Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013957.1 Corchorus capsularis cultivar CVL-1 contig13978, 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: 52861
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1208 original size:356 final size:357
Alignment explanation
Indices: 554--1214 Score: 1261
Period size: 356 Copynumber: 1.9 Consensus size: 357
544 GAAAAATCTG
554 AGTGTTCAGTTGCATTTGGACAATTCATGGTAATTGAAACTGAAAAAGAGCATGCCAACCTTCCA
1 AGTGTTCAGTTGCATTTGGACAATTCATGGTAATTGAAACTGAAAAAGAGCATGCCAACCTTCCA
619 GAAGTTCAACAAGGTGCAATTATGGCTGGTCTTCAGGCCATGATGCATGATCTAAAAAATCTAGA
66 GAAGTTCAACAAGGTGCAATTATGGCTGGTCTTCAGGCCATGATGCATGATCTAAAAAATCTAGA
*
684 GCAAAAGCTTGAGGCTCATCATACTCAAAAAGAAGAAGGCTTTGGAGAAATAATTAAGAGATTAC
131 GCAAAAGCTTGAGGCTCATCATACTCAAAAAGAAGAAGGCTTTGGAGAAATAATTAAAAGATTAC
*
749 AAGCAATGCCAGGGCGGCAAGAGAATTGGTGGTAAGGCCACTTGTTTTCACCAAGTTCATATAAA
196 AAGCAATGCCAGGGCGGCAAGAGAATTGGTGGTAAGGCCACTTGTTTTCACCAAATTCATATAAA
*
814 GCTTAGTGGACAAAGCCGCCCCAATTACAAATGTGGCTAATATTTAAAAAAAAAACAAACTGAAA
261 ACTTAGTGGACAAAGCCGCCCCAATTACAAATGTGGCTAATATTTAAAAAAAAAACAAACTGAAA
879 AAGAGCTGAAAAAGAAGGTGCAATTATCTAAA
326 AAGAGCTGAAAAAGAAGGTGCAATTATCTAAA
*
911 AGTGTTCAGTTGCATTTGGACAATTCATGGTAATTGGAACTG-AAAAGAGCATGCCAACCTTCCA
1 AGTGTTCAGTTGCATTTGGACAATTCATGGTAATTGAAACTGAAAAAGAGCATGCCAACCTTCCA
*
975 GAAGTTCAATAAGGTGCAATTATGGCTGGTCTTCAGGCCATGATGCATGATCTAAAAAATCTAGA
66 GAAGTTCAACAAGGTGCAATTATGGCTGGTCTTCAGGCCATGATGCATGATCTAAAAAATCTAGA
1040 GCAAAAGCTTGAGGCTCATCATACTCAAAAAGAAGAAGGCTTTGGAGAAATAATTAAAAGATTAC
131 GCAAAAGCTTGAGGCTCATCATACTCAAAAAGAAGAAGGCTTTGGAGAAATAATTAAAAGATTAC
*
1105 AAGCAATGCCAGGGTGGCAAGAGAATTGGTGGTAAGGCCACTTGTTTTCACCAAATTCATATAAA
196 AAGCAATGCCAGGGCGGCAAGAGAATTGGTGGTAAGGCCACTTGTTTTCACCAAATTCATATAAA
1170 ACTTAGTGGACAAAGCCGCCCCAATTACAAATGTGGCTAATATTT
261 ACTTAGTGGACAAAGCCGCCCCAATTACAAATGTGGCTAATATTT
1215 TTTTTTAAAA
Statistics
Matches: 298, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
356 257 0.86
357 41 0.14
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (357 bp):
AGTGTTCAGTTGCATTTGGACAATTCATGGTAATTGAAACTGAAAAAGAGCATGCCAACCTTCCA
GAAGTTCAACAAGGTGCAATTATGGCTGGTCTTCAGGCCATGATGCATGATCTAAAAAATCTAGA
GCAAAAGCTTGAGGCTCATCATACTCAAAAAGAAGAAGGCTTTGGAGAAATAATTAAAAGATTAC
AAGCAATGCCAGGGCGGCAAGAGAATTGGTGGTAAGGCCACTTGTTTTCACCAAATTCATATAAA
ACTTAGTGGACAAAGCCGCCCCAATTACAAATGTGGCTAATATTTAAAAAAAAAACAAACTGAAA
AAGAGCTGAAAAAGAAGGTGCAATTATCTAAA
Found at i:2282 original size:22 final size:22
Alignment explanation
Indices: 2257--2299 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2247 GGGTTAGTAT
*
2257 GTGGCCGTGAGATTCGCCCATG
1 GTGGCCATGAGATTCGCCCATG
* *
2279 GTGGTCATGAGATTCGGCCAT
1 GTGGCCATGAGATTCGCCCAT
2300 CGTTCAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.16, C:0.23, G:0.35, T:0.26
Consensus pattern (22 bp):
GTGGCCATGAGATTCGCCCATG
Found at i:2877 original size:17 final size:17
Alignment explanation
Indices: 2855--2902 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 17
2845 TTTTCTTTTG
*
2855 GACTCTTGTCTACTTTA
1 GACTCTTGTCTACTTAA
*
2872 GACTCTTGTCT-C-CAA
1 GACTCTTGTCTACTTAA
2887 GACTCTTGTCTACTTA
1 GACTCTTGTCTACTTA
2903 CTTGAGACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 12 0.46
16 2 0.08
17 12 0.46
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.42
Consensus pattern (17 bp):
GACTCTTGTCTACTTAA
Found at i:2896 original size:32 final size:35
Alignment explanation
Indices: 2855--2921 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
2845 TTTTCTTTTG
2855 GACTCTTGTCTAC-T-TT-AGACTCTTGTCTCCAA
1 GACTCTTGTCTACTTATTGAGACTCTTGTCTCCAA
2887 GACTCTTGTCTACTTACTTGAGACTCTTGTCTCCA
1 GACTCTTGTCTACTTA-TTGAGACTCTTGTCTCCA
2922 TCATTCCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 13 0.42
33 1 0.03
35 2 0.06
36 15 0.48
ACGTcount: A:0.18, C:0.28, G:0.13, T:0.40
Consensus pattern (35 bp):
GACTCTTGTCTACTTATTGAGACTCTTGTCTCCAA
Found at i:8681 original size:30 final size:30
Alignment explanation
Indices: 8647--8707 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
8637 AAAGTTCGTG
*
8647 ATTGAAGATTTATTGAAG-ATAATTTCAAGA
1 ATTGAAGA-TCATTGAAGAATAATTTCAAGA
*
8677 ATTGAAGATCATTGAAGAATTATTTCAAGA
1 ATTGAAGATCATTGAAGAATAATTTCAAGA
8707 A
1 A
8708 GCAATAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.34
Consensus pattern (30 bp):
ATTGAAGATCATTGAAGAATAATTTCAAGA
Found at i:14896 original size:31 final size:32
Alignment explanation
Indices: 14830--14955 Score: 173
Period size: 32 Copynumber: 4.0 Consensus size: 32
14820 TTGTCGGTGC
** *
14830 CGCCCTCCTGGGGCGGCTATGCCACGGCATGA
1 CGCCCTCCTAAGGCGGCTGTGCCACGGCATGA
**
14862 CGCCCTCCTGGGGCGGCTGTGCCACGG-ATGA
1 CGCCCTCCTAAGGCGGCTGTGCCACGGCATGA
**
14893 CGCCCTCCTAAGGCGGCTGAACCACGGCATGA
1 CGCCCTCCTAAGGCGGCTGTGCCACGGCATGA
*
14925 CGCCCTTCTAAGGCGGCTGTGCCACGGCATG
1 CGCCCTCCTAAGGCGGCTGTGCCACGGCATG
14956 CCATCCCAGA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
31 27 0.32
32 58 0.68
ACGTcount: A:0.14, C:0.37, G:0.33, T:0.16
Consensus pattern (32 bp):
CGCCCTCCTAAGGCGGCTGTGCCACGGCATGA
Found at i:14970 original size:32 final size:32
Alignment explanation
Indices: 14944--15053 Score: 114
Period size: 31 Copynumber: 3.4 Consensus size: 32
14934 AAGGCGGCTG
14944 TGCCACGGCATGCCATCCCAGAAAGGCGGTAA
1 TGCCACGGCATGCCATCCCAGAAAGGCGGTAA
* * * *
14976 TGCCATGGCATGCCGTCCCAG-AGGGTGGTAA
1 TGCCACGGCATGCCATCCCAGAAAGGCGGTAA
* * * * *
15007 TGCCATGGCATGCCGTCCCAGGAGGGCGGCAA
1 TGCCACGGCATGCCATCCCAGAAAGGCGGTAA
*
15039 TCGCCATGGCATGCC
1 T-GCCACGGCATGCC
15054 GCCCTCCTAG
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
31 29 0.41
32 28 0.40
33 13 0.19
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.15
Consensus pattern (32 bp):
TGCCACGGCATGCCATCCCAGAAAGGCGGTAA
Found at i:15009 original size:31 final size:31
Alignment explanation
Indices: 14944--15054 Score: 150
Period size: 32 Copynumber: 3.5 Consensus size: 31
14934 AAGGCGGCTG
* * *
14944 TGCCACGGCATGCCATCCCAGAAAGGCGGTAA
1 TGCCATGGCATGCCGTCCCAG-AGGGCGGTAA
*
14976 TGCCATGGCATGCCGTCCCAGAGGGTGGTAA
1 TGCCATGGCATGCCGTCCCAGAGGGCGGTAA
*
15007 TGCCATGGCATGCCGTCCCAGGAGGGCGGCAA
1 TGCCATGGCATGCCGTCCCA-GAGGGCGGTAA
15039 TCGCCATGGCATGCCG
1 T-GCCATGGCATGCCG
15055 CCCTCCTAGG
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
31 28 0.39
32 29 0.41
33 14 0.20
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.15
Consensus pattern (31 bp):
TGCCATGGCATGCCGTCCCAGAGGGCGGTAA
Found at i:22348 original size:31 final size:31
Alignment explanation
Indices: 22310--22384 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
22300 ATTTTTGGGT
* * * *
22310 ACCCGAACTCGAAATTACCCGAATCCAAACG
1 ACCCGAACCCGAAATGACCCAAACCCAAACG
*
22341 ACCCGAACCCGAAATGACCCAAACCCAAAATG
1 ACCCGAACCCGAAATGACCCAAACCC-AAACG
*
22373 ACCTGAACCCGA
1 ACCCGAACCCGA
22385 TCAACCCGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 22 0.59
32 15 0.41
ACGTcount: A:0.40, C:0.37, G:0.13, T:0.09
Consensus pattern (31 bp):
ACCCGAACCCGAAATGACCCAAACCCAAACG
Found at i:22381 original size:16 final size:16
Alignment explanation
Indices: 22310--22382 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 16
22300 ATTTTTGGGT
* * *
22310 ACCCGAACTCGAAATT
1 ACCCGAACCCAAAATG
* *
22326 ACCCGAATCC-AAACG
1 ACCCGAACCCAAAATG
*
22341 ACCCGAACCCGAAATG
1 ACCCGAACCCAAAATG
*
22357 ACCCAAACCCAAAATG
1 ACCCGAACCCAAAATG
*
22373 ACCTGAACCC
1 ACCCGAACCC
22383 GATCAACCCG
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
15 12 0.26
16 34 0.74
ACGTcount: A:0.40, C:0.38, G:0.12, T:0.10
Consensus pattern (16 bp):
ACCCGAACCCAAAATG
Found at i:23286 original size:340 final size:340
Alignment explanation
Indices: 22666--23348 Score: 1366
Period size: 340 Copynumber: 2.0 Consensus size: 340
22656 ACTTTAATAT
22666 AATATAGTTCATATAAAAAATCAATGCCAATGAATATTTCAATTAATACAATGTATTTATAAGTT
1 AATATAGTTCATATAAAAAATCAATGCCAATGAATATTTCAATTAATACAATGTATTTATAAGTT
22731 ATATAAGTTTAAAGAGGTAAATAAAATGGATTAAATTATATTGTGCAGAGTAGTTCTCAGTGTGT
66 ATATAAGTTTAAAGAGGTAAATAAAATGGATTAAATTATATTGTGCAGAGTAGTTCTCAGTGTGT
22796 AATGCAATTCAATCCCGAAATTCTCACATTTGTTCAAATTAGGGTTTGACAGATTTTAATTTGTT
131 AATGCAATTCAATCCCGAAATTCTCACATTTGTTCAAATTAGGGTTTGACAGATTTTAATTTGTT
22861 TGATTTAAAAGCTTGCATTTTCATAATTTGTTTAATTTAATGTTTAATTAGTTTTAATTTGAAAT
196 TGATTTAAAAGCTTGCATTTTCATAATTTGTTTAATTTAATGTTTAATTAGTTTTAATTTGAAAT
22926 AATTTACAATTAATTTTCATTAATTAGTTTAAATTAGTGTTAAAACATATGCATTACATATTTAA
261 AATTTACAATTAATTTTCATTAATTAGTTTAAATTAGTGTTAAAACATATGCATTACATATTTAA
22991 TTTATGTTAATTTAA
326 TTTATGTTAATTTAA
23006 AATATAGTTCATATAAAAAATCAATGCCAATGAATATTTCAATTAATACAATGTATTTATAAGTT
1 AATATAGTTCATATAAAAAATCAATGCCAATGAATATTTCAATTAATACAATGTATTTATAAGTT
23071 ATATAAGTTTAAAGAGGTAAATAAAATGGATTAAATTATATTGTGCAGAGTAGTTCTCAGTGTGT
66 ATATAAGTTTAAAGAGGTAAATAAAATGGATTAAATTATATTGTGCAGAGTAGTTCTCAGTGTGT
23136 AATGCAATTCAATCCCGAAATTCTCACATTTGTTCAAATTAGGGTTTGACAGATTTTAATTTGTT
131 AATGCAATTCAATCCCGAAATTCTCACATTTGTTCAAATTAGGGTTTGACAGATTTTAATTTGTT
23201 TGATTTAAAAGCTTGCATTTTCATAATTTGTTTAATTTAATGTTTAATTAGTTTTAATTTGAAAT
196 TGATTTAAAAGCTTGCATTTTCATAATTTGTTTAATTTAATGTTTAATTAGTTTTAATTTGAAAT
23266 AATTTACAATTAATTTTCATTAATTAGTTTAAATTAGTGTTAAAACATATGCATTACATATTTAA
261 AATTTACAATTAATTTTCATTAATTAGTTTAAATTAGTGTTAAAACATATGCATTACATATTTAA
23331 TTTATGTTAATTTAA
326 TTTATGTTAATTTAA
23346 AAT
1 AAT
23349 TTAAATGTTG
Statistics
Matches: 343, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
340 343 1.00
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.43
Consensus pattern (340 bp):
AATATAGTTCATATAAAAAATCAATGCCAATGAATATTTCAATTAATACAATGTATTTATAAGTT
ATATAAGTTTAAAGAGGTAAATAAAATGGATTAAATTATATTGTGCAGAGTAGTTCTCAGTGTGT
AATGCAATTCAATCCCGAAATTCTCACATTTGTTCAAATTAGGGTTTGACAGATTTTAATTTGTT
TGATTTAAAAGCTTGCATTTTCATAATTTGTTTAATTTAATGTTTAATTAGTTTTAATTTGAAAT
AATTTACAATTAATTTTCATTAATTAGTTTAAATTAGTGTTAAAACATATGCATTACATATTTAA
TTTATGTTAATTTAA
Found at i:24066 original size:15 final size:17
Alignment explanation
Indices: 24036--24068 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
24026 AAAACGACCT
24036 AACCCAGAATTGACCCG
1 AACCCAGAATTGACCCG
24053 AACCCAG-A-TGACCCG
1 AACCCAGAATTGACCCG
24068 A
1 A
24069 CATTTGAGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.36, C:0.36, G:0.18, T:0.09
Consensus pattern (17 bp):
AACCCAGAATTGACCCG
Found at i:29913 original size:13 final size:13
Alignment explanation
Indices: 29895--29919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29885 CTTGTGCAAA
29895 CAAAAGTTGTTTC
1 CAAAAGTTGTTTC
29908 CAAAAGTTGTTT
1 CAAAAGTTGTTT
29920 ACATTTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (13 bp):
CAAAAGTTGTTTC
Found at i:36167 original size:2 final size:2
Alignment explanation
Indices: 36160--36189 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
36150 ATTTATATGA
36160 AT AT AT AT AT -T 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 A
36190 ATAAATTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36781 original size:3 final size:3
Alignment explanation
Indices: 36775--36806 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
36765 TTTTGAAAAA
36775 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
36807 ATGGAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:37151 original size:16 final size:16
Alignment explanation
Indices: 37130--37160 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37120 TTGAAAAATA
37130 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
37146 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
37161 AATATGTAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:37934 original size:200 final size:197
Alignment explanation
Indices: 37500--38200 Score: 925
Period size: 195 Copynumber: 3.6 Consensus size: 197
37490 CATTATAATA
* * * *
37500 AGGATTATTATACAATACACCGTCAATGTAAATTTTGGACTTCATAAGCGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
* * *
37565 ACATACCCCATTTTATAATTAATTAAATATTTAATATTAATACATATTCTCTAAGGAGACACATG
66 ACAAACCACATTTCATAATTAATTAAATA-TTAATATTAATACATATTC-CTAAGG-GACACATG
** * * * *
37630 TCAA-TCCTTAAACCATGCACGTGCACTCTGCTAAACTCCACTGACGGTATATCGTATAATCTTT
128 TCAACTCCTTAAACCCCGCACGTGCAATCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTT
37694 TTTAT
193 TTTAT
* * * * *
37699 AGGATTATTATGCAATACACTGTTAGGGTAAATTTTGAACTCTATAAGCGGGATAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
*
37764 ACAAACCATATTTCATAATTAATTAAATATTAAATATTAATACATATTACCTAAGAGGACACATG
66 ACAAACCACATTTCATAATTAATTAAATATT-AATATTAATACATATT-CCTAAG-GGACACATG
** * *
37829 TCAACTCCAAAAACCCCGCACGTGCAGTCTACTAAACTCCACTGACGGTGTATTGTATAATTTTT
128 TCAACTCCTTAAACCCCGCACGTGCAATCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTT
37894 TTTAT
193 TTTAT
* * *
37899 ATGATTATTATACAATACACTGTTAGTGTAAATTTTGAACTCCATAAGCGGGTTAAAAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
* * *
37964 ACAAATCATATTTCATAATTAATT-AA-A-TAATATTAATACATATTCCCTAAGGGAATACATGT
66 ACAAACCACATTTCATAATTAATTAAATATTAATATTAATACATATT-CCTAAGGG-ACACATGT
* * *
38026 CAAC-CGTTAAACCCCGCACGTGCAATCTGCTAAACTCCACTGACGGTGTATTGTATAAATTTTC
129 CAACTCCTTAAACCCCGCACGTGCAATCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTT
38090 TTAT
194 TTAT
* * *
38094 AGGATTATTATACAATACGCTGTCAGTGTGAATTTTGAACTCCATAAACGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
* *
38159 ACATACCCCATTTC---A-TAATTAAATAGTTAATATTAATACATA
66 ACAAACCACATTTCATAATTAATTAAATA-TTAATATTAATACATA
38201 GGATACACAT
Statistics
Matches: 445, Mismatches: 48, Indels: 22
0.86 0.09 0.04
Matches are distributed among these distances:
191 5 0.01
192 3 0.01
193 1 0.00
195 143 0.32
196 33 0.07
197 1 0.00
198 3 0.01
199 116 0.26
200 140 0.31
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (197 bp):
AGGATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAGCGGGTTAAGAAGTTGAC
ACAAACCACATTTCATAATTAATTAAATATTAATATTAATACATATTCCTAAGGGACACATGTCA
ACTCCTTAAACCCCGCACGTGCAATCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTTTT
AT
Found at i:38501 original size:72 final size:72
Alignment explanation
Indices: 38420--38563 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
38410 TAACCTATTC
38420 TGAATGAAAAATCAAAATTTATCTTACTCCTTACCTCACAAAAATAAGGTAAACAGATGCCTATA
1 TGAATGAAAAATCAAAATTTATCTTACTCCTTACCTCACAAAAATAAGGTAAACAGATGCCTATA
38485 ATTAATA
66 ATTAATA
38492 TGAATGAAAAATCAAAATTTATCTTACTCCTTACCTCACAAAAATAAGGTAAACAGATGCCTATA
1 TGAATGAAAAATCAAAATTTATCTTACTCCTTACCTCACAAAAATAAGGTAAACAGATGCCTATA
38557 ATTAATA
66 ATTAATA
38564 AGAGTTGGAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (72 bp):
TGAATGAAAAATCAAAATTTATCTTACTCCTTACCTCACAAAAATAAGGTAAACAGATGCCTATA
ATTAATA
Found at i:38795 original size:31 final size:31
Alignment explanation
Indices: 38771--38875 Score: 174
Period size: 31 Copynumber: 3.4 Consensus size: 31
38761 TTCGGACGGG
*
38771 TTCGGGTTCGGGTACTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
*
38802 TTCGGGTTCGGGTATTTTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTA-TTTCGGGTTCGGGTATT
38834 TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
*
38865 TTCGGATTCGG
1 TTCGGGTTCGG
38876 ACTCGGATCG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 40 0.58
32 29 0.42
ACGTcount: A:0.06, C:0.14, G:0.38, T:0.42
Consensus pattern (31 bp):
TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
Found at i:38807 original size:16 final size:16
Alignment explanation
Indices: 38771--38875 Score: 169
Period size: 16 Copynumber: 6.7 Consensus size: 16
38761 TTCGGACGGG
*
38771 TTCGGGTTCGGGTA-C
1 TTCGGGTTCGGGTATT
38786 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
38802 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
38818 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTATT
38834 TTCGGGTTCGGGTA-T
1 TTCGGGTTCGGGTATT
38849 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
38865 TTCGGATTCGG
1 TTCGGGTTCGG
38876 ACTCGGATCG
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
15 29 0.35
16 55 0.65
ACGTcount: A:0.06, C:0.14, G:0.38, T:0.42
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:38826 original size:47 final size:47
Alignment explanation
Indices: 38771--38875 Score: 167
Period size: 47 Copynumber: 2.2 Consensus size: 47
38761 TTCGGACGGG
38771 TTCGGGTTCGGG-TACTTCGGGTTCGGGTATTTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTTACTTCGGGTTCGGGTA-TTTCGGGTTCGGGTATT
**
38818 TTCGGGTTCGGGTTTTTTCGGGTTCGGGTATTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTTACTTCGGGTTCGGGTATTTCGGGTTCGGGTATT
*
38865 TTCGGATTCGG
1 TTCGGGTTCGG
38876 ACTCGGATCG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 39 0.72
48 15 0.28
ACGTcount: A:0.06, C:0.14, G:0.38, T:0.42
Consensus pattern (47 bp):
TTCGGGTTCGGGTTACTTCGGGTTCGGGTATTTCGGGTTCGGGTATT
Found at i:38891 original size:17 final size:17
Alignment explanation
Indices: 38866--38909 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
38856 TCGGGTATTT
*
38866 TCGGATTCGGACTCGGA
1 TCGGGTTCGGACTCGGA
** *
38883 TCGGGTTCGGGTTCGGG
1 TCGGGTTCGGACTCGGA
38900 TCGGGTTCGG
1 TCGGGTTCGG
38910 GTTCACTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.07, C:0.20, G:0.45, T:0.27
Consensus pattern (17 bp):
TCGGGTTCGGACTCGGA
Found at i:38899 original size:6 final size:6
Alignment explanation
Indices: 38883--38913 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
38873 CGGACTCGGA
38883 TCGGGT TCGGGT TCGGG- TCGGGT TCGGGT TC
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TC
38914 ACTTTCGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.00, C:0.19, G:0.48, T:0.32
Consensus pattern (6 bp):
TCGGGT
Found at i:38910 original size:17 final size:17
Alignment explanation
Indices: 38878--38913 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
38868 GGATTCGGAC
38878 TCGGATCGGGTTCGGGT
1 TCGGATCGGGTTCGGGT
*
38895 TCGGGTCGGGTTCGGGT
1 TCGGATCGGGTTCGGGT
38912 TC
1 TC
38914 ACTTTCGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.19, G:0.47, T:0.31
Consensus pattern (17 bp):
TCGGATCGGGTTCGGGT
Found at i:39695 original size:16 final size:17
Alignment explanation
Indices: 39662--39706 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
39652 TATTTTGATC
*
39662 TCGGGCTCGGGTCGGGT
1 TCGGGTTCGGGTCGGGT
39679 TCGGGTTCGGG-CGGGT
1 TCGGGTTCGGGTCGGGT
*
39695 TCAGGTTCGGGT
1 TCGGGTTCGGGT
39707 TGTCTCGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.02, C:0.20, G:0.51, T:0.27
Consensus pattern (17 bp):
TCGGGTTCGGGTCGGGT
Found at i:39717 original size:16 final size:16
Alignment explanation
Indices: 39698--39754 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
39688 GGCGGGTTCA
39698 GGTTCGGGT-TGTCTCG
1 GGTTCGGGTAT-TCTCG
*
39714 GGTTCGGGTATTTTCG
1 GGTTCGGGTATTCTCG
*
39730 GGTTCGGGTAATT-TCA
1 GGTTCGGGT-ATTCTCG
39746 GGTTCGGGT
1 GGTTCGGGT
39755 TCGGGACGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 33 0.89
17 4 0.11
ACGTcount: A:0.07, C:0.14, G:0.40, T:0.39
Consensus pattern (16 bp):
GGTTCGGGTATTCTCG
Found at i:39738 original size:6 final size:6
Alignment explanation
Indices: 39662--39707 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
39652 TATTTTGATC
* *
39662 TCGGGC TCGGG- TCGGGT TCGGGT TCGGG- -CGGGT TCAGGT TCGGGT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT
39707 T
1 T
39708 GTCTCGGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 4 0.11
5 5 0.14
6 26 0.74
ACGTcount: A:0.02, C:0.20, G:0.50, T:0.28
Consensus pattern (6 bp):
TCGGGT
Found at i:40890 original size:26 final size:26
Alignment explanation
Indices: 40855--40916 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
40845 TGTATTGTAT
*
40855 AATTTTAGTAACCTCACATTCTTAGA
1 AATTTTAGTAACCTAACATTCTTAGA
* *
40881 ATTTTTAGTAACCTAATATTCTTAGA
1 AATTTTAGTAACCTAACATTCTTAGA
40907 AATTTTAGTA
1 AATTTTAGTA
40917 TAATATTCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (26 bp):
AATTTTAGTAACCTAACATTCTTAGA
Found at i:40924 original size:23 final size:25
Alignment explanation
Indices: 40855--40924 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
40845 TGTATTGTAT
* *
40855 AATTTTAGTAACCTCACATTCTTAGA
1 AATTTTAGTAA-CTAATATTCTTAGA
*
40881 ATTTTTAGTAACCTAATATTCTTAGA
1 AATTTTAGTAA-CTAATATTCTTAGA
40907 AATTTTAGT-A-TAATATTC
1 AATTTTAGTAACTAATATTC
40925 CCTTCGTCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 8 0.20
25 1 0.03
26 31 0.77
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (25 bp):
AATTTTAGTAACTAATATTCTTAGA
Found at i:44359 original size:29 final size:30
Alignment explanation
Indices: 44327--44384 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
44317 CACCATGAAT
44327 TGGGAAATAA-TTTTAAAAGTATAATACTA
1 TGGGAAATAAGTTTTAAAAGTATAATACTA
*
44356 TGGGAAATAAGTTTTCAAAGTATAATACT
1 TGGGAAATAAGTTTTAAAAGTATAATACT
44385 TAGGTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (30 bp):
TGGGAAATAAGTTTTAAAAGTATAATACTA
Found at i:47186 original size:7 final size:6
Alignment explanation
Indices: 47160--47184 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
47150 GTATTTGCTC
47160 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
47185 ATTGAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:47577 original size:81 final size:81
Alignment explanation
Indices: 47442--47604 Score: 301
Period size: 81 Copynumber: 2.0 Consensus size: 81
47432 TAGTATTTAT
*
47442 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAACACA
1 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTAAAATTAGGTTTAACACA
47507 ACAATT-AGCGAGAAAA
66 ACAATTAAG-GAGAAAA
47523 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTAAAATTAGGTTTAACACA
1 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTAAAATTAGGTTTAACACA
47588 ACAATTAAGGAGAAAA
66 ACAATTAAGGAGAAAA
47604 T
1 T
47605 TTTGGATCTA
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
81 78 0.98
82 2 0.03
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (81 bp):
TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTAAAATTAGGTTTAACACA
ACAATTAAGGAGAAAA
Found at i:48416 original size:14 final size:13
Alignment explanation
Indices: 48387--48422 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
48377 GTTTCATATC
48387 AAATCCAATTTGAA
1 AAAT-CAATTTGAA
48401 AAATCAATTTGAA
1 AAATCAATTTGAA
48414 AAATCAATT
1 AAATCAATT
48423 AATTTTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (13 bp):
AAATCAATTTGAA
Found at i:49436 original size:38 final size:36
Alignment explanation
Indices: 49364--49437 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 36
49354 GCCCCAAATT
**
49364 AATTTTTTTTATTCTAAGGGTAAATTTTAAAATTAA
1 AATTTTTTTTATTCTAAGGGTAAATTGCAAAATTAA
* *
49400 AATTTTATCTTTATTTTAAGGGTAAATTGCATAATTAA
1 AATTTT-T-TTTATTCTAAGGGTAAATTGCAAAATTAA
49438 TAATATATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 6 0.19
37 1 0.03
38 25 0.78
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (36 bp):
AATTTTTTTTATTCTAAGGGTAAATTGCAAAATTAA
Found at i:51767 original size:141 final size:138
Alignment explanation
Indices: 51506--51836 Score: 527
Period size: 141 Copynumber: 2.4 Consensus size: 138
51496 TACAACTTTG
* * * * *
51506 ATTAGATAATCATTAATCAATTAAAACTTTGATTGACAAAATTAATTAACAACATGTTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACATGTTCAATAAT
*
51571 TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTGGCGAT
66 TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTT--TAGCGA-
*
51636 TTTATGGTAAA
128 TTTATGGAAAA
*
51647 ATTATATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACATGTTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACATGTTCAATAAT
* *
51712 TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGTTAATTTTTTTTAGCGATTT
66 TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTTAGCGATTT
51777 ATGGAAAA
131 ATGGAAAA
* *
51785 ATTAAATAATTATCAATCAATTACAACTTTGATTGAAAAAATTAACTAACGA
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGA
51837 TCACTAACTT
Statistics
Matches: 178, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
138 59 0.33
139 5 0.03
141 114 0.64
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (138 bp):
ATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACATGTTCAATAAT
TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTTAGCGATTT
ATGGAAAA
Found at i:52493 original size:140 final size:141
Alignment explanation
Indices: 52116--52517 Score: 514
Period size: 140 Copynumber: 2.9 Consensus size: 141
52106 TAATTTTTTT
* ** * *
52116 TTGGC-AA-TTAACTAACGACTAATTTGATTCCCTAATTTATTTAGTATGTTCAATCAATCTATT
1 TTGGCAAAGTTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAAT-TATT
*
52179 TTTTTGCTAACATAATTACTAATTGATTCATTCATTTAT-GACAAAAATCAAATAATCATCAATC
65 TTTTTG-TAACATAATTACTAATTGATTCATTTATTTATGGA-AAAAAT-AAATAATCATCAATC
52243 AATTATAACCTTTGA
127 AATTATAACCTTTGA
* *
52258 TTGTACAAAGTTGA-TCAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAA-T-T
1 TTG-GCAAAGTTAACT-AACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTAT
* * * *
52320 TTTTTTGTAATATAATTACTAATTGGTTTATTTATTTATGGAAAAAATAAATAATCATCCATCAA
64 TTTTTTGTAACATAATTACTAATTGATTCATTTATTTATGGAAAAAATAAATAATCATCAATCAA
52385 TTATAA-CTTTGA
129 TTATAACCTTTGA
* * * *
52397 TTGGCAAAGTTAACTAAGGACTAACTTGATTCATTTACTTATTTTGGATGTTCAATCAATTTATT
1 TTGGCAAAGTTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAA-TTATT
* * *
52462 TTTTTGTAACATAA-TACTAATTGATTCATTTATTTGTGGCAAAATTAAATAATCAT
65 TTTTTGTAACATAATTACTAATTGATTCATTTATTTATGGAAAAAATAAATAATCAT
52518 TAGCTTTTGG
Statistics
Matches: 227, Mismatches: 24, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
138 48 0.21
139 10 0.04
140 60 0.26
141 49 0.22
142 13 0.06
143 2 0.01
144 3 0.01
145 42 0.19
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (141 bp):
TTGGCAAAGTTAACTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAATCAATTATTT
TTTTGTAACATAATTACTAATTGATTCATTTATTTATGGAAAAAATAAATAATCATCAATCAATT
ATAACCTTTGA
Done.