explanation
Indices: 1595242--1595267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1595232 AAGGGAAGAC
1595242 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1595268 ACATTCAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1596426 original size:26 final size:26
Alignment explanation
Indices: 1596390--1596495 Score: 103
Period size: 26 Copynumber: 4.1 Consensus size: 26
1596380 AATTCTAAGA
*
1596390 ATAATTTTACCATCAGAAGTGGATGG
1 ATAATTTTACCATCAGAAATGGATGG
**
1596416 ATAATTTTACCATCA-AAATCTA-GG
1 ATAATTTTACCATCAGAAATGGATGG
* *
1596440 AATGATTTTACCACCAGAAATGGAAT-G
1 -ATAATTTTACCATCAGAAATGG-ATGG
*
1596467 ATAATTTTACCA-CTAGAAGTGGATGG
1 ATAATTTTACCATC-AGAAATGGATGG
1596493 ATA
1 ATA
1596496 CCTTAACTTA
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
24 2 0.03
25 20 0.31
26 41 0.63
27 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (26 bp):
ATAATTTTACCATCAGAAATGGATGG
Found at i:1600870 original size:20 final size:19
Alignment explanation
Indices: 1600845--1600889 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1600835 TGAATAAGAT
*
1600845 CTTTCTACTCCTTCTAAATA
1 CTTTCT-CTCCGTCTAAATA
* *
1600865 CTTTCTCTTCGTCTAAGTA
1 CTTTCTCTCCGTCTAAATA
1600884 CTTTCT
1 CTTTCT
1600890 TTTATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.18, C:0.29, G:0.04, T:0.49
Consensus pattern (19 bp):
CTTTCTCTCCGTCTAAATA
Found at i:1603775 original size:21 final size:22
Alignment explanation
Indices: 1603740--1603783 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1603730 CTCTTAAAGT
1603740 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
1603762 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
1603783 A
1 A
1603784 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:1614241 original size:2 final size:2
Alignment explanation
Indices: 1614234--1614298 Score: 60
Period size: 2 Copynumber: 32.5 Consensus size: 2
1614224 ACATACATAC
** * * * *
1614234 AT AT AT AT GC AT AT AT AT AT AT AT AT AG AC AT AC AA 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
1614276 -T CAT AT AT AT AT AT AT AT AT AT A
1 AT -AT AT AT AT AT AT AT AT AT AT A
1614299 CACACACACA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
1 1 0.02
2 49 0.96
3 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1614248 original size:10 final size:9
Alignment explanation
Indices: 1614189--1614298 Score: 65
Period size: 8 Copynumber: 12.7 Consensus size: 9
1614179 TGATGCACAA
1614189 CATATATATT
1 CATATATA-T
1614199 CATATATAT
1 CATATATAT
* *
1614208 -ATATACACC
1 CATATATA-T
*
1614217 CATACATA-
1 CATATATAT
*
1614225 CATACATA-
1 CATATATAT
1614233 CATATATAT
1 CATATATAT
1614242 GCATATATAT
1 -CATATATAT
1614252 -ATATATAT
1 CATATATAT
* *
1614260 -AGACATA-
1 CATATATAT
*
1614267 CAAATATATT
1 CATATATA-T
1614277 CATATATAT
1 CATATATAT
1614286 -ATATATAT
1 CATATATAT
1614294 -ATATA
1 CATATA
1614299 CACACACACA
Statistics
Matches: 83, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
8 52 0.63
9 2 0.02
10 29 0.35
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (9 bp):
CATATATAT
Found at i:1614266 original size:34 final size:34
Alignment explanation
Indices: 1614228--1614294 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
1614218 ATACATACAT
*
1614228 ACATACATATATATGCATATATATATATATATAG
1 ACATACAAATATATGCATATATATATATATATAG
*
1614262 ACATACAAATATATTCATATATATATATATATA
1 ACATACAAATATATGCATATATATATATATATA
1614295 TATACACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (34 bp):
ACATACAAATATATGCATATATATATATATATAG
Found at i:1627809 original size:28 final size:27
Alignment explanation
Indices: 1627776--1627903 Score: 107
Period size: 27 Copynumber: 4.7 Consensus size: 27
1627766 TGTAACAACT
*
1627776 TTTTCATCATGACATGTAATAACTAAA
1 TTTTCAACATGACATGTAATAACTAAA
* *** *
1627803 TATTTCAATATAGTTGTGTAATAATTAAA
1 T-TTTCAACAT-GACATGTAATAACTAAA
* * * *
1627832 TCTTCAACATGACA--TAAAAATTATAT
1 TTTTCAACATGACATGTAATAACTA-AA
*
1627858 TTTTCAACATGACATGCAATAACTAAA
1 TTTTCAACATGACATGTAATAACTAAA
*
1627885 TTTTTAACATGACATGTAA
1 TTTTCAACATGACATGTAA
1627904 CAATTGCATT
Statistics
Matches: 76, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
25 8 0.11
26 14 0.18
27 20 0.26
28 20 0.26
29 14 0.18
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (27 bp):
TTTTCAACATGACATGTAATAACTAAA
Found at i:1627864 original size:26 final size:27
Alignment explanation
Indices: 1627834--1627899 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
1627824 TAATTAAATC
* *
1627834 TTCAACATGACAT-AAAAATTATATTT
1 TTCAACATGACATCAAAAACTAAATTT
*
1627860 TTCAACATGACATGCAATAACTAAATTT
1 TTCAACATGACAT-CAAAAACTAAATTT
1627888 TT-AACATGACAT
1 TTCAACATGACAT
1627900 GTAACAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.37
27 10 0.29
28 12 0.34
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (27 bp):
TTCAACATGACATCAAAAACTAAATTT
Found at i:1627896 original size:27 final size:26
Alignment explanation
Indices: 1627822--1627900 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 26
1627812 ATAGTTGTGT
* *
1627822 AATAATTAAATCTTCAACATGACAT-
1 AATAATTAAATTTTTAACATGACATG
* *
1627847 AAAAATTATATTTTTCAACATGACATG
1 AATAATTAAATTTTT-AACATGACATG
*
1627874 CAATAACTAAATTTTTAACATGACATG
1 -AATAATTAAATTTTTAACATGACATG
1627901 TAACAATTGC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 11 0.25
26 10 0.23
27 11 0.25
28 12 0.27
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (26 bp):
AATAATTAAATTTTTAACATGACATG
Found at i:1627986 original size:37 final size:37
Alignment explanation
Indices: 1627945--1628018 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
1627935 GTGTGATACG
*
1627945 TACTTCATTTATCTGTCAACTTAACCTTTAATTGTAA
1 TACTTCATCTATCTGTCAACTTAACCTTTAATTGTAA
1627982 TACTTCATCTATCTGTCAACTTAACCTTTAATTGTAA
1 TACTTCATCTATCTGTCAACTTAACCTTTAATTGTAA
1628019 GAAATCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (37 bp):
TACTTCATCTATCTGTCAACTTAACCTTTAATTGTAA
Found at i:1629205 original size:20 final size:21
Alignment explanation
Indices: 1629160--1629205 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1629150 TACTATTAAT
*
1629160 ATAAAATTATTTCTACAAATA
1 ATAAAATCATTTCTACAAATA
1629181 A-AAAATCATTTC-A-AATATA
1 ATAAAATCATTTCTACAA-ATA
1629200 ATAAAA
1 ATAAAA
1629206 ATAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 2 0.09
19 5 0.23
20 14 0.64
21 1 0.05
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAATCATTTCTACAAATA
Found at i:1629964 original size:7 final size:7
Alignment explanation
Indices: 1629952--1629979 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1629942 GATTAGGTGG
1629952 ATTAATT
1 ATTAATT
1629959 ATTAATT
1 ATTAATT
1629966 ATTAATT
1 ATTAATT
1629973 ATTAATT
1 ATTAATT
1629980 TAAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTAATT
Found at i:1631787 original size:18 final size:18
Alignment explanation
Indices: 1631760--1631799 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1631750 AATCGTTAAC
* *
1631760 TTATGAGTTATTTATGAA
1 TTATGAGTTACTTATAAA
*
1631778 TTATGTGTTACTTATAAA
1 TTATGAGTTACTTATAAA
1631796 TTAT
1 TTAT
1631800 TCGTGAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (18 bp):
TTATGAGTTACTTATAAA
Found at i:1634126 original size:29 final size:29
Alignment explanation
Indices: 1634094--1634149 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1634084 ATTTAAAAAA
1634094 ATTTAAATAAAATTTTAT-TTTTATATTAT
1 ATTTAAATAAAATTTTATATTTT-TATTAT
* *
1634123 ATTTAATTAAATTTTTATATTTTTATT
1 ATTTAAATAAAATTTTATATTTTTATT
1634150 TTAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTAAATAAAATTTTATATTTTTATTAT
Found at i:1652787 original size:28 final size:28
Alignment explanation
Indices: 1652755--1652808 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1652745 ATTTTTTAAA
1652755 ATTTTTTATTTTATAAAAAATAATATAT
1 ATTTTTTATTTTATAAAAAATAATATAT
* * *
1652783 ATTTTTTATTTTTTAGAAAATTATAT
1 ATTTTTTATTTTATAAAAAATAATAT
1652809 TTTTAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
ATTTTTTATTTTATAAAAAATAATATAT
Found at i:1653941 original size:2 final size:2
Alignment explanation
Indices: 1653934--1653962 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1653924 TTATCAAGTA
1653934 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
1653963 AAAGTCTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1669653 original size:15 final size:15
Alignment explanation
Indices: 1669625--1669670 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
1669615 TATAGCCAAT
1669625 TTTCCCT-C-AAATA
1 TTTCCCTCCAAAATA
1669638 TTTCCCTCCAAAATA
1 TTTCCCTCCAAAATA
1669653 TTTCCCTCCAAAATA
1 TTTCCCTCCAAAATA
1669668 TTT
1 TTT
1669671 AGGAGGGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.23
14 1 0.03
15 23 0.74
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (15 bp):
TTTCCCTCCAAAATA
Found at i:1670099 original size:30 final size:30
Alignment explanation
Indices: 1670059--1670123 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1670049 TCGGCCCTGC
* *
1670059 GTGCCTCGTACC-CATGCTGTGCGGGTTGGA
1 GTGCCACGTACCTC-TGCTGTGCGGGCTGGA
*
1670089 GTGCCACGTACCTCTGCTGTGCGGGCTGGC
1 GTGCCACGTACCTCTGCTGTGCGGGCTGGA
1670119 GTGCC
1 GTGCC
1670124 TGCGCACAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.08, C:0.31, G:0.37, T:0.25
Consensus pattern (30 bp):
GTGCCACGTACCTCTGCTGTGCGGGCTGGA
Found at i:1670204 original size:51 final size:50
Alignment explanation
Indices: 1670149--1670291 Score: 196
Period size: 51 Copynumber: 2.8 Consensus size: 50
1670139 TGGCTCTGTG
* *
1670149 CGGGCTGGCTCGCCCAGGGGCTTGTGTTGTGAGCCCCTGCTGGCACCCTGC
1 CGGGCTGGCTCGCCCAGGGGC-TGTGCTGTGCGCCCCTGCTGGCACCCTGC
* * *
1670200 CGGGCTGGCTCACCCAGGGCCTGTGCTGTGCGCCCCTGCTGGCACCCTGT
1 CGGGCTGGCTCGCCCAGGGGCTGTGCTGTGCGCCCCTGCTGGCACCCTGC
* * *
1670250 CGAGCTGGCTTGCCCAGGGGGCTGTGCTGTGCCCCCCTGCTG
1 CGGGCTGGCTCGCCCA-GGGGCTGTGCTGTGCGCCCCTGCTG
1670292 ACATCCTACA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 39 0.48
51 42 0.52
ACGTcount: A:0.06, C:0.37, G:0.36, T:0.21
Consensus pattern (50 bp):
CGGGCTGGCTCGCCCAGGGGCTGTGCTGTGCGCCCCTGCTGGCACCCTGC
Found at i:1670240 original size:50 final size:51
Alignment explanation
Indices: 1670149--1670291 Score: 198
Period size: 50 Copynumber: 2.8 Consensus size: 51
1670139 TGGCTCTGTG
* * *
1670149 CGGGCTGGCTCGCCCAGGGGCTTGTGTTGTGAGCCCCTGCTGGCACCCTGC
1 CGGGCTGGCTCGCCCAGGGGCCTGTGCTGTGCGCCCCTGCTGGCACCCTGC
* *
1670200 CGGGCTGGCTCACCCA-GGGCCTGTGCTGTGCGCCCCTGCTGGCACCCTGT
1 CGGGCTGGCTCGCCCAGGGGCCTGTGCTGTGCGCCCCTGCTGGCACCCTGC
* * * *
1670250 CGAGCTGGCTTGCCCAGGGGGCTGTGCTGTGCCCCCCTGCTG
1 CGGGCTGGCTCGCCCAGGGGCCTGTGCTGTGCGCCCCTGCTG
1670292 ACATCCTACA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 43 0.53
51 38 0.47
ACGTcount: A:0.06, C:0.37, G:0.36, T:0.21
Consensus pattern (51 bp):
CGGGCTGGCTCGCCCAGGGGCCTGTGCTGTGCGCCCCTGCTGGCACCCTGC
Found at i:1673960 original size:16 final size:15
Alignment explanation
Indices: 1673928--1673973 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
1673918 TATAGCCAAT
1673928 TTTTCCT-C-AAATA
1 TTTTCCTCCAAAATA
1673941 -TTTCCTTCCAAAATA
1 TTTTCC-TCCAAAATA
1673956 TTTTCCTCCAAAATA
1 TTTTCCTCCAAAATA
1673971 TTT
1 TTT
1673974 AAGAGGGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.17
13 1 0.03
14 1 0.03
15 17 0.59
16 5 0.17
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTTCCTCCAAAATA
Found at i:1685185 original size:10 final size:10
Alignment explanation
Indices: 1685170--1685195 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1685160 TTGTTATATT
1685170 ATTTTAAGTG
1 ATTTTAAGTG
1685180 ATTTTAAGTG
1 ATTTTAAGTG
1685190 ATTTTA
1 ATTTTA
1685196 CCACAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (10 bp):
ATTTTAAGTG
Found at i:1687458 original size:15 final size:15
Alignment explanation
Indices: 1687438--1687467 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1687428 ACTGACTTGT
*
1687438 CTTCTTTTGCTTTTG
1 CTTCTTTTCCTTTTG
1687453 CTTCTTTTCCTTTTG
1 CTTCTTTTCCTTTTG
1687468 AAAGACCGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.10, T:0.67
Consensus pattern (15 bp):
CTTCTTTTCCTTTTG
Found at i:1688107 original size:21 final size:22
Alignment explanation
Indices: 1688059--1688104 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1688049 TTAACAGGCC
*
1688059 AAACCAATTCCACCAGTATGTA
1 AAACCAATTCCACCAGTATATA
1688081 AAACCAATTCCACCAGTATATA
1 AAACCAATTCCACCAGTATATA
1688103 AA
1 AA
1688105 CCATAGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.26, G:0.07, T:0.22
Consensus pattern (22 bp):
AAACCAATTCCACCAGTATATA
Found at i:1689986 original size:15 final size:15
Alignment explanation
Indices: 1689966--1689995 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1689956 GCTAGCCATC
*
1689966 CAAAAGGAAAAGAAG
1 CAAAAGCAAAAGAAG
1689981 CAAAAGCAAAAGAAG
1 CAAAAGCAAAAGAAG
1689996 AGCAGCCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.10, G:0.23, T:0.00
Consensus pattern (15 bp):
CAAAAGCAAAAGAAG
Found at i:1690019 original size:35 final size:35
Alignment explanation
Indices: 1689980--1690083 Score: 117
Period size: 35 Copynumber: 3.0 Consensus size: 35
1689970 AGGAAAAGAA
1689980 GCAAAAGCAAAAGAAGAGC-AGCCAATCTTTCAAAT
1 GCAAAAGCAAAAGAAGA-CAAGCCAATCTTTCAAAT
*
1690015 GCAAAAGCAAAAGAAGACAAGCCAGTCTTTCAAAAT
1 GCAAAAGCAAAAGAAGACAAGCCAATCTTTC-AAAT
* *
1690051 --AATGAAG-AAAAGAAGACAAGCTAGTCTTTCAAA
1 GCAA--AAGCAAAAGAAGACAAGCCAATCTTTCAAA
1690084 AAGAAAAGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
34 6 0.10
35 50 0.79
36 7 0.11
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.15
Consensus pattern (35 bp):
GCAAAAGCAAAAGAAGACAAGCCAATCTTTCAAAT
Found at i:1690024 original size:114 final size:114
Alignment explanation
Indices: 1689898--1690127 Score: 336
Period size: 114 Copynumber: 2.0 Consensus size: 114
1689888 AAAACTCAAT
* ** *
1689898 AATGCAAAAGCAAAAGAAAACAAACCAGTCTTTCAAACTGGTGGAGAAAAGAAGACAAGCTAGCC
1 AATGCAAAAGCAAAAGAAAACAAACCAGTCTTTCAAAATAATGAAGAAAAGAAGACAAGCTAGCC
* *
1689963 ATCCAAAAGGAAAAGAAGCAAAAGCAAAAGAAGAGC-AGCCAATCTTTCA
66 ATCCAAAAAGAAAAGAAGCAAAAGCAAAAAAAGA-CAAGCCAATCTTTCA
* * *
1690012 AATGCAAAAGCAAAAGAAGACAAGCCAGTCTTTCAAAATAATGAAGAAAAGAAGACAAGCTAGTC
1 AATGCAAAAGCAAAAGAAAACAAACCAGTCTTTCAAAATAATGAAGAAAAGAAGACAAGCTAGCC
* * *
1690077 TTTCAAAAAGAAAAGAAGCAAAAGCAAAAAAAGACAAGCCAGTCTTTCA
66 ATCCAAAAAGAAAAGAAGCAAAAGCAAAAAAAGACAAGCCAATCTTTCA
1690126 AA
1 AA
1690128 ATGATGGAAG
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
113 1 0.01
114 102 0.99
ACGTcount: A:0.53, C:0.17, G:0.18, T:0.13
Consensus pattern (114 bp):
AATGCAAAAGCAAAAGAAAACAAACCAGTCTTTCAAAATAATGAAGAAAAGAAGACAAGCTAGCC
ATCCAAAAAGAAAAGAAGCAAAAGCAAAAAAAGACAAGCCAATCTTTCA
Found at i:1696347 original size:74 final size:72
Alignment explanation
Indices: 1696195--1696348 Score: 204
Period size: 74 Copynumber: 2.1 Consensus size: 72
1696185 AAACATAAAC
* * * *
1696195 TTATAAATATGTATTCATTAAATGACGATCATTGAAATTTTTTTTATAATTATTGGTAAGATTTA
1 TTATAAATATGTATTCATCAAATAACAATCATTGAAATTTTTTTTATAATTATTAGTAAGATTTA
1696260 ATTCTAT
66 ATTCTAT
* *
1696267 TT-TAAATGTGTATTCATCAAATAATAATCATTAGAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATAACAATCATT-GAA-ATTTTTT-TTATAATTATTAGTAAGAT
*
1696331 TTATTTC-AT
63 TTAATTCTAT
1696340 TTATAAATA
1 TTATAAATA
1696349 AAAATTTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
71 25 0.36
72 5 0.07
73 11 0.16
74 29 0.41
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (72 bp):
TTATAAATATGTATTCATCAAATAACAATCATTGAAATTTTTTTTATAATTATTAGTAAGATTTA
ATTCTAT
Found at i:1697468 original size:23 final size:23
Alignment explanation
Indices: 1697417--1697474 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1697407 ATTAACATAA
* *
1697417 AGTTCAA-CACAATGTCTTTTGT
1 AGTTCAAGCACAATGCCTTTTAT
*
1697439 -GAATCAAGCACAATGCCTTTTAT
1 AG-TTCAAGCACAATGCCTTTTAT
1697462 AGTTCAAGCACAA
1 AGTTCAAGCACAA
1697475 CTACTTTACC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 4 0.14
23 23 0.79
24 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (23 bp):
AGTTCAAGCACAATGCCTTTTAT
Found at i:1698200 original size:20 final size:20
Alignment explanation
Indices: 1698175--1698222 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1698165 TTCAATTTCT
1698175 ATCGATACTTGTCCGAATGA
1 ATCGATACTTGTCCGAATGA
1698195 ATCGATACTTGTCCGAATGA
1 ATCGATACTTGTCCGAATGA
1698215 ATCGATAC
1 ATCGATAC
1698223 ATGATGCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (20 bp):
ATCGATACTTGTCCGAATGA
Found at i:1703265 original size:60 final size:60
Alignment explanation
Indices: 1703146--1703265 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
1703136 TTCTATTAAG
* * * * * * *
1703146 AATGTATCAATACATTTGTTAATGTGTCCATACTTTTGAGGCGGTGAGCACTCTGTTGAA
1 AATGTATCAATACATTTGGTAATATATCAATACTTTAGAGGCAGTGAGCACTCTCTTGAA
* * * *
1703206 AATGTATCAGTACATTTGGTAATATATCAATACTTTAGAGGCATTGAGTACTTTCTTGAA
1 AATGTATCAATACATTTGGTAATATATCAATACTTTAGAGGCAGTGAGCACTCTCTTGAA
1703266 TTTTTATTGA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (60 bp):
AATGTATCAATACATTTGGTAATATATCAATACTTTAGAGGCAGTGAGCACTCTCTTGAA
Found at i:1718790 original size:16 final size:15
Alignment explanation
Indices: 1718752--1718794 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1718742 ACATAAAATT
* *
1718752 AAAATAACTTAATAA
1 AAAAAAACTAAATAA
*
1718767 AAATAAACTAAATAGA
1 AAAAAAACTAAATA-A
1718783 AAAAAAACTAAA
1 AAAAAAACTAAA
1718795 AATAATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAAAAACTAAATAA
Found at i:1719512 original size:20 final size:21
Alignment explanation
Indices: 1719481--1719520 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1719471 TGAAGCACAA
1719481 GTATCGATACCTTATTCAAAG
1 GTATCGATACCTTATTCAAAG
*
1719502 GTATC-ATACCTTTTTCAAA
1 GTATCGATACCTTATTCAAA
1719521 AATTACAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (21 bp):
GTATCGATACCTTATTCAAAG
Found at i:1728650 original size:50 final size:50
Alignment explanation
Indices: 1728513--1728671 Score: 205
Period size: 50 Copynumber: 3.2 Consensus size: 50
1728503 TTCAACCTGT
* * *
1728513 TTAAAAACAAA-AATCTCTTTATGGATTGTGTAAAGATTATTGCTTGATCTCG
1 TTAAAAAGAAAGAATCTCTTTATGGATTGTGTAAAGGTTATTGC-T--TCCCG
* **
1728565 TTAAAAAGCAAGAATC-CTTTATGGATTGTGTAAAGGTTATCACTTCCCG
1 TTAAAAAGAAAGAATCTCTTTATGGATTGTGTAAAGGTTATTGCTTCCCG
* *
1728614 TTAAAAAGAAAGAATCTCTTTATGCATTGTGTAAAGGTTATTGCTTCCCA
1 TTAAAAAGAAAGAATCTCTTTATGGATTGTGTAAAGGTTATTGCTTCCCG
1728664 TTAAAAAG
1 TTAAAAAG
1728672 CCAAAATCCT
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
49 19 0.20
50 37 0.39
51 1 0.01
52 33 0.35
53 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (50 bp):
TTAAAAAGAAAGAATCTCTTTATGGATTGTGTAAAGGTTATTGCTTCCCG
Found at i:1729499 original size:10 final size:11
Alignment explanation
Indices: 1729473--1729513 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
1729463 GAATGCTCAA
*
1729473 GAAATGTAAGT
1 GAAATGCAAGT
1729484 GAAATGCAAG-
1 GAAATGCAAGT
*
1729494 GAAATGCATGT
1 GAAATGCAAGT
1729505 GAAATGCAA
1 GAAATGCAA
1729514 ATTAGAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.46, C:0.07, G:0.27, T:0.20
Consensus pattern (11 bp):
GAAATGCAAGT
Found at i:1729499 original size:21 final size:21
Alignment explanation
Indices: 1729473--1729513 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1729463 GAATGCTCAA
*
1729473 GAAATGTAAGTGAAATGCAAG
1 GAAATGCAAGTGAAATGCAAG
*
1729494 GAAATGCATGTGAAATGCAA
1 GAAATGCAAGTGAAATGCAA
1729514 ATTAGAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.07, G:0.27, T:0.20
Consensus pattern (21 bp):
GAAATGCAAGTGAAATGCAAG
Found at i:1730790 original size:29 final size:31
Alignment explanation
Indices: 1730758--1730829 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 31
1730748 GGCCATTGAC
1730758 AGTGATGA-TA-ATTATATGGCATTGCCACT
1 AGTGATGATTAGATTATATGGCATTGCCACT
* * *
1730787 AGTGTTGATTATGATTATGTGGCATTGTCACT
1 AGTGATGATTA-GATTATATGGCATTGCCACT
* *
1730819 AATGTTGATTA
1 AGTGATGATTA
1730830 TGAATATGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 7 0.19
30 2 0.06
32 27 0.75
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (31 bp):
AGTGATGATTAGATTATATGGCATTGCCACT
Found at i:1730810 original size:32 final size:32
Alignment explanation
Indices: 1730768--1730936 Score: 119
Period size: 32 Copynumber: 5.3 Consensus size: 32
1730758 AGTGATGATA
* *
1730768 ATTATATGGCATTGCCACTAGTGTTGATTATG
1 ATTATGTGGCACTGCCACTAGTGTTGATTATG
* * *
1730800 ATTATGTGGCATTGTCACTAATGTTGATTATG
1 ATTATGTGGCACTGCCACTAGTGTTGATTATG
* * * * * * *
1730832 AATATGTGGTGA-GGCCACCAATATTGACTATG
1 ATTATGTGG-CACTGCCACTAGTGTTGATTATG
* * **
1730864 ATTATGTGGCGCAGCCACTAGAATT-ATCTATG
1 ATTATGTGGCACTGCCACTAGTGTTGAT-TATG
* * *
1730896 ATTATGTGGC-CCGACCATTAGTGATGATTATG
1 ATTATGTGGCACTG-CCACTAGTGTTGATTATG
1730928 ATTATGTGG
1 ATTATGTGG
1730937 TAAGGCCATT
Statistics
Matches: 109, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
31 3 0.03
32 103 0.94
33 3 0.03
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (32 bp):
ATTATGTGGCACTGCCACTAGTGTTGATTATG
Found at i:1730946 original size:32 final size:32
Alignment explanation
Indices: 1730892--1730969 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 32
1730882 TAGAATTATC
**
1730892 TATGATTATGTGGCCCGACCATT-AGT-GATGAT
1 TATGATTATGTGGCAAGACCATTGA-TAG-TGAT
* *
1730924 TATGATTATGTGGTAAGGCCATTGATAGTGAT
1 TATGATTATGTGGCAAGACCATTGATAGTGAT
*
1730956 GATGATTATGTGGC
1 TATGATTATGTGGC
1730970 GCTGCCATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
32 36 0.95
33 2 0.05
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (32 bp):
TATGATTATGTGGCAAGACCATTGATAGTGAT
Found at i:1732281 original size:71 final size:71
Alignment explanation
Indices: 1732198--1732386 Score: 204
Period size: 71 Copynumber: 2.7 Consensus size: 71
1732188 TTCAGATCAC
*
1732198 TAAGTATCGATACTTGTTCTTCAAGTATTAATAATTTTCACACAAAATGCTTCCCAAGACATTCT
1 TAAGTATTGATACTTGTTCTTCAAGTATTAATAATTTTCACACAAAATGCTTCCCAAGACATTCT
1732263 ATCTTT
66 ATCTTT
* * * * * * ** *
1732269 TAAGTGTTGATACTTCCTT-TTCAAGTATTGATACTTTTCACAAAAAATTCTTCTTAAGGCATTC
1 TAAGTATTGATACTT-GTTCTTCAAGTATTAATAATTTTCACACAAAATGCTTCCCAAGACATTC
*
1732333 TGTCTTT
65 TATCTTT
* * *
1732340 TAAGTATTGATACATGTTCTT-AAGATATCAATACTTTTTCA-ACAAAA
1 TAAGTATTGATACTTGTTCTTCAAG-TATTAATA-ATTTTCACACAAAA
1732387 CATGATTTTC
Statistics
Matches: 96, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
70 5 0.05
71 83 0.86
72 8 0.08
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (71 bp):
TAAGTATTGATACTTGTTCTTCAAGTATTAATAATTTTCACACAAAATGCTTCCCAAGACATTCT
ATCTTT
Found at i:1732299 original size:21 final size:20
Alignment explanation
Indices: 1732265--1732304 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1732255 GACATTCTAT
*
1732265 CTTTTAAGTGTTGATACTTC
1 CTTTTAAGTATTGATACTTC
1732285 CTTTTCAAGTATTGATACTT
1 CTTTT-AAGTATTGATACTT
1732305 TTCACAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (20 bp):
CTTTTAAGTATTGATACTTC
Found at i:1737334 original size:5 final size:5
Alignment explanation
Indices: 1737324--1737357 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1737314 GTTTACAAAC
1737324 TTATA TTATA TTATA TTATA TTATA TTATA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT
1737358 GTATTAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1742289 original size:68 final size:68
Alignment explanation
Indices: 1742159--1742303 Score: 179
Period size: 68 Copynumber: 2.2 Consensus size: 68
1742149 TTATTTTTTG
* * * *
1742159 TGAATCAGTCAAATAATTATCATTCATCAAATTAAAAAAAACCCTTTCTCTTATTCTCTTTTTTT
1 TGAATCAATCAAACAATTATCATTAATCAAATTAAAAAAAACCCTTTCTCCTATTCTCTTTTTTT
1742224 TCA
66 TCA
* * ** *
1742227 TGAATCAATCAAACAATTATCATTAATCAAATT-AGAAGAACGTTTTTTCCTATTCTC-TTTTTT
1 TGAATCAATCAAACAATTATCATTAATCAAATTAAAAAAAACCCTTTCTCCTATTCTCTTTTTTT
*
1742290 T-G
66 TCA
1742292 TGAATCAATCAA
1 TGAATCAATCAA
1742304 GCCATTTCTT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
65 12 0.18
66 7 0.10
67 18 0.27
68 30 0.45
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (68 bp):
TGAATCAATCAAACAATTATCATTAATCAAATTAAAAAAAACCCTTTCTCCTATTCTCTTTTTTT
TCA
Found at i:1742557 original size:65 final size:65
Alignment explanation
Indices: 1742409--1742565 Score: 187
Period size: 65 Copynumber: 2.4 Consensus size: 65
1742399 TCCTTTCTCT
* * * *
1742409 TCTTTTTT-GTAAATTAGTCAAATAATTATCATTCATCAAATTAGAAAAACCTTTTCTCTTATTC
1 TCTTTTTTCGTAAATCAATCAAACAATTATAATTCATCAAATTAGAAAAACCTTTTCTCTTATTC
* * * *
1742473 TC-TTTTTCTGTGAACCAATCAAACAATTATAATTTATCAAATTAGAAAAA-CTGTTT-TTTGTA
1 TCTTTTTTC-GTAAATCAATCAAACAATTATAATTCATCAAATTAGAAAAACCT-TTTCTCT-TA
1742535 TTC
63 TTC
1742538 TCTTTTTTCGTAAATCAATCAAACAATT
1 TCTTTTTTCGTAAATCAATCAAACAATT
1742566 TTCTTTCGTT
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
63 5 0.06
64 6 0.08
65 61 0.78
66 6 0.08
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (65 bp):
TCTTTTTTCGTAAATCAATCAAACAATTATAATTCATCAAATTAGAAAAACCTTTTCTCTTATTC
Found at i:1742592 original size:256 final size:259
Alignment explanation
Indices: 1742128--1742623 Score: 725
Period size: 256 Copynumber: 1.9 Consensus size: 259
1742118 ATCATTCACA
* * *
1742128 AAATTAGAAAAATCTTTTGTCTTATTTTTTGTGAATCAGTCAAATAATTATCATTCATCAAATTA
1 AAATTAGAAAAATCCTTTCTCTTATTTTTTGTAAATCAGTCAAATAATTATCATTCATCAAATTA
* * *
1742193 AAAAAAACCCTTTCTCTTATTCTCTTTTTTTTCATGAATCAATCAAACAATTATCATTAATCAAA
66 AAAAAAACCCTTTCTCTTATTCTCTTTTTTCTCATGAACCAATCAAACAATTATAATTAATCAAA
* * * * *
1742258 TTAGAAGAACGTTTTTTCCTATTCTCTTTTTTTGTGAATCAATCAAGCCATTTCTTGTCTTTATT
131 TTAGAAAAACGTTTTTTCCTATTCTCTTTTTTCGTAAATCAATCAAACAATTTCTTGTCTTTATT
* * *
1742323 TCTATCTAAACCAAATAATTTTATCCTATTCTCTTTTTTCGTGAAATTAGAAAAACCCTTCATC
196 TATATCTAAACCAAATAACTTTATCCTATTCTCTTTTCTCGTGAAATTAGAAAAACCCTTCATC
* * *
1742387 AAATTGGAAAAATCCTTTCTCTTCTTTTTTGTAAATTAGTCAAATAATTATCATTCATCAAATT-
1 AAATTAGAAAAATCCTTTCTCTTATTTTTTGTAAATCAGTCAAATAATTATCATTCATCAAATTA
* * * *
1742451 AGAAAAACCTTTTCTCTTATTCTC-TTTTTCT-GTGAACCAATCAAACAATTATAATTTATCAAA
66 AAAAAAACCCTTTCTCTTATTCTCTTTTTTCTCATGAACCAATCAAACAATTATAATTAATCAAA
*
1742514 TTAGAAAAACTGTTTTTT-GTATTCTCTTTTTTCGTAAATCAATCAAACAATTTTCTT-TCGTTT
131 TTAGAAAAAC-GTTTTTTCCTATTCTCTTTTTTCGTAAATCAATCAAACAA-TTTCTTGTC-TTT
1742577 -TTTATATCTAAACCAAATAACTTTATCCTATTCTCTTTTCTCGTGAA
193 ATTTATATCTAAACCAAATAACTTTATCCTATTCTCTTTTCTCGTGAA
1742624 TCAATTAAAC
Statistics
Matches: 212, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
256 110 0.52
257 22 0.10
258 22 0.10
259 58 0.27
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (259 bp):
AAATTAGAAAAATCCTTTCTCTTATTTTTTGTAAATCAGTCAAATAATTATCATTCATCAAATTA
AAAAAAACCCTTTCTCTTATTCTCTTTTTTCTCATGAACCAATCAAACAATTATAATTAATCAAA
TTAGAAAAACGTTTTTTCCTATTCTCTTTTTTCGTAAATCAATCAAACAATTTCTTGTCTTTATT
TATATCTAAACCAAATAACTTTATCCTATTCTCTTTTCTCGTGAAATTAGAAAAACCCTTCATC
Found at i:1742626 original size:72 final size:71
Alignment explanation
Indices: 1742533--1742666 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 71
1742523 CTGTTTTTTG
*
1742533 TATTCTCTTTTTTCGTAAATCAATCAAACAATTTTCTT-TCGTTTTTTATATCTAAACCAAATAA
1 TATTCTCTTTTCTCGTAAATCAATCAAACAATTTT-TTCTC-TTTTTTATATCTAAACCAAATAA
1742597 CTTTATCC
64 CTTTATCC
* * * *
1742605 TATTCTCTTTTCTCGTGAATCAATTAAACAATTTTTTCTCTTTTTTCTCTCTAAACCAAATA
1 TATTCTCTTTTCTCGTAAATCAATCAAACAATTTTTTCTCTTTTTTATATCTAAACCAAATA
1742667 GTATTAATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 22 0.39
72 34 0.61
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.48
Consensus pattern (71 bp):
TATTCTCTTTTCTCGTAAATCAATCAAACAATTTTTTCTCTTTTTTATATCTAAACCAAATAACT
TTATCC
Found at i:1747852 original size:22 final size:22
Alignment explanation
Indices: 1747799--1747855 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
1747789 ATATTTATTC
*
1747799 TTATAACTATTTACAATTAAAAA
1 TTATAAAT-TTTACAATTAAAAA
1747822 TATATTAAATTTTA-AATTAAAAAA
1 T-TA-TAAATTTTACAATT-AAAAA
1747846 TTATAAATTT
1 TTATAAATTT
1747856 GAATAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 7 0.23
23 7 0.23
24 12 0.40
25 4 0.13
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATAAATTTTACAATTAAAAA
Found at i:1753352 original size:15 final size:15
Alignment explanation
Indices: 1753332--1753368 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1753322 TTAACGCTAG
1753332 AGCATTTGCTTTTGA
1 AGCATTTGCTTTTGA
1753347 AGCATTTGCTTTTGA
1 AGCATTTGCTTTTGA
1753362 AGCATTT
1 AGCATTT
1753369 CGGGGCACTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (15 bp):
AGCATTTGCTTTTGA
Found at i:1757415 original size:16 final size:15
Alignment explanation
Indices: 1757389--1757424 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1757379 TTTAAAAATC
*
1757389 ATATTATTTATATTA
1 ATATTATTTATATAA
1757404 ATATTATATTATATAA
1 ATATTAT-TTATATAA
1757420 ATATT
1 ATATT
1757425 TTTGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTATTTATATAA
Found at i:1757693 original size:19 final size:19
Alignment explanation
Indices: 1757666--1757708 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1757656 ATTAACTTAA
*
1757666 AAAACTAAAATATT-AAAAT
1 AAAATTAAAAT-TTCAAAAT
*
1757685 AAAATTAAAATTTCCAAAT
1 AAAATTAAAATTTCAAAAT
1757704 AAAAT
1 AAAAT
1757709 ATCTAGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAATTAAAATTTCAAAAT
Found at i:1757788 original size:21 final size:21
Alignment explanation
Indices: 1757763--1757805 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1757753 AGATCCTTAG
*
1757763 ATTA-TATT-TTGAA-TAACA
1 ATTATTATTATTGAATTAAAA
1757781 ATTATTATTATTGAATTAAAA
1 ATTATTATTATTGAATTAAAA
1757802 ATTA
1 ATTA
1757806 AGGTTTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 4 0.19
20 5 0.24
21 8 0.38
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTATTATTATTGAATTAAAA
Found at i:1766473 original size:15 final size:13
Alignment explanation
Indices: 1766434--1766476 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
1766424 TTCCCCACCC
1766434 ATTTCCCTCCAAA
1 ATTTCCCTCCAAA
*
1766447 ATTTTCCTTCCAAA
1 A-TTTCCCTCCAAA
1766461 GGATTTCCCTCCAAA
1 --ATTTCCCTCCAAA
1766476 A
1 A
1766477 CCATTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 2 0.08
14 11 0.44
15 11 0.44
16 1 0.04
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.33
Consensus pattern (13 bp):
ATTTCCCTCCAAA
Found at i:1766557 original size:27 final size:27
Alignment explanation
Indices: 1766527--1766584 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
1766517 GGAGGGAAAT
*
1766527 CCCTACATGGGTCTTGGTGGGCTGGCA
1 CCCTACATGGGTCTTGGAGGGCTGGCA
1766554 CCCTACATGGGTCTTGGAGGGCTGGCA
1 CCCTACATGGGTCTTGGAGGGCTGGCA
1766581 CCCT
1 CCCT
1766585 CTTGGGCCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.12, C:0.29, G:0.34, T:0.24
Consensus pattern (27 bp):
CCCTACATGGGTCTTGGAGGGCTGGCA
Found at i:1766629 original size:14 final size:14
Alignment explanation
Indices: 1766610--1766637 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1766600 GGGTCTGGGC
1766610 TGTGGCCCGTGACA
1 TGTGGCCCGTGACA
1766624 TGTGGCCCGTGACA
1 TGTGGCCCGTGACA
1766638 CAAACATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.36, T:0.21
Consensus pattern (14 bp):
TGTGGCCCGTGACA
Found at i:1773949 original size:12 final size:12
Alignment explanation
Indices: 1773934--1773994 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
1773924 TGATACTATA
1773934 GATGTAAATGTT
1 GATGTAAATGTT
1773946 GATGTAAATGTT
1 GATGTAAATGTT
* *
1773958 GTTGCTAAA-GTA
1 GATG-TAAATGTT
* * *
1773970 AAAGTGAATGTT
1 GATGTAAATGTT
1773982 GATGTAAAT-TT
1 GATGTAAATGTT
1773993 GA
1 GA
1773995 ATACTAGAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
11 7 0.19
12 26 0.70
13 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.38
Consensus pattern (12 bp):
GATGTAAATGTT
Found at i:1778210 original size:30 final size:30
Alignment explanation
Indices: 1778174--1778232 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1778164 TGTGTATTTA
*
1778174 GATTGCTTGCTTTCATAATTCCAAAAAATG
1 GATTGCTTGCTTTCATAATTACAAAAAATG
* *
1778204 GATTGCTTGCTTTCGTAATTAGAAAAAAT
1 GATTGCTTGCTTTCATAATTACAAAAAAT
1778233 TTTGAAATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (30 bp):
GATTGCTTGCTTTCATAATTACAAAAAATG
Found at i:1779270 original size:36 final size:36
Alignment explanation
Indices: 1779230--1779298 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
1779220 AAGATTCTTT
1779230 CTTTTTAATG-GAATCAAGCGATAACCATTACACTGA
1 CTTTTTAATGAG-ATCAAGCGATAACCATTACACTGA
* * * *
1779266 CTTTTTCATGAGATCAAGTGATAATCTTTACAC
1 CTTTTTAATGAGATCAAGCGATAACCATTACAC
1779299 AATGGACAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 27 0.96
37 1 0.04
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (36 bp):
CTTTTTAATGAGATCAAGCGATAACCATTACACTGA
Found at i:1781044 original size:18 final size:19
Alignment explanation
Indices: 1781018--1781066 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1781008 GTGATAGGTA
*
1781018 AAAAGAATATTTTTA-AAT
1 AAAATAATATTTTTAGAAT
1781036 AAAATAATATTTTTATGAAT
1 AAAATAATATTTTTA-GAAT
*
1781056 AAAATATTATT
1 AAAATAATATT
1781067 AAAAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
AAAATAATATTTTTAGAAT
Found at i:1790357 original size:2 final size:2
Alignment explanation
Indices: 1790350--1790384 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1790340 ATGACTTTGA
*
1790350 AT AT AT AT AT AT AA 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
1790385 CATGTAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1801421 original size:12 final size:11
Alignment explanation
Indices: 1801404--1801448 Score: 63
Period size: 12 Copynumber: 3.9 Consensus size: 11
1801394 GAATAGTTTC
1801404 TTGCTGCCTCCT
1 TTGCTGCCT-CT
1801416 TTGCTGCCTCT
1 TTGCTGCCTCT
1801427 CTTGCTGCCTCT
1 -TTGCTGCCTCT
*
1801439 CTGCTGCCTC
1 TTGCTGCCTC
1801449 AAAAATCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.00, C:0.42, G:0.18, T:0.40
Consensus pattern (11 bp):
TTGCTGCCTCT
Found at i:1801431 original size:24 final size:23
Alignment explanation
Indices: 1801402--1801448 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1801392 CAGAATAGTT
*
1801402 TCTTGCTGCCTCCTTTGCTGCCTC
1 TCTTGCTGCCT-CTCTGCTGCCTC
1801426 TCTTGCTGCCTCTCTGCTGCCTC
1 TCTTGCTGCCTCTCTGCTGCCTC
1801449 AAAAATCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.00, C:0.43, G:0.17, T:0.40
Consensus pattern (23 bp):
TCTTGCTGCCTCTCTGCTGCCTC
Found at i:1802127 original size:21 final size:22
Alignment explanation
Indices: 1802092--1802135 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1802082 CTCTTAAAGT
1802092 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
1802114 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
1802135 A
1 A
1802136 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:1812545 original size:12 final size:12
Alignment explanation
Indices: 1812529--1812563 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1812519 CTGATGAAAC
1812529 CTTTGATTCTAG
1 CTTTGATTCTAG
*
1812541 TTTTGATTCTAG
1 CTTTGATTCTAG
*
1812553 CTTTAATTCTA
1 CTTTGATTCTA
1812564 ATGAATTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.54
Consensus pattern (12 bp):
CTTTGATTCTAG
Found at i:1814330 original size:37 final size:36
Alignment explanation
Indices: 1814289--1814393 Score: 104
Period size: 37 Copynumber: 2.8 Consensus size: 36
1814279 TTAATTCTTA
* *
1814289 AAAGGCATTTAGTTGTAAAGGTTATGATTGAACCTTG
1 AAAGGCATGT-GTTGTAAAGGTTATGCTTGAACCTTG
* * * *
1814326 AAAGGTAGTGTCTTGTAAAGGTTGTGCTTGATCCTTG
1 AAAGGCA-TGTGTTGTAAAGGTTATGCTTGAACCTTG
*
1814363 AAAAGCA-GTGGCTTGTAAAGGTTATGCTTGA
1 AAAGGCATGT-G-TTGTAAAGGTTATGCTTGA
1814394 TCCTAACAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
35 2 0.04
37 51 0.93
38 2 0.04
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.34
Consensus pattern (36 bp):
AAAGGCATGTGTTGTAAAGGTTATGCTTGAACCTTG
Found at i:1814394 original size:37 final size:37
Alignment explanation
Indices: 1814301--1814397 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
1814291 AGGCATTTAG
* * * * *
1814301 TTGTAAAGGTTATGATTGAACCTTGAAAGGTAGTGTC
1 TTGTAAAGGTTATGCTTGATCCTTGAAAAGCAGTGGC
*
1814338 TTGTAAAGGTTGTGCTTGATCCTTGAAAAGCAGTGGC
1 TTGTAAAGGTTATGCTTGATCCTTGAAAAGCAGTGGC
1814375 TTGTAAAGGTTATGCTTGATCCT
1 TTGTAAAGGTTATGCTTGATCCT
1814398 AACAAGGTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.36
Consensus pattern (37 bp):
TTGTAAAGGTTATGCTTGATCCTTGAAAAGCAGTGGC
Found at i:1814696 original size:21 final size:22
Alignment explanation
Indices: 1814671--1814714 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1814661 AAGTGATTAA
1814671 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
1814692 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1814714 T
1 T
1814715 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1817442 original size:39 final size:39
Alignment explanation
Indices: 1817383--1817524 Score: 151
Period size: 39 Copynumber: 3.6 Consensus size: 39
1817373 TAGTGCAAAA
* * * * * * *
1817383 CCACTTATGGCATATTAAAGTTATCGTCCAGTGCCATAA
1 CCACTGATGGAATATCAAAGTTATCGTCTAGTGTCGTAG
* *
1817422 CGACTGATGGAATATCAAAGTAATCGTCTAGTGTCGTAG
1 CCACTGATGGAATATCAAAGTTATCGTCTAGTGTCGTAG
* * * *
1817461 CCACTGACT-GAACATCAAAGTCATCATCTAGTGTTGTAG
1 CCACTGA-TGGAATATCAAAGTTATCGTCTAGTGTCGTAG
1817500 CCACTGATGGAATATCAAAGTTATC
1 CCACTGATGGAATATCAAAGTTATC
1817525 ATGCAAAATT
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.01
39 83 0.98
40 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (39 bp):
CCACTGATGGAATATCAAAGTTATCGTCTAGTGTCGTAG
Found at i:1828580 original size:36 final size:36
Alignment explanation
Indices: 1828504--1828580 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
1828494 TAAGATAGTG
* **
1828504 GTGGAGAATCAAATCACACATGTGCTGAAGTAACGG
1 GTGGAGAATCAAATCACACATGTGCTGAAGCAACAA
* *
1828540 GTGGAGAATGAAATCATACGA-GTGCTGAAGCAACAA
1 GTGGAGAATCAAATCACAC-ATGTGCTGAAGCAACAA
1828576 GTGGA
1 GTGGA
1828581 AAAACAAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.30, T:0.18
Consensus pattern (36 bp):
GTGGAGAATCAAATCACACATGTGCTGAAGCAACAA
Found at i:1832658 original size:34 final size:33
Alignment explanation
Indices: 1832620--1832683 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
1832610 ATTTGTTTCA
*
1832620 GTAATAAGGCATGACATGACTATTGTTTGTTAGG
1 GTAATAAGGCATGACATGA-TATTGTATGTTAGG
**
1832654 GTAATGGGGCATGACATGATATTGTATGTT
1 GTAATAAGGCATGACATGATATTGTATGTT
1832684 GTTCGTCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 10 0.37
34 17 0.63
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (33 bp):
GTAATAAGGCATGACATGATATTGTATGTTAGG
Found at i:1834073 original size:33 final size:33
Alignment explanation
Indices: 1834030--1834092 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1834020 GGTGACATTG
*
1834030 AGGATGATGATATACCCTA-ATATTAGAGATTTA
1 AGGATAATGATATACCCTATAT-TTAGAGATTTA
*
1834063 AGGATAATGATATGCCCTATATTTAGAGAT
1 AGGATAATGATATACCCTATATTTAGAGAT
1834093 GGTTGCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (33 bp):
AGGATAATGATATACCCTATATTTAGAGATTTA
Found at i:1841369 original size:15 final size:15
Alignment explanation
Indices: 1841349--1841384 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1841339 ACATTTTTAT
*
1841349 TGCCACATTAACAAC
1 TGCCACATCAACAAC
*
1841364 TGCCACATCAACATC
1 TGCCACATCAACAAC
1841379 TGCCAC
1 TGCCAC
1841385 GTCACTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.39, G:0.08, T:0.19
Consensus pattern (15 bp):
TGCCACATCAACAAC
Found at i:1846056 original size:26 final size:25
Alignment explanation
Indices: 1846027--1846078 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
1846017 AGTTCTTATT
1846027 TCTTAAT-TTTCTTTCATTTTTGTTTA
1 TCTTAATATTT-TTT-ATTTTTGTTTA
*
1846053 TCTTTATATTTTTTATTTTTGTTTA
1 TCTTAATATTTTTTATTTTTGTTTA
1846078 T
1 T
1846079 GCATTTGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 12 0.50
26 9 0.38
27 3 0.12
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.73
Consensus pattern (25 bp):
TCTTAATATTTTTTATTTTTGTTTA
Found at i:1857575 original size:40 final size:40
Alignment explanation
Indices: 1857521--1857601 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
1857511 CCTAATGCAA
*
1857521 AAGAGACAACTGAAGATATTTTCAAAAACACTATTAATGT
1 AAGAGACAACTGAAGATATTTTCAAAAACAATATTAATGT
*
1857561 AAGAGACAATTGAAGATATTTTCAAAAACAATATTAATGT
1 AAGAGACAACTGAAGATATTTTCAAAAACAATATTAATGT
1857601 A
1 A
1857602 TAAATTCTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.28
Consensus pattern (40 bp):
AAGAGACAACTGAAGATATTTTCAAAAACAATATTAATGT
Found at i:1858074 original size:33 final size:33
Alignment explanation
Indices: 1858032--1858103 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
1858022 CAATGCAAAA
*
1858032 GTCTTGGCTAAATTTAAAGTATAGATGAATGGT
1 GTCTTGGCTAAATCTAAAGTATAGATGAATGGT
1858065 GTCTTGGCTAAATCTAAAGTATAGATGAATGGT
1 GTCTTGGCTAAATCTAAAGTATAGATGAATGGT
*
1858098 GACTTG
1 GTCTTG
1858104 CTACAAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (33 bp):
GTCTTGGCTAAATCTAAAGTATAGATGAATGGT
Found at i:1860466 original size:39 final size:40
Alignment explanation
Indices: 1860412--1860491 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
1860402 CCGAATACAA
* * *
1860412 AAAAGACCATTGAAGATA-TTTCAAAAACACTCTTAATGT
1 AAAAGACAATTGAAGATATTTTCAAAAACAATATTAATGT
1860451 AAAAGACAATTGAAGATATTTTCAAAAACAATATTAATGT
1 AAAAGACAATTGAAGATATTTTCAAAAACAATATTAATGT
1860491 A
1 A
1860492 CAAATTCTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 17 0.46
40 20 0.54
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (40 bp):
AAAAGACAATTGAAGATATTTTCAAAAACAATATTAATGT
Found at i:1862413 original size:14 final size:15
Alignment explanation
Indices: 1862386--1862425 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1862376 TCTTTCAACT
1862386 TTTATTATTATTTTA
1 TTTATTATTATTTTA
*
1862401 TTTA-TATTTTTTTA
1 TTTATTATTATTTTA
1862415 TTT-TT-TTATTT
1 TTTATTATTATTT
1862426 CTATACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
15 4 0.18
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTATTATTATTTTA
Done.