Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 1811518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:1338117 original size:110 final size:110
Alignment explanation
Indices: 1337801--1338245 Score: 676
Period size: 110 Copynumber: 4.0 Consensus size: 110
1337791 TTGAGGAGTA
* *
1337801 AAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCA
1 AAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCA
* *
1337866 CCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACT-G
65 CCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG
* * * *
1337911 AAAGGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAA
1 AAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCGTCCTGCTCTTTGAGGACTGAAAG
* *
1337976 ATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG
59 GTGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG
* *
1338028 AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCAC
1 AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCAC
1338093 CAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG
66 CAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG
* *
1338138 AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCAC
1 AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCAC
*
1338203 CAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
66 CAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACT
1338246 AAAAAGCGGA
Statistics
Matches: 308, Mismatches: 19, Indels: 16
0.90 0.06 0.05
Matches are distributed among these distances:
110 204 0.66
111 4 0.01
115 4 0.01
116 92 0.30
117 4 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (110 bp):
AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCAC
CAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG
Found at i:1339219 original size:1 final size:1
Alignment explanation
Indices: 1339213--1339275 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
1339203 CTTAAGCAGA
* * * * * **
1339213 TTTTTTTTTTCTTTTTCTTTGTTTTGTTTTTTTTTTTTGTTTTTTTTTTTGCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1339276 GAAGAGAAGG
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.05, G:0.06, T:0.89
Consensus pattern (1 bp):
T
Found at i:1339245 original size:18 final size:17
Alignment explanation
Indices: 1339216--1339275 Score: 77
Period size: 18 Copynumber: 3.5 Consensus size: 17
1339206 AAGCAGATTT
1339216 TTTTTTTCTTTTTCTTTG
1 TTTTTTT-TTTTTCTTTG
*
1339234 TTTTGTTTTTTTTTTTTG
1 TTTT-TTTTTTTTCTTTG
*
1339252 TTTTTTTTTTTGCTTT-
1 TTTTTTTTTTTTCTTTG
1339268 TTTTTTTT
1 TTTTTTTT
1339276 GAAGAGAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 8 0.21
17 10 0.26
18 17 0.45
19 3 0.08
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTTTTCTTTG
Found at i:1339252 original size:13 final size:13
Alignment explanation
Indices: 1339213--1339276 Score: 85
Period size: 13 Copynumber: 4.8 Consensus size: 13
1339203 CTTAAGCAGA
*
1339213 TTTTTTTTTTCTT
1 TTTTTTTTTTGTT
1339226 TTTCTTTGTTTTGTT
1 TTT-TTT-TTTTGTT
1339241 TTTTTTTTTTG-T
1 TTTTTTTTTTGTT
*
1339253 TTTTTTTTTTGCT
1 TTTTTTTTTTGTT
1339266 TTTTTTTTTTG
1 TTTTTTTTTTG
1339277 AAGAGAAGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
12 12 0.26
13 20 0.43
14 6 0.13
15 9 0.19
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTGTT
Found at i:1339262 original size:25 final size:26
Alignment explanation
Indices: 1339213--1339276 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
1339203 CTTAAGCAGA
1339213 TTTTTTTTTTCTT-TTTCTTTGTTTTG
1 TTTTTTTTTT-TTGTTTCTTTGTTTTG
*
1339239 TTTTTTTTTTTTGTTT-TTTTTTTTG
1 TTTTTTTTTTTTGTTTCTTTGTTTTG
*
1339264 CTTTTTTTTTTTG
1 TTTTTTTTTTTTG
1339277 AAGAGAAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 22 0.63
26 13 0.37
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.88
Consensus pattern (26 bp):
TTTTTTTTTTTTGTTTCTTTGTTTTG
Found at i:1351889 original size:28 final size:28
Alignment explanation
Indices: 1351833--1351909 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
1351823 GGAATAAAGC
* *
1351833 CGAGGTTGGAGTATCCCCTCA-GAAGTAA
1 CGAGGTTGGAGTATCCCC-GATGAAATAA
1351861 C-AGGGTTGGAGTATCCCCGATGAAATAA
1 CGA-GGTTGGAGTATCCCCGATGAAATAA
* *
1351889 CGAGGTTGGAGCATCCTCGAT
1 CGAGGTTGGAGTATCCCCGAT
1351910 TGTGAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
27 2 0.05
28 39 0.93
29 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (28 bp):
CGAGGTTGGAGTATCCCCGATGAAATAA
Found at i:1354389 original size:13 final size:13
Alignment explanation
Indices: 1354371--1354396 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1354361 ACAAAGATCC
1354371 ATGTATCGATACA
1 ATGTATCGATACA
1354384 ATGTATCGATACA
1 ATGTATCGATACA
1354397 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1354392 original size:33 final size:33
Alignment explanation
Indices: 1354350--1354416 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1354340 AAAATTTCCA
***
1354350 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1354383 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1354416 A
1 A
1354417 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1354460 original size:19 final size:18
Alignment explanation
Indices: 1354436--1354503 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1354426 CAGTAGCTAA
1354436 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1354455 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1354470 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1354487 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1354504 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1354476 original size:13 final size:13
Alignment explanation
Indices: 1354458--1354482 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1354448 ACAATACTTA
1354458 TGTATCGATACAT
1 TGTATCGATACAT
1354471 TGTATCGATACA
1 TGTATCGATACA
1354483 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1354480 original size:32 final size:32
Alignment explanation
Indices: 1354439--1354501 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1354429 TAGCTAATTA
*
1354439 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1354471 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1354502 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1354582 original size:20 final size:20
Alignment explanation
Indices: 1354539--1354640 Score: 152
Period size: 20 Copynumber: 5.0 Consensus size: 20
1354529 GTTGGGACCC
1354539 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGT-GAA
1354560 TGTATCGATACATTTGTGAA
1 TGTATCGATACATTTGTGAA
1354580 TGTATCGATACATTTGTGAA
1 TGTATCGATACATTTGTGAA
***
1354600 TGTATCGATACATTCTACAAA
1 TGTATCGATACATT-TGTGAA
1354621 TGTATCGATACATTTG-GAA
1 TGTATCGATACATTTGTGAA
1354640 T
1 T
1354641 TTTTTTTTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
19 3 0.04
20 38 0.51
21 34 0.45
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTGTGAA
Found at i:1354596 original size:41 final size:41
Alignment explanation
Indices: 1354539--1354640 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
1354529 GTTGGGACCC
***
1354539 TGTATCGATACATTTGTAGAATGTATCGATACATT-TGTGAA
1 TGTATCGATACATTTGT-GAATGTATCGATACATTCTACAAA
1354580 TGTATCGATACATTTGTGAATGTATCGATACATTCTACAAA
1 TGTATCGATACATTTGTGAATGTATCGATACATTCTACAAA
1354621 TGTATCGATACATTTG-GAAT
1 TGTATCGATACATTTGTGAAT
1354641 TTTTTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 21 0.37
41 36 0.63
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (41 bp):
TGTATCGATACATTTGTGAATGTATCGATACATTCTACAAA
Found at i:1356608 original size:10 final size:10
Alignment explanation
Indices: 1356590--1356646 Score: 82
Period size: 10 Copynumber: 5.9 Consensus size: 10
1356580 TCCTCCACAA
*
1356590 AAAAAAAAAC
1 AAAACAAAAC
1356600 AAAACAAAAC
1 AAAACAAAAC
1356610 AAAACAAAA-
1 AAAACAAAAC
1356619 AAAACAAAAC
1 AAAACAAAAC
*
1356629 AAAACAATAC
1 AAAACAAAAC
1356639 AAAA-AAAA
1 AAAACAAAA
1356647 GGGTCCGGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
9 12 0.28
10 31 0.72
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (10 bp):
AAAACAAAAC
Found at i:1356613 original size:19 final size:19
Alignment explanation
Indices: 1356586--1356635 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
1356576 GGCGTCCTCC
*
1356586 ACAAAA-AAAA-AAACAAA
1 ACAAAACAAAACAAAAAAA
1356603 ACAAAACAAAACAAAAAAA
1 ACAAAACAAAACAAAAAAA
1356622 ACAAAACAAAACAA
1 ACAAAACAAAACAA
1356636 TACAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 6 0.20
18 4 0.13
19 20 0.67
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (19 bp):
ACAAAACAAAACAAAAAAA
Found at i:1356623 original size:24 final size:24
Alignment explanation
Indices: 1356591--1356646 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
1356581 CCTCCACAAA
1356591 AAAAAAAACAAAACAAAACAAAAC
1 AAAAAAAACAAAACAAAACAAAAC
*
1356615 AAAAAAAACAAAACAAAACAATAC
1 AAAAAAAACAAAACAAAACAAAAC
1356639 AAAAAAAA
1 AAAAAAAA
1356647 GGGTCCGGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (24 bp):
AAAAAAAACAAAACAAAACAAAAC
Found at i:1358125 original size:29 final size:30
Alignment explanation
Indices: 1358086--1358262 Score: 195
Period size: 29 Copynumber: 6.0 Consensus size: 30
1358076 TCACCCTTCA
1358086 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* *
1358115 AAAGCCCACAAGTCAGTGGCATGTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CTCTTTTTC
1358146 AAAAGCCCACAAGTCAGTGGCAAC-C---TTC
1 -AAAGCCCACAAGTCAGTGGC-ACTCTTTTTC
* *
1358174 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
1358204 GAAGCCCACAAGTCGGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
1358233 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
1358263 TTTTGTAAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.02
27 20 0.16
28 3 0.02
29 44 0.35
30 28 0.22
31 7 0.06
32 20 0.16
33 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTTTC
Found at i:1358156 original size:32 final size:30
Alignment explanation
Indices: 1358082--1358376 Score: 185
Period size: 30 Copynumber: 9.7 Consensus size: 30
1358072 TTCCTCACCC
1358082 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
*
1358112 TTC-AAAGCCCACAAGTCAGTGGCATGTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA--TCTTT
* *
1358143 TTCAAAAGCCCACAAGTCAGTGGCAAC--C
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
* *
1358171 TTC-AAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TCTTT
* *
1358201 TTC-GAAGCCCACAAGTCGGTGGCATC-TT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
* * * *
1358229 TTCCAAAGTCCACAACTCCGTGGCACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TCTTT
** * * * *
1358260 TTCTTTTGTAAGCTCACAACT-ATATAGCACTCTTT
1 TTC----AAAAGCCCACAAGTCA-GTGGCA-TCTTT
** * * *
1358295 TTCTTTTTAAGCCCACAAGTTAGTGGCACCCTT
1 TTC---AAAAGCCCACAAGTCAGTGGCATCTTT
* * *
1358328 TTCAAAAGCCCACAAGTTAGTGGCAAC-CT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
1358357 TT-AAAAGCCCACAAGTCAGT
1 TTCAAAAGCCCACAAGTCAGT
1358377 AGCAACCTTT
Statistics
Matches: 216, Mismatches: 34, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
27 20 0.09
28 26 0.12
29 42 0.19
30 47 0.22
31 12 0.06
32 21 0.10
33 6 0.03
34 18 0.08
35 24 0.11
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCATCTTT
Found at i:1358262 original size:59 final size:59
Alignment explanation
Indices: 1358082--1358262 Score: 222
Period size: 59 Copynumber: 3.1 Consensus size: 59
1358072 TTCCTCACCC
* * *
1358082 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATGTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATC-TTTTCAAAGCCCACAAATCAGTGGCA-CTCTTT
* * *
1358143 TTCAAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAATCAGTGGCACTCTTT
* * * * *
1358201 TTC-GAAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTTT-CAAAGCCCACAAATCAGTGGCACTCTTT
1358260 TTC
1 TTC
1358263 TTTTGTAAGC
Statistics
Matches: 104, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
57 20 0.19
58 8 0.08
59 50 0.48
61 26 0.25
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAATCAGTGGCACTCTTT
Found at i:1358371 original size:28 final size:29
Alignment explanation
Indices: 1358303--1358426 Score: 148
Period size: 28 Copynumber: 4.3 Consensus size: 29
1358293 TTTTCTTTTT
*
1358303 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTTAGTGGCAACC-TTTCAA
1358333 AAGCCCACAAGTTAGTGGCAACCTTT-AA
1 AAGCCCACAAGTTAGTGGCAACCTTTCAA
* *
1358361 AAGCCCACAAGTCAGTAGCAACCTTT-AA
1 AAGCCCACAAGTTAGTGGCAACCTTTCAA
*
1358389 AAGCACACAAGTT-GAT-GCAAACCTTTCAA
1 AAGCCCACAAGTTAG-TGGC-AACCTTTCAA
*
1358418 AAACCCACA
1 AAGCCCACA
1358427 CAAGTTGGTG
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.04
28 47 0.56
29 12 0.14
30 22 0.26
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.19
Consensus pattern (29 bp):
AAGCCCACAAGTTAGTGGCAACCTTTCAA
Found at i:1358603 original size:43 final size:43
Alignment explanation
Indices: 1358542--1358631 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
1358532 GCACCTTCAT
*
1358542 CTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
* *
1358585 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
1358628 CTTT
1 CTTT
1358632 TCCATCTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCAC
Found at i:1358626 original size:92 final size:95
Alignment explanation
Indices: 1358446--1358684 Score: 322
Period size: 92 Copynumber: 2.5 Consensus size: 95
1358436 GGCGTCTCCT
* * * * * *
1358446 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGTCCAATATCGC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATT-G-A-CAT-CCTTTAAGTCCAATATAGC
1358511 TGGCCTTAAATCAGCATATTGGCACC-TT-CATC
62 TGGCCTTAAATCAGCATATTGGCACCTTTCCATC
*
1358543 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCA-CCTTTAAGTCCAATATAGCTGGC
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTTAAGTCCAATATAGCTGGC
*
1358607 CTTGAATCAGCATATTGGCACCTTTTCCATC
66 CTTAAATCAGCATATTGGCACC-TTTCCATC
* *
1358638 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTT
1358685 TTCTCATCTT
Statistics
Matches: 127, Mismatches: 11, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
92 43 0.34
94 3 0.02
95 42 0.33
96 6 0.05
97 33 0.26
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (95 bp):
TTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGACATCCTTTAAGTCCAATATAGCTGGC
CTTAAATCAGCATATTGGCACCTTTCCATC
Found at i:1358663 original size:52 final size:53
Alignment explanation
Indices: 1358585--1358738 Score: 193
Period size: 52 Copynumber: 2.9 Consensus size: 53
1358575 ACATTGGCAC
1358585 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
1358637 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * * *
1358692 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
1358739 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 6 0.07
55 36 0.42
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:1359566 original size:33 final size:33
Alignment explanation
Indices: 1359523--1359589 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1359513 TTCAACGATT
1359523 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
* *** *
1359556 TGTATTGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1359589 T
1 T
1359590 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1359648 original size:13 final size:13
Alignment explanation
Indices: 1359630--1359654 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1359620 ATTACTCAAA
1359630 TGTATCGATACAT
1 TGTATCGATACAT
1359643 TGTATCGATACA
1 TGTATCGATACA
1359655 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1359702 original size:52 final size:51
Alignment explanation
Indices: 1359643--1359791 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
1359633 ATCGATACAT
** *
1359643 TGTATCGATACACTGATCTTTGTACCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
1359695 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1359747 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
1359792 TCATATTTCG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1365253 original size:21 final size:20
Alignment explanation
Indices: 1365229--1365269 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1365219 GCAAAATTTT
1365229 CAATTTAGTACTCCCCCTTAA
1 CAATTT-GTACTCCCCCTTAA
* *
1365250 CAATTTTTTCTCCCCCTTAA
1 CAATTTGTACTCCCCCTTAA
1365270 TAAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.24, C:0.34, G:0.02, T:0.39
Consensus pattern (20 bp):
CAATTTGTACTCCCCCTTAA
Found at i:1384976 original size:21 final size:21
Alignment explanation
Indices: 1384951--1385004 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1384941 CACTTGTAAC
*
1384951 TCATTTCTTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
1384972 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
*
1384993 TCACTTAATTTT
1 TCA-TTTATTTT
1385005 TTTTCAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.19, C:0.20, G:0.00, T:0.61
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:1385008 original size:21 final size:21
Alignment explanation
Indices: 1384966--1385009 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1384956 TCTTTTCTCC
*
1384966 TCTAATTCATTTATTTTCTTT
1 TCTAATTCATTAATTTTCTTT
1384987 TCTAATTCACTTAATTTT-TTT
1 TCTAATTCA-TTAATTTTCTTT
1385008 TC
1 TC
1385010 AAGAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (21 bp):
TCTAATTCATTAATTTTCTTT
Found at i:1386340 original size:13 final size:13
Alignment explanation
Indices: 1386322--1386350 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1386312 AAATAGTACC
1386322 CAATGTATCGATA
1 CAATGTATCGATA
1386335 CAATGTATCGATA
1 CAATGTATCGATA
1386348 CAA
1 CAA
1386351 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1388623 original size:10 final size:10
Alignment explanation
Indices: 1388608--1388660 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
1388598 AATCTCATTT
1388608 TCACTGTTCA
1 TCACTGTTCA
1388618 TCACTGTTCA
1 TCACTGTTCA
* * *
1388628 TGTATTGATGCA
1 T-CACTG-TTCA
1388640 TCACTGTTCA
1 TCACTGTTCA
1388650 TCACTGTTCA
1 TCACTGTTCA
1388660 T
1 T
1388661 GTATCGATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
10 25 0.71
11 6 0.17
12 4 0.11
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:1388649 original size:32 final size:32
Alignment explanation
Indices: 1388608--1388733 Score: 180
Period size: 32 Copynumber: 3.9 Consensus size: 32
1388598 AATCTCATTT
* **
1388608 TCACTGTTCATCACTGTTCATGTATTGATGCA
1 TCACTGTTCATCACTGTTCATGTATCGATAAA
1388640 TCACTGTTCATCACTGTTCATGTATCGATAAA
1 TCACTGTTCATCACTGTTCATGTATCGATAAA
* *
1388672 TCACTATTCATCACTATTCATGTATCGATAAA
1 TCACTGTTCATCACTGTTCATGTATCGATAAA
* **
1388704 TCATTGTTCATCACTGTTTGTGTATCGATA
1 TCACTGTTCATCACTGTTCATGTATCGATA
1388734 CATTGTGAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 84 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (32 bp):
TCACTGTTCATCACTGTTCATGTATCGATAAA
Found at i:1392680 original size:21 final size:21
Alignment explanation
Indices: 1392656--1392696 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1392646 AAATTAAAAA
*
1392656 ATAT-TTTTAT-ATTATATTT
1 ATATATTTTATAATTAAATTT
1392675 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
1392696 A
1 A
1392697 ATTAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:1392721 original size:30 final size:29
Alignment explanation
Indices: 1392675--1392735 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 29
1392665 TATTATATTT
1392675 ATATATTTTATAATTAAAT-TTAATTAAA
1 ATATATTTTATAATTAAATATTAATTAAA
*
1392703 ATATATTTTAAATTATTAAATATTAATTAAA
1 ATATATTTT--ATAATTAAATATTAATTAAA
1392734 AT
1 AT
1392736 CGAATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 9 0.31
30 9 0.31
31 11 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATATATTTTATAATTAAATATTAATTAAA
Found at i:1392735 original size:20 final size:21
Alignment explanation
Indices: 1392683--1392735 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
1392673 TTATATATTT
*
1392683 TATAATTAAATTTAATTAAAA
1 TATAATTAAAATTAATTAAAA
* *
1392704 TATATTTTAAATT-ATT-AAA
1 TATAATTAAAATTAATTAAAA
1392723 TATTAATTAAAAT
1 TA-TAATTAAAAT
1392736 CGAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 5 0.19
20 11 0.42
21 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAATTAAAATTAATTAAAA
Found at i:1398467 original size:2 final size:2
Alignment explanation
Indices: 1398460--1398619 Score: 104
Period size: 2 Copynumber: 80.0 Consensus size: 2
1398450 CTGCAGAAAA
* * * * * * *
1398460 AT AT AT AT AT AT AC AT AT AT AT AC AC AC AT AC AT AT AT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
1398502 GT AT AT GT AT AT AT AT AT AT AT GT GT GT GT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1398544 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT GT GT GT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1398586 AT AT AT GT GT GT GT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1398620 TTGTATATGC
Statistics
Matches: 138, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 138 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1398546 original size:50 final size:48
Alignment explanation
Indices: 1398492--1398619 Score: 193
Period size: 50 Copynumber: 2.6 Consensus size: 48
1398482 ACACACATAC
*
1398492 ATATATGTGTGTATATGTATATATATATATATGTGTGTGTATATATGTAT
1 ATATATGTGTGTATATATATATATATATATATGTGTGTGTATATA--TAT
* *
1398542 ATATATGTATATATATATATATATATATATATGTGTGTGTATATATAT
1 ATATATGTGTGTATATATATATATATATATATGTGTGTGTATATATAT
* *
1398590 ATGTGTGTGTGTATATATATATATATATAT
1 ATATATGTGTGTATATATATATATATATAT
1398620 TTGTATATGC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
48 29 0.41
50 42 0.59
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (48 bp):
ATATATGTGTGTATATATATATATATATATATGTGTGTGTATATATAT
Found at i:1398624 original size:22 final size:22
Alignment explanation
Indices: 1398492--1398627 Score: 128
Period size: 22 Copynumber: 6.0 Consensus size: 22
1398482 ACACACATAC
* * *
1398492 ATATATGTGTGTATATGTATAT
1 ATATATATATGTATGTGTATAT
*
1398514 ATATATATATGTGTGTGTATAT
1 ATATATATATGTATGTGTATAT
* *
1398536 ATGTATATATATGTATATATATAT
1 A--TATATATATGTATGTGTATAT
* *
1398560 ATATATATATATATGTGTGTGTAT
1 ATATATATATGTA--TGTGTATAT
* *
1398584 ATATATATGTGTGTGTGTATAT
1 ATATATATATGTATGTGTATAT
* *
1398606 ATATATATATATATTTGTATAT
1 ATATATATATGTATGTGTATAT
1398628 GCAAACGTAT
Statistics
Matches: 91, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
22 56 0.62
24 35 0.38
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.51
Consensus pattern (22 bp):
ATATATATATGTATGTGTATAT
Found at i:1408176 original size:7 final size:7
Alignment explanation
Indices: 1408166--1408197 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1408156 TTGTCTTTTT
1408166 TTTTTCC
1 TTTTTCC
1408173 TTTTTCC
1 TTTTTCC
1408180 TTTTTCC
1 TTTTTCC
1408187 -TTTTCC
1 TTTTTCC
1408193 TTTTT
1 TTTTT
1408198 TATATTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCC
Found at i:1408191 original size:13 final size:14
Alignment explanation
Indices: 1408166--1408197 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1408156 TTGTCTTTTT
1408166 TTTTTCCTTTTTCC
1 TTTTTCCTTTTTCC
1408180 TTTTTCC-TTTTCC
1 TTTTTCCTTTTTCC
1408193 TTTTT
1 TTTTT
1408198 TATATTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTCCTTTTTCC
Found at i:1409824 original size:25 final size:25
Alignment explanation
Indices: 1409796--1409846 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1409786 TCCATTGCCC
1409796 TTACATCACATGGAAGGGCTAGATT
1 TTACATCACATGGAAGGGCTAGATT
1409821 TTACATCACATGGAAGGGCTAGATT
1 TTACATCACATGGAAGGGCTAGATT
1409846 T
1 T
1409847 CAATTGAAAT
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:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (25 bp):
TTACATCACATGGAAGGGCTAGATT
Found at i:1410751 original size:2 final size:2
Alignment explanation
Indices: 1410744--1410781 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1410734 TCTTTTAGGC
*
1410744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1410782 GTGCTACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1412130 original size:24 final size:24
Alignment explanation
Indices: 1412103--1412153 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1412093 TGTACTAAGC
1412103 ATATT-TTGATAATCATATTTAAAT
1 ATATTATT-ATAATCATATTTAAAT
* *
1412127 ATATTATTTTAATTATATTTAAAT
1 ATATTATTATAATCATATTTAAAT
1412151 ATA
1 ATA
1412154 CTTGTGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
ATATTATTATAATCATATTTAAAT
Found at i:1412991 original size:39 final size:37
Alignment explanation
Indices: 1412916--1413023 Score: 112
Period size: 37 Copynumber: 2.9 Consensus size: 37
1412906 GAGCCAGCTC
* *
1412916 AAAACTTATTTTAATATTTAAA-AAAATTAAAATATAA
1 AAAATTTA-TTTAATATTTAAATAAAATTTAAATATAA
* *
1412953 AAAATTTATATTAATATTTATAATTAAATTTAATTATAA
1 AAAATTTAT-TTAATATTTA-AATAAAATTTAAATATAA
* *
1412992 AATATTT-TTTATTATTTAAATAATAATTTAAA
1 AAAATTTATTTAATATTTAAATAA-AATTTAAA
1413024 CTAGGTTAGC
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
36 5 0.08
37 33 0.56
38 3 0.05
39 18 0.31
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (37 bp):
AAAATTTATTTAATATTTAAATAAAATTTAAATATAA
Found at i:1413587 original size:6 final size:6
Alignment explanation
Indices: 1413578--1413644 Score: 66
Period size: 6 Copynumber: 11.2 Consensus size: 6
1413568 TTGATTAATG
* * * *
1413578 ATTTTA ATTTT- ATTATA ATTATGT- ACTTTA GTTTTG ATTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATT-T-TA ATTTTA ATTTTA ATTTTA ATTTTA
1413626 ATTTTA ATTTTA ATTTTA A
1 ATTTTA ATTTTA ATTTTA A
1413645 CATTACTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
5 5 0.10
6 41 0.84
7 2 0.04
8 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (6 bp):
ATTTTA
Found at i:1413654 original size:18 final size:18
Alignment explanation
Indices: 1413614--1413656 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1413604 TTTAGTTTTG
**
1413614 ATTTTAATTTTAATTTTA
1 ATTTTAATTTTAACATTA
1413632 ATTTTAATTTTAACATTA
1 ATTTTAATTTTAACATTA
*
1413650 CTTTTAA
1 ATTTTAA
1413657 ATGTTTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTAATTTTAACATTA
Found at i:1414570 original size:21 final size:20
Alignment explanation
Indices: 1414521--1414570 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1414511 ATATATATTT
* * *
1414521 AAAAATATGATTATAATATG
1 AAAAATATAATTAAAATATA
1414541 AAAAA-ATAATTAAAATATA
1 AAAAATATAATTAAAATATA
1414560 ATAAAATATAA
1 A-AAAATATAA
1414571 ATATAAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 12 0.48
20 9 0.36
21 4 0.16
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAAATATAATTAAAATATA
Found at i:1415366 original size:2 final size:2
Alignment explanation
Indices: 1415359--1415391 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1415349 CTATAGGTAA
1415359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1415392 AAAAAGAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1415712 original size:21 final size:20
Alignment explanation
Indices: 1415679--1415718 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1415669 AATAAAATGT
1415679 AAAATATAATATAACATAAA
1 AAAATATAATATAACATAAA
*
1415699 AAAATATAAATATAATATAA
1 AAAATAT-AATATAACATAA
1415719 TTATATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATATAATATAACATAAA
Found at i:1416099 original size:25 final size:23
Alignment explanation
Indices: 1416041--1416108 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 23
1416031 TTACCTATGC
* *
1416041 AAATATTAAATATGATTATAATATA
1 AAATA-TAAATAT-ATAAAAATATA
1416066 AAATA-AAATATATAAAAATAGTA
1 AAATATAAATATATAAAAATA-TA
1416089 TAAATATAAAT-TAGTAAAAA
1 -AAATATAAATATA-TAAAAA
1416109 AAGAAAGGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 7 0.19
25 15 0.41
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATATAAATATATAAAAATATA
Found at i:1417764 original size:3 final size:3
Alignment explanation
Indices: 1417756--1417800 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1417746 ATCAGTATAC
1417756 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1417801 GTAGTTTGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1418318 original size:30 final size:29
Alignment explanation
Indices: 1418283--1418353 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 29
1418273 AAAAAGTGAT
*
1418283 ATAATTATATGATATAA-ATATAATATAAAA
1 ATAATTATATGATATAAGA-AT-ATAAAAAA
1418313 ATAATTA-AT-ATATAAGAATATAAAAAA
1 ATAATTATATGATATAAGAATATAAAAAA
1418340 ATAATATAATATGA
1 ATAAT-T-ATATGA
1418354 GCATATTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
27 12 0.34
28 9 0.26
29 4 0.11
30 9 0.26
31 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (29 bp):
ATAATTATATGATATAAGAATATAAAAAA
Found at i:1420075 original size:26 final size:29
Alignment explanation
Indices: 1420042--1420102 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
1420032 AATTCTTTTT
*
1420042 AATAAAAAAATATATAAAT-TTAATA-AA
1 AATAAAAGAATATATAAATATTAATATAA
*
1420069 AATAAAATGTATATATAAATATTAATATAA
1 AATAAAA-GAATATATAAATATTAATATAA
1420099 AATA
1 AATA
1420103 TCTTCTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 7 0.24
28 10 0.34
29 6 0.21
30 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
AATAAAAGAATATATAAATATTAATATAA
Found at i:1420817 original size:8 final size:8
Alignment explanation
Indices: 1420798--1420836 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
1420788 AAATAAATTA
1420798 ATTTTATAT
1 ATTTT-TAT
1420807 ATTTTTAT
1 ATTTTTAT
1420815 ATTTTTAT
1 ATTTTTAT
*
1420823 ATAATTTAT
1 AT-TTTTAT
1420832 ATTTT
1 ATTTT
1420837 GTTAGTTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 15 0.56
9 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
ATTTTTAT
Found at i:1420822 original size:18 final size:17
Alignment explanation
Indices: 1420799--1420836 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1420789 AATAAATTAA
*
1420799 TTTTATATATTTTTATAT
1 TTTTATATA-ATTTATAT
1420817 TTTTATATAATTTATAT
1 TTTTATATAATTTATAT
1420834 TTT
1 TTT
1420837 GTTAGTTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATATAATTTATAT
Found at i:1421952 original size:15 final size:16
Alignment explanation
Indices: 1421928--1421960 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1421918 TGGTAAATTA
1421928 AAAAACTTAAGTGCTG
1 AAAAACTTAAGTGCTG
*
1421944 AAAAA-TTAAGTGTTG
1 AAAAACTTAAGTGCTG
1421959 AA
1 AA
1421961 TTGTTAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (16 bp):
AAAAACTTAAGTGCTG
Found at i:1422095 original size:6 final size:6
Alignment explanation
Indices: 1422070--1422110 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
1422060 AAATCTTAAA
*
1422070 AATTATT AATTTCA AATTTT AATTTT AATTTT AATTTT AAT
1 AATT-TT AATTT-T AATTTT AATTTT AATTTT AATTTT AAT
1422111 CATATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 22 0.71
7 9 0.29
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (6 bp):
AATTTT
Found at i:1428195 original size:23 final size:25
Alignment explanation
Indices: 1428163--1428209 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
1428153 AATTTTAATT
*
1428163 TTTTATTTATAT-AT-TTTTAAAAA
1 TTTTACTTATATGATATTTTAAAAA
*
1428186 TTTTACTTATTTGATATTTTAAAA
1 TTTTACTTATATGATATTTTAAAA
1428210 TTAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 2 0.10
25 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTACTTATATGATATTTTAAAAA
Found at i:1433337 original size:43 final size:43
Alignment explanation
Indices: 1433271--1433353 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
1433261 GCTCATTGAA
*
1433271 GTCACCATTATTAGCATCAATAGTATTTAATTCTTCTCCATAT
1 GTCACCATTATCAGCATCAATAGTATTTAATTCTTCTCCATAT
*
1433314 GTCAGCATTATCAGCATCAATAGTATTTAATTCTTCTCCA
1 GTCACCATTATCAGCATCAATAGTATTTAATTCTTCTCCA
1433354 GACGGGACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (43 bp):
GTCACCATTATCAGCATCAATAGTATTTAATTCTTCTCCATAT
Found at i:1438882 original size:23 final size:24
Alignment explanation
Indices: 1438845--1438892 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1438835 TTATAAATAA
1438845 TTTTATTATAATATTTAATATATT
1 TTTTATTATAATATTTAATATATT
* *
1438869 TTTTATTA-ATTATTTATTATATT
1 TTTTATTATAATATTTAATATATT
1438892 T
1 T
1438893 AATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTATTATAATATTTAATATATT
Found at i:1438898 original size:20 final size:19
Alignment explanation
Indices: 1438814--1438908 Score: 52
Period size: 23 Copynumber: 4.7 Consensus size: 19
1438804 ATGAGATTTA
*
1438814 AATTTTTAAT-T-TTTAAA
1 AATTTTTAATATATTTAAT
1438831 AATTTTATAA-ATAATTTTATTAT
1 AATTTT-TAATAT-A-TTTA--AT
* *
1438854 AATATTTAATATATTTTTTATT
1 AATTTTTAATATA---TTTAAT
*
1438876 AATTATTTATTATATTTAAT
1 AATT-TTTAATATATTTAAT
1438896 AATTTTTAATATA
1 AATTTTTAATATA
1438909 AAATATATTC
Statistics
Matches: 60, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
17 6 0.10
18 4 0.07
19 8 0.13
20 9 0.15
21 4 0.07
22 8 0.13
23 16 0.27
24 5 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTTTAATATATTTAAT
Found at i:1439336 original size:21 final size:21
Alignment explanation
Indices: 1439311--1439381 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
1439301 TAATTGATAT
1439311 TTTAATAAATTAATTATTA-AA
1 TTTAATAAATT-ATTATTATAA
* *
1439332 TTTAATTAA-TATTATTATAT
1 TTTAATAAATTATTATTATAA
*
1439352 TTTATATAAATTTATT-TAATAA
1 TTTA-ATAAA-TTATTATTATAA
*
1439374 TTTTATAA
1 TTTAATAA
1439382 CATCGATAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 7 0.17
20 6 0.15
21 16 0.40
22 7 0.17
23 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATAAATTATTATTATAA
Found at i:1439364 original size:30 final size:29
Alignment explanation
Indices: 1439324--1439380 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
1439314 AATAAATTAA
1439324 TTATTAAATTTAATTAAT-ATTATTATATT
1 TTATTAAATTTAATTAATAATT-TTATATT
*
1439353 TTATATAAATTTATTTAATAATTTTATA
1 TTAT-TAAATTTAATTAATAATTTTATA
1439381 ACATCGATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 4 0.16
30 18 0.72
31 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTATTAAATTTAATTAATAATTTTATATT
Found at i:1439376 original size:42 final size:38
Alignment explanation
Indices: 1439283--1439377 Score: 93
Period size: 42 Copynumber: 2.4 Consensus size: 38
1439273 TTAATTTATA
*
1439283 TATTTTATAATTTTTATATAATTGATATTTTAATAAAT
1 TATTTAATAATTTTTATATAATTGATATTTTAATAAAT
* * *
1439321 TAATTATTAAATTTAATTAATATTATT-ATATTTTATATAAATT
1 TATTTAAT-AATTT--TT-ATATAATTGATATTTTA-ATAAA-T
1439364 TATTTAATAATTTT
1 TATTTAATAATTTT
1439378 ATAACATCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
38 5 0.11
39 5 0.11
40 1 0.02
41 10 0.22
42 17 0.38
43 7 0.16
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (38 bp):
TATTTAATAATTTTTATATAATTGATATTTTAATAAAT
Found at i:1439432 original size:28 final size:26
Alignment explanation
Indices: 1439399--1439461 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 26
1439389 AGAAAAATAT
*
1439399 TATTTTTAATAAATAAATTAATAATTAAA
1 TATTTTTAAT--A-AAATAAATAATTAAA
1439428 T-TTTTT-ATAAAATAAATAATTAAA
1 TATTTTTAATAAAATAAATAATTAAA
1439452 TATTTTTAAT
1 TATTTTTAAT
1439462 TTATTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 15 0.48
25 6 0.19
26 2 0.06
27 2 0.06
28 5 0.16
29 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTTTTAATAAAATAAATAATTAAA
Found at i:1439440 original size:24 final size:25
Alignment explanation
Indices: 1439413--1439459 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1439403 TTTAATAAAT
*
1439413 AAATTAATAATTAAAT-TTTTTATA
1 AAATAAATAATTAAATATTTTTATA
1439437 AAATAAATAATTAAATATTTTTA
1 AAATAAATAATTAAATATTTTTA
1439460 ATTTATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATAAATAATTAAATATTTTTATA
Found at i:1440813 original size:27 final size:29
Alignment explanation
Indices: 1440751--1440813 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 29
1440741 GATTTACATA
*
1440751 ATAAAAA-ATAAAATATGATGATCAAATT
1 ATAAAAATATAAAATATGATGATAAAATT
*
1440779 A-AACAAATATAAATTAT-AT-ATAAAATT
1 ATAA-AAATATAAAATATGATGATAAAATT
1440806 ATAAAAAT
1 ATAAAAAT
1440814 GCATAAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
27 14 0.47
28 8 0.27
29 8 0.27
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
ATAAAAATATAAAATATGATGATAAAATT
Found at i:1442760 original size:14 final size:15
Alignment explanation
Indices: 1442743--1442780 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
1442733 AGATAATATA
1442743 AAAATAAT-AAAAAT
1 AAAATAATAAAAAAT
1442757 AAAATAATATAAAAAAT
1 AAAAT-A-ATAAAAAAT
1442774 AAAATAA
1 AAAATAA
1442781 ATACATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.24
15 2 0.10
16 3 0.14
17 11 0.52
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATAATAAAAAAT
Found at i:1442762 original size:22 final size:22
Alignment explanation
Indices: 1442737--1442799 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
1442727 GCATGAAGAT
1442737 AATATAAAAATAATAAAAATAA
1 AATATAAAAATAATAAAAATAA
1442759 AATAATATAAAA-AAT-AAAATAA
1 AAT-ATA-AAAATAATAAAAATAA
* *
1442781 ATACATATAAATATATAAA
1 A-ATATAAAAATA-ATAAA
1442800 TGTATCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
21 3 0.09
22 15 0.45
23 9 0.27
24 6 0.18
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (22 bp):
AATATAAAAATAATAAAAATAA
Found at i:1442800 original size:22 final size:22
Alignment explanation
Indices: 1442735--1442800 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 22
1442725 TGGCATGAAG
*
1442735 ATAATATAAAAATAATAAAAATAAA
1 ATAATAT--AAAT-ATATAAATAAA
*
1442760 ATAATATAAA-AAATAAA-ATAA
1 ATAATATAAATATATAAATA-AA
1442781 ATACATATAAATATATAAAT
1 ATA-ATATAAATATATAAAT
1442801 GTATCAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
20 1 0.03
21 10 0.29
22 7 0.21
23 9 0.26
25 7 0.21
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
ATAATATAAATATATAAATAAA
Found at i:1443348 original size:66 final size:66
Alignment explanation
Indices: 1443223--1443375 Score: 176
Period size: 66 Copynumber: 2.4 Consensus size: 66
1443213 ATCTATATAA
1443223 AATAAAATATTAAAATATATAAAAATTTATATAAATTTTGACACATTCAAAATATTAAAAATTTA
1 AATAAAATATTAAAATATATAAAAATTTATATAAATTTTGACACATTCAAAATATTAAAAATTTA
1443288 T
66 T
* *
1443289 AATACAAATGATT-AAA-ATATAAAAATTTATATAAATTTAT-A-ATATTTAAAATATATAAAAA
1 AATA-AAAT-ATTAAAATATATAAAAATTTATATAAATTT-TGACACATTCAAAATAT-TAAAAA
* *
1443350 -TAAC
62 TTTAT
*
1443354 AAAAAAATA-T-AAATATATAAAA
1 AATAAAATATTAAAATATATAAAA
1443376 TTTTCTCTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
62 4 0.05
63 9 0.12
64 4 0.05
65 16 0.21
66 33 0.43
67 8 0.10
68 3 0.04
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (66 bp):
AATAAAATATTAAAATATATAAAAATTTATATAAATTTTGACACATTCAAAATATTAAAAATTTA
T
Found at i:1444196 original size:22 final size:22
Alignment explanation
Indices: 1444171--1444243 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
1444161 TAATATGATT
*
1444171 ATATAATATAAAAATAATTTAA
1 ATATAATATAAAAATAATATAA
* *
1444193 ATATTATATAAAATATAACAT-A
1 ATATAATATAAAA-ATAATATAA
*
1444215 ATATTATATTAAAAAATAATATAA
1 ATATAATA-T-AAAAATAATATAA
1444239 ATATA
1 ATATA
1444244 TAAATATATC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
22 21 0.50
23 12 0.29
24 9 0.21
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATAATATAAAAATAATATAA
Found at i:1444223 original size:27 final size:26
Alignment explanation
Indices: 1444159--1444233 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 26
1444149 TAATTTTATA
* *
1444159 AATAATATGATTATATAATATAAAAAT
1 AATATTAT-ATTATATAAAATAAAAAT
*
1444186 AAT-TTAAATATTATATAAAATATAACAT
1 AATATT--ATATTATATAAAATA-AAAAT
1444214 AATATTATATTA-A-AAAATAA
1 AATATTATATTATATAAAATAA
1444234 TATAAATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
24 1 0.02
25 6 0.15
26 2 0.05
27 21 0.51
28 9 0.22
29 2 0.05
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (26 bp):
AATATTATATTATATAAAATAAAAAT
Found at i:1444246 original size:8 final size:8
Alignment explanation
Indices: 1444228--1444310 Score: 51
Period size: 8 Copynumber: 9.5 Consensus size: 8
1444218 TTATATTAAA
1444228 AAATAATAT
1 AAAT-ATAT
1444237 AAATATAT
1 AAATATAT
1444245 AAATATAT
1 AAATATAT
*
1444253 CAAAATTTAT
1 --AAATATAT
1444263 AAA-ATAT
1 AAATATAT
1444270 AAATTATTAT
1 AAA-TA-TAT
* *
1444280 TATTATATT
1 AAATATA-T
1444289 AAAATATAT
1 -AAATATAT
*
1444298 AAAAATAAT
1 AAATAT-AT
1444307 AAAT
1 AAAT
1444311 TAAATATGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
7 6 0.10
8 22 0.38
9 14 0.24
10 16 0.28
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATATAT
Found at i:1444324 original size:61 final size:57
Alignment explanation
Indices: 1444175--1444324 Score: 132
Period size: 61 Copynumber: 2.5 Consensus size: 57
1444165 ATGATTATAT
1444175 AATATAAAAATAAT---TTAAATAT-TATATAAAATATAACATAATATTATATTAAAA
1 AATATAAAAATAATAAATTAAATATAT-TATAAAATATAACATAATATTATATTAAAA
* *
1444229 AATAATATAAATATATAAATATATCAAAAT-TTATAAAATATAA-ATTATTATTATTATATTAAA
1 AAT-ATAAAAATA-ATAAAT-TA--AATATATTATAAAATATAACA-TA--A-TATTATATTAAA
1444292 A
57 A
*
1444293 TATATAAAAATAATAAATTAAATATGATTATA
1 AATATAAAAATAATAAATTAAATAT-ATTATA
1444325 TATAAAAATT
Statistics
Matches: 77, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
54 3 0.04
55 8 0.10
56 2 0.03
59 5 0.06
60 3 0.04
61 21 0.27
62 11 0.14
63 9 0.12
64 15 0.19
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (57 bp):
AATATAAAAATAATAAATTAAATATATTATAAAATATAACATAATATTATATTAAAA
Found at i:1446015 original size:32 final size:32
Alignment explanation
Indices: 1445977--1446080 Score: 88
Period size: 32 Copynumber: 3.2 Consensus size: 32
1445967 TATTGTAAGC
1445977 GAAAAGTTACTATCTTTTTAGGTTCCTCGTTA
1 GAAAAGTTACTATCTTTTTAGGTTCCTCGTTA
* * * * * * * *
1446009 GAAAAGTT-TTGTCCTATCT-CGTT-ATTGTAA
1 GAAAAGTTACTAT-CTTTTTAGGTTCCTCGTTA
1446039 GCGAAAAGTTACTATCTTTTTAGGTTCCTCGTTA
1 --GAAAAGTTACTATCTTTTTAGGTTCCTCGTTA
1446073 GAAAAGTT
1 GAAAAGTT
1446081 TGTCCTATCT
Statistics
Matches: 50, Mismatches: 16, Indels: 12
0.64 0.21 0.15
Matches are distributed among these distances:
30 4 0.08
31 5 0.10
32 32 0.64
33 5 0.10
34 4 0.08
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
GAAAAGTTACTATCTTTTTAGGTTCCTCGTTA
Found at i:1446044 original size:64 final size:64
Alignment explanation
Indices: 1445945--1446130 Score: 333
Period size: 63 Copynumber: 3.0 Consensus size: 64
1445935 CATATAGAAA
* *
1445945 AGAAAAGTTTTGTCC-GTCTTGTTATTGTAAGCGAAAAGTTACTATCTTTTTAGGTTCCTCGTT
1 AGAAAAGTTTTGTCCTATCTCGTTATTGTAAGCGAAAAGTTACTATCTTTTTAGGTTCCTCGTT
1446008 AGAAAAGTTTTGTCCTATCTCGTTATTGTAAGCGAAAAGTTACTATCTTTTTAGGTTCCTCGTT
1 AGAAAAGTTTTGTCCTATCTCGTTATTGTAAGCGAAAAGTTACTATCTTTTTAGGTTCCTCGTT
1446072 AGAAAAG-TTTGTCCTATCTCGTTATTGTAAGCGAAAAGTTACTATCTTTTT-GGTTCCTC
1 AGAAAAGTTTTGTCCTATCTCGTTATTGTAAGCGAAAAGTTACTATCTTTTTAGGTTCCTC
1446131 ATTTGTAAAT
Statistics
Matches: 120, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
62 8 0.07
63 59 0.49
64 53 0.44
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.42
Consensus pattern (64 bp):
AGAAAAGTTTTGTCCTATCTCGTTATTGTAAGCGAAAAGTTACTATCTTTTTAGGTTCCTCGTT
Found at i:1452238 original size:20 final size:20
Alignment explanation
Indices: 1452210--1452286 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
1452200 TAGATGTATC
1452210 GAATGTATCGATACATTGAA
1 GAATGTATCGATACATTGAA
* *
1452230 GAATATATCGATACATTCATA
1 GAATGTATCGATACATTGA-A
* *
1452251 -CATGTATCGATATATTGAA
1 GAATGTATCGATACATTGAA
*
1452270 AAATGTATCGATACATT
1 GAATGTATCGATACATT
1452287 TGGGTAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (20 bp):
GAATGTATCGATACATTGAA
Found at i:1452964 original size:29 final size:29
Alignment explanation
Indices: 1452844--1453544 Score: 837
Period size: 29 Copynumber: 23.9 Consensus size: 29
1452834 TTTTAAAATG
*
1452844 GTGCCACTAACTTGTGTGGGCTTTGAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAAGA
*
1452875 GTTGCCACTAACTCGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
* *
1452907 GTTGCCACTAATTCGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGA--CTTGTGGGCTTTGAAAAGA
** *
1452939 GTATCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1452967 GTGCCACTGACTTATGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
1452995 GTACCACTAACTTTTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1453024 GTGCCACTAACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1453052 GTGTCACTGACTTACGTGGGCTTTG-AAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
* *
1453082 GTGCCATTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1453111 -TG-CACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1453138 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1453167 GTTGCCACTGACTCGTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
* *
1453199 GTGCCACTGACTTATGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1453227 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1453256 GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1453285 GTGCCACCGACTCATGTGGGCTTTGAAAAGA
1 GTGCCACTGACT--TGTGGGCTTTGAAAAGA
* *
1453316 GTTGCCACCGACTCGTGTGGGCTTTGAAAAAA
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGA
* *
1453348 GTACCACT-ACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1453375 GTGCCACTGACTTGTGGGTTTTGAAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
1453404 GTGCCACTGAATTGTGGACTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1453432 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1453461 GTGCCACTAATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1453490 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1453519 GTGCCACTGACTCGTGAGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
1453545 GGGATGAACA
Statistics
Matches: 597, Mismatches: 53, Indels: 42
0.86 0.08 0.06
Matches are distributed among these distances:
27 32 0.05
28 154 0.26
29 224 0.38
30 40 0.07
31 42 0.07
32 104 0.17
34 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:1453028 original size:57 final size:58
Alignment explanation
Indices: 1452844--1453544 Score: 785
Period size: 57 Copynumber: 11.9 Consensus size: 58
1452834 TTTTAAAATG
* *
1452844 GTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACTAACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAAG-GGTGCCACTAACT--TGTGGGCTTTGAAAAGA
* * * ** * *
1452907 GTTGCCACTAATTCGTGTGGGCTTTGAAAAGAGTATCACTGACTTGTGGGCTTTG-AAAGG
1 G-TGCCACTGA--CTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA
* * *
1452967 GTGCCACTGACTTATGGGCTTTG-AAAGGGTACCACTAACTTTTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA
* * * *
1453024 GTGCCACTAACTTGTGGGCTTTG-AAAGGGTGTCACTGACTTACGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTT--GTGGGCTTTGAAAAGA
* *
1453082 GTGCCATTGACTTGTGGGCTTTG-AAAGGATG-CACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA
* *
1453138 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTCGTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAG-GGTGCCACTAACT--TGTGGGCTTTGAAAAGA
* *
1453199 GTGCCACTGACTTATGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA
* * **
1453256 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACCGACTCATGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACT--TGTGGGCTTTGAAAAGA
* ** * *
1453316 GTTGCCACCGACTCGTGTGGGCTTTGAAAAAAGTACCACT-ACTTGTGGGCTTTG-AAAGG
1 G-TGCCACTGACT--TGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA
* * *
1453375 GTGCCACTGACTTGTGGGTTTTGAAAAGGGTGCCACTGAA-TTGTGGACTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACT-AACTTGTGGGCTTTGAAAAGA
* *
1453432 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA
* * * * *
1453490 GTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTCGTGAGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAA
1453545 GGGATGAACA
Statistics
Matches: 559, Mismatches: 57, Indels: 49
0.84 0.09 0.07
Matches are distributed among these distances:
55 10 0.02
56 73 0.13
57 163 0.29
58 115 0.21
59 41 0.07
60 38 0.07
61 59 0.11
62 3 0.01
63 31 0.06
64 25 0.04
66 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (58 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGA
Found at i:1454788 original size:11 final size:10
Alignment explanation
Indices: 1454774--1454812 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1454764 TTTTTGCTAT
1454774 TTTTTTCTTTG
1 TTTTTT-TTTG
*
1454785 TTTTTTTGT-
1 TTTTTTTTTG
1454794 TTTTTTTTTG
1 TTTTTTTTTG
1454804 TTTTTTTTT
1 TTTTTTTTT
1454813 TAGGTGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 11 0.44
11 6 0.24
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:1454798 original size:19 final size:19
Alignment explanation
Indices: 1454774--1454810 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1454764 TTTTTGCTAT
1454774 TTTTTTCTTTGTTTTTTTG
1 TTTTTTCTTTGTTTTTTTG
*
1454793 TTTTTTTTTTGTTTTTTT
1 TTTTTTCTTTGTTTTTTT
1454811 TTTAGGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.89
Consensus pattern (19 bp):
TTTTTTCTTTGTTTTTTTG
Found at i:1454813 original size:11 final size:11
Alignment explanation
Indices: 1454763--1454813 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
1454753 GACCCATTTC
* *
1454763 TTTTTTGCTAT
1 TTTTTTGTTTT
*
1454774 TTTTTTCTTTGT
1 TTTTTTGTTT-T
1454786 TTTTTTGTTTT
1 TTTTTTGTTTT
1454797 TTTTTTGTTTT
1 TTTTTTGTTTT
1454808 TTTTTT
1 TTTTTT
1454814 AGGTGTAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.86
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:1470752 original size:20 final size:19
Alignment explanation
Indices: 1470723--1470797 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
1470713 AAAAAGATAT
1470723 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
1470742 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
1470763 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
1470783 AATGTATCGATACAT
1 AATGTATCGATACAT
1470798 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:1472319 original size:20 final size:19
Alignment explanation
Indices: 1472290--1472364 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
1472280 AAAAAGATAT
1472290 AATGTATCGATACATTGAA
1 AATGTATCGATACATTGAA
* *
1472309 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
* *
1472330 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-AA
1472350 AATGTATCGATACAT
1 AATGTATCGATACAT
1472365 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:1476983 original size:3 final size:3
Alignment explanation
Indices: 1476975--1477034 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
1476965 TCAGCTAAAT
1476975 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1477023 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1477035 GTCAAGCATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1479975 original size:2 final size:2
Alignment explanation
Indices: 1479968--1480001 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
1479958 TTTACAAGGG
1479968 TA TA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
1480002 TTAGCTGCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1480106 original size:13 final size:13
Alignment explanation
Indices: 1480080--1480119 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1480070 TGCTTATTTG
1480080 ATCATCTACCTTT
1 ATCATCTACCTTT
1480093 ATCA-CTACCTTTT
1 ATCATCTACC-TTT
*
1480106 ATCATCTGCCTTT
1 ATCATCTACCTTT
1480119 A
1 A
1480120 CCACACTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.21
13 15 0.62
14 4 0.17
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.45
Consensus pattern (13 bp):
ATCATCTACCTTT
Found at i:1482813 original size:5 final size:5
Alignment explanation
Indices: 1482803--1482835 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1482793 CAAGTTCATA
1482803 AAAAT AAAAT AAAAT AAAAT AAAA- AGAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAA
1482836 GTTCCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 24 0.92
6 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:1483573 original size:20 final size:20
Alignment explanation
Indices: 1483532--1483574 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1483522 ATTTCAATGG
*
1483532 ATTAATTATTTTTAAGAGAA
1 ATTAATTATTTTTAAGAAAA
* *
1483552 ATTAATTCTTTTTATGAAAA
1 ATTAATTATTTTTAAGAAAA
1483572 ATT
1 ATT
1483575 TTGATAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (20 bp):
ATTAATTATTTTTAAGAAAA
Found at i:1484224 original size:14 final size:15
Alignment explanation
Indices: 1484194--1484227 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1484184 TCGAGTTATT
*
1484194 TATTTGATTTAAATA
1 TATTTAATTTAAATA
1484209 TATTTAATTT-AATA
1 TATTTAATTTAAATA
1484223 TATTT
1 TATTT
1484228 TTTTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TATTTAATTTAAATA
Found at i:1484248 original size:18 final size:18
Alignment explanation
Indices: 1484211--1484267 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
1484201 TTTAAATATA
**
1484211 TTTAATTTAATATATTTT
1 TTTAATTTAATATAAATT
*
1484229 TTTAATTTAATCTAAA-T
1 TTTAATTTAATATAAATT
*
1484246 TTTAA-ATAA-ATAAATT
1 TTTAATTTAATATAAATT
1484262 TTTAAT
1 TTTAAT
1484268 AAAATTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 4 0.12
16 9 0.28
17 6 0.19
18 13 0.41
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATTTAATATAAATT
Found at i:1484272 original size:16 final size:15
Alignment explanation
Indices: 1484241--1484270 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1484231 TAATTTAATC
1484241 TAAATTTTAAATAAA
1 TAAATTTTAAATAAA
*
1484256 TAAATTTTTAATAAA
1 TAAATTTTAAATAAA
1484271 ATTTAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATTTTAAATAAA
Found at i:1485116 original size:33 final size:33
Alignment explanation
Indices: 1485079--1485161 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 33
1485069 AATAATACGA
* *
1485079 ATATAATATAAAAATA-TAATTATCTTAAAATTT
1 ATATAATATAAAAATATTAA-TATATTAAAAATT
*
1485112 ATATAATAT-AAATTATTAATATATTAAAAATT
1 ATATAATATAAAAATATTAATATATTAAAAATT
1485144 ATATAA-ATATAAAATATT
1 ATATAATATA-AAAATATT
1485162 TTAAACATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
31 2 0.05
32 22 0.51
33 19 0.44
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (33 bp):
ATATAATATAAAAATATTAATATATTAAAAATT
Found at i:1485133 original size:18 final size:20
Alignment explanation
Indices: 1485112--1485155 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1485102 CTTAAAATTT
*
1485112 ATATAATATAAATTAT-T-A
1 ATATAATAAAAATTATATAA
*
1485130 ATATATTAAAAATTATATAA
1 ATATAATAAAAATTATATAA
1485150 ATATAA
1 ATATAA
1485156 AATATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 14 0.67
19 1 0.05
20 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAATAAAAATTATATAA
Found at i:1485784 original size:41 final size:41
Alignment explanation
Indices: 1485727--1485808 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
1485717 ATTAAAAACG
1485727 ATTAGTTAGTAATTAATTAATTAATTAAGAAAGATGTACCA
1 ATTAGTTAGTAATTAATTAATTAATTAAGAAAGATGTACCA
1485768 ATTAGTTAGTAATTAATTAATTAATTAAGAAAGATGTACCA
1 ATTAGTTAGTAATTAATTAATTAATTAAGAAAGATGTACCA
1485809 TAACTGGAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (41 bp):
ATTAGTTAGTAATTAATTAATTAATTAAGAAAGATGTACCA
Found at i:1486504 original size:23 final size:23
Alignment explanation
Indices: 1486478--1486523 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1486468 AATATTTACT
1486478 TTTA-AAAATATATTTTTTAATTA
1 TTTATAAAATA-ATTTTTTAATTA
*
1486501 TTTATTAAATAATTTTTTAATTA
1 TTTATAAAATAATTTTTTAATTA
1486524 AATCAATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTATAAAATAATTTTTTAATTA
Found at i:1487066 original size:34 final size:34
Alignment explanation
Indices: 1487028--1487100 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
1487018 ATATGTGTAT
*
1487028 ATAATTAAAATAATTAAAATTATATTTATGTAAA
1 ATAATTAAAATAATTAAAATGATATTTATGTAAA
* *
1487062 ATAATTAAAATTATTAAAATGATATTTATGTTAA
1 ATAATTAAAATAATTAAAATGATATTTATGTAAA
1487096 ATAAT
1 ATAAT
1487101 AATTTAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (34 bp):
ATAATTAAAATAATTAAAATGATATTTATGTAAA
Found at i:1488357 original size:17 final size:18
Alignment explanation
Indices: 1488331--1488368 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1488321 TTTTATAGTA
*
1488331 TAATTTAATTAAT-TTTT
1 TAATTAAATTAATATTTT
1488348 TAATTAAATTAATATTTT
1 TAATTAAATTAATATTTT
1488366 TAA
1 TAA
1488369 ATTCATGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATTAAATTAATATTTT
Found at i:1492162 original size:42 final size:42
Alignment explanation
Indices: 1492104--1492187 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
1492094 AATCTTCATT
** *
1492104 TTTTTTTTTAGATTTGCTTAGATATGAAACAAACAGAAGATA
1 TTTTTTTAAAGATTTGCTTAGATATCAAACAAACAGAAGATA
1492146 TTTTTTTAAAGATTTGCTTAGATATCAAACAAACAGAAGATA
1 TTTTTTTAAAGATTTGCTTAGATATCAAACAAACAGAAGATA
1492188 AGAAACAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (42 bp):
TTTTTTTAAAGATTTGCTTAGATATCAAACAAACAGAAGATA
Found at i:1492661 original size:23 final size:23
Alignment explanation
Indices: 1492611--1492667 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1492601 TTAAATATTT
* *
1492611 AAATATATTTT-TAATTTAATAT
1 AAATATATTTTATAATTAAATAA
**
1492633 TTATATATTTTATAATTAAATAA
1 AAATATATTTTATAATTAAATAA
*
1492656 AAATATTTTTTA
1 AAATATATTTTA
1492668 AAATAATTCA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AAATATATTTTATAATTAAATAA
Found at i:1493719 original size:27 final size:28
Alignment explanation
Indices: 1493682--1493738 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
1493672 CATGTCGAAA
*
1493682 TTTTATTTATTTATCA-AA-TGTTTTAAT
1 TTTTATATATTTA-CATAATTGTTTTAAT
1493709 TTTTATATATTTACATAATTGTTTTAAT
1 TTTTATATATTTACATAATTGTTTTAAT
1493737 TT
1 TT
1493739 AAGAGGATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 2 0.07
27 14 0.52
28 11 0.41
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTTATATATTTACATAATTGTTTTAAT
Found at i:1496228 original size:3 final size:3
Alignment explanation
Indices: 1496220--1496247 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1496210 TTTGTAGTGG
1496220 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1496248 GTTTGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1496364 original size:2 final size:2
Alignment explanation
Indices: 1496357--1496381 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1496347 AGAGAATCTT
1496357 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
1496382 TAAGCAGTAG
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:1496726 original size:23 final size:23
Alignment explanation
Indices: 1496684--1496742 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
1496674 GTTACAAGTA
1496684 AAATTATATTAATTTAATTAA-AT
1 AAATTATA-TAATTTAATTAATAT
1496707 AAATTATA-AATTTAATATTAATAT
1 AAATTATATAATTT-A-ATTAATAT
*
1496731 AATATAATATAA
1 AA-ATTATATAA
1496743 ATATTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.17
22 1 0.03
23 13 0.43
24 4 0.13
25 5 0.17
26 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTATATAATTTAATTAATAT
Found at i:1496773 original size:16 final size:16
Alignment explanation
Indices: 1496740--1496784 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1496730 TAATATAATA
**
1496740 TAAATATTTATATTTT
1 TAAATATTTATAAATT
1496756 TAAATATTTATAAATT
1 TAAATATTTATAAATT
*
1496772 TATAT-TTTATAAA
1 TAAATATTTATAAA
1496785 AATTACTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATATTTATAAATT
Found at i:1496795 original size:24 final size:24
Alignment explanation
Indices: 1496701--1496789 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 24
1496691 ATTAATTTAA
1496701 TTAAATAAATTATAAATTTAATATTAAT
1 TTAAAT-AATTATAAATTT-ATATT--T
*
1496729 ATAATATAA-TATAAATATTTATATTT
1 TTAA-ATAATTAT-AA-ATTTATATTT
*
1496755 TTAAATATTTATAAATTTATATTT
1 TTAAATAATTATAAATTTATATTT
1496779 TATAAA-AATTA
1 T-TAAATAATTA
1496790 CTAATTCTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
24 15 0.29
25 9 0.17
26 7 0.13
27 3 0.06
28 12 0.23
29 6 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAAATAATTATAAATTTATATTT
Found at i:1496928 original size:2 final size:2
Alignment explanation
Indices: 1496921--1496958 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1496911 TACACAATAA
* *
1496921 AT AT AT AT AT AT AT AT AT AT AT GT CT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1496959 ATTAGCTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1497442 original size:2 final size:2
Alignment explanation
Indices: 1497435--1497469 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1497425 CAAACAGCTT
1497435 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1497470 TCAAGTACAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1497892 original size:18 final size:18
Alignment explanation
Indices: 1497869--1497917 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
1497859 TTATATTATT
1497869 TAAAATTAAAAATAATAA
1 TAAAATTAAAAATAATAA
*
1497887 TAAAATTAATTATTATAATAA
1 TAAAATTAA--A-AATAATAA
1497908 T-AAATTAAAA
1 TAAAATTAAAA
1497918 TCAGTAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
18 10 0.38
20 8 0.31
21 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATTAAAAATAATAA
Found at i:1498857 original size:232 final size:227
Alignment explanation
Indices: 1498556--1499291 Score: 710
Period size: 225 Copynumber: 3.2 Consensus size: 227
1498546 AATATAAACC
* * * * *
1498556 AGTATTACATACTTTTATTATAATTACGCATATATATTATTTATATT-CATAAATTATTATAAAA
1 AGTATTACATATTTTTCTTACAATTACACATATATATTATTTAT-TTACATAAATTATGATAAAA
* * *
1498620 AATAATAAAACTTTTAATACATAAATTTATTATATTTACATAAAATTTTTGTAAGTTACAAAAAT
65 AATAAT-AAAGTTTTAATATATAAATTTATTATATTTA-ATAAAA-TTTTGTAAGTTACATAAAT
* * * * *
1498685 ATATTATCAATAGGTAATAGAAAGTAGTATTATATAAAATATTACAATTATATAAATTGTATTAT
127 ATATTACCAATAAGTAATAGAAAGTAGTATTAAATAAAATATTA-AATTACATAAATTATATTAT
* *
1498750 CTACTATAAACGTTTATCATCGTA-AGGTAATAGAAATA
191 CTACTACAAACGTTTATCAT--AACAGGTAATAGAAATA
*
1498788 AGTATTACACATTTTTCTTACAATTACACATAT-TCATTATTTATTTACATAAATTATGATAAAA
1 AGTATTACATATTTTTCTTACAATTACACATATAT-ATTATTTATTTACATAAATTATGATAAAA
* * * *
1498852 AATAAT-AAGTTATT-ATGTATAAATTTA-TACATTTATATAAAAATTCTGTAAGTTACATAAAC
65 AATAATAAAGTT-TTAATATATAAATTTATTATATTTA-AT-AAAATTTTGTAAGTTACATAAAT
* * * * * *
1498914 ATATTACCAATAAGTAATAAAAAATAGTATTACATAAAATATTATAGTTACATACATTATAATAT
127 ATATTACCAATAAGTAATAGAAAGTAGTATTAAATAAAATATTA-AATTACATAAATTATATTAT
* * * * *
1498979 TTATTGCATACGTTTATCATAACAGGTAATAGAATTA
191 CTACTACAAACGTTTATCATAACAGGTAATAGAAATA
* * * * * *
1499016 AGTATTTCATGTTTTTCTTACAATTACAAATATATATTATATA-TTATATAAATTATGATAAAAG
1 AGTATTACATATTTTTCTTACAATTACACATATATATTATTTATTTACATAAATTATGATAAAAA
* * * * * *
1499080 ATAATAAAGTTGTAAAATATAAATTTATGATATTTAA-AAAATTTTATAAATTACTTAAATATAT
66 ATAATAAAGTTTTAATATATAAATTTATTATATTTAATAAAATTTTGTAAGTTACATAAATATAT
* *
1499144 TAGCAA-ATGTAATAGAAAGTAGTATTAAATAAAATATAATAAATT-CATAAATTATATTATCTA
131 TACCAATAAGTAATAGAAAGTAGTATTAAATAAAATAT--TAAATTACATAAATTATATTATCTA
* * *
1499207 -TAGCATAA-GTTTATTATCATACA--TAACAAAAATA
194 CTA-CA-AACGTTTATCAT-A-ACAGGTAATAGAAATA
* * * * * * *
1499241 TGTATTACATATTTTTATTATACTTACATATATACATTATGTA-TTACATAA
1 AGTATTACATATTTTTCTTACAATTACACATATATATTATTTATTTACATAA
1499292 TCATTAGAAT
Statistics
Matches: 415, Mismatches: 74, Indels: 37
0.79 0.14 0.07
Matches are distributed among these distances:
224 1 0.00
225 101 0.24
226 32 0.08
227 31 0.07
228 66 0.16
229 101 0.24
230 19 0.05
231 5 0.01
232 59 0.14
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (227 bp):
AGTATTACATATTTTTCTTACAATTACACATATATATTATTTATTTACATAAATTATGATAAAAA
ATAATAAAGTTTTAATATATAAATTTATTATATTTAATAAAATTTTGTAAGTTACATAAATATAT
TACCAATAAGTAATAGAAAGTAGTATTAAATAAAATATTAAATTACATAAATTATATTATCTACT
ACAAACGTTTATCATAACAGGTAATAGAAATA
Found at i:1499440 original size:20 final size:20
Alignment explanation
Indices: 1499382--1499442 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
1499372 TTATATGAAA
1499382 CAAATTACATAAAAATATTAT
1 CAAATTACAT-AAAATATTAT
*
1499403 CGAATTACATATAAATATTA-
1 CAAATTACATA-AAATATTAT
*
1499423 CAAAGTTATATAAAATATTA
1 CAAA-TTACATAAAATATTA
1499443 ATAAAATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 12 0.34
21 23 0.66
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
CAAATTACATAAAATATTAT
Found at i:1499634 original size:20 final size:20
Alignment explanation
Indices: 1499594--1499635 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1499584 TAAAAAATTT
* * *
1499594 TATATTTTTTATTTTATTAA
1 TATATTTTTAATATTAGTAA
1499614 TATATTTTTAATATTAGTAA
1 TATATTTTTAATATTAGTAA
1499634 TA
1 TA
1499636 AATATATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TATATTTTTAATATTAGTAA
Found at i:1499870 original size:21 final size:21
Alignment explanation
Indices: 1499818--1499871 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1499808 TTGTATGTAA
*
1499818 CAAATTACGT-AAAATATTAT
1 CAAATTACATAAAAATATTAT
*
1499838 CAAATTATATAAAAATATTA-
1 CAAATTACATAAAAATATTAT
*
1499858 CAGAGTTACATAAA
1 CA-AATTACATAAA
1499872 TCATTATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (21 bp):
CAAATTACATAAAAATATTAT
Found at i:1500024 original size:427 final size:422
Alignment explanation
Indices: 1499307--1500517 Score: 1503
Period size: 427 Copynumber: 2.9 Consensus size: 422
1499297 AGAATATAAG
* * ** * * * *
1499307 TAATATTTATATATAATATGTATTATCGGTAATATATTTATATAAAAAAT-ATTTGAAGGTAATG
1 TAATATTTATATATAAGATGTGTTATAAGTAATGTATTTGTATAAATAATCA-TTGAAGGTAATA
* * * *
1499371 TTTATATGAAACAAATTACATAAAAATATTATCGAATTACATATAAATATTACAAAGTTATATAA
65 TTT-TATG-AACAAATTAC-T-AAAATATTATCAAATTACATAAAAATATTACAGAGTTACAT-A
* *
1499436 AAT-ATTAAT-AAAATTATAATATACATATATATGTGTGTAAAACATTA-TTTCAAGAAAATTAA
125 AATCATT-ATCAAAACTATAATGTAC-T-TATA------TAAAACATTATTTTCAAGAAAATTAA
1499498 ATATAATTTTTTTCAAAA--TAATTTTTGATTATTTATTAAATATATTATATATGTAGGAAATTT
181 ATATAATTTTTTT-AAAATTTAATTTTTGATT-TTTATTAAATATATTATATATGTAGGAAA-TT
*
1499561 AATTTTTTATTAACTTTTGACGTTAAAAAATTTTATATTTTTTATTTTATTAATATATTTTTAAT
243 AATTTTTTATTAACTTTTGAAGTT-AAAAATTTTATATTTTTTATTTTATTAATATATTTTTAAT
* *
1499626 ATTAGTAATAAATATATTATATCAATAAAAATAAATTTATAATAATTTTTTTACTTTTTTATCAA
307 ATTAGTAATAAATATATTATAT-AATAAAAATAAATTTATAATAAATTTTGTACTTTTTTATCAA
*
1499691 TTACTGAAATTGCATAAAACTATTGAAATTACTAAAATCATTAGAGTGCAAA
371 TTACTGAAATTACATAAAACTATTGAAATTACTAAAATCATTAGAGTGCAAA
* *
1499743 TAATATTTATATGTAAGATGTGTTATAAGTAATGTATTTGTGTAAATAATCATTGAAGGTAATAT
1 TAATATTTATATATAAGATGTGTTATAAGTAATGTATTTGTATAAATAATCATTGAAGGTAATAT
*
1499808 TTGTATGTAACAAATTACGTAAAATATTATCAAATTATATAAAAATATTACAGAGTTACATAAAT
66 TT-TATG-AACAAATTAC-TAAAATATTATCAAATTACATAAAAATATTACAGAGTTACATAAAT
1499873 CATTATCAAAACTATAATGTACTTATATAAAACATTATTTTCAAGAAAATTAAATATAA-TTTTT
128 CATTATCAAAACTATAATGTACTTATATAAAACATTATTTTCAAGAAAATTAAATATAATTTTTT
* *
1499937 TAAAATTTAAATTTT-ATTTTCTATTATATATATTATATATGTAGGAAATTAAATTTTTTATTAA
193 TAAAATTTAATTTTTGATTTT-TATTAAATATATTATATATGTAGGAAATT-AATTTTTTATTAA
* *
1500001 CTTTTGAAGTTAAAACTTTTTATATTTTTTATTTTATTAATATATTTTTAATATTAGTAGTAAAT
256 CTTTTGAAGTTAAAA-ATTTTATATTTTTTATTTTATTAATATATTTTTAATATTAGTAATAAAT
*
1500066 ATATTATATTAATAAAAATAAATTTATAATAAATTTTGTACTTTTTTATCAATTACTGGAATTAC
320 ATATTATA-TAATAAAAATAAATTTATAATAAATTTTGTACTTTTTTATCAATTACTGAAATTAC
* *
1500131 ATGAAACTATTGAAATTACTAAAATTATTAGAGTGCAAA
384 ATAAAACTATTGAAATTACTAAAATCATTAGAGTGCAAA
* * * * *
1500170 TAATATTTGTTTCTAAGATATGTTATAAGTAATGTATTTGTATAAATAATCTTTGAAGGTAATA-
1 TAATATTTATATATAAGATGTGTTATAAGTAATGTATTTGTATAAATAATCATTGAAGGTAATAT
1500234 -TT-TG-------TA-T---ATA--A-CAAATTACATAAAAATATTACAGAGTTACATAAATCAT
66 TTTATGAACAAATTACTAAAATATTATCAAATTACATAAAAATATTACAGAGTTACATAAATCAT
* * * * * *
1500283 TACCAAAACTACAATGTACTTATGTAAAATATTATTTTCAAAAAAAATTAAATATAATTTTTTTC
131 TATCAAAACTATAATGTACTTATATAAAACATTATTTTC-AAGAAAATTAAATATAATTTTTTTA
* *
1500348 AAATTT-ATTTTTGGTTTTTTATTAAATATATTATATATGTAGGAAATT-ATTTTTTAGTAA-TT
195 AAATTTAATTTTT-GATTTTTATTAAATATATTATATATGTAGGAAATTAATTTTTTATTAACTT
* ** *
1500410 TTGAATTTAAAAAAATTATATTTTTTAGTTTATTAATATATTTTTTAATATTAGTAATAAATATA
259 TTGAAGTTAAAAATTTTATATTTTTTATTTTATTAATATA-TTTTTAATATTAGTAATAAATATA
* *
1500475 TTATAT--TAAAAATTAATTTTATAATAAAATTTGTA-TTTTTTAT
323 TTATATAATAAAAA-TAAATTTATAATAAATTTTGTACTTTTTTAT
1500518 TAGTTGGTAA
Statistics
Matches: 703, Mismatches: 56, Indels: 65
0.85 0.07 0.08
Matches are distributed among these distances:
403 14 0.02
404 20 0.03
405 25 0.04
406 41 0.06
407 83 0.12
408 22 0.03
409 40 0.06
410 7 0.01
413 1 0.00
415 2 0.00
423 2 0.00
424 1 0.00
425 1 0.00
426 12 0.02
427 269 0.38
428 29 0.04
433 4 0.01
434 7 0.01
435 52 0.07
436 70 0.10
437 1 0.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (422 bp):
TAATATTTATATATAAGATGTGTTATAAGTAATGTATTTGTATAAATAATCATTGAAGGTAATAT
TTTATGAACAAATTACTAAAATATTATCAAATTACATAAAAATATTACAGAGTTACATAAATCAT
TATCAAAACTATAATGTACTTATATAAAACATTATTTTCAAGAAAATTAAATATAATTTTTTTAA
AATTTAATTTTTGATTTTTATTAAATATATTATATATGTAGGAAATTAATTTTTTATTAACTTTT
GAAGTTAAAAATTTTATATTTTTTATTTTATTAATATATTTTTAATATTAGTAATAAATATATTA
TATAATAAAAATAAATTTATAATAAATTTTGTACTTTTTTATCAATTACTGAAATTACATAAAAC
TATTGAAATTACTAAAATCATTAGAGTGCAAA
Found at i:1500467 original size:21 final size:20
Alignment explanation
Indices: 1500426--1500468 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1500416 TTAAAAAAAT
* *
1500426 TATATTTTTTAGTTTATTAA
1 TATATTTTTTAATTTAGTAA
1500446 TATATTTTTTAATATTAGTAA
1 TATATTTTTTAAT-TTAGTAA
1500467 TA
1 TA
1500469 AATATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TATATTTTTTAATTTAGTAA
Found at i:1500982 original size:406 final size:409
Alignment explanation
Indices: 1500212--1500998 Score: 1005
Period size: 406 Copynumber: 1.9 Consensus size: 409
1500202 TGTATTTGTA
* *
1500212 TAAATAATCTTTGAAGGTAATATTTGTATATAACAAATTACATAAAAATATTACAGAGTTACATA
1 TAAAAAATCTTTAAAGGTAATATTTGTATATAACAAATTACATAAAAATATTACAGAGTTACATA
* * * *
1500277 AATCATTACCAAAACTACAATGTACTTATGTAAAATATTATTTTCAAAAAAAATTAAATATAATT
66 AATCATTACAAAAACTACAATGTACTTATGTAAAACATTAATTTCAAAAAAAATTAAATATAATA
* * * *
1500342 TTTTTCAAATTTATTTTTGGTTTTTTATTAAATATATTATATATGTAGGAAATTATTTTTTAGTA
131 TTTTTCAAAATTATTTTTGG-----TATTAAATATATTATACATGTAAGAAATTATTTTTTAGAA
*
1500407 ATTTTGAATTTAAAAAAATTATATTTTTTAGTTTATTAATATATTTTTTAATATTAGTAATAAAT
191 ATTTTGAATTTAAAAAAATTATATTTTTTAGTTTATTAATATATTTTTTAATATTAATAATAAAT
* *
1500472 ATATTATATTAAAAATTAATTTTATAATAAAATTTGTATTTTTTATTAGTTGGTAAGAATTACAA
256 ATATTATATAAAAAATTAATTTTATAATAAAATTAGTATTTTTTATTAGTTGGTAAGAATTACAA
* *
1500537 CTAAAAATTATCAAAATTATGCATATACATTATAATTTACATAAACTATTAGAGTGTACATAATA
321 CTAAAAATTACCAAAATTATGCATATACATTACAATTTACATAAACTATTAGAGTGTACATAATA
1500602 TTTGTTATGAGAAATATTTGTGTG
386 TTTGTTATGAGAAATATTTGTGTG
* * * *
1500626 TAAAAAATCTTTAAAGGTAATGTTTGTATGTAACAATTTATATAAAAATATTACTAGA-TTACAT
1 TAAAAAATCTTTAAAGGTAATATTTGTATATAACAAATTACATAAAAATATTAC-AGAGTTAC--
* * * *
1500690 ATAAAT-ATTACAAAAACTATAATGTATTTATGTAAAACA-TAATTTC-AAGAAATTTAAATATA
63 ATAAATCATTACAAAAACTACAATGTACTTATGTAAAACATTAATTTCAAAAAAAATTAAATATA
* *
1500752 A-ATTTTTCAAAATTA-TTTT-G-ATT-TATATA-T-TACGTGTAAGAAATTTATTTTTTCTA-A
128 ATATTTTTCAAAATTATTTTTGGTATTAAATATATTATACATGTAAGAAA-TTA-TTTTT-TAGA
*
1500809 AATTTTGAATTTAAAAAAATTATTATTTTTTATTTTATTAATATA-TTTTTAATATTAAT-ATAA
190 AATTTTGAATTTAAAAAAATTA-TATTTTTTAGTTTATTAATATATTTTTTAATATTAATAATAA
*
1500872 ATATATTGTACTAATAAAAAATTGATTTTATAATAAAATGTAG-ATTTTTTATTAGTTGGTAAGA
254 ATATA-T-TA-T-ATAAAAAATTAATTTTATAATAAAAT-TAGTATTTTTTATTAGTTGGTAAGA
* * * *
1500936 ATTATAACTAAAGATTACCAATA-T-TGCATATACACATTACAATTTACATAAATTATTAGAGTG
314 ATTACAACTAAAAATTACCAAAATTATGCATAT--ACATTACAATTTACATAAACTATTAGAGTG
1500999 CAAATAATGT
Statistics
Matches: 328, Mismatches: 31, Indels: 36
0.83 0.08 0.09
Matches are distributed among these distances:
401 10 0.03
402 13 0.04
403 46 0.14
404 35 0.11
405 2 0.01
406 92 0.28
407 2 0.01
410 1 0.00
411 4 0.01
412 12 0.04
413 15 0.05
414 58 0.18
415 32 0.10
416 6 0.02
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.44
Consensus pattern (409 bp):
TAAAAAATCTTTAAAGGTAATATTTGTATATAACAAATTACATAAAAATATTACAGAGTTACATA
AATCATTACAAAAACTACAATGTACTTATGTAAAACATTAATTTCAAAAAAAATTAAATATAATA
TTTTTCAAAATTATTTTTGGTATTAAATATATTATACATGTAAGAAATTATTTTTTAGAAATTTT
GAATTTAAAAAAATTATATTTTTTAGTTTATTAATATATTTTTTAATATTAATAATAAATATATT
ATATAAAAAATTAATTTTATAATAAAATTAGTATTTTTTATTAGTTGGTAAGAATTACAACTAAA
AATTACCAAAATTATGCATATACATTACAATTTACATAAACTATTAGAGTGTACATAATATTTGT
TATGAGAAATATTTGTGTG
Found at i:1501928 original size:19 final size:21
Alignment explanation
Indices: 1501883--1501944 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 21
1501873 TAGTGATAAA
*
1501883 TATATTATATTAATAAAAAAT
1 TATATTTTATTAATAAAAAAT
*
1501904 TA-ATTTTA-TAAT-AAAATT
1 TATATTTTATTAATAAAAAAT
*
1501922 TATATTTTTTATTAATAGAAAAT
1 TATA--TTTTATTAATAAAAAAT
1501945 AATTACTGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 7 0.22
19 5 0.16
20 5 0.16
21 7 0.22
22 4 0.12
23 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TATATTTTATTAATAAAAAAT
Found at i:1502334 original size:28 final size:28
Alignment explanation
Indices: 1502303--1502357 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1502293 ATTTTATACT
*
1502303 AATT-AAAAATAAAAAAATAAATGTTAAA
1 AATTAAAAAAT-AAAAAATAAATATTAAA
*
1502331 AATTAAAAAATTAAAAATAAATATTAA
1 AATTAAAAAATAAAAAATAAATATTAA
1502358 TTAATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (28 bp):
AATTAAAAAATAAAAAATAAATATTAAA
Found at i:1511546 original size:116 final size:110
Alignment explanation
Indices: 1511418--1511687 Score: 300
Period size: 116 Copynumber: 2.4 Consensus size: 110
1511408 AAATAATCTT
1511418 TAATATAT-ATAAATTTTAATTTTAATATTTATAATTTATTTTTATAACTTAAGATTATGGTAAT
1 TAATATATAATAAATTTTAATTTTAATATTTATAATTTATTTTTATAACTTAA-A--ATGGTAAT
* * *
1511482 TTTTTTATTAAAAAAATATTT-GAGAAGTAAGAAAT-TTTTGAAATTAAAAA
63 TTTTTTAAT-AAAAAATATTTAAAG-AGTAAGAAATCTATT-AAATT-AAAA
* *** *
1511532 GTAATAT-TCAATAAATTTAAATTTTAATATTTATAA-TTATTTTTTATTTTTTAAAATTGTAAT
1 -TAATATAT-AATAAATTTTAATTTTAATATTTATAATTTA-TTTTTATAACTTAAAATGGTAAT
1511595 TTTTTTAATAAAAAATATTTAAAGAGTAAGAAATCTATTAAATTAAAA
63 TTTTTTAATAAAAAATATTTAAAGAGTAAGAAATCTATTAAATTAAAA
* *
1511643 TACTATATAATAAATTTTAATTTTAAT-TTTAATATTTATATTTTT
1 TAATATATAATAAATTTTAATTTTAATATTT-ATAATT-TATTTTT
1511688 TTTCTTAAAA
Statistics
Matches: 135, Mismatches: 11, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
109 3 0.02
110 26 0.19
111 11 0.08
112 28 0.21
113 20 0.15
114 1 0.01
115 10 0.07
116 36 0.27
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (110 bp):
TAATATATAATAAATTTTAATTTTAATATTTATAATTTATTTTTATAACTTAAAATGGTAATTTT
TTTAATAAAAAATATTTAAAGAGTAAGAAATCTATTAAATTAAAA
Done.