Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001098.1 Hibiscus syriacus cultivar Beakdansim tig00002178_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: 91955
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:4304 original size:7 final size:7
Alignment explanation
Indices: 4292--4318 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4282 AGAAGTTTCT
4292 ATATAAA
1 ATATAAA
4299 ATATAAA
1 ATATAAA
4306 ATATAAA
1 ATATAAA
4313 ATATAA
1 ATATAA
4319 GAGAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATATAAA
Found at i:8166 original size:23 final size:23
Alignment explanation
Indices: 8140--8200 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
8130 CTCATATAAA
*
8140 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
8163 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
8186 TACACCGTAGTGCCA
1 TGCACCGTAGTGCCA
8201 TGTAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:8459 original size:102 final size:101
Alignment explanation
Indices: 8216--8429 Score: 333
Period size: 102 Copynumber: 2.1 Consensus size: 101
8206 TAATGTCCAT
* * * *
8216 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTGGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATAACACTCCTTAAG-ATCACATACATATACTAGGGATCAAGTATGTGTCTCACCA
8281 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATACA-ATATGTCCCG
* * *
8319 AAGGACCACATATCATTCCTTAAGATCATATACATATACTAGGGATCAAGTATGTGTCTCA-CAG
1 AAGGACCACATAACACTCCTTAAGATCACATACATATACTAGGGATCAAGTATGTGTCTCACCAG
8383 ACTTCACACATGTTCCAAAGAATAC-ATATGTCCCG
66 ACTTCACACATGTTCCAAAGAATACAATATGTCCCG
8418 AAGGACCACATA
1 AAGGACCACATA
8430 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
99 22 0.20
101 28 0.25
102 36 0.33
103 24 0.22
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (101 bp):
AAGGACCACATAACACTCCTTAAGATCACATACATATACTAGGGATCAAGTATGTGTCTCACCAG
ACTTCACACATGTTCCAAAGAATACAATATGTCCCG
Found at i:13127 original size:23 final size:23
Alignment explanation
Indices: 13101--13161 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
13091 CTCATATAAA
*
13101 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
13124 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
13147 TACACCGTAGTGCCA
1 TGCACCGTAGTGCCA
13162 TGTAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:13348 original size:103 final size:103
Alignment explanation
Indices: 13177--13394 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
13167 TAATGTCCAT
* * *
13177 AAGGACCACATATCATTCCTTAAGAATCATATACATATATTGGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAATATGTGTCTCACCA
13242 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
13280 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAATATGTGTCTCACTA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAATATGTGTCTCACCA
13345 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
13383 AAGGACCACATA
1 AAGGACCACATA
13395 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAATATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:14507 original size:16 final size:16
Alignment explanation
Indices: 14483--14513 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14473 TGTAATACAG
*
14483 ATAATCACACATAATT
1 ATAACCACACATAATT
14499 ATAACCACACATAAT
1 ATAACCACACATAAT
14514 CATGTCCATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAACCACACATAATT
Found at i:16409 original size:70 final size:70
Alignment explanation
Indices: 16296--16452 Score: 192
Period size: 70 Copynumber: 2.2 Consensus size: 70
16286 TAGTAAAACA
* * ** *
16296 TCCGTTCTAGTTGAATCGAAAGTGTGATGCCTCCTTTTGTTCGACTTGCATC-ATAAGTGCGATA
1 TCCGTTCTACTTGAATCGAAAATGTGATGCCTCCTTTCATTCGACTTGAATCGA-AAGTGCGATA
16360 CTTCCT
65 CTTCCT
* * * **
16366 TCCGTTCTACTTGGATTGAAAATGTGATGCCTTCTTTCATTCGACTTGAATCGAAAGTGCGATGT
1 TCCGTTCTACTTGAATCGAAAATGTGATGCCTCCTTTCATTCGACTTGAATCGAAAGTGCGATAC
16431 TTCCT
66 TTCCT
16436 TCCGTT-TAACTTGAATC
1 TCCGTTCT-ACTTGAATC
16453 TATGCAAACT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
69 1 0.01
70 71 0.97
71 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (70 bp):
TCCGTTCTACTTGAATCGAAAATGTGATGCCTCCTTTCATTCGACTTGAATCGAAAGTGCGATAC
TTCCT
Found at i:21406 original size:31 final size:31
Alignment explanation
Indices: 21371--21434 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
21361 TAAAATTATC
21371 AAGCTCGAATCAAACTAAAAATAAAAAATTG
1 AAGCTCGAATCAAACTAAAAATAAAAAATTG
* * * * *
21402 AAGCTGGACTCGAACTCAAAATCAAAAATTG
1 AAGCTCGAATCAAACTAAAAATAAAAAATTG
21433 AA
1 AA
21435 ACTATTGGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.53, C:0.16, G:0.12, T:0.19
Consensus pattern (31 bp):
AAGCTCGAATCAAACTAAAAATAAAAAATTG
Found at i:22040 original size:17 final size:17
Alignment explanation
Indices: 22018--22058 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
22008 TCATCAATAA
* *
22018 CTCGAGTCGAGTTCGAG
1 CTCGAGTAGAGTTCAAG
22035 CTCGAGTAGAGTTCAAG
1 CTCGAGTAGAGTTCAAG
*
22052 CTTGAGT
1 CTCGAGT
22059 TGAGACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.27
Consensus pattern (17 bp):
CTCGAGTAGAGTTCAAG
Found at i:22517 original size:2 final size:2
Alignment explanation
Indices: 22512--22537 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22502 TAGAGTTAAC
22512 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
22538 TAGTAATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23549 original size:30 final size:30
Alignment explanation
Indices: 23515--23585 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
23505 AACAAAATTC
*
23515 ATAATTTGGTGGTAAAAAAGAACTATCCCT
1 ATAATTTAGTGGTAAAAAAGAACTATCCCT
23545 ATAATTTAGTGGTAAAAAAGAACTATCCCT
1 ATAATTTAGTGGTAAAAAAGAACTATCCCT
23575 ATAATTTAGTG
1 ATAATTTAGTG
23586 ACTATACATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (30 bp):
ATAATTTAGTGGTAAAAAAGAACTATCCCT
Found at i:23724 original size:31 final size:31
Alignment explanation
Indices: 23681--23770 Score: 135
Period size: 31 Copynumber: 2.9 Consensus size: 31
23671 ATCTAACATA
23681 TTTTTGGGTCAAAATAAGTACATAAAGTTATC
1 TTTTT-GGTCAAAATAAGTACATAAAGTTATC
* *
23713 TTTTTGGTCAAAATATGTACTTAAAGTTATC
1 TTTTTGGTCAAAATAAGTACATAAAGTTATC
* *
23744 TTTTTGGTCAAAATAAGAACCTAAAGT
1 TTTTTGGTCAAAATAAGTACATAAAGT
23771 ATTTTATGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 48 0.91
32 5 0.09
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (31 bp):
TTTTTGGTCAAAATAAGTACATAAAGTTATC
Found at i:24308 original size:2 final size:2
Alignment explanation
Indices: 24301--24326 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24291 CTTGTTCTAC
24301 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
24327 TGTCTCTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29326 original size:190 final size:186
Alignment explanation
Indices: 28985--29329 Score: 435
Period size: 190 Copynumber: 1.8 Consensus size: 186
28975 AACAATTATC
* *
28985 TGACCCTTATTTCCATATGTAATGGGGTAAGAGGGAGGTAAGATAATAGGTTGTCCCCAACACCA
1 TGACCCTTATTCCCATATGTAATGGGGTAAGAGGGAGGTAAGATAATAGGTTAT-CCCAACACCA
* * * * *
29050 GGTTGAGAGCAGCTTCCGTACCTCCGAATTATGAAATGCCCTCCATGGGACTCGATCCCATGACC
65 GGTTGAGAACAGCTTCCGTACCTCCAAATTATGAAATGCCCACCATAGGACTCGATCCCACGACC
*
29115 ACAAGGTTAAGAACTTTGTGCTCTACCAACTGAGCTGAATGATCATTTCAAATTAGT
130 ACAAGGTTAAAAACTTTGTGCTCTACCAACTGAGCTGAATGATCATTTCAAATTAGT
* * *
29172 TGACCCTTATTCCCATATGTAATGGGGTAAGGGGGAGGT-AGAATAGTAGGTTAT-CCAACGCCA
1 TGACCCTTATTCCCATATGTAATGGGGTAAGAGGGAGGTAAG-ATAATAGGTTATCCCAACACCA
* * * * * *
29235 GGTTGAGAACATCTTCCGTGGGAAATCTCTAAATTATGAATTGTCCACCGTAGGACTCGATCCCA
65 GGTTGAGAACAGCTTCCGT-----ACCTCCAAATTATGAAATGCCCACCATAGGACTCGATCCCA
*
29300 CGACCTCAAGGTTAAAAA-TCTTGTGCTCTA
125 CGACCACAAGGTTAAAAACT-TTGTGCTCTA
29330 TCAAATTAAC
Statistics
Matches: 133, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
185 25 0.19
186 2 0.02
187 47 0.35
189 1 0.01
190 58 0.44
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (186 bp):
TGACCCTTATTCCCATATGTAATGGGGTAAGAGGGAGGTAAGATAATAGGTTATCCCAACACCAG
GTTGAGAACAGCTTCCGTACCTCCAAATTATGAAATGCCCACCATAGGACTCGATCCCACGACCA
CAAGGTTAAAAACTTTGTGCTCTACCAACTGAGCTGAATGATCATTTCAAATTAGT
Found at i:32935 original size:24 final size:24
Alignment explanation
Indices: 32908--32960 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
32898 AAATTAGATC
*
32908 AATTAGTA-TCAAAATATTATAAAT
1 AATTA-TACTCAAAATATTATAAAA
* *
32932 AATTATACTTAAAATTTTATAAAA
1 AATTATACTCAAAATATTATAAAA
32956 AATTA
1 AATTA
32961 AAATAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTATACTCAAAATATTATAAAA
Found at i:38912 original size:23 final size:23
Alignment explanation
Indices: 38885--38929 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
38875 ATTTAGAACT
38885 AAAATTA-AAAAAATTAATATTAA
1 AAAATTATAAAAAA-TAATATTAA
*
38908 AAAATTATCAAAAATAATATTA
1 AAAATTATAAAAAATAATATTA
38930 CATCTATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATTATAAAAAATAATATTAA
Found at i:39479 original size:59 final size:59
Alignment explanation
Indices: 39369--39482 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
39359 ACTGTGATTC
* * * * * *
39369 TCATTTTAAATTGGGCCTTAAACTTTTAAATATTCTAATTTCATCCTCAAACTATGCTT
1 TCATTTTAAATTAGGCCTCAAACTTTTAAACATCCAAATTTCATCCCCAAACTATGCTT
*
39428 TCATTTTAAATTAGTCCTCAAACTTTTAAACATACCAAATTT-ATCCCCAAACTAT
1 TCATTTTAAATTAGGCCTCAAACTTTTAAACAT-CCAAATTTCATCCCCAAACTAT
39483 AACCCTTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 41 0.87
60 6 0.13
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.40
Consensus pattern (59 bp):
TCATTTTAAATTAGGCCTCAAACTTTTAAACATCCAAATTTCATCCCCAAACTATGCTT
Found at i:43019 original size:29 final size:29
Alignment explanation
Indices: 42973--43050 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
42963 CACTAAATTA
*
42973 ATAACCT-TAAATCATAAACCATAACCTC
1 ATAACCTCTAAATCTTAAACCATAACCTC
*
43001 ATAACCTCTAAACCTTAAACCATAACCTC
1 ATAACCTCTAAATCTTAAACCATAACCTC
43030 ATAACCTCTAAATCTTAAACC
1 ATAACCTCTAAATCTTAAACC
43051 CTAAACATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 7 0.15
29 39 0.85
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.26
Consensus pattern (29 bp):
ATAACCTCTAAATCTTAAACCATAACCTC
Found at i:43035 original size:21 final size:22
Alignment explanation
Indices: 43000--43041 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
42990 ACCATAACCT
43000 CATAACCTCTAAACCT-TAAAC
1 CATAACCTCTAAACCTCTAAAC
43021 CATAACCTC-ATAACCTCTAAA
1 CATAACCTCTA-AACCTCTAAA
43042 TCTTAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.05
21 14 0.74
22 4 0.21
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (22 bp):
CATAACCTCTAAACCTCTAAAC
Found at i:46660 original size:28 final size:28
Alignment explanation
Indices: 46628--46682 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
46618 GTCCCTTCAA
*
46628 ATTTGAAAATATACAT-TAAACGTTAAGT
1 ATTTGAAAATATA-ATGTAAAAGTTAAGT
*
46656 ATTTGAAAGTATAATGTAAAAGTTAAG
1 ATTTGAAAATATAATGTAAAAGTTAAG
46683 CATATGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.35
Consensus pattern (28 bp):
ATTTGAAAATATAATGTAAAAGTTAAGT
Found at i:50755 original size:35 final size:35
Alignment explanation
Indices: 50708--50821 Score: 156
Period size: 35 Copynumber: 3.3 Consensus size: 35
50698 AAAACAGTCC
* * *
50708 TCAATTTTATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* *
50743 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * *
50778 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
50813 TCAATTTAA
1 TCAATTTAA
50822 GGTTTAGAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:52631 original size:35 final size:35
Alignment explanation
Indices: 52591--52702 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
52581 TCTAAACCTT
* * *
52591 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
52626 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
52661 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
52696 AAATTGA
1 AAATTGA
52703 GGATTGTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:53281 original size:15 final size:15
Alignment explanation
Indices: 53261--53290 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53251 AATGATAATT
53261 ACAATACTAATTGTG
1 ACAATACTAATTGTG
53276 ACAATACTAATTGTG
1 ACAATACTAATTGTG
53291 TAACAGGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
ACAATACTAATTGTG
Found at i:53463 original size:3 final size:3
Alignment explanation
Indices: 53455--53490 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
53445 TAAGTTGTAA
53455 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53491 TAATTAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:58474 original size:42 final size:42
Alignment explanation
Indices: 58421--58506 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
58411 AAATCCCTAT
58421 ATAACTTTTTAAGTACAATAGAAAATGTTACAAATTTATATA
1 ATAACTTTTTAAGTACAATAGAAAATGTTACAAATTTATATA
* * *
58463 ATAATTTTTTAATTACAATAGAAAATGTTATAAATTTATATA
1 ATAACTTTTTAAGTACAATAGAAAATGTTACAAATTTATATA
58505 AT
1 AT
58507 CTTTAAGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.42
Consensus pattern (42 bp):
ATAACTTTTTAAGTACAATAGAAAATGTTACAAATTTATATA
Found at i:58834 original size:2 final size:2
Alignment explanation
Indices: 58829--58856 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58819 TGTGTTATTA
58829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58857 GTCTACTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59631 original size:23 final size:24
Alignment explanation
Indices: 59596--59653 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
59586 GAGAATCGAG
*
59596 TAAACAAGCTTAT-AACGAGTCAA
1 TAAACAAGCTTATAAAAGAGTCAA
* *
59619 TAAATAAGTTTATAAAAGAGTCAA
1 TAAACAAGCTTATAAAAGAGTCAA
*
59643 TAAACGAGCTT
1 TAAACAAGCTT
59654 GTTTTTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (24 bp):
TAAACAAGCTTATAAAAGAGTCAA
Found at i:78831 original size:7 final size:7
Alignment explanation
Indices: 78780--78894 Score: 85
Period size: 7 Copynumber: 16.4 Consensus size: 7
78770 ACACCCCATG
78780 TCTT-CT
1 TCTTCCT
78786 TCTT-CT
1 TCTTCCT
*
78792 TCATTCAT
1 TC-TTCCT
*
78800 TCATTCTT
1 TC-TTCCT
*
78808 TCTTTCT
1 TCTTCCT
78815 T-TCTCCT
1 TCT-TCCT
*
78822 TCTCCCT
1 TCTTCCT
*
78829 TCTCCCT
1 TCTTCCT
78836 TC-TCCTT
1 TCTTCC-T
*
78843 TCTTCTT
1 TCTTCCT
*
78850 TCTTTCT
1 TCTTCCT
*
78857 TCTTTCT
1 TCTTCCT
78864 TCTTCCT
1 TCTTCCT
78871 TCTTCCT
1 TCTTCCT
78878 TCTTCCT
1 TCTTCCT
*
78885 TCTTCTT
1 TCTTCCT
78892 TCT
1 TCT
78895 CTTTTCACTT
Statistics
Matches: 91, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
6 11 0.12
7 67 0.74
8 13 0.14
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.61
Consensus pattern (7 bp):
TCTTCCT
Found at i:78854 original size:42 final size:42
Alignment explanation
Indices: 78803--78894 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
78793 CATTCATTCA
78803 TTCTTTCTTTCTT-TCTCCTTCTCCCTTCTCCCTTC-TCCTTTC
1 TTCTTTCTTTCTTCT-TCCTTCTCCCTTCTCCCTTCTTCC-TTC
* * *
78845 TTCTTTCTTTCTTCTTTCTTCTTCCTTCTTCCTTCTTCCTTC
1 TTCTTTCTTTCTTCTTCCTTCTCCCTTCTCCCTTCTTCCTTC
78887 TTCTTTCT
1 TTCTTTCT
78895 CTTTTCACTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
42 41 0.91
43 4 0.09
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (42 bp):
TTCTTTCTTTCTTCTTCCTTCTCCCTTCTCCCTTCTTCCTTC
Found at i:86581 original size:20 final size:20
Alignment explanation
Indices: 86558--86600 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
86548 AATCCACCAC
*
86558 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
86578 ATGCATCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
86598 ATG
1 ATG
86601 GTCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:87767 original size:7 final size:7
Alignment explanation
Indices: 87755--87839 Score: 93
Period size: 7 Copynumber: 12.3 Consensus size: 7
87745 GGAGGAGGAG
87755 GAAAGAA
1 GAAAGAA
87762 GAAAGAA
1 GAAAGAA
87769 GAAAGAA
1 GAAAGAA
*
87776 GAATGAA
1 GAAAGAA
87783 G-AAGAAA
1 GAAAG-AA
*
87790 GAAATAA
1 GAAAGAA
*
87797 GAAATAA
1 GAAAGAA
*
87804 GAAATAA
1 GAAAGAA
*
87811 AAAAGAA
1 GAAAGAA
87818 GAAAGAA
1 GAAAGAA
*
87825 GGAAGAA
1 GAAAGAA
87832 G-AAGAA
1 GAAAGAA
87838 GA
1 GA
87840 CGTGTGGGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
6 8 0.12
7 58 0.85
8 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (7 bp):
GAAAGAA
Found at i:90156 original size:20 final size:19
Alignment explanation
Indices: 90133--90174 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
90123 ATTTTACAAA
90133 TGATTTTCTA-AAAGTATATT
1 TGATTTTC-ACAAAGTAT-TT
90153 TGATTTTCACAAAGTATTT
1 TGATTTTCACAAAGTATTT
90172 TGA
1 TGA
90175 ACCAAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (19 bp):
TGATTTTCACAAAGTATTT
Found at i:90239 original size:20 final size:20
Alignment explanation
Indices: 90210--90265 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
90200 TTTCAGAGTG
*
90210 ATGCACCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
90230 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
*
90250 ATGCATCGATCCACCA
1 ATGCATCGATGCACCA
90266 TGAATTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.38, G:0.14, T:0.18
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:90305 original size:65 final size:64
Alignment explanation
Indices: 90229--90373 Score: 163
Period size: 65 Copynumber: 2.2 Consensus size: 64
90219 TGCACCAATC
*
90229 CATGCATCGATGCACCA-ATCCATGCATCGATCCACCATGA-ATTAAATTG-AACATCGAATGCA
1 CATGCATCGATGCACCATA-CCATGCACCGATCCA-C-TGAGATTAAA-TGAAACATCGAATGCA
90291 TTT
62 TTT
* **
90294 CATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGCATT
1 CATGCATCGATGCACCATACCATGCACCGATCCACTGA-GATTAAATG-AAACATCGAATGCATT
90358 T
64 T
*
90359 GATGCATCGATGCAC
1 CATGCATCGATGCAC
90374 TCTGGCTATT
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 19 0.28
65 44 0.64
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (64 bp):
CATGCATCGATGCACCATACCATGCACCGATCCACTGAGATTAAATGAAACATCGAATGCATTT
Found at i:90370 original size:46 final size:45
Alignment explanation
Indices: 90314--90420 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
90304 TGCACATACC
* * *
90314 ATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTG
* *
90360 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
*
90405 ATGCATAGATGCACTC
1 ATGCATCGATGCACTC
90421 TTAGTGCACC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
45 32 0.59
46 19 0.35
47 3 0.06
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTG
Found at i:91467 original size:7 final size:7
Alignment explanation
Indices: 91455--91510 Score: 69
Period size: 7 Copynumber: 8.0 Consensus size: 7
91445 GGAGGAGGAG
91455 GAAAGAA
1 GAAAGAA
91462 GAAAGAA
1 GAAAGAA
*
91469 GAAGGAA
1 GAAAGAA
*
91476 GAATGAA
1 GAAAGAA
91483 G-AAGAAA
1 GAAAG-AA
91490 GAAAGAA
1 GAAAGAA
*
91497 GGAAGAA
1 GAAAGAA
91504 GAAAGAA
1 GAAAGAA
91511 AGAATGAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 2 0.05
7 37 0.88
8 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (7 bp):
GAAAGAA
Found at i:91474 original size:18 final size:17
Alignment explanation
Indices: 91455--91536 Score: 96
Period size: 18 Copynumber: 4.7 Consensus size: 17
91445 GGAGGAGGAG
91455 GAAAGAAGAAAGAAG-AA
1 GAAAGAAG-AAGAAGAAA
*
91472 GGAAGAATGAAGAAGAAA
1 GAAAGAA-GAAGAAGAAA
91490 GAAAGAAGGAAGAAGAAA
1 GAAAGAA-GAAGAAGAAA
*
91508 GAAAGAATGAATAAGAAA
1 GAAAGAA-GAAGAAGAAA
91526 G-AAGAAGAAGA
1 GAAAGAAGAAGA
91537 CCTGTGGGGG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
16 4 0.07
17 17 0.30
18 36 0.63
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (17 bp):
GAAAGAAGAAGAAGAAA
Found at i:91476 original size:4 final size:3
Alignment explanation
Indices: 91457--91536 Score: 61
Period size: 3 Copynumber: 23.3 Consensus size: 3
91447 AGGAGGAGGA
91457 AAG AAG AAAG AAG AAGG AAG AATG AAG AAG AAAG AAAG AAGG AAG AAG
1 AAG AAG -AAG AAG AA-G AAG AA-G AAG AAG -AAG -AAG AA-G AAG AAG
*
91505 AAAG AAAG AATG AAT AAG AAAG AAG AAG AAG A
1 -AAG -AAG AA-G AAG AAG -AAG AAG AAG AAG A
91537 CCTGTGGGGG
Statistics
Matches: 67, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
3 35 0.52
4 32 0.48
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (3 bp):
AAG
Done.