Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004136.1 Hibiscus syriacus cultivar Beakdansim tig00009044_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: 74431
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1558 original size:30 final size:30
Alignment explanation
Indices: 1483--1558 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
1473 TTTGACCAAC
*
1483 TTTATAATAATTTGATAA-ATTTAATGATTAT
1 TTTAAAATAATTT-A-AATATTTAATGATTAT
** *
1514 TTTGTAATAGTTTAAATATTTAATGATT-T
1 TTTAAAATAATTTAAATATTTAATGATTAT
1543 TTTAAAATAAATTTAA
1 TTTAAAAT-AATTTAA
1559 CTTTGGTGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
29 9 0.24
30 18 0.47
31 11 0.29
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (30 bp):
TTTAAAATAATTTAAATATTTAATGATTAT
Found at i:5650 original size:2 final size:2
Alignment explanation
Indices: 5604--5632 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5594 AACATCTCTG
5604 TA 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 TA T
5633 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5948 original size:45 final size:45
Alignment explanation
Indices: 5897--5986 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
5887 TATATATAGA
*
5897 GATATTATTGTAATTATTCCTAAATATAAGGTAAAATTATATTTT
1 GATATTATTGTAATTATTCCTAAATATAAGATAAAATTATATTTT
*
5942 GATATTATTGTAATTATTCTTAAATATAAGATAAAATTATATTTT
1 GATATTATTGTAATTATTCCTAAATATAAGATAAAATTATATTTT
5987 TTTGGGTGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (45 bp):
GATATTATTGTAATTATTCCTAAATATAAGATAAAATTATATTTT
Found at i:5968 original size:22 final size:22
Alignment explanation
Indices: 5898--5968 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
5888 ATATATAGAG
*
5898 ATATTATTGTAATTATTCCTAA
1 ATATTATTGTAATTATTCTTAA
** **
5920 ATA-TAAGGTAAAATTATAT-TTTG
1 ATATTATTGT--AATTAT-TCTTAA
5943 ATATTATTGTAATTATTCTTAA
1 ATATTATTGTAATTATTCTTAA
5965 ATAT
1 ATAT
5969 AAGATAAAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
21 5 0.14
22 15 0.43
23 10 0.29
24 5 0.14
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (22 bp):
ATATTATTGTAATTATTCTTAA
Found at i:12446 original size:15 final size:16
Alignment explanation
Indices: 12410--12460 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
12400 TTCCTTTTGT
*
12410 TTATTTTT-T-TATTA
1 TTATTTTTATATATTG
12424 TT-TTTTTA-ATATTG
1 TTATTTTTATATATTG
*
12438 TTATTTTTATATATTT
1 TTATTTTTATATATTG
12454 TTATTTT
1 TTATTTT
12461 ATTTTTGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 8 0.26
15 6 0.19
16 12 0.39
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
TTATTTTTATATATTG
Found at i:12463 original size:11 final size:11
Alignment explanation
Indices: 12409--12466 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
12399 CTTCCTTTTG
12409 TTTATTTT-TT
1 TTTATTTTATT
12419 TATTATTTT-TT
1 T-TTATTTTATT
*
12430 TAATATTGTTATT
1 T-TTATT-TTATT
*
12443 TTTA-TATATT
1 TTTATTTTATT
12453 TTTATTTTATT
1 TTTATTTTATT
12464 TTT
1 TTT
12467 GTTGAAAACA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 9 0.22
11 24 0.60
12 4 0.10
13 3 0.08
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:13598 original size:2 final size:2
Alignment explanation
Indices: 13593--13625 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13583 TTTATTTATT
13593 TA TA TA 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 TA TA TA T
13626 CGTAGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13695 original size:15 final size:16
Alignment explanation
Indices: 13677--13722 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
13667 TAATTTTCTA
*
13677 TTTTCTGTTTTTTTGT
1 TTTTTTGTTTTTTTGT
*
13693 TTTTTTG-TTTTTTGG
1 TTTTTTGTTTTTTTGT
13708 TTTTTTGTTTATTTT
1 TTTTTTGTTT-TTTT
13723 TCTTATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 14 0.54
16 8 0.31
17 4 0.15
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (16 bp):
TTTTTTGTTTTTTTGT
Found at i:13696 original size:23 final size:23
Alignment explanation
Indices: 13647--13717 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 23
13637 TTTTTATTTA
* **
13647 TTTTCTATTTTTTAATTTTTTAA
1 TTTTCTATTTTTTGATTTTTTGT
* *
13670 TTTTCTATTTTCTGTTTTTTTGT
1 TTTTCTATTTTTTGATTTTTTGT
* * *
13693 TTTTTTGTTTTTTGGTTTTTTGT
1 TTTTCTATTTTTTGATTTTTTGT
13716 TT
1 TT
13718 ATTTTTCTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.08, C:0.04, G:0.08, T:0.79
Consensus pattern (23 bp):
TTTTCTATTTTTTGATTTTTTGT
Found at i:13735 original size:5 final size:5
Alignment explanation
Indices: 13715--13804 Score: 53
Period size: 5 Copynumber: 18.4 Consensus size: 5
13705 TGGTTTTTTG
* * * *
13715 TTTAT TTT-T CTTAT TTTAT TTCTGT TTTGT TTTGT TTTA- TTTAT TTTA-
1 TTTAT TTTAT TTTAT TTTAT TT-TAT TTTAT TTTAT TTTAT TTTAT TTTAT
* * * * *
13763 TCTAT TTTGTT TTTAT TGTAC TTTAT TTTAT GTTA- TTTAT TT
1 TTTAT TTT-AT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
13805 CATTACTTTC
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
4 13 0.20
5 44 0.68
6 8 0.12
ACGTcount: A:0.14, C:0.04, G:0.07, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:13761 original size:30 final size:31
Alignment explanation
Indices: 13725--13793 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
13715 TTTATTTTTC
*
13725 TTATTTTATTTCTGTTTTGTTTTGT-TT-TA-T
1 TTATTTTA-TTCTATTTTGTTTT-TATTGTACT
13755 TTATTTTA-TCTATTTTGTTTTTATTGTACT
1 TTATTTTATTCTATTTTGTTTTTATTGTACT
13785 TTATTTTAT
1 TTATTTTAT
13794 GTTATTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 1 0.03
28 14 0.41
29 2 0.06
30 17 0.50
ACGTcount: A:0.14, C:0.04, G:0.07, T:0.74
Consensus pattern (31 bp):
TTATTTTATTCTATTTTGTTTTTATTGTACT
Found at i:18239 original size:21 final size:21
Alignment explanation
Indices: 18197--18239 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
18187 TTTCTGGGCT
*
18197 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
18218 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
18239 A
1 A
18240 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:18292 original size:20 final size:20
Alignment explanation
Indices: 18267--18304 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18257 GAACGCTAGA
*
18267 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
18287 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
18305 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:19008 original size:103 final size:101
Alignment explanation
Indices: 18785--19000 Score: 387
Period size: 103 Copynumber: 2.1 Consensus size: 101
18775 GTAGAGGGTC
*
18785 TATGTGGTCCTTCGGGACATATATGTATTCTGGAACATGTGTAAAGTCTGGTGAGACACATACTT
1 TATGTGGTCCTTCGGGACATATATGTATTCTGGAACATGTGTAAAGTCTGGTGAGACACACACTT
18850 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
18886 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACACAC
1 TATGTGGTCCTTCGGGACATATATGTATTC--TGGAACATGTGTAAAGTCTGGTGAGACACACAC
18951 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
64 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
18989 TATGTGGTCCTT
1 TATGTGGTCCTT
19001 ATGGACATTA
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
101 29 0.27
103 80 0.73
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (101 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTGGAACATGTGTAAAGTCTGGTGAGACACACACTT
GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:25143 original size:21 final size:21
Alignment explanation
Indices: 25101--25143 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25091 TTTCTGGGCT
*
25101 AGGGAAATCGATACCCATTCA
1 AGGGAAATCGATACCCACTCA
* *
25122 AGGGGAATCGATACCCCCTCA
1 AGGGAAATCGATACCCACTCA
25143 A
1 A
25144 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (21 bp):
AGGGAAATCGATACCCACTCA
Found at i:25196 original size:20 final size:20
Alignment explanation
Indices: 25171--25208 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25161 GAATGCTAGA
*
25171 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
25191 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
25209 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:25856 original size:23 final size:23
Alignment explanation
Indices: 25820--25871 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
25810 ATTATTATAT
*
25820 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGATGCAATTCTACGC
* *
25843 GGCACTCCGATGCAATTCTACGT
1 GGCACTACGATGCAATTCTACGC
25866 GGCACT
1 GGCACT
25872 TAGGTGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (23 bp):
GGCACTACGATGCAATTCTACGC
Found at i:25879 original size:23 final size:23
Alignment explanation
Indices: 25819--25882 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
25809 CATTATTATA
25819 TGGCAC-TACGGTGCAATTCTACG
1 TGGCACTTA-GGTGCAATTCTACG
* ** *
25842 CGGCACTCCGATGCAATTCTACG
1 TGGCACTTAGGTGCAATTCTACG
25865 TGGCACTTAGGTGCAATT
1 TGGCACTTAGGTGCAATT
25883 ATATGAGCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:36381 original size:18 final size:18
Alignment explanation
Indices: 36355--36390 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
36345 TTTTTGTGTA
*
36355 CTTTTTTTCTTCCTTTTT
1 CTTTATTTCTTCCTTTTT
36373 CTTTATTTCTTCCTTTTT
1 CTTTATTTCTTCCTTTTT
36391 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (18 bp):
CTTTATTTCTTCCTTTTT
Found at i:36547 original size:12 final size:12
Alignment explanation
Indices: 36526--36580 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
36516 ATATAGTAGT
36526 TTTTTAAATTTTA
1 TTTTT-AATTTTA
36539 TTTTTAATTTTA
1 TTTTTAATTTTA
36551 TTTTCT-ATTTT-
1 TTTT-TAATTTTA
*
36562 TTAATTTAATTTAA
1 TT--TTTAATTTTA
36576 TTTTT
1 TTTTT
36581 TTGTTTTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
11 2 0.06
12 20 0.56
13 12 0.33
14 2 0.06
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTAATTTTA
Found at i:36562 original size:20 final size:18
Alignment explanation
Indices: 36539--36673 Score: 51
Period size: 20 Copynumber: 6.9 Consensus size: 18
36529 TTAAATTTTA
*
36539 TTTTTAATTTTATTTTCT
1 TTTTTTATTTTATTTTCT
* **
36557 ATTTTTTAATTTAATTTAAT
1 -TTTTTT-ATTTTATTTTCT
* *
36577 TTTTTTGTTTTGTTGTT-T
1 TTTTTTATTTTATT-TTCT
*
36595 TGTTTCTTTTTTTATTTAATCTT
1 T-TTT-TTATTTTATTT--TC-T
*
36618 CTTTTTCTTATTTTATTTTATT
1 --TTTT-TTATTTTATTTT-CT
36640 TTATTTTATTTTA-TTTCT
1 TT-TTTTATTTTATTTTCT
36658 ATTTTTTA-TTTATTTT
1 -TTTTTTATTTTATTTT
36674 TATCTATTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 29
0.68 0.10 0.22
Matches are distributed among these distances:
17 4 0.04
18 16 0.18
19 21 0.24
20 27 0.30
21 3 0.03
22 2 0.02
23 1 0.01
24 14 0.16
25 1 0.01
ACGTcount: A:0.16, C:0.04, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTTTATTTTATTTTCT
Found at i:36580 original size:19 final size:20
Alignment explanation
Indices: 36539--36582 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
36529 TTAAATTTTA
* **
36539 TTTTTAATTTTATTTTCTAT
1 TTTTTAATTTAATTTAATAT
36559 TTTTTAATTTAATTTAAT-T
1 TTTTTAATTTAATTTAATAT
36578 TTTTT
1 TTTTT
36583 GTTTTGTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTAATTTAATTTAATAT
Found at i:36635 original size:5 final size:5
Alignment explanation
Indices: 36625--36714 Score: 83
Period size: 5 Copynumber: 17.2 Consensus size: 5
36615 CTTCTTTTTC
*
36625 TTATT TTATT TTATT TTATT TTATT TTATT TCTATT TTTTAT TTATTT
1 TTATT TTATT TTATT TTATT TTATT TTATT T-TATT TTAT-T TTA-TT
* * * *
36673 TTATCT ATTTTT TTATT GTACT TTATT TTATG TTA-T TTATT T
1 TTAT-T -TTATT TTATT TTATT TTATT TTATT TTATT TTATT T
36715 CATTACTTTC
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
4 3 0.04
5 48 0.70
6 14 0.20
7 4 0.06
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:36674 original size:28 final size:28
Alignment explanation
Indices: 36592--36676 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 28
36582 TGTTTTGTTG
* *
36592 TTTTGTTTCT-TTTTTTATTTAATCTTCTTT
1 TTTTATTTCTATTTTTTATTT-AT-TT-TTA
*
36622 TTCTTATTT-TATTTTAT-TTTA-TTTTA
1 TT-TTATTTCTATTTTTTATTTATTTTTA
36648 TTTTATTTCTATTTTTTATTTATTTTTA
1 TTTTATTTCTATTTTTTATTTATTTTTA
36676 T
1 T
36677 CTATTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
25 6 0.13
26 11 0.24
27 6 0.13
28 6 0.13
29 1 0.02
30 6 0.13
31 10 0.22
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (28 bp):
TTTTATTTCTATTTTTTATTTATTTTTA
Found at i:37297 original size:19 final size:19
Alignment explanation
Indices: 37273--37322 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
37263 ATTCTCAAAA
37273 TAATATTATTTTATGT-ATT
1 TAATATTATTTTAT-TAATT
* *
37292 TAATATTAATATATTAATT
1 TAATATTATTTTATTAATT
37311 TAAT-TTATTTTA
1 TAATATTATTTTA
37323 ATAAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TAATATTATTTTATTAATT
Found at i:37312 original size:27 final size:27
Alignment explanation
Indices: 37274--37352 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
37264 TTCTCAAAAT
*
37274 AATATTATTTTATGTATTTAATATTAA
1 AATATTAATTTATGTATTTAATATTAA
* *
37301 TATATTAATTTAATTTATTTTAATA--AA
1 AATATTAATTT-ATGTA-TTTAATATTAA
*
37328 AATATTAA-TTATTGTATTCAATATT
1 AATATTAATTTA-TGTATTTAATATT
37353 TATAATAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
25 7 0.17
26 5 0.12
27 18 0.44
28 4 0.10
29 7 0.17
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (27 bp):
AATATTAATTTATGTATTTAATATTAA
Found at i:37411 original size:13 final size:13
Alignment explanation
Indices: 37389--37441 Score: 79
Period size: 13 Copynumber: 3.9 Consensus size: 13
37379 CTAACCAATG
*
37389 AAAATGATTTTCA
1 AAAATAATTTTCA
37402 AAAATAATTTTCTCA
1 AAAATAA-TTT-TCA
37417 AAAATAATTTTCA
1 AAAATAATTTTCA
37430 AAAATAATTTTC
1 AAAATAATTTTC
37442 TCAAAAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
13 21 0.57
14 6 0.16
15 10 0.27
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (13 bp):
AAAATAATTTTCA
Found at i:37419 original size:15 final size:15
Alignment explanation
Indices: 37399--37450 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
37389 AAAATGATTT
37399 TCAAAAATAATTTTC
1 TCAAAAATAATTTTC
37414 TCAAAAATAA-TTT-
1 TCAAAAATAATTTTC
37427 TCAAAAATAATTTTC
1 TCAAAAATAATTTTC
37442 TCAAAAATA
1 TCAAAAATA
37451 TAATTCATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.29
14 6 0.17
15 19 0.54
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.37
Consensus pattern (15 bp):
TCAAAAATAATTTTC
Found at i:37426 original size:28 final size:28
Alignment explanation
Indices: 37389--37450 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
37379 CTAACCAATG
*
37389 AAAATGATTTTCAAAAATAATTTTCTCA
1 AAAATAATTTTCAAAAATAATTTTCTCA
37417 AAAATAATTTTCAAAAATAATTTTCTCA
1 AAAATAATTTTCAAAAATAATTTTCTCA
37445 AAAATA
1 AAAATA
37451 TAATTCATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (28 bp):
AAAATAATTTTCAAAAATAATTTTCTCA
Found at i:38168 original size:60 final size:60
Alignment explanation
Indices: 38042--38200 Score: 151
Period size: 60 Copynumber: 2.6 Consensus size: 60
38032 TGAAATGTTC
* * ** * * ** *
38042 AAAAGTTTGGAGACTAATTTAGAATGAGGTTCATAGTTTGGGGATGATTTTTTAATGCTT
1 AAAAGTTTGAAGACTAATTTAGAATAAGGTTCATAGTTTACGAATGAATTTGGAATACTT
* * * * *
38102 ATAAGTTTGTAGACTAATTTAGAATAAGTTTCATTGTTTACGAATGAATTTGGAATATTT
1 AAAAGTTTGAAGACTAATTTAGAATAAGGTTCATAGTTTACGAATGAATTTGGAATACTT
*
38162 AAAAGTTT-AAGAACCAATTTAGAATAAGAG-TCATAGTTT
1 AAAAGTTTGAAG-ACTAATTTAGAATAAG-GTTCATAGTTT
38201 GAGGATGTGT
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
59 2 0.03
60 77 0.97
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (60 bp):
AAAAGTTTGAAGACTAATTTAGAATAAGGTTCATAGTTTACGAATGAATTTGGAATACTT
Found at i:40514 original size:20 final size:20
Alignment explanation
Indices: 40491--40542 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
40481 AACGCGATCC
40491 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
40511 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
40531 CCAAAATCGCAA
1 CCAGAATCGCAA
40543 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:40559 original size:21 final size:20
Alignment explanation
Indices: 40533--40630 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
40523 ATCAGTTTCC
40533 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * **
40554 AAAATCGCGATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
40573 ACAAATTCGCATTGCGATTTTCA
1 A-AAA-TCGCAACGCGATTTT-G
* *
40596 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
40616 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
40631 ACACATAAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
19 1 0.02
20 19 0.32
21 36 0.60
22 3 0.05
23 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:40644 original size:40 final size:40
Alignment explanation
Indices: 40597--40751 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
40587 CGATTTTCAA
* ** *
40597 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
40637 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
40677 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
40717 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
40752 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:40659 original size:20 final size:20
Alignment explanation
Indices: 40597--40750 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
40587 CGATTTTCAA
* ** *
40597 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
40617 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
40637 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
40657 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
40677 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
40697 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
40717 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
40738 AAATCGCAACGCG
1 AAATCGCAACGCG
40751 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:41176 original size:33 final size:32
Alignment explanation
Indices: 41132--41201 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
41122 TTCACTTAGA
*
41132 TTTCATTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTCGCGTTACGATTCTCTCGTTGCGAT
* *
41164 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCA-TTCGCGTTACGATTCTCTCGTTGCGAT
41197 TTTCA
1 TTTCA
41202 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 5 0.15
33 29 0.85
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (32 bp):
TTTCATTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:41341 original size:14 final size:14
Alignment explanation
Indices: 41322--41376 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
41312 AGAATGACTG
41322 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
41336 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
41355 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
41369 TCGCAACG
1 TCGCAACG
41377 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:41389 original size:33 final size:33
Alignment explanation
Indices: 41322--41392 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
41312 AGAATGACTG
***
41322 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
41355 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
41388 TCGCA
1 TCGCA
41393 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:41410 original size:19 final size:19
Alignment explanation
Indices: 41388--41485 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
41378 GAAACCAAAA
*
41388 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
41407 TCGCGTTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATT
41423 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
41440 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
41454 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
41473 TCGCGTTGCGATT
1 TCGCGTTGCGATT
41486 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 18 0.29
16 7 0.11
17 8 0.13
19 30 0.48
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:41429 original size:14 final size:14
Alignment explanation
Indices: 41410--41499 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
41400 TTTCATTTCG
*
41410 CGTTGCGATTCTAT
1 CGTTGCGATTCTCT
*
41424 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
41443 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
41457 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
41474 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
41490 CGTTGCGATT
1 CGTTGCGATT
41500 TTCATTTCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 20
0.73 0.03 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:41435 original size:33 final size:33
Alignment explanation
Indices: 41393--41507 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
41383 CAAAATCGCA
*
41393 TTGCGATTTTCATTTCGCGTTGCGATTCTATCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
41426 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
41459 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
41492 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
41508 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:43431 original size:185 final size:186
Alignment explanation
Indices: 43202--43673 Score: 930
Period size: 185 Copynumber: 2.5 Consensus size: 186
43192 TAGATTGCTT
43202 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43267 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
43331 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
43387 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43451 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
43516 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
43572 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43637 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
43674 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 62 0.22
185 184 0.65
186 39 0.14
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:43608 original size:93 final size:93
Alignment explanation
Indices: 43202--43673 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
43192 TAGATTGCTT
43202 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43267 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
43295 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43359 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
43387 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43451 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
43479 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43544 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
43572 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
43637 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
43665 AGTAAATTT
1 AGTAAATTT
43674 ATCCATTCAA
Statistics
Matches: 377, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.49
93 193 0.51
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:43742 original size:20 final size:19
Alignment explanation
Indices: 43717--43843 Score: 91
Period size: 18 Copynumber: 7.3 Consensus size: 19
43707 TAGTTTACTT
*
43717 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
43737 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
43755 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
43774 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACTAAAA
*
43788 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
*
43806 TCGCAA--CG--AC-AAGA
1 TCGCAACGCGAAACTAAAA
*
43820 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
43839 TCGCA
1 TCGCA
43844 TTGCGATTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 25
0.72 0.08 0.21
Matches are distributed among these distances:
14 19 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 28 0.33
19 17 0.20
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:43757 original size:18 final size:18
Alignment explanation
Indices: 43734--43843 Score: 96
Period size: 18 Copynumber: 6.4 Consensus size: 18
43724 ACGAAACTTA
43734 AAATCGCAACGCGAAACC
1 AAATCGCAACGCGAAACC
**
43752 AAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAA-CC
43771 AAATCGCAA--CG--A-C
1 AAATCGCAACGCGAAACC
43784 AGAATCGCAACGCGAAACC
1 A-AATCGCAACGCGAAACC
43803 AAATCGCAA--CG--A-C
1 AAATCGCAACGCGAAACC
43816 AAGATCGCAACGCGAAACC
1 AA-ATCGCAACGCGAAACC
43835 AAAATCGCA
1 -AAATCGCA
43844 TTGCGATTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 27
0.71 0.03 0.26
Matches are distributed among these distances:
13 4 0.05
14 16 0.21
15 1 0.01
16 6 0.08
17 2 0.03
18 26 0.35
19 18 0.24
20 2 0.03
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.07
Consensus pattern (18 bp):
AAATCGCAACGCGAAACC
Found at i:43812 original size:32 final size:31
Alignment explanation
Indices: 43751--43843 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 31
43741 AACGCGAAAC
**
43751 CAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAATCGCAACGCGAAA-CCAAATCGCAACGA
43783 CAGAATCGCAACGCGAAACCAAATCGCAACGA
1 CA-AATCGCAACGCGAAACCAAATCGCAACGA
43815 CAAGATCGCAACGCGAAACCAAAATCGCA
1 CAA-ATCGCAACGCGAAACC-AAATCGCA
43844 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 32 0.57
33 23 0.41
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.08
Consensus pattern (31 bp):
CAAATCGCAACGCGAAACCAAATCGCAACGA
Found at i:43841 original size:51 final size:51
Alignment explanation
Indices: 43717--43843 Score: 136
Period size: 51 Copynumber: 2.5 Consensus size: 51
43707 TAGTTTACTT
**
43717 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
* * *
43768 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAATCGCAACG-CGAA-A
*
43820 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
43844 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
49 3 0.05
50 6 0.10
51 41 0.67
52 3 0.05
53 6 0.10
54 2 0.03
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (51 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
Found at i:43861 original size:19 final size:19
Alignment explanation
Indices: 43839--43957 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
43829 GAAACCAAAA
*
43839 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
43858 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
43874 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
43891 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
43907 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
43924 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
43943 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
43958 AAGTTTCGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 46 0.55
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:43880 original size:14 final size:14
Alignment explanation
Indices: 43861--43917 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
43851 TTTCATTTCG
43861 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
43875 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
43892 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
43908 CGTTGCGATT
1 CGTTGCGATT
43918 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:43886 original size:33 final size:33
Alignment explanation
Indices: 43844--43936 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
43834 CAAAATCGCA
*
43844 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
43877 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
43910 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
43937 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:43972 original size:19 final size:19
Alignment explanation
Indices: 43908--43965 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
43898 GCGATTCTGT
43908 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
43927 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
43946 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
43966 TGTGCGAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 29 0.83
20 6 0.17
ACGTcount: A:0.10, C:0.17, G:0.26, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:47672 original size:12 final size:12
Alignment explanation
Indices: 47655--47679 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47645 TCTTCGGGGA
47655 CTTTTTCTTCTT
1 CTTTTTCTTCTT
47667 CTTTTTCTTCTT
1 CTTTTTCTTCTT
47679 C
1 C
47680 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:47888 original size:24 final size:24
Alignment explanation
Indices: 47854--47900 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47844 CTGAAACATC
47854 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
47878 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
47901 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:48601 original size:20 final size:20
Alignment explanation
Indices: 48573--48941 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
48563 AAATTTCAGT
* * * *
48573 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
48593 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
48613 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
48633 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
48653 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
48673 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
48693 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
48713 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
48733 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
48753 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
48773 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
48793 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
48813 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
48833 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
48853 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
48873 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
48893 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
48913 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
48933 GTTGCGATT
1 GTTGCGATT
48942 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:49581 original size:55 final size:55
Alignment explanation
Indices: 49497--49600 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 55
49487 CACATGTTTT
*
49497 AGAAGAAGAAGAAAGGTTGACGGGAGGTAACGTGTCACGTCAGATAAAACTAACG
1 AGAAGAAGAAGAAAGGTTGACGGGAGGTAACGTGCCACGTCAGATAAAACTAACG
* * *
49552 AGAAGAAGAAGAAAGGTT-AGTGGGAGGTAACGTGCCATGTTAGATAAAA
1 AGAAGAAGAAGAAAGGTTGA-CGGGAGGTAACGTGCCACGTCAGATAAAA
49601 TTAATGGGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 1 0.02
55 43 0.98
ACGTcount: A:0.42, C:0.10, G:0.32, T:0.16
Consensus pattern (55 bp):
AGAAGAAGAAGAAAGGTTGACGGGAGGTAACGTGCCACGTCAGATAAAACTAACG
Found at i:51434 original size:154 final size:154
Alignment explanation
Indices: 51220--51499 Score: 535
Period size: 154 Copynumber: 1.8 Consensus size: 154
51210 ATCCTAAAAG
51220 ATATAAATATCTAATTTTTTTGTGTGAATATTATATTTTTTTATGATTTATTGATTCTTTAGTTT
1 ATATAAATATCTAATTTTTTTGTGTGAATATTATATTTTTTTATGATTTATTGATTCTTTAGTTT
*
51285 TTAAATGCCTTTTTGTTAAAAAAATATTTCAAATATTTTTATACTTTATAAAAAACAATTTTTTT
66 TTAAATGCCTTTTTGTTAAAAAAATATTTCAAATATTTTTATACTTTATAAAAAAAAATTTTTTT
51350 ATAATTTTCTAAAAAATACGATGA
131 ATAATTTTCTAAAAAATACGATGA
51374 ATATATAATATCTAATTTTTTTGTGTGAATATTATA-TTTTTTATGATTTATTGATTCTTTAGTT
1 ATATA-AATATCTAATTTTTTTGTGTGAATATTATATTTTTTTATGATTTATTGATTCTTTAGTT
51438 TTTAAATGCCTTTTTGTTAAAAAAATATTTCAAATATTTTTATACTTTATAAAAAAAAATTT
65 TTTAAATGCCTTTTTGTTAAAAAAATATTTCAAATATTTTTATACTTTATAAAAAAAAATTT
51500 CAACCAAAAA
Statistics
Matches: 124, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
154 94 0.76
155 30 0.24
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.52
Consensus pattern (154 bp):
ATATAAATATCTAATTTTTTTGTGTGAATATTATATTTTTTTATGATTTATTGATTCTTTAGTTT
TTAAATGCCTTTTTGTTAAAAAAATATTTCAAATATTTTTATACTTTATAAAAAAAAATTTTTTT
ATAATTTTCTAAAAAATACGATGA
Found at i:72464 original size:34 final size:36
Alignment explanation
Indices: 72421--72492 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 36
72411 ACCCTTAGAT
*
72421 TAAACTTTTTAT-ATTTTCAATTTTGTAAA-AAAATA
1 TAAACTTTTTATGAATTT-AATTTTGTAAAGAAAATA
*
72456 TAAA-TTTTTATGAATTTAATTTTTTAAAGAAAATA
1 TAAACTTTTTATGAATTTAATTTTGTAAAGAAAATA
72491 TA
1 TA
72493 TAAATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (36 bp):
TAAACTTTTTATGAATTTAATTTTGTAAAGAAAATA
Found at i:72660 original size:18 final size:19
Alignment explanation
Indices: 72637--72679 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
72627 TCTCAGTCCT
72637 ATTCC-CTGATAATCTTAC
1 ATTCCACTGATAATCTTAC
*
72655 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGATAATCTTAC
72675 ATTCC
1 ATTCC
72680 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:74190 original size:2 final size:2
Alignment explanation
Indices: 74183--74253 Score: 119
Period size: 2 Copynumber: 36.5 Consensus size: 2
74173 ATAAATCATC
*
74183 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74224 A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
74254 AAAATAAGAA
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 63 0.97
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:74224 original size:29 final size:29
Alignment explanation
Indices: 74183--74254 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
74173 ATAAATCATC
74183 ATATATATATATAATATATATATATATAT
1 ATATATATATATAATATATATATATATAT
*
74212 ATATCTATATATAATATATATATATATAT
1 ATATATATATATAATATATATATATATAT
74241 ATATATATATATAA
1 ATATATATATATAA
74255 AAATAAGAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATATATATATAATATATATATATATAT
Found at i:74361 original size:20 final size:21
Alignment explanation
Indices: 74319--74367 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
74309 ATAAAATGAG
74319 ATAAAACAGTAACAAATTATA
1 ATAAAACAGTAACAAATTATA
*
74340 ATTAAACAGTGAA-AAA-TATA
1 ATAAAACAGT-AACAAATTATA
74360 ATAAAACA
1 ATAAAACA
74368 AAAACAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.44
21 12 0.48
22 2 0.08
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.22
Consensus pattern (21 bp):
ATAAAACAGTAACAAATTATA
Done.