Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007071.1 Hibiscus syriacus cultivar Beakdansim tig00018399_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: 144035
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:701 original size:35 final size:34
Alignment explanation
Indices: 607--715 Score: 139
Period size: 33 Copynumber: 3.2 Consensus size: 34
597 TCTAAACCTT
* * *
607 AAATTGAAGTATTTAGAATTTGGGGTTTAGAATT
1 AAATTGAAATATTTGGAATTTGGGGTTTAGAATG
* * *
641 TAA-TGAATTATTTGGAATTTAGGGTTTAGAATG
1 AAATTGAAATATTTGGAATTTGGGGTTTAGAATG
*
674 AAATTGAAATACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAAATA-TTTGGAATTTGGGGTTTAGAATG
709 AAATTGA
1 AAATTGA
716 GGACTGTTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
33 28 0.44
34 8 0.12
35 28 0.44
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.39
Consensus pattern (34 bp):
AAATTGAAATATTTGGAATTTGGGGTTTAGAATG
Found at i:1523 original size:16 final size:17
Alignment explanation
Indices: 1483--1528 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
1473 ATGTTATGAG
1483 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
*
1501 AGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
1517 GGAATTGGAATC
1 GGAATTGGAATC
1529 CAATTCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:2621 original size:217 final size:216
Alignment explanation
Indices: 2226--2674 Score: 629
Period size: 217 Copynumber: 2.0 Consensus size: 216
2216 TTAGAAATCT
* *
2226 ACCCGACCCGAAATAATAAAAAATTATTTTATTTAATAAAAACAGTGATTTAATCCGACCTGACC
1 ACCCGACCCAAAATAATAAAAAATTATTTTATTTAATAAAAACAGTGACTTAATCCGACCTGACC
* * *
2291 CGAATTATATATTTTCGGGTCGGTCCTTTTTTCAGCCTAAACCCGAACCTAACCCGATCCAACCC
66 CGAATTATATATTTTCAGATCGGTCCTTTTTTCACCCTAAACCC-AA-C-AACCCG----AACCC
* * * * *
2356 GAATATCACACTTAAAAGAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAGCCCGATTC
124 GAATATCACACTTAAAAAAAACCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCAATCC
*
2421 GACCCCGGAC-AAAATAAAGTTTCATCCG
189 GA-CCCGAACAAAAATAAAGTTTCATCCG
2449 ACCCGACCCAAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCTGAC
1 ACCCGACCCAAAATAATAAAAAATTA-TTTTATTTAATAAAAACAGTGACTTAATCCGACCTGAC
*
2514 TCGAATTATATATATTTCAGATCGGTCCGGTTTTTTTCACCCTAAACCC-A-AA-CCG-ACCCGA
65 CCGAATTATATAT-TTTCAGATCGGTCC---TTTTTTCACCCTAAACCCAACAACCCGAACCCGA
2575 ATATCACACTTAAAAAAAACCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCAATCCGA
126 ATATCACACTTAAAAAAAACCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCAATCCGA
*
2640 TCCGAACAAAAATAAAGTTTCATCCG
191 CCCGAACAAAAATAAAGTTTCATCCG
2666 ACCCGACCC
1 ACCCGACCC
2675 GAATATGAAT
Statistics
Matches: 207, Mismatches: 13, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
216 5 0.02
217 93 0.45
222 3 0.01
223 27 0.13
224 49 0.24
225 12 0.06
226 1 0.00
228 17 0.08
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (216 bp):
ACCCGACCCAAAATAATAAAAAATTATTTTATTTAATAAAAACAGTGACTTAATCCGACCTGACC
CGAATTATATATTTTCAGATCGGTCCTTTTTTCACCCTAAACCCAACAACCCGAACCCGAATATC
ACACTTAAAAAAAACCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCAATCCGACCCGA
ACAAAAATAAAGTTTCATCCG
Found at i:2928 original size:187 final size:181
Alignment explanation
Indices: 2636--3023 Score: 559
Period size: 187 Copynumber: 2.1 Consensus size: 181
2626 AAAACCCAAT
*
2636 CCGATCCGAACAAAAATAAAGTTTCATCCGACCCGACCCGAATATGAATTAGAAATCCAACCCGA
1 CCGACCCGAAC-AAAATAAAGTTTCATCCGACCCGACCCGAATATGAATTAGAAATCCAACCCGA
*
2701 CCGACCCGAAATAATAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCG
65 CCGACCCGAAATAATAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCCG
*
2766 AATTATATATATTTTCGGGTCGATCC-AGTTTTTTTCACCCTAAACCC-AAGCCTGAC
130 AA-T-TATATATTTTCGGGTCGATCCGA-TTTTTTT--CCCTAAACCCGAA-CCCGAC
* * *
2822 TCGACCCGAACAAAATAAAGTTTTCATCCGACCTGACTCGAATATATGAATTAG-AATCCAACCC
1 CCGACCCGAACAAAATAAAG-TTTCATCCGACCCGACCCG-A-ATATGAATTAGAAATCCAACCC
2886 GACCCGACCCGAAATAATAAAAAATA-TTTTATTTAATAAAAACAATGACTTAATCCGACCCGAC
63 GA-CCGACCCGAAATAATAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGAC
* *
2950 CTGAATTATATATTTTCGGGTCGGTCCGATTTTTTTCCCTAAACCCGAACCCGAC
127 CCGAATTATATATTTTCGGGTCGATCCGATTTTTTTCCCTAAACCCGAACCCGAC
*
3005 CCGACCCGACCCAAAATAA
1 CCGACCCGA-ACAAAATAA
3024 TAAAAAATAT
Statistics
Matches: 185, Mismatches: 10, Indels: 16
0.88 0.05 0.08
Matches are distributed among these distances:
183 23 0.12
184 10 0.05
185 36 0.19
186 28 0.15
187 54 0.29
188 34 0.18
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.25
Consensus pattern (181 bp):
CCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATGAATTAGAAATCCAACCCGAC
CGACCCGAAATAATAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCCGA
ATTATATATTTTCGGGTCGATCCGATTTTTTTCCCTAAACCCGAACCCGAC
Found at i:3410 original size:28 final size:28
Alignment explanation
Indices: 3350--3410 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
3340 ATTAGTAAAA
*
3350 AATTAATTTTATAGAATTATTAAATGAAT
1 AATT-ATTTTATAAAATTATTAAATGAAT
3379 -ATTATTTTCATAAAATTATCT-AAT-AAT
1 AATTATTTT-ATAAAATTAT-TAAATGAAT
3406 AATTA
1 AATTA
3411 GGTTTTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
27 8 0.29
28 19 0.68
29 1 0.04
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (28 bp):
AATTATTTTATAAAATTATTAAATGAAT
Found at i:11782 original size:3 final size:3
Alignment explanation
Indices: 11776--11815 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
11766 GAAGAAGGCC
11776 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11816 GAGGGTAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12055 original size:32 final size:32
Alignment explanation
Indices: 12009--12083 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 32
11999 AGGAGTTAAC
**
12009 TGTTGAGGGA-TAAAAATCAAACGGATTGATAA
1 TGTT-AGGGACTAAAAATCAAACAAATTGATAA
** *
12041 TGTTAGGGACT-AAAATTGAACAAATTTATAA
1 TGTTAGGGACTAAAAATCAAACAAATTGATAA
12072 TGTTAGGGACTA
1 TGTTAGGGACTA
12084 TTCCCCTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 31 0.86
32 5 0.14
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (32 bp):
TGTTAGGGACTAAAAATCAAACAAATTGATAA
Found at i:12382 original size:3 final size:3
Alignment explanation
Indices: 12374--12398 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12364 TCGTTTACCC
12374 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
12399 GCGAGAGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:14784 original size:20 final size:20
Alignment explanation
Indices: 14759--14799 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
14749 ATTGTAACGA
14759 TCAACGATGAAAAACGTTGG
1 TCAACGATGAAAAACGTTGG
*
14779 TCAACGATGAAAAATGTTGG
1 TCAACGATGAAAAACGTTGG
14799 T
1 T
14800 TAAAGATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (20 bp):
TCAACGATGAAAAACGTTGG
Found at i:17736 original size:21 final size:21
Alignment explanation
Indices: 17695--17736 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
17685 GTTATTAAGA
* *
17695 TTCAAGGATGTGTGTATTTAT
1 TTCAAGGATGTGTGAACTTAT
17716 TTCAAGGAT-TGCTGAACTTAT
1 TTCAAGGATGTG-TGAACTTAT
17737 GCTATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (21 bp):
TTCAAGGATGTGTGAACTTAT
Found at i:19272 original size:27 final size:27
Alignment explanation
Indices: 19241--19293 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
19231 TGAATGTGCG
**
19241 TTACGTGGCACTTGCTTAGAAAAAGAC
1 TTACGTGGCACTCACTTAGAAAAAGAC
19268 TTACGTGGCACTCACTTAGAAAAAGA
1 TTACGTGGCACTCACTTAGAAAAAGA
19294 AGTTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (27 bp):
TTACGTGGCACTCACTTAGAAAAAGAC
Found at i:19419 original size:42 final size:42
Alignment explanation
Indices: 19360--19445 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
19350 TACTTAAAAA
*
19360 AAGAACTTAATTTTTGAATCGA-TCATCAACAATAACACGATG
1 AAGAACTTAACTTTTGAATC-ACTCATCAACAATAACACGATG
* * *
19402 AAGAATTTAACTTTTGAATCACTGATCAACAATAATACGATG
1 AAGAACTTAACTTTTGAATCACTCATCAACAATAACACGATG
19444 AA
1 AA
19446 AAAAATTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (42 bp):
AAGAACTTAACTTTTGAATCACTCATCAACAATAACACGATG
Found at i:22319 original size:24 final size:24
Alignment explanation
Indices: 22287--22343 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
22277 ATGAACCAGC
22287 TCGTTTATGAGCTCCTGTATAAGT
1 TCGTTTATGAGCTCCTGTATAAGT
22311 TCGTTTATGAGCTCCTGTATAAGT
1 TCGTTTATGAGCTCCTGTATAAGT
22335 TCGTTTATG
1 TCGTTTATG
22344 TTCATGAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (24 bp):
TCGTTTATGAGCTCCTGTATAAGT
Found at i:25504 original size:2 final size:2
Alignment explanation
Indices: 25497--25524 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25487 ATGAAATCTT
25497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25525 ATTATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25928 original size:31 final size:30
Alignment explanation
Indices: 25881--25940 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
25871 TGATTTTGAA
25881 AAAAATGAAAGTTTAGGTACTAAAACGTGTC
1 AAAAATGAAAGTTTAGGTACTAAAA-GTGTC
* * *
25912 AAAACTGATAGTTTAGGTACTGAAAGTGT
1 AAAAATGAAAGTTTAGGTACTAAAAGTGT
25941 AGTTACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (30 bp):
AAAAATGAAAGTTTAGGTACTAAAAGTGTC
Found at i:26284 original size:31 final size:31
Alignment explanation
Indices: 26249--26325 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
26239 AAAAAATGAA
* *
26249 AGTTTAGGTACTAAAAAAGACCAATACTAAT
1 AGTTTAAGTACTAAAAAAGACCAAAACTAAT
** *
26280 AGTTTAAGTACTAAAACGGACCAAAACTTAT
1 AGTTTAAGTACTAAAAAAGACCAAAACTAAT
*
26311 AATTTAAGTACTAAA
1 AGTTTAAGTACTAAA
26326 TACGTAGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (31 bp):
AGTTTAAGTACTAAAAAAGACCAAAACTAAT
Found at i:31209 original size:75 final size:75
Alignment explanation
Indices: 31086--31235 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
31076 TCCAACCTAG
31086 AAACAATAACAAGATTTCTAGAGCAACTTGGAACATATAGACACTTCTGTAGAACAGGAAGTAGC
1 AAACAATAACAAGATTTCTAGAGCAACTTGGAACATATAGACACTTCTGTAGAACAGGAAGTAGC
31151 CCATATCTAA
66 CCATATCTAA
31161 AAACAATAACAAGATTTCTAGAGCAACTTGGAACATATAGACACTTCTGTAGAACAGGAAGTAGC
1 AAACAATAACAAGATTTCTAGAGCAACTTGGAACATATAGACACTTCTGTAGAACAGGAAGTAGC
31226 CCATATCTAA
66 CCATATCTAA
31236 CACAATTCTA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.23
Consensus pattern (75 bp):
AAACAATAACAAGATTTCTAGAGCAACTTGGAACATATAGACACTTCTGTAGAACAGGAAGTAGC
CCATATCTAA
Found at i:44730 original size:19 final size:21
Alignment explanation
Indices: 44691--44730 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
44681 ATAATCCTAT
44691 TATTTCAAAATTATATAAAAA
1 TATTTCAAAATTATATAAAAA
*
44712 TATTT-AAAA-TATCTAAAAA
1 TATTTCAAAATTATATAAAAA
44731 GGACTTCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 4 0.22
21 5 0.28
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTTCAAAATTATATAAAAA
Found at i:44917 original size:13 final size:13
Alignment explanation
Indices: 44880--44919 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
44870 TCGATATTGA
44880 AAAATAAATA-TT
1 AAAATAAATATTT
*
44892 AAAATAATTTATTT
1 AAAATAA-ATATTT
44906 AAAATAAATATTT
1 AAAATAAATATTT
44919 A
1 A
44920 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:46369 original size:3 final size:3
Alignment explanation
Indices: 46346--46422 Score: 73
Period size: 3 Copynumber: 25.0 Consensus size: 3
46336 AATTTTTTAT
* * * * * *
46346 TAA TAA TAT TAG TAA TAAA TAA TAA TAT TAG TAA TTA TAA TTA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
46392 TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
46423 ATAAATAAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
3 55 0.92
4 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:46370 original size:19 final size:19
Alignment explanation
Indices: 46346--46426 Score: 81
Period size: 19 Copynumber: 4.2 Consensus size: 19
46336 AATTTTTTAT
* *
46346 TAATAATATTAGTAATAAA
1 TAATAATAATAATAATAAA
* *
46365 TAATAATATTAGTAATTATAA
1 TAATAATAATAATAA-TA-AA
* * *
46386 TTATAATAATAATATTTAA
1 TAATAATAATAATAATAAA
46405 TAATAATAATAATAATAAA
1 TAATAATAATAATAATAAA
46424 TAA
1 TAA
46427 ATAAATTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
19 36 0.69
20 3 0.06
21 13 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TAATAATAATAATAATAAA
Found at i:46833 original size:113 final size:112
Alignment explanation
Indices: 46692--47337 Score: 755
Period size: 113 Copynumber: 5.6 Consensus size: 112
46682 TCTTGATGAG
*
46692 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTCTT-TC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACT-TTCTC
* * * * *
46755 TGGCAAGGCTGATCCATCAATTGATGAATTCATGTAAAAGGTTGAACAAG
64 TGGAAAAGCTGATCCATCAAATGATGAATT-ATGCAAAAGGTTGAACAAA
46805 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*** * *
46870 GAAAAGGCTGATGCTAATCTATCTCCTTCTGTGATAGAATTATGCAAAAAGTTGAACAAG
66 GAAAA-GCTGAT-C----C-A--T-C--AAATGAT-GAATTATGCAAAAGGTTGAACAAA
* * ** * *
46930 CTCTTCTTATTATGAACTTCTTCTT-CTTC-AGATGACGAGTTCTTCTCATTATGAACTCTAC-C
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCATTATGAACT-TTCTC
* * * * **
46992 TGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
64 TGGAAAAGCTGATCCATCAAATGATGAA-TTATGCAAAAGGTTGAACAAA
*
47042 TTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* **
47107 GAAAAGCTGATCCATCAAATGATGGATTTAAACAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAATGAT-GAATTATGCAAAAGGTTGAACAAA
* *
47155 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
47220 GAAAAGCTGATCCATCAAGTGATGGATT-TGAACAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAATGATGAATTATG--CAAAAGGTTGAACAAA
*
47268 TTCTTCTCATTATGAACTTCTTCTTCCTTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCC-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
47333 GGAAA
65 GGAAA
47338 TGTCAATCTA
Statistics
Matches: 460, Mismatches: 48, Indels: 49
0.83 0.09 0.09
Matches are distributed among these distances:
111 3 0.01
112 53 0.12
113 257 0.56
114 49 0.11
115 2 0.00
117 1 0.00
118 1 0.00
119 1 0.00
120 1 0.00
122 2 0.00
123 6 0.01
124 33 0.07
125 46 0.10
126 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAATGATGAATTATGCAAAAGGTTGAACAAA
Found at i:47009 original size:237 final size:223
Alignment explanation
Indices: 46693--47359 Score: 748
Period size: 237 Copynumber: 2.9 Consensus size: 223
46683 CTTGATGAGT
* ** **
46693 TCTTCTCATTATGAACTTCTTCATCCTTCTTTCGATGAGTTCTTCTCATTATGAACTCTTTCTGG
1 TCTTCTCATTATGAACTTCTTC-TTCTTCCAT-GATGAGTTCTTCTCATTATGAACTCTACCTGG
* * * *
46758 CAAGGCTGATCCATCAATTGATGAATTCATGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACT
64 CAAAGCTGATCCATCAAATGATGAATT-ATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
46823 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGGCTGATGCTAAT
128 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA-GCTGAT-C----
*** ** *
46888 CTATCTCCTTCTGTGATAGAATTATGCAAAAAGTTGAACAAGC
187 C-A--T-C--AAATGATAGAATTAAACAAAAAGTTGAACAAAC
* * *
46931 TCTTCTTATTATGAACTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGC
1 TCTTCTCATTATGAACTTCTTCTTCTTC-CATGATGAGTTCTTCTCATTATGAACTCTACCTGGC
* * * **
46996 AATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
65 AAAGCTGATCCATCAAATGATGAA-TTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
*
47061 ATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAA
129 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAA
* * * *
47126 TGATGGATTTAAACAAAAGGTTGAACAAAT
194 TGATAGAATTAAACAAAAAGTTGAACAAAC
* *
47156 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTTATTATGAACT-TCCTCT
1 TCTTCTCATTATGAACTTCTTCTT-CTTC--CATGATGAGTTCTTCTCATTATGAACTCTAC-CT
* * *
47219 GGAAAAGCTGATCCATCAAGTGATGGATT-TGAACAAAAGGTTGAACAAATTCTTCTCATTATGA
62 GGCAAAGCTGATCCATCAAATGATGAATTATG--CAAAAGGTTGAACAAATTCTTCTCATTATGA
* * * *
47283 ACTTCTTCTTCCTTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATG-TCAATCT
125 ACTTCTTCTTCC-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCT-GATCC
47347 ATCAAATGATAGA
188 ATCAAATGATAGA
47360 TTTGAATCTT
Statistics
Matches: 374, Mismatches: 46, Indels: 29
0.83 0.10 0.06
Matches are distributed among these distances:
225 50 0.13
226 92 0.25
227 59 0.16
228 1 0.00
230 1 0.00
231 1 0.00
235 1 0.00
236 6 0.02
237 139 0.37
238 24 0.06
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (223 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCCATGATGAGTTCTTCTCATTATGAACTCTACCTGGCA
AAGCTGATCCATCAAATGATGAATTATGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATG
ATAGAATTAAACAAAAAGTTGAACAAAC
Found at i:48223 original size:83 final size:83
Alignment explanation
Indices: 48084--48549 Score: 778
Period size: 83 Copynumber: 5.6 Consensus size: 83
48074 GTTCCTACCA
* * *
48084 AACCAGATCAGATAACTCAAAGATCAGTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATT
48149 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
48167 AACCAGACCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTC-AAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATT
* * *
48231 CAATGATTGATTCTGACA
66 CAATGATTGGTTCTGTCC
48249 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTC-AAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATT
* *
48313 TAATGATTGATTCTG-CC
66 CAATGATTGGTTCTGTCC
48330 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAAT
1 -AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAAT
*
48395 TCAATGATAGGTTCTGTCC
65 TCAATGATTGGTTCTGTCC
48414 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATT
48479 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
48497 AACCAGA-CTAGATAACTCAAAGAACAATTCCAGAAGATGCTATTGAGCACATT
1 AACCAGATC-AGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATT
48550 ACATTTGTTC
Statistics
Matches: 363, Mismatches: 15, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
81 1 0.00
82 157 0.43
83 193 0.53
84 12 0.03
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATT
CAATGATTGGTTCTGTCC
Found at i:49541 original size:13 final size:13
Alignment explanation
Indices: 49523--49560 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
49513 TTGACCTCCC
*
49523 CTTTTTCTTTTTT
1 CTTTTTCTCTTTT
49536 CTTTTTCTCTTTT
1 CTTTTTCTCTTTT
*
49549 -TTTTTCACTTTT
1 CTTTTTCTCTTTT
49561 TTTCTCTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTTTTCTCTTTT
Found at i:49552 original size:12 final size:12
Alignment explanation
Indices: 49524--49563 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
49514 TGACCTCCCC
*
49524 TTTTTCTTTTTT
1 TTTTTCTCTTTT
49536 CTTTTTCTCTTTT
1 -TTTTTCTCTTTT
*
49549 TTTTTCACTTTT
1 TTTTTCTCTTTT
49561 TTT
1 TTT
49564 CTCTTCAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:60928 original size:13 final size:12
Alignment explanation
Indices: 60898--60941 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
60888 CTTTTCTTCG
60898 ATATTGAAAATAA
1 ATATT-AAAATAA
60911 ATATTAAAATAA
1 ATATTAAAATAA
*
60923 TTTATTTAAAATAA
1 -ATA-TTAAAATAA
60937 ATATT
1 ATATT
60942 TATTATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.33
13 9 0.33
14 9 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
ATATTAAAATAA
Found at i:60942 original size:13 final size:13
Alignment explanation
Indices: 60898--60943 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
60888 CTTTTCTTCG
*
60898 ATATTGAAAATAA
1 ATATTTAAAATAA
60911 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
60923 TTTATTTAAAATAA
1 -ATATTTAAAATAA
60937 ATATTTA
1 ATATTTA
60944 TTATTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 8 0.29
13 11 0.39
14 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:62376 original size:3 final size:3
Alignment explanation
Indices: 62354--62422 Score: 79
Period size: 3 Copynumber: 23.0 Consensus size: 3
62344 AATTTTTTAT
* * *
62354 TAA TAA T-A TAG TAA TAAA TAA TAA T-A TAAA TTA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
62399 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
62423 ATAAATTAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
2 4 0.07
3 47 0.84
4 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:62432 original size:12 final size:11
Alignment explanation
Indices: 62366--62433 Score: 52
Period size: 12 Copynumber: 6.0 Consensus size: 11
62356 ATAATATAGT
62366 AATAAATAATA
1 AATAAATAATA
*
62377 ATATAAATTATA
1 A-ATAAATAATA
*
62389 ATTATAATAAT-
1 AATA-AATAATA
62400 AAT-AATAAT-
1 AATAAATAATA
62409 AATAATAATAATA
1 AAT-A-AATAATA
62422 AATAAATTAATA
1 AATAAA-TAATA
62434 TGGGTAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
9 9 0.20
11 7 0.15
12 27 0.59
13 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAAATAATA
Found at i:62432 original size:15 final size:15
Alignment explanation
Indices: 62352--62433 Score: 57
Period size: 15 Copynumber: 5.5 Consensus size: 15
62342 GTAATTTTTT
*
62352 ATTAATAATATAGT-A
1 ATTAATAATA-AATAA
*
62367 ATAAATAATAATATAA
1 ATTAATAATAA-ATAA
62383 ATT-ATAATTATAAT-A
1 ATTAATAA-TA-AATAA
62398 A-TAATAAT-AATAA
1 ATTAATAATAAATAA
*
62411 TAATAATAATAAATAA
1 -ATTAATAATAAATAA
62427 ATTAATA
1 ATTAATA
62434 TGGGTAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
12 3 0.06
13 1 0.02
14 4 0.07
15 33 0.61
16 12 0.22
17 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (15 bp):
ATTAATAATAAATAA
Found at i:63588 original size:3 final size:3
Alignment explanation
Indices: 63573--63640 Score: 84
Period size: 3 Copynumber: 22.0 Consensus size: 3
63563 CTATTTTAAT
* *
63573 TTA TTA CTA TTA TTA TT- TTGT TTA TTA TTA TTAA TTA TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT-A TTA TTA TT-A TTA
63620 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
63641 ATATAAATGG
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.03
3 48 0.83
4 8 0.14
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:63620 original size:35 final size:34
Alignment explanation
Indices: 63564--63642 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 34
63554 GGGTCTTTTC
*
63564 TATT-TTAATTTATTACTATTATTATT-TTGTTTAT
1 TATTATTAA-TTATTACTATTATTATTATT-ATTAT
*
63598 TATTATTAATTATTATTAATTATTATTATTATTAT
1 TATTATTAATTATTACT-ATTATTATTATTATTAT
63633 TATTATTAAT
1 TATTATTAAT
63643 ATAAATGGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 11 0.28
35 27 0.68
36 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (34 bp):
TATTATTAATTATTACTATTATTATTATTATTAT
Found at i:67823 original size:30 final size:30
Alignment explanation
Indices: 67766--67833 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
67756 ATGCATAAGT
* **
67766 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* *
67796 AAATGCATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
67826 ATATGCAT
1 AAATGCAT
67834 TCGAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:74838 original size:8 final size:8
Alignment explanation
Indices: 74827--74889 Score: 51
Period size: 8 Copynumber: 7.8 Consensus size: 8
74817 AAAAAAAGGA
74827 AAAAAATG
1 AAAAAATG
74835 AAAATATGATG
1 AAAA-A--ATG
*
74846 GAAAAATG
1 AAAAAATG
74854 AAAAAA-G
1 AAAAAATG
74861 AAGAAAATG
1 AA-AAAATG
74870 --AAAATG
1 AAAAAATG
*
74876 AAAAAAAG
1 AAAAAATG
74884 AAAAAA
1 AAAAAA
74890 ATAATAAAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
6 6 0.13
7 3 0.07
8 27 0.60
9 2 0.04
10 1 0.02
11 6 0.13
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:74876 original size:22 final size:23
Alignment explanation
Indices: 74848--74891 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
74838 ATATGATGGA
*
74848 AAAATG-AAAAAAGAAGAAAATG
1 AAAATGAAAAAAAGAAAAAAATG
74870 AAAATGAAAAAAAGAAAAAAAT
1 AAAATGAAAAAAAGAAAAAAAT
74892 AATAAAGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (23 bp):
AAAATGAAAAAAAGAAAAAAATG
Found at i:74887 original size:30 final size:28
Alignment explanation
Indices: 74817--74890 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
74807 ATTACACTTA
* **
74817 AAAAAAAGGAAAAAAATGAAAATATGATG
1 AAAAAAA-GAAAAAAAAGAAAATAAAATG
* *
74846 GAAAAATGAAAAAAGAAGAAAATGAAAATG
1 AAAAAAAGAAAAAA-AAGAAAAT-AAAATG
74876 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
74891 TAATAAAGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
28 7 0.19
29 13 0.36
30 16 0.44
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (28 bp):
AAAAAAAGAAAAAAAAGAAAATAAAATG
Found at i:76126 original size:133 final size:134
Alignment explanation
Indices: 75820--76259 Score: 552
Period size: 133 Copynumber: 3.3 Consensus size: 134
75810 AACATCAGCT
* *** * ** * *
75820 GACCAGATCTCCTCATCATGTAGGAGCAACGTCAACATTAGATAACCAGCCGTCCTCATTACGTA
1 GACCAGATCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTA
** *
75885 GGAACTATGTTATCG--C-T-ATAAA-ATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT
66 GGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT
75945 CCCC
131 CCCC
** *
75949 TGATTAGATCTCCTCATCACGTAGGAG-TCGTGTCACCCCTAGATAACCAGACATCCTCATCACG
1 -GACCAGATCTCCTCATCACGTAGGAGCT-GTGTCACCCCTAGATAACCAGACGTCCTCATCACG
* *
76013 TAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTATC
64 TAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTC
76077 ATCCCC
129 ATCCCC
* * *
76083 GACCAGATCTCCTCATCGCGTAGGAGCTGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTA
1 GACCAGATCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTA
* *
76148 GGAACCGAGTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT
66 GGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT
*
76213 CCCTT
131 CCC-C
* * * * *
76218 GACCATATTTCCTCATCACGTAGGAACCGTGTCACCCTTAGA
1 GACCAGATCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGA
76260 CGACCCGAAC
Statistics
Matches: 267, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
130 65 0.24
132 1 0.00
133 89 0.33
134 70 0.26
135 42 0.16
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (134 bp):
GACCAGATCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTA
GGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCAT
CCCC
Found at i:76293 original size:43 final size:40
Alignment explanation
Indices: 76182--76298 Score: 110
Period size: 43 Copynumber: 2.9 Consensus size: 40
76172 AAGATGGCCA
76182 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTTGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTTGACC
* ** * * * *
76222 ATATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAGACGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTT----GACC
* *
76265 CGAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC
76299 CAACAACTAA
Statistics
Matches: 56, Mismatches: 16, Indels: 6
0.72 0.21 0.08
Matches are distributed among these distances:
39 5 0.09
40 23 0.41
43 25 0.45
44 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTTGACC
Found at i:76462 original size:3 final size:3
Alignment explanation
Indices: 76447--76501 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
76437 CTATTTTAAT
* *
76447 TTA TTA CTA TTA TTA TT- TTGT TTA TTA TTA TTAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT-A TTA TTA TTA TTA
76493 TTA TTA TTA
1 TTA TTA TTA
76502 ATACAAATGG
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 5 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:76464 original size:22 final size:21
Alignment explanation
Indices: 76438--76501 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
76428 GGGTCTTTTC
*
76438 TATTTTAATTTATTACTATTAT
1 TATTTT-ATTTATTATTATTAT
*
76460 TATTTTGTTTATTATTATTAAT
1 TATTTTATTTATTATTATT-AT
76482 TATTATTA-TTATTATTATTA
1 TATT-TTATTTATTATTATTA
76502 ATACAAATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.32
22 23 0.62
23 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTTTATTTATTATTATTAT
Found at i:77393 original size:2 final size:2
Alignment explanation
Indices: 77382--77410 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
77372 ATGCTAATCG
77382 AT AT AT -T 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
77411 TAAACTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:89259 original size:14 final size:14
Alignment explanation
Indices: 89240--89267 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
89230 CAAAGGTGAT
89240 TAAAAAAATATTTA
1 TAAAAAAATATTTA
89254 TAAAAAAATATTTA
1 TAAAAAAATATTTA
89268 CACGCTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAAAAAATATTTA
Found at i:103706 original size:3 final size:3
Alignment explanation
Indices: 103698--103733 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
103688 AGGGTCTGTA
103698 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
103734 CAATATCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:106601 original size:15 final size:16
Alignment explanation
Indices: 106581--106610 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
106571 AATATCTTAA
106581 TTCATGTT-ATTTATT
1 TTCATGTTAATTTATT
106596 TTCATGTTAATTTAT
1 TTCATGTTAATTTAT
106611 ATTTGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (16 bp):
TTCATGTTAATTTATT
Found at i:106658 original size:4 final size:4
Alignment explanation
Indices: 106651--106685 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
106641 TATATATATA
106651 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
106686 ATTAATCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:109587 original size:60 final size:60
Alignment explanation
Indices: 109478--109591 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
109468 CTACATGATA
* * * * *
109478 TTACTTTATTAAGTCCATTGATTATTAAAAGTTATAATATGGTCCCTCGACTATAGGGAG
1 TTACTTTATTAAGTCCATTGACTATTAAAACTTACAAAATGGACCCTCGACTATAGGGAG
* * *
109538 TTACTTTGTTGAGTCCCTTGACTATTAAAACTTACAAAAT-GACCACTCGACTAT
1 TTACTTTATTAAGTCCATTGACTATTAAAACTTACAAAATGGACC-CTCGACTAT
109592 TCATTATGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
59 3 0.07
60 42 0.93
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (60 bp):
TTACTTTATTAAGTCCATTGACTATTAAAACTTACAAAATGGACCCTCGACTATAGGGAG
Found at i:110818 original size:21 final size:22
Alignment explanation
Indices: 110792--110833 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
110782 ACGATAAAAT
* *
110792 TTCAGGGTTGACAC-CATATAA
1 TTCAGGATGGACACACATATAA
110813 TTCAGGATGGACACACATATA
1 TTCAGGATGGACACACATATA
110834 TTAATTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (22 bp):
TTCAGGATGGACACACATATAA
Found at i:114032 original size:23 final size:24
Alignment explanation
Indices: 113974--114037 Score: 87
Period size: 25 Copynumber: 2.7 Consensus size: 24
113964 TCATTTTAAA
113974 TTTATTATTAATAATAAAATATCAT
1 TTTATTATTAATAATAAAATAT-AT
*
113999 TTTATTATTAATAATAAATTAT-T
1 TTTATTATTAATAATAAAATATAT
114022 TTTA-TAGTTAATAATA
1 TTTATTA-TTAATAATA
114038 TATGAAGATG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 2 0.05
23 14 0.38
25 21 0.57
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTATTATTAATAATAAAATATAT
Found at i:120338 original size:25 final size:25
Alignment explanation
Indices: 120310--120358 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
120300 ATACCTACTT
*
120310 AAATGATATTAAATTACTTACCACC
1 AAATGATATCAAATTACTTACCACC
120335 AAATGATATCAAATTACTTACCAC
1 AAATGATATCAAATTACTTACCAC
120359 TTGAACCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (25 bp):
AAATGATATCAAATTACTTACCACC
Found at i:125617 original size:20 final size:20
Alignment explanation
Indices: 125544--125615 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
125534 AAATGTTAAA
*
125544 AAAATATTAATATTTTAAGTT
1 AAAATAATAATATTTT-AGTT
*
125565 AAAATAATAATATTTTAGGT
1 AAAATAATAATATTTTAGTT
125585 AAAA-AA-AATTAATTTT-GTT
1 AAAATAATAA-T-ATTTTAGTT
125604 AAAATAATAATA
1 AAAATAATAATA
125616 ATAAAATCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
18 2 0.05
19 10 0.23
20 15 0.34
21 17 0.39
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (20 bp):
AAAATAATAATATTTTAGTT
Found at i:129045 original size:29 final size:30
Alignment explanation
Indices: 128988--129059 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
128978 GAAAACGGTC
*
128988 GAGTGAGCAAAATGATTCGATTGTAAAGTT
1 GAGTGAGCAAAATGATTCAATTGTAAAGTT
* *
129018 TAGTGAGCAAATTGA-TCAAATTG-AAAGTT
1 GAGTGAGCAAAATGATTC-AATTGTAAAGTT
*
129047 GAGTGAGGAAAAT
1 GAGTGAGCAAAAT
129060 AGGAGAGAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28
Consensus pattern (30 bp):
GAGTGAGCAAAATGATTCAATTGTAAAGTT
Found at i:129845 original size:61 final size:63
Alignment explanation
Indices: 129749--129876 Score: 224
Period size: 62 Copynumber: 2.1 Consensus size: 63
129739 ACACATTGAC
*
129749 CAAAAGAATTGATAGTGACATAATTTAATTTAAGTCAA-GGATTGATAAGAAAAAGGAATTTA
1 CAAAAGAATTGATAGTGACATAATTTAATTTAAGTCAAGGGATTGATAAGAAAAAGAAATTTA
*
129811 CAAAAGAATTGA-AGTGACATAATTTAATTTAAGTCAAGGGATTGATAAGAAAAAGAAATTTG
1 CAAAAGAATTGATAGTGACATAATTTAATTTAAGTCAAGGGATTGATAAGAAAAAGAAATTTA
129873 CAAA
1 CAAA
129877 GAGTTGTAGT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 25 0.40
62 38 0.60
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.27
Consensus pattern (63 bp):
CAAAAGAATTGATAGTGACATAATTTAATTTAAGTCAAGGGATTGATAAGAAAAAGAAATTTA
Done.