Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007160.1 Hibiscus syriacus cultivar Beakdansim tig00018749_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: 61495
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7131 original size:16 final size:16
Alignment explanation
Indices: 7112--7142 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7102 ATATAAATAC
*
7112 TATATAAAATAATATG
1 TATATAAAAAAATATG
7128 TATATAAAAAAATAT
1 TATATAAAAAAATAT
7143 AAATTAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TATATAAAAAAATATG
Found at i:7945 original size:18 final size:19
Alignment explanation
Indices: 7922--7960 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
7912 GCTATATATT
7922 AAAACA-ATAAAATAAATG
1 AAAACATATAAAATAAATG
*
7940 AAAACATTTAAAATAAATG
1 AAAACATATAAAATAAATG
7959 AA
1 AA
7961 TAAATTATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAACATATAAAATAAATG
Found at i:9031 original size:16 final size:15
Alignment explanation
Indices: 9006--9041 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
8996 GGACGTGGCA
9006 GCGGTGGAGGCAGAG
1 GCGGTGGAGGCAGAG
9021 GCGGCTGGAGGCAGAG
1 GCGG-TGGAGGCAGAG
9037 GCGGT
1 GCGGT
9042 TAGGGATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.17, C:0.17, G:0.58, T:0.08
Consensus pattern (15 bp):
GCGGTGGAGGCAGAG
Found at i:9161 original size:9 final size:10
Alignment explanation
Indices: 9128--9166 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
9118 TGGGCTTGTA
9128 ATTTAATATT
1 ATTTAATATT
9138 ATTTATATATGT
1 ATTTA-ATAT-T
9150 ATTTAATA-T
1 ATTTAATATT
9159 ATTTAATA
1 ATTTAATA
9167 ATAATAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:9170 original size:3 final size:3
Alignment explanation
Indices: 9162--9231 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
9152 TTAATATATT
* *
9162 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAAA TAA TAA TTA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
9207 TAA TAA TAA T-A TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
9232 TTTATAATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 53 0.88
4 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:11424 original size:30 final size:30
Alignment explanation
Indices: 11386--11444 Score: 91
Period size: 32 Copynumber: 1.9 Consensus size: 30
11376 CATATAATAT
11386 ATATATATATATATATATATTATTCTTTTTGC
1 ATATATATATATATAT-TA-TATTCTTTTTGC
*
11418 ATATATATGTATATATTATATTCTTTT
1 ATATATATATATATATTATATTCTTTT
11445 CGTTATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 9 0.35
31 2 0.08
32 15 0.58
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (30 bp):
ATATATATATATATATTATATTCTTTTTGC
Found at i:11425 original size:2 final size:2
Alignment explanation
Indices: 11377--11405 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11367 TTCTTTAACC
11377 AT AT A- 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
11406 TATTCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14860 original size:22 final size:22
Alignment explanation
Indices: 14815--14857 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
14805 TATAAAAAAT
14815 TATTTTTATTAAATATTTTTAA
1 TATTTTTATTAAATATTTTTAA
*
14837 TATTTTTATTTAAT-TTTTTAA
1 TATTTTTATTAAATATTTTTAA
14858 ATAATTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTTATTAAATATTTTTAA
Found at i:18274 original size:21 final size:22
Alignment explanation
Indices: 18238--18279 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
18228 TGTACAGAAG
18238 TCGGTTTTCAATCCGATCCGGA
1 TCGGTTTTCAATCCGATCCGGA
*
18260 TCGGTTTT-TATCCGATCCGG
1 TCGGTTTTCAATCCGATCCGG
18280 TTTTTTCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.14, C:0.26, G:0.24, T:0.36
Consensus pattern (22 bp):
TCGGTTTTCAATCCGATCCGGA
Found at i:18310 original size:16 final size:16
Alignment explanation
Indices: 18289--18319 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18279 GTTTTTTCCC
18289 ATAAAAAAACCGGTTT
1 ATAAAAAAACCGGTTT
*
18305 ATAAAATAACCGGTT
1 ATAAAAAAACCGGTT
18320 CGGTTTCTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (16 bp):
ATAAAAAAACCGGTTT
Found at i:18392 original size:20 final size:18
Alignment explanation
Indices: 18364--18409 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
18354 TAACCGGTGT
18364 AACCGGTTTCGGTTTTAAAA
1 AACCGGTTT--GTTTTAAAA
* *
18384 AATCGGTTTTTTTTAAAA
1 AACCGGTTTGTTTTAAAA
18402 AACCGGTT
1 AACCGGTT
18410 ATAAAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
20 8 0.35
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (18 bp):
AACCGGTTTGTTTTAAAA
Found at i:19648 original size:21 final size:21
Alignment explanation
Indices: 19624--19665 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
19614 ACTTCAAGTT
19624 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
19645 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
19666 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:21983 original size:11 final size:12
Alignment explanation
Indices: 21962--22001 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
21952 TCCGGATAAA
21962 AACCGGTTTTTT
1 AACCGGTTTTTT
21974 AACCGGTTTTTTT
1 AACCGG-TTTTTT
21987 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
22001 A
1 A
22002 TCAGGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 6 0.24
15 6 0.24
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:21992 original size:15 final size:14
Alignment explanation
Indices: 21961--22000 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
21951 TTCCGGATAA
21961 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
21974 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
21987 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
22001 ATCAGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:23264 original size:20 final size:19
Alignment explanation
Indices: 23241--23286 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
23231 CGATATACCA
23241 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
23261 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
*
23281 AGTAAA
1 GGTAAA
23287 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.83
21 3 0.12
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:23431 original size:20 final size:19
Alignment explanation
Indices: 23408--23454 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
23398 CGATATAACA
23408 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
23428 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
23448 GGTAAAA
1 GGTAAAA
23455 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:23456 original size:17 final size:19
Alignment explanation
Indices: 23417--23459 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
23407 AGGTAAAAAT
23417 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
23437 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
23454 ATGATA
1 ATGATA
23460 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:32438 original size:44 final size:44
Alignment explanation
Indices: 32383--32484 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 44
32373 TTCTACTAAT
* *
32383 AAACGCAGCTAAAAGTCAAGTTATGTAGCGACG-TTT-GTATAC
1 AAACGCCGCTAAAAGTCAAGTTATATAGCGACGTTTTAGTATAC
* * * *
32425 TAAAACGCCGCTAAAGGTTAGGTTATATAGCGGCGTTTTAGTATAC
1 --AAACGCCGCTAAAAGTCAAGTTATATAGCGACGTTTTAGTATAC
32471 AAACGCCGC-AAAAG
1 AAACGCCGCTAAAAG
32485 GTTTGCCAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
43 4 0.08
44 36 0.73
45 3 0.06
46 6 0.12
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (44 bp):
AAACGCCGCTAAAAGTCAAGTTATATAGCGACGTTTTAGTATAC
Found at i:32546 original size:43 final size:43
Alignment explanation
Indices: 32499--32624 Score: 112
Period size: 43 Copynumber: 3.2 Consensus size: 43
32489 GCCAAATAGC
32499 GGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATA
1 GGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATA
*** ** **
32542 GGCG-TTTT---CCCGAA---C-C-AT--GTTTTCTATTTAGC
1 GGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATA
32574 GGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATA
1 GGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATA
32617 GGCGTTTT
1 GGCGTTTT
32625 CCCGAACCAT
Statistics
Matches: 58, Mismatches: 14, Indels: 22
0.62 0.15 0.23
Matches are distributed among these distances:
32 14 0.24
33 4 0.07
34 2 0.03
35 1 0.02
36 4 0.07
39 4 0.07
40 1 0.02
41 2 0.03
42 4 0.07
43 22 0.38
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (43 bp):
GGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATA
Found at i:32618 original size:75 final size:75
Alignment explanation
Indices: 32495--32689 Score: 318
Period size: 75 Copynumber: 2.6 Consensus size: 75
32485 GTTTGCCAAA
32495 TAGCGGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATAGGCGTTTTCCCGAACCAT
1 TAGCGGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATAGGCGTTTTCCCGAACCAT
32560 GTTTTCTATT
66 GTTTTCTATT
32570 TAGCGGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATAGGCGTTTTCCCGAACCAT
1 TAGCGGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATAGGCGTTTTCCCGAACCAT
32635 GTTTTCTATT
66 GTTTTCTATT
* * ** * * * *
32645 TAGCAGTGTTTTCAGTCACAAACGCCGCAAAAGATTTGATATTTA
1 TAGCGGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTA
32690 GCGGTGTTTT
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 112 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (75 bp):
TAGCGGCGTTTTTGGGCATAAACGCCGCAATAGGTTTGATATTTATAGGCGTTTTCCCGAACCAT
GTTTTCTATT
Found at i:32732 original size:43 final size:43
Alignment explanation
Indices: 32642--32733 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 43
32632 CATGTTTTCT
* * *
32642 ATTTAGCAGTGTTTTCAGTCACAAACGCCGCAAAAGATTTGAT
1 ATTTAGCAGTGTTTTCAGTCACAAAAGCCGCAAAAGATTGGAC
* * * * * *
32685 ATTTAGCGGTGTTTTTAGTCACAAAAGCTGCAATAGGTTGGCC
1 ATTTAGCAGTGTTTTCAGTCACAAAAGCCGCAAAAGATTGGAC
32728 ATTTAG
1 ATTTAG
32734 TGACATTTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (43 bp):
ATTTAGCAGTGTTTTCAGTCACAAAAGCCGCAAAAGATTGGAC
Found at i:33145 original size:21 final size:21
Alignment explanation
Indices: 33115--33211 Score: 140
Period size: 21 Copynumber: 4.6 Consensus size: 21
33105 ACTGCTTCTG
* *
33115 TCTCTGCTTCTCTCACTGCTC
1 TCTCTACTTCTCTCGCTGCTC
33136 TCTCTACTTCTCTCGCTGCTC
1 TCTCTACTTCTCTCGCTGCTC
*
33157 TCTCTACTTCTCTCGTTGCTC
1 TCTCTACTTCTCTCGCTGCTC
* *
33178 TCTCTACTTCTCGCGCTACTC
1 TCTCTACTTCTCTCGCTGCTC
*
33199 TCTCTGCTTCTCT
1 TCTCTACTTCTCT
33212 TGCTTCAGCT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.05, C:0.41, G:0.09, T:0.44
Consensus pattern (21 bp):
TCTCTACTTCTCTCGCTGCTC
Found at i:33217 original size:9 final size:10
Alignment explanation
Indices: 33115--33217 Score: 63
Period size: 10 Copynumber: 10.0 Consensus size: 10
33105 ACTGCTTCTG
33115 TCTCTGCTTC
1 TCTCTGCTTC
33125 TCTCACTGC-TC
1 TCT--CTGCTTC
*
33136 TCTCTACTTC
1 TCTCTGCTTC
33146 TCTC-GCTGCTC
1 TCTCTGCT--TC
*
33157 TCTCTACTTC
1 TCTCTGCTTC
33167 TCTCGTTGC-TC
1 TCTC--TGCTTC
*
33178 TCTCTACTTC
1 TCTCTGCTTC
*
33188 TCGC-GCTACTC
1 TCTCTGCT--TC
33199 TCTCTGCTTC
1 TCTCTGCTTC
33209 TCT-TGCTTC
1 TCTCTGCTTC
33218 AGCTTCGGCT
Statistics
Matches: 73, Mismatches: 8, Indels: 25
0.69 0.08 0.24
Matches are distributed among these distances:
9 15 0.21
10 25 0.34
11 22 0.30
12 11 0.15
ACGTcount: A:0.05, C:0.41, G:0.10, T:0.45
Consensus pattern (10 bp):
TCTCTGCTTC
Found at i:45188 original size:55 final size:55
Alignment explanation
Indices: 45073--45397 Score: 440
Period size: 55 Copynumber: 5.9 Consensus size: 55
45063 TATATGGTAG
* * * * *
45073 TTCATCAACTCATAATGAATTCCGTGCG--TTGCACACATCGTGCCTGTATGGTTA
1 TTCATCAACTCATGATGAATTCCGTG-GATTTGCACACATAGTGCATGTACGATTA
* * * *
45127 TTCATCAACTAATGATGAATCCCGTGGATTTGCACATATAGTGCTTGTACGATTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGATTA
*
45182 TTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATGTAC-AGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGA-TTA
* * * *
45237 TTCATCAACTCATGATGAATTTCGTGGATTTACACACATAGTGCCTGTACGGTTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGATTA
* * *
45292 TTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCATTTACAATTA
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGATTA
* *
45347 TTTATCAACTCATGATGAATTACGTGGATTTGCACACATAGTGCATGTACG
1 TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACG
45398 GTTAGTGCAT
Statistics
Matches: 240, Mismatches: 27, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
53 1 0.00
54 24 0.10
55 215 0.90
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (55 bp):
TTCATCAACTCATGATGAATTCCGTGGATTTGCACACATAGTGCATGTACGATTA
Found at i:45309 original size:165 final size:164
Alignment explanation
Indices: 45073--45401 Score: 491
Period size: 165 Copynumber: 2.0 Consensus size: 164
45063 TATATGGTAG
* * *
45073 TTCATCAACTCATAATGAATTCCGTGCGTTGCACACATCGTGCCTGTATGGTTATTCATCAACTA
1 TTCATCAACTCATAATGAATTCCGTGCGTTACACACATAGTGCCTGTACGGTTATTCATCAACTA
* *
45138 ATGATGAATCCCGTGGATTTGCACATATAGTGC-TTGTACGATTATTCATCAACTCATGATGAAT
66 ATGATGAATCCCGTGGATTTGCACACATAGTGCATT-TACAATTATTCATCAACTCATGATGAAT
*
45202 TCCATGGATTTGCACACATAGTGCATGTACAGTTA
130 TACATGGATTTGCACACATAGTGCATGTACAGTTA
* *
45237 TTCATCAACTCATGATGAATTTCGTG-GATTTACACACATAGTGCCTGTACGGTTATTCATCAAC
1 TTCATCAACTCATAATGAATTCCGTGCG--TTACACACATAGTGCCTGTACGGTTATTCATCAAC
* ** *
45301 TCATGATGAATTTCGTGGATTTGCACACATAGTGCATTTACAATTATTTATCAACTCATGATGAA
64 TAATGATGAATCCCGTGGATTTGCACACATAGTGCATTTACAATTATTCATCAACTCATGATGAA
* *
45366 TTACGTGGATTTGCACACATAGTGCATGTACGGTTA
129 TTACATGGATTTGCACACATAGTGCATGTACAGTTA
45402 GTGCATGTAT
Statistics
Matches: 148, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
163 1 0.01
164 24 0.16
165 121 0.82
166 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (164 bp):
TTCATCAACTCATAATGAATTCCGTGCGTTACACACATAGTGCCTGTACGGTTATTCATCAACTA
ATGATGAATCCCGTGGATTTGCACACATAGTGCATTTACAATTATTCATCAACTCATGATGAATT
ACATGGATTTGCACACATAGTGCATGTACAGTTA
Found at i:45500 original size:125 final size:125
Alignment explanation
Indices: 45275--45520 Score: 348
Period size: 125 Copynumber: 2.0 Consensus size: 125
45265 TTTACACACA
* * * * *
45275 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCATTT
1 TAGTGCATGTACGATTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATAT
* *
45340 ACAATTATTTATCAACTCATGATGAATTACGTGGATTTGCACACATAGTGCATGTACGGT
66 ACAATTATTCATCAACTCATGATGAATTACATGGATTTGCACACATAGTGCATGTACGGT
* ** *
45400 TAGTGCATGTATGATTATTCATCAACTCATGATGAATTCCATGGATTTGCACGTATAGTGCCTAT
1 TAGTGCATGTACGATTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATAT
** * * *
45465 ACGGTTATTCATCAACTCCTGATGAATTATATGGATTTGCACACTTAGTGCATGTA
66 ACAATTATTCATCAACTCATGATGAATTACATGGATTTGCACACATAGTGCATGTA
45521 GTACACATAG
Statistics
Matches: 105, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
125 105 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (125 bp):
TAGTGCATGTACGATTATTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCATAT
ACAATTATTCATCAACTCATGATGAATTACATGGATTTGCACACATAGTGCATGTACGGT
Found at i:50215 original size:27 final size:27
Alignment explanation
Indices: 50184--50241 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
50174 ACTTTGGGTT
50184 ATTTTACACTTCAGGAG-CATTTTGGTC
1 ATTTTACACTTC-GGAGTCATTTTGGTC
*
50211 ATTTTACACTTCGGGGTCATTTTGGTC
1 ATTTTACACTTCGGAGTCATTTTGGTC
50238 ATTT
1 ATTT
50242 CCTTTAATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (27 bp):
ATTTTACACTTCGGAGTCATTTTGGTC
Found at i:50866 original size:20 final size:20
Alignment explanation
Indices: 50841--50885 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
50831 TCGAACATTT
50841 AAACTCATTAGATCACTCTC
1 AAACTCATTAGATCACTCTC
*
50861 AAACTCATTCGATCACTCTC
1 AAACTCATTAGATCACTCTC
50881 AAACT
1 AAACT
50886 TGAATCCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (20 bp):
AAACTCATTAGATCACTCTC
Found at i:53811 original size:24 final size:25
Alignment explanation
Indices: 53784--53836 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
53774 TAGTTTTCTT
*
53784 AAGATCTATTCAGTGATGATTCCGA
1 AAGATATATTCAGTGATGATTCCGA
*
53809 AGATGATATATTCATTGATGATTCCGA
1 A-A-GATATATTCAGTGATGATTCCGA
53836 A
1 A
53837 GATGGTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 1 0.04
27 22 0.92
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (25 bp):
AAGATATATTCAGTGATGATTCCGA
Found at i:54332 original size:24 final size:24
Alignment explanation
Indices: 54304--54388 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
54294 GAATATTTTA
* *
54304 TCTGATTTCTGAT-TTGAATTTTGT
1 TCTGATTTCTGATCTAG-ATTCTGT
*
54328 TCTGATTTTTGATCTAGATTCTGT
1 TCTGATTTCTGATCTAGATTCTGT
* * * *
54352 TCTGATATATGACCTAAATTCTGT
1 TCTGATTTCTGATCTAGATTCTGT
*
54376 TTTGATTTCTGAT
1 TCTGATTTCTGAT
54389 ATCTCCGTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
24 47 0.96
25 2 0.04
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.53
Consensus pattern (24 bp):
TCTGATTTCTGATCTAGATTCTGT
Done.