Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004194.1 Hibiscus syriacus cultivar Beakdansim tig00009172_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: 93596
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:545 original size:27 final size:27
Alignment explanation
Indices: 507--559 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
497 GTTACCATGC
507 ATCTTCTAGAATGTTTAATGCAACTTA
1 ATCTTCTAGAATGTTTAATGCAACTTA
534 ATCTTCTAGAATGTTTAATGCAACTT
1 ATCTTCTAGAATGTTTAATGCAACTT
560 CTTTGTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (27 bp):
ATCTTCTAGAATGTTTAATGCAACTTA
Found at i:560 original size:21 final size:21
Alignment explanation
Indices: 503--561 Score: 55
Period size: 27 Copynumber: 2.5 Consensus size: 21
493 TGTAGTTACC
*
503 ATGCATCTTCTAGAATGTTTA
1 ATGCAACTTCTAGAATGTTTA
524 ATGCAACTTAATCTTCTAGAATGTTTA
1 ATG---C--AA-CTTCTAGAATGTTTA
551 ATGCAACTTCT
1 ATGCAACTTCT
562 TTGTGTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
21 8 0.26
22 2 0.06
24 2 0.06
26 1 0.03
27 18 0.58
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGCAACTTCTAGAATGTTTA
Found at i:1369 original size:8 final size:8
Alignment explanation
Indices: 1356--1411 Score: 85
Period size: 8 Copynumber: 6.9 Consensus size: 8
1346 AATTCTCCAC
1356 ATGTATGA
1 ATGTATGA
1364 ATGTATGA
1 ATGTATGA
1372 ATGTATGA
1 ATGTATGA
1380 ATGTATGA
1 ATGTATGA
*
1388 ATGTATGT
1 ATGTATGA
*
1396 ATGTATTGT
1 ATGTA-TGA
1405 ATGTATG
1 ATGTATG
1412 CCAAATTTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
8 38 0.83
9 8 0.17
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (8 bp):
ATGTATGA
Found at i:1397 original size:4 final size:4
Alignment explanation
Indices: 1356--1411 Score: 67
Period size: 4 Copynumber: 13.8 Consensus size: 4
1346 AATTCTCCAC
* * * *
1356 ATGT ATGA ATGT ATGA ATGT ATGA ATGT ATGA ATGT ATGT ATGT ATTGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-TGT
1405 ATGT ATG
1 ATGT ATG
1412 CCAAATTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
4 39 0.91
5 4 0.09
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (4 bp):
ATGT
Found at i:1455 original size:9 final size:8
Alignment explanation
Indices: 1439--1489 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
1429 ATATGTGTTG
1439 TATGTATA
1 TATGTATA
1447 TATGT-TA
1 TATGTATA
*
1454 TATGGACTA
1 TATGTA-TA
*
1463 TATGT-TG
1 TATGTATA
1470 TATGTATA
1 TATGTATA
*
1478 TATGTATG
1 TATGTATA
1486 TATG
1 TATG
1490 AATTTTCCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 12 0.34
8 17 0.49
9 6 0.17
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (8 bp):
TATGTATA
Found at i:1466 original size:16 final size:15
Alignment explanation
Indices: 1429--1482 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1419 TGTCTTATAC
* * *
1429 ATATGTGTTGTATGT
1 ATATATGTTATATGG
1444 ATATATGTTATATGG
1 ATATATGTTATATGG
* *
1459 ACTATATGTTGTATGT
1 A-TATATGTTATATGG
1475 ATATATGT
1 ATATATGT
1483 ATGTATGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 20 0.61
16 13 0.39
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.50
Consensus pattern (15 bp):
ATATATGTTATATGG
Found at i:1487 original size:16 final size:16
Alignment explanation
Indices: 1356--1489 Score: 70
Period size: 16 Copynumber: 8.7 Consensus size: 16
1346 AATTCTCCAC
*
1356 ATGTATGAATGTATGA-
1 ATGTATGTATGTAT-AT
*
1372 ATGTATGAATGTATGA-
1 ATGTATGTATGTAT-AT
1388 ATGTATGTATG--TAT
1 ATGTATGTATGTATAT
* *
1402 -TGTATGTATGCCAAAT
1 ATGTATGTATG-TATAT
* * **
1418 TTGTCT-TATACATAT
1 ATGTATGTATGTATAT
*
1433 GTGT-TGTATGTATAT
1 ATGTATGTATGTATAT
* *
1448 ATGT-TATATGGACTAT
1 ATGTATGTATGTA-TAT
1464 ATGT-TGTATGTATAT
1 ATGTATGTATGTATAT
1479 ATGTATGTATG
1 ATGTATGTATG
1490 AATTTTCCGA
Statistics
Matches: 97, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
13 11 0.11
14 2 0.02
15 30 0.31
16 50 0.52
17 4 0.04
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.46
Consensus pattern (16 bp):
ATGTATGTATGTATAT
Found at i:4441 original size:19 final size:17
Alignment explanation
Indices: 4420--4451 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4410 TTTAAATATA
4420 ATAA-ATATGTGTTCTG
1 ATAATATATGTGTTCTG
4436 ATAATATATGTGTTCT
1 ATAATATATGTGTTCT
4452 TAGTGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (17 bp):
ATAATATATGTGTTCTG
Found at i:8558 original size:18 final size:18
Alignment explanation
Indices: 8523--8576 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
8513 GAGGGATTAT
**
8523 CAGTGGTCCTTCTAGACA
1 CAGTGGTCCTTCGGGACA
*
8541 TAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
* *
8559 CAGTGATCCTACGGGACA
1 CAGTGGTCCTTCGGGACA
8577 AATTTCTACG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Found at i:14377 original size:20 final size:20
Alignment explanation
Indices: 14352--14396 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
14342 TTATCTGGAA
*
14352 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGGTTT
14372 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTCTGAGGTTT
14392 AAAAA
1 AAAAA
14397 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGGTTT
Found at i:21255 original size:6 final size:6
Alignment explanation
Indices: 21246--21299 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
21236 CTTCATCTAT
* * *
21246 ATCCTC ATCCTC ATCCTC -TCC-C -TCCTC ATCATC ATCATC ATCATC
1 ATCCTC ATCCTC ATCCTC ATCCTC ATCCTC ATCCTC ATCCTC ATCCTC
*
21291 ATCCCC ATC
1 ATCCTC ATC
21300 ATCTGCCATG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 35 0.81
ACGTcount: A:0.20, C:0.48, G:0.00, T:0.31
Consensus pattern (6 bp):
ATCCTC
Found at i:21261 original size:12 final size:12
Alignment explanation
Indices: 21233--21302 Score: 58
Period size: 12 Copynumber: 6.1 Consensus size: 12
21223 ATTCCAGCAC
*
21233 CATCTTCATCTAT
1 CATCCTCATC-AT
*
21246 -ATCCTCATCCT
1 CATCCTCATCAT
21257 CATCCTC-TC--
1 CATCCTCATCAT
*
21266 CCTCCTCATCAT
1 CATCCTCATCAT
*
21278 CATCATCATCAT
1 CATCCTCATCAT
*
21290 CATCCCCATCAT
1 CATCCTCATCAT
21302 C
1 C
21303 TGCCATGTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
9 6 0.13
10 2 0.04
11 3 0.07
12 35 0.76
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.34
Consensus pattern (12 bp):
CATCCTCATCAT
Found at i:33540 original size:3 final size:3
Alignment explanation
Indices: 33534--33601 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
33524 TTTTTACCCA
* *
33534 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
33582 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
33602 AATATATATT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:33776 original size:16 final size:16
Alignment explanation
Indices: 33755--33809 Score: 103
Period size: 16 Copynumber: 3.5 Consensus size: 16
33745 TAATCCCATG
33755 CCAGCCGCCTCTGCCT
1 CCAGCCGCCTCTGCCT
33771 CCAGCCGCCTCTGCCT
1 CCAGCCGCCTCTGCCT
33787 CCAGCCGCCTCTGCCT
1 CCAGCCGCCTCTGCCT
33803 CCA-CCGC
1 CCAGCCGC
33810 TGCCACGTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
15 4 0.10
16 35 0.90
ACGTcount: A:0.07, C:0.58, G:0.18, T:0.16
Consensus pattern (16 bp):
CCAGCCGCCTCTGCCT
Found at i:34983 original size:13 final size:13
Alignment explanation
Indices: 34967--35013 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
34957 ATATAATAAA
34967 TAAATATTTATTT
1 TAAATATTTATTT
*
34980 TAAATAAATTATTT
1 TAAAT-ATTTATTT
34994 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
35007 TCAATAT
1 TAAATAT
35014 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:35718 original size:18 final size:18
Alignment explanation
Indices: 35677--35719 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
35667 AATTTTTATA
35677 TTTATTTATTATTTTCAT
1 TTTATTTATTATTTTCAT
**
35695 AATATTTA-TATGTTTCAT
1 TTTATTTATTAT-TTTCAT
35713 TTTATTT
1 TTTATTT
35720 TATTTGCAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTATTATTTTCAT
Found at i:35734 original size:15 final size:13
Alignment explanation
Indices: 35714--35751 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
35704 ATGTTTCATT
35714 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
35729 TTATTTTATTTCA
1 TTATTTTATTTCA
35742 TTA-TTTATTT
1 TTATTTTATTT
35752 TTCTGTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:44174 original size:18 final size:18
Alignment explanation
Indices: 44153--44200 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
44143 GCATGGGAAG
44153 CATGAGAGACATTCGGGC
1 CATGAGAGACATTCGGGC
44171 CATGAGAGACATTCGGGC
1 CATGAGAGACATTCGGGC
*
44189 CATGAGAAACAT
1 CATGAGAGACAT
44201 GATGAGCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (18 bp):
CATGAGAGACATTCGGGC
Found at i:45223 original size:19 final size:19
Alignment explanation
Indices: 45199--45237 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
45189 TCGAATGCAT
45199 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
45218 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
45237 T
1 T
45238 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:45362 original size:64 final size:65
Alignment explanation
Indices: 45185--45347 Score: 224
Period size: 65 Copynumber: 2.5 Consensus size: 65
45175 GAATTAATTG
* * *
45185 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTCAA
* ** *
45250 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CATG-CTATTTTTC
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTC-TGAATA-TTTTC
45313 -A
64 AA
45314 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
45348 TGGTGCACCG
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 35 0.41
65 51 0.59
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTCAA
Found at i:52633 original size:21 final size:21
Alignment explanation
Indices: 52591--52634 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
52581 ACCCCGAGAG
*
52591 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
*
52612 CTAGTTCTTCTCGTA-CTCCTC
1 CTAGTTCTTCACG-AGCTCCTC
52633 CT
1 CT
52635 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.11, C:0.36, G:0.14, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:53702 original size:19 final size:19
Alignment explanation
Indices: 53678--53716 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
53668 TCGAATGCAT
53678 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
53697 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
53716 T
1 T
53717 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:53733 original size:65 final size:64
Alignment explanation
Indices: 53615--53814 Score: 194
Period size: 65 Copynumber: 3.1 Consensus size: 64
53605 TATTCAAAGG
* *
53615 CATGCACCGATGCA-TCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGC
1 CATGCACCGATGCACTC--TCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGC
*
53676 ATTC
61 ATTT
53680 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * * *** * **
53745 GATTCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
53809 CATGCA
1 CATGCA
53815 TCTGTGCACA
Statistics
Matches: 115, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
63 7 0.06
64 42 0.37
65 64 0.56
66 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:57305 original size:21 final size:21
Alignment explanation
Indices: 57281--57341 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
57271 TTCAAAGAAA
57281 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
57302 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
57316 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
57337 CATTT
1 CATTT
57342 TCAAAGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:57308 original size:35 final size:36
Alignment explanation
Indices: 57205--57347 Score: 236
Period size: 35 Copynumber: 4.0 Consensus size: 36
57195 TAATTTCAAC
*
57205 AAACATCTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
57241 AAACATTTACCAAACTTTGAAAAAACATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAAACATTTTTCAAAG
*
57278 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
*
57313 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
57348 TTGGTTGCCA
Statistics
Matches: 104, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
35 44 0.42
36 24 0.23
37 36 0.35
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.29
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:61905 original size:21 final size:21
Alignment explanation
Indices: 61881--61941 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
61871 TTCAAAGAAA
61881 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
61902 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
61916 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
61937 TATTT
1 CATTT
61942 TCAAAGTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:61915 original size:35 final size:35
Alignment explanation
Indices: 61832--61947 Score: 191
Period size: 35 Copynumber: 3.3 Consensus size: 35
61822 TTACCCATTC
*
61832 CTATTTTC-AACAAAC-TTTACCAAACTTTGAAAA
1 CTATTTTCAAAGAAACATTTACCAAACTTTGAAAA
61865 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAA
1 CTA-TTTTCAAAGAAACATTTACCAAACTTTGAAAA
*
61901 CCATTTTCAAAGAAACATTTACCAAACTTTGAAAA
1 CTATTTTCAAAGAAACATTTACCAAACTTTGAAAA
61936 CTATTTTCAAAG
1 CTATTTTCAAAG
61948 TTGGTTGCCG
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
33 3 0.04
34 5 0.06
35 49 0.64
36 20 0.26
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (35 bp):
CTATTTTCAAAGAAACATTTACCAAACTTTGAAAA
Found at i:62158 original size:19 final size:19
Alignment explanation
Indices: 62131--62169 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
62121 GGAAGACAAT
*
62131 ACTCGACTTCTAAAACTGA
1 ACTCAACTTCTAAAACTGA
62150 ACTCAACTTCTAAAACTGA
1 ACTCAACTTCTAAAACTGA
62169 A
1 A
62170 GAGCACACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (19 bp):
ACTCAACTTCTAAAACTGA
Found at i:69167 original size:26 final size:27
Alignment explanation
Indices: 69121--69180 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
69111 CCATTCCCCA
69121 TCTTCTTCTCTTCTTCTTCTTCACTTT
1 TCTTCTTCTCTTCTTCTTCTTCACTTT
69148 TCTTCTTCT-TTCTT-TCTCTTCACTTT
1 TCTTCTTCTCTTCTTCT-TCTTCACTTT
*
69174 TCCTCTT
1 TCTTCTT
69181 ATCACACACA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 1 0.03
26 21 0.68
27 9 0.29
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (27 bp):
TCTTCTTCTCTTCTTCTTCTTCACTTT
Found at i:70122 original size:3 final size:3
Alignment explanation
Indices: 70114--70157 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
70104 GTGATAATAG
70114 GAA GAA GAA GAA G-A GAA G-A GAA -ATA -AA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA
70156 GA
1 GA
70158 TGGGGGGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:73959 original size:21 final size:21
Alignment explanation
Indices: 73925--73964 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
73915 CTTGTCAAAA
73925 TTAATTAAATGGTTTAATTTT
1 TTAATTAAATGGTTTAATTTT
73946 TTAATATAAA-GGTTTAATT
1 TTAAT-TAAATGGTTTAATT
73965 GAATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (21 bp):
TTAATTAAATGGTTTAATTTT
Found at i:74965 original size:23 final size:23
Alignment explanation
Indices: 74939--74994 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
74929 TTGAAAATAA
*
74939 TATTTATT-TTAAATATTATTAAT
1 TATTTATTAGTAAATATT-TTAAT
*
74962 TATTTATTAGTGAATATTTTAAT
1 TATTTATTAGTAAATATTTTAAT
74985 TATTTTATTA
1 TA-TTTATTA
74995 TCGTTATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
TATTTATTAGTAAATATTTTAAT
Found at i:76281 original size:12 final size:12
Alignment explanation
Indices: 76264--76294 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
76254 AGCTGATAAC
76264 GAAGATTTCGAG
1 GAAGATTTCGAG
76276 GAAGATTTCGAG
1 GAAGATTTCGAG
76288 GAAGATT
1 GAAGATT
76295 CATGTTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (12 bp):
GAAGATTTCGAG
Found at i:79248 original size:35 final size:34
Alignment explanation
Indices: 79163--79249 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
79153 ATTTGGTATT
* *
79163 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGA
* *
79197 TAAATGATAACCAAATTACAATAACTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGA
79235 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
79250 ACTGAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGA
Found at i:79466 original size:3 final size:3
Alignment explanation
Indices: 79458--79507 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
79448 CTCGCTGTTA
* * *
79458 TCG TCG TCG TCG TCG TCG TCG TCA TCA CCG TCG TCG TCG TCG TCG TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
79506 TC
1 TC
79508 CTGAGCAGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.04, C:0.36, G:0.28, T:0.32
Consensus pattern (3 bp):
TCG
Found at i:83490 original size:12 final size:12
Alignment explanation
Indices: 83473--83499 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
83463 ATTAGAAATT
83473 GGAATAGGAGGA
1 GGAATAGGAGGA
83485 GGAATAGGAGGA
1 GGAATAGGAGGA
83497 GGA
1 GGA
83500 TTTAGAGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.52, T:0.07
Consensus pattern (12 bp):
GGAATAGGAGGA
Found at i:84266 original size:20 final size:20
Alignment explanation
Indices: 84237--84274 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
84227 CCCCTTCAAA
*
84237 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
84257 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
84275 TACACCAAAA
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:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:91178 original size:50 final size:50
Alignment explanation
Indices: 91124--91249 Score: 180
Period size: 50 Copynumber: 2.5 Consensus size: 50
91114 AGATACCCAG
* *
91124 GTATAGCGTGGATCAGGGGGCGCGCTATACCCACGTGGCGACAGATCACC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGACAAATCACC
* ** * *
91174 GTATATCGCGGGGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAGC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGACAAATCACC
*
91224 GTATAGCGCGGTTCAGGGGGCGCGCT
1 GTATAGCGCGGATCAGGGGGCGCGCT
91250 TTACTGCTAC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.19, C:0.28, G:0.37, T:0.16
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGACAAATCACC
Done.