Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003907.1 Hibiscus syriacus cultivar Beakdansim tig00008450_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: 73337
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:3737 original size:21 final size:21
Alignment explanation
Indices: 3711--3757 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3701 CTCATAAACA
3711 TGCATTCCTTACATGAATGCT
1 TGCATTCCTTACATGAATGCT
3732 TGCATTCCTTACATGAATGCT
1 TGCATTCCTTACATGAATGCT
3753 TGCAT
1 TGCAT
3758 ACACATATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TGCATTCCTTACATGAATGCT
Found at i:33815 original size:20 final size:20
Alignment explanation
Indices: 33777--33815 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33767 ATTTCACCAC
**
33777 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGAACCTAA
*
33797 ATGCATCTATATGAACCTA
1 ATGCAACTATATGAACCTA
33816 TATGAGCTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (20 bp):
ATGCAACTATATGAACCTAA
Found at i:44100 original size:21 final size:21
Alignment explanation
Indices: 44049--44101 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
44039 ATTATTACTA
44049 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
44070 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
44091 TCGCAATGCGA
1 TCGCAATGCGA
44102 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:44138 original size:21 final size:20
Alignment explanation
Indices: 44091--44139 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
44081 TTTTCCCAAT
*
44091 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
44111 TCACAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
44132 TCGCAATG
1 TCGCAATG
44140 AGATACTGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:44156 original size:20 final size:20
Alignment explanation
Indices: 44131--44225 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
44121 AATTTGGAAA
* *
44131 ATCGCAATGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
44151 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
44172 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
44192 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
44212 TTCGCAACGAGATA
1 ATCGCAACGCGATA
44226 ATACATAATC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.70
21 15 0.23
22 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:44173 original size:41 final size:41
Alignment explanation
Indices: 44128--44205 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
44118 GCGAATTTGG
*
44128 AAAATCGCAATGAGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* *
44169 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
44206 CTGACTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:44753 original size:20 final size:20
Alignment explanation
Indices: 44704--44762 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
44694 TTTATTCTCT
* **
44704 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
44724 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
44744 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
44763 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:44953 original size:25 final size:24
Alignment explanation
Indices: 44899--44953 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
44889 TGTTTATTAT
* *
44899 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
44923 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
44949 TGTTT
1 TGTTT
44954 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:46102 original size:18 final size:18
Alignment explanation
Indices: 46081--46128 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
46071 TCCACTTTGG
46081 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
46099 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
46117 GAGCCATCACCT
1 GAGCCATCACCT
46129 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:46693 original size:20 final size:20
Alignment explanation
Indices: 46668--46713 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
46658 ATAATTACTT
46668 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
46688 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
46708 TCGCAA
1 TCGCAA
46714 TGCGATTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:46736 original size:19 final size:19
Alignment explanation
Indices: 46714--46849 Score: 93
Period size: 20 Copynumber: 7.3 Consensus size: 19
46704 GCTATCGCAA
46714 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
46733 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
*
46752 TGCGA-TTT--TGT--CGT
1 TGCGATTTTCATTTCGCGT
*
46766 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
** ***
46785 TTTGATAGCCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
***
46805 TGCGATAGCCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
**
46825 TGCGATAGTCATTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
46845 TGCGA
1 TGCGA
46850 AAGTAAACTA
Statistics
Matches: 96, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
14 7 0.07
15 3 0.03
16 2 0.02
17 2 0.02
18 3 0.03
19 34 0.35
20 42 0.44
21 3 0.03
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:46813 original size:20 final size:20
Alignment explanation
Indices: 46788--46849 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
46778 TTCGCATTTT
46788 GATAGCCATTTCCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
46808 GATAGCCATTTCCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
* *
46828 GATAGTCATTTTCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
46848 GA
1 GA
46850 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (20 bp):
GATAGCCATTTCCGCGTTGC
Found at i:47248 original size:21 final size:20
Alignment explanation
Indices: 47196--47251 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
47186 GACTCACCTG
*
47196 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGGCCCCT
* **
47216 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGGCCCCT
47237 ATCATCCCTCAAGAG
1 -TCATCCCTCAAGAG
47252 TCTCCCCCCA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGGCCCCT
Found at i:47267 original size:42 final size:42
Alignment explanation
Indices: 47196--47284 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
47186 GACTCACCTG
* *
47196 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* *
47238 TCATCCCTCAAGAGTCTCCC-CCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTC-CCCTCCAACCGTTCAAGAGGCCACTA
47280 TCATC
1 TCATC
47285 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:47304 original size:42 final size:41
Alignment explanation
Indices: 47196--47314 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 41
47186 GACTCACCTG
* * *
47196 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGT-CCCTCCCACCGTTCAAGAGGCCACTA
* *
47238 TCATCCCTCAAGAGTCTCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTC-CCTCCCACCGTTCAAGAGGCCACTA
** * * *
47280 TCATCGTTGAAGAGGTCCCTCCCACCATTCCAGAG
1 TCATCCCTCAAGA-GTCCCTCCCACCGTTCAAGAG
47315 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 60 0.94
43 3 0.05
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:48716 original size:14 final size:14
Alignment explanation
Indices: 48682--48720 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
48672 TTGATTGTTT
48682 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
48696 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
48710 TGTTGATTTGT
1 AATTGATTTGT
48721 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:48861 original size:19 final size:19
Alignment explanation
Indices: 48837--48904 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
48827 ATCGCAACGA
48837 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
48856 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
48875 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
48889 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
48905 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:48955 original size:20 final size:20
Alignment explanation
Indices: 48932--48998 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
48922 GATTTTCTCA
* *
48932 TTGCAATAGCCATTTTTGCG
1 TTGCGATAGCCATTTTCGCG
48952 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
* * *
48972 TTGCGATAGTCATTTTCACA
1 TTGCGATAGCCATTTTCGCG
48992 TTGCGAT
1 TTGCGAT
48999 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:49571 original size:20 final size:20
Alignment explanation
Indices: 49550--49637 Score: 140
Period size: 20 Copynumber: 4.4 Consensus size: 20
49540 TGTATTATCT
* *
49550 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
49570 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
49590 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
* *
49610 CGTTGCGAAAGTTAGTATCG
1 CGTTGCGAAAGTCAGAATCG
49630 CGTTGCGA
1 CGTTGCGA
49638 TTTTGTATTA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:49750 original size:21 final size:20
Alignment explanation
Indices: 49689--49750 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
49679 ATTTACTTAT
49689 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
* *
49710 TCGCAACT-CGAAATTAGAAAA
1 TCGC-ATTGCG-AATTGGAAAA
49731 TCGCATTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
49751 CTGATTTGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 5 0.15
21 22 0.67
22 6 0.18
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:51788 original size:63 final size:63
Alignment explanation
Indices: 51689--51813 Score: 196
Period size: 63 Copynumber: 2.0 Consensus size: 63
51679 TATTGAAAAT
* *
51689 CAAGTTGATAAGTCGGAGGAGCCACCGGAAAAGAAACAATGCCTTGAAACAGATACATCAAAC
1 CAAGTAGATAAGTCGGAGGAGCCACCAGAAAAGAAACAATGCCTTGAAACAGATACATCAAAC
* * * *
51752 CAAGTAGATAAGTTGGAGGAGCCATCAGCAAAGAAACAATGTCTTGAAACAGATACATCAAA
1 CAAGTAGATAAGTCGGAGGAGCCACCAGAAAAGAAACAATGCCTTGAAACAGATACATCAAA
51814 GAGTGCAACC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (63 bp):
CAAGTAGATAAGTCGGAGGAGCCACCAGAAAAGAAACAATGCCTTGAAACAGATACATCAAAC
Found at i:54482 original size:61 final size:61
Alignment explanation
Indices: 54399--54522 Score: 212
Period size: 61 Copynumber: 2.0 Consensus size: 61
54389 TTTATTTAAA
* * *
54399 ATTATGTATCCGTGTTAGTTTGTTTAATGTTCGTAAACAAGCTTATATAGTGTTCACTAAC
1 ATTACGTAGCCGTGTTAGTTTGTTTAATGTTCGTAAACAAGCTCATATAGTGTTCACTAAC
*
54460 ATTACGTAGCCGTGTTAGTTTGTTTAATGTTCGTAAACAAGCTCATTTAGTGTTCACTAAC
1 ATTACGTAGCCGTGTTAGTTTGTTTAATGTTCGTAAACAAGCTCATATAGTGTTCACTAAC
54521 AT
1 AT
54523 CTTAGCATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (61 bp):
ATTACGTAGCCGTGTTAGTTTGTTTAATGTTCGTAAACAAGCTCATATAGTGTTCACTAAC
Found at i:62315 original size:299 final size:298
Alignment explanation
Indices: 61265--62458 Score: 2176
Period size: 299 Copynumber: 4.0 Consensus size: 298
61255 GCTTGGGGCT
61265 TAAGATTATTTGGTTTCTT--AAA--AATTAATTTTTAAACTTTCTCCC-T-TTTTATGTGTG-T
1 TAAGATTATTTGGTTTCTTAAAAATGAATTAATTTTTAAACTTTCTCCCTTGTTTTATGTGTGTT
*
61323 TCTACAAATAATCGAAAAAAAAAAAGACAATTATTAAAGGTCACGTGTCACACATTTATTAGATA
66 TCTACAAATAATCG----AAAAAAAGACAATTATTAAAGGTCATGTGTCACACATTTATTAGATA
*
61388 ATTTTTTACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAGTT
127 ATTTTTTACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAATT
*
61453 GTTTATCTTTGTTCCCTTGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAAT
192 GTTTATCTTTGTTCCCTCGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAAT
61518 TCCTTCCTCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATA
257 TCCTTCCTCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATA
*
61560 TAAGATTATTTGGTTTCTTAAAAATGAATTAATTTTTAAACTTTCTTCCTTGTTTTATGTGTGTT
1 TAAGATTATTTGGTTTCTTAAAAATGAATTAATTTTTAAACTTTCTCCCTTGTTTTATGTGTGTT
*
61625 TCTACAAATAATCGAAAAAAAGACAATTATTAAAGGTCATGTGTCACATATTTATTAGATAATTT
66 TCTACAAATAATCGAAAAAAAGACAATTATTAAAGGTCATGTGTCACACATTTATTAGATAATTT
61690 TTTACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTTT
131 TTTACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTTT
61755 ATCTTTGTTCCCTCGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCCT
196 ATCTTTGTTCCCTCGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCCT
61820 TCCTCCTCCAGAATCTCCCCTT-CCCTT-CTCTC--TA
261 TCCTCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATA
*
61854 TAAGATTATTTGGTTTCTTAAAAATGAATTAATTTTTAAACTTTCTTCCTTGTTTTATGTGTGTT
1 TAAGATTATTTGGTTTCTTAAAAATGAATTAATTTTTAAACTTTCTCCCTTGTTTTATGTGTGTT
61919 TCTACAAATAATCGAAAAAAAGACAATTATTAAAGGTCATGTGTCACACATTTATTAGATAATTT
66 TCTACAAATAATCGAAAAAAAGACAATTATTAAAGGTCATGTGTCACACATTTATTAGATAATTT
*
61984 TTTACATACAACGTAAAAGTGTTTATGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTTT
131 TTTACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTTT
*
62049 ATCTTTGTTCCCTTGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCCT
196 ATCTTTGTTCCCTCGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCCT
62114 TCCTCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATA
261 TCCTCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATA
62152 TAAGATTATTTGGTTTCTTAAAAATGAATTAATTTTTTAAACTTTCTCCCTTGTTTTATGTGTGT
1 TAAGATTATTTGGTTTCTTAAAAATGAATTAA-TTTTTAAACTTTCTCCCTTGTTTTATGTGTGT
62217 TTCTACAAATAATCGAAAAAAAGACAATTATTAAAGGTCATGTGTCACACATTTATTAGATAATT
65 TTCTACAAATAATCGAAAAAAAGACAATTATTAAAGGTCATGTGTCACACATTTATTAGATAATT
62282 TTTTACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTT
130 TTTTACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTT
62347 TATCTTTGTTCCCTCGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCC
195 TATCTTTGTTCCCTCGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCC
* *
62412 TTCCTCCTCCATAGTCTCCCCTTCCCCTTCCTCTCTATA
260 TTCCTCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATA
62451 TAAGATTA
1 TAAGATTA
62459 GGGTGAGATT
Statistics
Matches: 874, Mismatches: 13, Indels: 20
0.96 0.01 0.02
Matches are distributed among these distances:
294 281 0.32
295 24 0.03
296 10 0.01
297 8 0.01
298 233 0.27
299 291 0.33
300 1 0.00
301 11 0.01
302 15 0.02
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (298 bp):
TAAGATTATTTGGTTTCTTAAAAATGAATTAATTTTTAAACTTTCTCCCTTGTTTTATGTGTGTT
TCTACAAATAATCGAAAAAAAGACAATTATTAAAGGTCATGTGTCACACATTTATTAGATAATTT
TTTACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTTT
ATCTTTGTTCCCTCGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCCT
TCCTCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATA
Found at i:62414 original size:593 final size:588
Alignment explanation
Indices: 61265--62450 Score: 2180
Period size: 593 Copynumber: 2.0 Consensus size: 588
61255 GCTTGGGGCT
61265 TAAGATTATTTGGTTTCTTAAAAATTAATTTTTAAACTTTCTCCCTTTTTATGTGTGTTCTACAA
1 TAAGATTATTTGGTTTCTTAAAAATTAATTTTTAAACTTTCTCCCTTTTTATGTGTGTTCTACAA
61330 ATAATCGAAAAAAAAAAAGACAATTATTAAAGGTCACGTGTCACACATTTATTAGATAATTTTTT
66 ATAATCG---AAAAAAAAGACAATTATTAAAGGTCACGTGTCACACATTTATTAGATAATTTTTT
*
61395 ACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAGTTGTTTATC
128 ACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTTTATC
61460 TTTGTTCCCTTGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCCTTCC
193 TTTGTTCCCTTGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCCTTCC
61525 TCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATATAAGATTATTTGGTTTCTTAAAAATGAATT
258 TCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATATAAGATTATTTGGTTTCTTAAAAATGAATT
*
61590 AATTTTTAAACTTTCTTCCTTGTTTTATGTGTGTTTCTACAAATAATCGAAAAAAAGACAATTAT
323 AATTTTTAAACTTTCTCCCTTGTTTTATGTGTGTTTCTACAAATAATCGAAAAAAAGACAATTAT
*
61655 TAAAGGTCATGTGTCACATATTTATTAGATAATTTTTTACATACAACGTAAAAGTGTTTACGAAG
388 TAAAGGTCATGTGTCACACATTTATTAGATAATTTTTTACATACAACGTAAAAGTGTTTACGAAG
61720 TCACAAGTATATTTGACTAGTTAATCAAATTGTTTATCTTTGTTCCCTCGTATACCCTTAGGTCA
453 TCACAAGTATATTTGACTAGTTAATCAAATTGTTTATCTTTGTTCCCTCGTATACCCTTAGGTCA
61785 CGAGTCTTACGTACACTAGGAGTACTTTAATTCCTTCCTCCTCCAGAATCTCCCCTT-CCCTT-C
518 CGAGTCTTACGTACACTAGGAGTACTTTAATTCCTTCCTCCTCCAGAATCTCCCCTTCCCCTTCC
61848 TCTCTA
583 TCTCTA
*
61854 TAAGATTATTTGGTTTCTTAAAAATGAATTAATTTTTAAACTTTCTTCCTTGTTTTATGTGTGTT
1 TAAGATTATTTGGTTTCTT--AAA--AATTAATTTTTAAACTTTC-TCCCT-TTTTATGTGTG-T
*
61919 TCTACAAATAATCG-AAAAAAAGACAATTATTAAAGGTCATGTGTCACACATTTATTAGATAATT
59 TCTACAAATAATCGAAAAAAAAGACAATTATTAAAGGTCACGTGTCACACATTTATTAGATAATT
*
61983 TTTTACATACAACGTAAAAGTGTTTATGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTT
124 TTTTACATACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTT
62048 TATCTTTGTTCCCTTGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCC
189 TATCTTTGTTCCCTTGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCC
62113 TTCCTCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATATAAGATTATTTGGTTTCTTAAAAATG
254 TTCCTCCTCCAGAATCTCCCCTTCCCCTTCCTCTCTATATAAGATTATTTGGTTTCTTAAAAATG
62178 AATTAATTTTTTAAACTTTCTCCCTTGTTTTATGTGTGTTTCTACAAATAATCGAAAAAAAGACA
319 AATTAA-TTTTTAAACTTTCTCCCTTGTTTTATGTGTGTTTCTACAAATAATCGAAAAAAAGACA
62243 ATTATTAAAGGTCATGTGTCACACATTTATTAGATAATTTTTTACATACAACGTAAAAGTGTTTA
383 ATTATTAAAGGTCATGTGTCACACATTTATTAGATAATTTTTTACATACAACGTAAAAGTGTTTA
62308 CGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTTTATCTTTGTTCCCTCGTATACCCTTA
448 CGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTTTATCTTTGTTCCCTCGTATACCCTTA
* *
62373 GGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCCTTCCTCCTCCATAGTCTCCCCTTCCC
513 GGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCCTTCCTCCTCCAGAATCTCCCCTTCCC
62438 CTTCCTCTCTA
578 CTTCCTCTCTA
62449 TA
1 TA
62451 TAAGATTAGG
Statistics
Matches: 579, Mismatches: 8, Indels: 14
0.96 0.01 0.02
Matches are distributed among these distances:
589 19 0.03
591 3 0.01
592 248 0.43
593 265 0.46
594 9 0.02
595 20 0.03
596 15 0.03
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (588 bp):
TAAGATTATTTGGTTTCTTAAAAATTAATTTTTAAACTTTCTCCCTTTTTATGTGTGTTCTACAA
ATAATCGAAAAAAAAGACAATTATTAAAGGTCACGTGTCACACATTTATTAGATAATTTTTTACA
TACAACGTAAAAGTGTTTACGAAGTCACAAGTATATTTGACTAGTTAATCAAATTGTTTATCTTT
GTTCCCTTGTATACCCTTAGGTCACGAGTCTTACGTACACTAGGAGTACTTTAATTCCTTCCTCC
TCCAGAATCTCCCCTTCCCCTTCCTCTCTATATAAGATTATTTGGTTTCTTAAAAATGAATTAAT
TTTTAAACTTTCTCCCTTGTTTTATGTGTGTTTCTACAAATAATCGAAAAAAAGACAATTATTAA
AGGTCATGTGTCACACATTTATTAGATAATTTTTTACATACAACGTAAAAGTGTTTACGAAGTCA
CAAGTATATTTGACTAGTTAATCAAATTGTTTATCTTTGTTCCCTCGTATACCCTTAGGTCACGA
GTCTTACGTACACTAGGAGTACTTTAATTCCTTCCTCCTCCAGAATCTCCCCTTCCCCTTCCTCT
CTA
Found at i:68830 original size:42 final size:42
Alignment explanation
Indices: 68771--68890 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
68761 TTTCCCCGGA
*
68771 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGGAAAATGTT
*
68813 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGAAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGGAAAATGTT
*
68855 TTCCAGTGTTTGTTTCACGTAATTGGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGGAA
68891 CGTAATTCAT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGGAAAATGTT
Found at i:69116 original size:28 final size:27
Alignment explanation
Indices: 69083--69218 Score: 98
Period size: 29 Copynumber: 4.7 Consensus size: 27
69073 TATTTATTTA
69083 TTAATATTTATAATAATATAATATTATT
1 TTAATATTT-TAATAATATAATATTATT
*
69111 TTAATATTATATAAAATAATCAATTATATTATAT
1 TTAATATT-T-T--AATAAT--ATAATATTAT-T
* *
69145 TT-TTATTTTAATAATAT-ATAATAATT
1 TTAATATTTTAATAATATAAT-ATTATT
*
69171 TTTATATATTTAATAATTAATAATATTA-T
1 TTAATAT-TTTAATAA-T-ATAATATTATT
69200 TTATATATTTTAATAATAT
1 TTA-ATATTTTAATAATAT
69219 TTTAATAAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 27
0.73 0.05 0.22
Matches are distributed among these distances:
26 5 0.06
27 11 0.12
28 17 0.19
29 21 0.24
30 9 0.10
31 9 0.10
32 1 0.01
33 13 0.15
34 3 0.03
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAATATTTTAATAATATAATATTATT
Found at i:69172 original size:60 final size:57
Alignment explanation
Indices: 69076--69218 Score: 146
Period size: 57 Copynumber: 2.4 Consensus size: 57
69066 TATTATTTAT
* *
69076 TTATTTATTAATATTTATAATAATATAATATTATTTTAATATTATATAAAATAATCAATTATA
1 TTATTTA-T-ATATTT-TAATAATATAATATAATTTT--TA-TATATAAAATAATCAATAATA
* ** *
69139 TTATATT-TTTATTTTAATAATAT-ATAATAATTTTTATATATTTAATAATTAATAATA
1 TTAT-TTATATATTTTAATAATATAAT-ATAATTTTTATATATAAAATAATCAATAATA
69196 TTATTTATATATTTTAATAATAT
1 TTATTTATATATTTTAATAATAT
69219 TTTAATAAAG
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
56 2 0.03
57 36 0.51
58 2 0.03
59 2 0.03
60 16 0.23
61 5 0.07
62 1 0.01
63 4 0.06
64 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.55
Consensus pattern (57 bp):
TTATTTATATATTTTAATAATATAATATAATTTTTATATATAAAATAATCAATAATA
Found at i:69216 original size:25 final size:26
Alignment explanation
Indices: 69143--69217 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 26
69133 ATTATATTAT
*
69143 ATTTTTAT-T-TTAATAATATATAATA
1 ATTTTTATATATTTATAATA-ATAATA
69168 ATTTTTATATATTTAATAATTAATAAT-
1 ATTTTTATATATTT-ATAA-TAATAATA
69195 ATTATTTATATATTT-TAATAATA
1 ATT-TTTATATATTTATAATAATA
69218 TTTTAATAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
25 13 0.30
26 4 0.09
27 5 0.11
28 20 0.45
29 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTTTATATATTTATAATAATAATA
Found at i:69219 original size:19 final size:19
Alignment explanation
Indices: 69149--69226 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
69139 TTATATTTTT
*
69149 ATTTTAATAATATATAATA
1 ATTTTAATAATATTTAATA
*
69168 ATTTTTAT-ATATTTAATA
1 ATTTTAATAATATTTAATA
* *
69186 ATTAATAATATTATTT-ATA
1 ATT-TTAATAATATTTAATA
69205 TATTTTAATAATATTTTAATA
1 -ATTTTAATAATA-TTTAATA
69226 A
1 A
69227 AGATATTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
18 12 0.26
19 20 0.43
20 12 0.26
21 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTAATAATATTTAATA
Found at i:69234 original size:14 final size:11
Alignment explanation
Indices: 69148--69226 Score: 61
Period size: 11 Copynumber: 8.0 Consensus size: 11
69138 ATTATATTTT
69148 TATTTTAATAA
1 TATTTTAATAA
*
69159 TA-TATAATAA
1 TATTTTAATAA
69169 T-TTTT-AT-A
1 TATTTTAATAA
69177 TA-TTTAAT-A
1 TATTTTAATAA
69186 -A--TTAATAA
1 TATTTTAATAA
*
69194 TATTATTTAT-A
1 TATT-TTAATAA
69205 TATTTTAATAA
1 TATTTTAATAA
69216 TATTTTAATAA
1 TATTTTAATAA
69227 AGATATTTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
7 5 0.09
8 7 0.13
9 6 0.11
10 14 0.25
11 19 0.35
12 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATTTTAATAA
Found at i:69247 original size:23 final size:23
Alignment explanation
Indices: 69221--69265 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
69211 AATAATATTT
69221 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
69244 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
69266 ATATAATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:69563 original size:14 final size:14
Alignment explanation
Indices: 69530--69557 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
69520 AAATGTAATT
69530 CATTTTACGGAAAA
1 CATTTTACGGAAAA
69544 CATTTTACGGAAAA
1 CATTTTACGGAAAA
69558 GGTTTTCCAT
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
CATTTTACGGAAAA
Found at i:69606 original size:15 final size:15
Alignment explanation
Indices: 69588--69651 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 15
69578 CATTTTCCAG
69588 AATTCAAATTTCAGT
1 AATTCAAATTTCAGT
*
69603 AATTCAAATTCCAGT
1 AATTCAAATTTCAGT
*
69618 AATTC-ATTTTCCAGT
1 AATTCAAATTT-CAGT
69633 AATTCAAA-TTCTAGT
1 AATTCAAATTTC-AGT
69648 AATT
1 AATT
69652 TATTTTCTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
14 4 0.10
15 37 0.88
16 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (15 bp):
AATTCAAATTTCAGT
Found at i:69633 original size:30 final size:30
Alignment explanation
Indices: 69573--69658 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
69563 TCCATAAATT
** *
69573 TAATTCATTTTCCAG-AATTCAAATTT-CAG
1 TAATTCAAATTCCAGTAATTC-ATTTTCCAG
69602 TAATTCAAATTCCAGTAATTCATTTTCCAG
1 TAATTCAAATTCCAGTAATTCATTTTCCAG
* *
69632 TAATTCAAATTCTAGTAATTTATTTTC
1 TAATTCAAATTCCAGTAATTCATTTTC
69659 TGGAAAACCA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 17 0.34
30 33 0.66
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (30 bp):
TAATTCAAATTCCAGTAATTCATTTTCCAG
Found at i:69659 original size:15 final size:15
Alignment explanation
Indices: 69573--69659 Score: 70
Period size: 15 Copynumber: 5.9 Consensus size: 15
69563 TCCATAAATT
*
69573 TAATTCATTTTCCAG
1 TAATTCATTTTCTAG
*
69588 -AATTCAAATTTC-AG
1 TAATTC-ATTTTCTAG
** *
69602 TAATTCAAATTCCAG
1 TAATTCATTTTCTAG
*
69617 TAATTCATTTTCCAG
1 TAATTCATTTTCTAG
**
69632 TAATTCAAATTCTAG
1 TAATTCATTTTCTAG
*
69647 TAATTTATTTTCT
1 TAATTCATTTTCT
69660 GGAAAACCAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (15 bp):
TAATTCATTTTCTAG
Done.