Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006653.1 Hibiscus syriacus cultivar Beakdansim tig00016424_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: 105476
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1041 original size:16 final size:17
Alignment explanation
Indices: 1011--1044 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1001 GGTTAATGTA
*
1011 AAAATAATATTAAATTT
1 AAAATAATATAAAATTT
1028 AAAA-AATATAAAATTT
1 AAAATAATATAAAATTT
1044 A
1 A
1045 TTAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATAATATAAAATTT
Found at i:7519 original size:6 final size:6
Alignment explanation
Indices: 7508--7574 Score: 89
Period size: 6 Copynumber: 11.2 Consensus size: 6
7498 GACACGTATT
* * * * *
7508 ACCACG ACCACG ACCACG ACCACG ACCTCG AACTCG ACCTCG ACCATG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
7556 ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG A
7575 GCCAAGCTGA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.31, C:0.46, G:0.16, T:0.06
Consensus pattern (6 bp):
ACCACG
Found at i:13302 original size:6 final size:6
Alignment explanation
Indices: 13291--13369 Score: 122
Period size: 6 Copynumber: 13.2 Consensus size: 6
13281 GACATGTATT
*
13291 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* * *
13339 ACCTCG ACCTCG ACCACG ACCACG ACAACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
13370 GCCGTGCATA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.32, C:0.48, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:19633 original size:2 final size:2
Alignment explanation
Indices: 19628--19702 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
19618 AAAAGATAAG
19628 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19703 AGATGATATT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19869 original size:2 final size:2
Alignment explanation
Indices: 19862--19925 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
19852 TTTAACATTA
19862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19904 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
19926 GTTTTGGATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22549 original size:12 final size:12
Alignment explanation
Indices: 22534--22560 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
22524 GAGAAGCAGA
22534 AGCCAAAGCTTG
1 AGCCAAAGCTTG
22546 AGCCAAAGCTTG
1 AGCCAAAGCTTG
22558 AGC
1 AGC
22561 TTGCATCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (12 bp):
AGCCAAAGCTTG
Found at i:23426 original size:60 final size:60
Alignment explanation
Indices: 23357--23472 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
23347 AAATATCATA
* * * *
23357 AAATTATGATCTGCT-TTTTAATTTAATCTCTAAATTTT-AAAATATTTTATAATAATTTTT
1 AAATTATGATCT--TATTCTAACTTAATCCCTAAATTTTCAAAATAGTTTATAATAATTTTT
* *
23417 AAATTATGATCTTATTCTAGCTTAATCCCTAAATTTTCAAAATAGTTTATATTAAT
1 AAATTATGATCTTATTCTAACTTAATCCCTAAATTTTCAAAATAGTTTATAATAAT
23473 CCTCGAACTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 1 0.02
59 19 0.40
60 28 0.58
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.49
Consensus pattern (60 bp):
AAATTATGATCTTATTCTAACTTAATCCCTAAATTTTCAAAATAGTTTATAATAATTTTT
Found at i:34747 original size:18 final size:18
Alignment explanation
Indices: 34724--34767 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
34714 TTAACTCCCT
34724 GTGCCCGGCTGCCGGCGA
1 GTGCCCGGCTGCCGGCGA
34742 GTGCCCGGCTGCCGGCGA
1 GTGCCCGGCTGCCGGCGA
*
34760 GTTCCCGG
1 GTGCCCGG
34768 AGCTCGAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.05, C:0.39, G:0.43, T:0.14
Consensus pattern (18 bp):
GTGCCCGGCTGCCGGCGA
Found at i:35756 original size:32 final size:32
Alignment explanation
Indices: 35707--35784 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
35697 CTTACCCAAT
*
35707 TTCAACAAAAATTAGCTGCCTACCATTCGATGC
1 TTCAAC-AAAATCAGCTGCCTACCATTCGATGC
*
35740 TTCAACAAAATCAGCTGCCTACCATTCGGTGC
1 TTCAACAAAATCAGCTGCCTACCATTCGATGC
35772 TTCAACAAAATCA
1 TTCAACAAAATCA
35785 ATTCCCTACC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 37 0.86
33 6 0.14
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.26
Consensus pattern (32 bp):
TTCAACAAAATCAGCTGCCTACCATTCGATGC
Found at i:35793 original size:32 final size:32
Alignment explanation
Indices: 35707--35794 Score: 104
Period size: 32 Copynumber: 2.7 Consensus size: 32
35697 CTTACCCAAT
* * *
35707 TTCAACAAAAATTAGCTGCCTACCATTCGATGC
1 TTCAAC-AAAATCAACTCCCTACCATTCGATGC
* * *
35740 TTCAACAAAATCAGCTGCCTACCATTCGGTGC
1 TTCAACAAAATCAACTCCCTACCATTCGATGC
*
35772 TTCAACAAAATCAATTCCCTACC
1 TTCAACAAAATCAACTCCCTACC
35795 CATCGAATGG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 44 0.88
33 6 0.12
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.26
Consensus pattern (32 bp):
TTCAACAAAATCAACTCCCTACCATTCGATGC
Found at i:38412 original size:34 final size:34
Alignment explanation
Indices: 38367--38433 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
38357 AATAGGAATT
*
38367 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATA
38402 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
38434 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:38644 original size:32 final size:32
Alignment explanation
Indices: 38601--38688 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
38591 CTTACCCAAT
*
38601 TTCAACAAAAATCAGCTGCCTACCATTCAGTGC
1 TTCAAC-AAAATCAGCTGTCTACCATTCAGTGC
* * * * *
38634 TTCAAGAAAATCAACTGTATGCCATTCGGTGC
1 TTCAACAAAATCAGCTGTCTACCATTCAGTGC
* *
38666 TTTAACAAAATCAGTTGTCTACC
1 TTCAACAAAATCAGCTGTCTACC
38689 CATCGAATGG
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
32 38 0.88
33 5 0.12
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (32 bp):
TTCAACAAAATCAGCTGTCTACCATTCAGTGC
Found at i:39138 original size:3 final size:3
Alignment explanation
Indices: 39132--39157 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39122 TTCAATTCTT
39132 CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CT
39158 TCTAAACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:39386 original size:38 final size:38
Alignment explanation
Indices: 39335--39412 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
39325 GGATTTTCAG
*
39335 TTAGATTGCATGGATATGGTAATTAACTAATTATTAGT
1 TTAGATTGCATGGATATGATAATTAACTAATTATTAGT
*
39373 TTAGATTGCATGGATATGATAATTAACTAATTATTGGT
1 TTAGATTGCATGGATATGATAATTAACTAATTATTAGT
39411 TT
1 TT
39413 GGTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (38 bp):
TTAGATTGCATGGATATGATAATTAACTAATTATTAGT
Found at i:41172 original size:82 final size:82
Alignment explanation
Indices: 41052--41214 Score: 249
Period size: 82 Copynumber: 2.0 Consensus size: 82
41042 GCGTATATCT
* *
41052 GTTTAATATTTTAAATTTTAAATATATTATTATATGTTTAAATTTAGATATT-AAAAGATCTATG
1 GTTTAATATTTTAAATTTTAAAAATATTATTATATGTTTAAATTTAGATATTAAAAAGAT-T-TA
*
41116 GTTGGAGTAAATCTCTCAG
64 GTTGGAGTAAAACTCTCAG
*
41135 GTTTAATATTTTAAA-TTTAAAAATATTATTATCTGTTTAAATTTAGATATTGAAAAAGATTTAG
1 GTTTAATATTTTAAATTTTAAAAATATTATTATATGTTTAAATTTAGATATT-AAAAAGATTTAG
41199 TTGGAGTAAAACTCTC
65 TTGGAGTAAAACTCTC
41215 TCGAAATTCT
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
82 51 0.69
83 16 0.22
84 7 0.09
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.45
Consensus pattern (82 bp):
GTTTAATATTTTAAATTTTAAAAATATTATTATATGTTTAAATTTAGATATTAAAAAGATTTAGT
TGGAGTAAAACTCTCAG
Found at i:45947 original size:19 final size:19
Alignment explanation
Indices: 45920--45959 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
45910 TTTCCGATTT
* *
45920 TATTATCAAGCAAGATCAA
1 TATTATCAAACAAAATCAA
*
45939 TATTCTCAAACAAAATCAA
1 TATTATCAAACAAAATCAA
45958 TA
1 TA
45960 ATCATAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (19 bp):
TATTATCAAACAAAATCAA
Found at i:47828 original size:18 final size:18
Alignment explanation
Indices: 47805--47860 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
47795 GGGCATTTGA
**
47805 TCCTCTGGTCGTGCTTGT
1 TCCTCTGGTCGAACTTGT
*
47823 TCCTCTGGTGGAACTTGT
1 TCCTCTGGTCGAACTTGT
*
47841 TCCTCTGGTGGAACTTGT
1 TCCTCTGGTCGAACTTGT
47859 TC
1 TC
47861 TTCGTGTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.07, C:0.25, G:0.27, T:0.41
Consensus pattern (18 bp):
TCCTCTGGTCGAACTTGT
Found at i:49462 original size:21 final size:21
Alignment explanation
Indices: 49434--49519 Score: 68
Period size: 23 Copynumber: 4.0 Consensus size: 21
49424 ATAGCCAAAA
49434 CCCT-CAGGGGGTATCGATTC
1 CCCTACAGGGGGTATCGATTC
*
49454 CCCTACAGGGGGAATC-ACTTC
1 CCCTACAGGGGGTATCGA-TTC
* * *
49475 CCCTTCAAAGGGGGGATCGGTTC
1 CCC-T-ACAGGGGGTATCGATTC
*
49498 CCCTTCAAGGGGGGTATCGATT
1 CCCTAC-A-GGGGGTATCGATT
49520 TCCTATGCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
20 5 0.10
21 16 0.31
22 3 0.06
23 27 0.53
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.23
Consensus pattern (21 bp):
CCCTACAGGGGGTATCGATTC
Found at i:49498 original size:23 final size:23
Alignment explanation
Indices: 49440--49516 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
49430 AAAACCCTCA
* *
49440 GGGGGTATCGATTCCCCTAC-A-
1 GGGGGTATCGGTTCCCCTTCAAG
* **
49461 GGGGGAATCACTTCCCCTTCAAAG
1 GGGGGTATCGGTTCCCCTTC-AAG
49485 GGGGG-ATCGGTTCCCCTTCAAG
1 GGGGGTATCGGTTCCCCTTCAAG
49507 GGGGGTATCG
1 GGGGGTATCG
49517 ATTTCCTATG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
21 16 0.35
22 8 0.17
23 17 0.37
24 5 0.11
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.22
Consensus pattern (23 bp):
GGGGGTATCGGTTCCCCTTCAAG
Found at i:54780 original size:113 final size:111
Alignment explanation
Indices: 54584--54807 Score: 385
Period size: 113 Copynumber: 2.0 Consensus size: 111
54574 TGATACCAAT
* * * *
54584 TGTTGAGTTAATCGATCGATGGAATTGGCCAAGAGGGGGTGAATTGGCAATTAAAATTTTGGTGG
1 TGTTGAGTTAATCGATCGACGGAATTAGCCAAGAGGGGGTGAATTGGCAATTAAAAATTCGGTGG
54649 AAGCTTTTGCAGAAAATTGAAAAGATTTGCACAGAGATTTAGAGTG
66 AAGCTTTTGCAGAAAATTGAAAAGATTTGCACAGAGATTTAGAGTG
54695 TGTTGAGTTAATCGATCGACGGAATTAGCCAAGAGGGGGGGTGAATTGGCAATTAAAAATTCGGT
1 TGTTGAGTTAATCGATCGACGGAATTAGCCAAGA--GGGGGTGAATTGGCAATTAAAAATTCGGT
*
54760 GGAAGCTTTTGCAGAAAATTGAAAAGATTTGCACAGCGATTTAGAGTG
64 GGAAGCTTTTGCAGAAAATTGAAAAGATTTGCACAGAGATTTAGAGTG
54808 GTTCGACTTT
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
111 32 0.30
113 74 0.70
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (111 bp):
TGTTGAGTTAATCGATCGACGGAATTAGCCAAGAGGGGGTGAATTGGCAATTAAAAATTCGGTGG
AAGCTTTTGCAGAAAATTGAAAAGATTTGCACAGAGATTTAGAGTG
Found at i:55857 original size:19 final size:19
Alignment explanation
Indices: 55833--55872 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
55823 ACACTTCTCC
55833 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
55852 CATTTATCATTTTAAAACA
1 CATTTATCATTTTAAAACA
55871 CA
1 CA
55873 CTTAAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
CATTTATCATTTTAAAACA
Found at i:55891 original size:12 final size:12
Alignment explanation
Indices: 55863--55897 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
55853 ATTTATCATT
55863 TTAAAACACAC-
1 TTAAAACACACA
55874 TTAAAACACACA
1 TTAAAACACACA
55886 TTAAAACACACA
1 TTAAAACACACA
55898 CTTACACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (12 bp):
TTAAAACACACA
Found at i:57000 original size:3 final size:3
Alignment explanation
Indices: 56992--57048 Score: 78
Period size: 3 Copynumber: 18.3 Consensus size: 3
56982 TTTTACTTAA
* *
56992 ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATT ATAT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT
57039 ATT ATT ATT A
1 ATT ATT ATT A
57049 AATATTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 42 0.86
4 7 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:63894 original size:7 final size:8
Alignment explanation
Indices: 63878--63910 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
63868 AAGAAAGAAT
63878 AAAACAAA
1 AAAACAAA
63886 AAAAC-AA
1 AAAACAAA
63893 AAAACAAA
1 AAAACAAA
63901 AAAACAAA
1 AAAACAAA
63909 AA
1 AA
63911 GGAAAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAACAAA
Found at i:63917 original size:15 final size:15
Alignment explanation
Indices: 63878--63910 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
63868 AAGAAAGAAT
63878 AAAACAAAAAAACAA
1 AAAACAAAAAAACAA
63893 AAAACAAAAAAACAA
1 AAAACAAAAAAACAA
63908 AAA
1 AAA
63911 GGAAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAAACAA
Found at i:69186 original size:22 final size:22
Alignment explanation
Indices: 69125--69197 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
69115 GCACTTTTTT
* **
69125 AAGATAATAGATTCTCACTTCA
1 AAGATGATAGATTCTCTTTTCA
* * * * *
69147 GAGATGACAAATTTTCTTTTTA
1 AAGATGATAGATTCTCTTTTCA
69169 AAGATGATAGATTCTCTTTTCA
1 AAGATGATAGATTCTCTTTTCA
*
69191 AAAATGA
1 AAGATGA
69198 AAGCTTTATG
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (22 bp):
AAGATGATAGATTCTCTTTTCA
Found at i:69958 original size:76 final size:76
Alignment explanation
Indices: 69876--70624 Score: 1446
Period size: 76 Copynumber: 9.9 Consensus size: 76
69866 CTATTTCTCA
* *
69876 CATCTGTAAGCCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
69941 AGCCTTCGGGT
66 AGCCTTCGGGT
69952 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
70017 AGCCTTCGGGT
66 AGCCTTCGGGT
70028 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
70093 AGCCTTCGGGT
66 AGCCTTCGGGT
70104 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
70169 AGCCTTCGGGT
66 AGCCTTCGGGT
*
70180 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
70245 AGCCTTCGGGT
66 AGCCTTCGGGT
70256 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
70321 AGCCTTCGGGT
66 AGCCTTCGGGT
70332 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
70397 AGCCTTC-GGT
66 AGCCTTCGGGT
70407 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
*
70472 AGCCTTCAGGT
66 AGCCTTCGGGT
70483 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
70548 AGCCTTCGGGT
66 AGCCTTCGGGT
*
70559 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTCCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
70624 A
66 A
70625 AAGCCTTCAG
Statistics
Matches: 666, Mismatches: 6, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 0.11
76 591 0.89
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:70618 original size:31 final size:31
Alignment explanation
Indices: 70581--70655 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
70571 CTTCAGTGCA
70581 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTT
70612 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTT
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTT
*
70643 TGATGTTTTCAAA
1 TGATGTTTCCAAA
70656 GCCTTCGGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (31 bp):
TGATGTTTCCAAAAAGCCTTCAGGAGCTTTT
Found at i:70622 original size:107 final size:107
Alignment explanation
Indices: 70505--70731 Score: 445
Period size: 107 Copynumber: 2.1 Consensus size: 107
70495 CTTCAGTGCA
70505 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
70570 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTT
70612 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
70677 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTT
66 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTT
*
70719 TGATGTTTTCAAA
1 TGATGTTTCCAAA
70732 GCCTTCGGGT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 119 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (107 bp):
TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTT
Found at i:70736 original size:259 final size:259
Alignment explanation
Indices: 70354--70894 Score: 1005
Period size: 259 Copynumber: 2.1 Consensus size: 259
70344 CTTCAGTGCA
70354 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGTCATCTGTAAGTC
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGTCATCTGTAAGTC
70419 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGTC
66 CTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGTC
*
70484 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAA
131 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTAAAA
70549 GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCAGGAGCTTTT
196 GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCAGGAGCTTTT
70612 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGT
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTC-GGTCATCTGTAAGT
*
70677 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
65 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGT
* *
70742 CATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTAAA
130 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTAAA
*
70807 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTT
195 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCAGGAGCTTTT
*
70872 TGATGTTTTCAAAAA-CCTTCAGG
1 TGATGTTTCCAAAAAGCCTTCAGG
70895 TCATCTGTAA
Statistics
Matches: 275, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
258 50 0.18
259 191 0.69
260 34 0.12
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (259 bp):
TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGTCATCTGTAAGTC
CTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCAGGTC
ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTAAAA
GCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCAGGAGCTTTT
Found at i:70932 original size:77 final size:77
Alignment explanation
Indices: 70612--71004 Score: 666
Period size: 76 Copynumber: 5.1 Consensus size: 77
70602 AGGAGCTTTT
70612 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTC-AAAGCCTTCGGGTCATCTGTAAG
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAAGCCTTCGGGTCATCTGTAAG
70676 TCCTTCAGTGCA
66 TCCTTCAGTGCA
70688 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTC-AAAGCCTTCGGGTCATCTGTAAG
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAAGCCTTCGGGTCATCTGTAAG
*
70752 TCCTTTAGTGCA
66 TCCTTCAGTGCA
*
70764 TGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-AAAAGCCTTCGGGTCATCTGTAAG
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAAGCCTTCGGGTCATCTGTAAG
70828 TCCTTCAGTGCA
66 TCCTTCAGTGCA
* * *
70840 TGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAACCTTCAGGTCATCTGTAA
1 TGATGTTTCC-AAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAAGCCTTCGGGTCATCTGTAA
*
70905 GTCCTACAGTGCA
65 GTCCTTCAGTGCA
* *
70918 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTAATGTTTTCAAAAACCTTCGGGTCATCTGTAAG
1 TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAAGCCTTCGGGTCATCTGTAAG
*
70983 CCCTTCAGTGCA
66 TCCTTCAGTGCA
70995 TGATGCTTTC
1 TGATG-TTTC
71005 AAACATTTCC
Statistics
Matches: 302, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
76 158 0.52
77 97 0.32
78 47 0.16
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (77 bp):
TGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAAGCCTTCGGGTCATCTGTAAG
TCCTTCAGTGCA
Found at i:71143 original size:3 final size:3
Alignment explanation
Indices: 71135--71187 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
71125 TTTTACTTAA
* *
71135 ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT A-T ATAT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT
71181 ATT ATT A
1 ATT ATT A
71188 AATATTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.80
4 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:82913 original size:83 final size:83
Alignment explanation
Indices: 82750--82915 Score: 244
Period size: 83 Copynumber: 2.0 Consensus size: 83
82740 GTGTATATCT
* * *
82750 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAATATATCTGA
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAAGAGATCTGA
* * *
82815 TTGGAGTAAATCTCTCAA
66 TTGAAATAAAACTCTCAA
* *
82833 GTTTAATATTTTAAATTTAAAAGATATTATTATTTATTTAAATTTAGATATTAAAAGAGAT-TTA
1 GTTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAAGAGATCTGA
82897 GTTGAAATAAAACTCTCAA
66 -TTGAAATAAAACTCTCAA
82916 AATTCCCCTA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 2 0.03
83 72 0.97
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (83 bp):
GTTTAATATTTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAAGAGATCTGA
TTGAAATAAAACTCTCAA
Found at i:91542 original size:24 final size:24
Alignment explanation
Indices: 91510--91572 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
91500 CAGTGAAAAT
*
91510 TGCCGCGTAGAATTTGCACCGAAG
1 TGCCACGTAGAATTTGCACCGAAG
* *
91534 TGCCACGTAAAATATGCACCGAAG
1 TGCCACGTAGAATTTGCACCGAAG
*
91558 TGCCACATAG-ATTTG
1 TGCCACGTAGAATTTG
91573 TCCCGAATGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (24 bp):
TGCCACGTAGAATTTGCACCGAAG
Found at i:91615 original size:23 final size:23
Alignment explanation
Indices: 91585--91632 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
91575 CCGAATGGCC
91585 AATTGTCCTGAAGGACCACATAG
1 AATTGTCCTGAAGGACCACATAG
*
91608 AATTGTCCTGAAGGACCACGTAG
1 AATTGTCCTGAAGGACCACATAG
91631 AA
1 AA
91633 CCCTCGACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (23 bp):
AATTGTCCTGAAGGACCACATAG
Found at i:94490 original size:54 final size:54
Alignment explanation
Indices: 94415--94528 Score: 192
Period size: 54 Copynumber: 2.1 Consensus size: 54
94405 AGAATCAGAC
* * *
94415 AAAAATTCGTTGTCTTGTCATTTTTATCATATTCTTGTTAAGATAAGAATGTGT
1 AAAAAATCGTTGTCTTATCATTTTTATCATATTCTTGTTAAGATAAAAATGTGT
*
94469 AAAAAATCGTTGTCTTATCATTTTTATCATATTCTTGTTAATATAAAAATGTGT
1 AAAAAATCGTTGTCTTATCATTTTTATCATATTCTTGTTAAGATAAAAATGTGT
94523 AAAAAA
1 AAAAAA
94529 AGACAGCTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (54 bp):
AAAAAATCGTTGTCTTATCATTTTTATCATATTCTTGTTAAGATAAAAATGTGT
Found at i:94600 original size:21 final size:21
Alignment explanation
Indices: 94574--94621 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
94564 ATTGTTTATT
94574 ATTATTATTATAGTAATAATA
1 ATTATTATTATAGTAATAATA
* *
94595 ATTATTATTTTATTAATAATA
1 ATTATTATTATAGTAATAATA
*
94616 TTTATT
1 ATTATT
94622 TACATTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTATTATTATAGTAATAATA
Found at i:94611 original size:18 final size:18
Alignment explanation
Indices: 94568--94614 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
94558 GTGTTAATTG
*
94568 TTTATT-ATTATTATTAT
1 TTTATTAATAATTATTAT
** *
94585 AGTAATAATAATTATTAT
1 TTTATTAATAATTATTAT
94603 TTTATTAATAAT
1 TTTATTAATAAT
94615 ATTTATTTAC
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTATTAATAATTATTAT
Done.