Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008996.1 Hibiscus syriacus cultivar Beakdansim tig00112372_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: 115512
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:22 original size:15 final size:15
Alignment explanation
Indices: 2--30 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1 T
2 TTGTTTTTCTTCTTC
1 TTGTTTTTCTTCTTC
17 TTGTTTTTCTTCTT
1 TTGTTTTTCTTCTT
31 TCTTTTGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (15 bp):
TTGTTTTTCTTCTTC
Found at i:443 original size:13 final size:14
Alignment explanation
Indices: 425--460 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
415 ATAGGCGTGA
425 ATGGTGATGG-AAG
1 ATGGTGATGGAAAG
438 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
*
452 ATGATGATG
1 ATGGTGATG
461 AAACAAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:954 original size:19 final size:20
Alignment explanation
Indices: 913--963 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
903 GAAACCCCTT
*
913 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
933 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
952 TGAAGATACATG
1 TGAAAATACATG
964 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:8196 original size:22 final size:20
Alignment explanation
Indices: 8171--8210 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
8161 ATGTTTGTTT
8171 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
8193 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
8211 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:11190 original size:23 final size:23
Alignment explanation
Indices: 11163--11215 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
11153 ACTTTGCAAC
11163 TTTC-TTCACTTCTTTTTCTTTGA
1 TTTCTTTCA-TTCTTTTTCTTTGA
* **
11186 TTTCTTTGATTCTTTTTCTTTTC
1 TTTCTTTCATTCTTTTTCTTTGA
11209 TTTCTTT
1 TTTCTTT
11216 TGCACTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTCTTTCATTCTTTTTCTTTGA
Found at i:11262 original size:12 final size:12
Alignment explanation
Indices: 11242--11282 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
11232 TGTAGGAGTC
11242 TTTTCTTTTGCT
1 TTTTCTTTTGCT
* *
11254 TTTTATTTTTCT
1 TTTTCTTTTGCT
11266 TCTTTCTTTTGCT
1 T-TTTCTTTTGCT
11279 TTTT
1 TTTT
11283 GTTGCAGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTGCT
Found at i:11654 original size:14 final size:14
Alignment explanation
Indices: 11625--11662 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
11615 ATAGGCGTGA
11625 ATGGTGATGG-AAG
1 ATGGTGATGGAAAG
11638 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
11652 ATGGTGATGGA
1 ATGGTGATGGA
11663 CAAATAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.32, C:0.00, G:0.45, T:0.24
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:12036 original size:19 final size:19
Alignment explanation
Indices: 12014--12050 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12004 AAATAAACGG
*
12014 TTTTGATGAAAATACATGA
1 TTTTAATGAAAATACATGA
*
12033 TTTTAATGAAGATACATG
1 TTTTAATGAAAATACATG
12051 CTCTTGGCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:12367 original size:24 final size:24
Alignment explanation
Indices: 12340--12422 Score: 148
Period size: 24 Copynumber: 3.5 Consensus size: 24
12330 TTCAACGGTA
*
12340 AGCTAGGTAAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
12364 AGCTAGGTGAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
12388 AGCTAGGTGAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
*
12412 AACTAGGTGAG
1 AGCTAGGTGAG
12423 CTATAGCTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.20, C:0.12, G:0.36, T:0.31
Consensus pattern (24 bp):
AGCTAGGTGAGTGTCTTGGTAGCT
Found at i:15188 original size:22 final size:23
Alignment explanation
Indices: 15162--15206 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
15152 ACTTTCTTCA
15162 CTTCTTTTTCTTTTATTT-TTTT
1 CTTCTTTTTCTTTTATTTCTTTT
*
15184 CTTCTTTTTCTTTTCTTTCTTTT
1 CTTCTTTTTCTTTTATTTCTTTT
15207 GCACTCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (23 bp):
CTTCTTTTTCTTTTATTTCTTTT
Found at i:15493 original size:15 final size:15
Alignment explanation
Indices: 15473--15503 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15463 TAAATTAAAG
15473 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
*
15488 GAAATGGATAGAATT
1 GAAATGGAAAGAATT
15503 G
1 G
15504 TTATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:18455 original size:16 final size:15
Alignment explanation
Indices: 18436--18469 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
18426 GTAAAAACAG
18436 TAAATAAAAAGATAAA
1 TAAATAAAAAGA-AAA
*
18452 TAAATAAGAAGAAAA
1 TAAATAAAAAGAAAA
18467 TAA
1 TAA
18470 TCCTCACGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (15 bp):
TAAATAAAAAGAAAA
Found at i:24139 original size:19 final size:20
Alignment explanation
Indices: 24117--24160 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
24107 GAGAAAAGGT
24117 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
24136 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
24156 AAAAG
1 AAAAG
24161 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:30527 original size:17 final size:16
Alignment explanation
Indices: 30505--30538 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
30495 TAAAAACAAT
30505 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
30522 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
30538 A
1 A
30539 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:31056 original size:24 final size:24
Alignment explanation
Indices: 31012--31058 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31002 ATAAAGAACC
*
31012 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
31036 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
31059 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:33060 original size:15 final size:15
Alignment explanation
Indices: 33040--33070 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33030 AAAGGAAATG
33040 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
*
33055 GAAATGGATAGAATT
1 GAAATGGAAAGAATT
33070 G
1 G
33071 TTATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:33235 original size:13 final size:14
Alignment explanation
Indices: 33217--33250 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
33207 AGGCGTGAAA
33217 GGTGATGG-AAGAT
1 GGTGATGGAAAGAT
33230 GGTGATGGAAAGAT
1 GGTGATGGAAAGAT
33244 GGTGATG
1 GGTGATG
33251 AACAAATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (14 bp):
GGTGATGGAAAGAT
Found at i:33615 original size:19 final size:19
Alignment explanation
Indices: 33591--33640 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
33581 GAAATCCCTT
*
33591 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
33610 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
33629 TGAAGATACATG
1 TGAAAATACATG
33641 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:33815 original size:17 final size:17
Alignment explanation
Indices: 33793--33834 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
33783 TCACATGGAG
33793 TGCACATGCTTGAATGA
1 TGCACATGCTTGAATGA
33810 TGCACATGCTTGAATGA
1 TGCACATGCTTGAATGA
33827 TGCACATG
1 TGCACATG
33835 GCAGCCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (17 bp):
TGCACATGCTTGAATGA
Found at i:33976 original size:24 final size:24
Alignment explanation
Indices: 33948--34006 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
33938 TTCAGTGGTA
33948 AGCTAGGTGAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
*
33972 AGCTAGGTAAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
*
33996 AACTAGGTGAG
1 AGCTAGGTGAG
34007 CTATAGCTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.22, C:0.12, G:0.36, T:0.31
Consensus pattern (24 bp):
AGCTAGGTGAGTGTCTTGGTAGCT
Found at i:36496 original size:15 final size:15
Alignment explanation
Indices: 36476--36506 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36466 AAAGTAAATG
36476 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
*
36491 GAAATGGATAGAATT
1 GAAATGGAAAGAATT
36506 G
1 G
36507 TTATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:36669 original size:13 final size:14
Alignment explanation
Indices: 36651--36686 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
36641 ATAGGCATGA
36651 ATGGTGATGG-AAG
1 ATGGTGATGGAAAG
36664 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
*
36678 ATTGTGATG
1 ATGGTGATG
36687 AACAAATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.42, T:0.28
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:37051 original size:19 final size:19
Alignment explanation
Indices: 37027--37076 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
37017 GAAATCCCTT
*
37027 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
37046 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
37065 TGAAGATACATG
1 TGAAAATACATG
37077 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:37345 original size:24 final size:24
Alignment explanation
Indices: 37317--37365 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
37307 TTCAATGGTA
37317 AGCTAGGTGAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
37341 AGCTAGGTGAGTGTCTTGGTAGCT
1 AGCTAGGTGAGTGTCTTGGTAGCT
37365 A
1 A
37366 ACTATGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.37, T:0.33
Consensus pattern (24 bp):
AGCTAGGTGAGTGTCTTGGTAGCT
Found at i:40266 original size:13 final size:14
Alignment explanation
Indices: 40248--40283 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
40238 ATAGGCGTGA
40248 ATGGTGATGG-AAG
1 ATGGTGATGGAAAG
40261 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
40275 ATGGTGATG
1 ATGGTGATG
40284 AACAAATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.44, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:40648 original size:19 final size:19
Alignment explanation
Indices: 40624--40673 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
40614 GAAATCCCTT
*
40624 TGAAAATACATGATTTTGA
1 TGAAAATACATGATTTTAA
40643 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
40662 TGAAGATACATG
1 TGAAAATACATG
40674 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:41421 original size:20 final size:21
Alignment explanation
Indices: 41383--41421 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
41373 GATCGTCTAG
*
41383 AAGCTAAGATAAAATGTATAT
1 AAGCTAAGATAAAAGGTATAT
*
41404 AAGCT-AGATAGAAGGTAT
1 AAGCTAAGATAAAAGGTAT
41422 TGGACGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.26
Consensus pattern (21 bp):
AAGCTAAGATAAAAGGTATAT
Found at i:42511 original size:24 final size:24
Alignment explanation
Indices: 42484--42529 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
42474 AATGTCAATG
*
42484 GACACAACTCTTGGCACTTCAAGT
1 GACACAACTCTTGGAACTTCAAGT
***
42508 GACATTTCTCTTGGAACTTCAA
1 GACACAACTCTTGGAACTTCAA
42530 ACGACATTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (24 bp):
GACACAACTCTTGGAACTTCAAGT
Found at i:42535 original size:24 final size:24
Alignment explanation
Indices: 42491--42537 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42481 ATGGACACAA
* **
42491 CTCTTGGCACTTCAAGTGACATTT
1 CTCTTGGAACTTCAAACGACATTT
42515 CTCTTGGAACTTCAAACGACATT
1 CTCTTGGAACTTCAAACGACATT
42538 ATCTTTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (24 bp):
CTCTTGGAACTTCAAACGACATTT
Found at i:42553 original size:24 final size:24
Alignment explanation
Indices: 42508--42553 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
42498 CACTTCAAGT
* *
42508 GACATTTCTCTTGGAACTTCAAAC
1 GACATTTCTCTTGAAACATCAAAC
42532 GACATTATCT-TTGAAACATCAA
1 GACATT-TCTCTTGAAACATCAA
42554 GAGATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (24 bp):
GACATTTCTCTTGAAACATCAAAC
Found at i:43697 original size:25 final size:25
Alignment explanation
Indices: 43650--43697 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
43640 ACTTTCTTCA
* *
43650 CTTCTTTTTCTTTGATTTTTTTTTT
1 CTTCTTATTCTTTGATTTCTTTTTT
**
43675 CTTCTTATTCTTTTCTTTCTTTT
1 CTTCTTATTCTTTGATTTCTTTT
43698 GCACTCCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (25 bp):
CTTCTTATTCTTTGATTTCTTTTTT
Found at i:44173 original size:14 final size:14
Alignment explanation
Indices: 44156--44192 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
44146 ATAGGCGTGA
44156 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
* *
44170 ATGGTGATGGAGAT
1 ATGGTGATGGAAAG
44184 ATGGTGATG
1 ATGGTGATG
44193 AACAAATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.43, T:0.27
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:44574 original size:19 final size:19
Alignment explanation
Indices: 44532--44581 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
44522 GAAACCCCTT
*
44532 TGAAAATACATTATTTTTTA
1 TGAAAATACATGA-TTTTTA
44552 TGAAAATACATGA-TTTTA
1 TGAAAATACATGATTTTTA
*
44570 GTGAAGATACAT
1 -TGAAAATACAT
44582 ACTCTTGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 5 0.19
19 10 0.37
20 12 0.44
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (19 bp):
TGAAAATACATGATTTTTA
Found at i:47517 original size:31 final size:31
Alignment explanation
Indices: 47461--47522 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
47451 AAGCAAAGAT
* **
47461 AAGGTAATGAAATAAGAAATGATGAA-ATAA
1 AAGGAAATGAAATAAGAAAAAATGAAGATAA
47491 AAGGAAATGAAATAGAGAAAAAATGAAGATAA
1 AAGGAAATGAAATA-AGAAAAAATGAAGATAA
47523 CTTACAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 13 0.48
31 10 0.37
32 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.16
Consensus pattern (31 bp):
AAGGAAATGAAATAAGAAAAAATGAAGATAA
Found at i:47675 original size:22 final size:23
Alignment explanation
Indices: 47649--47693 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
47639 ACTTTCTTCA
47649 CTTCTTTTTCTTTGATTT-TTTT
1 CTTCTTTTTCTTTGATTTCTTTT
*
47671 CTTCTTTTTCTTTTATTTCTTTT
1 CTTCTTTTTCTTTGATTTCTTTT
47694 GCACTCCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (23 bp):
CTTCTTTTTCTTTGATTTCTTTT
Found at i:47986 original size:15 final size:15
Alignment explanation
Indices: 47962--47995 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
47952 AAGAAATTAA
47962 AATT-AAATGGAAAG
1 AATTGAAATGGAAAG
*
47976 AATTGAAATGGATAG
1 AATTGAAATGGAAAG
47991 AATTG
1 AATTG
47996 TTAGCAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (15 bp):
AATTGAAATGGAAAG
Found at i:48163 original size:14 final size:14
Alignment explanation
Indices: 48144--48170 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48134 GCGTGAATGT
48144 TGATGGAAAGATGA
1 TGATGGAAAGATGA
48158 TGATGGAAAGATG
1 TGATGGAAAGATG
48171 GTTATGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.37, T:0.22
Consensus pattern (14 bp):
TGATGGAAAGATGA
Found at i:50764 original size:30 final size:31
Alignment explanation
Indices: 50723--50782 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
50713 ACATGCTGCC
*
50723 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAATCATATGCAAACATAATAA
*
50754 ATGA-ATCTAAATCATATGTAAACATAATA
1 ATGATATCTAAATCATATGCAAACATAATA
50783 TAAAGCTAAG
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:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (31 bp):
ATGATATCTAAATCATATGCAAACATAATAA
Found at i:53216 original size:18 final size:19
Alignment explanation
Indices: 53180--53220 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53170 CAGAAGTAAC
*
53180 AAAAAGAAAAAGAAAGAAG
1 AAAAACAAAAAGAAAGAAG
*
53199 AAAAACAAAAAG-AGGAAG
1 AAAAACAAAAAGAAAGAAG
53217 AAAA
1 AAAA
53221 GACTCCTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAGAAAGAAG
Found at i:73238 original size:33 final size:33
Alignment explanation
Indices: 73196--73264 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
73186 GTTGATGAAT
*
73196 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
73229 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
73262 GAA
1 GAA
73265 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:89797 original size:22 final size:22
Alignment explanation
Indices: 89771--89812 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
89761 TATTTATAGT
89771 TATGATGATGA-TATTATGAATG
1 TATGATG-TGATTATTATGAATG
*
89793 TATGATGTTATTATTATGAA
1 TATGATGTGATTATTATGAA
89813 CCACGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (22 bp):
TATGATGTGATTATTATGAATG
Found at i:92498 original size:40 final size:39
Alignment explanation
Indices: 92394--92513 Score: 206
Period size: 38 Copynumber: 3.1 Consensus size: 39
92384 TGCAGGTTTA
92394 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACAC-TTGGTGTATATGGTGGGCACGACCTTATGTG
92434 T-ATACACTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTGGTGTATATGGTGGGCACGACCTTATGTG
*
92472 TAATACAGTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTT-GGTGTATATGGTGGGCACGACCTTATGTG
92512 TA
1 TA
92514 GCACTGCGGT
Statistics
Matches: 77, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
38 32 0.42
39 13 0.17
40 32 0.42
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (39 bp):
TAATACACTTGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:92666 original size:44 final size:47
Alignment explanation
Indices: 92618--92728 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 47
92608 GTAACCATGC
*
92618 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTATATT-GGAA
1 AAATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATATTGGGAA
* * * *
92662 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGGTA
1 AAATAAGCTTACGAGCTTACGGAA-TTAAATGGCAAGTATATTGGGAA
*
92710 AAATAAGTTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
92729 TGAGATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
44 22 0.39
46 1 0.02
47 13 0.23
48 21 0.37
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.32
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATATTGGGAA
Found at i:92722 original size:48 final size:44
Alignment explanation
Indices: 92618--92730 Score: 136
Period size: 48 Copynumber: 2.5 Consensus size: 44
92608 GTAACCATGC
* *
92618 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGAA
* * *
92662 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATATT-GGAA
*
92710 AAATAAGTTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
92731 AGATAAATGG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
44 22 0.37
46 1 0.02
47 13 0.22
48 23 0.39
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGAA
Found at i:94372 original size:44 final size:44
Alignment explanation
Indices: 94309--94397 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
94299 CAATGAAATT
94309 TTCATTTGAGATGGAAAATGTTGTAAATGTTCAAGAATAATTCC
1 TTCATTTGAGATGGAAAATGTTGTAAATGTTCAAGAATAATTCC
94353 TTCATTTGAGATGGAAAATGTTGTAAATGTTCAAGAATAATTCC
1 TTCATTTGAGATGGAAAATGTTGTAAATGTTCAAGAATAATTCC
94397 T
1 T
94398 ATGGATCTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (44 bp):
TTCATTTGAGATGGAAAATGTTGTAAATGTTCAAGAATAATTCC
Found at i:99422 original size:38 final size:38
Alignment explanation
Indices: 99367--99484 Score: 182
Period size: 38 Copynumber: 3.0 Consensus size: 38
99357 CAGGTTTATA
*
99367 ATACACTTTGGTGTATATGGTGGGCATGACCTTATGTGT
1 ATACAC-TTGGTGTATATGGTGGGCACGACCTTATGTGT
* *
99406 ATACACTTAGTGTATATGGTGAGCACGACCTTATGTGT
1 ATACACTTGGTGTATATGGTGGGCACGACCTTATGTGT
99444 AATACACTTCGGTGTATATGGTGGGCACGACCTTATGTGT
1 -ATACACTT-GGTGTATATGGTGGGCACGACCTTATGTGT
99484 A
1 A
99485 GCACTACGGT
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
38 29 0.40
39 15 0.21
40 28 0.39
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (38 bp):
ATACACTTGGTGTATATGGTGGGCACGACCTTATGTGT
Found at i:99472 original size:40 final size:39
Alignment explanation
Indices: 99365--99484 Score: 188
Period size: 40 Copynumber: 3.1 Consensus size: 39
99355 TGCAGGTTTA
*
99365 TAATACACTTTGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACAC-TTGGTGTATATGGTGGGCACGACCTTATGTG
* *
99405 T-ATACACTTAGTGTATATGGTGAGCACGACCTTATGTG
1 TAATACACTTGGTGTATATGGTGGGCACGACCTTATGTG
99443 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTT-GGTGTATATGGTGGGCACGACCTTATGTG
99483 TA
1 TA
99485 GCACTACGGT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
38 29 0.40
39 14 0.19
40 30 0.41
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (39 bp):
TAATACACTTGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:99637 original size:44 final size:47
Alignment explanation
Indices: 99589--99699 Score: 147
Period size: 44 Copynumber: 2.4 Consensus size: 47
99579 GTAACCATGC
*
99589 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTATATT-GGAA
1 AAATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATATTGGGAA
* * * *
99633 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGGTA
1 AAATAAGCTTACGAGCTTACGGAA-TTAAATGGCAAGTATATTGGGAA
99681 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
99700 TGAGATAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 22 0.38
46 1 0.02
47 13 0.22
48 22 0.38
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.31
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTACGGAATTAAATGGCAAGTATATTGGGAA
Found at i:99691 original size:48 final size:44
Alignment explanation
Indices: 99589--99701 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 44
99579 GTAACCATGC
* *
99589 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGAA
* * *
99633 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATATT-GGAA
99681 AAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
99702 AGATAAATGG
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 22 0.37
46 1 0.02
47 13 0.22
48 24 0.40
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGGAA
Found at i:109644 original size:16 final size:16
Alignment explanation
Indices: 109610--109656 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
109600 ATAACATCTC
*
109610 TATCCATTTTATTTCT
1 TATCCATTTCATTTCT
109626 TATCC-TTTCATTTCT
1 TATCCATTTCATTTCT
109641 T-T--ATTTCATTTCT
1 TATCCATTTCATTTCT
109654 TAT
1 TAT
109657 TTCCAATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.39
14 2 0.07
15 10 0.36
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTCATTTCT
Found at i:109658 original size:12 final size:13
Alignment explanation
Indices: 109631--109659 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
109621 TTTCTTATCC
109631 TTTCATTTCTTTA
1 TTTCATTTCTTTA
109644 TTTCATTTC-TTA
1 TTTCATTTCTTTA
109656 TTTC
1 TTTC
109660 CAATACATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:112599 original size:27 final size:26
Alignment explanation
Indices: 112569--112645 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 26
112559 TAAGAAAGGA
* * *
112569 AAATGATTAATAAAAGAAGATGAAATT
1 AAATGATAAAGAAAAGAA-ATGAAATG
*
112596 AAATGATAAAGATAAGAAATGAAATG
1 AAATGATAAAGAAAAGAAATGAAATG
* *
112622 AAATGA-AATGAAATGAAATGAAAT
1 AAATGATAAAGAAAAGAAATGAAAT
112646 AAGGATGAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 15 0.35
26 13 0.30
27 15 0.35
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (26 bp):
AAATGATAAAGAAAAGAAATGAAATG
Found at i:112619 original size:5 final size:5
Alignment explanation
Indices: 112588--112645 Score: 73
Period size: 5 Copynumber: 11.4 Consensus size: 5
112578 ATAAAAGAAG
* *
112588 ATGAA ATTAA ATGATA AAGATA A-GAA ATGAA ATGAA ATGAA ATGAA ATGAA
1 ATGAA ATGAA ATGA-A ATGA-A ATGAA ATGAA ATGAA ATGAA ATGAA ATGAA
112639 ATGAA AT
1 ATGAA AT
112646 AAGGATGAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
4 2 0.04
5 39 0.81
6 7 0.15
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.22
Consensus pattern (5 bp):
ATGAA
Found at i:114121 original size:25 final size:22
Alignment explanation
Indices: 114071--114122 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 22
114061 AAGATGTGGA
*
114071 AACATATATTATGCATGAAAAT
1 AACATATAGTATGCATGAAAAT
114093 --CATATAGTATGCAAGTGAATAAT
1 AACATATAGTATGC-A-TGAA-AAT
114116 AACATAT
1 AACATAT
114123 TATTCAAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
20 11 0.46
21 1 0.04
22 4 0.17
23 3 0.12
25 5 0.21
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (22 bp):
AACATATAGTATGCATGAAAAT
Done.