Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002037.1 Hibiscus syriacus cultivar Beakdansim tig00004153_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: 58840
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1283 original size:3 final size:3
Alignment explanation
Indices: 1275--1323 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
1265 ATTTATCATT
* *
1275 TAA TAA TAA TAA TAA TAA TAT TAA T-A TAA TAA T-A TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1321 TAA
1 TAA
1324 ATGAGACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3240 original size:24 final size:24
Alignment explanation
Indices: 3212--3263 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
3202 AATGTTGCAA
3212 CATCATCTCAGTAATCCAGTCCAG
1 CATCATCTCAGTAATCCAGTCCAG
3236 CATCATCTCAGTAATCCAGTCCAG
1 CATCATCTCAGTAATCCAGTCCAG
3260 CATC
1 CATC
3264 GATGCTCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.35, G:0.12, T:0.25
Consensus pattern (24 bp):
CATCATCTCAGTAATCCAGTCCAG
Found at i:14164 original size:16 final size:16
Alignment explanation
Indices: 14139--14184 Score: 83
Period size: 16 Copynumber: 2.8 Consensus size: 16
14129 TCGCCGACCG
14139 AATTTCACTATTCACGA
1 AATTT-ACTATTCACGA
14156 AATTTACTATTCACGA
1 AATTTACTATTCACGA
14172 AATTTACTATTCA
1 AATTTACTATTCA
14185 TGTGAATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 24 0.83
17 5 0.17
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (16 bp):
AATTTACTATTCACGA
Found at i:19156 original size:23 final size:22
Alignment explanation
Indices: 19100--19185 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 22
19090 AAAACCCCAG
*
19100 GGGGGTATCGATTCCCC-T--A
1 GGGGGAATCGATTCCCCTTCAA
* *
19119 GGGGGACTCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
19142 GGGGGAATCGATTCCCCCTTCAA
1 GGGGGAATCGATT-CCCCTTCAA
* *
19165 GGGGGTATCAATTCCCTCTTC
1 GGGGGAATCGATTCCC-CTTC
19186 CCTATAATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 14 0.26
20 1 0.02
22 3 0.06
23 29 0.54
24 7 0.13
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:25606 original size:7 final size:7
Alignment explanation
Indices: 25589--25694 Score: 72
Period size: 7 Copynumber: 15.0 Consensus size: 7
25579 AAGAGATAAA
25589 GTTTA-G
1 GTTTAGG
25595 GTTTAGG
1 GTTTAGG
*
25602 GTTTATG
1 GTTTAGG
* *
25609 TTTTAAGAT
1 GTTT-AG-G
*
25618 GTTTAAG
1 GTTTAGG
*
25625 GTTTAGT
1 GTTTAGG
25632 GTTTAGG
1 GTTTAGG
*
25639 GATTAGG
1 GTTTAGG
*
25646 GGTTAGG
1 GTTTAGG
*
25653 GGTTAGG
1 GTTTAGG
*
25660 GGTTATGG
1 GTTTA-GG
25668 G-TTAGG
1 GTTTAGG
*
25674 GTTTAGA
1 GTTTAGG
25681 GTTTAGG
1 GTTTAGG
*
25688 TTTTAGG
1 GTTTAGG
25695 ATTTTTAATA
Statistics
Matches: 80, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
6 8 0.10
7 64 0.80
8 5 0.06
9 3 0.04
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:25783 original size:20 final size:20
Alignment explanation
Indices: 25754--25798 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
25744 ATATAACATT
*
25754 TTTTCGAGCTGCTCACGAAC
1 TTTTCAAGCTGCTCACGAAC
*
25774 TTTTCAAGCTGTTCACGAAC
1 TTTTCAAGCTGCTCACGAAC
25794 TTTTC
1 TTTTC
25799 GAGTCGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.38
Consensus pattern (20 bp):
TTTTCAAGCTGCTCACGAAC
Found at i:27020 original size:2 final size:2
Alignment explanation
Indices: 27013--27039 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27003 AATGTAAACT
27013 TA 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 TA T
27040 TTCTGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28369 original size:28 final size:29
Alignment explanation
Indices: 28287--28370 Score: 136
Period size: 29 Copynumber: 2.9 Consensus size: 29
28277 CATTGACAGC
*
28287 ATAGGTCGTCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
28316 ATAGGTCGCCATGCACGCCCGGCGTCC-T
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
28344 ATAAGGTCGCCATGCACGCCC-GCGTCC
1 AT-AGGTCGCCATGCACGCCCGGCGTCC
28371 AACATTCTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
28 9 0.17
29 44 0.83
ACGTcount: A:0.15, C:0.38, G:0.27, T:0.19
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCTT
Found at i:29163 original size:21 final size:21
Alignment explanation
Indices: 29138--29181 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
29128 AATCTAGTTA
29138 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
29159 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
29180 AT
1 AT
29182 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:29601 original size:14 final size:14
Alignment explanation
Indices: 29582--29608 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29572 AGTAATTTAT
29582 TATTTTTTGTTGTC
1 TATTTTTTGTTGTC
29596 TATTTTTTGTTGT
1 TATTTTTTGTTGT
29609 TGTGTATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
TATTTTTTGTTGTC
Found at i:29608 original size:17 final size:17
Alignment explanation
Indices: 29579--29611 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29569 GTGAGTAATT
29579 TATTATTTTTTGTTGTC
1 TATTATTTTTTGTTGTC
29596 TATT-TTTTGTTGTTGT
1 TATTATTTT-TTGTTGT
29612 GTATGTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.73
Consensus pattern (17 bp):
TATTATTTTTTGTTGTC
Found at i:32903 original size:60 final size:60
Alignment explanation
Indices: 32831--33624 Score: 1410
Period size: 60 Copynumber: 13.2 Consensus size: 60
32821 GTATTTATAA
* *
32831 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
* * * *
32891 GATTTATTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
* * *
32951 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTCATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
* *
33011 GA-TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
*
33070 GATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
33130 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
* *
33190 GATTTAGTAATGATTAGTTATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
33250 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
*
33310 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATAATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
* * *
33370 GATTTAATAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
*
33430 GATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
33490 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
33550 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
33610 GATTTAGTAATGATT
1 GATTTAGTAATGATT
33625 TGATAGTAAT
Statistics
Matches: 707, Mismatches: 26, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
59 58 0.08
60 649 0.92
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
Found at i:33017 original size:10 final size:10
Alignment explanation
Indices: 33004--33030 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
32994 AATGATTTCA
33004 TAGTAATGAT
1 TAGTAATGAT
33014 TAGTAATGAT
1 TAGTAATGAT
33024 TAGTAAT
1 TAGTAAT
33031 AATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:33057 original size:35 final size:34
Alignment explanation
Indices: 33017--33179 Score: 92
Period size: 35 Copynumber: 5.2 Consensus size: 34
33007 TAATGATTAG
33017 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAA-TTT
* * *
33052 TAATGATT--TGAT-A-GTAATGA-T-TTAA---
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
33077 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
* * * *
33112 TAATGATT--TGAT-A-GTAATGA-T-TT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
33137 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
33172 TAATGATT
1 TAATGATT
33180 TGATAGTAAT
Statistics
Matches: 91, Mismatches: 17, Indels: 40
0.61 0.11 0.27
Matches are distributed among these distances:
25 16 0.18
27 6 0.07
28 3 0.03
29 14 0.15
30 4 0.04
31 15 0.16
32 3 0.03
33 6 0.07
35 24 0.26
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (34 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTT
Found at i:33392 original size:13 final size:11
Alignment explanation
Indices: 33292--33455 Score: 57
Period size: 11 Copynumber: 13.5 Consensus size: 11
33282 TATTAATATT
33292 TAATGATTTGATA
1 TAATGATTT-A-A
*
33305 GTAATGATTTAG
1 -TAATGATTTAA
33317 TAATGATTAGTAA
1 TAATGATT--TAA
*
33330 TAATGAAATTGTTAT
1 TAATG--A-T-TTAA
33345 TAAT-ATTTAA
1 TAATGATTTAA
*
33355 TAAT--TTGATAG
1 TAATGATT--TAA
33366 TAATGATTTAA
1 TAATGATTTAA
33377 TAATGATTAGTAA
1 TAATGATT--TAA
* *
33390 TAATGAAATTAT
1 TAATG-ATTTAA
* * *
33402 TATTAATTT-T
1 TAATGATTTAA
33412 TAATGATTTGATA
1 TAATGATTT-A-A
33425 GTAATGATTTAA
1 -TAATGATTTAA
33437 TAATGATTAGTAA
1 TAATGATT--TAA
33450 TAATGA
1 TAATGA
33456 AATTGTTATT
Statistics
Matches: 117, Mismatches: 14, Indels: 39
0.69 0.08 0.23
Matches are distributed among these distances:
9 2 0.02
10 15 0.13
11 36 0.31
12 7 0.06
13 28 0.24
14 20 0.17
15 7 0.06
16 1 0.01
17 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:33416 original size:35 final size:34
Alignment explanation
Indices: 33377--33599 Score: 95
Period size: 35 Copynumber: 7.2 Consensus size: 34
33367 AATGATTTAA
33377 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAA-TTT
* * *
33412 TAATGATT--TGAT-A-GTAATGA-T-TTAA---
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
33437 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
* * * *
33472 TAATGATT--TGAT-A-GTAATGA-T-TT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
33497 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
* * * *
33532 TAATGATT--TGAT-A-GTAATGA-T-TT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
33557 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
33592 TAATGATT
1 TAATGATT
33600 TGATAGTAAT
Statistics
Matches: 131, Mismatches: 27, Indels: 60
0.60 0.12 0.28
Matches are distributed among these distances:
25 24 0.18
27 9 0.07
28 5 0.04
29 20 0.15
30 6 0.05
31 21 0.16
32 5 0.04
33 9 0.07
35 32 0.24
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (34 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTT
Found at i:33501 original size:25 final size:25
Alignment explanation
Indices: 33472--33640 Score: 94
Period size: 25 Copynumber: 7.0 Consensus size: 25
33462 TATTAATATT
33472 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
* * *
33497 TAATGATTAG-TAATAATGAAATT-G
1 TAATGATTTGATAGTAATG-ATTTAG
* *
33521 T--T-A-TTAATATTTAATGATTTGATAG
1 TAATGATTTGATA-GTAATGA-TT--TAG
*
33546 TAATGA-TT--TAGTAATGATTAGTAA
1 TAATGATTTGATAGTAATGATT--TAG
* * *
33570 TAATGAAATTGTTATTAAT-ATTTA-
1 TAATG-ATTTGATAGTAATGATTTAG
33594 -A-TGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
33617 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
33641 TTATAAATAT
Statistics
Matches: 111, Mismatches: 15, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
20 1 0.01
21 14 0.13
22 14 0.13
23 1 0.01
24 20 0.18
25 44 0.40
26 4 0.04
27 4 0.04
28 9 0.08
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:33611 original size:14 final size:14
Alignment explanation
Indices: 33592--33639 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
33582 TATTAATATT
33592 TAATGATTTGATAG
1 TAATGATTTGATAG
33606 TAATGA-TT--TAG
1 TAATGATTTGATAG
33617 TAATGATTTGATAG
1 TAATGATTTGATAG
33631 TAATGATTT
1 TAATGATTT
33640 ATTATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 2 0.06
14 18 0.58
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:34564 original size:23 final size:23
Alignment explanation
Indices: 34538--34582 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34528 AAAATTACAA
*
34538 AAATAATAAAATTTATTTAAATC
1 AAATAATAAAATTAATTTAAATC
* *
34561 AAATAATATAGTTAATTTAAAT
1 AAATAATAAAATTAATTTAAAT
34583 AATAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATAATAAAATTAATTTAAATC
Found at i:35796 original size:15 final size:16
Alignment explanation
Indices: 35776--35809 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
35766 CAAAAAAATT
35776 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
35791 TAATATAATAAACTTA
1 TAATATAATAAACTTA
35807 TAA
1 TAA
35810 AGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:35896 original size:30 final size:30
Alignment explanation
Indices: 35862--35967 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
35852 TTTCTTTAAA
35862 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
35892 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * *
35922 AAACTAATAAAATATTTTTTAATTATAA-TT
1 CAACTAATAAACTATTCTTTAA-TATAACTT
*
35952 CACTACTAAAAAACTA
1 CA--ACTAATAAACTA
35968 ATTAACTAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 52 0.78
31 5 0.07
32 10 0.15
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:35914 original size:15 final size:16
Alignment explanation
Indices: 35866--35920 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
35856 TTTAAACAAC
35866 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
35881 TAATATAAC--TTCAAC
1 TAATATAACTATTC-TT
35896 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
35911 TAATATAACT
1 TAATATAACT
35921 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:36368 original size:27 final size:27
Alignment explanation
Indices: 36330--36411 Score: 164
Period size: 27 Copynumber: 3.0 Consensus size: 27
36320 AGGGTCGGCT
36330 GCCATGCACCAATAATTGAAGAATCAC
1 GCCATGCACCAATAATTGAAGAATCAC
36357 GCCATGCACCAATAATTGAAGAATCAC
1 GCCATGCACCAATAATTGAAGAATCAC
36384 GCCATGCACCAATAATTGAAGAATCAC
1 GCCATGCACCAATAATTGAAGAATCAC
36411 G
1 G
36412 AGCCGTTGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (27 bp):
GCCATGCACCAATAATTGAAGAATCAC
Found at i:37218 original size:45 final size:45
Alignment explanation
Indices: 37158--37257 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
37148 CCATTCCTTT
* * *
37158 AAAATTTAAAATGATATATATATCTTTTAACCATTCAAAAATAAA
1 AAAATATATAATGATATATATATCTTTTAACCATACAAAAATAAA
*
37203 AAAATATATAATGATATATTTATCTTTTAACCATACAAAAATAAA
1 AAAATATATAATGATATATATATCTTTTAACCATACAAAAATAAA
*
37248 ATATATATAT
1 A-AAATATAT
37258 TATAAATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 42 0.86
46 7 0.14
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (45 bp):
AAAATATATAATGATATATATATCTTTTAACCATACAAAAATAAA
Found at i:37363 original size:17 final size:16
Alignment explanation
Indices: 37334--37372 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
37324 ATAAAAATAT
37334 TAATAAAATTATTATA
1 TAATAAAATTATTATA
*
37350 TAATAAAATATATTTTA
1 TAATAAAAT-TATTATA
37367 TAATAA
1 TAATAA
37373 CTTATTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAAAATTATTATA
Found at i:41384 original size:2 final size:2
Alignment explanation
Indices: 41377--41441 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
41367 TCATAGCGTG
41377 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41419 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
41442 TAAATGTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49172 original size:17 final size:18
Alignment explanation
Indices: 49150--49186 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
49140 AGTCCTTATA
49150 TTTTTATATA-TTTCATT
1 TTTTTATATATTTTCATT
*
49167 TTTTTATTTATTTTCATT
1 TTTTTATATATTTTCATT
49185 TT
1 TT
49187 ACCATGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTATATATTTTCATT
Found at i:49215 original size:3 final size:3
Alignment explanation
Indices: 49207--49282 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
49197 TATTTAGATG
49207 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49255 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
49283 ATGCCTGTAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:51766 original size:22 final size:22
Alignment explanation
Indices: 51740--51808 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
51730 GTAATGCTTG
51740 AATTAATATGTATATCATCAAC
1 AATTAATATGTATATCATCAAC
* * * * *
51762 AATTACAAAATATATATTATAAAT
1 AATT--AATATGTATATCATCAAC
51786 AATTAATATGTATATCATCAAC
1 AATTAATATGTATATCATCAAC
51808 A
1 A
51809 CTTATACAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
22 18 0.51
24 17 0.49
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (22 bp):
AATTAATATGTATATCATCAAC
Found at i:51872 original size:25 final size:26
Alignment explanation
Indices: 51844--51898 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
51834 TAATCGAGAT
*
51844 TTACAAA-ATTTAAATTAGTCTAAAC
1 TTACAAATATTTAAATTAGTCAAAAC
* * *
51869 TTACAAATTTTTGAATTAGTCAAAAT
1 TTACAAATATTTAAATTAGTCAAAAC
51895 TTAC
1 TTAC
51899 TATGTATTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (26 bp):
TTACAAATATTTAAATTAGTCAAAAC
Found at i:56159 original size:193 final size:190
Alignment explanation
Indices: 55826--56208 Score: 723
Period size: 193 Copynumber: 2.0 Consensus size: 190
55816 GCCAACGGAG
55826 AAGACGACAGTAACGCCGGTAATAATAGCGGCGGTAGCTCATCGGTTTATCCATGATCAAGACTG
1 AAGACGACAGTAACGCCGGTAATAATAGCGGCGGTAGCTCATCGGTTTATCCATGATCAAGACTG
55891 GTTAAGGAACCAACCGGCACAGACTCAGCGGAGGCCAAAACGACGGCGGCGCTTCACAGTCATTG
66 GTTAAGGAACCAACCGGCACAGACTCAGCGGAGGCCAAAACGACGGCGGCGCTTCACAGTCATTG
55956 TCTCTTTCCATGAGCACCGGTTCAC-AACAGGCTCCCCTTTACCCCTCCTCGCCACCACA
131 TCTCTTTCCATGAGCACCGGTTCACAAACAGGCTCCCCTTTACCCCTCCTCGCCACCACA
56015 AAGACGACAGTAACGCCGGTAATAATAGCGGCGGTAGCTCCATCGGTTTATCCATGATCAAGACT
1 AAGACGACAGTAACGCCGGTAATAATAGCGGCGGTAGCT-CATCGGTTTATCCATGATCAAGAC-
56080 TGGTTAAGGAACCAACCGGCACAGACTCAAGCGGAGGCCAAAAACGACGGCGGCGCTTCACAGTC
64 TGGTTAAGGAACCAACCGGCACAGACTC-AGCGGAGGCC-AAAACGACGGCGGCGCTTCACAGTC
56145 ATTGTCTCTTTCCATGAGCACCGGTTCACAAACAGGCTCCCCTTTACCCCTCCTCGCCACCACA
127 ATTGTCTCTTTCCATGAGCACCGGTTCACAAACAGGCTCCCCTTTACCCCTCCTCGCCACCACA
56209 CACCGTCGGC
Statistics
Matches: 189, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
189 39 0.21
190 24 0.13
191 28 0.15
192 10 0.05
193 54 0.29
194 34 0.18
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.19
Consensus pattern (190 bp):
AAGACGACAGTAACGCCGGTAATAATAGCGGCGGTAGCTCATCGGTTTATCCATGATCAAGACTG
GTTAAGGAACCAACCGGCACAGACTCAGCGGAGGCCAAAACGACGGCGGCGCTTCACAGTCATTG
TCTCTTTCCATGAGCACCGGTTCACAAACAGGCTCCCCTTTACCCCTCCTCGCCACCACA
Done.