Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015990.1 Corchorus capsularis cultivar CVL-1 contig16011, 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: 12360
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Found at i:242 original size:14 final size:14
Alignment explanation
Indices: 223--250 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
213 TGATAGTAAT
223 CTAAATGGACTAAA
1 CTAAATGGACTAAA
237 CTAAATGGACTAAA
1 CTAAATGGACTAAA
251 ATTAATATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
CTAAATGGACTAAA
Found at i:861 original size:11 final size:11
Alignment explanation
Indices: 841--907 Score: 71
Period size: 11 Copynumber: 5.7 Consensus size: 11
831 CATTTTTGGC
*
841 TTCTTCTTTTT
1 TTCTTTTTTTT
852 TTCTTTTTTTT
1 TTCTTTTTTTT
*
863 TTCCTTTTTTTC
1 TT-CTTTTTTTT
875 TTCTTTTTTTT
1 TTCTTTTTTTT
886 ATTCATTTTTTATT
1 -TTC-TTTTTT-TT
*
900 TTATTTTT
1 TTCTTTTT
908 ATTTGAAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
11 20 0.42
12 18 0.38
13 8 0.17
14 2 0.04
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:864 original size:12 final size:12
Alignment explanation
Indices: 847--907 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
837 TGGCTTCTTC
847 TTTTTTTC-TTT
1 TTTTTTTCTTTT
*
858 TTTTTTTCCTTT
1 TTTTTTTCTTTT
*
870 TTTTCTTCTTTT
1 TTTTTTTCTTTT
*
882 TTTTATTCATTTT
1 TTTTTTTC-TTTT
* *
895 TTATTTTATTTT
1 TTTTTTTCTTTT
907 T
1 T
908 ATTTGAAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
11 8 0.19
12 25 0.60
13 9 0.21
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:871 original size:20 final size:21
Alignment explanation
Indices: 846--885 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
836 TTGGCTTCTT
846 CTTTTTTTCTT-TTTTTTTTC
1 CTTTTTTTCTTCTTTTTTTTC
866 CTTTTTTTCTTCTTTTTTTT
1 CTTTTTTTCTTCTTTTTTTT
886 ATTCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (21 bp):
CTTTTTTTCTTCTTTTTTTTC
Found at i:873 original size:23 final size:24
Alignment explanation
Indices: 847--907 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
837 TGGCTTCTTC
*
847 TTTTTTTCTTTTTTTT-TTCCTTT
1 TTTTTTTCTTTTTTTTATTCATTT
*
870 TTTTCTTCTTTTTTTTATTCATTT
1 TTTTTTTCTTTTTTTTATTCATTT
*
894 TTTATTTTATTTTT
1 TTT-TTTTCTTTTT
908 ATTTGAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 15 0.47
24 9 0.28
25 8 0.25
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.84
Consensus pattern (24 bp):
TTTTTTTCTTTTTTTTATTCATTT
Found at i:1306 original size:69 final size:68
Alignment explanation
Indices: 1100--1452 Score: 414
Period size: 69 Copynumber: 5.2 Consensus size: 68
1090 GGAAATGAAC
* * * * * *
1100 TTGGCTTATGGAAAAGCCC--CTTCTTGGATGGAACCAAGGC-TAAACTAACTCATATGGAAACG
1 TTGGCTTGTGGAAAAGCCCTACTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAACG
1162 AGT
66 AGT
* * * * *
1165 TTGGCTAGTGGAAAAGCCTTTGCTGCTTGGATGGAACCAAGGC-TAAATTGACTCGTGTGGAAAC
1 TTGGCTTGTGGAAAAGCC-CTACTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAAC
1229 GAGT
65 GAGT
* * *
1233 TTGGCTTGTGG-AAAGCCCCTAAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
1 TTGGCTTGTGGAAAAG-CCCT-ACTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAA
1297 CGAGT
64 CGAGT
*
1302 TTGGCTTGTGGAAAAG--CTACTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAACA
1 TTGGCTTGTGGAAAAGCCCTACTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAACG
1365 AGT
66 AGT
* * * * * *
1368 TTGACTTATGGAAAAGCTGCTGCTGCTTGGATGAAACCAAAGCTTGAACTGACTCGTGTGGAAAC
1 TTGGCTTGTGGAAAAGC-CCTACTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAAC
1433 GAGT
65 GAGT
* *
1437 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
1453 TCAAAGCATT
Statistics
Matches: 252, Mismatches: 26, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
65 16 0.06
66 58 0.23
67 7 0.03
68 72 0.29
69 95 0.38
70 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (68 bp):
TTGGCTTGTGGAAAAGCCCTACTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAACG
AGT
Found at i:1395 original size:135 final size:136
Alignment explanation
Indices: 1122--1452 Score: 436
Period size: 135 Copynumber: 2.4 Consensus size: 136
1112 AAAGCCCCTT
* * * * *
1122 CTTGGATGGAACCAAGGC-TAAACTAACTCATATGGAAACGAGTTTGGCTAGTGGAAAAGCCTTT
1 CTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC-TT
* * * * *
1186 GCTGCTTGGATGGAACCAAGGCTAAATTGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAGCCC
65 ACTGCTTGGATGGAACCAAGGCTAAACTGACTCGTGTGGAAACAAGTTTGACTTATGGAAAGCCC
1251 CTAAATG
130 CTAAATG
1258 CTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG-C-TA
1 CTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTTA
* *
1321 CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTGTGGAAACAAGTTTGACTTATGGAAAAGCT
66 CTGCTTGGATGGAACCAAGGC-TAAACTGACTCGTGTGGAAACAAGTTTGACTTATGG-AAAGCC
* **
1386 GCT-GCTG
129 CCTAAATG
* * * *
1393 CTTGGATGAAACCAAAGCTTGAACTGACTCGTGTGGAAACGAGTTTGACTTATGGAAAAG
1 CTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
1453 TCAAAGCATT
Statistics
Matches: 173, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
134 22 0.13
135 89 0.51
136 25 0.14
137 37 0.21
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (136 bp):
CTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTTA
CTGCTTGGATGGAACCAAGGCTAAACTGACTCGTGTGGAAACAAGTTTGACTTATGGAAAGCCCC
TAAATG
Found at i:2000 original size:41 final size:41
Alignment explanation
Indices: 1955--2033 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
1945 TTTGAAAAGA
* * * *
1955 GAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTATC
1 GAATTTTCATATTGGACCCACAAATGAAATGCAATCTTATC
1996 GAATTTTCATATTGGACCCACAAATGAAATGCAATCTT
1 GAATTTTCATATTGGACCCACAAATGAAATGCAATCTT
2034 CTTATAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (41 bp):
GAATTTTCATATTGGACCCACAAATGAAATGCAATCTTATC
Found at i:2346 original size:21 final size:19
Alignment explanation
Indices: 2308--2351 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
2298 CTAGAGCCTC
2308 TTTTCTTCATTTTTTTTCT
1 TTTTCTTCATTTTTTTTCT
*
2327 TTTTCTCTCTTTTTTCTTTCT
1 TTTTCT-TCATTTTT-TTTCT
2348 TTTT
1 TTTT
2352 TTCTTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 7 0.32
21 9 0.41
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTTCATTTTTTTTCT
Found at i:2353 original size:12 final size:11
Alignment explanation
Indices: 2308--2358 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 11
2298 CTAGAGCCTC
*
2308 TTTTC-TTCAT
1 TTTTCTTTCTT
2318 TTTT-TTTC-T
1 TTTTCTTTCTT
*
2327 TTTTCTCTCTT
1 TTTTCTTTCTT
2338 TTTTCTTTCTTT
1 TTTTCTTTC-TT
2350 TTTTCTTTC
1 TTTTCTTTC
2359 ATTACGCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 5 0.14
10 10 0.29
11 9 0.26
12 11 0.31
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:3681 original size:6 final size:6
Alignment explanation
Indices: 3670--3736 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
3660 TTGTCTTTTC
* * * *
3670 TTTCTT TTTC-T TTTATT ATTCTT CTTCTT TTTCATT TTTCATT TATC--
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT TTTC-TT TTTCTT
3717 TTTCTT TTTC-T TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTT
3737 TCATTTTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 3 0.06
5 9 0.18
6 25 0.51
7 12 0.24
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:3697 original size:23 final size:23
Alignment explanation
Indices: 3668--3730 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
3658 TTTTGTCTTT
*
3668 TCTTTCTTTTTCTTTTATTATTCT-
1 TCTTTCTTTTTCTTTT-TCATT-TA
3692 TC-TTCTTTTTCATTTTTCATTTA
1 TCTTTCTTTTTC-TTTTTCATTTA
3715 TCTTTCTTTTTCTTTT
1 TCTTTCTTTTTCTTTT
3731 CTTTTTTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
22 1 0.03
23 19 0.54
24 15 0.43
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (23 bp):
TCTTTCTTTTTCTTTTTCATTTA
Found at i:3715 original size:30 final size:28
Alignment explanation
Indices: 3663--3742 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 28
3653 TTGCTTTTTG
*
3663 TCTT-TTC-TTTCTTTTTCTTTTAT-TAT
1 TCTTCTTCTTTTCTTTTTCATTTATCT-T
3689 TCTTCTTCTTTTTCATTTTTCATTTATCTT
1 TCTTCTTC-TTTTC-TTTTTCATTTATCTT
*
3719 TCTTTTTCTTTTCTTTTTTCATTT
1 TCTTCTTCTTTTC-TTTTTCATTT
3743 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
26 4 0.09
27 3 0.07
29 19 0.41
30 19 0.41
31 1 0.02
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (28 bp):
TCTTCTTCTTTTCTTTTTCATTTATCTT
Found at i:4269 original size:75 final size:75
Alignment explanation
Indices: 4141--4367 Score: 319
Period size: 75 Copynumber: 3.0 Consensus size: 75
4131 TGGATTTAAT
* * * * * ** *
4141 CACCTTGAAATCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAATACTTAACATC
1 CACCTCGAAACCATTGCTTTGATTAAAACTGATTTTGAAACATATTTTGATTAAAACCCAACATT
4206 CTTTTGCTCA
66 CTTTTGCTCA
* * * * *
4216 CACCTCGAAACCACTGCTTTGATTGAAACTTATTTTGAAACATGTTTTAATTAAAACCCAACATT
1 CACCTCGAAACCATTGCTTTGATTAAAACTGATTTTGAAACATATTTTGATTAAAACCCAACATT
*
4281 CTTTTGCTCT
66 CTTTTGCTCA
*
4291 CACCTCGAAACCATTGCTTTGATTAAAACTGATTTTGAAACATATTTTGATTAAAACCCATCATT
1 CACCTCGAAACCATTGCTTTGATTAAAACTGATTTTGAAACATATTTTGATTAAAACCCAACATT
4356 CTTTTGCTCA
66 CTTTTGCTCA
4366 CA
1 CA
4368 GTCCAGATAA
Statistics
Matches: 132, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 132 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (75 bp):
CACCTCGAAACCATTGCTTTGATTAAAACTGATTTTGAAACATATTTTGATTAAAACCCAACATT
CTTTTGCTCA
Found at i:10564 original size:64 final size:61
Alignment explanation
Indices: 10473--10919 Score: 214
Period size: 64 Copynumber: 7.2 Consensus size: 61
10463 TTTCACTGAA
* * * *
10473 TTACTAATTACCATCACTATTTTACTGATTAT-TCTTTACTTTGTACTGATTACTATTTTACTC
1 TTACTGATTACTATTACT-TTTTACTGATTATCT-TTTACTTT-TACTGATTACCATTTTACTC
** * *
10536 TTGTTGATTACCTTCTTACTTTTTACTGATTACCATTTTACTCTTTACTGATTACCATTTTACTT
1 TTACTGATTA-C-TATTACTTTTTACTGATTATC-TTTTACT-TTTACTGATTACCATTTTAC-T
10601 C
61 C
* * * *
10602 TTACTGATTACTATTACTTTCTACTGATTACTCTTTTAATTTTTGCTGATTACCATTTTACTTT
1 TTACTGATTACTATTACTTTTTACTGATTA-TCTTTT-ACTTTTACTGATTACCATTTTAC-TC
* * ** * * *
10666 TTACTAATTACCATTTTACCCTTTACTGATTACCTTTTACTTTTTACCAT-TTTACCTTTTTACT
1 TTACTGATTA-C-TATTACTTTTTACTGATTATCTTTTAC-TTTTA-C-TGATTACCATTTTACT
10730 C
61 C
* * * * *
10731 TTACT-ATCACTCTT--TCTTTA-TCATT-T-TTGT-C-TTTACTGATTA-C-TCTTTACTC
1 TTACTGATTACTATTACTTTTTACTGATTATCTTTTACTTTTACTGATTACCAT-TTTACTC
* * * *
10783 TTTAC-CA-T--T-TTACTCTTTT-CTAATTACTATTTTACTTTTTACTGATTACCTTTTTACTT
1 -TTACTGATTACTATTACT-TTTTACTGATTA-TCTTTTAC-TTTTACTGATTACCATTTTAC-T
*
10842 T
61 C
* * * * * *
10843 TTACTGATTACCATT-GTTTCTTACTAACT-TCTATTACTCTTTACTGATTACCATTTTACCTT
1 TTACTGATTACTATTACTTT-TTACTGATTATCTTTTACT-TTTACTGATTACCATTTTA-CTC
10905 TTACTGATTACTATT
1 TTACTGATTACTATT
10920 TTCTGCTCCT
Statistics
Matches: 298, Mismatches: 47, Indels: 79
0.70 0.11 0.19
Matches are distributed among these distances:
49 2 0.01
50 1 0.00
51 2 0.01
52 16 0.05
53 9 0.03
54 5 0.02
55 3 0.01
56 2 0.01
57 3 0.01
58 11 0.04
59 14 0.05
60 8 0.03
61 2 0.01
62 45 0.15
63 12 0.04
64 75 0.25
65 47 0.16
66 40 0.13
67 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.54
Consensus pattern (61 bp):
TTACTGATTACTATTACTTTTTACTGATTATCTTTTACTTTTACTGATTACCATTTTACTC
Found at i:10567 original size:22 final size:21
Alignment explanation
Indices: 10492--10854 Score: 226
Period size: 22 Copynumber: 16.7 Consensus size: 21
10482 ACCATCACTA
*
10492 TTTTACTGATTA-TTCTTTACT
1 TTTTACTGATTACCT-TTTACT
* *
10513 TTGTACTGATTACTATTTTACT
1 TTTTACTGATTAC-CTTTTACT
*
10535 CTTGT--TGATTACCTTCTTACT
1 -TTTTACTGATTACCTT-TTACT
10556 TTTTACTGATTACCATTTTACT
1 TTTTACTGATTACC-TTTTACT
*
10578 CTTTACTGATTACCATTTTACT
1 TTTTACTGATTACC-TTTTACT
* *
10600 TCTTACTGATTA-CTATTACT
1 TTTTACTGATTACCTTTTACT
* *
10620 TTCTACTGATTACTCTTTTAAT
1 TTTTACTGATTAC-CTTTTACT
*
10642 TTTTGCTGATTACCATTTTACT
1 TTTTACTGATTACC-TTTTACT
* *
10664 TTTTACTAATTACCATTTTACC
1 TTTTACTGATTACC-TTTTACT
*
10686 CTTTACTGATTACCTTTTACT
1 TTTTACTGATTACCTTTTACT
*
10707 TTTTACCAT-TTTACCTTTTTAC-
1 TTTTA-C-TGATTACC-TTTTACT
* *
10729 TCTTACT-ATCACTCTTTCTTTATCAT
1 TTTTACTGATTAC-C--T-TTTA-C-T
* *
10755 TTTTGTCT--TTA-CTGATTACT
1 TTTT-ACTGATTACCT-TTTACT
* **
10775 CTTTACTCTTTACCATTTTACT
1 TTTTACTGATTACC-TTTTACT
* *
10797 CTTTT-CTAATTACTATTTTACT
1 -TTTTACTGATTAC-CTTTTACT
10819 TTTTACTGATTACCTTTTTACT
1 TTTTACTGATTACC-TTTTACT
10841 TTTTACTGATTACC
1 TTTTACTGATTACC
10855 ATTGTTTCTT
Statistics
Matches: 274, Mismatches: 40, Indels: 55
0.74 0.11 0.15
Matches are distributed among these distances:
19 2 0.01
20 29 0.11
21 45 0.16
22 167 0.61
23 22 0.08
24 2 0.01
26 5 0.02
27 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTACTGATTACCTTTTACT
Found at i:10590 original size:44 final size:43
Alignment explanation
Indices: 10493--10921 Score: 246
Period size: 44 Copynumber: 9.9 Consensus size: 43
10483 CCATCACTAT
* * *
10493 TTTACTGATTA-TTCTTTACTTTGTACTGATTACTATTTTACTC
1 TTTACTGATTACCT-TTTACTTTTTACTGATTACCATTTTACTC
10536 TTGT--TGATTACCTTCTTACTTTTTACTGATTACCATTTTACTC
1 TT-TACTGATTACCTT-TTACTTTTTACTGATTACCATTTTACTC
* *
10579 TTTACTGATTACCATTTTACTTCTTACTGATTA-C-TATTACT-
1 TTTACTGATTACC-TTTTACTTTTTACTGATTACCATTTTACTC
* * *
10620 TTCTACTGATTACTCTTTTAATTTTTGCTGATTACCATTTTACTT
1 TT-TACTGATTAC-CTTTTACTTTTTACTGATTACCATTTTACTC
* ** *
10665 TTTACTAATTACCATTTTACCCTTTACTGATTACC-TTTTACTT
1 TTTACTGATTACC-TTTTACTTTTTACTGATTACCATTTTACTC
* * * *
10708 TTTACCAT-TTTACCTTTTTAC-TCTTACT-ATCACTCTTTCTTTA-TC
1 TTTA-C-TGATTACC-TTTTACTTTTTACTGATTAC-C-AT-TTTACTC
* * * * **
10753 ATTT-TTGTCTTTA-CTGATTACTCTTTACTCTTTACCATTTTACTC
1 -TTTACTG--ATTACCT-TTTACTTTTTACTGATTACCATTTTACTC
* * * * *
10798 TTTTCTAATTACTATTTTACTTTTTACTGATTACCTTTTTACTT
1 TTTACTGATTAC-CTTTTACTTTTTACTGATTACCATTTTACTC
* * * *
10842 TTTACTGATTACCATTGT--TTCTTACTAACTT--C-TATTACTC
1 TTTACTGATTACC-TTTTACTTTTTACTGA-TTACCATTTTACTC
* *
10882 TTTACTGATTACCATTTTACCTTTTACTGATTACTATTTT
1 TTTACTGATTACC-TTTTACTTTTTACTGATTACCATTTT
10922 CTGCTCCTTT
Statistics
Matches: 299, Mismatches: 51, Indels: 71
0.71 0.12 0.17
Matches are distributed among these distances:
40 23 0.08
41 5 0.02
42 59 0.20
43 59 0.20
44 116 0.39
45 17 0.06
46 17 0.06
47 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.04, T:0.55
Consensus pattern (43 bp):
TTTACTGATTACCTTTTACTTTTTACTGATTACCATTTTACTC
Found at i:10645 original size:86 final size:84
Alignment explanation
Indices: 10507--10708 Score: 239
Period size: 86 Copynumber: 2.3 Consensus size: 84
10497 CTGATTATTC
* *
10507 TTTACTT-TGTACTGATTACTATTTTACTCTTGTTGATTACCTTCTTACTTTTTACTGATTACCA
1 TTTACTTCT-TACTGATTACTA--TTACT-TTCTTGATTACCTTCTTAATTTTTACTGATTACCA
*
10571 TTTTACTCTTTACTGATTACCAT
62 TTTTACTCTTTACTAATTACCAT
*
10594 TTTACTTCTTACTGATTACTATTACTTTCTACTGATTACTCTT-TTAATTTTTGCTGATTACCAT
1 TTTACTTCTTACTGATTACTATTACTTTCT--TGATTAC-CTTCTTAATTTTTACTGATTACCAT
*
10658 TTTACTTTTTACTAATTACCAT
63 TTTACTCTTTACTAATTACCAT
* *
10680 TTTAC-CCTTTACTGATTACCTTTTACTTT
1 TTTACTTC-TTACTGATTA-CTATTACTTT
10709 TTACCATTTT
Statistics
Matches: 102, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
84 3 0.03
85 6 0.06
86 61 0.60
87 31 0.30
88 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.53
Consensus pattern (84 bp):
TTTACTTCTTACTGATTACTATTACTTTCTTGATTACCTTCTTAATTTTTACTGATTACCATTTT
ACTCTTTACTAATTACCAT
Found at i:10713 original size:36 final size:36
Alignment explanation
Indices: 10659--10824 Score: 104
Period size: 36 Copynumber: 4.5 Consensus size: 36
10649 GATTACCATT
* **
10659 TTACTTTTTACTAATTACCATTTTACCCTTTACTGA
1 TTACCTTTTACTTTTTACCATTTTACCCTTTACTGA
* *
10695 TTACCTTTTACTTTTTACCATTTTACCTTTTTACT-C
1 TTACCTTTTACTTTTTACCATTTTACC-CTTTACTGA
* * * ***
10731 TTA-CTATCACTCTTTCTTTATCATTTTTGTCTTTACTGA
1 TTACCTTTTA--C-TT-TTTACCATTTTACCCTTTACTGA
* * * *
10770 TTA-CTCTTTACTCTTTACCATTTTACTCTTTTCTAA
1 TTACCT-TTTACTTTTTACCATTTTACCCTTTACTGA
*
10806 TTACTATTTTACTTTTTAC
1 TTAC-CTTTTACTTTTTAC
10825 TGATTACCTT
Statistics
Matches: 98, Mismatches: 23, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
35 4 0.04
36 48 0.49
37 19 0.19
38 10 0.10
39 15 0.15
40 2 0.02
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.56
Consensus pattern (36 bp):
TTACCTTTTACTTTTTACCATTTTACCCTTTACTGA
Found at i:10824 original size:7 final size:7
Alignment explanation
Indices: 10770--10847 Score: 50
Period size: 7 Copynumber: 10.7 Consensus size: 7
10760 TCTTTACTGA
*
10770 TTACTCT
1 TTACTTT
*
10777 TTACTCT
1 TTACTTT
*
10784 TTACCATT
1 TTA-CTTT
10792 TTACTCTT
1 TTACT-TT
**
10800 TT-CTAA
1 TTACTTT
10806 TTACTATT
1 TTACT-TT
10814 TTACTTT
1 TTACTTT
**
10821 TTACTGA
1 TTACTTT
10828 TTACCTTT
1 TTA-CTTT
10836 TTACTTT
1 TTACTTT
10843 TTACT
1 TTACT
10848 GATTACCATT
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
6 2 0.04
7 34 0.62
8 19 0.35
ACGTcount: A:0.19, C:0.21, G:0.01, T:0.59
Consensus pattern (7 bp):
TTACTTT
Done.