Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014352.1 Corchorus capsularis cultivar CVL-1 contig14373, 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: 39661
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:399 original size:14 final size:14
Alignment explanation
Indices: 364--408 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
354 GAGTAGTAAA
*
364 AAGTAATAAGGTAA-
1 AAGTAATCAGG-AAG
378 AAGTAATCAGGAAG
1 AAGTAATCAGGAAG
*
392 AAGTAATCAGTAAG
1 AAGTAATCAGGAAG
406 AAG
1 AAG
409 GTCAAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 2 0.07
14 26 0.93
ACGTcount: A:0.53, C:0.04, G:0.24, T:0.18
Consensus pattern (14 bp):
AAGTAATCAGGAAG
Found at i:1249 original size:66 final size:65
Alignment explanation
Indices: 1143--1271 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 65
1133 TTAAACGCCA
*
1143 TAGAACACGAACATGGTAGAACGACAACATCGAAGATCGGCAGAAGTGTCAGATATGGAGATCCC
1 TAGAACACGAACAAGGTAGAACGACAACATCGAAGATCGGCA-AAGTGTCAGATATGGAGATCCC
1208 G
65 G
*
1209 TAGAACATGAACAAGGTAGAACGACAACATCGAAGATCGGCAAAGTGTCAGATATGGAGATCC
1 TAGAACACGAACAAGGTAGAACGACAACATCGAAGATCGGCAAAGTGTCAGATATGGAGATCC
1272 TTACGTTGGT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 21 0.34
66 40 0.66
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.16
Consensus pattern (65 bp):
TAGAACACGAACAAGGTAGAACGACAACATCGAAGATCGGCAAAGTGTCAGATATGGAGATCCCG
Found at i:1349 original size:165 final size:165
Alignment explanation
Indices: 1070--1370 Score: 460
Period size: 165 Copynumber: 1.8 Consensus size: 165
1060 GAGAACGGAT
* * * * *
1070 ACATCGTAGATCGGCAGATTTTCAGATATGGAGATCCTTGCGTTGATTACAGACTTGAAAGATTT
1 ACATCGAAGATCGGCAAAGTGTCAGATATGGAGATCCTTACGTTGATTACAGACTTGAAAGATTT
* *
1135 AAACGCCATAGAACACGAACATGGTAGAACGACAACATCGAAGATCGGCAGAAGTGTCAGATATG
66 AAACGCCATAGAACACGAACATGGAAGAACGACAACATCGAAGATCGGCAGAAGTGCCAGATATG
1200 GAGATCCCGTAGAACATGAACAAGGTAGAACGACA
131 GAGATCCCGTAGAACATGAACAAGGTAGAACGACA
*
1235 ACATCGAAGATCGGCAAAGTGTCAGATATGGAGATCCTTACGTTGGTTACA-AGCTTGAAAGATT
1 ACATCGAAGATCGGCAAAGTGTCAGATATGGAGATCCTTACGTTGATTACAGA-CTTGAAAGATT
* ** ** *
1299 TGATGGTGATAGAACCCGAACATGGAAGAACGACAACATCGAAGATCGGCAGAAGTGCCAGATAT
65 TAAACGCCATAGAACACGAACATGGAAGAACGACAACATCGAAGATCGGCAGAAGTGCCAGATAT
1364 GGAGATC
130 GGAGATC
1371 TTCCCTCGTG
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
164 1 0.01
165 120 0.99
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (165 bp):
ACATCGAAGATCGGCAAAGTGTCAGATATGGAGATCCTTACGTTGATTACAGACTTGAAAGATTT
AAACGCCATAGAACACGAACATGGAAGAACGACAACATCGAAGATCGGCAGAAGTGCCAGATATG
GAGATCCCGTAGAACATGAACAAGGTAGAACGACA
Found at i:1428 original size:100 final size:99
Alignment explanation
Indices: 1217--1411 Score: 241
Period size: 100 Copynumber: 2.0 Consensus size: 99
1207 CGTAGAACAT
* * * * *
1217 GAACAAGGTAGAACGACAACATCGAAGATCGGCAAAGTGTCAGATATGGAGATCCTTACGTTGGT
1 GAACAAGGAAGAACGACAACATCGAAGATCGGCAAAGTGCCAGATATGGAGATCCTTACCTCGGC
* * * *
1282 TACAAGCTTGAAAGATTTGATGGTGATAGAACCC
66 CACAAGCTTGAAAGATCTAATGGAGATAGAACCC
* *
1316 GAACATGGAAGAACGACAACATCGAAGATCGGCAGAAGTGCCAGATATGGAGAT-CTTCCCTCGT
1 GAACAAGGAAGAACGACAACATCGAAGATCGGCA-AAGTGCCAGATATGGAGATCCTTACCTCG-
*
1380 GCCACAAGGTTGGAAA-ATCTAATGGAGATAGA
64 GCCACAAGCTT-GAAAGATCTAATGGAGATAGA
1412 TTCGGAGGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
99 38 0.47
100 39 0.48
101 4 0.05
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.20
Consensus pattern (99 bp):
GAACAAGGAAGAACGACAACATCGAAGATCGGCAAAGTGCCAGATATGGAGATCCTTACCTCGGC
CACAAGCTTGAAAGATCTAATGGAGATAGAACCC
Found at i:11497 original size:27 final size:28
Alignment explanation
Indices: 11459--11536 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 28
11449 CGCTTCCTTT
* *
11459 TTTTTTATTGAATACTATTTTTTTAC-C
1 TTTTTTACTGAATACCATTTTTTTACTC
*
11486 TTTTTTACTGAATACCA-CTTTTTACTC
1 TTTTTTACTGAATACCATTTTTTTACTC
*
11513 TTTTTTACTGATTACCATTTTTTT
1 TTTTTTACTGAATACCATTTTTTT
11537 TCTACTGATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
26 7 0.16
27 32 0.73
28 5 0.11
ACGTcount: A:0.21, C:0.15, G:0.04, T:0.60
Consensus pattern (28 bp):
TTTTTTACTGAATACCATTTTTTTACTC
Found at i:11603 original size:36 final size:35
Alignment explanation
Indices: 11557--11648 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 35
11547 ACCCCTTTCA
11557 CTTTACTGATTACTATTTACTCTTTACCATTTTATT
1 CTTTACTGATTACTATTTACTCTTTACCATTTT-TT
* *
11593 TTTTATTGATTACTATTTACTCTTTACCATTTTTT
1 CTTTACTGATTACTATTTACTCTTTACCATTTTTT
* *
11628 CTTTGCTGATTACTCTTTACT
1 CTTTACTGATTACTATTTACT
11649 AATTAGTACT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
35 19 0.38
36 31 0.62
ACGTcount: A:0.20, C:0.18, G:0.04, T:0.58
Consensus pattern (35 bp):
CTTTACTGATTACTATTTACTCTTTACCATTTTTT
Found at i:11619 original size:14 final size:14
Alignment explanation
Indices: 11602--11820 Score: 60
Period size: 14 Copynumber: 15.1 Consensus size: 14
11592 TTTTTATTGA
11602 TTACTATTTACTCT
1 TTACTATTTACTCT
* **
11616 TTACCATTTTTTCT
1 TTACTATTTACTCT
*
11630 TTGCTGA-TTACTCT
1 TTACT-ATTTACTCT
**
11644 TTACTAATTAGTACTGA
1 TTACT-ATT--TACTCT
* *
11661 TTACCA-TTACTTT
1 TTACTATTTACTCT
*
11674 TTACCATTTTACT-T
1 TTACTA-TTTACTCT
11688 TCTACTGA-TTACTCT
1 T-TACT-ATTTACTCT
* **
11703 TTGCTAATTAGTACTGA
1 TTACT-ATT--TACTCT
* *
11720 TTACCA-TTACTTT
1 TTACTATTTACTCT
*
11733 TTACCATTTTACT-T
1 TTACTA-TTTACTCT
11747 TCTACTGA-TTACTCT
1 T-TACT-ATTTACTCT
*
11762 TTACTCTTTAC-CATT
1 TTACTATTTACTC--T
* *
11777 TTACTTTTTACTTT
1 TTACTATTTACTCT
11791 TTACTGA-TTACTCT
1 TTACT-ATTTACTCT
*
11805 TTACTTTTTACTCT
1 TTACTATTTACTCT
11819 TT
1 TT
11821 TTAACTTAAT
Statistics
Matches: 152, Mismatches: 30, Indels: 46
0.67 0.13 0.20
Matches are distributed among these distances:
13 21 0.14
14 76 0.50
15 36 0.24
16 4 0.03
17 15 0.10
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.54
Consensus pattern (14 bp):
TTACTATTTACTCT
Found at i:11677 original size:30 final size:30
Alignment explanation
Indices: 11636--11736 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
11626 TTCTTTGCTG
11636 ATTACTCTTTACTAATTAGTACTGATTACC
1 ATTACTCTTTACTAATTAGTACTGATTACC
* * * * *
11666 ATTACTTTTTAC-CATT-TTACT-TTCTACTG
1 ATTACTCTTTACTAATTAGTACTGAT-TAC-C
*
11695 ATTACTCTTTGCTAATTAGTACTGATTACC
1 ATTACTCTTTACTAATTAGTACTGATTACC
*
11725 ATTACTTTTTAC
1 ATTACTCTTTAC
11737 CATTTTACTT
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
27 1 0.02
28 7 0.13
29 13 0.25
30 24 0.45
31 7 0.13
32 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (30 bp):
ATTACTCTTTACTAATTAGTACTGATTACC
Found at i:11700 original size:59 final size:59
Alignment explanation
Indices: 11599--11766 Score: 259
Period size: 59 Copynumber: 2.8 Consensus size: 59
11589 TATTTTTTAT
* * * *
11599 TGATTACTATTTACTCTTTACCATTTT--TTCTTTGCTGATTACTCTTTACTAATTAGTAC
1 TGATTACCA-TTACTTTTTACCATTTTACTT-TCTACTGATTACTCTTTACTAATTAGTAC
*
11658 TGATTACCATTACTTTTTACCATTTTACTTTCTACTGATTACTCTTTGCTAATTAGTAC
1 TGATTACCATTACTTTTTACCATTTTACTTTCTACTGATTACTCTTTACTAATTAGTAC
11717 TGATTACCATTACTTTTTACCATTTTACTTTCTACTGATTACTCTTTACT
1 TGATTACCATTACTTTTTACCATTTTACTTTCTACTGATTACTCTTTACT
11767 CTTTACCATT
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
58 16 0.16
59 83 0.82
60 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.51
Consensus pattern (59 bp):
TGATTACCATTACTTTTTACCATTTTACTTTCTACTGATTACTCTTTACTAATTAGTAC
Found at i:11764 original size:29 final size:29
Alignment explanation
Indices: 11666--11765 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 29
11656 ACTGATTACC
*
11666 ATTACTTTTTACCATTTTACTTTCTACTG
1 ATTACTCTTTACCATTTTACTTTCTACTG
* * * * *
11695 ATTACTCTTTGCTAATTAGTACTGAT-TAC-C
1 ATTACTCTTTAC-CATT-TTACT-TTCTACTG
*
11725 ATTACTTTTTACCATTTTACTTTCTACTG
1 ATTACTCTTTACCATTTTACTTTCTACTG
11754 ATTACTCTTTAC
1 ATTACTCTTTAC
11766 TCTTTACCAT
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
27 1 0.02
28 7 0.13
29 24 0.45
30 13 0.25
31 7 0.13
32 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (29 bp):
ATTACTCTTTACCATTTTACTTTCTACTG
Found at i:11765 original size:7 final size:7
Alignment explanation
Indices: 11755--11820 Score: 62
Period size: 7 Copynumber: 9.3 Consensus size: 7
11745 TTTCTACTGA
11755 TTACTCT
1 TTACTCT
11762 TTACTCT
1 TTACTCT
11769 TTAC-CATT
1 TTACTC--T
*
11777 TTACTTT
1 TTACTCT
*
11784 TTACTTT
1 TTACTCT
**
11791 TTACTGA
1 TTACTCT
11798 TTACTCT
1 TTACTCT
*
11805 TTACTTT
1 TTACTCT
11812 TTACTCT
1 TTACTCT
11819 TT
1 TT
11821 TTAACTTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
6 1 0.02
7 43 0.88
8 5 0.10
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.61
Consensus pattern (7 bp):
TTACTCT
Found at i:11772 original size:36 final size:36
Alignment explanation
Indices: 11714--11816 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
11704 TGCTAATTAG
*
11714 TACTGATTAC-CATTACTTTTTACCATTTTACTTTC
1 TACTGATTACTCATTACTCTTTACCATTTTACTTTC
* *
11749 TACTGATTACTCTTTACTCTTTACCATTTTACTTTT
1 TACTGATTACTCATTACTCTTTACCATTTTACTTTC
** * *
11785 TACTTTTTACTGATTACTCTTTA-CTTTTTACT
1 TACTGATTACTCATTACTCTTTACCATTTTACT
11817 CTTTTTAACT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 18 0.31
36 41 0.69
ACGTcount: A:0.20, C:0.21, G:0.03, T:0.55
Consensus pattern (36 bp):
TACTGATTACTCATTACTCTTTACCATTTTACTTTC
Found at i:12580 original size:20 final size:20
Alignment explanation
Indices: 12557--12625 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
12547 ATATAAGCAT
12557 CAAAGCCCAAATATAAATGA
1 CAAAGCCCAAATATAAATGA
* *
12577 CAAAGCCC-AAGATAAATCAA
1 CAAAGCCCAAATATAAAT-GA
* *
12597 TAAAGCTCAAAT-TAAATGA
1 CAAAGCCCAAATATAAATGA
12616 CCAAA-CCCAA
1 -CAAAGCCCAA
12626 CCGAATCATT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 13 0.34
20 23 0.61
21 2 0.05
ACGTcount: A:0.54, C:0.23, G:0.09, T:0.14
Consensus pattern (20 bp):
CAAAGCCCAAATATAAATGA
Found at i:15101 original size:24 final size:24
Alignment explanation
Indices: 15051--15099 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
15041 CCCAAGGCAT
15051 AAGCCCAAAGCCCAAAATGGACTA
1 AAGCCCAAAGCCCAAAATGGACTA
*
15075 AAGCCCAGAA-CCCAAAA-GTACTA
1 AAGCCCA-AAGCCCAAAATGGACTA
15098 AA
1 AA
15100 AGGAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 14 0.61
25 2 0.09
ACGTcount: A:0.49, C:0.29, G:0.14, T:0.08
Consensus pattern (24 bp):
AAGCCCAAAGCCCAAAATGGACTA
Found at i:22905 original size:42 final size:40
Alignment explanation
Indices: 22834--22917 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 40
22824 TTAACAATAT
22834 ATATTTTTAATATATATTTATATTATTAGTAAATTAGTAA
1 ATATTTTTAATATATATTTATATTATTAGTAAATTAGTAA
*
22874 ATATTTATTAGTATATA-TTATTATTTATTAGTAAATTAGTAA
1 ATATTT-TTAATATATATTTA-TA-TTATTAGTAAATTAGTAA
22916 AT
1 AT
22918 TAGTAAAACA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
40 9 0.22
41 11 0.28
42 20 0.50
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (40 bp):
ATATTTTTAATATATATTTATATTATTAGTAAATTAGTAA
Found at i:22913 original size:8 final size:8
Alignment explanation
Indices: 22900--22924 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
22890 ATTATTATTT
22900 ATTAGTAA
1 ATTAGTAA
22908 ATTAGTAA
1 ATTAGTAA
22916 ATTAGTAA
1 ATTAGTAA
22924 A
1 A
22925 ACATATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (8 bp):
ATTAGTAA
Found at i:22962 original size:2 final size:2
Alignment explanation
Indices: 22957--22999 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
22947 TTTATTTAAC
*
22957 AT AT AT AT AT AT AT AT AC AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22998 AT
1 AT
23000 TTCAAGGCCG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24898 original size:33 final size:33
Alignment explanation
Indices: 24861--24934 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
24851 CTTTTTACCT
** *
24861 AAAACAGTCCTATTTTCAATGCTATGATCAACC
1 AAAACAGAACTATTTGCAATGCTATGATCAACC
*
24894 AAAACAGAATTATTTGCAATGCTATGATCAACC
1 AAAACAGAACTATTTGCAATGCTATGATCAACC
24927 AAAACAGA
1 AAAACAGA
24935 TTTATTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (33 bp):
AAAACAGAACTATTTGCAATGCTATGATCAACC
Found at i:24940 original size:33 final size:33
Alignment explanation
Indices: 24871--24941 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
24861 AAAACAGTCC
*
24871 TATTTTCAATGCTATGATCAACCAAAACAGAAT
1 TATTTGCAATGCTATGATCAACCAAAACAGAAT
*
24904 TATTTGCAATGCTATGATCAACCAAAACAGATT
1 TATTTGCAATGCTATGATCAACCAAAACAGAAT
24937 TATTT
1 TATTT
24942 TCATCACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (33 bp):
TATTTGCAATGCTATGATCAACCAAAACAGAAT
Found at i:36412 original size:3 final size:3
Alignment explanation
Indices: 36404--36438 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
36394 ATTTGCATTA
36404 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
36439 AGGGATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:37053 original size:9 final size:9
Alignment explanation
Indices: 37035--37098 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
37025 AAAAAAAATG
*
37035 AAATGGAAA
1 AAATGAAAA
37044 AAATG--AA
1 AAATGAAAA
37051 AAATGAAAA
1 AAATGAAAA
37060 AAGATGAAAA
1 AA-ATGAAAA
**
37070 TGATGAAAA
1 AAATGAAAA
37079 AAA-GAAAA
1 AAATGAAAA
37087 AAA-GAGAAA
1 AAATGA-AAA
37096 AAA
1 AAA
37099 AAAAAAAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
7 7 0.15
8 10 0.21
9 23 0.49
10 7 0.15
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.09
Consensus pattern (9 bp):
AAATGAAAA
Found at i:37054 original size:16 final size:15
Alignment explanation
Indices: 37027--37086 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 15
37017 AATTTCCCAA
37027 AAAAAATG-AAATGG
1 AAAAAATGAAAATGG
*
37041 AAAAAATGAAAAATGA
1 AAAAAATG-AAAATGG
37057 AAAAAGATGAAAATGATG
1 AAAAA-ATGAAAATG--G
*
37075 AAAAAAAGAAAA
1 AAAAAATGAAAA
37087 AAAGAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 8 0.21
16 16 0.42
17 9 0.24
18 5 0.13
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.12
Consensus pattern (15 bp):
AAAAAATGAAAATGG
Found at i:37085 original size:17 final size:15
Alignment explanation
Indices: 37035--37087 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 15
37025 AAAAAAAATG
*
37035 AAATGGAAAAAATGAA
1 AAAT-GAAAAAAAGAA
37051 AAATGAAAAAAGATGAA
1 AAATGAAAAAA-A-GAA
37068 AATGATGAAAAAAAGAA
1 AA--ATGAAAAAAAGAA
37085 AAA
1 AAA
37088 AAGAGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 8 0.25
16 4 0.12
17 10 0.31
18 1 0.03
19 9 0.28
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (15 bp):
AAATGAAAAAAAGAA
Found at i:37089 original size:8 final size:8
Alignment explanation
Indices: 37074--37108 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
37064 TGAAAATGAT
37074 GAAAAAAA
1 GAAAAAAA
37082 GAAAAAAA
1 GAAAAAAA
37090 GAGAAAAAA
1 GA-AAAAAA
37099 -AAAAAAA
1 GAAAAAAA
37106 GAA
1 GAA
37109 GAGAAAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 6 0.24
8 13 0.52
9 6 0.24
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:37096 original size:17 final size:18
Alignment explanation
Indices: 37076--37117 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
37066 AAAATGATGA
37076 AAAAAAGAAAAAAAG-AG
1 AAAAAAGAAAAAAAGAAG
37093 AAAAAA-AAAAAAAGAAG
1 AAAAAAGAAAAAAAGAAG
37110 AGAAAAAG
1 A-AAAAAG
37118 CAACGATGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.36
17 9 0.41
18 5 0.23
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAGAAG
Found at i:37102 original size:14 final size:15
Alignment explanation
Indices: 37078--37116 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
37068 AATGATGAAA
*
37078 AAAAGAAAAAAAGAG
1 AAAAGAAAAAAAAAG
37093 AAAA-AAAAAAAAAG
1 AAAAGAAAAAAAAAG
*
37107 AAGAGAAAAA
1 AAAAGAAAAA
37117 GCAACGATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:37110 original size:19 final size:18
Alignment explanation
Indices: 37074--37116 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
37064 TGAAAATGAT
*
37074 GAAAAAAAGAAAAAAAGA
1 GAAAAAAAAAAAAAAAGA
37092 GAAAAAAAAAAAAAGAAGA
1 GAAAAAAAAAAAAA-AAGA
37111 GAAAAA
1 GAAAAA
37117 GCAACGATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAAAAAAAGA
Found at i:37185 original size:45 final size:45
Alignment explanation
Indices: 37123--37226 Score: 174
Period size: 45 Copynumber: 2.3 Consensus size: 45
37113 AAAAGCAACG
* *
37123 ATGGTTTT-AAAAAAGAGTCATGGTTTTCAAAATGTTTTGATAAA
1 ATGGTTTTCCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
*
37167 ATGGTTTTCCAAAAAGAGTCATGGTTTTCGAAAGGTTTTGATAAA
1 ATGGTTTTCCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
37212 ATGGTTTTCCAAAAA
1 ATGGTTTTCCAAAAA
37227 TGATTTCAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 8 0.14
45 48 0.86
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (45 bp):
ATGGTTTTCCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
Found at i:37629 original size:25 final size:26
Alignment explanation
Indices: 37586--37639 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
37576 AAATAAAAAT
* *
37586 GAAAAAATGAAAATTGAAAGAGAAAG
1 GAAAAAATGAAAATAGAAACAGAAAG
* *
37612 GAAAAATTGAAAA-AGAAACTGAAAG
1 GAAAAAATGAAAATAGAAACAGAAAG
37637 GAA
1 GAA
37640 GGGTGAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.65, C:0.02, G:0.22, T:0.11
Consensus pattern (26 bp):
GAAAAAATGAAAATAGAAACAGAAAG
Found at i:37962 original size:6 final size:6
Alignment explanation
Indices: 37951--38000 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
37941 GTAAAAAATG
*
37951 AAAGAA AAAGAA AAAGAA AGAA-AA AGAAGAA AAAGAA AAA-AA AGAGAA
1 AAAGAA AAAGAA AAAGAA A-AAGAA A-AAGAA AAAGAA AAAGAA AAAGAA
37999 AA
1 AA
38001 TGAAGAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 4 0.10
6 30 0.77
7 5 0.13
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:37980 original size:9 final size:9
Alignment explanation
Indices: 37958--38009 Score: 70
Period size: 9 Copynumber: 5.8 Consensus size: 9
37948 ATGAAAGAAA
37958 AAGAAAAAG
1 AAGAAAAAG
37967 AAAGAAAAAG
1 -AAGAAAAAG
37977 AAGAAAAAG
1 AAGAAAAAG
*
37986 AAAAAAAAG
1 AAGAAAAAG
*
37995 -AGAAAATG
1 AAGAAAAAG
38003 AAGAAAA
1 AAGAAAA
38010 GAGGCTCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
8 6 0.16
9 23 0.61
10 9 0.24
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:37984 original size:26 final size:26
Alignment explanation
Indices: 37945--38009 Score: 98
Period size: 25 Copynumber: 2.5 Consensus size: 26
37935 GTGCATGTAA
37945 AAAATGAAAGAAAAAGAAAAAGAAAGA-
1 AAAATG-AAGAAAAAGAAAAA-AAAGAG
37972 AAAA-GAAGAAAAAGAAAAAAAAGAG
1 AAAATGAAGAAAAAGAAAAAAAAGAG
37997 AAAATGAAGAAAA
1 AAAATGAAGAAAA
38010 GAGGCTCTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.14
25 18 0.50
26 9 0.25
27 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.03
Consensus pattern (26 bp):
AAAATGAAGAAAAAGAAAAAAAAGAG
Found at i:38009 original size:16 final size:17
Alignment explanation
Indices: 37944--38012 Score: 79
Period size: 17 Copynumber: 4.0 Consensus size: 17
37934 AGTGCATGTA
37944 AAAAATGAAAGAAAA-AG
1 AAAAA-GAAAGAAAAGAG
37961 AAAAAGAAAGAAAAAGAAG
1 AAAAAGAAAG-AAAAG-AG
*
37980 AAAAAGAAAAAAAAGAG
1 AAAAAGAAAGAAAAGAG
*
37997 AAAATG-AAGAAAAGAG
1 AAAAAGAAAGAAAAGAG
38013 GCTCTAGGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
16 14 0.30
17 16 0.35
18 5 0.11
19 11 0.24
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAGAAAAGAG
Found at i:38891 original size:70 final size:70
Alignment explanation
Indices: 38804--39317 Score: 684
Period size: 70 Copynumber: 7.4 Consensus size: 70
38794 AATGCTTTGA
* * * *
38804 CTTTTCCATAAGTCAAACTCGCTTCCACACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
38869 AGGGG
66 AGGGG
* *
38874 TTTTTCCACAAGCCAAACTCGTTTCCATATGAGAT-AGTTCAAGCTTTGGTTCCATCCAAGCATG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAG-TCAGTTCAAGCTTTGGTTCCATCCAAGCATG
*
38938 TAGGGG
65 CAGGGG
38944 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCCAAAGCAT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAG-TCAGTTCAAGCTTTGGTTCCATCC-AAGCAT
*
39008 TCAGGGG
64 GCAGGGG
* * * *
39015 CTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAGTTTAA-CCTTGGTTCCATCCAAGCA-GT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
*
39078 AAGGG
66 AGGGG
* * * *
39083 CTTTTCCACAAGCCAAACTCGTTTCCGTACGAGGCAG-TCTAGCCTTGGTTCCATCCAAGCA-GC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
39146 AGGGG
66 AGGGG
* * * *
39151 CTTTTCCATAAGCCAAACTCATTTCCATACGAGTCAGTTCAAGCTTTGGTTCCACCCAAGCATTC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
*
39216 AAGGG
66 AGGGG
* * * *
39221 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGACAG-TCTAGCCTTGGTTCCATACAAGCA-GC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
**
39284 AATGG
66 AGGGG
*
39289 CTTTTCCACAAGCCAAACTCTTTTCCATA
1 CTTTTCCACAAGCCAAACTCGTTTCCATA
39318 AGCCAAGTTC
Statistics
Matches: 395, Mismatches: 43, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
67 2 0.01
68 128 0.32
69 46 0.12
70 169 0.43
71 50 0.13
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (70 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
AGGGG
Found at i:39273 original size:206 final size:209
Alignment explanation
Indices: 38804--39317 Score: 730
Period size: 206 Copynumber: 2.5 Consensus size: 209
38794 AATGCTTTGA
* * * * * *
38804 CTTTTCCATAAGTCAAACTCGCTTCCACACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAG-TCTAGCCTTGGTTCCATCCAAGCA-GC
* * * * *
38869 AGGGGTTTTTCCACAAGCCAAACTCGTTTCCATATGAGATAGTTCAAGCTTTGGTTCCATCCAAG
64 AAGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGACAGTTCAAGCCTTGGTTCCATCCAAG
* *
38934 CATGTAGGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCAT
129 CATGCAGGGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGATAGTTCAAGCTTTGGTTCCAT
*
38999 CCAAAGCATTCAGGGG
194 CCAAAGCATTCAAGGG
* * * *
39015 CTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAGTTTAACCTTGGTTCCATCCAAGCAGTAA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTCTAGCCTTGGTTCCATCCAAGCAGCAA
* * *
39080 GGGCTTTTCCACAAGCCAAACTCGTTTCCGTACGAGGCAG-TCTAGCCTTGGTTCCATCCAAGCA
66 GGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGACAGTTCAAGCCTTGGTTCCATCCAAGCA
*
39144 -GCAGGGGCTTTTCCATAAGCCAAACTCATTTCCATACGAG-TCAGTTCAAGCTTTGGTTCCA-C
131 TGCAGGGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATC
*
39206 CCAAGCATTCAAGGG
195 CAAAGCATTCAAGGG
* *
39221 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGACAGTCTAGCCTTGGTTCCATACAAGCAGCAA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTCTAGCCTTGGTTCCATCCAAGCAGCAA
* *
39286 TGGCTTTTCCACAAGCCAAACTCTTTTCCATA
66 GGGCTTTTCCACAAGCCAAACTCGTTTCCATA
39318 AGCCAAGTTC
Statistics
Matches: 270, Mismatches: 32, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
206 103 0.38
207 56 0.21
208 22 0.08
209 37 0.14
210 20 0.07
211 32 0.12
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (209 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTCTAGCCTTGGTTCCATCCAAGCAGCAA
GGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGACAGTTCAAGCCTTGGTTCCATCCAAGCA
TGCAGGGGCTTTTCCACAAGCCAAACTCATTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCC
AAAGCATTCAAGGG
Done.