Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005193.1 Hibiscus syriacus cultivar Beakdansim tig00011732_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: 65637
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1115 original size:45 final size:45
Alignment explanation
Indices: 1064--1354 Score: 167
Period size: 45 Copynumber: 6.5 Consensus size: 45
1054 ATTTATGTTG
*
1064 ATAATGCACCCATATGCATT-TCAACTATGAAATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTAT-AACTATGAAATCATTTCATGCCA
* * * **
1109 ATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCA
1 ATAATGCACCCATATGCATTATAACTATGAAATCATTTCATGCCA
* * * * * ** *
1154 ATAATGCACCCATATTCTTTATTATTTTGGGAT-ACTTTCATGCTA
1 ATAATGCACCCATATGCATTATAACTATGAAATCA-TTTCATGCCA
* * * * * ** * * *
1199 ATAATGCACCTATATTCATTATTATTTTGGCATCCTTTCATGTCG
1 ATAATGCACCCATATGCATTATAACTATGAAATCATTTCATGCCA
* * * * * ** *
1244 ATAATGCACCTATATGGATTATTATTTTGGCATCCTTTCATGCCA
1 ATAATGCACCCATATGCATTATAACTATGAAATCATTTCATGCCA
* * * ** * *
1289 ATAATGCA-CC-TATCGCATTATTATTTTGGTATCCTTTCATGCCG
1 ATAATGCACCCATAT-GCATTATAACTATGAAATCATTTCATGCCA
*
1333 ATAATGCACCCATATTCATTAT
1 ATAATGCACCCATATGCATTAT
1355 TATTTTGTTC
Statistics
Matches: 214, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
43 3 0.01
44 37 0.17
45 170 0.79
46 4 0.02
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.40
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTATAACTATGAAATCATTTCATGCCA
Found at i:1192 original size:90 final size:90
Alignment explanation
Indices: 1098--1361 Score: 388
Period size: 90 Copynumber: 2.9 Consensus size: 90
1088 CTATGAAATC
* *
1098 CTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCATTTCATGCCAATAATGCAC
1 CTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCGATAATGCAC
* *
1163 CCATATTCTTTATTATTTTGGGATA
66 CCATATTCATTATTATTTTGGCATA
* * * *
1188 CTTTCATGCTAATAATGCACCTATATTCATTATTATTTTGGCATCCTTTCATGTCGATAATGCAC
1 CTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCGATAATGCAC
* ** *
1253 CTATATGGATTATTATTTTGGCATC
66 CCATATTCATTATTATTTTGGCATA
*
1278 CTTTCATGCCAATAATGCA-CC-TATCGCATTATTATTTTGGTATCCTTTCATGCCGATAATGCA
1 CTTTCATGCCAATAATGCACCCATAT-GCATTATTATTTTGGCATCCTTTCATGCCGATAATGCA
1341 CCCATATTCATTATTATTTTG
65 CCCATATTCATTATTATTTTG
1362 TTCATTCATT
Statistics
Matches: 153, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
88 3 0.02
89 54 0.35
90 96 0.63
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (90 bp):
CTTTCATGCCAATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCGATAATGCAC
CCATATTCATTATTATTTTGGCATA
Found at i:1793 original size:22 final size:21
Alignment explanation
Indices: 1751--1821 Score: 85
Period size: 22 Copynumber: 3.5 Consensus size: 21
1741 TGGCTCCTCA
*
1751 GTATCGATAC-CCATACCATG
1 GTATCGATACTCCATACTATG
1771 GTATCGATACTACCATACTATG
1 GTATCGATACT-CCATACTATG
* *
1793 GTACCGATACT--ATGCTATG
1 GTATCGATACTCCATACTATG
1812 GTATCGATAC
1 GTATCGATAC
1822 CATTTTTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 16 0.36
20 10 0.22
22 19 0.42
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (21 bp):
GTATCGATACTCCATACTATG
Found at i:4822 original size:25 final size:24
Alignment explanation
Indices: 4766--4827 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
4756 TATATATATA
4766 ATTTGAA-A-ATATTTTTGAAAAC
1 ATTTGAATATATATTTTTGAAAAC
4788 ATATAT-AATATATAGTTTTTGAAAAC
1 AT-T-TGAATATATA-TTTTTGAAAAC
4814 ATTTGAATATATAT
1 ATTTGAATATATAT
4828 ATATATAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
22 2 0.06
23 3 0.09
24 4 0.12
25 12 0.35
26 13 0.38
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (24 bp):
ATTTGAATATATATTTTTGAAAAC
Found at i:4856 original size:69 final size:70
Alignment explanation
Indices: 4621--4913 Score: 219
Period size: 69 Copynumber: 4.1 Consensus size: 70
4611 ATAGTATATT
* ** * * *
4621 TTTTGAAAATA-TTTTCAAAAAAACGTATAACATATAGTTTTTAAAACGGTTATTGAAAACGTAT
1 TTTTGAAAATAGTTTT-AAAAACATATATAATATATAGTTTTGAAAAC-ATT-TTGAAAA--TAT
*
4685 A-ATATAGAG
61 ATATATATAG
* ** * *
4694 TTTTTGAAAAAACCAGTTTTTGAAA-ATATAT-ATAATATGGTTTTGAAATACGA-TTT-AAAAC
1 -TTTTG--AAAA-TAGTTTTAAAAACATATATAAT-ATATAGTTTTGAAA-AC-ATTTTGAAAAT
4755 ATATATATATA-
59 ATATATATATAG
* * * *
4766 ATTTGAAAATATTTTTGAAAACATATATAATATATAGTTTTTGAAAACA-TTTGAATATATATAT
1 TTTTGAAAATAGTTTTAAAAACATATATAATATATAG-TTTTGAAAACATTTTGAAAATATATAT
4830 ATATAG
65 ATATAG
* * *
4836 TTTTTAAAAT-GTTTTAAAAACATATATTATATATAGTTTTGAAAATATTTTTGAAAATATAT-T
1 TTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTGAAAACA-TTTTGAAAATATATAT
4899 ATATAG
65 ATATAG
4905 TTTTGAAAA
1 TTTTGAAAA
4914 ATGGGTTTTG
Statistics
Matches: 178, Mismatches: 27, Indels: 33
0.75 0.11 0.14
Matches are distributed among these distances:
68 22 0.12
69 69 0.39
70 30 0.17
71 4 0.02
72 3 0.02
73 6 0.03
74 9 0.05
75 3 0.02
76 21 0.12
77 7 0.04
78 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (70 bp):
TTTTGAAAATAGTTTTAAAAACATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATA
TATAG
Found at i:4923 original size:35 final size:34
Alignment explanation
Indices: 4711--4927 Score: 173
Period size: 33 Copynumber: 6.3 Consensus size: 34
4701 AAAAACCAGT
* * *
4711 TTTTGAAAATATATATAATATGGTTTTGAAATACG
1 TTTTGAAAATATATAT-ATATAGTTTTGAAAAATG
* * *
4746 ATTT-AAAACATATATATATA-ATTTGAAAATAT-
1 TTTTGAAAATATATATATATAGTTTTGAAAA-ATG
4778 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA--
1 TTTTG-AAA-ATATAT-ATATATAG-TTTTGAAAA-ATG
* *
4815 -TTTGAATATATATATATATAGTTTT-TAAAATG
1 TTTTGAAAATATATATATATAGTTTTGAAAAATG
*
4847 TTTTAAAAACATATATTATATATAGTTTTGAAAATAT-
1 TTTT-GAAA-ATATA-TATATATAGTTTTGAAAA-ATG
4884 TTTTGAAAATATAT-TATATAGTTTTGAAAAATGGG
1 TTTTGAAAATATATATATATAGTTTTGAAAAAT--G
4919 TTTTGAAAA
1 TTTTGAAAA
4928 CATTTTTGGA
Statistics
Matches: 148, Mismatches: 16, Indels: 36
0.74 0.08 0.18
Matches are distributed among these distances:
30 1 0.01
31 3 0.02
32 16 0.11
33 32 0.22
34 22 0.15
35 29 0.20
36 27 0.18
37 7 0.05
38 11 0.07
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (34 bp):
TTTTGAAAATATATATATATAGTTTTGAAAAATG
Found at i:4958 original size:3 final size:3
Alignment explanation
Indices: 4952--5034 Score: 80
Period size: 3 Copynumber: 25.7 Consensus size: 3
4942 TATTTTTTTG
4952 TTA TTA TTA TTA TTA TTCA TTA -TA TTTA TTTA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA -TTA -TTA TTA T-TA TTA TTA TTA
5000 TTA TTCA TTA -TA TTTA TTTA TTA TTTA TTA TTA TT
1 TTA TT-A TTA TTA -TTA -TTA TTA -TTA TTA TTA TT
5035 TCTTTTAGGG
Statistics
Matches: 72, Mismatches: 0, Indels: 16
0.82 0.00 0.18
Matches are distributed among these distances:
2 4 0.06
3 44 0.61
4 24 0.33
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4980 original size:13 final size:12
Alignment explanation
Indices: 4952--5034 Score: 73
Period size: 13 Copynumber: 6.7 Consensus size: 12
4942 TATTTTTTTG
4952 TTATTATTAT-T
1 TTATTATTATAT
4963 ATTATTCATTATAT
1 -TTATT-ATTATAT
4977 TTATTTATTATAT
1 TTA-TTATTATAT
4990 ATTATTATTATTAT
1 -TTATTATTA-TAT
* *
5004 TCATTATATTTAT
1 TTATTAT-TATAT
5017 TTATTATT-TA-
1 TTATTATTATAT
5027 TTATTATT
1 TTATTATT
5035 TCTTTTAGGG
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
10 8 0.13
11 2 0.03
12 6 0.10
13 36 0.58
14 10 0.16
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTATTATAT
Found at i:4993 original size:36 final size:36
Alignment explanation
Indices: 4953--5034 Score: 155
Period size: 36 Copynumber: 2.3 Consensus size: 36
4943 ATTTTTTTGT
4953 TATTATTATTATTATTCATTATATTTATTTATTATA
1 TATTATTATTATTATTCATTATATTTATTTATTATA
*
4989 TATTATTATTATTATTCATTATATTTATTTATTATT
1 TATTATTATTATTATTCATTATATTTATTTATTATA
5025 TATTATTATT
1 TATTATTATT
5035 TCTTTTAGGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (36 bp):
TATTATTATTATTATTCATTATATTTATTTATTATA
Found at i:6213 original size:29 final size:29
Alignment explanation
Indices: 6161--6219 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
6151 TTACTCTCTA
* * *
6161 AAATTACCATTTTTTCTTCGTTTTTCTTT
1 AAATTAACATTTTTTCATCGTTTTTATTT
6190 AAATTAACATTTTTGTCATC-TTTTTATTT
1 AAATTAACATTTTT-TCATCGTTTTTATTT
6219 A
1 A
6220 TTTATTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.24, C:0.14, G:0.03, T:0.59
Consensus pattern (29 bp):
AAATTAACATTTTTTCATCGTTTTTATTT
Found at i:6272 original size:20 final size:20
Alignment explanation
Indices: 6249--6286 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6239 CTCATTATTC
*
6249 TTTCTTTTAGCTTTATTTGT
1 TTTCTTTCAGCTTTATTTGT
6269 TTTCTTTCAGCTTTATTT
1 TTTCTTTCAGCTTTATTT
6287 CCTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.13, G:0.08, T:0.68
Consensus pattern (20 bp):
TTTCTTTCAGCTTTATTTGT
Found at i:12926 original size:24 final size:25
Alignment explanation
Indices: 12892--12950 Score: 102
Period size: 24 Copynumber: 2.4 Consensus size: 25
12882 AGGTTTTGCT
12892 CCTTAAACCCGCTAGGAGCTCCGCC
1 CCTTAAACCCGCTAGGAGCTCCGCC
12917 CCTT-AACCCGCTAGGAGCTCCGCC
1 CCTTAAACCCGCTAGGAGCTCCGCC
*
12941 CCTTGAACCC
1 CCTTAAACCC
12951 TTAGTAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 24 0.73
25 9 0.27
ACGTcount: A:0.19, C:0.46, G:0.19, T:0.17
Consensus pattern (25 bp):
CCTTAAACCCGCTAGGAGCTCCGCC
Found at i:17151 original size:34 final size:34
Alignment explanation
Indices: 17108--17208 Score: 166
Period size: 34 Copynumber: 3.0 Consensus size: 34
17098 GGTTTCTGCC
*
17108 TATGAGACATTGTATTTCTCTTTCGAAGGAAATG
1 TATGAGACATGGTATTTCTCTTTCGAAGGAAATG
**
17142 TATGAGACATGGTATTTCTCTTTCGAAAAAAATG
1 TATGAGACATGGTATTTCTCTTTCGAAGGAAATG
*
17176 TATGAGACATGGTATTTCTCTTTAGAAGGAAAT
1 TATGAGACATGGTATTTCTCTTTCGAAGGAAAT
17209 TTATCCTTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 61 1.00
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (34 bp):
TATGAGACATGGTATTTCTCTTTCGAAGGAAATG
Found at i:20449 original size:90 final size:88
Alignment explanation
Indices: 20335--20508 Score: 303
Period size: 90 Copynumber: 2.0 Consensus size: 88
20325 TCCCGAATAT
* *
20335 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
20400 GGTAACTTGGATATAAAAGGATTA
65 GGTAACTTGGATATAAAAGGATTA
20424 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
20489 GGTAACTTGGCTATAAAAGG
65 GGTAACTTGGATATAAAAGG
20509 GTGCGTTGGG
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
89 40 0.49
90 41 0.51
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAAAGGATTA
Found at i:31533 original size:35 final size:36
Alignment explanation
Indices: 31465--31535 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
31455 AATTTAAAAT
*
31465 GGGTATTTTTCAAATACAACTGTCCCACAAAACATC
1 GGGTATTTTTCAAATACAACTGCCCCACAAAACATC
* *
31501 GGGTGTTTTTCAAATA-AATTGCCCCACAAAACATC
1 GGGTATTTTTCAAATACAACTGCCCCACAAAACATC
31536 AAGTGCAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (36 bp):
GGGTATTTTTCAAATACAACTGCCCCACAAAACATC
Found at i:32094 original size:63 final size:63
Alignment explanation
Indices: 31995--32140 Score: 240
Period size: 63 Copynumber: 2.3 Consensus size: 63
31985 TTGACGAGGA
* * *
31995 AGATCATTCAACAAATCT-ATTCCAATACAGTTTGATGGGGAAGATCATTCAAAAAGTATTTGT
1 AGATCACTCAACAAAT-TGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT
32058 AGATCACTCAACAAATTGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT
1 AGATCACTCAACAAATTGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT
*
32121 AAATCACTCAACAAATTGAT
1 AGATCACTCAACAAATTGAT
32141 GAGGAAGATC
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
62 1 0.01
63 77 0.99
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (63 bp):
AGATCACTCAACAAATTGATTCCAATACAGTTTGATGAGGAAGATAATTCAAAAAGTATTTGT
Found at i:33388 original size:30 final size:30
Alignment explanation
Indices: 33344--33418 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
33334 GCACAAACTT
33344 AAACATAAAGGACTAAAATA-ATAAAAATAG
1 AAACATAAAGGACTAAAATAGA-AAAAATAG
*
33374 AAAC-TAAAGGGACTAAAATAGAAAAATTAG
1 AAACATAAA-GGACTAAAATAGAAAAAATAG
*
33404 AAACTTAAAGGACTA
1 AAACATAAAGGACTA
33419 TACATTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
29 4 0.10
30 32 0.78
31 5 0.12
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.17
Consensus pattern (30 bp):
AAACATAAAGGACTAAAATAGAAAAAATAG
Found at i:34676 original size:3 final size:3
Alignment explanation
Indices: 34658--34696 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
34648 GTAAATTGTA
34658 AAT AA- AAT ATAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
34697 TAAAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35112 original size:134 final size:134
Alignment explanation
Indices: 34939--35216 Score: 346
Period size: 134 Copynumber: 2.1 Consensus size: 134
34929 GAGTTCTTTT
* **
34939 CATCTTTAGGAAGGGTGATAACTCGATTCTTACGCGATGAAGACAGTTGGTTATCTAGGGGTGAC
1 CATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGAC
* * * *
35004 ACGGCTCCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGTTCCTACGTG-ATGAGGAT-G
66 ACAGATCCTACGTGATAAGGAGGTCTAGTCAAGGGATGACACGGTTCCTACG-GAATGAGG-TCG
*
35067 GTTGGC
129 ATTGGC
* * * * * *
35073 CATCTTTAGG-AGTGGTGATAACTCGGTTCCTACGTGATGACGACGGCAGGTTATCTATGGTTGA
1 CATCTTTAGGAAG-GGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGA
* * *
35137 CACAGATCCTACGTTATAAGGAGGTCTAGTCAGGGGATGACATGGTTCCTACGGAATGAGGTCGA
65 CACAGATCCTACGTGATAAGGAGGTCTAGTCAAGGGATGACACGGTTCCTACGGAATGAGGTCGA
35202 TTGGC
130 TTGGC
*
35207 CATCCTTAGG
1 CATCTTTAGG
35217 GATTATGGTT
Statistics
Matches: 123, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
133 4 0.03
134 119 0.97
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.27
Consensus pattern (134 bp):
CATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAAGACAGCAGGTTATCTAGGGGTGAC
ACAGATCCTACGTGATAAGGAGGTCTAGTCAAGGGATGACACGGTTCCTACGGAATGAGGTCGAT
TGGC
Found at i:35264 original size:28 final size:28
Alignment explanation
Indices: 35232--35320 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 28
35222 TGGTTTCAGG
35232 AGAAACCAACTCAAAGATTTGTTTCAAA
1 AGAAACCAACTCAAAGATTTGTTTCAAA
* *
35260 AGAAA-CATACTTAAAGATTTATTTCAAGA
1 AGAAACCA-ACTCAAAGATTTGTTTCAA-A
*
35289 A-AAACAAACTCAAAGATGATGTGTTTCAAA
1 AGAAACCAACTCAAAGAT--T-TGTTTCAAA
35319 AG
1 AG
35321 CAACTGTCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
27 2 0.04
28 34 0.69
29 3 0.06
30 3 0.06
31 7 0.14
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.26
Consensus pattern (28 bp):
AGAAACCAACTCAAAGATTTGTTTCAAA
Found at i:35402 original size:63 final size:67
Alignment explanation
Indices: 35280--35408 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 67
35270 TTAAAGATTT
* *
35280 ATTTCAAGAAAAACAAACTCAAAGATGATGTGTTTCAAAAGCAACTGTCTCAAAAGAGACAAAAT
1 ATTTCAAGAAAAACAAACTCAAAGATGATCTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAAT
35345 TC
66 TC
* * * **
35347 ATTTCAAGAGAAAC-GACTCAAAGATGA-CT-TTT-AAAGGAAACTGTCTCAAGCGAGACAAAAT
1 ATTTCAAGAAAAACAAACTCAAAGATGATCTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAAT
35408 T
66 T
35409 TGTTTTTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 26 0.47
64 3 0.05
65 1 0.02
66 12 0.22
67 13 0.24
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (67 bp):
ATTTCAAGAAAAACAAACTCAAAGATGATCTGTTTCAAAAGAAACTGTCTCAAAAGAGACAAAAT
TC
Found at i:35840 original size:28 final size:28
Alignment explanation
Indices: 35779--35832 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
35769 AGAGAAATAA
* *
35779 ACTCAAAGATTTTTTTCAAAAGGAACAG
1 ACTCAAAGATTTGTTTCAAAAGAAACAG
*
35807 ACTCAAAGATTTGTTTCAAGAGAAAC
1 ACTCAAAGATTTGTTTCAAAAGAAAC
35833 TGTCTCAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (28 bp):
ACTCAAAGATTTGTTTCAAAAGAAACAG
Found at i:43442 original size:3 final size:3
Alignment explanation
Indices: 43434--43464 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
43424 AATTGTAAAT
*
43434 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
43465 ATATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:43470 original size:15 final size:15
Alignment explanation
Indices: 43429--43488 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 15
43419 GTGTAAATTG
*
43429 TAAATATAATAATAA
1 TAAATATAACAATAA
43444 TAATAATAATAACAATAA
1 T-A-AAT-ATAACAATAA
43462 TAAATATAA-AATAAA
1 TAAATATAACAAT-AA
*
43477 TAAATAAAACAA
1 TAAATATAACAA
43489 AAAAAAAGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.08
15 15 0.39
16 6 0.16
17 4 0.11
18 10 0.26
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAATATAACAATAA
Found at i:47575 original size:28 final size:28
Alignment explanation
Indices: 47517--47607 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 28
47507 TGAATAAAAT
* * *
47517 TTTATAGGGTTTTTGAGATTATGATATAA
1 TTTATAGGG-TTTAGAGTTTATGATGTAA
47546 TTTATAGGGTTTAGAGTTTATGATGTAA
1 TTTATAGGGTTTAGAGTTTATGATGTAA
* * * *
47574 TTTATAGGATTTGGAATTTATGACGTAA
1 TTTATAGGGTTTAGAGTTTATGATGTAA
47602 TTTATA
1 TTTATA
47608 TGATTTGGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 46 0.84
29 9 0.16
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (28 bp):
TTTATAGGGTTTAGAGTTTATGATGTAA
Found at i:47612 original size:28 final size:28
Alignment explanation
Indices: 47543--47616 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
47533 GATTATGATA
* * * *
47543 TAATTTATAGGGTTTAGAGTTTATGATG
1 TAATTTATAGGATTTGGAATTTATGACG
47571 TAATTTATAGGATTTGGAATTTATGACG
1 TAATTTATAGGATTTGGAATTTATGACG
*
47599 TAATTTATATGATTTGGA
1 TAATTTATAGGATTTGGA
47617 CTAATTTACA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (28 bp):
TAATTTATAGGATTTGGAATTTATGACG
Found at i:47849 original size:3 final size:3
Alignment explanation
Indices: 47841--47905 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
47831 ACCATTATAT
* ** *
47841 TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA CAAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
47887 TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA -TTA TTA
47906 CAAACCCAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
3 50 0.93
4 4 0.07
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:48690 original size:19 final size:19
Alignment explanation
Indices: 48663--48699 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
48653 TCAGCCGAGC
*
48663 AGAGGAAAAGAGAGAGTTG
1 AGAGAAAAAGAGAGAGTTG
*
48682 AGAGAAAAAGGGAGAGTT
1 AGAGAAAAAGAGAGAGTT
48700 TTTTTGGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.41, T:0.11
Consensus pattern (19 bp):
AGAGAAAAAGAGAGAGTTG
Found at i:62126 original size:78 final size:79
Alignment explanation
Indices: 62032--62201 Score: 247
Period size: 78 Copynumber: 2.2 Consensus size: 79
62022 GAAAGTTCAA
* *
62032 AATGAGAAGAACTTATTTAACCTTAGCTAGATTCCATCATAG-AATGAGGTTG-ATCAACATTTC
1 AATGAGAAGAACTTATTCAACCTTAGCTAGATTCCATCACAGAAAT-AGG-TGAATCAACATTTC
62095 CAATGGAAGGGTT-GT
64 CAATGGAAGGGTTCGT
* * *
62110 AATGAGAAGAACTTATTCAACCTTAGCTCGATTCCATCACAGAAATATGTGAATCAATATTTCCA
1 AATGAGAAGAACTTATTCAACCTTAGCTAGATTCCATCACAGAAATAGGTGAATCAACATTTCCA
62175 ATGGAAGGGTTCGT
66 ATGGAAGGGTTCGT
*
62189 AATAAGAAGAACT
1 AATGAGAAGAACT
62202 CGTCCTATGA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
77 2 0.02
78 64 0.77
79 17 0.20
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (79 bp):
AATGAGAAGAACTTATTCAACCTTAGCTAGATTCCATCACAGAAATAGGTGAATCAACATTTCCA
ATGGAAGGGTTCGT
Found at i:62317 original size:118 final size:118
Alignment explanation
Indices: 62109--62497 Score: 565
Period size: 118 Copynumber: 3.3 Consensus size: 118
62099 GGAAGGGTTG
* * * *
62109 TAATGAGAAGAACTTATTCAACCTTAGCTCGATTCCATCACAGAAAT-ATGTGAATCAATATTTC
1 TAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAG-AATGAGGTGGATCAACATTTC
* * *
62173 CAATGGAAGGGTTCGTAATAAGAAGAACTCGTCCTATGAGGGAGAAGAAGTTCA
65 CAATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
* * * *
62227 TAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCATAGAATGAGGAGGGTTAACATTTCC
1 TAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAATGAGGTGGATCAACATTTCC
*
62292 AATGGAAGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
66 AATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
* * *
62345 TAAT--GAAGAACTTATTCAACCTTATCTCAATTCCATCACAGAAGGAGGTGGATCAACATTTCT
1 TAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAATGAGGTGGATCAACATTTCC
* *
62408 AATAGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAG-A-AA-TTCG
66 AATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
*
62458 TAATGAGAAGAACTTATTCAACCTTAGCTCGATTCCATCA
1 TAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCA
62498 TATAAGGAGT
Statistics
Matches: 244, Mismatches: 24, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
113 7 0.03
114 2 0.01
115 33 0.14
116 93 0.38
117 3 0.01
118 106 0.43
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (118 bp):
TAATGAGAAGAACTTATTCAACCTTAGCTCAATTCCATCACAGAATGAGGTGGATCAACATTTCC
AATGGAAGGGTTCGTAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCA
Found at i:62853 original size:19 final size:19
Alignment explanation
Indices: 62831--62899 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
62821 AAATATTATT
62831 ATTATTATTATTATTATAA
1 ATTATTATTATTATTATAA
*
62850 ATTATTTTTATT-TT-T--
1 ATTATTATTATTATTATAA
*
62865 ATTATTATTATTTATTACAA
1 ATTATTATTA-TTATTATAA
*
62885 AATATTATTATTATT
1 ATTATTATTATTATT
62900 TATGACAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 9 0.22
16 2 0.05
17 3 0.07
18 2 0.05
19 16 0.39
20 9 0.22
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTATTATTATTATAA
Found at i:62879 original size:25 final size:25
Alignment explanation
Indices: 62801--62881 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
62791 ATTTTCAACC
*
62801 ATTA-TATTATTATTATTA-TAAAA
1 ATTATTATTATTATTATTATTATAA
62824 TATTATTATTATTATTATTATTATAA
1 -ATTATTATTATTATTATTATTATAA
* * *
62850 ATTATTTTTATTTTTATTATTATTA
1 ATTATTATTATTATTATTATTATAA
*
62875 TTTATTA
1 ATTATTA
62882 CAAAATATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
24 4 0.08
25 41 0.84
26 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTATTATTATTATTATTATTATAA
Found at i:62881 original size:28 final size:28
Alignment explanation
Indices: 62801--62875 Score: 116
Period size: 28 Copynumber: 2.7 Consensus size: 28
62791 ATTTTCAACC
*
62801 ATTA-TATTATTATTATTATAAAATATT
1 ATTATTATTATTATTATTATAAATTATT
62828 ATTATTATTATTATTATTATAAATTATT
1 ATTATTATTATTATTATTATAAATTATT
* *
62856 TTTATTTTTATTATTATTAT
1 ATTATTATTATTATTATTAT
62876 TTATTACAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 4 0.09
28 40 0.91
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (28 bp):
ATTATTATTATTATTATTATAAATTATT
Found at i:62894 original size:23 final size:23
Alignment explanation
Indices: 62864--62908 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
62854 TTTTTATTTT
*
62864 TATTATTATTATTTATTACAAAA
1 TATTATTATTATTTATGACAAAA
62887 TATTATTATTATTTATGACAAA
1 TATTATTATTATTTATGACAAA
62909 CCCAATACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TATTATTATTATTTATGACAAAA
Found at i:62899 original size:3 final size:3
Alignment explanation
Indices: 62801--62881 Score: 83
Period size: 3 Copynumber: 26.3 Consensus size: 3
62791 ATTTTCAACC
* *
62801 ATT A-T ATT ATT ATT ATT ATAA AAT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* * *
62846 ATAA ATT ATT TTT ATT TTT ATT ATT ATT ATTT ATT A
1 AT-T ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A
62882 CAAAATATTA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 2 0.03
3 56 0.88
4 6 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Done.