Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006104.1 Hibiscus syriacus cultivar Beakdansim tig00014464_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: 61612
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:6117 original size:16 final size:17
Alignment explanation
Indices: 6096--6132 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
6086 AATGAAGGAG
6096 ATTATAT-AT-TTTTTA
1 ATTATATAATGTTTTTA
6111 TATTATATAATGTTTTTA
1 -ATTATATAATGTTTTTA
6129 ATTA
1 ATTA
6133 ATTAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 6 0.32
18 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTATATAATGTTTTTA
Found at i:8883 original size:14 final size:14
Alignment explanation
Indices: 8864--8905 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
8854 AATAAAATAT
8864 AATAAAAAAATTAA
1 AATAAAAAAATTAA
*
8878 AATAAAAAAAATAA
1 AATAAAAAAATTAA
*
8892 AAAATAAAAAATTA
1 AATA-AAAAAATTA
8906 TAGCGTTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AATAAAAAAATTAA
Found at i:10560 original size:18 final size:18
Alignment explanation
Indices: 10537--10572 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10527 TGATTGATGA
*
10537 AGACGACGGGAGAGATAT
1 AGACGACGAGAGAGATAT
*
10555 AGACGACGAGAGGGATAT
1 AGACGACGAGAGAGATAT
10573 TAAAGAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.39, T:0.11
Consensus pattern (18 bp):
AGACGACGAGAGAGATAT
Found at i:14178 original size:24 final size:24
Alignment explanation
Indices: 14151--14220 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
14141 ACGGAGATAT
14151 CATAAATCAAAACAGAATTCAGAA
1 CATAAATCAAAACAGAATTCAGAA
* * * *
14175 CATATATCATAACATAA-TCTAGAT
1 CATAAATCAAAACAGAATTC-AGAA
* *
14199 CAGAAATCAGAACAGAATTCAG
1 CATAAATCAAAACAGAATTCAG
14221 GTCATGTATC
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 2 0.06
24 32 0.89
25 2 0.06
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.21
Consensus pattern (24 bp):
CATAAATCAAAACAGAATTCAGAA
Found at i:22363 original size:48 final size:48
Alignment explanation
Indices: 22306--22402 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
22296 ATATATAACT
22306 AAATTTAAAATGTTAAGAA-AAAATAAATAATTTGATAAAAAAACTTGA
1 AAATTTAAAATGTTAAGAACAAAA-AAATAATTTGATAAAAAAACTTGA
* * *
22354 AAATTTAAAATTTTAAGAACAAAAAAATAATTTGATAAACAAATTTGA
1 AAATTTAAAATGTTAAGAACAAAAAAATAATTTGATAAAAAAACTTGA
22402 A
1 A
22403 TGTTGTGCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 41 0.91
49 4 0.09
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (48 bp):
AAATTTAAAATGTTAAGAACAAAAAAATAATTTGATAAAAAAACTTGA
Found at i:23314 original size:34 final size:33
Alignment explanation
Indices: 23263--23397 Score: 101
Period size: 34 Copynumber: 3.9 Consensus size: 33
23253 AGTCGTGTCA
* *
23263 AGAAAATGA-CTCGAGTGAGACATAATTTTTCAAG
1 AGAAAAT-ATCTCAAGTGAGACAAAATTTTT-AAG
*** *
23297 AGAAAATATCTCAAGTGAGTTGAAATTTTTATTCG
1 AGAAAATATCTCAAGTGAGACAAAATTTTTA--AG
* *
23332 AGGAAACTGTCTCAAGTGAGACAAAATTTATTAAG
1 A-GAAAATATCTCAAGTGAGACAAAATTT-TTAAG
* * *
23367 AGAAAACTATCTAAAGCGAGATAAAATTTTT
1 AGAAAA-TATCTCAAGTGAGACAAAATTTTT
23398 CTTTCGAGAG
Statistics
Matches: 78, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
33 2 0.03
34 29 0.37
35 22 0.28
36 22 0.28
37 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (33 bp):
AGAAAATATCTCAAGTGAGACAAAATTTTTAAG
Found at i:23523 original size:39 final size:38
Alignment explanation
Indices: 23431--23527 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 38
23421 TGAGACAATA
** *
23431 ATAAAAATTTTGTTCCAAGAGAAACTGTCTCGAGTGAG
1 ATAAAAATTTTGTTCCAAGAGAAACAATCTCAAGTGAG
** * *
23469 A-CGAAA-CTT-TT-CAAGAGAAAGCAATCTCAATTGAG
1 ATAAAAATTTTGTTCCAAGAGAAA-CAATCTCAAGTGAG
23504 ATAAAAATTTTGTTCCAAGAGAAA
1 ATAAAAATTTTGTTCCAAGAGAAA
23528 TTTCATTTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
34 9 0.20
35 13 0.30
36 5 0.11
37 5 0.11
38 3 0.07
39 9 0.20
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (38 bp):
ATAAAAATTTTGTTCCAAGAGAAACAATCTCAAGTGAG
Found at i:23595 original size:15 final size:15
Alignment explanation
Indices: 23575--23607 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
23565 TTGGTGTTTT
23575 AAGGGAGACTATCTC
1 AAGGGAGACTATCTC
23590 AAGGGAGACTATCTC
1 AAGGGAGACTATCTC
23605 AAG
1 AAG
23608 AGAGGCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (15 bp):
AAGGGAGACTATCTC
Found at i:23725 original size:38 final size:37
Alignment explanation
Indices: 23639--23725 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 37
23629 GGGAAACAAT
* *
23639 TGTTTCAAGTA-AAACTATCTCAAGGGAGACAAATTGG
1 TGTTTCAAG-AGAAACAATCTCAAGGGAGACAAATTAG
* * * *
23676 TATTTCAAGAGAAACAATTTCAAGTGAGATAAATTTAG
1 TGTTTCAAGAGAAACAATCTCAAGGGAGACAAA-TTAG
23714 TGTTTCAAGAGA
1 TGTTTCAAGAGA
23726 CGGGATGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
36 1 0.02
37 26 0.63
38 14 0.34
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGAGAAACAATCTCAAGGGAGACAAATTAG
Found at i:27099 original size:18 final size:18
Alignment explanation
Indices: 27056--27090 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27046 ATTCCAATAC
27056 TGGAATTTCTTGAATTTA
1 TGGAATTTCTTGAATTTA
*
27074 TGGAATTTGTTGAATTT
1 TGGAATTTCTTGAATTT
27091 TTGGTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.51
Consensus pattern (18 bp):
TGGAATTTCTTGAATTTA
Found at i:28150 original size:31 final size:31
Alignment explanation
Indices: 28112--28296 Score: 289
Period size: 31 Copynumber: 6.0 Consensus size: 31
28102 TAGTCGAGGG
*
28112 TTACCTATGTTCTTCGGGACATATAGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
*
28143 TTACCTATGTTATTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
*
28174 TTACCTATGTTCTTCGGGACATATGAACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGT
* **
28205 TTACCTATGTTCTCCGGGACATATGGACAAA
1 TTACCTATGTTCTTCGGGACATATGGACAGT
* *
28236 TTACCTATGTTCTTCGGGACATATAGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGT
*
28267 TTACTTATGTTCTTCGGGACATATGGACAG
1 TTACCTATGTTCTTCGGGACATATGGACAG
28297 ATTATTATAC
Statistics
Matches: 141, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 141 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGT
Found at i:28399 original size:30 final size:30
Alignment explanation
Indices: 28363--28423 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
28353 TACCTTGAGT
28363 TCTCAGTAATGTACATGGGCTTATAAAAGA
1 TCTCAGTAATGTACATGGGCTTATAAAAGA
*
28393 TCTCAGTAATGTTCATGGGCTTATAAAAGA
1 TCTCAGTAATGTACATGGGCTTATAAAAGA
28423 T
1 T
28424 ATCAATACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (30 bp):
TCTCAGTAATGTACATGGGCTTATAAAAGA
Found at i:28441 original size:30 final size:30
Alignment explanation
Indices: 28376--28458 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
28366 CAGTAATGTA
* * *
28376 CATGGGCTTATAAAAGATCTCAGTAATGTT
1 CATGGGCTTATAAAAGATATCAATAATATT
*
28406 CATGGGCTTATAAAAGATATCAATACTATAT
1 CATGGGCTTATAAAAGATATCAATAATAT-T
* *
28437 -ATGGGCCTACAAAAGATATCAA
1 CATGGGCTTATAAAAGATATCAA
28459 ACGTATACAC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 45 0.98
31 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (30 bp):
CATGGGCTTATAAAAGATATCAATAATATT
Found at i:28912 original size:28 final size:28
Alignment explanation
Indices: 28876--28936 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
28866 ATGATTCTAT
* *
28876 ATGTCACAAATG-TTAATTGCAAGATGAC
1 ATGTCACAAA-GATTAAGTACAAGATGAC
* *
28904 ATGTTACAAAGATTAAGTACAAGATGAT
1 ATGTCACAAAGATTAAGTACAAGATGAC
28932 ATGTC
1 ATGTC
28937 TGAAATTGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (28 bp):
ATGTCACAAAGATTAAGTACAAGATGAC
Found at i:33106 original size:24 final size:24
Alignment explanation
Indices: 33079--33220 Score: 198
Period size: 24 Copynumber: 5.9 Consensus size: 24
33069 TCGATTTAAT
*
33079 TTCTGATCTGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
33103 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
33127 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
33151 TTCTGATATGATACTTGACTTAGA
1 TTCTGATATGATACTTGACATGGA
* *
33175 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
33199 TTTTGATATGATACTTGACATG
1 TTCTGATATGATACTTGACATG
33221 AATTAATATT
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
23 1 0.01
24 105 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:33131 original size:12 final size:12
Alignment explanation
Indices: 33094--33156 Score: 76
Period size: 12 Copynumber: 5.2 Consensus size: 12
33084 ATCTGATACT
33094 TGACATGGATTC
1 TGACATGGATTC
*
33106 TGATAT-GATATC
1 TGACATGGAT-TC
33118 TGACATGGATTC
1 TGACATGGATTC
*
33130 TGATAT-GATATC
1 TGACATGGAT-TC
33142 TGACATGGATTC
1 TGACATGGATTC
33154 TGA
1 TGA
33157 TATGATACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 6 0.14
12 31 0.72
13 6 0.14
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.37
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:35873 original size:7 final size:7
Alignment explanation
Indices: 35863--35950 Score: 63
Period size: 7 Copynumber: 12.0 Consensus size: 7
35853 GAGCTAAGGG
35863 GAAAAAA
1 GAAAAAA
35870 GAAAGAATA
1 GAAA-AA-A
*
35879 GAAAGAA
1 GAAAAAA
35886 GAAAAAA
1 GAAAAAA
*
35893 AAGAAAAA
1 GA-AAAAA
35901 G-AAAAA
1 GAAAAAA
35907 GAAAGAAA
1 GAAA-AAA
*
35915 -AAAGAA
1 GAAAAAA
*
35921 GAAAGAA
1 GAAAAAA
35928 GAAAAAAA
1 G-AAAAAA
*
35936 GGAAAAAT
1 -GAAAAAA
35944 GAAAAAA
1 GAAAAAA
35951 ATGAATGAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
6 8 0.12
7 30 0.46
8 21 0.32
9 6 0.09
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.02
Consensus pattern (7 bp):
GAAAAAA
Found at i:35890 original size:21 final size:21
Alignment explanation
Indices: 35866--35941 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
35856 CTAAGGGGAA
*
35866 AAAAGAAAGAATAGAAAGAAG
1 AAAAGAAAGAAAAGAAAGAAG
*
35887 AAAAAAAAGAAAAAGAAA-AAG
1 AAAAGAAAG-AAAAGAAAGAAG
*
35908 -AAAGAAAAAAGAAGAAAGAAG
1 AAAAGAAAGAA-AAGAAAGAAG
35929 AAAA-AAAGGAAAA
1 AAAAGAAA-GAAAA
35942 ATGAAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.04
20 12 0.27
21 19 0.42
22 12 0.27
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (21 bp):
AAAAGAAAGAAAAGAAAGAAG
Found at i:35936 original size:25 final size:24
Alignment explanation
Indices: 35864--35942 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
35854 AGCTAAGGGG
* *
35864 AAAAAAGAAAGAATAGAAAGAAGAA
1 AAAAAAGAAAGAAGA-AAAAAAGAA
35889 AAAAAAGAAA-AAGAAAAAGAAAGAA
1 AAAAAAGAAAGAAG-AAAA-AAAGAA
*
35914 AAAAGAAGAAAGAAGAAAAAAAGGA
1 AAAA-AAGAAAGAAGAAAAAAAGAA
35939 AAAA
1 AAAA
35943 TGAAAAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 5 0.11
25 29 0.62
26 10 0.21
27 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (24 bp):
AAAAAAGAAAGAAGAAAAAAAGAA
Found at i:37862 original size:32 final size:31
Alignment explanation
Indices: 37792--37865 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
37782 TCTACAAGCC
*
37792 TTAGAAAA-TTTGGGGACCATTCTGTAATTT
1 TTAGAAAAGTTGGGGGACCATTCTGTAATTT
*
37822 TTAAAAAAGTTGGGGGACCAATT-TGTAATTTT
1 TTAGAAAAGTTGGGGGACC-ATTCTGTAA-TTT
*
37854 TTTGAAAAGTTG
1 TTAGAAAAGTTG
37866 TAAATGGTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 7 0.19
31 14 0.38
32 16 0.43
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (31 bp):
TTAGAAAAGTTGGGGGACCATTCTGTAATTT
Found at i:39338 original size:31 final size:31
Alignment explanation
Indices: 39120--39339 Score: 316
Period size: 31 Copynumber: 7.1 Consensus size: 31
39110 GAGTCGAGGG
* **
39120 TTACCTATGTTCTTTGGGACACGTGGACA-A
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* *
39150 TTTACCTATGTTCTTCGGGACATATGAACAGT
1 -TTACCTATGTTCTTCGGGACATATGGACAGA
* *
39182 TTACCTATGTTCTTCGGGACAAATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* *
39213 TTACCTATGTTATTCGGGACATATGGACAGT
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
39244 TTACCTATGTTATTCGGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
39275 TTACCTATGTTCTTCGGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* *
39306 TTACCTATGTTCTTCGGGATATATGGATAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
39337 TTA
1 TTA
39340 TTATACGAGC
Statistics
Matches: 175, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
31 175 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGA
Found at i:39436 original size:30 final size:30
Alignment explanation
Indices: 39402--39492 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
39392 TACCTTGAGT
* *
39402 TCTCATTAATGTAGATGAGCTTATAAAAGA
1 TCTCAGTAATGTACATGAGCTTATAAAAGA
* * *
39432 TCTCAGTAATGTTCATGGGCTTATAAAATA
1 TCTCAGTAATGTACATGAGCTTATAAAAGA
* * * * * *
39462 TATCAGTACTGTATATGGGCCTACAAAAGA
1 TCTCAGTAATGTACATGAGCTTATAAAAGA
39492 T
1 T
39493 ATCAAACGTA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (30 bp):
TCTCAGTAATGTACATGAGCTTATAAAAGA
Found at i:41869 original size:36 final size:36
Alignment explanation
Indices: 41782--41898 Score: 98
Period size: 36 Copynumber: 3.3 Consensus size: 36
41772 ATCAAGCTGG
*
41782 TAATTCC-TATATAGGTTC-AGCATCGATCAACTAG
1 TAATTCCTTATATAGGTTCAAGCATCGATCAACTAA
* ** *
41816 TAATTCCTTATTGTAGGTTCAATTAT-GATTAAGCTAA
1 TAATTCCTTA-TATAGGTTCAAGCATCGATCAA-CTAA
* * * *
41853 TAATTCCTTATATAGGTTC-AGTACCGATCAGCTGA
1 TAATTCCTTATATAGGTTCAAGCATCGATCAACTAA
*
41888 TAATTTCTTAT
1 TAATTCCTTAT
41899 GAATCTAAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
34 7 0.11
35 18 0.27
36 25 0.38
37 16 0.24
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (36 bp):
TAATTCCTTATATAGGTTCAAGCATCGATCAACTAA
Found at i:43180 original size:18 final size:18
Alignment explanation
Indices: 43157--43196 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
43147 TAACCGGTAA
* *
43157 AAAAATAAAAATTTAAAT
1 AAAAATAAAAAATAAAAT
43175 AAAAATAAAAAATAAAAT
1 AAAAATAAAAAATAAAAT
43193 AAAA
1 AAAA
43197 CAAATAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATAAAAAATAAAAT
Found at i:43191 original size:12 final size:13
Alignment explanation
Indices: 43156--43196 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
43146 ATAACCGGTA
43156 AAAAAATAAAAAT
1 AAAAAATAAAAAT
**
43169 -TTAAATAAAAAT
1 AAAAAATAAAAAT
43181 AAAAAAT-AAAAT
1 AAAAAATAAAAAT
43193 AAAA
1 AAAA
43197 CAAATAATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:46258 original size:23 final size:23
Alignment explanation
Indices: 46228--46304 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
46218 CATCTTATAT
*
46228 GGCACTTCGGTGCATTTCTACAC
1 GGCACTTCGGTGCATTTCTACGC
46251 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * * *
46274 GTCACTTTGGTGTAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
46297 GGCACTTC
1 GGCACTTC
46305 AGTATATTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.16, C:0.27, G:0.23, T:0.34
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:48395 original size:34 final size:34
Alignment explanation
Indices: 48357--48478 Score: 106
Period size: 35 Copynumber: 3.5 Consensus size: 34
48347 AAATGTCTTG
* *
48357 AGTGAGACAGAATTTTTCAAGAGAAAATATCTAA
1 AGTGAGACAAAATTTTTCAAGAGAAAATATCTCA
* *
48391 AGTGAGATGAAAA--TTTCATATGAGGAAAATGTCTCA
1 AGTGAGA-CAAAATTTTTCA-A-GA-GAAAATATCTCA
*
48427 AGTGAGACAAAATTAATT-AAGAGAAAACTATCTCA
1 AGTGAGACAAAATT-TTTCAAGAGAAAA-TATCTCA
* *
48462 AGCGAGATAAAATTTTT
1 AGTGAGACAAAATTTTT
48479 GTTTTGAGAG
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
33 5 0.07
34 15 0.21
35 29 0.41
36 18 0.26
37 1 0.01
38 2 0.03
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (34 bp):
AGTGAGACAAAATTTTTCAAGAGAAAATATCTCA
Found at i:48474 original size:70 final size:70
Alignment explanation
Indices: 48345--48476 Score: 178
Period size: 70 Copynumber: 1.9 Consensus size: 70
48335 GTCGTGCCAA
** * * *
48345 GAAAATGTCTTGAGTGAGACAGAATTTTTCAAGAGAAAATATCTAAAGTGAGATGAAAATTTCAT
1 GAAAATGTCTCAAGTGAGACAAAATTATTCAAGAGAAAATATCTAAAGCGAGATGAAAATTTCAT
48410 ATGAG
66 ATGAG
*
48415 GAAAATGTCTCAAGTGAGACAAAATTAATT-AAGAGAAAACTATCTCAAGCGAGAT-AAAATTT
1 GAAAATGTCTCAAGTGAGACAAAATT-ATTCAAGAGAAAA-TATCTAAAGCGAGATGAAAATTT
48477 TTGTTTTGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
70 39 0.72
71 15 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (70 bp):
GAAAATGTCTCAAGTGAGACAAAATTATTCAAGAGAAAATATCTAAAGCGAGATGAAAATTTCAT
ATGAG
Found at i:48784 original size:51 final size:52
Alignment explanation
Indices: 48552--48883 Score: 251
Period size: 53 Copynumber: 6.2 Consensus size: 52
48542 GAGCGAGACA
* * * * *
48552 AAAC-ATTTAAAGAGAAAACAATCTCAAGCGAGAGAAAAATT-TTGTTCCAAGAG
1 AAACAATTTCAAG-GAAAACTATCTCAAG-G-GAGATAAATTAGTGTTTCAAGAG
* * * *
48605 AAATTTC-ATTTCAAGGAAAACTATATCAAGAGAGATACATTTGGTGTTTCAAGAG
1 AAA---CAATTTCAAGGAAAACTATCTCAAGGGAGATA-AATTAGTGTTTCAAGAG
* * * * ** * *
48660 AAACAATCTCAATGG-AGACTACCTTAAGGGAGGCAAACTAGTGTTTCAAGGG
1 AAACAATTTCAA-GGAAAACTATCTCAAGGGAGATAAATTAGTGTTTCAAGAG
* * * *
48712 AAACAATTCTTTCAAGGAAAACTGTCTCAAGGGAGACAAACT-GTATTTCAAGAG
1 AAACAA---TTTCAAGGAAAACTATCTCAAGGGAGATAAATTAGTGTTTCAAGAG
* * * *
48766 AAATAGTTTCAAGGAAAACAATCTCAAGTGAGATAAATTTAGTGTTTCAAGAG
1 AAACAATTTCAAGGAAAACTATCTCAAGGGAGATAAA-TTAGTGTTTCAAGAG
* * * *
48819 AAACAATCTCAAGGAAGACTATTTCAAGGGAGATAAATTGGTGTTTCAAGAG
1 AAACAATTTCAAGGAAAACTATCTCAAGGGAGATAAATTAGTGTTTCAAGAG
*
48871 AAACAATCTCAAG
1 AAACAATTTCAAG
48884 TGAGATAAAA
Statistics
Matches: 222, Mismatches: 44, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
51 27 0.12
52 48 0.22
53 68 0.31
54 21 0.09
55 50 0.23
56 8 0.04
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.25
Consensus pattern (52 bp):
AAACAATTTCAAGGAAAACTATCTCAAGGGAGATAAATTAGTGTTTCAAGAG
Found at i:48834 original size:53 final size:52
Alignment explanation
Indices: 48615--48883 Score: 263
Period size: 53 Copynumber: 5.1 Consensus size: 52
48605 AAATTTCATT
* * * *
48615 TCAAGGAAAACTATATCAAGAGAGATACATTTGGTGTTTCAAGAGAAACAATC
1 TCAAGGAAAACTATCTCAAGGGAGATA-AATTAGTGTTTCAAGAGAAACAATC
* * * ** * *
48668 TCAATGG-AGACTACCTTAAGGGAGGCAAACTAGTGTTTCAAGGGAAACAATTC
1 TCAA-GGAAAACTATCTCAAGGGAGATAAATTAGTGTTTCAAGAGAAACAA-TC
* * * * * * *
48721 TTTCAAGGAAAACTGTCTCAAGGGAGACAAACT-GTATTTCAAGAGAAATAGTT
1 --TCAAGGAAAACTATCTCAAGGGAGATAAATTAGTGTTTCAAGAGAAACAATC
* *
48774 TCAAGGAAAACAATCTCAAGTGAGATAAATTTAGTGTTTCAAGAGAAACAATC
1 TCAAGGAAAACTATCTCAAGGGAGATAAA-TTAGTGTTTCAAGAGAAACAATC
* * *
48827 TCAAGGAAGACTATTTCAAGGGAGATAAATTGGTGTTTCAAGAGAAACAATC
1 TCAAGGAAAACTATCTCAAGGGAGATAAATTAGTGTTTCAAGAGAAACAATC
48879 TCAAG
1 TCAAG
48884 TGAGATAAAA
Statistics
Matches: 174, Mismatches: 35, Indels: 15
0.78 0.16 0.07
Matches are distributed among these distances:
51 25 0.14
52 47 0.27
53 61 0.35
54 18 0.10
55 23 0.13
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.25
Consensus pattern (52 bp):
TCAAGGAAAACTATCTCAAGGGAGATAAATTAGTGTTTCAAGAGAAACAATC
Found at i:48912 original size:159 final size:160
Alignment explanation
Indices: 48613--48978 Score: 356
Period size: 159 Copynumber: 2.3 Consensus size: 160
48603 AGAAATTTCA
* * *
48613 TTTCAAGGAAAACTATATCAAGAGAGATACATTTGGTGTTTCAAGAGAAACAATCTCAATGGAGA
1 TTTCAAGGAAAACTATCTCAAGTGAGATAAATTT-GTGTTTCAAGAGAAACAATCTCAATGGAGA
* * *
48678 CTACCTTAAGGGAGGCAAACTAGTGTTTCAAGGGAAACAATTCTTTCAAGGAAAACTGTCTCAAG
65 CTACCTTAAGGGAGACAAACTAGTGTTTCAAGAGAAACAATTC-TTCAAGGAAAAATGTCTCAAG
* *
48743 GGAGACAAACTG-T-ATTTCAAGA-GAAA-TAG
129 GGAGAAAAACTGCTCAATT-AAGACGAAATTAG
*
48772 TTTCAAGGAAAACAATCTCAAGTGAGATAAATTTAGTGTTTCAAGAGAAACAATCTCAA-GGAAG
1 TTTCAAGGAAAACTATCTCAAGTGAGATAAATTT-GTGTTTCAAGAGAAACAATCTCAATGG-AG
* * * *
48836 ACTA-TTTCAAGGGAGATAAATTGGTGTTTCAAGAGAAACAA-TC-TCAAGTGAGATAAAAT-T-
64 ACTACCTT-AAGGGAGACAAACTAGTGTTTCAAGAGAAACAATTCTTCAA--G-GA-AAAATGTC
* *** * *
48896 TTATTTTGAGAAAAACTGTCTCAATTGAGACGAAATTTG
124 TCA-AGGGAGAAAAACTG-CTCAATTAAGACGAAATTAG
* *
48935 TTTCAAGGAAAACTATCTCAAGTGATATAAAATTTTTGTTTCAA
1 TTTCAAGGAAAACTATCTCAAGTGAGAT-AAATTTGTGTTTCAA
48979 TGGAAATTAT
Statistics
Matches: 171, Mismatches: 23, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
156 4 0.02
158 9 0.05
159 101 0.59
160 4 0.02
161 4 0.02
162 7 0.04
163 36 0.21
164 6 0.04
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (160 bp):
TTTCAAGGAAAACTATCTCAAGTGAGATAAATTTGTGTTTCAAGAGAAACAATCTCAATGGAGAC
TACCTTAAGGGAGACAAACTAGTGTTTCAAGAGAAACAATTCTTCAAGGAAAAATGTCTCAAGGG
AGAAAAACTGCTCAATTAAGACGAAATTAG
Found at i:48918 original size:37 final size:37
Alignment explanation
Indices: 48827--48970 Score: 112
Period size: 37 Copynumber: 3.9 Consensus size: 37
48817 AGAAACAATC
* * * * * *
48827 TCAAGGAAGACTATTTCAAGGGAGAT-AAATTGGTGTT
1 TCAAGAAAAACTATCTCAAGTGAGATAAAATT-TTATT
* *
48864 TCAAGAGAAACAATCTCAAGTGAGATAAAATTTTATT
1 TCAAGAAAAACTATCTCAAGTGAGATAAAATTTTATT
** * * ** *
48901 TTGAGAAAAACTGTCTCAATTGAGACGAAA-TTTGTT
1 TCAAGAAAAACTATCTCAAGTGAGATAAAATTTTATT
* *
48937 TCAAGGAAAACTATCTCAAGTGATATAAAATTTT
1 TCAAGAAAAACTATCTCAAGTGAGATAAAATTTT
48971 TGTTTCAATG
Statistics
Matches: 80, Mismatches: 25, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
36 27 0.34
37 48 0.60
38 5 0.06
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (37 bp):
TCAAGAAAAACTATCTCAAGTGAGATAAAATTTTATT
Found at i:48954 original size:36 final size:35
Alignment explanation
Indices: 48907--49020 Score: 104
Period size: 36 Copynumber: 3.1 Consensus size: 35
48897 TATTTTGAGA
*
48907 AAAACTGTCTCAATTGAGACGAAATTTGTTTCAAGG
1 AAAACTATCTCAA-TGAGACGAAATTTGTTTCAAGG
* **
48943 AAAACTATCTCAAGTGATATAAAATTTTTGTTTCAATGG
1 AAAACTATCTCAA-TGAGACGAAA--TTTGTTTCAA-GG
* *
48982 -AAATTATCTCGAATAAGACGAAATTTGTTTCAAGAG
1 AAAACTATCTC-AATGAGACGAAATTTGTTTCAAG-G
49018 AAA
1 AAA
49021 CAATCTTAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
35 1 0.02
36 30 0.48
37 2 0.03
38 25 0.40
39 4 0.06
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (35 bp):
AAAACTATCTCAATGAGACGAAATTTGTTTCAAGG
Found at i:49112 original size:61 final size:60
Alignment explanation
Indices: 49046--49160 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
49036 CAATGTTTTT
* *
49046 TTAAGAAAGACAAAATTATTTGGAAAATTTTAAAGATATCTTCAAGAGAGTAAAAATGATC
1 TTAAGAAAGACAAAATTATTT-GAAAATATTAAAGATATCTTCAAGAGAATAAAAATGATC
** * * * *
49107 TTAAGAAAGATGAGATTCTTTGAAAATATTGAAGATGTCTTCAAGAGAATAAAA
1 TTAAGAAAGACAAAATTATTTGAAAATATTAAAGATATCTTCAAGAGAATAAAA
49161 TAGTCTCGAG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
60 29 0.63
61 17 0.37
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.30
Consensus pattern (60 bp):
TTAAGAAAGACAAAATTATTTGAAAATATTAAAGATATCTTCAAGAGAATAAAAATGATC
Found at i:54975 original size:17 final size:17
Alignment explanation
Indices: 54950--54985 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54940 CAAACGACTC
* *
54950 AATTTACAAAATTTAAA
1 AATTAACAAAACTTAAA
54967 AATTAACAAAACTTAAA
1 AATTAACAAAACTTAAA
54984 AA
1 AA
54986 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (17 bp):
AATTAACAAAACTTAAA
Found at i:57813 original size:138 final size:136
Alignment explanation
Indices: 57315--57868 Score: 631
Period size: 138 Copynumber: 4.0 Consensus size: 136
57305 ATTTTTAGTA
* * * * * ** * * *
57315 AATTATTGAATCGAATAGTCAAAGTGGAACCTCGAGCATAAGCGGGGATCAAATAAAAAATTCTC
1 AATTATTTATTCGAATAATTAAAATGGAACCTC-AGCA-AAGCGATGACCAAATTAAAAATTCCC
* * * ** * *
57380 ATAGAA-TAAAGGACT-AG-TTATAAAATTAAACCTAAAATGGAGGCTCTAAAAAATAACATAGT
64 CTA-AATTTAAGGACTAAGCTT-T-AAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTAGT
57442 CAATTTTAACC
126 CAATTTTAACC
*
57453 AATTATTTGATTCGAATAATTTAAAATGGAACCTCGAGCAATGCGATGACCAAATTAAAAATTCC
1 AATTATTT-ATTCGAATAA-TTAAAATGGAACCTC-AGCAAAGCGATGACCAAATTAAAAATTCC
* *
57518 CCTAAATTTAAGGAC-AAGCTTGAAATTAAGCCT-AAATGGAGGCTCTAATTATTAACGTAGTC-
63 CCTAAATTTAAGGACTAAGCTTTAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTAGTCA
57580 ATTTTAACC
128 ATTTTAACC
* * * *
57589 AAATATTTATTCGAATAATTAAAATAGAACCTCAGCAAAGTGAGGACCAAATTAAAAATTCCCCT
1 AATTATTTATTCGAATAATTAAAATGGAACCTCAGCAAAGCGATGACCAAATTAAAAATTCCCCT
*
57654 AAATTTAAGGACTAAGTTTTAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTAGTCAATT
66 AAATTTAAGGACTAAGCTTTAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTAGTCAATT
57719 TTAAACC
131 TT-AACC
*
57726 AATTATTTATTTCGAATAATTAAAATGGAACCTTAGCAAAAGCGATGACCAAATTAAAAAATTCC
1 AATTATTTA-TTCGAATAATTAAAATGGAACCTCAGC-AAAGCGATGACCAAATT-AAAAATTCC
* * * * * *
57791 TCT-AATTTAAGGACTAAG-TTTAAATTAGGCCTAAAGTGGAGACTCTAATTA-TAATCCTAATT
63 CCTAAATTTAAGGACTAAGCTTTAAATTAAGCCTAAAATGGAGGCTCTAATTATTAA-CCTAGTC
*
57853 AATTTTAATC
127 AATTTTAACC
57863 AATTAT
1 AATTAT
57869 GATTTGAATC
Statistics
Matches: 364, Mismatches: 39, Indels: 27
0.85 0.09 0.06
Matches are distributed among these distances:
133 41 0.11
134 30 0.08
135 38 0.10
136 21 0.06
137 49 0.13
138 85 0.23
139 69 0.19
140 31 0.09
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (136 bp):
AATTATTTATTCGAATAATTAAAATGGAACCTCAGCAAAGCGATGACCAAATTAAAAATTCCCCT
AAATTTAAGGACTAAGCTTTAAATTAAGCCTAAAATGGAGGCTCTAATTATTAACCTAGTCAATT
TTAACC
Found at i:58253 original size:13 final size:13
Alignment explanation
Indices: 58220--58266 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
58210 TTTAAGAAAG
*
58220 AAATTAAAATAACA
1 AAATT-AAATGACA
*
58234 AAA-TAAATGGCA
1 AAATTAAATGACA
58246 AAATTAAATGACA
1 AAATTAAATGACA
58259 AACATTAA
1 AA-ATTAA
58267 GTCAATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 9 0.32
13 11 0.39
14 8 0.29
ACGTcount: A:0.64, C:0.09, G:0.06, T:0.21
Consensus pattern (13 bp):
AAATTAAATGACA
Found at i:58856 original size:11 final size:11
Alignment explanation
Indices: 58840--58871 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
58830 AAATTGTGAT
58840 CTGAACCCGAC
1 CTGAACCCGAC
58851 CTGAACCCGAC
1 CTGAACCCGAC
*
58862 CTGCACCCGA
1 CTGAACCCGA
58872 TTTGAGAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.47, G:0.19, T:0.09
Consensus pattern (11 bp):
CTGAACCCGAC
Found at i:59141 original size:27 final size:27
Alignment explanation
Indices: 59111--59163 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
59101 TATATATACC
59111 ATTGATGAAATTATAAGATT-TAATAAA
1 ATTG-TGAAATTATAAGATTATAATAAA
* * *
59138 ATTGTGAGATTTTAAGTTTATAATAA
1 ATTGTGAAATTATAAGATTATAATAA
59164 GCATACTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (27 bp):
ATTGTGAAATTATAAGATTATAATAAA
Done.