Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008557.1 Hibiscus syriacus cultivar Beakdansim tig00111462_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: 126703
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:667 original size:69 final size:68
Alignment explanation
Indices: 584--728 Score: 177
Period size: 69 Copynumber: 2.1 Consensus size: 68
574 TTACTGGTTA
* * ** *
584 TATAGGCGTTAAATGGTGATAGAAGTTGGTGATG-TATAGGCGTG-CAATGGTGATGGAATATGG
1 TATAGGCGTGAAATGGTGATAGAAGAT-GTGATGTTATA-GAATGAAAATGGTGATGGAA-ATGG
647 TGATGT
63 TGATGT
*
653 TATAGGCGTGAAATGGTGATGGAAGATGTGATGTTATAGAATGAAAAAATGGTGATGGAAATGGT
1 TATAGGCGTGAAATGGTGATAGAAGATGTGATGTTATAGAATG--AAAATGGTGATGGAAATGGT
718 GATGT
64 GATGT
723 TATAGG
1 TATAGG
729 TATATCTTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
68 9 0.14
69 28 0.42
70 16 0.24
71 13 0.20
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.30
Consensus pattern (68 bp):
TATAGGCGTGAAATGGTGATAGAAGATGTGATGTTATAGAATGAAAATGGTGATGGAAATGGTGA
TGT
Found at i:668 original size:35 final size:35
Alignment explanation
Indices: 584--728 Score: 165
Period size: 34 Copynumber: 4.2 Consensus size: 35
574 TTACTGGTTA
* *
584 TATAGGCGTTAAATGGTGATAGAAGT-TGGTGATG-
1 TATAGGCGTGAAATGGTGATGGAA-TATGGTGATGT
*
618 TATAGGCGTGCAATGGTGATGGAATATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAATATGGTGATGT
*
653 TATAGGCGTGAAATGGTGATGGAAGAT-GTGATGT
1 TATAGGCGTGAAATGGTGATGGAATATGGTGATGT
**
687 TATA-GAATGAAAAAATGGTGATGGAA-ATGGTGATGT
1 TATAGGCGTG---AAATGGTGATGGAATATGGTGATGT
723 TATAGG
1 TATAGG
729 TATATCTTAT
Statistics
Matches: 97, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 4 0.04
34 40 0.41
35 27 0.28
36 25 0.26
37 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.30
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAATATGGTGATGT
Found at i:4746 original size:20 final size:19
Alignment explanation
Indices: 4696--4747 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
4686 GATGTAATAC
*
4696 TCTTTTTA-TTTTCTTTTT
1 TCTTTTTATTTTTCTTCTT
* *
4714 TTTTTTGTGTTTTTCTTCTT
1 TCTTTT-TATTTTTCTTCTT
4734 TCTTTTCTATTTTT
1 TCTTTT-TATTTTT
4748 GTTGTTGCTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 20 0.77
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.81
Consensus pattern (19 bp):
TCTTTTTATTTTTCTTCTT
Found at i:4978 original size:26 final size:26
Alignment explanation
Indices: 4933--4984 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
4923 AAGTTGTTAA
4933 ATAAATGGATAATTAAGAAA-GGAAAT
1 ATAAATGGATAATT-AGAAATGGAAAT
4959 ATAAATGGAAATAATT-GAAATGGAAA
1 ATAAATGG--ATAATTAGAAATGGAAA
4985 GAAATGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
26 12 0.52
27 5 0.22
28 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (26 bp):
ATAAATGGATAATTAGAAATGGAAAT
Found at i:5234 original size:36 final size:35
Alignment explanation
Indices: 5136--5254 Score: 148
Period size: 35 Copynumber: 3.4 Consensus size: 35
5126 TTGTTGGTTA
* * * * *
5136 TATAGGCATAAAATGGTGATAGAAGTTGGTGATGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* *
5171 TATAGGCGTGCAATGATGATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
*
5206 TATAGACGTGAATATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTGAA-ATGGTGATGGAAGATGGTGATGT
*
5242 TGTAGGCGTGAAA
1 TATAGGCGTGAAA
5255 AAATGGTGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 39 0.55
36 32 0.45
ACGTcount: A:0.32, C:0.04, G:0.35, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:8387 original size:11 final size:13
Alignment explanation
Indices: 8355--8384 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
8345 TGGCCAAAGA
8355 TGAAAAGGTATGT
1 TGAAAAGGTATGT
8368 TGAAAAGGTATG-
1 TGAAAAGGTATGT
8380 TGAAA
1 TGAAA
8385 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:12617 original size:20 final size:19
Alignment explanation
Indices: 12582--12623 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
12572 AGCATTTATC
*
12582 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTATT
*
12601 TTCATTAAAAATCATGTGTT
1 TTCATT-AAAATCATGTATT
12621 TTC
1 TTC
12624 GAAGGAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (19 bp):
TTCATTAAAATCATGTATT
Found at i:17745 original size:14 final size:14
Alignment explanation
Indices: 17728--17761 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
17718 CAGTACTCAA
17728 AAAGAAAA-AAAAG
1 AAAGAAAAGAAAAG
17741 CAAAGAAAAGAAAAG
1 -AAAGAAAAGAAAAG
17756 AAAGAA
1 AAAGAA
17762 GTTGAAGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:27144 original size:17 final size:17
Alignment explanation
Indices: 27119--27158 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
27109 GTATGTTGTT
*
27119 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
27136 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
27153 CATTTA
1 CATTTA
27159 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:27185 original size:17 final size:17
Alignment explanation
Indices: 27165--27223 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
27155 TTTAGGGAAG
27165 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
27182 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
27198 TACTTCATTCATGCATT
1 TAGTTCATTTATGCATC
27215 TAGTTCATT
1 TAGTTCATT
27224 GAATAATGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:38653 original size:35 final size:34
Alignment explanation
Indices: 38614--38729 Score: 160
Period size: 35 Copynumber: 3.3 Consensus size: 34
38604 TGGTAAGGGA
* *
38614 ATGGTGATGATATAGGCGTGATATGGTGATAGTAG
1 ATGGTGATGATATAGGCGTGAAATGGTGAT-GAAG
*
38649 ATGGTGATGATATAGGCGTGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGAT-GAAG
*
38684 ATGGTGATGTTATAGGCGTGAAAATGGTGATGAAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATG-AAG
38720 ATGGTGATGA
1 ATGGTGATGA
38730 ACAGATAGTA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
35 51 0.71
36 21 0.29
ACGTcount: A:0.30, C:0.03, G:0.38, T:0.28
Consensus pattern (34 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGAAG
Found at i:38725 original size:13 final size:13
Alignment explanation
Indices: 38671--38735 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
38661 TAGGCGTGCA
*
38671 ATGGTGATGGAAG
1 ATGGTGATGAAAG
** *
38684 ATGGTGATGTTAT
1 ATGGTGATGAAAG
*
38697 A-GGCG-TGAAA-
1 ATGGTGATGAAAG
38707 ATGGTGATGAAAG
1 ATGGTGATGAAAG
38720 ATGGTGATGAACAG
1 ATGGTGATGAA-AG
38734 AT
1 AT
38736 AGTATCTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
10 1 0.02
11 6 0.15
12 8 0.20
13 22 0.54
14 4 0.10
ACGTcount: A:0.34, C:0.03, G:0.37, T:0.26
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:39114 original size:19 final size:20
Alignment explanation
Indices: 39073--39123 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
39063 GAAACCCCTT
* *
39073 TGAAAATACATGATTTTTTA
1 TGAAAATACATGAATTTTAA
39093 TGAAAATACAT-AATTTTAA
1 TGAAAATACATGAATTTTAA
*
39112 TGAAGATACATG
1 TGAAAATACATG
39124 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGAATTTTAA
Found at i:42124 original size:30 final size:30
Alignment explanation
Indices: 42063--42124 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
42053 ATGGTTAAGC
* * * *
42063 AAAGATAAGGTAATGAAATAAGAAAGGATG
1 AAAGAAAAGGAAATAAAATAAGAAAGAATG
42093 AAAGAAAAGGAAATAAAATAGAGAAA-AATG
1 AAAGAAAAGGAAATAAAATA-AGAAAGAATG
42123 AA
1 AA
42125 GATAACTTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.13
Consensus pattern (30 bp):
AAAGAAAAGGAAATAAAATAAGAAAGAATG
Found at i:42756 original size:35 final size:35
Alignment explanation
Indices: 42711--42826 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
42701 TGGTAAGGGA
*
42711 ATGGTGATGATATAGGTGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGTGTGAAATGGTGATGGAAG
*
42746 ATGGTGATGATATAGGTGTGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGTGTGAAATGGTGATGGAAG
* * *
42781 ATGGTGATGTTATAGGAGTGAAAATGATGATGGAAG
1 ATGGTGATGATATAGGTGTG-AAATGGTGATGGAAG
42817 ATGGTGATGA
1 ATGGTGATGA
42827 ACAGATAGTA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 51 0.70
36 22 0.30
ACGTcount: A:0.33, C:0.01, G:0.38, T:0.28
Consensus pattern (35 bp):
ATGGTGATGATATAGGTGTGAAATGGTGATGGAAG
Found at i:43216 original size:19 final size:20
Alignment explanation
Indices: 43169--43219 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
43159 GAAACCCCTT
**
43169 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
43189 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
43208 TGAAGATACATG
1 TGAAAATACATG
43220 CTCTTTGTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:45145 original size:2 final size:2
Alignment explanation
Indices: 45138--45170 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
45128 AGTTATTTTC
*
45138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45171 GTTATTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50173 original size:22 final size:20
Alignment explanation
Indices: 50148--50187 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
50138 ATGTTTGTTT
50148 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
50170 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
50188 CTTCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:51439 original size:13 final size:13
Alignment explanation
Indices: 51417--51446 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
51407 ACTAAACACC
51417 TTTC-ACATACCT
1 TTTCAACATACCT
51429 TTTCAACATACCT
1 TTTCAACATACCT
51442 TTTCA
1 TTTCA
51447 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:55613 original size:22 final size:20
Alignment explanation
Indices: 55588--55627 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55578 ATGTTTGTTT
55588 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
55610 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
55628 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:57154 original size:22 final size:22
Alignment explanation
Indices: 57126--57167 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
57116 AGTGAAACTG
*
57126 AAATTAATCCGAACCAAAATCA
1 AAATTAACCCGAACCAAAATCA
57148 AAATTAACCCGAACCAAAAT
1 AAATTAACCCGAACCAAAAT
57168 TTAACCCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.24, G:0.05, T:0.17
Consensus pattern (22 bp):
AAATTAACCCGAACCAAAATCA
Found at i:61808 original size:13 final size:13
Alignment explanation
Indices: 61790--61849 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
61780 TCTTCTTGAA
61790 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
*
61803 TTCTTTTCTTCTT
1 TTCTTTTTTTCTT
* *
61816 TTCTGATTTTTCTC
1 TTCT-TTTTTTCTT
*
61830 TTCTTTTTCTCTTT
1 TTCTTTTTTTC-TT
61844 TTCTTT
1 TTCTTT
61850 CGTTTTGCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 21 0.55
14 17 0.45
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.77
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:61844 original size:19 final size:18
Alignment explanation
Indices: 61791--61847 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
61781 CTTCTTGAAT
*
61791 TCTT-TTTTTCTTTTCTTT
1 TCTTCTTTTTCTTTT-TTC
61809 TCTTC-TTTTCTGATTTTTC
1 TCTTCTTTTTCT--TTTTTC
61828 TCTTCTTTTTCTCTTTTTC
1 TCTTCTTTTTCT-TTTTTC
61847 T
1 T
61848 TTCGTTTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 10 0.30
19 14 0.42
20 9 0.27
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (18 bp):
TCTTCTTTTTCTTTTTTC
Found at i:78655 original size:10 final size:9
Alignment explanation
Indices: 78635--78691 Score: 60
Period size: 10 Copynumber: 6.0 Consensus size: 9
78625 CTTGGAGTAC
78635 AAAAAGAAA
1 AAAAAGAAA
78644 AAAAAGACAA
1 AAAAAGA-AA
78654 AAAAAGAAA
1 AAAAAGAAA
**
78663 AAAATCATAA
1 AAAAAGA-AA
*
78673 AAGAAGAAAA
1 AAAAAG-AAA
78683 AAAAAGAAA
1 AAAAAGAAA
78692 TTCAAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 17 0.44
10 21 0.54
11 1 0.03
ACGTcount: A:0.82, C:0.04, G:0.11, T:0.04
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:78655 original size:17 final size:17
Alignment explanation
Indices: 78633--78685 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
78623 AACTTGGAGT
78633 ACAAAAAGAA-AAAAAA
1 ACAAAAAGAAGAAAAAA
78649 GACAAAAA-AAGAAAAAA
1 -ACAAAAAGAAGAAAAAA
78666 ATCATAAAAGAAGAAAAAA
1 A-CA-AAAAGAAGAAAAAA
78685 A
1 A
78686 AAGAAATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.09
17 15 0.47
18 4 0.12
19 10 0.31
ACGTcount: A:0.81, C:0.06, G:0.09, T:0.04
Consensus pattern (17 bp):
ACAAAAAGAAGAAAAAA
Found at i:78659 original size:19 final size:19
Alignment explanation
Indices: 78635--78686 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
78625 CTTGGAGTAC
*
78635 AAAAAGAAAAAAAAGACAA
1 AAAAAGAAAAAAAACACAA
* *
78654 AAAAAGAAAAAAATCATAA
1 AAAAAGAAAAAAAACACAA
*
78673 AAGAAGAAAAAAAA
1 AAAAAGAAAAAAAA
78687 AGAAATTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.83, C:0.04, G:0.10, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAAAAACACAA
Found at i:78706 original size:26 final size:27
Alignment explanation
Indices: 78642--78707 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
78632 TACAAAAAGA
*
78642 AAAAAAAGACAAAAAAAGAAAAAAATC
1 AAAAAAAGAGAAAAAAAGAAAAAAATC
* * *
78669 -ATAAAAGAAGAAAAAAA-AAGAAATTC
1 AAAAAAAG-AGAAAAAAAGAAAAAAATC
78695 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
78708 GCAAGACAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 18 0.56
27 14 0.44
ACGTcount: A:0.79, C:0.05, G:0.11, T:0.06
Consensus pattern (27 bp):
AAAAAAAGAGAAAAAAAGAAAAAAATC
Found at i:80068 original size:21 final size:21
Alignment explanation
Indices: 80044--80091 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
80034 ATCGAGGAAA
*
80044 AGACATCCCTGAATGATCAAG
1 AGACATCCCTGAACGATCAAG
80065 AGACATCCCTGAACGATCAAG
1 AGACATCCCTGAACGATCAAG
80086 AGACAT
1 AGACAT
80092 TAGGTGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.17
Consensus pattern (21 bp):
AGACATCCCTGAACGATCAAG
Found at i:82229 original size:35 final size:35
Alignment explanation
Indices: 82181--82256 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
82171 ATACTATCTA
* * *
82181 TACCATCTACCATCTCCATATCATGCCTATATCAT
1 TACCATATACCATCTCCATATCACGCCTATATAAT
* *
82216 TACCATATTCCATCTCCATTTCACGCCTATATAAT
1 TACCATATACCATCTCCATATCACGCCTATATAAT
*
82251 GACCAT
1 TACCAT
82257 CCCATTATCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.33, G:0.04, T:0.34
Consensus pattern (35 bp):
TACCATATACCATCTCCATATCACGCCTATATAAT
Found at i:92910 original size:20 final size:20
Alignment explanation
Indices: 92887--92929 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
92877 AATAGTACCC
92887 GTGAACAGTGAACAAT-AACA
1 GTGAACAGT-AACAATGAACA
* *
92907 GTGAATAGTTACAATGAACA
1 GTGAACAGTAACAATGAACA
92927 GTG
1 GTG
92930 CTTGTGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (20 bp):
GTGAACAGTAACAATGAACA
Found at i:96048 original size:24 final size:23
Alignment explanation
Indices: 96017--96071 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
96007 CAAATCCAGC
96017 AAAG-AAAATCAAAACACTCAAAA
1 AAAGAAAAATC-AAACACTCAAAA
* *
96040 AAAGAAAAATCCAGCACTCAAAA
1 AAAGAAAAATCAAACACTCAAAA
96063 ATAAGAAAA
1 A-AAGAAAA
96072 GAAAAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.67, C:0.16, G:0.07, T:0.09
Consensus pattern (23 bp):
AAAGAAAAATCAAACACTCAAAA
Found at i:96093 original size:4 final size:5
Alignment explanation
Indices: 96065--96090 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
96055 ACTCAAAAAT
96065 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
96091 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:98955 original size:15 final size:15
Alignment explanation
Indices: 98930--98964 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
98920 TGCTTCAACT
98930 TCTTT-CTTTTCTTA
1 TCTTTGCTTTTCTTA
98944 TCTTTGCTTTTCTTA
1 TCTTTGCTTTTCTTA
*
98959 TTTTTG
1 TCTTTG
98965 AGCGCTGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.71
Consensus pattern (15 bp):
TCTTTGCTTTTCTTA
Found at i:102514 original size:21 final size:20
Alignment explanation
Indices: 102488--102526 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
102478 TATTCCATCT
*
102488 TTATTTCATTTATTATCTTTA
1 TTATTTCATTAATT-TCTTTA
102509 TTATTTCATTAATTTCTT
1 TTATTTCATTAATTTCTT
102527 CCTTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTCATTAATTTCTTTA
Found at i:102533 original size:21 final size:21
Alignment explanation
Indices: 102485--102534 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
102475 CTCTATTCCA
*
102485 TCTTTATTTCATTTATTATCT
1 TCTTTATTTCATTAATTATCT
102506 T-TATTATTTCATTAATT-TCT
1 TCT-TTATTTCATTAATTATCT
102526 TCCTTTATT
1 T-CTTTATT
102535 AACCATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 5 0.20
21 19 0.76
22 1 0.04
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (21 bp):
TCTTTATTTCATTAATTATCT
Found at i:115421 original size:8 final size:8
Alignment explanation
Indices: 115410--115457 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
115400 TCTTTTTCTT
115410 TTCTTTTC
1 TTCTTTTC
115418 TTCTTTTC
1 TTCTTTTC
115426 TTCTTTTC
1 TTCTTTTC
115434 TTC-TTTC
1 TTCTTTTC
115441 TGTCTTTTC
1 T-TCTTTTC
115450 TTTCTTTT
1 -TTCTTTT
115458 TGTACTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 5 0.14
8 21 0.57
9 10 0.27
10 1 0.03
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (8 bp):
TTCTTTTC
Found at i:115427 original size:24 final size:23
Alignment explanation
Indices: 115400--115452 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
115390 TTTGAACTTC
*
115400 TCTTTTTCTTTTCTTTTCT-TCTTT
1 TCTTTTT-TCTTC-TTTCTGTCTTT
115424 TCTTCTTTTCTTCTTTCTGTCTTT
1 TCTT-TTTTCTTCTTTCTGTCTTT
115448 TCTTT
1 TCTTT
115453 CTTTTTGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 6 0.23
24 17 0.65
25 3 0.12
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (23 bp):
TCTTTTTTCTTCTTTCTGTCTTT
Found at i:115453 original size:13 final size:12
Alignment explanation
Indices: 115400--115455 Score: 64
Period size: 13 Copynumber: 4.7 Consensus size: 12
115390 TTTGAACTTC
115400 TCTTT-TTCTTT
1 TCTTTCTTCTTT
115411 TCTTTTCTTCTTT
1 TC-TTTCTTCTTT
115424 TC-TTCTT-TTCT
1 TCTTTCTTCTT-T
115435 TCTTTCTGTCTTT
1 TCTTTCT-TCTTT
115448 TCTTTCTT
1 TCTTTCTT
115456 TTTGTACTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.05
11 10 0.26
12 8 0.21
13 17 0.44
14 2 0.05
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (12 bp):
TCTTTCTTCTTT
Found at i:120874 original size:14 final size:14
Alignment explanation
Indices: 120857--120891 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
120847 TTTATTTCTT
120857 TTCTTTTCT-TTTTC
1 TTCTTTT-TGTTTTC
120871 TTCTTTTTGTTTTC
1 TTCTTTTTGTTTTC
120885 TTCTTTT
1 TTCTTTT
120892 GGAGTGCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 1 0.05
14 19 0.95
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (14 bp):
TTCTTTTTGTTTTC
Found at i:123087 original size:4 final size:5
Alignment explanation
Indices: 123059--123084 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
123049 ACTCAAAAAG
123059 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
123085 GAAGTTGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Done.