Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006188.1 Hibiscus syriacus cultivar Beakdansim tig00014726_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: 96270
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1481 original size:62 final size:62
Alignment explanation
Indices: 1344--1546 Score: 313
Period size: 62 Copynumber: 3.3 Consensus size: 62
1334 GACTATTTAA
**
1344 AAAACTACAAATCTTAC--TTTATTACTACCATACCTATCCAAGTGCTTTCTAATGAGATCTT
1 AAAACTACAAGCCTTACTATTTATTACTACCATACCTATCCAAGTGC-TTCTAATGAGATCTT
1405 AAAACTACAAGCCTTACTATTTATTACTACCATACCTATCCAAGTGCTTCTAATGAGATCTT
1 AAAACTACAAGCCTTACTATTTATTACTACCATACCTATCCAAGTGCTTCTAATGAGATCTT
* ** *
1467 AAAACTACAAGCCTTACTATTTATTACTACCATACCTATCCAACTGCTAAT-ACGAGATCTT
1 AAAACTACAAGCCTTACTATTTATTACTACCATACCTATCCAAGTGCTTCTAATGAGATCTT
*
1528 AAAACCACAAGCCTTACTA
1 AAAACTACAAGCCTTACTA
1547 ATTTTGCAAT
Statistics
Matches: 133, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
61 42 0.32
62 63 0.47
63 28 0.21
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (62 bp):
AAAACTACAAGCCTTACTATTTATTACTACCATACCTATCCAAGTGCTTCTAATGAGATCTT
Found at i:3091 original size:84 final size:84
Alignment explanation
Indices: 2950--3123 Score: 312
Period size: 84 Copynumber: 2.1 Consensus size: 84
2940 TTTCCACTGA
*
2950 TATAAGTTCAATGTATTATATAAGGACGGTACTAACATTCAACCCTCTTTTGCTTTAGTTTTTCA
1 TATAAGTTCAATGTATTATATAAGGACCGTACTAACATTCAACCCTCTTTTGCTTTAGTTTTTCA
*
3015 ACCATGCATTGTGATTACT
66 ACCATGCATTGTGATTAAT
*
3034 TATAAGTTCAATGTATTATATAAGGACCGTACTAACATTTAACCCTCTTTTGCTTTAGTTTTTCA
1 TATAAGTTCAATGTATTATATAAGGACCGTACTAACATTCAACCCTCTTTTGCTTTAGTTTTTCA
*
3099 ACCATTCATTGTGATTAAT
66 ACCATGCATTGTGATTAAT
3118 TATAAG
1 TATAAG
3124 CTACTGGGAT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (84 bp):
TATAAGTTCAATGTATTATATAAGGACCGTACTAACATTCAACCCTCTTTTGCTTTAGTTTTTCA
ACCATGCATTGTGATTAAT
Found at i:5404 original size:24 final size:24
Alignment explanation
Indices: 5377--5432 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
5367 TTTAACGATT
* *
5377 TAATTTTTAGTATTTTCATTTTA-A
1 TAATTTTTA-TATTTTAAATTTATA
5401 TAATTTTTTATATTTTAAATTTATA
1 TAA-TTTTTATATTTTAAATTTATA
5426 TAATTTT
1 TAATTTT
5433 AAATAAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TAATTTTTATATTTTAAATTTATA
Found at i:5422 original size:25 final size:25
Alignment explanation
Indices: 5380--5432 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
5370 AACGATTTAA
*
5380 TTTTTAGTATTTTCATTT-TAATAAT
1 TTTTTAGTATTTTAATTTAT-ATAAT
5405 TTTTTA-TATTTTAAATTTATATAAT
1 TTTTTAGTATTTT-AATTTATATAAT
5430 TTT
1 TTT
5433 AAATAAGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 6 0.24
25 18 0.72
26 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTTAGTATTTTAATTTATATAAT
Found at i:5524 original size:21 final size:21
Alignment explanation
Indices: 5495--5535 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5485 CTGTATATTA
*
5495 TCATGTCAACATCGTAAACTG
1 TCATATCAACATCGTAAACTG
* *
5516 TCATATCAATATTGTAAACT
1 TCATATCAACATCGTAAACT
5536 TTCACTCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.34
Consensus pattern (21 bp):
TCATATCAACATCGTAAACTG
Found at i:26355 original size:44 final size:44
Alignment explanation
Indices: 26292--26433 Score: 239
Period size: 44 Copynumber: 3.2 Consensus size: 44
26282 AACCGAATTA
*
26292 ATAACTAAAATGCATAATGGTGCATTAAGGCATGAAAGGACGTC
1 ATAACTAAAATGCATAATGGTGCATTAAGGCATGAAAGGATGTC
*
26336 ATAACTAAAATGCATAATGGTGCATTAAGGCATGAAATGATGTC
1 ATAACTAAAATGCATAATGGTGCATTAAGGCATGAAAGGATGTC
* *
26380 ATAACTGAAATGCATAATGGTCCATTAAGGCATGAAAGGATGTC
1 ATAACTAAAATGCATAATGGTGCATTAAGGCATGAAAGGATGTC
*
26424 ATAAATAAAA
1 ATAACTAAAA
26434 ATAATAAATA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 91 1.00
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (44 bp):
ATAACTAAAATGCATAATGGTGCATTAAGGCATGAAAGGATGTC
Found at i:27861 original size:30 final size:31
Alignment explanation
Indices: 27820--27885 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 31
27810 GATAACGACA
27820 AAAATAACCTCTAAATGATCACCTAGAGGAT
1 AAAATAACCTCTAAATGATCACCTAGAGGAT
27851 AAAAT-ACCTCTAAATGATCACCTAGAGGAT
1 AAAATAACCTCTAAATGATCACCTAGAGGAT
27881 AAAAT
1 AAAAT
27886 CTCAATCACT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (31 bp):
AAAATAACCTCTAAATGATCACCTAGAGGAT
Found at i:31025 original size:39 final size:39
Alignment explanation
Indices: 30982--31200 Score: 175
Period size: 39 Copynumber: 6.0 Consensus size: 39
30972 CCATTTATAT
*
30982 ATATATATATATATTATAG-TTTGAAAACATTTTTAAAAA
1 ATATATATATATA-TATAGTTTTGAAAACATTTTGAAAAA
*
31021 ATATATATA-ATATATAGTTTTGAAAACATGTTTGAAAAC
1 ATATATATATATATATAGTTTTGAAAACAT-TTTGAAAAA
* * *
31060 GTTTATATAT-TATATAGTTTTTAAAACATTTTG--AAA
1 ATATATATATATATATAGTTTTGAAAACATTTTGAAAAA
** * *
31096 ATA-A-ATATAGCT-T--TTTT-AAAATATTTTGAAAAC
1 ATATATATATATATATAGTTTTGAAAACATTTTGAAAAA
*
31129 ATATATAT-TATATA-A-TTTTGAAATCATTTTG-AAAA
1 ATATATATATATATATAGTTTTGAAAACATTTTGAAAAA
* * *
31164 CT-TATATA-GTATATAGTTTTAAAAACATTTTTGAAAA
1 ATATATATATATATATAGTTTTGAAAACA-TTTTGAAAA
31201 CTATATAGTT
Statistics
Matches: 143, Mismatches: 21, Indels: 33
0.73 0.11 0.17
Matches are distributed among these distances:
31 10 0.07
32 4 0.03
33 5 0.03
34 18 0.13
35 13 0.09
36 21 0.15
37 10 0.07
38 21 0.15
39 41 0.29
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (39 bp):
ATATATATATATATATAGTTTTGAAAACATTTTGAAAAA
Found at i:31135 original size:31 final size:29
Alignment explanation
Indices: 31070--31135 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
31060 GTTTATATAT
*
31070 TATATAGTTTTTAAAACATTTTGAAAATA
1 TATATAGTTTTTAAAACATTTTGAAAACA
* *
31099 AATATAGCTTTTTTAAAATATTTTGAAAACA
1 TATATAG--TTTTTAAAACATTTTGAAAACA
31130 TATATA
1 TATATA
31136 TTATATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 6 0.19
31 25 0.81
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (29 bp):
TATATAGTTTTTAAAACATTTTGAAAACA
Found at i:31189 original size:103 final size:102
Alignment explanation
Indices: 30996--31259 Score: 306
Period size: 103 Copynumber: 2.5 Consensus size: 102
30986 ATATATATAT
* * *
30996 TATAG-TTTGAAAACATTTTTAAAAAATATATATAATATATAGTTTTGAAAACATGTTTGAAAAC
1 TATAGTTTTG-AAACATTTTTCAAAAA-ATATATAATATATAATTTTGAAATCAT-TTTGAAAAC
* *
31060 GTTTATATATTATATAGTTTTTAAAACA-TTTTGAAAA-TAAA
63 G-TTATATAGTATATAGTTTTAAAAACATTTTTGAAAACT--A
* * * *
31101 TATAGCTTTTTTAAA-ATATTTTGAAAACATATATATTATATAATTTTGAAATCATTTTGAAAAC
1 TATAG--TTTTGAAACAT-TTTTCAAAAAATATATAATATATAATTTTGAAATCATTTTGAAAAC
31165 -TTATATAGTATATAGTTTTAAAAACATTTTTGAAAACTA
63 GTTATATAGTATATAGTTTTAAAAACATTTTTGAAAACTA
*
31204 TATAGTTTTGAAAGCATTTTTCAAAAAATATATAATATATAATTTTAAAAT-ATTTT
1 TATAGTTTTGAAA-CATTTTTCAAAAAATATATAATATATAATTTTGAAATCATTTT
31260 TTTGAAAATA
Statistics
Matches: 138, Mismatches: 13, Indels: 20
0.81 0.08 0.12
Matches are distributed among these distances:
101 12 0.09
102 30 0.22
103 32 0.23
104 9 0.07
105 15 0.11
106 26 0.19
107 11 0.08
108 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (102 bp):
TATAGTTTTGAAACATTTTTCAAAAAATATATAATATATAATTTTGAAATCATTTTGAAAACGTT
ATATAGTATATAGTTTTAAAAACATTTTTGAAAACTA
Found at i:31209 original size:36 final size:35
Alignment explanation
Indices: 30987--31207 Score: 193
Period size: 36 Copynumber: 6.2 Consensus size: 35
30977 TATATATATA
* *
30987 TATATATATTATAG-TTTGAAAACATTTTTAAAAAAT
1 TATATATA-TATAGTTTTGAAAACA-TTTTGAAAACT
31023 ATATATAATATATAGTTTTGAAAACATGTTTGAAAACGTT
1 -TATAT-ATATATAGTTTTGAAAACAT-TTTGAAAAC--T
*
31063 TATATATTATATAGTTTTTAAAACATTTTGAAAA--
1 TATATA-TATATAGTTTTGAAAACATTTTGAAAACT
*** * * *
31097 TA-A-ATATAGCTTTTTTAAAATATTTTGAAAACA
1 TATATATATATAGTTTTGAAAACATTTTGAAAACT
* *
31130 TATATATTATATAATTTTGAAATCATTTTGAAAACT
1 TATATA-TATATAGTTTTGAAAACATTTTGAAAACT
*
31166 TATATAGTATATAGTTTTAAAAACATTTTTGAAAAC-
1 TATATA-TATATAGTTTTGAAAACA-TTTTGAAAACT
31202 TATATA
1 TATATA
31208 GTTTTGAAAG
Statistics
Matches: 154, Mismatches: 18, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
31 23 0.15
32 1 0.01
33 3 0.02
34 3 0.02
35 1 0.01
36 49 0.32
37 21 0.14
38 29 0.19
39 23 0.15
40 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (35 bp):
TATATATATATAGTTTTGAAAACATTTTGAAAACT
Found at i:31221 original size:29 final size:29
Alignment explanation
Indices: 31173--31229 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
31163 ACTTATATAG
*
31173 TATATAGTTTTAAAAACATTTTTGAAAAC
1 TATATAGTTTTAAAAACATTTTTCAAAAC
* *
31202 TATATAGTTTTGAAAGCATTTTTCAAAA
1 TATATAGTTTTAAAAACATTTTTCAAAA
31230 AATATATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (29 bp):
TATATAGTTTTAAAAACATTTTTCAAAAC
Found at i:31253 original size:66 final size:65
Alignment explanation
Indices: 31137--31273 Score: 168
Period size: 66 Copynumber: 2.1 Consensus size: 65
31127 ACATATATAT
* * ** * *
31137 TATATAATTTTGAAATCATTTTGAAAACTTATATAGTATATAGTTTTAAAA-ACATTTTTGAAAA
1 TATATAATTTTGAAAGCATTTTCAAAAAATATATAATATATAATTTTAAAATACATTTTTGAAAA
* **
31201 CTATATAGTTTTGAAAGCATTTTTCAAAAAATATATAATATATAATTTTAAAATATTTTTTTGAA
1 -TATATAATTTTGAAAGCA-TTTTCAAAAAATATATAATATATAATTTTAAAATACATTTTTGAA
31266 AA
64 AA
31268 TATATA
1 TATATA
31274 TTATATAGGT
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
65 16 0.26
66 34 0.56
67 11 0.18
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (65 bp):
TATATAATTTTGAAAGCATTTTCAAAAAATATATAATATATAATTTTAAAATACATTTTTGAAAA
Found at i:31364 original size:20 final size:21
Alignment explanation
Indices: 31320--31371 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
31310 ATCTTTATTA
*
31320 TTATTATTATTTATTTCCTTTT
1 TTATT-TTATTAATTTCCTTTT
31342 TTATTTTATTAATTTCC-TTT
1 TTATTTTATTAATTTCCTTTT
31362 TTATTTTATT
1 TTATTTTATT
31372 TTTCTTTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 13 0.45
21 11 0.38
22 5 0.17
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATTTTATTAATTTCCTTTT
Found at i:32650 original size:3 final size:3
Alignment explanation
Indices: 32644--32675 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
32634 TTTTGTTTTT
*
32644 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
32676 CTTTTGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:33178 original size:6 final size:6
Alignment explanation
Indices: 33167--33191 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
33157 CGAAAATTAC
33167 AAATTT AAATTT AAATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
33192 TTTATTCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:37645 original size:84 final size:84
Alignment explanation
Indices: 37521--38905 Score: 1707
Period size: 84 Copynumber: 16.7 Consensus size: 84
37511 GCTCAATGCT
* * *
37521 AGAAGGGCTATCTGCCAACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
37586 TACAGCATAACTCAAGGT-T
66 TGCAGCATAACTTAA-GTCG
* * * * * *
37605 AAAAAGGTTATCTGTCATA-AAAAGACCTTCGAGTTTGACTATGCTCAGCTCCAAGGCACATCAT
1 AGAAGGGTTATCTGCCA-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
*
37669 TTGTAGCATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCG
* * * *
37689 AGAAGGGTTATCTACCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATTATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
37754 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * * *
37773 AGAAGGGTTATCTG----CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
*
37834 TTGCAGCATAACTTAATTCG
65 TTGCAGCATAACTTAAGTCG
* * * *
37854 AAAAGAGTTATCTACCAACCAAAGACCTTCGAGTTCGAGTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
37919 TACAACATAGCTTAAGTTG
66 TGCAGCATAACTTAAGTCG
* * * * * * * * * * *
37938 ATAAAGGCTATCT----TCCAAAGACCCTCGAGTTCGATTACACTTAGCTTCGAGGGCATATCAT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* * * *
37999 TTACAACATAACTTAAGGCT
65 TTGCAGCATAACTTAAGTCG
* * *
38019 ATAAGGGTTATCTG-C-ACCAAAAGAACTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCAT
1 AGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
*
38082 TTGCATCATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCG
* **
38102 ATAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTTAAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
38166 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * *
38185 AGAAGGGTTATCTTCCAACCAAATACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
38250 TGCAGCATAAATTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * * *
38269 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGACATATAATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
38334 TGCAGCATAGCTTAAGCCG
66 TGCAGCATAACTTAAGTCG
*
38353 AGAAGGGTTATCTG----CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
38414 TGCAACATAACTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * *
38433 AAAAGGGTTATCTGCCAA-CAAAGACCTTCAAGTTCGACTACGCTCAGCTCAAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
38497 TGCAGTATAACTTAAGTTG
66 TGCAGCATAACTTAAGTCG
* * * *
38516 ATAAGGGCTATCTGCCAACTAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
38581 TGCAGCATAACTTAAGTTG
66 TGCAGCATAACTTAAGTCG
** * **
38600 AGAAGAATTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGAATGTCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
38665 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * *
38684 AGAATGGTTATCT----ACCAAAGACCTTCGAGTTCGACTACGATCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
38745 TGCAACATAACTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * *
38764 AGAAGGGTTATTTGCCAACCAAAGACCTTCGAGTTTGACTACGCTTAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
38829 TGCAGCATAGCTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * * * * *
38848 AAAAGGGCTATCTGCCAACCGAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
38906 AACCAAATTT
Statistics
Matches: 1124, Mismatches: 153, Indels: 48
0.85 0.12 0.04
Matches are distributed among these distances:
80 201 0.18
81 79 0.07
83 197 0.18
84 616 0.55
85 31 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (84 bp):
AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAACTTAAGTCG
Found at i:38345 original size:415 final size:413
Alignment explanation
Indices: 37539--38905 Score: 1692
Period size: 415 Copynumber: 3.3 Consensus size: 413
37529 TATCTGCCAA
* * * * * * * *
37539 CCAAATACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGT
1 CCAAAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTACAACATAACTTAAGGC
* * * *
37604 TAAAAAGGTTATCTGTCATAAAAAGACCTTCGAGTTTGACTATGCTCAGCTCCAAGGCACATCAT
66 TAAAAGGGTTATCTG-CACAAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * * * *
37669 TTGTAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTTGAGTTCGACTACGCT
130 TTGCATCATAACTTAAGTCGATAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTACGCT
* * *
37734 CAGCTCCAAGGCATATTATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATC-T---GCCAAAGAC
194 CAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGAC
* * * * * * *
37795 CTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAATTCGAAAAGA
259 CTTCGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
* * *
37860 GTTATCTACCAACCAAAGACCTTCGAGTTCGAGTACGCTCAGCTCCAAGGCACATCATTTACAAC
323 GTTATCT-CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAAC
* * *
37925 ATAGCTTAAGTTGATAAAGGCTATCTT
387 ATAGCTTAAGTCGAGAAAGGCTATCTG
* * * *
37952 CCAAAGACCCTCGAGTTCGATTACACTTAGCTTCGAGGGCATATCATTTACAACATAACTTAAGG
1 CCAAAGACCCTCGAGTTCGACTACACTCAGC-TCCAAGGCATATCATTTACAACATAACTTAAGG
* * * *
38017 CTATAAGGGTTATCTGCACCAAAAGAACTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCAT
65 CTAAAAGGGTTATCTGCACAAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
38082 TTGCATCATAACTTAAGTCGATAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTC
130 TTGCATCATAACTTAAGTCGATAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTC
** *
38147 AGCTTAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTTCCAACCAAATACC
195 AGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACC
*
38212 TTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAAATTAAGTCGAGAAGGGT
260 TTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
* * * *
38277 TATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGACATATAATTTGCAGCAT
325 TATCT-CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACAT
* * *
38342 AGCTTAAGCCGAGAAGGGTTATCTG
389 AGCTTAAGTCGAGAAAGGCTATCTG
* * * *
38367 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTC
1 CCAAAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTACAACATAACTTAAGGC
* * *
38432 GAAAAGGGTTATCTGC-CAACAAAGACCTTCAAGTTCGACTACGCTCAGCTCAAAGGCACATCAT
66 TAAAAGGGTTATCTGCACAA-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * *
38496 TTGCAGT-ATAACTTAAGTTGATAAGGGCTATCTGCCAACTAAAGACCTTCGAGTTTGACTACGC
130 TTGCA-TCATAACTTAAGTCGATAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTACGC
* * ** *
38560 TCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTTGAGAAGAATTATCTGCCAACCAAAGA
193 TCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGA
* * ** * *
38625 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGAATGTCATTTGCAGCATAGCTTAAGTCGAGAATG
258 CCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
*
38690 GTTATCT---ACCAAAGACCTTCGAGTTCGACTACGATCAGCTCCAAGGCATATCATTTGCAACA
323 GTTATCTCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACA
* * * *
38752 TAACTTAAGTCGAGAAGGGTTATTTG
388 TAGCTTAAGTCGAGAAAGGCTATCTG
* * * * * * * *
38778 CCAACCAAAGACCTTCGAGTTTGACTACGCTTAGCTCCAAGGCACATCATTTGCAGCATAGCTTA
1 ----CCAAAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTACAACATAACTTA
* * * * * * *
38843 AGTCGAAAAGGGCTATCTGC-CAACCGAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
62 AGGCTAAAAGGGTTATCTGCACAA--AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
38906 AACCAAATTT
Statistics
Matches: 837, Mismatches: 104, Indels: 23
0.87 0.11 0.02
Matches are distributed among these distances:
411 73 0.09
412 72 0.09
413 105 0.13
414 160 0.19
415 364 0.43
416 63 0.08
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (413 bp):
CCAAAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTACAACATAACTTAAGGC
TAAAAGGGTTATCTGCACAAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCATCATAACTTAAGTCGATAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCA
GCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCT
TCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTT
ATCTCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAG
CTTAAGTCGAGAAAGGCTATCTG
Found at i:38381 original size:331 final size:331
Alignment explanation
Indices: 37523--38905 Score: 1825
Period size: 331 Copynumber: 4.2 Consensus size: 331
37513 TCAATGCTAG
* *
37523 AAGGGCTATCTGCCAACCAAATACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTA
1 AAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * * * * *
37588 CAGCATAACTCAAGGTT-AAAAAGGTTATCTGTCATA-AAAAGACCTTCGAGTTTGACTATGCTC
66 CAGCATAACTTAA-GTTGAGAAAGGTTATCTGCCA-ACCAAAGACCTTCGAGTTCGACTACGCTC
* * *
37651 AGCTCCAAGGCACATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACC
129 AGCTCCAAGACATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT----ACCAAAGACC
* * * *
37716 TTTGAGTTCGACTACGCTCAGCTCCAAGGCATATTATTTGCAGCATAGCTTAAGTCGAGAAGGGT
190 TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGT
* * * *
37781 TATCTG-C--CAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCAT
255 TATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATTTGCAGCAT
* *
37843 AACTTAATTCGAA
319 AGCTTAAGTCGAA
* * * *
37856 AAGAGTTATCTACCAACCAAAGACCTTCGAGTTCGAGTACGCTCAGCTCCAAGGCACATCATTTA
1 AAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * * * * * * * *
37921 CAACATAGCTTAAGTTGATAAAGGCTATCT----TCCAAAGACCCTCGAGTTCGATTACACTTAG
66 CAGCATAACTTAAGTTGAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
* * * * * * * * *
37982 CTTCGAGGGCATATCATTTACAACATAACTTAAGGCTATAAGGGTTATCTGCACCAAAAGAACTT
131 C-TCCAAGACATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT--ACC-AAAGACCTT
* *
38047 CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCATCATAACTTAAGTCGATAAGGGTTA
192 CGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTA
*
38112 TCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTTAAAGGCACATCATTTGCAGCATAGC
257 TCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGC
*
38177 TTAAGTCGAG
322 TTAAGTCGAA
* * * * *
38187 AAGGGTTATCTTCCAACCAAATACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTG
1 AAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
* * * *
38252 CAGCATAAATTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAG
66 CAGCATAACTTAAGTTGAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
* * * *
38317 CTCCAAGACATATAATTTGCAGCATAGCTTAAGCCGAGAAGGGTTATCTGCCAAAGACCTTCGAG
131 CTCCAAGACATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAAAGACCTTCGAG
*
38382 TTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAAAAGGGTTATCTG
196 TTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTG
* * *
38447 CCAACAAAGACCTTCAAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGTATAACTTAA
261 CCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAA
* *
38512 GTTGAT
326 GTCGAA
* * *
38518 AAGGGCTATCTGCCAACTAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTG
1 AAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
*
38583 CAGCATAACTTAAGTTGAG-AAGAATTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
66 CAGCATAACTTAAGTTGAGAAAG-GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA
* * *
38647 GCTCCAAGGA-ATGTCATTTGCAGCATAGCTTAAGTCGAGAATGGTTATCTACCAAAGACCTTCG
130 GCTCCAA-GACATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAAAGACCTTCG
* *
38711 AGTTCGACTACGATCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATT
194 AGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATC
* * *
38776 TGCCAACCAAAGACCTTCGAGTTTGACTACGCTTAGCTCCAAGGCACATCATTTGCAGCATAGCT
259 TGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
38841 TAAGTCGAA
323 TAAGTCGAA
* * * *
38850 AAGGGCTATCTGCCAACCGAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
1 AAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
38906 AACCAAATTT
Statistics
Matches: 920, Mismatches: 116, Indels: 29
0.86 0.11 0.03
Matches are distributed among these distances:
328 3 0.00
329 95 0.10
330 42 0.05
331 492 0.53
332 144 0.16
333 80 0.09
334 38 0.04
335 26 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (331 bp):
AAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTA
CAGCATAACTTAAGTTGAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
CTCCAAGACATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAAAGACCTTCGAG
TTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTG
CCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAA
GTCGAA
Found at i:39480 original size:2 final size:2
Alignment explanation
Indices: 39473--39515 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
39463 TTTGTCCCAT
* * *
39473 TA TA TA TA TA TA TA TA TA TA TA TA CA TA CA TA TA AA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39514 TA
1 TA
39516 GTTTGAAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:39551 original size:37 final size:36
Alignment explanation
Indices: 39502--39845 Score: 185
Period size: 35 Copynumber: 9.8 Consensus size: 36
39492 ATATACATAC
* *
39502 ATATA-AATTATATAG-TTTGAAAACATTTTTAAAAA
1 ATATATAA-TATATAGTTTTTAAAACATTTTGAAAAA
* *
39537 ATATATGTAATATATAGTTTTGAAAACATATTTGAAAATGT
1 ATATA--TAATATATAGTTTTTAAAACAT-TTTGAAAA--A
* *
39578 TTATATATTATATAGTTTTTAAAACATTTTGAAAATA
1 ATATATAATATATAGTTTTTAAAACATTTTGAAAA-A
*
39615 A-ATATAATATATAGTTTTTAAAACGTTTTTG--AAA
1 ATATATAATATATAGTTTTTAAAAC-ATTTTGAAAAA
* *
39649 ATGTATATTATATAGTTTTTAAAACATTTTGAAAATA
1 ATATATAATATATAGTTTTTAAAACATTTTGAAAA-A
* ** *
39686 A-ATATAGT-T-T--TTTAAAAAAACATTTT-AAAAC
1 ATATATAATATATAGTTT-TTAAAACATTTTGAAAAA
* * * * *
39717 AGATATATTATAAAGTTTTGAAATCATTTTG-AAAA
1 ATATATAATATATAGTTTTTAAAACATTTTGAAAAA
* *
39752 CT-TAT-ATAGTATAGTTTTAAAAACATTTTTG----A
1 ATATATAATA-TATAGTTTTTAAAACA-TTTTGAAAAA
* * *
39784 A-A-AT--TATATAGTTTTGAAAGCATTTTTCAAAAA
1 ATATATAATATATAGTTTTTAAAACA-TTTTGAAAAA
* *
39817 ATATATAATATATA-ATTTTAAAATATTTT
1 ATATATAATATATAGTTTTTAAAACATTTT
39846 TTTTGAAAAT
Statistics
Matches: 241, Mismatches: 38, Indels: 60
0.71 0.11 0.18
Matches are distributed among these distances:
29 19 0.08
30 2 0.01
31 3 0.01
32 14 0.06
33 15 0.06
34 25 0.10
35 52 0.22
36 39 0.16
37 20 0.08
38 21 0.09
39 27 0.11
41 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (36 bp):
ATATATAATATATAGTTTTTAAAACATTTTGAAAAA
Found at i:39627 original size:36 final size:36
Alignment explanation
Indices: 39510--39787 Score: 195
Period size: 35 Copynumber: 7.8 Consensus size: 36
39500 ACATATAAAT
*
39510 TATATAG-TTTGAAAACATTTTTAAAA-AATATATGTAA
1 TATATAGTTTTGAAAACATTTTGAAAATAA-ATA--TAA
** *
39547 TATATAGTTTTGAAAACATATTTGAAAATGTTTATATAT
1 TATATAGTTTTGAAAACAT-TTTGAAAA--TAAATATAA
*
39586 TATATAGTTTTTAAAACATTTTGAAAATAAATATAA
1 TATATAGTTTTGAAAACATTTTGAAAATAAATATAA
* * * *
39622 TATATAGTTTTTAAAACGTTTTTGAAAAT--GTATAT
1 TATATAGTTTTGAAAAC-ATTTTGAAAATAAATATAA
* *
39657 TATATAGTTTTTAAAACATTTTGAAAATAAATATAG
1 TATATAGTTTTGAAAACATTTTGAAAATAAATATAA
** * * *
39693 T-T-T--TTTAAAAAAACATTTT-AAAACAGATATAT
1 TATATAGTTT-TGAAAACATTTTGAAAATAAATATAA
* *
39725 TATAAAGTTTTGAAATCATTTTGAAAACT---TAT-A
1 TATATAGTTTTGAAAACATTTTGAAAA-TAAATATAA
*
39758 TAGTATAGTTTTAAAAACATTTTTGAAAAT
1 TA-TATAGTTTTGAAAACA-TTTTGAAAAT
39788 TATATAGTTT
Statistics
Matches: 196, Mismatches: 28, Indels: 37
0.75 0.11 0.14
Matches are distributed among these distances:
32 14 0.07
33 13 0.07
34 28 0.14
35 40 0.20
36 35 0.18
37 17 0.09
38 19 0.10
39 27 0.14
41 3 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (36 bp):
TATATAGTTTTGAAAACATTTTGAAAATAAATATAA
Found at i:39679 original size:34 final size:33
Alignment explanation
Indices: 39547--39792 Score: 196
Period size: 35 Copynumber: 7.0 Consensus size: 33
39537 ATATATGTAA
*
39547 TATATAGTTTTGAAAACATATTTGAAAATGTTTATATAT
1 TATATAGTTTTTAAAACAT-TTTGAAAA----T-TATAT
*
39586 TATATAGTTTTTAAAACATTTTGAAAATAAATATAA
1 TATATAGTTTTTAAAACATTTTGAAAAT---TATAT
*
39622 TATATAGTTTTTAAAACGTTTTTGAAAATGTATAT
1 TATATAGTTTTTAAAAC-ATTTTGAAAAT-TATAT
39657 TATATAGTTTTTAAAACATTTTGAAAA-TA-A-
1 TATATAGTTTTTAAAACATTTTGAAAATTATAT
* *
39687 -ATATAGTTTTTTAAAAAAACATTTTAAAACAGATATAT
1 TATATAG-TTTTT---AAAACATTTTGAAA-A-TTATAT
* * *
39725 TATAAAGTTTTGAAATCATTTTGAAAACTTATA-
1 TATATAGTTTTTAAAACATTTTGAAAA-TTATAT
*
39758 TAGTATAGTTTTAAAAACATTTTTGAAAATTATAT
1 TA-TATAGTTTTTAAAACA-TTTTGAAAATTATAT
39793 AGTTTTGAAA
Statistics
Matches: 175, Mismatches: 16, Indels: 36
0.77 0.07 0.16
Matches are distributed among these distances:
29 6 0.03
30 5 0.03
31 1 0.01
32 2 0.01
33 15 0.09
34 34 0.19
35 42 0.24
36 24 0.14
37 11 0.06
38 12 0.07
39 23 0.13
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (33 bp):
TATATAGTTTTTAAAACATTTTGAAAATTATAT
Found at i:39687 original size:71 final size:72
Alignment explanation
Indices: 39508--39691 Score: 248
Period size: 71 Copynumber: 2.5 Consensus size: 72
39498 ATACATATAA
* *
39508 ATTATATAG-TTTGAAAACATTTTTAAAA-AATATATGTAATATATAGTTTTGAAAACATATTTG
1 ATTATATAGTTTTTAAAACATTTTGAAAATAA-ATA--TAATATATAGTTTTGAAAACATATTTG
39571 AAAATGTTTATAT
63 AAAATG--T-TAT
* * *
39584 ATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAACGTTTTTGAAA
1 ATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTGAAAACATATTTGAAA
39649 ATG-TAT
66 ATGTTAT
39655 ATTATATAGTTTTTAAAACATTTTGAAAATAAATATA
1 ATTATATAGTTTTTAAAACATTTTGAAAATAAATATA
39692 GTTTTTTAAA
Statistics
Matches: 101, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
71 40 0.40
75 30 0.30
76 9 0.09
77 20 0.20
78 2 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (72 bp):
ATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTGAAAACATATTTGAAA
ATGTTAT
Found at i:39757 original size:29 final size:29
Alignment explanation
Indices: 39724--39809 Score: 75
Period size: 29 Copynumber: 2.8 Consensus size: 29
39714 AACAGATATA
*
39724 TTATAAAGTTTTGAAATCATTTTGAAAACT
1 TTATAAAGTTTTGAAAACATTTTGAAAA-T
*
39754 TATATAGTATAGTTTTAAAAACATTTTTGAAAA-
1 T-TATA--A-AGTTTTGAAAACA-TTTTGAAAAT
* *
39787 TTATATAGTTTTGAAAGCATTTT
1 TTATAAAGTTTTGAAAACATTTT
39810 TCAAAAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
28 4 0.09
29 11 0.24
30 1 0.02
31 4 0.09
32 4 0.09
33 2 0.04
34 11 0.24
35 9 0.20
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (29 bp):
TTATAAAGTTTTGAAAACATTTTGAAAAT
Found at i:39758 original size:102 final size:104
Alignment explanation
Indices: 39598--39798 Score: 259
Period size: 102 Copynumber: 2.0 Consensus size: 104
39588 TATAGTTTTT
* * * *
39598 AAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAACGTTTTTGAAAATGTATATTA-TAT
1 AAAACATTTTGAAAACAAATATAATATAAAGTTTTGAAAACGATTTTGAAAATGTATA-TAGTAT
*
39662 AGTTTTTAAAACA-TTTTGAAAATAAATATAGTTTTTTAAA
65 AGTTTTAAAAACATTTTTGAAAAT-AATATAGTTTTTTAAA
* * *
39702 AAAACATTTT-AAAACAGATATATTATAAAGTTTTGAAATC-ATTTTGAAAACT-TATATAGTAT
1 AAAACATTTTGAAAACAAATATAATATAAAGTTTTGAAAACGATTTTGAAAA-TGTATATAGTAT
*
39764 AGTTTTAAAAACATTTTTGAAAATTATATAGTTTT
65 AGTTTTAAAAACATTTTTGAAAATAATATAGTTTT
39799 GAAAGCATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 38 0.45
103 35 0.41
104 10 0.12
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (104 bp):
AAAACATTTTGAAAACAAATATAATATAAAGTTTTGAAAACGATTTTGAAAATGTATATAGTATA
GTTTTAAAAACATTTTTGAAAATAATATAGTTTTTTAAA
Found at i:39831 original size:102 final size:99
Alignment explanation
Indices: 39584--39831 Score: 240
Period size: 102 Copynumber: 2.4 Consensus size: 99
39574 ATGTTTATAT
* * *
39584 ATTATATAGTTTTTAAAACATTTTGAAAATAAATATAATATAT--AGTTTTTAAAACGTTTTTGA
1 ATTATATAGTTTTAAAAACATTTT-AAAA-AAATATAATATATAAAGTTTTGAAAACGATTTTGA
*
39647 AAATGTATATTATATAGTTTTTAAAACATTTTGAAA
64 AAATGTATATTATATAGTTTTAAAAACATTTTGAAA
* * *
39683 ATAAATATAGTTTTTTAAAAAAACATTTTAAAACAGATAT-AT-TATAAAGTTTTGAAATC-ATT
1 AT-TATATAG--TTTT--AAAAACATTTTAAAA-AAATATAATATATAAAGTTTTGAAAACGATT
39745 TTGAAAACT-TATA-TAGTATAGTTTTAAAAACATTTTTGAAA
60 TTGAAAA-TGTATATTA-TATAGTTTTAAAAACA-TTTTGAAA
* *
39786 ATTATATAGTTTTGAAAGCATTTTTCAAAAAATATATAATATATAA
1 ATTATATAGTTTTAAAAACA-TTTT-AAAAAA-ATATAATATATAA
39832 TTTTAAAATA
Statistics
Matches: 122, Mismatches: 12, Indels: 27
0.76 0.07 0.17
Matches are distributed among these distances:
98 5 0.04
99 7 0.06
100 18 0.15
101 7 0.06
102 45 0.37
103 30 0.25
104 10 0.08
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.43
Consensus pattern (99 bp):
ATTATATAGTTTTAAAAACATTTTAAAAAAATATAATATATAAAGTTTTGAAAACGATTTTGAAA
ATGTATATTATATAGTTTTAAAAACATTTTGAAA
Found at i:39925 original size:36 final size:37
Alignment explanation
Indices: 39885--39955 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 37
39875 GGAAAATATT
39885 TTATTTTA-T-ATTT-ATTATTATTATTTATTTCTTTTC
1 TTATTTTATTAATTTCATTATTATT-TTT-TTTCTTTTC
*
39921 TTATTTTATTAATTTCATTTTTATTTTTTTTCTTT
1 TTATTTTATTAATTTCATTATTATTTTTTTTCTTT
39956 CCAGGTCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 8 0.26
37 8 0.26
38 7 0.23
39 8 0.26
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.75
Consensus pattern (37 bp):
TTATTTTATTAATTTCATTATTATTTTTTTTCTTTTC
Found at i:39935 original size:21 final size:20
Alignment explanation
Indices: 39894--39947 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
39884 TTTATTTTAT
*
39894 ATTTATTATTATTATTTATTTC
1 ATTT-TTATT-TTATTAATTTC
*
39916 TTTTCTTATTTTATTAATTTC
1 ATTT-TTATTTTATTAATTTC
39937 ATTTTTATTTT
1 ATTTTTATTTT
39948 TTTTCTTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.25
21 13 0.46
22 8 0.29
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTATTTTATTAATTTC
Found at i:41164 original size:7 final size:6
Alignment explanation
Indices: 41147--41271 Score: 58
Period size: 6 Copynumber: 19.8 Consensus size: 6
41137 TCTACGTATC
*
41147 ATTTTT ATTTTT ACTTTT ATTTTT -TTTCTT CATTTTGT -TTTTGT -TTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT-TT -ATTTT-T ATTTT-T ATTTTT
* * * * * * *
41196 AATTATT ATTGTT ATTATT ATTATT ATTGTT ATTATT ATTATT ATTATTCT
1 -ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT-TT-T
* *
41247 TTTGTTT ATTTCTT TTTTTT ATTTT
1 ATT-TTT ATTT-TT ATTTTT ATTTT
41272 ATCTTGTTTC
Statistics
Matches: 97, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
5 4 0.04
6 70 0.72
7 14 0.14
8 9 0.09
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.74
Consensus pattern (6 bp):
ATTTTT
Found at i:41205 original size:3 final size:3
Alignment explanation
Indices: 41197--41244 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
41187 TTGTTTTTTA
* *
41197 ATT ATT ATT GTT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41245 CTTTTGTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41220 original size:18 final size:18
Alignment explanation
Indices: 41197--41241 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
41187 TTGTTTTTTA
41197 ATTATTATTGTTATTATT
1 ATTATTATTGTTATTATT
41215 ATTATTATTGTTATTATT
1 ATTATTATTGTTATTATT
41233 ATTATTATT
1 ATTATTATT
41242 ATTCTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
ATTATTATTGTTATTATT
Found at i:44594 original size:20 final size:20
Alignment explanation
Indices: 44557--44594 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44547 TACTGAATTA
* *
44557 ATAAAATAAATTACATTTTC
1 ATAAAATAAAATAAATTTTC
44577 ATAAAATAAAATAAATTT
1 ATAAAATAAAATAAATTT
44595 CAGTGTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAAATAAAATAAATTTTC
Found at i:48396 original size:18 final size:17
Alignment explanation
Indices: 48357--48399 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
48347 ATTATATAGA
48357 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
48373 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
48391 TATTATTAT
1 TATTATTAT
48400 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:48911 original size:2 final size:2
Alignment explanation
Indices: 48904--48937 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
48894 TAATACTTTG
48904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48938 TTTCTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53598 original size:182 final size:183
Alignment explanation
Indices: 53121--53656 Score: 950
Period size: 183 Copynumber: 2.9 Consensus size: 183
53111 ATTAAATCCG
53121 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
53186 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTTGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
53251 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* *
53304 TAAAGCTGAGCTATTCCACTAAGGTAATTGGTTATAGAGGAAACTCGAAATCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
53369 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTATTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
53434 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTTAGTGATTTGT-CCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
53486 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
53551 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGTAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
53615 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
53657 TAAACCTGAT
Statistics
Matches: 336, Mismatches: 16, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
181 1 0.00
182 163 0.49
183 172 0.51
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:54876 original size:36 final size:36
Alignment explanation
Indices: 54836--54952 Score: 108
Period size: 36 Copynumber: 3.1 Consensus size: 36
54826 ATACTTTGTC
*
54836 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGATTGTTTTTCTCGAAAGAAGATTTATT
** ** * * *
54872 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTC
1 TCACTTGAGATTGTTTTTCTCGAAAGAAGATTTATT
* *
54908 TCGCTTGAGATTGTTTTCACTCGAAAGAAGGCATTTCATT
1 TCACTTGAGATTGTTTT-TCTCGAAAGAA-G-ATTT-ATT
54948 TCACT
1 TCACT
54953 CAATGCTATT
Statistics
Matches: 59, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
36 42 0.71
37 7 0.12
38 1 0.02
39 4 0.07
40 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (36 bp):
TCACTTGAGATTGTTTTTCTCGAAAGAAGATTTATT
Found at i:54889 original size:72 final size:74
Alignment explanation
Indices: 54796--54955 Score: 202
Period size: 72 Copynumber: 2.2 Consensus size: 74
54786 ATACAGATGA
* * * * *
54796 TTATCTCACTCAAATTTTTTTTCTTAAAATATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCGA
1 TTATTTCACTCAAATTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACTGTTTTCACTCGA
54859 AAGAA-G-AT
65 AAGAAGGCAT
* *
54867 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGATTGTTTTCACTCGA
1 TTATTTCACTCAA-ATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACTGTTTTCACTCGA
54932 AAGAAGGCAT
65 AAGAAGGCAT
54942 TTCATTTCACTCAA
1 TT-ATTTCACTCAA
54956 TGCTATTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
71 13 0.17
72 37 0.49
73 10 0.13
74 1 0.01
75 4 0.05
76 11 0.14
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (74 bp):
TTATTTCACTCAAATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACTGTTTTCACTCGAA
AGAAGGCAT
Found at i:55071 original size:104 final size:104
Alignment explanation
Indices: 54975--55358 Score: 439
Period size: 104 Copynumber: 3.9 Consensus size: 104
54965 TTTTAAGAAT
*
54975 ATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAAAGAAAATTTCGTCTCCCTTGAGACAGTTTCT
1 ATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAAAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
*** * *
55040 CTTGAAAACATTTCCCTTG--AA-A-TT--ATT----T-
66 CTTGAAAACATAAACATTGAAAACATTTCCCTTGAAATG
* * *
55068 -TTTTCTC-T-CCTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
1 ATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAAAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
55130 CTT-AAAACATAAACATTGAAAACATTTCCCTTGAAATG
66 CTTGAAAACATAAACATTGAAAACATTTCCCTTGAAATG
* * * *
55168 ATTTTTTTTTCTCTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGACAGTTTC
1 ATTTTATCTT-GCTTGAGATAGTTTCCCTCGAAAAAGAAAATTTTGTCTCCCTTGAGACAGTTTC
55233 TCTTG-AAACATAAACATTGAAAACATTTCCCTTGAAATG
65 TCTTGAAAACATAAACATTGAAAACATTTCCCTTGAAATG
* * *
55272 AATTTTATCTCGCTTGAGATAGTTTCCCTTG-AAACG--AATTTTGTCTCCCTTGAGACAGTTTC
1 -ATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAAAGAAAATTTTGTCTCCCTTGAGACAGTTTC
** *
55334 TC-TCCAAACATAAACTTTGAAAACA
65 TCTTGAAAACATAAACATTGAAAACA
55359 ATTTAACGAA
Statistics
Matches: 252, Mismatches: 21, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
89 11 0.04
90 54 0.21
91 3 0.01
92 7 0.03
93 2 0.01
95 2 0.01
99 1 0.00
100 1 0.00
101 52 0.21
102 1 0.00
103 3 0.01
104 108 0.43
105 7 0.03
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (104 bp):
ATTTTATCTTGCTTGAGATAGTTTCCCTCGAAAAAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
CTTGAAAACATAAACATTGAAAACATTTCCCTTGAAATG
Found at i:55305 original size:36 final size:36
Alignment explanation
Indices: 55258--55333 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
55248 ATTGAAAACA
* * *
55258 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
55294 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
55330 TTTC
1 TTTC
55334 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:55690 original size:106 final size:106
Alignment explanation
Indices: 55533--56590 Score: 1707
Period size: 106 Copynumber: 10.0 Consensus size: 106
55523 ATATCGTGAC
* * * * *
55533 ACTCGAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
55598 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
55639 ACTCCAGACAATGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAAATTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
55704 AATTTCAGTTCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
55745 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
55810 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
55851 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
55916 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
55957 ACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
56022 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
56063 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
56128 AATTTCTGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
56169 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
56234 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
56275 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
56340 AATTTCAGAGCCAATTTCAACTTCATAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
56381 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
56446 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * ** *
56487 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGATCGCTTCTTGTCAAC-AA-AA-TT-TC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
56548 -A-TCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
56587 ACTC
1 ACTC
56591 GAAACAATGC
Statistics
Matches: 895, Mismatches: 56, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
100 38 0.04
101 1 0.00
102 1 0.00
103 2 0.00
104 2 0.00
105 2 0.00
106 849 0.95
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:57227 original size:37 final size:37
Alignment explanation
Indices: 57133--57229 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
57123 CATTTTCGTC
57133 CTACTAGGATTCAAACTCCTAAAAATAAGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAAAATT
* * * * *
57170 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAAAATT
* * *
57207 CTACTAAGATTTAAATTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
57230 GATAGGATCC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAAGATAAAATT
Found at i:57895 original size:18 final size:16
Alignment explanation
Indices: 57881--57938 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 16
57871 ATCTTATATA
57881 TTTATTATTTTTTATT
1 TTTATTATTTTTTATT
*
57897 TTT-TTATTTTTT-TA
1 TTTATTATTTTTTATT
* *
57911 TTCATTA-TTATTA-T
1 TTTATTATTTTTTATT
57925 TTTATTATTTTTTA
1 TTTATTATTTTTTA
57939 AAAAAAACAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
14 13 0.39
15 17 0.52
16 3 0.09
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTATTTTTTATT
Found at i:57899 original size:8 final size:8
Alignment explanation
Indices: 57888--57936 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
57878 ATATTTATTA
57888 TTTTTTAT
1 TTTTTTAT
57896 TTTTTTAT
1 TTTTTTAT
57904 TTTTTTAT
1 TTTTTTAT
*
57912 TCATTATTAT
1 T--TTTTTAT
*
57922 TATTTTAT
1 TTTTTTAT
57930 TATTTTT
1 T-TTTTT
57937 TAAAAAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 23 0.68
9 4 0.12
10 7 0.21
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTAT
Found at i:57911 original size:48 final size:43
Alignment explanation
Indices: 57815--57938 Score: 108
Period size: 48 Copynumber: 2.7 Consensus size: 43
57805 TATATACCTA
* *
57815 TTATTAAATA-TATATATCTTAATTATTTTTTGATTATTTCTTTAT
1 TTATTAATTATTATATAT-TT-ATTATTTTTT-ATTATTTATTTAT
* *
57860 TTATGTAATATATCTTATATATTTATTATTTTTTATTTTTTTATTTTT
1 TTAT-TAAT-TA--TTATATATTTATTATTTTTTA-TTATTTATTTAT
*
57908 TTATTCATTATTAT-TATTTTATTATTTTTTA
1 TTATTAATTATTATATA-TTTATTATTTTTTA
57939 AAAAAAACAT
Statistics
Matches: 67, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
43 2 0.03
44 18 0.27
45 4 0.06
46 5 0.07
47 6 0.09
48 23 0.34
49 2 0.03
50 7 0.10
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (43 bp):
TTATTAATTATTATATATTTATTATTTTTTATTATTTATTTAT
Found at i:58133 original size:2 final size:2
Alignment explanation
Indices: 58126--58177 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
58116 TAATGCTTTG
58126 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58168 AT AT AT AT AT
1 AT AT AT AT AT
58178 TTTTTTTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61301 original size:20 final size:20
Alignment explanation
Indices: 61276--61330 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
61266 CATATTCCCT
61276 GATAATCTTACATTCTCACC
1 GATAATCTTACATTCTCACC
*
61296 GATAATCTTACATTATCACC
1 GATAATCTTACATTCTCACC
*
61316 GATAATCTTATATTC
1 GATAATCTTACATTC
61331 CATAAATCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (20 bp):
GATAATCTTACATTCTCACC
Found at i:61885 original size:24 final size:24
Alignment explanation
Indices: 61858--61912 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
61848 ATGTGTCATC
**
61858 TTTATAAAATTTTAAAAAT-TTAT
1 TTTATAAAAACTTAAAAATATTAT
61881 ATTTA-AAAAACTTAAAAATATTAT
1 -TTTATAAAAACTTAAAAATATTAT
61905 TTT-TAAAA
1 TTTATAAAA
61913 CCCTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTATAAAAACTTAAAAATATTAT
Found at i:71745 original size:21 final size:20
Alignment explanation
Indices: 71721--71759 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
71711 CCCTTACGCC
*
71721 TTAAAATTATTATTTTTTTTA
1 TTAAAATCATT-TTTTTTTTA
*
71742 TTAATATCATTTTTTTTT
1 TTAAAATCATTTTTTTTT
71760 ATTTTGAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (20 bp):
TTAAAATCATTTTTTTTTTA
Found at i:75405 original size:21 final size:22
Alignment explanation
Indices: 75366--75410 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
75356 TCCATTTTTC
*
75366 ATAATCTAGTTTTCTAAAAATT
1 ATAATCCAGTTTTCTAAAAATT
* *
75388 ATAATCCATTTTTC-AAAATTT
1 ATAATCCAGTTTTCTAAAAATT
75409 AT
1 AT
75411 TTTCAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAATCCAGTTTTCTAAAAATT
Found at i:78816 original size:25 final size:22
Alignment explanation
Indices: 78768--78835 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 22
78758 TAATAAACAA
78768 TTAA-ATAATTTTTTAAATATT
1 TTAATATAATTTTTTAAATATT
78789 TTAAATATAACTTTTTTAGAATGA-T
1 TT-AATATAA-TTTTTTA-AAT-ATT
*
78814 TTAATATAAATTTTATAAATAT
1 TTAATAT-AATTTTTTAAATAT
78836 ATATATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
21 2 0.05
22 3 0.08
23 7 0.18
24 18 0.46
25 8 0.21
26 1 0.03
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
TTAATATAATTTTTTAAATATT
Found at i:80764 original size:42 final size:43
Alignment explanation
Indices: 80717--80809 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 43
80707 ATATTTTAAT
* * * *
80717 TAATTAATTCATAAAATATAACGATCGCGCTAA-TAATAATTA
1 TAATTAACTAATAAAATATAACAATCGCACTAACTAATAATTA
80759 TAATTAACTAATAAAATATAACAATCGCACTAACTAATAATTA
1 TAATTAACTAATAAAATATAACAATCGCACTAACTAATAATTA
*
80802 CAATTAAC
1 TAATTAAC
80810 AATTGCATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 29 0.64
43 16 0.36
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (43 bp):
TAATTAACTAATAAAATATAACAATCGCACTAACTAATAATTA
Found at i:80790 original size:22 final size:22
Alignment explanation
Indices: 80727--80791 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
80717 TAATTAATTC
* *
80727 ATAAAATATAACGATCGCGCTA
1 ATAAAATATAACAATCGCACTA
* **
80749 ATAATAAT-T-ATAAT-TAACTA
1 ATAA-AATATAACAATCGCACTA
80769 ATAAAATATAACAATCGCACTA
1 ATAAAATATAACAATCGCACTA
80791 A
1 A
80792 CTAATAATTA
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
19 3 0.10
20 8 0.26
21 7 0.23
22 10 0.32
23 3 0.10
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (22 bp):
ATAAAATATAACAATCGCACTA
Found at i:81841 original size:24 final size:24
Alignment explanation
Indices: 81804--81868 Score: 121
Period size: 24 Copynumber: 2.7 Consensus size: 24
81794 AGGAGAAATG
81804 GAGCCTTTTGCATGGTTATGGAGGA
1 GAGCC-TTTGCATGGTTATGGAGGA
81829 GAGCCTTTGCATGGTTATGGAGGA
1 GAGCCTTTGCATGGTTATGGAGGA
81853 GAGCCTTTGCATGGTT
1 GAGCCTTTGCATGGTT
81869 TTATATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 35 0.88
25 5 0.12
ACGTcount: A:0.18, C:0.14, G:0.35, T:0.32
Consensus pattern (24 bp):
GAGCCTTTGCATGGTTATGGAGGA
Found at i:86443 original size:17 final size:18
Alignment explanation
Indices: 86404--86444 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
86394 AATCATTTTC
*
86404 TTGTT-ATTATATTCTCT
1 TTGTTCATTATATTCTAT
86421 TATGTTCATTAT-TTCTAT
1 T-TGTTCATTATATTCTAT
86439 TTGTTC
1 TTGTTC
86445 TTTTTCCCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 10 0.48
19 5 0.24
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.63
Consensus pattern (18 bp):
TTGTTCATTATATTCTAT
Found at i:92937 original size:13 final size:13
Alignment explanation
Indices: 92913--92949 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
92903 TTTTTATTTA
92913 ATATTTTA--ATT
1 ATATTTTAGTATT
92924 ATATTTTAGTATT
1 ATATTTTAGTATT
92937 ATATTTTAGTATT
1 ATATTTTAGTATT
92950 TAAAGTAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.33
13 16 0.67
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (13 bp):
ATATTTTAGTATT
Found at i:93437 original size:24 final size:25
Alignment explanation
Indices: 93384--93437 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
93374 TGTCATCTGT
93384 TCGAACATAAATGAACGGACATAAA
1 TCGAACATAAATGAACGGACATAAA
*
93409 T-GAACATAAATG-A-GGAACGTAAA
1 TCGAACATAAATGAACGG-ACATAAA
93432 TCGAAC
1 TCGAAC
93438 GTTCACGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 8 0.31
24 15 0.58
25 1 0.04
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.17
Consensus pattern (25 bp):
TCGAACATAAATGAACGGACATAAA
Done.