Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008846.1 Hibiscus syriacus cultivar Beakdansim tig00112053_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: 75029
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:4248 original size:30 final size:31
Alignment explanation
Indices: 4212--4278 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
4202 ATTTAAGCTA
* *
4212 AGGGACT-AAATGGAACGGATCAATAATATT
1 AGGGACTAAAATCGAACAGATCAATAATATT
* * *
4242 AGGGACTAAAATCGAATAGATTAATAATGTT
1 AGGGACTAAAATCGAACAGATCAATAATATT
4273 AGGGAC
1 AGGGAC
4279 CATTTATACT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (31 bp):
AGGGACTAAAATCGAACAGATCAATAATATT
Found at i:4390 original size:18 final size:18
Alignment explanation
Indices: 4367--4401 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4357 ACCGCATAGT
4367 TTACCCATATTAAAAAGC
1 TTACCCATATTAAAAAGC
4385 TTACCCATATTAAAAAG
1 TTACCCATATTAAAAAG
4402 TTTGACGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.29
Consensus pattern (18 bp):
TTACCCATATTAAAAAGC
Found at i:5205 original size:19 final size:20
Alignment explanation
Indices: 5183--5222 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5173 TCCATTTGTA
5183 AACCCAAA-CGCCATGAATC
1 AACCCAAAGCGCCATGAATC
*
5202 AACCCAAAGCGCCATTAATC
1 AACCCAAAGCGCCATGAATC
5222 A
1 A
5223 TGACTGTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.42, C:0.35, G:0.10, T:0.12
Consensus pattern (20 bp):
AACCCAAAGCGCCATGAATC
Found at i:10265 original size:20 final size:19
Alignment explanation
Indices: 10240--10279 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
10230 TAAACATTTT
10240 TTTCTGCCCAGTTTCAAAAC
1 TTTCTG-CCAGTTTCAAAAC
**
10260 TTTCTGGGAGTTTCAAAAC
1 TTTCTGCCAGTTTCAAAAC
10279 T
1 T
10280 ATGACCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTCTGCCAGTTTCAAAAC
Found at i:10943 original size:21 final size:20
Alignment explanation
Indices: 10919--10958 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
10909 TGGCTACAAC
*
10919 AAACTAAGCTTAGAATACTTG
1 AAACTAAGCTT-GAAAACTTG
10940 AAACTAAGCTTGAAAACTT
1 AAACTAAGCTTGAAAACTT
10959 ACAAAATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (20 bp):
AAACTAAGCTTGAAAACTTG
Found at i:12550 original size:57 final size:57
Alignment explanation
Indices: 12455--12613 Score: 237
Period size: 57 Copynumber: 2.8 Consensus size: 57
12445 CATAGTTTCC
* *
12455 AAAATCGCGTTGCGATGGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
1 AAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATTAGCGTTGCGAATTTG
* ** * *
12512 AAAATCGTGTTGCGATAACACTGTTTACCTACAGCGGTAATTAGCGTTGTGAATTTG
1 AAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATTAGCGTTGCGAATTTG
* *
12569 AAAATCGCGCTGCGATAGTACTATTTACCTACATCGGTAATTAGC
1 AAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATTAGC
12614 ATATTTCGAT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 89 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (57 bp):
AAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATTAGCGTTGCGAATTTG
Found at i:12677 original size:20 final size:20
Alignment explanation
Indices: 12654--12697 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
12644 GTAATTAGCT
12654 TTGCGAATTTGTAAATCGCG
1 TTGCGAATTTGTAAATCGCG
*
12674 TTGCGAATTTTTAAATCGCG
1 TTGCGAATTTGTAAATCGCG
12694 TTGC
1 TTGC
12698 TCCTGTGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (20 bp):
TTGCGAATTTGTAAATCGCG
Found at i:14364 original size:20 final size:20
Alignment explanation
Indices: 14339--14377 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
14329 CGGTAATTAG
14339 CGTTGCGAATTTGAAAATCT
1 CGTTGCGAATTTGAAAATCT
14359 CGTTGCGAATTTGAAAATC
1 CGTTGCGAATTTGAAAATC
14378 GCATTGCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAATCT
Found at i:14384 original size:20 final size:20
Alignment explanation
Indices: 14341--14386 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
14331 GTAATTAGCG
* *
14341 TTGCGAATTTGAAAATCTCG
1 TTGCGAATTTGAAAATCGCA
14361 TTGCGAATTTGAAAATCGCA
1 TTGCGAATTTGAAAATCGCA
14381 TTGCGA
1 TTGCGA
14387 TAGTACTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCGCA
Found at i:14394 original size:77 final size:78
Alignment explanation
Indices: 14295--14454 Score: 218
Period size: 77 Copynumber: 2.1 Consensus size: 78
14285 CACAGTTTCC
** * *
14295 AAAATCGTGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGA-A-AATC
1 AAAATCGCATTGCGATAGTACTGTTTACCTACATCGGTAATCAGCGTTGCG-ATTT-ACATAATC
*
14358 TCGTTGCGAATTT-G
64 GCGTTGCGAATTTGG
* *
14372 AAAATCGCATTGCGATAGTACTGTTTACCTACATCGGTAATCAGTGTTGCGATTTACATATTCGC
1 AAAATCGCATTGCGATAGTACTGTTTACCTACATCGGTAATCAGCGTTGCGATTTACATAATCGC
14437 GTTGCGAATTTGG
66 GTTGCGAATTTGG
14450 AAAAT
1 AAAAT
14455 GGCGCTGCGA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
75 1 0.01
76 5 0.07
77 61 0.84
78 6 0.08
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (78 bp):
AAAATCGCATTGCGATAGTACTGTTTACCTACATCGGTAATCAGCGTTGCGATTTACATAATCGC
GTTGCGAATTTGG
Found at i:14442 original size:20 final size:20
Alignment explanation
Indices: 14417--14504 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
14407 GGTAATCAGT
14417 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
** * * *
14437 GTTGCGAATTTGGAAAATGGC
1 GTTGCG-ATTTACATATTCGC
* **
14458 GCTGCGATTTACATATTATC
1 GTTGCGATTTACATATTCGC
*
14478 ATTGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
14498 GTTGCGA
1 GTTGCGA
14505 ATTTGGAAAA
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
20 36 0.72
21 14 0.28
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:14545 original size:61 final size:60
Alignment explanation
Indices: 14415--14528 Score: 156
Period size: 61 Copynumber: 1.9 Consensus size: 60
14405 TCGGTAATCA
** * *
14415 GTGTTGCGATTTACATATTCGCGTTGCGAATTTGGAAAATGGCGCTGCGATTTACATATT
1 GTGTTGCGATTTACATATTCGCGTTGCGAATTTGGAAAATCACACTGCGATTTACATACT
* * *
14475 ATCATTGCGATTTACATATTCGCGTTGCGAATTTGGAAAATCACATTGCGATTT
1 GT-GTTGCGATTTACATATTCGCGTTGCGAATTTGGAAAATCACACTGCGATTT
14529 TGGAACCTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 1 0.02
61 46 0.98
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (60 bp):
GTGTTGCGATTTACATATTCGCGTTGCGAATTTGGAAAATCACACTGCGATTTACATACT
Found at i:15323 original size:23 final size:23
Alignment explanation
Indices: 15258--15326 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
15248 CACCACAGCT
* * *
15258 CGTATAATTGCACAGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
*
15281 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
* *
15304 CGTAGAATTGCATCGTAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
15327 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:16975 original size:20 final size:20
Alignment explanation
Indices: 16950--17021 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
16940 ACAGGTTCCA
*
16950 AAATCGCAACGCAAATAGGT
1 AAATCGCAACGCAAATATGT
***
16970 AAATCGCAACATGAATATGT
1 AAATCGCAACGCAAATATGT
*
16990 AAATCGCAACG-ATAATTTGT
1 AAATCGCAACGCA-AATATGT
17010 AAATCGCAACGC
1 AAATCGCAACGC
17022 TAACTACCGA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCAAATATGT
Found at i:17200 original size:41 final size:41
Alignment explanation
Indices: 17134--17214 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
17124 TTATCGAAAC
17134 GCGATTTTCCAAATTCACAAGGCGAATA-GATAAATCGCAAT
1 GCGATTTTCCAAATTCACAAGGCGAATATG-TAAATCGCAAT
* *
17175 GCGATTTTCCAAATTCGCAATGCGAATATGTAAATCGCAA
1 GCGATTTTCCAAATTCACAAGGCGAATATGTAAATCGCAA
17215 CGATAATATG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (41 bp):
GCGATTTTCCAAATTCACAAGGCGAATATGTAAATCGCAAT
Found at i:17209 original size:21 final size:21
Alignment explanation
Indices: 17144--17229 Score: 61
Period size: 20 Copynumber: 4.2 Consensus size: 21
17134 GCGATTTTCC
* *
17144 AAATTCACAAGGCGAATA-GAT
1 AAATTCGCAATGCGAATATG-T
* * **
17165 AAA-TCGCAATGCGATTTTCC
1 AAATTCGCAATGCGAATATGT
17185 AAATTCGCAATGCGAATATGT
1 AAATTCGCAATGCGAATATGT
* **
17206 AAA-TCGCAACGATAATATGT
1 AAATTCGCAATGCGAATATGT
17226 AAAT
1 AAAT
17230 CACAACGCGA
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
20 30 0.61
21 19 0.39
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (21 bp):
AAATTCGCAATGCGAATATGT
Found at i:17214 original size:20 final size:20
Alignment explanation
Indices: 17155--17230 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
17145 AATTCACAAG
17155 GCGAATA-GATAAATCGCAAT
1 GCGAATATG-TAAATCGCAAT
* * **
17175 GCGATTTTCCAAATTCGCAAT
1 GCGAATATGTAAA-TCGCAAT
*
17196 GCGAATATGTAAATCGCAAC
1 GCGAATATGTAAATCGCAAT
**
17216 GATAATATGTAAATC
1 GCGAATATGTAAATC
17231 ACAACGCGAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (20 bp):
GCGAATATGTAAATCGCAAT
Found at i:17235 original size:20 final size:20
Alignment explanation
Indices: 17199--17236 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17189 TCGCAATGCG
*
17199 AATATGTAAATCGCAACGAT
1 AATATGTAAATCACAACGAT
17219 AATATGTAAATCACAACG
1 AATATGTAAATCACAACG
17237 CGATTTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (20 bp):
AATATGTAAATCACAACGAT
Found at i:17321 original size:57 final size:57
Alignment explanation
Indices: 17232--17415 Score: 287
Period size: 57 Copynumber: 3.2 Consensus size: 57
17222 ATGTAAATCA
* * *
17232 CAACGCGATTTTCCAAAATCGCAACGCTAATTACCGATGTAGGTAAACAGAACTATCG
1 CAACGCGATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG
* **
17290 CAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTGTTATCG
1 CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG
*
17347 CAACGCGATTTTCAAATTCGCAATGCTAATTACCGATATAGGTAAACAGTACTATCG
1 CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG
*
17404 TAACGCGATTTT
1 CAACGCGATTTT
17416 GGAAAATGTG
Statistics
Matches: 115, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
57 104 0.90
58 11 0.10
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (57 bp):
CAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG
Found at i:17435 original size:21 final size:21
Alignment explanation
Indices: 17411--17476 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
17401 TCGTAACGCG
17411 ATTTTGGAAAATGTGTTGCGA
1 ATTTTGGAAAATGTGTTGCGA
** *
17432 A-TTTACAAATTCGTGTTGCG-
1 ATTTTGGAAAAT-GTGTTGCGA
*
17452 ATTTTGGAAACTGTGTTGCGA
1 ATTTTGGAAAATGTGTTGCGA
17473 ATTT
1 ATTT
17477 ACAAATTTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (21 bp):
ATTTTGGAAAATGTGTTGCGA
Found at i:17467 original size:20 final size:20
Alignment explanation
Indices: 17408--17472 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
17398 CTATCGTAAC
17408 GCGATTTTGGAAAATGTGTT
1 GCGATTTTGGAAAATGTGTT
* ** *
17428 GCGAATTTACAAATTCGTGTT
1 GCGATTTTGGAAAAT-GTGTT
*
17449 GCGATTTTGGAAACTGTGTT
1 GCGATTTTGGAAAATGTGTT
17469 GCGA
1 GCGA
17473 ATTTACAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.37
Consensus pattern (20 bp):
GCGATTTTGGAAAATGTGTT
Found at i:17493 original size:41 final size:41
Alignment explanation
Indices: 17408--17496 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
17398 CTATCGTAAC
* *
17408 GCGATTTTGGAAAATGTGTTGCGAATTTACAAATTCGTGTT
1 GCGATTTTGGAAAATGTGTTGCGAATTTACAAATTCGCGGT
* *
17449 GCGATTTTGGAAACTGTGTTGCGAATTTACAAATTTGCGGT
1 GCGATTTTGGAAAATGTGTTGCGAATTTACAAATTCGCGGT
17490 GCGATTT
1 GCGATTT
17497 ACCTATTCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (41 bp):
GCGATTTTGGAAAATGTGTTGCGAATTTACAAATTCGCGGT
Found at i:35834 original size:31 final size:31
Alignment explanation
Indices: 35796--35871 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
35786 TTAACTCGGG
*
35796 GTGACCACATCTTAATTAAATAAAAACGAAA
1 GTGACCACATCTTAATTAAATAAAAAAGAAA
*
35827 GTGACCACATCGTAATTAAATAAAAAAGAAA
1 GTGACCACATCTTAATTAAATAAAAAAGAAA
* *
35858 GTGATCATATCTTA
1 GTGACCACATCTTA
35872 TATTGTTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (31 bp):
GTGACCACATCTTAATTAAATAAAAAAGAAA
Found at i:38437 original size:23 final size:23
Alignment explanation
Indices: 38359--38446 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
38349 AACCATAAAG
* *
38359 AACATGTCACAAGAGCAAGAGAAAA
1 AACATGTCACAATAACAA-A-AAAA
* *
38384 AACGTATCACAATAACAAAAAAA
1 AACATGTCACAATAACAAAAAAA
* *
38407 AACGTGTCACAATAACAAAGAAA
1 AACATGTCACAATAACAAAAAAA
* *
38430 AATATGTCACAAGAACA
1 AACATGTCACAATAACA
38447 TATATTCTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 39 0.72
24 1 0.02
25 14 0.26
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.12
Consensus pattern (23 bp):
AACATGTCACAATAACAAAAAAA
Found at i:38558 original size:13 final size:13
Alignment explanation
Indices: 38542--38566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38532 TATTAAAATT
38542 ATAAAATAAAAAA
1 ATAAAATAAAAAA
38555 ATAAAATAAAAA
1 ATAAAATAAAAA
38567 GAAGACGACA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
ATAAAATAAAAAA
Found at i:40396 original size:5 final size:5
Alignment explanation
Indices: 40386--40453 Score: 82
Period size: 5 Copynumber: 12.8 Consensus size: 5
40376 AACGGTCAAC
* *
40386 GGTCG GGTCG GGTCG GGTCAAT GGTCG GGTCG GGTCG GGTCG GGTCG GGTCAAC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTC--G
40440 GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC
40454 AGACCGGTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 47 0.85
7 8 0.15
ACGTcount: A:0.06, C:0.21, G:0.53, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:40411 original size:22 final size:22
Alignment explanation
Indices: 40379--40426 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
40369 AACGGTCAAC
40379 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
40401 GGTCAATGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
40423 GGTC
1 GGTC
40427 GGGTCGGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.08, C:0.21, G:0.50, T:0.21
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:40427 original size:32 final size:32
Alignment explanation
Indices: 40386--40453 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
40376 AACGGTCAAC
*
40386 GGTCGGGTCGGGTCGGGTCAATGGTCGGGTCG
1 GGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
40418 GGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
1 GGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
40450 GGTC
1 GGTC
40454 AGACCGGTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.06, C:0.21, G:0.53, T:0.21
Consensus pattern (32 bp):
GGTCGGGTCGGGTCGGGTCAACGGTCGGGTCG
Found at i:40474 original size:19 final size:19
Alignment explanation
Indices: 40452--40529 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
40442 TCGGGTCGGG
40452 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
40471 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
* *
40490 TC-GAACCGGTTGAAATCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
40509 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
40529 T
1 T
40530 TCCAGCAGCC
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
18 3 0.06
19 37 0.79
20 7 0.15
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:40525 original size:10 final size:10
Alignment explanation
Indices: 40450--40528 Score: 55
Period size: 10 Copynumber: 8.3 Consensus size: 10
40440 GGTCGGGTCG
40450 GGTCAG-ACC
1 GGTCAGAACC
40459 GGTCA-AACC
1 GGTCAGAACC
40468 GGTTCAG-ACC
1 GG-TCAGAACC
40478 GGTCA-AACC
1 GGTCAGAACC
*
40487 GATTC-GAACC
1 G-GTCAGAACC
* *
40497 GGT-TGAAATC
1 GGTCAG-AACC
40507 GGTCA-AACC
1 GGTCAGAACC
40516 GGTCAGAACC
1 GGTCAGAACC
40526 GGT
1 GGT
40529 TTCCAGCAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
9 27 0.49
10 28 0.51
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (10 bp):
GGTCAGAACC
Found at i:47721 original size:17 final size:17
Alignment explanation
Indices: 47701--47739 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
47691 GAAAGTCAAC
47701 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
47718 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
47735 AGTCA
1 GGTCA
47740 GACCGGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.23, G:0.44, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:47753 original size:9 final size:9
Alignment explanation
Indices: 47736--47803 Score: 73
Period size: 9 Copynumber: 7.2 Consensus size: 9
47726 GTCGGGTCGA
*
47736 GTCAGACCG
1 GTCAAACCG
47745 GTCAAACCG
1 GTCAAACCG
*
47754 GTTCAGACCG
1 G-TCAAACCG
47764 GTCAAACCG
1 GTCAAACCG
*
47773 GTTCAGACCG
1 G-TCAAACCG
47783 GTCAAACCG
1 GTCAAACCG
*
47792 GTTCGAACCG
1 G-TCAAACCG
47802 GT
1 GT
47804 TGAAAACCGG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
9 26 0.52
10 24 0.48
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.16
Consensus pattern (9 bp):
GTCAAACCG
Found at i:47765 original size:10 final size:10
Alignment explanation
Indices: 47737--47804 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
47727 TCGGGTCGAG
47737 TCAGACCGG-
1 TCAGACCGGT
*
47746 TCAAACCGGT
1 TCAGACCGGT
47756 TCAGACCGG-
1 TCAGACCGGT
*
47765 TCAAACCGGT
1 TCAGACCGGT
47775 TCAGACCGG-
1 TCAGACCGGT
*
47784 TCAAACCGGT
1 TCAGACCGGT
47794 TC-GAACCGGT
1 TCAG-ACCGGT
47804 T
1 T
47805 GAAAACCGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
9 24 0.49
10 25 0.51
ACGTcount: A:0.25, C:0.31, G:0.26, T:0.18
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:47803 original size:19 final size:19
Alignment explanation
Indices: 47737--47795 Score: 118
Period size: 19 Copynumber: 3.1 Consensus size: 19
47727 TCGGGTCGAG
47737 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
47756 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
47775 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
47794 TC
1 TC
47796 GAACCGGTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:48981 original size:225 final size:225
Alignment explanation
Indices: 48587--49120 Score: 680
Period size: 225 Copynumber: 2.4 Consensus size: 225
48577 ATAACATCTT
* * * * * *
48587 TTTAAAGCTGATAAGGCCTTAAAAATCCGACGATAACAAAATAGGTTAATTACTTGATTTGTTAT
1 TTTAAAGTTGATGAGACCTTAGAAATTCGACGATAACAAAATAAGTTAATTACTTGATTTGTTAT
** * * * * *
48652 CAATATTATCAACATATTAGGTAGGGCCTAAAATGTTACCAAAGTTTAATCTGATGGAGTTTTAG
66 CAATATTATCAACATATTAGGTAGCACCTAAAATATTACCAAAATTTAAGCTGATGGACTTATAG
* *
48717 AAATCTGACGACGATAAAATAGGTTAATTACTGAAACATTATCAACCATAATAACATAACAAGTA
131 AAATCTGACGACAACAAAATAGGTTAATTACTGAAACATTATCAACCATAATAACATAACAAGTA
* * *
48782 ACGCTTATTTAATGTAATAGGCAGTGTCTG
196 ACGCTTACTTAATGTAATAGGCAGAGTCTA
* *
48812 TTTAAAGTTGATGAGACCTTAGAAATTCGACGATAACAAAATAAGTTAATTACATAATTTGTTAT
1 TTTAAAGTTGATGAGACCTTAGAAATTCGACGATAACAAAATAAGTTAATTACTTGATTTGTTAT
* *
48877 CAATATTATCAACATATTAGGTAGCACTTAAAATATTACCAAAATTTAAGCTGATAGGCCTTATA
66 CAATATTATCAACATATTAGGTAGCACCTAAAATATTACCAAAATTTAAGCTGAT-GGACTTATA
* * * *
48942 -AATTC-GACGATAACAAAATATGTTAATTACTGAAAACATTATCAACCATAATAACATAACATG
130 GAAATCTGACGACAACAAAATAGGTTAATTACTG-AAACATTATCAACCATAATAACATAACAAG
* * *
49005 TAGCGCTTACTTAATGTAATATGTAGAGTCTA
194 TAACGCTTACTTAATGTAATAGGCAGAGTCTA
* * * * *
49037 TTTGAAGTTGACGGGACATTAGAAA-TCTGACGATAACAAAAT-AGATTAATTACTTGATTTATT
1 TTTAAAGTTGATGAGACCTTAGAAATTC-GACGATAACAAAATAAG-TTAATTACTTGATTTGTT
* *
49100 TTCAATATTATCAATATATTA
64 ATCAATATTATCAACATATTA
49121 CTGTATACCT
Statistics
Matches: 267, Mismatches: 38, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
224 27 0.10
225 234 0.88
226 6 0.02
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (225 bp):
TTTAAAGTTGATGAGACCTTAGAAATTCGACGATAACAAAATAAGTTAATTACTTGATTTGTTAT
CAATATTATCAACATATTAGGTAGCACCTAAAATATTACCAAAATTTAAGCTGATGGACTTATAG
AAATCTGACGACAACAAAATAGGTTAATTACTGAAACATTATCAACCATAATAACATAACAAGTA
ACGCTTACTTAATGTAATAGGCAGAGTCTA
Found at i:49215 original size:23 final size:23
Alignment explanation
Indices: 49185--49243 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
49175 CAATAGCTAG
*
49185 TTTAACGTAATAGGTA-AGATTTA
1 TTTAACGTAATAGGTAGAGA-CTA
49208 TTTAACGTAATAGGTAGAGACTA
1 TTTAACGTAATAGGTAGAGACTA
*
49231 TTTAACATAATAG
1 TTTAACGTAATAG
49244 ATAACGTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 30 0.91
24 3 0.09
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.36
Consensus pattern (23 bp):
TTTAACGTAATAGGTAGAGACTA
Found at i:49391 original size:74 final size:75
Alignment explanation
Indices: 49231--49412 Score: 224
Period size: 74 Copynumber: 2.4 Consensus size: 75
49221 GTAGAGACTA
* * * * *
49231 TTTAACATAATAGATAACGTCTATTTTATTTTATCGTTTACATTATTATTAACCTTTAAACAAAT
1 TTTAACATAATAGATAACGTCTATTTTATTTTATCGTTGAAATTATTAATAACCTTCAAACAAAA
49296 CAATAGCTAG
66 CAATAGCTAG
** * *
49306 TTTAATGTAATAGATAACGCCCATTTTATTTTATC-TTGAAATTATTAATAACCTTCAAACAAAA
1 TTTAACATAATAGATAACGTCTATTTTATTTTATCGTTGAAATTATTAATAACCTTCAAACAAAA
**
49370 CGGTAAG-TAG
66 CAAT-AGCTAG
* *
49380 TTTAACATAATAGGTATCGTCTATTTTATTTTA
1 TTTAACATAATAGATAACGTCTATTTTATTTTA
49413 ATTGGTTAAG
Statistics
Matches: 89, Mismatches: 17, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
74 56 0.63
75 33 0.37
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (75 bp):
TTTAACATAATAGATAACGTCTATTTTATTTTATCGTTGAAATTATTAATAACCTTCAAACAAAA
CAATAGCTAG
Found at i:49885 original size:2 final size:2
Alignment explanation
Indices: 49878--49908 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49868 TGGATACTTT
49878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49909 CGATACTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53958 original size:31 final size:31
Alignment explanation
Indices: 53910--53977 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
53900 TTAAAGGAGA
* * *
53910 ATAGTCTTTAACGTTATCGATTT-GTTTGATT
1 ATAGTCTCTAACATTATCG-TTTCGTTCGATT
53941 ATAGTCTCTAACATTATCGTTTCGTTCGATT
1 ATAGTCTCTAACATTATCGTTTCGTTCGATT
*
53972 TTAGTC
1 ATAGTC
53978 ATTTGATCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.49
Consensus pattern (31 bp):
ATAGTCTCTAACATTATCGTTTCGTTCGATT
Found at i:61641 original size:20 final size:20
Alignment explanation
Indices: 61617--61689 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
61607 GCAGCCTTAG
* *
61617 TGCATGGATGCACAGCAGGG
1 TGCATCGATGCACAGCAGGA
*
61637 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
61657 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
61677 TGCATCGATGCAC
1 TGCATCGATGCAC
61690 TAATTGTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.29, C:0.22, G:0.33, T:0.16
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:62436 original size:86 final size:86
Alignment explanation
Indices: 62291--62486 Score: 329
Period size: 86 Copynumber: 2.3 Consensus size: 86
62281 AGGGGATGAT
* **
62291 ACTGCTCATATGTGATGAGTCTTGACCATATAAAGGTGATAACATGGTTCCTACGTGATGAGGAA
1 ACTGCTCATATGCGATGAGTCTTGACCATATAAAGGTGATAACACAGTTCCTACGTGATGAGGAA
*
62356 AGATTGTTATCAAGGGTTGAC
66 AGATGGTTATCAAGGGTTGAC
* *
62377 ACTGCTCATATGCGATGAGTCTTGACCATATAAGGGTGATAACACAGTTCCTACGTGATGAGGAC
1 ACTGCTCATATGCGATGAGTCTTGACCATATAAAGGTGATAACACAGTTCCTACGTGATGAGGAA
*
62442 GGATGGTTATCAAGGGTTGAC
66 AGATGGTTATCAAGGGTTGAC
62463 ACTGCTCATATGCGATGAGTCTTG
1 ACTGCTCATATGCGATGAGTCTTG
62487 GCCAGGGAAT
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 103 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (86 bp):
ACTGCTCATATGCGATGAGTCTTGACCATATAAAGGTGATAACACAGTTCCTACGTGATGAGGAA
AGATGGTTATCAAGGGTTGAC
Found at i:62437 original size:43 final size:43
Alignment explanation
Indices: 62302--62438 Score: 98
Period size: 43 Copynumber: 3.2 Consensus size: 43
62292 CTGCTCATAT
* **
62302 GTGATGAGTCTTGACCATATAAAGGTGATAACATGGTTCCTAC
1 GTGATGAGTCTTGACCATATAAGGGTGATAACACAGTTCCTAC
**** *** * * * * *
62345 GTGATGAGGAAAGATTGTTATCAAGGGT--TGACACTGCTCATAT
1 GTGATGAGTCTTGA-CCATAT-AAGGGTGATAACACAGTTCCTAC
*
62388 GCGATGAGTCTTGACCATATAAGGGTGATAACACAGTTCCTAC
1 GTGATGAGTCTTGACCATATAAGGGTGATAACACAGTTCCTAC
62431 GTGATGAG
1 GTGATGAG
62439 GACGGATGGT
Statistics
Matches: 62, Mismatches: 28, Indels: 8
0.63 0.29 0.08
Matches are distributed among these distances:
41 6 0.10
42 3 0.05
43 45 0.73
44 3 0.05
45 5 0.08
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (43 bp):
GTGATGAGTCTTGACCATATAAGGGTGATAACACAGTTCCTAC
Found at i:63644 original size:14 final size:14
Alignment explanation
Indices: 63625--63656 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
63615 TGCTTCATGT
63625 ATGTATGTTGATGG
1 ATGTATGTTGATGG
*
63639 ATGTATGTTGATGT
1 ATGTATGTTGATGG
63653 ATGT
1 ATGT
63657 CTTGATCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (14 bp):
ATGTATGTTGATGG
Found at i:67685 original size:39 final size:38
Alignment explanation
Indices: 67625--67703 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 38
67615 TACCACGCCT
* *
67625 CCTCCACCACTGTGTATTCACCTCCCCCGCCACCAACA
1 CCTCCACCACCGTGTACTCACCTCCCCCGCCACCAACA
* *
67663 CCTCCACCACCCGTGTACTCACCTCCCCCGCCGCCACCA
1 CCTCCACCA-CCGTGTACTCACCTCCCCCGCCACCAACA
67702 CC
1 CC
67704 ATATCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 9 0.25
39 27 0.75
ACGTcount: A:0.18, C:0.58, G:0.09, T:0.15
Consensus pattern (38 bp):
CCTCCACCACCGTGTACTCACCTCCCCCGCCACCAACA
Found at i:67730 original size:45 final size:40
Alignment explanation
Indices: 67624--67730 Score: 119
Period size: 45 Copynumber: 2.6 Consensus size: 40
67614 TTACCACGCC
67624 TCCTCCACCA-CTGTGTATTCACCTCCCCCGCCACCAACA
1 TCCTCCACCACCTGTGTATTCACCTCCCCCGCCACCAACA
* * *
67663 -CCTCCACCACCCGTGTACTCACCTCCCCCGCCGCCACCACCATA
1 TCCTCCACCACCTGTGTATTCACCT--CCC-CCGCCACCA--ACA
*
67707 TCCTCCACCACCTGAGTATTCACC
1 TCCTCCACCACCTGTGTATTCACC
67731 ACCTCCACCT
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
38 9 0.16
39 12 0.22
41 3 0.05
42 9 0.16
44 2 0.04
45 20 0.36
ACGTcount: A:0.20, C:0.53, G:0.08, T:0.19
Consensus pattern (40 bp):
TCCTCCACCACCTGTGTATTCACCTCCCCCGCCACCAACA
Found at i:67987 original size:21 final size:21
Alignment explanation
Indices: 67949--67988 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
67939 CACCTCCGGT
*
67949 ACATTCTCCACCACCACCACC
1 ACATTCACCACCACCACCACC
* *
67970 ACATTCACCTCCAGCACCA
1 ACATTCACCACCACCACCA
67989 ATCTATCCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.53, G:0.03, T:0.15
Consensus pattern (21 bp):
ACATTCACCACCACCACCACC
Done.