Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006827.1 Hibiscus syriacus cultivar Beakdansim tig00017356_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: 64561
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1334 original size:15 final size:17
Alignment explanation
Indices: 1314--1350 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1304 AAACTTAAGG
1314 AGCTT-AAG-AATTAGA
1 AGCTTAAAGAAATTAGA
1329 AGCTTAAAGATAATTAGA
1 AGCTTAAAGA-AATTAGA
1347 AGCT
1 AGCT
1351 AAGGATTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.26
16 3 0.16
18 11 0.58
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.27
Consensus pattern (17 bp):
AGCTTAAAGAAATTAGA
Found at i:1437 original size:50 final size:50
Alignment explanation
Indices: 1379--1484 Score: 212
Period size: 50 Copynumber: 2.1 Consensus size: 50
1369 GGTGAATTAG
1379 TAAAGTGCGTTTTTAAGTGAAAGGATGAAATTTGGTTAGTAACTTGATTC
1 TAAAGTGCGTTTTTAAGTGAAAGGATGAAATTTGGTTAGTAACTTGATTC
1429 TAAAGTGCGTTTTTAAGTGAAAGGATGAAATTTGGTTAGTAACTTGATTC
1 TAAAGTGCGTTTTTAAGTGAAAGGATGAAATTTGGTTAGTAACTTGATTC
1479 TAAAGT
1 TAAAGT
1485 CATATTTGAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.38
Consensus pattern (50 bp):
TAAAGTGCGTTTTTAAGTGAAAGGATGAAATTTGGTTAGTAACTTGATTC
Found at i:1960 original size:20 final size:22
Alignment explanation
Indices: 1917--1963 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
1907 AATTCCAGAA
*
1917 TGCTACAGGGGTATCGATATCC
1 TGCTACAGGGGTATCGATACCC
*
1939 TGCTACA-GTGTA-CGATACCC
1 TGCTACAGGGGTATCGATACCC
1959 TGCTA
1 TGCTA
1964 TAGTAATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
21 4 0.17
22 7 0.30
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (22 bp):
TGCTACAGGGGTATCGATACCC
Found at i:2512 original size:31 final size:30
Alignment explanation
Indices: 2473--2532 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
2463 CCCGAAGTAC
* *
2473 CAGTCATATGTTCAAAAGAATATAGGTAAT
1 CAGTCATATGTCCAAAAGAACATAGGTAAT
**
2503 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGT-CATATGTCCAAAAGAACATAGGTAA
2533 CCCTCGACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (30 bp):
CAGTCATATGTCCAAAAGAACATAGGTAAT
Found at i:4705 original size:22 final size:20
Alignment explanation
Indices: 4677--4732 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 20
4667 ATAATAGTAC
4677 CGATACCCTGCTACAGGGGTA
1 CGATACCCTGCTACA-GGGTA
*
4698 TCGATACCCTGCTACAGTGTA
1 -CGATACCCTGCTACAGGGTA
4719 CTGATACCCTGCTA
1 C-GATACCCTGCTA
4733 TAGTAATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 1 0.03
21 16 0.50
22 15 0.47
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.25
Consensus pattern (20 bp):
CGATACCCTGCTACAGGGTA
Found at i:4726 original size:21 final size:22
Alignment explanation
Indices: 4673--4732 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
4663 TTTAATAATA
*
4673 GTACCGATACCCTGCTACAGGG
1 GTACTGATACCCTGCTACAGGG
*
4695 GTA-TCGATACCCTGCTACA-GT
1 GTACT-GATACCCTGCTACAGGG
4716 GTACTGATACCCTGCTA
1 GTACTGATACCCTGCTA
4733 TAGTAATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (22 bp):
GTACTGATACCCTGCTACAGGG
Found at i:5287 original size:31 final size:31
Alignment explanation
Indices: 5249--5340 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 31
5239 CCCGAAGGAC
*
5249 CAGTCCATATGTTCCGAAGAATATAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAT
5280 CAGTCCATATG-TCCTGAAGAACATAGGTAAT
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAT
* * *
5311 CAGTCTATATGTCCCGAAGAACATAAGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
5341 CCCTCGACTA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
30 3 0.05
31 50 0.91
32 2 0.04
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAT
Found at i:5453 original size:39 final size:38
Alignment explanation
Indices: 5389--5463 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 38
5379 AACATGTATC
*
5389 ACATATTGCATATTCATGTAGTTCATGTCACATATAATA
1 ACATATTGCATATTCATGTAGTTCATG-CACACATAATA
5428 ACATA-TGCATGATTTCATGTA-TTCATGCACACATAA
1 ACATATTGCAT-A-TTCATGTAGTTCATGCACACATAA
5464 GAATAATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
38 13 0.39
39 12 0.36
40 8 0.24
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (38 bp):
ACATATTGCATATTCATGTAGTTCATGCACACATAATA
Found at i:6765 original size:21 final size:20
Alignment explanation
Indices: 6741--6792 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
6731 GGATGAACAA
*
6741 TATCGATATTGAT-TGAAGAAT
1 TATCGATATTGATGTGAAG--G
*
6762 TATCGATACTGATGTGAAGG
1 TATCGATATTGATGTGAAGG
6782 TATCGATATTG
1 TATCGATATTG
6793 TAAGTAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (20 bp):
TATCGATATTGATGTGAAGG
Found at i:7606 original size:23 final size:23
Alignment explanation
Indices: 7580--7645 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
7570 TTCTATGGGA
7580 TCCTTCGGGACAAATCTATATGG
1 TCCTTCGGGACAAATCTATATGG
*
7603 TCCTTCGGGACAAACCTATATGG
1 TCCTTCGGGACAAATCTATATGG
* *
7626 TCATTCGAGACAAATTCTAT
1 TCCTTCGGGACAAA-TCTAT
7646 GTGGCACTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
23 34 0.89
24 4 0.11
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (23 bp):
TCCTTCGGGACAAATCTATATGG
Found at i:10757 original size:24 final size:24
Alignment explanation
Indices: 10730--10812 Score: 148
Period size: 24 Copynumber: 3.5 Consensus size: 24
10720 TACCGAGTGA
10730 GTATCGATACCTCCCTTACCTTTG
1 GTATCGATACCTCCCTTACCTTTG
*
10754 GTATCGATACCTCCCTTATCTTTG
1 GTATCGATACCTCCCTTACCTTTG
10778 GTATCGATACCTCCCTTACCTTTG
1 GTATCGATACCTCCCTTACCTTTG
*
10802 GTATCAATACC
1 GTATCGATACC
10813 ATATGAACAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.37
Consensus pattern (24 bp):
GTATCGATACCTCCCTTACCTTTG
Found at i:12792 original size:3 final size:3
Alignment explanation
Indices: 12779--12829 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
12769 ATCCTAAACT
12779 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
12824 TT- TTA T
1 TTA TTA T
12830 GGGGGTTGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:23839 original size:29 final size:30
Alignment explanation
Indices: 23807--23878 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
23797 TTGCATTTAG
23807 GTCCCCCAACTTTTAAAAC-TTGCAATATA
1 GTCCCCCAACTTTTAAAACGTTGCAATATA
* *** *
23836 GTCCCCCAACATTTATTCCGTTTGCAATATG
1 GTCCCCCAACTTTTAAAACG-TTGCAATATA
23867 GTCCCCCAACTT
1 GTCCCCCAACTT
23879 AAACTACTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 15 0.43
31 20 0.57
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.32
Consensus pattern (30 bp):
GTCCCCCAACTTTTAAAACGTTGCAATATA
Found at i:24050 original size:34 final size:35
Alignment explanation
Indices: 23981--24128 Score: 163
Period size: 35 Copynumber: 4.3 Consensus size: 35
23971 AAAACAACCA
* * * *
23981 TCAATTTCATTCTAAACCTCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* *
24016 TCAATTTCATTCTAAA-CCCTAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * *
24050 TCAATTAAATTTTAAACCCCAAATTCTAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
24085 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
24120 TTAATTTAA
1 TCAATTTAA
24129 GGTTTAGAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
34 27 0.27
35 73 0.73
ACGTcount: A:0.43, C:0.20, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:32506 original size:29 final size:28
Alignment explanation
Indices: 32464--32519 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
32454 TATTTATAAA
*
32464 AATAAAATATTATATATAA-AAATTTAAC
1 AATAAAATATTATA-ATAATAAAATTAAC
*
32492 AATAATAATTTTATAATAATAAAATTAA
1 AATAA-AATATTATAATAATAAAATTAA
32520 TTCAATTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
AATAAAATATTATAATAATAAAATTAAC
Found at i:32963 original size:21 final size:24
Alignment explanation
Indices: 32914--32969 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 24
32904 TGGTTTTATG
32914 TTTAGGGTTTTACGTTAAAGTGAT
1 TTTAGGGTTTTACGTTAAAGTGAT
* *
32938 TTTAGGGTTTT-CG-T-AATTGGT
1 TTTAGGGTTTTACGTTAAAGTGAT
32959 TTTAGGGTTTT
1 TTTAGGGTTTT
32970 TAGTGTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 16 0.53
22 1 0.03
23 2 0.07
24 11 0.37
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.52
Consensus pattern (24 bp):
TTTAGGGTTTTACGTTAAAGTGAT
Found at i:36969 original size:6 final size:6
Alignment explanation
Indices: 36933--37015 Score: 51
Period size: 6 Copynumber: 13.8 Consensus size: 6
36923 TGTATACTTC
* * * * * * * *
36933 TCCTCA TCGTCC TCATCA TCTTCA ACCTCA TCCTCA TCTTCG TCGTCA
1 TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA TCCTCA
* * *
36981 TCATCA -CCATCA TCCTCA TCCTCC TCCTCC TCCTC
1 TCCTCA TCC-TCA TCCTCA TCCTCA TCCTCA TCCTC
37016 CTCATTGTCA
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
5 1 0.02
6 57 0.95
7 2 0.03
ACGTcount: A:0.16, C:0.47, G:0.04, T:0.34
Consensus pattern (6 bp):
TCCTCA
Found at i:38960 original size:14 final size:14
Alignment explanation
Indices: 38941--38971 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38931 CAAAATTATT
38941 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
38955 TAAATAAATTCTAA
1 TAAATAAATTCAAA
38969 TAA
1 TAA
38972 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Found at i:38988 original size:19 final size:19
Alignment explanation
Indices: 38966--39015 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
38956 AAATAAATTC
38966 TAAT-AATTTAAATAATAT
1 TAATAAATTTAAATAATAT
* *
38984 ATAATCAATTT-CATAATAT
1 -TAATAAATTTAAATAATAT
*
39003 TCATAAATTTAAA
1 TAATAAATTTAAA
39016 AACAATACAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.32
19 12 0.48
20 5 0.20
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATAAATTTAAATAATAT
Found at i:39889 original size:7 final size:6
Alignment explanation
Indices: 39857--39890 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
39847 ACATAAACTC
*
39857 AATTTA AATTTA AATTCA AATTTA AACTTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AA-TTTA AAT
39891 ACATGAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:42347 original size:13 final size:13
Alignment explanation
Indices: 42307--42387 Score: 60
Period size: 13 Copynumber: 6.2 Consensus size: 13
42297 ACATAAAATT
* *
42307 TATAAATTCAAAT
1 TATAAATTAAAAA
42320 TATATAATCTAAAAA
1 TATA-AAT-TAAAAA
42335 TA-AAATATAAAAA
1 TATAAAT-TAAAAA
*
42348 TATAAATTAAAAT
1 TATAAATTAAAAA
*
42361 TATAAAGTT-ACAA
1 TATAAA-TTAAAAA
*
42374 T-TAAATTTAAAA
1 TATAAATTAAAAA
42386 TA
1 TA
42388 ATAAGACTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
11 2 0.04
12 8 0.15
13 29 0.53
14 10 0.18
15 6 0.11
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (13 bp):
TATAAATTAAAAA
Found at i:48703 original size:13 final size:12
Alignment explanation
Indices: 48683--48747 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
48673 ATATAGGTGT
48683 GATATGGTGATG
1 GATATGGTGATG
48695 GACTATGGTGAT-
1 GA-TATGGTGATG
*
48707 GATATAGGCG-T-
1 GATAT-GGTGATG
48718 GATAATGGTGATG
1 GAT-ATGGTGATG
48731 GAATATGGTGAT-
1 G-ATATGGTGATG
48743 GATAT
1 GATAT
48748 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 11 0.24
13 18 0.40
14 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:48738 original size:36 final size:36
Alignment explanation
Indices: 48665--48768 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
48655 ATTTAGAAGT
* * *
48665 TGGTGATAATATAGGTGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
48700 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
48736 TGGTGATGATATAGGCGTGATAATGGCGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
48769 CAGATTGTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:54435 original size:36 final size:36
Alignment explanation
Indices: 54362--54463 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
54352 ATTTAGAAGT
* * * *
54362 TGGTGATAATATAGACGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGAAATA
54397 TGGTGATGATATAGGCGTGATAATGGTGATGAAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGAAATA
54433 TGGTGATGATATAGGCGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGATAATGGTGATG
54464 GACAGATTGT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.31
36 43 0.69
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGAAATA
Found at i:54437 original size:13 final size:13
Alignment explanation
Indices: 54381--54441 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
54371 TATAGACGTG
*
54381 ATATGGTGATGGA
1 ATATGGTGATGAA
* *
54394 CTATGGTGATGAT
1 ATATGGTGATGAA
* *
54407 ATA-GGCG-TGAT
1 ATATGGTGATGAA
54418 A-ATGGTGATGAA
1 ATATGGTGATGAA
54430 ATATGGTGATGA
1 ATATGGTGATGA
54442 TATAGGCGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 1 0.03
11 8 0.21
12 7 0.18
13 22 0.58
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.31
Consensus pattern (13 bp):
ATATGGTGATGAA
Found at i:54453 original size:11 final size:13
Alignment explanation
Indices: 54395--54463 Score: 51
Period size: 11 Copynumber: 5.8 Consensus size: 13
54385 GGTGATGGAC
*
54395 TATGGTGATGATA
1 TATGGCGATGATA
54408 TA-GGCG-TGATA
1 TATGGCGATGATA
* *
54419 -ATGGTGATGAAA
1 TATGGCGATGATA
*
54431 TATGGTGATGATA
1 TATGGCGATGATA
54444 TA-GGCG-TGATA
1 TATGGCGATGATA
*
54455 -ATGGTGATG
1 TATGGCGATG
54464 GACAGATTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
10 2 0.04
11 16 0.36
12 12 0.27
13 15 0.33
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.32
Consensus pattern (13 bp):
TATGGCGATGATA
Found at i:55949 original size:17 final size:17
Alignment explanation
Indices: 55929--55966 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
55919 AGGGCATCTT
55929 CCACGCCACACGTGCCG
1 CCACGCCACACGTGCCG
* *
55946 CCACTCCATACGTGCCG
1 CCACGCCACACGTGCCG
55963 CCAC
1 CCAC
55967 TGCACGTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.53, G:0.18, T:0.11
Consensus pattern (17 bp):
CCACGCCACACGTGCCG
Found at i:56186 original size:20 final size:20
Alignment explanation
Indices: 56141--56188 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
56131 TTTTATACTG
*
56141 TTGACTTTGACCGTTGACTA
1 TTGACTTTGACCGTTGACCA
* *
56161 TCGACTTTGA-CTTTGACACA
1 TTGACTTTGACCGTTGAC-CA
56181 TTGACTTT
1 TTGACTTT
56189 TTCTAAAGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (20 bp):
TTGACTTTGACCGTTGACCA
Found at i:58389 original size:29 final size:29
Alignment explanation
Indices: 58356--58465 Score: 125
Period size: 29 Copynumber: 3.9 Consensus size: 29
58346 AATCCCGTTA
* *
58356 TGATTATGCATGAGATTATATCCCCATCC
1 TGATTCTGCATGAGATTGTATCCCCATCC
* * *
58385 TGATTCTACATGGGATTGTAT--CCGTCC
1 TGATTCTGCATGAGATTGTATCCCCATCC
* *
58412 TAATTTTGCATGAGATTGTATCCCCATCC
1 TGATTCTGCATGAGATTGTATCCCCATCC
* *
58441 TGATTCTGCATGATATTTTATCCCC
1 TGATTCTGCATGAGATTGTATCCCC
58466 GTTCTATTTT
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
27 22 0.34
29 43 0.66
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (29 bp):
TGATTCTGCATGAGATTGTATCCCCATCC
Found at i:62544 original size:29 final size:29
Alignment explanation
Indices: 62509--62590 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
62499 AAACTAAATT
*
62509 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
62538 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
62567 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
62591 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Done.