Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007221.1 Corchorus capsularis cultivar CVL-1 contig07242, 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: 35078
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Found at i:3035 original size:33 final size:33
Alignment explanation
Indices: 2971--3035 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
2961 ATCGCAAATA
* * **
2971 TTTTTTTATATAAAAATCGGAAAAAGGAAAACT
1 TTTTTTTATAGAAAAAACGGAAAAACAAAAACT
*
3004 TTTTTTTTTAGAAAAAACGGAAAAACAAAAAC
1 TTTTTTTATAGAAAAAACGGAAAAACAAAAAC
3036 AAAAAAACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.31
Consensus pattern (33 bp):
TTTTTTTATAGAAAAAACGGAAAAACAAAAACT
Found at i:3332 original size:6 final size:6
Alignment explanation
Indices: 3323--3361 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
3313 AAAGCAAAGC
3323 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT AAA
3362 GCAGATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:13345 original size:137 final size:137
Alignment explanation
Indices: 13085--13336 Score: 504
Period size: 137 Copynumber: 1.8 Consensus size: 137
13075 GCATTTTAGA
13085 ATTAAGGCAATCACATCATATATTTCCTTAATTTCATGCATATCATCACATCATTTGACAGTTTG
1 ATTAAGGCAATCACATCATATATTTCCTTAATTTCATGCATATCATCACATCATTTGACAGTTTG
13150 TTGACTTAGATTTTGCATGAATAAGGTTTGCATCTTTACTAGTTTACATGAATTTCATGCATATA
66 TTGACTTAGATTTTGCATGAATAAGGTTTGCATCTTTACTAGTTTACATGAATTTCATGCATATA
13215 TTTCATG
131 TTTCATG
13222 ATTAAGGCAATCACATCATATATTTCCTTAATTTCATGCATATCATCACATCATTTGACAGTTTG
1 ATTAAGGCAATCACATCATATATTTCCTTAATTTCATGCATATCATCACATCATTTGACAGTTTG
13287 TTGACTTAGATTTTGCATGAATAAGGTTTGCATCTTTACTAGTTTACATG
66 TTGACTTAGATTTTGCATGAATAAGGTTTGCATCTTTACTAGTTTACATG
13337 GGATTCATGG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 115 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (137 bp):
ATTAAGGCAATCACATCATATATTTCCTTAATTTCATGCATATCATCACATCATTTGACAGTTTG
TTGACTTAGATTTTGCATGAATAAGGTTTGCATCTTTACTAGTTTACATGAATTTCATGCATATA
TTTCATG
Found at i:15704 original size:10 final size:10
Alignment explanation
Indices: 15689--15713 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15679 GAGGACTCTA
15689 GAATTTTCTG
1 GAATTTTCTG
15699 GAATTTTCTG
1 GAATTTTCTG
15709 GAATT
1 GAATT
15714 GGGCAGGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:17288 original size:24 final size:24
Alignment explanation
Indices: 17243--17289 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
17233 AATCATTCTT
*
17243 AAAAATTCAAAGCAATCATCAATC
1 AAAAATTCAAAGCAATAATCAATC
*
17267 AAAAA-TCAAATCAATAACTCAAT
1 AAAAATTCAAAGCAATAA-TCAAT
17290 ATAAGCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAAATTCAAAGCAATAATCAATC
Found at i:22595 original size:10 final size:10
Alignment explanation
Indices: 22580--22604 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
22570 GAGGACTCTA
22580 GAATTTTCTG
1 GAATTTTCTG
22590 GAATTTTCTG
1 GAATTTTCTG
22600 GAATT
1 GAATT
22605 GTGCAGGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:23063 original size:40 final size:40
Alignment explanation
Indices: 23006--23097 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
22996 TCTTCAATTG
*
23006 TCTTCAAATCTTCAAAATATCTTCAATCACGAACTTCGCA
1 TCTTCAAATCTTAAAAATATCTTCAATCACGAACTTCGCA
*
23046 TCTTCAAATCTTAAAAATATCTTCAATCACGAAGTTCGCA
1 TCTTCAAATCTTAAAAATATCTTCAATCACGAACTTCGCA
23086 TCTTCAAATCTT
1 TCTTCAAATCTT
23098 CATTCCAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (40 bp):
TCTTCAAATCTTAAAAATATCTTCAATCACGAACTTCGCA
Found at i:24639 original size:51 final size:51
Alignment explanation
Indices: 24579--24752 Score: 217
Period size: 51 Copynumber: 3.4 Consensus size: 51
24569 TTATAGGTTG
24579 ATAATAAAGATTCAATTTTTAAGGTAAAAGGCTTTAGTTTTTGGTTAATCA
1 ATAATAAAGATTCAATTTTTAAGGTAAAAGGCTTTAGTTTTTGGTTAATCA
* * * * **
24630 ATAATAAAGATTCAATTCTTGATGTAAAAGGCTTTAGCTTTTGGTTAGCCA
1 ATAATAAAGATTCAATTTTTAAGGTAAAAGGCTTTAGTTTTTGGTTAATCA
* * *
24681 ATAATAAAGATTCGATTTTT-AGTGTAAAAGGCCTT-GATTTGTGGTTAATCA
1 ATAATAAAGATTCAATTTTTAAG-GTAAAAGGCTTTAG-TTTTTGGTTAATCA
* *
24732 GTAAAAAAGATTCAATTTTTA
1 ATAATAAAGATTCAATTTTTA
24753 GTGTGAAAGA
Statistics
Matches: 103, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
50 2 0.02
51 101 0.98
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (51 bp):
ATAATAAAGATTCAATTTTTAAGGTAAAAGGCTTTAGTTTTTGGTTAATCA
Found at i:24767 original size:102 final size:102
Alignment explanation
Indices: 24579--24767 Score: 258
Period size: 102 Copynumber: 1.9 Consensus size: 102
24569 TTATAGGTTG
* * *
24579 ATAATAAAGATTCAATTTTTAAGGTAAAAGGCTTTAGTTTTTGGTTAATCAATAATAAAGATTCA
1 ATAATAAAGATTCAATTTTTAAGGTAAAAGGCTTGAGTTTGTGGTTAATCAATAAAAAAGATTCA
*
24644 ATTCTTGATGTAAAAGGCTTTAGCTTTTGGTTAGCCA
66 ATTCTTGATGTAAAAGACTTTAGCTTTTGGTTAGCCA
* *
24681 ATAATAAAGATTCGATTTTT-AGTGTAAAAGGCCTTGA-TTTGTGGTTAATCAGTAAAAAAGATT
1 ATAATAAAGATTCAATTTTTAAG-GTAAAAGG-CTTGAGTTTGTGGTTAATCAATAAAAAAGATT
* *
24744 CAATT-TTTAGTGTGAAAGACTTTA
64 CAATTCTTGA-TGTAAAAGACTTTA
24768 ATTTTGGGGT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
101 5 0.07
102 67 0.88
103 4 0.05
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (102 bp):
ATAATAAAGATTCAATTTTTAAGGTAAAAGGCTTGAGTTTGTGGTTAATCAATAAAAAAGATTCA
ATTCTTGATGTAAAAGACTTTAGCTTTTGGTTAGCCA
Found at i:25731 original size:46 final size:44
Alignment explanation
Indices: 25572--25824 Score: 209
Period size: 46 Copynumber: 5.7 Consensus size: 44
25562 AATTTTCGGT
* **
25572 TTTGCCCTT-CCCAGTCAGAAGGTGTTGTCTAGTTGTCAAATTCCTAG
1 TTTGCCCTTCCCCA-TCGGAAGGTGTTGT-TAGTTGTC-TTTTCC-AG
* * * *
25619 TTTGTCCTTCCCCACCGAAAGGTGTTGTCTAGTTGTCATTTCC-G
1 TTTGCCCTTCCCCATCGGAAGGTGTTGT-TAGTTGTCTTTTCCAG
** * ** *
25663 ATTCACCCTTCCCCA-CTAGAAGGTACTGCTTAGTTGTCTTATTCTAG
1 -TTTGCCCTTCCCCATC-GGAAGGTGTTG-TTAGTTGTCTT-TTCCAG
25710 TTTGCCCTTCCCCATCGGAAGGTGTTGTTCAGTTG-CTTTTTCCCAG
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTT-AGTTGTC-TTTT-CCAG
25756 TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTT-TC----CCAG
1 TTTGCCCTTCCCCATCGGAAGGTGTTG-TTAGTTGTCTTTTCCAG
25796 TTTGCCCTTCCCCATCGGAAGGTGTTGTT
1 TTTGCCCTTCCCCATCGGAAGGTGTTGTT
25825 TACATTCCTA
Statistics
Matches: 174, Mismatches: 20, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
39 2 0.01
40 31 0.18
44 2 0.01
45 32 0.18
46 71 0.41
47 32 0.18
48 4 0.02
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.38
Consensus pattern (44 bp):
TTTGCCCTTCCCCATCGGAAGGTGTTGTTAGTTGTCTTTTCCAG
Found at i:25803 original size:40 final size:40
Alignment explanation
Indices: 25748--25862 Score: 178
Period size: 40 Copynumber: 2.9 Consensus size: 40
25738 TCAGTTGCTT
*
25748 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAG
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAC
25788 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAC
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAC
* * *
25828 ATTCCTAGTTTGCCCTTCCCCA-CTAGAAGGTGTTG
1 TTTCCCAGTTTGCCCTTCCCCATC-GGAAGGTGTTG
25863 CTTAAATTCA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
39 1 0.01
40 69 0.99
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.37
Consensus pattern (40 bp):
TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAC
Found at i:25975 original size:49 final size:49
Alignment explanation
Indices: 25921--26788 Score: 541
Period size: 50 Copynumber: 17.6 Consensus size: 49
25911 TCTTGTTCCC
* * *
25921 AAAATGCCCCTTCCCAGTCGGAAGGTCACAGCCTTCTTTACTTATTGTA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATTCTA
* * * * *
25970 AAAATGCCCATTCCCGATCGAAAGGTCACGGTCTTCTTTACTTATTGTA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATTCTA
* * **
26019 AAAATGCCCCTTCCCGGTCGGAAGGTAACGGTCTTCTTCCCTTATTCTA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATTCTA
* *
26068 AAAATGCCCATTCCCGGTCGGAAGGTCACGGTCTTC-TTACCTTATTCTA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTA-CTTATTCTA
* ** *
26117 AAAATGCCCCTTCCCGGTCGGAAGGTCACGGTCTTCTTCCCTTATTCCA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATTCTA
* ** * * * *
26166 AAAATACCTATTCCCAGTCGGAAGGTCATAGT-TCTCTTTTA-TTGTTCCA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCT-TC-TTTACTTATTCTA
* * * **
26215 AAAATGCCCCTTCCCAGTCGAAAGGTCACAGTTTTCTACACTTATTCCT-
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATT-CTA
* * * *
26264 AAAA-GCCCCTTCCCGGTCGGAAGTTCATAGTCTTCTTTATTTATTC-C
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATTCTA
* * * * * * * *
26311 AAAATGCCCCTTCTCGGTCGGAAGGTCCCCGTTTTATTTATTTGTTTCCA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTT-ATTCTA
** * * * * * * * *
26361 AAAATGCCCCTTCCTTGTTGGAAGGTCCCTGTTTTATTTATTTGTTTCCA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTT-ATTCTA
* * * * * * * *
26411 AAAATGCCCCTTCCTGGTCGAAAGGTCCCTGGT-TTATTTATTTGTTTTCA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCAC-AGTCTTCTTTACTTATTCT-A
* * * * **
26461 AAAATGCCCCTTCCCGGTCGGAAGGTC-CATGTTTTCTTAATTTGTTTTCCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACA-GTCTTCTTTA-CT-TATTCTA
** * * * * * * * *
26512 AAAATGCCCCTTCCTAGTGGGAAGGTCCCTGTTTTATTTATTTGTTTCCA
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTT-ATTCTA
* * * * * * **
26562 AAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTATTTATTTCCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTA-TTCTA
* * * * **
26612 AAAATGCCCCTTCCCGGTCGGAAGGTCCCTGT-TCTCTTTATTTGTTTCCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCT-TCTTTACTT-ATTCTA
* * **
26662 AAAATGCCCCTTCCCGGTCGGAAGGTC-CATGTTTTCTTTATTTATTTCCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACA-GTCTTCTTTACTTA-TTCTA
* * * * * * * ** * **
26712 AAAATGCCCCTTCCTGATTGGCAGGTCCCTGTTTTCTTTGTTTGTTTCCC
1 AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTT-ATTCTA
*
26762 AAAATGCCCCTTCCTGGTCGGAAGGTC
1 AAAATGCCCCTTCCCGGTCGGAAGGTC
26789 CCTATTTTTC
Statistics
Matches: 688, Mismatches: 104, Indels: 53
0.81 0.12 0.06
Matches are distributed among these distances:
47 5 0.01
48 68 0.10
49 254 0.37
50 319 0.46
51 38 0.06
52 4 0.01
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (49 bp):
AAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTATTCTA
Found at i:26093 original size:98 final size:98
Alignment explanation
Indices: 25916--26725 Score: 542
Period size: 98 Copynumber: 8.2 Consensus size: 98
25906 GCTCTTCTTG
* * * * *
25916 TTCCCAAAATGCCCCTTCCCAGTCGGAAGGTCACAGCCTTCTTTACTTATTGTAAAAATGCCCAT
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTCACTTATTCTAAAAATGCCCAT
* * *
25981 TCCCGATCGAAAGGTCACGGTCTTCTTTACTTA
66 TCCCGGTCGGAAGGTCACAGTCTTCTTTACTTA
** * * *
26014 TTGTAAAAATGCCCCTTCCCGGTCGGAAGGTAACGGTCTTCTTCCCTTATTCTAAAAATGCCCAT
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTCACTTATTCTAAAAATGCCCAT
*
26079 TCCCGGTCGGAAGGTCACGGTCTTC-TTACCTTA
66 TCCCGGTCGGAAGGTCACAGTCTTCTTTA-CTTA
* * * * * *
26112 TTCTAAAAATGCCCCTTCCCGGTCGGAAGGTCACGGTCTTCTTCCCTTATTCCAAAAATACCTAT
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTCACTTATTCTAAAAATGCCCAT
* * *
26177 TCCCAGTCGGAAGGTCATAGT-TCTCTTTTA-TTG
66 TCCCGGTCGGAAGGTCACAGTCT-TC-TTTACTTA
* * * * *
26210 TTCCAAAAATGCCCCTTCCCAGTCGAAAGGTCACAGTTTTCTACACTTATTCCT-AAAA-GCCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTCACTTATT-CTAAAAATGCCCA
* * *
26273 TTCCCGGTCGGAAGTTCATAGTCTTCTTTATTTA
65 TTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTA
* * * * * * * * * *
26307 TTCC-AAAATGCCCCTTCTCGGTCGGAAGGTCCCCGTTTTATTTATTTGTTTCCAAAAATGCCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTCACTT-ATTCTAAAAATGCCCA
** * * * * * * *
26371 TTCCTTGTTGGAAGGTCCCTGTTTTATTTATTTGT
65 TTCCCGGTCGGAAGGTCACAGTCTTCTTTACTT-A
* * * * * * * * *
26406 TTCCAAAAATGCCCCTTCCTGGTCGAAAGGTCCCTGGT-TTATTTATTTGTTTTCAAAAATGCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCAC-AGTCTTCTTCACTTATTCT-AAAAATGCCC
* * * * *
26470 CTTCCCGGTCGGAAGGTC-CATGTTTTCTTAATTTGTT
64 ATTCCCGGTCGGAAGGTCACA-GTCTTCTTTA-CT-TA
* ** * * * * * * * * * *
26507 TTCCCAAAATGCCCCTTCCTAGTGGGAAGGTCCCTGTTTTATTTATTTGTTTCCAAAAATGCCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTCACTT-ATTCTAAAAATGCCCA
* * * * * *
26572 TTCCTGGTTGGAAGGTCCCTGTTTTCTTTATTTA
65 TTCCCGGTCGGAAGGTCACAGTCTTCTTTACTTA
* * * * * * **
26606 TTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGT-TCTCTTTATTTGTTTCCCAAAATGCC
1 -TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCT-TCTTCACTT-ATTCTAAAAATGCC
* * *
26670 CCTTCCCGGTCGGAAGGTC-CATGTTTTCTTTATTTA
63 CATTCCCGGTCGGAAGGTCACA-GTCTTCTTTACTTA
*
26706 TTTCCCAAAATGCCCCTTCC
1 -TTCCAAAAATGCCCCTTCC
26726 TGATTGGCAG
Statistics
Matches: 599, Mismatches: 90, Indels: 44
0.82 0.12 0.06
Matches are distributed among these distances:
96 39 0.07
97 40 0.07
98 242 0.40
99 11 0.02
100 183 0.31
101 80 0.13
102 4 0.01
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (98 bp):
TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTCACTTATTCTAAAAATGCCCAT
TCCCGGTCGGAAGGTCACAGTCTTCTTTACTTA
Found at i:26188 original size:147 final size:147
Alignment explanation
Indices: 25916--26337 Score: 453
Period size: 147 Copynumber: 2.9 Consensus size: 147
25906 GCTCTTCTTG
* * * *
25916 TTCCCAAAATGCCCCTTCCCAGTCGGAAGGTCACAGCCTTCTTTA-CTTATTGTAAAAATGCCCA
1 TTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCACAGTCTTC-TTACCTTATTCTAAAAATGCCCC
* * ** * * *
25980 TTCCCGATCGAAAGGTCACGGTCTTCTTTACTTATTGTAAAAATGCCCCTTCCCGGTCGGAAGGT
65 TTCCCGGTCGGAAGGTCACGGTCTTCTTTACTTATTCCAAAAATACCCATTCCCAGTCGGAAGGT
*
26045 -A-ACGGTCTTCTTCCCTTA
130 CATA-GGTC-TCTTCCATTA
* * * *
26063 TTCTAAAAATGCCCATTCCCGGTCGGAAGGTCACGGTCTTCTTACCTTATTCTAAAAATGCCCCT
1 TTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCACAGTCTTCTTACCTTATTCTAAAAATGCCCCT
** *
26128 TCCCGGTCGGAAGGTCACGGTCTTCTTCCCTTATTCCAAAAATACCTATTCCCAGTCGGAAGGTC
66 TCCCGGTCGGAAGGTCACGGTCTTCTTTACTTATTCCAAAAATACCCATTCCCAGTCGGAAGGTC
* ** *
26193 ATAGTTCTCTTTTATTG
131 ATAGGTCTCTTCCATTA
* *
26210 TTCCAAAAATGCCCCTTCCCAGTCGAAAGGTCACAGTTTTC-TACACTTATTCCT-AAAA-GCCC
1 TTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCACAGTCTTCTTAC-CTTATT-CTAAAAATGCCC
* ** * * * * *
26272 CTTCCCGGTCGGAAGTTCATAGTCTTCTTTATTTATTCC-AAAATGCCCCTTCTCGGTCGGAAGG
64 CTTCCCGGTCGGAAGGTCACGGTCTTCTTTACTTATTCCAAAAATACCCATTCCCAGTCGGAAGG
26336 TC
129 TC
26338 CCCGTTTTAT
Statistics
Matches: 230, Mismatches: 40, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
145 22 0.10
146 43 0.19
147 158 0.69
148 6 0.03
149 1 0.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.32
Consensus pattern (147 bp):
TTCCAAAAATGCCCCTTCCCAGTCGGAAGGTCACAGTCTTCTTACCTTATTCTAAAAATGCCCCT
TCCCGGTCGGAAGGTCACGGTCTTCTTTACTTATTCCAAAAATACCCATTCCCAGTCGGAAGGTC
ATAGGTCTCTTCCATTA
Found at i:26384 original size:50 final size:50
Alignment explanation
Indices: 26203--26840 Score: 736
Period size: 50 Copynumber: 12.8 Consensus size: 50
26193 ATAGTTCTCT
* ** * * *
26203 TTTA-TTG-TTCCAAAAATGCCCCTTCCCAGTCGAAAGGTCACAGTTTTC
1 TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC
** * * * * * * *
26251 TACACTT-ATTCCTAAAA-GCCCCTTCCCGGTCGGAA-GTTCATAGTCTTC
1 TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCT-GTTTTC
* * *
26299 TTTATTT-ATT-CCAAAATGCCCCTT-CTCGGTCGGAAGGTCCCCGTTTTA
1 TTTATTTGTTTCCCAAAATGCCCCTTCCT-GGTCGGAAGGTCCCTGTTTTC
* * * *
26347 TTTATTTGTTTCCAAAAATGCCCCTTCCTTGTTGGAAGGTCCCTGTTTTA
1 TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC
* * * *
26397 TTTATTTGTTTCCAAAAATGCCCCTTCCTGGTCGAAAGGTCCCTGGTTTA
1 TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC
* * * *
26447 TTTATTTGTTTTCAAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTTTC
1 TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC
* * * *
26497 TTAATTTGTTTTCCCAAAATGCCCCTTCCTAGTGGGAAGGTCCCTGTTTTA
1 TTTATTTG-TTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC
* *
26548 TTTATTTGTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTC
1 TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC
* * *
26598 TTTATTTATTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTCTC
1 TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC
* *
26648 TTTATTTGTTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTTTC
1 TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC
* * * *
26698 TTTATTTATTTCCCAAAATGCCCCTTCCTGATTGGCAGGTCCCTGTTTTC
1 TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC
* *
26748 TTTGTTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTATTTTTC
1 TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCT-GTTTTC
*
26799 TTAATTTGTTTCCCAAAATGCCCCTTCCAT-GTCGGAAGGTCC
1 TTTATTTGTTTCCCAAAATGCCCCTTCC-TGGTCGGAAGGTCC
26841 AATTTTCTCT
Statistics
Matches: 508, Mismatches: 70, Indels: 21
0.85 0.12 0.04
Matches are distributed among these distances:
47 8 0.02
48 56 0.11
49 15 0.03
50 341 0.67
51 87 0.17
52 1 0.00
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (50 bp):
TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTTC
Found at i:26548 original size:201 final size:198
Alignment explanation
Indices: 26259--26840 Score: 807
Period size: 201 Copynumber: 2.9 Consensus size: 198
26249 TCTACACTTA
* * * *
26259 TTCCTAAAA-GCCCCTTCCCGGTCGGAA-GTTCATAGTCTTCTTTA-TTTATT-CCAAAATGCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCAT-GTTTTCTTTATTTTTTTCCCAAAATGCCC
* * *
26320 CTTCTCGGTCGGAAGGTCCCCGTTTTATTTATTTGTTTCCAAAAATGCCCCTTCCTTGTTGGAAG
65 CTTC-CTGTCGGAAGGTCCCTGTTTTATTTATTTGTTTCCAAAAATGCCCCTTCCTGGTTGGAAG
* *
26385 GTCCCTGTTTTATTTATTTGTTTCCAAAAATGCCCCTTCCTGGTCGAAAGGTCCCTGGTT-TATT
129 GTCCCTGTTTT-TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCT-GTTCTATT
26449 TATTTGT
192 TATTTGT
* *
26456 TTTCAAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTTTCTTAATTTGTTTTCCCAAAATGCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTTTCTTTATTT-TTTTCCCAAAATGCCC
*
26521 CTTCCTAGTGGGAAGGTCCCTGTTTTATTTATTTGTTTCCAAAAATGCCCCTTCCTGGTTGGAAG
65 CTTCCT-GTCGGAAGGTCCCTGTTTTATTTATTTGTTTCCAAAAATGCCCCTTCCTGGTTGGAAG
* * *
26586 GTCCCTGTTTTCTTTATTTATTTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTCTCTTT
129 GTCCCTGTTTT-TTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTCTATTT
26651 ATTTGT
193 ATTTGT
* *
26657 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTTTCTTTATTTATTTCCCAAAATGCCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTTTCTTTATTTTTTTCCCAAAATGCCCC
* * * * * *
26722 TTCCTGATTGGCAGGTCCCTGTTTTCTTTGTTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGG
66 TTCCTG-TCGGAAGGTCCCTGTTTTATTTATTTGTTTCCAAAAATGCCCCTTCCTGGTTGGAAGG
*
26787 TCCCTATTTTTCTTAATTTGTTTCCCAAAATGCCCCTTCCAT-GTCGGAAGGTCC
130 TCCCTGTTTTT-TT-ATTTGTTTCCCAAAATGCCCCTTCC-TGGTCGGAAGGTCC
26841 AATTTTCTCT
Statistics
Matches: 345, Mismatches: 29, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
197 7 0.02
198 26 0.08
199 9 0.03
200 91 0.26
201 212 0.61
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.39
Consensus pattern (198 bp):
TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCATGTTTTCTTTATTTTTTTCCCAAAATGCCCC
TTCCTGTCGGAAGGTCCCTGTTTTATTTATTTGTTTCCAAAAATGCCCCTTCCTGGTTGGAAGGT
CCCTGTTTTTTTATTTGTTTCCCAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTCTATTTATT
TGT
Found at i:34179 original size:8 final size:9
Alignment explanation
Indices: 34159--34183 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
34149 CCATTACCCT
34159 AAAACAAGA
1 AAAACAAGA
34168 AAAACAAGA
1 AAAACAAGA
34177 AAAACAA
1 AAAACAA
34184 CACAAGATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAACAAGA
Done.