Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005994.1 Hibiscus syriacus cultivar Beakdansim tig00014108_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: 139534
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:68 original size:24 final size:22
Alignment explanation
Indices: 19--60 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
9 ACAGAATGTC
19 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
40 TAGGAGGGAACCGATTCCCCC
1 AAGGAGGGAACCGATACCCCC
61 CTAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.29, C:0.33, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:1078 original size:31 final size:31
Alignment explanation
Indices: 994--1117 Score: 110
Period size: 31 Copynumber: 4.0 Consensus size: 31
984 GTCGAGGGTT
*
994 TACCTATGTTCTACGGAACATATGGACA-TAA
1 TACCTATGTTCTAAGGAACATATGGACAGT-A
* * *
1025 TTACTTATG-TCT-TGCGAGACATATGGATAGTA
1 -TACCTATGTTCTAAG-GA-ACATATGGACAGTA
1057 TACCTATGTTCTAAGGAACATATGGACAGTA
1 TACCTATGTTCTAAGGAACATATGGACAGTA
* ** * *
1088 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGT
1118 TGCCGAGGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
30 1 0.01
31 50 0.66
32 23 0.30
33 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:1159 original size:30 final size:30
Alignment explanation
Indices: 1104--1206 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
1094 GGTTCTTCGG
* * * *
1104 GACCTATGGACAGTTGCCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGATGATCTTTAT
1134 GACCTCTGGATAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGATGATCTTTAT
1164 GACCTCTGGATAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGATGATCTTTAT
1194 GACCTCTGGATAG
1 GACCTCTGGATAG
1207 GTCCTTCGGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGATGATCTTTAT
Found at i:2861 original size:31 final size:30
Alignment explanation
Indices: 2806--2864 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
2796 TTAGGTCCAT
2806 AAGGAATTACCAGTCGATGATGAACCTATAC
1 AAGGAATTACCAGTCGAT-ATGAACCTATAC
2837 AAGGAATTACCAGTAGCGAT-TGAACCTA
1 AAGGAATTACCAGT--CGATATGAACCTA
2865 CCAGAGTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 22 0.85
33 4 0.15
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (30 bp):
AAGGAATTACCAGTCGATATGAACCTATAC
Found at i:5817 original size:14 final size:15
Alignment explanation
Indices: 5798--5833 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
5788 ATTAATTAAA
5798 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
5812 TATTTTATGTTAATT
1 TATTTTATGTTAATT
5827 TAGTTTT
1 TA-TTTT
5834 TTTTATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.55
15 5 0.25
16 4 0.20
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:8452 original size:2 final size:2
Alignment explanation
Indices: 8441--8475 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
8431 TGATTTACTT
8441 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
8476 TTGATATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12223 original size:31 final size:31
Alignment explanation
Indices: 12168--12226 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
12158 TTAGGTCCAT
* *
12168 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
12199 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
12227 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:15212 original size:14 final size:15
Alignment explanation
Indices: 15193--15223 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
15183 ATTAATTAAA
15193 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
15207 TATTTTATGTTAATT
1 TATTTTATGTTAATT
15222 TA
1 TA
15224 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:17855 original size:2 final size:2
Alignment explanation
Indices: 17848--17883 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
17838 TGATTTACTT
17848 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
17884 TTGATATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21639 original size:31 final size:31
Alignment explanation
Indices: 21584--21642 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
21574 TTAGGTCCAT
* *
21584 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
21615 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
21643 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:24633 original size:14 final size:15
Alignment explanation
Indices: 24614--24644 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
24604 ATTAATTAAA
24614 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
24628 TATTTTATGTTAATT
1 TATTTTATGTTAATT
24643 TA
1 TA
24645 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:31057 original size:31 final size:31
Alignment explanation
Indices: 31002--31060 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
30992 TTAGGTCCAT
* *
31002 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
31033 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
31061 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:34056 original size:14 final size:15
Alignment explanation
Indices: 34037--34067 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
34027 ATTAATTAAA
34037 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
34051 TATTTTATGTTAATT
1 TATTTTATGTTAATT
34066 TA
1 TA
34068 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:36710 original size:2 final size:2
Alignment explanation
Indices: 36699--36731 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
36689 TGATTTACTT
36699 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
36732 TTGATATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:40475 original size:31 final size:31
Alignment explanation
Indices: 40420--40478 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
40410 TTAGGTCCAT
* *
40420 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
40451 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
40479 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:43475 original size:14 final size:15
Alignment explanation
Indices: 43456--43486 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
43446 ATTAATTAAA
43456 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
43470 TATTTTATGTTAATT
1 TATTTTATGTTAATT
43485 TA
1 TA
43487 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:49893 original size:31 final size:31
Alignment explanation
Indices: 49838--49896 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
49828 TTAGGTCCAT
* *
49838 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
49869 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
49897 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:56811 original size:24 final size:25
Alignment explanation
Indices: 56767--56814 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
56757 TTCATATTAC
56767 TAATTAATCTATTAATATATTATTT
1 TAATTAATCTATTAATATATTATTT
*
56792 TAATTAAT-TATTAATCTATTATT
1 TAATTAATCTATTAATATATTATT
56815 GATCATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TAATTAATCTATTAATATATTATTT
Found at i:59305 original size:31 final size:31
Alignment explanation
Indices: 59250--59308 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
59240 TTAGGTCCAT
* *
59250 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
59281 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
59309 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:62288 original size:14 final size:15
Alignment explanation
Indices: 62269--62299 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
62259 ATTAATTAAA
62269 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
62283 TATTTTATGTTAATT
1 TATTTTATGTTAATT
62298 TA
1 TA
62300 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:67296 original size:30 final size:30
Alignment explanation
Indices: 67262--67329 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
67252 TGGCAGATGT
*
67262 GTTGATGGAGCAGGTACTGGTGGAACACAC
1 GTTGATGGAGCAGGCACTGGTGGAACACAC
*
67292 GTTGATGGAGCAGGCACTGGTGGAACGCAC
1 GTTGATGGAGCAGGCACTGGTGGAACACAC
67322 GTTGATGG
1 GTTGATGG
67330 GACTTGCAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.21
Consensus pattern (30 bp):
GTTGATGGAGCAGGCACTGGTGGAACACAC
Found at i:70632 original size:2 final size:2
Alignment explanation
Indices: 70621--70671 Score: 86
Period size: 2 Copynumber: 25.5 Consensus size: 2
70611 TGATTTACTT
70621 TA TA -A 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
70662 TA TA TGA TA T
1 TA TA T-A TA T
70672 TCGATATTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 44 0.94
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:74399 original size:31 final size:31
Alignment explanation
Indices: 74344--74402 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
74334 TTAGGTCCAT
* *
74344 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
74375 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
74403 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:75971 original size:2 final size:2
Alignment explanation
Indices: 75959--75995 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
75949 TCAATATCAA
75959 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75996 AAGTAAATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:78641 original size:14 final size:15
Alignment explanation
Indices: 78617--78647 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
78607 AAAAACAAAC
78617 TAAATTAACATAAAA
1 TAAATTAACATAAAA
78632 TAAA-TAACATAAAA
1 TAAATTAACATAAAA
78646 TA
1 TA
78648 TTTAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATTAACATAAAA
Found at i:83346 original size:34 final size:33
Alignment explanation
Indices: 83282--83348 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
83272 TTCATATTAC
*
83282 TAATTAATCTATTAATAATATTATTTTAATTAAT
1 TAATTAATCTATTAATAATATTA-TCTAATTAAT
*
83316 TAATTAATCTATTATGATCATATTA-CTAATTAA
1 TAATTAATCTATTA--ATAATATTATCTAATTAA
83349 GTAGAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 21 0.72
36 8 0.28
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.49
Consensus pattern (33 bp):
TAATTAATCTATTAATAATATTATCTAATTAAT
Found at i:87536 original size:13 final size:13
Alignment explanation
Indices: 87518--87551 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
87508 TGATTTACTT
87518 TATATATATATAA
1 TATATATATATAA
*
87531 TATATATATATTA
1 TATATATATATAA
87544 TATGATAT
1 TAT-ATAT
87552 TTGATATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TATATATATATAA
Found at i:93413 original size:158 final size:154
Alignment explanation
Indices: 93128--93439 Score: 579
Period size: 158 Copynumber: 2.0 Consensus size: 154
93118 CGATATTTGA
93128 ATCAAGTATCTTTTCACAAAAGAATCATATTAATATGAAGATCTTCAAATTCTCTTTCACGTTGT
1 ATCAAGTATCTTTTCACAAAAGAATCATATTAATATGAAGATCTTCAAATTCTCTTTCACGTTGT
93193 GTTTTCTTCAATTATATTCATGTTAATGCTCACAATGTCACTCACGATTCGAGATCAATCATCAT
66 GTTTTCTTCAATTATATTCATGTTAATGCTCACAATGTCACTCACGATTCGAGATCAATCATCAT
93258 GATGGAAACTCATCGAATCATTCTC
131 GATGG-AACTCATCGAATCATTCTC
*
93283 ATCAATTATCTTTTCACAAAAGAATCATATTAATATGAAGATCTTCAAATTCTTCTTTCACGTTG
1 ATCAAGTATCTTTTCACAAAAGAATCATATTAATATGAAGATCTTCAAATTC-TCTTTCACGTTG
93348 TTGTTTCTCTTCAATTATATTCATGTTAATGCTCACAATGTCACTCACGATTCGAGATCAATCAT
65 -TGTTT-TCTTCAATTATATTCATGTTAATGCTCACAATGTCACTCACGATTCGAGATCAATCAT
93413 CATGATGGAACTCATCGAATCATTCTC
128 CATGATGGAACTCATCGAATCATTCTC
93440 TCGGGTTCAA
Statistics
Matches: 153, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
155 51 0.33
156 12 0.08
157 24 0.16
158 66 0.43
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (154 bp):
ATCAAGTATCTTTTCACAAAAGAATCATATTAATATGAAGATCTTCAAATTCTCTTTCACGTTGT
GTTTTCTTCAATTATATTCATGTTAATGCTCACAATGTCACTCACGATTCGAGATCAATCATCAT
GATGGAACTCATCGAATCATTCTC
Found at i:94249 original size:14 final size:15
Alignment explanation
Indices: 94230--94260 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
94220 ATTAATTAAA
94230 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
94244 TATTTTATGTTAATT
1 TATTTTATGTTAATT
94259 TA
1 TA
94261 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:100642 original size:31 final size:31
Alignment explanation
Indices: 100587--100645 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
100577 TTAGGTCCAT
* *
100587 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
100618 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
100646 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:103635 original size:14 final size:15
Alignment explanation
Indices: 103616--103646 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
103606 ATTAATTAAA
103616 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
103630 TATTTTATGTTAATT
1 TATTTTATGTTAATT
103645 TA
1 TA
103647 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:106283 original size:2 final size:2
Alignment explanation
Indices: 106272--106304 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
106262 TGATTTACTT
106272 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
106305 TTGATATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:110056 original size:31 final size:31
Alignment explanation
Indices: 110001--110059 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
109991 TTAGGTCCAT
* *
110001 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
110032 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
110060 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:113052 original size:14 final size:15
Alignment explanation
Indices: 113033--113063 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
113023 ATTAATTAAA
113033 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
113047 TATTTTATGTTAATT
1 TATTTTATGTTAATT
113062 TA
1 TA
113064 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:115701 original size:2 final size:2
Alignment explanation
Indices: 115690--115722 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
115680 TGATTTACTT
115690 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
115723 TTGATATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:119475 original size:31 final size:31
Alignment explanation
Indices: 119420--119478 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
119410 TTAGGTCCAT
* *
119420 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
119451 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
119479 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:122473 original size:14 final size:15
Alignment explanation
Indices: 122454--122484 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
122444 ATTAATTAAA
122454 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
122468 TATTTTATGTTAATT
1 TATTTTATGTTAATT
122483 TA
1 TA
122485 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:125118 original size:2 final size:2
Alignment explanation
Indices: 125107--125140 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
125097 TGATTTACTT
125107 TA TA -A 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 TA T
125141 TGATATTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:128892 original size:31 final size:31
Alignment explanation
Indices: 128837--128895 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
128827 TTAGGTCCAT
* *
128837 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
128868 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
128896 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Found at i:131894 original size:14 final size:15
Alignment explanation
Indices: 131875--131905 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
131865 ATTAATTAAA
131875 TATTTTATGTT-ATT
1 TATTTTATGTTAATT
131889 TATTTTATGTTAATT
1 TATTTTATGTTAATT
131904 TA
1 TA
131906 GTTTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATGTTAATT
Found at i:134542 original size:2 final size:2
Alignment explanation
Indices: 134531--134562 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
134521 TGATTTACTT
134531 TA TA -A 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
134563 TGATATTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:138309 original size:31 final size:31
Alignment explanation
Indices: 138254--138312 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
138244 TTAGGTCCAT
* *
138254 AAGGAATTACCAGTCGGTGATGAACCTATAC
1 AAGGAATTACCAGTCAGCGATGAACCTATAC
138285 AAGGAATTACCAGT-AGCGATTGAACCTA
1 AAGGAATTACCAGTCAGCGA-TGAACCTA
138313 CCAGAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGCGATGAACCTATAC
Done.