Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005736.1 Hibiscus syriacus cultivar Beakdansim tig00013411_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: 121025
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2360 original size:16 final size:16
Alignment explanation
Indices: 2339--2371 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2329 GGCATGGCCG
2339 AATGGTCTGATTACAA
1 AATGGTCTGATTACAA
2355 AATGGTCTGATTACAA
1 AATGGTCTGATTACAA
2371 A
1 A
2372 TGAAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (16 bp):
AATGGTCTGATTACAA
Found at i:4471 original size:24 final size:25
Alignment explanation
Indices: 4425--4472 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
4415 CACCATGATC
* * *
4425 TGCATTTTCTTCAGTTTCTTCATCT
1 TGCATTGTCTTCAGGTTCCTCATCT
4450 TGCATTGT-TTCAGGTTCCTCATC
1 TGCATTGTCTTCAGGTTCCTCATC
4473 AAAAATAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.50
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCCTCATCT
Found at i:6968 original size:17 final size:16
Alignment explanation
Indices: 6946--6979 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
6936 CGACTAAAGG
6946 AAATGGATATGGTATAA
1 AAATGGATATGGT-TAA
6963 AAATGGATATGGTTAA
1 AAATGGATATGGTTAA
6979 A
1 A
6980 GGTAAGATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (16 bp):
AAATGGATATGGTTAA
Found at i:7710 original size:13 final size:13
Alignment explanation
Indices: 7692--7728 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
7682 ATGTTGGCAT
*
7692 GAAGGTGGTGGAA
1 GAAGGTGATGGAA
7705 GAAGGTGATGGAA
1 GAAGGTGATGGAA
*
7718 GATGGTGATGG
1 GAAGGTGATGG
7729 TTTAAGTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.51, T:0.19
Consensus pattern (13 bp):
GAAGGTGATGGAA
Found at i:11687 original size:18 final size:18
Alignment explanation
Indices: 11645--11690 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
11635 TAGTTTGATT
*
11645 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
11663 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
11681 AATGAACTAA
1 AATGAACTAA
11691 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:11766 original size:17 final size:17
Alignment explanation
Indices: 11746--11787 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
11736 ACTACTTCCC
11746 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
*
11763 TAAATGCAATACATGCT
1 TAAATGAAATACATGCT
*
11780 TTAATGAA
1 TAAATGAA
11788 CAACATACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:12137 original size:17 final size:17
Alignment explanation
Indices: 12115--12167 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
12105 AATTAAGAGT
12115 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
12132 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
12149 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
12166 TA
1 TA
12168 ACTTTATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:12180 original size:18 final size:18
Alignment explanation
Indices: 12118--12186 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
12108 TAAGAGTTAG
* *
12118 TTTAATAAATGAACT-AG
1 TTTAATTAATGAACTAAC
* * *
12135 TTTGATGAATGAACT-AG
1 TTTAATTAATGAACTAAC
12152 TTTAATTAATGAACTAAC
1 TTTAATTAATGAACTAAC
12170 TTT-ATTCAATGAACTAA
1 TTTAATT-AATGAACTAA
12187 ATGCATGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
17 31 0.69
18 14 0.31
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTAATTAATGAACTAAC
Found at i:18048 original size:13 final size:13
Alignment explanation
Indices: 18030--18115 Score: 63
Period size: 14 Copynumber: 6.7 Consensus size: 13
18020 ACTATATGTT
18030 CATCACCATCTTC
1 CATCACCATCTTC
*
18043 CATCACCAT-TTT
1 CATCACCATCTTC
* **
18055 CA-CACC-TATAA
1 CATCACCATCTTC
*
18066 CATCACCATCTTTT
1 CATCACCATC-TTC
18080 CATCACCATCTTTC
1 CATCACCATC-TTC
18094 CATCACCAT-TATC
1 CATCACCATCT-TC
*
18107 TATCACCAT
1 CATCACCAT
18116 TCACGCCTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
10 1 0.02
11 7 0.12
12 9 0.15
13 20 0.33
14 23 0.38
ACGTcount: A:0.28, C:0.38, G:0.00, T:0.34
Consensus pattern (13 bp):
CATCACCATCTTC
Found at i:18083 original size:14 final size:14
Alignment explanation
Indices: 18066--18115 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
18056 ACACCTATAA
*
18066 CATCACCATCTTTT
1 CATCACCATCTTTC
18080 CATCACCATCTTTC
1 CATCACCATCTTTC
*
18094 CATCACCAT-TATC
1 CATCACCATCTTTC
*
18107 TATCACCAT
1 CATCACCAT
18116 TCACGCCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 11 0.33
14 22 0.67
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:18293 original size:15 final size:15
Alignment explanation
Indices: 18273--18303 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18263 TCTTTGATAA
18273 CATTTCTTTCCATTT
1 CATTTCTTTCCATTT
18288 CATTTCTTTCCATTT
1 CATTTCTTTCCATTT
18303 C
1 C
18304 TATTACCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (15 bp):
CATTTCTTTCCATTT
Found at i:25222 original size:11 final size:11
Alignment explanation
Indices: 25208--25232 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25198 AATTTTTGTA
25208 ATTTTTTTAAT
1 ATTTTTTTAAT
25219 ATTTTTTTAAT
1 ATTTTTTTAAT
25230 ATT
1 ATT
25233 CAAAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTTTTAAT
Found at i:27435 original size:21 final size:20
Alignment explanation
Indices: 27409--27455 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
27399 ATTTTTTTTC
27409 AAAAAAAA-CAAAAAAAGGCAA
1 AAAAAAAAGCAAAAAAA--CAA
27430 AAAAAAAAGGCAAAAAAACAA
1 AAAAAAAA-GCAAAAAAACAA
27451 AAAAA
1 AAAAA
27456 GAGCCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 16 0.67
23 8 0.33
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGCAAAAAAACAA
Found at i:27436 original size:13 final size:13
Alignment explanation
Indices: 27418--27447 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
27408 CAAAAAAAAC
27418 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
27431 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
27444 AAAA
1 AAAA
27448 CAAAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAGGCAAA
Found at i:27473 original size:20 final size:20
Alignment explanation
Indices: 27429--27466 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27419 AAAAAAGGCA
*
27429 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
27449 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
27467 TCCAAAATTT
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:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:40347 original size:29 final size:29
Alignment explanation
Indices: 40302--40357 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
40292 GTTCAAATAC
40302 AAAAGAAGAAAAAAATTT-AGAAAAGAAGA
1 AAAAGAAGAAAAAAATTTCA-AAAAGAAGA
*
40331 AAAAGAA-AAGAAGAATTTCAAAAAGAA
1 AAAAGAAGAA-AAAAATTTCAAAAAGAA
40358 AGCAAAGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 2 0.08
29 21 0.88
30 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.11
Consensus pattern (29 bp):
AAAAGAAGAAAAAAATTTCAAAAAGAAGA
Found at i:46469 original size:23 final size:23
Alignment explanation
Indices: 46441--46561 Score: 74
Period size: 23 Copynumber: 5.1 Consensus size: 23
46431 ACAATTTGTC
46441 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCGCC-ATAT
*
46464 CATCACCA-TAGTCCATCTCCAT-T
1 CATCACCATTA-T-CATCGCCATAT
* *
46487 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCGCCATA-T
46512 CCATCACCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCGCC-ATAT
*
46536 CATCACCA-TATTCCATCACCATAT
1 CATCACCATTA-T-CATCGCCATAT
46560 CA
1 CA
46562 CGCCTATATT
Statistics
Matches: 78, Mismatches: 6, Indels: 27
0.70 0.05 0.24
Matches are distributed among these distances:
22 9 0.12
23 28 0.36
24 17 0.22
25 17 0.22
26 2 0.03
27 5 0.06
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (23 bp):
CATCACCATTATCATCGCCATAT
Found at i:46486 original size:36 final size:36
Alignment explanation
Indices: 46438--46570 Score: 241
Period size: 36 Copynumber: 3.7 Consensus size: 36
46428 GATACAATTT
46438 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
46474 GTCCATCTCCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
46510 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
46546 TTCCATCACCA-TATCACGCCTATAT
1 GTCCATCACCATTATCACGCCTATAT
46571 TAACATCAAC
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 14 0.15
36 80 0.85
ACGTcount: A:0.29, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:46518 original size:13 final size:11
Alignment explanation
Indices: 46441--46561 Score: 77
Period size: 11 Copynumber: 10.2 Consensus size: 11
46431 ACAATTTGTC
46441 CATCACCATTAT
1 CATCACCA-TAT
*
46453 CA-CGCCTATAT
1 CATCACC-ATAT
46464 CATCACCATAGT
1 CATCACCATA-T
*
46476 CCATCTCCATTAT
1 -CATCACCA-TAT
*
46489 CA-CGCCTATAT
1 CATCACC-ATAT
46500 CATCACCATAGT
1 CATCACCATA-T
46512 CCATCACCATTAT
1 -CATCACCA-TAT
*
46525 CA-CGCCTATAT
1 CATCACC-ATAT
46536 CATCACCATATT
1 CATCACCATA-T
46548 CCATCACCATAT
1 -CATCACCATAT
46560 CA
1 CA
46562 CGCCTATATT
Statistics
Matches: 88, Mismatches: 7, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
11 35 0.40
12 22 0.25
13 27 0.31
14 4 0.05
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:46996 original size:17 final size:17
Alignment explanation
Indices: 46976--47008 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
46966 CAAAAAGAGA
46976 AAAAGA-AAGAAGAAAAT
1 AAAAGAGAA-AAGAAAAT
46993 AAAAGAGAAAAGAAAA
1 AAAAGAGAAAAGAAAA
47009 AGACTCCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAAGAGAAAAGAAAAT
Found at i:47009 original size:13 final size:12
Alignment explanation
Indices: 46967--47011 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
46957 CAAAAGCAAC
46967 AAAAAGAGAAAA
1 AAAAAGAGAAAA
*
46979 AGAAAGAAGAAAA
1 AAAAAG-AGAAAA
*
46992 TAAAAGAGAAAA
1 AAAAAGAGAAAA
47004 GAAAAAGA
1 -AAAAAGA
47012 CTCCTACATC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:51023 original size:23 final size:23
Alignment explanation
Indices: 50994--51098 Score: 76
Period size: 23 Copynumber: 4.4 Consensus size: 23
50984 TACAATCTGT
50994 TCATCACCATTATCA-CGCCTATA
1 TCATCACCATTATCATCGCC-ATA
*
51017 TCATCACCA-TAGTCCATCTCCAT-
1 TCATCACCATTA-T-CATCGCCATA
* *
51040 T-ATCACGCCTATATCATCACCATA
1 TCATCAC-CAT-TATCATCGCCATA
51064 GTCCATCACCATTATCA-CGCCTATA
1 -T-CATCACCATTATCATCGCC-ATA
51089 TCATCACCAT
1 TCATCACCAT
51099 ATTCCATCAC
Statistics
Matches: 66, Mismatches: 5, Indels: 22
0.71 0.05 0.24
Matches are distributed among these distances:
22 7 0.11
23 29 0.44
24 9 0.14
25 14 0.21
26 2 0.03
27 5 0.08
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (23 bp):
TCATCACCATTATCATCGCCATA
Found at i:51047 original size:36 final size:36
Alignment explanation
Indices: 50995--51132 Score: 224
Period size: 36 Copynumber: 3.9 Consensus size: 36
50985 ACAATCTGTT
50995 CATCACCATTATCACGCCTATATCATCACCATAGTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
*
51031 CATCTCCATTATCACGCCTATATCATCACCATAGTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
*
51067 CATCACCATTATCACGCCTATATCATCACCATATTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
* * *
51103 CATCACCA-TATTATGCCTATATTATCACCA
1 CATCACCATTATCACGCCTATATCATCACCA
51133 ACTTATAAAT
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.20
36 77 0.80
ACGTcount: A:0.30, C:0.35, G:0.04, T:0.30
Consensus pattern (36 bp):
CATCACCATTATCACGCCTATATCATCACCATAGTC
Found at i:51072 original size:13 final size:11
Alignment explanation
Indices: 50994--51113 Score: 75
Period size: 11 Copynumber: 10.1 Consensus size: 11
50984 TACAATCTGT
50994 TCATCACCATTA
1 TCATCACCA-TA
*
51006 TCA-CGCCTATA
1 TCATCACC-ATA
51017 TCATCACCATA
1 TCATCACCATA
*
51028 GTCCATCTCCATTA
1 -T-CATCACCA-TA
*
51042 TCA-CGCCTATA
1 TCATCACC-ATA
51053 TCATCACCATA
1 TCATCACCATA
51064 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
51078 TCA-CGCCTATA
1 TCATCACC-ATA
51089 TCATCACCATA
1 TCATCACCATA
51100 TTCCATCACCATA
1 -T-CATCACCATA
51113 T
1 T
51114 TATGCCTATA
Statistics
Matches: 87, Mismatches: 7, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
11 33 0.38
12 23 0.26
13 27 0.31
14 4 0.05
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.30
Consensus pattern (11 bp):
TCATCACCATA
Found at i:60372 original size:22 final size:21
Alignment explanation
Indices: 60346--60386 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
60336 GCTGCGGATA
60346 TGATGGTCTTGATGGATGAAGT
1 TGATGGTCTTGAT-GATGAAGT
*
60368 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
60387 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGT
Found at i:63925 original size:22 final size:22
Alignment explanation
Indices: 63877--63925 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
63867 CTTTGGTTGT
*
63877 TCTTCTAGGAAGGTGGTGAGTA
1 TCTTTTAGGAAGGTGGTGAGTA
63899 TCTTTTAGGAAGGTGGTGAGTA
1 TCTTTTAGGAAGGTGGTGAGTA
63921 TCTTT
1 TCTTT
63926 GCATAGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.08, G:0.33, T:0.39
Consensus pattern (22 bp):
TCTTTTAGGAAGGTGGTGAGTA
Found at i:69629 original size:10 final size:9
Alignment explanation
Indices: 69613--69674 Score: 61
Period size: 10 Copynumber: 6.2 Consensus size: 9
69603 TTTGAAATTG
69613 TTTTTCTTT
1 TTTTTCTTT
69622 TCTTTTCTTT
1 T-TTTTCTTT
*
69632 TCTTTCTGATT
1 TTTTTCT--TT
69643 TTTTTCTTCT
1 TTTTTCTT-T
69653 TTTTGTCTTT
1 TTTT-TCTTT
69663 TTCTTTCTTT
1 TT-TTTCTTT
69673 TT
1 TT
69675 GCACTACAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
9 7 0.16
10 24 0.53
11 14 0.31
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:69673 original size:18 final size:19
Alignment explanation
Indices: 69624--69675 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
69614 TTTTCTTTTC
* *
69624 TTTTCTTTTCTTTCTGATTT
1 TTTTC-TTTCTTTTTGATCT
69644 TTTTC-TTCTTTTTG-TCT
1 TTTTCTTTCTTTTTGATCT
69661 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
69676 CACTACAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 7 0.24
18 17 0.59
20 5 0.17
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCTTTTTGATCT
Found at i:70000 original size:22 final size:21
Alignment explanation
Indices: 69974--70014 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
69964 GTTGCGAAAA
69974 TGATGGTCTTGATGGATGAAGT
1 TGATGGTCTTGAT-GATGAAGT
*
69996 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
70015 AAGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGT
Found at i:74193 original size:20 final size:19
Alignment explanation
Indices: 74140--74212 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 19
74130 TTGCTTTCTC
* *
74140 TTTTTGAATTTATTT-TTA
1 TTTTTGATTTTTTTTCTTA
74158 -TTTT-ATTTTCTTTTCTTA
1 TTTTTGATTTT-TTTTCTTA
*
74176 TTTTCTGATTTTTTTTCTTC
1 TTTT-TGATTTTTTTTCTTA
*
74196 TTTTTG-TCTTTTTTCTT
1 TTTTTGATTTTTTTTCTT
74213 TCTTTTTGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
16 4 0.09
17 7 0.15
18 13 0.28
19 5 0.11
20 12 0.26
21 5 0.11
ACGTcount: A:0.10, C:0.10, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTTTGATTTTTTTTCTTA
Found at i:84306 original size:20 final size:20
Alignment explanation
Indices: 84256--84307 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
84246 TTTGAATTTA
84256 TTTT-TCTTTTCTTTTATTCT
1 TTTTGTCTTTT-TTTTATTCT
* *
84276 TTTCTG-ATTTTTTTTCTTCT
1 TTT-TGTCTTTTTTTTATTCT
84296 TTTTGTCTTTTT
1 TTTTGTCTTTTT
84308 CTCTCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTTGTCTTTTTTTTATTCT
Found at i:85341 original size:16 final size:15
Alignment explanation
Indices: 85300--85341 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
85290 AGATGGAAAG
85300 GCATCTTCATGGGAA
1 GCATCTTCATGGGAA
* *
85315 GTATCTTCATGGGCA
1 GCATCTTCATGGGAA
85330 GCATCATTCATG
1 GCATC-TTCATG
85342 AAAGGTCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (15 bp):
GCATCTTCATGGGAA
Found at i:88857 original size:10 final size:9
Alignment explanation
Indices: 88841--88901 Score: 59
Period size: 10 Copynumber: 6.2 Consensus size: 9
88831 TTTGAATTTC
88841 TTTTTCTTT
1 TTTTTCTTT
88850 TCTTTTCTTCT
1 T-TTTTCTT-T
**
88861 TTTTTGATT
1 TTTTTCTTT
88870 TTTTTCTTCT
1 TTTTTCTT-T
88880 TTTTATCTTT
1 TTTT-TCTTT
88890 TTCTTTCTTT
1 TT-TTTCTTT
88900 TT
1 TT
88902 GCACTCCAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
9 8 0.19
10 27 0.63
11 8 0.19
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:88862 original size:19 final size:18
Alignment explanation
Indices: 88838--88901 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
88828 CTTTTTGAAT
88838 TTCTTTTTCT-TTTCTTTTC
1 TTCTTTTT-TATTT-TTTTC
88857 TTCTTTTTTGATTTTTTTC
1 TTCTTTTTT-ATTTTTTTC
*
88876 TTC-TTTTTATCTTTTTC
1 TTCTTTTTTATTTTTTTC
88893 TTTCTTTTT
1 -TTCTTTTT
88902 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
17 8 0.20
18 9 0.22
19 20 0.50
20 3 0.08
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.80
Consensus pattern (18 bp):
TTCTTTTTTATTTTTTTC
Found at i:88900 original size:27 final size:27
Alignment explanation
Indices: 88837--88901 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 27
88827 TCTTTTTGAA
88837 TTTCTTTTTCTTTTCTTTTCTTCTTTTT
1 TTTCTTTTTC-TTTCTTTTCTTCTTTTT
88865 TGATT-TTTTTC-TTCTTTT-TATCTTTTT
1 T--TTCTTTTTCTTTCTTTTCT-TCTTTTT
88892 CTTTCTTTTT
1 -TTTCTTTTT
88902 GCACTCCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
26 3 0.09
27 19 0.59
28 2 0.06
29 6 0.19
30 2 0.06
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (27 bp):
TTTCTTTTTCTTTCTTTTCTTCTTTTT
Found at i:89227 original size:22 final size:21
Alignment explanation
Indices: 89201--89241 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
89191 GTTACGAAAA
89201 TGATGGTCTTGATGGATGAAGT
1 TGATGGTCTTGAT-GATGAAGT
*
89223 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
89242 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGT
Found at i:90505 original size:15 final size:16
Alignment explanation
Indices: 90485--90527 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
90475 AGTTATCATC
90485 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
90500 ATAATATA-TATAGATG
1 ATAATA-ACTATAGATG
*
90516 AAAATAACTATA
1 ATAATAACTATA
90528 TTAAAACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:97451 original size:2 final size:2
Alignment explanation
Indices: 97444--97493 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
97434 TATTACATTC
97444 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
97486 AT AT AT AT
1 AT AT AT AT
97494 TCTTATAACG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98050 original size:17 final size:17
Alignment explanation
Indices: 98018--98157 Score: 127
Period size: 17 Copynumber: 8.1 Consensus size: 17
98008 TTTAACTAAG
*
98018 TAGTTCATTGATTAAAC
1 TAGTTCATTCATTAAAC
* *
98035 TTGTTTATTCATTAAAC
1 TAGTTCATTCATTAAAC
*
98052 TAGTTCATTCATCAAAC
1 TAGTTCATTCATTAAAC
** *
98069 TAGTTCATTCAAGATTAC
1 TAGTTCATTCATTA-AAC
* * * *
98087 AAGTTCATTAAATAAAGT
1 TAGTTCATTCATTAAA-C
*
98105 TAGTTCATTAATTAAAC
1 TAGTTCATTCATTAAAC
* *
98122 TATTTCATTCATCAAAC
1 TAGTTCATTCATTAAAC
*
98139 TAGTTCATTTATTAAAC
1 TAGTTCATTCATTAAAC
98156 TA
1 TA
98158 ACTCTTAATT
Statistics
Matches: 98, Mismatches: 23, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
17 71 0.72
18 27 0.28
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.41
Consensus pattern (17 bp):
TAGTTCATTCATTAAAC
Found at i:109380 original size:17 final size:17
Alignment explanation
Indices: 109358--109397 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
109348 CAGCTCACAA
*
109358 GGAACATGGCATCTCAT
1 GGAACATGGCAGCTCAT
* *
109375 GGAACATTGTAGCTCAT
1 GGAACATGGCAGCTCAT
109392 GGAACA
1 GGAACA
109398 CTAAGGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (17 bp):
GGAACATGGCAGCTCAT
Found at i:110880 original size:16 final size:15
Alignment explanation
Indices: 110842--110880 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
110832 TAAGATTAGA
110842 ATAAATAAACAAAAG
1 ATAAATAAACAAAAG
**
110857 ATAAATAAACGGAAG
1 ATAAATAAACAAAAG
110872 ATGAAATAA
1 AT-AAATAA
110881 GATAATAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.67, C:0.05, G:0.13, T:0.15
Consensus pattern (15 bp):
ATAAATAAACAAAAG
Found at i:115158 original size:18 final size:18
Alignment explanation
Indices: 115137--115194 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
115127 AATTTTGGCT
115137 TTTTTGGCTCTTTTTTTG
1 TTTTTGGCTCTTTTTTTG
*
115155 TTTTTTTGC-CTTTTTTT-
1 -TTTTTGGCTCTTTTTTTG
* *
115172 TTTTTGCCTTTTTTTTTG
1 TTTTTGGCTCTTTTTTTG
115190 TTTTT
1 TTTTT
115195 TTTGTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 13 0.39
19 7 0.21
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.79
Consensus pattern (18 bp):
TTTTTGGCTCTTTTTTTG
Found at i:115159 original size:20 final size:20
Alignment explanation
Indices: 115136--115196 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
115126 AAATTTTGGC
115136 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGGCTCTTTTTTTGT
115156 TTTTTT-GC-C--TTTTT-T
1 TTTTTTGGCTCTTTTTTTGT
* *
115171 TTTTTTGCCTTTTTTTTTGT
1 TTTTTTGGCTCTTTTTTTGT
115191 TTTTTT
1 TTTTTT
115197 TGTTTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
15 7 0.21
16 6 0.18
18 1 0.03
19 7 0.21
20 13 0.38
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (20 bp):
TTTTTTGGCTCTTTTTTTGT
Found at i:115170 original size:12 final size:10
Alignment explanation
Indices: 115147--115205 Score: 57
Period size: 10 Copynumber: 5.5 Consensus size: 10
115137 TTTTTGGCTC
115147 TTTTTTTGTT
1 TTTTTTTGTT
*
115157 TTTTTGCCTTTTT
1 TTTTT---TTGTT
115170 TTTTTTTGCCTT
1 TTTTTTTG--TT
115182 TTTTTTTG-T
1 TTTTTTTGTT
115191 TTTTTTTGTT
1 TTTTTTTGTT
115201 TTTTT
1 TTTTT
115206 GAAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
9 9 0.22
10 13 0.32
12 10 0.24
13 9 0.22
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:115173 original size:15 final size:15
Alignment explanation
Indices: 115149--115188 Score: 71
Period size: 15 Copynumber: 2.6 Consensus size: 15
115139 TTTGGCTCTT
115149 TTTTTGTTTTTTTGCC
1 TTTTT-TTTTTTTGCC
115165 TTTTTTTTTTTTGCC
1 TTTTTTTTTTTTGCC
115180 TTTTTTTTT
1 TTTTTTTTT
115189 GTTTTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTGCC
Found at i:117776 original size:23 final size:22
Alignment explanation
Indices: 117733--117776 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
117723 TTCAATTTCT
* * *
117733 TAATCTTTTTTTTATCTTGTTC
1 TAATATTTTTTTTACCGTGTTC
117755 TAATATTTTTTCTTACCGTGTT
1 TAATATTTTTT-TTACCGTGTT
117777 TCCAGCACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.16, C:0.14, G:0.07, T:0.64
Consensus pattern (22 bp):
TAATATTTTTTTTACCGTGTTC
Found at i:117893 original size:25 final size:25
Alignment explanation
Indices: 117859--117909 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
117849 CATCGAGTAT
117859 AGAGCTTTCTAGGTTTGATTCTTCA
1 AGAGCTTTCTAGGTTTGATTCTTCA
117884 AGAGCTTTCTAGGTTTGATTCTTCA
1 AGAGCTTTCTAGGTTTGATTCTTCA
117909 A
1 A
117910 CAAGAACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.43
Consensus pattern (25 bp):
AGAGCTTTCTAGGTTTGATTCTTCA
Done.