Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011770.1 Corchorus olitorius cultivar O-4 contig11803, 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: 2649
ACGTcount: A:0.18, C:0.30, G:0.29, T:0.23
Found at i:27 original size:13 final size:13
Alignment explanation
Indices: 9--63 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
1 CTTGCCGA
9 TGGCACTCGGCCT
1 TGGCACTCGGCCT
22 TGGCACTCGGGCTTGCT
1 TGGCACTC-GGC---CT
39 GATGGCACTCGGCCT
1 --TGGCACTCGGCCT
54 TGGCACTCGG
1 TGGCACTCGG
64 GACTTGCCGA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 18 0.50
14 3 0.08
15 2 0.06
17 2 0.06
18 3 0.08
19 8 0.22
ACGTcount: A:0.09, C:0.33, G:0.35, T:0.24
Consensus pattern (13 bp):
TGGCACTCGGCCT
Found at i:76 original size:33 final size:33
Alignment explanation
Indices: 1--1442 Score: 587
Period size: 33 Copynumber: 40.5 Consensus size: 33
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGG-
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
*
33 CTTGCTGATGGCACTCGGCCTTGGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
66 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
*
99 CTTGCTGATGGCACTCGGCCTTGGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
*
132 CTTGCCGATGGCACTCGGCACCTGCCGATGGCACTCGGCA
1 CTTGCCGATGGCACTCGG--CCT-----TGGCACTCGGGA
* * * *
172 -TTGGC-ACTCGGGACT-TGCCGATGGCACTCGGGA
1 CTTGCCGA-T-GGCACTCGGCC-TTGGCACTCGGGA
* *
205 CTTGCCGATGGCACTCGACACTTGCCGACTGGCACTCGGCA
1 CTTGCCGATGGCACTCG------GCC--TTGGCACTCGGGA
*
246 CTTGCCGATGGCACTAGGCCTTGGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
* *
279 GTTGCCGATGGCACTCGGGAGTTGCCGATGGCACTCGGGA
1 CTTGCCGATGGCACTC----G--GCC-TTGGCACTCGGGA
*
319 CTTGCCGATGGCACTCGGGACTTGCCGATGGCACTCGGGA
1 CTTGCCGATGGCACTC--G----GCC-TTGGCACTCGGGA
359 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
* *
392 CTTGCCGATGGCACTCGAGACTTGCCGATGGCAACTC-GGC
1 CTTGCCGATGGCACTC--G----GCC-TTGGC-ACTCGGGA
* * * * **
432 CTTGGC-ACTCGGGACT-TGCCGATGGCACTCGACA
1 CTTGCCGA-T-GGCACTCGGCC-TTGGCACTCGGGA
* *
466 CTTGCCGATGGCACTCGGCACTTGCCGA-T-GGCA
1 CTTGCCGATGGCACTCGGC-CTTGGC-ACTCGGGA
* * * *
499 CTGGCC-TTGGCACTCGGCACTTGCCGA-T-GGCA
1 CTTGCCGATGGCACTCGGC-CTTGGC-ACTCGGGA
* * *
531 CTAGGCC-TTGGCACTCGGGAGTTGCCGATGGCACTCGGGA
1 CT-TGCCGATGGCACTC----G--GCC-TTGGCACTCGGGA
* * *
571 GTTGCCGATGGCACTCGGGACTTGCCGATGGCACTC-GGC
1 CTTGCCGATGGCACTC--G----GCC-TTGGCACTCGGGA
* * * *
610 CTTGGC-ACTCGGCACT-TGCCGATGGCACTCGGCA
1 CTTGCCGA-T-GGCACTCGGCC-TTGGCACTCGGGA
*
644 CTTGCCGATGGCACTCGGGACTTGCTGATGGCACTCGGCA
1 CTTGCCGATGGCACTC-GG-C---CT--TGGCACTCGGGA
**
684 CTTGCCGATGGCACTCGGCCTAAGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
*
717 CATGCCGATGGCACTCGGCCTTGGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
* *
750 CTTGCCGATGG-ACT-TG-CTGATGGCACTC-GGC
1 CTTGCCGATGGCACTCGGCCT--TGGCACTCGGGA
* * * *
781 CTTGGC-ACTCGGGACT-TGCCGATGGCACTCGGGA
1 CTTGCCGA-T-GGCACTCGGCC-TTGGCACTCGGGA
* *
815 CTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGCA
1 CTTGCCGATGGCACTCG------GCC-TTGGCACTCGGGA
* *
855 CTTGCCGATGGCACTAGGCCTTGGCACTCGGCA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
*
888 CTTGCCGATGGCACTAGGCCTTGGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
* * **
921 -TTGCCGATGGCACTCGGGACTTGCCGA-T-GACA
1 CTTGCCGATGGCACTC-GGCCTTGGC-ACTCGGGA
* * *
953 CTCGGCC-TTGGCACTCGGGACTTGCTGATGGCACTC-GGC
1 CT-TGCCGATGGCACTC-GG-C---CT--TGGCACTCGGGA
* * * * *
992 CTTGGC-ACTCGGGACT-TGCCGATGGCACTCGGCA
1 CTTGCCGA-T-GGCACTCGGCC-TTGGCACTCGGGA
* *
1026 CCTGCCGATGGCACTCGGCATTGGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
* **
1059 CTTGCCGATGGCACTCGGGACTTGCCGATAGCACTCGACA
1 CTTGCCGATGGCACTC-GGCCTT---G---GCACTCGGGA
* *
1099 CTTGCCGATGGCACTCGGCACTTGCCGA-T-GGCA
1 CTTGCCGATGGCACTCGGC-CTTGGC-ACTCGGGA
* * *
1132 CTAGGCC-TTGGCACTCGGGAGTTGCCGATGGCACTCGGGA
1 CT-TGCCGATGGCACTC----G--GCC-TTGGCACTCGGGA
* *
1172 GTTGCCGATGGCACTCGGGACTTGCCGATGGCACTCGGGA
1 CTTGCCGATGGCACTC--G----GCC-TTGGCACTCGGGA
* *
1212 CCTTGCCGATGGCACTCGGGACTTGCCGATGGCACTC-GGC
1 -CTTGCCGATGGCACTC--G----GCC-TTGGCACTCGGGA
* * * * *
1252 CTTGGC-ACTCGGGACT-TGCCGATGGCACTCGAGA
1 CTTGCCGA-T-GGCACTCGGCC-TTGGCACTCGGGA
1286 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
* *
1319 CTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGCA
1 CTTGCCGATGGCACTCG------GCC-TTGGCACTCGGGA
* *
1359 CTTGCCGATGGCACTAGGCCTTGGCACTCGGCA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
*
1392 CTTGCCGATGGCACTAGGCCTTGGCACTCGGGA
1 CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
*
1425 GTTGCCGATGGCACTCGG
1 CTTGCCGATGGCACTCGG
1443 GACTTGCCGA
Statistics
Matches: 1132, Mismatches: 139, Indels: 277
0.73 0.09 0.18
Matches are distributed among these distances:
30 3 0.00
31 9 0.01
32 87 0.08
33 488 0.43
34 83 0.07
35 19 0.02
36 1 0.00
37 10 0.01
38 19 0.02
39 59 0.05
40 283 0.25
41 71 0.06
ACGTcount: A:0.15, C:0.32, G:0.33, T:0.21
Consensus pattern (33 bp):
CTTGCCGATGGCACTCGGCCTTGGCACTCGGGA
Found at i:79 original size:20 final size:20
Alignment explanation
Indices: 54--1462 Score: 1032
Period size: 20 Copynumber: 77.5 Consensus size: 20
44 CACTCGGCCT
54 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
74 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
*
87 TGGCACTCGGGACTTGCTGA
1 TGGCACTCGGGACTTGCCGA
*
107 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
120 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
140 TGGCACTCGGCACCTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
160 TGGCACTC-GG-CAT-----
1 TGGCACTCGGGACTTGCCGA
173 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
193 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
**
213 TGGCACTCGACACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
233 CTGGCACTCGGCACTTGCCGA
1 -TGGCACTCGGGACTTGCCGA
* *
254 TGGCACT----A--GGCC-T
1 TGGCACTCGGGACTTGCCGA
*
267 TGGCACTCGGGAGTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
287 TGGCACTCGGGAGTTGCCGA
1 TGGCACTCGGGACTTGCCGA
307 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
327 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
347 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
367 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
380 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
400 TGGCACTCGAGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
420 TGGCAACTC--G----GCC-T
1 TGGC-ACTCGGGACTTGCCGA
434 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
**
454 TGGCACTCGACACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
474 TGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
494 TGGCACT---G----GCC-T
1 TGGCACTCGGGACTTGCCGA
*
506 TGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
526 TGGCACT----A--GGCC-T
1 TGGCACTCGGGACTTGCCGA
*
539 TGGCACTCGGGAGTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
559 TGGCACTCGGGAGTTGCCGA
1 TGGCACTCGGGACTTGCCGA
579 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
599 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
*
612 TGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
632 TGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
652 TGGCACTCGGGACTTGCTGA
1 TGGCACTCGGGACTTGCCGA
*
672 TGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
692 TGGCACTC--G----GCCTA
1 TGGCACTCGGGACTTGCCGA
* *
706 -AGCACTCGGGACATGCCGA
1 TGGCACTCGGGACTTGCCGA
*
725 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
738 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
758 TGG-ACTTGCTGATGGCACTCGGCC-T
1 TGGCAC-T-C-G--GG-ACT-TGCCGA
783 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
803 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
**
823 TGGCACTCGACACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
843 TGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
863 TGGCACT----A--GGCC-T
1 TGGCACTCGGGACTTGCCGA
*
876 TGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
896 TGGCACT----A--GGCC-T
1 TGGCACTCGGGACTTGCCGA
909 TGGCACTCGGGA-TTGCCGA
1 TGGCACTCGGGACTTGCCGA
928 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
948 TGACACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
*
961 TGGCACTCGGGACTTGCTGA
1 TGGCACTCGGGACTTGCCGA
*
981 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
994 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
1014 TGGCACTCGGCACCTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
1034 TGGCACTC-GG-CAT-----
1 TGGCACTCGGGACTTGCCGA
1047 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
1067 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* **
1087 TAGCACTCGACACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
1107 TGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
1127 TGGCACT----A--GGCC-T
1 TGGCACTCGGGACTTGCCGA
*
1140 TGGCACTCGGGAGTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
1160 TGGCACTCGGGAGTTGCCGA
1 TGGCACTCGGGACTTGCCGA
1180 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
1200 TGGCACTCGGGACCTTGCCGA
1 TGGCACTCGGGA-CTTGCCGA
1221 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
1241 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
1254 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
1274 TGGCACTCGAGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
1294 TGGCACTC--G----GCC-T
1 TGGCACTCGGGACTTGCCGA
1307 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
**
1327 TGGCACTCGACACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
*
1347 TGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
1367 TGGCACT----A--GGCC-T
1 TGGCACTCGGGACTTGCCGA
*
1380 TGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
* *
1400 TGGCACT----A--GGCC-T
1 TGGCACTCGGGACTTGCCGA
*
1413 TGGCACTCGGGAGTTGCCGA
1 TGGCACTCGGGACTTGCCGA
1433 TGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA
1453 TGGCACTCGG
1 TGGCACTCGG
1463 CCTTGACACT
Statistics
Matches: 1124, Mismatches: 105, Indels: 320
0.73 0.07 0.21
Matches are distributed among these distances:
12 7 0.01
13 149 0.13
14 58 0.05
15 17 0.02
16 7 0.01
17 7 0.01
18 16 0.01
19 73 0.06
20 727 0.65
21 46 0.04
22 1 0.00
23 1 0.00
24 3 0.00
25 7 0.01
26 5 0.00
ACGTcount: A:0.15, C:0.32, G:0.33, T:0.21
Consensus pattern (20 bp):
TGGCACTCGGGACTTGCCGA
Found at i:116 original size:53 final size:54
Alignment explanation
Indices: 54--1462 Score: 701
Period size: 53 Copynumber: 26.2 Consensus size: 54
44 CACTCGGCCT
* *
54 TGGCACTCGGGACTTGCCGATGGCACTCGGCC-TTGGCACTCGGGACTTGCTGA
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCGATGGCACTCGGGACTTGCCGA
* * * * * *
107 TGGCACTC-GGCCTTGGC-ACTCGGGACT-TGCCGATGGCACTCGGCACCTGCCGA
1 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCCGATGGCACTCGGGACTTGCCGA
* * * *
160 TGGCACTCGGCA-TTGGC-ACTCGGGACT-TGCCGATGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCCGATGGCACTCGGGACTTGCCGA
** * * * * *
213 TGGCACTCGACACTTGCCGACTGGCACTCGGCAC-TTGCCGA-T-GGCACTAGGCC-T
1 TGGCACTCGGGACTTGCCGA-TGGCACTCGGC-CGATGGC-ACTCGGGACT-TGCCGA
*
267 TGGCACTCGGGAGTTGCCGATGGCACTCGGGAGTTGCCGATGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTC----G--GCCGATGGCACTCGGGACTTGCCGA
* * * *
327 TGGCACTCGGGACTTGCCGATGGCACTCGG--GACTTGC-CGAT-GGCACTCGGCC-T
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCGA-TGGCAC--TCGGGACT-TGCCGA
* * * * * *
380 TGGCACTCGGGACTTGCCGATGGCACTCGAGAC-TTGCCGA-T-GGCAACTCGGCC-T
1 TGGCACTCGGGACTTGCCGATGGCACTCG-GCCGATGGC-ACTCGG-GACT-TGCCGA
*
434 TGGCACTCGGGACTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTCG------GCCGATGGCACTCGGGACTTGCCGA
* * * * *
494 TGGCACT--GGCCTTGGC-ACTCGGCACT-TGCCGATGGCACT----A--GGCC-T
1 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCCGATGGCACTCGGGACTTGCCGA
*
539 TGGCACTCGGGAGTTGCCGATGGCACTCGGGAGTTGCCGATGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTC----G--GCCGATGGCACTCGGGACTTGCCGA
* * * *
599 TGGCACTC-GGCCTTGGC-ACTCGGCACT-TGCCGATGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCCGATGGCACTCGGGACTTGCCGA
* * * * * *
652 TGGCACTCGGGACTTGCTGATGGCACTCGGCAC-TTGCCGA-T-GGCACTCGGCCTA
1 TGGCACTCGGGACTTGCCGATGGCACTCGGC-CGATGGC-ACTCGGGACT-TGCCGA
* * *
706 -AGCACTCGGGACATGCCGATGGCACTCGGCC-TTGGCACTCGGGACTTGCC--
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCGATGGCACTCGGGACTTGCCGA
* *
756 --G-A-T--GGACTTGCTGATGGCACTCGGCC-TTGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCGATGGCACTCGGGACTTGCCGA
*
803 TGGCACTCGGGACTTGCCGATGGCACTCGACACTTGCCGATGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTCG------GCCGATGGCACTCGGGACTTGCCGA
* * * * * *
863 TGGCACT-AGGCCTTGGC-ACTCGGCACT-TGCCGATGGCACT----A--GGCC-T
1 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCCGATGGCACTCGGGACTTGCCGA
* ** * *
909 TGGCACTCGGGA-TTGCCGATGGCACTCGG--GACTTGC-CGAT-GACACTCGGCC-T
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCGA-TGGCAC--TCGGGACT-TGCCGA
* *
961 TGGCACTCGGGACTTGCTGATGGCACTCGGCC-TTGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCGATGGCACTCGGGACTTGCCGA
* *
1014 TGGCACTCGGCACCTGCCGATGGCACTCGG-C-ATTGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCGA-TGGCACTCGGGACTTGCCGA
* *
1067 TGGCACTCGGGACTTGCCGATAGCACTCGACACTTGCCGATGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTCG------GCCGATGGCACTCGGGACTTGCCGA
* * * * * * *
1127 TGGCACT-AGGCCTTGGC-ACTCGGGAGT-TGCCGATGGCACTCGGGAGTTGCCGA
1 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCCGATGGCACTCGGGACTTGCCGA
1180 TGGCACTCGGGACTTGCCGATGGCACTCGGGACCTTGCCGATGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTC--G-----GCCGATGGCACTCGGGACTTGCCGA
* * * * *
1241 TGGCACTC-GGCCTTGGC-ACTCGGGACT-TGCCGATGGCACTCGAGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCCGATGGCACTCGGGACTTGCCGA
* * * * **
1294 TGGCACTC-GGCCTTGGC-ACTCGGGACT-TGCCGATGGCACTCGACACTTGCCGA
1 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCCGATGGCACTCGGGACTTGCCGA
* * * *
1347 TGGCACTCGGCACTTGCCGATGGCACTAGGCC-TTGGCACTCGGCACTTGCCGA
1 TGGCACTCGGGACTTGCCGATGGCACTCGGCCGATGGCACTCGGGACTTGCCGA
* * * * * *
1400 TGGCACT-AGGCCTTGGC-ACTCGGGAGT-TGCCGATGGCACTCGGGACTTGCCGA
1 TGGCACTCGGGACTTGCCGA-T-GGCACTCGGCCGATGGCACTCGGGACTTGCCGA
1453 TGGCACTCGG
1 TGGCACTCGG
1463 CCTTGACACT
Statistics
Matches: 1078, Mismatches: 145, Indels: 265
0.72 0.10 0.18
Matches are distributed among these distances:
44 3 0.00
45 56 0.05
46 23 0.02
47 14 0.01
48 3 0.00
49 4 0.00
50 1 0.00
51 4 0.00
52 67 0.06
53 530 0.49
54 115 0.11
55 17 0.02
56 3 0.00
57 3 0.00
58 13 0.01
59 52 0.05
60 130 0.12
61 40 0.04
ACGTcount: A:0.15, C:0.32, G:0.33, T:0.21
Consensus pattern (54 bp):
TGGCACTCGGGACTTGCCGATGGCACTCGGCCGATGGCACTCGGGACTTGCCGA
Found at i:617 original size:13 final size:14
Alignment explanation
Indices: 599--627 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
589 GACTTGCCGA
599 TGGCACTCGGC-CT
1 TGGCACTCGGCACT
612 TGGCACTCGGCACT
1 TGGCACTCGGCACT
626 TG
1 TG
628 CCGATGGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.10, C:0.34, G:0.31, T:0.24
Consensus pattern (14 bp):
TGGCACTCGGCACT
Done.