Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011570.1 Corchorus capsularis cultivar CVL-1 contig11591, 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: 37447
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:903 original size:9 final size:9
Alignment explanation
Indices: 889--921 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
879 TTAGTTTGTA
889 ATTTGGTTT
1 ATTTGGTTT
898 ATTTGGTTT
1 ATTTGGTTT
*
907 ATTT-GTGT
1 ATTTGGTTT
915 ATTTGGT
1 ATTTGGT
922 ATGTAGATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (9 bp):
ATTTGGTTT
Found at i:1188 original size:9 final size:9
Alignment explanation
Indices: 1174--1216 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
1164 AACACATATC
1174 TATACTAAT
1 TATACTAAT
1183 TATACTAAT
1 TATACTAAT
*
1192 TATAATGTGAAT
1 TAT-A-CT-AAT
1204 TATACTAAT
1 TATACTAAT
1213 TATA
1 TATA
1217 ATGTGAAGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 19 0.66
10 2 0.07
11 2 0.07
12 6 0.21
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (9 bp):
TATACTAAT
Found at i:1204 original size:21 final size:21
Alignment explanation
Indices: 1180--1223 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1170 TATCTATACT
1180 AATTATACTAATTATAATGTG
1 AATTATACTAATTATAATGTG
1201 AATTATACTAATTATAATGTG
1 AATTATACTAATTATAATGTG
1222 AA
1 AA
1224 GTCCTGAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (21 bp):
AATTATACTAATTATAATGTG
Found at i:2031 original size:12 final size:12
Alignment explanation
Indices: 2014--2050 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
2004 TCTAAATTAT
2014 ACACGAAACACG
1 ACACGAAACACG
2026 ACACGAAACACG
1 ACACGAAACACG
2038 ACACGAAACACG
1 ACACGAAACACG
2050 A
1 A
2051 ATTGCCAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.32, G:0.16, T:0.00
Consensus pattern (12 bp):
ACACGAAACACG
Found at i:3092 original size:11 final size:11
Alignment explanation
Indices: 3076--3104 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3066 TCTAATTCTC
3076 TTTGAAAAATG
1 TTTGAAAAATG
3087 TTTGAAAAATG
1 TTTGAAAAATG
3098 TTTGAAA
1 TTTGAAA
3105 CATTCCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (11 bp):
TTTGAAAAATG
Found at i:4383 original size:68 final size:69
Alignment explanation
Indices: 4311--4455 Score: 195
Period size: 69 Copynumber: 2.1 Consensus size: 69
4301 TAATTAAAAT
* * * * *
4311 AGTAAAATGGTAAAAT-ATA-AGTAATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATAAAATAGTAATAAAGATATTAGATTGAATTAAAT-AAAATAGAGTTTTT
*
4374 AGTTG
65 AGTTA
* *
4379 AGTAAAATAGTAAAATAAAATAGTTATAAAGATATTATATTGAATTAAATAAAATAGAGTTTTTA
1 AGTAAAATAGTAAAATAAAATAGTAATAAAGATATTAGATTGAATTAAATAAAATAGAGTTTTTA
4444 GTTA
66 GTTA
4448 AGTAAAAT
1 AGTAAAAT
4456 TATAAAAACC
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
68 15 0.22
69 28 0.42
70 24 0.36
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (69 bp):
AGTAAAATAGTAAAATAAAATAGTAATAAAGATATTAGATTGAATTAAATAAAATAGAGTTTTTA
GTTA
Found at i:13430 original size:33 final size:33
Alignment explanation
Indices: 13388--13490 Score: 163
Period size: 33 Copynumber: 3.1 Consensus size: 33
13378 CCTCTTTTTC
* **
13388 AGCCGTGACAGGGGGTTCAGAGTCCACTTCCAT
1 AGCCGTGACAGGGGGTACAGTCTCCACTTCCAT
13421 AGCCGTGACAGGGGGTACAGTCTCCACTTCCAT
1 AGCCGTGACAGGGGGTACAGTCTCCACTTCCAT
13454 AGCC-TCGACAGGGGGTACAGTCTCCACTTCCAT
1 AGCCGT-GACAGGGGGTACAGTCTCCACTTCCAT
13487 AGCC
1 AGCC
13491 ATGGATTTGT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
32 1 0.02
33 65 0.98
ACGTcount: A:0.21, C:0.31, G:0.27, T:0.20
Consensus pattern (33 bp):
AGCCGTGACAGGGGGTACAGTCTCCACTTCCAT
Found at i:13639 original size:33 final size:33
Alignment explanation
Indices: 13611--14082 Score: 288
Period size: 33 Copynumber: 14.3 Consensus size: 33
13601 TAAGGTCATT
*
13611 GGATTAGTTGGAGTTTCCTCATGCAAGGTGGTG
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* *
13644 GGGTCAGATGGAGTTTCCTCATGCAAGGTGGTG
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * *
13677 GGATCAGTTGTAGTTTCCTCA-CCCAGATTAGTG
1 GGATCAGTTGGAGTTTCCTCATGCAAG-GTGGTG
*** * **
13710 GGATCAGTTGGAGTTTCCTCGCCCAAAGTGGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * ** *
13743 GAATCATTTGGAGTTTCCTCACCCAATGTTGG-G
1 GGATCAGTTGGAGTTTCCTCATGCAA-GGTGGTG
*
13776 GGATCAGTTGGAGTTTCCT--TGCTCAATGTTGG-G
1 GGATCAGTTGGAGTTTCCTCATG--CAA-GGTGGTG
* * ** * **
13809 GGATCAGTTGTAGCTTCCTCATGCAAAATTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * *
13842 GGTTCGGTTGTAGTTTCCTCATGCAAGGTTGTA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * **
13875 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * **
13908 GGTTCAGTTGTAGTTTCCTCATGCAAGATTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * * **
13941 GGTTCAGTTGTAGTTTCCTCGTGCAAGATTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * **
13974 GGTTCAGTTGTAGTTTCCTCGTGCAAGGTTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * * * **
14007 GGTTCAGTTGCAGTTTCCTCGTGCAAGGTTGCA
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
* * *
14040 GGTTCAGTTGCAGTTTCCTCATGCAAGGTTGTG
1 GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
14073 GGATCAGTTG
1 GGATCAGTTG
14083 TCGCTTCCAC
Statistics
Matches: 379, Mismatches: 52, Indels: 16
0.85 0.12 0.04
Matches are distributed among these distances:
32 5 0.01
33 366 0.97
34 6 0.02
35 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.33
Consensus pattern (33 bp):
GGATCAGTTGGAGTTTCCTCATGCAAGGTGGTG
Found at i:14107 original size:66 final size:66
Alignment explanation
Indices: 13611--14083 Score: 375
Period size: 66 Copynumber: 7.2 Consensus size: 66
13601 TAAGGTCATT
* * * ** * * * *
13611 GGATTAGTTGGAGTTTCCTC-ATGCAAGGTGGTGGGGTCAGATGGAGTTTCCTCATGCAAGGTGG
1 GGATCAGTTGTAGTTTCCTCGA-GCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCATGCAAGGTTG
**
13675 TG
65 CA
* * * ** * * *** * *
13677 GGATCAGTTGTAGTTTCCTC-ACCCAGATTAGTGGGATCAGTTGGAGTTTCCTCGCCCAAAGTGG
1 GGATCAGTTGTAGTTTCCTCGAGCAAGGTT-GCAGGTTCAGTTGTAGTTTCCTCATGCAAGGTTG
13741 CA
65 CA
* * * * * ** * * *
13743 GAATCATTTGGAGTTTCCTC-ACCCAATGTTGGGGGATCAGTTGGAGTTTCCT--TGCTCAATGT
1 GGATCAGTTGTAGTTTCCTCGA-GCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCATG--CAAGGT
**
13805 TGGG
63 TGCA
* ** *
13809 GGATCAGTTGTAGCTTCCTC-ATGCAAAATTGCAGGTTCGGTTGTAGTTTCCTCATGCAAGGTTG
1 GGATCAGTTGTAGTTTCCTCGA-GCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCATGCAAGGTTG
*
13873 TA
65 CA
*
13875 GGATCAGTTGTAGTTTCCTC-ATGCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCATGCAAGATTG
1 GGATCAGTTGTAGTTTCCTCGA-GCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCATGCAAGGTTG
13939 CA
65 CA
* * * *
13941 GGTTCAGTTGTAGTTTCCTCGTGCAAGATTGCAGGTTCAGTTGTAGTTTCCTCGTGCAAGGTTGC
1 GGATCAGTTGTAGTTTCCTCGAGCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCATGCAAGGTTGC
14006 A
66 A
* * * * *
14007 GGTTCAGTTGCAGTTTCCTCGTGCAAGGTTGCAGGTTCAGTTGCAGTTTCCTCATGCAAGGTTGT
1 GGATCAGTTGTAGTTTCCTCGAGCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCATGCAAGGTTGC
*
14072 G
66 A
14073 GGATCAGTTGT
1 GGATCAGTTGT
14084 CGCTTCCACA
Statistics
Matches: 338, Mismatches: 62, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
65 4 0.01
66 327 0.97
67 5 0.01
68 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (66 bp):
GGATCAGTTGTAGTTTCCTCGAGCAAGGTTGCAGGTTCAGTTGTAGTTTCCTCATGCAAGGTTGC
A
Found at i:14121 original size:99 final size:99
Alignment explanation
Indices: 13611--14122 Score: 454
Period size: 99 Copynumber: 5.2 Consensus size: 99
13601 TAAGGTCATT
* * * ** * * *
13611 GGATTAGTTGGAGTTTCCTCATGCAAGGTGGTGGGGTCAGATGGAGTTTCCTCATGCAAGGTGGT
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGGAGTTTCCTCATGCAAGGTTGT
* **
13676 GGGATCAGTTGTAGTTTCCTCACCCAGAT-TAGTG
66 GGGATCAGTTGTAGTTTCCTCACCCAG-TGTTGCA
* *** * * ** * ** * *
13710 GGATCAGTTGGAGTTTCCTCGCCCAAAGTGGCAGAATCATTTGGAGTTTCCTCACCCAATGTTGG
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGGAGTTTCCTCATGCAAGGTTGT
* ** * * **
13775 GGGATCAGTTGGAGTTTCCTTGCTCAATGTTGGG
66 GGGATCAGTTGTAGTTTCCTCACCCAGTGTTGCA
* ** * *
13809 GGATCAGTTGTAGCTTCCTCATGCAAAATTGCAGGTTCGGTTGTAGTTTCCTCATGCAAGGTTGT
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGGAGTTTCCTCATGCAAGGTTGT
* * *
13874 AGGATCAGTTGTAGTTTCCTCATGCAAG-GTTGCA
66 GGGATCAGTTGTAGTTTCCTCA-CCCAGTGTTGCA
* * * * * *
13908 GGTTCAGTTGTAGTTTCCTCATGCAAGATTGCAGGTTCAGTTGTAGTTTCCTCGTGCAAGATTGC
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGGAGTTTCCTCATGCAAGGTTGT
* * ** *
13973 AGGTTCAGTTGTAGTTTCCTCGTGCAAG-GTTGCA
66 GGGATCAGTTGTAGTTTCCTC-ACCCAGTGTTGCA
* * * *
14007 GGTTCAGTTGCAGTTTCCTCGTGCAAGGTTGCAGGTTCAGTTGCAGTTTCCTCATGCAAGGTTGT
1 GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGGAGTTTCCTCATGCAAGGTTGT
* * *
14072 GGGATCAGTTGTCGCTTCCACACCCAGTGTTGCA
66 GGGATCAGTTGTAGTTTCCTCACCCAGTGTTGCA
*
14106 GGATCAGTTTTAGTTTC
1 GGATCAGTTGTAGTTTC
14123 AACACCCGTT
Statistics
Matches: 333, Mismatches: 76, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
98 4 0.01
99 328 0.98
100 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.34
Consensus pattern (99 bp):
GGATCAGTTGTAGTTTCCTCATGCAAGGTTGCAGGTTCAGTTGGAGTTTCCTCATGCAAGGTTGT
GGGATCAGTTGTAGTTTCCTCACCCAGTGTTGCA
Found at i:14287 original size:33 final size:32
Alignment explanation
Indices: 14250--14386 Score: 148
Period size: 33 Copynumber: 4.2 Consensus size: 32
14240 AACATTTGGT
* *
14250 GTTTCTTCTGCCAAGGTCACGGAATAGGTAGGA
1 GTTTCTTCAGCCAAGGTCACGGAAT-GCTAGGA
***
14283 GTTTCTTCAGCCAAGGTTGTGGGAATGCTAGGA
1 GTTTCTTCAGCCAAGG-TCACGGAATGCTAGGA
**
14316 GTTTCTTCAGCCAAGGTTGCGGGAATGCTAGGA
1 GTTTCTTCAGCCAAGGTCAC-GGAATGCTAGGA
* **
14349 GTTTCTTCGGCCAAGGTTGCGGGAATGCTAGGA
1 GTTTCTTCAGCCAAGGTCAC-GGAATGCTAGGA
14382 GTTTC
1 GTTTC
14387 GGCACTCAAG
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 86 0.92
34 6 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (32 bp):
GTTTCTTCAGCCAAGGTCACGGAATGCTAGGA
Found at i:14299 original size:66 final size:66
Alignment explanation
Indices: 14250--14386 Score: 168
Period size: 66 Copynumber: 2.1 Consensus size: 66
14240 AACATTTGGT
* * **
14250 GTTTCTTCTGCCAAGGTCAC-GGAATAGGTAGGAGTTTCTTCAGCCAAGGTTGTGGGAATGCTAG
1 GTTTCTTCAGCCAAGGTCACGGGAAT-GCTAGGAGTTTCTTCAGCCAAGGTTGTGGGAACACTAG
14314 GA
65 GA
** * * **
14316 GTTTCTTCAGCCAAGGTTGCGGGAATGCTAGGAGTTTCTTCGGCCAAGGTTGCGGGAATGCTAGG
1 GTTTCTTCAGCCAAGGTCACGGGAATGCTAGGAGTTTCTTCAGCCAAGGTTGTGGGAACACTAGG
14381 A
66 A
14382 GTTTC
1 GTTTC
14387 GGCACTCAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 59 0.92
67 5 0.08
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (66 bp):
GTTTCTTCAGCCAAGGTCACGGGAATGCTAGGAGTTTCTTCAGCCAAGGTTGTGGGAACACTAGG
A
Found at i:14353 original size:99 final size:99
Alignment explanation
Indices: 14250--14431 Score: 226
Period size: 99 Copynumber: 1.8 Consensus size: 99
14240 AACATTTGGT
* * ** *
14250 GTTTCTTCTGCCAAGGTCAC-GGAATAGGTAGGAGTTTCTTCAGC-CAAGGTTGTGGGAATGCTA
1 GTTTCTTCGGCCAAGGTCACGGGAAT-GCTAGGAGTTTCGGCA-CTCAAGGCTGTGGGAATGCTA
*
14313 GGAGTTTCTTCAGCC-AAGGTTGCGGGAATGCTAGGA
64 GAAGTTTCTTCA-CCTAAGGTTGCGGGAATGCTAGGA
** * *
14349 GTTTCTTCGGCCAAGGTTGCGGGAATGCTAGGAGTTTCGGCACTCAAGGCTGTGGGAATGGTTGA
1 GTTTCTTCGGCCAAGGTCACGGGAATGCTAGGAGTTTCGGCACTCAAGGCTGTGGGAATGCTAGA
14414 AGTTTCTTCACCTAAGGT
66 AGTTTCTTCACCTAAGGT
14432 AGTAATGCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
98 3 0.04
99 62 0.89
100 5 0.07
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (99 bp):
GTTTCTTCGGCCAAGGTCACGGGAATGCTAGGAGTTTCGGCACTCAAGGCTGTGGGAATGCTAGA
AGTTTCTTCACCTAAGGTTGCGGGAATGCTAGGA
Found at i:14397 original size:33 final size:32
Alignment explanation
Indices: 14278--14431 Score: 182
Period size: 33 Copynumber: 4.7 Consensus size: 32
14268 ACGGAATAGG
*
14278 TAGGAGTTTCTTCAGCCAAGGTTGTGGGAATGC
1 TAGGAGTTTCTTCA-CCAAGGTTGCGGGAATGC
14311 TAGGAGTTTCTTCAGCCAAGGTTGCGGGAATGC
1 TAGGAGTTTCTTCA-CCAAGGTTGCGGGAATGC
*
14344 TAGGAGTTTCTTCGGCCAAGGTTGCGGGAATGC
1 TAGGAGTTTCTTC-ACCAAGGTTGCGGGAATGC
** * * *
14377 TAGGAGTTTCGGCACTCAAGGCTGTGGGAATGG
1 TAGGAGTTTCTTCAC-CAAGGTTGCGGGAATGC
* *
14410 TTGAAGTTTCTTCACCTAAGGT
1 TAGGAGTTTCTTCACC-AAGGT
14432 AGTAATGCTT
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.02
33 103 0.98
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (32 bp):
TAGGAGTTTCTTCACCAAGGTTGCGGGAATGC
Found at i:22669 original size:16 final size:17
Alignment explanation
Indices: 22648--22680 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
22638 AATTAATAAA
*
22648 TCTAGCACATT-ATATT
1 TCTAGCAAATTCATATT
22664 TCTAGCAAATTCATATT
1 TCTAGCAAATTCATATT
22681 ATATAATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (17 bp):
TCTAGCAAATTCATATT
Found at i:24680 original size:20 final size:22
Alignment explanation
Indices: 24641--24692 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
24631 TCGAAAAGGG
24641 AAAAAAA-AAT-CAAGGACCTT
1 AAAAAAATAATACAAGGACCTT
*
24661 -CAAAAATAATACAAGG-CCTT
1 AAAAAAATAATACAAGGACCTT
24681 AAAAAAATAATA
1 AAAAAAATAATA
24693 AGCCCAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 7 0.26
21 15 0.56
ACGTcount: A:0.62, C:0.13, G:0.08, T:0.17
Consensus pattern (22 bp):
AAAAAAATAATACAAGGACCTT
Found at i:28064 original size:65 final size:65
Alignment explanation
Indices: 27958--28101 Score: 225
Period size: 65 Copynumber: 2.2 Consensus size: 65
27948 GTAATTGAAA
* *
27958 ATTCGAATTATTCGAGTTAATCCAACAATACTGAGTCAACAATAGAAAACGCGTGAAAAGAGAAT
1 ATTCGAATTATTCAAGTTAATCCAACAATACTGAGTCAACAATAGAAAACACGTGAAAAGAGAAT
* * * * *
28023 ATTCGAATGATTCAAGTTAGTCCAATAATAGTGAGTTAACAATAGAAAACACGTGAAAAGAGAAT
1 ATTCGAATTATTCAAGTTAATCCAACAATACTGAGTCAACAATAGAAAACACGTGAAAAGAGAAT
28088 ATTCGAATTATTCA
1 ATTCGAATTATTCA
28102 TAGAAGACAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 71 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (65 bp):
ATTCGAATTATTCAAGTTAATCCAACAATACTGAGTCAACAATAGAAAACACGTGAAAAGAGAAT
Found at i:29676 original size:82 final size:83
Alignment explanation
Indices: 29546--29700 Score: 294
Period size: 82 Copynumber: 1.9 Consensus size: 83
29536 GGCGATTTGA
29546 GAAAGAATTTGTCTGCATTTTTTTGACACTGTCGTGGTGTAAGTTCCTTACTTTTGCACTTGCTT
1 GAAAGAATTTGTCTGCATTTTTTTGACACTGTCGTGGTGTAAGTTCCTTACTTTTGCACTTGCTT
29611 CTGTGATTGAATTTGTCT
66 CTGTGATTGAATTTGTCT
*
29629 GAAAGAATTTGTCTGCA-TTTTTTGACATTGTCGTGGTGTAAGTTCCTTACTTTTGCACTTGCTT
1 GAAAGAATTTGTCTGCATTTTTTTGACACTGTCGTGGTGTAAGTTCCTTACTTTTGCACTTGCTT
29693 CTGTGATT
66 CTGTGATT
29701 TGAGAAAGAA
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
82 54 0.76
83 17 0.24
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.46
Consensus pattern (83 bp):
GAAAGAATTTGTCTGCATTTTTTTGACACTGTCGTGGTGTAAGTTCCTTACTTTTGCACTTGCTT
CTGTGATTGAATTTGTCT
Found at i:33215 original size:1 final size:1
Alignment explanation
Indices: 33209--33245 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
33199 AGATAATAAT
33209 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33246 GAGAATGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.