Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005074.1 Hibiscus syriacus cultivar Beakdansim tig00011392_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: 60858
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:859 original size:14 final size:14
Alignment explanation
Indices: 814--859 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
804 ACACGAAAAT
*
814 GAAAATCGCAACAC
1 GAAAATCGCAACGC
* *
828 CAAAATCGCAACGA
1 GAAAATCGCAACGC
842 GAAAATCGCAACGC
1 GAAAATCGCAACGC
856 GAAA
1 GAAA
860 CTAAAATTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.26, G:0.17, T:0.07
Consensus pattern (14 bp):
GAAAATCGCAACGC
Found at i:1416 original size:20 final size:20
Alignment explanation
Indices: 1388--1567 Score: 159
Period size: 20 Copynumber: 8.9 Consensus size: 20
1378 TAATTGTGTT
*
1388 TCGCTTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
* *
1408 TCGCATTGCGAA-TTGA-AA
1 TCGCGTTGCGAATTTGACTA
*
1426 TTCAGTGTTGCGAATTTGACTA
1 -TC-GCGTTGCGAATTTGACTA
* *
1448 TCGCGTTGCGAATTTAACTT
1 TCGCGTTGCGAATTTGACTA
* * *
1468 TTGTGTTGCGAATTTGA-AA
1 TCGCGTTGCGAATTTGACTA
**
1487 TTCAGTATTGCGAATTTGACTA
1 -TC-GCGTTGCGAATTTGACTA
* *
1509 TCGCGTTGCGAAGTTGACTT
1 TCGCGTTGCGAATTTGACTA
* * *
1529 TTGTGTTGCGGATTTGACTA
1 TCGCGTTGCGAATTTGACTA
1549 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
1568 TCTGTGTTGC
Statistics
Matches: 125, Mismatches: 28, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
18 1 0.01
19 6 0.05
20 94 0.75
21 22 0.18
22 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:1500 original size:61 final size:61
Alignment explanation
Indices: 1413--1545 Score: 223
Period size: 61 Copynumber: 2.2 Consensus size: 61
1403 GACTATCGCA
* *
1413 TTGCGAA-TTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCGAATTTAACTTTTGTG
1 TTGCGAATTTGAAATTCAGTATTGCGAATTTGACTATCGCGTTGCGAAGTTAACTTTTGTG
*
1473 TTGCGAATTTGAAATTCAGTATTGCGAATTTGACTATCGCGTTGCGAAGTTGACTTTTGTG
1 TTGCGAATTTGAAATTCAGTATTGCGAATTTGACTATCGCGTTGCGAAGTTAACTTTTGTG
*
1534 TTGCGGATTTGA
1 TTGCGAATTTGA
1546 CTATCGCGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
60 7 0.10
61 61 0.90
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.40
Consensus pattern (61 bp):
TTGCGAATTTGAAATTCAGTATTGCGAATTTGACTATCGCGTTGCGAAGTTAACTTTTGTG
Found at i:1544 original size:40 final size:40
Alignment explanation
Indices: 1432--1599 Score: 144
Period size: 40 Copynumber: 4.2 Consensus size: 40
1422 GAAATTCAGT
* * * * * * *
1432 GTTGCGAATTTGACTATC-GCGTTGCGAATTTAACTTTTGT
1 GTTGCGAAGTTGACT-TCTGTGTTGCGGATTTGACTATCGC
* * * * *
1472 GTTGCGAATTTGAAATTCAGTATTGCGAATTTGACTATCGC
1 GTTGCGAAGTTG-ACTTCTGTGTTGCGGATTTGACTATCGC
*
1513 GTTGCGAAGTTGACTTTTGTGTTGCGGATTTGACTATCGC
1 GTTGCGAAGTTGACTTCTGTGTTGCGGATTTGACTATCGC
* *
1553 GTTGCGAATTTGACTTCTGTGTTGC-GATTT-ACAAATTCGC
1 GTTGCGAAGTTGACTTCTGTGTTGCGGATTTGAC-TA-TCGC
1593 GTTGCGA
1 GTTGCGA
1600 TATTGGAAAC
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
38 2 0.02
39 6 0.06
40 71 0.66
41 29 0.27
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.39
Consensus pattern (40 bp):
GTTGCGAAGTTGACTTCTGTGTTGCGGATTTGACTATCGC
Found at i:1544 original size:101 final size:101
Alignment explanation
Indices: 1393--1579 Score: 295
Period size: 101 Copynumber: 1.9 Consensus size: 101
1383 GTGTTTCGCT
1393 TTGCGAATTTGACTATCGCATTGCGAATTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCG
1 TTGCGAATTTGACTATCGCATTGCGAATTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCG
*
1458 AATTTAACTTTTGTGTTGCGAATTTGAAATTCAGTA
66 AATTTAACTTCTGTGTTGCGAATTTGAAATTCAGTA
* * ** *
1494 TTGCGAATTTGACTATCGCGTTGCGAAGTTG-ACTTTTGTGTTGCGGATTTGACTATCGCGTTGC
1 TTGCGAATTTGACTATCGCATTGCGAA-TTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGC
*
1558 GAATTTGACTTCTGTGTTGCGA
65 GAATTTAACTTCTGTGTTGCGA
1580 TTTACAAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 75 0.96
102 3 0.04
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (101 bp):
TTGCGAATTTGACTATCGCATTGCGAATTGAAATTCAGTGTTGCGAATTTGACTATCGCGTTGCG
AATTTAACTTCTGTGTTGCGAATTTGAAATTCAGTA
Found at i:3507 original size:3 final size:3
Alignment explanation
Indices: 3501--3534 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3491 CAAAATAATA
3501 TAT TAT TAT TA- TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3535 CTCGGATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3515 original size:11 final size:11
Alignment explanation
Indices: 3499--3534 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
3489 TACAAAATAA
3499 TATATTATTAT
1 TATATTATTAT
3510 TATATTATTAT
1 TATATTATTAT
3521 TATTATTA-TAT
1 TA-TATTATTAT
3532 TAT
1 TAT
3535 CTCGGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 1 0.04
11 18 0.75
12 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTATTAT
Found at i:3523 original size:17 final size:17
Alignment explanation
Indices: 3501--3534 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3491 CAAAATAATA
3501 TATTATTATTATATTAT
1 TATTATTATTATATTAT
3518 TATTATTATTATATTAT
1 TATTATTATTATATTAT
3535 CTCGGATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATTATATTAT
Found at i:8227 original size:14 final size:14
Alignment explanation
Indices: 8208--8237 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8198 TTTCAAAAAC
*
8208 TTAAATTGTCAATA
1 TTAAATTGTAAATA
8222 TTAAATTGTAAATA
1 TTAAATTGTAAATA
8236 TT
1 TT
8238 TTTATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (14 bp):
TTAAATTGTAAATA
Found at i:11443 original size:18 final size:18
Alignment explanation
Indices: 11420--11526 Score: 169
Period size: 18 Copynumber: 5.9 Consensus size: 18
11410 AGGGATTATC
*
11420 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
*
11438 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
*
11456 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
*
11474 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
11492 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
11510 AGTGGTCCTTCGTGACA
1 AGTGGTCCTTCGGGACA
11527 AATATTCAGT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 85 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:20366 original size:21 final size:21
Alignment explanation
Indices: 20323--20366 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20313 TTATGAACTA
* **
20323 TGGCTTTGTAATAGAGCTGCT
1 TGGCTTTGTAATAAAGCACCT
20344 TGGCTTTGTAATAAAGCACCT
1 TGGCTTTGTAATAAAGCACCT
20365 TG
1 TG
20367 ATTCTTGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (21 bp):
TGGCTTTGTAATAAAGCACCT
Found at i:28073 original size:18 final size:18
Alignment explanation
Indices: 28046--28092 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
28036 ATTCCTCGAA
*
28046 TACA-TAGAAACTGAATT
1 TACATTAGAAACTGAACT
28063 TACATTAGAAACTGAACT
1 TACATTAGAAACTGAACT
28081 TA-ATTGAGAAAC
1 TACATT-AGAAAC
28093 CAATTTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.28
Consensus pattern (18 bp):
TACATTAGAAACTGAACT
Found at i:28335 original size:20 final size:20
Alignment explanation
Indices: 28294--28340 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
28284 ACGAGTCGGG
*
28294 TCGGGTC-GGTTGACTTGTT
1 TCGGGTCAGGTTGACTAGTT
28313 TCGGGTCAGGTTGACTCAG-T
1 TCGGGTCAGGTTGACT-AGTT
28333 TCGGGTCA
1 TCGGGTCA
28341 ATAGACCCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 7 0.28
20 17 0.68
21 1 0.04
ACGTcount: A:0.11, C:0.19, G:0.36, T:0.34
Consensus pattern (20 bp):
TCGGGTCAGGTTGACTAGTT
Found at i:34761 original size:29 final size:30
Alignment explanation
Indices: 34690--34762 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
34680 GATTTAACGA
*
34690 TTCAGTGGTATAATTGAAACGAAAATCAAAG
1 TTCAGTGGTATAATTGAAAC-AAAATAAAAG
* *
34721 TTCAGTGCTATAATTGAAA-AAATTAAAAG
1 TTCAGTGGTATAATTGAAACAAAATAAAAG
*
34750 TTTAGTGGTATAA
1 TTCAGTGGTATAA
34763 ACAATACAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.51
31 18 0.49
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.32
Consensus pattern (30 bp):
TTCAGTGGTATAATTGAAACAAAATAAAAG
Found at i:38689 original size:2 final size:2
Alignment explanation
Indices: 38682--38717 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
38672 AGCATAAGTG
* *
38682 CA CA CA CA CG CA CG CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
38718 TATATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.50, G:0.06, T:0.00
Consensus pattern (2 bp):
CA
Found at i:38722 original size:2 final size:2
Alignment explanation
Indices: 38717--38760 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
38707 ACACACACAC
38717 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38758 AT A
1 AT A
38761 ATCAGCATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38992 original size:23 final size:23
Alignment explanation
Indices: 38955--39000 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
38945 CACCGAAGTG
38955 CCACATAGAAATGT-CTCGAAGGA
1 CCACATAGAAATGTCCT-GAAGGA
* *
38978 CCACATAGTATTGTCCTGAAGGA
1 CCACATAGAAATGTCCTGAAGGA
39001 TCGTGAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (23 bp):
CCACATAGAAATGTCCTGAAGGA
Found at i:39023 original size:43 final size:43
Alignment explanation
Indices: 38962--39043 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
38952 GTGCCACATA
* * * *
38962 GAAATGTCTCGAAGGACCACATAGTATTGTCCTGAAGGATCGT
1 GAAATGTCCCGAAAGACCACATAGTATTATCCCGAAGGATCGT
*
39005 GAAATGTCCCGAAAGACCACGTAGTATTATCCCGAAGGA
1 GAAATGTCCCGAAAGACCACATAGTATTATCCCGAAGGA
39044 CCGCGTAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (43 bp):
GAAATGTCCCGAAAGACCACATAGTATTATCCCGAAGGATCGT
Found at i:39207 original size:45 final size:45
Alignment explanation
Indices: 39157--39308 Score: 114
Period size: 45 Copynumber: 3.2 Consensus size: 45
39147 ACTTAGTTCA
39157 ATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTT
1 ATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTT
* * * * *
39202 ATATCACAT-GTTCATATAATCACTTATGTCAATACCATATAACCACT-TAGTTT
1 ATATCACATAG-ACATATAAGCACATA-G---AT-CC-T-T-ATCA-TATAGCTT
*
39255 CAATTTCACATAGAC--ATAAGCACATAGATCCTTATCATATAGCTT
1 --ATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTT
39300 ATATCACAT
1 ATATCACAT
39309 GTTCATATAA
Statistics
Matches: 81, Mismatches: 12, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
43 8 0.10
44 2 0.02
45 29 0.36
46 2 0.02
47 1 0.01
48 2 0.02
49 4 0.05
50 2 0.02
51 1 0.01
52 2 0.02
53 17 0.21
54 1 0.01
55 9 0.11
56 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (45 bp):
ATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTT
Found at i:39294 original size:98 final size:98
Alignment explanation
Indices: 39139--39340 Score: 352
Period size: 98 Copynumber: 2.1 Consensus size: 98
39129 TCACATATTT
39139 ATATAACCACTTAGTTCAATATCACATAGACATATAAGCACATAGATCCTTATCATATAGCTTAT
1 ATATAACCACTTAGTTCAATATCACATAGACA-ATAAGCACATAGATCCTTATCATATAGCTTAT
*
39204 ATCACATGTTCATATAATCACTTATGTCAATACC
65 ATCACATGTTCATATAATCACTTATGTCAATACA
*
39238 ATATAACCACTTAGTTTCAATTTCACATAGAC-ATAAGCACATAGATCCTTATCATATAGCTTAT
1 ATATAACCACTTAG-TTCAATATCACATAGACAATAAGCACATAGATCCTTATCATATAGCTTAT
*
39302 ATCACATGTTCATATAATCACTTGTGTCAATACA
65 ATCACATGTTCATATAATCACTTATGTCAATACA
39336 ATATA
1 ATATA
39341 GCTTATATCA
Statistics
Matches: 99, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
98 69 0.70
99 14 0.14
100 16 0.16
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.34
Consensus pattern (98 bp):
ATATAACCACTTAGTTCAATATCACATAGACAATAAGCACATAGATCCTTATCATATAGCTTATA
TCACATGTTCATATAATCACTTATGTCAATACA
Found at i:41533 original size:17 final size:17
Alignment explanation
Indices: 41513--41550 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
41503 GGAAGTCAAC
41513 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
41530 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
41547 GGTC
1 GGTC
41551 GAGTCGGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:41604 original size:19 final size:19
Alignment explanation
Indices: 41563--41607 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41553 GTCGGGTCAG
*
41563 ACCGGTTAAACCGGTTCAT
1 ACCGGTCAAACCGGTTCAT
*
41582 ACCGGTCAAACTGGTTCGA-
1 ACCGGTCAAACCGGTTC-AT
41601 ACCGGTC
1 ACCGGTC
41608 GGAACCGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAT
Found at i:43966 original size:14 final size:14
Alignment explanation
Indices: 43934--43974 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
43924 ATAGGCATGA
* *
43934 ATGGTGATAGAGA-
1 ATGGTGATGGAAAG
43947 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
43961 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
43975 GTAGTATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:44369 original size:77 final size:76
Alignment explanation
Indices: 44268--44424 Score: 269
Period size: 77 Copynumber: 2.1 Consensus size: 76
44258 TTTAGGCCGA
*
44268 ATACTTATGGTTCAGCCAAGGTTGAAACCCCTTTGAAAATACATGATTTTTTATGAAAATACATG
1 ATACTTATGGTTCAGCCAAGGTTGAAACCCCTTTGAAAATACATGATTTTTGATG-AAATACATG
44333 ATTTAAATAAAG
65 ATTTAAATAAAG
* *
44345 ATACTTATGGTTCGGCCAATGTTGAAACCCCTTTGAAAATACATGATTTTTGATGAAATACATGA
1 ATACTTATGGTTCAGCCAAGGTTGAAACCCCTTTGAAAATACATGATTTTTGATGAAATACATGA
*
44410 TTTAAATGAAG
66 TTTAAATAAAG
44421 ATAC
1 ATAC
44425 ATGCTCTTGG
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
76 24 0.32
77 52 0.68
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (76 bp):
ATACTTATGGTTCAGCCAAGGTTGAAACCCCTTTGAAAATACATGATTTTTGATGAAATACATGA
TTTAAATAAAG
Found at i:44424 original size:19 final size:19
Alignment explanation
Indices: 44381--44427 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
44371 ACCCCTTTGA
**
44381 AAATACATGATTTTTGATG
1 AAATACATGATTTTAAATG
44400 AAATACATGA-TTTAAATG
1 AAATACATGATTTTAAATG
44418 AAGATACATG
1 AA-ATACATG
44428 CTCTTGGCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (19 bp):
AAATACATGATTTTAAATG
Found at i:47354 original size:15 final size:15
Alignment explanation
Indices: 47334--47372 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
47324 AGGATAAGGT
*
47334 AATGAAATAAGAAAG
1 AATGAAATAAGAAAA
* *
47349 AATGAAAGAATAAAA
1 AATGAAATAAGAAAA
47364 AATGAAATA
1 AATGAAATA
47373 GTAAGAAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AATGAAATAAGAAAA
Found at i:51916 original size:3 final size:3
Alignment explanation
Indices: 51901--51952 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
51891 ATATATATAT
* * * * *
51901 ATC ATC ATT ATC ATC ATC ATC AT- ATC ATT ATC ATT ATC AAC ATC ATT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
51948 ATC AT
1 ATC AT
51953 TGTCACTATA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (3 bp):
ATC
Found at i:51918 original size:12 final size:12
Alignment explanation
Indices: 51901--51952 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
51891 ATATATATAT
51901 ATCATCATTATC
1 ATCATCATTATC
51913 ATCATCATCATATC
1 ATCATCAT--TATC
*
51927 ATTATCATTATC
1 ATCATCATTATC
*
51939 AACATCATTATC
1 ATCATCATTATC
51951 AT
1 AT
51953 TGTCACTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 23 0.68
14 11 0.32
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (12 bp):
ATCATCATTATC
Found at i:55999 original size:23 final size:23
Alignment explanation
Indices: 55973--56025 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
55963 CGAATGATCG
*
55973 CGTAGAAATATCCCGAAGTACCA
1 CGTAGAAATATCCCGAAGGACCA
* * *
55996 CGTAGTATTATCCCGAAGGACCG
1 CGTAGAAATATCCCGAAGGACCA
56019 CGTAGAA
1 CGTAGAA
56026 CCCTCGACTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATATCCCGAAGGACCA
Done.