Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 5 of 160
Found at i:1321016 original size:11 final size:11
Alignment explanation
Indices: 1321000--1321025 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1320990 ATAATACAAC
1321000 GAAAAATGCGA
1 GAAAAATGCGA
1321011 GAAAAATGCGA
1 GAAAAATGCGA
1321022 GAAA
1 GAAA
1321026 CACTTGAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.08, G:0.27, T:0.08
Consensus pattern (11 bp):
GAAAAATGCGA
Found at i:1333402 original size:12 final size:13
Alignment explanation
Indices: 1333387--1333446 Score: 65
Period size: 12 Copynumber: 4.7 Consensus size: 13
1333377 AAATTATTTT
1333387 TTTAATTT-TATA
1 TTTAATTTATATA
1333399 TTTAATTATATATA
1 TTTAATT-TATATA
1333413 TTT--TTATATATA
1 TTTAATT-TATATA
1333425 TTTAATTT-TATA
1 TTTAATTTATATA
1333437 TTTATATTTA
1 TTTA-ATTTA
1333447 AAATAATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
12 27 0.64
13 6 0.14
14 9 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTAATTTATATA
Found at i:1333419 original size:22 final size:22
Alignment explanation
Indices: 1333392--1333447 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1333382 ATTTTTTTAA
1333392 TTTTATATTTAATT-ATATATAT
1 TTTTATATTTAATTAAT-TATAT
* * *
1333414 TTTTATATATATTTAATTTTAT
1 TTTTATATTTAATTAATTATAT
*
1333436 ATTTATATTTAA
1 TTTTATATTTAA
1333448 AATAATATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATATTTAATTAATTATAT
Found at i:1333424 original size:16 final size:16
Alignment explanation
Indices: 1333405--1333443 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1333395 TATATTTAAT
*
1333405 TATATATATTTTTATA
1 TATATATAATTTTATA
*
1333421 TATATTTAATTTTATA
1 TATATATAATTTTATA
*
1333437 TTTATAT
1 TATATAT
1333444 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATATAATTTTATA
Found at i:1340240 original size:2 final size:2
Alignment explanation
Indices: 1340233--1340257 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1340223 GGTATCTATT
1340233 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1340258 GCTAGAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1347026 original size:22 final size:22
Alignment explanation
Indices: 1346998--1347046 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1346988 GATTTCAAAT
* **
1346998 AATTTAAATCAATTTAATTTTA
1 AATTTAAACCAATTTAAAATTA
1347020 AATTTAAACCAATTTAAAATTA
1 AATTTAAACCAATTTAAAATTA
1347042 AATTT
1 AATTT
1347047 TTATTGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTAAACCAATTTAAAATTA
Found at i:1347535 original size:19 final size:19
Alignment explanation
Indices: 1347497--1347535 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1347487 AAATTTAAAA
*
1347497 TTATTAATAATAGTATTTT
1 TTATTAATAATAGTAATTT
1347516 TTATTAATTAATA-TAATTT
1 TTATTAA-TAATAGTAATTT
1347535 T
1 T
1347536 GGTTTTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATTAATAATAGTAATTT
Found at i:1347593 original size:28 final size:29
Alignment explanation
Indices: 1347545--1347601 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 29
1347535 TGGTTTTACA
1347545 AAAAAAATCACAATTTGAACT-TTGAAAAT
1 AAAAAAATCACAATTTGAACTATT-AAAAT
*
1347574 AAAAAAAT-ATAATTAT-AACTATTAAAAT
1 AAAAAAATCACAATT-TGAACTATTAAAAT
1347602 TTAAATAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAAAAATCACAATTTGAACTATTAAAAT
Found at i:1348440 original size:10 final size:10
Alignment explanation
Indices: 1348421--1348457 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
1348411 ATCTCTCTCC
1348421 CTTTTTTTTT
1 CTTTTTTTTT
*
1348431 CTTTTCTTTT
1 CTTTTTTTTT
1348441 CTTTTTTTTT
1 CTTTTTTTTT
1348451 CTATTTT
1 CT-TTTT
1348458 GATTGATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:1350044 original size:11 final size:11
Alignment explanation
Indices: 1350028--1350093 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
1350018 CATGCAGGCC
1350028 TTTTCTTTTCT
1 TTTTCTTTTCT
*
1350039 TTTTCTTTTTT
1 TTTTCTTTTCT
*
1350050 TTTTTTTTTCCT
1 TTTTCTTTT-CT
*
1350062 TTTTACTTGTCT
1 TTTT-CTTTTCT
*
1350074 TTTTATTTTC-
1 TTTTCTTTTCT
*
1350084 TCTTCTTTTC
1 TTTTCTTTTC
1350094 CCATCCTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
10 8 0.18
11 22 0.50
12 11 0.25
13 3 0.07
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:1351403 original size:3 final size:3
Alignment explanation
Indices: 1351397--1351423 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1351387 TCTCGTGGTC
1351397 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1351424 GTGGTGGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:1361063 original size:2 final size:2
Alignment explanation
Indices: 1361056--1361093 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1361046 GAGTTGGGAC
1361056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1361094 CACACATACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1361343 original size:2 final size:2
Alignment explanation
Indices: 1361338--1361370 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1361328 ATGGTGTGTG
1361338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1361371 ATTGACATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1382041 original size:2 final size:2
Alignment explanation
Indices: 1382034--1382058 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1382024 GGTATCTATT
1382034 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1382059 GCTAAGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1385373 original size:51 final size:51
Alignment explanation
Indices: 1385297--1385398 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
1385287 CTCATGCAAG
*
1385297 GAACTGAAAGAGAGAATATCAGGCCTTACACTGATGGTGATCTGGTAACTT
1 GAACTGAAAGAGAGAATATCAGGCCTTACACTGATAGTGATCTGGTAACTT
1385348 GAACTGAAAGAGAGAATATCAGGCCTTACACTGATAGTGATCTGGTAACTT
1 GAACTGAAAGAGAGAATATCAGGCCTTACACTGATAGTGATCTGGTAACTT
1385399 ATGCTGATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (51 bp):
GAACTGAAAGAGAGAATATCAGGCCTTACACTGATAGTGATCTGGTAACTT
Found at i:1389292 original size:19 final size:19
Alignment explanation
Indices: 1389254--1389292 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1389244 AAATTTAAAA
*
1389254 TTATTAATAATAGTATTTT
1 TTATTAATAATAGTAATTT
1389273 TTATTAATTAATA-TAATTT
1 TTATTAA-TAATAGTAATTT
1389292 T
1 T
1389293 GGTTTTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATTAATAATAGTAATTT
Found at i:1390188 original size:10 final size:10
Alignment explanation
Indices: 1390169--1390205 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
1390159 ATCTCTCTCC
1390169 CTTTTTTTTT
1 CTTTTTTTTT
*
1390179 CTTTTCTTTT
1 CTTTTTTTTT
1390189 CTTTTTTTTT
1 CTTTTTTTTT
1390199 CTATTTT
1 CT-TTTT
1390206 GATTGATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 20 0.83
11 4 0.17
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:1391791 original size:11 final size:11
Alignment explanation
Indices: 1391775--1391840 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
1391765 CATGCAGGCC
1391775 TTTTCTTTTCT
1 TTTTCTTTTCT
*
1391786 TTTTCTTTTTT
1 TTTTCTTTTCT
*
1391797 TTTTTTTTTCCT
1 TTTTCTTTT-CT
*
1391809 TTTTACTTGTCT
1 TTTT-CTTTTCT
*
1391821 TTTTATTTTC-
1 TTTTCTTTTCT
*
1391831 TCTTCTTTTC
1 TTTTCTTTTC
1391841 CCATCCTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
10 8 0.18
11 22 0.50
12 11 0.25
13 3 0.07
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:1399841 original size:105 final size:105
Alignment explanation
Indices: 1399659--1399869 Score: 422
Period size: 105 Copynumber: 2.0 Consensus size: 105
1399649 TTAAAGTAAG
1399659 TACTGATTTAGTGGTGAAGCAAAATATGTCAGTGAAGAAAAGCTTCCATAGTTTACCCAAGTACA
1 TACTGATTTAGTGGTGAAGCAAAATATGTCAGTGAAGAAAAGCTTCCATAGTTTACCCAAGTACA
1399724 GAAAATATCATCATTGTAGCATAAGTCGACTCTGTTTTAC
66 GAAAATATCATCATTGTAGCATAAGTCGACTCTGTTTTAC
1399764 TACTGATTTAGTGGTGAAGCAAAATATGTCAGTGAAGAAAAGCTTCCATAGTTTACCCAAGTACA
1 TACTGATTTAGTGGTGAAGCAAAATATGTCAGTGAAGAAAAGCTTCCATAGTTTACCCAAGTACA
1399829 GAAAATATCATCATTGTAGCATAAGTCGACTCTGTTTTAC
66 GAAAATATCATCATTGTAGCATAAGTCGACTCTGTTTTAC
1399869 T
1 T
1399870 TAGTTTTAAT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (105 bp):
TACTGATTTAGTGGTGAAGCAAAATATGTCAGTGAAGAAAAGCTTCCATAGTTTACCCAAGTACA
GAAAATATCATCATTGTAGCATAAGTCGACTCTGTTTTAC
Found at i:1402291 original size:21 final size:21
Alignment explanation
Indices: 1402267--1402306 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1402257 CTGCCACCAT
**
1402267 CTCAAAGTTATCCACCATCAA
1 CTCAAAGCCATCCACCATCAA
*
1402288 CTCAAGGCCATCCACCATC
1 CTCAAAGCCATCCACCATC
1402307 CTCTCACGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.40, G:0.07, T:0.20
Consensus pattern (21 bp):
CTCAAAGCCATCCACCATCAA
Found at i:1403137 original size:2 final size:2
Alignment explanation
Indices: 1403132--1403170 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1403122 GGTGTGTGTG
1403132 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1403171 ATTGACATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1411155 original size:9 final size:9
Alignment explanation
Indices: 1411141--1411165 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1411131 AATCAGGGTG
1411141 CTGCTACTA
1 CTGCTACTA
1411150 CTGCTACTA
1 CTGCTACTA
1411159 CTGCTAC
1 CTGCTAC
1411166 AACGGCCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.36, G:0.12, T:0.32
Consensus pattern (9 bp):
CTGCTACTA
Found at i:1424787 original size:15 final size:15
Alignment explanation
Indices: 1424765--1424801 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1424755 TTGTTCGTTT
1424765 TAATTTTTGATATCA
1 TAATTTTTGATATCA
*
1424780 TGATTTTTGATATCA
1 TAATTTTTGATATCA
1424795 TAATTTT
1 TAATTTT
1424802 ATCTTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (15 bp):
TAATTTTTGATATCA
Found at i:1433464 original size:30 final size:30
Alignment explanation
Indices: 1433430--1433490 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1433420 TGTGTCGGCC
1433430 CAACTCAAAATGATATACTTCAAACCCAAT
1 CAACTCAAAATGATATACTTCAAACCCAAT
1433460 CAACTCAAAATGATATACTTCAAACCCAAT
1 CAACTCAAAATGATATACTTCAAACCCAAT
1433490 C
1 C
1433491 CAATAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.28, G:0.03, T:0.23
Consensus pattern (30 bp):
CAACTCAAAATGATATACTTCAAACCCAAT
Found at i:1442179 original size:21 final size:22
Alignment explanation
Indices: 1442130--1442180 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1442120 AGTTTTTTTG
*
1442130 AATTTTA-AATAAAAAATTATT
1 AATTTTATAATAAAAAAATATT
*
1442151 AATATTTATAA-AAAAAAATCTT
1 AAT-TTTATAATAAAAAAATATT
1442173 AATTTTAT
1 AATTTTAT
1442181 TCTCTAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTTTATAATAAAAAAATATT
Found at i:1443049 original size:48 final size:48
Alignment explanation
Indices: 1442962--1443059 Score: 128
Period size: 48 Copynumber: 2.0 Consensus size: 48
1442952 CATATACACC
* * *
1442962 CATGCATCATACTTATGTGGACCATTTCAGTCTCTTCTAGTTCACTCA
1 CATGCATCATACTTATGTGGACCATTTCAATCTCCTCTAGTCCACTCA
*
1443010 CATGCATCATAAC-TATGTGGACCCTCTT-AATCTCCTCTAGTCCACTCA
1 CATGCATCAT-ACTTATGTGGACCAT-TTCAATCTCCTCTAGTCCACTCA
1443058 CA
1 CA
1443060 AACATTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
48 40 0.91
49 4 0.09
ACGTcount: A:0.24, C:0.31, G:0.11, T:0.34
Consensus pattern (48 bp):
CATGCATCATACTTATGTGGACCATTTCAATCTCCTCTAGTCCACTCA
Found at i:1444111 original size:24 final size:22
Alignment explanation
Indices: 1444078--1444139 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 22
1444068 CAACTTCAAG
*
1444078 AAATGTAATATTAGTCATGCAAT
1 AAATATAATATTA-TCATGCAAT
1444101 AATATATAATATCATATCATGCAAT
1 AA-ATATAATAT--TATCATGCAAT
*
1444126 AAATATAAAATTAT
1 AAATATAATATTAT
1444140 GCAACAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 3 0.09
23 2 0.06
24 16 0.47
25 11 0.32
26 2 0.06
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (22 bp):
AAATATAATATTATCATGCAAT
Found at i:1444265 original size:21 final size:21
Alignment explanation
Indices: 1444239--1444281 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1444229 TTAAATATAT
*
1444239 AATCATGCA-ATTAACAATGTA
1 AATCATGCAGATAAAC-ATGTA
1444260 AATCATGCAGATAAACATGTA
1 AATCATGCAGATAAACATGTA
1444281 A
1 A
1444282 TTAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (21 bp):
AATCATGCAGATAAACATGTA
Found at i:1444299 original size:21 final size:20
Alignment explanation
Indices: 1444270--1444311 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1444260 AATCATGCAG
* *
1444270 ATAAACATGTAATTAAATAT
1 ATAAACATGCAAGTAAATAT
1444290 ATAAACCATGCAAGTAAATAT
1 ATAAA-CATGCAAGTAAATAT
1444311 A
1 A
1444312 CAATTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.29
Consensus pattern (20 bp):
ATAAACATGCAAGTAAATAT
Found at i:1444300 original size:33 final size:33
Alignment explanation
Indices: 1444258--1444334 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
1444248 ATTAACAATG
* **
1444258 TAAATCATGC-AGATAAACATGTAATTAAATATA
1 TAAACCATGCAAG-TAAACATACAATTAAATATA
*
1444291 TAAACCATGCAAGTAAATATACAATTAAATATA
1 TAAACCATGCAAGTAAACATACAATTAAATATA
*
1444324 T-AATCATGCAA
1 TAAACCATGCAA
1444335 TCATAGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 9 0.24
33 27 0.71
34 2 0.05
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.29
Consensus pattern (33 bp):
TAAACCATGCAAGTAAACATACAATTAAATATA
Found at i:1444352 original size:32 final size:32
Alignment explanation
Indices: 1444316--1444398 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 32
1444306 AATATACAAT
*
1444316 TAAATATATAATCATGCAATCATAGA-AA-TAAA
1 TAAATATATAATCATGCAAT--TAGACAAGCAAA
*
1444348 TAAAT-TAATAATCATGCAATTAGACAAGCAAT
1 TAAATAT-ATAATCATGCAATTAGACAAGCAAA
1444380 TAAATATATAATCATGCAA
1 TAAATATATAATCATGCAA
1444399 ATAATATTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
30 4 0.09
31 3 0.07
32 37 0.82
33 1 0.02
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (32 bp):
TAAATATATAATCATGCAATTAGACAAGCAAA
Found at i:1444401 original size:56 final size:55
Alignment explanation
Indices: 1444333--1444592 Score: 246
Period size: 56 Copynumber: 4.7 Consensus size: 55
1444323 ATAATCATGC
* * *
1444333 AATCATAG-AAATAAATAAATTAATAATCATGCAATTAGACAAGCAATTAAATATAT
1 AATCAT-GCAAAT-AATAAATTAATAATCATGCAAATAAACATGCAATTAAATATAT
* * * * *
1444389 AATCATGCAAATAATATTATTAATAATCATACAAATAAACATGTAACTAAATATGT
1 AATCATGCAAATAATA-AATTAATAATCATGCAAATAAACATGCAATTAAATATAT
* * *
1444445 AAGT-ATGC-AACAA-AAATATATATATACCATGCAAATAAATATGCAATTAAATATAT
1 AA-TCATGCAAATAATAAAT-TA-ATA-ATCATGCAAATAAACATGCAATTAAATATAT
* * *
1444501 AATCATGCCAATAGT-AATATATTAATCATGCAAATAAACATGCAATTAAATATAT
1 AATCATGCAAATAATAAAT-TAATAATCATGCAAATAAACATGCAATTAAATATAT
*
1444556 AATCATGCAACTAAT-AA-TACATAAATCATGCAAATAA
1 AATCATGCAAATAATAAATTA-AT-AATCATGCAAATAA
1444593 TAATATATAA
Statistics
Matches: 168, Mismatches: 25, Indels: 23
0.78 0.12 0.11
Matches are distributed among these distances:
53 4 0.02
54 4 0.02
55 70 0.42
56 80 0.48
57 10 0.06
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.29
Consensus pattern (55 bp):
AATCATGCAAATAATAAATTAATAATCATGCAAATAAACATGCAATTAAATATAT
Found at i:1444522 original size:22 final size:23
Alignment explanation
Indices: 1444494--1444536 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1444484 TATGCAATTA
*
1444494 AATATA-TAATCATGCCAATAGT
1 AATATATTAATCATGCAAATAGT
1444516 AATATATTAATCATGCAAATA
1 AATATATTAATCATGCAAATA
1444537 AACATGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.33
Consensus pattern (23 bp):
AATATATTAATCATGCAAATAGT
Found at i:1444535 original size:55 final size:54
Alignment explanation
Indices: 1444356--1444592 Score: 260
Period size: 55 Copynumber: 4.3 Consensus size: 54
1444346 AATAAATTAA
* * * * *
1444356 TAATCATGCAATTAGACAAGCAATTAAATATATAATCATGCAAATAATATTATTAA
1 TAATCATGCAAATAAACATGCAATTAAATATATAATCATGC-AATAATAATA-TAT
* * * * * *
1444412 TAATCATACAAATAAACATGTAACTAAATATGTAAGT-ATGCAACAAAAATATAT
1 TAATCATGCAAATAAACATGCAATTAAATATATAA-TCATGCAATAATAATATAT
* * *
1444466 ATATACCATGCAAATAAATATGCAATTAAATATATAATCATGCCAATAGTAATATAT
1 -TA-ATCATGCAAATAAACATGCAATTAAATATATAATCATG-CAATAATAATATAT
*
1444523 TAATCATGCAAATAAACATGCAATTAAATATATAATCATGCAACTAATAATACAT
1 TAATCATGCAAATAAACATGCAATTAAATATATAATCATGCAA-TAATAATATAT
*
1444578 AAATCATGCAAATAA
1 TAATCATGCAAATAA
1444593 TAATATATAA
Statistics
Matches: 150, Mismatches: 25, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
54 5 0.03
55 69 0.46
56 64 0.43
57 12 0.08
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (54 bp):
TAATCATGCAAATAAACATGCAATTAAATATATAATCATGCAATAATAATATAT
Found at i:1444586 original size:23 final size:23
Alignment explanation
Indices: 1444556--1444611 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1444546 TTAAATATAT
*
1444556 AATCATGCAACTAATAATACATA
1 AATCATGCAAATAATAATACATA
*
1444579 AATCATGCAAATAATAATATATA
1 AATCATGCAAATAATAATACATA
1444602 AATCATGCAA
1 AATCATGCAA
1444612 TCATGTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27
Consensus pattern (23 bp):
AATCATGCAAATAATAATACATA
Found at i:1444614 original size:31 final size:31
Alignment explanation
Indices: 1444579--1444642 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1444569 ATAATACATA
*
1444579 AATCATGCAAATAATAATATATAAATCATGC
1 AATCATGCAAATAATAATATATAAACCATGC
* *
1444610 AATCATGTAACTAATAATATATAAACCATGC
1 AATCATGCAAATAATAATATATAAACCATGC
1444641 AA
1 AA
1444643 CATATGCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (31 bp):
AATCATGCAAATAATAATATATAAACCATGC
Found at i:1445255 original size:14 final size:13
Alignment explanation
Indices: 1445224--1445261 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1445214 CTTTTGACAA
1445224 AAAAAAATTAAAC
1 AAAAAAATTAAAC
*
1445237 -CAAAAATTAAAC
1 AAAAAAATTAAAC
1445249 TAAAAAAATTAAA
1 -AAAAAAATTAAA
1445262 ATACAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 11 0.52
14 10 0.48
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAAATTAAAC
Found at i:1445644 original size:37 final size:37
Alignment explanation
Indices: 1445591--1445719 Score: 161
Period size: 37 Copynumber: 3.4 Consensus size: 37
1445581 GTACCCCTTT
*
1445591 AACTTTGAGAAAATAAAGTACTCCTTCACCGAGATTTC
1 AACTTTGA-AAAATAAAGTACTCCTCCACCGAGATTTC
* * *
1445629 AACTTTGAAAAATAAAGAACTTCTCCACCGAAGCTTT-
1 AACTTTGAAAAATAAAGTACTCCTCCACCG-AGATTTC
* **
1445666 AACTTTGAAAAATAAAGTACTCCTCCATCGAGGCTTC
1 AACTTTGAAAAATAAAGTACTCCTCCACCGAGATTTC
1445703 AACTTTGAAAAAATAAA
1 AACTTTG-AAAAATAAA
1445720 AAACTCATCC
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
36 4 0.05
37 53 0.67
38 22 0.28
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (37 bp):
AACTTTGAAAAATAAAGTACTCCTCCACCGAGATTTC
Found at i:1445672 original size:75 final size:75
Alignment explanation
Indices: 1445587--1445749 Score: 231
Period size: 75 Copynumber: 2.2 Consensus size: 75
1445577 AAAAGTACCC
* * *
1445587 CTTTAACTTTGAGAAAATAAAGTACTCCTTCACCGAGATTTCAACTTTG-AAAAATAAAGAACTT
1 CTTTAACTTTGA-AAAATAAAGTACTCCTCCACCGAGACTTCAACTTTGAAAAAATAAAAAAC-T
1445651 C-TCCACCGAAG
64 CATCCACCGAAG
* *
1445662 CTTTAACTTTGAAAAATAAAGTACTCCTCCATCGAGGCTTCAACTTTGAAAAAATAAAAAACTCA
1 CTTTAACTTTGAAAAATAAAGTACTCCTCCACCGAGACTTCAACTTTGAAAAAATAAAAAACTCA
* *
1445727 TCCACTGAGG
66 TCCACCGAAG
1445737 CTTTAACTTTGAA
1 CTTTAACTTTGAA
1445750 CTTTTGAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
74 34 0.43
75 45 0.57
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.29
Consensus pattern (75 bp):
CTTTAACTTTGAAAAATAAAGTACTCCTCCACCGAGACTTCAACTTTGAAAAAATAAAAAACTCA
TCCACCGAAG
Found at i:1445737 original size:38 final size:36
Alignment explanation
Indices: 1445591--1445749 Score: 149
Period size: 37 Copynumber: 4.2 Consensus size: 36
1445581 GTACCCCTTT
* * * **
1445591 AACTTTGAGAAAATAAAGTACTCCTTCACCGAGATTTC
1 AACTTTGA-AAAATAAAGAACT-CTCCACTGAGGCTTC
* * *
1445629 AACTTTGAAAAATAAAGAACTTCTCCACCGAAGCTTT
1 AACTTTGAAAAATAAAGAAC-TCTCCACTGAGGCTTC
*
1445666 AACTTTGAAAAATAAAGTACTCCTCCA-TCGAGGCTTC
1 AACTTTGAAAAATAAAGAACT-CTCCACT-GAGGCTTC
* *
1445703 AACTTTGAAAAAATAAAAAACTCATCCACTGAGGCTTT
1 AACTTTG-AAAAATAAAGAACTC-TCCACTGAGGCTTC
1445741 AACTTTGAA
1 AACTTTGAA
1445750 CTTTTGAAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
36 1 0.01
37 61 0.60
38 39 0.38
39 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (36 bp):
AACTTTGAAAAATAAAGAACTCTCCACTGAGGCTTC
Found at i:1445802 original size:42 final size:43
Alignment explanation
Indices: 1445752--1445852 Score: 136
Period size: 42 Copynumber: 2.4 Consensus size: 43
1445742 ACTTTGAACT
1445752 TTTG-AAAAATAAAATGCTACCCCACAACTGA-GACTTTAAAAC
1 TTTGAAAAAATAAAATGCTACCCCACAACTGAGGA-TTTAAAAC
* * * *
1445794 TTT-AAAAAATAAAATGCTCCCCCATAATTGAGGATTTGAAAC
1 TTTGAAAAAATAAAATGCTACCCCACAACTGAGGATTTAAAAC
1445836 TTTGAAAAAATAAAATG
1 TTTGAAAAAATAAAATG
1445853 AAATCATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
42 37 0.71
43 15 0.29
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.27
Consensus pattern (43 bp):
TTTGAAAAAATAAAATGCTACCCCACAACTGAGGATTTAAAAC
Found at i:1446781 original size:12 final size:12
Alignment explanation
Indices: 1446766--1446790 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1446756 ATTTTTTGCT
1446766 TTTTTTTGCACA
1 TTTTTTTGCACA
1446778 TTTTTTTGCACA
1 TTTTTTTGCACA
1446790 T
1 T
1446791 ACTTTCCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTTTTTGCACA
Found at i:1448355 original size:17 final size:19
Alignment explanation
Indices: 1448321--1448360 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
1448311 TGAGTATCTT
1448321 TTTTTTTTAGCACAACCA-
1 TTTTTTTTAGCACAACCAC
1448339 TTTTTTTTA-CATC-ACCAC
1 TTTTTTTTAGCA-CAACCAC
1448357 TTTT
1 TTTT
1448361 AAGCTTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.53
Consensus pattern (19 bp):
TTTTTTTTAGCACAACCAC
Found at i:1455032 original size:19 final size:20
Alignment explanation
Indices: 1455010--1455100 Score: 59
Period size: 20 Copynumber: 4.7 Consensus size: 20
1455000 TAATGTAAAT
*
1455010 ATATAAT-ATTATTATGCAA
1 ATATAATAATTATCATGCAA
*
1455029 ATATATTAATTATCATGCAATA
1 ATATAATAATTATCATGC-A-A
**
1455051 ATATAA-AA-TGCCATGCGACA
1 ATATAATAATTATCATGC-A-A
*
1455071 ATATAA-AA-TACCATGCAA
1 ATATAATAATTATCATGCAA
1455089 ATAT-ATAATTAT
1 ATATAATAATTAT
1455101 GAAATCAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
17 1 0.02
18 7 0.12
19 9 0.16
20 32 0.55
21 3 0.05
22 6 0.10
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (20 bp):
ATATAATAATTATCATGCAA
Found at i:1455046 original size:20 final size:20
Alignment explanation
Indices: 1454963--1455048 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
1454953 TGCAAGAATG
*
1454963 TCATGCAAATATGTTAATAA
1 TCATGCAAATATATTAATAA
*
1454983 TCATGC-AATA-A-TAACAA
1 TCATGCAAATATATTAATAA
* *
1455000 TAATGTAAATATA-TAATATTA
1 TCATGCAAATATATTAATA--A
* *
1455021 TTATGCAAATATATTAATTA
1 TCATGCAAATATATTAATAA
1455041 TCATGCAA
1 TCATGCAA
1455049 TAATATAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
17 9 0.17
18 4 0.08
19 9 0.17
20 14 0.27
21 12 0.23
22 4 0.08
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (20 bp):
TCATGCAAATATATTAATAA
Found at i:1455094 original size:20 final size:20
Alignment explanation
Indices: 1455023--1455096 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
1455013 TAATATTATT
* * *
1455023 ATGCAAATATATTAATTATC
1 ATGCAAATATATAAAATACC
*
1455043 ATGC-AATAATATAAAATGCC
1 ATGCAAAT-ATATAAAATACC
*
1455063 ATGCGACA-ATATAAAATACC
1 ATGC-AAATATATAAAATACC
1455083 ATGCAAATATATAA
1 ATGCAAATATATAA
1455097 TTATGAAATC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 5 0.12
20 37 0.86
22 1 0.02
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (20 bp):
ATGCAAATATATAAAATACC
Found at i:1455230 original size:24 final size:24
Alignment explanation
Indices: 1455201--1455252 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1455191 TCATTCAAAC
*
1455201 ATAATATTA-ATCATGCAATAACAT
1 ATAATATCATATCATGCAATAA-AT
1455225 ATAATATCATATCATGCAATAAAT
1 ATAATATCATATCATGCAATAAAT
1455249 ATAA
1 ATAA
1455253 ATCGTACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAATATCATATCATGCAATAAAT
Found at i:1455419 original size:21 final size:20
Alignment explanation
Indices: 1455388--1455429 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1455378 AATCATGCAA
*
1455388 ATAAACATGTAATTAAATAT
1 ATAAACATGTAAATAAATAT
1455408 ATAAACCATGTAAATAAATAT
1 ATAAA-CATGTAAATAAATAT
1455429 A
1 A
1455430 CAATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (20 bp):
ATAAACATGTAAATAAATAT
Found at i:1455528 original size:55 final size:55
Alignment explanation
Indices: 1455471--1455707 Score: 302
Period size: 55 Copynumber: 4.3 Consensus size: 55
1455461 ATAAATAAAT
** * *
1455471 TAATAATCATATAATTAGACATGCAATTAAATATATAATCATGCAA-TAATAATA
1 TAATAATCATGCAAATAAACATGCAATTAAATATATAATCATGCAACTAATAATA
*
1455525 TTAATAATCATGCAAATAAACATGCAATTAAATATATAATCATGCAACTAAAAATA
1 -TAATAATCATGCAAATAAACATGCAATTAAATATATAATCATGCAACTAATAATA
* * * *
1455581 T-ATAAACCATGCAAATAAATATGCAA-TAAATATATAATCATGCAAATAGTAATA
1 TAAT-AATCATGCAAATAAACATGCAATTAAATATATAATCATGCAACTAATAATA
* * *
1455635 TATTAATCATGCGAATAAACATGAAATTAAATATATAATCATGCAACTAATAATA
1 TAATAATCATGCAAATAAACATGCAATTAAATATATAATCATGCAACTAATAATA
*
1455690 -CATAAATCATGCAAATAA
1 TAAT-AATCATGCAAATAA
1455708 TAATATATAA
Statistics
Matches: 157, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
54 47 0.30
55 103 0.66
56 7 0.04
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (55 bp):
TAATAATCATGCAAATAAACATGCAATTAAATATATAATCATGCAACTAATAATA
Found at i:1455535 original size:23 final size:20
Alignment explanation
Indices: 1455490--1455727 Score: 99
Period size: 23 Copynumber: 12.4 Consensus size: 20
1455480 TATAATTAGA
*
1455490 CATGCAATTAAATATATAAT
1 CATGCAATAAAATATATAAT
1455510 CATGCAATAATAATAT-TAAT
1 CATGCAATAA-AATATATAAT
* **
1455530 AAT-C-ATGCAA-ATA-AA-
1 CATGCAATAAAATATATAAT
*
1455545 CATGCAATTAAATATATAAT
1 CATGCAATAAAATATATAAT
*
1455565 CATGCAACTAAAAATATATAAAC
1 CATGCAA-T-AAAATATAT-AAT
1455588 CATGC-----AA-ATA-AAT
1 CATGCAATAAAATATATAAT
1455601 -ATGCAAT-AAATATATAAT
1 CATGCAATAAAATATATAAT
*
1455619 CATGCAAATAGTAATATATTAAT
1 CATGC-AATA-AAATATA-TAAT
*
1455642 CATGC-----GA-ATA-AA-
1 CATGCAATAAAATATATAAT
* *
1455654 CATGAAATTAAATATATAAT
1 CATGCAATAAAATATATAAT
*
1455674 CATGCAACTAATAATACATAAAT
1 CATGCAA-TAA-AATATAT-AAT
1455697 CATGCAAATAATAATATATAAAT
1 CATGC-AATAA-AATATAT-AAT
1455720 CATGCAAT
1 CATGCAAT
1455728 CATGTAAATA
Statistics
Matches: 167, Mismatches: 18, Indels: 64
0.67 0.07 0.26
Matches are distributed among these distances:
12 8 0.05
13 4 0.02
15 8 0.05
16 10 0.06
17 10 0.06
18 11 0.07
19 9 0.05
20 31 0.19
21 8 0.05
22 23 0.14
23 43 0.26
24 2 0.01
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (20 bp):
CATGCAATAAAATATATAAT
Found at i:1455617 original size:109 final size:110
Alignment explanation
Indices: 1455491--1455707 Score: 348
Period size: 109 Copynumber: 2.0 Consensus size: 110
1455481 ATAATTAGAC
*
1455491 ATGCAATTAAATATATAATCATGC-AATAATAATATTAATAATCATGCAAATAAACATGCAATTA
1 ATGCAATTAAATATATAATCATGCAAATAATAATA-TAATAATCATGCAAATAAACATGAAATTA
*
1455555 AATATATAATCATGCAACTAAAAATATATAAACCATGCAAATAAAT
65 AATATATAATCATGCAACTAAAAATACATAAACCATGCAAATAAAT
* * *
1455601 ATGCAA-TAAATATATAATCATGCAAATAGTAATATATTAATCATGCGAATAAACATGAAATTAA
1 ATGCAATTAAATATATAATCATGCAAATAATAATATAATAATCATGCAAATAAACATGAAATTAA
* *
1455665 ATATATAATCATGCAACTAATAATACATAAATCATGCAAATAA
66 ATATATAATCATGCAACTAAAAATACATAAACCATGCAAATAA
1455708 TAATATATAA
Statistics
Matches: 99, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
109 84 0.85
110 15 0.15
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (110 bp):
ATGCAATTAAATATATAATCATGCAAATAATAATATAATAATCATGCAAATAAACATGAAATTAA
ATATATAATCATGCAACTAAAAATACATAAACCATGCAAATAAAT
Found at i:1455729 original size:109 final size:108
Alignment explanation
Indices: 1455498--1455743 Score: 327
Period size: 109 Copynumber: 2.3 Consensus size: 108
1455488 GACATGCAAT
* *
1455498 TAAATATATAATCATGC-AATAATAATATTAATAATCATGCAAATAAACATGCAATTAAATATAT
1 TAAATATACAATCATGCAAATAATAATATTAATAATCATGCAAATAAACATGAAATTAAATATAT
*
1455562 AATCATGCAACTAAAAATATATAAACCATGCAAATAAATATGCAA
66 AATCATGCAACTAAAAATACATAAACCATGCAAATAAATAT--AA
* * * *
1455607 TAAATATATAATCATGCAAATAGTAATA-TATTAATCATGCGAATAAACATGAAATTAAATATAT
1 TAAATATACAATCATGCAAATAATAATATTAATAATCATGCAAATAAACATGAAATTAAATATAT
* *
1455671 AATCATGCAACTAATAATACATAAATCATGCAAAT-AATAATATA
66 AATCATGCAACTAAAAATACATAAACCATGCAAATAAAT-ATA-A
* *
1455715 TAAATCATGCAATCATGTAAATAATAATA
1 TAAAT-ATACAATCATGCAAATAATAATA
1455744 ATATAGAAAC
Statistics
Matches: 122, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
107 1 0.01
108 9 0.07
109 103 0.84
110 9 0.07
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (108 bp):
TAAATATACAATCATGCAAATAATAATATTAATAATCATGCAAATAAACATGAAATTAAATATAT
AATCATGCAACTAAAAATACATAAACCATGCAAATAAATATAA
Found at i:1455772 original size:109 final size:107
Alignment explanation
Indices: 1455498--1455781 Score: 296
Period size: 109 Copynumber: 2.6 Consensus size: 107
1455488 GACATGCAAT
* *
1455498 TAAATATATAATCATGC-AATAATAATAT-TAATAATCATGCAAATAAACATG-CAATTAAATAT
1 TAAATATACAATCATGCAAATAATAATATAT-A-AACCATGC-AATAAACATGACAATTAAATAT
*
1455560 ATAATCATGCAACTAAAAATATATAAACCATGCAAATAAATATGCAA
63 ATAATCATGCAACTAAAAATACATAAACCATGCAAATAAATAT--AA
* * * *
1455607 TAAATATATAATCATGCAAATAGTAATATATTAATCATGCGAATAAACATGA-AATTAAATATAT
1 TAAATATACAATCATGCAAATAATAATATATAAACCATGC-AATAAACATGACAATTAAATATAT
* *
1455671 AATCATGCAACTAATAATACATAAATCATGCAAAT-AATAATATA
65 AATCATGCAACTAAAAATACATAAACCATGCAAATAAAT-ATA-A
* * *
1455715 TAAATCATGCAATCATGTAAATAATAATAATATAGAAACCATGC-A-AAATAT-ACAATTAAATA
1 TAAAT-ATACAATCATGCAAATAATAAT-ATAT--AAACCATGCAATAAACATGACAATTAAATA
1455777 TATAA
62 TATAA
1455782 AAGTTATGCA
Statistics
Matches: 152, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
107 1 0.01
108 10 0.07
109 118 0.78
110 15 0.10
111 1 0.01
112 7 0.05
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (107 bp):
TAAATATACAATCATGCAAATAATAATATATAAACCATGCAATAAACATGACAATTAAATATATA
ATCATGCAACTAAAAATACATAAACCATGCAAATAAATATAA
Found at i:1456355 original size:12 final size:11
Alignment explanation
Indices: 1456317--1456363 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
1456307 TTTGACTCTT
1456317 ATAAATAAA-AA
1 ATAAA-AAATAA
1456328 ATAAAAAATAA
1 ATAAAAAATAA
*
1456339 ATAAAAATTAA
1 ATAAAAAATAA
1456350 ACTAAAAAAATAA
1 A-T-AAAAAATAA
1456363 A
1 A
1456364 ATATAAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 3 0.10
11 18 0.58
12 1 0.03
13 9 0.29
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAAAATAA
Found at i:1456381 original size:31 final size:31
Alignment explanation
Indices: 1456323--1456381 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1456313 TCTTATAAAT
*
1456323 AAAAAATAAAAAATAAATAAAAATTAAACTA
1 AAAAAATAAAAAATAAACAAAAATTAAACTA
* * *
1456354 AAAAAATAAAATATAAACATAATTTAAA
1 AAAAAATAAAAAATAAACAAAAATTAAA
1456382 GCTTAATCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (31 bp):
AAAAAATAAAAAATAAACAAAAATTAAACTA
Found at i:1459074 original size:2 final size:2
Alignment explanation
Indices: 1459067--1459096 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1459057 CAATTTAACA
1459067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1459097 TGCAGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1461902 original size:6 final size:5
Alignment explanation
Indices: 1461865--1461929 Score: 62
Period size: 5 Copynumber: 12.4 Consensus size: 5
1461855 ATCACAAACA
*
1461865 ATTTT ATTTT ATTTT ATTTTCT ATTTT GATTTT A-ATT -TTTT ATTTT
1 ATTTT ATTTT ATTTT A-TTT-T ATTTT -ATTTT ATTTT ATTTT ATTTT
1461911 ATTTT GATTTT ATTATT AT
1 ATTTT -ATTTT ATT-TT AT
1461930 GTATATATCT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
4 4 0.08
5 25 0.49
6 20 0.39
7 2 0.04
ACGTcount: A:0.22, C:0.02, G:0.03, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:1461913 original size:24 final size:24
Alignment explanation
Indices: 1461865--1461922 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1461855 ATCACAAACA
1461865 ATTTT-ATTTT-ATTTTATTTTCT
1 ATTTTGATTTTAATTTTATTTTCT
*
1461887 ATTTTGATTTTAATTTT-TTATTTT
1 ATTTTGATTTTAATTTTATT-TTCT
1461911 ATTTTGATTTTA
1 ATTTTGATTTTA
1461923 TTATTATGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 5 0.16
23 7 0.22
24 20 0.62
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (24 bp):
ATTTTGATTTTAATTTTATTTTCT
Found at i:1462336 original size:21 final size:20
Alignment explanation
Indices: 1462312--1462350 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1462302 ATATCAAAAT
1462312 AAAATCTTATCATATTATTAA
1 AAAATCTTATCA-ATTATTAA
* *
1462333 AAAATTTTATTAATTATT
1 AAAATCTTATCAATTATT
1462351 TCTTTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATCTTATCAATTATTAA
Found at i:1466813 original size:3 final size:3
Alignment explanation
Indices: 1466807--1466847 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1466797 ATATAATAAA
1466807 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1466848 AGAAATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1470948 original size:20 final size:20
Alignment explanation
Indices: 1470908--1470945 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1470898 TATAATATTG
*
1470908 ATCATGCAATAATATATAAT
1 ATCATGCAACAATATATAAT
1470928 ATCATGCAACAATA-ATAA
1 ATCATGCAACAATATATAA
1470946 ATAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (20 bp):
ATCATGCAACAATATATAAT
Found at i:1471020 original size:56 final size:52
Alignment explanation
Indices: 1470918--1471031 Score: 133
Period size: 56 Copynumber: 2.1 Consensus size: 52
1470908 ATCATGCAAT
* *
1470918 AATATA-TAATATCATGCAACAATAATAAATAAATAAATAACTATGTAAATA
1 AATATATTAATATCATACAACAATAATAAAAAAATAAATAACTATGTAAATA
* *
1470969 AATATATTAATAATCATACAATCACATAAATAAAAAAATTAATAA-TCATGTAATTA
1 AATATATTAAT-ATCATACAA-CA-AT-AATAAAAAAATAAATAACT-ATGTAAATA
1471025 AATATAT
1 AATATAT
1471032 AATCATGCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
51 6 0.11
52 4 0.08
53 8 0.15
54 2 0.04
55 3 0.06
56 30 0.57
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (52 bp):
AATATATTAATATCATACAACAATAATAAAAAAATAAATAACTATGTAAATA
Found at i:1471072 original size:21 final size:21
Alignment explanation
Indices: 1471032--1471074 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1471022 TTAAATATAT
*
1471032 AATCATGCAATTAACAATGTA
1 AATCATGCAATAAACAATGTA
1471053 AATCATGCAAATAAAC-ATGTA
1 AATCATGC-AATAAACAATGTA
1471074 A
1 A
1471075 TTAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCATGCAATAAACAATGTA
Found at i:1471078 original size:33 final size:33
Alignment explanation
Indices: 1471030--1471159 Score: 149
Period size: 33 Copynumber: 4.0 Consensus size: 33
1471020 AATTAAATAT
* * *
1471030 ATAATCATGCAATTAACA-ATGTAAATCATGCAA
1 ATAAACATGCAATTAA-ATATATAAACCATGCAA
*
1471063 ATAAACATGTAATTAAATATATAAACCATGCAA
1 ATAAACATGCAATTAAATATATAAACCATGCAA
* *
1471096 ATAAA-ATACAATTAAATATATAAACCATGTAA
1 ATAAACATGCAATTAAATATATAAACCATGCAA
* * *
1471128 ATAAATATACAATTAAATATAT-AATCATGCAA
1 ATAAACATGCAATTAAATATATAAACCATGCAA
1471160 TCACACAAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
32 38 0.44
33 48 0.56
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (33 bp):
ATAAACATGCAATTAAATATATAAACCATGCAA
Found at i:1471114 original size:32 final size:33
Alignment explanation
Indices: 1471051--1471159 Score: 150
Period size: 32 Copynumber: 3.4 Consensus size: 33
1471041 ATTAACAATG
* **
1471051 TAAATCATGCAAATAAACATGTAATTAAATATA
1 TAAACCATGCAAATAAACATACAATTAAATATA
1471084 TAAACCATGCAAATAAA-ATACAATTAAATATA
1 TAAACCATGCAAATAAACATACAATTAAATATA
* *
1471116 TAAACCATGTAAATAAATATACAATTAAATATA
1 TAAACCATGCAAATAAACATACAATTAAATATA
*
1471149 T-AATCATGCAA
1 TAAACCATGCAA
1471160 TCACACAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
32 37 0.54
33 32 0.46
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.28
Consensus pattern (33 bp):
TAAACCATGCAAATAAACATACAATTAAATATA
Found at i:1471226 original size:32 final size:31
Alignment explanation
Indices: 1471053--1471227 Score: 120
Period size: 32 Copynumber: 5.5 Consensus size: 31
1471043 TAACAATGTA
* **
1471053 AATCATGCAAATAAACATGTAATTAAATATAT
1 AATCATGCAATTAAACA-ACAATTAAATATAT
* *
1471085 AAACCATGCAAATAAA-ATACAATTAAATATAT
1 -AATCATGCAATTAAACA-ACAATTAAATATAT
* * * *
1471117 AAACCATGTAAATAAATATACAATTAAATATAT
1 -AATCATGCAATTAAACA-ACAATTAAATATAT
* * * *
1471150 AATCATGCAATCACACAAATAAATAAAT-TAAT
1 AATCATGCAATTAAAC-AACAATTAAATAT-AT
* *
1471182 AATCACGCAATTAGACAAGCAATTAAATATAT
1 AATCATGCAATTAAACAA-CAATTAAATATAT
*
1471214 AATCATGTAATTAA
1 AATCATGCAATTAA
1471228 TGATATTAAT
Statistics
Matches: 117, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
31 3 0.03
32 82 0.70
33 32 0.27
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (31 bp):
AATCATGCAATTAAACAACAATTAAATATAT
Found at i:1471277 original size:20 final size:19
Alignment explanation
Indices: 1471254--1471325 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 19
1471244 ACAAATAAAC
1471254 ATGCAACTAAATATATAAGT
1 ATGCAACTAAATATATAA-T
* *
1471274 ATGCAACAAAAATATATAAACC
1 ATGCAAC-TAAATATAT-AA-T
*
1471296 ATGCAATTAAATATATAAT
1 ATGCAACTAAATATATAAT
1471315 CATGCAACTAA
1 -ATGCAACTAA
1471326 TAATACATAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 18 0.43
21 16 0.38
22 8 0.19
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (19 bp):
ATGCAACTAAATATATAAT
Found at i:1471288 original size:21 final size:20
Alignment explanation
Indices: 1471254--1471292 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1471244 ACAAATAAAC
*
1471254 ATGCAACTAAATATATAAGT
1 ATGCAACAAAATATATAAGT
1471274 ATGCAACAAAAATATATAA
1 ATGCAAC-AAAATATATAA
1471293 ACCATGCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (20 bp):
ATGCAACAAAATATATAAGT
Found at i:1471307 original size:42 final size:42
Alignment explanation
Indices: 1471248--1471358 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 42
1471238 AATCATACAA
* *
1471248 ATAAACATGCAACTAAATATATAAGT-ATGCAAC-AAAAATAT
1 ATAAACATGCAATTAAATATATAA-TCATGCAACTAAAAATAC
*
1471289 ATAAACCATGCAATTAAATATATAATCATGCAACTAATAATAC
1 ATAAA-CATGCAATTAAATATATAATCATGCAACTAAAAATAC
*
1471332 ATAAATCATGCAAATAATAATATATAA
1 ATAAA-CATGC-AATTA-AATATATAA
1471359 ATCAGACAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
41 6 0.10
42 25 0.42
43 16 0.27
44 4 0.07
45 9 0.15
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (42 bp):
ATAAACATGCAATTAAATATATAATCATGCAACTAAAAATAC
Found at i:1471342 original size:23 final size:22
Alignment explanation
Indices: 1471248--1471362 Score: 123
Period size: 23 Copynumber: 5.4 Consensus size: 22
1471238 AATCATACAA
1471248 ATAAA-CATGCAACT-AAATAT
1 ATAAATCATGCAACTAAAATAT
* *
1471268 ATAAGT-ATGCAACAAAAATAT
1 ATAAATCATGCAACTAAAATAT
* *
1471289 ATAAACCATGCAA-TTAAATAT
1 ATAAATCATGCAACTAAAATAT
*
1471310 AT-AATCATGCAACTAATAATAC
1 ATAAATCATGCAACTAA-AATAT
*
1471332 ATAAATCATGCAAATAATAATAT
1 ATAAATCATGCAACTAA-AATAT
1471355 ATAAATCA
1 ATAAATCA
1471363 GACAATCATG
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
20 20 0.26
21 20 0.26
22 12 0.15
23 26 0.33
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (22 bp):
ATAAATCATGCAACTAAAATAT
Found at i:1471349 original size:20 final size:20
Alignment explanation
Indices: 1471248--1471355 Score: 69
Period size: 20 Copynumber: 5.2 Consensus size: 20
1471238 AATCATACAA
*
1471248 ATAAA-CATGCAACTAAATAT
1 ATAAATCATGCAAAT-AATAT
* *
1471268 ATAAGT-ATGCAACAAAAATAT
1 ATAAATCATGC-A-AATAATAT
* *
1471289 ATAAACCATGCAATTAA-AT
1 ATAAATCATGCAAATAATAT
*
1471308 ATATAATCATGCAACTAATAATAC
1 ATA-AATCATGC-A--AATAATAT
1471332 ATAAATCATGCAAATAATAAT
1 ATAAATCATGCAAATAAT-AT
1471353 ATA
1 ATA
1471356 TAAATCAGAC
Statistics
Matches: 67, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
19 5 0.07
20 24 0.36
21 16 0.24
22 6 0.09
23 12 0.18
24 4 0.06
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.27
Consensus pattern (20 bp):
ATAAATCATGCAAATAATAT
Found at i:1471981 original size:13 final size:13
Alignment explanation
Indices: 1471951--1471984 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1471941 AATAAAAAAA
1471951 TAAAAAATTAAAC
1 TAAAAAATTAAAC
*
1471964 -CAAAAATTAAAC
1 TAAAAAATTAAAC
1471976 TAAAAAATT
1 TAAAAAATT
1471985 TAAATACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAAATTAAAC
Found at i:1472362 original size:37 final size:37
Alignment explanation
Indices: 1472316--1472510 Score: 227
Period size: 37 Copynumber: 5.3 Consensus size: 37
1472306 CTCTATCGAA
* *
1472316 GCTTAAAC-TTGAGAAAATAAAGTA-TTCCTCCACCAAG
1 GCTTCAACTTTGA-AAAATAAAGAACTT-CTCCACCAAG
*
1472353 GCTTCAACTTTGAAAAATAAAGAACTTCTTCACCAAG
1 GCTTCAACTTTGAAAAATAAAGAACTTCTCCACCAAG
* * * *
1472390 GTTTCAAC-TTGAAAAATAAAGAACTCCTTCACCAAA
1 GCTTCAACTTTGAAAAATAAAGAACTTCTCCACCAAG
*
1472426 GCTTCAACTTTGAAAAATAAAGTACTTCTCCACCAAG
1 GCTTCAACTTTGAAAAATAAAGAACTTCTCCACCAAG
* * *
1472463 GCTTCAACTTTGAAAAAATAAAAAAC-TCATCCTCCGAG
1 GCTTCAACTTTG-AAAAATAAAGAACTTC-TCCACCAAG
1472501 GCTTCAACTT
1 GCTTCAACTT
1472511 AGAACTTTTG
Statistics
Matches: 138, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
36 33 0.24
37 71 0.51
38 34 0.25
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (37 bp):
GCTTCAACTTTGAAAAATAAAGAACTTCTCCACCAAG
Found at i:1472423 original size:73 final size:73
Alignment explanation
Indices: 1472316--1472510 Score: 255
Period size: 73 Copynumber: 2.6 Consensus size: 73
1472306 CTCTATCGAA
* * *
1472316 GCTTAAACTTGAGAAAATAAAGTATTCCTCCACCAAGGCTTCAACTTTGAAAAATAAAGAACTTC
1 GCTTCAACTTGA-AAAATAAAGAACTCCTCCACCAAGGCTTCAACTTTGAAAAATAAAGAACTTC
*
1472381 TTCACCAAG
65 TCCACCAAG
* * * *
1472390 GTTTCAACTTGAAAAATAAAGAACTCCTTCACCAAAGCTTCAACTTTGAAAAATAAAGTACTTCT
1 GCTTCAACTTGAAAAATAAAGAACTCCTCCACCAAGGCTTCAACTTTGAAAAATAAAGAACTTCT
1472455 CCACCAAG
66 CCACCAAG
* * * *
1472463 GCTTCAACTTTGAAAAAATAAAAAACTCATCCTCCGAGGCTTCAACTT
1 GCTTCAAC-TTG-AAAAATAAAGAACTCCTCCACCAAGGCTTCAACTT
1472511 AGAACTTTTG
Statistics
Matches: 104, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
73 62 0.60
74 13 0.12
75 29 0.28
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (73 bp):
GCTTCAACTTGAAAAATAAAGAACTCCTCCACCAAGGCTTCAACTTTGAAAAATAAAGAACTTCT
CCACCAAG
Found at i:1472568 original size:42 final size:42
Alignment explanation
Indices: 1472517--1472616 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
1472507 ACTTAGAACT
1472517 TTTGAAAAATAAAATGCTACCCCACAA-CTGA-GACTTTGAAAC
1 TTTGAAAAATAAAATGCTACCCCACAATC-GAGGA-TTTGAAAC
* *
1472559 TTTGAAAAATAAAATGCTCCCCCATAATCGAGGATTTGAAAC
1 TTTGAAAAATAAAATGCTACCCCACAATCGAGGATTTGAAAC
1472601 TTTGAAAAAATAAAAT
1 TTTG-AAAAATAAAAT
1472617 AATATCATTC
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
42 39 0.74
43 14 0.26
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (42 bp):
TTTGAAAAATAAAATGCTACCCCACAATCGAGGATTTGAAAC
Found at i:1472806 original size:13 final size:13
Alignment explanation
Indices: 1472788--1472812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1472778 TTCCAAACAT
1472788 ATGCAATGAATGC
1 ATGCAATGAATGC
1472801 ATGCAATGAATG
1 ATGCAATGAATG
1472813 AAAAGATTTT
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:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATGCAATGAATGC
Found at i:1482327 original size:18 final size:19
Alignment explanation
Indices: 1482285--1482331 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1482275 GTTGATTATC
1482285 ATGC-AATA-ATAACAATA
1 ATGCAAATATATAACAATA
* *
1482302 ATGTAAATATATAAC-ATT
1 ATGCAAATATATAACAATA
1482320 ATGCAAATATAT
1 ATGCAAATATAT
1482332 TAATTATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 17 0.68
19 5 0.20
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (19 bp):
ATGCAAATATATAACAATA
Found at i:1482391 original size:20 final size:20
Alignment explanation
Indices: 1482320--1482393 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
1482310 ATATAACATT
* * *
1482320 ATGCAAATATATTAATTATC
1 ATGCAAATATATAAAATACC
* *
1482340 ATAC-AATAATATAAAATGCC
1 ATGCAAAT-ATATAAAATACC
1482360 ATGCAACA-ATATAAAATACC
1 ATGCAA-ATATATAAAATACC
1482380 ATGCAAATATATAA
1 ATGCAAATATATAA
1482394 TCATATTAGC
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.09
20 37 0.86
21 1 0.02
22 1 0.02
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (20 bp):
ATGCAAATATATAAAATACC
Found at i:1482687 original size:33 final size:32
Alignment explanation
Indices: 1482650--1482722 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 32
1482640 ACAACGTAAG
*
1482650 TCATGCAAATAAACATGCAATTAAATATATAAA
1 TCATGCAAATAAACATACAATTAAATATAT-AA
* *
1482683 TCATGTAAATAAATATACAATTAAATATATAA
1 TCATGCAAATAAACATACAATTAAATATATAA
1482715 TCATGCAA
1 TCATGCAA
1482723 TCACATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 9 0.25
33 27 0.75
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.30
Consensus pattern (32 bp):
TCATGCAAATAAACATACAATTAAATATATAA
Found at i:1482695 original size:21 final size:20
Alignment explanation
Indices: 1482658--1482699 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1482648 AGTCATGCAA
*
1482658 ATAAACATGCAATTAAATAT
1 ATAAACATGCAAATAAATAT
*
1482678 ATAAATCATGTAAATAAATAT
1 ATAAA-CATGCAAATAAATAT
1482699 A
1 A
1482700 CAATTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (20 bp):
ATAAACATGCAAATAAATAT
Found at i:1482785 original size:20 final size:20
Alignment explanation
Indices: 1482760--1482912 Score: 75
Period size: 20 Copynumber: 7.6 Consensus size: 20
1482750 TATAGTTAGA
1482760 CATGCAAATAAAAATATAAT
1 CATGCAAATAAAAATATAAT
*
1482780 CATGC-AATAATAATATTAATAAC
1 CATGCAAATAA-AA-A-T-ATAAT
* *
1482803 CATGCAATTAAATATATAAT
1 CATGCAAATAAAAATATAAT
* *
1482823 CATGTAACTAAAAATAT-AT
1 CATGCAAATAAAAATATAAT
** * **
1482842 -AAAC-TATGCAAATA-AAT
1 CATGCAAATAAAAATATAAT
* * *
1482859 -AGGCAATTAAATATATAAT
1 CATGCAAATAAAAATATAAT
*
1482878 CATGCAAATAGTAATATATTAAT
1 CATGCAAATA--AAAATA-TAAT
1482901 CATGCAAATAAA
1 CATGCAAATAAA
1482913 CATGCAATTA
Statistics
Matches: 98, Mismatches: 23, Indels: 23
0.68 0.16 0.16
Matches are distributed among these distances:
17 10 0.10
18 6 0.06
19 10 0.10
20 32 0.33
21 4 0.04
22 8 0.08
23 24 0.24
24 4 0.04
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (20 bp):
CATGCAAATAAAAATATAAT
Found at i:1482822 original size:23 final size:23
Alignment explanation
Indices: 1482760--1482822 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
1482750 TATAGTTAGA
* *
1482760 CATGCAAATAAA-A-AT-ATAAT
1 CATGCAATTAAATATATAATAAC
*
1482780 CATGCAATAATAATAT-TAATAAC
1 CATGCAATTA-AATATATAATAAC
1482803 CATGCAATTAAATATATAAT
1 CATGCAATTAAATATATAAT
1482823 CATGTAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 8 0.24
21 2 0.06
22 7 0.21
23 17 0.50
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (23 bp):
CATGCAATTAAATATATAATAAC
Found at i:1482858 original size:43 final size:43
Alignment explanation
Indices: 1482760--1482859 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 43
1482750 TATAGTTAGA
* *
1482760 CATGCAAATAAAAATATAATCATGCAATAATAATATTAATAAC
1 CATGCAAATAAATATATAATCATGCAATAAAAATATTAATAAC
* *
1482803 CATGCAATTAAATATATAATCATGTAACTAAAAATA-T-ATAAAC
1 CATGCAAATAAATATATAATCATGCAA-TAAAAATATTAAT-AAC
*
1482846 TATGCAAATAAATA
1 CATGCAAATAAATA
1482860 GGCAATTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 2 0.04
43 40 0.82
44 7 0.14
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (43 bp):
CATGCAAATAAATATATAATCATGCAATAAAAATATTAATAAC
Found at i:1482896 original size:22 final size:23
Alignment explanation
Indices: 1482868--1482910 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1482858 TAGGCAATTA
1482868 AATATA-TAATCATGCAAATAGT
1 AATATATTAATCATGCAAATAGT
1482890 AATATATTAATCATGCAAATA
1 AATATATTAATCATGCAAATA
1482911 AACATGCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (23 bp):
AATATATTAATCATGCAAATAGT
Found at i:1482967 original size:23 final size:23
Alignment explanation
Indices: 1482941--1482984 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1482931 TTGTGCAACA
*
1482941 AATAATACATAAATCATGCAAAT
1 AATAATACATAAATAATGCAAAT
*
1482964 AATAATATATAAATAATGCAA
1 AATAATACATAAATAATGCAA
1482985 TCATGTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (23 bp):
AATAATACATAAATAATGCAAAT
Found at i:1482978 original size:34 final size:31
Alignment explanation
Indices: 1482944--1483007 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1482934 TGCAACAAAT
1482944 AATACATA-AATCATGCAAATAATAATATATA
1 AATA-ATACAATCATGCAAATAATAATATATA
* *
1482975 AATAATGCAATCATGTAAATAATAATATATA
1 AATAATACAATCATGCAAATAATAATATATA
1483006 AA
1 AA
1483008 CCATGCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.30
Consensus pattern (31 bp):
AATAATACAATCATGCAAATAATAATATATA
Found at i:1482979 original size:14 final size:14
Alignment explanation
Indices: 1482960--1483007 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
1482950 TAAATCATGC
1482960 AAATAATAATATAT
1 AAATAATAATATAT
*
1482974 AAATAATGCAATCATGT
1 AAATAAT--AAT-ATAT
1482991 AAATAATAATATAT
1 AAATAATAATATAT
1483005 AAA
1 AAA
1483008 CCATGCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 13 0.45
15 3 0.10
16 3 0.10
17 10 0.34
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (14 bp):
AAATAATAATATAT
Found at i:1482995 original size:17 final size:15
Alignment explanation
Indices: 1482952--1483000 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 15
1482942 ATAATACATA
*
1482952 AATCATGCAAATAAT
1 AATCATGTAAATAAT
*
1482967 AAT-ATATAAATAAT
1 AATCATGTAAATAAT
1482981 GCAATCATGTAAATAAT
1 --AATCATGTAAATAAT
1482998 AAT
1 AAT
1483001 ATATAAACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 3 0.11
17 10 0.36
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (15 bp):
AATCATGTAAATAAT
Found at i:1483014 original size:31 final size:31
Alignment explanation
Indices: 1482952--1483015 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1482942 ATAATACATA
*
1482952 AATCATGCAAATAATAATATATAAATAATGC
1 AATCATGCAAATAATAATATATAAACAATGC
* *
1482983 AATCATGTAAATAATAATATATAAACCATGC
1 AATCATGCAAATAATAATATATAAACAATGC
1483014 AA
1 AA
1483016 AATATGCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (31 bp):
AATCATGCAAATAATAATATATAAACAATGC
Found at i:1491174 original size:2 final size:2
Alignment explanation
Indices: 1491167--1491195 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1491157 GCCATGATAA
1491167 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1491196 GGGCCAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1500588 original size:20 final size:20
Alignment explanation
Indices: 1500545--1500618 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 20
1500535 TATTTGCAAG
* * * *
1500545 TATTATAATTTAAAATTTAT
1 TATTAAAATTAAAAAATTAA
1500565 TATTAAAATTAAAAAATTAA
1 TATTAAAATTAAAAAATTAA
** *
1500585 TATT-TTATTAATAAATT-A
1 TATTAAAATTAAAAAATTAA
1500603 T-TTAAAATTTAAAAAA
1 TATTAAAA-TTAAAAAA
1500619 AATTTATATA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
17 2 0.05
18 3 0.07
19 17 0.40
20 20 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTAAAATTAAAAAATTAA
Found at i:1500640 original size:30 final size:35
Alignment explanation
Indices: 1500563--1500645 Score: 97
Period size: 37 Copynumber: 2.5 Consensus size: 35
1500553 TTTAAAATTT
*
1500563 ATTATTAAAATTAAAAAATTAATATTTTATTAATAA
1 ATTATTAAAATTTAAAAA-TAATATTTTATTAATAA
1500599 ATTATTTAAAATTTAAAAA-AA-A-TTTA-T-ATAA
1 ATTA-TTAAAATTTAAAAATAATATTTTATTAATAA
1500630 ATTATTAAAA-TTAAAA
1 ATTATTAAAATTTAAAA
1500646 TTTTAATCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
29 6 0.13
30 6 0.13
31 8 0.18
32 1 0.02
33 4 0.09
34 1 0.02
35 2 0.04
36 4 0.09
37 13 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
ATTATTAAAATTTAAAAATAATATTTTATTAATAA
Found at i:1503635 original size:2 final size:2
Alignment explanation
Indices: 1503628--1503663 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1503618 TTCATTACTT
*
1503628 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1503664 CATGATGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1509228 original size:16 final size:16
Alignment explanation
Indices: 1509207--1509241 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1509197 TCAATTAATT
1509207 TTATAATAAAAAATAA
1 TTATAATAAAAAATAA
**
1509223 TTATAATAGTAAATAA
1 TTATAATAAAAAATAA
1509239 TTA
1 TTA
1509242 AAATTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
TTATAATAAAAAATAA
Found at i:1512614 original size:6 final size:6
Alignment explanation
Indices: 1512603--1512655 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
1512593 AATATTATTT
* * *
1512603 TAAATA TAAATA TAAAT- TAAATA TATATA AAAATA TATATAA TTAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAAT-A -TAAATA
1512652 TAAA
1 TAAA
1512656 ATTAAAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 5 0.13
6 27 0.71
7 2 0.05
8 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAATA
Found at i:1512658 original size:12 final size:13
Alignment explanation
Indices: 1512612--1512671 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 13
1512602 TTAAATATAA
1512612 ATATAAATTAAAT
1 ATATAAATTAAAT
1512625 ATATATAA--AAAT
1 ATATA-AATTAAAT
1512637 ATATATAATTAAAT
1 ATATA-AATTAAAT
*
1512651 ATA-AAATTAAAA
1 ATATAAATTAAAT
*
1512663 AAATAAATT
1 ATATAAATT
1512672 TTTTATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 21 0.51
13 11 0.27
14 9 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATTAAAT
Found at i:1514835 original size:23 final size:23
Alignment explanation
Indices: 1514783--1514842 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
1514773 TTTATAAAAT
1514783 AAATAAA-TAAAATAAAATTCAA
1 AAATAAATTAAAATAAAATTCAA
** *
1514805 AAGGAAATTAACATAATAATT-AA
1 AAATAAATTAAAATAA-AATTCAA
1514828 AAATAAA-T-AAATAAA
1 AAATAAATTAAAATAAA
1514843 TAATAATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
20 1 0.03
21 5 0.17
22 6 0.20
23 14 0.47
24 4 0.13
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (23 bp):
AAATAAATTAAAATAAAATTCAA
Found at i:1515765 original size:3 final size:3
Alignment explanation
Indices: 1515757--1515785 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1515747 AAAAACAAAC
1515757 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1515786 TGGGCCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1516227 original size:66 final size:66
Alignment explanation
Indices: 1516157--1516287 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 66
1516147 ATTCGAGGTT
** * * * *
1516157 AAAAATGAGTGACC-GAGATCGAACCATG-AGTCAGAAAAATAAAATGATTTGGACTGAGCCAAG
1 AAAAATGAGTGACCAG-GAAAGAACAATGTA-TCAGAAAAATAAAATCATCTGGACCGAGCCAAG
1516220 ATA
64 ATA
*
1516223 AAAAATGAGTGACCAGGAAAGAACAATGTATCAGAAAAATAAAATCATCTGGACCGAGCCGAGAT
1 AAAAATGAGTGACCAGGAAAGAACAATGTATCAGAAAAATAAAATCATCTGGACCGAGCCAAGAT
1516288 TAGAAGCAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 54 0.96
67 2 0.04
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.17
Consensus pattern (66 bp):
AAAAATGAGTGACCAGGAAAGAACAATGTATCAGAAAAATAAAATCATCTGGACCGAGCCAAGAT
A
Found at i:1516454 original size:64 final size:62
Alignment explanation
Indices: 1516319--1516480 Score: 159
Period size: 65 Copynumber: 2.5 Consensus size: 62
1516309 GAACCGCGAG
* * * * *
1516319 TCAAAAAATAAATGATTTGGATTGAATCAAGATTGAAGATGAATGTCAAGATTGAACCACGAA
1 TCAAAAAATAAATGATCTAGATTGAACCAAGATCGAAGATGAATGTAAAGATTGAACCAC-AA
* *
1516382 TTAGAAAAATAAATGATGTAGATTGAACCAAGATCGAAGAT-AA-GTAAAGGGGATTGAACCGTA
1 TCA-AAAAATAAATGATCTAGATTGAACCAAGATCGAAGATGAATGTAAA---GATTGAACC--A
1516445 C-A
60 CAA
*
1516447 TCAAAAAAATAAATGATCCAGATTGAACCAAGAT
1 TC-AAAAAATAAATGATCTAGATTGAACCAAGAT
1516481 TAAACTACAG
Statistics
Matches: 83, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
62 4 0.05
63 4 0.05
64 33 0.40
65 39 0.47
66 1 0.01
67 2 0.02
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (62 bp):
TCAAAAAATAAATGATCTAGATTGAACCAAGATCGAAGATGAATGTAAAGATTGAACCACAA
Found at i:1516662 original size:74 final size:74
Alignment explanation
Indices: 1516578--1516741 Score: 204
Period size: 74 Copynumber: 2.2 Consensus size: 74
1516568 AAGTTGAAAG
* * * * * * *
1516578 ATTTTAAGTTTCGCAAAAAATTCACAAAGATTTCAAAATTCGCAAAAAGTCAGGATTCATAAATG
1 ATTTCAAGTTTCACAAAAAATTCACAAAAATTTCAAAATTCACAAAAAGTCAAGATTCACAAAAG
*
1516643 TTTGCAAGA
66 TTTACAAGA
* * *
1516652 ATTTCAAGTTTTACAAAAAATTCACAAAAATTTTAAAATTCACAAAAGGTCAAGATTCACAAAAG
1 ATTTCAAGTTTCACAAAAAATTCACAAAAATTTCAAAATTCACAAAAAGTCAAGATTCACAAAAG
1516717 TTTACAAGA
66 TTTACAAGA
*
1516726 A-TTCTAATTTTCACAA
1 ATTTC-AAGTTTCACAA
1516742 TAGTTTCAAG
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
73 3 0.04
74 73 0.96
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (74 bp):
ATTTCAAGTTTCACAAAAAATTCACAAAAATTTCAAAATTCACAAAAAGTCAAGATTCACAAAAG
TTTACAAGA
Found at i:1516895 original size:34 final size:34
Alignment explanation
Indices: 1516829--1516895 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
1516819 TAAAAACTAT
* * * * *
1516829 ATATTCGTAAGAGTTTTAGGTTTGTAAGAATTTC
1 ATATTCGGAAAAGTTTCAAGTTCGTAAGAATTTC
*
1516863 ATATTCGGAAAAGTTTCAAGTTCGTAATAATTT
1 ATATTCGGAAAAGTTTCAAGTTCGTAAGAATTT
1516896 AAGGTTCATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (34 bp):
ATATTCGGAAAAGTTTCAAGTTCGTAAGAATTTC
Found at i:1517170 original size:43 final size:43
Alignment explanation
Indices: 1517087--1517181 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 43
1517077 GGGCACACCT
1517087 CCAAAATTCAAAGATTCTTATTCGAAAATTTTTTAAATTCACAC
1 CCAAAATTCAAAGATTCTTATTCGAAAA-TTTTTAAATTCACAC
* *
1517131 CCAAAAGTT-AAAGATT-TTATTTGAAAA-TTTTAAGGATTCACAT
1 CCAAAA-TTCAAAGATTCTTATTCGAAAATTTTTAA--ATTCACAC
1517174 CCAAAATT
1 CCAAAATT
1517182 TATATTTGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
41 6 0.13
42 2 0.04
43 23 0.50
44 13 0.28
45 2 0.04
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (43 bp):
CCAAAATTCAAAGATTCTTATTCGAAAATTTTTAAATTCACAC
Found at i:1517193 original size:36 final size:35
Alignment explanation
Indices: 1517144--1517215 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
1517134 AAAGTTAAAG
*
1517144 ATTTTATTTGAAAATTTTA-AGGATTCACATCCAAA
1 ATTTTATTTGAAAATTTTATA-AATTCACATCCAAA
*
1517179 ATTTATATTTGAAAATTTTATAAATTCACATTCAAA
1 ATTT-TATTTGAAAATTTTATAAATTCACATCCAAA
1517215 A
1 A
1517216 GTTAAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 4 0.12
36 28 0.85
37 1 0.03
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.42
Consensus pattern (35 bp):
ATTTTATTTGAAAATTTTATAAATTCACATCCAAA
Found at i:1518368 original size:35 final size:35
Alignment explanation
Indices: 1518318--1518387 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
1518308 AGTTTTCTTT
1518318 TTTTTCTCTTTTCTTTGTATTT-T-TTTTACACATC
1 TTTTTCTCTTTTCTTTGTATTTCTCTTTTAC-CATC
* *
1518352 TTTTTCTTTTTATCTTTTTATTTCTCTTTTACCATC
1 TTTTTCTCTTT-TCTTTGTATTTCTCTTTTACCATC
1518388 AATTTATTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 10 0.32
35 10 0.32
36 5 0.16
37 6 0.19
ACGTcount: A:0.11, C:0.19, G:0.01, T:0.69
Consensus pattern (35 bp):
TTTTTCTCTTTTCTTTGTATTTCTCTTTTACCATC
Found at i:1518379 original size:26 final size:25
Alignment explanation
Indices: 1518313--1518381 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 25
1518303 GTTTAAGTTT
1518313 TCTTTTTTTTCTC-TTTTCTTTGTA
1 TCTTTTTTTTCTCTTTTTCTTTGTA
* *
1518337 T-TTTTTTTACACATCTTTTTCTTTTTA
1 TCTTTTTTT--TC-TCTTTTTCTTTGTA
1518364 TCTTTTTATTTCTCTTTT
1 TCTTTTT-TTTCTCTTTT
1518382 ACCATCAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
23 7 0.19
24 1 0.03
25 1 0.03
26 8 0.22
27 12 0.33
28 5 0.14
29 2 0.06
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.74
Consensus pattern (25 bp):
TCTTTTTTTTCTCTTTTTCTTTGTA
Found at i:1522161 original size:33 final size:36
Alignment explanation
Indices: 1522095--1522162 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
1522085 TAAAATCTTT
1522095 CAATAATTTGATAAGATTTATTTTGATGCAGATTTTC
1 CAATAATTTGATAAGATTTATTTTGAT-CAGATTTTC
* *
1522132 CAATAATTTGGTGAGATTT-TTTTG-T-AGATTT
1 CAATAATTTGATAAGATTTATTTTGATCAGATTT
1522163 ATTTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 6 0.21
35 1 0.03
36 5 0.17
37 17 0.59
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (36 bp):
CAATAATTTGATAAGATTTATTTTGATCAGATTTTC
Found at i:1522468 original size:6 final size:6
Alignment explanation
Indices: 1522457--1522509 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
1522447 GAAGATCAAA
* * * * *
1522457 AATAGT AATAGT AATAGT AGTAGT AGTAAT AATAGT AATAAT AATAAT
1 AATAGT AATAGT AATAGT AATAGT AATAGT AATAGT AATAGT AATAGT
1522505 AATAG
1 AATAG
1522510 GTAAAATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (6 bp):
AATAGT
Found at i:1522483 original size:15 final size:15
Alignment explanation
Indices: 1522457--1522505 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1522447 GAAGATCAAA
1522457 AATAGTAATAGTAAT
1 AATAGTAATAGTAAT
* *
1522472 AGTAGTAGTAGTAAT
1 AATAGTAATAGTAAT
*
1522487 AATAGTAATAATAAT
1 AATAGTAATAGTAAT
1522502 AATA
1 AATA
1522506 ATAGGTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (15 bp):
AATAGTAATAGTAAT
Found at i:1522492 original size:9 final size:9
Alignment explanation
Indices: 1522468--1522509 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
1522458 ATAGTAATAG
*
1522468 TAATAGTAG
1 TAATAGTAA
*
1522477 TAGTAGTAA
1 TAATAGTAA
1522486 TAATAGTAA
1 TAATAGTAA
*
1522495 TAATAATAA
1 TAATAGTAA
1522504 TAATAG
1 TAATAG
1522510 GTAAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.33
Consensus pattern (9 bp):
TAATAGTAA
Found at i:1522559 original size:19 final size:19
Alignment explanation
Indices: 1522537--1522583 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
1522527 TTAAATAAAT
*
1522537 AAAATAAAT-AAAAAAAAA
1 AAAAAAAATGAAAAAAAAA
1522555 CAAAAAAAATGAAAAAAAAA
1 -AAAAAAAATGAAAAAAAAA
1522575 AAAAGAAAA
1 AAAA-AAAA
1522584 CCTACGATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.87, C:0.02, G:0.04, T:0.06
Consensus pattern (19 bp):
AAAAAAAATGAAAAAAAAA
Found at i:1522583 original size:23 final size:23
Alignment explanation
Indices: 1522537--1522583 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1522527 TTAAATAAAT
1522537 AAAATAAATAAAAAAAAACAAAA
1 AAAATAAATAAAAAAAAACAAAA
* *
1522560 AAAATGAAAAAAAAAAAAAGAAAA
1 AAAAT-AAATAAAAAAAAACAAAA
1522584 CCTACGATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.87, C:0.02, G:0.04, T:0.06
Consensus pattern (23 bp):
AAAATAAATAAAAAAAAACAAAA
Found at i:1523494 original size:3 final size:3
Alignment explanation
Indices: 1523448--1523481 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1523438 AAATAAACAA
1523448 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1523482 TATTACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1527277 original size:28 final size:28
Alignment explanation
Indices: 1527245--1527301 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1527235 TGACTTACAA
1527245 AGTCGGATAAGCATGGTCCACAGAAATC
1 AGTCGGATAAGCATGGTCCACAGAAATC
1527273 AGTCGGATAAGCATGGTCCACAGAAATC
1 AGTCGGATAAGCATGGTCCACAGAAATC
1527301 A
1 A
1527302 ATGACGATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.18
Consensus pattern (28 bp):
AGTCGGATAAGCATGGTCCACAGAAATC
Found at i:1528419 original size:2 final size:2
Alignment explanation
Indices: 1528412--1528437 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1528402 GAGTTAATTG
1528412 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1528438 GACAATGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1531031 original size:24 final size:24
Alignment explanation
Indices: 1531004--1531088 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
1530994 CAGGCAACAA
1531004 AGATCTACGATGTATAGGTGAAGG
1 AGATCTACGATGTATAGGTGAAGG
* *
1531028 AGATCTACG--GTACCTACGCGAAGG
1 AGATCTACGATGTA--TAGGTGAAGG
* ***
1531052 AGATCTATGATACCTAGGTGAAGG
1 AGATCTACGATGTATAGGTGAAGG
*
1531076 AGATCTATGATGT
1 AGATCTACGATGT
1531089 CGAACAGGAG
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
22 3 0.06
24 44 0.94
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (24 bp):
AGATCTACGATGTATAGGTGAAGG
Found at i:1533600 original size:2 final size:2
Alignment explanation
Indices: 1533595--1533629 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1533585 ATACACACAA
1533595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1533630 CACACAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1533858 original size:6 final size:6
Alignment explanation
Indices: 1533849--1533875 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1533839 GAATATCATG
1533849 TTGGGT TTGGGT TTGGGT TTGGGT TTG
1 TTGGGT TTGGGT TTGGGT TTGGGT TTG
1533876 ACTGTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TTGGGT
Found at i:1534901 original size:42 final size:42
Alignment explanation
Indices: 1534833--1534937 Score: 103
Period size: 42 Copynumber: 2.5 Consensus size: 42
1534823 TTATTATTAT
*
1534833 TTATTTAATTTTATAGTTTTAAATATTATA-TTAATAAAGTTA
1 TTATTTAATTTTATAGATTTAAATATTA-ACTTAATAAAGTTA
**
1534875 TTATTTAATATTT-TA-ATTTAAGATATTAACTTAATAAAAATA
1 TTATTTAAT-TTTATAGATTTAA-ATATTAACTTAATAAAGTTA
*
1534917 TTA--TAATTTTTATATATTTAA
1 TTATTTAA-TTTTATAGATTTAA
1534938 CTGTAATTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
40 6 0.11
41 9 0.17
42 36 0.67
43 3 0.06
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (42 bp):
TTATTTAATTTTATAGATTTAAATATTAACTTAATAAAGTTA
Found at i:1553790 original size:11 final size:12
Alignment explanation
Indices: 1553770--1553798 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1553760 TATAAGATTA
1553770 ATATTAGTATTT
1 ATATTAGTATTT
1553782 ATATT-GTATTT
1 ATATTAGTATTT
1553793 ATATTA
1 ATATTA
1553799 TTAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
ATATTAGTATTT
Done.