Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012570.1 Corchorus capsularis cultivar CVL-1 contig12591, 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: 43158
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Found at i:1322 original size:13 final size:13
Alignment explanation
Indices: 1304--1337 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1294 TTAACTATTG
1304 TTTGCTTTAATAA
1 TTTGCTTTAATAA
1317 TTTGCTTT-ATAA
1 TTTGCTTTAATAA
*
1329 TCTGCTTTA
1 TTTGCTTTA
1338 GATTTAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (13 bp):
TTTGCTTTAATAA
Found at i:1345 original size:6 final size:6
Alignment explanation
Indices: 1334--1360 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1324 TATAATCTGC
1334 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1361 GCTTTACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:4037 original size:25 final size:26
Alignment explanation
Indices: 3992--4042 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
3982 AACACGTTTA
*
3992 AATAAAAATATTTAAATAATTGAAATT
1 AATAAAAATATTTAAAGAATT-AAATT
4019 AATAAAAA-A-TTAAAGAATTAAATT
1 AATAAAAATATTTAAAGAATTAAATT
4043 GTTATATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 9 0.39
26 1 0.04
27 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (26 bp):
AATAAAAATATTTAAAGAATTAAATT
Found at i:5260 original size:2 final size:2
Alignment explanation
Indices: 5255--5288 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5245 TTTTAGTGTA
5255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5289 TTTTTGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5777 original size:30 final size:31
Alignment explanation
Indices: 5723--5787 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
5713 TTGCAATTTA
* * *
5723 GAAATATGTTTTTTAAAAAGGGGTATAATCG
1 GAAATATGTTTTTAAAAAAAGGGTACAATCG
5754 GAAATATG-TTTTAAAAAAAGGGTACAATCG
1 GAAATATGTTTTTAAAAAAAGGGTACAATCG
5784 GAAA
1 GAAA
5788 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTTAAAAAAAGGGTACAATCG
Found at i:5881 original size:12 final size:12
Alignment explanation
Indices: 5837--5905 Score: 51
Period size: 11 Copynumber: 6.2 Consensus size: 12
5827 TAGATTATTA
5837 TTTCT-TTCTCT
1 TTTCTCTTCTCT
*
5848 TTT-ACTTC-CT
1 TTTCTCTTCTCT
*
5858 TTT-TCTTTTCT
1 TTTCTCTTCTCT
5869 TTTCTCTTCTCT
1 TTTCTCTTCTCT
* *
5881 TCTCTCCTCTC-
1 TTTCTCTTCTCT
*
5892 TCTCTCTTCT-T
1 TTTCTCTTCTCT
5903 TTT
1 TTT
5906 TTTTTTTAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 8 0.17
11 22 0.48
12 16 0.35
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCTCTTCTCT
Found at i:6222 original size:17 final size:18
Alignment explanation
Indices: 6200--6233 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6190 TAACAACCCC
*
6200 AAACCATCA-CAAACATA
1 AAACCAACATCAAACATA
6217 AAACCAACATCAAACAT
1 AAACCAACATCAAACAT
6234 CCATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.29, G:0.00, T:0.12
Consensus pattern (18 bp):
AAACCAACATCAAACATA
Found at i:6916 original size:2 final size:2
Alignment explanation
Indices: 6909--6942 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6899 TTATAAATAC
6909 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6943 AAAGTTAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7721 original size:16 final size:16
Alignment explanation
Indices: 7690--7740 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
7680 ACTAAATACC
* *
7690 ACTTTATACCATTTTT
1 ACTTAATACCAATTTT
*
7706 ACTTAATGCCAATTTT
1 ACTTAATACCAATTTT
*
7722 ACTTAATACCATTTTT
1 ACTTAATACCAATTTT
7738 ACT
1 ACT
7741 CTTTTGCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (16 bp):
ACTTAATACCAATTTT
Found at i:7767 original size:25 final size:24
Alignment explanation
Indices: 7718--7813 Score: 94
Period size: 24 Copynumber: 4.1 Consensus size: 24
7708 TTAATGCCAA
7718 TTTTACTTAATACCATTTTTACTC
1 TTTTACTTAATACCATTTTTACTC
* * *
7742 TTTTGCTTAATATCATTTTT-CAC
1 TTTTACTTAATACCATTTTTACTC
*
7765 ---T-CTTAATACCATTTATTGCTC
1 TTTTACTTAATACCATTT-TTACTC
7786 TTTTTACTATAATACCATTTTTACTC
1 -TTTTACT-TAATACCATTTTTACTC
7812 TT
1 TT
7814 AAGACCATCC
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
19 12 0.21
20 3 0.05
21 2 0.03
23 2 0.03
24 18 0.31
25 3 0.05
26 7 0.12
27 11 0.19
ACGTcount: A:0.24, C:0.20, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTACTTAATACCATTTTTACTC
Found at i:7821 original size:45 final size:43
Alignment explanation
Indices: 7684--7821 Score: 140
Period size: 45 Copynumber: 3.2 Consensus size: 43
7674 TTTTTTACTA
* * *
7684 AATACCACTTTATAC-CATTTTTACTTAATGCCAATTTTA--CTT
1 AATACCA-TTTTTACTC-TTTTTACTTAATACCATTTTTACTCTT
* *
7726 AATACCATTTTTACTC-TTTTGCTTAATATCATTTTTCACTCTT
1 AATACCATTTTTACTCTTTTTACTTAATACCATTTTT-ACTCTT
*
7769 AATACCATTTATTGCTCTTTTTACTATAATACCATTTTTACTCTT
1 AATACCATTT-TTACTCTTTTTACT-TAATACCATTTTTACTCTT
*
7814 AAGACCAT
1 AATACCAT
7822 CCTTTTTTAC
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
40 16 0.20
41 7 0.09
42 8 0.10
43 13 0.16
44 5 0.06
45 19 0.24
46 12 0.15
ACGTcount: A:0.28, C:0.21, G:0.03, T:0.48
Consensus pattern (43 bp):
AATACCATTTTTACTCTTTTTACTTAATACCATTTTTACTCTT
Found at i:7930 original size:15 final size:15
Alignment explanation
Indices: 7910--7949 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
7900 TCACTACTTC
7910 TTTTACTTTTACCAT
1 TTTTACTTTTACCAT
* *
7925 TTTTACTAATTACCTT
1 TTTTACT-TTTACCAT
7941 TTTTACTTT
1 TTTTACTTT
7950 CTATCTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTACTTTTACCAT
Found at i:8041 original size:14 final size:15
Alignment explanation
Indices: 8022--8050 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
8012 TTAACTTACC
8022 TTTACTTT-TAATTA
1 TTTACTTTCTAATTA
8036 TTTACTTTCTAATTA
1 TTTACTTTCTAATTA
8051 CTCCTTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTACTTTCTAATTA
Found at i:8246 original size:34 final size:36
Alignment explanation
Indices: 8206--8298 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 36
8196 TTACTCCCTT
*
8206 TCTTAATTATCAATTTACTGATTA-ATCAC-TCAAC
1 TCTTAATTATCGATTTACTGATTACATCACTTCAAC
* **
8240 TCTTAATTA-CTGATTTGCTGATTACTATCACTTTGAC
1 TCTTAATTATC-GATTTACTGATTAC-ATCACTTCAAC
8277 TCTTAATTATCGATTTACTGAT
1 TCTTAATTATCGATTTACTGAT
8299 GACTCTTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
33 1 0.02
34 20 0.41
36 5 0.10
37 22 0.45
38 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (36 bp):
TCTTAATTATCGATTTACTGATTACATCACTTCAAC
Found at i:8293 original size:71 final size:69
Alignment explanation
Indices: 8206--8436 Score: 214
Period size: 63 Copynumber: 3.4 Consensus size: 69
8196 TTACTCCCTT
*
8206 TCTTAATTATCAATTTACTGATTAATCACTCAACTCTTAATTACTGATTTGCTGATTACTATCAC
1 TCTTAATTATCAATTTACTGATTAATCACT-AACTCTTAATTACTGATTTACTGATTACTAT-AC
8271 TTTGAC
64 TTTGAC
* * *
8277 TCTTAATTATCGATTTACTG-------A-TGACTCTTAATTACTAACTTTACTGATTACTATTA-
1 TCTTAATTATCAATTTACTGATTAATCACTAACTCTTAATTACTGA-TTTACTGATTACTA-TAC
8333 TCTTGAC
64 T-TTGAC
* *** *
8340 TCTTAATTATCAATTTACTGATTAATCTCTTTTTACTTAATTACTGATTTACTAATTAC--TACT
1 TCTTAATTATCAATTTACTGATTAATCACTAACT-CTTAATTACTGATTTACTGATTACTATACT
*
8403 TTTAC
65 TTGAC
*
8408 TTCCTTAATTAACAATTTACTGATTAATC
1 -T-CTTAATTATCAATTTACTGATTAATC
8437 TTTTTACTTT
Statistics
Matches: 132, Mismatches: 13, Indels: 31
0.75 0.07 0.18
Matches are distributed among these distances:
62 15 0.11
63 39 0.30
64 2 0.02
68 6 0.05
69 2 0.02
70 25 0.19
71 32 0.24
72 11 0.08
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.47
Consensus pattern (69 bp):
TCTTAATTATCAATTTACTGATTAATCACTAACTCTTAATTACTGATTTACTGATTACTATACTT
TGAC
Found at i:8442 original size:36 final size:36
Alignment explanation
Indices: 8341--8445 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
8331 TATCTTGACT
* *
8341 CTTAATTATCAATTTACTGATTAATCTCTTT--TTA
1 CTTAATTAACAATTTACTGATTAATCTTTTTACTTA
* * * *
8375 CTTAATT-ACTGATTTACTAATTACTAC-TTTTACTTC
1 CTTAATTAAC-AATTTACTGATTAAT-CTTTTTACTTA
8411 CTTAATTAACAATTTACTGATTAATCTTTTTACTT
1 CTTAATTAACAATTTACTGATTAATCTTTTTACTT
8446 TTACTTTTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
33 1 0.02
34 22 0.39
35 2 0.04
36 29 0.52
37 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (36 bp):
CTTAATTAACAATTTACTGATTAATCTTTTTACTTA
Found at i:18716 original size:3 final size:3
Alignment explanation
Indices: 18708--18748 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
18698 AAGGTCAAAA
*
18708 ATT ATT ATT ATT GCTT ATT ATT ATTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT -ATT ATT ATT A-TT ATT ATT ATT ATT ATT
18749 TTAAAATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.85
4 5 0.15
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:18727 original size:10 final size:9
Alignment explanation
Indices: 18708--18748 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
18698 AAGGTCAAAA
18708 ATTATTATT
1 ATTATTATT
*
18717 ATTGCTTATT
1 ATT-ATTATT
18727 ATTATTTATT
1 ATTA-TTATT
18737 ATTATTATT
1 ATTATTATT
18746 ATT
1 ATT
18749 TTAAAATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 11 0.39
10 17 0.61
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
ATTATTATT
Found at i:18727 original size:13 final size:13
Alignment explanation
Indices: 18708--18745 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
18698 AAGGTCAAAA
18708 ATTATTATTATTG
1 ATTATTATTATTG
* *
18721 CTTATTATTATTT
1 ATTATTATTATTG
18734 ATTATTATTATT
1 ATTATTATTATT
18746 ATTTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (13 bp):
ATTATTATTATTG
Found at i:18749 original size:16 final size:17
Alignment explanation
Indices: 18708--18749 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
18698 AAGGTCAAAA
*
18708 ATTATTA-TTATTGCTT
1 ATTATTATTTATTGATT
18724 ATTATTATTTATT-ATT
1 ATTATTATTTATTGATT
18740 ATTATTATTT
1 ATTATTATTT
18750 TAAAATGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTATTATTTATTGATT
Found at i:21805 original size:45 final size:43
Alignment explanation
Indices: 21707--21805 Score: 128
Period size: 45 Copynumber: 2.3 Consensus size: 43
21697 ACTGTCCTTA
* *
21707 CTTAATACCATTTTTACTCTTTTGCTTAATATCATTTTTCACT
1 CTTAATACCATTTTTACTCTTTTACTTAATACCATTTTTCACT
*
21750 CTTAATACCATTTATTGCTCTTTTTACTATAATACCATTTTT-ACT
1 CTTAATACCATTT-TTACTC-TTTTACT-TAATACCATTTTTCACT
*
21795 CTTAAGACCAT
1 CTTAATACCAT
21806 CCTTTTTTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
43 13 0.27
44 5 0.10
45 19 0.39
46 12 0.24
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.49
Consensus pattern (43 bp):
CTTAATACCATTTTTACTCTTTTACTTAATACCATTTTTCACT
Found at i:21914 original size:15 final size:15
Alignment explanation
Indices: 21894--21933 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
21884 TCACTACTTC
21894 TTTTACTTTTACCAT
1 TTTTACTTTTACCAT
* *
21909 TTTTACTAATTACCTT
1 TTTTACT-TTTACCAT
21925 TTTTACTTT
1 TTTTACTTT
21934 CTATCTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTACTTTTACCAT
Found at i:22230 original size:34 final size:36
Alignment explanation
Indices: 22190--22282 Score: 102
Period size: 37 Copynumber: 2.6 Consensus size: 36
22180 TTGCTCCCTT
*
22190 TCTTAATTATCAATTTACTGATTA-ATCAC-TCAAC
1 TCTTAATTATCGATTTACTGATTACATCACTTCAAC
* **
22224 TCTTAATTA-CTGATTTGCTGATTACCATCACTTTGAC
1 TCTTAATTATC-GATTTACTGATTA-CATCACTTCAAC
*
22261 ACTTAATTATCGATTTACTGAT
1 TCTTAATTATCGATTTACTGAT
22283 GACTCTTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
33 1 0.02
34 20 0.42
36 5 0.10
37 21 0.44
38 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (36 bp):
TCTTAATTATCGATTTACTGATTACATCACTTCAAC
Found at i:22277 original size:71 final size:69
Alignment explanation
Indices: 22191--22420 Score: 219
Period size: 63 Copynumber: 3.4 Consensus size: 69
22181 TGCTCCCTTT
*
22191 CTTAATTATCAATTTACTGATTAATCACTCAACTCTTAATTACTGATTTGCTGATTACCATCACT
1 CTTAATTATCAATTTACTGATTAATCACT-AACTCTTAATTACTGATTTACTGATTACCAT-ACT
22256 TTGACA
64 TTGACA
* * *
22262 CTTAATTATCGATTTACTG-------A-TGACTCTTAATTACTGACTTTACTGATTACTATTACT
1 CTTAATTATCAATTTACTGATTAATCACTAACTCTTAATTACTGA-TTTACTGATTACCA-TACT
*
22319 TTGACT
64 TTGACA
* * ***
22325 CTTAATTATCAATTCACTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTA-C-TACTT
1 CTTAATTATCAATTTACTGATTAATCACTAACT-CTTAATTACTGATTTACTGATTACCATACTT
* *
22388 TTACTTC
65 TGAC--A
22395 CTTAATTATCAATTTACTGATTAATC
1 CTTAATTATCAATTTACTGATTAATC
22421 TTTTTACTTT
Statistics
Matches: 131, Mismatches: 15, Indels: 27
0.76 0.09 0.16
Matches are distributed among these distances:
62 15 0.11
63 38 0.29
64 2 0.02
68 8 0.06
70 25 0.19
71 31 0.24
72 12 0.09
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.46
Consensus pattern (69 bp):
CTTAATTATCAATTTACTGATTAATCACTAACTCTTAATTACTGATTTACTGATTACCATACTTT
GACA
Found at i:22285 original size:25 final size:26
Alignment explanation
Indices: 22257--22308 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
22247 ACCATCACTT
22257 TGACACTTAATTA-TCGA-TTTACTGA
1 TGACACTTAATTACT-GACTTTACTGA
*
22282 TGACTCTTAATTACTGACTTTACTGA
1 TGACACTTAATTACTGACTTTACTGA
22308 T
1 T
22309 TACTATTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (26 bp):
TGACACTTAATTACTGACTTTACTGA
Found at i:22402 original size:36 final size:35
Alignment explanation
Indices: 22286--22417 Score: 103
Period size: 36 Copynumber: 3.7 Consensus size: 35
22276 TACTGATGAC
* * *
22286 TCTTAATTACTGACTTTACTGATTACTATTACTTTGAC-
1 TCTTAATTA-TCAATTTACTGATTAC---TACTTTTACT
*
22324 TCTTAATTATCAATTCACTGATTAATCT-CTTTT--T
1 TCTTAATTATCAATTTACTGATT-A-CTACTTTTACT
* *
22358 ACTTAATTA-CTGATTTACTGATTACTACTTTTACT
1 TCTTAATTATC-AATTTACTGATTACTACTTTTACT
22393 TCCTTAATTATCAATTTACTGATTA
1 T-CTTAATTATCAATTTACTGATTA
22418 ATCTTTTTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
32 2 0.03
33 7 0.09
34 18 0.24
35 5 0.07
36 21 0.28
37 12 0.16
38 10 0.13
39 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.49
Consensus pattern (35 bp):
TCTTAATTATCAATTTACTGATTACTACTTTTACT
Found at i:22408 original size:70 final size:68
Alignment explanation
Indices: 22287--22429 Score: 200
Period size: 70 Copynumber: 2.0 Consensus size: 68
22277 ACTGATGACT
22287 CTTAATTACTGACTTTACTGATTACTATTACTTTGACTCTTAATTATCAATTCACTGATTAATCT
1 CTTAATTACTGACTTTACTGATTAC--TTACTTTGACTCTTAATTATCAATTCACTGATTAA--T
22352 CTTTTTA
62 CTTTTTA
* *
22359 CTTAATTACTGA-TTTACTGATTAC-TACTTTTACTTCCTTAATTATCAATTTACTGATTAATCT
1 CTTAATTACTGACTTTACTGATTACTTACTTTGAC-T-CTTAATTATCAATTCACTGATTAATCT
22422 TTTTA
64 TTTTA
22427 CTT
1 CTT
22430 TACTTTTTGC
Statistics
Matches: 67, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
68 19 0.28
69 1 0.01
70 23 0.34
71 12 0.18
72 12 0.18
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.50
Consensus pattern (68 bp):
CTTAATTACTGACTTTACTGATTACTTACTTTGACTCTTAATTATCAATTCACTGATTAATCTTT
TTA
Found at i:22426 original size:36 final size:36
Alignment explanation
Indices: 22325--22434 Score: 120
Period size: 36 Copynumber: 3.1 Consensus size: 36
22315 TACTTTGACT
* *
22325 CTTAATTATCAATTCACTGATTAATCTCTTT--TTA
1 CTTAATTATCAATTTACTGATTAATCTTTTTACTTA
* * *
22359 CTTAATTA-CTGATTTACTGATTACTAC-TTTTACTTC
1 CTTAATTATC-AATTTACTGATTAAT-CTTTTTACTTA
22395 CTTAATTATCAATTTACTGATTAATCTTTTTACTTTA
1 CTTAATTATCAATTTACTGATTAATCTTTTTAC-TTA
22432 CTT
1 CTT
22435 TTTGCTTCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
33 1 0.02
34 23 0.38
35 2 0.03
36 29 0.48
37 6 0.10
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (36 bp):
CTTAATTATCAATTTACTGATTAATCTTTTTACTTA
Found at i:27509 original size:34 final size:29
Alignment explanation
Indices: 27445--27502 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
27435 TAAAAGGATA
27445 ATTCCATTTTCAACTTTAATATATGTTAT
1 ATTCCATTTTCAACTTTAATATATGTTAT
*
27474 ATTCCATTTTCAACTTTAATACATGTTAT
1 ATTCCATTTTCAACTTTAATATATGTTAT
27503 GTTATATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.03, T:0.50
Consensus pattern (29 bp):
ATTCCATTTTCAACTTTAATATATGTTAT
Found at i:28925 original size:13 final size:13
Alignment explanation
Indices: 28907--28936 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28897 ACGGAGGTAG
*
28907 GAAGGAAGGAGAA
1 GAAGGAAGGAAAA
28920 GAAGGAAGGAAAA
1 GAAGGAAGGAAAA
28933 GAAG
1 GAAG
28937 TGAGATAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (13 bp):
GAAGGAAGGAAAA
Found at i:32927 original size:68 final size:67
Alignment explanation
Indices: 32819--32952 Score: 241
Period size: 68 Copynumber: 2.0 Consensus size: 67
32809 TGAATGACAA
*
32819 CTTTGTAAATGGCACAAAGTTTAAGGGAATGTGTTATTTTGGTATGTACTTTCCAATAATACCCT
1 CTTTGTAAATGACACAAAGTTTAAGGGAATGTGTTATTTTGGTATGTACTTTCCAATAATACCCT
32884 TG
66 TG
*
32886 CTTTGTAAATGACACAAAGTTTTAAGGGAATGTGTTATTTTGGTATGTGCTTTCCAATAATACCC
1 CTTTGTAAATGACACAAAG-TTTAAGGGAATGTGTTATTTTGGTATGTACTTTCCAATAATACCC
32951 TT
65 TT
32953 AAAAGTGTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 18 0.28
68 46 0.72
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (67 bp):
CTTTGTAAATGACACAAAGTTTAAGGGAATGTGTTATTTTGGTATGTACTTTCCAATAATACCCT
TG
Found at i:33658 original size:32 final size:35
Alignment explanation
Indices: 33606--33715 Score: 128
Period size: 34 Copynumber: 3.4 Consensus size: 35
33596 CCCAAGAGGG
33606 CGGCTT-AA-CAT-GGCGAAGCCGCCCCACTGGGA
1 CGGCTTCAACCATAGGCGAAGCCGCCCCACTGGGA
33638 -GGC-TCAACCA-AGGCGAAGCCGCCCCACTGGGA
1 CGGCTTCAACCATAGGCGAAGCCGCCCCACTGGGA
* * * *
33670 CGGCTTCACCCATCGGC-AGGCCGCCCCACTGGGG
1 CGGCTTCAACCATAGGCGAAGCCGCCCCACTGGGA
33704 CGGCTTC-ACCAT
1 CGGCTTCAACCAT
33716 GAAAAGGCCG
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
30 1 0.01
31 5 0.07
32 23 0.34
33 7 0.10
34 28 0.42
35 3 0.04
ACGTcount: A:0.19, C:0.39, G:0.30, T:0.12
Consensus pattern (35 bp):
CGGCTTCAACCATAGGCGAAGCCGCCCCACTGGGA
Found at i:33729 original size:33 final size:34
Alignment explanation
Indices: 33655--33739 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 34
33645 CCAAGGCGAA
* **
33655 GCCGCCCCACTGGGACGGCTTCACCCATCGGCAG
1 GCCGCCCCACTGGGGCGGCTTCACCCATCGAAAG
33689 GCCGCCCCACTGGGGCGGCTTCA-CCAT-GAAAAG
1 GCCGCCCCACTGGGGCGGCTTCACCCATCG-AAAG
**
33722 GCCGCCCCGGTGGGGCGG
1 GCCGCCCCACTGGGGCGG
33740 GTCGGCTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.02
33 22 0.49
34 22 0.49
ACGTcount: A:0.14, C:0.40, G:0.35, T:0.11
Consensus pattern (34 bp):
GCCGCCCCACTGGGGCGGCTTCACCCATCGAAAG
Found at i:34140 original size:21 final size:21
Alignment explanation
Indices: 34115--34159 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
34105 AGATACTGGA
34115 TTGCTAAATACCGCCCCATTT
1 TTGCTAAATACCGCCCCATTT
**
34136 TTGCTATTTACCGCCCCATTT
1 TTGCTAAATACCGCCCCATTT
34157 TTG
1 TTG
34160 ATGCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.31, G:0.11, T:0.40
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCATTT
Found at i:34428 original size:32 final size:31
Alignment explanation
Indices: 34392--34493 Score: 123
Period size: 32 Copynumber: 3.2 Consensus size: 31
34382 CACTTGGGAC
*
34392 GCTTCGCCACGGCAAGCCACCCTCATGGGGCG
1 GCTTCGCCACGGCAAGCCGCCC-CATGGGGCG
* * * *
34424 GCTTCACCATGGGTAGGCCGCCCCACTGGGGCG
1 GCTTCGCCA-CGGCAAGCCGCCCCA-TGGGGCG
34457 GCTTCGCCACGGCAAGCCGCCCCATGAGGGCG
1 GCTTCGCCACGGCAAGCCGCCCCATG-GGGCG
34489 GCTTC
1 GCTTC
34494 CCCATGAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
31 2 0.03
32 32 0.55
33 24 0.41
ACGTcount: A:0.14, C:0.39, G:0.33, T:0.14
Consensus pattern (31 bp):
GCTTCGCCACGGCAAGCCGCCCCATGGGGCG
Found at i:34454 original size:33 final size:33
Alignment explanation
Indices: 34417--34520 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
34407 GCCACCCTCA
*
34417 TGGGGCGGCTTCACCATGGGTAGGCCGCCCCAC
1 TGGGGCGGCTTCACCATGGGAAGGCCGCCCCAC
* * *
34450 TGGGGCGGCTTCGCCACGGCAA-GCCGCCCCA-
1 TGGGGCGGCTTCACCATGGGAAGGCCGCCCCAC
* ** *
34481 TGAGGGCGGCTTCCCCATGAAAAGGGCGCCCCAC
1 TG-GGGCGGCTTCACCATGGGAAGGCCGCCCCAC
34515 TGGGGC
1 TGGGGC
34521 AGTTTAGCCA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.03
32 25 0.42
33 30 0.51
34 2 0.03
ACGTcount: A:0.14, C:0.37, G:0.37, T:0.12
Consensus pattern (33 bp):
TGGGGCGGCTTCACCATGGGAAGGCCGCCCCAC
Found at i:34462 original size:65 final size:64
Alignment explanation
Indices: 34379--34520 Score: 187
Period size: 65 Copynumber: 2.2 Consensus size: 64
34369 GGCGAAGCCA
* ***
34379 CCCCACTTGGGACGCTTCGCCACGGCAAGCCACCCTCATG-GGGCGGCTTCACCATGGGTAGGCC
1 CCCCAC-TGGGGCGCTTCGCCACGGCAAGCCACCC-CATGAGGGCGGCTTCACCATGAAAAGGCC
34443 G
64 G
* * *
34444 CCCCACTGGGGCGGCTTCGCCACGGCAAGCCGCCCCATGAGGGCGGCTTCCCCATGAAAAGGGCG
1 CCCCACTGGGGC-GCTTCGCCACGGCAAGCCACCCCATGAGGGCGGCTTCACCATGAAAAGGCCG
34509 CCCCACTGGGGC
1 CCCCACTGGGGC
34521 AGTTTAGCCA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 9 0.13
65 59 0.87
ACGTcount: A:0.15, C:0.39, G:0.32, T:0.13
Consensus pattern (64 bp):
CCCCACTGGGGCGCTTCGCCACGGCAAGCCACCCCATGAGGGCGGCTTCACCATGAAAAGGCCG
Found at i:34553 original size:65 final size:64
Alignment explanation
Indices: 34379--34556 Score: 178
Period size: 65 Copynumber: 2.7 Consensus size: 64
34369 GGCGAAGCCA
* * * ***
34379 CCCCACTTGGG-ACGCTTCGCCACGGCAAGCCACCCTCATGGGGCGGCTTCACCATGGGTAGGCC
1 CCCCACTGGGGCA-GCTTAGCCACGGCAAGCCGCCC-CATGGGGCGGCTTCACCATGAAAAGGCC
34443 G
64 G
* * * *
34444 CCCCACTGGGGCGGCTTCGCCACGGCAAGCCGCCCCATGAGGGCGGCTTCCCCATGAAAAGGGCG
1 CCCCACTGGGGCAGCTTAGCCACGGCAAGCCGCCCCATG-GGGCGGCTTCACCATGAAAAGGCCG
* * * **
34509 CCCCACTGGGGCAGTTTAGCCAGGGCAGGCCGTCCCGGTGGGGCGGCT
1 CCCCACTGGGGCAGCTTAGCCACGGCAAGCCG-CCCCATGGGGCGGCT
34557 CGGCTATTTT
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
64 4 0.04
65 86 0.91
66 5 0.05
ACGTcount: A:0.15, C:0.37, G:0.35, T:0.13
Consensus pattern (64 bp):
CCCCACTGGGGCAGCTTAGCCACGGCAAGCCGCCCCATGGGGCGGCTTCACCATGAAAAGGCCG
Found at i:34651 original size:33 final size:33
Alignment explanation
Indices: 34609--34690 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
34599 ATTTTGGTCT
34609 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
34642 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
* *
34675 AGTCGCCCTAGTGGGG
1 AGCCGCCCCAGTGGGG
34691 AGGCTCCGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.12, C:0.34, G:0.40, T:0.13
Consensus pattern (33 bp):
AGCCGCCCCAGTGGGGCGGCCTGCCCATGGTGA
Found at i:34703 original size:33 final size:34
Alignment explanation
Indices: 34609--34729 Score: 133
Period size: 33 Copynumber: 3.6 Consensus size: 34
34599 ATTTTGGTCT
* * *
34609 AGCCGCCCCAGTGGGGCGGC-CTGCCCATGGTGA
1 AGCCGCCCTAGTGGGGAGGCTCCGCCCATGGTGA
* * *
34642 AGCCGCCCCAGTGGGGCGGC-CTGCCCATGGTGA
1 AGCCGCCCTAGTGGGGAGGCTCCGCCCATGGTGA
*
34675 AGTCGCCCTAGTGGGGAGGCTCCG-CCATGGCTGA
1 AGCCGCCCTAGTGGGGAGGCTCCGCCCATGG-TGA
*
34709 A-CCGTCCTAGTGGGGAGGCTC
1 AGCCGCCCTAGTGGGGAGGCTC
34730 AGTGCAAAAG
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
33 74 0.93
34 6 0.08
ACGTcount: A:0.13, C:0.33, G:0.39, T:0.15
Consensus pattern (34 bp):
AGCCGCCCTAGTGGGGAGGCTCCGCCCATGGTGA
Found at i:35089 original size:15 final size:14
Alignment explanation
Indices: 35066--35095 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
35056 AATAAAATTA
35066 AATATTTTTATTTT
1 AATATTTTTATTTT
35080 AATATATTTTATTTT
1 AATAT-TTTTATTTT
35095 A
1 A
35096 TTTAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:35096 original size:20 final size:20
Alignment explanation
Indices: 35071--35109 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35061 AATTAAATAT
*
35071 TTTTATTTTAATATATTTTA
1 TTTTATTTAAATATATTTTA
*
35091 TTTTATTTAAATTTATTTT
1 TTTTATTTAAATATATTTT
35110 TAAAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTTAAATATATTTTA
Found at i:36079 original size:20 final size:20
Alignment explanation
Indices: 36054--36091 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36044 ATTATTATTT
*
36054 TAAAATAAATTTAAATAAGA
1 TAAAATAAATTAAAATAAGA
*
36074 TAAAATATATTAAAATAA
1 TAAAATAAATTAAAATAA
36092 AAATATTCAA
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:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
TAAAATAAATTAAAATAAGA
Found at i:36759 original size:2 final size:2
Alignment explanation
Indices: 36752--36780 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36742 ATTTAATCTG
36752 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36781 ACAAACAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37413 original size:21 final size:21
Alignment explanation
Indices: 37388--37429 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
37378 AATTAAGTAT
37388 TATATATTATAATATCTATACAA
1 TATATA-TAT-ATATCTATACAA
37411 TATATATATATATCTATAC
1 TATATATATATATCTATAC
37430 CCTAATTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
TATATATATATATCTATACAA
Found at i:38361 original size:24 final size:24
Alignment explanation
Indices: 38329--38379 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
38319 TTTGTTTTCT
38329 TTTTTGTTCTTTCCTCATTCCATG
1 TTTTTGTTCTTTCCTCATTCCATG
38353 TTTTTGTTCTTTCCTCATTCCATG
1 TTTTTGTTCTTTCCTCATTCCATG
38377 TTT
1 TTT
38380 GTCTTCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.61
Consensus pattern (24 bp):
TTTTTGTTCTTTCCTCATTCCATG
Done.