Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001877.1 Hibiscus syriacus cultivar Beakdansim tig00003813_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: 102219
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:2143 original size:113 final size:113
Alignment explanation
Indices: 1849--2457 Score: 861
Period size: 113 Copynumber: 5.5 Consensus size: 113
1839 TTGAATAAGC
* *
1849 TCTTCTTATTATGAAC-T-TTC-T-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT-G
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGG
* * * * *
1909 TAAAGGTTGATCCATTAAGTGATGAATTTGAA-CAAAGGGTTAAACAAGT
66 CAAA-GCTGATCCATCAAATGATGAA-TTCAAGCAAAGGGTTAAACAAGT
*
1958 TCTTCTCATTATGAAC-TC--CTTCCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGG
***
2020 CGCTGCTGATCCATCAAATGATGAATTCAAGCAAAGGGTTAAACAAGT
66 CAAAGCTGATCCATCAAATGATGAATTCAAGCAAAGGGTTAAACAAGT
2068 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGG
* * *
2133 CAAAGCTGATCCATCAAATGATGAGTTCAAGCAAA-AGTTGAACAAGT
66 CAAAGCTGATCCATCAAATGATGAATTCAAGCAAAGGGTTAAACAAGT
*
2180 TCTTCTTATTATGAACTTCTTCTT-C--C-TCAGATGAGTTCTTCTCATTATGAACTTTCTTTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGG
*** * *
2241 CGCTGTTGATCCATCAAATGATGAATTCAAGTAAAGGGTTAAACAAGT
66 CAAAGCTGATCCATCAAATGATGAATTCAAGCAAAGGGTTAAACAAGT
* *
2289 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGG
* *
2354 CAAAGCTGATCCATCAAATGATGAATTCAAGCAAA-AGTTGAACAAGT
66 CAAAGCTGATCCATCAAATGATGAATTCAAGCAAAGGGTTAAACAAGT
* *
2401 TCTTCTTATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
2458 CTAACTGGAA
Statistics
Matches: 448, Mismatches: 39, Indels: 23
0.88 0.08 0.05
Matches are distributed among these distances:
108 65 0.15
109 55 0.12
110 88 0.20
111 4 0.01
112 98 0.22
113 138 0.31
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGG
CAAAGCTGATCCATCAAATGATGAATTCAAGCAAAGGGTTAAACAAGT
Found at i:2255 original size:221 final size:221
Alignment explanation
Indices: 1849--2457 Score: 960
Period size: 221 Copynumber: 2.7 Consensus size: 221
1839 TTGAATAAGC
* *
1849 TCTTCTTATTATGAAC-T-TTC-TCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT-GT
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
* * * * * * *
1910 AAAGGTTGATCCATTAAGTGATGAATTTGAA-CAAAGGGTTAAACAAGTTCTTCTCATTATGAAC
66 AAA-GCTGATCCATCAAATGATGAA-TTCAAGCAAA-AGTTGAACAAGTTCTTCTTATTATGAAC
* *
1974 TCCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGGCGCTGCTGATCCATCAAAT
128 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGGCGCTGCTGATCCATCAAAT
2039 GATGAATTCAAGCAAAGGGTTAAACAAGT
193 GATGAATTCAAGCAAAGGGTTAAACAAGT
*
2068 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGG
1 TCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
*
2133 CAAAGCTGATCCATCAAATGATGAGTTCAAGCAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
65 CAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
* *
2198 CTT-CTTCCTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGGCGCTGTTGATCCATCAAATGA
130 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGGCGCTGCTGATCCATCAAATGA
*
2262 TGAATTCAAGTAAAGGGTTAAACAAGT
195 TGAATTCAAGCAAAGGGTTAAACAAGT
2289 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
2354 CAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
65 CAAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGTTGAACAAGTTCTTCTTATTATGAACTT
2419 CTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
130 C---TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
2458 CTAACTGGAA
Statistics
Matches: 360, Mismatches: 19, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
219 15 0.04
220 1 0.00
221 213 0.59
222 36 0.10
223 58 0.16
224 6 0.02
225 31 0.09
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (221 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGC
AAAGCTGATCCATCAAATGATGAATTCAAGCAAAAGTTGAACAAGTTCTTCTTATTATGAACTTC
TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGGCGCTGCTGATCCATCAAATGAT
GAATTCAAGCAAAGGGTTAAACAAGT
Found at i:3463 original size:83 final size:84
Alignment explanation
Indices: 3312--3534 Score: 412
Period size: 83 Copynumber: 2.7 Consensus size: 84
3302 TTTAGGGTTA
*
3312 TACCAAACCAGATCAGATAACTCAAAGGACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
*
3377 AAATTCAATGATTGGTTTT
66 AAATTCAAGGATTGGTTTT
3396 TACCAAACCAGATCAGATAACTCAAAGAACACTT-CAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
3460 AAATTCAAGGATTGGTTTT
66 AAATTCAAGGATTGGTTTT
*
3479 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAGCACAT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
3535 GGCATTTGTT
Statistics
Matches: 135, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
83 82 0.61
84 53 0.39
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.26
Consensus pattern (84 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
AAATTCAAGGATTGGTTTT
Found at i:4925 original size:13 final size:12
Alignment explanation
Indices: 4902--4966 Score: 69
Period size: 12 Copynumber: 5.3 Consensus size: 12
4892 CCTTGACCCC
4902 CTTTTTCTTTTTT
1 CTTTTT-TTTTTT
*
4915 CTTTCTTTTTTT
1 CTTTTTTTTTTT
4927 CTTTTCTTTTTTT
1 CTTTT-TTTTTTT
*
4940 CTTTTTTTCTTT
1 CTTTTTTTTTTT
* *
4952 -TTTCTTTTTCT
1 CTTTTTTTTTTT
4963 CTTT
1 CTTT
4967 AAGCATAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
11 8 0.18
12 19 0.43
13 17 0.39
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:4927 original size:8 final size:8
Alignment explanation
Indices: 4903--4966 Score: 80
Period size: 8 Copynumber: 8.1 Consensus size: 8
4893 CTTGACCCCC
4903 TTTTTC-T
1 TTTTTCTT
4910 TTTTTCTT
1 TTTTTCTT
4918 TCTTTT-TT
1 T-TTTTCTT
4926 TCTTTTCTT
1 T-TTTTCTT
4935 TTTTTCTT
1 TTTTTCTT
4943 TTTTTC-T
1 TTTTTCTT
4950 TTTTTCTT
1 TTTTTCTT
*
4958 TTTCTCTT
1 TTTTTCTT
4966 T
1 T
4967 AAGCATAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
7 13 0.25
8 32 0.62
9 7 0.13
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:4942 original size:21 final size:20
Alignment explanation
Indices: 4903--4962 Score: 86
Period size: 21 Copynumber: 3.0 Consensus size: 20
4893 CTTGACCCCC
*
4903 TTTTTC-TTTTTTCTTTCTT
1 TTTTTCTTTTTTTTTTTCTT
4922 TTTTTCTTTTCTTTTTTTCTT
1 TTTTTCTTTT-TTTTTTTCTT
4943 TTTTTCTTTTTTCTTTTTCT
1 TTTTTCTTTTTT-TTTTTCT
4963 CTTTAAGCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 6 0.16
20 5 0.14
21 26 0.70
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTTTCTT
Found at i:17741 original size:3 final size:3
Alignment explanation
Indices: 17735--17784 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
17725 TAATATTTAT
17735 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
17779 TAA TAA
1 TAA TAA
17785 AAAAATGAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 38 0.86
4 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:25534 original size:98 final size:98
Alignment explanation
Indices: 25365--25556 Score: 348
Period size: 98 Copynumber: 2.0 Consensus size: 98
25355 TATTGACCGA
25365 AGAACCCTAATTTTGGGAACAAAGTTGTAGGACAAATTATACATGTGGCTGGGTATCCTTGGAGG
1 AGAACCCTAATTTTGGGAACAAAGTTGTAGGACAAATTATACATGTGGCTGGGTATCCTTGGAGG
25430 ATAAATATGTAATTATCATTCTTTTAAGATAGG
66 ATAAATATGTAATTATCATTCTTTTAAGATAGG
* * * *
25463 AGAACCCTAATTTTGGGAACCAAGTTGTAGGACAAATTATACCTTTGGTTGGGTATCCTTGGAGG
1 AGAACCCTAATTTTGGGAACAAAGTTGTAGGACAAATTATACATGTGGCTGGGTATCCTTGGAGG
25528 ATAAATATGTAATTATCATTCTTTTAAGA
66 ATAAATATGTAATTATCATTCTTTTAAGA
25557 CAGTTTCATG
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (98 bp):
AGAACCCTAATTTTGGGAACAAAGTTGTAGGACAAATTATACATGTGGCTGGGTATCCTTGGAGG
ATAAATATGTAATTATCATTCTTTTAAGATAGG
Found at i:26596 original size:19 final size:18
Alignment explanation
Indices: 26572--26616 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
26562 ATATATAATG
26572 TTATTTAATAAAT-TAAATA
1 TTATTTAA-AAATATAAA-A
26591 TTATTTAAAAATATAAAA
1 TTATTTAAAAATATAAAA
26609 TATATTTA
1 T-TATTTA
26617 TAATGTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATTTAAAAATATAAAA
Found at i:27544 original size:15 final size:15
Alignment explanation
Indices: 27523--27560 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
27513 TTGAGACTTT
*
27523 ACCCGCCCCGCATCC
1 ACCCGCCCCACATCC
*
27538 GCCCGCCCCACATCC
1 ACCCGCCCCACATCC
27553 ACCCGCCC
1 ACCCGCCC
27561 AGCTAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.13, C:0.68, G:0.13, T:0.05
Consensus pattern (15 bp):
ACCCGCCCCACATCC
Found at i:29556 original size:4 final size:4
Alignment explanation
Indices: 29547--29599 Score: 61
Period size: 4 Copynumber: 13.2 Consensus size: 4
29537 ATCTTGTAGA
* ** * *
29547 TATG TATG TATG TATG TATG TATG TATG CATG TGCG CATG TATG TGTG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
29595 TATG T
1 TATG T
29600 GTGTGTATGT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.21, C:0.06, G:0.28, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:29604 original size:12 final size:12
Alignment explanation
Indices: 29547--29609 Score: 67
Period size: 12 Copynumber: 5.4 Consensus size: 12
29537 ATCTTGTAGA
*
29547 TATGTATGTATG
1 TATGTATGTGTG
*
29559 TATGTATGTATG
1 TATGTATGTGTG
* *
29571 TATGCATGTGCG
1 TATGTATGTGTG
*
29583 CATGTATGTGTG
1 TATGTATGTGTG
29595 TATG--TGTGTG
1 TATGTATGTGTG
29605 TATGT
1 TATGT
29610 TATTTGTCTA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
10 10 0.23
12 33 0.77
ACGTcount: A:0.19, C:0.05, G:0.30, T:0.46
Consensus pattern (12 bp):
TATGTATGTGTG
Found at i:56773 original size:2 final size:2
Alignment explanation
Indices: 56766--56792 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56756 TCTTGAGAAT
56766 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 T
56793 CTTAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58156 original size:47 final size:47
Alignment explanation
Indices: 58105--58203 Score: 157
Period size: 47 Copynumber: 2.1 Consensus size: 47
58095 AAGGACAAAG
58105 AAGATAGAAAATGTAGAAATTGATGTAAAAACAAA-GAGTGT-GATAGA
1 AAGATAGAAAATGTAGAAATTGATGTAAAAACAAACG-GT-TCGATAGA
*
58152 AAGATAGAAAATGTAGAAATTGGTGTAAAAACAAACGGTTCGATAGA
1 AAGATAGAAAATGTAGAAATTGATGTAAAAACAAACGGTTCGATAGA
58199 AAGAT
1 AAGAT
58204 TGAACAACGG
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
46 1 0.02
47 47 0.96
48 1 0.02
ACGTcount: A:0.52, C:0.04, G:0.23, T:0.21
Consensus pattern (47 bp):
AAGATAGAAAATGTAGAAATTGATGTAAAAACAAACGGTTCGATAGA
Found at i:58412 original size:37 final size:37
Alignment explanation
Indices: 58341--58413 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
58331 TCTTCAGTAA
* *
58341 AGTATATATGCATAAGCAGCTGTACAAAGCCAACAAT
1 AGTAAATAGGCATAAGCAGCTGTACAAAGCCAACAAT
* * *
58378 AGTAAATAGGCATAAGCAGCTTTATAAAGGCAACAA
1 AGTAAATAGGCATAAGCAGCTGTACAAAGCCAACAA
58414 CTTTTAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (37 bp):
AGTAAATAGGCATAAGCAGCTGTACAAAGCCAACAAT
Found at i:58603 original size:24 final size:24
Alignment explanation
Indices: 58576--58626 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
58566 TTTCACCGAA
58576 AATATTATTTGTGTT-AGTAATAAT
1 AATATTATTTGTGTTGA-TAATAAT
58600 AATATTATTTGTGTTGATAATAAT
1 AATATTATTTGTGTTGATAATAAT
58624 AAT
1 AAT
58627 GGTAATAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (24 bp):
AATATTATTTGTGTTGATAATAAT
Found at i:60523 original size:31 final size:32
Alignment explanation
Indices: 60462--60520 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
60452 GTTTCAAAAA
* *
60462 TTATAAAATAGTCATTAAATTTTATCAAATTG
1 TTATAAAATAGTCATTAAATCTAATCAAATTG
*
60494 TTAT-AAATCGTCATTAAA-CTAATCAAA
1 TTATAAAATAGTCATTAAATCTAATCAAA
60521 ATTTATCCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.29
31 13 0.54
32 4 0.17
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (32 bp):
TTATAAAATAGTCATTAAATCTAATCAAATTG
Found at i:67289 original size:20 final size:20
Alignment explanation
Indices: 67209--67309 Score: 76
Period size: 21 Copynumber: 5.0 Consensus size: 20
67199 CGCAAATCAG
67209 TTTCCAAATCGCAACGCGAT
1 TTTCCAAATCGCAACGCGAT
** *
67229 TCTTTAAAATCGCAATGCGAT
1 T-TTCCAAATCGCAACGCGAT
** * **
67250 AGTACAAATTCGCATTGCGAT
1 TTTCCAAA-TCGCAACGCGAT
*
67271 TTTCCAAATCGCAACGCGAA
1 TTTCCAAATCGCAACGCGAT
* **
67291 TATGAAAATCGCAACGCGA
1 TTTCCAAATCGCAACGCGA
67310 ACACATAAAT
Statistics
Matches: 62, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 30 0.48
21 32 0.52
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (20 bp):
TTTCCAAATCGCAACGCGAT
Found at i:67310 original size:20 final size:20
Alignment explanation
Indices: 67276--67470 Score: 78
Period size: 20 Copynumber: 9.7 Consensus size: 20
67266 GCGATTTTCC
* *
67276 AAATCGCAACGCGAATATGA-
1 AAATCGCAACGCGAACA-CAT
67296 AAATCGCAACGCGAACACAT
1 AAATCGCAACGCGAACACAT
* *
67316 AAATCGCAACGCGTATC-CGT
1 AAATCGCAACGCG-AACACAT
* * *
67336 AAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCG-AACACAT
* ****
67356 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAACACAT
* * *
67376 AAATCGCAATGCGTATC-CGT
1 AAATCGCAACGCG-AACACAT
* * *
67396 ATATCGCAACGCGTATC-CGT
1 AAATCGCAACGCG-AACACAT
** *
67416 AAATCGCAACGATAATACAT
1 AAATCGCAACGCGAACACAT
* *
67436 AAAATCGCAACGCGTATC-CGT
1 -AAATCGCAACGCG-AACACAT
67457 AAATCGCAACGCGA
1 AAATCGCAACGCGA
67471 TATTTAAAGC
Statistics
Matches: 140, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 121 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAACACAT
Found at i:67320 original size:40 final size:39
Alignment explanation
Indices: 67276--67470 Score: 201
Period size: 40 Copynumber: 4.9 Consensus size: 39
67266 GCGATTTTCC
* ** *
67276 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * *
67316 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
67356 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* ** *
67396 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
67436 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
67471 TATTTAAAGC
Statistics
Matches: 129, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 95 0.74
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:67360 original size:60 final size:60
Alignment explanation
Indices: 67276--67469 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
67266 GCGATTTTCC
* ** * *
67276 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
67336 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
67396 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
67457 AAATCGCAACGCG
1 AAATCGCAACGCG
67470 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:67888 original size:33 final size:33
Alignment explanation
Indices: 67849--67919 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
67839 TTCACTTAGA
*
67849 TTTCATTTCGCGTTACAATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACAATTCTCTCGTTGCGAT
* *
67882 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACAATTCTCTCGTTGCGAT
67915 TTTCA
1 TTTCA
67920 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACAATTCTCTCGTTGCGAT
Found at i:68043 original size:20 final size:20
Alignment explanation
Indices: 67999--68108 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
67989 TGCAGAAGAG
*
67999 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
68020 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
68040 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
68061 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
68075 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
68094 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
68109 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:68056 original size:41 final size:38
Alignment explanation
Indices: 67992--68108 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
67982 TTCAATTTGC
* *
67992 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
68030 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
68071 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
68104 AGAAT
1 AGAAT
68109 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:68078 original size:14 final size:14
Alignment explanation
Indices: 68059--68115 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
68049 GAGAAATGAA
68059 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
68073 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
68092 AATCGCAACGAGAG
1 AATCGCAACGAGAG
68106 AATCGCAACG
1 AATCGCAACG
68116 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:68091 original size:33 final size:33
Alignment explanation
Indices: 68051--68131 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
68041 CGCAACGAGA
68051 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
68084 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
68117 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
68132 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:68216 original size:19 final size:17
Alignment explanation
Indices: 68127--68240 Score: 79
Period size: 14 Copynumber: 7.1 Consensus size: 17
68117 GAAACCAAAA
*
68127 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCA-T
68146 TCGCGTTGCGA-TTC--
1 TCGCGTTGCGATTTCAT
68160 T--CGTTGCGATTTCAT
1 TCGCGTTGCGATTTCAT
68175 TCGCGTTGCGA-TTC--
1 TCGCGTTGCGATTTCAT
*
68189 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATT-TCA-T
68208 TCGCGTTGCGA-TTC--
1 TCGCGTTGCGATTTCAT
*
68222 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGA-TTTCAT
68240 T
1 T
68241 TCAACCAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 29
0.70 0.04 0.26
Matches are distributed among these distances:
12 8 0.10
13 3 0.04
14 21 0.27
15 2 0.03
16 8 0.10
17 13 0.17
18 2 0.03
19 20 0.26
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.44
Consensus pattern (17 bp):
TCGCGTTGCGATTTCAT
Found at i:68216 original size:33 final size:33
Alignment explanation
Indices: 68132--68242 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
68122 CAAAATCGCA
68132 TTGCGATTTTCATTTCGCGTTGCGA-T-TCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
68163 TTGCGA-TTTCA-TTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
68194 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
68227 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
68243 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
29 12 0.16
30 6 0.08
31 17 0.23
32 4 0.05
33 35 0.47
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:69919 original size:93 final size:93
Alignment explanation
Indices: 69760--70016 Score: 514
Period size: 93 Copynumber: 2.8 Consensus size: 93
69750 TAGATTGCTT
69760 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
69825 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
69853 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
69918 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
69946 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
70011 TTTGTC
66 TTTGTC
70017 AAGTTTTCAA
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 164 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:70094 original size:19 final size:19
Alignment explanation
Indices: 70054--70182 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
70044 TAGTTTACTT
* *
70054 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
70074 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
70093 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
70112 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
70126 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
70145 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
70159 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
70178 TCGCA
1 TCGCA
70183 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:70133 original size:33 final size:32
Alignment explanation
Indices: 70090--70182 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
70080 CGCGAAACCA
**
70090 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
70122 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
70155 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
70183 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:70180 original size:52 final size:52
Alignment explanation
Indices: 70054--70182 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
70044 TAGTTTACTT
**
70054 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
70106 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
70159 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
70183 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:70219 original size:14 final size:14
Alignment explanation
Indices: 70200--70256 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
70190 TTTCATTTCG
70200 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
70214 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
70231 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
70247 CGTTGCGATT
1 CGTTGCGATT
70257 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:70225 original size:33 final size:33
Alignment explanation
Indices: 70183--70275 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
70173 CAAAATCGCA
*
70183 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
70216 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
70249 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
70276 TTGGTTTCGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:70283 original size:19 final size:19
Alignment explanation
Indices: 70178--70292 Score: 106
Period size: 19 Copynumber: 6.6 Consensus size: 19
70168 GAAACCAAAA
*
70178 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
70197 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
70213 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
70230 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
70246 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
70263 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
70282 TCGTGTTGCGA
1 TCGCGTTGCGA
70293 AAGTAAACTA
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
14 15 0.19
16 11 0.14
17 11 0.14
19 41 0.53
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:72231 original size:14 final size:14
Alignment explanation
Indices: 72212--72247 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
72202 CTTGTTTAAT
72212 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
72226 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
72240 TGATTTGT
1 TGATTTGT
72248 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:72370 original size:19 final size:19
Alignment explanation
Indices: 72354--72451 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
72344 AAAAATGACT
72354 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
72373 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
72392 ATCGCAA--C--TA-GAGA
1 ATCGCAATGCGAAATGAAA
72406 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
72425 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
72445 ATCGCAA
1 ATCGCAA
72452 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 39 0.57
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:72483 original size:53 final size:53
Alignment explanation
Indices: 72354--72469 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
72344 AAAAATGACT
*
72354 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACTAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
72406 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
72459 ATCGCAATGCG
1 ATCGCAATGCG
72470 TTTATAATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:72503 original size:14 final size:14
Alignment explanation
Indices: 72484--72538 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
72474 TAATTTCGCA
72484 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
72498 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
72515 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
72531 TTGCGATT
1 TTGCGATT
72539 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:72513 original size:33 final size:33
Alignment explanation
Indices: 72476--72623 Score: 210
Period size: 33 Copynumber: 4.5 Consensus size: 33
72466 TGCGTTTATA
72476 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
72509 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
72542 ATTTCCGCATTGCGATTTTCAT-GTTGGGA-TTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
* *
72575 ATTTCGCATTGCGATTCTCTCGTTGCGATTGTA
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
72608 ATTTCCGTATTGCGAT
1 ATTT-CGCATTGCGAT
72624 AGTCAAATGC
Statistics
Matches: 103, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
31 1 0.01
32 20 0.19
33 51 0.50
34 30 0.29
35 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.45
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:72556 original size:20 final size:19
Alignment explanation
Indices: 72498--72590 Score: 82
Period size: 20 Copynumber: 5.4 Consensus size: 19
72488 GATTCTCTCG
72498 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
72517 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
72531 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
72551 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
72565 TTGGGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
72583 TTGCGATT
1 TTGCGATT
72591 CTCTCGTTGC
Statistics
Matches: 58, Mismatches: 4, Indels: 24
0.67 0.05 0.28
Matches are distributed among these distances:
13 5 0.09
14 11 0.19
15 1 0.02
16 9 0.16
17 5 0.09
18 8 0.14
19 7 0.12
20 12 0.21
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:74901 original size:12 final size:12
Alignment explanation
Indices: 74884--74908 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
74874 TCTTCGGGGA
74884 CTTTTTCTTCTT
1 CTTTTTCTTCTT
74896 CTTTTTCTTCTT
1 CTTTTTCTTCTT
74908 C
1 C
74909 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:75116 original size:24 final size:24
Alignment explanation
Indices: 75082--75128 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
75072 CTGAAACATC
75082 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
75106 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
75129 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:75839 original size:20 final size:20
Alignment explanation
Indices: 75811--76000 Score: 204
Period size: 20 Copynumber: 9.5 Consensus size: 20
75801 AAATTTCAGT
* * * *
75811 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
75831 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
75851 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
75871 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
75891 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
75911 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
75931 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
75951 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
75971 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
75991 GTTGCGATTT
1 GTTGCGATTT
76001 TGGAAAATCG
Statistics
Matches: 146, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 142 0.97
21 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:76017 original size:21 final size:21
Alignment explanation
Indices: 75987--76069 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
75977 ATTTTCATAT
*
75987 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
76008 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
76029 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
76050 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
76070 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:76060 original size:42 final size:43
Alignment explanation
Indices: 75967--76065 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
75957 ATTTATGTGT
* *
75967 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
76008 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
76050 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
76066 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:90646 original size:28 final size:29
Alignment explanation
Indices: 90612--90679 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 29
90602 ATTCAGTCCG
*
90612 GTTTTTCACTATATTTTTTTATTTTGCGA
1 GTTTTTCACTATATTTTTTTATTCTGCGA
*
90641 G-TTTTCACTATCTTTTTTTATTCTGCGA
1 GTTTTTCACTATATTTTTTTATTCTGCGA
90669 GTTTTTCACTA
1 GTTTTTCACTA
90680 CAGATCTGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 26 0.72
29 10 0.28
ACGTcount: A:0.16, C:0.15, G:0.10, T:0.59
Consensus pattern (29 bp):
GTTTTTCACTATATTTTTTTATTCTGCGA
Found at i:95016 original size:2 final size:2
Alignment explanation
Indices: 95009--95080 Score: 116
Period size: 2 Copynumber: 38.0 Consensus size: 2
94999 CATTTTTAAT
95009 TA TA TA TA TA TA T- TA T- TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
95048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
95081 CAGTTTCTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
1 4 0.06
2 62 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:99204 original size:21 final size:21
Alignment explanation
Indices: 99178--99222 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
99168 GATTTCTGGG
* *
99178 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
99199 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
99220 CAA
1 CAA
99223 CGAACAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:100814 original size:145 final size:146
Alignment explanation
Indices: 100496--100795 Score: 477
Period size: 146 Copynumber: 2.1 Consensus size: 146
100486 GAGTCGAGGG
* * *
100496 TCTACGCGGTCCTTCGGG--ACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACAC
1 TCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACAC
*
100559 ATACTTGATCCCTAGTATGTATATGATCTTAAGGAATAATATGTGGTCCTTATGGACATATATAT
66 ATACTTGATCCCTAGTATGTATATAATCTTAAGGAATAATATGTGGTCCTTATGGACATATATAT
100624 GGCACTACGGTGCAAT
131 GGCACTACGGTGCAAT
100640 TCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTG-AGTCTTG-AA-ACAC
1 TCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACAC
100702 ATACTTGATCCCTAGTATATGTATATAATTCTTAAGGAATAATATG-GGTCCTTATGGACATTAT
66 ATACTTGATCCCTAG--TATGTATATAA-TCTTAAGGAATAATATGTGGTCCTTATGGACA-TA-
100766 TATATGGCACTACGGTGCAAT
126 TATATGGCACTACGGTGCAAT
100787 TCTACGCGG
1 TCTACGCGG
100796 CACTTCAGTG
Statistics
Matches: 145, Mismatches: 4, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
143 19 0.13
144 20 0.14
145 31 0.21
146 45 0.31
147 30 0.21
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (146 bp):
TCTACGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACAC
ATACTTGATCCCTAGTATGTATATAATCTTAAGGAATAATATGTGGTCCTTATGGACATATATAT
GGCACTACGGTGCAAT
Done.