Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000474.1 Hibiscus syriacus cultivar Beakdansim tig00000882_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: 109455
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2993 original size:171 final size:171
Alignment explanation
Indices: 2708--3051 Score: 661
Period size: 171 Copynumber: 2.0 Consensus size: 171
2698 TTTTCTCTTG
2708 TCGAAGGAGAAGATACAGATTCTTGGGTTTTTTTCCTTCTAAATTTACGTGCACATGTTATCACG
1 TCGAAGGAGAAGATACAGATTCTTGGGTTTTTTTCCTTCTAAATTTACGTGCACATGTTATCACG
*
2773 AGGGAAAACATTTGTGTCATTTCAGATCGTGGAGCTGGGATCAAAGCAGTAATGGAGTCTTTGGG
66 AGGGAAAACATTTGTGTCATTTCAGATCGTGGAGCTGGAATCAAAGCAGTAATGGAGTCTTTGGG
* *
2838 TCTAATGTGGTAACCAAATTTTGTCCAACATAGGTATTATC
131 TCCAATGTAGTAACCAAATTTTGTCCAACATAGGTATTATC
2879 TCGAAGGAGAAGATACAGATTCTTGGGTTTTTTTCCTTCTAAATTTACGTGCACATGTTATCACG
1 TCGAAGGAGAAGATACAGATTCTTGGGTTTTTTTCCTTCTAAATTTACGTGCACATGTTATCACG
2944 AGGGAAAACATTTGTGTCATTTCAGATCGTGGAGCTGGAATCAAAGCAGTAATGGAGTCTTTGGG
66 AGGGAAAACATTTGTGTCATTTCAGATCGTGGAGCTGGAATCAAAGCAGTAATGGAGTCTTTGGG
3009 TCCAATGTAGTAACCAAATTTTGTCCAACATAGGTATTATC
131 TCCAATGTAGTAACCAAATTTTGTCCAACATAGGTATTATC
3050 TC
1 TC
3052 CGACACATTG
Statistics
Matches: 170, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
171 170 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (171 bp):
TCGAAGGAGAAGATACAGATTCTTGGGTTTTTTTCCTTCTAAATTTACGTGCACATGTTATCACG
AGGGAAAACATTTGTGTCATTTCAGATCGTGGAGCTGGAATCAAAGCAGTAATGGAGTCTTTGGG
TCCAATGTAGTAACCAAATTTTGTCCAACATAGGTATTATC
Found at i:4281 original size:35 final size:34
Alignment explanation
Indices: 4196--4282 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
4186 ATTTGGTATT
*
4196 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
4230 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
4268 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
4283 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:4506 original size:3 final size:3
Alignment explanation
Indices: 4500--4540 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
4490 GCTGTCATCA
*
4500 TCG TCG TCG TCG TCG TCG TCG TCA TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
4541 ATGAGCAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.02, C:0.34, G:0.29, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:6622 original size:17 final size:18
Alignment explanation
Indices: 6602--6637 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
6592 GAATTATATT
6602 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
6619 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
6637 A
1 A
6638 TTACATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.28
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:6708 original size:10 final size:10
Alignment explanation
Indices: 6695--6720 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6685 AGAGTATTTA
6695 AGAGAAATTG
1 AGAGAAATTG
6705 AGAGAAATTG
1 AGAGAAATTG
6715 AGAGAA
1 AGAGAA
6721 TTTGGTGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (10 bp):
AGAGAAATTG
Found at i:18850 original size:18 final size:18
Alignment explanation
Indices: 18819--18863 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
18809 ACTGAAAATT
* *
18819 TGTCCCTAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
18837 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
18855 TGTCCCGAA
1 TGTCCCGAA
18864 TGACAACTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:20394 original size:30 final size:31
Alignment explanation
Indices: 20356--20446 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 31
20346 CCGAAGAACC
* *
20356 TATCCATATGTTCCTAAGAACATAGGTAAT-
1 TATCCATATGTCCCGAAGAACATAGGTAATA
*
20386 TGTCCATATGTCCCGAATG-ACATAGGTAATA
1 TATCCATATGTCCCGAA-GAACATAGGTAATA
20417 CTATCCATATGTCCCGAA-AGACATAGGTAA
1 -TATCCATATGTCCCGAAGA-ACATAGGTAA
20447 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
30 25 0.48
31 1 0.02
32 26 0.50
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (31 bp):
TATCCATATGTCCCGAAGAACATAGGTAATA
Found at i:20429 original size:32 final size:30
Alignment explanation
Indices: 20355--20446 Score: 114
Period size: 30 Copynumber: 3.0 Consensus size: 30
20345 CCCGAAGAAC
* *
20355 CTATCCATATGTTCCTAAGAACATAGGTAAT
1 CTATCCATATGTCCCGAAG-ACATAGGTAAT
*
20386 -TGTCCATATGTCCCGAATGACATAGGTAAT
1 CTATCCATATGTCCCGAA-GACATAGGTAAT
20416 ACTATCCATATGTCCCGAAAGACATAGGTAA
1 -CTATCCATATGTCCCG-AAGACATAGGTAA
20447 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
30 25 0.47
31 1 0.02
32 25 0.47
33 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (30 bp):
CTATCCATATGTCCCGAAGACATAGGTAAT
Found at i:23585 original size:21 final size:21
Alignment explanation
Indices: 23559--23603 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23549 GATTTCTGGG
* *
23559 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
23580 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
23601 CAA
1 CAA
23604 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:24441 original size:31 final size:31
Alignment explanation
Indices: 24403--24558 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
24393 AGGGTCGAGG
24403 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
24434 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
24465 ATTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
24496 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
24527 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
24558 G
1 G
24559 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:27725 original size:21 final size:21
Alignment explanation
Indices: 27699--27743 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27689 GATTTCTGGG
* *
27699 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
27720 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
27741 CAA
1 CAA
27744 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:28583 original size:31 final size:31
Alignment explanation
Indices: 28545--28700 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
28535 AGGGTCGAGG
*
28545 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
28576 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
28607 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
28638 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
28669 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
28700 G
1 G
28701 GTCCTTTGGG
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
31 113 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:30300 original size:32 final size:31
Alignment explanation
Indices: 30226--30303 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 31
30216 CCATATGTTT
* * *
30226 CGAAAAACATAGGT-AACTGTCCATATGTCC
1 CGAAAGACATAGGTAAACTGTCAATATATCC
* * *
30256 CGAATGATATAGGTAATATTGTCAATATATCC
1 CGAAAGACATAGGTAA-ACTGTCAATATATCC
30288 CGAAAGACATAGGTAA
1 CGAAAGACATAGGTAA
30304 CCATCGACTC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 11 0.29
31 1 0.03
32 26 0.68
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (31 bp):
CGAAAGACATAGGTAAACTGTCAATATATCC
Found at i:31436 original size:19 final size:20
Alignment explanation
Indices: 31409--31450 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
31399 CCTTGCCCAT
*
31409 AAATCACTT-TTTGAGCTCA
1 AAATCACTTATTTCAGCTCA
*
31428 AAATTACTTCATTTCAGCTCA
1 AAATCACTT-ATTTCAGCTCA
31449 AA
1 AA
31451 TGCTTCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (20 bp):
AAATCACTTATTTCAGCTCA
Found at i:34748 original size:14 final size:15
Alignment explanation
Indices: 34731--34770 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
34721 ATAATTAAAG
34731 TAAAAT-ATAAATAT
1 TAAAATAATAAATAT
*
34745 T-AAATAATTAA-AT
1 TAAAATAATAAATAT
34758 TAAAATAATAAAT
1 TAAAATAATAAAT
34771 TTTATATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAATAATAAATAT
Found at i:40222 original size:13 final size:13
Alignment explanation
Indices: 40204--40228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40194 TGCAGTACCT
40204 TGTTTCTAAATTG
1 TGTTTCTAAATTG
40217 TGTTTCTAAATT
1 TGTTTCTAAATT
40229 CCTTGACCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (13 bp):
TGTTTCTAAATTG
Found at i:41412 original size:4 final size:4
Alignment explanation
Indices: 41405--41430 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41395 TTAAGACTGG
41405 TTGA TTGA TTGA TTGA TTGA TTGA TT
1 TTGA TTGA TTGA TTGA TTGA TTGA TT
41431 CCATATACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (4 bp):
TTGA
Found at i:44678 original size:3 final size:3
Alignment explanation
Indices: 44670--44735 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
44660 GCTCTCACCT
44670 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44718 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
44736 AACATTGTAG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:46385 original size:185 final size:184
Alignment explanation
Indices: 46074--46463 Score: 588
Period size: 185 Copynumber: 2.1 Consensus size: 184
46064 TTTTCTAATT
* * * *
46074 TATATAAAA-ATTAAATGTTTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 TATATAAAATATTTAAT-ATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
46138 TTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* * * *
46203 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTT-AGCCCATATGTTA
130 TAGATCTTAAATTATTAATTGGATTTTAAATGATTTG-GCTTGAACCCATATGTTA
*
46258 TATATAATATATTTAATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAAAATATTTAATATTTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* * *
46323 TTATAAAATAAAAAATTT-ATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 TTATAAAAT-AAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
* * *
46387 TTAGATCTTAAATTATTAATTTGATTTTAAATGATTTGGGTTGAATCCATATGTTA
129 TTAGATCTTAAATTATTAATTGGATTTTAAATGATTTGGCTTGAACCCATATGTTA
46443 TATATAAAATATTTAATATTT
1 TATATAAAATATTTAATATTT
46464 AATTTCGGTT
Statistics
Matches: 186, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
184 27 0.15
185 151 0.81
186 8 0.04
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAAAATATTTAATATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
AGATCTTAAATTATTAATTGGATTTTAAATGATTTGGCTTGAACCCATATGTTA
Found at i:47177 original size:29 final size:29
Alignment explanation
Indices: 47144--47207 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
47134 TGGTGGAGTG
* * *
47144 GGTGGAAAGAAATATGATAGTGGAAGGTT
1 GGTGGAAACAAATAGGATAGTGGAAGCTT
* *
47173 GGTGGAAACAAATGGGATGGTGGAAGCTT
1 GGTGGAAACAAATAGGATAGTGGAAGCTT
47202 GGTGGA
1 GGTGGA
47208 GGATGGGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.03, G:0.42, T:0.22
Consensus pattern (29 bp):
GGTGGAAACAAATAGGATAGTGGAAGCTT
Found at i:48025 original size:73 final size:74
Alignment explanation
Indices: 47889--48088 Score: 178
Period size: 72 Copynumber: 2.7 Consensus size: 74
47879 AGAGAAGCTC
* * * * * *
47889 TCTCGAGTGAGATAAAATTTCTTGTTTCATGGGAAAATTGTCTC--AAGCGA-GAAATTGGTTTT
1 TCTCAAGTGAGAT--AATTTCTTGTTTCAAGGG-AAATTGTCTCAAAAGAGACAAAACTCGTTTT
47951 -AAGAAAAACCA
63 AAAGAAAAACCA
47962 TCTCAAGTGAGATACATTTCTTGTTTCAAGGGAAATTGTCTCAAAAGAGACAAAACTCG-TTTAA
1 TCTCAAGTGAGATA-ATTTCTTGTTTCAAGGGAAATTGTCTCAAAAGAGACAAAACTCGTTTTAA
** *
48026 AGGGAAACTA
65 AGAAAAACCA
* * ** * * *
48036 TCTCAAGCGAGACAAAAT-TTGTTTCAAGGGAAACTGTCACAAGAGAGACAAAA
1 TCTCAAGTGAGATAATTTCTTGTTTCAAGGGAAATTGTCTCAAAAGAGACAAAA
48089 TTTGTTTCAA
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
71 11 0.10
72 48 0.45
73 22 0.21
74 25 0.24
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (74 bp):
TCTCAAGTGAGATAATTTCTTGTTTCAAGGGAAATTGTCTCAAAAGAGACAAAACTCGTTTTAAA
GAAAAACCA
Found at i:48178 original size:39 final size:39
Alignment explanation
Indices: 48026--48478 Score: 602
Period size: 39 Copynumber: 11.8 Consensus size: 39
48016 ACTCGTTTAA
* *
48026 AGGGAAACTATCTCAAGCGAGACAAAA--TT-TGTTTCA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * * * *
48062 AGGGAAACTGTCACAAGAGAGACAAAA--TT-TGTTTCA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* ** *
48098 AGGGAAACTGTCTCAATAGAGACAAAA-C-TC-GTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
48134 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* *
48173 AGGGAATCTATCTCAAGCAAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
48212 AGGGAAACTATCTCAAGCGAGATAAAATATTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* ** * * *
48251 AGAGAAACTATCTCAAGAAAGATAAAACCTTTTGTTTCA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* *
48290 AGGGAAACTATCTCAAGTGAGATAAAATCTTCTGTTTTG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* *
48329 AGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
48368 AGGGAAACTATCTCAA-CTGAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGC-GAGATAAAATCTTCTGTTTCG
*
48407 AGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
48446 AGGGAAACTATCTCAAGCGAGATAAAATCTTCT
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCT
48479 TTAAAAACAA
Statistics
Matches: 373, Mismatches: 37, Indels: 11
0.89 0.09 0.03
Matches are distributed among these distances:
36 87 0.23
37 1 0.00
38 3 0.01
39 281 0.75
40 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28
Consensus pattern (39 bp):
AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
Found at i:48576 original size:78 final size:77
Alignment explanation
Indices: 48481--48875 Score: 426
Period size: 78 Copynumber: 5.1 Consensus size: 77
48471 AATCTTCTTT
*
48481 AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTTGAGTAAAAAAATCGTCTCAAGCAAGACAA
1 AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTTGAGTAAAAAAAT-GTCTCAAGCGAGACAA
48546 ATCTTGTTTTAAG
65 ATCTTGTTTTAAG
* * * * ** *
48559 AAAAACAA-CATGTAGTGAAGTGAAATGTCTTGTTTTGAAT-AAAACCTGTCTCAAGCGAGAAAA
1 AAAAACAATCTTG-AGTGAAATGAAATGTCTTCTTTTGAGTAAAAAAATGTCTCAAGCGAG-ACA
* *
48622 AATTTTGCTTTAAG
64 AATCTTGTTTTAAG
* * * *
48636 AAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGTAAAAAAATCATCTCAAGCGAGACAT
1 AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTTGAGTAAAAAAAT-GTCTCAAGCGAGACAA
*
48701 ATCTTGTGTTAAG
65 ATCTTGTTTTAAG
* * * * **
48714 AAAAACAA-CATGTAGTGAAGTGAAATGTCTTGTTTTGAAT-AAAACCTGTCTCAAGCGAGACAA
1 AAAAACAATCTTG-AGTGAAATGAAATGTCTTCTTTTGAGTAAAAAAATGTCTCAAGCGAGACAA
* *
48777 ATTTTATTTTAAG
65 ATCTTGTTTTAAG
* * ** * *
48790 AAAAACAATCTTGAGTAAAATGAAATGTATTCTTTCAAGTAAAACAA--TCTCAAGTGAGACAAA
1 AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTTGAGTAAAAAAATGTCTCAAGCGAGACAAA
48853 GTC-TGTTTTAAG
66 -TCTTGTTTTAAG
48865 AAAAACAATCT
1 AAAAACAATCT
48876 CCAATGAGAT
Statistics
Matches: 257, Mismatches: 51, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
75 34 0.13
76 64 0.25
77 66 0.26
78 82 0.32
79 11 0.04
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (77 bp):
AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTTGAGTAAAAAAATGTCTCAAGCGAGACAAA
TCTTGTTTTAAG
Found at i:48643 original size:155 final size:153
Alignment explanation
Indices: 48456--48872 Score: 614
Period size: 155 Copynumber: 2.7 Consensus size: 153
48446 AGGGAAACTA
* * * *
48456 TCTCAAGCGAGATAAAATCTTCTTT---AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTTG
1 TCTCAAGCGAGAAAAAATTTTCTTTAAGAAAAACAATCTTGAGTAAAATGAAATGTCTTCTTTCG
*
48518 AGTAAAAAAATCGTCTCAAGCAAGACAAATCTTGTTTTAAGAAAAACAACATGTAGTGAAGTGAA
66 AGTAAAAAAATC-TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAACATGTAGTGAAGTGAA
48583 ATGTCTTGTTTTGAATAAAACCTG
130 ATGTCTTGTTTTGAATAAAACCTG
*
48607 TCTCAAGCGAGAAAAAATTTTGCTTTAAGAAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTC
1 TCTCAAGCGAGAAAAAATTTT-CTTTAAGAAAAACAATCTTGAGTAAAATGAAATGTCTTCTTTC
* *
48672 GAGTAAAAAAATCATCTCAAGCGAGACATATCTTGTGTTAAGAAAAACAACATGTAGTGAAGTGA
65 GAGTAAAAAAATC-TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAACATGTAGTGAAGTGA
48737 AATGTCTTGTTTTGAATAAAACCTG
129 AATGTCTTGTTTTGAATAAAACCTG
* * *
48762 TCTCAAGCGAG-ACAAATTTTATTTTAAGAAAAACAATCTTGAGTAAAATGAAATGTATTCTTTC
1 TCTCAAGCGAGAAAAAATTTT-CTTTAAGAAAAACAATCTTGAGTAAAATGAAATGTCTTCTTTC
* * *
48826 AAGTAAAACAA--TCTCAAGTGAGACAAAGTC-TGTTTTAAGAAAAACAA
65 GAGTAAAAAAATCTCTCAAGCGAGACAAA-TCTTGTTTTAAGAAAAACAA
48873 TCTCCAATGA
Statistics
Matches: 243, Mismatches: 18, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
151 49 0.20
152 6 0.02
154 57 0.23
155 131 0.54
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (153 bp):
TCTCAAGCGAGAAAAAATTTTCTTTAAGAAAAACAATCTTGAGTAAAATGAAATGTCTTCTTTCG
AGTAAAAAAATCTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAACATGTAGTGAAGTGAAA
TGTCTTGTTTTGAATAAAACCTG
Found at i:59007 original size:22 final size:21
Alignment explanation
Indices: 58965--59004 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
58955 GAGTTTATTT
*
58965 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
58986 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
59005 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:65836 original size:29 final size:29
Alignment explanation
Indices: 65803--65858 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
65793 TGGTGGAGTG
*
65803 GGTGGAAAGAAATATGATAGTGGAAGCTT
1 GGTGGAAAGAAATAGGATAGTGGAAGCTT
* *
65832 GGTGGAAAGAAATGGGATGGTGGAAGC
1 GGTGGAAAGAAATAGGATAGTGGAAGC
65859 CTGTTGGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.41, T:0.20
Consensus pattern (29 bp):
GGTGGAAAGAAATAGGATAGTGGAAGCTT
Found at i:65866 original size:29 final size:29
Alignment explanation
Indices: 65803--65866 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
65793 TGGTGGAGTG
* *
65803 GGTGGAAAGAAATATGATAGTGGAAGCTT
1 GGTGGAAAGAAATAGGATAGTGGAAGCCT
* *
65832 GGTGGAAAGAAATGGGATGGTGGAAGCCT
1 GGTGGAAAGAAATAGGATAGTGGAAGCCT
*
65861 GTTGGA
1 GGTGGA
65867 GGATGGGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.41, T:0.22
Consensus pattern (29 bp):
GGTGGAAAGAAATAGGATAGTGGAAGCCT
Found at i:69006 original size:23 final size:23
Alignment explanation
Indices: 68946--69006 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
68936 TATGGAACTA
68946 CGGTGTATTTCTACGCGGCACTT
1 CGGTGTATTTCTACGCGGCACTT
* *
68969 CGGTGTAATTCTACGTGGCACTT
1 CGGTGTATTTCTACGCGGCACTT
* *
68992 CGGTGCATTTATACG
1 CGGTGTATTTCTACG
69007 AGCTGTGGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.34
Consensus pattern (23 bp):
CGGTGTATTTCTACGCGGCACTT
Found at i:69644 original size:35 final size:35
Alignment explanation
Indices: 69605--69677 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
69595 GTAAATGATA
*
69605 AATGTATAGCGGTGAAAGGTTAAATTTTAAGAGTT
1 AATGTATAGCGATGAAAGGTTAAATTTTAAGAGTT
69640 AATGTATAGCGATGAAAGGTTAAATTTTAAGAGTT
1 AATGTATAGCGATGAAAGGTTAAATTTTAAGAGTT
69675 AAT
1 AAT
69678 ATCGATACCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (35 bp):
AATGTATAGCGATGAAAGGTTAAATTTTAAGAGTT
Found at i:72826 original size:27 final size:27
Alignment explanation
Indices: 72795--72850 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
72785 AGTGTGACAT
*
72795 TAATTTTATGATAAAATTTAAATTTAA
1 TAATTATATGATAAAATTTAAATTTAA
* *
72822 TAATTATATTATAAATTTTAAATTTAA
1 TAATTATATGATAAAATTTAAATTTAA
72849 TA
1 TA
72851 TCTAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TAATTATATGATAAAATTTAAATTTAA
Found at i:74483 original size:15 final size:12
Alignment explanation
Indices: 74451--74479 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
74441 TGTTGTTGTT
74451 GTGGTTTCCATC
1 GTGGTTTCCATC
74463 GTGGTTTCCATC
1 GTGGTTTCCATC
74475 GTGGT
1 GTGGT
74480 GGTTAGGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.21, G:0.31, T:0.41
Consensus pattern (12 bp):
GTGGTTTCCATC
Found at i:76696 original size:33 final size:33
Alignment explanation
Indices: 76653--76724 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
76643 ATATTTTAGC
*
76653 TTTACATTCTTTTTTTTATTG-AATTTTATTCATT
1 TTTA-ATTC-TTTTTATATTGTAATTTTATTCATT
* *
76687 TTTAATTCTTTTTATATTGTATTTTTATTGATT
1 TTTAATTCTTTTTATATTGTAATTTTATTCATT
76720 TTTAA
1 TTTAA
76725 ATATGAGAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 10 0.29
33 20 0.59
34 4 0.12
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.68
Consensus pattern (33 bp):
TTTAATTCTTTTTATATTGTAATTTTATTCATT
Found at i:76966 original size:68 final size:68
Alignment explanation
Indices: 76891--77031 Score: 282
Period size: 68 Copynumber: 2.1 Consensus size: 68
76881 AAAATTCAAT
76891 AAAAAAAGAATGTAAAACTAAAAAATATCACCTATATATTTACAATATTCTTTCTAATATTAATT
1 AAAAAAAGAATGTAAAACTAAAAAATATCACCTATATATTTACAATATTCTTTCTAATATTAATT
76956 TTA
66 TTA
76959 AAAAAAAGAATGTAAAACTAAAAAATATCACCTATATATTTACAATATTCTTTCTAATATTAATT
1 AAAAAAAGAATGTAAAACTAAAAAATATCACCTATATATTTACAATATTCTTTCTAATATTAATT
77024 TTA
66 TTA
77027 AAAAA
1 AAAAA
77032 TACAAAATAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 73 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (68 bp):
AAAAAAAGAATGTAAAACTAAAAAATATCACCTATATATTTACAATATTCTTTCTAATATTAATT
TTA
Found at i:81576 original size:22 final size:20
Alignment explanation
Indices: 81541--81580 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
81531 TAAGTAATAA
81541 AATAAAATAAATAATTAAGT
1 AATAAAATAAATAATTAAGT
81561 AATAAAAGGTAAATAATTAA
1 AATAAAA--TAAATAATTAA
81581 AAATACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (20 bp):
AATAAAATAAATAATTAAGT
Found at i:81749 original size:3 final size:3
Alignment explanation
Indices: 81741--81783 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
81731 CTCATTATCG
* * *
81741 TCA TCA TCA TCA TCA TCA TCA CCG TCA TTA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
81784 TAGGAGCAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.30, C:0.33, G:0.02, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:83703 original size:33 final size:31
Alignment explanation
Indices: 83662--83730 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
83652 ATAAATATTA
*
83662 TAAAAATTAATATATAAACTAAT-ATTAAAAAT
1 TAAAAATTAAAATATAAAC-AATAATT-AAAAT
*
83694 TAAATAATTAAAATATTAACAATAATTAAAAT
1 TAAA-AATTAAAATATAAACAATAATTAAAAT
83726 TAAAA
1 TAAAA
83731 TAGAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 1 0.03
32 16 0.48
33 16 0.48
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (31 bp):
TAAAAATTAAAATATAAACAATAATTAAAAT
Found at i:83732 original size:33 final size:33
Alignment explanation
Indices: 83653--83732 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 33
83643 CCTAATTTAA
*
83653 TAAATATTATAAA-AATTAATATATAAACTAATAT
1 TAAA-ATTA-AAATAATTAAAATATAAACTAATAT
*
83687 TAAAAATT-AAATAATTAAAATATTAAC-AATAAT
1 T-AAAATTAAAATAATTAAAATATAAACTAAT-AT
83720 TAAAATTAAAATA
1 TAAAATTAAAATA
83733 GAATTTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
32 12 0.30
33 21 0.52
34 4 0.10
35 3 0.08
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (33 bp):
TAAAATTAAAATAATTAAAATATAAACTAATAT
Found at i:85156 original size:16 final size:16
Alignment explanation
Indices: 85135--85167 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
85125 TAATAAATAA
85135 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
85151 ACGAACATAAACTAAC
1 ACGAACATAAACGAAC
85167 A
1 A
85168 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.24, G:0.09, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:85257 original size:16 final size:16
Alignment explanation
Indices: 85236--85296 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
85226 TAATAAATAA
85236 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
85252 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
85268 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
85284 ACGAACATAAACG
1 ACGAACATAAACG
85297 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:85728 original size:10 final size:10
Alignment explanation
Indices: 85713--85760 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
85703 ATAAATGAAT
85713 GAACATAAAC
1 GAACATAAAC
85723 GAACATTACCGAAC
1 GAACA-TA---AAC
85737 GAACATAAAC
1 GAACATAAAC
*
85747 GAACATAACC
1 GAACATAAAC
85757 GAAC
1 GAAC
85761 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 21 0.64
11 2 0.06
13 2 0.06
14 8 0.24
ACGTcount: A:0.52, C:0.25, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:85740 original size:24 final size:24
Alignment explanation
Indices: 85713--85768 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
85703 ATAAATGAAT
*
85713 GAACATAAACGAACATTACCGAAC
1 GAACATAAACGAACATAACCGAAC
85737 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
85761 GAACATAA
1 GAACATAA
85769 CCAAACGTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:85767 original size:14 final size:14
Alignment explanation
Indices: 85720--85775 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
85710 AATGAACATA
*
85720 AACGAACATTACCG
1 AACGAACATAACCG
85734 AACGAACAT-A---
1 AACGAACATAACCG
85744 AACGAACATAACCG
1 AACGAACATAACCG
*
85758 AACGAACATAACCA
1 AACGAACATAACCG
85772 AACG
1 AACG
85776 TTCATGAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.52, C:0.27, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:93083 original size:25 final size:25
Alignment explanation
Indices: 93055--93126 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 25
93045 AAAGTCCAAC
**
93055 AAATTTAACAAAATAAGTAAGTATT
1 AAATTTAACAAAATAAGTAAAAATT
*
93080 AAA-TGAGA-AATAATAA-TAAAAATT
1 AAATTTA-ACAA-AATAAGTAAAAATT
93104 ACAATTTAACAAAATAAAGTAAA
1 A-AATTTAACAAAAT-AAGTAAA
93127 TACAAACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
24 11 0.31
25 15 0.42
26 6 0.17
27 4 0.11
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.26
Consensus pattern (25 bp):
AAATTTAACAAAATAAGTAAAAATT
Found at i:93635 original size:18 final size:18
Alignment explanation
Indices: 93612--93651 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
93602 AAAGGCGATG
*
93612 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGCT
93630 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
93648 GCGG
1 GCGG
93652 TGGCTGCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:96553 original size:110 final size:111
Alignment explanation
Indices: 96359--96579 Score: 390
Period size: 110 Copynumber: 2.0 Consensus size: 111
96349 ATTACAAAAA
* * *
96359 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
96424 AATTAAAACGTTAAAATGTTATCGTATCAGTAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTAGAGATAT
96470 TTAATTCTTAATCTAATAATCATACATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
96534 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTAGAGATAT
96580 ATGATTTCCA
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 34 0.32
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTAGAGATAT
Found at i:96732 original size:20 final size:19
Alignment explanation
Indices: 96704--96742 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
96694 CCTTAAAAAG
*
96704 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGA-AAATTT
96724 AGAGAATTTGAGAAAATTT
1 AGAGAATTTGAGAAAATTT
96743 GGTGTGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
AGAGAATTTGAGAAAATTT
Found at i:96921 original size:50 final size:51
Alignment explanation
Indices: 96867--96992 Score: 182
Period size: 51 Copynumber: 2.5 Consensus size: 51
96857 GATATACATA
* * * **
96867 TATAGCACGCTGCAGGGGCCGCGCTATA-CCCACGTGACGCCAGCTCACCG
1 TATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCACCG
* *
96917 TATAGTGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCATCG
1 TATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCACCG
96968 TATAGCGCGGTGCAGGGGGCGCGCT
1 TATAGCGCGGTGCAGGGGGCGCGCT
96993 TTACTGCTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 24 0.36
51 43 0.64
ACGTcount: A:0.19, C:0.32, G:0.33, T:0.16
Consensus pattern (51 bp):
TATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCACCG
Found at i:100478 original size:4 final size:4
Alignment explanation
Indices: 100469--100498 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
100459 GGCCAACCCT
100469 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
100499 CCATTCTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:102477 original size:60 final size:59
Alignment explanation
Indices: 102353--102510 Score: 147
Period size: 60 Copynumber: 2.7 Consensus size: 59
102343 ATGTCCCCAT
* * * * *
102353 ACTATGATTTTCATTCTAAATAGTTCCTAAACCTTTGAATACTCTAATTTCATCCTCAA
1 ACTATGATATTCATTCTAAATAGTTCCTAAACCTTTAAACAATCCAATTTCATCCTCAA
* * * *
102412 GCTATGATATTCATTTTAAATAAG-TCCTTAAACTTTTAAACAATCCAATTTCATCCTTAA
1 ACTATGATATTCATTCTAAAT-AGTTCC-TAAACCTTTAAACAATCCAATTTCATCCTCAA
*** * * * *
102472 ACTATGACCCTCATTCTAAATTGGTCCCAAACTTTTAAA
1 ACTATGATATTCATTCTAAATAGTTCCTAAACCTTTAAA
102511 TCTTCTAATT
Statistics
Matches: 80, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
59 33 0.41
60 47 0.59
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.39
Consensus pattern (59 bp):
ACTATGATATTCATTCTAAATAGTTCCTAAACCTTTAAACAATCCAATTTCATCCTCAA
Done.