Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004180.1 Hibiscus syriacus cultivar Beakdansim tig00009142_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: 61656
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2568 original size:36 final size:35
Alignment explanation
Indices: 2471--2582 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
2461 TTGGTGGTTA
* * * *
2471 TATAGGCGTGAAATTGTGATAGAAGTTGGTGATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
2506 TATAGGCGTGCAATGGTGATGAAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
2541 TATAGGCGTAAAAATGGTGATGGAAGATGGTGGTGT
1 TATAGGCGT-GAAATGGTGATGGAAGATGGTGATGT
2577 TATAGG
1 TATAGG
2583 TAGTATCTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 38 0.58
36 28 0.42
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:5530 original size:21 final size:21
Alignment explanation
Indices: 5506--5545 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5496 TTTAGAGTGC
*
5506 AAAAGAAAGAAAAGAAAAAAG
1 AAAAAAAAGAAAAGAAAAAAG
*
5527 AAAAAAAATAAAAGAAAAA
1 AAAAAAAAGAAAAGAAAAA
5546 GAAGTGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (21 bp):
AAAAAAAAGAAAAGAAAAAAG
Found at i:25709 original size:19 final size:21
Alignment explanation
Indices: 25685--25736 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
25675 CGGCCAAGAG
*
25685 CATGTATATTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
25704 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
25725 CATGTATTTTCA
1 CATGTATTTTCA
25737 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:27935 original size:22 final size:22
Alignment explanation
Indices: 27910--27953 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27900 TGTTGATGGT
27910 CGAATGCCTTGATGATGATTGA
1 CGAATGCCTTGATGATGATTGA
27932 CGAATGCCTTGATGATGATTGA
1 CGAATGCCTTGATGATGATTGA
27954 AGGATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (22 bp):
CGAATGCCTTGATGATGATTGA
Found at i:28433 original size:19 final size:20
Alignment explanation
Indices: 28392--28434 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
28382 GAAACCCCTT
**
28392 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
*
28412 TGAAATTACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
28431 TGAA
1 TGAA
28435 GGTACATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:31363 original size:36 final size:36
Alignment explanation
Indices: 31311--31423 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
31301 GATACTATTT
*
31311 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
31347 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
31383 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
31418 ACATCA
1 TCATCA
31424 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:31366 original size:13 final size:11
Alignment explanation
Indices: 31311--31409 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
31301 GATACTATTT
31311 TCATCACCATAA
1 TCATCACCAT-A
*
31323 TCCATCTCCATTA
1 T-CATCACCA-TA
*
31336 TCA-CGCCTATA
1 TCATCACC-ATA
31347 TCATCACCATA
1 TCATCACCATA
31358 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
31372 TCA-CGCCTATA
1 TCATCACC-ATA
31383 TCATCACCATA
1 TCATCACCATA
31394 TTCCATCACCATA
1 -T-CATCACCATA
31407 TCA
1 TCA
31410 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:31438 original size:33 final size:33
Alignment explanation
Indices: 31323--31462 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
31313 ATCACCATAA
* * *
31323 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
31357 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
31395 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
31428 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
31461 TC
1 TC
31463 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:35341 original size:36 final size:36
Alignment explanation
Indices: 35289--35401 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
35279 GATACTATTT
*
35289 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
35325 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
35361 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
35396 ACATCA
1 TCATCA
35402 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:35344 original size:13 final size:11
Alignment explanation
Indices: 35289--35387 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
35279 GATACTATTT
35289 TCATCACCATAA
1 TCATCACCAT-A
*
35301 TCCATCTCCATTA
1 T-CATCACCA-TA
*
35314 TCA-CGCCTATA
1 TCATCACC-ATA
35325 TCATCACCATA
1 TCATCACCATA
35336 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
35350 TCA-CGCCTATA
1 TCATCACC-ATA
35361 TCATCACCATA
1 TCATCACCATA
35372 TTCCATCACCATA
1 -T-CATCACCATA
35385 TCA
1 TCA
35388 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:35416 original size:33 final size:33
Alignment explanation
Indices: 35301--35440 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
35291 ATCACCATAA
* * *
35301 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
35335 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
35373 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
35406 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
35439 TC
1 TC
35441 ATTCATCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:37824 original size:15 final size:16
Alignment explanation
Indices: 37804--37836 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
37794 GTGATGGACT
37804 ATGGTGATAGAAA-AG
1 ATGGTGATAGAAATAG
*
37819 ATGGTGATGGAAATAG
1 ATGGTGATAGAAATAG
37835 AT
1 AT
37837 AGTATCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.24
Consensus pattern (16 bp):
ATGGTGATAGAAATAG
Found at i:40256 original size:30 final size:31
Alignment explanation
Indices: 40220--40279 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
40210 CTTAGCTTTA
**
40220 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
40250 TATTATGTTTACATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
40280 GGCAGCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:42731 original size:19 final size:21
Alignment explanation
Indices: 42707--42758 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
42697 CAGCCAAGAG
*
42707 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
42726 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
42747 CATGTATTTTCA
1 CATGTATTTTCA
42759 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:43400 original size:19 final size:20
Alignment explanation
Indices: 43359--43409 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
43349 GACACCCCTT
**
43359 TGAATATACATGATTTTTTA
1 TGAATATACATGATTTTAAA
*
43379 TGAAAATACATG-TTTTAAA
1 TGAATATACATGATTTTAAA
43398 TGAATATACATG
1 TGAATATACATG
43410 CTCTTGGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (20 bp):
TGAATATACATGATTTTAAA
Found at i:43851 original size:302 final size:301
Alignment explanation
Indices: 43306--43886 Score: 1126
Period size: 302 Copynumber: 1.9 Consensus size: 301
43296 GGGACACAAT
43306 AAGGGTTTAGGCCGAATAAAAAATTGATGGTTCGGCCAAGGTTGACACCCCTTTGAATATACATG
1 AAGGGTTTAGGCCGAATAAAAAATTGATGGTTCGGCCAAGGTTGACACCCCTTTGAATATACATG
43371 ATTTTTTATGAAAATACATGTTTTAAATGAATATACATGCTCTTGGTGATGCAAGCACGTTTTCA
66 ATTTTTTATGAAAATACATGTTTTAAATGAATATACATGCTCTTGGTGATGCAAGCACGTTTTCA
43436 CCTATAAAGAGAGTACTCTTGAACACCTTTATATTGAATTTACTATATATTAGTTATATACTATA
131 CCTATAAAGAGAGTACTCTTGAACACCTTTATATTGAATTTACTATATATTAGTTATATACTATA
*
43501 TGCTTTTATAATACAATTCATAATAAGAATTCTTGTTATATAGTTAAAAATAACTTAATATGAAT
196 TGCTTTTATAATACAATTCATAATAAGAATTCTTGTTATATAGTTAAAAATAACTTAATATGAAC
43566 ACAACATGCACATTGATATGATGGCCTATTTATAGTTTTCA
261 ACAACATGCACATTGATATGATGGCCTATTTATAGTTTTCA
*
43607 AAGGGTTTAGGCCGAATAAAAAATTGATGGTTTGGCCAAGGTTGACACCCCTTTGAATATACATG
1 AAGGGTTTAGGCCGAATAAAAAATTGATGGTTCGGCCAAGGTTGACACCCCTTTGAATATACATG
43672 ATTTTTTTATGAAAATACATGTTTTAAATGAATATACATGCTCTTGGTGATGCAAGCACGTTTTC
66 A-TTTTTTATGAAAATACATGTTTTAAATGAATATACATGCTCTTGGTGATGCAAGCACGTTTTC
*
43737 ACCTATAAAGATAGTACTCTTGAACACCTTTATATTGAATTTACTATATATTAGTTATATACTAT
130 ACCTATAAAGAGAGTACTCTTGAACACCTTTATATTGAATTTACTATATATTAGTTATATACTAT
43802 ATGCTTTTATAATACAATTCATAATAAGAATTCTTGTTATATAGTTAAAAATAACTTAATATGAA
195 ATGCTTTTATAATACAATTCATAATAAGAATTCTTGTTATATAGTTAAAAATAACTTAATATGAA
43867 CACAACATGCACATTGATAT
260 CACAACATGCACATTGATAT
43887 TTAAGCATGT
Statistics
Matches: 276, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
301 65 0.24
302 211 0.76
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (301 bp):
AAGGGTTTAGGCCGAATAAAAAATTGATGGTTCGGCCAAGGTTGACACCCCTTTGAATATACATG
ATTTTTTATGAAAATACATGTTTTAAATGAATATACATGCTCTTGGTGATGCAAGCACGTTTTCA
CCTATAAAGAGAGTACTCTTGAACACCTTTATATTGAATTTACTATATATTAGTTATATACTATA
TGCTTTTATAATACAATTCATAATAAGAATTCTTGTTATATAGTTAAAAATAACTTAATATGAAC
ACAACATGCACATTGATATGATGGCCTATTTATAGTTTTCA
Found at i:45433 original size:15 final size:15
Alignment explanation
Indices: 45422--45450 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45412 ACTCAAAAAG
45422 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
45437 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
45451 GTTGAAGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:47900 original size:2 final size:2
Alignment explanation
Indices: 47893--47919 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47883 TTTTAAAAGT
47893 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
47920 GTTGGTCCAT
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:50071 original size:16 final size:18
Alignment explanation
Indices: 50039--50073 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
50029 ATATAAAAAC
50039 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
50057 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
50073 A
1 A
50074 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:50109 original size:20 final size:20
Alignment explanation
Indices: 50084--50121 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
50074 AATGAGTAAA
50084 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
50104 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
50122 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:50694 original size:37 final size:36
Alignment explanation
Indices: 50651--50752 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
50641 ATAGTAGAAC
50651 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
50688 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
50722 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
50753 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:51605 original size:105 final size:105
Alignment explanation
Indices: 51298--51919 Score: 862
Period size: 105 Copynumber: 6.0 Consensus size: 105
51288 CATTGTTCCA
* * ** * *
51298 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTATTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTT-GTTGTTGACAA
* * * *
51362 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * ** *
51404 AGTCTAATATCCTTCGTTGTGAAGTTAAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
51464 AGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
51504 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
51569 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
51609 AGTCCAATATCGTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTGGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* * *
51674 AGCGGTCCCTTCTTTGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
51714 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
51779 AGCGGTCCCTTCATCATGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
51819 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
* * *
51884 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
51920 CCTCGAGTGC
Statistics
Matches: 467, Mismatches: 41, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
99 1 0.00
100 81 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 299 0.64
106 73 0.16
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:52410 original size:29 final size:26
Alignment explanation
Indices: 52345--52411 Score: 62
Period size: 29 Copynumber: 2.3 Consensus size: 26
52335 GCTTGTCTGG
*
52345 AATCTTGATTCTTGAATCTTCAAATTTT
1 AATC-TGA-TCTTGAATCTTCAAATTTA
52373 AATCCCTGATCTTGAATTCTTCAAATGTTCA
1 AAT--CTGATCTTGAA-TCTTCAAAT-TT-A
52404 AATCTGAT
1 AATCTGAT
52412 GTGCACATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
28 10 0.30
29 17 0.52
30 3 0.09
31 3 0.09
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (26 bp):
AATCTGATCTTGAATCTTCAAATTTA
Found at i:52695 original size:67 final size:67
Alignment explanation
Indices: 52549--52883 Score: 254
Period size: 65 Copynumber: 4.9 Consensus size: 67
52539 GGAAACGATC
* * * *
52549 TCAAAGATATCTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAA
52614 TAAAT
63 TAAAT
** * *
52619 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAA
52684 AT
66 AT
* ** * *
52686 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATTTGTTTTAAGGGAAA--
52748 GTCTCAAGAGT
63 ---T-AA-A-T
* * * * * * * * * *
52759 GACAAA-A-CTT-AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACA
1 -TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATA
*
52821 TAT
65 AAT
* * *
52824 TCAAATA-TTT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
52884 CTGTCTCAAG
Statistics
Matches: 213, Mismatches: 40, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
64 4 0.02
65 85 0.40
66 8 0.04
67 24 0.11
68 32 0.15
69 3 0.01
70 7 0.03
71 2 0.01
72 4 0.02
73 40 0.19
74 4 0.02
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAA
AT
Found at i:52746 original size:36 final size:35
Alignment explanation
Indices: 52695--52903 Score: 191
Period size: 36 Copynumber: 6.0 Consensus size: 35
52685 TTCAAAGATT
* *
52695 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
52731 TTGTTTCAAGAGAAACTGTCTCAAGAGTGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
52766 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
52804 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
52833 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
52868 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
52904 CTCTTCTAGT
Statistics
Matches: 141, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
28 2 0.01
29 17 0.12
30 2 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 7 0.05
36 76 0.54
37 29 0.21
38 3 0.02
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:52791 original size:37 final size:36
Alignment explanation
Indices: 52706--52817 Score: 122
Period size: 37 Copynumber: 3.1 Consensus size: 36
52696 TGTTTCAAGG
* *
52706 GAAACTGTCTCAAGATAGACGAAAATTGTTTCAAGA
1 GAAACTGTCTCAAGATAGACGAAAATTGTTCCAAAA
52742 GAAACTGTCTCAAGAGT-GAC-AAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGA-TAGACGAAAA-TT-GTTCCAAAA
** * *
52779 GAAACTGTCTCAAGGGAGACGAAATTTGTTTC-AAA
1 GAAACTGTCTCAAGATAGACGAAAATTGTTCCAAAA
52814 GAAA
1 GAAA
52818 ACATATTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
35 11 0.17
36 24 0.37
37 27 0.42
38 3 0.05
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (36 bp):
GAAACTGTCTCAAGATAGACGAAAATTGTTCCAAAA
Found at i:52804 original size:138 final size:138
Alignment explanation
Indices: 52643--52905 Score: 402
Period size: 138 Copynumber: 1.9 Consensus size: 138
52633 TTTCAAGAGT
* ** * * *
52643 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGAGA
* *
52708 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGTGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
52772 TCCAAAAGA
130 TCCAAAAGA
* * *
52781 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGAGA
1 AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGAGA
*
52846 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
66 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
52906 CTTCTAGTGA
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
137 4 0.04
138 108 0.96
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (138 bp):
AACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGAGA
AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
CCAAAAGA
Found at i:52925 original size:35 final size:36
Alignment explanation
Indices: 52837--52937 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 36
52827 AATATTTTGT
* *
52837 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
52873 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
52907 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
52938 TCTTGTTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
34 5 0.09
35 22 0.39
36 28 0.50
37 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:52953 original size:35 final size:35
Alignment explanation
Indices: 52833--52953 Score: 113
Period size: 35 Copynumber: 3.4 Consensus size: 35
52823 TTCAAATATT
52833 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT-
1 TTGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATC
* *
52869 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATC
* * * *
52905 -T-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAATC
1 TTGTTTC-A-AGAAAACTGTCTCAAGAGAGACAAATC
*
52940 TTGTTTTAAGAAAA
1 TTGTTTCAAGAAAA
52954 ACAATCATGA
Statistics
Matches: 68, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
34 3 0.04
35 32 0.47
36 30 0.44
37 3 0.04
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAAAACTGTCTCAAGAGAGACAAATC
Found at i:53410 original size:18 final size:18
Alignment explanation
Indices: 53383--53418 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53373 TGTTGAATCC
* *
53383 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
53401 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
53419 TTGATGTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:54526 original size:16 final size:15
Alignment explanation
Indices: 54507--54559 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
54497 TTCTTTTTGA
*
54507 TTTTTGTTCTTTATTT
1 TTTTTGTTCTTT-TCT
54523 TTTTTGTT-TTCTTCT
1 TTTTTGTTCTT-TTCT
54538 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
54554 TTTTTG
1 TTTTTG
54560 GTTTTTTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.30
16 21 0.64
17 2 0.06
ACGTcount: A:0.02, C:0.11, G:0.08, T:0.79
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:54567 original size:16 final size:16
Alignment explanation
Indices: 54521--54567 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
54511 TGTTCTTTAT
* *
54521 TTTTTTTGTTTTCTTC
1 TTTTTTGGTTTTTTTC
* *
54537 TTTTTTGCTTCTTTTC
1 TTTTTTGGTTTTTTTC
54553 TTTTTTGGTTTTTTT
1 TTTTTTGGTTTTTTT
54568 GCCCTTTTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.81
Consensus pattern (16 bp):
TTTTTTGGTTTTTTTC
Found at i:58984 original size:16 final size:18
Alignment explanation
Indices: 58952--58986 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
58942 ATATAAAAAC
58952 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
58970 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
58986 A
1 A
58987 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:59568 original size:37 final size:35
Alignment explanation
Indices: 59553--59654 Score: 170
Period size: 34 Copynumber: 2.9 Consensus size: 35
59543 ATAGTAGAAC
59553 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG--AAAT
*
59590 TTTATCCTATTTTTAGGAGTTTGAATCCTA-AAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAT
59624 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
59655 TAGGACAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 33 0.53
37 29 0.47
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAT
Found at i:60510 original size:18 final size:18
Alignment explanation
Indices: 60487--60525 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
60477 AAATATTTTA
*
60487 TTTGATATATTATATTGT
1 TTTGATATATTATATTAT
* *
60505 TTTGATTTGTTATATTAT
1 TTTGATATATTATATTAT
60523 TTT
1 TTT
60526 TATGCTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (18 bp):
TTTGATATATTATATTAT
Done.