Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001163.1 Hibiscus syriacus cultivar Beakdansim tig00002318_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: 88318
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2781 original size:18 final size:18
Alignment explanation
Indices: 2758--2822 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
2748 GAGTGCACAA
2758 GGAAGAAGGTTCGAGCAT
1 GGAAGAAGGTTCGAGCAT
* *
2776 GGAAGAAGGTACGAGTAT
1 GGAAGAAGGTTCGAGCAT
* * *
2794 GGAAGAAGGGTGGAGCAC
1 GGAAGAAGGTTCGAGCAT
2812 GGAAGAAGGTT
1 GGAAGAAGGTT
2823 TGAAGCTGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.35, C:0.08, G:0.43, T:0.14
Consensus pattern (18 bp):
GGAAGAAGGTTCGAGCAT
Found at i:3286 original size:3 final size:3
Alignment explanation
Indices: 3278--3303 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3268 TACAATAAAA
3278 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
3304 ATGTTCTAAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:8751 original size:53 final size:53
Alignment explanation
Indices: 8683--8786 Score: 199
Period size: 53 Copynumber: 2.0 Consensus size: 53
8673 TACATTTGGT
8683 TGTTCTCCATGATTTGAACCGGACTAATCGAGCTTGTAATAGTGTCAGCAATA
1 TGTTCTCCATGATTTGAACCGGACTAATCGAGCTTGTAATAGTGTCAGCAATA
*
8736 TGTTTTCCATGATTTGAACCGGACTAATCGAGCTTGTAATAGTGTCAGCAA
1 TGTTCTCCATGATTTGAACCGGACTAATCGAGCTTGTAATAGTGTCAGCAA
8787 AGATCCGCCA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (53 bp):
TGTTCTCCATGATTTGAACCGGACTAATCGAGCTTGTAATAGTGTCAGCAATA
Found at i:12339 original size:30 final size:31
Alignment explanation
Indices: 12303--12371 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
12293 AAATTTAGGG
*
12303 TTAAATTAGTTAAAATTTTA-AATTTTAA-AA
1 TTAAATTAATT-AAATTTTATAATTTTAATAA
* *
12333 TTAAATTAATTAATTTTTATTAATTTTAATTA
1 TTAAATTAATTAAATTTTA-TAATTTTAATAA
12365 TTAAATT
1 TTAAATT
12372 TCAATAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 7 0.21
30 10 0.30
31 8 0.24
32 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TTAAATTAATTAAATTTTATAATTTTAATAA
Found at i:12480 original size:20 final size:19
Alignment explanation
Indices: 12455--12502 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
12445 ATAAATATAT
12455 TTTTAAAAATT-CTAAAATAA
1 TTTTAAAAATTAC-AAAAT-A
*
12475 TTTTAAGAATTAACAAAATA
1 TTTTAAAAATT-ACAAAATA
12495 TTTTAAAA
1 TTTTAAAA
12503 TACTATGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 18 0.75
21 5 0.21
22 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
TTTTAAAAATTACAAAATA
Found at i:21158 original size:56 final size:55
Alignment explanation
Indices: 21068--21183 Score: 198
Period size: 56 Copynumber: 2.1 Consensus size: 55
21058 TTCCCCGTCG
*
21068 GTGGCGGCTGCGCCTGCCTGACTCGGTTTTCTGAAACCGAAATCATCTCATAAGA
1 GTGGCGGCTGCGCCTGCCTGACTCAGTTTTCTGAAACCGAAATCATCTCATAAGA
21123 GTGGTCGGCTGCGCCTGCCCT-ACTCAGTTTTCTGAAACCGAAATCATCTCATAAGA
1 GTGG-CGGCTGCGCCTG-CCTGACTCAGTTTTCTGAAACCGAAATCATCTCATAAGA
21179 GTGGC
1 GTGGC
21184 CGGGCTGGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
55 5 0.09
56 50 0.86
57 3 0.05
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.26
Consensus pattern (55 bp):
GTGGCGGCTGCGCCTGCCTGACTCAGTTTTCTGAAACCGAAATCATCTCATAAGA
Found at i:21982 original size:7 final size:7
Alignment explanation
Indices: 21967--22011 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
21957 TCATCAGAGC
21967 TTCTTCT
1 TTCTTCT
*
21974 TTCTCCT
1 TTCTTCT
21981 TT-TTCT
1 TTCTTCT
21987 TTCTTCT
1 TTCTTCT
*
21994 TTCTCCT
1 TTCTTCT
22001 TT-TTCT
1 TTCTTCT
22007 TTCTT
1 TTCTT
22012 TCTTCCATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 10 0.31
7 22 0.69
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
TTCTTCT
Found at i:22022 original size:24 final size:20
Alignment explanation
Indices: 21967--22011 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
21957 TCATCAGAGC
21967 TTCTTCTTTCTCCTTTTTCT
1 TTCTTCTTTCTCCTTTTTCT
21987 TTCTTCTTTCTCCTTTTTCT
1 TTCTTCTTTCTCCTTTTTCT
22007 TTCTT
1 TTCTT
22012 TCTTCCATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
TTCTTCTTTCTCCTTTTTCT
Found at i:24731 original size:2 final size:2
Alignment explanation
Indices: 24724--24757 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
24714 TGCATCAATA
24724 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
24758 CATGATTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26067 original size:3 final size:3
Alignment explanation
Indices: 26059--26099 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
26049 GTAGGATCTC
26059 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
26100 ATGAAATTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:31509 original size:13 final size:13
Alignment explanation
Indices: 31491--31515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31481 TCATAACCCG
31491 ACCCGACCCGTTT
1 ACCCGACCCGTTT
31504 ACCCGACCCGTT
1 ACCCGACCCGTT
31516 GACCGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:31532 original size:15 final size:15
Alignment explanation
Indices: 31508--31551 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
31498 CCGTTTACCC
31508 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
*
31523 GACCCTTTGACCGTT
1 GACCCGTTGACCGTT
31538 GACCGACGTTGACC
1 GACC--CGTTGACC
31552 AAAACTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 18 0.72
17 7 0.28
ACGTcount: A:0.16, C:0.34, G:0.25, T:0.25
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:34069 original size:23 final size:24
Alignment explanation
Indices: 34022--34112 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
34012 TCAAATTTGA
* * *
34022 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
34046 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATCTGATACTTGACCTGG
*
34069 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
34093 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
34113 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:34091 original size:47 final size:48
Alignment explanation
Indices: 34022--34112 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
34012 TCAAATTTGA
* * *
34022 ATTCTGTTATGATACCTGACCTGGATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
34069 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
34113 TTGAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:36253 original size:13 final size:13
Alignment explanation
Indices: 36227--36267 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
36217 AACCCGACCC
*
36227 GACCCGACCTGTT
1 GACCCGACCCGTT
*
36240 GACCCAACCCGTT
1 GACCCGACCCGTT
*
36253 GACCCGACTCGTT
1 GACCCGACCCGTT
36266 GA
1 GA
36268 TCGTTGACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.20, C:0.39, G:0.22, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:38843 original size:24 final size:24
Alignment explanation
Indices: 38781--38862 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
38771 AATTATGTTA
* *
38781 TGATACCTGACTTGGATTCTGATC
1 TGATACTTGACATGGATTCTGATC
38805 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACATGGATTCTGATC
* * * *
38828 TGATACATGACCTGGATTCTAATA
1 TGATACTTGACATGGATTCTGATC
38852 TGATACTTGAC
1 TGATACTTGAC
38863 TTGAATTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.42
24 29 0.58
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (24 bp):
TGATACTTGACATGGATTCTGATC
Found at i:48931 original size:25 final size:26
Alignment explanation
Indices: 48903--48951 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
48893 TGTTTGTGAT
48903 TAGTTT-GTCTTTTGTAT-TATTCAGA
1 TAGTTTAGTCTTTT-TATGTATTCAGA
*
48928 TAGTTTAGTGTTTTTATGTATTCA
1 TAGTTTAGTCTTTTTATGTATTCA
48952 TTTAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.20, C:0.06, G:0.16, T:0.57
Consensus pattern (26 bp):
TAGTTTAGTCTTTTTATGTATTCAGA
Found at i:51915 original size:106 final size:107
Alignment explanation
Indices: 51729--51942 Score: 405
Period size: 106 Copynumber: 2.0 Consensus size: 107
51719 TGTGTGTAAT
51729 CGCTACAATGGACGAACAACCCCCTGAGGTTAACACGGCTCTCCAAGAATTCCGTACACCCGAAA
1 CGCTACAATGGACGAACAACCCCCTGAGGTTAACACGGCTCTCCAAGAATTCCGTACACCCGAAA
51794 ACTGGAGTGAACTTGGTGGTATTGCTCTTCTCTCAACTCAAA
66 ACTGGAGTGAACTTGGTGGTATTGCTCTTCTCTCAACTCAAA
51836 CGCTACAATGGACG-ACAACCCCCTGAGGTTAACACGGCTCTCCAAGAATTCCGTACA-CCGAAA
1 CGCTACAATGGACGAACAACCCCCTGAGGTTAACACGGCTCTCCAAGAATTCCGTACACCCG-AA
51899 AACTGGAGTGAACTTGGTGGTATTGCTCTTCTCTCAACTCAAA
65 AACTGGAGTGAACTTGGTGGTATTGCTCTTCTCTCAACTCAAA
51942 C
1 C
51943 AACACTCAAA
Statistics
Matches: 106, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
105 3 0.03
106 89 0.84
107 14 0.13
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (107 bp):
CGCTACAATGGACGAACAACCCCCTGAGGTTAACACGGCTCTCCAAGAATTCCGTACACCCGAAA
ACTGGAGTGAACTTGGTGGTATTGCTCTTCTCTCAACTCAAA
Found at i:53455 original size:59 final size:61
Alignment explanation
Indices: 53308--53458 Score: 209
Period size: 59 Copynumber: 2.5 Consensus size: 61
53298 TCCGAAGTAC
* * * * *
53308 CAGTCCATA-GATTCCGAAGAACCTAGGCAATCAATCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAA-CAGTCCATATGTCCCGAAGAACATAGGTAAA
53370 CAGTCCATATGTCCCGAAGAACATAGGTAACAGTCCATATGTCCCGAAGAACATAGGT-AA
1 CAGTCCATATGTCCCGAAGAACATAGGTAACAGTCCATATGTCCCGAAGAACATAGGTAAA
*
53430 -AGTCCATATGTCCTGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
53459 ACCCTCGACC
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
59 28 0.34
60 2 0.02
61 26 0.32
62 25 0.30
63 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (61 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAACAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:53459 original size:29 final size:30
Alignment explanation
Indices: 53308--53458 Score: 207
Period size: 31 Copynumber: 5.0 Consensus size: 30
53298 TCCGAAGTAC
* * *
53308 CAGTCCATA-GATTCCGAAGAACCTAGGCAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAA
* *
53338 TCAATCTATATGTCCCGAAGAACATAGGTAAA
1 -CAGTCCATATGTCCCGAAGAACATAGGT-AA
53370 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
53400 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
*
53430 -AGTCCATATGTCCTGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
53459 ACCCTCGACC
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
29 28 0.25
30 32 0.29
31 47 0.43
32 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (30 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAA
Found at i:54370 original size:20 final size:20
Alignment explanation
Indices: 54329--54404 Score: 125
Period size: 20 Copynumber: 3.7 Consensus size: 20
54319 TTCGCTTGAG
*
54329 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATT-CCC-TTGAAT
54351 GGGTACCGATTCCCTTGAAT
1 GGGTACCGATTCCCTTGAAT
54371 GGGTACCGATTCCCTTGAAT
1 GGGTACCGATTCCCTTGAAT
54391 GGGTACCGATTCCC
1 GGGTACCGATTCCC
54405 CTTGCCCAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
20 40 0.75
21 3 0.06
22 10 0.19
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (20 bp):
GGGTACCGATTCCCTTGAAT
Found at i:55336 original size:16 final size:16
Alignment explanation
Indices: 55297--55339 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
55287 AGCATCAGTT
*
55297 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
55313 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
55330 CTTATCAATC
1 CTTATCAATC
55340 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:57973 original size:23 final size:23
Alignment explanation
Indices: 57932--57975 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
57922 AGTGAGGCAT
**
57932 ATAAAACATAATATTCATATAAC
1 ATAAAACATAATAAACATATAAC
*
57955 ATAAAGCATAATAAACATATA
1 ATAAAACATAATAAACATATA
57976 CCATCATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (23 bp):
ATAAAACATAATAAACATATAAC
Found at i:58252 original size:30 final size:30
Alignment explanation
Indices: 58216--58365 Score: 209
Period size: 30 Copynumber: 5.0 Consensus size: 30
58206 CCCGAAGGAC
*
58216 CAGTCCATA-GATTCCGAAGAAC-TAGGTAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAA
58245 TCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 -CAGTCCATATGTCCCGAAGAACATAGGT-AA
*
58277 CAGTCCATA--TCCTGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
58305 GCAGTCCATATGTCCCGAAGAACATAGGTAA
1 -CAGTCCATATGTCCCGAAGAACATAGGTAA
*
58336 CAATCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
58366 ACCCTCGACC
Statistics
Matches: 110, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
28 2 0.02
29 25 0.23
30 48 0.44
31 33 0.30
32 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (30 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAA
Found at i:59198 original size:21 final size:23
Alignment explanation
Indices: 59155--59198 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
59145 TTTACAATTT
*
59155 TCCTGTAGGGGGAATCGATTTCC
1 TCCTGTAGGGGGAATCGAGTTCC
59178 TCCTGT-GGGGGAATCG-GTTCC
1 TCCTGTAGGGGGAATCGAGTTCC
59199 CCTATGAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 10 0.50
23 6 0.30
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.30
Consensus pattern (23 bp):
TCCTGTAGGGGGAATCGAGTTCC
Found at i:59265 original size:22 final size:21
Alignment explanation
Indices: 59234--59292 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
59224 TCGCTTAAGG
59234 GGTATCGATTCCCCTATGAATA
1 GGTATCGATTCCCCT-TGAATA
* *
59256 GGTATAGATT-CCCTTGAATG
1 GGTATCGATTCCCCTTGAATA
*
59276 GGTACCGATTCCCCTTG
1 GGTATCGATTCCCCTTG
59293 CCCAGAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 13 0.41
21 10 0.31
22 9 0.28
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (21 bp):
GGTATCGATTCCCCTTGAATA
Found at i:65003 original size:19 final size:19
Alignment explanation
Indices: 64971--65010 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
64961 TTATAACTCA
** *
64971 AAATTCTCCGATTTATTAT
1 AAATTCTCAAATTTATAAT
64990 AAATTCTCAAATTTATAAT
1 AAATTCTCAAATTTATAAT
65009 AA
1 AA
65011 TATTATAATT
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:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (19 bp):
AAATTCTCAAATTTATAAT
Found at i:66963 original size:18 final size:17
Alignment explanation
Indices: 66936--66979 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
66926 GTTATATATG
*
66936 TCCCGTAGGACCACTACA
1 TCCCGAAGGA-CACTACA
66954 TCCCGAAGG--ACTACA
1 TCCCGAAGGACACTACA
66969 TCCCGAAGGAC
1 TCCCGAAGGAC
66980 TATTATACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 15 0.65
18 8 0.35
ACGTcount: A:0.30, C:0.36, G:0.20, T:0.14
Consensus pattern (17 bp):
TCCCGAAGGACACTACA
Found at i:66968 original size:15 final size:15
Alignment explanation
Indices: 66948--66981 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
66938 CCGTAGGACC
66948 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
66963 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
66978 ACTA
1 ACTA
66982 TTATACCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:67577 original size:64 final size:62
Alignment explanation
Indices: 67508--67663 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 62
67498 TAATGAAGGT
* * **
67508 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATGTTTTATTATTAATGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTAGATGTTTTATT-TTAA-AAG
* * *
67572 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTAGATGTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTAGATGTTTTATTTTAAAAG
* *
67634 AGTGCATCGATGCCCTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
67664 ACACCTTCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
62 2 0.03
63 27 0.35
64 47 0.61
65 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTAGATGTTTTATTTTAAAAG
Found at i:70953 original size:64 final size:64
Alignment explanation
Indices: 70801--70962 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 64
70791 TAATGAAGGT
* * * * *
70801 ATGCATCGATGCACTACTTGTGTATCGGTTCA-TAAAATGCATTCGATGTTTTATTATTAATGG
1 ATGCATCGATGCACTACCTGTGCATCGATACACTAAAATGCATTCGATGTTTTATTATTAATAG
* * * *
70864 CATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTTTATT-TTAAA
1 -ATGCATCGATGCACTACC-TGTGCATCGATACACTAAAATGCATTCGATG-TTTTATTATT--A
70926 ATAG
61 ATAG
70930 -TGCATCGATGCACTACCTGTGCATCGATACACT
1 ATGCATCGATGCACTACCTGTGCATCGATACACT
70963 TTCAAACAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
63 2 0.02
64 64 0.79
65 11 0.14
66 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATACACTAAAATGCATTCGATGTTTTATTATTAATAG
Found at i:73777 original size:21 final size:21
Alignment explanation
Indices: 73751--73907 Score: 171
Period size: 21 Copynumber: 7.6 Consensus size: 21
73741 GTTTCCAGAT
*
73751 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
73772 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
73792 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
73813 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
73834 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
73855 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
73875 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
73896 TCGCAATGCGAA
1 TCGCAATGCGAA
73908 TATGTAAATT
Statistics
Matches: 112, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
20 33 0.29
21 79 0.71
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:73796 original size:41 final size:41
Alignment explanation
Indices: 73751--73926 Score: 239
Period size: 41 Copynumber: 4.3 Consensus size: 41
73741 GTTTCCAGAT
* *
73751 TCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAA
* * *
73792 TCGCAATGCGATA-GTCGACTATCGCAATGCGAACT-TGGACTA
1 TCGCAATGCGA-ACTTCGACTATCGCAATGCGAA-TATGTA-AA
*
73834 TCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAA
*
73875 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAA
*
73916 TTGCAATGCGA
1 TCGCAATGCGA
73927 TAGTCGAAGT
Statistics
Matches: 118, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
41 83 0.70
42 35 0.30
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.23
Consensus pattern (41 bp):
TCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAA
Found at i:73845 original size:83 final size:83
Alignment explanation
Indices: 73751--73907 Score: 271
Period size: 83 Copynumber: 1.9 Consensus size: 83
73741 GTTTCCAGAT
*
73751 TCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATA-GTCGACTATC
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGA-ACGTCGACTATC
73815 GCAATGCGAACTTGGACTA
65 GCAATGCGAACTTGGACTA
* *
73834 TCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGAACTTGGACTATCG
1 TCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGAACGTCGACTATCG
73899 CAATGCGAA
66 CAATGCGAA
73908 TATGTAAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
82 1 0.01
83 69 0.99
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (83 bp):
TCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGAACGTCGACTATCG
CAATGCGAACTTGGACTA
Found at i:73946 original size:21 final size:21
Alignment explanation
Indices: 73922--74050 Score: 124
Period size: 21 Copynumber: 6.3 Consensus size: 21
73912 TAAATTGCAA
*
73922 TGCGATAGTCGAAGTTTGCGT
1 TGCGATAGTCGAAGTTCGCGT
*
73943 TGCGATAGTCGAAGTTCGCAT
1 TGCGATAGTCGAAGTTCGCGT
* *
73964 TGCGAT-TTAC-ATA-TTCGCAT
1 TGCGATAGT-CGA-AGTTCGCGT
73984 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
** * *
74005 TGCGATTTTCCAAATT--CGT
1 TGCGATAGTCGAAGTTCGCGT
*
74024 TGCGATAGTCGAAGTCCGCGT
1 TGCGATAGTCGAAGTTCGCGT
74045 TGCGAT
1 TGCGAT
74051 TTATTCCAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
19 14 0.16
20 17 0.20
21 56 0.64
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:73987 original size:41 final size:39
Alignment explanation
Indices: 73940--74053 Score: 165
Period size: 40 Copynumber: 2.8 Consensus size: 39
73930 TCGAAGTTTG
* *
73940 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTACATATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTACAAATT
*
73979 CGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATT
1 CG--TTGCGATAGTCGAAGTTCGCGTTGCGA-TTTACAAATT
*
74021 CGTTGCGATAGTCGAAGTCCGCGTTGCGATTTA
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
74054 TTCCAAATTC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
39 5 0.07
40 26 0.39
41 26 0.39
42 10 0.15
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (39 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTACAAATT
Found at i:74356 original size:128 final size:130
Alignment explanation
Indices: 74125--74362 Score: 426
Period size: 128 Copynumber: 1.8 Consensus size: 130
74115 TAGTATTCGC
74125 ATTACCACGACCACGACCACGACCCGACCCGAGAAGAGACGGACGACGACGGCGGCGGCGCGCGA
1 ATTACCACGACCACGACCACGACCCGACCCGAGAAGAGACGGACGA-GACGGCGGCGGCGCGCGA
74190 GAGTCCCCCTTGTTCTCTATCACTCAACAAGGAAGTGGGAAAGCCCAAGACGTGTCGAATACACG
65 GAGTCCCCCTTGTTCTCTATCACTCAACAAGGAAGTGGGAAAGCCCAAGACGTGTCGAATACACG
74255 T
130 T
* *
74256 ATTACCACGACCACGACCACGACCCGACCCGAGACGAGACGGACG-G-CGGCGGCGGCTCGCGAG
1 ATTACCACGACCACGACCACGACCCGACCCGAGAAGAGACGGACGAGACGGCGGCGGCGCGCGAG
*
74319 AGTCTCCCTTGTTCTCTATCACTCAACAAGGAAGTGGGAAAGCC
66 AGTCCCCCTTGTTCTCTATCACTCAACAAGGAAGTGGGAAAGCC
74363 AAGCCTTAAA
Statistics
Matches: 104, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
128 59 0.57
129 1 0.01
131 44 0.42
ACGTcount: A:0.27, C:0.33, G:0.28, T:0.13
Consensus pattern (130 bp):
ATTACCACGACCACGACCACGACCCGACCCGAGAAGAGACGGACGAGACGGCGGCGGCGCGCGAG
AGTCCCCCTTGTTCTCTATCACTCAACAAGGAAGTGGGAAAGCCCAAGACGTGTCGAATACACGT
Found at i:74967 original size:42 final size:42
Alignment explanation
Indices: 74908--75089 Score: 180
Period size: 42 Copynumber: 4.4 Consensus size: 42
74898 TGCGATTTTG
74908 GACTATCGCAA-CGAATTTAGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAAGCGAATTT-GAATAAATCGCAACGCGAACTTC
*
74950 GACTATCGCAA-CGAATTTGGA-AAATCGCAACGCGAACTTC
1 GACTATCGCAAGCGAATTTGAATAAATCGCAACGCGAACTTC
** * * * * *
74990 GACTATTACAATGCGAATATG--TAAATCACAATGTGAACTTG
1 GACTATCGCAA-GCGAATTTGAATAAATCGCAACGCGAACTTC
* *
75031 GACTATCGCAACGCGAACTTCGACT--ATCGCAACGCGAACTTC
1 GACTATCGCAA-GCGAA-TTTGAATAAATCGCAACGCGAACTTC
75073 GACTATCGCAATGCGAA
1 GACTATCGCAA-GCGAA
75090 CTTCGACTAT
Statistics
Matches: 116, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
40 28 0.24
41 31 0.27
42 56 0.48
44 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (42 bp):
GACTATCGCAAGCGAATTTGAATAAATCGCAACGCGAACTTC
Found at i:74976 original size:19 final size:19
Alignment explanation
Indices: 74912--74981 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
74902 ATTTTGGACT
*
74912 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAATTT-GGA-AA
* * **
74933 ATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAATTTGGAAA
74954 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
74973 ATCGCAACG
1 ATCGCAACG
74982 CGAACTTCGA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 17 0.45
21 14 0.37
22 1 0.03
23 6 0.16
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.20
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:75109 original size:21 final size:21
Alignment explanation
Indices: 74933--75103 Score: 172
Period size: 21 Copynumber: 8.3 Consensus size: 21
74923 TTTAGAATAA
74933 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
74954 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
74973 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
** * *
74994 ATTACAATGCGAA-TAT-GTA-A
1 ATCGCAACGCGAACT-TCG-ACT
* * * *
75014 ATCACAATGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
75035 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
75056 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
75077 ATCGCAATGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
75098 ATCGCA
1 ATCGCA
75104 TTGCGATTTA
Statistics
Matches: 123, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
19 15 0.12
20 15 0.12
21 93 0.76
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:75151 original size:21 final size:21
Alignment explanation
Indices: 75118--75337 Score: 245
Period size: 21 Copynumber: 10.6 Consensus size: 21
75108 GATTTACATA
75118 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * * *
75139 TTGGCATTACGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
75159 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
*
75180 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
75201 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
75222 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
75242 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
75263 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
75284 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
75305 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
75326 TTCGCGTTGCGA
1 TTCGCATTGCGA
75338 ATCTGGAAAC
Statistics
Matches: 168, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
20 34 0.20
21 132 0.79
22 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:75158 original size:62 final size:63
Alignment explanation
Indices: 75099--75337 Score: 260
Period size: 62 Copynumber: 3.8 Consensus size: 63
75089 ACTTCGACTA
* * * *
75099 TCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCCAAGTTGGCATTACGATAGT-CGACT
1 TCGCATTGCGATAGTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAACT
* * * *
75160 ATCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGT
1 -TCGCATTGCGATAGTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAACT
* * *
75223 TCGCATTGCGATAGT-CGACTA-TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAG
1 TCGCATTGCGATAGTAC-A-TATTCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCCAAC
75284 T
63 T
* *
75285 TCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCCAAGTTCGCGTTGCGA
1 TCGCATTGCGATAGTACATA-TTCGCATTGCGATAGTCCAAGTTCGCATTGCGA
75338 ATCTGGAAAC
Statistics
Matches: 153, Mismatches: 14, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
60 1 0.01
62 117 0.76
63 33 0.22
64 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (63 bp):
TCGCATTGCGATAGTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAACT
Found at i:75337 original size:83 final size:83
Alignment explanation
Indices: 75118--75321 Score: 372
Period size: 83 Copynumber: 2.5 Consensus size: 83
75108 GATTTACATA
* *
75118 TTCGCATTGCGATAGTCCAAGTTGGCATTACGATAGTCGACTATCGCATTGCGATTTACATATTC
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
*
75183 GCATTGCGATAGTCGAAG
66 GCATTGCGATAGTCCAAG
*
75201 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
75266 GCATTGCGATAGTCCAAG
66 GCATTGCGATAGTCCAAG
75284 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
75322 CAAGTTCGCG
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 116 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (83 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTC
GCATTGCGATAGTCCAAG
Done.