Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015575.1 Corchorus capsularis cultivar CVL-1 contig15596, 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: 44569
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3347 original size:44 final size:46
Alignment explanation
Indices: 3260--3359 Score: 159
Period size: 45 Copynumber: 2.2 Consensus size: 46
3250 ATTTGCTATC
* * *
3260 AAAAGAAAGAGGGATAATGAGTGTTTTTTTTAATACAAAATTC-TT
1 AAAAAAAAAAGGGATAATGAGTGATTTTTTTAATACAAAATTCTTT
3305 AAAAAAAAAAGGGATAATGAGT-ATTTTTTTAATACAAAATTCTTT
1 AAAAAAAAAAGGGATAATGAGTGATTTTTTTAATACAAAATTCTTT
3350 AAAAAAAAAA
1 AAAAAAAAAA
3360 AAAACCCACT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
44 19 0.37
45 32 0.63
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (46 bp):
AAAAAAAAAAGGGATAATGAGTGATTTTTTTAATACAAAATTCTTT
Found at i:7863 original size:2 final size:2
Alignment explanation
Indices: 7852--7887 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
7842 GAATATATGA
*
7852 AT AT AA 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 AT
7888 CTGTGTGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14304 original size:2 final size:2
Alignment explanation
Indices: 14292--14364 Score: 74
Period size: 2 Copynumber: 40.5 Consensus size: 2
14282 ATTTTCTACG
14292 TA TA T- TA TA TA TA TA -A TA -A TA TA -A TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14329 TA -A TA -A TA TA TA TA TA TA TA TA T- TA T- TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
14365 TATTTTTGTC
Statistics
Matches: 61, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
1 9 0.15
2 50 0.82
3 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:14349 original size:8 final size:8
Alignment explanation
Indices: 14292--14364 Score: 74
Period size: 7 Copynumber: 10.1 Consensus size: 8
14282 ATTTTCTACG
14292 TATAT-TA
1 TATATATA
14299 TATATATA
1 TATATATA
14307 -ATA-ATA
1 TATATATA
14313 TA-ATA-A
1 TATATATA
14319 TATATATA
1 TATATATA
14327 TATA-ATA
1 TATATATA
14334 -ATATATA
1 TATATATA
14341 TATATATA
1 TATATATA
14349 TAT-TAT-
1 TATATATA
14355 TACTATATA
1 TA-TATATA
14364 T
1 T
14365 TATTTTTGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
6 12 0.21
7 23 0.41
8 20 0.36
9 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (8 bp):
TATATATA
Found at i:15725 original size:713 final size:719
Alignment explanation
Indices: 14353--15785 Score: 2736
Period size: 713 Copynumber: 2.0 Consensus size: 719
14343 TATATATATT
14353 ATTACTATATATTATTTTTGTCTCCTATGGAATTTACTCACAGGTCCTTTTAACTTTTAACCTGA
1 ATTACTATATATTATTTTTGTCTCCTATGGAATTTACTCACAGGTCCTTTTAACTTTTAACCTGA
14418 AACAACCTTATCGCCCCATTTTGGTCTTTTTGCAAATGGCTTATTACTTTAAAAAAAATTCCTTT
66 AACAACCTTATCGCCCCATTTTGGTCTTTTTGCAAATGGCTTATTACTTT-AAAAAAATTCCTTT
14483 TAATCTTAATCCTTTTTCTAAAAATACAATGTCTTTTTATGTAATTTTAGAATCTAACTTCAATT
130 TAATCTTAATCCTTTTTCTAAAAATACAATGTCTTTTTATGTAATTTTAGAATCTAACTTCAATT
*
14548 AATAGTGTTCCCATCATTTTAAATGCATGATTAATGGTGTTCCCACCTTTTTAAATTCTACATAT
195 AATAGTGTTCCCATCATTTTAAATGCATGATTAATGGTGTTCCCACCTTTTTAAATTCCACATAT
14613 GCTAATCTATTGACTATTAGGCTTCATGAGGATTCAGTAATTTTAAATGTTGCTCAAGGCTTTTT
260 GCTAATCTATTGACTATTAGGCTTCATGAGGATTCAGTAATTTTAAATGTTGCTCAAGGCTTTTT
*
14678 CCTTCTTCAACCCATTTTTCCAGTCCATTTTCATTGGGTCCGTTTACGGTTTGCATCAGAAATAT
325 CCTTCTTCAACCCATTTTCCCAGTCCATTTTCATTGGGTCCGTTTACGGTTTGCATCAGAAATAT
14743 TCAGTTTACAGTTAGTACGACCTCTATGATGTTATTCTTTGATGATTGAGTGTGTTGGGTTATTA
390 TCAGTTTACAGTTAGTACGACCTCTATGATGTTATTCTTTGATGATTGAGTGTGTTGGGTTATTA
14808 GACTAAATTGCATTTTCTGAAATTATTAACATACTAAGTGCGCTTTTTATAGACCCTGTTAATTG
455 GACTAAATTGCATTTTCTGAAATTATTAACATACTAAGTGCGCTTTTTATAGACCCTGTTAATTG
14873 TTTTTCAAGATGGTGCTTACTGAAAGTTCCTTTCAACTTTTCACCTGGGACAACATTTTCGTCCC
520 TTTTTCAAGATGGTGCTTACTGAAAGTTCCTTTCAACTTTTCACCTGGGACAACATTTTCGTCCC
*
14938 GTTTGGTCTTTTCTCCATTTATTAATTACTAATCCTTATGTTCTATATCGATCTATTTTATTACC
585 GTTTGGTCTTTTCTCCATTTACTAATTACTAATCCTTATGTTCTATATCGATCTATTTTATTACC
15003 TAAAATGACCCTTGTGCTGCATTCTCTGATGCTTTGCTTGGTTGGGCTATTACAATAATTTGAAA
650 TAAAATGACCCTTGTGCTGCATTCTCTGATGCTTTGCTTGGTTGGGCTATTACAATAATTTGAAA
15068 TTCCC
715 TTCCC
15073 ATTACTATATATTATTTTTGTC-CCTTATGGAATTTACTCACAGGTCCTTTTAACTTTTAACCTG
1 ATTACTATATATTATTTTTGTCTCC-TATGGAATTTACTCACAGGTCCTTTTAACTTTTAACCTG
15137 AAACAACCTTATCGCCCCATTTTGGTCTTTTTGCAAATGGCTTATTACTTT-AAAAAA-TCCTTT
65 AAACAACCTTATCGCCCCATTTTGGTCTTTTTGCAAATGGCTTATTACTTTAAAAAAATTCCTTT
15200 TAATCTTAATCCTTTTTCTAAAAATACAATGTCTTTTTATGTAATTTTAGAATCTAACTTCAATT
130 TAATCTTAATCCTTTTTCTAAAAATACAATGTCTTTTTATGTAATTTTAGAATCTAACTTCAATT
*
15265 AATAGTGTTCCCATCATTTTAAATGCATGATTCAT-G-GTTCCCACCTTTTTAAATTCCACATAT
195 AATAGTGTTCCCATCATTTTAAATGCATGATTAATGGTGTTCCCACCTTTTTAAATTCCACATAT
15328 GCTAATCTATTGACTATTAGGCTTCATGAGGATTCAGTAATTTTAAATGTTGCTCAAGGCTTTTT
260 GCTAATCTATTGACTATTAGGCTTCATGAGGATTCAGTAATTTTAAATGTTGCTCAAGGCTTTTT
15393 CCTTCTTCAACCCATTTTCCCAGTCCATTTTCATTGGGTCCGTTTACGGTTTGCA-CAGAAATAT
325 CCTTCTTCAACCCATTTTCCCAGTCCATTTTCATTGGGTCCGTTTACGGTTTGCATCAGAAATAT
15457 TCAGTTTACAGTTAGTACGACCTCTATGATG-TATTCTTTGATGATTGAGTGTGTTGGGTTATTA
390 TCAGTTTACAGTTAGTACGACCTCTATGATGTTATTCTTTGATGATTGAGTGTGTTGGGTTATTA
* *
15521 GAGTAAATTGCATTTTCTGAAATTATTAACATACTAAGTGCGCTTTTTATAGACTCTGTTAATTG
455 GACTAAATTGCATTTTCTGAAATTATTAACATACTAAGTGCGCTTTTTATAGACCCTGTTAATTG
15586 TTTTTCAAGATGGTGCTTACTGAAAGTTCCTTTCAACTTTTCACCTGGGACAACATTTTCGTCCC
520 TTTTTCAAGATGGTGCTTACTGAAAGTTCCTTTCAACTTTTCACCTGGGACAACATTTTCGTCCC
15651 GTTTGGTCTTTTCTCCATTTACTAATTACTAATCCTTATGTTCTATATCGATCTATTTTATTACC
585 GTTTGGTCTTTTCTCCATTTACTAATTACTAATCCTTATGTTCTATATCGATCTATTTTATTACC
*
15716 TAAAATGACCTTTGTGCTGCATTCTCTGATGCTTTGCTTGGTTGGGCTATTACAATAATTTGAAA
650 TAAAATGACCCTTGTGCTGCATTCTCTGATGCTTTGCTTGGTTGGGCTATTACAATAATTTGAAA
15781 TTCCC
715 TTCCC
15786 TTTAATTATT
Statistics
Matches: 705, Mismatches: 7, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
713 294 0.42
714 40 0.06
715 145 0.21
716 1 0.00
717 105 0.15
718 6 0.01
719 2 0.00
720 112 0.16
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (719 bp):
ATTACTATATATTATTTTTGTCTCCTATGGAATTTACTCACAGGTCCTTTTAACTTTTAACCTGA
AACAACCTTATCGCCCCATTTTGGTCTTTTTGCAAATGGCTTATTACTTTAAAAAAATTCCTTTT
AATCTTAATCCTTTTTCTAAAAATACAATGTCTTTTTATGTAATTTTAGAATCTAACTTCAATTA
ATAGTGTTCCCATCATTTTAAATGCATGATTAATGGTGTTCCCACCTTTTTAAATTCCACATATG
CTAATCTATTGACTATTAGGCTTCATGAGGATTCAGTAATTTTAAATGTTGCTCAAGGCTTTTTC
CTTCTTCAACCCATTTTCCCAGTCCATTTTCATTGGGTCCGTTTACGGTTTGCATCAGAAATATT
CAGTTTACAGTTAGTACGACCTCTATGATGTTATTCTTTGATGATTGAGTGTGTTGGGTTATTAG
ACTAAATTGCATTTTCTGAAATTATTAACATACTAAGTGCGCTTTTTATAGACCCTGTTAATTGT
TTTTCAAGATGGTGCTTACTGAAAGTTCCTTTCAACTTTTCACCTGGGACAACATTTTCGTCCCG
TTTGGTCTTTTCTCCATTTACTAATTACTAATCCTTATGTTCTATATCGATCTATTTTATTACCT
AAAATGACCCTTGTGCTGCATTCTCTGATGCTTTGCTTGGTTGGGCTATTACAATAATTTGAAAT
TCCC
Found at i:16146 original size:53 final size:52
Alignment explanation
Indices: 16080--16183 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 52
16070 GGTCTTTGTA
16080 GAGATTATTTTATGATTCT-ATAAATTGTTTAGGG-AAAAAAAATAAAAAGAC
1 GAGATTATTTTATGATTCTAAT-AATTGTTTAGGGAAAAAAAAATAAAAAGAC
* *
16131 GAGATTAATTTTTATGGTTCTAATAATTGTTTNGGGAAAAAAAAAATAAAAAG
1 GAGATT-A-TTTTATGATTCTAATAATTGTTTAGGG-AAAAAAAAATAAAAAG
16184 CGCCTGACGC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
51 6 0.13
52 1 0.02
53 22 0.48
54 2 0.04
55 15 0.33
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.34
Consensus pattern (52 bp):
GAGATTATTTTATGATTCTAATAATTGTTTAGGGAAAAAAAAATAAAAAGAC
Found at i:16229 original size:2 final size:2
Alignment explanation
Indices: 16217--16285 Score: 90
Period size: 2 Copynumber: 36.0 Consensus size: 2
16207 ATCCACTTGT
*
16217 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA GA T- TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
16256 TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16286 AGTGTAGTCC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
1 3 0.05
2 55 0.95
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16259 original size:32 final size:32
Alignment explanation
Indices: 16216--16277 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
16206 TATCCACTTG
*
16216 TTATATTATATATATATATATATATATATAGA
1 TTATATAATATATATATATATATATATATAGA
*
16248 TTATATAATATATATATATATATATGTATA
1 TTATATAATATATATATATATATATATATA
16278 TGTATATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (32 bp):
TTATATAATATATATATATATATATATATAGA
Found at i:16686 original size:2 final size:2
Alignment explanation
Indices: 16681--16709 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16671 CCTCTTCCAC
16681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16710 TAAATATGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18095 original size:12 final size:12
Alignment explanation
Indices: 18078--18120 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
18068 TTAATACAGG
*
18078 TATCGATGGATA
1 TATCGACGGATA
*
18090 TATCGAACAGATA
1 TATCG-ACGGATA
18103 TATCGACGGATA
1 TATCGACGGATA
18115 TATCGA
1 TATCGA
18121 GGTATCGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:19191 original size:3 final size:3
Alignment explanation
Indices: 19183--19222 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
19173 TTCATTTCCC
19183 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA -CA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
19223 TTCCGTGAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:20230 original size:10 final size:10
Alignment explanation
Indices: 20215--20240 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20205 AATTTAATAT
20215 GGATATTTAC
1 GGATATTTAC
20225 GGATATTTAC
1 GGATATTTAC
20235 GGATAT
1 GGATAT
20241 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:34489 original size:26 final size:26
Alignment explanation
Indices: 34454--34504 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
34444 AAGTGTAAAT
34454 AATGGGGCTGCATTGAATTATCCAAA
1 AATGGGGCTGCATTGAATTATCCAAA
34480 AATGGGGCTGCATTGAATTATCCAA
1 AATGGGGCTGCATTGAATTATCCAA
34505 CCTATCACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (26 bp):
AATGGGGCTGCATTGAATTATCCAAA
Found at i:39995 original size:7 final size:7
Alignment explanation
Indices: 39985--40189 Score: 69
Period size: 7 Copynumber: 28.7 Consensus size: 7
39975 TCTTTACTGA
39985 TTACTTT
1 TTACTTT
*
39992 TTACTCT
1 TTACTTT
*
39999 TTACTCT
1 TTACTTT
**
40006 TTACTGA
1 TTACTTT
*
40013 TTACTCT
1 TTACTTT
40020 TTACTATT
1 TTACT-TT
40028 TT--TTCT
1 TTACTT-T
**
40034 TTACTGA
1 TTACTTT
*
40041 TTACTCT
1 TTACTTT
40048 TTACTTT
1 TTACTTT
**
40055 TTACTAA
1 TTACTTT
*
40062 TTACCATT
1 TTA-CTTT
40070 TTACTTT
1 TTACTTT
**
40077 TTACTGA
1 TTACTTT
*
40084 TTACCCTT
1 TTA-CTTT
40092 TTACTCTT
1 TTACT-TT
**
40100 TT-CTAA
1 TTACTTT
*
40106 TTACCATT
1 TTA-CTTT
40114 TTACTTT
1 TTACTTT
* **
40121 TCACTGA
1 TTACTTT
*
40128 TTAC-CT
1 TTACTTT
40134 TTACTTT
1 TTACTTT
**
40141 TTACTGA
1 TTACTTT
*
40148 TTACCATT
1 TTA-CTTT
40156 TTACTTT
1 TTACTTT
*
40163 TTA-TTGA
1 TTACTT-T
40170 TTACATTT
1 TTAC-TTT
40178 TTACTTT
1 TTACTTT
40185 TTACT
1 TTACT
40190 GATTACCATT
Statistics
Matches: 140, Mismatches: 44, Indels: 28
0.66 0.21 0.13
Matches are distributed among these distances:
5 1 0.01
6 12 0.09
7 97 0.69
8 28 0.20
9 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (7 bp):
TTACTTT
Found at i:40007 original size:28 final size:28
Alignment explanation
Indices: 39975--40059 Score: 125
Period size: 28 Copynumber: 3.0 Consensus size: 28
39965 CTATTTTTTT
* *
39975 TCTTTACTGATTACTTTTTACTCTTTAC
1 TCTTTACTGATTACTCTTTACTATTTAC
**
40003 TCTTTACTGATTACTCTTTACTATTTTT
1 TCTTTACTGATTACTCTTTACTATTTAC
*
40031 TCTTTACTGATTACTCTTTACTTTTTAC
1 TCTTTACTGATTACTCTTTACTATTTAC
40059 T
1 T
40060 AATTACCATT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.18, C:0.20, G:0.04, T:0.59
Consensus pattern (28 bp):
TCTTTACTGATTACTCTTTACTATTTAC
Found at i:40065 original size:14 final size:14
Alignment explanation
Indices: 39975--40052 Score: 95
Period size: 14 Copynumber: 5.6 Consensus size: 14
39965 CTATTTTTTT
39975 TCTTTACTGATTAC
1 TCTTTACTGATTAC
* **
39989 TTTTTACTCTTTAC
1 TCTTTACTGATTAC
40003 TCTTTACTGATTAC
1 TCTTTACTGATTAC
**
40017 TCTTTACT-ATTTTT
1 TCTTTACTGA-TTAC
40031 TCTTTACTGATTAC
1 TCTTTACTGATTAC
40045 TCTTTACT
1 TCTTTACT
40053 TTTTACTAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
13 1 0.02
14 50 0.96
15 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.04, T:0.58
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:40075 original size:22 final size:22
Alignment explanation
Indices: 40033--40293 Score: 275
Period size: 22 Copynumber: 12.4 Consensus size: 22
40023 CTATTTTTTC
40033 TTTACTGATTA-C-TCTTTACTT
1 TTTACTGATTACCAT-TTTACTT
*
40054 TTTACTAATTACCATTTTACTT
1 TTTACTGATTACCATTTTACTT
*
40076 TTTACTGATTACCCTTTTACTCT
1 TTTACTGATTACCATTTTACT-T
*
40099 TTT-CTAATTACCATTTTACTT
1 TTTACTGATTACCATTTTACTT
*
40120 TTCACTGATTACC--TTTACTT
1 TTTACTGATTACCATTTTACTT
40140 TTTACTGATTACCATTTTACTT
1 TTTACTGATTACCATTTTACTT
*
40162 TTTATTGATTA-CATTTTTACTT
1 TTTACTGATTACCA-TTTTACTT
40184 TTTACTGATTACCA--TTACTT
1 TTTACTGATTACCATTTTACTT
* * *
40204 CTTACTGATTA-C-TATTACTC
1 TTTACTGATTACCATTTTACTT
40224 TTTACTGATTACCATTTT--TT
1 TTTACTGATTACCATTTTACTT
*
40244 CTTTACTGATTA-CTTTTTAC--
1 -TTTACTGATTACCATTTTACTT
**
40264 TTTACTCTTTACCATTTT-CTT
1 TTTACTGATTACCATTTTACTT
40285 TTTACTGAT
1 TTTACTGAT
40294 CTCTCTTTAC
Statistics
Matches: 201, Mismatches: 21, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
19 11 0.05
20 61 0.30
21 34 0.17
22 88 0.44
23 7 0.03
ACGTcount: A:0.21, C:0.20, G:0.04, T:0.55
Consensus pattern (22 bp):
TTTACTGATTACCATTTTACTT
Found at i:40137 original size:64 final size:64
Alignment explanation
Indices: 40031--40266 Score: 254
Period size: 64 Copynumber: 3.7 Consensus size: 64
40021 TACTATTTTT
* *
40031 TCTTTACTGATTA-C-TCTTTACTTTTTACTAATTACCATTTTACTTTTTACTGATTACCCTTTT
1 TCTTTTCTGATTACCAT-TTTACTTTTTACTGATTACC--TTTACTTTTTACTGATTACCCTTTT
40094 AC
63 AC
* * *
40096 TCTTTTCTAATTACCATTTTACTTTTCACTGATTACCTTTACTTTTTACTGATTACCATTTTAC
1 TCTTTTCTGATTACCATTTTACTTTTTACTGATTACCTTTACTTTTTACTGATTACCCTTTTAC
* * * *
40160 T-TTTTATTGATTA-CATTTTTACTTTTTACTGATTACCATTACTTCTTACTGATTA--CTATTA
1 TCTTTT-CTGATTACCA-TTTTACTTTTTACTGATTACCTTTACTTTTTACTGATTACCCTTTTA
40221 C
64 C
* *
40222 TCTTTACTGATTACCATTTT--TTCTTTACTGATTACTTTTTACTTT
1 TCTTTTCTGATTACCATTTTACTT-TTTACTGATTAC-CTTTACTTT
40267 ACTCTTTACC
Statistics
Matches: 146, Mismatches: 17, Indels: 19
0.80 0.09 0.10
Matches are distributed among these distances:
60 2 0.01
61 12 0.08
62 22 0.15
63 11 0.08
64 68 0.47
65 11 0.08
66 19 0.13
67 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.04, T:0.55
Consensus pattern (64 bp):
TCTTTTCTGATTACCATTTTACTTTTTACTGATTACCTTTACTTTTTACTGATTACCCTTTTAC
Found at i:40415 original size:14 final size:14
Alignment explanation
Indices: 40393--40447 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
40383 TTACCACTTT
*
40393 TCTTCACTGATTAC
1 TCTTTACTGATTAC
*
40407 TCTTTACTGATCAC
1 TCTTTACTGATTAC
**
40421 TGATTACT-ATTAC
1 TCTTTACTGATTAC
*
40434 TC-TTACTAATTAC
1 TCTTTACTGATTAC
40447 T
1 T
40448 ATTACTCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
12 5 0.15
13 11 0.32
14 18 0.53
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.45
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:40461 original size:20 final size:20
Alignment explanation
Indices: 40423--40531 Score: 87
Period size: 22 Copynumber: 5.3 Consensus size: 20
40413 CTGATCACTG
40423 ATTACTATTACTC-TTACTA
1 ATTACTATTACTCTTTACTA
40442 ATTACTATTACTCTTTACTA
1 ATTACTATTACTCTTTACTA
* ** *
40462 ATTACCATTTTTCCTTTTACTG
1 ATTACTATTACT-C-TTTACTA
* * *
40484 ATCA-TCATTACTTTTTACTG
1 ATTACT-ATTACTCTTTACTA
*
40504 ATTACTATTTTACTCTTTTCTA
1 ATTACTA--TTACTCTTTACTA
40526 ATTACT
1 ATTACT
40532 CTGATTATCA
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
19 13 0.19
20 26 0.37
21 2 0.03
22 29 0.41
ACGTcount: A:0.26, C:0.20, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTACTATTACTCTTTACTA
Found at i:43488 original size:20 final size:21
Alignment explanation
Indices: 43450--43489 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
43440 ATTGTTAAAT
43450 TTCATGGTTATATAAGAGAGA
1 TTCATGGTTATATAAGAGAGA
43471 TTCATTGGTT-TA-AAGAGAG
1 TTCA-TGGTTATATAAGAGAG
43490 GTAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (21 bp):
TTCATGGTTATATAAGAGAGA
Found at i:44048 original size:6 final size:6
Alignment explanation
Indices: 44046--44094 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
44036 AAAAAAATGA
* *
44046 AAAAGG AAAAGG AAAAGG AAAA-G AAAA-G AAATGA AAAAGG AAAAGG
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG
44092 AAA
1 AAA
44095 TTAGGAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 9 0.24
6 29 0.76
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (6 bp):
AAAAGG
Found at i:44076 original size:22 final size:23
Alignment explanation
Indices: 44046--44090 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
44036 AAAAAAATGA
*
44046 AAAAGGAAAAGGAAAAGGAAAAG
1 AAAAGGAAAAGAAAAAGGAAAAG
*
44069 AAAA-GAAATGAAAAAGGAAAAG
1 AAAAGGAAAAGAAAAAGGAAAAG
44091 GAAATTAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (23 bp):
AAAAGGAAAAGAAAAAGGAAAAG
Found at i:44083 original size:34 final size:35
Alignment explanation
Indices: 44030--44104 Score: 118
Period size: 34 Copynumber: 2.1 Consensus size: 35
44020 GCAAGAAAAA
44030 AAAATGAAAAAAATGAAAAAGGAAAAGGAAA-AGG
1 AAAATGAAAAAAATGAAAAAGGAAAAGGAAATAGG
44064 AAAA-GAAAAGAAATGAAAAAGGAAAAGGAAATTAGG
1 AAAATGAAAA-AAATGAAAAAGGAAAAGGAAA-TAGG
44100 AAAAT
1 AAAAT
44105 AATAATAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
33 5 0.14
34 25 0.68
36 7 0.19
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (35 bp):
AAAATGAAAAAAATGAAAAAGGAAAAGGAAATAGG
Done.