Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002847.1 Hibiscus syriacus cultivar Beakdansim tig00005859_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: 91233
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:233 original size:35 final size:38
Alignment explanation
Indices: 183--266 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 38
173 TGACTTTTCA
183 GTCAAAGTCAAAGTCA-A-CAGTCAA-AGGTATGACCT-
1 GTCAAAGTCAAAGTCAGACCAGTCAACA-GTATGACCTG
* * *
218 GTCAAAGTCACAGTCAGACCAGTCAACAGTTTGACTTG
1 GTCAAAGTCAAAGTCAGACCAGTCAACAGTATGACCTG
256 GTCAAAGTCAA
1 GTCAAAGTCAA
267 CGAGTTGACT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 15 0.37
36 1 0.02
37 14 0.34
38 11 0.27
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (38 bp):
GTCAAAGTCAAAGTCAGACCAGTCAACAGTATGACCTG
Found at i:300 original size:27 final size:23
Alignment explanation
Indices: 238--303 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 23
228 CAGTCAGACC
238 AGTCAAC-AGTTTGACTTGGTCAA
1 AGTCAACGAG-TTGACTTGGTCAA
*
261 AGTCAACGAGTTGACTTGGTGAA
1 AGTCAACGAGTTGACTTGGTCAA
284 ATGACTCAATCGAGTTGACT
1 A-G--TCAA-CGAGTTGACT
304 CATTGATTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 20 0.54
24 3 0.08
26 4 0.11
27 10 0.27
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (23 bp):
AGTCAACGAGTTGACTTGGTCAA
Found at i:3855 original size:36 final size:36
Alignment explanation
Indices: 3803--3877 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
3793 CCATTCCACG
3803 TGGCAAGAGGAGATTGTTAATGCTATTGGAAGAACC
1 TGGCAAGAGGAGATTGTTAATGCTATTGGAAGAACC
* *
3839 TGGCAAGAGGATATTGTTGATGCTATTGGAAGAACC
1 TGGCAAGAGGAGATTGTTAATGCTATTGGAAGAACC
3875 TGG
1 TGG
3878 TGTTGGATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.32, T:0.27
Consensus pattern (36 bp):
TGGCAAGAGGAGATTGTTAATGCTATTGGAAGAACC
Found at i:6844 original size:443 final size:441
Alignment explanation
Indices: 6020--6893 Score: 1694
Period size: 443 Copynumber: 2.0 Consensus size: 441
6010 AATGATCAAT
6020 AAAACCACAACCCGTACCGATTAATCCAACGTTTCTTCCATTAACACAAAGAAGAGTTACAAAAA
1 AAAACCACAACCCGTACCGATTAATCCAACGTTTCTTCCATTAACACAAAGAAGAGTTACAAAAA
6085 ACTACAAGAGACTCATAAATATGAACAGACTCTATCTCATTATGCAGCTGGTAAGCATCCGATGA
66 ACTACAAGAGACTCATAAATATGAACAGACTCTATCTCATTATGCAGCTGGTAAGCATCCGATGA
*
6150 CATACTCCCAGATCCGCATTTGGCATCATCCATATACTGGCTCACAAACACATAGATTGCATAAC
131 CATACTCCCAGATCCGCATTTGGCATCATCCATATACTGGCCCACAAACACATAGATTGCATAAC
6215 AAAGAATTACCATAGCCAGTTCACATTTCCCTCATAAGATCATGACAACAATTTAACAATGCTCC
196 AAAGAATTACCATAGCCAGTTCACATTTCCCTCATAAGATCATGACAACAATTTAACAATGCTCC
*
6280 ATATCCTAGGCAATTTTCCAGACCACATTATCATCAATCCTAGCTTATAGCTTAGACAGGTCACC
261 ATATCCTAGGCAATTTTCCAGACCACATTATCATCAATCCTAGCTTATAGCTTAAACAGGTCACC
6345 TGAAATTATTATTGAAGTCCTTCCCTAGTGTCCATAATCTATAAACATCAATAATGAGCAACTCC
326 TGAAATTATTATTGAAGTCCTTCCCTAGTGTCCATAATCTATAAACATCAATAATGAGCAACTCC
*
6410 AATAATAGGTTGAAACACTAGCCATTAGATCAAAACCAAGAAGAGTTACAA
391 AACAATAGGTTGAAACACTAGCCATTAGATCAAAACCAAGAAGAGTTACAA
6461 AAAACCACAACCCGTACCGATTAATCCAACGTTTCTTCCATTAACACAAAGAAGAGTTACAAAAA
1 AAAACCACAACCCGTACCGATTAATCCAACGTTTCTTCCATTAACACAAAGAAGAGTTACAAAAA
6526 ACTACAAGAGACTCATAAATATGAACAGACTCTATCTCATTATGCAGCTGGTAAGCATCCGATGA
66 ACTACAAGAGACTCATAAATATGAACAGACTCTATCTCATTATGCAGCTGGTAAGCATCCGATGA
6591 CATACTCCCCAGATCCGCATTTGGCATCATCCATATACTGGCCCACAAACACATAGATTGCATAA
131 CATACT-CCCAGATCCGCATTTGGCATCATCCATATACTGGCCCACAAACACATAGATTGCATAA
6656 TCAAAGAATTACCATAGCCAGTTCACATTTCCCTCATAAGATCATGACAACAATTTAACAATGCT
195 -CAAAGAATTACCATAGCCAGTTCACATTTCCCTCATAAGATCATGACAACAATTTAACAATGCT
*
6721 CCATATCCTAGGCAATTTTCCAGACCACATTATCATCAATCCTAGCTTATAGCTTAAACAGTTCA
259 CCATATCCTAGGCAATTTTCCAGACCACATTATCATCAATCCTAGCTTATAGCTTAAACAGGTCA
6786 CCTGAAATTATTATTGAAGTCCTTCCCTAGTGTCCATAATCTATAAACATCAATAATGAGCAACT
324 CCTGAAATTATTATTGAAGTCCTTCCCTAGTGTCCATAATCTATAAACATCAATAATGAGCAACT
6851 CCAACAATAGGTTGAAACACTAGCCATTAGATCAAAACCAAGA
389 CCAACAATAGGTTGAAACACTAGCCATTAGATCAAAACCAAGA
6894 CTGGCCCCAA
Statistics
Matches: 427, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
441 136 0.32
442 57 0.13
443 234 0.55
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (441 bp):
AAAACCACAACCCGTACCGATTAATCCAACGTTTCTTCCATTAACACAAAGAAGAGTTACAAAAA
ACTACAAGAGACTCATAAATATGAACAGACTCTATCTCATTATGCAGCTGGTAAGCATCCGATGA
CATACTCCCAGATCCGCATTTGGCATCATCCATATACTGGCCCACAAACACATAGATTGCATAAC
AAAGAATTACCATAGCCAGTTCACATTTCCCTCATAAGATCATGACAACAATTTAACAATGCTCC
ATATCCTAGGCAATTTTCCAGACCACATTATCATCAATCCTAGCTTATAGCTTAAACAGGTCACC
TGAAATTATTATTGAAGTCCTTCCCTAGTGTCCATAATCTATAAACATCAATAATGAGCAACTCC
AACAATAGGTTGAAACACTAGCCATTAGATCAAAACCAAGAAGAGTTACAA
Found at i:8768 original size:14 final size:15
Alignment explanation
Indices: 8719--8766 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
8709 AAATATTAAA
*
8719 TTTTGATTTGAAATT
1 TTTTAATTTGAAATT
8734 TTTTAATTTGAAATT
1 TTTTAATTTGAAATT
*
8749 TTTTAATTTAAAATT
1 TTTTAATTTGAAATT
8764 TTT
1 TTT
8767 AAGTTTCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTTAATTTGAAATT
Found at i:8997 original size:17 final size:17
Alignment explanation
Indices: 8975--9009 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
8965 GATACGTTAA
8975 AAATTCAAATCAAATTT
1 AAATTCAAATCAAATTT
*
8992 AAATTCAAATTAAATTT
1 AAATTCAAATCAAATTT
9009 A
1 A
9010 TTAAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTCAAATCAAATTT
Found at i:9025 original size:22 final size:22
Alignment explanation
Indices: 8990--9048 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
8980 CAAATCAAAT
*
8990 TTAAATTC-AA-ATTAAATTTA
1 TTAAATTCTAATATTAAATCTA
9010 TTAAATTCTAATATTAAATCTA
1 TTAAATTCTAATATTAAATCTA
*
9032 TTTAATT-TAAATATTAA
1 TTAAATTCT-AATATTAA
9049 TTGAATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.24
21 3 0.09
22 23 0.68
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATTCTAATATTAAATCTA
Found at i:10158 original size:228 final size:228
Alignment explanation
Indices: 9756--10241 Score: 875
Period size: 228 Copynumber: 2.1 Consensus size: 228
9746 GTAAATTATC
* * *
9756 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
9821 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
9886 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
*
9951 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTTAAAAAAAGTATA
*
9984 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
10049 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTAT-AAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
* *
10113 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
10178 GAAACATAAATTACATAACTTTAAAAAAAGTATA
195 GAAACATAAATTACATAACTTTAAAAAAAGTATA
10212 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
10242 AAAAGTAGGT
Statistics
Matches: 248, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
228 187 0.75
229 61 0.25
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAAGTATA
Found at i:10545 original size:18 final size:18
Alignment explanation
Indices: 10506--10563 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
10496 GTATCGATCC
* *
10506 AAAACGATATACCAGGTAA
1 AAAATGATAAACC-GGTAA
10525 AAATATGATAAAACC-GTAA
1 AAA-ATGAT-AAACCGGTAA
10544 AAAATGATAAACCGGTAA
1 AAAATGATAAACCGGTAA
10562 AA
1 AA
10564 CGTTACCGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 5 0.15
18 11 0.32
19 10 0.29
20 4 0.12
21 4 0.12
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.17
Consensus pattern (18 bp):
AAAATGATAAACCGGTAA
Found at i:10557 original size:17 final size:20
Alignment explanation
Indices: 10520--10563 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
10510 CGATATACCA
10520 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
10540 -GTAAAAA-ATGAT-AAACC
1 GGTAAAAATATGATAAAACC
10557 GGTAAAA
1 GGTAAAA
10564 CGTTACCGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 11 0.48
19 7 0.30
ACGTcount: A:0.57, C:0.09, G:0.16, T:0.18
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:10659 original size:178 final size:179
Alignment explanation
Indices: 10308--10772 Score: 659
Period size: 176 Copynumber: 2.6 Consensus size: 179
10298 GATCCAAATT
* * * *
10308 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATAGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTA-AAAAATGAT-
* * * * * *
10373 AAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
64 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
10438 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
129 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATAC-TTTA
*
10490 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACC-GTAAAAAATGATAA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAAAAAATGATAA
* *
10554 ACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTTGT
66 ACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGT
** *
10618 GAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTTA
131 GAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTA
* * **
10667 AAAAA-ATATCGATCCACAACGATATAACAGGTAAAAATATGAT-AAACCGGTATCAAATGATAA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAAAAAATGATAA
* *
10730 ACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 ACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
10773 CGTAAGTACG
Statistics
Matches: 257, Mismatches: 25, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
175 5 0.02
176 87 0.34
177 9 0.04
178 60 0.23
179 39 0.15
180 8 0.03
181 3 0.01
182 46 0.18
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (179 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAAAAAATGATAA
ACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGT
GAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTA
Found at i:10742 original size:16 final size:17
Alignment explanation
Indices: 10705--10744 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
10695 AGGTAAAAAT
10705 ATGATAAACCGGTATCAA
1 ATGATAAACCGGTA-CAA
10723 ATGATAAACCGGTA-AA
1 ATGATAAACCGGTACAA
10739 ATGATA
1 ATGATA
10745 CCGGATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.23
Consensus pattern (17 bp):
ATGATAAACCGGTACAA
Found at i:11555 original size:18 final size:18
Alignment explanation
Indices: 11534--11570 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11524 GTAATTGGAG
11534 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
11552 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
11570 T
1 T
11571 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:11578 original size:24 final size:24
Alignment explanation
Indices: 11526--11572 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11516 TTTCATATGT
* *
11526 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
11550 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
11573 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:11872 original size:39 final size:39
Alignment explanation
Indices: 11829--11914 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
11819 TCCGATGCTC
*
11829 ATCAAAATTCAAAGCTCATATGGTGCCAAACAAAAGGAA
1 ATCAAAATTCAAAGCTCATATGATGCCAAACAAAAGGAA
* *
11868 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATTCAAAGCTCATATGATGCCAAACAAAAGGAA
11907 ATCAAAAT
1 ATCAAAAT
11915 CTACAACTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (39 bp):
ATCAAAATTCAAAGCTCATATGATGCCAAACAAAAGGAA
Found at i:12366 original size:23 final size:23
Alignment explanation
Indices: 12335--12407 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
12325 ATAGGTAAAC
*
12335 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
12358 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
12381 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
12404 ATAT
1 ATAT
12408 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:16719 original size:15 final size:15
Alignment explanation
Indices: 16699--16728 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16689 CTTTCTCATA
16699 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
16714 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
16729 CCAGCCTCGT
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:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:17616 original size:19 final size:19
Alignment explanation
Indices: 17573--17617 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
17563 ACTTGGACGG
17573 CTCGGTCAATAGGCTTACGA
1 CTCGGTCAATAGGCTTAC-A
*
17593 CTCGGTCAACTTGGCTTA-A
1 CTCGGTCAA-TAGGCTTACA
17612 CTCGGT
1 CTCGGT
17618 GAGTCAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 9 0.39
21 7 0.30
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (19 bp):
CTCGGTCAATAGGCTTACA
Found at i:17888 original size:45 final size:45
Alignment explanation
Indices: 17825--17916 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
17815 AGCACTCTCA
17825 CTCAAAAACAAGATACTACAACTCACTCTTTCTAAGACTTTGCTT
1 CTCAAAAACAAGATACTACAACTCACTCTTTCTAAGACTTTGCTT
17870 CTCAAAAACAAGATACTACAACTCACTCTTTCTAAGACTTTGCTT
1 CTCAAAAACAAGATACTACAACTCACTCTTTCTAAGACTTTGCTT
17915 CT
1 CT
17917 TCACTCACTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.32
Consensus pattern (45 bp):
CTCAAAAACAAGATACTACAACTCACTCTTTCTAAGACTTTGCTT
Found at i:31308 original size:23 final size:23
Alignment explanation
Indices: 31278--31362 Score: 93
Period size: 23 Copynumber: 3.7 Consensus size: 23
31268 TTAGTACAAA
31278 GGGAATCGATACCCCCCTTGATG
1 GGGAATCGATACCCCCCTTGATG
* *
31301 GGGAATCGATTCCCCCCTTTGAAG
1 GGGAATCGATACCCCCC-TTGATG
* * *
31325 GGGAACCGAT-TCCCCCATG-TAG
1 GGGAATCGATACCCCCCTTGAT-G
31347 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
31363 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
22 12 0.24
23 25 0.49
24 14 0.27
ACGTcount: A:0.22, C:0.32, G:0.26, T:0.20
Consensus pattern (23 bp):
GGGAATCGATACCCCCCTTGATG
Found at i:31322 original size:24 final size:23
Alignment explanation
Indices: 31278--31362 Score: 93
Period size: 24 Copynumber: 3.7 Consensus size: 23
31268 TTAGTACAAA
31278 GGGAATCGATACCCCCC-TTGATG
1 GGGAATCGATACCCCCCTTTGA-G
*
31301 GGGAATCGATTCCCCCCTTTGAAG
1 GGGAATCGATACCCCCCTTTG-AG
* * * *
31325 GGGAACCGATTCCCCCATGT-AG
1 GGGAATCGATACCCCCCTTTGAG
31347 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
31363 TGGGGTTCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
22 16 0.30
23 16 0.30
24 21 0.39
25 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.26, T:0.20
Consensus pattern (23 bp):
GGGAATCGATACCCCCCTTTGAG
Found at i:32704 original size:18 final size:18
Alignment explanation
Indices: 32683--32723 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
32673 AGAACAACAC
* *
32683 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACAACCA
32701 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
32719 GAGGA
1 GAGGA
32724 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.32, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:40620 original size:29 final size:24
Alignment explanation
Indices: 40561--40611 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
40551 ATATACATAT
40561 AATATAATAAATGCATTTCATGAA
1 AATATAATAAATGCATTTCATGAA
40585 AATATAATAAATGCATTTCATGAA
1 AATATAATAAATGCATTTCATGAA
40609 AAT
1 AAT
40612 GGTATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (24 bp):
AATATAATAAATGCATTTCATGAA
Found at i:40724 original size:19 final size:19
Alignment explanation
Indices: 40700--40738 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40690 TTAATACCAT
40700 ATGATTTGTTTTTTAACAA
1 ATGATTTGTTTTTTAACAA
40719 ATGATTTGTTTTTTAACAA
1 ATGATTTGTTTTTTAACAA
40738 A
1 A
40739 AGAAATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
ATGATTTGTTTTTTAACAA
Found at i:42201 original size:24 final size:24
Alignment explanation
Indices: 42169--42216 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42159 AACTTCTTTG
42169 ATAATAAATGCATTTCATGAAAAT
1 ATAATAAATGCATTTCATGAAAAT
42193 ATAATAAATGCATTTCATGAAAAT
1 ATAATAAATGCATTTCATGAAAAT
42217 GGTATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (24 bp):
ATAATAAATGCATTTCATGAAAAT
Found at i:42329 original size:19 final size:19
Alignment explanation
Indices: 42305--42343 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
42295 TTAATACCAT
42305 ATGATTTGTTTTTTAACAA
1 ATGATTTGTTTTTTAACAA
42324 ATGATTTGTTTTTTAACAA
1 ATGATTTGTTTTTTAACAA
42343 A
1 A
42344 AGAAATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
ATGATTTGTTTTTTAACAA
Found at i:46137 original size:25 final size:25
Alignment explanation
Indices: 46108--46184 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
46098 ATTGAACCTT
*
46108 ACCCTAAACCACTTTAACCTACACA
1 ACCCTAAACCACTTTAACCTACAAA
** * *
46133 ACCCTTGACCACTCTAACCTTAAAAA
1 ACCCTAAACCACTTTAACC-TACAAA
*
46159 ACCCTAAACAACTTTAACCTACAAA
1 ACCCTAAACCACTTTAACCTACAAA
46184 A
1 A
46185 TCATTCACCA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 22 0.54
26 19 0.46
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.21
Consensus pattern (25 bp):
ACCCTAAACCACTTTAACCTACAAA
Found at i:46184 original size:26 final size:26
Alignment explanation
Indices: 46108--46184 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
46098 ATTGAACCTT
*
46108 ACCCTAAACCACTTTAACCTAC-ACA
1 ACCCTAAACCACTTTAACCTACAAAA
** *
46133 ACCCTTGACCACTCTAACCTTA-AAAA
1 ACCCTAAACCACTTTAACC-TACAAAA
*
46159 ACCCTAAACAACTTTAACCTACAAAA
1 ACCCTAAACCACTTTAACCTACAAAA
46185 TCATTCACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
25 18 0.44
26 23 0.56
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.21
Consensus pattern (26 bp):
ACCCTAAACCACTTTAACCTACAAAA
Found at i:46197 original size:25 final size:25
Alignment explanation
Indices: 46108--46198 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
46098 ATTGAACCTT
* *
46108 ACCCTAAACCACTTTAACCTACACA
1 ACCCTTAACCACTTTAACCTACAAA
* * *
46133 ACCCTTGACCACTCTAACCTTAAAAA
1 ACCCTTAACCACTTTAACC-TACAAA
* *
46159 ACCCTAAACAACTTTAACCTACAAA
1 ACCCTTAACCACTTTAACCTACAAA
* * *
46184 ATCATTCACCACTTT
1 ACCCTTAACCACTTT
46199 CATCTTAAGG
Statistics
Matches: 50, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
25 31 0.62
26 19 0.38
ACGTcount: A:0.40, C:0.35, G:0.01, T:0.24
Consensus pattern (25 bp):
ACCCTTAACCACTTTAACCTACAAA
Found at i:46793 original size:28 final size:31
Alignment explanation
Indices: 46743--46804 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 31
46733 CCCTTAAAAA
*
46743 TTTTAATTTAATATATATAATTTTTATATTT
1 TTTTAAATTAATATATATAATTTTTATATTT
*
46774 TTTTAAATTAA-A-ATAT-ATTTTTGTATTT
1 TTTTAAATTAATATATATAATTTTTATATTT
46802 TTT
1 TTT
46805 GTATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 14 0.48
29 4 0.14
30 1 0.03
31 10 0.34
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (31 bp):
TTTTAAATTAATATATATAATTTTTATATTT
Found at i:47478 original size:2 final size:2
Alignment explanation
Indices: 47471--47512 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
47461 TGGTGTATGT
47471 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47512 T
1 T
47513 CCCATGCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64482 original size:21 final size:21
Alignment explanation
Indices: 64458--64502 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
64448 CATTTTAATT
*
64458 TATTTTTTTAT-TTGAAAAAAA
1 TATTTTTTAATATT-AAAAAAA
64479 TATTTTTTAATATTAAAAAAA
1 TATTTTTTAATATTAAAAAAA
64500 TAT
1 TAT
64503 GCCACATGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTTTTTAATATTAAAAAAA
Found at i:65324 original size:32 final size:32
Alignment explanation
Indices: 65239--65330 Score: 121
Period size: 32 Copynumber: 2.9 Consensus size: 32
65229 ATTGACACTC
* *
65239 ATGTGCATTATCTAAATGTAACACTAACTCTG
1 ATGTACATTATCTAAATGTAATACTAACTCTG
* *
65271 TTGTACATTATCTAAATGTAATACTTACTCTG
1 ATGTACATTATCTAAATGTAATACTAACTCTG
* * *
65303 ATGTACATTATTTGAATGTAATCCTAAC
1 ATGTACATTATCTAAATGTAATACTAAC
65331 ACTACTATGC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (32 bp):
ATGTACATTATCTAAATGTAATACTAACTCTG
Found at i:75223 original size:24 final size:24
Alignment explanation
Indices: 75195--75367 Score: 98
Period size: 24 Copynumber: 7.2 Consensus size: 24
75185 GAATATGTCA
*
75195 ATATTTTAAAATAATTAAAATAAT
1 ATATTTTAAAATAATTATAATAAT
*
75219 ATATTTTATAGTAATATATTTATAATCATT
1 ATATTTTA-A--AATA-A-TTATAAT-AAT
*
75249 ATTATTTTTAAAATTATTATAATAAT
1 A-TA-TTTTAAAATAATTATAATAAT
* *
75275 ATATTTTATAAT-ATT-TATTAA-
1 ATATTTTAAAATAATTATAATAAT
75296 AT-TTTT--AATAATTA-AATAAT
1 ATATTTTAAAATAATTATAATAAT
* *
75316 ATATTTTAACATTATAAATATAAAAAT
1 ATATTTTAA-A--ATAATTATAATAAT
75343 -TA-TTTAAAAT-ATTA-AATATAT
1 ATATTTTAAAATAATTATAATA-AT
75364 ATAT
1 ATAT
75368 ATATATATAT
Statistics
Matches: 117, Mismatches: 11, Indels: 43
0.68 0.06 0.25
Matches are distributed among these distances:
18 3 0.03
19 7 0.06
20 9 0.08
21 11 0.09
22 9 0.08
23 3 0.03
24 18 0.15
25 8 0.07
26 11 0.09
27 16 0.14
28 2 0.02
29 9 0.08
30 3 0.03
31 3 0.03
32 5 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (24 bp):
ATATTTTAAAATAATTATAATAAT
Found at i:75275 original size:41 final size:40
Alignment explanation
Indices: 75224--75330 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 40
75214 ATAATATATT
* *
75224 TTATAGTAATATATTTATAATCATTATT-ATTTTTAAAATTA
1 TTATAATAATATATTTATAATCATTATTAATTTTT--AATAA
75265 TTATAATAATATATTTTATAAT-ATTTATTAAATTTTTAATAA
1 TTATAATAATATA-TTTATAATCA-TTATT-AATTTTTAATAA
75307 TTA-AATAATATATTT-TAA-CATTAT
1 TTATAATAATATATTTATAATCATTAT
75331 AAATATAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
38 4 0.07
39 4 0.07
40 3 0.05
41 22 0.37
42 20 0.34
44 6 0.10
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (40 bp):
TTATAATAATATATTTATAATCATTATTAATTTTTAATAA
Found at i:75283 original size:15 final size:15
Alignment explanation
Indices: 75213--75287 Score: 72
Period size: 15 Copynumber: 5.3 Consensus size: 15
75203 AAATAATTAA
75213 AATAATATATTTTAT
1 AATAATATATTTTAT
*
75228 AGTAATATA-TTTAT
1 AATAATATATTTTAT
*
75242 AATCATTATTATTTT-T
1 AAT-AATA-TATTTTAT
75258 AA-AAT-TA--TTAT
1 AATAATATATTTTAT
75269 AATAATATATTTTAT
1 AATAATATATTTTAT
75284 AATA
1 AATA
75288 TTTATTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
10 2 0.04
11 3 0.06
12 5 0.10
13 2 0.04
14 9 0.19
15 19 0.40
16 5 0.10
17 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:76659 original size:24 final size:24
Alignment explanation
Indices: 76632--76694 Score: 108
Period size: 24 Copynumber: 2.5 Consensus size: 24
76622 TGCATCGTAA
76632 GATAAATGTCATTAGCTATGTAGG
1 GATAAATGTCATTAGCTATGTAGG
76656 GATAAATGTCATTAGCTATGTAGG
1 GATAAATGTCATTAGCTATGTAGG
76680 GATAAAATAGTCATT
1 GAT-AAAT-GTCATT
76695 TCACATTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
24 27 0.73
25 4 0.11
26 6 0.16
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (24 bp):
GATAAATGTCATTAGCTATGTAGG
Found at i:77867 original size:149 final size:149
Alignment explanation
Indices: 77597--77895 Score: 546
Period size: 149 Copynumber: 2.0 Consensus size: 149
77587 ACATAAAAAT
*
77597 TCATCATTTCATTATTCATTCAACAATCAAAGTATAACATAATTTATTATAGGTCATTTATACAA
1 TCATCATTTCATTATTCATTCAACAATCAAAGTATAACACAATTTATTATAGGTCATTTATACAA
77662 TAGCAAATGTAAAAAGAGTAAATTAGCATACACTTAATCAAGGATCCCATATTACCTCAAAATAA
66 TAGCAAATGTAAAAAGAGTAAATTAGCATACACTTAATCAAGGATCCCATATTACCTCAAAATAA
77727 AACCAAGGTTCAAAATAAC
131 AACCAAGGTTCAAAATAAC
**
77746 TCATCATTTCATTATTCATTCAAGGATCAAAGTATAACACAATTTATTATAGGTCATTTATACAA
1 TCATCATTTCATTATTCATTCAACAATCAAAGTATAACACAATTTATTATAGGTCATTTATACAA
77811 TAG-AAAGTGTAAAAAGAGTAAATTAGCATACACTTAATCAAGGATCCCATATTACCTCAAAATA
66 TAGCAAA-TGTAAAAAGAGTAAATTAGCATACACTTAATCAAGGATCCCATATTACCTCAAAATA
*
77875 AAACCAATGTTCAAAATAAC
130 AAACCAAGGTTCAAAATAAC
77895 T
1 T
77896 TTCCAAAAGC
Statistics
Matches: 145, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 3 0.02
149 142 0.98
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.30
Consensus pattern (149 bp):
TCATCATTTCATTATTCATTCAACAATCAAAGTATAACACAATTTATTATAGGTCATTTATACAA
TAGCAAATGTAAAAAGAGTAAATTAGCATACACTTAATCAAGGATCCCATATTACCTCAAAATAA
AACCAAGGTTCAAAATAAC
Found at i:82521 original size:28 final size:28
Alignment explanation
Indices: 82481--82544 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
82471 CTTAGCTCTC
82481 AACCCAAATCTAAAGTCCCCTACCCCAA
1 AACCCAAATCTAAAGTCCCCTACCCCAA
82509 AACCCAAATCTAAAGTCCCCTACCCCAA
1 AACCCAAATCTAAAGTCCCCTACCCCAA
82537 AACCCAAA
1 AACCCAAA
82545 CAGAAAACCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.42, C:0.42, G:0.03, T:0.12
Consensus pattern (28 bp):
AACCCAAATCTAAAGTCCCCTACCCCAA
Found at i:83178 original size:3 final size:3
Alignment explanation
Indices: 83170--83207 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
83160 ATGTACATTA
*
83170 AAT AAT AAT AAT AAT AAT AAT AATT AA- AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA
83208 AAAAGACCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:83210 original size:12 final size:12
Alignment explanation
Indices: 83168--83210 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
83158 AAATGTACAT
83168 TAAATAATAATAA
1 TAAA-AATAATAA
*
83181 TAATAATAATAA
1 TAAAAATAATAA
* *
83193 TTAAAATAAAAA
1 TAAAAATAATAA
83205 TAAAAA
1 TAAAAA
83211 AGACCCGGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 22 0.88
13 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAAAATAATAA
Found at i:83603 original size:134 final size:134
Alignment explanation
Indices: 83349--83838 Score: 730
Period size: 134 Copynumber: 3.7 Consensus size: 134
83339 GTTTGATGGT
** * * * *
83349 GGGGATGACACTTCTCATATGTGATGAAGAATTCGTGGCCATCTTTAAGAAGGGTGATAACTCGA
1 GGGGATGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGTGATAACTCGG
* * * * *
83414 TTCCTACGTGATGAGGACGACTGGTTAACT-GGGGTGACACGGTTCATACGTGATGAGGAGTTCT
65 TTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCT
83478 GGTCG
130 GGTCG
* * *
83483 GTGGATGACACGGCTCATACGTGATGAAGAGTTCTAGCCATCTTTAGGAAGGGTGATAACTTGGT
1 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGT
* *
83548 TCCTACGCGATGAGGACAACTGGTTATCTAGGGGTGACACGACTCATACGTGATGAAGAGATCTG
66 TCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTG
83613 GTCG
131 GTCG
* *
83617 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGTCATCTTTAGGAAGGGTGATAACTCGGT
1 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGT
* * *
83682 TCCTACGCGATGAGGATGGCTGGTTATCTAGGGGTTACACGGCTCATACGTGATGAAGAGATCTG
66 TCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTG
83747 GTCG
131 GTCG
* * *
83751 GGGGATGACACGGCTCATACATAATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGT
1 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGT
* *
83816 TCCTAAGCGATGAGGACGGCTGG
66 TCCTACGCGATGAGGACGACTGG
83839 CCATCTTTAA
Statistics
Matches: 325, Mismatches: 30, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
133 53 0.16
134 272 0.84
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (134 bp):
GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGT
TCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAAGAGATCTG
GTCG
Found at i:83634 original size:40 final size:41
Alignment explanation
Indices: 83578--83789 Score: 130
Period size: 40 Copynumber: 5.0 Consensus size: 41
83568 TGGTTATCTA
*
83578 GGGG-TGACACGACTCATACGTGATGAAGAGATCTGGTC-G
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTCTG
* *
83617 GGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGTCATCTTTAGG
1 GGGGATGACACGGCTCATACGTGATGAAGAGATC-TG--GTC--T--G
* * * * * *
83665 AAGGGTGATAACTCGGTTCCTACGCGATG-AG-GATGGCTGGTTATCTA
1 --GGG-GATGACACGGCTCATACGTGATGAAGAGAT--CTGG---TCTG
*
83712 GGGG-TTACACGGCTCATACGTGATGAAGAGATCTGGTC-G
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTCTG
* * *
83751 GGGGATGACACGGCTCATACATAATGAAGAGTTCTGGTC
1 GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTC
83790 ATCTTTAGGA
Statistics
Matches: 132, Mismatches: 21, Indels: 39
0.69 0.11 0.20
Matches are distributed among these distances:
39 8 0.06
40 59 0.45
41 2 0.02
43 22 0.17
44 3 0.02
45 6 0.05
48 1 0.01
49 3 0.02
50 7 0.05
51 21 0.16
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (41 bp):
GGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTCTG
Found at i:84334 original size:132 final size:133
Alignment explanation
Indices: 84198--84511 Score: 415
Period size: 131 Copynumber: 2.4 Consensus size: 133
84188 TATGAAAAAT
* * * *
84198 TGTCTCAAGAGAGACAAAACTTTGTTTCAAAAGAAAAACACTCAAAGATGGGTTTTGTTTC-AAG
1 TGTCTCAAGAGAGACAAAATTTTGTTTCAAAAGAAAAAGACTCAAAGATGGCTTTTGTTTCAAAA
** * *
84262 GGAAACAGACTCACGGATGGTAAATGTTGTTTCCAAAGAAACAGACTCAAAGA-TTTT-TCAAAA
66 GG-AA-AGACTCAAAGATGATAAATGTTGTTTCCAAAGAAACAGAATCAAAGATTTTTCTCAAAA
84325 GAAAC
129 GAAAC
* * *
84330 TGTCTCAAGAGAGACAAAATTTTGTTTCAACAGAAATAGAATCAAAGAT--CTTTTGTTTCAAAA
1 TGTCTCAAGAGAGACAAAATTTTGTTTCAAAAGAAAAAGACTCAAAGATGGCTTTTGTTTCAAAA
* *
84393 GGAAATACTCAAAGATGATAAATTTTGTTTCCAAAGAAACAGAATCAAAGATTTTTCTCAAAAGA
66 GGAAAGACTCAAAGATGATAAATGTTGTTTCCAAAGAAACAGAATCAAAGATTTTTCTCAAAAGA
84458 AAC
131 AAC
* * *
84461 TGTCTCAAGAGTGACAAAATTTTGTTT-ACAGAGAAACAGACTCAAAGATGG
1 TGTCTCAAGAGAGACAAAATTTTGTTTCA-AAAGAAAAAGACTCAAAGATGG
84512 ATTATGTCTT
Statistics
Matches: 159, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
129 41 0.26
130 16 0.10
131 58 0.36
132 44 0.28
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (133 bp):
TGTCTCAAGAGAGACAAAATTTTGTTTCAAAAGAAAAAGACTCAAAGATGGCTTTTGTTTCAAAA
GGAAAGACTCAAAGATGATAAATGTTGTTTCCAAAGAAACAGAATCAAAGATTTTTCTCAAAAGA
AAC
Found at i:84407 original size:30 final size:30
Alignment explanation
Indices: 84349--84408 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
84339 AGAGACAAAA
*
84349 TTTTGTTTCAACAGAAATAGAATCAAAGATC
1 TTTTGTTTCAAAAGAAATA-AATCAAAGATC
*
84380 TTTTGTTTCAAAAGGAAAT-ACTCAAAGAT
1 TTTTGTTTCAAAA-GAAATAAATCAAAGAT
84409 GATAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 9 0.35
31 12 0.46
32 5 0.19
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAATAAATCAAAGATC
Found at i:84678 original size:29 final size:28
Alignment explanation
Indices: 84633--84705 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
84623 TCAAATATGA
84633 TTTTGTTAAAAGAAACAAACCCAAAGAT
1 TTTTGTTAAAAGAAACAAACCCAAAGAT
* * *
84661 TTTTGTTCAAAAGGAACAGACTCAAAGAT
1 TTTTGTT-AAAAGAAACAAACCCAAAGAT
*
84690 TTGTT-TTAAGAGAAAC
1 TT-TTGTTAAAAGAAAC
84706 TGTCTCAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 14 0.37
29 22 0.58
30 2 0.05
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (28 bp):
TTTTGTTAAAAGAAACAAACCCAAAGAT
Found at i:85058 original size:104 final size:104
Alignment explanation
Indices: 84870--85174 Score: 362
Period size: 104 Copynumber: 2.9 Consensus size: 104
84860 ATTGATTTTG
* * * * * *
84870 ACAATCTCAAGTGAAATTAATTTTGTTTCAAGTAAAACAACTTTGAAATTTGTATTCTAAGGGAA
1 ACAATCTCAAGTGAAATTAATTTTGTTTAAAGTGAAACAAATTCGAAATTTGTATTCAAAGGAAA
* * *
84935 AATGTCTCAAGTGAGACGAAATTTGTTTTGAAATAAACA
66 AATGTCTCAAGCGAAACGAAATTTGTTTTGAAAGAAACA
* * * *
84974 ACAATCTCAAGTGAGATTAATTTTG-TTAAAGTGAAGCAAATTCAAAATTTGCATATCAAAGGAA
1 ACAATCTCAAGTGAAATTAATTTTGTTTAAAGTGAAACAAATTCGAAATTTGTAT-TCAAAGGAA
* *
85038 AAATGTCTCAAGCGAAACGAAATATGTTTTGAAAGAAATA
65 AAATGTCTCAAGCGAAACGAAATTTGTTTTGAAAGAAACA
* * * *
85078 ACAATATCAAGTGATATTAATTTTGTTTAAAGTGAATCAAATTCGAAATTTGTATCTCAAAGAAA
1 ACAATCTCAAGTGAAATTAATTTTGTTTAAAGTGAAACAAATTCGAAATTTGTAT-TCAAAG--G
* *
85143 AAAAATGTCTCAAAC-AAGATGAAATTTGTTTT
63 AAAAATGTCTCAAGCGAA-ACGAAATTTGTTTT
85175 TTAGAGAAAT
Statistics
Matches: 171, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
103 22 0.13
104 89 0.52
105 32 0.19
106 2 0.01
107 26 0.15
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (104 bp):
ACAATCTCAAGTGAAATTAATTTTGTTTAAAGTGAAACAAATTCGAAATTTGTATTCAAAGGAAA
AATGTCTCAAGCGAAACGAAATTTGTTTTGAAAGAAACA
Found at i:85453 original size:35 final size:36
Alignment explanation
Indices: 85351--85498 Score: 149
Period size: 35 Copynumber: 4.0 Consensus size: 36
85341 GAAACAAATT
* * *
85351 CAAAATTTGTATCTCAAAGGAAAATGTCTCAAGCGAGA
1 CAAAATTTGTTTTTC-AA-GAAATTGTCTCAAGCGAGA
* * *
85389 CGAAATTTGTTTTTCAAGAAATTGTCTCAAACGATA
1 CAAAATTTGTTTTTCAAGAAATTGTCTCAAGCGAGA
*
85425 CAAAATTTGTTTTT--AGAAAATTTTCTCAAGCGAGA
1 CAAAATTTGTTTTTCAAG-AAATTGTCTCAAGCGAGA
*
85460 CAAAATTTGTTTTTCAAAAGAAGTTGTCT-ATAGCGAGA
1 CAAAATTTGTTTTTC--AAGAAATTGTCTCA-AGCGAGA
85498 C
1 C
85499 GACATTTTGT
Statistics
Matches: 92, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
34 2 0.02
35 29 0.32
36 29 0.32
37 3 0.03
38 27 0.29
39 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (36 bp):
CAAAATTTGTTTTTCAAGAAATTGTCTCAAGCGAGA
Found at i:87163 original size:16 final size:16
Alignment explanation
Indices: 87142--87230 Score: 60
Period size: 18 Copynumber: 5.4 Consensus size: 16
87132 GCTCTTTGTC
87142 CTCTTTTTGTTCTTTG
1 CTCTTTTTGTTCTTTG
87158 CTCTTTTCTTTGTT-TTTG
1 CTC--TT-TTTGTTCTTTG
*
87176 CT-TTTTT-TTCTTTT
1 CTCTTTTTGTTCTTTG
* *
87190 TTCTTTTTTTTC-TTG
1 CTCTTTTTGTTCTTTG
*
87205 CTCTTTGTTTTTTCTTTG
1 CTC-TT-TTTGTTCTTTG
87223 CTTCTTTT
1 C-TCTTTT
87231 CTCTTTATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
13 2 0.03
14 7 0.12
15 11 0.19
16 8 0.14
17 9 0.15
18 14 0.24
19 8 0.14
ACGTcount: A:0.00, C:0.17, G:0.08, T:0.75
Consensus pattern (16 bp):
CTCTTTTTGTTCTTTG
Found at i:87173 original size:9 final size:9
Alignment explanation
Indices: 87161--87203 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
87151 TTCTTTGCTC
87161 TTTTCTTTGT
1 TTTTCTTT-T
87171 TTTTGCTTTT
1 TTTT-CTTTT
87181 TTTTC--TT
1 TTTTCTTTT
87188 TTTTCTTTT
1 TTTTCTTTT
87197 TTTTCTT
1 TTTTCTT
87204 GCTCTTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.23
9 10 0.33
10 9 0.30
11 4 0.13
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.84
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:87187 original size:32 final size:31
Alignment explanation
Indices: 87142--87232 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 31
87132 GCTCTTTGTC
* * *
87142 CTCTTTTTGTTCTTTGCTCTTTTCTTTGTTT
1 CTCTTTTTTTTCTTTGCTCTTTTCTTTCTTG
* ** *
87173 TTGCTTTTTTTTCTTTTTTCTTTTTTTTCTTG
1 CT-CTTTTTTTTCTTTGCTCTTTTCTTTCTTG
87205 CTCTTTGTTTTTTCTTTGCTTCTTTTCT
1 CTC-TT-TTTTTTCTTTGC-TCTTTTCT
87233 CTTTATTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
31 2 0.04
32 26 0.58
33 10 0.22
34 7 0.16
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.75
Consensus pattern (31 bp):
CTCTTTTTTTTCTTTGCTCTTTTCTTTCTTG
Found at i:87223 original size:18 final size:18
Alignment explanation
Indices: 87195--87229 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
87185 CTTTTTTCTT
87195 TTTTTTCTTGC-TCTTTG
1 TTTTTTCTTGCTTCTTTG
87212 TTTTTTCTTTGCTTCTTT
1 TTTTTTC-TTGCTTCTTT
87230 TCTCTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (18 bp):
TTTTTTCTTGCTTCTTTG
Found at i:87223 original size:47 final size:49
Alignment explanation
Indices: 87143--87249 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 49
87133 CTCTTTGTCC
*
87143 TCTTTTTGTTCTTTGCTCTTTTCTTTGTTTTTGCTT-TTTTTTCTTTTT
1 TCTTTTTGTTCTTTGCTCTTTTCTTTGTTTTTGCTTCTTTTCTCTTTTT
* *
87191 TCTTTTTTTTC-TTGCTCTTTGT-TTT-TTCTTTGCTTCTTTTCTCTTTAT
1 TCTTTTTGTTCTTTGCTCTTT-TCTTTGTT-TTTGCTTCTTTTCTCTTTTT
*
87239 T-TTTCTGTTCT
1 TCTTTTTGTTCT
87250 CTTCACTTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
46 2 0.04
47 26 0.52
48 22 0.44
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (49 bp):
TCTTTTTGTTCTTTGCTCTTTTCTTTGTTTTTGCTTCTTTTCTCTTTTT
Found at i:87228 original size:41 final size:43
Alignment explanation
Indices: 87164--87244 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
87154 TTTGCTCTTT
** *
87164 TCTTTGTTTTTGCTTTTTTTTCTTTTTTCTTT-TTTTTCTTGC
1 TCTTTGTTTTTGCTTTTGCTTCTTTTCTCTTTATTTTTCTTGC
*
87206 TCTTTGTTTTTTC-TTTGCTTCTTTTCTCTTTATTTTTCT
1 TCTTTGTTTTTGCTTTTGCTTCTTTTCTCTTTATTTTTCT
87245 GTTCTCTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 15 0.44
42 19 0.56
ACGTcount: A:0.01, C:0.16, G:0.06, T:0.77
Consensus pattern (43 bp):
TCTTTGTTTTTGCTTTTGCTTCTTTTCTCTTTATTTTTCTTGC
Found at i:88543 original size:14 final size:12
Alignment explanation
Indices: 88506--88539 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
88496 CAAAATGCAA
*
88506 AGATGAAAATGC
1 AGATAAAAATGC
88518 AGATAAAAATGC
1 AGATAAAAATGC
88530 AGATACAAAA
1 AGATA-AAAA
88540 ATGCTGATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.59, C:0.09, G:0.18, T:0.15
Consensus pattern (12 bp):
AGATAAAAATGC
Done.