Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004713.1 Hibiscus syriacus cultivar Beakdansim tig00010622_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: 47938
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2208 original size:36 final size:35
Alignment explanation
Indices: 2090--2553 Score: 473
Period size: 36 Copynumber: 12.5 Consensus size: 35
2080 ATATACACAT
* *
2090 TATATAG-TTTGAAAACATTTTTAAAATATATATATAA
1 TATATAGTTTTTAAAACA-TTTTGAAA-ATA-ATATAA
* * * * *
2127 TATATAGTTTTGACAAGCATGTTTAAAAACATTTATATAT
1 TATATAGTTTTTA-AAACAT-TTT-GAAA-A-TAATATAA
2167 TATATAGTTTTTAAAACATTTTGAAAACTAATATAA
1 TATATAGTTTTTAAAACATTTTGAAAA-TAATATAA
*
2203 TATATAGTTTTTAAAACATTTTTTGAAAATATATATAT
1 TATATAGTTTTTAAAACA--TTTTGAAAATA-ATATAA
2241 TATATAGTTTTTAAAACATTTTGAAAACTAATATAA
1 TATATAGTTTTTAAAACATTTTGAAAA-TAATATAA
*
2277 TATATAGTTTTTAAAACATTTTTGAAAATATATATAT
1 TATATAGTTTTTAAAACA-TTTTGAAAATA-ATATAA
*
2314 TATATAGTTTTTAAAACATCTTGAAAACTAATATAA
1 TATATAGTTTTTAAAACATTTTGAAAA-TAATATAA
* *
2350 TATATAGTTTTTAAAATATTTTTTGAAAATATATATAT
1 TATATAGTTTTTAAAACA--TTTTGAAAATA-ATATAA
*
2388 TATATAATTTTTAAAACATTTTGAAAATAAATATAA
1 TATATAGTTTTTAAAACATTTTGAAAAT-AATATAA
* * *
2424 TATATAATTTTTAAAATATTTTTGAAAAT-ATATAT
1 TATATAGTTTTTAAAACA-TTTTGAAAATAATATAA
*
2459 TATATAGTTTTTAAAACATTTTGGAAATATATATAATAT
1 TATATAGTTTTTAAAACATTTT-GAAA-ATA-AT-ATAA
* *
2498 TATATAGTTTTTGAAAAATCTTTTTGGAAAATGCATATAA
1 TATATAGTTTTT--AAAA-CATTTT-GAAAAT-AATATAA
2538 TATATAGTTTTTAAAA
1 TATATAGTTTTTAAAA
2554 TAATATTTTA
Statistics
Matches: 373, Mismatches: 28, Indels: 51
0.83 0.06 0.11
Matches are distributed among these distances:
34 4 0.01
35 25 0.07
36 123 0.33
37 61 0.16
38 76 0.20
39 28 0.08
40 37 0.10
41 9 0.02
42 10 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (35 bp):
TATATAGTTTTTAAAACATTTTGAAAATAATATAA
Found at i:2250 original size:74 final size:74
Alignment explanation
Indices: 2088--2553 Score: 606
Period size: 74 Copynumber: 6.2 Consensus size: 74
2078 ATATATACAC
* * * * * * *
2088 ATTATATAG-TTTGAAAACATTTTTAAAATATATATATAATATATAGTTTTGACAAGCATGTTTA
1 ATTATATAGTTTTTAAAACATTTTGAAAA-CTA-ATATAATATATAGTTTTTA-AAACATTTTTT
* *
2152 AAAACATTTATAT
63 GAAA-ATATATAT
2165 ATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAACATTTTTTGAA
1 ATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAACATTTTTTGAA
2230 AATATATAT
66 AATATATAT
2239 ATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAACA-TTTTTGAA
1 ATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAACATTTTTTGAA
2303 AATATATAT
66 AATATATAT
* *
2312 ATTATATAGTTTTTAAAACATCTTGAAAACTAATATAATATATAGTTTTTAAAATATTTTTTGAA
1 ATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAACATTTTTTGAA
2377 AATATATAT
66 AATATATAT
* * *
2386 ATTATATAATTTTTAAAACATTTTGAAAA-TAAATATAATATATAATTTTTAAAATA-TTTTTG-
1 ATTATATAGTTTTTAAAACATTTTGAAAACT-AATATAATATATAGTTTTTAAAACATTTTTTGA
2448 AAA-ATATAT
65 AAATATATAT
*
2457 ATTATATAGTTTTTAAAACATTTTGGAAATA-TATATAATATTATATAGTTTTTGAAAA-ATCTT
1 ATTATATAGTTTTTAAAACATTTT-GAAA-ACTA-AT-ATAATATATAGTTTTT-AAAACAT-TT
**
2520 TTTGGAAAATGCATAT
60 TTT-GAAAATATATAT
*
2536 AATATATAGTTTTTAAAA
1 ATTATATAGTTTTTAAAA
2554 TAATATTTTA
Statistics
Matches: 356, Mismatches: 20, Indels: 24
0.89 0.05 0.06
Matches are distributed among these distances:
71 29 0.08
72 8 0.02
73 82 0.23
74 146 0.41
75 15 0.04
76 23 0.06
77 12 0.03
78 20 0.06
79 21 0.06
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (74 bp):
ATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAACATTTTTTGAA
AATATATAT
Found at i:2330 original size:147 final size:145
Alignment explanation
Indices: 2088--2553 Score: 616
Period size: 147 Copynumber: 3.1 Consensus size: 145
2078 ATATATACAC
* * * * *
2088 ATTATATAG-TTTGAAAACATTTTTAAAATATATATATAATATATAGTTTTGACAAGCATGTTTA
1 ATTATATAGTTTTTAAAACA-TTTTGAAA-ATA-ATATAATATATAGTTTTTA-AAACAT-TTTT
* *
2152 AAAACATTTATATATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAA
61 GAAA-ATATATATATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAA
2217 AACATTTTTTGAAAATATATAT
125 AA-ATTTTTTGAAAATATATAT
2239 ATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAACATTTTTGAAA
1 ATTATATAGTTTTTAAAACATTTTGAAAA-TAATATAATATATAGTTTTTAAAACATTTTTGAAA
*
2304 ATATATATATTATATAGTTTTTAAAACATCTTGAAAACTAATATAATATATAGTTTTTAAAATAT
65 ATATATATATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAA-AT
2369 TTTTTGAAAATATATAT
129 TTTTTGAAAATATATAT
* * *
2386 ATTATATAATTTTTAAAACATTTTGAAAATAAATATAATATATAATTTTTAAAATATTTTTG-AA
1 ATTATATAGTTTTTAAAACATTTTGAAAAT-AATATAATATATAGTTTTTAAAACATTTTTGAAA
*
2450 A-ATATATATTATATAGTTTTTAAAACATTTTGGAAATA-TATATAATATTATATAGTTTTTGAA
65 ATATATATATTATATAGTTTTTAAAACATTTT-GAAA-ACTA-AT-ATAATATATAGTTTTT-AA
**
2513 AAATCTTTTTGGAAAATGCATAT
125 AAAT-TTTTT-GAAAATATATAT
*
2536 AATATATAGTTTTTAAAA
1 ATTATATAGTTTTTAAAA
2554 TAATATTTTA
Statistics
Matches: 287, Mismatches: 18, Indels: 21
0.88 0.06 0.06
Matches are distributed among these distances:
145 29 0.10
146 10 0.03
147 139 0.48
148 23 0.08
149 14 0.05
150 45 0.16
151 18 0.06
152 9 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (145 bp):
ATTATATAGTTTTTAAAACATTTTGAAAATAATATAATATATAGTTTTTAAAACATTTTTGAAAA
TATATATATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAAATTT
TTTGAAAATATATAT
Found at i:2610 original size:10 final size:10
Alignment explanation
Indices: 2597--2634 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2587 CAAATTTGTT
2597 TTTATTTTTA
1 TTTATTTTTA
2607 TTTATTTATTA
1 TTTATTT-TTA
*
2618 TTAATTTTTA
1 TTTATTTTTA
2628 TTTATTT
1 TTTATTT
2635 ATTTTTTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:4055 original size:12 final size:11
Alignment explanation
Indices: 3988--4062 Score: 60
Period size: 12 Copynumber: 6.5 Consensus size: 11
3978 TTTCTTTACC
*
3988 TTTTTATTATTC
1 TTTTT-TTATTA
4000 TTTTTTTATTTA
1 TTTTTTTA-TTA
* *
4012 TTATTTTATCA
1 TTTTTTTATTA
*
4023 TTTTTTTAAGTA
1 TTTTTTT-ATTA
**
4035 TTGGTTTATTA
1 TTTTTTTATTA
4046 TTTTTATTATTA
1 TTTTT-TTATTA
4058 TTTTT
1 TTTTT
4063 GCCTAACATC
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
11 17 0.35
12 32 0.65
ACGTcount: A:0.20, C:0.03, G:0.04, T:0.73
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:4059 original size:23 final size:22
Alignment explanation
Indices: 3994--4059 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
3984 TACCTTTTTA
* *
3994 TTATTCTTTTTTTATTTATTATT
1 TTATTATTTTTTTA-TTATTAGT
* * *
4017 TTATCATTTTTTTAAGTATTGGT
1 TTATTATTTTTTT-ATTATTAGT
4040 TTATTATTTTTATTATTATT
1 TTATTATTTTT-TTATTATT
4060 TTTGCCTAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 31 0.91
24 3 0.09
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (22 bp):
TTATTATTTTTTTATTATTAGT
Found at i:15088 original size:3 final size:3
Alignment explanation
Indices: 15082--15122 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
15072 TTTTTTTCAA
* *
15082 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TTT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15123 AATAATTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:15227 original size:11 final size:11
Alignment explanation
Indices: 15211--15240 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
15201 CCCGTCTAGG
15211 TCCAGACCCGA
1 TCCAGACCCGA
15222 TCCAGACCCGA
1 TCCAGACCCGA
15233 TCC-GACCC
1 TCCAGACCC
15241 AGTAAGGCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.23, C:0.50, G:0.17, T:0.10
Consensus pattern (11 bp):
TCCAGACCCGA
Found at i:17069 original size:2 final size:2
Alignment explanation
Indices: 17062--17109 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
17052 AAACCTTAGG
17062 TA TA TA 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
17104 TA TA TA
1 TA TA TA
17110 CTTTAGTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22292 original size:11 final size:11
Alignment explanation
Indices: 22276--22303 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
22266 ATGTCAAGTA
22276 AAAATGGTAAG
1 AAAATGGTAAG
22287 AAAATGGTAAG
1 AAAATGGTAAG
22298 AAAATG
1 AAAATG
22304 TCAAGTAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.18
Consensus pattern (11 bp):
AAAATGGTAAG
Found at i:24577 original size:2 final size:2
Alignment explanation
Indices: 24570--24598 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24560 TTGTACGGAA
24570 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24599 AACAAGAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28186 original size:91 final size:91
Alignment explanation
Indices: 28031--28215 Score: 343
Period size: 91 Copynumber: 2.0 Consensus size: 91
28021 GAGTACTTAG
28031 AGAGCCAACAAATTGAGGATAACCCAAAATATTTTTCATTGATCAAGCAGCTGGTCATGAATACT
1 AGAGCCAACAAATTGAGGATAACCCAAAATATTTTTCATTGATCAAGCAGCTGGTCATGAATACT
*
28096 ACCTGGTTTCAAGAGGGGAAAAATGA
66 ACCTGGTTTCAAGAGGGAAAAAATGA
28122 AGAGCCAACAAATTGAGGATAACCCAAAATATTTTTCATTGATCAAGCAGCTGGTCATGAATACT
1 AGAGCCAACAAATTGAGGATAACCCAAAATATTTTTCATTGATCAAGCAGCTGGTCATGAATACT
* *
28187 ATCTGGTTTCAATAGGGAAAAAATGA
66 ACCTGGTTTCAAGAGGGAAAAAATGA
28213 AGA
1 AGA
28216 TTATGTCCAA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (91 bp):
AGAGCCAACAAATTGAGGATAACCCAAAATATTTTTCATTGATCAAGCAGCTGGTCATGAATACT
ACCTGGTTTCAAGAGGGAAAAAATGA
Found at i:30165 original size:17 final size:17
Alignment explanation
Indices: 30143--30177 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
30133 AAATCCCCGT
30143 AATCTTGCAAATGAGGA
1 AATCTTGCAAATGAGGA
30160 AATCTTGCAAATGAGGA
1 AATCTTGCAAATGAGGA
30177 A
1 A
30178 TACAATCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (17 bp):
AATCTTGCAAATGAGGA
Found at i:31038 original size:16 final size:17
Alignment explanation
Indices: 31017--31049 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31007 GCTCCATTAC
31017 ATTTATGTA-TATTTTT
1 ATTTATGTAGTATTTTT
*
31033 ATTTATTTAGTATTTTT
1 ATTTATGTAGTATTTTT
31050 GTTATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
ATTTATGTAGTATTTTT
Found at i:31054 original size:20 final size:20
Alignment explanation
Indices: 31017--31056 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31007 GCTCCATTAC
31017 ATTTATGTATATTTTTATTT
1 ATTTATGTATATTTTTATTT
*
31037 ATTTA-GTATTTTTGTTATTT
1 ATTTATGTATATTT-TTATTT
31057 TATGTGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (20 bp):
ATTTATGTATATTTTTATTT
Found at i:33610 original size:82 final size:84
Alignment explanation
Indices: 33451--33612 Score: 193
Period size: 82 Copynumber: 2.0 Consensus size: 84
33441 ACGTTTCTTT
* * *
33451 AACAAATACCGTGATAGAATAGTAATTTAGCGGCGTTTTTAGCACAAACGCCATAATAGGGTTTA
1 AACAAATACCGCGATAGAAGAGTAATTTAGCGGCGTTTTTAGCACAAACGCCATAATAGGGTTCA
***
33516 TTTGTAGAGGCGTTTTTCC
66 TCAATAGAGGCGTTTTTCC
* * * ** *
33535 AACAAATGCCGCGATA-AAGAGTACTTTAGCGGTGTTTTTAG-ACAAATTCTATAATAGGGTTCA
1 AACAAATACCGCGATAGAAGAGTAATTTAGCGGCGTTTTTAGCACAAACGCCATAATAGGGTTCA
*
33598 TCAATAGTGGCGTTT
66 TCAATAGAGGCGTTT
33613 GTTATAAAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
82 29 0.45
83 22 0.34
84 14 0.22
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (84 bp):
AACAAATACCGCGATAGAAGAGTAATTTAGCGGCGTTTTTAGCACAAACGCCATAATAGGGTTCA
TCAATAGAGGCGTTTTTCC
Found at i:33784 original size:41 final size:41
Alignment explanation
Indices: 33717--34139 Score: 376
Period size: 41 Copynumber: 10.3 Consensus size: 41
33707 ACATGTGCTA
** * *
33717 TAGTGGCGTTTTT-TTTAAACGCCGCTAAATACTCATATTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTATTT
* * * *
33757 TAGTGGTGTTTTTATATAAACGCCGCTAAAGA-TTGTAATT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTATTT
* * *
33797 TAGTGGGGGTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTATTT
* * *
33838 TAGTGGCATTTTTTTGTACAAACGCCGCTAAA-AAT-G-AGTTCAT
1 TAGTGGC--GTTTTTATACAAACGCCGCTAAAGACTCGTA-TT--T
* * *
33881 TAGTGGCATTTTTGA-ACAAACGCTGCTAAA-ATCTAGT-TATT
1 TAGTGGCGTTTTT-ATACAAACGCCGCTAAAGA-CTCGTAT-TT
*
33922 TAGTGGCGTTTTTATACAAACGCCGCTAATGACTCGTATTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTATTT
* * *
33963 TAGTGGCGTTTTTGTTTACAAACGCTGCTAAAGACTCGTAATT
1 TAGTGGCG-TTTT-TATACAAACGCCGCTAAAGACTCGTATTT
* * * * * * *
34006 CAGTGGCGTTTTTATATAAATGCCGCTATAGAGTCATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTATTT
* * * *
34047 CAGTGGCGTTTTTATACAAACGTCGCTTAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTATTT
* * * *
34088 CAGTGGCGTTTTTATACAAACGCCACTAAAGACTTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTATTT
34129 TAGTGGCGTTT
1 TAGTGGCGTTT
34140 GTAAACACAA
Statistics
Matches: 316, Mismatches: 50, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
40 48 0.15
41 192 0.61
42 14 0.04
43 62 0.20
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTATTT
Found at i:33975 original size:82 final size:82
Alignment explanation
Indices: 33717--34139 Score: 392
Period size: 84 Copynumber: 5.1 Consensus size: 82
33707 ACATGTGCTA
** * * * * * *
33717 TAGTGGCGTTTTT-TTTAAACGCCGCTAAATACTCATATTTTAGTGGTGTTTTTATATAAACGCC
1 TAGTGGCGTTTTTATACAAACGCTGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCC
* *
33781 GCTAAAGA-TTGTAATT
66 GCTAAAGACTCGTACTT
* * * * *
33797 TAGTGGGGGTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTTTGTACAAACG
1 TAGTGGCGTTTTTATACAAACGCTGCTAAAGACTCGTACTTTAGTGGC--GTTTTTATACAAACG
* * * *
33862 CCGCTAAA-AATGAGTTCAT
64 CCGCTAAAGACT-CGTACTT
* *
33881 TAGTGGCATTTTTGA-ACAAACGCTGCTAAA-ATCTAGTTA-TTTAGTGGCGTTTTTATACAAAC
1 TAGTGGCGTTTTT-ATACAAACGCTGCTAAAGA-CTCG-TACTTTAGTGGCGTTTTTATACAAAC
* *
33943 GCCGCTAATGACTCGTATTT
63 GCCGCTAAAGACTCGTACTT
* * * * *
33963 TAGTGGCGTTTTTGTTTACAAACGCTGCTAAAGACTCGTAATTCAGTGGCGTTTTTATATAAATG
1 TAGTGGCG-TTTT-TATACAAACGCTGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACG
* * *
34028 CCGCTATAGAGTCATACTT
64 CCGCTAAAGACTCGTACTT
* * *
34047 CAGTGGCGTTTTTATACAAACG-TCGCTTAAGACTCGTACTTCAGTGGCGTTTTTATACAAACGC
1 TAGTGGCGTTTTTATACAAACGCT-GCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* *
34111 CACTAAAGACTTGTACTT
65 CGCTAAAGACTCGTACTT
34129 TAGTGGCGTTT
1 TAGTGGCGTTT
34140 GTAAACACAA
Statistics
Matches: 277, Mismatches: 51, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
80 11 0.04
81 29 0.10
82 99 0.36
83 34 0.12
84 100 0.36
85 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (82 bp):
TAGTGGCGTTTTTATACAAACGCTGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCC
GCTAAAGACTCGTACTT
Found at i:34011 original size:125 final size:123
Alignment explanation
Indices: 33717--34139 Score: 427
Period size: 125 Copynumber: 3.4 Consensus size: 123
33707 ACATGTGCTA
* * * *
33717 TAGTGGCGTTTTTTTT--AAACGCCGCTAAATACTCATATTTTAGTGGTGTTTTTATATAAACGC
1 TAGTGGCGTTTTTTTTACAAACGCCGCTAAAGACTCGTAATTTAGTGGCGTTTTTATATAAACGC
* * *
33780 CGCTAAAGAT-T-GTAATTTAGTGGGGGTTTTATACAAACGCCGCTAAAGACTCGTACTT
66 CGCTAAA-ATCTAGTTATTTAGTGGCGTTTTTATACAAACGCCGCT-AAGACTCGTACTT
* * * * * *
33838 TAGTGGCATTTTTTTGTACAAACGCCGCTAAA-AATGAGTTCA-TTAGTGGCATTTTTGA-ACAA
1 TAGTGGCGTTTTTTT-TACAAACGCCGCTAAAGACT-CG-TAATTTAGTGGCGTTTTT-ATATAA
* *
33900 ACGCTGCTAAAATCTAGTTATTTAGTGGCGTTTTTATACAAACGCCGCTAATGACTCGTATTT
62 ACGCCGCTAAAATCTAGTTATTTAGTGGCGTTTTTATACAAACGCCGCTAA-GACTCGTACTT
* * *
33963 TAGTGGCGTTTTTGTTTACAAACGCTGCTAAAGACTCGTAATTCAGTGGCGTTTTTATATAAATG
1 TAGTGGCGTTTTT-TTTACAAACGCCGCTAAAGACTCGTAATTTAGTGGCGTTTTTATATAAACG
* * *
34028 CCGCTATAGAGTC-A--TACTTCAGTGGCGTTTTTATACAAACGTCGCTTAAGACTCGTACTT
65 CCGCTA-A-AATCTAGTTA-TTTAGTGGCGTTTTTATACAAACGCCGC-TAAGACTCGTACTT
* * * * *
34088 CAGTGGCG-TTTTTATACAAACGCCACTAAAGACTTGTACTTTAGTGGCGTTT
1 TAGTGGCGTTTTTTTTACAAACGCCGCTAAAGACTCGTAATTTAGTGGCGTTT
34140 GTAAACACAA
Statistics
Matches: 250, Mismatches: 35, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
121 14 0.06
122 1 0.00
123 38 0.15
124 50 0.20
125 135 0.54
126 9 0.04
127 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (123 bp):
TAGTGGCGTTTTTTTTACAAACGCCGCTAAAGACTCGTAATTTAGTGGCGTTTTTATATAAACGC
CGCTAAAATCTAGTTATTTAGTGGCGTTTTTATACAAACGCCGCTAAGACTCGTACTT
Found at i:37291 original size:43 final size:43
Alignment explanation
Indices: 37164--37424 Score: 341
Period size: 43 Copynumber: 6.1 Consensus size: 43
37154 TTGTGGATAC
* *
37164 AAACGCCGCTATAGATATTGACCTTTTGTGGCATTTGTTCC-A
1 AAACGCCGCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAA
* *
37206 AAACGCCGCTATAGATATTGACTTTTTGAGGCGTTTGTTCCAA
1 AAACGCCGCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAA
* * * *
37249 AAACGCAGCTATAGATCTT-TCCTTTCGCGGCGTTTGTATCCAA
1 AAACGCCGCTATAGATATTGACCTTTTGCGGCGTTTGT-TCCAA
* *
37292 AAATGCCGCTATA-AGTCTT-ACCTTTTGCGGCGTTTGTTCCAA
1 AAACGCCGCTATAGA-TATTGACCTTTTGCGGCGTTTGTTCCAA
* * *
37334 AAACGCCGCTATAGATATTGACCTTTTGCGGCATTTGATCTAA
1 AAACGCCGCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAA
* *
37377 AAACGCCGCTATAGATATCGACCTTTTGCGGTGTTTGTTCCAA
1 AAACGCCGCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAA
37420 AAACG
1 AAACG
37425 ACGCACTAAA
Statistics
Matches: 191, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
42 73 0.38
43 118 0.62
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (43 bp):
AAACGCCGCTATAGATATTGACCTTTTGCGGCGTTTGTTCCAA
Found at i:37293 original size:85 final size:86
Alignment explanation
Indices: 37164--37424 Score: 343
Period size: 85 Copynumber: 3.1 Consensus size: 86
37154 TTGTGGATAC
*
37164 AAACGCCGCTATAGATATTGACCTTTTGTGGCATTTGT-TCCAAAACGCCGCTATAGATATTGAC
1 AAACGCCGCTATAGATATTGACCTTTTGCGGCATTTGTATCCAAAACGCCGCTATAGATATTGAC
* *
37228 TTTTTGAGGCGTTTGTTCCAA
66 CTTTTGCGGCGTTTGTTCCAA
* * * * * * *
37249 AAACGCAGCTATAGATCTT-TCCTTTCGCGGCGTTTGTATCCAAAAATGCCGCTATA-AGTCTT-
1 AAACGCCGCTATAGATATTGACCTTTTGCGGCATTTGTATCC-AAAACGCCGCTATAGA-TATTG
37311 ACCTTTTGCGGCGTTTGTTCCAA
64 ACCTTTTGCGGCGTTTGTTCCAA
* *
37334 AAACGCCGCTATAGATATTGACCTTTTGCGGCATTTG-ATCTAAAAACGCCGCTATAGATATCGA
1 AAACGCCGCTATAGATATTGACCTTTTGCGGCATTTGTATC-CAAAACGCCGCTATAGATATTGA
*
37398 CCTTTTGCGGTGTTTGTTCCAA
65 CCTTTTGCGGCGTTTGTTCCAA
37420 AAACG
1 AAACG
37425 ACGCACTAAA
Statistics
Matches: 149, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
84 14 0.09
85 77 0.52
86 58 0.39
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (86 bp):
AAACGCCGCTATAGATATTGACCTTTTGCGGCATTTGTATCCAAAACGCCGCTATAGATATTGAC
CTTTTGCGGCGTTTGTTCCAA
Found at i:37419 original size:128 final size:127
Alignment explanation
Indices: 37184--37422 Score: 336
Period size: 128 Copynumber: 1.9 Consensus size: 127
37174 ATAGATATTG
* * * *
37184 ACCTTTTGTGGCATTTGTTCCAAAACGCCGCTATAGATATTGACTTTTTGAGGCGTTTGTTCCAA
1 ACCTTTTGCGGCATTTGTTCCAAAACGCCGCTATAGATATTGACCTTTTGAGGCATTTGATCCAA
* **
37249 AAACGCAGCTATAGATCTTTCCTTTCGCGGCGTTTGTATCCAAAAATGCCGCTATAAGTCTT
66 AAACGCAGCTATAGATATGACCTTTCGCGGCGTTTGTATCCAAAAATGCCGCTATAAGTCTT
* * *
37311 ACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATTGACCTTTTGCGGCATTTGATCTA
1 ACCTTTTGCGGCATTTGTTCC-AAAACGCCGCTATAGATATTGACCTTTTGAGGCATTTGATCCA
* * *
37376 AAAACGCCGCTATAGATATCGACCTTTTGCGGTGTTTGT-TCCAAAAA
65 AAAACGCAGCTATAGATAT-GACCTTTCGCGGCGTTTGTATCCAAAAA
37423 CGACGCACTA
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
127 19 0.20
128 63 0.65
129 15 0.15
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (127 bp):
ACCTTTTGCGGCATTTGTTCCAAAACGCCGCTATAGATATTGACCTTTTGAGGCATTTGATCCAA
AAACGCAGCTATAGATATGACCTTTCGCGGCGTTTGTATCCAAAAATGCCGCTATAAGTCTT
Found at i:38039 original size:13 final size:13
Alignment explanation
Indices: 38018--38050 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
38008 ATGTCACTTT
*
38018 TTATCTTTTAAAA
1 TTATTTTTTAAAA
38031 TTATTTTTTAAAA
1 TTATTTTTTAAAA
38044 TTATTTT
1 TTATTTT
38051 AATTGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTTTTAAAA
Found at i:41265 original size:56 final size:55
Alignment explanation
Indices: 41186--41572 Score: 544
Period size: 57 Copynumber: 7.1 Consensus size: 55
41176 TTTCTTAGTT
* * *
41186 TTTTTCACATAAAGTGCCTATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
1 TTTTT-ACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
*
41242 TTTTGTACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAAC
1 TTTT-TACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
41298 TTTTTTCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
1 -TTTTT-ACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
* *
41355 TTTTTACACACAAAGTGCCCATACGAAAATTCATAAACCAATTATGAATTTCTTAAC
1 TTTTT--ACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
41412 TTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
1 TTTTT--ACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
*
41469 ---TT---C---TTG--CATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
1 TTTTTACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
* *
41513 ATTTCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
1 TTTTTACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
41568 TTTTT
1 TTTTT
41573 GTACACTCAG
Statistics
Matches: 303, Mismatches: 13, Indels: 31
0.87 0.04 0.09
Matches are distributed among these distances:
44 38 0.13
46 2 0.01
47 1 0.00
49 1 0.00
50 1 0.00
53 2 0.01
54 2 0.01
55 41 0.14
56 58 0.19
57 157 0.52
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (55 bp):
TTTTTACACAAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC
Found at i:41494 original size:44 final size:47
Alignment explanation
Indices: 41425--41569 Score: 179
Period size: 44 Copynumber: 3.0 Consensus size: 47
41415 TTGCACACAA
41425 AGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAACTT-C
1 AGTG-CCATACGGAAATTCATAAACTAATTATGAATTTCTTAACTTAC
*
41472 -TTG-CATACGGAAATTCATAAACTAATTATGAATTTCTTAACATTTCACAC
1 AGTGCCATACGGAAATTCATAAACTAATTATGAATTTCTTAAC--TT---AC
41522 AAAGTGCCCATACGGAAATTCATAAACTAATTATGAATTTCTTAACTT
1 --AGTG-CCATACGGAAATTCATAAACTAATTATGAATTTCTTAACTT
41570 TTTGTACACT
Statistics
Matches: 85, Mismatches: 2, Indels: 16
0.83 0.02 0.16
Matches are distributed among these distances:
44 38 0.45
46 4 0.05
50 1 0.01
53 4 0.05
55 38 0.45
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (47 bp):
AGTGCCATACGGAAATTCATAAACTAATTATGAATTTCTTAACTTAC
Found at i:41552 original size:99 final size:101
Alignment explanation
Indices: 41374--41569 Score: 351
Period size: 99 Copynumber: 2.0 Consensus size: 101
41364 ACAAAGTGCC
*
41374 CATACGAAAATTCATAAACCAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGA
1 CATACGAAAATTCATAAACCAATTATGAATTTCTTAACTATTTGCACACAAAGTGCCCATACGGA
41439 AATTCATAAACTAATTATGAATTTCTTAACTTCTTG
66 AATTCATAAACTAATTATGAATTTCTTAACTTCTTG
* *
41475 CATACGGAAATTCATAAACTAATTATGAATTTCTTAAC-ATTT-CACACAAAGTGCCCATACGGA
1 CATACGAAAATTCATAAACCAATTATGAATTTCTTAACTATTTGCACACAAAGTGCCCATACGGA
41538 AATTCATAAACTAATTATGAATTTCTTAACTT
66 AATTCATAAACTAATTATGAATTTCTTAACTT
41570 TTTGTACACT
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
99 53 0.58
100 3 0.03
101 36 0.39
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (101 bp):
CATACGAAAATTCATAAACCAATTATGAATTTCTTAACTATTTGCACACAAAGTGCCCATACGGA
AATTCATAAACTAATTATGAATTTCTTAACTTCTTG
Found at i:44759 original size:3 final size:3
Alignment explanation
Indices: 44751--44810 Score: 111
Period size: 3 Copynumber: 19.7 Consensus size: 3
44741 AGGTTAATAA
44751 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
44799 ATT ATAT ATT AT
1 ATT AT-T ATT AT
44811 ACAATAAAGC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:47383 original size:42 final size:41
Alignment explanation
Indices: 47296--47917 Score: 280
Period size: 42 Copynumber: 14.6 Consensus size: 41
47286 ACTGACGACC
* * * *
47296 CGTGAAGAGGAGTCAATCTTTCAATATATTC-TGACTCCCT
1 CGTGAAGAAGAGTCAATCTTTCAATGTTTTCTTGACTCTCT
* *
47336 TGTGAAGAAGAGTCATTCTTTTCAATGTTTTCTTGACTCTCT
1 CGTGAAGAAGAGTCAATC-TTTCAATGTTTTCTTGACTCTCT
* * *
47378 CGTGAAGAGGAGTCAATCTTTCAATGTTATTATTGACTTTCT
1 CGTGAAGAAGAGTCAATCTTTCAATGTT-TTCTTGACTCTCT
* * *
47420 TGTGAAGATA-AGTC-ATCTTTCAATATTGTCATTCTGACT-TCT
1 CGTGAAGA-AGAGTCAATCTTTCAATGTTTTC--T-TGACTCTCT
* * * *
47462 CATGAAG-AGAAGTCAATC-TTCAGTATTTTCTTTCTTGAATTTCT
1 CGTGAAGAAG-AGTCAATCTTTCA--A-TGT-TTTCTTGACTCTCT
*
47506 CGTGAAG-AGAAGTTAATCTTTCAGTAT-TGTTTCTTGACT-T-T
1 CGTGAAGAAG-AGTCAATCTTTCA--ATGT-TTTCTTGACTCTCT
* * * *
47547 CATG-AG-AGAAGTCAATCTTTCAGTATTGTCATTCTTGGCTTTCT
1 CGTGAAGAAG-AGTCAATCTTTCA--A-TGT-TTTCTTGACTCTCT
*
47591 CGTGAAG-AGAATTCAATCTTTCAATATTGTCTTTCTTGACT-TCT
1 CGTGAAGAAG-AGTCAATCTTTC-A-A-TGT-TTTCTTGACTCTCT
* *
47635 CGTGAAG-AGAAGTCAATCTTTCAGTGCTTTCATTCTGACTC-CT
1 CGTGAAGAAG-AGTCAATCTTTCAATGTTTTC--T-TGACTCTCT
** * * * *
47678 TATGAAGATGAGTTAATATTTCAATGTTATTCTTGGCTCTCT
1 CGTGAAGAAGAGTCAATCTTTCAATGTT-TTCTTGACTCTCT
*
47720 CGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACT-TCT
1 CGTGAAGAAGAGTCAATCTTTCAATGTT-TTCTTGACTCTCT
* ** *
47761 CATGAAG-AGAAGTCAATCTTTCAGTATTGGCATTCTT-ACTTTCT
1 CGTGAAGAAG-AGTCAATCTTTCA--A-T-GTTTTCTTGACTCTCT
* *
47805 CTTGAA-AAGAAGTCAATCTTTCAGTATTGTTATTCTTGACTTTCT
1 CGTGAAGAAG-AGTCAATCTTTCA--A-TGTT-TTCTTGACTCTCT
* * * * *
47850 CGCGAAG-AGAATTCAATC-TTCAAGTATTGTCATTCTTGATTTTCT
1 CGTGAAGAAG-AGTCAATCTTTC-A--A-TGT-TTTCTTGACTCTCT
*
47895 CGTGAAGAAAAGTCAATCTTTCA
1 CGTGAAGAAGAGTCAATCTTTCA
47918 GTATTTCTTT
Statistics
Matches: 473, Mismatches: 66, Indels: 81
0.76 0.11 0.13
Matches are distributed among these distances:
40 42 0.09
41 67 0.14
42 108 0.23
43 55 0.12
44 97 0.21
45 96 0.20
46 8 0.02
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (41 bp):
CGTGAAGAAGAGTCAATCTTTCAATGTTTTCTTGACTCTCT
Found at i:47512 original size:44 final size:45
Alignment explanation
Indices: 47365--47932 Score: 443
Period size: 44 Copynumber: 13.2 Consensus size: 45
47355 TTTCAATGTT
* * * *
47365 TTCTTGACTCTCTCGTGAAGAGGAGTCAATCTTTCA--ATGTT-A
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
* * * * * *
47407 TTATTGACTTTCTTGTGAAGATAAGTC-ATCTTTCAATATTGTCA
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
* * *
47451 TTC-TG-ACTTCTCATGAAGAGAAGTCAATC-TTCAGTATTTTCT
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
* *
47493 TTCTTGAATTTCTCGTGAAGAGAAGTTAATCTTTCAGTATTGT--
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
* * *
47536 TTCTTG-ACTT-TCATG-AGAGAAGTCAATCTTTCAGTATTGTCA
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
** * * * *
47578 TTCTTGGCTTTCTCGTGAAGAGAATTCAATCTTTCAATATTGTCT
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
* **
47623 TTCTTG-ACTTCTCGTGAAGAGAAGTCAATCTTTCAGTGCTTTCA
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
* * ** * * *
47667 TTC-TG-ACTCCTTATGAAGATG-AGTTAATATTTCA--ATGTT-A
1 TTCTTGAATTTCTCGTGAAGA-GAAGTCAATCTTTCAGTATTTTCA
** * * *
47707 TTCTTGGCTCTCTCGTGAAGAGGAGTCAATCTTTCA--ATGTT-A
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
* * **
47749 TTCTTG-ACTTCTCATGAAGAGAAGTCAATCTTTCAGTATTGGCA
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
* * *
47793 TTCTT-ACTTTCTCTTGAAAAGAAGTCAATCTTTCAGTATTGTT-A
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATT-TTCA
* * * *
47837 TTCTTGACTTTCTCGCGAAGAGAATTCAATC-TTCAAGTATTGTCA
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTC-AGTATTTTCA
* * *
47882 TTCTTGATTTTCTCGTGAAGAAAAGTCAATCTTTCAGTA-TTTCT
1 TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
47926 TTCTTGA
1 TTCTTGA
47933 CTTTTT
Statistics
Matches: 423, Mismatches: 78, Indels: 48
0.77 0.14 0.09
Matches are distributed among these distances:
40 28 0.07
41 41 0.10
42 90 0.21
43 44 0.10
44 118 0.28
45 99 0.23
46 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (45 bp):
TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTCA
Found at i:47582 original size:85 final size:87
Alignment explanation
Indices: 47364--47932 Score: 489
Period size: 85 Copynumber: 6.6 Consensus size: 87
47354 TTTTCAATGT
* * * * *
47364 TTTCTTGACTCTCTCGTGAAGAGGAGTCAATCTTTCA--A-TGTTATTATTGACTTTCTTGTGAA
1 TTTCTTGACT-TCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGAATTTCTCGTGAA
* *
47426 GATAAG-TCATCTTTCAATATTG
65 GAGAAGTTAATCTTTCAATATTG
* * *
47448 TCATTC-TGACTTCTCATGAAGAGAAGTCAATC-TTCAGTATTTTCTTTCTTGAATTTCTCGTGA
1 T--TTCTTGACTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGAATTTCTCGTGA
*
47511 AGAGAAGTTAATCTTTCAGTATTG
64 AGAGAAGTTAATCTTTCAATATTG
* **
47535 TTTCTTGACTT-TCATG-AGAGAAGTCAATCTTTCAGTATTGTCATTCTTGGCTTTCTCGTGAAG
1 TTTCTTGACTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGAATTTCTCGTGAAG
47598 AGAA-TTCAATCTTTCAATATTG
66 AGAAGTT-AATCTTTCAATATTG
* * * **
47620 TCTTTCTTGACTTCTCGTGAAGAGAAGTCAATCTTTCAGTGCTT-TCATTC-TG-ACTCCTTATG
1 --TTTCTTGACTTCTCGTGAAGAGAAGTCAATCTTTCAGT-ATTGTCATTCTTGAATTTCTCGTG
* *
47682 AAGATG-AGTTAATATTTCAATGTT-
63 AAGA-GAAGTTAATCTTTCAATATTG
* * * * * *
47706 ATTCTTGGCTCTCTCGTGAAGAGGAGTCAATCTTTCA--A-TGTTATTCTTG-ACTTCTCATGAA
1 TTTCTTGACT-TCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGAATTTCTCGTGAA
* *
47767 GAGAAGTCAATCTTTCAGTATTGG
65 GAGAAGTTAATCTTTCAATATT-G
* * * * * *
47791 CATTCTT-ACTTTCTCTTGAAAAGAAGTCAATCTTTCAGTATTGTTATTCTTGACTTTCTCGCGA
1 -TTTCTTGAC-TTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGAATTTCTCGTGA
47855 AGAGAA-TTCAATC-TTCAAGTATTG
64 AGAGAAGTT-AATCTTTCAA-TATTG
* * *
47879 TCATTCTTGATTTTCTCGTGAAGAAAAGTCAATCTTTCAGTATT-TCTTTCTTGA
1 T--TTCTTGA-CTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGA
47933 CTTTTT
Statistics
Matches: 398, Mismatches: 53, Indels: 63
0.77 0.10 0.12
Matches are distributed among these distances:
81 1 0.00
82 6 0.02
83 32 0.08
84 43 0.11
85 110 0.28
86 39 0.10
87 49 0.12
88 26 0.07
89 60 0.15
90 32 0.08
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (87 bp):
TTTCTTGACTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTCATTCTTGAATTTCTCGTGAAG
AGAAGTTAATCTTTCAATATTG
Found at i:47608 original size:129 final size:130
Alignment explanation
Indices: 47364--47936 Score: 536
Period size: 129 Copynumber: 4.4 Consensus size: 130
47354 TTTTCAATGT
* * * * * * * * *
47364 TTTCTTGACTCTCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTATTGACTTTCTTGTGAAGAT
1 TTTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTTCTTGACTTTC--ATGAAGAG
* * *
47429 AAGTC-ATCTTTCAATATTGTCATTC-TGAC-TTCTCATGAAGAGAAGTCAATC-TTCAGTATTT
64 AAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTG
47490 TC
129 TC
*
47492 TTTCTTGAATTTCTCGTGAAGAGAAGTTAATCTTTCAGTATTGTTTCTTGACTTTCATG-AGAGA
1 TTTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATT-TTTCTTGACTTTCATGAAGAGA
* * *
47556 AGTCAATCTTTCAGTATTGTCATTCTTGGCTTTCTCGTGAAGAGAATTCAATCTTTCAATATTGT
65 AGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGT
47621 C
130 C
* *
47622 TTTCTTG-ACTTCTCGTGAAGAGAAGTCAATCTTTCAGTGCTTTCATTC-TGACTCCTT-ATGAA
1 TTTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGT-ATTT--TTCTTGACT--TTCATGAA
* * * * * *
47684 GATG-AGTTAATATTTCA--A-TGTTATTCTTGGCTCTCTCGTGAAGAGGAGTCAATCTTTCA--
61 GA-GAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGT
47743 A-TGT-
125 ATTGTC
* * * *
47747 TATTCTTG-ACTTCTCATGAAGAGAAGTCAATCTTTCAGTATTGGCATTCTT-ACTTTCTCTTGA
1 T-TTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATT---TTTCTTGAC-TT-TCATGA
* * * *
47810 AAAGAAGTCAATCTTTCAGTATTGTTATTCTTGACTTTCTCGCGAAGAGAATTCAATC-TTCAAG
60 AGAGAAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTC-AG
47874 TATTGTC
124 TATTGTC
* * *
47881 ATTCTTGATTTTCTCGTGAAGAAAAGTCAATCTTTCAGTATTTCTTTCTTGACTTT
1 TTTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTA-TT-TTTCTTGACTTT
47937 TT
Statistics
Matches: 370, Mismatches: 43, Indels: 60
0.78 0.09 0.13
Matches are distributed among these distances:
125 4 0.01
126 54 0.15
127 40 0.11
128 39 0.11
129 102 0.28
130 57 0.15
131 6 0.02
132 18 0.05
133 18 0.05
134 30 0.08
135 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (130 bp):
TTTCTTGAATTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTTTTCTTGACTTTCATGAAGAGAA
GTCAATCTTTCAGTATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCAGTATTGTC
Done.