Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009372.1 Hibiscus syriacus cultivar Beakdansim tig00113243_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: 80083
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2396 original size:18 final size:16
Alignment explanation
Indices: 2375--2414 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
2365 TGATTATATG
2375 TATATGCATGACATGAAT
1 TATATGCATG-CATG-AT
*
2393 TATATGTATGCATGAT
1 TATATGCATGCATGAT
2409 TATATG
1 TATATG
2415 TATTAACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 4 0.19
18 9 0.43
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (16 bp):
TATATGCATGCATGAT
Found at i:2412 original size:16 final size:18
Alignment explanation
Indices: 2375--2417 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
2365 TGATTATATG
*
2375 TATATGCATGACATGAAT
1 TATATGTATGACATGAAT
2393 TATATGTATG-CATG-AT
1 TATATGTATGACATGAAT
2409 TATATGTAT
1 TATATGTAT
2418 TAACATGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 11 0.46
17 4 0.17
18 9 0.38
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (18 bp):
TATATGTATGACATGAAT
Found at i:2991 original size:2 final size:2
Alignment explanation
Indices: 2984--3038 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
2974 AAGAGATAAC
2984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
3025 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
3039 TACATGTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4063 original size:23 final size:23
Alignment explanation
Indices: 4036--4097 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
4026 ATTTTATATG
4036 GCACTTCGGTGCATTTCTACGCA
1 GCACTTCGGTGCATTTCTACGCA
** * **
4059 GCACTTCGGTATAATTCTACGTG
1 GCACTTCGGTGCATTTCTACGCA
4082 GCACTTCGGTGCATTT
1 GCACTTCGGTGCATTT
4098 ATAAGAGTTG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.34
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCA
Found at i:5352 original size:20 final size:20
Alignment explanation
Indices: 5316--5353 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5306 TCTAAATCAT
*
5316 TTTTCAAAACATCATTTTTG
1 TTTTCAAAACATAATTTTTG
5336 TTTTCAAAATC-TAATTTT
1 TTTTCAAAA-CATAATTTT
5354 GCCTTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTCAAAACATAATTTTTG
Found at i:6645 original size:31 final size:31
Alignment explanation
Indices: 6578--6637 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
6568 CAATTTAAGG
*
6578 CAAAATGGTTTTTGGACTTGAATTAAATTTA
1 CAAAATGGTATTTGGACTTGAATTAAATTTA
*
6609 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTAAATTTA
6638 TTCAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTAAATTTA
Found at i:6882 original size:21 final size:21
Alignment explanation
Indices: 6856--6897 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6846 ATTTGAATAT
*
6856 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
6877 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
6898 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:6960 original size:21 final size:21
Alignment explanation
Indices: 6927--6966 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
6917 TTTTTGCAGA
*
6927 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
6949 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
6967 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:15441 original size:13 final size:13
Alignment explanation
Indices: 15423--15451 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
15413 TTTTAACTCC
15423 TTATCATCTGGAA
1 TTATCATCTGGAA
15436 TTATCATCTGGAA
1 TTATCATCTGGAA
15449 TTA
1 TTA
15452 CTAGTCTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (13 bp):
TTATCATCTGGAA
Found at i:19180 original size:3 final size:3
Alignment explanation
Indices: 19172--19205 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
19162 GTGAGGCAAT
*
19172 ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19206 CAATGAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:32947 original size:27 final size:27
Alignment explanation
Indices: 32892--32952 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
32882 TAGTAGTTCA
*
32892 TTAAATATATTTTATTATTAACTTAAT
1 TTAAAAATATTTTATTATTAACTTAAT
* ** *
32919 TTAAAAATATTTTATTTTTATTTTGAT
1 TTAAAAATATTTTATTATTAACTTAAT
32946 TTAAAAA
1 TTAAAAA
32953 ATATATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAAAAATATTTTATTATTAACTTAAT
Found at i:34486 original size:48 final size:48
Alignment explanation
Indices: 34395--34777 Score: 240
Period size: 48 Copynumber: 7.9 Consensus size: 48
34385 ATTGATTTGA
* * * *
34395 ACTCCTCAGGACAGATATCAGAGTTCTGATCATCTTCAACAACAACATC
1 ACTCCT-AGGAAAGTTATCAGAGTTCTGATCGTCTTCAACAACAGCATC
* * *
34444 A-TCCTAAGGAAAGTTATCAGAGTTCTGATCGCCTCCAGCAACAGCATC
1 ACTCCT-AGGAAAGTTATCAGAGTTCTGATCGTCTTCAACAACAGCATC
* * *
34492 AGT-CTCGAGAAAGTTATCAGACTTCTGATCGTCTTCAACAACAGCATC
1 ACTCCTAG-GAAAGTTATCAGAGTTCTGATCGTCTTCAACAACAGCATC
*
34540 GGACTCCTCAGGAAAGTTATCAGAGTTCTGAT-GATCTTGAACAACAGCATC
1 --ACTCCT-AGGAAAGTTATCAGAGTTCTGATCG-TCTTCAACAACAGCATC
* * * * ** * *
34591 A-GCCTCGGAAAAGTT-TGATGACTTCCAATCATCTTCATCAACAGCATC
1 ACTCCTAGG-AAAGTTATCA-GAGTTCTGATCGTCTTCAACAACAGCATC
* ** * * * **
34639 AGCTTC-AGGAAAGTTATCAGAGTTCCAATCATCTCCAACAATAGTGTC
1 A-CTCCTAGGAAAGTTATCAGAGTTCTGATCGTCTTCAACAACAGCATC
* * * * * * *
34687 AGGATCCTTGATAAAGTAATGAGAGTTCTTATCATCTTCAACAACAGCATC
1 A--CTCCTAG-GAAAGTTATCAGAGTTCTGATCGTCTTCAACAACAGCATC
* * * * * *
34738 A-GCCTCGAAAAGTTATCAGAGTTTTGATCATCTTGAACAA
1 ACTCCTAGGAAAGTTATCAGAGTTCTGATCGTCTTCAACAA
34778 GTGCAGGCTA
Statistics
Matches: 262, Mismatches: 56, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
47 32 0.12
48 144 0.55
49 10 0.04
50 5 0.02
51 70 0.27
52 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (48 bp):
ACTCCTAGGAAAGTTATCAGAGTTCTGATCGTCTTCAACAACAGCATC
Found at i:34585 original size:99 final size:96
Alignment explanation
Indices: 34410--34770 Score: 350
Period size: 99 Copynumber: 3.7 Consensus size: 96
34400 TCAGGACAGA
* * * *
34410 TATCAGAGTTCTGATCATCTTCAACAACAACATCATCCTAAGGAAAGTTATCAGAGTTCTGATCG
1 TATCAGACTTCTGATCATCTTCAACAACAGCATCATCCTCAGGAAAGTTATCAGAGTTCTGATCA
* *
34475 CCTCCAGCAACAGCATCAGTCTCGAGAAAGT
66 TCTCCAACAACAGCATCAGTCTCGAGAAAGT
*
34506 TATCAGACTTCTGATCGTCTTCAACAACAGCATCGGACTCCTCAGGAAAGTTATCAGAGTTCTGA
1 TATCAGACTTCTGATCATCTTCAACAACAGCATC--A-TCCTCAGGAAAGTTATCAGAGTTCTGA
* ** *
34571 TGATCTTGAACAACAGCATCAGCCTCG-GAAAAGT
63 TCATCTCCAACAACAGCATCAGTCTCGAG-AAAGT
* ** * * * **
34605 T-TGATGACTTCCAATCATCTTCATCAACAGCATCAGCTTCAGGAAAGTTATCAGAGTTCCAATC
1 TATCA-GACTTCTGATCATCTTCAACAACAGCATCATCCTCAGGAAAGTTATCAGAGTTCTGATC
* ** * *
34669 ATCTCCAACAATAGTGTCAGGATCCTTGATAAAGT
65 ATCTCCAACAACAGCATCA-G-T-CTCGAGAAAGT
* * * * * * *
34704 AATGAGAGTTCTTATCATCTTCAACAACAGCATCAGCCTC-GAAAAGTTATCAGAGTTTTGATCA
1 TATCAGACTTCTGATCATCTTCAACAACAGCATCATCCTCAGGAAAGTTATCAGAGTTCTGATCA
34768 TCT
66 TCT
34771 TGAACAAGTG
Statistics
Matches: 216, Mismatches: 39, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
96 69 0.32
97 2 0.01
98 27 0.12
99 115 0.53
100 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (96 bp):
TATCAGACTTCTGATCATCTTCAACAACAGCATCATCCTCAGGAAAGTTATCAGAGTTCTGATCA
TCTCCAACAACAGCATCAGTCTCGAGAAAGT
Found at i:34678 original size:147 final size:148
Alignment explanation
Indices: 34395--34757 Score: 373
Period size: 147 Copynumber: 2.5 Consensus size: 148
34385 ATTGATTTGA
* * * * *
34395 ACTCCTCAGGACAGATATCAGAGTTCTGATCATCTTCAACAACAACATCATCCTAAGG-AAAGTT
1 ACTCCTCAGGAAAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCT-CGGAAAAGTT
* ** * ** *
34459 ATCAGAGTTCTGATCGCCTCCAGCAACAGCATCAGTCTCGAGAAAGTTATCAGACTTCTGATCGT
65 ATCAGACTTCCAATCACCTCCAGCAACAGCATCAGTCTCGAGAAAGTTATCAGACTTCCAATCAT
*
34524 CTTCAACAACAGCATC-GG
130 CTCCAACAACAGCATCAGG
* *
34542 ACTCCTCAGGAAAGTTATCAGAGTTCTGATGATCTTGAACAACAGCATCAGCCTCGGAAAAGTT-
1 ACTCCTCAGGAAAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCGGAAAAGTTA
* * * * *
34606 TGATGACTTCCAATCATCTTCATCAACAGCATCAG-CTTC-AGGAAAGTTATCAGAGTTCCAATC
66 TCA-GACTTCCAATCACCTCCAGCAACAGCATCAGTC-TCGA-GAAAGTTATCAGACTTCCAATC
* **
34669 ATCTCCAACAATAGTGTCAGG
128 ATCTCCAACAACAGCATCAGG
* * * * *
34690 A-TCCT-TGATAAAGTAATGAGAGTTCTTATCATCTTCAACAACAGCATCAGCCTC-GAAAAGTT
1 ACTCCTCAG-GAAAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCGGAAAAGTT
34752 ATCAGA
65 ATCAGA
34758 GTTTTGATCA
Statistics
Matches: 178, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
146 17 0.10
147 158 0.89
148 3 0.02
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (148 bp):
ACTCCTCAGGAAAGTTATCAGAGTTCTGATCATCTTCAACAACAGCATCAGCCTCGGAAAAGTTA
TCAGACTTCCAATCACCTCCAGCAACAGCATCAGTCTCGAGAAAGTTATCAGACTTCCAATCATC
TCCAACAACAGCATCAGG
Found at i:38351 original size:21 final size:21
Alignment explanation
Indices: 38327--38473 Score: 122
Period size: 21 Copynumber: 7.1 Consensus size: 21
38317 CGCAAATTCG
*
38327 AGTTGCATTTCGCGTTGCGAT
1 AGTTCCATTTCGCGTTGCGAT
** **
38348 AGTTGAAAATCGCGTTGCGAT
1 AGTTCCATTTCGCGTTGCGAT
*
38369 -TTTCCATTTCGCGTTGCGAT
1 AGTTCCATTTCGCGTTGCGAT
** **
38389 AGTTGAAAATCGCGTTGCGAT
1 AGTTCCATTTCGCGTTGCGAT
*
38410 -TTTCCATTTCGCGTTGCGAT
1 AGTTCCATTTCGCGTTGCGAT
* * *
38430 AGTCTACA-GTCGCGTTACGAT
1 AGT-TCCATTTCGCGTTGCGAT
*
38451 -TTTCCATTTCGCGTTGCGAT
1 AGTTCCATTTCGCGTTGCGAT
38471 AGT
1 AGT
38474 CTACGGTTGT
Statistics
Matches: 94, Mismatches: 27, Indels: 10
0.72 0.21 0.08
Matches are distributed among these distances:
19 3 0.03
20 42 0.45
21 46 0.49
22 3 0.03
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.37
Consensus pattern (21 bp):
AGTTCCATTTCGCGTTGCGAT
Found at i:38382 original size:20 final size:20
Alignment explanation
Indices: 38357--38470 Score: 113
Period size: 20 Copynumber: 5.6 Consensus size: 20
38347 TAGTTGAAAA
38357 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
38377 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
38398 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
38418 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
*
38439 TCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
38459 TCGCGTTGCGAT
1 TCGCGTTGCGAT
38471 AGTCTACGGT
Statistics
Matches: 72, Mismatches: 18, Indels: 8
0.73 0.18 0.08
Matches are distributed among these distances:
19 4 0.06
20 38 0.53
21 26 0.36
22 4 0.06
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:38477 original size:41 final size:41
Alignment explanation
Indices: 38332--38473 Score: 241
Period size: 41 Copynumber: 3.5 Consensus size: 41
38322 ATTCGAGTTG
38332 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
38373 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * *
38414 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTACGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
38455 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
38474 CTACGGTTGT
Statistics
Matches: 97, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
41 96 0.99
42 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:38514 original size:41 final size:40
Alignment explanation
Indices: 38332--38498 Score: 194
Period size: 41 Copynumber: 4.0 Consensus size: 40
38322 ATTCGAGTTG
* *
38332 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
* *
38373 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
*
38414 CATTTCGCGTTGCGATAGTCTACAGTCGCGTTACGATTTTC
1 CATTTC-CGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
* *
38455 CATTTCGCGTTGCGATAGTCTACGGTTGTCGTTGCGATTTTC
1 CATTTC-CGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTC
38497 CA
1 CA
38499 AATTCGTTGT
Statistics
Matches: 118, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
41 103 0.87
42 15 0.13
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (40 bp):
CATTTCCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
Found at i:38653 original size:5 final size:6
Alignment explanation
Indices: 38591--38650 Score: 81
Period size: 6 Copynumber: 10.5 Consensus size: 6
38581 GACACGTATT
* *
38591 ACCACT ACCACT ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
38638 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
38651 CGAGACAAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 15 0.28
6 38 0.72
ACGTcount: A:0.30, C:0.53, G:0.13, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:38661 original size:5 final size:5
Alignment explanation
Indices: 38651--38691 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
38641 CGACCCGACC
* *
38651 CGAGA CAAGA CGAGA CGAGA CGAGA CTAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
38692 GCGGCGGCGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.39, C:0.22, G:0.37, T:0.02
Consensus pattern (5 bp):
CGAGA
Found at i:39189 original size:6 final size:6
Alignment explanation
Indices: 39173--39205 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
39163 TCTCGTCTCG
39173 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
39206 ATACGTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.18, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:39342 original size:20 final size:20
Alignment explanation
Indices: 39317--39389 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
39307 ACTGTAGACT
39317 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
39337 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
39358 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
39378 ATCACAACGCGA
1 ATCGCAACGCGA
39390 TTTTCAACTA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:39418 original size:21 final size:21
Alignment explanation
Indices: 39314--39418 Score: 97
Period size: 21 Copynumber: 5.1 Consensus size: 21
39304 ACAACTGTAG
*
39314 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
39335 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
39355 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
39376 A-AATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
39396 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
39417 AC
1 AC
39419 GCGAATTTGC
Statistics
Matches: 61, Mismatches: 21, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
20 29 0.48
21 32 0.52
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:39431 original size:41 final size:41
Alignment explanation
Indices: 39314--39414 Score: 193
Period size: 41 Copynumber: 2.5 Consensus size: 41
39304 ACAACTGTAG
*
39314 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
39355 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
39396 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
39415 CAACGCGAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
Found at i:39513 original size:41 final size:41
Alignment explanation
Indices: 39454--39556 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
39444 GTTGCGATTT
* *
39454 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACCCGAAATGGAAAAACGCAACGCGATCTC
* * * *
39495 CAACTATCGTAACCCGAAATGGAAAAACTCAACGCGATTTT
1 CAACTATCGCAACCCGAAATGGAAAAACGCAACGCGATCTC
**
39536 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACCCGAAATG
39557 CAACGTGAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.18
Consensus pattern (41 bp):
CAACTATCGCAACCCGAAATGGAAAAACGCAACGCGATCTC
Found at i:39570 original size:142 final size:142
Alignment explanation
Indices: 39314--39585 Score: 456
Period size: 142 Copynumber: 1.9 Consensus size: 142
39304 ACAACTGTAG
* * *
39314 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACCCGAAATGGAAAA
*
39379 TCACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGAT-GATGGAGATCG
66 ACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAG-TGGAGATCG
39443 CGTTGCGATTTCA
130 CGTTGCGATTTCA
*
39456 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGTAACCCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACCCGAAATGGAAAA
* * *
39521 ACTCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGATAGTGGAGATCGC
66 ACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGC
39586 AATGTGAATT
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
142 120 0.99
143 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (142 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATCGCAACCCGAAATGGAAAA
ACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGC
GTTGCGATTTCA
Found at i:40364 original size:19 final size:19
Alignment explanation
Indices: 40330--40378 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
40320 AAAACGTTTT
*
40330 TATGAACAATAATATACGG
1 TATGAACAGTAATATACGG
* **
40349 TATGAACAGTATTATATTG
1 TATGAACAGTAATATACGG
*
40368 TATGAATAGTA
1 TATGAACAGTA
40379 CTGTGAACAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (19 bp):
TATGAACAGTAATATACGG
Found at i:40418 original size:22 final size:22
Alignment explanation
Indices: 40369--40412 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40359 ATTATATTGT
*
40369 ATGAATAGTACTGTGAACAGTA
1 ATGAATAGTACTGTGAACAATA
40391 ATGAATAGTA-TCGTGAACAATA
1 ATGAATAGTACT-GTGAACAATA
40413 TCGAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.27
Consensus pattern (22 bp):
ATGAATAGTACTGTGAACAATA
Found at i:40507 original size:22 final size:21
Alignment explanation
Indices: 40446--40509 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
40436 TTAAACAATG
* * *
40446 GTACCAATATCCTGCTACAAT
1 GTACCGATACCCTGCTACAGT
*
40467 GTACTGATACCCTGCTACAGT
1 GTACCGATACCCTGCTACAGT
40488 GTACCGATACCCTTGCTACAGT
1 GTACCGATACCC-TGCTACAGT
40510 AACTTTCGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 28 0.76
22 9 0.24
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (21 bp):
GTACCGATACCCTGCTACAGT
Found at i:44193 original size:27 final size:27
Alignment explanation
Indices: 44163--44216 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
44153 TGGATTTATA
44163 AAAATGCCCCTAAAGTGTAAAATGACC
1 AAAATGCCCCTAAAGTGTAAAATGACC
* *
44190 AAAATGCTCCTAAAGTGTTAAATGACC
1 AAAATGCCCCTAAAGTGTAAAATGACC
44217 TAAAGTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (27 bp):
AAAATGCCCCTAAAGTGTAAAATGACC
Found at i:46653 original size:28 final size:27
Alignment explanation
Indices: 46622--46716 Score: 81
Period size: 28 Copynumber: 3.6 Consensus size: 27
46612 GAAAGCAAAG
46622 ATAAAATAGTAAGTAAAAAAAACAAATA
1 ATAAAATAGTAA-TAAAAAAAACAAATA
* *
46650 ATAAAATA-T-ATATAAAAAAGAAA-A
1 ATAAAATAGTAATAAAAAAAACAAATA
* * *
46674 AGAAAA-AGAAAATAAATAAAACAAATAA
1 ATAAAATAG-TAATAAAAAAAACAAAT-A
*
46702 ATAAAATAATAATAA
1 ATAAAATAGTAATAA
46717 CAAAGTACGA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
23 1 0.02
24 6 0.12
25 11 0.22
26 12 0.24
27 1 0.02
28 19 0.37
29 1 0.02
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (27 bp):
ATAAAATAGTAATAAAAAAAACAAATA
Found at i:46699 original size:13 final size:13
Alignment explanation
Indices: 46683--46707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46673 AAGAAAAAGA
46683 AAATAAATAAAAC
1 AAATAAATAAAAC
46696 AAATAAATAAAA
1 AAATAAATAAAA
46708 TAATAATAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAATAAAAC
Found at i:47251 original size:11 final size:10
Alignment explanation
Indices: 47235--47325 Score: 51
Period size: 11 Copynumber: 8.5 Consensus size: 10
47225 ATAACAAAAT
47235 AAATAATATAA
1 AAATAATA-AA
47246 AAATAATAAA
1 AAATAATAAA
47256 AGTAATAATACAA
1 A--AATAATA-AA
*
47269 GAATAATAAA
1 AAATAATAAA
* *
47279 AAA-AAGAGA
1 AAATAATAAA
*
47288 AAGTAA-AAA
1 AAATAATAAA
47297 AATATAATAATA
1 AA-ATAATAA-A
*
47309 ATAAAATATAAA
1 A-AATA-ATAAA
47321 AAATA
1 AAATA
47326 TACATATATA
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
9 10 0.16
10 12 0.19
11 20 0.32
12 13 0.21
13 7 0.11
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (10 bp):
AAATAATAAA
Found at i:47251 original size:23 final size:23
Alignment explanation
Indices: 47236--47279 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
47226 TAACAAAATA
*
47236 AATAATATAAAAATAATAAAAGT
1 AATAATACAAAAATAATAAAAGT
*
47259 AATAATACAAGAATAATAAAA
1 AATAATACAAAAATAATAAAA
47280 AAAAGAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (23 bp):
AATAATACAAAAATAATAAAAGT
Found at i:47264 original size:12 final size:11
Alignment explanation
Indices: 47236--47279 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
47226 TAACAAAATA
47236 AATAATATAAA-
1 AATAATA-AAAG
47247 AATAATAAAAG
1 AATAATAAAAG
*
47258 TAATAATACAAG
1 -AATAATAAAAG
47270 AATAATAAAA
1 AATAATAAAA
47280 AAAAGAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 3 0.10
11 16 0.55
12 10 0.34
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (11 bp):
AATAATAAAAG
Found at i:47322 original size:27 final size:28
Alignment explanation
Indices: 47293--47344 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
47283 AGAGAAAGTA
47293 AAAAAATATA-ATA-ATAATA-AAATAT
1 AAAAAATATACATATATAATATAAATAT
47318 AAAAAATATACATATATAATATAAATA
1 AAAAAATATACATATATAATATAAATA
47345 AGTAGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (28 bp):
AAAAAATATACATATATAATATAAATAT
Found at i:47381 original size:12 final size:12
Alignment explanation
Indices: 47359--47403 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
47349 GAATAAAAGG
47359 AAAATATAATAGT
1 AAAA-ATAATAGT
*
47372 AAAAATAATAAT
1 AAAAATAATAGT
*
47384 AAATATAATAGT
1 AAAAATAATAGT
*
47396 AATAATAA
1 AAAAATAA
47404 AAATGCAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:48011 original size:37 final size:37
Alignment explanation
Indices: 47957--48060 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
47947 GTGCTTGTGG
* * *
47957 ATCATA-TCTTTAAGAGTTTAAATCATAGTAGAACTCT
1 ATCATAGT-TTTAGGAGTTTAAATCCTAGTAAAACTCT
* * * *
47994 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCATAGTTTTAGGAGTTTAAATCCTAGTAAAACTCT
*
48031 ATCATAGTTTTAGGAGTTTGAATCCTAGTA
1 ATCATAGTTTTAGGAGTTTAAATCCTAGTA
48061 TGACGAAAAG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 55 0.98
38 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (37 bp):
ATCATAGTTTTAGGAGTTTAAATCCTAGTAAAACTCT
Found at i:49228 original size:106 final size:106
Alignment explanation
Indices: 48778--50479 Score: 2393
Period size: 106 Copynumber: 16.0 Consensus size: 106
48768 GCATTGTTCT
* * * ** *
48778 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTTTGGAACCGTGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** * * * *
48842 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
48884 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
** * * * * *
48943 TTAGCTG-CCTATTCGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * * * *
48985 G-GTTCAAGATCATTCGCTGAGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
49049 CCAGCGGTCCCTTCATCGTGAAGTTGAATTTGCGTAAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAA---G---TT--G--AACTTGCGTTGTCTG
* * * *
49100 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
49165 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
49206 GAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTGGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
49271 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
49312 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
49377 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
49418 GAGTCCAATATCCTTCGCTGTTAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
49483 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
49524 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
49589 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
49630 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
49695 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
49736 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
49801 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
49842 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGATAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
49907 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGCCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
49948 TAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
50013 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
50054 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA-TGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
50118 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
50159 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATT-GGAAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACA
*
50223 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
50265 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGATTTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
50330 CCAGCGGTCCCTTCGTCGTGAAGTTTAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
50371 GAGTCCAATATCCTTCGCTGTTAAGTTGAAATTAGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * *
50435 CTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
50476 GAGT
1 GAGT
50480 GGCACGATAT
Statistics
Matches: 1447, Mismatches: 125, Indels: 49
0.89 0.08 0.03
Matches are distributed among these distances:
99 2 0.00
100 71 0.05
101 5 0.00
102 5 0.00
104 3 0.00
105 154 0.11
106 1105 0.76
107 8 0.01
108 1 0.00
109 1 0.00
110 2 0.00
112 2 0.00
113 1 0.00
114 1 0.00
115 2 0.00
116 84 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:51330 original size:22 final size:22
Alignment explanation
Indices: 51304--51373 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
51294 TTATGTTTGG
51304 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
**
51326 TCAAAGGTTTGGCATGGGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
51348 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
51370 TCAA
1 TCAA
51374 CGATTTGATG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:51994 original size:6 final size:6
Alignment explanation
Indices: 51983--52041 Score: 55
Period size: 6 Copynumber: 9.0 Consensus size: 6
51973 TTTTTTGTCC
* *
51983 CTTTTT CTTTTT GATTTTT GTTCTTT CTTTTT CTTTTT CTTTTT GCTTCTTTT
1 CTTTTT CTTTTT -CTTTTT CTT-TTT CTTTTT CTTTTT CTTTTT -C-T-TTTT
52036 CTTTTT
1 CTTTTT
52042 TGTTTTTGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
6 27 0.60
7 12 0.27
8 2 0.04
9 4 0.09
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:52016 original size:26 final size:27
Alignment explanation
Indices: 51983--52041 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 27
51973 TTTTTTGTCC
51983 CTTTTTCTTTTTGATTTTTG-TTC-TTT
1 CTTTTTCTTTTT-ATTTTTGCTTCTTTT
*
52009 CTTTTTCTTTTTCTTTTTGCTTCTTTT
1 CTTTTTCTTTTTATTTTTGCTTCTTTT
52036 CTTTTT
1 CTTTTT
52042 TGTTTTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 6 0.20
26 15 0.50
27 9 0.30
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (27 bp):
CTTTTTCTTTTTATTTTTGCTTCTTTT
Found at i:52032 original size:16 final size:16
Alignment explanation
Indices: 51983--52041 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
51973 TTTTTTGTCC
51983 CTTTTTCTTTTTGATT
1 CTTTTTCTTTTTGATT
*
51999 -TTTGTTCTTTCTT-TTT
1 CTTT-TTCTTT-TTGATT
*
52015 CTTTTTCTTTTTGCTT
1 CTTTTTCTTTTTGATT
52031 C-TTTTCTTTTT
1 CTTTTTCTTTTT
52042 TGTTTTTGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 15 0.41
16 17 0.46
17 5 0.14
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (16 bp):
CTTTTTCTTTTTGATT
Found at i:52035 original size:22 final size:23
Alignment explanation
Indices: 51983--52050 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 23
51973 TTTTTTGTCC
51983 CTTTTTCTTTTTGATTTTTGTTCTTT
1 CTTTTTCTTTTT-ATTTTTG--CTTT
*
52009 CTTTTTCTTTTTCTTTTTGC-TT
1 CTTTTTCTTTTTATTTTTGCTTT
*
52031 C-TTTTCTTTTTTGTTTTTGC
1 CTTTTTC-TTTTTATTTTTGC
52051 CCTTTTTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.13
22 15 0.38
23 1 0.03
25 6 0.15
26 12 0.31
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.76
Consensus pattern (23 bp):
CTTTTTCTTTTTATTTTTGCTTT
Found at i:52055 original size:21 final size:21
Alignment explanation
Indices: 52011--52056 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
52001 TGTTCTTTCT
*
52011 TTTTCTTTTTCTTTTTGCTTC
1 TTTTCTTTTTCTTTTTGCTCC
*
52032 TTTTCTTTTTTGTTTTTGC-CC
1 TTTTC-TTTTTCTTTTTGCTCC
52053 TTTT
1 TTTT
52057 TGTTCTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTTCTTTTTGCTCC
Found at i:52057 original size:22 final size:22
Alignment explanation
Indices: 51974--52057 Score: 57
Period size: 22 Copynumber: 3.7 Consensus size: 22
51964 TGCATGTGCT
*
51974 TTTTTG-TCCCTTTTTCTTTTTGA
1 TTTTTGCT-CCTTTTTCTTTTT-C
*
51997 TTTTTGTTCTTTCTTTTTCTTTTTC
1 TTTTTG--C-TCCTTTTTCTTTTTC
* *
52022 TTTTTGCTTC-TTTTCTTTTTTG
1 TTTTTGCTCCTTTTTC-TTTTTC
52044 TTTTTGC-CCTTTTT
1 TTTTTGCTCCTTTTT
52058 GTTCTGATTG
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
21 6 0.12
22 19 0.37
23 7 0.14
25 6 0.12
26 12 0.24
27 1 0.02
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (22 bp):
TTTTTGCTCCTTTTTCTTTTTC
Found at i:56540 original size:22 final size:21
Alignment explanation
Indices: 56475--56553 Score: 65
Period size: 22 Copynumber: 3.6 Consensus size: 21
56465 AAATAGTAAG
56475 TAAA-AAAACAAATAATAAAATA
1 TAAATAAAACAAATAA-AAAA-A
* *
56497 TATATAAAA-AAGAAAAAGAAAA
1 TAAATAAAACAA-ATAAA-AAAA
56519 TAAATAAAACAAATAAACAAAA
1 TAAATAAAACAAATAAA-AAAA
56541 T-AATAATAACAAA
1 TAAATAA-AACAAA
56554 GTACGAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
21 5 0.11
22 30 0.64
23 12 0.26
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (21 bp):
TAAATAAAACAAATAAAAAAA
Found at i:56596 original size:23 final size:23
Alignment explanation
Indices: 56569--56617 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
56559 AATAATATAT
56569 ATATATAATAAA-TAAAAAAGTAA
1 ATATAT-ATAAATTAAAAAAGTAA
* *
56592 ATATATATAAATTAATAAATTAA
1 ATATATATAAATTAAAAAAGTAA
56615 ATA
1 ATA
56618 ACGAAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
ATATATATAAATTAAAAAAGTAA
Found at i:57095 original size:12 final size:11
Alignment explanation
Indices: 57080--57109 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
57070 TAAATATAAA
57080 AATAATACAAG
1 AATAATACAAG
57091 TAATAATACAAG
1 -AATAATACAAG
57103 AATAATA
1 AATAATA
57110 AAAAGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (11 bp):
AATAATACAAG
Found at i:57210 original size:12 final size:12
Alignment explanation
Indices: 57188--57242 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
57178 GAATAAAAGG
*
57188 AAAATATAATAGT
1 AAAA-ATAATAAT
57201 AAAAATAATAAT
1 AAAAATAATAAT
* *
57213 AAATATAATAGT
1 AAAAATAATAAT
* *
57225 AATAATAAAAAT
1 AAAAATAATAAT
57237 AAAAAT
1 AAAAAT
57243 GCAAAGAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
12 30 0.88
13 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:57216 original size:24 final size:24
Alignment explanation
Indices: 57189--57239 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
57179 AATAAAAGGA
*
57189 AAATATAATAGTAAAAATAATAAT
1 AAATATAATAGTAAAAATAAAAAT
*
57213 AAATATAATAGTAATAATAAAAAT
1 AAATATAATAGTAAAAATAAAAAT
57237 AAA
1 AAA
57240 AATGCAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (24 bp):
AAATATAATAGTAAAAATAAAAAT
Found at i:57841 original size:37 final size:37
Alignment explanation
Indices: 57800--57903 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
57790 GTGCTTGTGG
* * *
57800 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAACTCT
* *
57837 ATCCTATTTTTAGGAGTTTAAATCCTAGAAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAACTCT
* *
57874 ATCCTATTTTTATGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTA
57904 CGACGAAAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAACTCT
Found at i:61492 original size:21 final size:20
Alignment explanation
Indices: 61456--61518 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
61446 AAAACCAGAA
61456 CCCTATGGGGGTATCGATTC
1 CCCTATGGGGGTATCGATTC
* *
61476 CCCTATAGGGGGAATCGGTTC
1 CCCTAT-GGGGGTATCGATTC
*
61497 CCTTATGGGGGTATCGATTC
1 CCCTATGGGGGTATCGATTC
61517 CC
1 CC
61519 TCTGCCAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (20 bp):
CCCTATGGGGGTATCGATTC
Found at i:70560 original size:45 final size:46
Alignment explanation
Indices: 70496--70599 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 46
70486 GCACTAAGGA
*
70496 TGCATCGATGCATAAAATGCATTCGATG-TTTGAAAAATAGCCTG-G
1 TGCATCGATGCATAAAATGCATTCGATGTTTTG-AAAATAGCCAGAG
* **
70541 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAATAGCCAGAG
70587 TGCATCGATGCAT
1 TGCATCGATGCAT
70600 GGAGAGTGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
45 35 0.66
46 18 0.34
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (46 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAATAGCCAGAG
Found at i:70607 original size:19 final size:19
Alignment explanation
Indices: 70583--70633 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
70573 GAAAATATTC
70583 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
70602 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
70621 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
70634 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:71049 original size:31 final size:31
Alignment explanation
Indices: 71011--71090 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
71001 ATTGATTTTG
71011 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
71042 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
** * *
71073 TTAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
71091 TTTGTTAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:75530 original size:22 final size:21
Alignment explanation
Indices: 75504--75550 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
75494 AAGGTCAAAA
*
75504 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
75526 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
75546 ATCAA
1 ATCAA
75551 TTACATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:77727 original size:19 final size:19
Alignment explanation
Indices: 77703--77739 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
77693 AAATATTCAT
77703 AGTGCATCGGTGCATGGAG
1 AGTGCATCGGTGCATGGAG
77722 AGTGCATCGGTGCATGGA
1 AGTGCATCGGTGCATGGA
77740 ATGCATTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.22
Consensus pattern (19 bp):
AGTGCATCGGTGCATGGAG
Done.