Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011688.1 Corchorus capsularis cultivar CVL-1 contig11709, 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: 93540
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:965 original size:67 final size:67
Alignment explanation
Indices: 857--991 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
847 CTGGCCAAAA
*
857 ACCGACCGCAGCGACTTGAATGATGCAAACGGTGCAAATGGTTTCTCGGGGTCGGTGGCGGTTCA
1 ACCGACCGCAGCGACTTGAATGATACAAACGGTGCAAATGGTTTCTCGGGGTCGGTGGCGGTTCA
922 CT
66 CT
924 ACCGACCGCAGCGACTTGAATGATACAAACGGTGCAAATGGTTTCTCGGGGTCGGTGGCGGTTCA
1 ACCGACCGCAGCGACTTGAATGATACAAACGGTGCAAATGGTTTCTCGGGGTCGGTGGCGGTTCA
989 CT
66 CT
991 A
1 A
992 ATTAGTGAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.22, C:0.24, G:0.32, T:0.22
Consensus pattern (67 bp):
ACCGACCGCAGCGACTTGAATGATACAAACGGTGCAAATGGTTTCTCGGGGTCGGTGGCGGTTCA
CT
Found at i:8139 original size:2 final size:2
Alignment explanation
Indices: 8132--8171 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
8122 CTCATATTAT
8132 TA TA TA 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 TA TA TA
8172 CACACACTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10582 original size:2 final size:2
Alignment explanation
Indices: 10575--10612 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
10565 TTTTCCAATC
10575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
10613 CATTTATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21744 original size:22 final size:20
Alignment explanation
Indices: 21719--21760 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
21709 GTAAGAATTT
21719 TATT-TTAATATATAATATA
1 TATTATTAATATATAATATA
*
21738 TATTATTAATATGTAATATA
1 TATTATTAATATATAATATA
21758 TAT
1 TAT
21761 CTTTATACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTATTAATATATAATATA
Found at i:21748 original size:20 final size:19
Alignment explanation
Indices: 21719--21765 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
21709 GTAAGAATTT
21719 TATTTTAATATATAATATA
1 TATTTTAATATATAATATA
*
21738 TATTATTAATATGTAATATA
1 TATT-TTAATATATAATATA
21758 TATCTTTA
1 TAT-TTTA
21766 TACTCTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 20 0.80
21 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TATTTTAATATATAATATA
Found at i:21999 original size:18 final size:18
Alignment explanation
Indices: 21950--21999 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
21940 ATTAAACTTC
21950 TTATTA-TTATAATAATAA
1 TTATTAGTTATAA-AATAA
* *
21968 TAATTAG-TAGTAAAATTA
1 TTATTAGTTA-TAAAATAA
21986 TTATTAGTTATAAA
1 TTATTAGTTATAAA
22000 CTTCTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
TTATTAGTTATAAAATAA
Found at i:24837 original size:22 final size:22
Alignment explanation
Indices: 24811--24852 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
24801 GATAATAATC
24811 TACTTTTTAGAATAATCACTTA
1 TACTTTTTAGAATAATCACTTA
24833 TACTTTTTAGAATAATCACT
1 TACTTTTTAGAATAATCACT
24853 GCAGTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (22 bp):
TACTTTTTAGAATAATCACTTA
Found at i:24862 original size:23 final size:22
Alignment explanation
Indices: 24811--24865 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
24801 GATAATAATC
*
24811 TACTTTTTAGAATAATCACTTA
1 TACTTTTTAGAATAATCACTCA
24833 TACTTTTTAGAATAATCACTGCA
1 TACTTTTTAGAATAATCACT-CA
24856 GTA-TTTTTAG
1 -TACTTTTTAG
24866 TAACTTCAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 20 0.67
23 8 0.27
24 2 0.07
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (22 bp):
TACTTTTTAGAATAATCACTCA
Found at i:25150 original size:31 final size:31
Alignment explanation
Indices: 25112--25276 Score: 148
Period size: 31 Copynumber: 5.5 Consensus size: 31
25102 TTGGGCTAAT
* *
25112 TGCTCAAATAAGGGTCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * **
25143 TGCTCAAATAAGGGCCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCCAAAA
25172 TGGCT-AAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * **
25203 TGCTCAAATAAGGGCCCGATC-TTTG--AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGCCAAAA
25232 TGGCT-AAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
25263 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
25277 TCTATCTCAT
Statistics
Matches: 105, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 6 0.06
29 34 0.32
30 12 0.11
31 47 0.45
32 6 0.06
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:25185 original size:60 final size:60
Alignment explanation
Indices: 25117--25276 Score: 284
Period size: 60 Copynumber: 2.7 Consensus size: 60
25107 CTAATTGCTC
* * * *
25117 AAATAAGGGTCTAACGTTTGTCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCT
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGCT
25177 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGCT
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGCT
25237 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
25277 TCTATCTCAT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (60 bp):
AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGCT
Found at i:25347 original size:31 final size:31
Alignment explanation
Indices: 25309--25477 Score: 154
Period size: 31 Copynumber: 5.6 Consensus size: 31
25299 CTGAAACCAA
* *
25309 GCCCTTATTTGAGCATTTTCGATAACGTTAG
1 GCCCTTATTTGAGCATTTTAGATAACATTAG
*
25340 GCCCTTATTTGAGCATTTTAAATAACATTAG
1 GCCCTTATTTGAGCATTTTAGATAACATTAG
** * **
25371 GCCCTTATTTG-GCCAAATTAG--AAGATCGG
1 GCCCTTATTTGAG-CATTTTAGATAACATTAG
*
25400 GCCCTTATTTGAGCA-TTTCGATAACATTAG
1 GCCCTTATTTGAGCATTTTAGATAACATTAG
** * *
25430 GCCCTTATTTG-GCCAAATTA-A-AAGATCAG
1 GCCCTTATTTGAG-CATTTTAGATAACATTAG
25459 GCCCTTATTTGAGCATTTT
1 GCCCTTATTTGAGCATTTT
25478 GGCAAACGTT
Statistics
Matches: 111, Mismatches: 20, Indels: 16
0.76 0.14 0.11
Matches are distributed among these distances:
28 3 0.03
29 40 0.36
30 22 0.20
31 46 0.41
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (31 bp):
GCCCTTATTTGAGCATTTTAGATAACATTAG
Found at i:25468 original size:29 final size:29
Alignment explanation
Indices: 25369--25469 Score: 107
Period size: 29 Copynumber: 3.4 Consensus size: 29
25359 AAATAACATT
*
25369 AGGCCCTTATTTGGCCAAATTAGAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
* * * * *
25398 GGGCCCTTATTTGAG-C-ATTTCGATAACATT
1 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
25428 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
25457 AGGCCCTTATTTG
1 AGGCCCTTATTTG
25470 AGCATTTTGG
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
28 3 0.05
29 32 0.56
30 19 0.33
31 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:25508 original size:59 final size:59
Alignment explanation
Indices: 25338--25478 Score: 237
Period size: 59 Copynumber: 2.4 Consensus size: 59
25328 CGATAACGTT
* *
25338 AGGCCCTTATTTGAGCATTTTAAATAACATTAGGCCCTTATTTGGCCAAATTAGAAGATC
1 AGGCCCTTATTTGAGCATTTT-GATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATC
* *
25398 GGGCCCTTATTTGAGCATTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATC
25457 AGGCCCTTATTTGAGCATTTTG
1 AGGCCCTTATTTGAGCATTTTG
25479 GCAAACGTTA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
59 56 0.75
60 19 0.25
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (59 bp):
AGGCCCTTATTTGAGCATTTTGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:26136 original size:2 final size:2
Alignment explanation
Indices: 26129--26155 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26119 TTACACTACC
26129 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 A
26156 ATGTTTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28995 original size:31 final size:32
Alignment explanation
Indices: 28957--29037 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 32
28947 GTATTGCTGG
*
28957 CGTGGCAATGCCACGTCGGACCAAAATG-CCA
1 CGTGGCAATGCCACGTCAGACCAAAATGTCCA
* * * * **
28988 CGTGGCAAGGCCACATCAGACGAAGATGTTGA
1 CGTGGCAATGCCACGTCAGACCAAAATGTCCA
29020 CGTGGCAATGCCACGTCA
1 CGTGGCAATGCCACGTCA
29038 ACAATATTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.57
32 17 0.43
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.15
Consensus pattern (32 bp):
CGTGGCAATGCCACGTCAGACCAAAATGTCCA
Found at i:29112 original size:29 final size:30
Alignment explanation
Indices: 29077--29156 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
29067 CCTCATATTG
*
29077 CAAGTTTAGGGGGCAAAAAGTCCCAAAT-TA
1 CAAGTTTAGGGGGCAAAAAGT-CAAAATATA
* *
29107 -AAGTTTAGGGGACAAAACGTCAAAATCATA
1 CAAGTTTAGGGGGCAAAAAGTCAAAAT-ATA
*
29137 CAAGTTCAGGGGGCAAAAAG
1 CAAGTTTAGGGGGCAAAAAG
29157 GGCATTAAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
28 5 0.12
29 18 0.44
30 2 0.05
31 16 0.39
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.17
Consensus pattern (30 bp):
CAAGTTTAGGGGGCAAAAAGTCAAAATATA
Found at i:34259 original size:29 final size:29
Alignment explanation
Indices: 34189--34263 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
34179 GTCCTTTCAC
**
34189 CTCTAAAGACAATTCGCCTATCGGCTCAT
1 CTCTAAAGACCCTTCGCCTATCGGCTCAT
*
34218 C-CTATCATG-CCCTTCGCCT-TACGGCTCAT
1 CTCTA--AAGACCCTTCGCCTAT-CGGCTCAT
34247 CTCTAAAGACCCTTCGC
1 CTCTAAAGACCCTTCGC
34264 TTCGGATTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
28 6 0.16
29 26 0.70
30 5 0.14
ACGTcount: A:0.21, C:0.37, G:0.13, T:0.28
Consensus pattern (29 bp):
CTCTAAAGACCCTTCGCCTATCGGCTCAT
Found at i:42244 original size:2 final size:2
Alignment explanation
Indices: 42231--42264 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
42221 GACAAAAATA
42231 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
42265 GGTGACAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42807 original size:18 final size:18
Alignment explanation
Indices: 42786--42821 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42776 TTTTCTTCTC
*
42786 TTTTTTTGAAAAAAATTA
1 TTTTTCTGAAAAAAATTA
*
42804 TTTTTCTGAAAAATATTA
1 TTTTTCTGAAAAAAATTA
42822 ACTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTTCTGAAAAAAATTA
Found at i:45483 original size:2 final size:2
Alignment explanation
Indices: 45448--45473 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45438 TCGTATATTG
45448 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
45474 TTCCATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50409 original size:303 final size:303
Alignment explanation
Indices: 49862--50456 Score: 1127
Period size: 303 Copynumber: 2.0 Consensus size: 303
49852 CAACAGAGTG
49862 TCCTCGAAAGACGCTGGTGTCTCTTACACCACCGAGACATCCACCTCCTGCTCCCCTAGGGCCTT
1 TCCTCGAAAGACGCTGGTGTCTCTTACACCACCGAGACATCCACCTCCTGCTCCCCTAGGGCCTT
49927 AATCTTCTTCGTCTTATGTTCGAGATAATCAGTTTTCTCCATCGTGAGCAACTCACTTTGAGTGA
66 AATCTTCTTCGTCTTATGTTCGAGATAATCAGTTTTCTCCATCGTGAGCAACTCACTTTGAGTGA
49992 GAGCAAACCATTGCCAACAATATCTTATCGTGGGAACAATAGGGTATTCCGAAATGATTGCTTAA
131 GAGCAAACCATTGCCAACAATATCTTATCGTGGGAACAATAGGGTATTCCGAAATGATTGCTTAA
*
50057 GGCAAGAAGGTTAAAATTAAGTCCAACTTAATGTTGTAATTGTGTCTAATTTTGAAAGGAATGTG
196 GGCAAGAAGGTTAAAATTAAGTCCAACTTAATGTTGCAATTGTGTCTAATTTTGAAAGGAATGTG
*
50122 TTATGATCAACATTTTTACTACTGTTCATGATCCTTAGTATTT
261 TTATGATCAACATTTATACTACTGTTCATGATCCTTAGTATTT
*
50165 TCCTCGAAAGACGCTGGTGTCTCTTACACCACCGAGACATCCACCTCGTGCTCCCCTAGGGCCTT
1 TCCTCGAAAGACGCTGGTGTCTCTTACACCACCGAGACATCCACCTCCTGCTCCCCTAGGGCCTT
*
50230 AATCTTCTTCGTCTTATGTTCGAGATAATTAGTTTTCTCCATCGTGAGCAACTCACTTTGAGTGA
66 AATCTTCTTCGTCTTATGTTCGAGATAATCAGTTTTCTCCATCGTGAGCAACTCACTTTGAGTGA
*
50295 GAGCAAACCATTGCCAACAATATCTTATCGTGGGAACAATAGGGTATTCTGAAATGATTGCTTAA
131 GAGCAAACCATTGCCAACAATATCTTATCGTGGGAACAATAGGGTATTCCGAAATGATTGCTTAA
* *
50360 GGCAAGAAGGTTAAAATTATGTCCAATTTAATGTTGCAATTGTGTCTAATTTTGAAAGGAATGTG
196 GGCAAGAAGGTTAAAATTAAGTCCAACTTAATGTTGCAATTGTGTCTAATTTTGAAAGGAATGTG
50425 TTATGATCAACATTTATACTACTGTTCATGAT
261 TTATGATCAACATTTATACTACTGTTCATGAT
50457 GTAGTTTCTC
Statistics
Matches: 285, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
303 285 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (303 bp):
TCCTCGAAAGACGCTGGTGTCTCTTACACCACCGAGACATCCACCTCCTGCTCCCCTAGGGCCTT
AATCTTCTTCGTCTTATGTTCGAGATAATCAGTTTTCTCCATCGTGAGCAACTCACTTTGAGTGA
GAGCAAACCATTGCCAACAATATCTTATCGTGGGAACAATAGGGTATTCCGAAATGATTGCTTAA
GGCAAGAAGGTTAAAATTAAGTCCAACTTAATGTTGCAATTGTGTCTAATTTTGAAAGGAATGTG
TTATGATCAACATTTATACTACTGTTCATGATCCTTAGTATTT
Found at i:55231 original size:27 final size:27
Alignment explanation
Indices: 55201--55253 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
55191 GATGCAGAAT
*
55201 ATCTGACTTTTGAAATTAGAAGTAGAC
1 ATCTCACTTTTGAAATTAGAAGTAGAC
55228 ATCTCACTTTTGAAATTAGAAGTAGA
1 ATCTCACTTTTGAAATTAGAAGTAGA
55254 ATTTAGCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (27 bp):
ATCTCACTTTTGAAATTAGAAGTAGAC
Found at i:57322 original size:6 final size:6
Alignment explanation
Indices: 57311--57336 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
57301 AAGTTGTGAT
57311 TTTGGA TTTGGA TTTGGA TTTGGA TT
1 TTTGGA TTTGGA TTTGGA TTTGGA TT
57337 CCATAGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (6 bp):
TTTGGA
Found at i:58070 original size:3 final size:3
Alignment explanation
Indices: 58062--58095 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
58052 CACGGACTTG
58062 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGCA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA
58096 TTGGGATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:68009 original size:2 final size:2
Alignment explanation
Indices: 68002--68043 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
67992 TGACATCAAC
68002 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68042 AT
1 AT
68044 GGGGATCTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:70024 original size:50 final size:50
Alignment explanation
Indices: 69965--70063 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
69955 ACTTTATGTG
* * *
69965 AAACAGTGTTGTCAAATCC-GGACTGGATCGGTCGGGTGACCGGTTCAACT
1 AAACAGTGTTGTCAAA-CCTGGACCGGATCGGTCGAGTAACCGGTTCAACT
*
70015 AAACAGTGTTGTCAAACCTGGACCGGATCGGTCGAGTAATCGGTTCAAC
1 AAACAGTGTTGTCAAACCTGGACCGGATCGGTCGAGTAACCGGTTCAAC
70064 CGGAACCCGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 2 0.05
50 42 0.95
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
AAACAGTGTTGTCAAACCTGGACCGGATCGGTCGAGTAACCGGTTCAACT
Found at i:73591 original size:12 final size:12
Alignment explanation
Indices: 73574--73604 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
73564 TACTAAACCA
73574 ATCCTCCTCAAT
1 ATCCTCCTCAAT
*
73586 ATCCTCTTCAAT
1 ATCCTCCTCAAT
73598 ATCCTCC
1 ATCCTCC
73605 AAAACTCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (12 bp):
ATCCTCCTCAAT
Found at i:75565 original size:20 final size:21
Alignment explanation
Indices: 75521--75565 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
75511 GTGCAAAATA
*
75521 TCAAGCTCCACGCTTTTTCTC
1 TCAAGCTCCACGCTTTTTATC
*
75542 TCAAGCTCCATGCTTTTTAT-
1 TCAAGCTCCACGCTTTTTATC
75562 TCAA
1 TCAA
75566 ACTCTCTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (21 bp):
TCAAGCTCCACGCTTTTTATC
Found at i:78764 original size:16 final size:16
Alignment explanation
Indices: 78743--78777 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
78733 ACAATTCAGA
78743 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
78759 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
78775 AAG
1 AAG
78778 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:80752 original size:67 final size:66
Alignment explanation
Indices: 80633--80782 Score: 194
Period size: 67 Copynumber: 2.2 Consensus size: 66
80623 TCACTCAACC
* * *
80633 CAAAAAAAAAAAAATAGCTCGCTAAGTTGAAAATCTTGTAAACGACGACTTAGGCAAAAGC-TAA
1 CAAAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAACGACGACTTAGGCAAAA-CTTAA
80697 AG
65 AG
* * * *
80699 CAAAAAAAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGGACGGCTTAGGTAAAACTTAG
1 CAAAAAAAAAAAAAAA-GCTCGCTAAGTTGAAAATCCTGCAAACGACGACTTAGGCAAAACTTAA
80764 AG
65 AG
*
80766 CACAAAGAAAAAAAAAA
1 CA-AAAAAAAAAAAAAA
80783 CAATGAACTA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 16 0.22
67 44 0.60
68 13 0.18
ACGTcount: A:0.53, C:0.15, G:0.17, T:0.15
Consensus pattern (66 bp):
CAAAAAAAAAAAAAAAGCTCGCTAAGTTGAAAATCCTGCAAACGACGACTTAGGCAAAACTTAAA
G
Found at i:81554 original size:16 final size:16
Alignment explanation
Indices: 81533--81567 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
81523 ACAATTCAGA
81533 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
*
81549 AAGCAGAAAAGCTTTG
1 AAGCAGAAAAGCTCTG
81565 AAG
1 AAG
81568 TATTTCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.26, T:0.14
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:91478 original size:31 final size:31
Alignment explanation
Indices: 91443--91508 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 31
91433 AACTTTATGT
91443 TTTCCAATTGTACCCTTATTTT-TAAAACATA
1 TTTCCAATTGTACCCTT-TTTTCTAAAACATA
91474 TTTCCAATTGTACCCTTTTTTCTAAAACATA
1 TTTCCAATTGTACCCTTTTTTCTAAAACATA
91505 TTTC
1 TTTC
91509 TAAATTTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTTTCTAAAACATA
Found at i:92004 original size:22 final size:22
Alignment explanation
Indices: 91974--92188 Score: 144
Period size: 22 Copynumber: 9.9 Consensus size: 22
91964 CACTTTGCAA
91974 ATTATCAAAATTTCATAGTGTG
1 ATTATCAAAATTTCATAGTGTG
* *
91996 ACTATCAAAATTTCATAATGTG
1 ATTATCAAAATTTCATAGTGTG
* *
92018 ATTATCCAAATTTCATAATGTG
1 ATTATCAAAATTTCATAGTGTG
* *
92040 GTTA-CAAAAATTTCATAGAAG-G
1 ATTATC-AAAATTTCATAG-TGTG
* *
92062 -TAATCAAAATTTGAT-GTTGTG
1 ATTATCAAAATTTCATAG-TGTG
* *
92083 CTTATCAAAATTTCATAGTGAG
1 ATTATCAAAATTTCATAGTGTG
*
92105 ATTAACAAAA-TTCTATAG-G-G
1 ATTATCAAAATTTC-ATAGTGTG
* *
92125 AAGTTATCAACA-TTCCTAG-G-G
1 -A-TTATCAAAATTTCATAGTGTG
*
92146 AAGTTATCAAAATTTCATAGTATG
1 -A-TTATCAAAATTTCATAGTGTG
* *
92170 GTTATCCAAATTTCATAGT
1 ATTATCAAAATTTCATAGT
92189 TTACCAAATC
Statistics
Matches: 156, Mismatches: 25, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.02
21 34 0.22
22 116 0.74
23 2 0.01
24 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGTGTG
Found at i:92245 original size:22 final size:22
Alignment explanation
Indices: 92219--92364 Score: 107
Period size: 22 Copynumber: 6.5 Consensus size: 22
92209 CAATTATTGT
92219 GGTTATCAAAATTTTATAGTGA
1 GGTTATCAAAATTTTATAGTGA
* *
92241 AGTTAGCAAAATTAATT-TCATGTAGA
1 GGTTATCAAAATT--TTAT-A-GT-GA
** *
92267 GGTTATCACTATTTTATAGTGT
1 GGTTATCAAAATTTTATAGTGA
* * *
92289 GGTTATCAAAGTTTCATAGTGT
1 GGTTATCAAAATTTTATAGTGA
* *
92311 GGTAATCAAAATTTAATAG-GA
1 GGTTATCAAAATTTTATAGTGA
* *
92332 TGGTTATCGAAATTTTATAGTGT
1 -GGTTATCAAAATTTTATAGTGA
*
92355 GGGTATCAAA
1 GGTTATCAAA
92365 GTTTCACAGG
Statistics
Matches: 95, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
21 1 0.01
22 70 0.74
23 4 0.04
24 6 0.06
25 3 0.03
26 11 0.12
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (22 bp):
GGTTATCAAAATTTTATAGTGA
Found at i:93456 original size:34 final size:35
Alignment explanation
Indices: 93408--93478 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 35
93398 AATAAAAAAG
93408 TATATAATATATATAATATATTTTAAA-ATATATT
1 TATATAATATATATAATATATTTTAAATATATATT
93442 TATAT-ATATAATATAATATATTTTAAATATATATT
1 TATATAATAT-ATATAATATATTTTAAATATATATT
93477 TA
1 TA
93479 GGGATGGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
33 4 0.11
34 22 0.63
35 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TATATAATATATATAATATATTTTAAATATATATT
Found at i:93478 original size:12 final size:12
Alignment explanation
Indices: 93422--93478 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
93412 TAATATATAT
93422 AATATAT-TTTA
1 AATATATATTTA
93433 AA-ATATATTTA
1 AATATATATTTA
* *
93444 TATATATA-ATA
1 AATATATATTTA
93455 TAATATAT-TTTA
1 -AATATATATTTA
93467 AATATATATTTA
1 AATATATATTTA
93479 GGGATGGGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
10 4 0.11
11 16 0.43
12 17 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AATATATATTTA
Done.