Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008544.1 Corchorus capsularis cultivar CVL-1 contig08565, 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: 95905
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:211 original size:2 final size:2
Alignment explanation
Indices: 166--200 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
156 TACGGTTTTA
166 AT AT AT 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 AT AT AT A
201 AAAGATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10385 original size:116 final size:116
Alignment explanation
Indices: 10181--10414 Score: 468
Period size: 116 Copynumber: 2.0 Consensus size: 116
10171 TCAAAAAAAT
10181 TACTGACAAATTGATATTATAACCTTAATGTCTAATTTAAGTTAGAAAACATATATATAGGCAAT
1 TACTGACAAATTGATATTATAACCTTAATGTCTAATTTAAGTTAGAAAACATATATATAGGCAAT
10246 ATATAGATATAGTATATAGTTTTAAATTAAAAAAAGGGAGAAGAGTTTAGC
66 ATATAGATATAGTATATAGTTTTAAATTAAAAAAAGGGAGAAGAGTTTAGC
10297 TACTGACAAATTGATATTATAACCTTAATGTCTAATTTAAGTTAGAAAACATATATATAGGCAAT
1 TACTGACAAATTGATATTATAACCTTAATGTCTAATTTAAGTTAGAAAACATATATATAGGCAAT
10362 ATATAGATATAGTATATAGTTTTAAATTAAAAAAAGGGAGAAGAGTTTAGC
66 ATATAGATATAGTATATAGTTTTAAATTAAAAAAAGGGAGAAGAGTTTAGC
10413 TA
1 TA
10415 GGGAAAAGCA
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.34
Consensus pattern (116 bp):
TACTGACAAATTGATATTATAACCTTAATGTCTAATTTAAGTTAGAAAACATATATATAGGCAAT
ATATAGATATAGTATATAGTTTTAAATTAAAAAAAGGGAGAAGAGTTTAGC
Found at i:27918 original size:216 final size:213
Alignment explanation
Indices: 27298--27946 Score: 767
Period size: 210 Copynumber: 3.0 Consensus size: 213
27288 AACTCATGGT
* * * * * * *
27298 GTCTTGGTTGATGTCTTGGTTACTAGCCATAGGATTGGTTCTCATTGGAGGAAAAAAAAGAGGTT
1 GTCTTGGTTGGTGTCTTGGTTGCTAGCCATAGGATCGGTTCTCATTAGAGG--GAAAAAGTGGCT
* * *
27363 ATGATATTGTAAACACAAATTTCGCGTCGAAACAAGAACAAAAAATTCAGAAACAAATACCAACT
64 ATGATACTGTAAACACAAATTTCGCGTCGAAACAATAAC-AAAAATTCGGAAACAAATACCAACT
* *
27428 TTACTGATTATTGTGGATACAATCTCTAGAATGAATTAC-AGTAAATATCTAT-CATCTGATTCT
128 TTATTGATAATTGTGGATACAATCTCTAGAATGAATTACAAG-AAATATCT-TCCAT-TGATTCT
*
27491 TTCTTCGATAAATTTGCTTCAAGG
190 TTCTTCGATAAATTCGCTTCAAGG
* * * * *
27515 GTCTTAGTTGGCGTCTTGGTTGCTAGCCATTGGATCGGTTCTTATTAG-GGG--AAAGTGGCTCT
1 GTCTTGGTTGGTGTCTTGGTTGCTAGCCATAGGATCGGTTCTCATTAGAGGGAAAAAGTGGCTAT
* * ** * * * **
27577 GATACTTTAAACACAAATTTCACG-AAAAAAAAGTAA-AAAATTTTAGG-AACAAATAATAACTT
66 GATACTGTAAACACAAATTTCGCGTCGAAACAA-TAACAAAA-ATTCGGAAACAAATACCAACTT
* * * * *
27639 TATTGATGATTGTGGTTACAATCTTTAGAATGAATTACAAGAAATATCAATCCTTTGATTCTTTC
129 TATTGATAATTGTGGATACAATCTCTAGAATGAATTACAAGAAATATC-TTCCATTGATTCTTTC
* *
27704 TTCGACAAATTCGTTTCAAGG
193 TTCGATAAATTCGCTTCAAGG
*
27725 GTCTTGGTTGGTGTCTTGGTTGCTAGCCATAGGATCAGTTCTCATTAGAGGGTAAAAAGTGGCTA
1 GTCTTGGTTGGTGTCTTGGTTGCTAGCCATAGGATCGGTTCTCATTAGAGGG-AAAAAGTGGCTA
*
27790 TGATACTGTAAACACAAATTTCGCGTCGAAACAATAACAAGAAATTCGGAAACAACTACCAACTT
65 TGATACTGTAAACACAAATTTCGCGTCGAAACAATAACAA-AAATTCGGAAACAAATACCAACTT
* *
27855 TATTGATAATTGTAGG-TACAATCTCTAGAATGTATTACAAGAAATATCGTTCCATTAATTCTTT
129 TATTGATAATTGT-GGATACAATCTCTAGAATGAATTACAAGAAATATC-TTCCATTGATTCTTT
*
27919 CTTCGATAAATTCACTTCAAGG
192 CTTCGATAAATTCGCTTCAAGG
27941 GTCTTG
1 GTCTTG
27947 ATAGATTTGA
Statistics
Matches: 359, Mismatches: 59, Indels: 29
0.80 0.13 0.06
Matches are distributed among these distances:
210 130 0.36
211 15 0.04
212 31 0.09
214 35 0.10
215 11 0.03
216 95 0.26
217 42 0.12
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (213 bp):
GTCTTGGTTGGTGTCTTGGTTGCTAGCCATAGGATCGGTTCTCATTAGAGGGAAAAAGTGGCTAT
GATACTGTAAACACAAATTTCGCGTCGAAACAATAACAAAAATTCGGAAACAAATACCAACTTTA
TTGATAATTGTGGATACAATCTCTAGAATGAATTACAAGAAATATCTTCCATTGATTCTTTCTTC
GATAAATTCGCTTCAAGG
Found at i:28120 original size:33 final size:35
Alignment explanation
Indices: 28057--28134 Score: 110
Period size: 33 Copynumber: 2.3 Consensus size: 35
28047 CGAACAAACA
28057 AAAATGAT--TTTCTTTGAATAAGTTGGTGAAGATC
1 AAAATGATAATTTCTTTGAAT-AGTTGGTGAAGATC
28091 AAAATGATAATTTC-TTGAAT-GTTGGTGAAGATC
1 AAAATGATAATTTCTTTGAATAGTTGGTGAAGATC
*
28124 AAAATAATAAT
1 AAAATGATAAT
28135 ATCTCGACTA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
33 23 0.56
34 8 0.20
35 6 0.15
36 4 0.10
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (35 bp):
AAAATGATAATTTCTTTGAATAGTTGGTGAAGATC
Found at i:31925 original size:2 final size:2
Alignment explanation
Indices: 31920--31957 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
31910 AGAGAGAGAA
* *
31920 AT AT AT AA AT AT AA 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 AT AT
31958 GAACCACAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:33135 original size:11 final size:10
Alignment explanation
Indices: 33119--33171 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
33109 AAGTTCGTGT
33119 TTGAAGACTTA
1 TTGAAGA-TTA
*
33130 TTGAAGATAA
1 TTGAAGATTA
33140 TTTGAAGA-T-
1 -TTGAAGATTA
33149 TTGAAGATTA
1 TTGAAGATTA
33159 TTGAAGAATTA
1 TTGAAG-ATTA
33170 TT
1 TT
33172 TCAAGGAGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 8 0.22
11 20 0.56
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:33146 original size:22 final size:21
Alignment explanation
Indices: 33118--33171 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
33108 AAAGTTCGTG
33118 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
33140 TTTGAAGA-T-TTGAAGATTA
1 TTTGAAGATTATTGAAGATAA
33159 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
33172 TCAAGGAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.41
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:41040 original size:15 final size:15
Alignment explanation
Indices: 41020--41049 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41010 GGATGGTAAG
41020 TGATTAGAGCTACTT
1 TGATTAGAGCTACTT
*
41035 TGATTATAGCTACTT
1 TGATTAGAGCTACTT
41050 AAGAATGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (15 bp):
TGATTAGAGCTACTT
Found at i:41488 original size:11 final size:10
Alignment explanation
Indices: 41472--41524 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
41462 AAGTTCGTGT
41472 TTGAAGACTTA
1 TTGAAGA-TTA
*
41483 TTGAAGATAA
1 TTGAAGATTA
41493 TTTGAAGA-T-
1 -TTGAAGATTA
41502 TTGAAGATTA
1 TTGAAGATTA
41512 TTGAAGAATTA
1 TTGAAG-ATTA
41523 TT
1 TT
41525 TCAAGGAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 8 0.22
11 20 0.56
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:41499 original size:22 final size:21
Alignment explanation
Indices: 41471--41524 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
41461 AAAGTTCGTG
41471 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
41493 TTTGAAGA-T-TTGAAGATTA
1 TTTGAAGATTATTGAAGATAA
41512 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
41525 TCAAGGAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.41
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:45538 original size:2 final size:2
Alignment explanation
Indices: 45527--45564 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
45517 GTTCTTTTAC
45527 AT AT -T AT AT AT AT -T 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 AT AT AT
45565 TAATAGTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:46290 original size:2 final size:2
Alignment explanation
Indices: 46283--46311 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46273 TTCCGAAACA
46283 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
46312 GTAACTGCAA
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:48299 original size:11 final size:11
Alignment explanation
Indices: 48283--48342 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
48273 TGTTAGCTTT
48283 TAATTAACCTC
1 TAATTAACCTC
**
48294 TAATTATTCTC
1 TAATTAACCTC
*
48305 TAATTAGCCT-
1 TAATTAACCTC
*
48315 TAATTAACTTC
1 TAATTAACCTC
**
48326 TAATTAAGTTC
1 TAATTAACCTC
48337 TAATTA
1 TAATTA
48343 GCTGCTAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 8 0.20
11 33 0.80
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (11 bp):
TAATTAACCTC
Found at i:48310 original size:22 final size:22
Alignment explanation
Indices: 48283--48398 Score: 78
Period size: 22 Copynumber: 5.3 Consensus size: 22
48273 TGTTAGCTTT
48283 TAATTAACCTCTAATTATTCTC
1 TAATTAACCTCTAATTATTCTC
* *
48305 TAATTAGCCT-TAATTA-ACTTC
1 TAATTAACCTCTAATTATTC-TC
** *
48326 TAATTAAGTTCTAATTA-GCTGC
1 TAATTAACCTCTAATTATTCT-C
** * *
48348 TAATTATTCTCTAATTGTCTTTC
1 TAATTAACCTCTAATTAT-TCTC
*
48371 TAACTAACC-CTAATTATTCTCC
1 TAATTAACCTCTAATTATTCT-C
48393 TAATTA
1 TAATTA
48399 GGATCTAATT
Statistics
Matches: 70, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
20 1 0.01
21 18 0.26
22 43 0.61
23 7 0.10
24 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (22 bp):
TAATTAACCTCTAATTATTCTC
Found at i:48318 original size:32 final size:32
Alignment explanation
Indices: 48282--48344 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
48272 TTGTTAGCTT
*
48282 TTAATTAACCTCTAATT-ATTCTCTAATTAGCC
1 TTAATTAACCTCTAATTAAGT-TCTAATTAGCC
*
48314 TTAATTAACTTCTAATTAAGTTCTAATTAGC
1 TTAATTAACCTCTAATTAAGTTCTAATTAGC
48345 TGCTAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.44
Consensus pattern (32 bp):
TTAATTAACCTCTAATTAAGTTCTAATTAGCC
Found at i:53548 original size:18 final size:17
Alignment explanation
Indices: 53521--53555 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53511 GTAAGAATTT
53521 TATTTTAATATATAATA
1 TATTTTAATATATAATA
*
53538 TATTGTTAATATGTAATA
1 TATT-TTAATATATAATA
53556 CATATATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
TATTTTAATATATAATA
Found at i:55838 original size:11 final size:11
Alignment explanation
Indices: 55824--55884 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
55814 TTGATTAGCT
55824 TCTAATTAACC
1 TCTAATTAACC
**
55835 TCTAATTATTC
1 TCTAATTAACC
*
55846 TCTAATTAGCC
1 TCTAATTAACC
*
55857 T-TAATTAACT
1 TCTAATTAACC
**
55867 TCT-ATTAAGT
1 TCTAATTAACC
55877 TCTAATTA
1 TCTAATTA
55885 GCTGCTAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
10 17 0.41
11 24 0.59
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (11 bp):
TCTAATTAACC
Found at i:55849 original size:22 final size:22
Alignment explanation
Indices: 55824--55951 Score: 77
Period size: 22 Copynumber: 5.9 Consensus size: 22
55814 TTGATTAGCT
55824 TCTAATTAACCTCTAATTATTC
1 TCTAATTAACCTCTAATTATTC
* *
55846 TCTAATTAGCCT-TAATTA-AC
1 TCTAATTAACCTCTAATTATTC
** *
55866 TTCT-ATTAAGTTCTAATTA-GC
1 -TCTAATTAACCTCTAATTATTC
** * *
55887 TGCTAATTATTCTCTAATTGTCTT
1 T-CTAATTAACCTCTAATTAT-TC
*
55911 TCTAACTAACC-CTAATTATTC
1 TCTAATTAACCTCTAATTATTC
**
55932 TCCTAATTAGGCTCTAATTA
1 T-CTAATTAACCTCTAATTA
55952 CACTGAATCA
Statistics
Matches: 78, Mismatches: 20, Indels: 15
0.69 0.18 0.13
Matches are distributed among these distances:
20 7 0.09
21 20 0.26
22 36 0.46
23 14 0.18
24 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (22 bp):
TCTAATTAACCTCTAATTATTC
Found at i:56029 original size:39 final size:38
Alignment explanation
Indices: 55984--56077 Score: 118
Period size: 38 Copynumber: 2.4 Consensus size: 38
55974 CTAACTACCC
*
55984 CCATTATTACCAAATTACCGAAGTTTG-CCTAAATTACTT
1 CCATTATTACCAAATTACCGAA--ATGACCTAAATTACTT
** *
56023 CCATTATTACCAAATTGTCTAAATGACCTAAATTACTT
1 CCATTATTACCAAATTACCGAAATGACCTAAATTACTT
*
56061 CAATTATTACCAAATTA
1 CCATTATTACCAAATTA
56078 ACATCAAGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.04
38 27 0.56
39 19 0.40
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36
Consensus pattern (38 bp):
CCATTATTACCAAATTACCGAAATGACCTAAATTACTT
Found at i:56077 original size:20 final size:20
Alignment explanation
Indices: 56014--56077 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
56004 AAGTTTGCCT
*
56014 AAATTACTTCCATTATTACC
1 AAATTACTTCAATTATTACC
* *
56034 AAATT--GTCTAA--ATGACC
1 AAATTACTTC-AATTATTACC
56051 TAAATTACTTCAATTATTACC
1 -AAATTACTTCAATTATTACC
56072 AAATTA
1 AAATTA
56078 ACATCAAGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
17 5 0.15
18 7 0.21
19 3 0.09
20 13 0.39
21 5 0.15
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATTACTTCAATTATTACC
Found at i:57153 original size:30 final size:29
Alignment explanation
Indices: 57091--57160 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
57081 ACCGAACCGT
* ***
57091 CAAATAAGCCCCTGAACTTTTATTTCGGC
1 CAAATAAGCCCCTGAACTTTAAAAACGGC
*
57120 CAAATAAGCCCCTGAACTCTTAAAAAGGGC
1 CAAATAAGCCCCTGAACT-TTAAAAACGGC
57150 CAAATAAGCCC
1 CAAATAAGCCC
57161 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTTTAAAAACGGC
Found at i:70074 original size:72 final size:72
Alignment explanation
Indices: 69957--70097 Score: 255
Period size: 72 Copynumber: 2.0 Consensus size: 72
69947 GATATTAATT
69957 TTGAACCATTTATTGTCCATTTCTTTATAAATTATGCAATCAATCTCCTCAAAGGATTCTTAAGA
1 TTGAACCATTTATTGTCCATTTCTTTATAAATTATGCAATCAATCTCCTCAAAGGATTCTTAAGA
70022 GTACATG
66 GTACATG
* * *
70029 TTGAACCATTTATTGTCCTTTTCTTTATAAATTATGCAATTAATCTCCTTAAAGGATTCTTAAGA
1 TTGAACCATTTATTGTCCATTTCTTTATAAATTATGCAATCAATCTCCTCAAAGGATTCTTAAGA
70094 GTAC
66 GTAC
70098 CTAATGTTGA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (72 bp):
TTGAACCATTTATTGTCCATTTCTTTATAAATTATGCAATCAATCTCCTCAAAGGATTCTTAAGA
GTACATG
Found at i:72288 original size:27 final size:27
Alignment explanation
Indices: 72256--72310 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
72246 GTATAATTTG
*
72256 AAACTAATTCATTTATATA-ATATATAT
1 AAACTAATTC-TTCATATATATATATAT
72283 AAACTAATTCTTCATATATATATATAT
1 AAACTAATTCTTCATATATATATATAT
72310 A
1 A
72311 TATTCAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (27 bp):
AAACTAATTCTTCATATATATATATAT
Found at i:73001 original size:3 final size:3
Alignment explanation
Indices: 72993--73034 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
72983 TTTTTGTCTA
72993 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
73035 AGGATATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:73632 original size:53 final size:53
Alignment explanation
Indices: 73575--73720 Score: 221
Period size: 52 Copynumber: 2.8 Consensus size: 53
73565 ATTAGAAGCG
73575 TATATCTTTCATTTCTTTTTTTTTAATTTAACCGATATATATATATATATATA
1 TATATCTTTCATTTCTTTTTTTTTAATTTAACCGATATATATATATATATATA
73628 TATATC-TTCATTT-TATTTTTTTTAATTTAACCG---TATATATATATATATA
1 TATATCTTTCATTTCT-TTTTTTTTAATTTAACCGATATATATATATATATATA
*
73677 TATATCTTTCTATTTCTTTTTTTGTTAATTTAACCTATATATAT
1 TATATCTTTC-ATTTCTTTTTTT-TTAATTTAACCGATATATAT
73721 CTCCAAGTCT
Statistics
Matches: 84, Mismatches: 1, Indels: 14
0.85 0.01 0.14
Matches are distributed among these distances:
49 22 0.26
50 3 0.04
51 11 0.13
52 37 0.44
53 6 0.07
55 5 0.06
ACGTcount: A:0.30, C:0.10, G:0.02, T:0.58
Consensus pattern (53 bp):
TATATCTTTCATTTCTTTTTTTTTAATTTAACCGATATATATATATATATATA
Found at i:73831 original size:2 final size:2
Alignment explanation
Indices: 73824--73853 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
73814 TACTATTACC
73824 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
73854 CTCCAAGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73855 original size:133 final size:135
Alignment explanation
Indices: 73712--73959 Score: 455
Period size: 135 Copynumber: 1.9 Consensus size: 135
73702 TAATTTAACC
73712 TATATATATCTCCAAGTCTTGGTGATTTGAGACTAAGGGATCG-AA-ATATAGCAGGGTTAAAGT
1 TATATATATCTCCAAGTCTTGGTGATTTGAGACTAAGGGATCGAAACATATAGCAGGGTTAAAGT
* *
73775 CTTCTCAATGAGAATTTAGAGGAGATCAAATTGTATTCTTACTATTACCATATATATATATATAT
66 CTTCTCAATGAGAACTTAGAGGAGATCAAATTGTATTCTTAATATTACCATATATATATATATAT
73840 ATATA
131 ATATA
73845 TATATATATCTCCAAGTCTTGGTGATTTGAGACTAAGGGATCGAAACATATAGCAGGGTTAAAGT
1 TATATATATCTCCAAGTCTTGGTGATTTGAGACTAAGGGATCGAAACATATAGCAGGGTTAAAGT
*
73910 CTTCTCAATGAGAACTTAGAGGAGATCGAATTGTATTCTTAATATTACCA
66 CTTCTCAATGAGAACTTAGAGGAGATCAAATTGTATTCTTAATATTACCA
73960 AGATAGAGAC
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
133 43 0.39
134 2 0.02
135 65 0.59
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (135 bp):
TATATATATCTCCAAGTCTTGGTGATTTGAGACTAAGGGATCGAAACATATAGCAGGGTTAAAGT
CTTCTCAATGAGAACTTAGAGGAGATCAAATTGTATTCTTAATATTACCATATATATATATATAT
ATATA
Found at i:74365 original size:2 final size:2
Alignment explanation
Indices: 74358--74382 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
74348 ATTCTTTTTA
74358 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 A
74383 AGTAGGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80698 original size:15 final size:16
Alignment explanation
Indices: 80666--80699 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
80656 AAAGAAGAAT
*
80666 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
80682 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
80697 TAA
1 TAA
80700 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:82015 original size:19 final size:18
Alignment explanation
Indices: 81982--82017 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
81972 TTGAAATAAT
81982 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
82000 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
82018 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:83656 original size:32 final size:34
Alignment explanation
Indices: 83590--83657 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
83580 CCTATGATGC
83590 TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
1 TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
* * *
83624 TTAAAATTAAAATCCT-AAT-TTGAAAACCTAAA
1 TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
83656 TT
1 TT
83658 TGTTTAGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 13 0.42
33 3 0.10
34 15 0.48
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (34 bp):
TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
Found at i:90917 original size:11 final size:11
Alignment explanation
Indices: 90881--90918 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
90871 TGTTGGCGTA
90881 CACGTGTCATC
1 CACGTGTCATC
* *
90892 CACCTGTCACC
1 CACGTGTCATC
90903 CACGTGTCATC
1 CACGTGTCATC
90914 CACGT
1 CACGT
90919 CAGCATGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.18, C:0.42, G:0.16, T:0.24
Consensus pattern (11 bp):
CACGTGTCATC
Found at i:93955 original size:20 final size:20
Alignment explanation
Indices: 93927--93976 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
93917 AATGAATGAT
*
93927 ATTTTCAATCCATACTCTCA
1 ATTTACAATCCATACTCTCA
93947 ATTTACAATCCATACTCTCA
1 ATTTACAATCCATACTCTCA
93967 ATTTACAATC
1 ATTTACAATC
93977 ATCTACATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTACAATCCATACTCTCA
Done.