Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000248.1 Hibiscus syriacus cultivar Beakdansim tig00000443_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: 79089
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:6889 original size:28 final size:27
Alignment explanation
Indices: 6815--6889 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 27
6805 AGTTGAATGC
* *
6815 CTAATTGCACCCAAAAAAATGTTGGGTA
1 CTAATTGCA-CCAAAAAAAAGTTAGGTA
* * *
6843 CGAAATTGCATCATTAAAAAAGTTAGGTA
1 C-TAATTGCACCA-AAAAAAAGTTAGGTA
*
6872 CTAATTGCACCAGAAAAA
1 CTAATTGCACCAAAAAAA
6890 GCTGGAAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
27 5 0.14
28 12 0.32
29 20 0.54
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (27 bp):
CTAATTGCACCAAAAAAAAGTTAGGTA
Found at i:7001 original size:49 final size:49
Alignment explanation
Indices: 6929--7026 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
6919 AGGTAGCAAA
6929 AGTTATATTAACCCTAATTTAATCTATACTTATGGTAAGGAGATTGTTT
1 AGTTATATTAACCCTAATTTAATCTATACTTATGGTAAGGAGATTGTTT
6978 AGTTATATTAACCCTAATTTAATCTATACTTATGGTAAGGAGATTGTTT
1 AGTTATATTAACCCTAATTTAATCTATACTTATGGTAAGGAGATTGTTT
7027 TGAGATTTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (49 bp):
AGTTATATTAACCCTAATTTAATCTATACTTATGGTAAGGAGATTGTTT
Found at i:11436 original size:2 final size:2
Alignment explanation
Indices: 11429--11454 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11419 TTAAATCAAC
11429 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
11455 TTAAATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18160 original size:23 final size:23
Alignment explanation
Indices: 18134--18201 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
18124 TTCATGTTTG
* ** *
18134 TTTATTTATTGTTCGTGAACATT
1 TTTATTTAATGTTCACGAACATA
18157 TTTATTTAATGTTCACGAACATA
1 TTTATTTAATGTTCACGAACATA
* * *
18180 TTCATTTAGTGTTCACAAACAT
1 TTTATTTAATGTTCACGAACAT
18202 GTTCGTTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.47
Consensus pattern (23 bp):
TTTATTTAATGTTCACGAACATA
Found at i:18210 original size:23 final size:23
Alignment explanation
Indices: 18151--18212 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
18141 ATTGTTCGTG
* * *
18151 AACATTTTTATTTAATGTTCACG
1 AACATATTCATTTAATGTTCACA
*
18174 AACATATTCATTTAGTGTTCACA
1 AACATATTCATTTAATGTTCACA
* *
18197 AACATGTTCGTTTAAT
1 AACATATTCATTTAAT
18213 ATTTATTTAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.44
Consensus pattern (23 bp):
AACATATTCATTTAATGTTCACA
Found at i:18657 original size:41 final size:41
Alignment explanation
Indices: 18600--18682 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
18590 TAACAAATAG
18600 TTAATTGAACGCTGAGTTGATTTACACCCTTACGTTTAGGT
1 TTAATTGAACGCTGAGTTGATTTACACCCTTACGTTTAGGT
* *
18641 TTAATTGAACGTTGAGTTGATTTACTCCCTTACGTTTAGGT
1 TTAATTGAACGCTGAGTTGATTTACACCCTTACGTTTAGGT
18682 T
1 T
18683 ACCCAGAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (41 bp):
TTAATTGAACGCTGAGTTGATTTACACCCTTACGTTTAGGT
Found at i:23271 original size:27 final size:29
Alignment explanation
Indices: 23240--23295 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
23230 ACAAGTCCCC
*
23240 CCCCCCTTTTT-CTGCTTTGTACTCTAGA
1 CCCCCTTTTTTCCTGCTTTGTACTCTAGA
23268 CCCCCTTTTTTTCCTGCTTTGTACTCTA
1 CCCCC-TTTTTTCCTGCTTTGTACTCTA
23296 AAAAAGGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
29 5 0.20
30 15 0.60
ACGTcount: A:0.09, C:0.36, G:0.09, T:0.46
Consensus pattern (29 bp):
CCCCCTTTTTTCCTGCTTTGTACTCTAGA
Found at i:27035 original size:20 final size:19
Alignment explanation
Indices: 26977--27035 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
26967 GATTGAAGTA
*
26977 GTATCGATACTGAAGTGAAG
1 GTATCGATACTAAAGT-AAG
* *
26997 GTAACGATACCAAAGGTAAG
1 GTATCGATACTAAA-GTAAG
27017 GTATCGATACTATAAGTAA
1 GTATCGATACTA-AAGTAA
27036 AGATGAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (19 bp):
GTATCGATACTAAAGTAAG
Found at i:27524 original size:15 final size:15
Alignment explanation
Indices: 27496--27588 Score: 105
Period size: 15 Copynumber: 6.1 Consensus size: 15
27486 GTTTGTGAGT
* *
27496 ATGTTTTATATGAAA
1 ATGTTCTATGTGAAA
27511 ATGTTCTATGTGAAA
1 ATGTTCTATGTGAAA
* * *
27526 ATGTGCTAAGTTAAA
1 ATGTTCTATGTGAAA
27541 ATGTTCTATGTGAAAA
1 ATGTTCTATGTG-AAA
* * *
27557 ATATGCTAAGTGAAA
1 ATGTTCTATGTGAAA
27572 ATGTTCTATGTGAAA
1 ATGTTCTATGTGAAA
27587 AT
1 AT
27589 ACCCTATGTG
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
15 51 0.81
16 12 0.19
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (15 bp):
ATGTTCTATGTGAAA
Found at i:27542 original size:30 final size:30
Alignment explanation
Indices: 27506--27589 Score: 141
Period size: 31 Copynumber: 2.8 Consensus size: 30
27496 ATGTTTTATA
*
27506 TGAAAATGTTCTATGTGAAAATGTGCTAAG
1 TGAAAATGTTCTATGTGAAAATATGCTAAG
*
27536 TTAAAATGTTCTATGTGAAAAATATGCTAAG
1 TGAAAATGTTCTATGTG-AAAATATGCTAAG
27567 TGAAAATGTTCTATGTGAAAATA
1 TGAAAATGTTCTATGTGAAAATA
27590 CCCTATGTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
30 22 0.44
31 28 0.56
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (30 bp):
TGAAAATGTTCTATGTGAAAATATGCTAAG
Found at i:28021 original size:22 final size:22
Alignment explanation
Indices: 27982--28023 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
27972 CCATATTGCC
**
27982 CAGATGGTACCGGTACCCCCCT
1 CAGATGGTACCGACACCCCCCT
28004 CAGATGGTACCGACACCCCC
1 CAGATGGTACCGACACCCCC
28024 ATGACAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.43, G:0.21, T:0.14
Consensus pattern (22 bp):
CAGATGGTACCGACACCCCCCT
Found at i:30618 original size:20 final size:20
Alignment explanation
Indices: 30593--30633 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30583 TTTCTGGGCA
* *
30593 AGGGGAATCGGTACCCATTC
1 AGGGGAACCGATACCCATTC
*
30613 AGGGGAACCGATACCCCTTC
1 AGGGGAACCGATACCCATTC
30633 A
1 A
30634 AACGACAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (20 bp):
AGGGGAACCGATACCCATTC
Found at i:31139 original size:18 final size:18
Alignment explanation
Indices: 31116--31150 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31106 CTAGGAGATT
31116 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
31134 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
31151 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:31236 original size:21 final size:22
Alignment explanation
Indices: 31207--31250 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31197 GTTGTATGAT
31207 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
31228 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
31250 A
1 A
31251 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:32306 original size:146 final size:149
Alignment explanation
Indices: 32130--32430 Score: 554
Period size: 146 Copynumber: 2.0 Consensus size: 149
32120 GAGTCGAGGG
32130 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
32195 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTA-T-
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
32258 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
32277 TCTACGCGGTTCTTCG-GACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
32341 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
32406 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
32425 TCTACG
1 TCTACG
32431 GGGCACTTCG
Statistics
Matches: 149, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
146 107 0.72
147 17 0.11
148 25 0.17
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:32453 original size:23 final size:23
Alignment explanation
Indices: 32409--32453 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
32399 ATCATTATAT
*
32409 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
32432 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
32454 AGCTGTGGTG
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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:34684 original size:16 final size:15
Alignment explanation
Indices: 34654--34697 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
34644 GGTAATTAAA
34654 GATTGATAAGAATTT
1 GATTGATAAGAATTT
*
34669 GATTGATTAAGGATTTT
1 GATTGA-TAA-GAATTT
*
34686 GAGTGATAAGAA
1 GATTGATAAGAA
34698 CTGATGCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (15 bp):
GATTGATAAGAATTT
Found at i:35604 original size:21 final size:21
Alignment explanation
Indices: 35578--35622 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
35568 GATTTATGGG
* *
35578 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
35599 CAAGGGGAACCGATACCCATT
1 CAAGGGGAACCGATACCCATT
35620 CAA
1 CAA
35623 ACGACAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:36225 original size:18 final size:18
Alignment explanation
Indices: 36202--36236 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36192 CTAGGAGATT
36202 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
36220 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
36237 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:36322 original size:21 final size:22
Alignment explanation
Indices: 36293--36336 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
36283 GTTGTATGAT
36293 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
36314 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
36336 A
1 A
36337 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:37399 original size:149 final size:149
Alignment explanation
Indices: 37218--37521 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
37208 GAGTCGAGGG
37218 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
37283 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
37348 TATGGCACTACGGTACAAT
131 TATGGCACTACGGTACAAT
* *
37367 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
37432 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
*
37497 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTACAAT
37516 TCTACG
1 TCTACG
37522 GGGCACTTCG
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTACAAT
Found at i:37544 original size:23 final size:23
Alignment explanation
Indices: 37500--37544 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
37490 ATCATTATAT
*
37500 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
37523 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
37545 AGCTGTGGTG
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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:42221 original size:23 final size:22
Alignment explanation
Indices: 42195--42248 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
42185 CTAGGTATCA
* * *
42195 ATACCCCCTTTGCATGGGTACTG
1 ATACCCCC-TTGAATGGATACCG
*
42218 ATACCATCCTTGAATGGATACCG
1 ATACC-CCCTTGAATGGATACCG
42241 ATACCCCC
1 ATACCCCC
42249 ATGAGGGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.08
23 21 0.84
24 2 0.08
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (22 bp):
ATACCCCCTTGAATGGATACCG
Found at i:42733 original size:13 final size:13
Alignment explanation
Indices: 42708--42748 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
42698 TGAAAACTAC
42708 ACATTGATTTTCAA
1 ACATTG-TTTTCAA
*
42722 ATATTGTTTTCAA
1 ACATTGTTTTCAA
*
42735 ACATAGTTTTCAA
1 ACATTGTTTTCAA
42748 A
1 A
42749 ATTTGCCCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (13 bp):
ACATTGTTTTCAA
Found at i:42923 original size:20 final size:20
Alignment explanation
Indices: 42900--42939 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42890 GACATCCTCT
42900 AGTTGTTCAAACCATCCACC
1 AGTTGTTCAAACCATCCACC
42920 AGTTGTTCAAACCATCCACC
1 AGTTGTTCAAACCATCCACC
42940 TAACCCACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.35, G:0.10, T:0.25
Consensus pattern (20 bp):
AGTTGTTCAAACCATCCACC
Found at i:45741 original size:23 final size:24
Alignment explanation
Indices: 45687--45757 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
45677 TAACTCAACA
*
45687 CTACGTGGTCCTTCGGGACAAATT
1 CTACGTGGTCATTCGGGACAAATT
45711 CTACGTGGTCATTCGGGACAAA-T
1 CTACGTGGTCATTCGGGACAAATT
*
45734 CTATGTGG-CACTTCGGTG-CAAATT
1 CTACGTGGTCA-TTCGG-GACAAATT
45758 ATATGAGCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.05
23 17 0.40
24 23 0.55
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (24 bp):
CTACGTGGTCATTCGGGACAAATT
Found at i:52021 original size:20 final size:20
Alignment explanation
Indices: 51996--52049 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
51986 CGATCTCAAA
51996 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
52016 TTCGCAAC-CCAGCTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
52036 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
52050 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:53081 original size:24 final size:24
Alignment explanation
Indices: 53054--53107 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
53044 GTATTCGAAA
*
53054 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGATCAATACCCGGAC
* *
53078 TTTGATCTTGATCAATACTCGGAT
1 TTTGATCTTGATCAATACCCGGAC
53102 TTTGAT
1 TTTGAT
53108 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGATCAATACCCGGAC
Found at i:55743 original size:20 final size:20
Alignment explanation
Indices: 55715--55755 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
55705 CGCGAAATAA
*
55715 GCGTTGCGAATTTGACTATC
1 GCGTAGCGAATTTGACTATC
55735 GCGTAGCGAATTTGACTATC
1 GCGTAGCGAATTTGACTATC
55755 G
1 G
55756 TATCGCTTAT
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:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (20 bp):
GCGTAGCGAATTTGACTATC
Found at i:55879 original size:25 final size:25
Alignment explanation
Indices: 55847--55895 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
55837 AAATCAATTA
*
55847 AACATTGTTGTGGGTACATTATTTT
1 AACATTGTTATGGGTACATTATTTT
55872 AACATTGTTATGGGTACATTATTT
1 AACATTGTTATGGGTACATTATTT
55896 GGAAAAATAA
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:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTT
Found at i:56304 original size:18 final size:18
Alignment explanation
Indices: 56283--56319 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56273 GTAATTGGAG
56283 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
56301 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
56319 T
1 T
56320 ACAACTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:56671 original size:39 final size:39
Alignment explanation
Indices: 56586--56672 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
56576 TTCGATGCTC
* * *
56586 ATCAAAAGCCAAAGCTCATTTGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
*
56625 ATCAAAATCCAAATCTCATATGGTGCCAAACAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
56664 ATCAAAATC
1 ATCAAAATC
56673 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
Found at i:60813 original size:13 final size:13
Alignment explanation
Indices: 60795--60826 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
60785 GGGTTTCTTC
60795 AACAAAAAGACAA
1 AACAAAAAGACAA
*
60808 AACAAAAAGATAA
1 AACAAAAAGACAA
60821 AACAAA
1 AACAAA
60827 GACAAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.03
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:61068 original size:22 final size:22
Alignment explanation
Indices: 61040--61085 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
61030 GATGGAGATA
61040 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
61062 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
61084 GA
1 GA
61086 TGAATATCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:61243 original size:20 final size:20
Alignment explanation
Indices: 61218--61302 Score: 143
Period size: 20 Copynumber: 4.2 Consensus size: 20
61208 ACGTAAAAAC
*
61218 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
61238 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
* *
61258 ATTTGATTATCGCGTTGAGA
1 ATTTGACTATCGCGTTGCGA
61278 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
61298 ATTTG
1 ATTTG
61303 GAAAATCACA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:66848 original size:2 final size:2
Alignment explanation
Indices: 66841--66878 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
66831 TTAACAATAA
66841 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
66879 CACTTAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67733 original size:32 final size:32
Alignment explanation
Indices: 67697--67778 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
67687 ATAATATAAT
67697 ATATATCACATCAATATTTT-AAGTAACATATC
1 ATATATCACATCAATATTTTGAA-TAACATATC
* * *
67729 ATATATCACAT-TATCATTTTGAATAATATATT
1 ATATATCACATCAAT-ATTTTGAATAACATATC
* *
67761 ATATATCAAATCATTATT
1 ATATATCACATCAATATT
67779 ATAGGTATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
31 2 0.05
32 36 0.88
33 3 0.07
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (32 bp):
ATATATCACATCAATATTTTGAATAACATATC
Found at i:71215 original size:42 final size:42
Alignment explanation
Indices: 71168--71283 Score: 196
Period size: 42 Copynumber: 2.8 Consensus size: 42
71158 CCCGAAATCT
* * *
71168 CGTGTTTGTTTCATGTAATTCGTTTTTCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
*
71210 CGTGTTTGTTTCAGGTAATTCGTTTTCCGGAAAATATTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
71252 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
71284 TGTAATTCAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTTTCC
Found at i:71516 original size:22 final size:23
Alignment explanation
Indices: 71469--71529 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
71459 TAATTATTAA
* *
71469 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
71490 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
71513 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
71530 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:71536 original size:26 final size:26
Alignment explanation
Indices: 71452--71536 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 26
71442 TATCATTTTC
* *
71452 AAAATATTA-ATTATTAA-AATATTT
1 AAAATATTATATTATTAATATTATAT
71476 AAAATA-TAT-TTATTAATATTTATAAT
1 AAAATATTATATTATTAATA-TTAT-AT
*
71502 AATATAATATTATATTTTTAATATTATAT
1 -A-A-AATATTATATTATTAATATTATAT
71531 AAAATA
1 AAAATA
71537 ATCAATTATA
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
23 9 0.18
24 7 0.14
25 3 0.06
26 5 0.10
27 2 0.04
28 2 0.04
29 6 0.12
30 7 0.14
31 8 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AAAATATTATATTATTAATATTATAT
Found at i:71559 original size:23 final size:22
Alignment explanation
Indices: 71522--71571 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 22
71512 TATATTTTTA
71522 ATATTATATAAAATAATCAATT
1 ATATTATATAAAATAATCAATT
71544 ATATTATAATAAAATAATCAATT
1 ATATTAT-ATAAAATAATCAATT
71567 ATATT
1 ATATT
71572 TTTATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATTATATAAAATAATCAATT
Found at i:71592 original size:54 final size:52
Alignment explanation
Indices: 71495--71597 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 52
71485 TTATTAATAT
* *
71495 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAAAATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
*
71547 TTATAATAAAATAATCAATTATATTTTT-ATTTTA-ATAATATATAATAAATT
1 TTATAATAAAATAAT--ATTATATTTTTAATATTATATAA-A-ATAATAAATT
71598 TTTTTATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
52 18 0.41
53 6 0.14
54 20 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (52 bp):
TTATAATAAAATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
Found at i:71612 original size:31 final size:29
Alignment explanation
Indices: 71543--71646 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 29
71533 AATAATCAAT
71543 TATATTATAATAA-AATAATCAATTATATTTT-
1 TATATT-TAATAATAATAAT-AATT-T-TTTTA
71574 TAT-TTTAATAATATATAATAAATTTTTTTA
1 TATATTTAATAATA-ATAAT-AATTTTTTTA
*
71604 TATATTTAATAATGAATAAT-A-TTATTTA
1 TATATTTAATAAT-AATAATAATTTTTTTA
71632 TATATTTAAATAATA
1 TATATTT-AATAATA
71647 TTTTCGTAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
28 14 0.22
29 17 0.26
30 7 0.11
31 26 0.40
32 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
TATATTTAATAATAATAATAATTTTTTTA
Found at i:73652 original size:2 final size:2
Alignment explanation
Indices: 73645--73670 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
73635 TTAAAATGGA
73645 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
73671 TAAAAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74216 original size:16 final size:16
Alignment explanation
Indices: 74195--74259 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
74185 TAATAAATAA
74195 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
74211 ACGAACATAAGCGAAT
1 ACGAACATAAACGAAC
*
74227 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
74243 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
74259 A
1 A
74260 TAAACGTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.55, C:0.22, G:0.14, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:75333 original size:14 final size:14
Alignment explanation
Indices: 75316--75360 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
75306 GATTGGGTTA
75316 AACATAACCGAACG
1 AACATAACCGAACG
75330 AACAT-A---AACG
1 AACATAACCGAACG
75340 AACATAACCGAACG
1 AACATAACCGAACG
75354 AACATAA
1 AACATAA
75361 ACAAACATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
10 9 0.33
11 1 0.04
13 1 0.04
14 16 0.59
ACGTcount: A:0.56, C:0.24, G:0.11, T:0.09
Consensus pattern (14 bp):
AACATAACCGAACG
Found at i:75348 original size:24 final size:24
Alignment explanation
Indices: 75315--75377 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
75305 AGATTGGGTT
75315 AAACATAACCGAACGAACATAAAC
1 AAACATAACCGAACGAACATAAAC
*
75339 GAACATAACCGAACGAACATAAAC
1 AAACATAACCGAACGAACATAAAC
75363 AAACATAACCGAACG
1 AAACATAACCGAACG
75378 TTCACGAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.56, C:0.25, G:0.11, T:0.08
Consensus pattern (24 bp):
AAACATAACCGAACGAACATAAAC
Found at i:76726 original size:23 final size:21
Alignment explanation
Indices: 76699--76741 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
76689 ATATAAAAAA
76699 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
76720 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
76741 T
1 T
76742 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Done.