Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005103.1 Hibiscus syriacus cultivar Beakdansim tig00011472_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: 77010
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5271 original size:20 final size:20
Alignment explanation
Indices: 5234--5272 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5224 AGATTGAGTG
* * *
5234 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
5254 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
5273 AGTTTAGGAG
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:5497 original size:20 final size:20
Alignment explanation
Indices: 5423--5525 Score: 100
Period size: 20 Copynumber: 4.9 Consensus size: 20
5413 CAGAACCCCA
*
5423 GGGGGGTATCGATTCCC-CTGT
1 GGGGGG-ATCGATTCCCTC-AT
* *
5444 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGATT-CCC-TC-AT
* *
5468 GGGGGAATCGGTTCCCTCAT
1 GGGGGGATCGATTCCCTCAT
5488 GGGGGGATCGATTCCCTCAT
1 GGGGGGATCGATTCCCTCAT
5508 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
5526 TGCACCAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
20 37 0.53
21 14 0.20
22 6 0.09
23 7 0.10
24 6 0.09
ACGTcount: A:0.15, C:0.25, G:0.36, T:0.24
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAT
Found at i:14155 original size:31 final size:31
Alignment explanation
Indices: 14060--14155 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
14050 AGAGTCGAGG
*
14060 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTATGTTC-TTCGGGACATATGGACA
* ** *
14091 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
* *
14122 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
14153 GTT
1 GTT
14156 GTCGGGGTTC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 51 0.96
32 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACA
Found at i:14676 original size:11 final size:11
Alignment explanation
Indices: 14662--14696 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
14652 ATTTTATGAA
14662 AGTATTGTAGC
1 AGTATTGTAGC
14673 AGTATTGTAGC
1 AGTATTGTAGC
*
14684 AGTACTGTAGC
1 AGTATTGTAGC
14695 AG
1 AG
14697 GGAATCTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (11 bp):
AGTATTGTAGC
Found at i:16325 original size:22 final size:21
Alignment explanation
Indices: 16274--16326 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
16264 TATACTTCTT
16274 TTCCTATAATTGATACATTAA
1 TTCCTATAATTGATACATTAA
* * **
16295 TGTCATATAATTTATATTTCTAA
1 T-TCCTATAATTGATACAT-TAA
16318 TTCCTATAA
1 TTCCTATAA
16327 CATCCTCACA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 20 0.80
23 4 0.16
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (21 bp):
TTCCTATAATTGATACATTAA
Found at i:21793 original size:30 final size:31
Alignment explanation
Indices: 21754--21811 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
21744 GTTTAGATTA
*
21754 GGTTAGGGTTT-TAAATTTGGT-TTGGGCCCG
1 GGTTAGGGTTTGT-AATTGGGTATTGGGCCCG
*
21784 GGTTTGGGTTTGTAATTGGGTATTGGGC
1 GGTTAGGGTTTGTAATTGGGTATTGGGC
21812 TTGAATATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 17 0.71
31 7 0.29
ACGTcount: A:0.12, C:0.07, G:0.40, T:0.41
Consensus pattern (31 bp):
GGTTAGGGTTTGTAATTGGGTATTGGGCCCG
Found at i:22371 original size:118 final size:117
Alignment explanation
Indices: 22146--22473 Score: 469
Period size: 118 Copynumber: 2.8 Consensus size: 117
22136 CAACTTCTTA
* **
22146 TGTGATGGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATTATAAATTTTTTCTCCCTTATCGGA
1 TGTGATGGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAA-CCTTTCTCCCTTATCGGA
* * **
22211 TGAGTTCTTCTTATTACGAACCTTTCTATTGGAAATGTTGATCCACCTCCTTC
65 TGAGTTCTTCTTATTACGAACCTTTCCATTGAAAATAATGATCCACCTCCTTC
* **
22264 TGTGATGGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAACAGTTTCTCCCTTATCATA
1 TGTGATGGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAAC-CTTTCTCCCTTATCGGA
* *
22329 TGAGTTCTTCTTATTAAGAA-CTCTTCCATTGAAAATAATGATCCACCTTCTTC
65 TGAGTTCTTCTTATTACGAACCT-TTCCATTGAAAATAATGATCCACCTCCTTC
* *
22382 TATGATGGAATCGAGCTAAGGTTGAATAAGTTATTCTCATTATGAACCTCTTCTCCCTTATCGGA
1 TGTGATGGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAACCT-TTCTCCCTTATCGGA
*
22447 TGAGTTCTTCTCATTACGAACCCTTTC
65 TGAGTTCTTCTTATTACGAA-CCTTTC
22474 TCAAAAATGT
Statistics
Matches: 187, Mismatches: 18, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
117 3 0.02
118 179 0.96
119 3 0.02
120 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (117 bp):
TGTGATGGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATTATGAACCTTTCTCCCTTATCGGAT
GAGTTCTTCTTATTACGAACCTTTCCATTGAAAATAATGATCCACCTCCTTC
Found at i:33048 original size:22 final size:22
Alignment explanation
Indices: 33023--33073 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
33013 CACCACAGCT
*
33023 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
33045 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
33067 CGTAGAA
1 CGTAGAA
33074 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:33074 original size:22 final size:22
Alignment explanation
Indices: 33031--33075 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
33021 CTCGTATAAA
33031 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
33053 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
33075 T
1 T
33076 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:33345 original size:30 final size:31
Alignment explanation
Indices: 33295--33354 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
33285 TAGACATAGT
*
33295 ATTTCCATAACTTTAACACATAG-GCATATC
1 ATTTACATAACTTTAACACATAGTGCATATC
* *
33325 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATAACTTTAACACATAGTGCATAT
33355 AACTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATAACTTTAACACATAGTGCATATC
Found at i:33831 original size:66 final size:66
Alignment explanation
Indices: 33715--33864 Score: 203
Period size: 66 Copynumber: 2.3 Consensus size: 66
33705 TCTTTTTCAT
* *
33715 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACGA
33780 TGA
64 TGA
** * * *
33783 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
33847 A
66 A
*
33848 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
33865 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 22 0.30
66 33 0.45
67 7 0.09
68 12 0.16
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
A
Found at i:33874 original size:21 final size:21
Alignment explanation
Indices: 33844--33886 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
33834 ATTCATTTCG
* *
33844 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
33865 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
33886 T
1 T
33887 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:39930 original size:22 final size:22
Alignment explanation
Indices: 39905--39955 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
39895 CACCACAGCT
*
39905 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
* *
39927 CGTAGAATTGCACCGAAGTTCC
1 CGTAGAAATGCACCGAAGTGCC
39949 CGTAGAA
1 CGTAGAA
39956 TTATGTCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:39956 original size:22 final size:22
Alignment explanation
Indices: 39913--39957 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
39903 CTCGTATAAA
39913 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
39935 TGCACCGAAGTTCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
39957 T
1 T
39958 ATGTCCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:40227 original size:30 final size:31
Alignment explanation
Indices: 40177--40236 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
40167 TAGACATAGT
*
40177 ATTTCCATAACTTTAACACATAG-GCATATC
1 ATTTACATAACTTTAACACATAGTGCATATC
* *
40207 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATAACTTTAACACATAGTGCATAT
40237 AACTTTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATAACTTTAACACATAGTGCATATC
Found at i:40717 original size:68 final size:67
Alignment explanation
Indices: 40598--40750 Score: 216
Period size: 68 Copynumber: 2.3 Consensus size: 67
40588 TTTTTTTCAT
* *
40598 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT-CCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACG
40663 ATGA
64 ATGA
** * * *
40667 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCGTT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGAT
40732 GA
66 GA
*
40734 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
40751 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
67 22 0.29
68 42 0.55
69 12 0.16
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGAT
GA
Found at i:40760 original size:21 final size:21
Alignment explanation
Indices: 40730--40772 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40720 ATTCATTTCG
* *
40730 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
40751 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
40772 T
1 T
40773 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:44927 original size:6 final size:6
Alignment explanation
Indices: 44916--44943 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
44906 ATGTTGGATA
44916 TTTTGG TTTTGG TTTTGG TTTTGG TTTT
1 TTTTGG TTTTGG TTTTGG TTTTGG TTTT
44944 AAATATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (6 bp):
TTTTGG
Found at i:45330 original size:14 final size:15
Alignment explanation
Indices: 45306--45336 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
45296 ACAAGAAGAT
45306 TAATAATATAATGGA
1 TAATAATATAATGGA
45321 TAAT-ATATAATGGA
1 TAATAATATAATGGA
45335 TA
1 TA
45337 TGTAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (15 bp):
TAATAATATAATGGA
Found at i:45957 original size:16 final size:17
Alignment explanation
Indices: 45936--45968 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45926 AATCAATAAA
45936 AATATTGA-AAAATCTT
1 AATATTGATAAAATCTT
*
45952 AATATTTATAAAATCTT
1 AATATTGATAAAATCTT
45969 GTATTAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
AATATTGATAAAATCTT
Found at i:48955 original size:22 final size:22
Alignment explanation
Indices: 48921--48962 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
48911 ATAAACTTAG
48921 ATTTTTTTGCATTGTGCATTTA
1 ATTTTTTTGCATTGTGCATTTA
*
48943 ATTTTTCTT-CATTTTGCATT
1 ATTTTT-TTGCATTGTGCATT
48963 GAACTGTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.62
Consensus pattern (22 bp):
ATTTTTTTGCATTGTGCATTTA
Found at i:50197 original size:23 final size:23
Alignment explanation
Indices: 50168--50233 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
50158 ATGGTCTCAA
50168 CATATCTCAACATATTTCAACAG
1 CATATCTCAACATATTTCAACAG
* * *
50191 CATATCTTAACATATTT-GATAG
1 CATATCTCAACATATTTCAACAG
* * *
50213 CATATGTCAGCATATCTCAAC
1 CATATCTCAACATATTTCAAC
50234 GAAAAATTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (23 bp):
CATATCTCAACATATTTCAACAG
Found at i:52116 original size:15 final size:15
Alignment explanation
Indices: 52098--52267 Score: 62
Period size: 15 Copynumber: 11.3 Consensus size: 15
52088 ATATTGTCCC
52098 TTTCAACACTACCCA
1 TTTCAACACTACCCA
* * *
52113 TTTCAACATTGTCTC-
1 TTTCAACACT-ACCCA
*
52128 TTTCTACACTACCCA
1 TTTCAACACTACCCA
* *
52143 TTTCAGCATTATCCC-
1 TTTCAACACTA-CCCA
*
52158 TTTCTACACTACCCA
1 TTTCAACACTACCCA
* * * *
52173 TATCAGCATTATCCA
1 TTTCAACACTACCCA
* * * *
52188 TTTCTAGACCA-TCA
1 TTTCAACACTACCCA
* *
52202 CTTTCAGCACTATCCA
1 -TTTCAACACTACCCA
* *
52218 TTTCTACACCA-CCA
1 TTTCAACACTACCCA
* * *
52232 CTTTCAGCATTGTCCC-
1 -TTTCAACACT-ACCCA
52248 TTTCAACACTACCCA
1 TTTCAACACTACCCA
52263 TTTCA
1 TTTCA
52268 GTAGTGTCCC
Statistics
Matches: 104, Mismatches: 41, Indels: 20
0.63 0.25 0.12
Matches are distributed among these distances:
14 13 0.12
15 82 0.79
16 7 0.07
17 2 0.02
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (15 bp):
TTTCAACACTACCCA
Found at i:52191 original size:45 final size:43
Alignment explanation
Indices: 52140--52268 Score: 109
Period size: 45 Copynumber: 2.9 Consensus size: 43
52130 TCTACACTAC
* **
52140 CCATTTCAGCATTATCCCTTTCTACACTACCCATATCAGCATTA
1 CCATTTCAGCATTATCCCTTTC-ACACTACCCATTTCAGCACCA
** * *
52184 TCCATTTCTAG-ACCATCACTTTCAGCACTATCCATTTCTA-CACCA
1 -CCATTTC-AGCATTATCCCTTTCA-CACTACCCATTTC-AGCACCA
*
52229 CCACTTTCAGCATTGTCCCTTTCAACACTACCCATTTCAG
1 CCA-TTTCAGCATTATCCCTTTC-ACACTACCCATTTCAG
52269 TAGTGTCCCT
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
44 7 0.11
45 54 0.83
46 4 0.06
ACGTcount: A:0.26, C:0.36, G:0.05, T:0.33
Consensus pattern (43 bp):
CCATTTCAGCATTATCCCTTTCACACTACCCATTTCAGCACCA
Found at i:52356 original size:15 final size:15
Alignment explanation
Indices: 52314--52402 Score: 58
Period size: 15 Copynumber: 5.9 Consensus size: 15
52304 TCCATTTCTG
*
52314 CACCACCACTTTCAT
1 CACCACCACTTTCAA
**
52329 CATTATCCA-TTTCAA
1 CACCA-CCACTTTCAA
*
52344 CACCACCACTTTCAG
1 CACCACCACTTTCAA
** *
52359 CATTATCCAC-TTCTA
1 CACCA-CCACTTTCAA
52374 CACCACCACTTTCATA
1 CACCACCACTTTCA-A
*
52390 -ACAACCACTTTCA
1 CACCACCACTTTCA
52403 GTTATACCCT
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
14 7 0.13
15 40 0.73
16 8 0.15
ACGTcount: A:0.30, C:0.39, G:0.01, T:0.29
Consensus pattern (15 bp):
CACCACCACTTTCAA
Found at i:52377 original size:30 final size:30
Alignment explanation
Indices: 52053--52387 Score: 295
Period size: 30 Copynumber: 11.2 Consensus size: 30
52043 ACATTACTCA
*
52053 TTTCAGCATTATCCATTTCTACACCAACAC
1 TTTCAGCATTATCCATTTCTACACCACCAC
** * * * *
52083 TTTCAATATTGTCCCTTTCAACACTACC-C
1 TTTCAGCATTATCCATTTCTACACCACCAC
* * *
52112 ATTTCAACATTGTCTC-TTTCTACACTACC-C
1 -TTTCAGCATTATC-CATTTCTACACCACCAC
* *
52142 ATTTCAGCATTATCCCTTTCTACACTACC-C
1 -TTTCAGCATTATCCATTTCTACACCACCAC
* * *
52172 ATATCAGCATTATCCATTTCTAGACCATCAC
1 -TTTCAGCATTATCCATTTCTACACCACCAC
*
52203 TTTCAGCACTATCCATTTCTACACCACCAC
1 TTTCAGCATTATCCATTTCTACACCACCAC
* * * *
52233 TTTCAGCATTGTCCCTTTCAACACTACC-C
1 TTTCAGCATTATCCATTTCTACACCACCAC
* * * * *
52262 ATTTCAGTAGTGTCCCTTTCTACACTACC-C
1 -TTTCAGCATTATCCATTTCTACACCACCAC
* * *
52292 ATTTTAGCAGTATCCATTTCTGCACCACCAC
1 -TTTCAGCATTATCCATTTCTACACCACCAC
* *
52323 TTTCATCATTATCCATTTCAACACCACCAC
1 TTTCAGCATTATCCATTTCTACACCACCAC
*
52353 TTTCAGCATTATCCACTTCTACACCACCAC
1 TTTCAGCATTATCCATTTCTACACCACCAC
52383 TTTCA
1 TTTCA
52388 TAACAACCAC
Statistics
Matches: 257, Mismatches: 42, Indels: 12
0.83 0.14 0.04
Matches are distributed among these distances:
29 3 0.01
30 251 0.98
31 3 0.01
ACGTcount: A:0.26, C:0.35, G:0.05, T:0.35
Consensus pattern (30 bp):
TTTCAGCATTATCCATTTCTACACCACCAC
Found at i:52387 original size:120 final size:119
Alignment explanation
Indices: 52032--52376 Score: 408
Period size: 120 Copynumber: 2.9 Consensus size: 119
52022 TCTTTCTCAT
* * * * * *
52032 TGTCCCTGTCAACATTACTCATTTCAGCATTATCCATTTCTACACCAACACTTTCAAT-ATTGTC
1 TGTCCCTTTCTACACTACCCATTTCAGCATTATCCATTTCTGCACCAACACTTTC-ATCATTATC
* * * * *
52096 CCTTTCAACACTACC-CATTTCAACATTGTCTCTTTCTACACTACCCATTTCAGCAT
65 CATTTCAACACCACCAC-TTTCAGCATTGTC-CCTTCTACACTACCCATTTCAGCAG
* * * * *
52152 TATCCCTTTCTACACTACCCATATCAGCATTATCCATTTCTAG-ACCATCACTTTCAGCACTATC
1 TGTCCCTTTCTACACTACCCATTTCAGCATTATCCATTTCT-GCACCAACACTTTCATCATTATC
* * *
52216 CATTTCTACACCACCACTTTCAGCATTGTCCCTTTCAACACTACCCATTTCAGTAG
65 CATTTCAACACCACCACTTTCAGCATTGTCCC-TTCTACACTACCCATTTCAGCAG
* * *
52272 TGTCCCTTTCTACACTACCCATTTTAGCAGTATCCATTTCTGCACCACCACTTTCATCATTATCC
1 TGTCCCTTTCTACACTACCCATTTCAGCATTATCCATTTCTGCACCAACACTTTCATCATTATCC
*
52337 ATTTCAACACCACCACTTTCAGCATTATCCACTTCTACAC
66 ATTTCAACACCACCACTTTCAGCATTGTCC-CTTCTACAC
52377 CACCACTTTC
Statistics
Matches: 190, Mismatches: 29, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
119 3 0.02
120 185 0.97
121 2 0.01
ACGTcount: A:0.26, C:0.34, G:0.05, T:0.35
Consensus pattern (119 bp):
TGTCCCTTTCTACACTACCCATTTCAGCATTATCCATTTCTGCACCAACACTTTCATCATTATCC
ATTTCAACACCACCACTTTCAGCATTGTCCCTTCTACACTACCCATTTCAGCAG
Found at i:58332 original size:23 final size:23
Alignment explanation
Indices: 58280--58332 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
58270 GGAATCGATA
*
58280 CCCCCATTGAAGGGGAACTGATT
1 CCCCCTTTGAAGGGGAACTGATT
*
58303 CCCCCTTTGAATGGGAACTGATT
1 CCCCCTTTGAAGGGGAACTGATT
*
58326 CCTCCTT
1 CCCCCTT
58333 GAGGGAATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (23 bp):
CCCCCTTTGAAGGGGAACTGATT
Found at i:60143 original size:25 final size:24
Alignment explanation
Indices: 60093--60141 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
60083 AAAAAGGGGA
60093 GAAATATTAAAGTGTTTTTAAAGG
1 GAAATATTAAAGTGTTTTTAAAGG
60117 GAAATATTAAAGTGTTTTTAAAGG
1 GAAATATTAAAGTGTTTTTAAAGG
60141 G
1 G
60142 GAGAAGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (24 bp):
GAAATATTAAAGTGTTTTTAAAGG
Found at i:60558 original size:20 final size:21
Alignment explanation
Indices: 60533--60575 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
60523 CAGTATGCTC
*
60533 GGAGGGAATCGA-TACCCCTA
1 GGAGGGAACCGATTACCCCTA
*
60553 GGAGGGAACCGATTCCCCCTA
1 GGAGGGAACCGATTACCCCTA
60574 GG
1 GG
60576 GGTATCGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.26, C:0.28, G:0.33, T:0.14
Consensus pattern (21 bp):
GGAGGGAACCGATTACCCCTA
Found at i:64109 original size:21 final size:21
Alignment explanation
Indices: 64085--64126 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
64075 TAATGTAAAA
*
64085 TTATTTTTTA-TTATATTATAT
1 TTATTTTATATTTA-ATTATAT
64106 TTATTTTATATTTAATTATAT
1 TTATTTTATATTTAATTATAT
64127 GAACAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATTTTATATTTAATTATAT
Found at i:67476 original size:13 final size:14
Alignment explanation
Indices: 67450--67479 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
67440 CAATTCAAAC
67450 AATAAAAACAATTA
1 AATAAAAACAATTA
67464 AATAAAAAC-ATTA
1 AATAAAAACAATTA
67477 AAT
1 AAT
67480 GCAGACAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAAAACAATTA
Found at i:70944 original size:17 final size:17
Alignment explanation
Indices: 70909--70954 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
70899 GGCTTCATTC
* *
70909 TTTCTTTTT-TTTTCTT
1 TTTCTTTTTCTCTTCAT
70925 TTTCTTTTTCTCTTCAT
1 TTTCTTTTTCTCTTCAT
70942 TTTCTTGTTTCTC
1 TTTCTT-TTTCTC
70955 AAGCGGGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 9 0.35
17 11 0.42
18 6 0.23
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTCTTTTTCTCTTCAT
Done.