Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 5 of 279
Found at i:1335588 original size:24 final size:24
Alignment explanation
Indices: 1335561--1335606 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1335551 AGGAAGTAAG
1335561 CCATATCTCCAAGACCAAACATAT
1 CCATATCTCCAAGACCAAACATAT
1335585 CCATATCTCCAAGACCAAACAT
1 CCATATCTCCAAGACCAAACAT
1335607 TTCAAATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.35, G:0.04, T:0.20
Consensus pattern (24 bp):
CCATATCTCCAAGACCAAACATAT
Found at i:1339737 original size:25 final size:25
Alignment explanation
Indices: 1339709--1339759 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1339699 ATGATTATGG
1339709 TTCGATAAATCTTGAGGCATTGGTA
1 TTCGATAAATCTTGAGGCATTGGTA
1339734 TTCGATAAATCTTGAGGCATTGGTA
1 TTCGATAAATCTTGAGGCATTGGTA
1339759 T
1 T
1339760 AGGTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (25 bp):
TTCGATAAATCTTGAGGCATTGGTA
Found at i:1341670 original size:46 final size:46
Alignment explanation
Indices: 1341480--1341790 Score: 204
Period size: 46 Copynumber: 6.6 Consensus size: 46
1341470 GTATAATGCT
* * * * *
1341480 GATGCCATGTCCCAGATATGGTCTTACATTGGCTCATC-CATC-AAGTC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTC-TCATATCGAGGCC
* * * *
1341527 GATGCCATGTCCCAAACATGGTCTTACGCTAGCTCTCGCATATCTG-TGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCT--CATATC-GAGGCC
* * * *
1341577 GATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTCGAAGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATATCGAGGCC
*
1341623 GATGCATGTCCCAGACATGTCTTATACTGGCT-TACATATCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATATCGAGGCC
* * * * * * * *
1341669 GATACATGTCCCAGACATGTCTTATACTAGCTCTCGTCTCAATGCT
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATCGAGGCC
* * *
1341715 GATGCCATGTCCCAGACATGGTCTTACGCTGGCTCTCATAAT-GTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-ATCGAGGCC
**
1341763 GATAAATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
1341791 AGTACACAAA
Statistics
Matches: 213, Mismatches: 38, Indels: 27
0.77 0.14 0.10
Matches are distributed among these distances:
44 9 0.04
45 16 0.08
46 72 0.34
47 58 0.27
48 23 0.11
49 5 0.02
50 30 0.14
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCTCATATCGAGGCC
Found at i:1341772 original size:94 final size:93
Alignment explanation
Indices: 1341526--1341798 Score: 288
Period size: 94 Copynumber: 2.9 Consensus size: 93
1341516 TCCATCAAGT
* * * * *
1341526 CGATGCCATGTCCCAAACATGGTCTTACGCTAGCTCTCGCATATCTGTGCCGATGCCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACGCTGGCTCT-ACATATGTG-GCCGAT-ACATGTCCCA
1341591 GACATGGTCTTACACT-GACACATCTCGAAGC
63 GACAT-GTCTTACACTAGACACATCTCGAAGC
** *
1341622 CGATG-CATGTCCCAGACAT-GTCTTATACTGGCT-TACATATCGAGGCCGATACATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACGCTGGCTCTACATAT-GTGGCCGATACATGTCCCAGA
* * * *
1341684 CATGTCTTATACTAGCTCTCGTCTC-AATGC
65 CATGTCTTACACTAG-ACACATCTCGAA-GC
* * *
1341714 TGATGCCATGTCCCAGACATGGTCTTACGCTGGCTCT-CATAATGTGGCTGATAAATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACGCTGGCTCTACAT-ATGTGGCCGATACATGTCCCAGA
1341778 CATGTCTTACACTAGTACACA
65 CATGTCTTACACTAG-ACACA
1341799 AATAACCCGA
Statistics
Matches: 146, Mismatches: 23, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
90 9 0.06
91 17 0.12
92 23 0.16
93 16 0.11
94 60 0.41
95 16 0.11
96 5 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (93 bp):
CGATGCCATGTCCCAGACATGGTCTTACGCTGGCTCTACATATGTGGCCGATACATGTCCCAGAC
ATGTCTTACACTAGACACATCTCGAAGC
Found at i:1342520 original size:13 final size:13
Alignment explanation
Indices: 1342502--1342526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1342492 CTAAAAGTAC
1342502 AAAAATCATCAAG
1 AAAAATCATCAAG
1342515 AAAAATCATCAA
1 AAAAATCATCAA
1342527 AATCTCTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:1345584 original size:26 final size:25
Alignment explanation
Indices: 1345550--1345611 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
1345540 TAGCTCTTAA
*
1345550 GAGCGTCCCGATATATGGCTCTTCGC
1 GAGCTTCCCGATATA-GGCTCTTCGC
* *
1345576 GAGCTTCCC-A-ATAGGCTCTTTGT
1 GAGCTTCCCGATATAGGCTCTTCGC
1345599 GAGCTTCCCGATA
1 GAGCTTCCCGATA
1345612 GTGCTCGCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 17 0.55
24 4 0.13
25 2 0.06
26 8 0.26
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (25 bp):
GAGCTTCCCGATATAGGCTCTTCGC
Found at i:1345602 original size:23 final size:23
Alignment explanation
Indices: 1345566--1345617 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1345556 CCCGATATAT
1345566 GGCTCTTCGCGAGCTTCCCAATA
1 GGCTCTTCGCGAGCTTCCCAATA
* * *
1345589 GGCTCTTTGTGAGCTTCCCGATA
1 GGCTCTTCGCGAGCTTCCCAATA
1345612 GTGCTC
1 G-GCTC
1345618 GCTTGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.13, C:0.31, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCTCTTCGCGAGCTTCCCAATA
Found at i:1346147 original size:46 final size:46
Alignment explanation
Indices: 1346076--1346346 Score: 364
Period size: 46 Copynumber: 5.9 Consensus size: 46
1346066 CTCTGAAATC
* * * * *
1346076 AAATGTGTAAGACCATAGTTGAAAGATACCATGACAACCTGATATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATG
* * * * *
1346122 AAATGTGTAAGACCATGGTTAAAAGATATCATGGCAACCTGATATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATG
*
1346168 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATG
* *
1346214 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATG
*
1346260 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-G
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATG
* * * *
1346305 AAAACGAGTAAGACCATAGTTGAAAGATACTATGGCATCATG
1 -AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
1346347 TCGAAGATAA
Statistics
Matches: 207, Mismatches: 17, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
45 1 0.00
46 206 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (46 bp):
AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATG
Found at i:1346742 original size:78 final size:78
Alignment explanation
Indices: 1346652--1346806 Score: 283
Period size: 78 Copynumber: 2.0 Consensus size: 78
1346642 TGAAATATTG
* *
1346652 ATATAACGAAATGAATAATATATGCTTATGAAGAAACAGTAAGAGAATAATATATTTTGTGACAT
1 ATATAACAAAATGAATAATATATGATTATGAAGAAACAGTAAGAGAATAATATATTTTGTGACAT
1346717 GTACATATATAAA
66 GTACATATATAAA
*
1346730 ATATAACAAAATGAATAATATATGATTATGAAGAAATAGTAAGAGAATAATATATTTTGTGACAT
1 ATATAACAAAATGAATAATATATGATTATGAAGAAACAGTAAGAGAATAATATATTTTGTGACAT
1346795 GTACATATATAA
66 GTACATATATAA
1346807 TTATCTTTGA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.32
Consensus pattern (78 bp):
ATATAACAAAATGAATAATATATGATTATGAAGAAACAGTAAGAGAATAATATATTTTGTGACAT
GTACATATATAAA
Found at i:1347358 original size:14 final size:14
Alignment explanation
Indices: 1347339--1347368 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1347329 TTATATCGAG
1347339 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
1347353 ACCAATCCAATTCA
1 ACCAATCCAAATCA
1347367 AC
1 AC
1347369 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:1369378 original size:47 final size:49
Alignment explanation
Indices: 1369306--1369436 Score: 142
Period size: 49 Copynumber: 2.7 Consensus size: 49
1369296 GTATAATACC
* * *
1369306 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC-AATC-AAGTT
1 GATGCCATATCCCAAACATGGTCTTACACTGGCTCATCAAATCGAAGCT
* * * *
1369353 GATGCCATATACCAAACATGTTCTTACACTGACT-ATCGAAATCGAGGCT
1 GATGCCATATCCCAAACATGGTCTTACACTGGCTCATC-AAATCGAAGCT
* * *
1369402 GACGTCATATCCCAAACATGGTCTTACACTAGCTC
1 GATGCCATATCCCAAACATGGTCTTACACTGGCTC
1369437 TCACATATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
46 3 0.04
47 29 0.43
48 4 0.06
49 31 0.46
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (49 bp):
GATGCCATATCCCAAACATGGTCTTACACTGGCTCATCAAATCGAAGCT
Found at i:1369662 original size:46 final size:46
Alignment explanation
Indices: 1369411--1369665 Score: 185
Period size: 46 Copynumber: 5.5 Consensus size: 46
1369401 TGACGTCATA
* * * *
1369411 TCCCAAACATGGTCTTACACTAGCTCTCACATATTTGT-GTCGATACCATG
1 TCCCAGACAT-GTCTTACACTAGCTCT--CATA-ATGTAGCCGAT-GCATG
*
1369461 TCCCAGACATGGTCTTACACTA-C-ATC-T--TGTAGCCGATGCATG
1 TCCCAGACAT-GTCTTACACTAGCTCTCATAATGTAGCCGATGCATG
*
1369503 TCCCAGACATGTCTTACACT-GACT-TACAT-CTCG-AGGCCGATGCATG
1 TCCCAGACATGTCTTACACTAG-CTCT-CATAAT-GTA-GCCGATGCATG
* * *
1369549 TCCCAGACATGTCTTATACTAGCTCTCGTCTCAATGTA---GATACCATG
1 TCCCAGACATGTCTTACACTAGCTCTC--AT-AATGTAGCCGAT-GCATG
1369596 TCCCAGACATGGTCTTACACTAGCTCTCATAATGTAGCCGATGCATG
1 TCCCAGACAT-GTCTTACACTAGCTCTCATAATGTAGCCGATGCATG
* *
1369643 TCCCGGACTTGTCTTACACTAGC
1 TCCCAGACATGTCTTACACTAGC
1369666 ACACAAATAA
Statistics
Matches: 171, Mismatches: 13, Indels: 46
0.74 0.06 0.20
Matches are distributed among these distances:
41 10 0.06
42 19 0.11
43 6 0.04
44 1 0.01
45 9 0.05
46 52 0.30
47 28 0.16
48 21 0.12
49 2 0.01
50 23 0.13
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (46 bp):
TCCCAGACATGTCTTACACTAGCTCTCATAATGTAGCCGATGCATG
Found at i:1375086 original size:32 final size:32
Alignment explanation
Indices: 1375050--1375114 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
1375040 AGTACAAAAG
*
1375050 AATGGTTCACATATGCATTTCATTAAAACATT
1 AATGGTTCACATATGCATTTCATCAAAACATT
1375082 AATGGTTCACATATGCATTTCATCAAAACATT
1 AATGGTTCACATATGCATTTCATCAAAACATT
1375114 A
1 A
1375115 CATCTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.35
Consensus pattern (32 bp):
AATGGTTCACATATGCATTTCATCAAAACATT
Found at i:1380289 original size:43 final size:42
Alignment explanation
Indices: 1380223--1380333 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 42
1380213 AGCTCGTACA
* * *
1380223 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTAAACGGAATCAAATA-CG
1380266 ATGCC-ACAGTCCCAGACAG-GGTCTTAAACGGAATCAAATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTAAACGGAATCAAATACG
* * * * *
1380308 ATGTCGATGTCCCAGACATCGTCTTA
1 ATGCCAACGTCCCAGACGTGGTCTTA
1380334 CACATAAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
42 23 0.40
43 33 0.58
44 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTAAACGGAATCAAATACG
Found at i:1380325 original size:42 final size:44
Alignment explanation
Indices: 1380223--1380310 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 44
1380213 AGCTCGTACA
* * *
1380223 ATGCCA-ACGTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCACA-GTCCCAGACAGTGGTCTTAAACGGAATCAAATATCG
1380266 ATGCCACAGTCCCAGACAG-GGTCTTAAACGGAATCAAATA-CG
1 ATGCCACAGTCCCAGACAGTGGTCTTAAACGGAATCAAATATCG
1380308 ATG
1 ATG
1380311 TCGATGTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
42 5 0.12
43 33 0.82
44 2 0.05
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (44 bp):
ATGCCACAGTCCCAGACAGTGGTCTTAAACGGAATCAAATATCG
Found at i:1387804 original size:27 final size:26
Alignment explanation
Indices: 1387767--1387877 Score: 123
Period size: 27 Copynumber: 4.1 Consensus size: 26
1387757 AGCATGGCTG
* *
1387767 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
1387793 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
1387821 CCAGAACAGATATATGTGGCAGGGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * * *
1387848 CCAGATCCGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
1387875 CCA
1 CCA
1387878 AAACGCTTCC
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.07
27 52 0.70
28 17 0.23
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:1387826 original size:54 final size:54
Alignment explanation
Indices: 1387767--1387877 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
1387757 AGCATGGCTG
*
1387767 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * * *
1387821 CCAGAACAGATATATGTGGCAGGGCCACCAGATCCGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
1387875 CCA
1 CCA
1387878 AAACGCTTCC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
54 32 0.65
55 17 0.35
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:1389261 original size:26 final size:26
Alignment explanation
Indices: 1389100--1389253 Score: 299
Period size: 26 Copynumber: 5.9 Consensus size: 26
1389090 CATGAAATTC
*
1389100 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
1389126 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
1389152 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
1389178 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
1389204 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
1389230 TTATCATGGAACATTTACCTAACC
1 TTATCATGGAACATTTACCTAACC
1389254 TTTTATCAAT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 127 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:1390730 original size:43 final size:42
Alignment explanation
Indices: 1390673--1390781 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
1390663 AATGCCAACG
* * *
1390673 TCCCAGACATGGTCTTACATGTAATGAAATATCGATGCC-ACTG
1 TCCCAGACAGGGTCTTACATGTAATCAAATA-CGATGCCGA-TA
** *
1390716 TCCCAGTTAGGGTCTTACATGAAATCAAATACGATGCCGATA
1 TCCCAGACAGGGTCTTACATGTAATCAAATACGATGCCGATA
*
1390758 TCCCAGACATGGTCTTACATGTAA
1 TCCCAGACAGGGTCTTACATGTAA
1390782 ATCTCAAATC
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 28 0.51
43 27 0.49
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (42 bp):
TCCCAGACAGGGTCTTACATGTAATCAAATACGATGCCGATA
Found at i:1402765 original size:21 final size:21
Alignment explanation
Indices: 1402739--1402783 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1402729 AATTGACTCG
1402739 ATTTATTCGATATGGAATTAA
1 ATTTATTCGATATGGAATTAA
1402760 ATTTATTCGATATGGAATTAA
1 ATTTATTCGATATGGAATTAA
1402781 ATT
1 ATT
1402784 AGGTGGTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (21 bp):
ATTTATTCGATATGGAATTAA
Found at i:1403421 original size:31 final size:30
Alignment explanation
Indices: 1403383--1403454 Score: 117
Period size: 31 Copynumber: 2.4 Consensus size: 30
1403373 TGTTTTAATA
*
1403383 AATTTAATATTTATCTAGATAGTATTTTATT
1 AATTTAATATTTATCTAGATAATATTTT-TT
*
1403414 AATTTAATATTTATTTAGATAATATTTTTT
1 AATTTAATATTTATCTAGATAATATTTTTT
1403444 AATTTAATATT
1 AATTTAATATT
1403455 AATGTGATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 13 0.33
31 26 0.67
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (30 bp):
AATTTAATATTTATCTAGATAATATTTTTT
Found at i:1403426 original size:15 final size:15
Alignment explanation
Indices: 1403408--1403454 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1403398 TAGATAGTAT
1403408 TTTATTAATTTAATA
1 TTTATTAATTTAATA
* **
1403423 TTTATTTAGATAATA
1 TTTATTAATTTAATA
*
1403438 TTTTTTAATTTAATA
1 TTTATTAATTTAATA
1403453 TT
1 TT
1403455 AATGTGATTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTATTAATTTAATA
Found at i:1403451 original size:35 final size:34
Alignment explanation
Indices: 1403364--1403457 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 34
1403354 ACTTTTCTAA
*
1403364 AGATAATATTGTTTTAATAAATTTAATATTTATCT
1 AGATAATATT-TTTTAATTAATTTAATATTTATCT
* *
1403399 AGATAGTA--TTTT-ATTAATTTAATATTTATTT
1 AGATAATATTTTTTAATTAATTTAATATTTATCT
1403430 AGATAATATTTTTTAATTTAATATTAAT
1 AGATAATATTTTTTAA-TTAAT-TTAAT
1403458 GTGATTAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
31 24 0.48
32 4 0.08
33 4 0.08
34 1 0.02
35 12 0.24
36 5 0.10
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.54
Consensus pattern (34 bp):
AGATAATATTTTTTAATTAATTTAATATTTATCT
Found at i:1412420 original size:2 final size:2
Alignment explanation
Indices: 1412413--1412445 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1412403 GGGAATACTA
1412413 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1412446 AGCAGTAGTT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1413183 original size:26 final size:26
Alignment explanation
Indices: 1413154--1413203 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1413144 TTAACATCAG
* *
1413154 AAACTCGAATCTTAAATCCTAAACTT
1 AAACTCGAAACTCAAATCCTAAACTT
**
1413180 AAACTTTAAACTCAAATCCTAAAC
1 AAACTCGAAACTCAAATCCTAAAC
1413204 ACCAAGAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (26 bp):
AAACTCGAAACTCAAATCCTAAACTT
Found at i:1413357 original size:22 final size:24
Alignment explanation
Indices: 1413318--1413371 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
1413308 ACAAAATTAC
*
1413318 AAAAATTATATATTAATAAT-ATAA
1 AAAAATTATATATAAAT-ATCATAA
*
1413342 AAAAATTAT-TA-AAATATCATTA
1 AAAAATTATATATAAATATCATAA
1413364 AAAAATTA
1 AAAAATTA
1413372 AAAAATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 14 0.52
23 2 0.07
24 9 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAAATTATATATAAATATCATAA
Found at i:1420870 original size:22 final size:22
Alignment explanation
Indices: 1420845--1420889 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1420835 TATATTAAGT
1420845 ATACCTTAGTTTCAGTTAGTTA
1 ATACCTTAGTTTCAGTTAGTTA
1420867 ATACCTTAGTTTCAGTTAGTTA
1 ATACCTTAGTTTCAGTTAGTTA
1420889 A
1 A
1420890 GTTTCTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (22 bp):
ATACCTTAGTTTCAGTTAGTTA
Found at i:1421127 original size:54 final size:54
Alignment explanation
Indices: 1421041--1421291 Score: 220
Period size: 54 Copynumber: 4.6 Consensus size: 54
1421031 TGGATTCACG
** ** * * * **
1421041 GATTTACGATCGCAACCTCCCA-TATACAAGATTTTCAAAATTTTATGGTTCATT
1 GATTTACGATCGCAACCTCTTACT-TATGAGATTTTCAAAATATCATGATTTGTT
** * *
1421095 GATTTACGATCGTGACCTCTTACTTATGAGATTTTCAGAATATCATGATTTGTC
1 GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCATGATTTGTT
* * * *
1421149 GATTTACGATGGCAAACT-TCTACTTATGAGATTTTCAGAATCTCACT-ATTTGTT
1 GATTTACGATCGCAACCTCT-TACTTATGAGATTTTCAAAATATCA-TGATTTGTT
* * * ** *
1421203 GATTTATGATCGCAACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTC
1 GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCATGATTTGTT
* * *
1421257 GATTTACGATTGCAACCTCCTACTTATAAGATTTT
1 GATTTACGATCGCAACCTCTTACTTATGAGATTTT
1421292 TAGAATCTTA
Statistics
Matches: 161, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
53 1 0.01
54 157 0.98
55 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (54 bp):
GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCATGATTTGTT
Found at i:1421230 original size:108 final size:108
Alignment explanation
Indices: 1421092--1421351 Score: 306
Period size: 108 Copynumber: 2.4 Consensus size: 108
1421082 TTTATGGTTC
** * *
1421092 ATTGATTTACGATCGTGACCTCTTACTTATGAGATTTTCAGAATATCATGATTTGTCGATTTACG
1 ATTGATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCACGATTTGTCGATTTACG
* *
1421157 ATGGCAAACTTCTACTTATGAGATTTTCAGAATCTCACTA-TTT
66 ATGGCAAACTCCTACTTATAAGATTTTCAGAATCTCAC-AGTTT
* * * * *
1421200 GTTGATTTATGATCGCAACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTCGATTTACG
1 ATTGATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCACGATTTGTCGATTTACG
* * * *
1421265 ATTGCAACCTCCTACTTATAAGATTTTTAGAATCTTACAGTTT
66 ATGGCAAACTCCTACTTATAAGATTTTCAGAATCTCACAGTTT
** * * * **
1421308 ATCAATTTAGGATCGCAACCTCTCATTTACAAGATTTTCAAAAT
1 ATTGATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAAT
1421352 CTTGTGGTTT
Statistics
Matches: 127, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
107 1 0.01
108 126 0.99
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (108 bp):
ATTGATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCACGATTTGTCGATTTACG
ATGGCAAACTCCTACTTATAAGATTTTCAGAATCTCACAGTTT
Found at i:1421292 original size:54 final size:54
Alignment explanation
Indices: 1421095--1421329 Score: 256
Period size: 54 Copynumber: 4.4 Consensus size: 54
1421085 ATGGTTCATT
** * * *
1421095 GATTTACGATCGTGACCTCTTACTTATGAGATTTTCAGAATATCATGATTTGTC
1 GATTTACGATCGCAACCTCCTACTTATGAGATTTTCAGAATCTCACGATTTGTC
* * * * *
1421149 GATTTACGATGGCAAACTTCTACTTATGAGATTTTCAGAATCTCACTATTTGTT
1 GATTTACGATCGCAACCTCCTACTTATGAGATTTTCAGAATCTCACGATTTGTC
* * * * *
1421203 GATTTATGATCGCAACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTC
1 GATTTACGATCGCAACCTCCTACTTATGAGATTTTCAGAATCTCACGATTTGTC
* * * * *
1421257 GATTTACGATTGCAACCTCCTACTTATAAGATTTTTAGAATCTTAC-AGTTTATC
1 GATTTACGATCGCAACCTCCTACTTATGAGATTTTCAGAATCTCACGA-TTTGTC
* *
1421311 AATTTAGGATCGCAACCTC
1 GATTTACGATCGCAACCTC
1421330 TCATTTACAA
Statistics
Matches: 149, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
53 1 0.01
54 148 0.99
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (54 bp):
GATTTACGATCGCAACCTCCTACTTATGAGATTTTCAGAATCTCACGATTTGTC
Found at i:1421342 original size:54 final size:54
Alignment explanation
Indices: 1421042--1421354 Score: 175
Period size: 54 Copynumber: 5.8 Consensus size: 54
1421032 GGATTCACGG
* * * * * * * **
1421042 ATTTACGATCGCAACCTCCCA-TATACAAGATTTTCAAAATTTTATGGTTCATTG
1 ATTTACGATCGCAACCTCTCACT-TATAAGATTTTTAAAATCTTACGATTTATCA
** * * * * * * * * *
1421096 ATTTACGATCGTGACCTCTTACTTATGAGATTTTCAGAATATCATGATTTGTCG
1 ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTACGATTTATCA
* * * * * * * * **
1421150 ATTTACGATGGCAAACT-TCTACTTATGAGATTTTCAGAATCTCACTATTTGTTG
1 ATTTACGATCGCAACCTCTC-ACTTATAAGATTTTTAAAATCTTACGATTTATCA
* * * ** * *
1421204 ATTTATGATCGCAACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTCG
1 ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTACGATTTATCA
* *
1421258 ATTTACGATTGCAACCTC-CTACTTATAAGATTTTTAGAATCTTAC-AGTTTATCA
1 ATTTACGATCGCAACCTCTC-ACTTATAAGATTTTTAAAATCTTACGA-TTTATCA
* * * *
1421312 ATTTAGGATCGCAACCTCTCATTTACAAGATTTTCAAAATCTT
1 ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTT
1421355 GTGGTTTATC
Statistics
Matches: 207, Mismatches: 46, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
53 2 0.01
54 202 0.98
55 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (54 bp):
ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTACGATTTATCA
Found at i:1421362 original size:54 final size:54
Alignment explanation
Indices: 1421204--1421408 Score: 164
Period size: 54 Copynumber: 3.8 Consensus size: 54
1421194 CTATTTGTTG
* * * * * * *
1421204 ATTTATGATCGCAACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTCG
1 ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTGCGGTTTATCA
* * * *
1421258 ATTTACGATTGCAACCTC-CTACTTATAAGATTTTTAGAATCTTACAGTTTATCA
1 ATTTACGATCGCAACCTCTC-ACTTATAAGATTTTTAAAATCTTGCGGTTTATCA
* * * * * *
1421312 ATTTAGGATCGCAACCTCTCATTTACAAGATTTTCAAAATCTTGTGGTTTATCG
1 ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTGCGGTTTATCA
* * * * * *
1421366 ATATGCAATCGCAACCTAC-CGCTTACAAGA-TTTTAGAATCTTG
1 ATTTACGATCGCAACCT-CTCACTTATAAGATTTTTAAAATCTTG
1421409 TTGATGCCAA
Statistics
Matches: 119, Mismatches: 29, Indels: 7
0.77 0.19 0.05
Matches are distributed among these distances:
53 11 0.09
54 106 0.89
55 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (54 bp):
ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTGCGGTTTATCA
Found at i:1421367 original size:108 final size:108
Alignment explanation
Indices: 1421109--1421407 Score: 262
Period size: 108 Copynumber: 2.8 Consensus size: 108
1421099 TACGATCGTG
* ** * * ** * * * *
1421109 ACCTCTTACTTATGAGATTTTCAGAATATCATGATTTGTCGATTTACGATGGCAAACTTCTACTT
1 ACCTCTCACTTACAAGATTTTCAAAATCTCGCGATTTATCGATTTACGATCGCAACCTCCTACTT
* * * * ** *
1421174 ATGAGATTTTCAGAATCTCACTATTTGTTGATTTATGATCGCA
66 ATAAGATTTTTAGAATCTTACTATTTATCAATTTAGGATCGCA
* ** * * *
1421217 ACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTCGATTTACGATTGCAACCTCCTACTT
1 ACCTCTCACTTACAAGATTTTCAAAATCTCGCGATTTATCGATTTACGATCGCAACCTCCTACTT
1421282 ATAAGATTTTTAGAATCTTAC-AGTTTATCAATTTAGGATCGCA
66 ATAAGATTTTTAGAATCTTACTA-TTTATCAATTTAGGATCGCA
* * * * * * * *
1421325 ACCTCTCATTTACAAGATTTTCAAAATCTTGTGGTTTATCGATATGCAATCGCAACCTACC-GCT
1 ACCTCTCACTTACAAGATTTTCAAAATCTCGCGATTTATCGATTTACGATCGCAACCT-CCTACT
*
1421389 TACAAGA-TTTTAGAATCTT
65 TATAAGATTTTTAGAATCTT
1421408 GTTGATGCCA
Statistics
Matches: 159, Mismatches: 30, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
107 13 0.08
108 144 0.91
109 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (108 bp):
ACCTCTCACTTACAAGATTTTCAAAATCTCGCGATTTATCGATTTACGATCGCAACCTCCTACTT
ATAAGATTTTTAGAATCTTACTATTTATCAATTTAGGATCGCA
Found at i:1421774 original size:24 final size:23
Alignment explanation
Indices: 1421746--1421969 Score: 142
Period size: 24 Copynumber: 9.4 Consensus size: 23
1421736 GCACAGGTGG
1421746 CATAATTTTCTGCTGTATAGCTCA
1 CATAATTTTCTGCTGTATAGCT-A
* * **
1421770 TATAATTTTCTACTACATAGCTAA
1 CATAATTTTCTGCTGTATAGCT-A
* *
1421794 CATAATTTTCTGTTGTATAGCTTG
1 CATAATTTTCTGCTGTATAGC-TA
* *
1421818 CATAATTTTCTGCTGCACAGCTA
1 CATAATTTTCTGCTGTATAGCTA
* * *
1421841 GCATAATTTTCTGTTGTATAGTTT
1 -CATAATTTTCTGCTGTATAGCTA
* * * *
1421865 CATATTTTTTTGTTGTAGAGCTA
1 CATAATTTTCTGCTGTATAGCTA
* * ** *
1421888 GCATAATCTTCTACTCCACAGCTA
1 -CATAATTTTCTGCTGTATAGCTA
* * *
1421912 GCATAATTTTCTGCTATACAGTTTA
1 -CATAATTTTCTGCTGTATAG-CTA
* * *
1421937 CATAATTTTCTACTGCACAGCTA
1 CATAATTTTCTGCTGTATAGCTA
1421960 GCATAATTTT
1 -CATAATTTT
1421970 TTGTTGTAGA
Statistics
Matches: 153, Mismatches: 42, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
23 21 0.14
24 129 0.84
25 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (23 bp):
CATAATTTTCTGCTGTATAGCTA
Found at i:1421774 original size:48 final size:48
Alignment explanation
Indices: 1421696--1421861 Score: 188
Period size: 48 Copynumber: 3.4 Consensus size: 48
1421686 TCACCAGTTC
* * * * * *
1421696 GCATAATTTTTTTACTGTATAGTTCGTATAAATTTCTACTGCACAGGTG
1 GCATAA-TTTTCTGCTGTATAGCTCGTATAATTTTCTACTGCACAGCTA
* * *
1421745 GCATAATTTTCTGCTGTATAGCTCATATAATTTTCTACTACATAGCTA
1 GCATAATTTTCTGCTGTATAGCTCGTATAATTTTCTACTGCACAGCTA
* * * * *
1421793 ACATAATTTTCTGTTGTATAGCTTGCATAATTTTCTGCTGCACAGCTA
1 GCATAATTTTCTGCTGTATAGCTCGTATAATTTTCTACTGCACAGCTA
*
1421841 GCATAATTTTCTGTTGTATAG
1 GCATAATTTTCTGCTGTATAG
1421862 TTTCATATTT
Statistics
Matches: 99, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
48 93 0.94
49 6 0.06
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (48 bp):
GCATAATTTTCTGCTGTATAGCTCGTATAATTTTCTACTGCACAGCTA
Found at i:1421918 original size:119 final size:120
Alignment explanation
Indices: 1421745--1421994 Score: 324
Period size: 119 Copynumber: 2.1 Consensus size: 120
1421735 TGCACAGGTG
* * * * * * * *
1421745 GCATAATTTTCTGCTGTATAGCTCA-TATAATTTTCTACTACATAGCTAACATAATTTTCTGTTG
1 GCATAATTTTTTGTTGTAGAGCT-AGCATAATCTTCTACTACACAGCTAACATAATTTTCTGCTA
* * * *
1421809 TATAGCTTGCATAATTTTCTGCTGCACAGCTAGCATAATTTTCTGTTGTATAGTTT
65 TACAGCTTACATAATTTTCTACTGCACAGCTAGCATAATTTTCTGTTGTAGAGTTT
* * *
1421865 -CATATTTTTTTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAGCATAATTTTCTGCTAT
1 GCATAATTTTTTGTTGTAGAGCTAGCATAATCTTCTACTACACAGCTAACATAATTTTCTGCTAT
* *
1421929 ACAGTTTACATAATTTTCTACTGCACAGCTAGCATAATTTTTTGTTGTAGAGTTT
66 ACAGCTTACATAATTTTCTACTGCACAGCTAGCATAATTTTCTGTTGTAGAGTTT
1421984 GCATAATTTTT
1 GCATAATTTTT
1421995 CGCTACACAA
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
118 1 0.01
119 100 0.91
120 9 0.08
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (120 bp):
GCATAATTTTTTGTTGTAGAGCTAGCATAATCTTCTACTACACAGCTAACATAATTTTCTGCTAT
ACAGCTTACATAATTTTCTACTGCACAGCTAGCATAATTTTCTGTTGTAGAGTTT
Found at i:1421935 original size:71 final size:72
Alignment explanation
Indices: 1421793--1421966 Score: 215
Period size: 71 Copynumber: 2.4 Consensus size: 72
1421783 TACATAGCTA
* * * * * * *
1421793 ACATAATTTTCTGTTGTATAGCTTGCATAATTTTCTGCTGCACAGCTAGCATAATTTTCTGTTGT
1 ACATAATTTTCTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAGCATAATTTTCTGCTAT
*
1421858 ATAGTTT
66 ACAGTTT
* *
1421865 -CATATTTTTTTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAGCATAATTTTCTGCTAT
1 ACATAATTTTCTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAGCATAATTTTCTGCTAT
1421929 ACAGTTT
66 ACAGTTT
** * *
1421936 ACATAATTTTCTACTGCACAGCTAGCATAAT
1 ACATAATTTTCTGTTGTAGAGCTAGCATAAT
1421967 TTTTTGTTGT
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
71 61 0.72
72 24 0.28
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (72 bp):
ACATAATTTTCTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAGCATAATTTTCTGCTAT
ACAGTTT
Found at i:1422018 original size:48 final size:48
Alignment explanation
Indices: 1421865--1422019 Score: 177
Period size: 48 Copynumber: 3.2 Consensus size: 48
1421855 TGTATAGTTT
* * * * *
1421865 CATATTTTTTTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAG
1 CATAATTTTTTGTTGTAGAGTTTGCATAATTTTCTACTACACAGCTAG
* * * * * *
1421913 CATAATTTTCTGCTATACAGTTTACATAATTTTCTACTGCACAGCTAG
1 CATAATTTTTTGTTGTAGAGTTTGCATAATTTTCTACTACACAGCTAG
* *
1421961 CATAATTTTTTGTTGTAGAGTTTGCATAATTTT-TCGCTACACAACTAG
1 CATAATTTTTTGTTGTAGAGTTTGCATAATTTTCT-ACTACACAGCTAG
1422009 CATAATTTTTT
1 CATAATTTTTT
1422020 ACTACATAGC
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
47 1 0.01
48 87 0.99
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (48 bp):
CATAATTTTTTGTTGTAGAGTTTGCATAATTTTCTACTACACAGCTAG
Found at i:1422729 original size:12 final size:12
Alignment explanation
Indices: 1422712--1422745 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1422702 TTCCCTTTAA
1422712 AATAGTAAA-ATT
1 AATAGTAAAGA-T
1422724 AATAGTAAAGAT
1 AATAGTAAAGAT
1422736 AATAGTAAAG
1 AATAGTAAAG
1422746 GAGAAGTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 20 0.95
13 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (12 bp):
AATAGTAAAGAT
Found at i:1423658 original size:20 final size:20
Alignment explanation
Indices: 1423620--1423667 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1423610 TAAATTCTAA
* **
1423620 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
1423640 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
1423660 AAA-ATAAA
1 AAAGATAAA
1423668 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:1423678 original size:19 final size:18
Alignment explanation
Indices: 1423654--1423697 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1423644 ATAAATAAAG
1423654 ATAATTAAAATAAAATCCTA
1 ATAATTAAAAT--AATCCTA
*
1423674 A-AATTTAAATAATCCTA
1 ATAATTAAAATAATCCTA
1423691 ATAATTA
1 ATAATTA
1423698 TCCTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 8 0.38
20 1 0.05
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATTAAAATAATCCTA
Found at i:1423712 original size:15 final size:15
Alignment explanation
Indices: 1423692--1423721 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1423682 ATAATCCTAA
1423692 TAATTATCCTAATAT
1 TAATTATCCTAATAT
1423707 TAATTATCCTAATAT
1 TAATTATCCTAATAT
1423722 AAATAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:1425254 original size:39 final size:38
Alignment explanation
Indices: 1425165--1425260 Score: 120
Period size: 39 Copynumber: 2.5 Consensus size: 38
1425155 ATCCTTGTTG
* * *
1425165 TAATTATTGTAATTATAATTTATGATCGAATATTATTA
1 TAATTATTGTAATTATAATTTATCATCAAACATTATTA
* * *
1425203 TAACTATTGTAATTGTAATTTTTCAGTCAAACATTATTA
1 TAATTATTGTAATTATAATTTATCA-TCAAACATTATTA
*
1425242 TAATTATGGTAATTATAAT
1 TAATTATTGTAATTATAAT
1425261 CGATTAATTG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (38 bp):
TAATTATTGTAATTATAATTTATCATCAAACATTATTA
Found at i:1426548 original size:38 final size:39
Alignment explanation
Indices: 1426498--1426579 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 39
1426488 CAATTTGATC
* * *
1426498 TAATTTGATTCTTGTACATAATGTCATTATTTAGCCATA
1 TAATTTGATTCTTCTACAGAATATCATTATTTAGCCATA
* *
1426537 TAATTT-ATTCTTCTACAGAATATCATTATTTATCCTTA
1 TAATTTGATTCTTCTACAGAATATCATTATTTAGCCATA
1426575 TAATT
1 TAATT
1426580 GACACTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
38 32 0.84
39 6 0.16
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (39 bp):
TAATTTGATTCTTCTACAGAATATCATTATTTAGCCATA
Found at i:1428666 original size:41 final size:42
Alignment explanation
Indices: 1428606--1428783 Score: 226
Period size: 41 Copynumber: 4.4 Consensus size: 42
1428596 GACGTTTTTT
** *
1428606 AAAACGCCGCTAAAAACAGAGCAACAGCGGCG-TTTTAGTAA
1 AAAACGCCGCTAAAAACAGAGCATTAGCGGCGCTTTTGGTAA
*
1428647 AAAATGCCGCTAAAAACAGAGCATTAGCGGCGCTTTTGGT--
1 AAAACGCCGCTAAAAACAGAGCATTAGCGGCGCTTTTGGTAA
* *
1428687 AAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT--
1 AAAACGCCGCTAAAAA-CAGAGCATTAGCGGCGCTTTTGGTAA
*
1428728 AAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT--
1 AAAACGCCGCTAAAAA-CAGAGCATTAGCGGCGCTTTTGGTAA
1428769 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
1428784 GTCATATAAC
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 15 0.12
41 103 0.83
42 6 0.05
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (42 bp):
AAAACGCCGCTAAAAACAGAGCATTAGCGGCGCTTTTGGTAA
Found at i:1428699 original size:81 final size:81
Alignment explanation
Indices: 1428577--1428783 Score: 269
Period size: 82 Copynumber: 2.6 Consensus size: 81
1428567 GCAAAAATTT
* * * * *
1428577 TAAAATACAGAGCAATAGCGACG-TTTT-TTAAAACGCCGCTAAAAA-CAGAGCAACAGCGGCG-
1 TAAAA-ACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCAACAACGACGC
1428638 TTTTAGTAAAAAATGCCGC
65 TTTTAGTAAAAAA--CCGC
**
1428657 TAAAAACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAACGACGCT
1 TAAAAACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCAACAACGACGCT
* *
1428722 TTTGGTAAAACACCGC
66 TTTAGTAAAAAACCGC
1428738 TAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
1 TAAAAA-CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
1428784 GTCATATAAC
Statistics
Matches: 113, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
79 15 0.13
80 9 0.08
81 27 0.24
82 51 0.45
83 11 0.10
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (81 bp):
TAAAAACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCAACAACGACGCT
TTTAGTAAAAAACCGC
Found at i:1428963 original size:14 final size:14
Alignment explanation
Indices: 1428941--1428985 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1428931 TTAATTATCA
*
1428941 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
1428955 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
* *
1428969 ATATGGTTTAGGGT
1 TTATGGTTTAAGGT
1428983 TTA
1 TTA
1428986 AGCAGGTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:1428976 original size:21 final size:21
Alignment explanation
Indices: 1428952--1429036 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 21
1428942 TATAGTTTAA
*
1428952 GGTTTATGGTTTAAGATATAT
1 GGTTTAGGGTTTAAGATATAT
*
1428973 GGTTTAGGGTTTAAGCAGGTTTAT
1 GGTTTAGGGTTTAAG-A--TATAT
*
1428997 GAGTTAACTATGGTTTAAGATATAT
1 G-GTT---TAGGGTTTAAGATATAT
*
1429022 AGTTTAGGGTTTAAG
1 GGTTTAGGGTTTAAG
1429037 GTTTAAGAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
21 24 0.47
22 1 0.02
24 8 0.16
25 7 0.14
27 1 0.02
28 10 0.20
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.42
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGATATAT
Found at i:1429014 original size:49 final size:46
Alignment explanation
Indices: 1428956--1429051 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 46
1428946 GTTTAAGGTT
* *
1428956 TATGGTTTAAGATATATGGTTTAGGGTTTAAGCAGGTTTATGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTT-A--AGGTTTAAGAGTTAAC
1429005 TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAAGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAAGAGTTAAC
1429051 T
1 T
1429052 TGTATTTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 16 0.36
48 1 0.02
49 28 0.62
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.42
Consensus pattern (46 bp):
TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAAGAGTTAAC
Found at i:1429101 original size:14 final size:15
Alignment explanation
Indices: 1429074--1429102 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1429064 TTTGTGATGA
1429074 ATTATGATTTTAGGG
1 ATTATGATTTTAGGG
1429089 ATTATGA-TTTAGGG
1 ATTATGATTTTAGGG
1429103 TTTAAGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (15 bp):
ATTATGATTTTAGGG
Found at i:1429972 original size:16 final size:16
Alignment explanation
Indices: 1429951--1429994 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1429941 TTCTTTTTTT
1429951 TATAAATTTAAAAAAA
1 TATAAATTTAAAAAAA
* *
1429967 TATAAATTTAAAATAT
1 TATAAATTTAAAAAAA
*
1429983 TATAAATATAAA
1 TATAAATTTAAA
1429995 TTTAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TATAAATTTAAAAAAA
Found at i:1433868 original size:22 final size:23
Alignment explanation
Indices: 1433826--1433868 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1433816 TTTCAAAAAT
*
1433826 TAAACATAATATAATATTTAACA
1 TAAAAATAATATAATATTTAACA
*
1433849 TAAAAATAA-ATATTATTTAA
1 TAAAAATAATATAATATTTAA
1433869 TTAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAAAATAATATAATATTTAACA
Found at i:1433998 original size:43 final size:43
Alignment explanation
Indices: 1433888--1434004 Score: 162
Period size: 43 Copynumber: 2.7 Consensus size: 43
1433878 AATAATTTTT
* * * * * * *
1433888 TTAAAGTTCATGATTTTTAGCGGCATTTGTAGGAAAAGTGCTG
1 TTAAAGGTCATGATCTTTAGCGGCGTTTTTTGGAAAAGCGCCG
*
1433931 TTAAAGGTCATGACCTTTAGCGGCGTTTTTTGGAAAAGCGCCG
1 TTAAAGGTCATGATCTTTAGCGGCGTTTTTTGGAAAAGCGCCG
1433974 TTAAAGGTCATGATCTTTAGCGGCGTTTTTT
1 TTAAAGGTCATGATCTTTAGCGGCGTTTTTT
1434005 TTTAAAAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.37
Consensus pattern (43 bp):
TTAAAGGTCATGATCTTTAGCGGCGTTTTTTGGAAAAGCGCCG
Found at i:1439623 original size:25 final size:27
Alignment explanation
Indices: 1439580--1439633 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
1439570 TAATAAATTA
1439580 TTAATATAATTAATATAAT-TTATTAAT
1 TTAATATAATTAATATAATATT-TTAAT
*
1439607 TTAATA-AATT-ATTTAATATTTTAAT
1 TTAATATAATTAATATAATATTTTAAT
1439632 TT
1 TT
1439634 TATTTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 13 0.52
26 6 0.24
27 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTAATATAATTAATATAATATTTTAAT
Found at i:1439631 original size:38 final size:40
Alignment explanation
Indices: 1439540--1439631 Score: 113
Period size: 38 Copynumber: 2.4 Consensus size: 40
1439530 TAAACATATA
*
1439540 TATTTAAT-TATTT-ATATATATTTAGTCATATAATAAAT
1 TATTTAATATATTTAATATATATTTAGTAATATAATAAAT
* * *
1439578 TA-TTAATATAATTAATATA-ATTTATTAATTTAATAAAT
1 TATTTAATATATTTAATATATATTTAGTAATATAATAAAT
1439616 TATTTAATAT-TTTAAT
1 TATTTAATATATTTAAT
1439632 TTTATTTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
37 5 0.11
38 29 0.63
39 12 0.26
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (40 bp):
TATTTAATATATTTAATATATATTTAGTAATATAATAAAT
Found at i:1439668 original size:16 final size:17
Alignment explanation
Indices: 1439640--1439676 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1439630 ATTTTATTTT
1439640 AATAATAAATTTTAAAA
1 AATAATAAATTTTAAAA
*
1439657 AATAAT-AATTTTAAAT
1 AATAATAAATTTTAAAA
1439673 AATA
1 AATA
1439677 TTCTTCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAATAAATTTTAAAA
Found at i:1440268 original size:50 final size:51
Alignment explanation
Indices: 1440210--1440306 Score: 151
Period size: 50 Copynumber: 1.9 Consensus size: 51
1440200 TTCGAAAATC
* * * *
1440210 ATTTTCGGTGAAACAAATAGACTTTTAAA-TTAAAAAAAATCAATCACACT
1 ATTTTCGGTGAAACAAACACACCTTTAAATTTAAAAAAAAACAATCACACT
1440260 ATTTTCGGTGAAACAAACACACCTTTAAATTTAAAAAAAAACAATCA
1 ATTTTCGGTGAAACAAACACACCTTTAAATTTAAAAAAAAACAATCA
1440307 TTATAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 26 0.62
51 16 0.38
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.28
Consensus pattern (51 bp):
ATTTTCGGTGAAACAAACACACCTTTAAATTTAAAAAAAAACAATCACACT
Found at i:1453126 original size:17 final size:17
Alignment explanation
Indices: 1453104--1453142 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1453094 TTTCAAGCTA
1453104 AAGCCTTTACACCTTGC
1 AAGCCTTTACACCTTGC
1453121 AAGCCTTTACACCTTGC
1 AAGCCTTTACACCTTGC
1453138 AAGCC
1 AAGCC
1453143 AACCACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.36, G:0.13, T:0.26
Consensus pattern (17 bp):
AAGCCTTTACACCTTGC
Found at i:1456554 original size:10 final size:9
Alignment explanation
Indices: 1456540--1456703 Score: 75
Period size: 9 Copynumber: 17.2 Consensus size: 9
1456530 AATAAAAGTA
1456540 ATAAAAATT
1 ATAAAAATT
**
1456549 ATTAAATTTT
1 A-TAAAAATT
1456559 AATAAAAA-T
1 -ATAAAAATT
1456568 ATAAAAATAT
1 ATAAAAAT-T
1456578 ATTTAAAAATT
1 A--TAAAAATT
*
1456589 ATAAAAATC
1 ATAAAAATT
1456598 ATAAAACA-T
1 ATAAAA-ATT
*
1456607 ATAGAAA-T
1 ATAAAAATT
**
1456615 ATAAAAAAA
1 ATAAAAATT
1456624 ATAGAAAATT
1 ATA-AAAATT
* *
1456634 GTATAAATT
1 ATAAAAATT
1456643 CATAAGAAAATT
1 -AT-A-AAAATT
*
1456655 ATAAAAAAT
1 ATAAAAATT
* *
1456664 GTAAAGAAAT
1 ATAAA-AATT
1456674 AT-AAAATT
1 ATAAAAATT
*
1456682 CATAAAAAAAT
1 -AT-AAAAATT
1456693 ATAAAAATT
1 ATAAAAATT
1456702 AT
1 AT
1456704 CGTATAAAAA
Statistics
Matches: 118, Mismatches: 21, Indels: 32
0.69 0.12 0.19
Matches are distributed among these distances:
8 18 0.15
9 49 0.42
10 28 0.24
11 11 0.09
12 12 0.10
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:1456618 original size:17 final size:18
Alignment explanation
Indices: 1456581--1456630 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1456571 AAAATATATT
* *
1456581 TAAAAATTATAAAAATCA
1 TAAAAAATATAGAAATCA
*
1456599 TAAAACATATAGAAAT-A
1 TAAAAAATATAGAAATCA
*
1456616 TAAAAAAAATAGAAA
1 TAAAAAATATAGAAA
1456631 ATTGTATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (18 bp):
TAAAAAATATAGAAATCA
Found at i:1456905 original size:29 final size:29
Alignment explanation
Indices: 1456873--1456954 Score: 101
Period size: 30 Copynumber: 2.8 Consensus size: 29
1456863 TTTTTGATGT
*
1456873 ATTTTATAATTTTTTAAATTTTTAATAAA
1 ATTTAATAATTTTTTAAATTTTTAATAAA
* * *
1456902 ATTTAAATATTTTTTTATATTTTTATTAAA
1 ATTT-AATAATTTTTTAAATTTTTAATAAA
*
1456932 ATTTAATAATTTTTATAACTTTT
1 ATTTAATAATTTTT-TAAATTTT
1456955 ATTGATTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 13 0.30
30 31 0.70
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTAATAATTTTTTAAATTTTTAATAAA
Found at i:1456946 original size:10 final size:10
Alignment explanation
Indices: 1456874--1456980 Score: 50
Period size: 9 Copynumber: 11.4 Consensus size: 10
1456864 TTTTGATGTA
1456874 TTTT-ATAAT
1 TTTTAATAAT
*
1456883 TTTTTA-AAT
1 TTTTAATAAT
*
1456892 TTTTAATAAAA
1 TTTTAAT-AAT
* *
1456903 TTTAAATATT
1 TTTTAATAAT
*
1456913 TTTTTAT-AT
1 TTTTAATAAT
* *
1456922 TTTTATTAAA
1 TTTTAATAAT
*
1456932 ATTTAATAAT
1 TTTTAATAAT
*
1456942 TTTT-ATAAC
1 TTTTAATAAT
* *
1456951 TTTTATTGAT
1 TTTTAATAAT
1456961 TTTT-AT--T
1 TTTTAATAAT
1456968 TTTT-ATAAT
1 TTTTAATAAT
1456977 TTTT
1 TTTT
1456981 GCCACGTGTC
Statistics
Matches: 71, Mismatches: 20, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
7 7 0.10
9 32 0.45
10 24 0.34
11 8 0.11
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:1469473 original size:47 final size:47
Alignment explanation
Indices: 1469420--1469513 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
1469410 AAGGTCAAGT
*
1469420 TAGCCAACTC-CTCCTCCATTGTGCATAAGAAGAAATAACAGGCCGTG
1 TAGCCAACTCTC-CCTCCATTGCGCATAAGAAGAAATAACAGGCCGTG
1469467 TAGCCAACTCTCCCTCCATTGCGCATAAGAAGAAATAACAGGCCGTG
1 TAGCCAACTCTCCCTCCATTGCGCATAAGAAGAAATAACAGGCCGTG
1469514 CCAAACAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 44 0.98
48 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (47 bp):
TAGCCAACTCTCCCTCCATTGCGCATAAGAAGAAATAACAGGCCGTG
Found at i:1469598 original size:24 final size:26
Alignment explanation
Indices: 1469565--1469617 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
1469555 TCAAAAAACC
* *
1469565 AAAACCGCGTGTCACACGATAGAC-G
1 AAAACCGCGTGTCAAACGACAGACTG
1469590 AAAA-CGCGTGTCAAACGACAGACTG
1 AAAACCGCGTGTCAAACGACAGACTG
1469615 AAA
1 AAA
1469618 GGATTGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.42, C:0.25, G:0.23, T:0.11
Consensus pattern (26 bp):
AAAACCGCGTGTCAAACGACAGACTG
Found at i:1478318 original size:62 final size:62
Alignment explanation
Indices: 1478252--1478373 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 62
1478242 CACGTATCTC
* *
1478252 TTCATTCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
1 TTCATGCATCAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
* * *
1478314 TTCATGCATCAACATTACATTTTATTGCATACAATAAATTTCCTAAAATCCAAAAGTACG
1 TTCATGCATCAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACG
1478374 TCGAGTTTAG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (62 bp):
TTCATGCATCAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
Found at i:1493136 original size:40 final size:39
Alignment explanation
Indices: 1493076--1493216 Score: 119
Period size: 40 Copynumber: 3.6 Consensus size: 39
1493066 AATACACCAG
* *
1493076 TTTGGCACCCAGTGCCTCATCGAATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGAATAATCCGAAGTAA-AA
* * *
1493116 TTTGACACCCAGTGTCTCATC-AGTTAAACCGAAGT-AAA
1 TTTGACACCCAGTGCCTCATCGA-ATAATCCGAAGTAAAA
* *
1493154 -TTGGCACCCAGTGCCTCATTGAATTAATCCGAAGTAGCAAA
1 TTTGACACCCAGTGCCTCATCGAA-TAATCCGAAGTA--AAA
* * *
1493195 -TTGACATCTAGTGTCTCATCGA
1 TTTGACACCCAGTGCCTCATCGA
1493217 CTCGAAGTCG
Statistics
Matches: 80, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
37 17 0.21
38 13 0.16
39 2 0.03
40 28 0.35
41 20 0.25
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (39 bp):
TTTGACACCCAGTGCCTCATCGAATAATCCGAAGTAAAA
Found at i:1495293 original size:19 final size:22
Alignment explanation
Indices: 1495269--1495310 Score: 63
Period size: 19 Copynumber: 2.0 Consensus size: 22
1495259 AATACATGGT
1495269 ATTCATC-AT-AAAA-TTCAAA
1 ATTCATCAATGAAAACTTCAAA
1495288 ATTCATCAATGAAAACTTCAAA
1 ATTCATCAATGAAAACTTCAAA
1495310 A
1 A
1495311 AATTTTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 4 0.20
22 7 0.35
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (22 bp):
ATTCATCAATGAAAACTTCAAA
Found at i:1498885 original size:17 final size:17
Alignment explanation
Indices: 1498863--1498898 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1498853 AATATTATTT
*
1498863 ATTAAATTAAATTTTCA
1 ATTAAATAAAATTTTCA
1498880 ATTAAATAAAATTTTCA
1 ATTAAATAAAATTTTCA
1498897 AT
1 AT
1498899 CTAATTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTAAATAAAATTTTCA
Found at i:1499229 original size:21 final size:22
Alignment explanation
Indices: 1499196--1499238 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1499186 CATATATATA
1499196 TATAATTAGAGTTAAAATATTT
1 TATAATTAGAGTTAAAATATTT
* *
1499218 TATAATTA-AGTTTAATTATTT
1 TATAATTAGAGTTAAAATATTT
1499239 ATCTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TATAATTAGAGTTAAAATATTT
Found at i:1509837 original size:10 final size:10
Alignment explanation
Indices: 1509789--1509842 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
1509779 TAAAAGTAAT
1509789 AAAATTTTAA
1 AAAATTTTAA
1509799 AAAATATATTATA
1 AAAAT-T-TTA-A
**
1509812 AAAATCATAA
1 AAAATTTTAA
1509822 AAAATTTTAA
1 AAAATTTTAA
1509832 AAAA-TTTAA
1 AAAATTTTAA
1509841 AA
1 AA
1509843 TTCATTATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
9 7 0.19
10 18 0.49
11 3 0.08
12 3 0.08
13 6 0.16
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:1509982 original size:19 final size:21
Alignment explanation
Indices: 1509941--1509988 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1509931 TTAAAATTTT
1509941 AACTAAAAATATTAAAATAAA
1 AACTAAAAATATTAAAATAAA
* *
1509962 AA-TAAAAAT-TTAGAATCAA
1 AACTAAAAATATTAAAATAAA
1509981 AACTAAAA
1 AACTAAAA
1509989 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (21 bp):
AACTAAAAATATTAAAATAAA
Found at i:1510492 original size:44 final size:44
Alignment explanation
Indices: 1510429--1510517 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
1510419 CTATAGCATC
1510429 ATATAAGGCATAACATCTGTTAAAATAAAGTTGACACCTAAATG
1 ATATAAGGCATAACATCTGTTAAAATAAAGTTGACACCTAAATG
1510473 ATATAAGGCATAACATCTGTTAAAATAAAGTTGACACCTAAATG
1 ATATAAGGCATAACATCTGTTAAAATAAAGTTGACACCTAAATG
1510517 A
1 A
1510518 AAGCGATAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.27
Consensus pattern (44 bp):
ATATAAGGCATAACATCTGTTAAAATAAAGTTGACACCTAAATG
Found at i:1514972 original size:16 final size:14
Alignment explanation
Indices: 1514952--1514993 Score: 59
Period size: 13 Copynumber: 3.0 Consensus size: 14
1514942 TACGGCGCTA
1514952 ATTTTTATTTTATAT
1 ATTTTTATTTT-TAT
1514967 ATTTTTATTTTTAT
1 ATTTTTATTTTTAT
*
1514981 A-TTTCATTTTTAT
1 ATTTTTATTTTTAT
1514994 TTATTATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTTATTTTTAT
Found at i:1515009 original size:19 final size:20
Alignment explanation
Indices: 1514987--1515034 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
1514977 TTATATTTCA
*
1514987 TTTTTATTTA-TTATTAATG
1 TTTTTATTTATTTATCAATG
1515006 TTTTTATTTATTTATCAATG
1 TTTTTATTTATTTATCAATG
1515026 TTTTT-TTTA
1 TTTTTATTTA
1515035 AATCTAATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTTTATTTATTTATCAATG
Found at i:1515515 original size:41 final size:41
Alignment explanation
Indices: 1515470--1515621 Score: 200
Period size: 41 Copynumber: 3.7 Consensus size: 41
1515460 ATTATATGAC
* * *
1515470 TTTTAGCGGCGTTTTACTAAAAACGCCGCTATTACTCTGGT
1 TTTTAGCGGCGCTTTACCAAAAACGCCGCTATTGCTCTGGT
* * * *
1515511 TTTTAGTGGCACTTTGCCAAAAACGCCGCTATTGCTCTAGT
1 TTTTAGCGGCGCTTTACCAAAAACGCCGCTATTGCTCTGGT
*
1515552 TTTTAGCGGCGCTTTGA-CAAAAACGCAGCTATTGCTCTGG-
1 TTTTAGCGGCGCTTT-ACCAAAAACGCCGCTATTGCTCTGGT
*
1515592 TTTTAGCGGCGCTTTGCCAAAAACGCCGCT
1 TTTTAGCGGCGCTTTACCAAAAACGCCGCT
1515622 CATGTATGAT
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
40 27 0.28
41 68 0.72
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (41 bp):
TTTTAGCGGCGCTTTACCAAAAACGCCGCTATTGCTCTGGT
Found at i:1517307 original size:58 final size:58
Alignment explanation
Indices: 1517215--1517561 Score: 313
Period size: 58 Copynumber: 6.0 Consensus size: 58
1517205 TGTGAGTCTG
* * *
1517215 CAAGCTGTTTTAAACTTAAGCAAATTTTCCAAAATAATCAGCTAGGAATATAAATCTA
1 CAAGCTGTTTTAAACTTAAGCATATTTTCTAAAATAATCAGCTGGGAATATAAATCTA
* * * * * *
1517273 CGAGCTGTTTTGAACTTAAGCATATTTTTTAAAATAATTAGTTGGGAATATAAATCTG
1 CAAGCTGTTTTAAACTTAAGCATATTTTCTAAAATAATCAGCTGGGAATATAAATCTA
* * * * * * * *
1517331 CAAGCTGTTATGAACTTCAA-CAAATTTTCAAGAAATTATTAGTTGGGAATATAAATCCA
1 CAAGCTGTTTTAAACTT-AAGCATATTTTCTA-AAATAATCAGCTGGGAATATAAATCTA
* * **
1517390 CAAGCTGTTTTGAACTTAAGCATATTTTCTAAAATAATCAACTAAGAATATAAATCTGA
1 CAAGCTGTTTTAAACTTAAGCATATTTTCTAAAATAATCAGCTGGGAATATAAATCT-A
* * * * * * * *
1517449 -GAGCTATTCTAAACTTAAACGA-ATTTTCCAAAATCATCAACTGGGAATATAAATCCA
1 CAAGCTGTTTTAAACTTAAGC-ATATTTTCTAAAATAATCAGCTGGGAATATAAATCTA
* * * * * * *
1517506 CAAGTTGTTCTAAAATTAAACATATTCTCTAAAATAATTAGTTGGGAATATAAATC
1 CAAGCTGTTTTAAACTTAAGCATATTTTCTAAAATAATCAGCTGGGAATATAAATC
1517562 CGTGAGCCGT
Statistics
Matches: 235, Mismatches: 47, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
57 2 0.01
58 180 0.77
59 53 0.23
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (58 bp):
CAAGCTGTTTTAAACTTAAGCATATTTTCTAAAATAATCAGCTGGGAATATAAATCTA
Found at i:1517647 original size:70 final size:70
Alignment explanation
Indices: 1517570--1518353 Score: 637
Period size: 70 Copynumber: 11.2 Consensus size: 70
1517560 TCCGTGAGCC
* * * * * *
1517570 GTTTGGAGGCAGCGATATGGAATCAACAAGCCTTAAAATTACAGGTGGGAGCTTTTAATTCTCGC
1 GTTTGGAGGCAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGC
1517635 TAACT
66 TAACT
* * * *
1517640 GTTTGGAGGCCA-CGATATGAAATCAGCGAGCTTTGCAATTACAGTTGGGAGCTTTTAACTATC-
1 GTTTGGAGG-CAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCG
* * *
1517703 ATTAGT
65 CTAACT
* **** * * * ** * * * * * *
1517709 AGTTTAGAGATTTCAACATGAAATCAGCAAGTGTTGGAATTACAACCGAGAGCTTTTAACTATTG
1 -GTTTGGAGGCAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCG
1517774 CTAACT
65 CTAACT
* * * * * * * *
1517780 GTTTAGAGGC-TCGATATGAAATCAACGAGTCTTGAAATTACAGCTAGGAGCATTTAGCTTTCGC
1 GTTTGGAGGCAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGC
1517844 TAACT
66 TAACT
* * * * * * * *
1517849 GTTTGGAGGCCA-CAATATGAAATTAGCGAGCCTTGAAGTTACAACTAGAAGCTTTTAACTTTTG
1 GTTTGGAGG-CAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCG
1517913 CTAACT
65 CTAACT
** * * * * *
1517919 GTTTGGAGGTTGTGATATGAAATCAGTGAGCCTTGAAATTATAGCTGAGAGCTTTTAACTCTCAC
1 GTTTGGAGGCAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGC
1517984 TAACT
66 TAACT
* * * * *
1517989 GTTTGGAGGCCA-CGATATGAAATCAGCAAGCTTTGAAATTATAGTTGAGAGCTTTTAACTCTCG
1 GTTTGGAGG-CAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCG
*
1518053 TTAACT
65 CTAACT
* * * * * * * *
1518059 GTTTGGAGGTCA-CAATATGAAATCAACAAGCTTTGAAATTACAACTGTGAGGTTTTAACTCTAG
1 GTTTGGAGG-CAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCG
1518123 CTAACT
65 CTAACT
* * * * * * * *
1518129 ATCTAGAGGCCGCGATATGAAATCAGCGAGCCTTGAAATTATAGTTGAGAGCTTTTAACTATCGC
1 GTTTGGAGGCAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGC
1518194 TAAACCTTT
66 T-AA-C--T
* ** * * * *
1518203 GTTTGGAGGTC-GCGATATGAAATTAATGAGCCTTGAAATTACAACTGTGAGCTTTTAACTATTG
1 GTTTGGAGG-CAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCG
*
1518267 GTAACT
65 CTAACT
* * * *
1518273 ATTTGGAGGCCGCAATATGAAATCAGCGAGCCTTGAAATTACAGGTGGGAGCTTTTAACTCTCGC
1 GTTTGGAGGCAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGC
1518338 TAACT
66 TAACT
* *
1518343 ATTTGAAGGCA
1 GTTTGGAGGCA
1518354 CATCATGATA
Statistics
Matches: 568, Mismatches: 131, Indels: 30
0.78 0.18 0.04
Matches are distributed among these distances:
69 58 0.10
70 445 0.78
71 7 0.01
72 2 0.00
73 2 0.00
74 53 0.09
75 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (70 bp):
GTTTGGAGGCAGCGATATGAAATCAGCGAGCCTTGAAATTACAGCTGGGAGCTTTTAACTCTCGC
TAACT
Found at i:1531416 original size:15 final size:15
Alignment explanation
Indices: 1531396--1531427 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1531386 TGATTGTAGA
*
1531396 TATTGAAATTTGAAC
1 TATTGAAATTCGAAC
1531411 TATTGAAATTCGAAC
1 TATTGAAATTCGAAC
1531426 TA
1 TA
1531428 GGAATGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (15 bp):
TATTGAAATTCGAAC
Found at i:1533627 original size:9 final size:9
Alignment explanation
Indices: 1533615--1533657 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1533605 TCTCTTTAAA
1533615 CTCTCAATT
1 CTCTCAATT
*
1533624 CTCTCAACT
1 CTCTCAATT
1533633 C-CTTCAATT
1 CTC-TCAATT
1533642 CTCTCAATT
1 CTCTCAATT
*
1533651 TTCTCAA
1 CTCTCAA
1533658 CTTTTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 1 0.03
9 27 0.93
10 1 0.03
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (9 bp):
CTCTCAATT
Found at i:1535512 original size:50 final size:50
Alignment explanation
Indices: 1535450--1535678 Score: 232
Period size: 50 Copynumber: 4.6 Consensus size: 50
1535440 TATAAGAGTC
** * * *
1535450 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCAAGATATGAAAGCT
1 AGTGTAAGACCATGTCTAGGACATGGCATCAACCTCGACATATGAGAGCT
* * *
1535500 AGTGTAAGACCATGTCTGGGACATGGCATCAACAC-CGACAGATGAGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCAAC-CTCGACATATGAGAGCT
* * *
1535550 AGTGTAAGACCATGTCTAGAACATGGCATCATCCTCGATATATGAGAG-T
1 AGTGTAAGACCATGTCTAGGACATGGCATCAACCTCGACATATGAGAGCT
* * * ** *
1535599 CAGTGTAAGACCATGTCTGGGACATGGCATCGACCTTGATGTGTGAG-GC-
1 -AGTGTAAGACCATGTCTAGGACATGGCATCAACCTCGACATATGAGAGCT
* **
1535648 AATGTAAGACCATGTCCGGGACATGGCATCA
1 AGTGTAAGACCATGTCTAGGACATGGCATCA
1535679 GTATCTTACC
Statistics
Matches: 151, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
48 28 0.19
49 2 0.01
50 120 0.79
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (50 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCAACCTCGACATATGAGAGCT
Found at i:1535593 original size:100 final size:100
Alignment explanation
Indices: 1535444--1535629 Score: 293
Period size: 100 Copynumber: 1.9 Consensus size: 100
1535434 CCACATTATA
* * *
1535444 AGAGTCAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCAAGATATGAAAG-CTAGTGTAAG
1 AGAGCCAGTGTAAGACCATGTCTAGAACATGGCATCAGCCTCAAGATATGAAAGTC-AGTGTAAG
1535508 ACCATGTCTGGGACATGGCATCAACACCGACAGATG
65 ACCATGTCTGGGACATGGCATCAACACCGACAGATG
* * * *
1535544 AGAGCCAGTGTAAGACCATGTCTAGAACATGGCATCATCCTCGATATATGAGAGTCAGTGTAAGA
1 AGAGCCAGTGTAAGACCATGTCTAGAACATGGCATCAGCCTCAAGATATGAAAGTCAGTGTAAGA
1535609 CCATGTCTGGGACATGGCATC
66 CCATGTCTGGGACATGGCATC
1535630 GACCTTGATG
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 77 0.99
101 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (100 bp):
AGAGCCAGTGTAAGACCATGTCTAGAACATGGCATCAGCCTCAAGATATGAAAGTCAGTGTAAGA
CCATGTCTGGGACATGGCATCAACACCGACAGATG
Found at i:1536106 original size:44 final size:44
Alignment explanation
Indices: 1536040--1536127 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
1536030 TGCAGTAGTC
*
1536040 CAACTTGGAAAATGCACAAAAAATAGTGGAATA-AGGGTTAAAGA
1 CAACTTGGAAAATACACAAAAAATAGTGGAA-AGAGGGTTAAAGA
*
1536084 CAACTTGGAAAATACACCAAAAATAGTGGAAAGAGGGTTAAAGA
1 CAACTTGGAAAATACACAAAAAATAGTGGAAAGAGGGTTAAAGA
1536128 TTGAATGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.50, C:0.10, G:0.23, T:0.17
Consensus pattern (44 bp):
CAACTTGGAAAATACACAAAAAATAGTGGAAAGAGGGTTAAAGA
Found at i:1539773 original size:44 final size:44
Alignment explanation
Indices: 1539710--1539796 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
1539700 GCAGTAGTCC
1539710 AACTTGGAAAATACACAAAAAATAGT-GAACAAAGGGTTAAAGAA
1 AACTTGGAAAATACACAAAAAATAGTGGAA-AAAGGGTTAAAGAA
*
1539754 AACTTGGAAAATACACAAAAAATAGTGGAAAGAGGGTTAAAGA
1 AACTTGGAAAATACACAAAAAATAGTGGAAAAAGGGTTAAAGA
1539797 TTGAATGAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 38 0.93
45 3 0.07
ACGTcount: A:0.55, C:0.08, G:0.21, T:0.16
Consensus pattern (44 bp):
AACTTGGAAAATACACAAAAAATAGTGGAAAAAGGGTTAAAGAA
Found at i:1543242 original size:24 final size:24
Alignment explanation
Indices: 1543215--1543266 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1543205 GAAGGCGATA
* *
1543215 AAGACGAAGCCGATAGTAGAGATG
1 AAGACGAAGACAATAGTAGAGATG
* * *
1543239 AAGATGAAGACAATGGTGGAGATG
1 AAGACGAAGACAATAGTAGAGATG
1543263 AAGA
1 AAGA
1543267 TGAGTACAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.35, T:0.13
Consensus pattern (24 bp):
AAGACGAAGACAATAGTAGAGATG
Found at i:1546101 original size:405 final size:405
Alignment explanation
Indices: 1545343--1546113 Score: 960
Period size: 405 Copynumber: 1.9 Consensus size: 405
1545333 CTAGCTACAG
* *
1545343 ATGTTGGCAATCAACATCGGGACGAGAATTTTGGGACTTGTTTTCACCATAGGTAGAATTATGTT
1 ATGTTGGCAATCAACATCGGGACGAGAATTTTGGGACTCGCTTTCACCATAGGTAGAATTATGTT
* * * * *
1545408 AGATATCATGTTGGAGTTTAGCCTCGGATGATCTTGGCTTACACCTATGAAGTATACCCATAAAG
66 AGATATCACGTCGGAGTCTAGCCTCGGATGATCCTGACTTACACCTATGAAGTATACCCATAAAG
* ** * * *
1545473 TTATGTTATTCGAAAAAACGAAGACCTTGGTTAGGTCACATTATGTTAGAAAATCGGGTGATCAC
131 TTATGTTATTAGAAAAAACGAAGACCTTAATCAGGTCACATTATGTTACAAAATCGAGTGATCAC
* * ** *
1545538 ATTGCATACTTACTTCAACACAAGTATGTGACCAAAATACTTCTTTATTGTCCACAAACTTGTCT
196 ATCGCATACTTACTTCAACACAAGTATATGACCAAAATACTTCTTTATCATCCACAAACTTATCT
* * *
1545603 TCTTCCAAAAAGATGTCATGATTTTCCATTTGTACCTTCCGTCACGCATTGCACATTTTCCCTCA
261 TCTTCCAAAAAGATGCCATGATTTTCCATTTGTACCTTCCGTCACACATTGCAAATTTTCCCTCA
* ** * *
1545668 AATTTTTTTGAACGGGATTTTGTGACGTGATAGTTCACGCCATCTTATAGTATGATGACGTGAAA
326 AATTTCTCCGAACGAGATTTTATGACGTGATAGTTCACGCCATCTTATAGTATGATGACGTGAAA
1545733 TCATACTGGCTATGA
391 TCATACTGGCTATGA
* *
1545748 ATGTTGGTAATCAACATCGGGATGAGAATTTTGGGACTCGCTTTCACCATAGGTAGAATTATGTT
1 ATGTTGGCAATCAACATCGGGACGAGAATTTTGGGACTCGCTTTCACCATAGGTAGAATTATGTT
* * * ** *
1545813 AGATTTCACGTCGGAGTCTAGCCTTGGATTATCCTGACTTACA-C-ATGCAAAGTATACGTATGA
66 AGATATCACGTCGGAGTCTAGCCTCGGATGATCCTGACTTACACCTATG--AAGTATACCCATAA
* * * * *
1545876 ATTTATGTTTTTAGAAAAAACGAATATCTTAATCAGGTTACATTATGTTACAAAATCGAGTGATC
129 AGTTATGTTATTAGAAAAAACGAAGACCTTAATCAGGTCACATTATGTTACAAAATCGAGTGATC
* * * * * *
1545941 ACATCGCGTACTTA-TTGTAACACAAGTATATAGACCAGAATACTTCTTTATCATTCA-GAAGTC
194 ACATCGCATACTTACTT-CAACACAAGTATAT-GACCAAAATACTTCTTTATCATCCACAAACT-
* * ** *
1546004 TATCTTCTTCCAAAATGATGCCATGATTTTCCATTTG-ATCTTTTGTCGCACATTGCATAATTTT
256 TATCTTCTTCCAAAAAGATGCCATGATTTTCCATTTGTACCTTCCGTCACACATTGCA-AATTTT
** * *
1546068 -CCTTGAATTTCTCCGAATGAGATTTTATGACGTGATAGTTTACGCC
320 CCCTCAAATTTCTCCGAACGAGATTTTATGACGTGATAGTTCACGCC
1546114 GTTCTTGAAA
Statistics
Matches: 306, Mismatches: 54, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
403 3 0.01
404 3 0.01
405 240 0.78
406 60 0.20
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (405 bp):
ATGTTGGCAATCAACATCGGGACGAGAATTTTGGGACTCGCTTTCACCATAGGTAGAATTATGTT
AGATATCACGTCGGAGTCTAGCCTCGGATGATCCTGACTTACACCTATGAAGTATACCCATAAAG
TTATGTTATTAGAAAAAACGAAGACCTTAATCAGGTCACATTATGTTACAAAATCGAGTGATCAC
ATCGCATACTTACTTCAACACAAGTATATGACCAAAATACTTCTTTATCATCCACAAACTTATCT
TCTTCCAAAAAGATGCCATGATTTTCCATTTGTACCTTCCGTCACACATTGCAAATTTTCCCTCA
AATTTCTCCGAACGAGATTTTATGACGTGATAGTTCACGCCATCTTATAGTATGATGACGTGAAA
TCATACTGGCTATGA
Found at i:1551115 original size:29 final size:29
Alignment explanation
Indices: 1551073--1551131 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1551063 CATTATGACT
1551073 TAAAACTTTGTTAAAGATAGACTCCAATA
1 TAAAACTTTGTTAAAGATAGACTCCAATA
*
1551102 TAAAACTTTGTTAAAGATGGACTCCAATA
1 TAAAACTTTGTTAAAGATAGACTCCAATA
1551131 T
1 T
1551132 GGCATAGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (29 bp):
TAAAACTTTGTTAAAGATAGACTCCAATA
Found at i:1559837 original size:40 final size:40
Alignment explanation
Indices: 1559806--1560055 Score: 292
Period size: 40 Copynumber: 6.3 Consensus size: 40
1559796 GGACTAAGAT
* *
1559806 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATATCAAA-TCCGGGTTAAGTC
* *
1559846 CCGAAGGCCTTTGTGCGAGATA-CTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATC-AAATCCGGGTTAAGTC
* *
1559886 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
* *
1559926 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
* * * *
1559966 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
* * * * *
1560006 CCGAAGGCATT-GTGTGAGTTA-CTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATATC-AAATCCGGGTTAAGTC
1560045 CCGAAGGCATT
1 CCGAAGGCATT
1560056 TGAACGAGGA
Statistics
Matches: 194, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
39 33 0.17
40 158 0.81
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
Found at i:1559890 original size:80 final size:79
Alignment explanation
Indices: 1559753--1560055 Score: 342
Period size: 80 Copynumber: 3.8 Consensus size: 79
1559743 TTGAATGCTG
* * * * * **
1559753 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
* * *
1559816 TTGTGCGAGATACAAA
64 TCGTGCGAGTTATAAA
* *
1559832 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1559897 CGTGCGAGTTATTAAA
65 CGTGCGAGTTA-TAAA
* * *
1559913 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
*
1559978 GTGCGAGTTGTTAAA
66 GTGCGAGTT-ATAAA
* * * * * *
1559993 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1560056 TGAACGAGGA
Statistics
Matches: 192, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
79 36 0.19
80 145 0.76
81 11 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
GTGCGAGTTATAAA
Found at i:1559969 original size:120 final size:119
Alignment explanation
Indices: 1559753--1560055 Score: 358
Period size: 120 Copynumber: 2.5 Consensus size: 119
1559743 TTGAATGCTG
* * * * * *
1559753 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGCTAAG-TCCCGAAGGCATT
* * *
1559817 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
64 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAA
* *
1559873 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTC
* * * * **
1559938 GTGCGAGTTATTAAA-TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
65 GTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAA
* * * * *
1559993 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATT
1560056 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
119 35 0.22
120 115 0.73
121 7 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAA
Found at i:1567829 original size:40 final size:39
Alignment explanation
Indices: 1567798--1568007 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
1567788 GGACTAAGAT
* *
1567798 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
1567838 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
1567878 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
1567918 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
1567958 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
1567997 CCGAAGGCATT
1 CCGAAGGCATT
1568008 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:1567961 original size:120 final size:120
Alignment explanation
Indices: 1567745--1568007 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
1567735 TTGAATGCTG
* *
1567745 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
1567809 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
1567865 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
1567928 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
1567984 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
1568008 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:1568027 original size:79 final size:80
Alignment explanation
Indices: 1567746--1568042 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
1567736 TGAATGCTGT
* ** * * * **
1567746 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
1567809 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
1567826 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
1567890 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
1567906 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
1567970 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
1567985 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
1568043 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:1571430 original size:46 final size:45
Alignment explanation
Indices: 1571375--1571545 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 45
1571365 ATTGTGAGTT
* *
1571375 AGTGTAAGACATGTTTGGGACATGCATCGGCCACATTACGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACA-AACGAGAGCC
* * *
1571421 AGTGTAAGACCATGT-TCGGGACATAGCATTGG-CAGTAAGACGAGAGCT
1 AGTGTAAGA-CATGTCT-GGGACAT-GCATCGGCCA-CAA-ACGAGAGCC
* * * *
1571469 AGTGTAAGACATGTCTGGGACATACATCAGCCTCGAAATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-AAACG-AGAGCC
1571515 AGTGTAAGACATGTCTGGGACATGCATCGGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC
1571546 TACGAGTTAA
Statistics
Matches: 103, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
46 48 0.47
47 30 0.29
48 25 0.24
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.22
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACAAACGAGAGCC
Found at i:1571473 original size:48 final size:47
Alignment explanation
Indices: 1571374--1571588 Score: 144
Period size: 46 Copynumber: 4.6 Consensus size: 47
1571364 CATTGTGAGT
* **
1571374 TAGTGTAAGACATGTTTGGGACAT-GCATCGGCCACATTACGAGAGC
1 TAGTGTAAGACATGTTCGGGACATAGCATCGGCCACAAGACGAGAGC
* * *
1571420 CAGTGTAAGACCATGTTCGGGACATAGCATTGG-CAGTAAGACGAGAGC
1 TAGTGTAAGA-CATGTTCGGGACATAGCATCGGCCA-CAAGACGAGAGC
* * *
1571468 TAGTGTAAGACATG-TCTGGGACATA-CATCAGCCTCGAA-ATGTA-AGC
1 TAGTGTAAGACATGTTC-GGGACATAGCATCGGCCAC-AAGACG-AGAGC
* * * **
1571514 CAGTGTAAGACATG-TCTGGGACAT-GCATCGGCTACGAG-TTA-AGC
1 TAGTGTAAGACATGTTC-GGGACATAGCATCGGCCACAAGACGAGAGC
* * *
1571558 TAGTGTAAGACCATGTCCAGGACATGGCATC
1 TAGTGTAAGA-CATGTTCGGGACATAGCATC
1571589 AGCATCCTAT
Statistics
Matches: 136, Mismatches: 21, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
44 13 0.10
45 12 0.09
46 56 0.41
47 31 0.23
48 24 0.18
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (47 bp):
TAGTGTAAGACATGTTCGGGACATAGCATCGGCCACAAGACGAGAGC
Found at i:1574295 original size:85 final size:85
Alignment explanation
Indices: 1574152--1574320 Score: 320
Period size: 85 Copynumber: 2.0 Consensus size: 85
1574142 GAGTCTATTT
1574152 TCATATGGATTGAACAAAACAGGTATATGAATTATATTTTATGAGATATTTGAAATTTTGTGAAA
1 TCATATGGATTGAACAAAACAGGTATATGAATTATATTTTATGAGATATTTGAAATTTTGTGAAA
*
1574217 TAGGTCCAGAGTGATTTCTA
66 TAGGACCAGAGTGATTTCTA
1574237 TCATATGGATTGAACAAAACAGGTATATGAATTATATTTTATGAGATATTTGAAATTTTGTGAAA
1 TCATATGGATTGAACAAAACAGGTATATGAATTATATTTTATGAGATATTTGAAATTTTGTGAAA
*
1574302 TAGGACTAGAGTGATTTCT
66 TAGGACCAGAGTGATTTCT
1574321 GGATCCCCTG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.38
Consensus pattern (85 bp):
TCATATGGATTGAACAAAACAGGTATATGAATTATATTTTATGAGATATTTGAAATTTTGTGAAA
TAGGACCAGAGTGATTTCTA
Found at i:1583291 original size:283 final size:284
Alignment explanation
Indices: 1582783--1583360 Score: 1113
Period size: 283 Copynumber: 2.0 Consensus size: 284
1582773 AAGAGTTAAC
1582783 TTACCAACATAAAAGTTTCGAACAAAGAATCGAAGTGTCGTCGAGGGTCTGAAATTTAGTTTCTT
1 TTACCAACATAAAAGTTTCGAACAAAGAATCGAAGTGTCGTCGAGGGTCTGAAATTTAGTTTCTT
1582848 TACTAGTACGGTCTCGATCATGTCGAACACCGGCATTGCATAGATCTACATAAAACCAAAATTAA
66 TACTAGTACGGTCTCGATCATGTCGAACACCGGCATTGCATAGATCTACATAAAACCAAAATTAA
*
1582913 GATAGAATCTAAAACAATAATGATGAGAAATATTGATGATTGATCTATATAAACCTGGTAGCTTC
131 GATAGAATCTAAAACAAGAATGATGAGAAATATTGATGATTGATCTATATAAACCTGGTAGCTTC
1582978 CAATCACGTGAATAACTACAAATATGTTAGCCATTGCAATAAGCCATGCTGGTTTCTCCAATGAG
196 CAATCACGTGAATAACTACAAATATGTTAGCCATTGCAATAAGCCATGCTGGTTTCTCCAATGAG
*
1583043 ATGAGAATGTTGTCTTCGATAGAA
261 ATGAGAATGTTATCTTCGATAGAA
1583067 -TACCAACATAAAAGTTTCGAACAAAGAATCGAAGTGTCGTCGAGGGTCTGAAATTTAGTTTCTT
1 TTACCAACATAAAAGTTTCGAACAAAGAATCGAAGTGTCGTCGAGGGTCTGAAATTTAGTTTCTT
*
1583131 TACTAGTACGGTCTCGATCATGTCGAACACCGGCATTGCATAGATCTACATAAAACCAAAATTAT
66 TACTAGTACGGTCTCGATCATGTCGAACACCGGCATTGCATAGATCTACATAAAACCAAAATTAA
1583196 GATAGAATCTAAAACAAGAATGATGAGAAATATTGATGATTGATCTATATAAACCTGGTAGCTTC
131 GATAGAATCTAAAACAAGAATGATGAGAAATATTGATGATTGATCTATATAAACCTGGTAGCTTC
1583261 CAATCACGTGAATAACTACAAATATGTTAGCCATTGCAATAAGCCATGCTGGTTTCTCCAATGAG
196 CAATCACGTGAATAACTACAAATATGTTAGCCATTGCAATAAGCCATGCTGGTTTCTCCAATGAG
1583326 ATGAGAATGTTATCTTCGATAGAA
261 ATGAGAATGTTATCTTCGATAGAA
1583350 TTACCGAACAT
1 TTACC-AACAT
1583361 CCAGTAGCCA
Statistics
Matches: 289, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
283 280 0.97
284 4 0.01
285 5 0.02
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (284 bp):
TTACCAACATAAAAGTTTCGAACAAAGAATCGAAGTGTCGTCGAGGGTCTGAAATTTAGTTTCTT
TACTAGTACGGTCTCGATCATGTCGAACACCGGCATTGCATAGATCTACATAAAACCAAAATTAA
GATAGAATCTAAAACAAGAATGATGAGAAATATTGATGATTGATCTATATAAACCTGGTAGCTTC
CAATCACGTGAATAACTACAAATATGTTAGCCATTGCAATAAGCCATGCTGGTTTCTCCAATGAG
ATGAGAATGTTATCTTCGATAGAA
Found at i:1583692 original size:4 final size:4
Alignment explanation
Indices: 1583683--1583737 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
1583673 TGCATTGGAC
1583683 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1583731 ATAG ATA
1 ATAG ATA
1583738 CCTCAAGGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:1587118 original size:3 final size:3
Alignment explanation
Indices: 1587110--1587158 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1587100 AACAACGGGT
1587110 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1587158 A
1 A
1587159 ACAAAAAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1588803 original size:64 final size:65
Alignment explanation
Indices: 1588678--1588802 Score: 166
Period size: 64 Copynumber: 2.0 Consensus size: 65
1588668 TAAAATTTAT
** * *
1588678 AAAAATATGTAAGTACGTGTTTTGTTTATTATGATTTTTTTTACATAATTATGAATTTTTTTAGA
1 AAAAATATGTAAGTACGTGTTTTGTTTATTATGATAATGTTTAAATAATTATGAATTTTTTTAGA
* *
1588743 AAAAAT-TGTAAGTATGTGTTTTGTTTATTAT-ATAATGTTTAGAAT-TTTATGAATTTTTTT
1 AAAAATATGTAAGTACGTGTTTTGTTTATTATGATAATGTTTA-AATAATTATGAATTTTTTT
1588803 TTTACTTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 21 0.40
64 26 0.49
65 6 0.11
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.54
Consensus pattern (65 bp):
AAAAATATGTAAGTACGTGTTTTGTTTATTATGATAATGTTTAAATAATTATGAATTTTTTTAGA
Found at i:1589031 original size:50 final size:50
Alignment explanation
Indices: 1588972--1589070 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
1588962 CAAAATGGAT
1588972 ATTAACCCTTGAATTAATGTCCCACCTCACTTTTTCGTTAAGGTTGTTAC
1 ATTAACCCTTGAATTAATGTCCCACCTCACTTTTTCGTTAAGGTTGTTAC
*
1589022 ATTAACCCTTGAATTAATGTCCTACCTCACTTTTTCGTTAAGGTTGTTA
1 ATTAACCCTTGAATTAATGTCCCACCTCACTTTTTCGTTAAGGTTGTTA
1589071 AGACAATTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.41
Consensus pattern (50 bp):
ATTAACCCTTGAATTAATGTCCCACCTCACTTTTTCGTTAAGGTTGTTAC
Found at i:1592063 original size:20 final size:22
Alignment explanation
Indices: 1592035--1592075 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1592025 AAATATCTCA
1592035 ATTAGTTTAATA-ATAAAAATT
1 ATTAGTTTAATATATAAAAATT
1592056 ATTA-TTTAATATATAAAAAT
1 ATTAGTTTAATATATAAAAAT
1592076 CTAACTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTAGTTTAATATATAAAAATT
Found at i:1600397 original size:39 final size:39
Alignment explanation
Indices: 1600327--1600442 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 39
1600317 TCACATATAG
* * * * *
1600327 TCACCTAACATACAAGCATAAATCACCATACTCATATAA
1 TCACATAACATTCAAGCATATATCACAATACTCATAAAA
* * * * * *
1600366 TCTCTTAACGTTTAAGCATATGTCACAATACTCGTAAAA
1 TCACATAACATTCAAGCATATATCACAATACTCATAAAA
*
1600405 TCACATAACATTCAAGCATATACCACAATACTC-TAAAA
1 TCACATAACATTCAAGCATATATCACAATACTCATAAAA
1600443 CGTCTTTATA
Statistics
Matches: 61, Mismatches: 16, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
38 5 0.08
39 56 0.92
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.27
Consensus pattern (39 bp):
TCACATAACATTCAAGCATATATCACAATACTCATAAAA
Found at i:1605548 original size:928 final size:928
Alignment explanation
Indices: 1603753--1605608 Score: 3712
Period size: 928 Copynumber: 2.0 Consensus size: 928
1603743 AATTAGTAAA
1603753 AGTAAAATTCTACTTTGACCCCTTTAAAATTATAAAAATTTTATTTAATCCTTTAAAAATTATAA
1 AGTAAAATTCTACTTTGACCCCTTTAAAATTATAAAAATTTTATTTAATCCTTTAAAAATTATAA
1603818 ATATATAGATTATAAAAAATTAAAATTTCATTCGGCCCCCTAAATATTTGTTCTGGCTTCGCCCC
66 ATATATAGATTATAAAAAATTAAAATTTCATTCGGCCCCCTAAATATTTGTTCTGGCTTCGCCCC
1603883 TGAACTCAAGGTACGTTCTCACGCTTGATACCCTCTGCTACTACATCACGAGCAAGCAGCGGCCA
131 TGAACTCAAGGTACGTTCTCACGCTTGATACCCTCTGCTACTACATCACGAGCAAGCAGCGGCCA
1603948 GCCCCTTGGCTCCGGATCAACTAGCACCGAAGGGCGACACCCCTCTTGCGAAATGCCTTAGCAAC
196 GCCCCTTGGCTCCGGATCAACTAGCACCGAAGGGCGACACCCCTCTTGCGAAATGCCTTAGCAAC
1604013 AAAGTCAGCTGCTTTGGTGCTCTCCCTAGTAATGTGTCTAATATACATCTCCCATTAAAGCTTTA
261 AAAGTCAGCTGCTTTGGTGCTCTCCCTAGTAATGTGTCTAATATACATCTCCCATTAAAGCTTTA
1604078 ACATAGCCCGAATGCGACGAACCAAGCTACAGCCAGTATCCACAACACCATTCGCCATGACGAGT
326 ACATAGCCCGAATGCGACGAACCAAGCTACAGCCAGTATCCACAACACCATTCGCCATGACGAGT
1604143 TCCGTTGCTTCTTTATTGCCGCTCTCCAGCATTTAACTTAGTTATATATTAACATTTAGATAAAT
391 TCCGTTGCTTCTTTATTGCCGCTCTCCAGCATTTAACTTAGTTATATATTAACATTTAGATAAAT
1604208 TCTTTAAATTATTTTTATATAAAATTAATTAACTAGTATTATTTAAAAAGTTGTAATGAAGAGAA
456 TCTTTAAATTATTTTTATATAAAATTAATTAACTAGTATTATTTAAAAAGTTGTAATGAAGAGAA
1604273 ATTGATTAAAATATAAAACTAAAAAAAAACTCAACTCAAAATTAATATTAAATTTAAATATTTAA
521 ATTGATTAAAATATAAAACTAAAAAAAAACTCAACTCAAAATTAATATTAAATTTAAATATTTAA
1604338 CATATATTTGCAGAAAATAATTTTTTTTCAAAATATCTAGGCCCTAAAAATTTTAACATCTTCTC
586 CATATATTTGCAGAAAATAATTTTTTTTCAAAATATCTAGGCCCTAAAAATTTTAACATCTTCTC
1604403 CTCCTTTGTAACCATGTGTGCATTCTTTTTTGTTGCTACCCAATCAAGCTGTCTTTAAGAAGAAA
651 CTCCTTTGTAACCATGTGTGCATTCTTTTTTGTTGCTACCCAATCAAGCTGTCTTTAAGAAGAAA
1604468 ATAAAAACATATATTTAACATTAGAGGCCGTTGACGCCCATCTTGACACTTCTATGTATGCATAT
716 ATAAAAACATATATTTAACATTAGAGGCCGTTGACGCCCATCTTGACACTTCTATGTATGCATAT
1604533 TTCATTGGTCCCATTCTATCGTCGATTATGCTTACATTGCCAAGTCTCCTGATATCCTCTACCAA
781 TTCATTGGTCCCATTCTATCGTCGATTATGCTTACATTGCCAAGTCTCCTGATATCCTCTACCAA
1604598 TGTCTTGATTTTCCAATTGATAATGTACTTGTCTTGCCTTCTAGTACTTGTCCCAAGATTTTAAT
846 TGTCTTGATTTTCCAATTGATAATGTACTTGTCTTGCCTTCTAGTACTTGTCCCAAGATTTTAAT
1604663 GTTCTCCTTGAAAATTCC
911 GTTCTCCTTGAAAATTCC
1604681 AGTAAAATTCTACTTTGACCCCTTTAAAATTATAAAAATTTTATTTAATCCTTTAAAAATTATAA
1 AGTAAAATTCTACTTTGACCCCTTTAAAATTATAAAAATTTTATTTAATCCTTTAAAAATTATAA
1604746 ATATATAGATTATAAAAAATTAAAATTTCATTCGGCCCCCTAAATATTTGTTCTGGCTTCGCCCC
66 ATATATAGATTATAAAAAATTAAAATTTCATTCGGCCCCCTAAATATTTGTTCTGGCTTCGCCCC
1604811 TGAACTCAAGGTACGTTCTCACGCTTGATACCCTCTGCTACTACATCACGAGCAAGCAGCGGCCA
131 TGAACTCAAGGTACGTTCTCACGCTTGATACCCTCTGCTACTACATCACGAGCAAGCAGCGGCCA
1604876 GCCCCTTGGCTCCGGATCAACTAGCACCGAAGGGCGACACCCCTCTTGCGAAATGCCTTAGCAAC
196 GCCCCTTGGCTCCGGATCAACTAGCACCGAAGGGCGACACCCCTCTTGCGAAATGCCTTAGCAAC
1604941 AAAGTCAGCTGCTTTGGTGCTCTCCCTAGTAATGTGTCTAATATACATCTCCCATTAAAGCTTTA
261 AAAGTCAGCTGCTTTGGTGCTCTCCCTAGTAATGTGTCTAATATACATCTCCCATTAAAGCTTTA
1605006 ACATAGCCCGAATGCGACGAACCAAGCTACAGCCAGTATCCACAACACCATTCGCCATGACGAGT
326 ACATAGCCCGAATGCGACGAACCAAGCTACAGCCAGTATCCACAACACCATTCGCCATGACGAGT
1605071 TCCGTTGCTTCTTTATTGCCGCTCTCCAGCATTTAACTTAGTTATATATTAACATTTAGATAAAT
391 TCCGTTGCTTCTTTATTGCCGCTCTCCAGCATTTAACTTAGTTATATATTAACATTTAGATAAAT
1605136 TCTTTAAATTATTTTTATATAAAATTAATTAACTAGTATTATTTAAAAAGTTGTAATGAAGAGAA
456 TCTTTAAATTATTTTTATATAAAATTAATTAACTAGTATTATTTAAAAAGTTGTAATGAAGAGAA
1605201 ATTGATTAAAATATAAAACTAAAAAAAAACTCAACTCAAAATTAATATTAAATTTAAATATTTAA
521 ATTGATTAAAATATAAAACTAAAAAAAAACTCAACTCAAAATTAATATTAAATTTAAATATTTAA
1605266 CATATATTTGCAGAAAATAATTTTTTTTCAAAATATCTAGGCCCTAAAAATTTTAACATCTTCTC
586 CATATATTTGCAGAAAATAATTTTTTTTCAAAATATCTAGGCCCTAAAAATTTTAACATCTTCTC
1605331 CTCCTTTGTAACCATGTGTGCATTCTTTTTTGTTGCTACCCAATCAAGCTGTCTTTAAGAAGAAA
651 CTCCTTTGTAACCATGTGTGCATTCTTTTTTGTTGCTACCCAATCAAGCTGTCTTTAAGAAGAAA
1605396 ATAAAAACATATATTTAACATTAGAGGCCGTTGACGCCCATCTTGACACTTCTATGTATGCATAT
716 ATAAAAACATATATTTAACATTAGAGGCCGTTGACGCCCATCTTGACACTTCTATGTATGCATAT
1605461 TTCATTGGTCCCATTCTATCGTCGATTATGCTTACATTGCCAAGTCTCCTGATATCCTCTACCAA
781 TTCATTGGTCCCATTCTATCGTCGATTATGCTTACATTGCCAAGTCTCCTGATATCCTCTACCAA
1605526 TGTCTTGATTTTCCAATTGATAATGTACTTGTCTTGCCTTCTAGTACTTGTCCCAAGATTTTAAT
846 TGTCTTGATTTTCCAATTGATAATGTACTTGTCTTGCCTTCTAGTACTTGTCCCAAGATTTTAAT
1605591 GTTCTCCTTGAAAATTCC
911 GTTCTCCTTGAAAATTCC
1605609 CACAGTAAGG
Statistics
Matches: 928, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
928 928 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (928 bp):
AGTAAAATTCTACTTTGACCCCTTTAAAATTATAAAAATTTTATTTAATCCTTTAAAAATTATAA
ATATATAGATTATAAAAAATTAAAATTTCATTCGGCCCCCTAAATATTTGTTCTGGCTTCGCCCC
TGAACTCAAGGTACGTTCTCACGCTTGATACCCTCTGCTACTACATCACGAGCAAGCAGCGGCCA
GCCCCTTGGCTCCGGATCAACTAGCACCGAAGGGCGACACCCCTCTTGCGAAATGCCTTAGCAAC
AAAGTCAGCTGCTTTGGTGCTCTCCCTAGTAATGTGTCTAATATACATCTCCCATTAAAGCTTTA
ACATAGCCCGAATGCGACGAACCAAGCTACAGCCAGTATCCACAACACCATTCGCCATGACGAGT
TCCGTTGCTTCTTTATTGCCGCTCTCCAGCATTTAACTTAGTTATATATTAACATTTAGATAAAT
TCTTTAAATTATTTTTATATAAAATTAATTAACTAGTATTATTTAAAAAGTTGTAATGAAGAGAA
ATTGATTAAAATATAAAACTAAAAAAAAACTCAACTCAAAATTAATATTAAATTTAAATATTTAA
CATATATTTGCAGAAAATAATTTTTTTTCAAAATATCTAGGCCCTAAAAATTTTAACATCTTCTC
CTCCTTTGTAACCATGTGTGCATTCTTTTTTGTTGCTACCCAATCAAGCTGTCTTTAAGAAGAAA
ATAAAAACATATATTTAACATTAGAGGCCGTTGACGCCCATCTTGACACTTCTATGTATGCATAT
TTCATTGGTCCCATTCTATCGTCGATTATGCTTACATTGCCAAGTCTCCTGATATCCTCTACCAA
TGTCTTGATTTTCCAATTGATAATGTACTTGTCTTGCCTTCTAGTACTTGTCCCAAGATTTTAAT
GTTCTCCTTGAAAATTCC
Found at i:1606769 original size:20 final size:20
Alignment explanation
Indices: 1606736--1606780 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1606726 AATCAAAATG
1606736 TTTTTATTACTAA-TTATATT
1 TTTTTATTACTAATTTA-ATT
**
1606756 TTTTTATTTTTAATTTAATT
1 TTTTTATTACTAATTTAATT
1606776 TTTTT
1 TTTTT
1606781 TAACATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTATTACTAATTTAATT
Found at i:1614038 original size:22 final size:22
Alignment explanation
Indices: 1614007--1614050 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1613997 AAAAGTTTGT
1614007 ATGCTAATTCATGAAATCAAAG
1 ATGCTAATTCATGAAATCAAAG
*
1614029 ATGCTCATTCATGAAATCAAAG
1 ATGCTAATTCATGAAATCAAAG
1614051 CTACTAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (22 bp):
ATGCTAATTCATGAAATCAAAG
Found at i:1615391 original size:3 final size:3
Alignment explanation
Indices: 1615383--1615408 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1615373 GGGTGAGTAT
1615383 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
1615409 AATTTCAAAA
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:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1622858 original size:47 final size:47
Alignment explanation
Indices: 1622793--1623244 Score: 600
Period size: 47 Copynumber: 9.4 Consensus size: 47
1622783 CAGCCAAGAG
*
1622793 AGTGTATATATGTGATAAGGCCTAAT-GACCGATGTGATGAATGTGGA
1 AGTGTATATATGTGATAAGGCCTAATAG-CCGATGTGATGAATGTGAA
* * *
1622840 AGTGTATGTATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
1622887 AGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTA--TATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
1622936 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1622987 AGTGTATGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTA--TATA--TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * *
1623038 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGCGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
1623085 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
1623132 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * * * * * * *
1623179 AGTGTATATATGTGACAAGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
1623226 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
1623245 TCCCGAAAGG
Statistics
Matches: 371, Mismatches: 23, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
47 233 0.63
48 1 0.00
49 48 0.13
51 85 0.23
53 4 0.01
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:1623419 original size:37 final size:37
Alignment explanation
Indices: 1623363--1623441 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
1623353 CCGAGCTCTA
* * *
1623363 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
1623400 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
1623437 AAGAC
1 AAGAC
1623442 TTTGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:1625009 original size:255 final size:252
Alignment explanation
Indices: 1624542--1625048 Score: 951
Period size: 255 Copynumber: 2.0 Consensus size: 252
1624532 CATGGGAGAC
1624542 TTTGACTAATAAACTGTAATTGGCCTGACCAAAAATTCTAGAAAAAAATATGTAGATGGGCATAT
1 TTTGACTAATAAACTGTAATTGGCCTGACCAAAAATTCTAGAAAAAAATATGTAGATGGGCATAT
*
1624607 GAGTCTAGTTTCATGGAAAAATTACGAAACTGATTTTCAAGTTGTGAAACTCAAGATATGATTTT
66 GAGTCTAGTTTCAGGGAAAAATTACGAAACTGATTTTCAAGTTGTGAAACTCAAGATATGATTTT
1624672 TAAAGCGACTAGTACGCAGATTGGCAGTGTCTGGGAAATTTTTTTTATAAGTGGTTAAAGTCTGC
131 TAAAGCGACTAGTACGCAGATTGGCAGTGTCTGGGAAATTTTTTTTATAAGTGGTTAAAGTCTGC
1624737 TAACACCTCGTGTTCGACTCCGGTGACGGTCTCGGGTTCAGGGTGTTACATTTGATT
196 TAACACCTCGTGTTCGACTCCGGTGACGGTCTCGGGTTCAGGGTGTTACATTTGATT
*
1624794 TTTGACTAATAAACTGTACTAATTGGCCTGACCAAAAATTCTAGAAAAAAATATGTAGATGGTCA
1 TTTGACTAATAAACTG---TAATTGGCCTGACCAAAAATTCTAGAAAAAAATATGTAGATGGGCA
**
1624859 TATGAGTCTAGTTTCAGGGAAAAATTATTAAACTGATTTTCAAGTTGTGAAACTCAAGATATGAT
63 TATGAGTCTAGTTTCAGGGAAAAATTACGAAACTGATTTTCAAGTTGTGAAACTCAAGATATGAT
1624924 TTTTAAAGCGACTAGTACGCAGATTGGCAGTGTCTGGGAAATTTTTTTTATAAGTGGTTAAAGTC
128 TTTTAAAGCGACTAGTACGCAGATTGGCAGTGTCTGGGAAATTTTTTTTATAAGTGGTTAAAGTC
1624989 TGCTAACACCTCGTGTTCGACTCCGGTGACGGTCTCGGGTTCAGGGTGTTACATTTGATT
193 TGCTAACACCTCGTGTTCGACTCCGGTGACGGTCTCGGGTTCAGGGTGTTACATTTGATT
1625049 GGTATCAGAG
Statistics
Matches: 248, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
252 16 0.06
255 232 0.94
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (252 bp):
TTTGACTAATAAACTGTAATTGGCCTGACCAAAAATTCTAGAAAAAAATATGTAGATGGGCATAT
GAGTCTAGTTTCAGGGAAAAATTACGAAACTGATTTTCAAGTTGTGAAACTCAAGATATGATTTT
TAAAGCGACTAGTACGCAGATTGGCAGTGTCTGGGAAATTTTTTTTATAAGTGGTTAAAGTCTGC
TAACACCTCGTGTTCGACTCCGGTGACGGTCTCGGGTTCAGGGTGTTACATTTGATT
Found at i:1625411 original size:50 final size:49
Alignment explanation
Indices: 1625289--1625561 Score: 262
Period size: 50 Copynumber: 5.5 Consensus size: 49
1625279 TATGAGTGCT
* * * * **
1625289 AGTGTAAGACCATGTCTAGGACATGGCATCGGCAC-CGGTAAATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGACATC-GC-CTCGATACGTGAGAGCC
* * * * * *
1625339 -TTGTAAGACCATATTTGGGACATGACATCGGCTGCAATATGCGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGACATCGCCT-CGATACGTGAGAGCC
** * * *
1625388 AGTGTAAGACCATGTCCGGGACATGGCATCGGCCTCGATATGTGAGAGCT
1 AGTGTAAGACCATGTTTGGGACATGACATC-GCCTCGATACGTGAGAGCC
* * *
1625438 AGTGTAAGACCATATTTGGGACATGACATCGACCTTGATACGTGAGGGCC
1 AGTGTAAGACCATGTTTGGGACATGACATCG-CCTCGATACGTGAGAGCC
* * *
1625488 AGTGTAAGATCATGTTTGGGACATGGCATCAGCCTCGATACGTGAGAGTC
1 AGTGTAAGACCATGTTTGGGACATGACATC-GCCTCGATACGTGAGAGCC
*
1625538 AGTGTAAGACCATGTCTGGGACAT
1 AGTGTAAGACCATGTTTGGGACAT
1625562 AGCATCGACT
Statistics
Matches: 181, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 35 0.19
50 140 0.77
51 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCATGTTTGGGACATGACATCGCCTCGATACGTGAGAGCC
Found at i:1625493 original size:100 final size:100
Alignment explanation
Indices: 1625289--1625570 Score: 326
Period size: 100 Copynumber: 2.8 Consensus size: 100
1625279 TATGAGTGCT
* * *
1625289 AGTGTAAGACCATGTCTAGGACATGGCATCGGCAC-CGGTAAATGAGAGCCT--TGTAAGACCAT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGATAAGTGAGAG-CTAGTGTAAGACCAT
* *
1625351 ATTTGGGACATGACATCG-GCTGCAATATGCGAGAGCC
64 ATTTGGGACATGACATCGACCTG-AATACGCGAGAGCC
* *
1625388 AGTGTAAGACCATGTCCGGGACATGGCATCGGCCTCGATATGTGAGAGCTAGTGTAAGACCATAT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAAGTGAGAGCTAGTGTAAGACCATAT
* *
1625453 TTGGGACATGACATCGACCTTG-ATACGTGAGGGCC
66 TTGGGACATGACATCGACC-TGAATACGCGAGAGCC
* * * * *
1625488 AGTGTAAGATCATGTTTGGGACATGGCATCAGCCTCGATACGTGAGAG-TCAGTGTAAGACCATG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAAGTGAGAGCT-AGTGTAAGACCATA
*
1625552 TCTGGGACAT-AGCATCGAC
65 TTTGGGACATGA-CATCGAC
1625571 TTTTATGTAT
Statistics
Matches: 160, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
98 3 0.02
99 43 0.27
100 111 0.69
101 1 0.01
102 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (100 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAAGTGAGAGCTAGTGTAAGACCATAT
TTGGGACATGACATCGACCTGAATACGCGAGAGCC
Found at i:1633456 original size:14 final size:14
Alignment explanation
Indices: 1633437--1633476 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1633427 ATATTTTTAA
1633437 TAATAATTTTATAT
1 TAATAATTTTATAT
1633451 TAATAATTTTATAT
1 TAATAATTTTATAT
1633465 TAA-AATTATTAT
1 TAATAATT-TTAT
1633477 TAAATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATAATTTTATAT
Found at i:1633479 original size:12 final size:13
Alignment explanation
Indices: 1633437--1633501 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 13
1633427 ATATTTTTAA
*
1633437 TAATAATTTTATAT
1 TAATAATTAT-TAT
*
1633451 TAATAATTTTATAT
1 TAATAATTAT-TAT
1633465 TAA-AATTATTAT
1 TAATAATTATTAT
1633477 T-A-AA-TATTAT
1 TAATAATTATTAT
1633487 TAATAATTA-TAT
1 TAATAATTATTAT
1633499 TAA
1 TAA
1633502 GAATGTTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
10 7 0.15
11 4 0.09
12 12 0.26
13 7 0.15
14 17 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATAATTATTAT
Found at i:1633485 original size:13 final size:12
Alignment explanation
Indices: 1633448--1633524 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 12
1633438 AATAATTTTA
*
1633448 TATTAATAATTTT
1 TATTAA-AATTAT
1633461 ATATTAAAATTAT
1 -TATTAAAATTAT
1633474 TATT-AAA-TAT
1 TATTAAAATTAT
1633484 TATTAATAATTA-
1 TATTAA-AATTAT
*
1633496 TATTAAGAA-TGT
1 TATTAA-AATTAT
1633508 TATT-AAATTAT
1 TATTAAAATTAT
1633519 ATATTA
1 -TATTA
1633525 TTTTATAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
10 9 0.17
11 8 0.15
12 22 0.42
13 7 0.13
14 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
TATTAAAATTAT
Found at i:1633489 original size:22 final size:23
Alignment explanation
Indices: 1633462--1633524 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
1633452 AATAATTTTA
1633462 TATTAAAATTATTATTA-AATAT
1 TATTAAAATTATTATTAGAATAT
*
1633484 TATTAATAATTA-TATTAAGAATGT
1 TATTAA-AATTATTATT-AGAATAT
1633508 TATT-AAATTATATATTA
1 TATTAAAATTAT-TATTA
1633525 TTTTATAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 15 0.43
23 8 0.23
24 12 0.34
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (23 bp):
TATTAAAATTATTATTAGAATAT
Found at i:1633497 original size:34 final size:37
Alignment explanation
Indices: 1633441--1633524 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 37
1633431 TTTTAATAAT
*
1633441 AATTTTATATTAATAATTTTATATTAA-AATTATTATTA
1 AATTATATATTAATAA-TTTATATTAAGAA-TATTATTA
*
1633479 AA-TAT-TATTAATAA-TTATATTAAGAATGTTATTA
1 AATTATATATTAATAATTTATATTAAGAATATTATTA
1633513 AATTATATATTA
1 AATTATATATTA
1633525 TTTTATAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
34 18 0.44
35 5 0.12
36 14 0.34
37 2 0.05
38 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (37 bp):
AATTATATATTAATAATTTATATTAAGAATATTATTA
Found at i:1633603 original size:61 final size:58
Alignment explanation
Indices: 1633487--1633620 Score: 139
Period size: 61 Copynumber: 2.3 Consensus size: 58
1633477 TAAATATTAT
* * *
1633487 TAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATAAAATTGTATTTAA
1 TAATAATTATATTAAGAATATGATTAAATTATATATTATTTTATAAAATTATATTTAA
* *
1633545 TAATAATTATGTTAA-AATATGATTAAATTATTTATTTTTATTTTTATTAAAA-TATATTTAA
1 TAATAATTATATTAAGAATATGATTAAATTA--TA-TATTA-TTTTA-TAAAATTATATTTAA
*
1633606 CAATAATCT-TATTAA
1 TAATAAT-TATATTAA
1633621 AACTTAATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
57 13 0.21
58 14 0.22
59 2 0.03
60 4 0.06
61 24 0.38
62 6 0.10
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (58 bp):
TAATAATTATATTAAGAATATGATTAAATTATATATTATTTTATAAAATTATATTTAA
Found at i:1633764 original size:44 final size:46
Alignment explanation
Indices: 1633708--1633800 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
1633698 TATTACATCT
1633708 ATTCCATTCAACCAAACACAAGAATT-CT-ATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTCC
***
1633752 ATTCCATTCAACCAAACAGTTGAATTACTGATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTCC
1633798 ATT
1 ATT
1633801 ACAGTTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.52
45 2 0.05
46 19 0.43
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.32
Consensus pattern (46 bp):
ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTCC
Found at i:1633803 original size:16 final size:16
Alignment explanation
Indices: 1633782--1633868 Score: 120
Period size: 16 Copynumber: 5.4 Consensus size: 16
1633772 TGAATTACTG
1633782 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
1633798 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
* *
1633814 ATTACAGTTCTATTTC
1 ATTACAGCTCTATTCC
* *
1633830 ATTACATCTCTATTCA
1 ATTACAGCTCTATTCC
*
1633846 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
1633862 ATTACAG
1 ATTACAG
1633869 TGAAACAAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 62 1.00
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:1635180 original size:34 final size:34
Alignment explanation
Indices: 1635137--1635204 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
1635127 ACAAATATAA
* *
1635137 CATAATCACAAGATAT-CAATTTAAGTAGAGAAAC
1 CATAATCACAACATATGC-ATTAAAGTAGAGAAAC
1635171 CATAATCACAACATATGCATTAAAGTAGAGAAAC
1 CATAATCACAACATATGCATTAAAGTAGAGAAAC
1635205 AACTGCAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 30 0.97
35 1 0.03
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (34 bp):
CATAATCACAACATATGCATTAAAGTAGAGAAAC
Done.