Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004372.1 Hibiscus syriacus cultivar Beakdansim tig00009577_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 111654
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5036 original size:32 final size:32
Alignment explanation
Indices: 4974--5036 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
4964 AAGAGAGGCA
* * *
4974 TAGAGTATTAAATATATTTTAAACGTATTAAC
1 TAGAGTATTAAAGATATTTGAAACGAATTAAC
*
5006 TAGAGTATTAAAGA-ATTTGACAATGAATTAA
1 TAGAGTATTAAAGATATTTGA-AACGAATTAA
5037 TTTGGCAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.37
Consensus pattern (32 bp):
TAGAGTATTAAAGATATTTGAAACGAATTAAC
Found at i:15405 original size:21 final size:20
Alignment explanation
Indices: 15381--15419 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
15371 ACAAGAGCAC
* *
15381 TTGTATAACAGACTTTAACAG
1 TTGTACAACA-ACCTTAACAG
15402 TTGTACAACAACCTTAAC
1 TTGTACAACAACCTTAAC
15420 CAACTTAGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (20 bp):
TTGTACAACAACCTTAACAG
Found at i:15454 original size:22 final size:21
Alignment explanation
Indices: 15408--15455 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
15398 ACAGTTGTAC
*
15408 AACAACCTTAACCAACTTAGTT
1 AACAACCTTAACCAACCTAG-T
15430 AACAACCTCATAACCAACCTA-T
1 AACAACCT--TAACCAACCTAGT
15452 AACA
1 AACA
15456 GACACAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 13 0.57
24 10 0.43
ACGTcount: A:0.46, C:0.31, G:0.02, T:0.21
Consensus pattern (21 bp):
AACAACCTTAACCAACCTAGT
Found at i:21046 original size:40 final size:40
Alignment explanation
Indices: 20991--21112 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
20981 TGCAGGTTTA
20991 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
*
21031 TAATACACTTTGGTGTATATAGTGGGCACGACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
*
21071 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
21111 TA
1 TA
21113 GCACTACGGT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:21318 original size:47 final size:44
Alignment explanation
Indices: 21217--21341 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 44
21207 GTAACCATGC
* *
21217 AAATAAGCTTATGAGCTTATGGAAT-AATGGCAAGTATATATGA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATATGA
*
21260 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTAT-TTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAT-G-A
*
21307 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
21342 AGATTTTATA
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
43 23 0.32
45 14 0.19
46 12 0.16
47 24 0.33
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATATGA
Found at i:24186 original size:15 final size:15
Alignment explanation
Indices: 24168--24213 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
24158 AGAAGAAGAA
*
24168 AAAAAATAGAAAAGG
1 AAAAAATAGAAAAAG
*
24183 AAAATATAGAAAAAG
1 AAAAAATAGAAAAAG
24198 --AAAAT-GAAAAAG
1 AAAAAATAGAAAAAG
24210 AAAA
1 AAAA
24214 TGAAAACGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 2 0.08
15 13 0.50
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (15 bp):
AAAAAATAGAAAAAG
Found at i:24186 original size:16 final size:16
Alignment explanation
Indices: 24150--24201 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
24140 AAGAAGAAGA
* *
24150 AAAAAAACAGAAGAAGA
1 AAAAAAATAGAA-AAGG
24167 AAAAAAATAGAAAAGG
1 AAAAAAATAGAAAAGG
* *
24183 -AAAATATAGAAAAAG
1 AAAAAAATAGAAAAGG
24198 AAAA
1 AAAA
24202 TGAAAAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 13 0.43
16 6 0.20
17 11 0.37
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (16 bp):
AAAAAAATAGAAAAGG
Found at i:24186 original size:17 final size:17
Alignment explanation
Indices: 24141--24178 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
24131 ATATATTATA
24141 AGAAGAAGAAAAAAAAC
1 AGAAGAAGAAAAAAAAC
*
24158 AGAAGAAGAAAAAAAAT
1 AGAAGAAGAAAAAAAAC
24175 AGAA
1 AGAA
24179 AAGGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (17 bp):
AGAAGAAGAAAAAAAAC
Found at i:24199 original size:6 final size:6
Alignment explanation
Indices: 24140--24244 Score: 72
Period size: 6 Copynumber: 17.3 Consensus size: 6
24130 CATATATTAT
* * * * *
24140 AAGAAG AAGAAA AA-AAA CAGAAG AAGAAA AA-AAA TAGAAA AGGAAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG-AAA
* * * *
24187 TATAGAAA AAGAAA ATGAAA AAGAAA ATGAAA ACGAGA AAG-AA AAGAAA
1 -A-AGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
24236 AAGAGAA AA
1 AAGA-AA AA
24245 AAATGAGAGA
Statistics
Matches: 76, Mismatches: 16, Indels: 13
0.72 0.15 0.12
Matches are distributed among these distances:
5 12 0.16
6 51 0.67
7 8 0.11
8 4 0.05
9 1 0.01
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:24219 original size:33 final size:32
Alignment explanation
Indices: 24158--24219 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
24148 GAAAAAAAAC
*
24158 AGAAGAAGAAAAAAAATAGAAAAGGAAAATAT
1 AGAAAAAGAAAAAAAATAGAAAAGGAAAATAT
*
24190 AGAAAAAGAAAATGAAAA-AGAAAATGAAAA
1 AGAAAAAGAAAA--AAAATAGAAAAGGAAAA
24220 CGAGAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 11 0.42
33 11 0.42
34 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (32 bp):
AGAAAAAGAAAAAAAATAGAAAAGGAAAATAT
Found at i:27874 original size:40 final size:40
Alignment explanation
Indices: 27818--27899 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 40
27808 TGCAGGTTTA
*
27818 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGAACGACCTTATGTG
27858 TAATACACTTCT-GTGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTT-TGGTGTATATGGTGGGAACGACCTTATGTG
27898 TA
1 TA
27900 GCACTACGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (40 bp):
TAATACACTTTGGTGTATATGGTGGGAACGACCTTATGTG
Found at i:28098 original size:47 final size:45
Alignment explanation
Indices: 28004--28129 Score: 166
Period size: 47 Copynumber: 2.8 Consensus size: 45
27994 GTAACCATGC
* *
28004 AAATAAGCTTATGAGCTTATGGAAT-AATGGCAAGTATATATGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATATGAA
* *
28048 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTAT-TTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAT-GAA
*
28095 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
28130 AGATTTTATA
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
44 23 0.32
45 11 0.15
46 3 0.04
47 36 0.49
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATATGAA
Found at i:28591 original size:23 final size:23
Alignment explanation
Indices: 28565--28625 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
28555 AGATTGTTAA
*
28565 AGGGGTACCGATTCCCCTGCTAC
1 AGGGGAACCGATTCCCCTGCTAC
*
28588 A-GGGAATCGATTCCCCTGCTAC
1 AGGGGAACCGATTCCCCTGCTAC
*
28610 A-GGGAATCGATTCCCC
1 AGGGGAACCGATTCCCC
28626 CACTGTTCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.21, C:0.33, G:0.25, T:0.21
Consensus pattern (23 bp):
AGGGGAACCGATTCCCCTGCTAC
Found at i:28598 original size:22 final size:22
Alignment explanation
Indices: 28573--28625 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
28563 AAAGGGGTAC
28573 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
28595 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCTGCTACAGGGAAT
28617 CGATTCCCC
1 CGATTCCCC
28626 CACTGTTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.23
Consensus pattern (22 bp):
CGATTCCCCTGCTACAGGGAAT
Found at i:30108 original size:22 final size:22
Alignment explanation
Indices: 30079--30132 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
30069 ATAATAGACT
30079 TTAA-CAACTT-GTACAACAACC
1 TTAACCAACTTAGT-CAACAACC
*
30100 TTAACCAACTTAGTTAACAACC
1 TTAACCAACTTAGTCAACAACC
30122 TCATAACCAAC
1 T--TAACCAAC
30133 CTATAACAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.14
22 14 0.50
23 2 0.07
24 8 0.29
ACGTcount: A:0.43, C:0.30, G:0.04, T:0.24
Consensus pattern (22 bp):
TTAACCAACTTAGTCAACAACC
Found at i:30139 original size:22 final size:21
Alignment explanation
Indices: 30093--30140 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
30083 CAACTTGTAC
*
30093 AACAACCTTAACCAACTTAGTT
1 AACAACCTTAACCAACCTAG-T
30115 AACAACCTCATAACCAACCTA-T
1 AACAACCT--TAACCAACCTAGT
30137 AACA
1 AACA
30141 GACACAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 13 0.57
24 10 0.43
ACGTcount: A:0.46, C:0.31, G:0.02, T:0.21
Consensus pattern (21 bp):
AACAACCTTAACCAACCTAGT
Found at i:33705 original size:19 final size:19
Alignment explanation
Indices: 33681--33717 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
33671 ATGACCAATA
*
33681 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
33700 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
33718 CATTATCGCA
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:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:34068 original size:22 final size:22
Alignment explanation
Indices: 34043--34093 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
34033 CTACGGCGAC
34043 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
34065 ATCCATCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
34087 ATCCGTC
1 ATCCGTC
34094 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.45, G:0.12, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:34538 original size:20 final size:20
Alignment explanation
Indices: 34513--34550 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34503 CGATTTTCAT
34513 TTCTCGTTCCGATAGTCAAA
1 TTCTCGTTCCGATAGTCAAA
*
34533 TTCTCGTTGCGATAGTCA
1 TTCTCGTTCCGATAGTCA
34551 TTTTCGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (20 bp):
TTCTCGTTCCGATAGTCAAA
Found at i:34586 original size:20 final size:20
Alignment explanation
Indices: 34538--34588 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
34528 TCAAATTCTC
**
34538 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
34558 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
34578 GTTGCGATTTT
1 GTTGCGATTTT
34589 AAGTTTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:34595 original size:20 final size:20
Alignment explanation
Indices: 34552--34595 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
34542 CGATAGTCAT
* *
34552 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
34572 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
34592 TTTC
1 TTTC
34596 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:36670 original size:20 final size:20
Alignment explanation
Indices: 36623--36710 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
36613 CGATTATCCC
** *
36623 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGT
* * *
36643 GTTACGATAGACATTTCCGT
1 GTTGCGATAGTCATTTTCGT
*
36663 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGT
*
36683 ATTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
36703 GTTGCGAT
1 GTTGCGAT
36711 TTTAAGTTTC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:36682 original size:40 final size:40
Alignment explanation
Indices: 36623--36710 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
36613 CGATTATCCC
*
36623 GTTGCGATAGTCAAATTCGCGTTACGATAGACATTTCCGT
1 GTTGCGATAGTCAAATTCGCATTACGATAGACATTTCCGT
** * * *
36663 GTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCAAATTCGCATTACGATAGACATTTCCGT
36703 GTTGCGAT
1 GTTGCGAT
36711 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (40 bp):
GTTGCGATAGTCAAATTCGCATTACGATAGACATTTCCGT
Found at i:37240 original size:42 final size:42
Alignment explanation
Indices: 37171--37282 Score: 116
Period size: 42 Copynumber: 2.7 Consensus size: 42
37161 CTGTCATCGT
* * * *
37171 TCAAGAGGCCTCTCCTATCGTTTAAGAGGCCCCTATCATCCC
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * **
37213 TCAAGAGTCCCCTCCCACCGTTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * * *
37255 TGAAGAGGTCCCTCCCACCATTCTAGAG
1 TCAAGAGGCCCCTCCCACCGTTCAAGAG
37283 TCCGATTCAC
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
TCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:37255 original size:21 final size:21
Alignment explanation
Indices: 37160--37267 Score: 92
Period size: 21 Copynumber: 5.1 Consensus size: 21
37150 GCCCGACTCA
37160 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* * *
37181 TCT-CCTATCGTTTAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
37202 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
37223 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
37244 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
37265 CCT
1 CCT
37268 CCCACCATTC
Statistics
Matches: 65, Mismatches: 20, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:38607 original size:14 final size:14
Alignment explanation
Indices: 38588--38624 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
38578 TTATATTTAA
38588 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
38602 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
38616 TTGATTTGT
1 TTGATTTGT
38625 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:38791 original size:20 final size:20
Alignment explanation
Indices: 38766--39182 Score: 272
Period size: 20 Copynumber: 21.6 Consensus size: 20
38756 TTTCTAGTTT
*
38766 CGATAGTCAAATTCCCGTTG
1 CGATAGTCAAATTCGCGTTG
*
38786 CGATAGTCAAATTCCCGTTG
1 CGATAGTCAAATTCGCGTTG
* *
38806 CGATAATCAAATTCACGTTG
1 CGATAGTCAAATTCGCGTTG
* ***
38826 CGATAGTCAAAATCGCAACG
1 CGATAGTCAAATTCGCGTTG
* * ***
38846 CGAAAGTCAAAATCGCAACG
1 CGATAGTCAAATTCGCGTTG
*
38866 CGAAAGTC-AATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
* * * *
38885 CGATGGTCTAATACGCTTTG
1 CGATAGTCAAATTCGCGTTG
*
38905 CGAT--T----TTCTCGTTG
1 CGATAGTCAAATTCGCGTTG
* * *
38919 CGTTAGTAAAATTCCCGTTG
1 CGATAGTCAAATTCGCGTTG
* *
38939 CGATAATCAAATTCACGTTG
1 CGATAGTCAAATTCGCGTTG
* **
38959 CGATAGTCAAAATCGCAATG
1 CGATAGTCAAATTCGCGTTG
* * * ***
38979 TGAAAG-CTAAAATCGCAACG
1 CGATAGTC-AAATTCGCGTTG
* *
38999 CGAAAGTC-AATTTGCGTTG
1 CGATAGTCAAATTCGCGTTG
* * * * *
39018 CGATGGTCTAATACACTTTG
1 CGATAGTCAAATTCGCGTTG
* *
39038 CG--A-T---ATTCTCGTTA
1 CGATAGTCAAATTCGCGTTG
* *
39052 CGATAATCAAATTCACGTTG
1 CGATAGTCAAATTCGCGTTG
*
39072 CAATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
*
39092 CGATAGTGAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
*
39112 CGATAGTCAAATTCGAGTTG
1 CGATAGTCAAATTCGCGTTG
*
39132 CGATAGTC-AATTTGCGTTG
1 CGATAGTCAAATTCGCGTTG
39151 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
*
39171 CGATATTCAAAT
1 CGATAGTCAAAT
39183 AAATGTGTAA
Statistics
Matches: 316, Mismatches: 64, Indels: 34
0.76 0.15 0.08
Matches are distributed among these distances:
14 17 0.05
16 2 0.01
17 2 0.01
18 1 0.00
19 43 0.14
20 250 0.79
21 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:38962 original size:133 final size:133
Alignment explanation
Indices: 38776--39178 Score: 531
Period size: 133 Copynumber: 3.0 Consensus size: 133
38766 CGATAGTCAA
*
38776 ATTCCCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCG
1 ATTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCG
* *
38841 CAACGCGAAAGTCAAAATCGCAACGCGAAAGTCAATTCGCGTTGCGATGGTCTAATACGCTTTGC
66 CAATGCGAAAGTCAAAATCGCAACGCGAAAGTCAATTTGCGTTGCGATGGTCTAATACGCTTTGC
38906 GAT
131 GAT
* * *
38909 TTTCTCGTTGCGTTAGTAAAATTCCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCG
1 ATTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCG
* *
38974 CAATGTGAAAG-CTAAAATCGCAACGCGAAAGTCAATTTGCGTTGCGATGGTCTAATACACTTTG
66 CAATGCGAAAGTC-AAAATCGCAACGCGAAAGTCAATTTGCGTTGCGATGGTCTAATACGCTTTG
39038 CGAT
130 CGAT
* * * * * * * *
39042 ATTCTCGTTACGATAATCAAATTCACGTTGCAATAGTCAAATTCGCGTTGCGATAGTGAAATTCG
1 ATTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCG
** * * ** * * * * *
39107 CGTTGCGATAGTCAAATTCG-AGTTGCGATAGTCAATTTGCGTTGCGATAGTCAAATTCGCGTTG
66 CAATGCGAAAGTCAAAATCGCA-ACGCGAAAGTCAATTTGCGTTGCGATGGTCTAATACGCTTTG
39171 CGAT
130 CGAT
39175 ATTC
1 ATTC
39179 AAATAAATGT
Statistics
Matches: 235, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
132 2 0.01
133 232 0.99
134 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (133 bp):
ATTCTCGTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCG
CAATGCGAAAGTCAAAATCGCAACGCGAAAGTCAATTTGCGTTGCGATGGTCTAATACGCTTTGC
GAT
Found at i:39007 original size:153 final size:153
Alignment explanation
Indices: 38729--39008 Score: 418
Period size: 153 Copynumber: 1.8 Consensus size: 153
38719 GCAAAAGACA
* * *
38729 TTGCGATAGTCTAATACGCTTTGCGATTTTCTAGTTTCGATAGTCAAATTCCCGTTGCGATAGTC
1 TTGCGATAGTCTAATACGCTTTGCGATTTTCTAGTTGCGATAGTAAAATTCCCGTTGCGATAATC
* * ** *
38794 AAATTCCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCGCAACGCGAAAGTCAAAAT
66 AAATTCACGTTGCGATAATCAAAATCACAATGCGAAAGTCAAAATCGCAACGCGAAAGTCAAAAT
38859 CGCAACGCGAAAGTCAATTCGCG
131 CGCAACGCGAAAGTCAATTCGCG
* * *
38882 TTGCGATGGTCTAATACGCTTTGCGATTTTCTCGTTGCGTTAGTAAAATTCCCGTTGCGATAATC
1 TTGCGATAGTCTAATACGCTTTGCGATTTTCTAGTTGCGATAGTAAAATTCCCGTTGCGATAATC
* * *
38947 AAATTCACGTTGCGATAGTCAAAATCGCAATGTGAAAG-CTAAAATCGCAACGCGAAAGTCAA
66 AAATTCACGTTGCGATAATCAAAATCACAATGCGAAAGTC-AAAATCGCAACGCGAAAGTCAA
39009 TTTGCGTTGC
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
152 1 0.01
153 111 0.99
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (153 bp):
TTGCGATAGTCTAATACGCTTTGCGATTTTCTAGTTGCGATAGTAAAATTCCCGTTGCGATAATC
AAATTCACGTTGCGATAATCAAAATCACAATGCGAAAGTCAAAATCGCAACGCGAAAGTCAAAAT
CGCAACGCGAAAGTCAATTCGCG
Found at i:39120 original size:113 final size:114
Alignment explanation
Indices: 38929--39135 Score: 256
Period size: 113 Copynumber: 1.8 Consensus size: 114
38919 CGTTAGTAAA
* * *
38929 ATTCCCGTTGCGATAATCAAATTCACGTTGCGATAGTCAAAATCGCAATGTGAAAGCTAAAATCG
1 ATTCCCGTTACGATAATCAAATTCACGTTGCAATAGTCAAAATCGCAATGCGAAAGCTAAAATCG
* *
38994 CAACGCGAAAGTC-AATTTGCGTTGCGATGGTCTAATACACTTTGCGAT
66 CAACGCGAAAGTCAAATTCGAGTTGCGATGGTCTAATACACTTTGCGAT
* * ** * *
39042 ATTCTCGTTACGATAATCAAATTCACGTTGCAATAGTCAAATTCGCGTTGCGATAG-TGAAATTC
1 ATTCCCGTTACGATAATCAAATTCACGTTGCAATAGTCAAAATCGCAATGCGAAAGCT-AAAATC
*** *
39106 GCGTTGCGATAGTCAAATTCGAGTTGCGAT
65 GCAACGCGAAAGTCAAATTCGAGTTGCGAT
39136 AGTCAATTTG
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
112 1 0.01
113 63 0.82
114 13 0.17
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (114 bp):
ATTCCCGTTACGATAATCAAATTCACGTTGCAATAGTCAAAATCGCAATGCGAAAGCTAAAATCG
CAACGCGAAAGTCAAATTCGAGTTGCGATGGTCTAATACACTTTGCGAT
Found at i:39171 original size:59 final size:60
Alignment explanation
Indices: 39042--39182 Score: 196
Period size: 59 Copynumber: 2.4 Consensus size: 60
39032 ACTTTGCGAT
* * *
39042 ATTCTCGTTACGATAATCAAATTCACGTTGCAATAGTCAAATTCGCGTTGCGATAGTGAA
1 ATTCGCGTTGCGATAATCAAATTCACGTTGCAATAGTCAAATTCGCGTTGCGATAGTCAA
* * *
39102 ATTCGCGTTGCGATAGTCAAATTCGA-GTTGCGATAGTC-AATTTGCGTTGCGATAGTCAA
1 ATTCGCGTTGCGATAATCAAATTC-ACGTTGCAATAGTCAAATTCGCGTTGCGATAGTCAA
*
39161 ATTCGCGTTGCGATATTCAAAT
1 ATTCGCGTTGCGATAATCAAAT
39183 AAATGTGTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
59 40 0.55
60 32 0.44
61 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (60 bp):
ATTCGCGTTGCGATAATCAAATTCACGTTGCAATAGTCAAATTCGCGTTGCGATAGTCAA
Found at i:39405 original size:140 final size:140
Alignment explanation
Indices: 39153--39435 Score: 503
Period size: 140 Copynumber: 2.0 Consensus size: 140
39143 TTGCGTTGCG
*
39153 ATAGTCAAATTCGCGTTGCGATATTCAAATAAATGTGTAATAAGTGATAACAACTAAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATAAATGTGTAACAAGTGATAACAACTAAACAGATCA
* * *
39218 TAGTAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
39283 AATACACATA
131 AATACACATA
* * *
39293 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAACAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATAAATGTGTAACAAGTGATAACAACTAAACAGATCA
39358 TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
39423 AATACACATA
131 AATACACATA
39433 ATA
1 ATA
39436 AAACGTTTGA
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 136 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATAAATGTGTAACAAGTGATAACAACTAAACAGATCA
TAGCAATGTTCAAAATCAAGTTACTAATAAATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:41481 original size:14 final size:15
Alignment explanation
Indices: 41462--41498 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
41452 TCCCGTGGTA
41462 TTTTCTTCGGGGA-C
1 TTTTCTTCGGGGATC
*
41476 TTTTCTTCGGGGATT
1 TTTTCTTCGGGGATC
41491 TTTTCTTC
1 TTTTCTTC
41499 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.05, C:0.19, G:0.22, T:0.54
Consensus pattern (15 bp):
TTTTCTTCGGGGATC
Found at i:42611 original size:20 final size:20
Alignment explanation
Indices: 42588--42628 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
42578 TCGCAACGCA
*
42588 ATAGTCAGAATCGCGTTGCG
1 ATAGTCAAAATCGCGTTGCG
*
42608 ATAGTCAAAATTGCGTTGCG
1 ATAGTCAAAATCGCGTTGCG
42628 A
1 A
42629 ATCTGGAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (20 bp):
ATAGTCAAAATCGCGTTGCG
Found at i:42678 original size:19 final size:19
Alignment explanation
Indices: 42654--42690 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42644 TGCGATAATG
*
42654 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
42673 GAGATCGTATTGCGATTT
1 GAGATCGCATTGCGATTT
42691 TATTGATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:54814 original size:21 final size:21
Alignment explanation
Indices: 54788--54880 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
54778 TGACAATCAG
**
54788 AGATGAGAAAACAGCCATCCA
1 AGATGAGAAAACAGCCGCCCA
*
54809 ATATGAGAAAACAGCCGCCCA
1 AGATGAGAAAACAGCCGCCCA
54830 AGATGAGAAAACAGCCGCCCA
1 AGATGAGAAAACAGCCGCCCA
54851 AGATGAGAAAACAGCCGCCCA
1 AGATGAGAAAACAGCCGCCCA
54872 AGATGAGAA
1 AGATGAGAA
54881 GGTGATTTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.45, C:0.25, G:0.23, T:0.08
Consensus pattern (21 bp):
AGATGAGAAAACAGCCGCCCA
Found at i:55442 original size:39 final size:39
Alignment explanation
Indices: 55389--55511 Score: 203
Period size: 39 Copynumber: 3.2 Consensus size: 39
55379 GGAAATGGAA
*
55389 CAGAA-GCAGGTCAGATTAGTTCATCTACTAGTGTGGGT
1 CAGAATGCAGGTCAGATAAGTTCATCTACTAGTGTGGGT
*
55427 CAGAATGCAGGTCAGATAAGTTCATCTACTTGTGTGGGT
1 CAGAATGCAGGTCAGATAAGTTCATCTACTAGTGTGGGT
**
55466 CAGAATGCAGGTCAGATAAGTTCATCTACTAAAGTGGGT
1 CAGAATGCAGGTCAGATAAGTTCATCTACTAGTGTGGGT
55505 CAGAATG
1 CAGAATG
55512 GACAACCAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
38 5 0.06
39 74 0.94
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (39 bp):
CAGAATGCAGGTCAGATAAGTTCATCTACTAGTGTGGGT
Found at i:59136 original size:2 final size:2
Alignment explanation
Indices: 59129--59160 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
59119 TGTAAATCAA
59129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59161 GTTCTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61977 original size:29 final size:29
Alignment explanation
Indices: 61943--62033 Score: 77
Period size: 29 Copynumber: 3.3 Consensus size: 29
61933 CTTCTGCAGT
61943 TTTTCTCCTCTTTCAAATTGGTTCTGGCA
1 TTTTCTCCTCTTTCAAATTGGTTCTGGCA
** * * *
61972 TTTTCTCC-C--TCGGCATCT--TCCTAG-T
1 TTTTCTCCTCTTTC-AAAT-TGGTTCTGGCA
61997 TTTTCTCCTCTTTCAAATTGGTTCTGGCA
1 TTTTCTCCTCTTTCAAATTGGTTCTGGCA
62026 TTTTCTCC
1 TTTTCTCC
62034 CTCGGCATCT
Statistics
Matches: 44, Mismatches: 10, Indels: 16
0.63 0.14 0.23
Matches are distributed among these distances:
25 8 0.18
26 8 0.18
27 4 0.09
28 8 0.18
29 16 0.36
ACGTcount: A:0.11, C:0.29, G:0.12, T:0.48
Consensus pattern (29 bp):
TTTTCTCCTCTTTCAAATTGGTTCTGGCA
Found at i:62000 original size:54 final size:54
Alignment explanation
Indices: 61940--62047 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
61930 TTTCTTCTGC
61940 AGTTTTTCTCCTCTTTCAAATTGGTTCTGGCATTTTCTCCCTCGGCATCTTCCT
1 AGTTTTTCTCCTCTTTCAAATTGGTTCTGGCATTTTCTCCCTCGGCATCTTCCT
61994 AGTTTTTCTCCTCTTTCAAATTGGTTCTGGCATTTTCTCCCTCGGCATCTTCCT
1 AGTTTTTCTCCTCTTTCAAATTGGTTCTGGCATTTTCTCCCTCGGCATCTTCCT
62048 GTTATATACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.11, C:0.30, G:0.13, T:0.46
Consensus pattern (54 bp):
AGTTTTTCTCCTCTTTCAAATTGGTTCTGGCATTTTCTCCCTCGGCATCTTCCT
Found at i:63245 original size:21 final size:21
Alignment explanation
Indices: 63219--63332 Score: 101
Period size: 21 Copynumber: 5.4 Consensus size: 21
63209 GTCTTCGACT
63219 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * **
63240 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAATTTGGAATAA
63261 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
63282 ATCGCAACACGAACTTCGACT--
1 ATCGC-A-ACGAATTTGGAATAA
63303 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
63324 ATCGCAACG
1 ATCGCAACG
63333 CGAACTTCGA
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
19 18 0.25
20 1 0.01
21 33 0.46
22 1 0.01
23 18 0.25
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:63270 original size:42 final size:42
Alignment explanation
Indices: 63211--63388 Score: 297
Period size: 42 Copynumber: 4.3 Consensus size: 42
63201 TAATACGTGT
63211 CTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAA
1 CTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAA
* *
63253 CTTCGCCTATCGCAACGAATTTGGAATAAATCGCAACACGAA
1 CTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAA
63295 CTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAA
1 CTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAA
* *
63337 CTTCGACTATCGCAATGAATTT-GAA-AAATCGCAACTCGAA
1 CTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAA
*
63377 CTTGGACTATCG
1 CTTCGACTATCG
63389 TAATGCGAAT
Statistics
Matches: 129, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
40 25 0.19
41 3 0.02
42 101 0.78
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (42 bp):
CTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAA
Found at i:63348 original size:21 final size:20
Alignment explanation
Indices: 63211--63351 Score: 90
Period size: 21 Copynumber: 6.8 Consensus size: 20
63201 TAATACGTGT
63211 CTTCGACTATCGCAA-CGAA
1 CTTCGACTATCGCAACCGAA
* * *
63230 TTTGGAATAAATCGCAACGCGAA
1 CTTCGACT--ATCGCAAC-CGAA
*
63253 CTTCGCCTATCGCAA-CGAA
1 CTTCGACTATCGCAACCGAA
* * *
63272 TTTGGAATAAATCGCAACACGAA
1 CTTCGACT--ATCGCAAC-CGAA
63295 CTTCGACTATCGCAA-CGAA
1 CTTCGACTATCGCAACCGAA
* * *
63314 TTTGGAATAAATCGCAACGCGAA
1 CTTCGACT--ATCGCAAC-CGAA
63337 CTTCGACTATCGCAA
1 CTTCGACTATCGCAA
63352 TGAATTTGAA
Statistics
Matches: 90, Mismatches: 20, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
19 22 0.24
21 42 0.47
23 26 0.29
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (20 bp):
CTTCGACTATCGCAACCGAA
Found at i:63487 original size:19 final size:20
Alignment explanation
Indices: 63452--63497 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
63442 GGAAACTGAT
* *
63452 TTGCGATATTGGAGATCGCG
1 TTGCGATATTAGAGATCGCA
63472 TTGCGA-ATTAGAGATCGCA
1 TTGCGATATTAGAGATCGCA
63491 TTGCGAT
1 TTGCGAT
63498 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (20 bp):
TTGCGATATTAGAGATCGCA
Found at i:73802 original size:20 final size:20
Alignment explanation
Indices: 73777--73821 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
73767 GGTGCGTTTA
73777 ATCAGTGTGAATAAAAGATT
1 ATCAGTGTGAATAAAAGATT
73797 ATCAGTGTGAATAAAAGATT
1 ATCAGTGTGAATAAAAGATT
73817 ATCAG
1 ATCAG
73822 GGAATATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (20 bp):
ATCAGTGTGAATAAAAGATT
Found at i:73965 original size:15 final size:15
Alignment explanation
Indices: 73940--74011 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
73930 TGGTTTTCCA
73940 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
73955 GAATTTGAATTACTG
1 GAAAATGAATTACTG
73970 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
73985 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
73999 GAAAATGAATTAC
1 GAAAATGAATTAC
74012 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.25
15 36 0.75
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:74009 original size:29 final size:30
Alignment explanation
Indices: 73940--74011 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
73930 TGGTTTTCCA
73940 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
73970 GAAAATGAATTACTGGAATTTGAATT-CTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
73999 GAAAATGAATTAC
1 GAAAATGAATTAC
74012 ATTTCTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (30 bp):
GAAAATGAATTACTGGAATTTGAATTACTG
Found at i:74017 original size:20 final size:20
Alignment explanation
Indices: 73994--74063 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
73984 GGAATTTGAA
73994 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
* *
74014 TTCTGTAAAATGAATTATAT
1 TTCTGGAAAATGAATTACAT
74034 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
74054 TTCTAGAAAA
1 TTCTGGAAAA
74064 CATTTGGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:74273 original size:28 final size:30
Alignment explanation
Indices: 74231--74379 Score: 114
Period size: 29 Copynumber: 5.0 Consensus size: 30
74221 CTTTACTAAA
*
74231 ATATTATTGAAATATATAAATAA-TATTAT
1 ATATTATTAAAATATATAAATAATTATTAT
*
74260 -TCATTATTAAATATATATAAAAAATTATTAT
1 AT-ATTATTAAA-ATATATAAATAATTATTAT
*
74291 ATATTATTAAAATA-A-AAATATAATATCT-T
1 ATATTATTAAAATATATAAATA-ATTAT-TAT
* ** * *
74320 ATATTATTATAATATAATTGATTATTTTTAT
1 ATATTATTAAAATAT-ATAAATAATTATTAT
*
74351 ATAATATTAAAA-ATATAATATAA-TATTAT
1 ATATTATTAAAATATATAA-ATAATTATTAT
74380 TATAAATATT
Statistics
Matches: 93, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
28 5 0.05
29 34 0.37
30 21 0.23
31 30 0.32
32 3 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (30 bp):
ATATTATTAAAATATATAAATAATTATTAT
Found at i:74286 original size:21 final size:20
Alignment explanation
Indices: 74262--74302 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
74252 AATATTATTC
74262 ATTATTAAATATATATAAAAA
1 ATTATTAAATAT-TATAAAAA
*
74283 ATTATTATATATTATTAAAA
1 ATTATTAAATATTA-TAAAA
74303 TAAAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTATTAAATATTATAAAAA
Found at i:74314 original size:60 final size:60
Alignment explanation
Indices: 74231--74382 Score: 161
Period size: 60 Copynumber: 2.5 Consensus size: 60
74221 CTTTACTAAA
*
74231 ATATTATTGAAATATATAA-ATAATATTATTCATTATTA-AATATATATAAAAAATTATTAT
1 ATATTATTAAAATATATAATATAATATTATT-ATTATTATAATATA-ATAAAAAATTATTAT
* ** ** *
74291 ATATTATTAAAATA-AAAATATAATATCT-TATATTATTATAATATAATTGATTATTTTTAT
1 ATATTATTAAAATATATAATATAATAT-TAT-TATTATTATAATATAATAAAAAATTATTAT
*
74351 ATAATATTAAAA-ATATAATATAATATTATTAT
1 ATATTATTAAAATATATAATATAATATTATTAT
74383 AAATATTAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
59 8 0.10
60 61 0.79
61 8 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (60 bp):
ATATTATTAAAATATATAATATAATATTATTATTATTATAATATAATAAAAAATTATTAT
Found at i:74359 original size:34 final size:31
Alignment explanation
Indices: 74262--74399 Score: 97
Period size: 32 Copynumber: 4.4 Consensus size: 31
74252 AATATTATTC
* * *
74262 ATTATTAAATATATATAAAAAATTATTATATATT
1 ATTA-TAAATATA-ATATAATATTATTATA-AAT
* * *
74296 ATTA-AAATAAAAATATAATA-TCTTAT-ATT
1 ATTATAAAT-ATAATATAATATTATTATAAAT
* *
74325 ATTAT-AATATAAT-TGATTATTTTTATATAAT
1 ATTATAAATATAATAT-AATATTATTATA-AAT
*
74356 ATTAAAAATATAATATAATATTATTATAAAT
1 ATTATAAATATAATATAATATTATTATAAAT
74387 ATTAATAAATATA
1 ATT-ATAAATATA
74400 TTTTAAATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
27 1 0.01
28 7 0.08
29 15 0.18
31 17 0.20
32 36 0.43
33 3 0.04
34 4 0.05
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (31 bp):
ATTATAAATATAATATAATATTATTATAAAT
Found at i:74394 original size:10 final size:10
Alignment explanation
Indices: 74353--74398 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
74343 ATTTTTATAT
74353 AATATTAA-A
1 AATATTAATA
74362 AATA-TAATA
1 AATATTAATA
74371 TAATATTATTATA
1 -AATATTA--ATA
74384 AATATTAATA
1 AATATTAATA
74394 AATAT
1 AATAT
74399 ATTTTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 3 0.09
9 5 0.16
10 12 0.38
11 2 0.06
12 7 0.22
13 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATTAATA
Found at i:74401 original size:21 final size:22
Alignment explanation
Indices: 74354--74410 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
74344 TTTTTATATA
*
74354 ATATTAAAAATA-TAATATAAT
1 ATATTATAAATATTAATATAAT
74375 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
74397 ATATTTTAAATATT
1 ATATTATAAATATT
74411 TTAATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 13 0.41
22 14 0.44
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:74415 original size:23 final size:21
Alignment explanation
Indices: 74361--74410 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
74351 ATAATATTAA
*
74361 AAATA-TAATATAATATTATTAT
1 AAATATTAATA-AATA-TATTTT
74383 AAATATTAATAAATATATTTT
1 AAATATTAATAAATATATTTT
74404 AAATATT
1 AAATATT
74411 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATATTAATAAATATATTTT
Found at i:74662 original size:42 final size:42
Alignment explanation
Indices: 74603--74715 Score: 199
Period size: 42 Copynumber: 2.7 Consensus size: 42
74593 AATTACATTT
*
74603 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTTTTC
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
**
74645 CGGAAAACGAATTACGTGAAACAAACACATGAAAACATTTTC
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
74687 CGGAAAACGAATTACGTGAAACAAACACG
1 CGGAAAACGAATTACGTGAAACAAACACG
74716 AGAATTCGGG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (42 bp):
CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTC
Found at i:75759 original size:18 final size:19
Alignment explanation
Indices: 75736--75772 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
75726 CCAGTAATCC
75736 TATTCT-CTGGTAATCTTT
1 TATTCTACTGGTAATCTTT
75754 TATTCTCACTGGTAATCTT
1 TATTCT-ACTGGTAATCTT
75773 ACATTTCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (19 bp):
TATTCTACTGGTAATCTTT
Found at i:81209 original size:2 final size:2
Alignment explanation
Indices: 81202--81228 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
81192 AACATTTTCA
81202 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 A
81229 AAGATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:81301 original size:15 final size:15
Alignment explanation
Indices: 81281--81310 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
81271 CCTACATTAT
81281 TTTTTTGCTCATCCA
1 TTTTTTGCTCATCCA
81296 TTTTTTGCTCATCCA
1 TTTTTTGCTCATCCA
81311 GGTGTCTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.07, T:0.53
Consensus pattern (15 bp):
TTTTTTGCTCATCCA
Found at i:84992 original size:2 final size:2
Alignment explanation
Indices: 84944--84975 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
84934 TCATCTTTAA
84944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84976 TCTTTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85083 original size:2 final size:2
Alignment explanation
Indices: 85076--85100 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
85066 AGTACTTGTT
85076 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
85101 TTAAAATTTT
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:88063 original size:3 final size:3
Alignment explanation
Indices: 88040--88090 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
88030 TGTGCAAAAA
* * *
88040 AAT AATT AAT ATT AGT AAT AAT AAT AAT -AT AAT AAT AAAT ATT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
88086 AAT AA
1 AAT AA
88091 ATAAATCCGG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:88085 original size:21 final size:20
Alignment explanation
Indices: 88056--88094 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
88046 TAATATTAGT
88056 AATAATAATAATATAATAATA
1 AATAATAATAATA-AATAATA
*
88077 AATATTAATAATAAATAA
1 AATAATAATAATAAATAA
88095 ATCCGGACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATAATAATAAATAATA
Found at i:88087 original size:13 final size:12
Alignment explanation
Indices: 88057--88093 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
88047 AATATTAGTA
88057 ATAATAAT-AAT
1 ATAATAATAAAT
88068 ATAATAATAAAT
1 ATAATAATAAAT
88080 ATTAATAATAAAT
1 A-TAATAATAAAT
88093 A
1 A
88094 AATCCGGACG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.33
12 4 0.17
13 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:89458 original size:2 final size:2
Alignment explanation
Indices: 89451--89480 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
89441 TGCACCTTTC
*
89451 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89481 CCACGCATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:89898 original size:30 final size:30
Alignment explanation
Indices: 89753--89881 Score: 224
Period size: 30 Copynumber: 4.3 Consensus size: 30
89743 GAAGGACCTA
* *
89753 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
89782 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
89812 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
89842 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
89872 TCCATAGGTC
1 TCCAGAGGTC
89882 CCGAAGAACC
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 16 0.17
30 80 0.83
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:89898 original size:60 final size:60
Alignment explanation
Indices: 89753--89898 Score: 213
Period size: 60 Copynumber: 2.5 Consensus size: 60
89743 GAAGGACCTA
**
89753 TCCAGAGGTCACAAAG-ACCCCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
89812 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
89872 TCCATAGGTCCCGAAGAACCTAGGTAA
1 TCCAGAGGTCACAAAGAACCTAGGTAA
89899 ACTTTCCATA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 15 0.19
60 62 0.81
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:91111 original size:21 final size:21
Alignment explanation
Indices: 91081--91125 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
91071 ATTCTGTCGT
* *
91081 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
91102 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
91123 TTG
1 TTG
91126 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:93041 original size:105 final size:111
Alignment explanation
Indices: 92912--93193 Score: 369
Period size: 114 Copynumber: 2.6 Consensus size: 111
92902 GCTTCCGGAC
* *
92912 CATTGATTGGGGATTCTCTTCTTCTGTAATCTGACAGAAAGCAACAGTGTGGCAGTTGTGTCCAC
1 CATTGATTGGGGATTCTCTTCTTCTGTAATCTGACAGAAAGCAACAGTGCGGCGGTTGTGTCCAC
* *
92977 GTCG-CC-C-AC-A-G-CGGTATTTTCCTTGTGGAGGTATAGGAAT
66 GTCGACCACAACGACGACGGTATTTTCCTAGCGGAGGTATAGGAAT
* * * *
93017 CATTGACTGGCGATTCTCTTCTTCTGTAATCAGACACAAAGCAACAGTGCGGCGGTTGTGTCCAC
1 CATTGATTGGGGATTCTCTTCTTCTGTAATCTGACAGAAAGCAACAGTGCGGCGGTTGTGTCCAC
* *
93082 GTCGACCACAACGACTGCATCGGTATTTTCCTAGCGGAGGTGTAGGGAT
66 GTCGACCACAACGAC-G-A-CGGTATTTTCCTAGCGGAGGTATAGGAAT
* * * *
93131 CATAGGTTGGGGATTCCCTTCTTCTGTAATCTGACAGAAAACAACAGTGCGGCGGTTGTGTCC
1 CATTGATTGGGGATTCTCTTCTTCTGTAATCTGACAGAAAGCAACAGTGCGGCGGTTGTGTCC
93194 CTGTTGACCA
Statistics
Matches: 150, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
105 63 0.42
106 2 0.01
107 1 0.01
108 2 0.01
109 1 0.01
111 1 0.01
114 80 0.53
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (111 bp):
CATTGATTGGGGATTCTCTTCTTCTGTAATCTGACAGAAAGCAACAGTGCGGCGGTTGTGTCCAC
GTCGACCACAACGACGACGGTATTTTCCTAGCGGAGGTATAGGAAT
Found at i:93188 original size:114 final size:114
Alignment explanation
Indices: 92988--93225 Score: 318
Period size: 114 Copynumber: 2.1 Consensus size: 114
92978 TCGCCCACAG
* * * *
92988 CGGTATTTTCCTTGTGGAGGTATAGGAATCATTGACTGGCGATTCTCTTCTTCTGTAATCAGACA
1 CGGTATTTTCCTAGCGGAGGTATAGGAATCATAGACTGGCGATTCCCTTCTTCTGTAATCAGACA
*
93053 CAAAGCAACAGTGCGGCGGTTGTGTCCAC-GTCGACCACAA-CGACTGCAT
66 CAAAACAACAGTGCGGCGGTTGTGTCC-CTGTCGACCA-AAGCGACTGCAT
* * ** * *
93102 CGGTATTTTCCTAGCGGAGGTGTAGGGATCATAGGTTGGGGATTCCCTTCTTCTGTAATCTGACA
1 CGGTATTTTCCTAGCGGAGGTATAGGAATCATAGACTGGCGATTCCCTTCTTCTGTAATCAGACA
* *
93167 GAAAACAACAGTGCGGCGGTTGTGTCCCTGTTGACCAAAGCGACTGCAT
66 CAAAACAACAGTGCGGCGGTTGTGTCCCTGTCGACCAAAGCGACTGCAT
*
93216 CGATATTTTC
1 CGGTATTTTC
93226 GTTTTGGGTG
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
113 3 0.03
114 105 0.97
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (114 bp):
CGGTATTTTCCTAGCGGAGGTATAGGAATCATAGACTGGCGATTCCCTTCTTCTGTAATCAGACA
CAAAACAACAGTGCGGCGGTTGTGTCCCTGTCGACCAAAGCGACTGCAT
Found at i:93242 original size:114 final size:114
Alignment explanation
Indices: 92991--93265 Score: 304
Period size: 114 Copynumber: 2.4 Consensus size: 114
92981 CCCACAGCGG
* * * * * * * * *
92991 TATTTTCCTTGTGGAGGTATAGGAATCATTGACTGGCGATTCTCTTCTTCTGTAATCAGACACAA
1 TATTTTCCTAGCGGAGGTGTAGGGACCATAGGCTGGGGATTCCCTTCTTCTGTAATCAGACACAA
* *
93056 AGCAACAGTGCGGCGGTTGTGTCCACGTCGACCACAACGACTGCATCGG
66 AACAACAGTGCGGCGGTTGTGTCCACGTCGACCACAACGACTGCATCGA
* * * *
93105 TATTTTCCTAGCGGAGGTGTAGGGATCATAGGTTGGGGATTCCCTTCTTCTGTAATCTGACAGAA
1 TATTTTCCTAGCGGAGGTGTAGGGACCATAGGCTGGGGATTCCCTTCTTCTGTAATCAGACACAA
*
93170 AACAACAGTGCGGCGGTTGTGTCC-CTGTTGACCA-AAGCGACTGCATCGA
66 AACAACAGTGCGGCGGTTGTGTCCAC-GTCGACCACAA-CGACTGCATCGA
* *** * *
93219 TATTTTCGTTTTGG-GTGTTTAGGGACCATTGGCTGGGGATTCCCTTC
1 TATTTTCCTAGCGGAG-GTGTAGGGACCATAGGCTGGGGATTCCCTTC
93266 GGCAATCTGG
Statistics
Matches: 136, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
113 4 0.03
114 132 0.97
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (114 bp):
TATTTTCCTAGCGGAGGTGTAGGGACCATAGGCTGGGGATTCCCTTCTTCTGTAATCAGACACAA
AACAACAGTGCGGCGGTTGTGTCCACGTCGACCACAACGACTGCATCGA
Found at i:93532 original size:45 final size:45
Alignment explanation
Indices: 93471--93575 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 45
93461 TTCTCTCTCA
* * **
93471 AGAGATCAGAACGTTCC-AGAGTTATTGGAGGAGCTGGCTCTCGCC
1 AGAGATCAGGACGTTCCGA-ACTTACAGGAGGAGCTGGCTCTCGCC
* * *
93516 AGAGATCAGGATGTTCCGAACTTACAGGAGGAGCTGGCTCTTGCG
1 AGAGATCAGGACGTTCCGAACTTACAGGAGGAGCTGGCTCTCGCC
*
93561 AGAGACCAGGACGTT
1 AGAGATCAGGACGTT
93576 TAGGACTTAC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 49 0.98
46 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (45 bp):
AGAGATCAGGACGTTCCGAACTTACAGGAGGAGCTGGCTCTCGCC
Found at i:93597 original size:45 final size:45
Alignment explanation
Indices: 93497--93585 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
93487 CAGAGTTATT
* * *
93497 GGAGGAGCTGGCTCTCGCCAGAGATCAGGATGTTCCGAACTTACA
1 GGAGGAGCTGGCTCTCGCCAGAGACCAGGACGTTCAGAACTTACA
* * * *
93542 GGAGGAGCTGGCTCTTGCGAGAGACCAGGACGTTTAGGACTTAC
1 GGAGGAGCTGGCTCTCGCCAGAGACCAGGACGTTCAGAACTTAC
93586 CATAGGAGCT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.34, T:0.20
Consensus pattern (45 bp):
GGAGGAGCTGGCTCTCGCCAGAGACCAGGACGTTCAGAACTTACA
Found at i:94652 original size:13 final size:13
Alignment explanation
Indices: 94634--94660 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
94624 CGAATGATGC
94634 ACTTGACTTACCA
1 ACTTGACTTACCA
94647 ACTTGACTTACCA
1 ACTTGACTTACCA
94660 A
1 A
94661 TTTCTACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTGACTTACCA
Found at i:95921 original size:22 final size:22
Alignment explanation
Indices: 95891--95934 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
95881 CATTCAAAAC
95891 GGTGAAGAATCATACGAGAGAT
1 GGTGAAGAATCATACGAGAGAT
*
95913 GGTGGAGAATCATACGAGAGAT
1 GGTGAAGAATCATACGAGAGAT
95935 ATGAAACAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.09, G:0.34, T:0.18
Consensus pattern (22 bp):
GGTGAAGAATCATACGAGAGAT
Found at i:96084 original size:29 final size:28
Alignment explanation
Indices: 96051--96105 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
96041 ATTAATCTGA
*
96051 TTGTCAGAGAATAGATTTAACTGATAATT
1 TTGTCAGAGAATAAATTTAAC-GATAATT
*
96080 TTGTCAGATAATAAATTTAACGATAA
1 TTGTCAGAGAATAAATTTAACGATAA
96106 ATCACGTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (28 bp):
TTGTCAGAGAATAAATTTAACGATAATT
Found at i:96642 original size:22 final size:23
Alignment explanation
Indices: 96606--96648 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
96596 CTAAATATAT
96606 AAATATGTTAAGAAAT-AATTCC
1 AAATATGTTAAGAAATGAATTCC
**
96628 AAATATGTTTTGAAATGAATT
1 AAATATGTTAAGAAATGAATT
96649 TACAAAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (23 bp):
AAATATGTTAAGAAATGAATTCC
Found at i:101714 original size:19 final size:18
Alignment explanation
Indices: 101679--101735 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
101669 TACATTCAAT
* *
101679 TTAATATATTATATTTTCA
1 TTAATATTTTAT-TTTTTA
101698 TTAATATTTTATTTTTTA
1 TTAATATTTTATTTTTTA
*
101716 -TCATATTTT-TATTTTTA
1 TTAATATTTTAT-TTTTTA
101733 TTA
1 TTA
101736 TTTTTTAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 1 0.03
17 14 0.44
18 6 0.19
19 11 0.34
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAATATTTTATTTTTTA
Found at i:101732 original size:17 final size:17
Alignment explanation
Indices: 101704--101742 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
101694 TTCATTAATA
101704 TTTTATTTTTTATCATAT
1 TTTTATTTTTTATCAT-T
*
101722 TTTTA-TTTTTATTATT
1 TTTTATTTTTTATCATT
101738 TTTTA
1 TTTTA
101743 ATCTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATTTTTTATCATT
Found at i:104221 original size:2 final size:2
Alignment explanation
Indices: 104175--104201 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
104165 TGATATTAAT
104175 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 T
104202 TAAAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:106144 original size:35 final size:36
Alignment explanation
Indices: 106098--106166 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
106088 TCTTATTCTA
106098 TTTGGGAAACTTTTAT-TTGCTTGACATTGTTTTAT
1 TTTGGGAAACTTTTATATTGCTTGACATTGTTTTAT
* *
106133 TTTGGGGAACTTTTTTATTGCTTGACATTGTTTT
1 TTTGGGAAACTTTTATATTGCTTGACATTGTTTT
106167 TGCTTCGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 14 0.45
36 17 0.55
ACGTcount: A:0.17, C:0.09, G:0.19, T:0.55
Consensus pattern (36 bp):
TTTGGGAAACTTTTATATTGCTTGACATTGTTTTAT
Found at i:108413 original size:31 final size:30
Alignment explanation
Indices: 108377--108493 Score: 112
Period size: 31 Copynumber: 3.8 Consensus size: 30
108367 TTACAAAATG
* *
108377 ATTAAATTTATTAAATTATTAGAATATAATT
1 ATTAAATTTATTAAATTATTATAA-ATAATC
* *
108408 ATTAAAGTTTAATAAACTATTATAAAATAATC
1 ATTAAA-TTTATTAAATTATTAT-AAATAATC
* **
108440 ATTAAATTT-TAATAATTAACATAAAGTAATC
1 ATTAAATTTATTA-AATTATTATAAA-TAATC
108471 ATTAAATTTATTAAATT-TTATAA
1 ATTAAATTTATTAAATTATTATAA
108494 CATTTTAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
30 8 0.12
31 33 0.48
32 26 0.38
33 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (30 bp):
ATTAAATTTATTAAATTATTATAAATAATC
Found at i:108438 original size:32 final size:31
Alignment explanation
Indices: 108377--108485 Score: 94
Period size: 32 Copynumber: 3.5 Consensus size: 31
108367 TTACAAAATG
* * * *
108377 ATTAAATTTATTAAATTATTAGAATATAATT
1 ATTAAATTTAATAAACTATTAGAAAATAATC
*
108408 ATTAAAGTTTAATAAACTATTATAAAATAATC
1 ATTAAA-TTTAATAAACTATTAGAAAATAATC
* ** * *
108440 ATTAAATTTTAAT-AATTAACATAAAGTAATC
1 ATTAAA-TTTAATAAACTATTAGAAAATAATC
*
108471 ATTAAATTTATTAAA
1 ATTAAATTTAATAAA
108486 TTTTATAACA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
30 5 0.08
31 28 0.43
32 32 0.49
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTAAATTTAATAAACTATTAGAAAATAATC
Found at i:108690 original size:13 final size:13
Alignment explanation
Indices: 108661--108699 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
108651 GTTCGGTAAT
*
108661 TGTTCGTTCATTTA
1 TGTTCGTTC-GTTA
108675 TGTTCGTTCGTTA
1 TGTTCGTTCGTTA
*
108688 TGTTCATTCGTT
1 TGTTCGTTCGTT
108700 TATATTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.10, C:0.15, G:0.18, T:0.56
Consensus pattern (13 bp):
TGTTCGTTCGTTA
Found at i:108707 original size:14 final size:14
Alignment explanation
Indices: 108661--108709 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
108651 GTTCGGTAAT
* *
108661 TGTTCGTTCATTTA
1 TGTTCATTCGTTTA
*
108675 TGTTCGTTCG-TTA
1 TGTTCATTCGTTTA
108688 TGTTCATTCGTTTA
1 TGTTCATTCGTTTA
*
108702 TATTCATT
1 TGTTCATT
108710 TATGTGTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
13 12 0.39
14 19 0.61
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
TGTTCATTCGTTTA
Found at i:108909 original size:10 final size:10
Alignment explanation
Indices: 108894--108960 Score: 53
Period size: 10 Copynumber: 5.9 Consensus size: 10
108884 AAAATATATT
108894 TTCATTTATG
1 TTCATTTATG
108904 TTCATTTACATCCG
1 TTCATTT--AT--G
108918 TTCATTTATG
1 TTCATTTATG
108928 TTCATTTACATCCG
1 TTCATTT--AT--G
108942 TTCATTTATG
1 TTCATTTATG
*
108952 TTCGTTTAT
1 TTCATTTAT
108961 CATTTAAATG
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
10 24 0.50
12 8 0.17
14 16 0.33
ACGTcount: A:0.19, C:0.18, G:0.09, T:0.54
Consensus pattern (10 bp):
TTCATTTATG
Found at i:108922 original size:14 final size:14
Alignment explanation
Indices: 108903--108949 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
108893 TTTCATTTAT
108903 GTTCATTTACATCC
1 GTTCATTTACATCC
108917 GTTCATTT--AT--
1 GTTCATTTACATCC
108927 GTTCATTTACATCC
1 GTTCATTTACATCC
108941 GTTCATTTA
1 GTTCATTTA
108950 TGTTCGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 8 0.28
12 4 0.14
14 17 0.59
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (14 bp):
GTTCATTTACATCC
Found at i:108926 original size:24 final size:24
Alignment explanation
Indices: 108894--108959 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
108884 AAAATATATT
108894 TTCATTTATGTTCATTTACATCCG
1 TTCATTTATGTTCATTTACATCCG
108918 TTCATTTATGTTCATTTACATCCG
1 TTCATTTATGTTCATTTACATCCG
*
108942 TTCATTTATGTTCGTTTA
1 TTCATTTATGTTCATTTA
108960 TCATTTAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.53
Consensus pattern (24 bp):
TTCATTTATGTTCATTTACATCCG
Found at i:109408 original size:3 final size:3
Alignment explanation
Indices: 109400--109427 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
109390 TACCAGAAAG
109400 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
109428 GAAAAAAATG
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:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Done.