Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015909.1 Corchorus capsularis cultivar CVL-1 contig15930, 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: 58759
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:1821 original size:13 final size:14
Alignment explanation
Indices: 1803--1839 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1793 TTTTCATTAC
1803 TGTTTTATTAAT-A
1 TGTTTTATTAATGA
*
1816 TGTTTTATAAATGA
1 TGTTTTATTAATGA
1830 T-TTTTATTAA
1 TGTTTTATTAA
1840 ATAATTTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 19 0.90
14 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (14 bp):
TGTTTTATTAATGA
Found at i:6352 original size:2 final size:2
Alignment explanation
Indices: 6345--6402 Score: 56
Period size: 2 Copynumber: 31.5 Consensus size: 2
6335 ATAAATATTA
6345 AT AT AT AT AT AT AT A- AT AT A- AT ACT A- AT A- AT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
6382 AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
6403 ATTTATCGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
1 6 0.13
2 39 0.83
3 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:6372 original size:11 final size:11
Alignment explanation
Indices: 6345--6404 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
6335 ATAAATATTA
6345 ATAT-ATATAT
1 ATATAATATAT
6355 ATATAATATA-
1 ATATAATATAT
6365 ATACTAATA-AT
1 ATA-TAATATAT
6376 AT-TAATATAT
1 ATATAATATAT
*
6386 ATATATAAATAT
1 ATATA-ATATAT
6398 ATATAAT
1 ATATAAT
6405 TTATCGGTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
9 5 0.12
10 12 0.29
11 15 0.36
12 10 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATAATATAT
Found at i:17081 original size:45 final size:45
Alignment explanation
Indices: 17030--17119 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
17020 TAATAGAGTA
* *
17030 GTGGAATTACTAAAAGATTCCTACCACATATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCACAGATTAATGATGAGCTGG
* *
17075 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCACAGATTAATGATGAGCTGG
17120 AGAACTAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCACAGATTAATGATGAGCTGG
Found at i:25658 original size:116 final size:114
Alignment explanation
Indices: 25508--25761 Score: 373
Period size: 116 Copynumber: 2.2 Consensus size: 114
25498 ACCCTTTATC
* * * *
25508 TTACTATTGATTACCGTTTTACTTCTTAATTAACCTTATTACTTTGAATTAAGCTAATTACTACT
1 TTACTATTGTTTACCCTTTTACTTCTTAATTAACCTAATTACTCTGAATTAAGCTAATTACTACT
* *
25573 GTTTACTCCTTTTACTCCTTGATTAACTTAATTTACTCTGAATTAAGCTAA
66 GTTT-CCCCTTTTACTCCTTGATTAACCTAA-TTACTCTGAATTAAGCTAA
* * *
25624 TTACTATTGTTTCCCCTTTTATTTCTTGATTAACCTAATTACTCTGAATTAAGCTAATTACTACT
1 TTACTATTGTTTACCCTTTTACTTCTTAATTAACCTAATTACTCTGAATTAAGCTAATTACTACT
* *
25689 GTTTCCCCTTTTATTTCTTGATTAACCTAATTACTCTGAATTAAGCTAA
66 GTTTCCCCTTTTACTCCTTGATTAACCTAATTACTCTGAATTAAGCTAA
*
25738 TTACTATTGTTTACTCCTCTTACT
1 TTACTATTGTTTAC-CCTTTTACT
25762 ACTTTTACTC
Statistics
Matches: 123, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
114 32 0.26
115 29 0.24
116 62 0.50
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (114 bp):
TTACTATTGTTTACCCTTTTACTTCTTAATTAACCTAATTACTCTGAATTAAGCTAATTACTACT
GTTTCCCCTTTTACTCCTTGATTAACCTAATTACTCTGAATTAAGCTAA
Found at i:25680 original size:19 final size:18
Alignment explanation
Indices: 25650--25742 Score: 71
Period size: 19 Copynumber: 4.9 Consensus size: 18
25640 TTTTATTTCT
25650 TGATTAACCTAATTACTC
1 TGATTAACCTAATTACTC
*
25668 TGAATTAAGCTAATTACTAC
1 TG-ATTAACCTAATTACT-C
* ** * *
25688 TGTTTCCCCT-TTTATTTC
1 TGATTAACCTAATTA-CTC
25706 TTGATTAACCTAATTACTC
1 -TGATTAACCTAATTACTC
*
25725 TGAATTAAGCTAATTACT
1 TG-ATTAACCTAATTACT
25743 ATTGTTTACT
Statistics
Matches: 56, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
18 8 0.14
19 42 0.75
20 6 0.11
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (18 bp):
TGATTAACCTAATTACTC
Found at i:25685 original size:57 final size:57
Alignment explanation
Indices: 25508--25749 Score: 349
Period size: 57 Copynumber: 4.2 Consensus size: 57
25498 ACCCTTTATC
* * * * * *
25508 TTACTATTGATTACCGTTTTACTTCTTAATTAACCTTATTACTTTGAATTAAGCTAA
1 TTACTATTGTTTCCCCTTTTACTTCTTGATTAACCTAATTACTCTGAATTAAGCTAA
* * * *
25565 TTACTACTGTTTACTCCTTTTACTCCTTGATTAACTTAATTTACTCTGAATTAAGCTAA
1 TTACTATTGTTT-CCCCTTTTACTTCTTGATTAACCTAA-TTACTCTGAATTAAGCTAA
*
25624 TTACTATTGTTTCCCCTTTTATTTCTTGATTAACCTAATTACTCTGAATTAAGCTAA
1 TTACTATTGTTTCCCCTTTTACTTCTTGATTAACCTAATTACTCTGAATTAAGCTAA
* *
25681 TTACTACTGTTTCCCCTTTTATTTCTTGATTAACCTAATTACTCTGAATTAAGCTAA
1 TTACTATTGTTTCCCCTTTTACTTCTTGATTAACCTAATTACTCTGAATTAAGCTAA
25738 TTACTATTGTTT
1 TTACTATTGTTT
25750 ACTCCTCTTA
Statistics
Matches: 166, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
57 96 0.58
58 41 0.25
59 29 0.17
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.48
Consensus pattern (57 bp):
TTACTATTGTTTCCCCTTTTACTTCTTGATTAACCTAATTACTCTGAATTAAGCTAA
Found at i:25769 original size:9 final size:9
Alignment explanation
Indices: 25747--25860 Score: 167
Period size: 9 Copynumber: 12.7 Consensus size: 9
25737 ATTACTATTG
25747 TTTACTCCT
1 TTTACTCCT
* *
25756 CTTACTACT
1 TTTACTCCT
25765 TTTACTCCT
1 TTTACTCCT
25774 TTTACTCCT
1 TTTACTCCT
25783 TTTACT-CT
1 TTTACTCCT
25791 TTTACTCCT
1 TTTACTCCT
25800 TTTACTCCCT
1 TTTACT-CCT
*
25810 TTTACTTCT
1 TTTACTCCT
25819 TTTACTCCT
1 TTTACTCCT
*
25828 TTTACTCTT
1 TTTACTCCT
*
25837 TTTACTCAT
1 TTTACTCCT
25846 TTTACTCCT
1 TTTACTCCT
25855 TTTACT
1 TTTACT
25861 TCTACTTCAT
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
8 8 0.09
9 77 0.82
10 9 0.10
ACGTcount: A:0.13, C:0.30, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTACTCCT
Found at i:25885 original size:17 final size:17
Alignment explanation
Indices: 25863--25917 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
25853 CTTTTACTTC
25863 TACTTCATTCTGCTGAT
1 TACTTCATTCTGCTGAT
* * *
25880 TACTTC-TTTTACT-TT
1 TACTTCATTCTGCTGAT
25895 TACTTCATTCTGCTGAT
1 TACTTCATTCTGCTGAT
25912 TACTTC
1 TACTTC
25918 TTTTACTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 7 0.23
16 10 0.33
17 13 0.43
ACGTcount: A:0.16, C:0.24, G:0.07, T:0.53
Consensus pattern (17 bp):
TACTTCATTCTGCTGAT
Found at i:25921 original size:64 final size:64
Alignment explanation
Indices: 25847--26197 Score: 310
Period size: 64 Copynumber: 5.2 Consensus size: 64
25837 TTTACTCATT
* * * * * * *
25847 TTACTCCTTTTACTTCTACTTCATTCTGCTGATTACTTCTTTTACTTTTACTTCATTCTGCTGA
1 TTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTTACTTTTACTTCTTTCTACTGA
* * * * *
25911 TTACTTCTTTTACTTTTACTTTACTCTACTAATTACTCCTTTTATTTTTAC-TCTTTTTTACTGT
1 TTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTTACTTTTACTTC-TTTCTACTGA
*
25975 TTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTT-CTTTCTACTCTTTTTAGCCTT
1 TTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTTACTTT-TACT-TCTTT---C--
*
26039 TACTAA
59 TACTGA
* * * * * * * *
26045 CTACTTCCTTTTACTCTTACTCTTTTACTTTTACTGATAACTTCTTTTACTTTCACTTCCTTCTA
1 TTACTT-CTTTTACTTTTA--C-TTTAC-TCTGCTGATTACTCCTTTTACTTTTACTTCTTTCTA
26110 CTGA
61 CTGA
* *
26114 TTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTTACTTCTACTCCTTTACTTCTAC
1 TTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTTACTTTTACT--TCT--TTCTAC
26179 TGA
62 TGA
*
26182 TTATTTCTTTTACTTT
1 TTACTTCTTTTACTTT
26198 CACTCTTTTA
Statistics
Matches: 228, Mismatches: 40, Indels: 34
0.75 0.13 0.11
Matches are distributed among these distances:
63 5 0.02
64 115 0.50
65 8 0.04
66 3 0.01
68 35 0.15
69 10 0.04
70 9 0.04
71 12 0.05
73 1 0.00
74 8 0.04
75 18 0.08
76 4 0.02
ACGTcount: A:0.16, C:0.24, G:0.04, T:0.56
Consensus pattern (64 bp):
TTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTTACTTTTACTTCTTTCTACTGA
Found at i:25927 original size:38 final size:32
Alignment explanation
Indices: 25847--26197 Score: 222
Period size: 32 Copynumber: 10.5 Consensus size: 32
25837 TTTACTCATT
* *
25847 TTACTCCTTTTACTTCTACTTCATTCTGCTGA
1 TTACTTCTTTTACTTTTACTTCATTCTGCTGA
25879 TTACTTCTTTTACTTTTACTTCATTCTGCTGA
1 TTACTTCTTTTACTTTTACTTCATTCTGCTGA
* * * *
25911 TTACTTCTTTTACTTTTACTTTACTCTACTAA
1 TTACTTCTTTTACTTTTACTTCATTCTGCTGA
* * * * * *
25943 TTACTCCTTTTATTTTTAC-TCTTTTTTACTGT
1 TTACTTCTTTTACTTTTACTTC-ATTCTGCTGA
* *
25975 TTACTTCTTTTACTTTTACTTTACTCTGCTGA
1 TTACTTCTTTTACTTTTACTTCATTCTGCTGA
* * * *
26007 TTACTCCTTTT-CTTTCTAC-TCTTTTTAGCCTTTA
1 TTACTTCTTTTACTTT-TACTTCATTCT-G-C-TGA
* * * *
26041 CTAACTACTTCCTTTTACTCTTACTCTTTTACTTTTACTGA
1 -T---TACTT-CTTTTACTTTTA--C-TTCA-TTCTGCTGA
* * * *
26082 TAACTTCTTTTACTTTCACTTCCTTCTACTGA
1 TTACTTCTTTTACTTTTACTTCATTCTGCTGA
* *
26114 TTACTTCTTTTACTTTTACTTTACTCTGCTGA
1 TTACTTCTTTTACTTTTACTTCATTCTGCTGA
* * * *
26146 TTACTCCTTTTACTTCTACTCCTTTACTTCTACTGA
1 TTACTTCTTTTACTT-T--TACTTCA-TTCTGCTGA
*
26182 TTATTTCTTTTACTTT
1 TTACTTCTTTTACTTT
26198 CACTCTTTTA
Statistics
Matches: 246, Mismatches: 52, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
31 8 0.03
32 164 0.67
33 5 0.02
34 3 0.01
35 8 0.03
36 30 0.12
37 4 0.02
38 4 0.02
39 7 0.03
40 4 0.02
41 3 0.01
42 1 0.00
43 1 0.00
44 4 0.02
ACGTcount: A:0.16, C:0.24, G:0.04, T:0.56
Consensus pattern (32 bp):
TTACTTCTTTTACTTTTACTTCATTCTGCTGA
Found at i:26093 original size:16 final size:16
Alignment explanation
Indices: 26072--26127 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
26062 TACTCTTTTA
26072 CTTTTACTGATAACTT
1 CTTTTACTGATAACTT
* *
26088 CTTTTACT-TTCACTT
1 CTTTTACTGATAACTT
* *
26103 CCTTCTACTGATTACTT
1 -CTTTTACTGATAACTT
26120 CTTTTACT
1 CTTTTACT
26128 TTTACTTTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 5 0.16
16 22 0.69
17 5 0.16
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.54
Consensus pattern (16 bp):
CTTTTACTGATAACTT
Found at i:26118 original size:139 final size:136
Alignment explanation
Indices: 25967--26259 Score: 373
Period size: 139 Copynumber: 2.1 Consensus size: 136
25957 TTTACTCTTT
* *
25967 TTTACTGTTTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTT-CTTTCTACTCTTT
1 TTTACTGATTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTTAC-TTCTACTC-CT
* *
26031 TTAGCCTT-TACTAACTACTTCCTTTTACTCTT-ACTCTTTTACTTTTACTGA-TA-ACTTCTTT
64 TTA--CTTCTACTAACTA-TTCCTTTTACT-TTCACTCTTTTAATTCTACTGATTACACTTCTTT
*
26092 TACT-TTCACTTCC
125 TACTCTT--CTACC
26105 TTCTACTGATTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTTACTTCTACTCCTT
1 TT-TACTGATTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTTACTTCTACTCCTT
* * * *
26170 TACTTCTACTGATTATTTCTTTTACTTTCACTCTTTTAATTCTACTGATTACTTCTTCTTTTACT
65 TACTTCTACTAACTATTCCTTTTACTTTCACTCTTTTAATTCTACTGATTAC-ACTTCTTTTACT
26235 CTTCTACC
129 CTTCTACC
26243 TTTACTGATTACTTCTT
1 TTTACTGATTACTTCTT
26260 CTTTTTACTT
Statistics
Matches: 138, Mismatches: 9, Indels: 17
0.84 0.05 0.10
Matches are distributed among these distances:
135 2 0.01
136 30 0.22
137 24 0.17
138 12 0.09
139 67 0.49
140 3 0.02
ACGTcount: A:0.16, C:0.25, G:0.04, T:0.55
Consensus pattern (136 bp):
TTTACTGATTACTTCTTTTACTTTTACTTTACTCTGCTGATTACTCCTTTTACTTCTACTCCTTT
ACTTCTACTAACTATTCCTTTTACTTTCACTCTTTTAATTCTACTGATTACACTTCTTTTACTCT
TCTACC
Found at i:26173 original size:14 final size:15
Alignment explanation
Indices: 26147--26179 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
26137 CTCTGCTGAT
26147 TACTCCTTTTACTTC
1 TACTCCTTTTACTTC
26162 TACTCC-TTTACTTC
1 TACTCCTTTTACTTC
26176 TACT
1 TACT
26180 GATTATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (15 bp):
TACTCCTTTTACTTC
Found at i:26412 original size:57 final size:57
Alignment explanation
Indices: 26244--26438 Score: 238
Period size: 57 Copynumber: 3.4 Consensus size: 57
26234 TCTTCTACCT
* * * *
26244 TTACTGATTACTTCTTCTTTT--TACTTTTCTAGCTTAATTTCTCTGAATTAAAC-CA
1 TTACTGTTTACTTCTTCTTTTACT-CTTTTTTAGCTTAATTACTCTGAATTAAACTAA
* * *
26299 TATACTGCTTACTTCTTCCTTTACTTTCTTTTTAG-TCTAATTACTCTGAATTAAACTAA
1 T-TACTGTTTACTTCTTCTTTTACTCT-TTTTTAGCT-TAATTACTCTGAATTAAACTAA
*
26358 TTACTGTTTACTACTTCTTTTACTCTTTTTTAGCTTAATTACTCTGAATTAAACTAA
1 TTACTGTTTACTTCTTCTTTTACTCTTTTTTAGCTTAATTACTCTGAATTAAACTAA
26415 TTACTGTTTACTT-TTCCTTTTACT
1 TTACTGTTTACTTCTT-CTTTTACT
26439 TAATGGCATT
Statistics
Matches: 121, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
55 1 0.01
56 20 0.17
57 51 0.42
58 47 0.39
59 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (57 bp):
TTACTGTTTACTTCTTCTTTTACTCTTTTTTAGCTTAATTACTCTGAATTAAACTAA
Found at i:39161 original size:22 final size:22
Alignment explanation
Indices: 39139--39188 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
39129 CCATAATTAA
39139 TATATTATACTAATTATGGTAAT
1 TATATTATA-TAATTATGGTAAT
39162 TATATTATATAATTAT--TAAT
1 TATATTATATAATTATGGTAAT
39182 T-TATTAT
1 TATATTAT
39189 TGCTATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.22
20 5 0.19
22 7 0.26
23 9 0.33
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (22 bp):
TATATTATATAATTATGGTAAT
Found at i:44544 original size:26 final size:26
Alignment explanation
Indices: 44469--44537 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
44459 GAGAATTGAT
* *
44469 ATTGAGATTTTTGATAACCTCATGAA
1 ATTGAGATTTTTGATAACATCATAAA
44495 ATTGAGATTTTTGATAACATCATAAA
1 ATTGAGATTTTTGATAACATCATAAA
*
44521 ATTGAGGTTTTTG-TAAC
1 ATTGAGATTTTTGATAAC
44538 TTTCATATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 4 0.10
26 36 0.90
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.41
Consensus pattern (26 bp):
ATTGAGATTTTTGATAACATCATAAA
Found at i:44558 original size:22 final size:21
Alignment explanation
Indices: 44529--44687 Score: 108
Period size: 22 Copynumber: 7.3 Consensus size: 21
44519 AAATTGAGGT
44529 TTTTG-TAACTTTCATATGAAA
1 TTTTGATAAC-TTCATATGAAA
* ** *
44550 TTTTGGTAACCACACTACGAAA
1 TTTTGATAACTTCA-TATGAAA
* *
44572 TTTTGATAAGC-ACAATATGACA
1 TTTTGATAA-CTTC-ATATGAAA
*
44594 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAA-CTTCATATGAAA
*
44616 TTTT-AGTAACCTTCTTATGAAA
1 TTTTGA-TAA-CTTCATATGAAA
44638 TTTTGATAACTTCACTATGAAA
1 TTTTGATAACTTCA-TATGAAA
* * * *
44660 TTCTAATAACCTCGCTATGAAA
1 TTTTGATAACTTC-ATATGAAA
44682 TTTTGA
1 TTTTGA
44688 AATCCCATGA
Statistics
Matches: 111, Mismatches: 18, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
21 12 0.11
22 95 0.86
23 4 0.04
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (21 bp):
TTTTGATAACTTCATATGAAA
Found at i:44616 original size:44 final size:45
Alignment explanation
Indices: 44541--44687 Score: 135
Period size: 44 Copynumber: 3.3 Consensus size: 45
44531 TTGTAACTTT
* * * *
44541 CATATGAAATTTTGGTAACC-ACACTACGAAATTTT-GATAAGC-A
1 CATATGAAATTTTGATAACCTTCACTATGAAATTTTAG-TAACCTA
* *
44584 CAATATGACATTTTGATAACCTTC-CTATGAAATTTTAGTAACCTT
1 C-ATATGAAATTTTGATAACCTTCACTATGAAATTTTAGTAACCTA
* * *
44629 CTTATGAAATTTTGATAA-CTTCACTATGAAATTCTAATAACCT-
1 CATATGAAATTTTGATAACCTTCACTATGAAATTTTAGTAACCTA
*
44672 CGCTATGAAATTTTGA
1 C-ATATGAAATTTTGA
44688 AATCCCATGA
Statistics
Matches: 87, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.07
44 78 0.90
45 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (45 bp):
CATATGAAATTTTGATAACCTTCACTATGAAATTTTAGTAACCTA
Found at i:44617 original size:66 final size:66
Alignment explanation
Indices: 44529--44686 Score: 162
Period size: 66 Copynumber: 2.4 Consensus size: 66
44519 AAATTGAGGT
* *
44529 TTTTG-TAACTTTCATATGAAATTTTGGTAACC-ACACTACGAAATTTTGATAAGC-ACAATATG
1 TTTTGATAACCTTCCTATGAAATTTTGGTAACCTAC-CTACGAAATTTTGATAA-CTACAATATG
*
44591 ACA
64 AAA
* * * * * *
44594 TTTTGATAACCTTCCTATGAAATTTTAGTAACCTTCTTATGAAATTTTGATAACTTCACTATGAA
1 TTTTGATAACCTTCCTATGAAATTTTGGTAACCTACCTACGAAATTTTGATAACTACAATATGAA
44659 A
66 A
* *
44660 TTCTAATAACC-TCGCTATGAAATTTTG
1 TTTTGATAACCTTC-CTATGAAATTTTG
44687 AAATCCCATG
Statistics
Matches: 77, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
65 8 0.10
66 68 0.88
67 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (66 bp):
TTTTGATAACCTTCCTATGAAATTTTGGTAACCTACCTACGAAATTTTGATAACTACAATATGAA
A
Found at i:44905 original size:22 final size:22
Alignment explanation
Indices: 44851--45011 Score: 144
Period size: 22 Copynumber: 7.3 Consensus size: 22
44841 CATAGAGTGA
44851 TTATCAAAATTTCATAGGATCAGG
1 TTATCAAAATTTCATAGGA--AGG
* * *
44875 TTGTTAAAATTCCATAGGAAGG
1 TTATCAAAATTTCATAGGAAGG
* ** *
44897 TTATCAAAATGTCATAATATGG
1 TTATCAAAATTTCATAGGAAGG
* *
44919 TTATCAAAATTTCATTGG-GGG
1 TTATCAAAATTTCATAGGAAGG
***
44940 TTATCAAAATTTCATATTTAGG
1 TTATCAAAATTTCATAGGAAGG
* * *
44962 TTTTTAAAATTTCATAGAAAGG
1 TTATCAAAATTTCATAGGAAGG
*
44984 TTAACAAAATTTCATAGGAAGG
1 TTATCAAAATTTCATAGGAAGG
*
45006 GTATCA
1 TTATCA
45012 TCGTCAATCT
Statistics
Matches: 106, Mismatches: 30, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
21 17 0.16
22 73 0.69
24 16 0.15
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGAAGG
Found at i:45011 original size:87 final size:88
Alignment explanation
Indices: 44851--45011 Score: 207
Period size: 87 Copynumber: 1.8 Consensus size: 88
44841 CATAGAGTGA
* * *
44851 TTATCAAAATTTCATAGGATCAGGTTGTTAAAATTCCATAGGAAGGTTATCAAAATGTCATAATA
1 TTATCAAAATTTCATA-GATCAGGTTGTTAAAATTCCATAGAAAGGTTAACAAAATGTCATAAGA
* *
44916 TGGTTATCAAAATTTCATTGGGGG
65 AGGGTATCAAAATTTCATTGGGGG
* * * * * *
44940 TTATCAAAATTTCATA-TTTAGGTTTTTAAAATTTCATAGAAAGGTTAACAAAATTTCATAGGAA
1 TTATCAAAATTTCATAGATCAGGTTGTTAAAATTCCATAGAAAGGTTAACAAAATGTCATAAGAA
45004 GGGTATCA
66 GGGTATCA
45012 TCGTCAATCT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
87 45 0.74
89 16 0.26
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (88 bp):
TTATCAAAATTTCATAGATCAGGTTGTTAAAATTCCATAGAAAGGTTAACAAAATGTCATAAGAA
GGGTATCAAAATTTCATTGGGGG
Done.