Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006119.1 Hibiscus syriacus cultivar Beakdansim tig00014513_pilon, 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: 56703
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Found at i:1595 original size:58 final size:55
Alignment explanation
Indices: 1505--1617 Score: 172
Period size: 58 Copynumber: 2.0 Consensus size: 55
1495 CCATATCAAG
*
1505 ACTTGGAAGGATTTAACCAAGTCTTTTATGGAACAATACAAACACGTCAATGACATGA
1 ACTTGGAAGGATTTAACCAAGTCGTTTATGGAACAATAC--A-ACGTCAATGACATGA
* *
1563 ACTTGGAAGGATTTAGCCAAGTCGTTTCTGGAACAATACAACGTCAATGACATGA
1 ACTTGGAAGGATTTAACCAAGTCGTTTATGGAACAATACAACGTCAATGACATGA
1618 GGCCAGATCA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
55 15 0.29
56 1 0.02
58 36 0.69
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (55 bp):
ACTTGGAAGGATTTAACCAAGTCGTTTATGGAACAATACAACGTCAATGACATGA
Found at i:13576 original size:21 final size:21
Alignment explanation
Indices: 13550--13612 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
13540 TTTTGGTGCA
*
13550 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
13571 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
13592 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
13613 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:13620 original size:21 final size:21
Alignment explanation
Indices: 13594--13633 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13584 CCCCCTTTGA
*
13594 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
13615 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
13634 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:26911 original size:2 final size:2
Alignment explanation
Indices: 26895--26933 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
26885 TTTATATCAC
*
26895 AT AT TT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26934 TTATGTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:28163 original size:22 final size:21
Alignment explanation
Indices: 28138--28194 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
28128 CTATTTATTT
*
28138 TATTTATTCGTTTTATTTTTAC
1 TATTTATTCGTTTTAGTTTT-C
* *
28160 TATTT-TTCTTTTTGGTTTTC
1 TATTTATTCGTTTTAGTTTTC
*
28180 TATATTATTGGTTTT
1 TAT-TTATTCGTTTT
28195 CCTAACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 4 0.14
21 13 0.46
22 11 0.39
ACGTcount: A:0.14, C:0.07, G:0.09, T:0.70
Consensus pattern (21 bp):
TATTTATTCGTTTTAGTTTTC
Found at i:28215 original size:2 final size:2
Alignment explanation
Indices: 28208--28232 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28198 AACATTTTAT
28208 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28233 TTACTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28263 original size:4 final size:4
Alignment explanation
Indices: 28256--28471 Score: 60
Period size: 4 Copynumber: 52.8 Consensus size: 4
28246 CTTTTTTTTC
* * * *
28256 TTTA TTTA TTTA TTTA TTTCT TTTC TTTC TTTT TTTA TTTA TTTA CTTTA
1 TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA -TTTA
* *
28306 TCTTTA CCTTA -TT- TTTA TTTCC TTTA --TA TTTA TTTTA TTTTA TTTA
1 --TTTA -TTTA TTTA TTTA TTT-A TTTA TTTA TTTA -TTTA -TTTA TTTA
*
28352 TTTTCA TTCTA TTCT- TGTT- TTTA TTTA TTTA TTTA TTATA TATA TTT-
1 -TTT-A TT-TA TT-TA T-TTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA
* * * * * *
28399 TTT- TTAA TTTT TTTA TTTTC TTTA TTT- TTTCC TTTA TTTTC TTTA TCT-
1 TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTT-A TTTA -TTTA TTTA TTTA
* *
28447 TTTA TTTC TTTA TCT- TTT- TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
28472 TCTTTATCTC
Statistics
Matches: 166, Mismatches: 24, Indels: 44
0.71 0.10 0.19
Matches are distributed among these distances:
2 2 0.01
3 21 0.13
4 90 0.54
5 46 0.28
6 7 0.04
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:28275 original size:29 final size:29
Alignment explanation
Indices: 28243--28300 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
28233 TTACTATTAT
*
28243 TTTCTTTTTTTTCTTTATTTATTTATTTA
1 TTTCTTTTCTTTCTTTATTTATTTATTTA
*
28272 TTTCTTTTCTTTCTTTTTTTATTTATTTA
1 TTTCTTTTCTTTCTTTATTTATTTATTTA
28301 CTTTATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (29 bp):
TTTCTTTTCTTTCTTTATTTATTTATTTA
Found at i:28299 original size:55 final size:54
Alignment explanation
Indices: 28239--28528 Score: 164
Period size: 55 Copynumber: 5.3 Consensus size: 54
28229 ATATTTACTA
*
28239 TTATTTTCTTTTTTTTCTTTATTTATTTATTTATTTCTTTTCTTTCTTTTTTTAT
1 TTATTTTCTTTTTTTTCTTTATTTATTTATTTATTTCTTTTATTT-TTTTTTTAT
* * * * * *
28294 TTATTTACTTTATCTTTACCTTA-TT-TTTATTTCCTTTATATTTA-TTTTATTTTAT
1 TTATTTTCTTT-T-TTTTCTTTATTTATTTATTT-ATTTCT-TTTATTTTTTTTTTAT
* * * * * * * *
28349 TTATTTTCATTCTATTCTTGTTTTTATTTATTTATTTATTATATATATTTTTT-T
1 TTATTTTCTTTTTTTTCTT-TATTTATTTATTTATTTCTTTTATTTTTTTTTTAT
* * * * * *
28403 TAATTTT-TTTATTTTCTTTATTT-TTTCCTTTATTT-TCTTTATCTTTTATTTCT
1 TTATTTTCTTTTTTTTCTTTATTTATTT-ATTTATTTCT-TTTATTTTTTTTTTAT
* * * * * * *
28456 TTATCTTT-TTTTATTTTCTTTATCTCATTTTTTTGTTTCATTTGTTTTTATTTTCT
1 TTAT-TTTCTTTT-TTTTCTTTAT-TTATTTATTTATTTCTTTTATTTTTTTTTTAT
*
28512 TTATTTTCTTTATTTTC
1 TTATTTTCTTTTTTTTC
28529 ATTACCTTTT
Statistics
Matches: 178, Mismatches: 40, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
51 4 0.02
52 21 0.12
53 16 0.09
54 17 0.10
55 65 0.37
56 42 0.24
57 13 0.07
ACGTcount: A:0.15, C:0.10, G:0.01, T:0.74
Consensus pattern (54 bp):
TTATTTTCTTTTTTTTCTTTATTTATTTATTTATTTCTTTTATTTTTTTTTTAT
Found at i:28414 original size:31 final size:28
Alignment explanation
Indices: 28317--28532 Score: 104
Period size: 28 Copynumber: 7.5 Consensus size: 28
28307 CTTTACCTTA
* * *
28317 TTTTTATTTCCTTTATATTTATTTTATT
1 TTTTTATTTTCATTATATTTTTTTTATT
*
28345 TTATTTATTTTCATTCTATTCTTGTTTTTATT
1 TT-TTTATTTTCATTATA-T-TT-TTTTTATT
* *
28377 TATTTATTTATTATATATATTTTTTTTAATT
1 TTTTTATTT-TCAT-TATATTTTTTTT-ATT
*
28408 TTTTTATTTTCTTTAT-TTTTTCCTTTATT
1 TTTTTATTTTCATTATATTTTT--TTTATT
* * * *
28437 TTCTTTATCTT--TTAT-TTCTTTATCTT
1 TT-TTTATTTTCATTATATTTTTTTTATT
* * **
28463 TTTTTATTTTCTTTATCTCATTTTT-TT
1 TTTTTATTTTCATTATATTTTTTTTATT
* * * *
28490 GTTTCATTTGT--TTTTATTTTCTTTATT
1 TTTTTATTT-TCATTATATTTTTTTTATT
28517 TTCTTTATTTTCATTA
1 TT-TTTATTTTCATTA
28533 CCTTTTCTTC
Statistics
Matches: 142, Mismatches: 28, Indels: 35
0.69 0.14 0.17
Matches are distributed among these distances:
25 7 0.05
26 14 0.10
27 17 0.12
28 27 0.19
29 22 0.15
30 18 0.13
31 22 0.15
32 12 0.08
33 3 0.02
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (28 bp):
TTTTTATTTTCATTATATTTTTTTTATT
Found at i:28426 original size:15 final size:15
Alignment explanation
Indices: 28314--28518 Score: 56
Period size: 15 Copynumber: 13.5 Consensus size: 15
28304 TATCTTTACC
*
28314 TTATTTTTATTTCCT
1 TTATTTTTATTTTCT
* *
28329 TTATATTTATTTTAT
1 TTATTTTTATTTTCT
*
28344 TT-TATTTATTTTCAT
1 TTATTTTTATTTTC-T
*
28359 TCTATTCTTGT-TTTTAT
1 T-TATT-TT-TATTTTCT
*
28376 TTATTTATTTATTATATAT
1 TTA-TT-TTTATT-T-TCT
*
28395 ATTTTTTTTAATTTT-T
1 -TTATTTTT-ATTTTCT
28411 TTATTTTCT-TTATT-T
1 TTATTTT-TATT-TTCT
*
28426 TT-TCCTTTATTTTCT
1 TTAT-TTTTATTTTCT
28441 TTATCTTTTA-TTTCT
1 TTAT-TTTTATTTTCT
* *
28456 TTATCTTT-TTTTAT
1 TTATTTTTATTTTCT
* * *
28470 TT-TCTTTA-TCTCA
1 TTATTTTTATTTTCT
*
28483 TT-TTTTT-GTTTCAT
1 TTATTTTTATTTTC-T
*
28497 TTGTTTTTATTTTCT
1 TTATTTTTATTTTCT
28512 TTATTTT
1 TTATTTT
28519 CTTTATTTTC
Statistics
Matches: 146, Mismatches: 21, Indels: 46
0.69 0.10 0.22
Matches are distributed among these distances:
13 16 0.11
14 27 0.18
15 55 0.38
16 16 0.11
17 10 0.07
18 11 0.08
19 9 0.06
20 2 0.01
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (15 bp):
TTATTTTTATTTTCT
Found at i:28488 original size:21 final size:20
Alignment explanation
Indices: 28237--28527 Score: 86
Period size: 21 Copynumber: 14.3 Consensus size: 20
28227 ATATATTTAC
*
28237 TATTATTTTCTTTTTTTTCTT
1 TATT-TTTTCTTTATTTTCTT
*
28258 TATTTATTTATTTA-TTTCTTT
1 TATTT-TTTCTTTATTTTC-TT
* * *
28279 TCTTTCTTTTTTTA-TTTATT
1 TATTT-TTTCTTTATTTTCTT
* * ** *
28299 TACTTTATCTTTACCTTATT
1 TATTTTTTCTTTATTTTCTT
* *
28319 T-TTATTTCCTTTATATTTATT
1 TATT-TTTTCTTTAT-TTTCTT
* *
28340 T-TATTTTATTTATTTTCATT
1 TATTTTTTCTTTATTTTC-TT
*
28360 CTATTCTTGTT-TTTA-TTTATT
1 -TATT-TT-TTCTTTATTTTCTT
* * *
28381 TATTTATTATATATATTTTTTT
1 TATTT-TT-TCTTTATTTTCTT
*
28403 TA-ATTTT-TTTATTTTCTT
1 TATTTTTTCTTTATTTTCTT
28421 TATTTTTTCCTTTATTTTCTT
1 TATTTTTT-CTTTATTTTCTT
* * *
28442 TATCTTTTATTTCTTTATCTTT
1 TATTTTTTCTTTATTT-TC-TT
* *
28464 TTTTATTTTCTTTA-TCTCATT
1 TATT-TTTTCTTTATTTTC-TT
* *
28485 T-TTTTGT-TTCATTTGT-TT
1 TATTTTTTCTTTATTT-TCTT
*
28503 T-TATTTTCTTTATTTTCTT
1 TATTTTTTCTTTATTTTCTT
28522 TATTTT
1 TATTTT
28528 CATTACCTTT
Statistics
Matches: 201, Mismatches: 44, Indels: 51
0.68 0.15 0.17
Matches are distributed among these distances:
18 22 0.11
19 30 0.15
20 53 0.26
21 65 0.32
22 16 0.08
23 13 0.06
24 2 0.01
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.75
Consensus pattern (20 bp):
TATTTTTTCTTTATTTTCTT
Found at i:28528 original size:9 final size:9
Alignment explanation
Indices: 28239--28528 Score: 138
Period size: 9 Copynumber: 31.9 Consensus size: 9
28229 ATATTTACTA
28239 TTATTTTCT
1 TTATTTTCT
*
28248 TTTTTTTCT
1 TTATTTTCT
*
28257 TTA-TTTAT
1 TTATTTTCT
*
28265 TTA-TTTAT
1 TTATTTTCT
*
28273 TTCTTTTCT
1 TTATTTTCT
*
28282 TTCTTTT-T
1 TTATTTTCT
*
28290 TTA-TTTAT
1 TTATTTTCT
28298 TTACTTTATCT
1 TTA-TTT-TCT
28309 TTACCTTATT-T
1 TTA--TT-TTCT
*
28320 TTATTTCCT
1 TTATTTTCT
*
28329 TTATATTTATT
1 TTAT-TTT-CT
*
28340 TTATTTTAT
1 TTATTTTCT
*
28349 TTATTTTCA
1 TTATTTTCT
* *
28358 TTCTATTCT
1 TTATTTTCT
*
28367 TGT-TTTTAT
1 T-TATTTTCT
*
28376 TTA-TTTAT
1 TTATTTTCT
* *
28384 TTATTATAT
1 TTATTTTCT
* *
28393 ATATTTTTT
1 TTATTTTCT
28402 TTAATTTT-T
1 TT-ATTTTCT
28411 TTATTTTCT
1 TTATTTTCT
28420 TTATTTTTTCCT
1 TTA--TTTT-CT
28432 TTATTTTCT
1 TTATTTTCT
*
28441 TTA-TCT-T
1 TTATTTTCT
28448 TTA-TTTCT
1 TTATTTTCT
*
28456 TTATCTTTTT
1 TTAT-TTTCT
28466 TTATTTTCT
1 TTATTTTCT
*
28475 TTA-TCTCAT
1 TTATTTTC-T
*
28484 TT-TTTTGT
1 TTATTTTCT
*
28492 TTCATTTGTTT
1 TT-ATTT-TCT
28503 TTATTTTCT
1 TTATTTTCT
28512 TTATTTTCT
1 TTATTTTCT
28521 TTATTTTC
1 TTATTTTC
28529 ATTACCTTTT
Statistics
Matches: 223, Mismatches: 32, Indels: 52
0.73 0.10 0.17
Matches are distributed among these distances:
7 9 0.04
8 48 0.22
9 102 0.46
10 32 0.14
11 22 0.10
12 9 0.04
13 1 0.00
ACGTcount: A:0.15, C:0.10, G:0.01, T:0.74
Consensus pattern (9 bp):
TTATTTTCT
Found at i:30393 original size:19 final size:19
Alignment explanation
Indices: 30360--30398 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30350 TTTAGTGTAG
30360 TGATTATAAATTTTTATTA
1 TGATTATAAATTTTTATTA
*
30379 TGATT-TAAATATTTTTTTA
1 TGATTATAAAT-TTTTATTA
30398 T
1 T
30399 TTTTAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TGATTATAAATTTTTATTA
Found at i:32006 original size:15 final size:15
Alignment explanation
Indices: 31986--32021 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
31976 AAGGGAGATG
31986 AGCCTCTCTTCCGAC
1 AGCCTCTCTTCCGAC
*
32001 AGCCTCTCTTCTGAC
1 AGCCTCTCTTCCGAC
32016 AGCCTC
1 AGCCTC
32022 CCTAAACGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.44, G:0.14, T:0.28
Consensus pattern (15 bp):
AGCCTCTCTTCCGAC
Found at i:32757 original size:18 final size:18
Alignment explanation
Indices: 32727--32762 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
32717 TGTAACCATT
32727 AAATAATAAAATAATTTA
1 AAATAATAAAATAATTTA
32745 AAAT-ATAATAATAATTTA
1 AAATAATAA-AATAATTTA
32763 TTATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAATAAAATAATTTA
Found at i:34568 original size:29 final size:30
Alignment explanation
Indices: 34526--34591 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
34516 CCCGAAGGAC
34526 CTATCCAAAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAAAGGTCACAAAGAACCCCGGTAA
*
34555 CTATCCAAAGGTCACAAAGAACCTCGGTAA
1 CTATCCAAAGGTCACAAAGAACCCCGGTAA
*
34585 CTGTCCA
1 CTATCCA
34592 TAGATCTCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (30 bp):
CTATCCAAAGGTCACAAAGAACCCCGGTAA
Found at i:34585 original size:30 final size:30
Alignment explanation
Indices: 34526--34614 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
34516 CCCGAAGGAC
*
34526 CTATCCAAAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAAAGGTCACAAAGAACCTCGGTAA
34555 CTATCCAAAGGTCACAAAGAACCTCGGTAA
1 CTATCCAAAGGTCACAAAGAACCTCGGTAA
* * * * * *
34585 CTGTCCATAGATCTCGAAGAACCTAGGTAA
1 CTATCCAAAGGTCACAAAGAACCTCGGTAA
34615 ACTGTCCATA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
29 19 0.37
30 33 0.63
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (30 bp):
CTATCCAAAGGTCACAAAGAACCTCGGTAA
Found at i:34621 original size:31 final size:31
Alignment explanation
Indices: 34571--34647 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
34561 AAAGGTCACA
*
34571 AAGAACCTCGGT-AACTGTCCATA-GATCTCG
1 AAGAACCTAGGTAAACTGTCCATATG-TCTCG
34601 AAGAACCTAGGTAAACTGTCCATATGTCTCG
1 AAGAACCTAGGTAAACTGTCCATATGTCTCG
*
34632 AA-AGACATAGGTAAAC
1 AAGA-ACCTAGGTAAAC
34648 CCTCAACTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 12 0.29
31 29 0.69
32 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (31 bp):
AAGAACCTAGGTAAACTGTCCATATGTCTCG
Found at i:34998 original size:12 final size:12
Alignment explanation
Indices: 34981--35005 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34971 ATATATCATG
34981 TCACATAACTTA
1 TCACATAACTTA
34993 TCACATAACTTA
1 TCACATAACTTA
35005 T
1 T
35006 TTGATATTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCACATAACTTA
Found at i:35650 original size:64 final size:63
Alignment explanation
Indices: 35571--35732 Score: 166
Period size: 64 Copynumber: 2.5 Consensus size: 63
35561 TATTTAACAT
* * * * *
35571 GTGCATTGATGCACTACTCATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTAATCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * ** *
35634 GATGCATCGATGCACTAATTATGCATCGATGCATTAATTACATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTAATCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
*
35698 GTGCATCGATGCATATTGAAT-ATGCATCGATACAC
1 GTGCATCGATGC--ACT-AATCATGCATCGATACAC
35733 CTTGCCCATA
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
63 17 0.21
64 47 0.58
65 14 0.17
66 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (63 bp):
GTGCATCGATGCACTAATCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:35659 original size:19 final size:19
Alignment explanation
Indices: 35635--35673 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
35625 TTTTAAGGGG
35635 ATGCATCGATGCACTAATT
1 ATGCATCGATGCACTAATT
*
35654 ATGCATCGATGCATTAATT
1 ATGCATCGATGCACTAATT
35673 A
1 A
35674 CATTCGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (19 bp):
ATGCATCGATGCACTAATT
Found at i:39107 original size:31 final size:31
Alignment explanation
Indices: 39060--39124 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
39050 GAACCTCTGC
* * *
39060 AACTGTCCATAGGTCTCGAA-GAACCTAGGTA
1 AACTATCCATAGGTCTCAAATGAA-ATAGGTA
*
39091 AACTATCCATATGTCTCAAATGAAATAGGTA
1 AACTATCCATAGGTCTCAAATGAAATAGGTA
39122 AAC
1 AAC
39125 CCTCAACTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (31 bp):
AACTATCCATAGGTCTCAAATGAAATAGGTA
Found at i:40030 original size:20 final size:22
Alignment explanation
Indices: 40005--40062 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
39995 TTCCCCTTGA
40005 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
40025 AGTGCATCGATACATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
40048 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
40063 CTACTCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:40058 original size:24 final size:20
Alignment explanation
Indices: 40005--40081 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
39995 TTCCCCTTGA
*
40005 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATACATTCTAC
40025 AGTGCATCGATACATTCTTTAAC
1 AGTGCATCGATACATTC--T-AC
* *
40048 ATGTGCATCGATGCACTACT-C
1 A-GTGCATCGATACA-TTCTAC
40069 A-TGCATCGATACA
1 AGTGCATCGATACA
40082 CAAATTACTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
19 11 0.23
20 16 0.33
21 2 0.04
22 1 0.02
23 4 0.08
24 12 0.25
25 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:40128 original size:64 final size:63
Alignment explanation
Indices: 40050--40190 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
40040 TCTTTAACAT
* * *
40050 GTGCATCGATGCACTACTCATGCATCGATACA-CAAATTACTTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACTCATGCATCGATACATC-AATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
40113 GATGCATCGATGCACTCCTTATGCATCGATGCATCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACTCATGCATCGATACATCAATTACATTCGATGTTTCATCTTTAAAGA
40177 GTGCATCGATGCAC
1 GTGCATCGATGCAC
40191 ATTGAATATG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 19 0.28
64 47 0.70
65 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACTCATGCATCGATACATCAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:44783 original size:18 final size:18
Alignment explanation
Indices: 44755--44804 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
44745 ATGACTTTAT
*
44755 CTCTT-GATCGTTCTTAA
1 CTCTTCGATCGTTCCTAA
44772 CTCTTCGATCGTTCCTAA
1 CTCTTCGATCGTTCCTAA
*
44790 CTCTTCGATTGTTCC
1 CTCTTCGATCGTTCC
44805 AGAACTTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 5 0.17
18 25 0.83
ACGTcount: A:0.14, C:0.30, G:0.12, T:0.44
Consensus pattern (18 bp):
CTCTTCGATCGTTCCTAA
Found at i:48154 original size:191 final size:190
Alignment explanation
Indices: 47890--48312 Score: 632
Period size: 191 Copynumber: 2.2 Consensus size: 190
47880 AGGATGACTA
* * * *
47890 ACTTGAACAAAATCT-ATTTGACTACTCTTCCGTGAAGATCATACTCGAAATTAGATTGCTTCAC
1 ACTTG-ACAAAATCTAATTTCACTACTCTTTCGTGAAAATCAAACTCGAAATTAGATTGCTTCAC
* *
47954 TATTCTTCCGTGAAGGTTTCATACTTTACTGAAAAATTCATTCCACTACTCTTCCGTGGAGAGCG
65 TACTCTTCCGTGAAGGTTTCATACTTTACTGAAAAATCCATTCCACTACTCTTCCGTGGAGAGCG
* * * *
48019 AATTTTGATCTTACTTCTGAATTTTTCTTCACTACTCTTTCTTGAAGACTGAAAATGATTG
130 AATTTTGATCTTACTTCTGAATTTTGCTTCACTACTCTTCCATGAAGACTAAAAATGATTG
* * *
48080 GCTTGACAAGAATCTAATTTCACTACTCTTTCGTGAAAATCAAACTCGCAATTTGATTGCTTCAC
1 ACTTGACAA-AATCTAATTTCACTACTCTTTCGTGAAAATCAAACTCGAAATTAGATTGCTTCAC
* *
48145 TACTCTTCCGTGAAGGTTTCATACTTTGCTGTAAAATCCATTCCACTACTCTTCCGTGGAGAGCG
65 TACTCTTCCGTGAAGGTTTCATACTTTACTGAAAAATCCATTCCACTACTCTTCCGTGGAGAGCG
* *
48210 AATTTTGATCTTGCTTCTGACTTTTGCTTCACTACTCTTCCATGAAGACTAAAAATGATTG
130 AATTTTGATCTTACTTCTGAATTTTGCTTCACTACTCTTCCATGAAGACTAAAAATGATTG
* * *
48271 ACTTGACAAAAATCTAATTTCACTATTCTTTAGTGAATATCA
1 ACTTGAC-AAAATCTAATTTCACTACTCTTTCGTGAAAATCA
48313 GATTGATTTG
Statistics
Matches: 209, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
189 4 0.02
190 9 0.04
191 194 0.93
192 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (190 bp):
ACTTGACAAAATCTAATTTCACTACTCTTTCGTGAAAATCAAACTCGAAATTAGATTGCTTCACT
ACTCTTCCGTGAAGGTTTCATACTTTACTGAAAAATCCATTCCACTACTCTTCCGTGGAGAGCGA
ATTTTGATCTTACTTCTGAATTTTGCTTCACTACTCTTCCATGAAGACTAAAAATGATTG
Found at i:48421 original size:20 final size:20
Alignment explanation
Indices: 48395--48496 Score: 168
Period size: 20 Copynumber: 5.1 Consensus size: 20
48385 AGACTGACAG
* *
48395 ATGACCCGAAGGATTTACTA
1 ATGACCCGAAGGCTTTACAA
*
48415 CTGACCCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
*
48435 ATGACCAGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
48455 ATGACCCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
48475 ATGACCCGAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
48495 AT
1 AT
48497 TTGTGGGAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
ATGACCCGAAGGCTTTACAA
Found at i:49099 original size:22 final size:22
Alignment explanation
Indices: 49073--49169 Score: 140
Period size: 22 Copynumber: 4.4 Consensus size: 22
49063 GATAAAGCTG
* *
49073 TCATCTTTGTAAAGATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
49095 TCATCTTTGAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
49117 TCATCTTTGAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
49139 TTAACTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
49161 TCATCTTTG
1 TCATCTTTG
49170 CAACATGTAG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 67 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:49353 original size:55 final size:56
Alignment explanation
Indices: 49255--49364 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 56
49245 CTTGAAACAA
* *
49255 TTCACAATAATGATTTATCATAATTCCTTTCATGTCTCCACATCTAATAAGATCTC
1 TTCACAAGAAGGATTTATCATAATTCCTTTCATGTCTCCACATCTAATAAGATCTC
* *
49311 TTCACAAGAAGGATTTATCCTAA-TCCTTTCATGTCTCTACATCTAATAAGATCT
1 TTCACAAGAAGGATTTATCATAATTCCTTTCATGTCTCCACATCTAATAAGATCT
49365 TGAACAAGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
55 30 0.60
56 20 0.40
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (56 bp):
TTCACAAGAAGGATTTATCATAATTCCTTTCATGTCTCCACATCTAATAAGATCTC
Found at i:53249 original size:18 final size:18
Alignment explanation
Indices: 53199--53249 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
53189 TTATCATGCT
53199 ATGCATAATCATGAATGTAA
1 ATGCAT-AT-ATGAATGTAA
*
53219 ATGCA-ACTGTGAATGTAA
1 ATGCATA-TATGAATGTAA
53237 ATGCATATATGAA
1 ATGCATATATGAA
53250 AGAGTGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 20 0.74
19 2 0.07
20 5 0.19
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (18 bp):
ATGCATATATGAATGTAA
Found at i:55541 original size:22 final size:25
Alignment explanation
Indices: 55495--55549 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 25
55485 ATACTAATAT
*
55495 TAATTAATCATATAATAATAGTTAA
1 TAATTAATAATATAATAATAGTTAA
55520 TAATTAA-AATATAA-AATA-TTAA
1 TAATTAATAATATAATAATAGTTAA
*
55542 AAATTAAT
1 TAATTAAT
55550 TAACTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 10 0.37
23 4 0.15
24 6 0.22
25 7 0.26
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
TAATTAATAATATAATAATAGTTAA
Found at i:55707 original size:15 final size:17
Alignment explanation
Indices: 55687--55722 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
55677 TAGCAGTGAC
55687 TAAAAT-AAAA-AAAAT
1 TAAAATAAAAACAAAAT
55702 TAAAATAAAAACAAAAT
1 TAAAATAAAAACAAAAT
55719 TAAA
1 TAAA
55723 GGTATGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
17 9 0.47
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (17 bp):
TAAAATAAAAACAAAAT
Done.