Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005859.1 Hibiscus syriacus cultivar Beakdansim tig00013771_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: 67836
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4000 original size:2 final size:2
Alignment explanation
Indices: 3995--4065 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
3985 TGTGTGTGTG
3995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
4037 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 T
4066 TCATATTGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6798 original size:14 final size:16
Alignment explanation
Indices: 6769--6802 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
6759 TTTTTAAATT
6769 TTAATAAATGATTTAA
1 TTAATAAATGATTTAA
6785 TTAA-AAAT-ATTTAA
1 TTAATAAATGATTTAA
6799 TTAA
1 TTAA
6803 GACATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 4 0.22
16 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TTAATAAATGATTTAA
Found at i:10786 original size:319 final size:318
Alignment explanation
Indices: 10193--10831 Score: 1260
Period size: 319 Copynumber: 2.0 Consensus size: 318
10183 GATGGTTTTA
*
10193 GACAGAAATATACTAAAAAATATGGTTAATTTGTAAATCTAAAGCCAGAGGGGGACACAATCACT
1 GACAGAAATATACTAAAAAATATGGTTAACTTGTAAATCTAAAGCCAGAGGGGGACACAATCACT
10258 CTGAAGTCTGAACAGCTAACGTGCCTCTCCAAACTCCTTTAATATGCCATGAACCATATTCAAGG
66 CTGAAGTCTGAACAGCTAACGTGCCTCTCCAAACTCCTTTAATATGCCATGAACCATATTCAAGG
10323 GAGCATGTACATGTATGACATTCAGAACCAAATAAACATTCATTAAAACCATAAAAGCTTAGCTT
131 GAGCATGTACATGTATGACATTCAGAACCAAATAAACATTCATTAAAACCATAAAAGCTTAGCTT
10388 AAGGTGTTTGCTCCAAAGAATCTCACCTAAACCTGATTGTGTGATGACAGAACATAAAGGAGATA
196 AAGGTGTTTGCTCCAAAGAATCTCACCTAAACCTGATTGTGTGATGACAGAACATAAAGGAGATA
10453 AACGAGTTCTTCTAATAAAATTACCTCTTCATCTGAGAGATACATCAGCAGCAAATTG
261 AACGAGTTCTTCTAATAAAATTACCTCTTCATCTGAGAGATACATCAGCAGCAAATTG
10511 GACAGAAATATACTAAAAAAATATGGTTAACTTGTAAATCTAAAGCCAGAGGGGGACACAATCAC
1 GACAGAAATATACT-AAAAAATATGGTTAACTTGTAAATCTAAAGCCAGAGGGGGACACAATCAC
10576 TCTGAAGTCTGAACAGCTAACGTGCCTCTCCAAACTCCTTTAATATGCCATGAACCATATTCAAG
65 TCTGAAGTCTGAACAGCTAACGTGCCTCTCCAAACTCCTTTAATATGCCATGAACCATATTCAAG
10641 GGAGCATGTACATGTATGACATTCAGAACCAAATAAACATTCATTAAAACCATAAAAGCTTAGCT
130 GGAGCATGTACATGTATGACATTCAGAACCAAATAAACATTCATTAAAACCATAAAAGCTTAGCT
10706 TAAGGTGTTTGCTCCAAAGAATCTCACCTAAACCTGATTGTGTGATGACAGAACATAAAGGAGAT
195 TAAGGTGTTTGCTCCAAAGAATCTCACCTAAACCTGATTGTGTGATGACAGAACATAAAGGAGAT
10771 AAACGAGTTCTTCTAATAAAATTACCTCTTCATCTGAGAGATACATCAGCAGCAAATTG
260 AAACGAGTTCTTCTAATAAAATTACCTCTTCATCTGAGAGATACATCAGCAGCAAATTG
10830 GA
1 GA
10832 AAATATCAAG
Statistics
Matches: 319, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
318 14 0.04
319 305 0.96
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (318 bp):
GACAGAAATATACTAAAAAATATGGTTAACTTGTAAATCTAAAGCCAGAGGGGGACACAATCACT
CTGAAGTCTGAACAGCTAACGTGCCTCTCCAAACTCCTTTAATATGCCATGAACCATATTCAAGG
GAGCATGTACATGTATGACATTCAGAACCAAATAAACATTCATTAAAACCATAAAAGCTTAGCTT
AAGGTGTTTGCTCCAAAGAATCTCACCTAAACCTGATTGTGTGATGACAGAACATAAAGGAGATA
AACGAGTTCTTCTAATAAAATTACCTCTTCATCTGAGAGATACATCAGCAGCAAATTG
Found at i:20393 original size:19 final size:19
Alignment explanation
Indices: 20363--20407 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
20353 TATTAGAACA
20363 TTATTA-TTTTTA-TTGATT
1 TTATTATTTTTTACTTG-TT
20381 TTATTATTTTTTACTTGTT
1 TTATTATTTTTTACTTGTT
20400 TTATTATT
1 TTATTATT
20408 GTTGGACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.24
19 16 0.64
20 3 0.12
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (19 bp):
TTATTATTTTTTACTTGTT
Found at i:41504 original size:287 final size:289
Alignment explanation
Indices: 40982--41561 Score: 1011
Period size: 287 Copynumber: 2.0 Consensus size: 289
40972 GAACCGCCCT
* *
40982 TTCGGTACCAATTAATTTGTCGGTTGTCTTTAATTGTGAAAATTAAGAATTTAAATTTAAATTTA
1 TTCGGTACCAATTAATTTGTCGATTGTCTTTAATTGCGAAAATTAAG-----AAATTTAAATTTA
*
41047 AAAATTTGATTCGAATAATTACCTTTGACCGATTGAAATTACCCCTTTTGAAGGTTCTTGGCTCT
61 AAAATTTGATTCGAATAATTACCTTTGACCGATTGAAATTACCCCTTTTGAAGGTTATTGGCTCT
41112 AGTGAACGAAAATTGCCTTATTCGAATGGAAAGGTCAGGTTTTTTACTTGGATCTTTGTTTCCTT
126 AGTGAACGAAAATTGCCTTATTCGAATGGAAAGGTCAGGTTTTTTACTTGGATCTTTGTTTCCTT
41177 CTTTGTATTTGAGAAATGATTTCTGGTTTTCTCCAATGGATCCCCTCGAACGGTTCTC-TTTTTT
191 CTTTGTATTTGAGAAATGATTTCTGGTTTTCTCCAATGGATCCCCTCGAACGGTTCTCTTTTTTT
41241 TTAACTTCGAATGAATCTGGTACCCTTTTTTTTA
256 TTAACTTCGAATGAATCTGGTACCCTTTTTTTTA
*
41275 TTCGGTACCAATTAATTTTTCGATTGTCTTTAATTGCGAAAATTAAG-AATTTAAATTTAAAAAT
1 TTCGGTACCAATTAATTTGTCGATTGTCTTTAATTGCGAAAATTAAGAAATTTAAATTTAAAAAT
* * *
41339 TTGATTCGAATAATTACCTTTGATCGATTGAAATTACCCCTTTTGAAGGTTATTGGCTGTGGTGA
66 TTGATTCGAATAATTACCTTTGACCGATTGAAATTACCCCTTTTGAAGGTTATTGGCTCTAGTGA
* *
41404 ACGAAAATTGCCTTCTTCGAATGGAAAGGTCAGGTTTTTTACTTGGCTCTTTGTTTCCTTCTTTG
131 ACGAAAATTGCCTTATTCGAATGGAAAGGTCAGGTTTTTTACTTGGATCTTTGTTTCCTTCTTTG
*
41469 TATTTGAGATATGATTTCTGGTTTTCTCCAATGGATCCCCTCGAACGGTTCTCTTTTTTTTTAAC
196 TATTTGAGAAATGATTTCTGGTTTTCTCCAATGGATCCCCTCGAACGGTTCTCTTTTTTTTTAAC
41534 TTCGAATGAATCTGGTACCCTTTTTTTT
261 TTCGAATGAATCTGGTACCCTTTTTTTT
41562 CTTTTCTTTT
Statistics
Matches: 276, Mismatches: 10, Indels: 7
0.94 0.03 0.02
Matches are distributed among these distances:
287 193 0.70
288 39 0.14
293 44 0.16
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (289 bp):
TTCGGTACCAATTAATTTGTCGATTGTCTTTAATTGCGAAAATTAAGAAATTTAAATTTAAAAAT
TTGATTCGAATAATTACCTTTGACCGATTGAAATTACCCCTTTTGAAGGTTATTGGCTCTAGTGA
ACGAAAATTGCCTTATTCGAATGGAAAGGTCAGGTTTTTTACTTGGATCTTTGTTTCCTTCTTTG
TATTTGAGAAATGATTTCTGGTTTTCTCCAATGGATCCCCTCGAACGGTTCTCTTTTTTTTTAAC
TTCGAATGAATCTGGTACCCTTTTTTTTA
Found at i:42128 original size:7 final size:7
Alignment explanation
Indices: 42110--42145 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
42100 ATATGTTTAT
42110 TATAAT-
1 TATAATA
42116 TATAATA
1 TATAATA
42123 TATAATA
1 TATAATA
42130 TATAATA
1 TATAATA
42137 TATAATA
1 TATAATA
42144 TA
1 TA
42146 ATATTCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATAATA
Found at i:42677 original size:30 final size:30
Alignment explanation
Indices: 42641--42700 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
42631 AGATTCAGGG
* *
42641 TTTCAAGAGAAATATTTTCAAAGGTTTTTT
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTT
42671 TTTCAAGAGAAACAATTTCAAAGGTTTTTT
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTT
42701 GTGTTTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.43
Consensus pattern (30 bp):
TTTCAAGAGAAACAATTTCAAAGGTTTTTT
Found at i:42791 original size:34 final size:33
Alignment explanation
Indices: 42640--42794 Score: 158
Period size: 34 Copynumber: 4.7 Consensus size: 33
42630 AAGATTCAGG
* *
42640 GTTTCAAGAGAAATATTTTCAAAGG-TTTTT-T
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTGT
42671 -TTTCAAGAGAAACAATTTCAAAGGTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTGT
* **
42703 GTTTCAAAAG-AA-AATTTCCCAAGATTTTTTTTGT
1 GTTTCAAGAGAAACAATTT--CAA-AGGTTTTTTGT
* ***
42737 GTTTCAAGAAAAATTGTTTCAAAGGTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGG-TTTTTTGT
42771 GTTTCAAGAGAAACAATTTCAAAG
1 GTTTCAAGAGAAACAATTTCAAAG
42795 ATTGGTGCTT
Statistics
Matches: 100, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
30 22 0.22
31 10 0.10
32 3 0.03
33 12 0.12
34 48 0.48
35 2 0.02
36 3 0.03
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.41
Consensus pattern (33 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTGT
Found at i:42851 original size:66 final size:66
Alignment explanation
Indices: 42788--42914 Score: 157
Period size: 65 Copynumber: 1.9 Consensus size: 66
42778 GAGAAACAAT
* * * *
42788 TTCAAAGATTGGTGCTTCAAGAGAAACTATCTCGAGAGAGACGAAATTTG-TTTAAAGGAAAACA
1 TTCAAAGATT-GTGCTTCAAGAGAAACCATCTCAAGAGAGACAAAATTTGTTTTAAAAGAAAACA
42852 TA
65 TA
* * * * *
42854 TTCAAGGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAA
1 TTCAAAGATTGTGCTTCAAGAGAAACCATCTCAAGAGAGACAAAATTTGTTTTAAAAGAAA
42915 CTGTCTCAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 32 0.63
66 19 0.37
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (66 bp):
TTCAAAGATTGTGCTTCAAGAGAAACCATCTCAAGAGAGACAAAATTTGTTTTAAAAGAAAACAT
A
Found at i:42915 original size:36 final size:36
Alignment explanation
Indices: 42863--43071 Score: 220
Period size: 36 Copynumber: 6.0 Consensus size: 36
42853 ATTCAAGGAT
* * *
42863 TTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
42899 TTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
42935 TTTGTTTTAAG-GAAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTTAAGAG-AAACTG-TCTCAAGAGAGACAAAA
* * *
42964 TTTGTTTCAAGGGAAACTGTCTCAATAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
*
43000 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
*
43036 TTTGTTTTAAGAGAAGCTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
43072 CTCTATTTCA
Statistics
Matches: 143, Mismatches: 19, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
28 1 0.01
29 18 0.13
30 2 0.01
31 1 0.01
32 2 0.01
33 2 0.01
35 2 0.01
36 114 0.80
37 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (36 bp):
TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:43043 original size:101 final size:101
Alignment explanation
Indices: 42806--43046 Score: 383
Period size: 101 Copynumber: 2.4 Consensus size: 101
42796 TTGGTGCTTC
* * * * *
42806 AAGAGAAACTATCTCGAGAGAGACGAAATTTGTTTAAAGGAAAACATATTCAAGGATTTTGTTTC
1 AAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTC
42871 AAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTT
66 AAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTT
* *
42907 AAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTC
1 AAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTC
* *
42972 AAGGGAAACTGTCTCAATAGAGACAAAATTTGTTTT
66 AAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTT
* *
43008 AAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAG
1 AAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTTAAG
43047 AGAAGCTGTC
Statistics
Matches: 127, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 127 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (101 bp):
AAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTC
AAGGGAAACCGTCTCAAGAGAGACAAAATTTGTTTT
Found at i:43048 original size:19 final size:19
Alignment explanation
Indices: 42990--43049 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
42980 CTGTCTCAAT
42990 AGAGACAAAATTTGTTTTA
1 AGAGACAAAATTTGTTTTA
**
43009 AGAG--AAAA--TGTCTCAA
1 AGAGACAAAATTTGT-TTTA
43025 GAGAGACAAAATTTGTTTTA
1 -AGAGACAAAATTTGTTTTA
43045 AGAGA
1 AGAGA
43050 AGCTGTCTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 3 0.10
16 2 0.06
17 8 0.26
19 13 0.42
20 2 0.06
21 3 0.10
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (19 bp):
AGAGACAAAATTTGTTTTA
Found at i:43146 original size:138 final size:137
Alignment explanation
Indices: 42881--43182 Score: 451
Period size: 138 Copynumber: 2.2 Consensus size: 137
42871 AAGGGAAACC
* * * * *
42881 GTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTTAAG
1 GTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAATCTATTTCAAG
* * * * *
42946 GAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAATAGAGACAAAATTTGTTTTAAG
66 GAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAAAGACAAAATTTATTTTAAG
43011 AGAAAAT
131 AGAAAAT
* *
43018 GTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAGCTGTCTCAAGAGAGACAAAACTCTATTTCAA
1 GTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAA-TCTATTTCAA
* *
43083 GGAAAACAAATTCGAAGTTTTTGTTTCAAGGGAAACCGTCTCAAGAAAGACAAAATTTATTTTAA
65 GGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAAAGACAAAATTTATTTTAA
43148 GAGAAAAT
130 GAGAAAAT
*
43156 GTCTCGAGAGAGACAAAACTTTGTTTT
1 GTCTCAAGAGAGACAAAA-TTTGTTTT
43183 GAGTAAATTA
Statistics
Matches: 148, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
137 50 0.34
138 90 0.61
139 8 0.05
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (137 bp):
GTCTCAAGAGAGACAAAATTTGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAATCTATTTCAAG
GAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAAAGACAAAATTTATTTTAAG
AGAAAAT
Found at i:44573 original size:15 final size:15
Alignment explanation
Indices: 44549--44655 Score: 187
Period size: 15 Copynumber: 7.1 Consensus size: 15
44539 GTAGGACTCA
44549 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
*
44564 TACTTCCCGAAGGAC
1 TACATCCCGAAGGAC
44579 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
*
44594 TACGTCCCGAAGGAC
1 TACATCCCGAAGGAC
44609 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
*
44624 TACGTCCCGAAGGAC
1 TACATCCCGAAGGAC
44639 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
44654 TA
1 TA
44656 TAATACCCTC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 86 1.00
ACGTcount: A:0.31, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:45384 original size:64 final size:63
Alignment explanation
Indices: 45277--45434 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
45267 TAATGAAGGT
* * * * * **
45277 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCTATGTTTCATTA-A-TAACGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTTT--TTATATTAA-AA
45340 G
63 G
* *
45341 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTTTTTATATTTAAAAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTTTTTATA-TTAAAAG
*
45405 AGTGCATCGATGCACTACCTATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
45435 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
62 3 0.04
63 1 0.01
64 46 0.57
65 30 0.38
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTTTTTATATTAAAAG
Found at i:48965 original size:15 final size:15
Alignment explanation
Indices: 48942--49034 Score: 168
Period size: 15 Copynumber: 6.2 Consensus size: 15
48932 CGTAGGACTC
48942 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
48957 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
48972 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
48987 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
49002 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
49017 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
49032 CTA
1 CTA
49035 TAATACCCTC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 74 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.14
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:49746 original size:64 final size:65
Alignment explanation
Indices: 49656--49812 Score: 187
Period size: 64 Copynumber: 2.4 Consensus size: 65
49646 TAATGAAGGT
* * * *
49656 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATG-TTT-CA-TTAATAACG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTTTTACATTTAA-AA-G
*
49718 GG
64 AG
* * *
49720 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTTTTATATTTAAAAGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTTTTACATTTAAAAGAG
*
49785 -TGCATCGATGCACTACCTATGCATCGAT
1 ATGCATCGATGCACTACTTATGCATCGAT
49813 ACACCTTCAA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
64 69 0.85
65 5 0.06
66 3 0.04
67 4 0.05
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTTTTACATTTAAAAGAG
Found at i:51442 original size:83 final size:88
Alignment explanation
Indices: 51319--51541 Score: 244
Period size: 95 Copynumber: 2.5 Consensus size: 88
51309 GGCTAGCCGA
* *
51319 ATCCATAAAGCCGGGGTGTTT-ACCAATTGCTCTAGAGGGACAACTCAA-TA-TG-TA-AAT-AC
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATTGATATAATCAC
* *
51378 CTTTATCAGGTTAGCTGAATCTT
66 CTTTATCAGGCTAGCTGAATATT
* * *
51401 ATCCATAAAGTCAGGGCGTTTAACTAATTGC-CTTAGAGGGACAGCTCAAGCTTTATTGTATAAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTCAA---TTATTG----AT
51465 ATAATCACCTTTATCAGGCTAGCTGAATATT
58 ATAATCACCTTTATCAGGCTAGCTGAATATT
* *
51496 ATCCATAAAGTCGGGGCGTTTAACCAATTACTCTAGAAGGACAACT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACT
51542 AAAGCTTTAT
Statistics
Matches: 114, Mismatches: 12, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
82 19 0.17
83 23 0.20
87 2 0.02
88 2 0.02
93 2 0.02
94 3 0.03
95 62 0.54
96 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (88 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATTGATATAATCAC
CTTTATCAGGCTAGCTGAATATT
Found at i:51547 original size:95 final size:95
Alignment explanation
Indices: 51376--51557 Score: 276
Period size: 95 Copynumber: 1.9 Consensus size: 95
51366 ATATGTAAAT
* * * * *
51376 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACTAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCAGGGCGTTTAACCAATTACCTTAGAAGG
* *
51441 ACAGCTCAAGCTTTATTGTATAATATAATC
66 ACAACTAAAGCTTTATTGTATAATATAATC
*
51471 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCGGGGCGTTTAACCAATTA-CTCTAGAAG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCAGGGCGTTTAACCAATTACCT-TAGAAG
51535 GACAACTAAAGCTTTATTGTATA
65 GACAACTAAAGCTTTATTGTATA
51558 TAAATAATAT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 2 0.03
95 76 0.97
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGTCAGGGCGTTTAACCAATTACCTTAGAAGG
ACAACTAAAGCTTTATTGTATAATATAATC
Found at i:59341 original size:17 final size:17
Alignment explanation
Indices: 59319--59361 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
59309 GAAATGATGT
59319 CAATAATGATACGTGGA
1 CAATAATGATACGTGGA
59336 CAATAATGATACGTGGA
1 CAATAATGATACGTGGA
59353 CAATAATGA
1 CAATAATGA
59362 GCCTTAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (17 bp):
CAATAATGATACGTGGA
Done.