Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013840.1 Corchorus capsularis cultivar CVL-1 contig13861, 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: 49460
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:13501 original size:31 final size:31
Alignment explanation
Indices: 13466--13532 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
13456 AAAATTACTA
* * *
13466 ATTGACCTCACTAAAATGAACGATTTATTGT
1 ATTGACCCCACTAAAATGAAAGATTTATAGT
* *
13497 ATTGACCCCATTAAAATGAAAGTTTTATAGT
1 ATTGACCCCACTAAAATGAAAGATTTATAGT
13528 ATTGA
1 ATTGA
13533 TCTTAGTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (31 bp):
ATTGACCCCACTAAAATGAAAGATTTATAGT
Found at i:14373 original size:31 final size:31
Alignment explanation
Indices: 14328--14404 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
14318 GCCAAATTAC
* * ** *
14328 CAATTTAAGGCTAAACCTTTCAAAAGTTGCT
1 CAATTTGAGCCTAAACAATTCAAAAATTGCT
* *
14359 CAGTTTGAGCCTAAACAATTCAAAAATTGTT
1 CAATTTGAGCCTAAACAATTCAAAAATTGCT
*
14390 CAATTTGAGTCTAAA
1 CAATTTGAGCCTAAA
14405 AACAGAAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (31 bp):
CAATTTGAGCCTAAACAATTCAAAAATTGCT
Found at i:15519 original size:17 final size:17
Alignment explanation
Indices: 15497--15533 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
15487 AATATTTGAA
15497 AATTGAATTTCAACTTT
1 AATTGAATTTCAACTTT
15514 AATTGAATTTCAACTTT
1 AATTGAATTTCAACTTT
15531 AAT
1 AAT
15534 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (17 bp):
AATTGAATTTCAACTTT
Found at i:18449 original size:17 final size:17
Alignment explanation
Indices: 18411--18443 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18401 CTCATAGTAC
*
18411 CTAGGTAGTATGAGGTA
1 CTAGGTAGCATGAGGTA
18428 CTAGGTAGCATGAGGT
1 CTAGGTAGCATGAGGT
18444 GATAGGCTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (17 bp):
CTAGGTAGCATGAGGTA
Found at i:20027 original size:31 final size:31
Alignment explanation
Indices: 19992--20156 Score: 139
Period size: 31 Copynumber: 5.5 Consensus size: 31
19982 TTTGGCTAAT
19992 TGCTCAAATAAGGGTCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGTCTAACGTTTGCCAAAA
* * **
20023 TGCTCAAATAAGGGTCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGTCT-AACGTTTGCCAAAA
*
20052 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGTCTAACGTTTGCCAAAA
* * **
20083 TGCTCAAATAAGGGTCCCATC-TTTG--AATT
1 TGCTCAAATAAGGGT-CTAACGTTTGCCAAAA
* *
20112 TGGC-CAAATAAGGGCCTAACGTTTACCAAAA
1 T-GCTCAAATAAGGGTCTAACGTTTGCCAAAA
20143 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
20157 CATGTCTCAC
Statistics
Matches: 102, Mismatches: 20, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
28 5 0.05
29 34 0.33
30 8 0.08
31 50 0.49
32 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGTCTAACGTTTGCCAAAA
Found at i:20062 original size:60 final size:60
Alignment explanation
Indices: 19996--20156 Score: 277
Period size: 60 Copynumber: 2.7 Consensus size: 60
19986 GCTAATTGCT
* ** *
19996 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCCATCTTTGAATTTGGC
20056 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCCATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCCATCTTTGAATTTGGC
*
20116 CAAATAAGGGCCTAACGTTTACCAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
20157 CATGTCTCAC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCCATCTTTGAATTTGGC
Found at i:20125 original size:29 final size:29
Alignment explanation
Indices: 20027--20125 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
20017 CCAAAATGCT
** *
20027 CAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGTCCCATCTTTGAATTTGGC
* * **
20056 CAAATAAGGG-CCTAACGTTTGCCAAAAT-GC
1 CAAATAAGGGTCCCATC-TTTG--AATTTGGC
20086 TCAAATAAGGGTCCCATCTTTGAATTTGGC
1 -CAAATAAGGGTCCCATCTTTGAATTTGGC
20116 CAAATAAGGG
1 CAAATAAGGG
20126 CCTAACGTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 3 0.06
29 26 0.48
30 4 0.07
31 17 0.31
32 4 0.07
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGTCCCATCTTTGAATTTGGC
Found at i:20231 original size:31 final size:30
Alignment explanation
Indices: 20193--20385 Score: 155
Period size: 31 Copynumber: 6.4 Consensus size: 30
20183 CACCAGACCA
20193 TTATTTGAGCATTTTCGATAACGTTAGGCCC
1 TTATTTGAGCATTTTCGA-AACGTTAGGCCC
* *
20224 TTATTTGAGCATTTTCGATAACGTTGGGCCT
1 TTATTTGAGCATTTTCGA-AACGTTAGGCCC
** * * *
20255 TTATTTG-GCCAAATT--AAAAGATCGGACCC
1 TTATTTGAG-CATTTTCGAAACGTTAGG-CCC
20284 TTATTTGAGCATTTTCGATAACGTTAGGCCC
1 TTATTTGAGCATTTTCGA-AACGTTAGGCCC
** * * *
20315 TTATTTG-GCCAAATT--AAAAGATCGGACCC
1 TTATTTGAG-CATTTTCGAAACGTTAGG-CCC
*
20344 TTATTTGAGCATTTTAGCAAACGTTAGGCCC
1 TTATTTGAGCATTTTCG-AAACGTTAGGCCC
20375 TTATTTGAGCA
1 TTATTTGAGCA
20386 ATTAACCTAA
Statistics
Matches: 127, Mismatches: 23, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
28 12 0.09
29 29 0.23
30 4 0.03
31 69 0.54
32 13 0.10
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (30 bp):
TTATTTGAGCATTTTCGAAACGTTAGGCCC
Found at i:20290 original size:29 final size:29
Alignment explanation
Indices: 20255--20350 Score: 97
Period size: 29 Copynumber: 3.2 Consensus size: 29
20245 CGTTGGGCCT
20255 TTATTTGGCCAAATTAAAAGATCGGACCC
1 TTATTTGGCCAAATTAAAAGATCGGACCC
** * * *
20284 TTATTTGAG-CATTTTCGATAACGTTAGG-CCC
1 TTATTTG-GCCAAATT--A-AAAGATCGGACCC
20315 TTATTTGGCCAAATTAAAAGATCGGACCC
1 TTATTTGGCCAAATTAAAAGATCGGACCC
20344 TTATTTG
1 TTATTTG
20351 AGCATTTTAG
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 6 0.12
29 22 0.43
30 2 0.04
31 15 0.29
32 6 0.12
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (29 bp):
TTATTTGGCCAAATTAAAAGATCGGACCC
Found at i:20292 original size:60 final size:60
Alignment explanation
Indices: 20221--20381 Score: 279
Period size: 60 Copynumber: 2.7 Consensus size: 60
20211 TAACGTTAGG
* *
20221 CCCTTATTTGAGCATTTTCGATAACGTTGGGCCTTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
20281 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
*
20341 CCCTTATTTGAGCATTTTAGCA-AACGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
20382 AGCAATTAAC
Statistics
Matches: 97, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
60 96 0.99
61 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
Found at i:23456 original size:21 final size:22
Alignment explanation
Indices: 23420--23461 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
23410 GGAACTAAAA
23420 GTCCAACACTCTACTAATATCGT
1 GTCCAACAC-CTACTAATATCGT
23443 GTCCAACA-CTACTAATATC
1 GTCCAACACCTACTAATATC
23462 ATGATTGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.33, C:0.31, G:0.07, T:0.29
Consensus pattern (22 bp):
GTCCAACACCTACTAATATCGT
Found at i:25453 original size:19 final size:19
Alignment explanation
Indices: 25418--25455 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25408 GCATTGGTGA
*
25418 TTGCACGTGCTTGGGGGAG
1 TTGCACGTGCTTAGGGGAG
25437 TTGCACGTG-TTCAGGGGAG
1 TTGCACGTGCTT-AGGGGAG
25456 CATTCGGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.13, C:0.16, G:0.45, T:0.26
Consensus pattern (19 bp):
TTGCACGTGCTTAGGGGAG
Found at i:25456 original size:119 final size:119
Alignment explanation
Indices: 25239--25736 Score: 690
Period size: 119 Copynumber: 4.2 Consensus size: 119
25229 TCGGTGCTAC
* *** * * *
25239 CATTCTTCACTCGCGCGGTCGGCACTCCAAATTGAGCACTCTACTTTCGCGCGTTGGTAATTGCA
1 CATTCTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTCGCGCATTGGTGATTGCA
* **
25304 CGTGCTTAGGGGAGTTACACGTGTTCAAAGGAGCATTCGGTGCTCTTCATTAAG
66 CGTGCTTGGGGGAGTTACACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAG
*
25358 CATTCTTCACTCGCGCGGTTGGCACTCTTCATTAAGCACTCTTCTTTCGCGCATTGGTGATTGCA
1 CATTCTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTCGCGCATTGGTGATTGCA
* *
25423 CGTGCTTGGGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAT
66 CGTGCTTGGGGGAGTTACACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAG
* * * *
25477 CAGTCTCCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCCTCTTTCGCACATTGGTGATTGCA
1 CATTCTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTCGCGCATTGGTGATTGCA
* * * * * *
25542 CGTGCTTCGAGGAGTTGCACATGTTCAGGGGAGCATTCGGTGCTCATCATTAAT
66 CGTGCTTGGGGGAGTTACACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAG
* * * * * * *
25596 CATTCTTCACTCGCACAGTTGTCACTTTTCATTGAGCGCTCTTCTTTCCCGCATTGGTGATTTCA
1 CATTCTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTCGCGCATTGGTGATTGCA
* ** *
25661 CGTGCTTGGGGGAATTACACGTGTTCAGGGGAGCACCCAGTGCTCTTCATTAAG
66 CGTGCTTGGGGGAGTTACACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAG
25715 CATTCTTCACTCGCGCGGTTGG
1 CATTCTTCACTCGCGCGGTTGG
25737 TCATCATGCG
Statistics
Matches: 333, Mismatches: 46, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
119 333 1.00
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (119 bp):
CATTCTTCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCTTCTTTCGCGCATTGGTGATTGCA
CGTGCTTGGGGGAGTTACACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAAG
Found at i:25594 original size:238 final size:236
Alignment explanation
Indices: 25181--25736 Score: 705
Period size: 238 Copynumber: 2.4 Consensus size: 236
25171 CATGTATAAG
* * * *
25181 TTGGTGATTGCACGTGCTTGAGGGAGTTGCTCTTGTTCAGGAGAGCATTCGGTGCTAC--CA-T-
1 TTGGTGATTGCACGTGCTTGGGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCT-CTTCATTA
* * *
25242 -TC-T-TCACTCGCGCGGTCGGCACTCCAAATTGAGCACTCTACTTTCGCGCGTTGGTAATTGCA
65 ATCATCTCACTCGCGCGGTTGGCACTCCAAATTGAGCACTCTACTTTCGCACATTGGTAATTGCA
* * *
25304 CGTGCTTAGGGGAGTTACACGTGTTCAAAGGAGCATTCGGTGCTCTTCATTAAGCATTCTTCACT
130 CGTGCTTAGAGGAGTTACACATGTTCAAAGGAGCATTCGGTGCTCATCATTAAGCATTCTTCACT
* * *
25369 CGCGCGGTTGGCACTCTTCATTAAGCACTCTTCTTTCGCGCA
195 CGCACAGTTGGCACTCTTCATTAAGCACTCTTCTTTCCCGCA
25411 TTGGTGATTGCACGTGCTTGGGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAA
1 TTGGTGATTGCACGTGCTTGGGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAA
*** *
25476 TCAGTCTCCACTCGCGCGGTTGGCACTCTTCATTGAGCACTCCT-CTTTCGCACATTGGTGATTG
66 TCA-TCT-CACTCGCGCGGTTGGCACTCCAAATTGAGCACT-CTACTTTCGCACATTGGTAATTG
* * ** *
25540 CACGTGCTTCGAGGAGTTGCACATGTTCAGGGGAGCATTCGGTGCTCATCATTAATCATTCTTCA
128 CACGTGCTTAGAGGAGTTACACATGTTCAAAGGAGCATTCGGTGCTCATCATTAAGCATTCTTCA
* * * *
25605 CTCGCACAGTTGTCACTTTTCATTGAGCGCTCTTCTTTCCCGCA
193 CTCGCACAGTTGGCACTCTTCATTAAGCACTCTTCTTTCCCGCA
* * * ** *
25649 TTGGTGATTTCACGTGCTTGGGGGAATTACACGTGTTCAGGGGAGCACCCAGTGCTCTTCATTAA
1 TTGGTGATTGCACGTGCTTGGGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAA
*
25714 GCATTCTTCACTCGCGCGGTTGG
66 TCA-TC-TCACTCGCGCGGTTGG
25737 TCATCATGCG
Statistics
Matches: 281, Mismatches: 34, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
229 1 0.00
230 52 0.19
231 2 0.01
232 1 0.00
234 2 0.01
236 1 0.00
237 1 0.00
238 218 0.78
239 3 0.01
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (236 bp):
TTGGTGATTGCACGTGCTTGGGGGAGTTGCACGTGTTCAGGGGAGCATTCGGTGCTCTTCATTAA
TCATCTCACTCGCGCGGTTGGCACTCCAAATTGAGCACTCTACTTTCGCACATTGGTAATTGCAC
GTGCTTAGAGGAGTTACACATGTTCAAAGGAGCATTCGGTGCTCATCATTAAGCATTCTTCACTC
GCACAGTTGGCACTCTTCATTAAGCACTCTTCTTTCCCGCA
Found at i:26390 original size:24 final size:24
Alignment explanation
Indices: 26358--26403 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
26348 TTTTATAATT
*
26358 GCTCGCCCTTTTGACTTGTTGGTC
1 GCTCACCCTTTTGACTTGTTGGTC
26382 GCTCACCCTTTTGACTTGTTGG
1 GCTCACCCTTTTGACTTGTTGG
26404 AGATGGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.07, C:0.28, G:0.24, T:0.41
Consensus pattern (24 bp):
GCTCACCCTTTTGACTTGTTGGTC
Found at i:35197 original size:2 final size:2
Alignment explanation
Indices: 35190--35244 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
35180 TCTGTGTTTT
35190 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
35232 TG TG TG TG TG TG T
1 TG TG TG TG TG TG T
35245 AGGCAGTTAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:35380 original size:17 final size:16
Alignment explanation
Indices: 35358--35393 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
35348 ATTAATTTGC
35358 TTTTCTTGAAATTAAGT
1 TTTTC-TGAAATTAAGT
35375 TTTTCTGAAATTAAGT
1 TTTTCTGAAATTAAGT
35391 TTT
1 TTT
35394 ACTTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (16 bp):
TTTTCTGAAATTAAGT
Found at i:41851 original size:21 final size:21
Alignment explanation
Indices: 41810--41853 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
41800 AATTTTGTTG
**
41810 TTTATTTATTTATTTTTAATA
1 TTTATTTATTTATTTGCAATA
41831 TTTA-TTATTTAATTTGCAATA
1 TTTATTTATTT-ATTTGCAATA
41852 TT
1 TT
41854 ATCCTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTATTTATTTATTTGCAATA
Found at i:42546 original size:21 final size:21
Alignment explanation
Indices: 42520--42560 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42510 GAACTGGATT
42520 GCTAAACACCGCCCCCCTTTC
1 GCTAAACACCGCCCCCCTTTC
* *
42541 GCTAAATACCGCCCTCCTTT
1 GCTAAACACCGCCCCCCTTT
42561 TTACACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.46, G:0.10, T:0.24
Consensus pattern (21 bp):
GCTAAACACCGCCCCCCTTTC
Found at i:42786 original size:33 final size:33
Alignment explanation
Indices: 42725--42787 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
42715 TTTAGGACTG
* *
42725 TGCCGCCCAAATTAGGCGGCTAGGCCATGGGTA
1 TGCCGCCCAAATTAGGCAGCTAGCCCATGGGTA
* * *
42758 TGCCGCCCAAATTGGGCAGTTTGCCCATGG
1 TGCCGCCCAAATTAGGCAGCTAGCCCATGG
42788 TAGCGGCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.19, C:0.29, G:0.32, T:0.21
Consensus pattern (33 bp):
TGCCGCCCAAATTAGGCAGCTAGCCCATGGGTA
Found at i:42836 original size:15 final size:15
Alignment explanation
Indices: 42818--42856 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
42808 TTTTTAAAAA
42818 AATTAATTTTTAATT
1 AATTAATTTTTAATT
* *
42833 AATTAGTATTTAATT
1 AATTAATTTTTAATT
*
42848 ACTTAATTT
1 AATTAATTT
42857 ATTAGTTTTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (15 bp):
AATTAATTTTTAATT
Found at i:42878 original size:22 final size:23
Alignment explanation
Indices: 42827--42880 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
42817 AAATTAATTT
*
42827 TTAATTAATTAGTATTTAATTAC
1 TTAATTTATTAGTATTTAATTAC
*
42850 TTAATTTATTAGT-TTTAATTAG
1 TTAATTTATTAGTATTTAATTAC
42872 TTAATTTAT
1 TTAATTTAT
42881 GATCAACTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (23 bp):
TTAATTTATTAGTATTTAATTAC
Found at i:47870 original size:16 final size:16
Alignment explanation
Indices: 47850--47967 Score: 134
Period size: 16 Copynumber: 7.4 Consensus size: 16
47840 GGACCCGCCC
*
47850 GACCCGAGACCCG-AC
1 GACCCGAGACCCGAAT
*
47865 GAACCCGTGACCCGAAT
1 G-ACCCGAGACCCGAAT
47882 GACCCGCA-ACCC-AGAT
1 GACCCG-AGACCCGA-AT
47898 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
47914 GACCCGAAACCCGAAT
1 GACCCGAGACCCGAAT
*
47930 GACCCGAGACCCGTAT
1 GACCCGAGACCCGAAT
*
47946 GACCCGAAACCCGAAT
1 GACCCGAGACCCGAAT
*
47962 AACCCG
1 GACCCG
47968 GGACATTAAC
Statistics
Matches: 88, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
15 3 0.03
16 82 0.93
17 3 0.03
ACGTcount: A:0.31, C:0.40, G:0.22, T:0.07
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:47960 original size:32 final size:32
Alignment explanation
Indices: 47850--47967 Score: 150
Period size: 32 Copynumber: 3.7 Consensus size: 32
47840 GGACCCGCCC
* * *
47850 GACCCGAGACCCG-ACGAACCCGTGACCCGAAT
1 GACCCGAAACCCGAATG-ACCCGAGACCCGAAT
*
47882 GACCCGCAACCC-AGATGACCCGAGACCCGAAT
1 GACCCGAAACCCGA-ATGACCCGAGACCCGAAT
*
47914 GACCCGAAACCCGAATGACCCGAGACCCGTAT
1 GACCCGAAACCCGAATGACCCGAGACCCGAAT
*
47946 GACCCGAAACCCGAATAACCCG
1 GACCCGAAACCCGAATGACCCG
47968 GGACATTAAC
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
32 73 0.96
33 3 0.04
ACGTcount: A:0.31, C:0.40, G:0.22, T:0.07
Consensus pattern (32 bp):
GACCCGAAACCCGAATGACCCGAGACCCGAAT
Found at i:48102 original size:21 final size:21
Alignment explanation
Indices: 48077--48123 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
48067 TACAATTTAT
48077 ATTATTGTTATAATTTTACCA
1 ATTATTGTTATAATTTTACCA
* *
48098 ATTATTGTTATGATTTTACCT
1 ATTATTGTTATAATTTTACCA
48119 ATTAT
1 ATTAT
48124 AAATTGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTGTTATAATTTTACCA
Found at i:48589 original size:16 final size:16
Alignment explanation
Indices: 48570--48718 Score: 207
Period size: 16 Copynumber: 9.4 Consensus size: 16
48560 AACCCGCCCA
*
48570 ACCCGAGACCCG-GTAG
1 ACCCGAGACCCGAAT-G
48586 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
*
48602 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
48618 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
*
48634 ACCCGAGACCCGTATG
1 ACCCGAGACCCGAATG
48650 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
*
48666 ACCCGAGACCCGAATA
1 ACCCGAGACCCGAATG
48682 ACCCGA-ACCC-AGATG
1 ACCCGAGACCCGA-ATG
48697 ACCCGTA-ACCCGAATG
1 ACCCG-AGACCCGAATG
48713 ACCCGA
1 ACCCGA
48719 AAAACTGCAT
Statistics
Matches: 122, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
14 1 0.01
15 12 0.10
16 107 0.88
17 2 0.02
ACGTcount: A:0.32, C:0.38, G:0.23, T:0.07
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Done.