Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006358.1 Hibiscus syriacus cultivar Beakdansim tig00015240_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: 153993
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:883 original size:17 final size:17
Alignment explanation
Indices: 858--896 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
848 ATGATAGAAA
*
858 TGGAGCACCCAAGCCAC
1 TGGACCACCCAAGCCAC
*
875 TGGACCACCCAAGCTAC
1 TGGACCACCCAAGCCAC
892 TGGAC
1 TGGAC
897 TAAATGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.38, G:0.23, T:0.10
Consensus pattern (17 bp):
TGGACCACCCAAGCCAC
Found at i:1670 original size:18 final size:18
Alignment explanation
Indices: 1647--1681 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1637 TTGGACCGAA
*
1647 CAGAGTTAGGTTTTTGAC
1 CAGAGTCAGGTTTTTGAC
*
1665 CAGAGTCATGTTTTTGA
1 CAGAGTCAGGTTTTTGA
1682 AGATTGCTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (18 bp):
CAGAGTCAGGTTTTTGAC
Found at i:2351 original size:20 final size:20
Alignment explanation
Indices: 2326--2372 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2316 GGTGCTCGAT
2326 GAAACAAACTTCTTGTTGTG
1 GAAACAAACTTCTTGTTGTG
*
2346 GAAACAAACTTCTTGTTGTT
1 GAAACAAACTTCTTGTTGTG
2366 GAAACAA
1 GAAACAA
2373 CAAGTCTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (20 bp):
GAAACAAACTTCTTGTTGTG
Found at i:12637 original size:60 final size:61
Alignment explanation
Indices: 12543--12658 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 61
12533 AATAGTCGGT
** * * * * *
12543 GACCATTTTTGTAACTTTTTATAGTCGAAGGACTCAATAAAGTAATTTCTTATAGTTAGAG
1 GACCATTTTTGTAACTTTACATAGTCCAAGGACTCAACAAAATAATATCCTATAGTTAGAG
12604 GACCA-TTTTGTAACTTTACATAGTCC-AGAGACTCAACAAAATAATATCCTATAGT
1 GACCATTTTTGTAACTTTACATAGTCCAAG-GACTCAACAAAATAATATCCTATAGT
12659 CAAGGTACAG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
59 2 0.04
60 40 0.85
61 5 0.11
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (61 bp):
GACCATTTTTGTAACTTTACATAGTCCAAGGACTCAACAAAATAATATCCTATAGTTAGAG
Found at i:21967 original size:32 final size:32
Alignment explanation
Indices: 21931--21992 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
21921 TTCGGTGAGT
* *
21931 TTAACGAA-CAATGTGCTTAATGAGCAACGAAC
1 TTAAC-AAGCAATGAGCTTAACGAGCAACGAAC
*
21963 TTAACAAGTAATGAGCTTAACGAGCAACGA
1 TTAACAAGCAATGAGCTTAACGAGCAACGA
21993 GTCGAGCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (32 bp):
TTAACAAGCAATGAGCTTAACGAGCAACGAAC
Found at i:25293 original size:20 final size:20
Alignment explanation
Indices: 25268--25305 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25258 TGAAAAATTA
25268 ATTGGTACATCGATGCATGG
1 ATTGGTACATCGATGCATGG
* *
25288 ATTGGTGCATCGGTGCAT
1 ATTGGTACATCGATGCAT
25306 CACTTTGAAA
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:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
ATTGGTACATCGATGCATGG
Found at i:25296 original size:91 final size:91
Alignment explanation
Indices: 25134--25307 Score: 219
Period size: 91 Copynumber: 1.9 Consensus size: 91
25124 GGTGCACTAA
* * ** *
25134 GAGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTC
1 GAGTGCATCGATGCATAAAATGAATTCGATGTTTTGAAAAAAACTGAGTACATCGATGCATGGTC
*
25199 TTGTGCATCGATGCATCAAATGCATT
66 TGGTGCATCGATGCATCAAATGCATT
* *
25225 GAGTGCATCGATGCATAAAATGAATTTGATG-TTTGAAAAATTAATTG-GTACATCGATGCATGG
1 GAGTGCATCGATGCATAAAATGAATTCGATGTTTTGAAAAA--AACTGAGTACATCGATGCATGG
*
25288 AT-TGGTGCATCGGTGCATCA
64 -TCTGGTGCATCGATGCATCA
25308 CTTTGAAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
90 9 0.13
91 59 0.83
92 3 0.04
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (91 bp):
GAGTGCATCGATGCATAAAATGAATTCGATGTTTTGAAAAAAACTGAGTACATCGATGCATGGTC
TGGTGCATCGATGCATCAAATGCATT
Found at i:26261 original size:21 final size:21
Alignment explanation
Indices: 26237--26280 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
26227 CCAGAGGAGG
* *
26237 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
* *
26258 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
26279 AG
1 AG
26281 CTCTCGGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:30232 original size:22 final size:23
Alignment explanation
Indices: 30207--30266 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
30197 AACAAAATGC
30207 TAATAAAAAAAAAAAATAAT-AA
1 TAATAAAAAAAAAAAATAATAAA
*
30229 TAATAATGAAAGAAAGAAATAATAGAA
1 TAATAA--AAA-AAAAAAATAATA-AA
*
30256 TAATAATAAAA
1 TAATAAAAAAA
30267 GGTTAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 6 0.19
24 5 0.16
25 12 0.39
27 8 0.26
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (23 bp):
TAATAAAAAAAAAAAATAATAAA
Found at i:31446 original size:15 final size:14
Alignment explanation
Indices: 31414--31442 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31404 CTAAAAAAAC
31414 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
31428 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
31442 A
1 A
31443 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:31520 original size:33 final size:31
Alignment explanation
Indices: 31504--31615 Score: 104
Period size: 33 Copynumber: 3.5 Consensus size: 31
31494 ATATTTTTTT
31504 AAACTATATATTATATTTAAAAAAGTTTTCA
1 AAACTATATATTATATTTAAAAAAGTTTTCA
* *
31535 AAACTATAT-TATATAGTTTTCAAAATGTTTT-A
1 AAACTATATAT-TATA--TTTAAAAAAGTTTTCA
* * *
31567 AAAATATTATATAAGT-TTTAAAAAACGTTTTTA
1 AAACTA-TATATTA-TATTTAAAAAA-GTTTTCA
31600 AAACTATATATTATAT
1 AAACTATATATTATAT
31616 AATTTATTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
30 1 0.02
31 21 0.33
32 18 0.28
33 22 0.34
34 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (31 bp):
AAACTATATATTATATTTAAAAAAGTTTTCA
Found at i:31610 original size:32 final size:31
Alignment explanation
Indices: 31498--31610 Score: 113
Period size: 31 Copynumber: 3.5 Consensus size: 31
31488 TCAAAAATAT
* *
31498 TTTTTTAAACTATATATTA-TATTTAAAAAAG
1 TTTTTAAAACTATATATAAGT-TTTAAAAAAG
* * *
31529 TTTTCAAAACTATATTATATAGTTTTCAAAATG
1 TTTTTAAAACTATA-TATA-AGTTTTAAAAAAG
*
31562 -TTTTAAAAATATTATATAAGTTTTAAAAAACG
1 TTTTTAAAACTA-TATATAAGTTTTAAAAAA-G
31594 TTTTTAAAACTATATAT
1 TTTTTAAAACTATATAT
31611 TATATAATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
31 22 0.33
32 22 0.33
33 21 0.32
34 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (31 bp):
TTTTTAAAACTATATATAAGTTTTAAAAAAG
Found at i:31614 original size:37 final size:37
Alignment explanation
Indices: 31519--31763 Score: 201
Period size: 37 Copynumber: 6.8 Consensus size: 37
31509 ATATATTATA
*
31519 TTTAAAAAA-GTTTTCAAAAC--TATATTATAT-AGT
1 TTTAAAAAATGTTTTTAAAACTATATATTATATAAGT
*
31552 TTT-CAAAATG-TTTT-AAA--A-ATATTATATAAGT
1 TTTAAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
31583 TTTAAAAAACGTTTTTAAAACTATATATTATATAATT
1 TTTAAAAAATGTTTTTAAAACTATATATTATATAAGT
** *
31620 TATTCAAAATTTTTTTTTTAAAACTATATATTATATAAGT
1 T-TT-AAAA-AATGTTTTTAAAACTATATATTATATAAGT
* * *
31660 TTT-TAAAATGATTTTAAAACTATATGTTATATATA-T
1 TTTAAAAAATGTTTTTAAAACTATATATTATATA-AGT
** * *
31696 TTTCTAAAATGTTTTAAAAACTATATGTTATAT-AGT
1 TTTAAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
31732 TTTCAAAAAATATTTTAAAAAACTATATATTA
1 TTT-AAAAAATGTTTT-TAAAACTATATATTA
31764 CCCATATTTT
Statistics
Matches: 173, Mismatches: 22, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
30 9 0.05
31 9 0.05
32 12 0.07
33 8 0.05
34 3 0.02
35 1 0.01
36 31 0.18
37 52 0.30
38 16 0.09
39 6 0.03
40 26 0.15
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAAAAAATGTTTTTAAAACTATATATTATATAAGT
Found at i:31710 original size:113 final size:105
Alignment explanation
Indices: 31539--31784 Score: 262
Period size: 111 Copynumber: 2.3 Consensus size: 105
31529 TTTTCAAAAC
*
31539 TATATTATATAGTTTTCAAAATGTTTTAAAAATATTATATAAGTTTTAAAAAACGTTTTTAAAAC
1 TATATTATATAGTTTTCAAAATGTTTTAAAAATATTATATAAGTTTTAAAAAACGTTTTAAAAAC
* ** * **
31604 TATATATTATATAATTTATTCAAAATTTTTTTTTTAAAACTA
66 TATATATTATAT-AGTT-TTCAAAAAATATTTTAAAAAACTA
* ** *
31646 TATATTATATAAGTTTTTAAAATGATTTTAAAACTATATGTTATATATA-TTTTCTAAAATGTTT
1 TATATTATAT-AGTTTTCAAAATG-TTTTAAAA--ATA--TTATATA-AGTTTTAAAAAACGTTT
*
31710 TAAAAACTATATGTTATATAGTTTTCAAAAAATATTTTAAAAAACTA
59 TAAAAACTATATATTATATAGTTTTCAAAAAATATTTTAAAAAACTA
*
31757 TATATTACCCATA-TTTTCAAAATGTTTT
1 TATATTA--TATAGTTTTCAAAATGTTTT
31785 CTTTTTAAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
107 10 0.09
108 12 0.10
109 8 0.07
110 4 0.03
111 39 0.34
112 4 0.03
113 38 0.33
114 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (105 bp):
TATATTATATAGTTTTCAAAATGTTTTAAAAATATTATATAAGTTTTAAAAAACGTTTTAAAAAC
TATATATTATATAGTTTTCAAAAAATATTTTAAAAAACTA
Found at i:32630 original size:84 final size:83
Alignment explanation
Indices: 32421--33752 Score: 1222
Period size: 84 Copynumber: 16.1 Consensus size: 83
32411 TGACAAATAG
* * * * * * * * * * *
32421 CCCTTCTTGCCATAAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACTC-GG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
*
32485 GAGTCTTTG--GCAGATAG
66 G-GTCTTTGTAGCAGATAA
* ** * * * **
32502 CCCTTCTTGACTTAAGCTATGCTGCAAATGATGCGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
*
32567 GGTCTTTGCTAACAGATAA
66 GGTCTTTG-TAGCAGATAA
* * * * * * * *
32586 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
*
32651 GGTCTTTG--GCAGATAG
66 GGTCTTTGTAGCAGATAA
* * * * * *
32667 CCCTTCTCGACTTAAGCTATTCTGCAAATG--ATGCGCCTAGGAGCTGAGCGTAGTCGAACCCAA
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGC-CCTTGAAGCTGAGCGTAGTCGAACTCAA
* *
32730 AGGTCTTTGCTAACAGATAA
65 GGGTCTTTG-TAGCAGATAA
* * * * * * * *
32750 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
*
32815 GGTCTTTG--GCAGATAG
66 GGTCTTTGTAGCAGATAA
* * * * * *
32831 CCCTTCTCGACTTAAGCTATTCTGCAAATG--ATGCGCCTAGGAGCTGAGCGTAGTCGAACCCAA
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGC-CCTTGAAGCTGAGCGTAGTCGAACTCAA
* *
32894 AGGTCTTTGCTAACAGATAA
65 GGGTCTTTG-TAGCAGATAA
* * * * * * * *
32914 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
*
32979 GGTCTTTG--GCAGATAG
66 GGTCTTTGTAGCAGATAA
* * * * * *
32995 CCCTTCTCGACTTAAGCTATTCTGCAAATG--ATGCGCCTAGGAGCTGAGCGTAGTCGAACCCAA
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGC-CCTTGAAGCTGAGCGTAGTCGAACTCAA
* *
33058 AGGTCTTTGCTAACAGATAA
65 GGGTCTTTG-TAGCAGATAA
* * * * * * * *
33078 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
*
33143 GGTCTTTAGTTGGCAGATAA
66 GGTCTTT-G-TAGCAGATAA
* * * *
33163 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTG-CCTTCGAAGCTGAACGTAGTCGAACTCGA
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTT-GAAGCTGAGCGTAGTCGAACTCAA
*
33227 GGGTCTTTG--GCAGATAG
65 GGGTCTTTGTAGCAGATAA
* * * * * *
33244 CCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAA
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
33308 GGTCTTTTGTTAGCAGATAA
66 GGTC-TTTG-TAGCAGATAA
* * * *
33328 CCCTTCTTGACTTAAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
*
33393 GGTCTTTAGTTGGCAGATAA
66 GGTCTTT-G-TAGCAGATAA
* * * *
33413 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTG-CCTTCGAAGCTGAACGTAGTCGAACTCGA
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTT-GAAGCTGAGCGTAGTCGAACTCAA
*
33477 GGGTCTTTG--GCAGATAG
65 GGGTCTTTGTAGCAGATAA
* * * * * *
33494 CCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAA
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
33558 GGTCTTTTGTTAGCAGATAA
66 GGTC-TTTG-TAGCAGATAA
* * *
33578 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAA
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
33642 GGTCTTTTGTTAGCAGATAA
66 GGTC-TTTG-TAGCAGATAA
* * *
33662 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGTG-CCTTCAAAGCTGAACGTAGTCGAACTCGA
1 CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTT-GAAGCTGAGCGTAGTCGAACTC-A
* * *
33726 A-GGTCTTGGTGGACAGATAG
64 AGGGTCTTTGTAG-CAGATAA
33746 CCCTTCT
1 CCCTTCT
33753 GGCCTTGAGC
Statistics
Matches: 1040, Mismatches: 173, Indels: 73
0.81 0.13 0.06
Matches are distributed among these distances:
79 12 0.01
80 140 0.13
81 245 0.24
82 3 0.00
83 92 0.09
84 349 0.34
85 197 0.19
86 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (83 bp):
CCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGCGTAGTCGAACTCAAG
GGTCTTTGTAGCAGATAA
Found at i:32789 original size:164 final size:164
Alignment explanation
Indices: 32438--33761 Score: 1498
Period size: 164 Copynumber: 8.0 Consensus size: 164
32428 TGCCATAAGC
* * * * **
32438 TATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAAC-TCGGGAGTCTTTGGCAGATAG
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGG-GTCTTTGGCAGATAG
* * * * * ***
32502 CCCTTCTTGACTTAAGCTATGCTGCAAATGATGCGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
65 CCCTTCTCGACTTAAGCTATTCTGCAAATGATGCG-CCTAGAAGCTGAGCGTAGTCGAACTCAAA
32567 GGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
129 GGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
*
32603 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGC
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGC
* *
32668 CCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCCTAGGAGCTGAGCGTAGTCGAACCCAAAGG
66 CCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCCTAGAAGCTGAGCGTAGTCGAACTCAAAGG
32733 TCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
131 TCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
*
32767 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGC
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGC
* *
32832 CCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCCTAGGAGCTGAGCGTAGTCGAACCCAAAGG
66 CCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCCTAGAAGCTGAGCGTAGTCGAACTCAAAGG
32897 TCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
131 TCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
*
32931 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGC
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGC
* *
32996 CCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCCTAGGAGCTGAGCGTAGTCGAACCCAAAGG
66 CCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCCTAGAAGCTGAGCGTAGTCGAACTCAAAGG
33061 TCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
131 TCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
*
33095 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGA
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC--T--TTGGCAGA
* * * * * * *
33160 TAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTC
62 TAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCC-TAGAAGCTGAGCGTAGTCGAACTC
* * * * * * * *
33225 GAGGGTCTTTG---GCAGATAGCCCTTCTCGACTTAAGC
126 AAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
* * * * * * * *
33261 TATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGA
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC-TTTG---GCAGA
* * * * * * * *
33325 TAACCCTTCTTGACTTAAGTTATGCTGTAAATGATATGC-CCTTGAAGCTGAGTGTAATCGAACT
62 TAGCCCTTCTCGACTTAAGCTATTCTGCAAATG--ATGCGCCTAGAAGCTGAGCGTAGTCGAACT
* * * ** * * *
33389 TAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGT
125 CAAAGGTCTTT-GCTAACAGATAACCCTTCTAGCCTTGAGT
* * * ** * **
33430 TATACTGCAAATGATGTG-CCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAG
1 TATGCTGTAAATGATATGCCCTT-GAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAG
* * *
33494 CCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
65 CCCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCCTAGAAGCTGAGCGTAGTCGAACTCAAAG
* * * * *
33559 GTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGT
130 GTC-TTTGCTAACAGATAACCCTTCTAGCCTTGAGT
* * * * * * *
33595 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGA
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC-TTTG---GCAGA
* * * * * *
33659 TAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTCA-AAGCTGAACGTAGTCGAACT
62 TAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCC-T-AGAAGCTGAGCGTAGTCGAACT
* * * * *
33723 CGAAGGTC-TTGGTGGACAGATAGCCCTTCTGGCCTTGAG
125 CAAAGGTCTTTGCT-AACAGATAACCCTTCTAGCCTTGAG
33762 CTAAGCTGCA
Statistics
Matches: 1042, Mismatches: 92, Indels: 47
0.88 0.08 0.04
Matches are distributed among these distances:
162 3 0.00
164 467 0.45
165 259 0.25
166 76 0.07
167 7 0.01
168 103 0.10
169 102 0.10
170 25 0.02
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (164 bp):
TATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGC
CCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCCTAGAAGCTGAGCGTAGTCGAACTCAAAGG
TCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
Found at i:33425 original size:250 final size:248
Alignment explanation
Indices: 32475--33752 Score: 1527
Period size: 250 Copynumber: 5.1 Consensus size: 248
32465 TTGAGTGTAA
* * *
32475 TCGAACTCG-GGAGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGCGCC
1 TCGAACTCGAGG-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-C
* * * * *** * * *
32539 CTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTT
64 CTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAGCAGATAACCCTTCTAGACTTAAGTT
*
32604 ATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC--T-TTGGCAGATA
129 ATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGTTGGCAGATA
* * * * * * * *
32666 GCCCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCC-TAGGAGCTGAGCGTAG
194 ACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
* * * * * * * * * * * * *
32720 TCGAACCCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATG
1 TCGAACTCGAGGGTCTTTG---GCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
* * * * * * *
32785 CCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTG---GCAGATAGCCCTTCTCGACTTAAG
63 -CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAGCAGATAACCCTTCTAGACTTAAG
* * * * * * * ** * * **
32847 CTATTCTGCAAATG--ATGCGCCTAGGAGCTGAGCGTAGTCGAACCCAAAGGTCTTTGCTAACAG
127 TTATGCTGTAAATGATATGC-CCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGTTGGCAG
* * * * * * * ** *
32910 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTT-GAAGCTGAGTGTAA
191 ATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTG-CCTTCGAAGCTGAACGTAG
** *
32968 TCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGCGCCT
1 TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
* * * * *
33033 AGGAGCTGAGCGTAGTCGAACCCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTAT
66 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAGCAGATAACCCTTCTAGACTTAAGTTAT
*
33098 GCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATAA
131 GCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTT-GTTGGCAGATAA
33163 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
195 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
33217 TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
1 TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
* *
33282 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTA
66 TGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTAGCAGATAACCCTTCTAGACTTAAGTTA
33347 TGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTGGCAGATA
130 TGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTT-GTTGGCAGATA
33412 ACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
194 ACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
33467 TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
1 TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
* *
33532 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTA
66 TGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTAGCAGATAACCCTTCTAGACTTAAGTTA
* * * * * * * *
33597 TGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATA
130 TGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC-TTTGTTGGCAGATA
* *
33661 ACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTCAAAGCTGAACGTAG
194 ACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
*
33716 TCGAACTCGAAGGTCTTGGTGGACAGATAGCCCTTCT
1 TCGAACTCGAGGGTCTT--TGG-CAGATAGCCCTTCT
33753 GGCCTTGAGC
Statistics
Matches: 892, Mismatches: 119, Indels: 37
0.85 0.11 0.04
Matches are distributed among these distances:
243 4 0.00
244 56 0.06
245 76 0.09
246 2 0.00
247 63 0.07
248 129 0.14
249 250 0.28
250 295 0.33
251 3 0.00
252 14 0.02
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (248 bp):
TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAGCAGATAACCCTTCTAGACTTAAGTTAT
GCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGTTGGCAGATAAC
CCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAG
Found at i:37122 original size:19 final size:19
Alignment explanation
Indices: 37098--37143 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
37088 AGTTAATGTG
37098 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
37117 AATGCAAAGAAAATAACGA
1 AATGCAAAGAAAATAACAA
37136 AATGCAAA
1 AATGCAAA
37144 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:38876 original size:22 final size:23
Alignment explanation
Indices: 38851--38910 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
38841 AACAAAATGC
38851 TAATAAAAAAAAAAAATAAT-AA
1 TAATAAAAAAAAAAAATAATAAA
*
38873 TAATAATGAAAGAAAGAAATAATAGAA
1 TAATAA--AAA-AAAAAAATAATA-AA
*
38900 TAATAATAAAA
1 TAATAAAAAAA
38911 GGTTAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 6 0.19
24 5 0.16
25 12 0.39
27 8 0.26
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (23 bp):
TAATAAAAAAAAAAAATAATAAA
Found at i:40089 original size:15 final size:14
Alignment explanation
Indices: 40057--40085 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40047 CTAAAAAAAC
40057 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
40071 ATAAAAAGAAAATA
1 ATAAAAAGAAAATA
40085 A
1 A
40086 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
ATAAAAAGAAAATA
Found at i:40163 original size:33 final size:31
Alignment explanation
Indices: 40147--40258 Score: 104
Period size: 33 Copynumber: 3.5 Consensus size: 31
40137 ATATTTTTTT
40147 AAACTATATATTATATTTAAAAAAGTTTTCA
1 AAACTATATATTATATTTAAAAAAGTTTTCA
* *
40178 AAACTATAT-TATATAGTTTTCAAAATGTTTT-A
1 AAACTATATAT-TATA--TTTAAAAAAGTTTTCA
* * *
40210 AAAATATTATATAAGT-TTTAAAAAACGTTTTTA
1 AAACTA-TATATTA-TATTTAAAAAA-GTTTTCA
40243 AAACTATATATTATAT
1 AAACTATATATTATAT
40259 AATTTATTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
30 1 0.02
31 21 0.33
32 18 0.28
33 22 0.34
34 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (31 bp):
AAACTATATATTATATTTAAAAAAGTTTTCA
Found at i:40253 original size:32 final size:31
Alignment explanation
Indices: 40141--40253 Score: 113
Period size: 31 Copynumber: 3.5 Consensus size: 31
40131 TCAAAAATAT
* *
40141 TTTTTTAAACTATATATTA-TATTTAAAAAAG
1 TTTTTAAAACTATATATAAGT-TTTAAAAAAG
* * *
40172 TTTTCAAAACTATATTATATAGTTTTCAAAATG
1 TTTTTAAAACTATA-TATA-AGTTTTAAAAAAG
*
40205 -TTTTAAAAATATTATATAAGTTTTAAAAAACG
1 TTTTTAAAACTA-TATATAAGTTTTAAAAAA-G
40237 TTTTTAAAACTATATAT
1 TTTTTAAAACTATATAT
40254 TATATAATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
31 22 0.33
32 22 0.33
33 21 0.32
34 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (31 bp):
TTTTTAAAACTATATATAAGTTTTAAAAAAG
Found at i:40257 original size:37 final size:37
Alignment explanation
Indices: 40162--40406 Score: 210
Period size: 37 Copynumber: 6.8 Consensus size: 37
40152 ATATATTATA
*
40162 TTTAAAAAA-GTTTTCAAAAC--TATATTATAT-AGT
1 TTTAAAAAATGTTTTTAAAACTATATATTATATAAGT
*
40195 TTT-CAAAATG-TTTT-AAA--A-ATATTATATAAGT
1 TTTAAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
40226 TTTAAAAAACGTTTTTAAAACTATATATTATATAATT
1 TTTAAAAAATGTTTTTAAAACTATATATTATATAAGT
**
40263 TATTCAAAAAAAAATTTTTAAAACTATATATTATATAAGT
1 T-TT--AAAAAATGTTTTTAAAACTATATATTATATAAGT
* * *
40303 TTT-TAAAATGATTTTAAAACTATATGTTATATATA-T
1 TTTAAAAAATGTTTTTAAAACTATATATTATATA-AGT
** * *
40339 TTTCTAAAATGTTTTAAAAACTATATGTTATAT-AGT
1 TTTAAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
40375 TTTCAAAAAATATTTTAAAAAACTATATATTA
1 TTT-AAAAAATGTTTT-TAAAACTATATATTA
40407 CCCATATTTT
Statistics
Matches: 176, Mismatches: 19, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
30 9 0.05
31 9 0.05
32 12 0.07
33 8 0.05
34 3 0.02
35 1 0.01
36 34 0.19
37 50 0.28
38 16 0.09
39 2 0.01
40 32 0.18
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (37 bp):
TTTAAAAAATGTTTTTAAAACTATATATTATATAAGT
Found at i:40423 original size:111 final size:108
Alignment explanation
Indices: 40165--40427 Score: 265
Period size: 113 Copynumber: 2.4 Consensus size: 108
40155 TATTATATTT
* * *
40165 AAAAAAGTTTTCAAAACTATA--TTATAT-AGTTTTCAAAATGTTTTAAAAATATTATATAAGTT
1 AAAAAAATTTTAAAAACTATATATTACATAAGTTTTCAAAATGTTTTAAAAATATTATATAAGTT
* *
40227 TTAAAAAACGTTTTTAAAACTATATATTATATAATTTATTCAA
66 TTAAAAAACGTTTTAAAAACTATATATTATATAAGTTATTCAA
* * *
40270 AAAAAAATTTTTAAAACTATATATTATATAAGTTTTTAAAATGATTTTAAAACTATATGTTATAT
1 AAAAAAATTTTAAAAACTATATATTACATAAGTTTTCAAAATG-TTTTAAAA--ATA--TTATAT
** * *
40335 ATA-TTTTCTAAAATGTTTTAAAAACTATATGTTATAT-AGTT-TTC-A
61 A-AGTTTTAAAAAACGTTTTAAAAACTATATATTATATAAGTTATTCAA
*
40380 AAAAATATTTTAAAAAACTATATATTACCCAT-A-TTTTCAAAATGTTTT
1 AAAAAAATTTT-AAAAACTATATATTA--CATAAGTTTTCAAAATGTTTT
40428 CTTTTTAAAA
Statistics
Matches: 133, Mismatches: 13, Indels: 19
0.81 0.08 0.12
Matches are distributed among these distances:
105 19 0.14
107 6 0.05
108 12 0.09
109 8 0.06
110 15 0.11
111 30 0.23
112 4 0.03
113 38 0.29
114 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (108 bp):
AAAAAAATTTTAAAAACTATATATTACATAAGTTTTCAAAATGTTTTAAAAATATTATATAAGTT
TTAAAAAACGTTTTAAAAACTATATATTATATAAGTTATTCAA
Found at i:42648 original size:22 final size:21
Alignment explanation
Indices: 42606--42645 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42596 GAGTTTATTT
* *
42606 TCATTTTTTTATTTTGAAACA
1 TCATTTTTATATTTTAAAACA
42627 TCATTTTTATATTTTAAAA
1 TCATTTTTATATTTTAAAA
42646 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (21 bp):
TCATTTTTATATTTTAAAACA
Found at i:44702 original size:19 final size:19
Alignment explanation
Indices: 44663--44702 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
44653 AATGCATTGA
***
44663 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAAT
44682 GTGCATCGATGCATAAAAT
1 GTGCATCGATGCATAAAAT
44701 GT
1 GT
44703 ATTCGATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (19 bp):
GTGCATCGATGCATAAAAT
Found at i:44748 original size:20 final size:20
Alignment explanation
Indices: 44723--44760 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
44713 TGAAAAATTA
44723 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
44743 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
44761 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:46142 original size:2 final size:2
Alignment explanation
Indices: 46135--46200 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
46125 CCATTAACTG
46135 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
46177 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
46201 CATAATGTAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50727 original size:29 final size:29
Alignment explanation
Indices: 50683--50768 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
50673 AGTGTTGGCC
*
50683 GTAGGTCGCCAGGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
*
50712 GTAGGTCGCCATGCACTCCGGGCGATCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
* *
50741 GTAGGTCGCCATGTACTCAGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
50769 ACCCTTACTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:50872 original size:29 final size:29
Alignment explanation
Indices: 50839--50923 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
50829 TCCCAACACA
* *
50839 TAGGTCGCCATGCCCTCCGGACGACTTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
50868 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
50897 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
50924 ACCCTCGCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.13, C:0.36, G:0.29, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:50992 original size:14 final size:14
Alignment explanation
Indices: 50975--51002 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50965 TCGGTTGCCC
50975 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
50989 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
51003 ATACTCTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:51102 original size:29 final size:29
Alignment explanation
Indices: 51065--51122 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
51055 GCAATCTCTT
*
51065 GTAGCTCG-CCGGAAAGACATGGCGACCTA
1 GTAGCTCGCCCAG-AAGACATGGCGACCTA
* *
51094 GTAGGTCGCCCAGAAGGCATGGCGACCTA
1 GTAGCTCGCCCAGAAGACATGGCGACCTA
51123 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.26, C:0.28, G:0.33, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCAGAAGACATGGCGACCTA
Found at i:52997 original size:57 final size:57
Alignment explanation
Indices: 52909--53023 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
52899 TTTTATCTCA
* *
52909 TCAAACCATTAAGGAAACACATTAAATACTTAAATAAATTCTATTCCTTTTGGTATT
1 TCAAACCATTAAGGAAACACATTAAATACTTAAATAAATTATATTCCTCTTGGTATT
*
52966 TCAAACCATTAAGGAAACGCATTAAATACTTAAATAAATTATATTCCTCTTGGTATT
1 TCAAACCATTAAGGAAACACATTAAATACTTAAATAAATTATATTCCTCTTGGTATT
53023 T
1 T
53024 GATTTATAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (57 bp):
TCAAACCATTAAGGAAACACATTAAATACTTAAATAAATTATATTCCTCTTGGTATT
Found at i:53127 original size:42 final size:43
Alignment explanation
Indices: 53049--53142 Score: 154
Period size: 42 Copynumber: 2.2 Consensus size: 43
53039 CTTGTACGTA
53049 CAGGCCACAGGCTGTGCAACAACAAGGATTACTGAATCAAACTCC
1 CAGGCCACAGGCTGTG--ACAACAAGGATTACTGAATCAAACTCC
*
53094 CAGGCCACAGGCTGTG-CAACAAGGATTGCTGAATCAAACTCC
1 CAGGCCACAGGCTGTGACAACAAGGATTACTGAATCAAACTCC
53136 CAGGCCA
1 CAGGCCA
53143 AATGCTACAT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
42 32 0.67
45 16 0.33
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.15
Consensus pattern (43 bp):
CAGGCCACAGGCTGTGACAACAAGGATTACTGAATCAAACTCC
Found at i:56351 original size:16 final size:16
Alignment explanation
Indices: 56330--56366 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
56320 TTAAAACTTG
56330 AACTCGAAAAGGCTTA
1 AACTCGAAAAGGCTTA
*
56346 AACTCGAAAAGGCTTG
1 AACTCGAAAAGGCTTA
56362 AACTC
1 AACTC
56367 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (16 bp):
AACTCGAAAAGGCTTA
Found at i:59220 original size:23 final size:23
Alignment explanation
Indices: 59194--59265 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
59184 GAGTAAAAAT
59194 AAATGACTGAGATTAATAGTAGA
1 AAATGACTGAGATTAATAGTAGA
* *
59217 AAATGA--GAAGA-TATTA--AAA
1 AAATGACTG-AGATTAATAGTAGA
59236 TAAATGACTGAGATTAATAGTAGA
1 -AAATGACTGAGATTAATAGTAGA
59260 AAATGA
1 AAATGA
59266 GAAGATATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 2 0.05
20 6 0.16
21 8 0.21
22 8 0.21
23 12 0.32
24 2 0.05
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (23 bp):
AAATGACTGAGATTAATAGTAGA
Found at i:59249 original size:43 final size:43
Alignment explanation
Indices: 59189--59274 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
59179 TGAATGAGTA
59189 AAAATAAATGACTGAGATTAATAGTAGAAAATGAGAAGATATT
1 AAAATAAATGACTGAGATTAATAGTAGAAAATGAGAAGATATT
59232 AAAATAAATGACTGAGATTAATAGTAGAAAATGAGAAGATATT
1 AAAATAAATGACTGAGATTAATAGTAGAAAATGAGAAGATATT
59275 CACTTGGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.53, C:0.02, G:0.19, T:0.26
Consensus pattern (43 bp):
AAAATAAATGACTGAGATTAATAGTAGAAAATGAGAAGATATT
Found at i:59393 original size:2 final size:2
Alignment explanation
Indices: 59386--59412 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59376 ATCTTAACCT
59386 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
59413 TTATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60152 original size:22 final size:20
Alignment explanation
Indices: 60117--60161 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 20
60107 CTTGTGATAA
60117 ATTAATTTTTTTTA-TGTAAT
1 ATTAATTTTTTTTATTG-AAT
60137 ATTAAGTTATTTTTTATTGAAT
1 ATTAA-TT-TTTTTTATTGAAT
60159 ATT
1 ATT
60162 CTTTATATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.23
21 2 0.09
22 13 0.59
23 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (20 bp):
ATTAATTTTTTTTATTGAAT
Found at i:69418 original size:11 final size:10
Alignment explanation
Indices: 69388--69428 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
69378 GGGCTTTGTA
69388 ATTTAATATT
1 ATTTAATATT
69398 ATTTATATATGT
1 ATTTA-ATAT-T
69410 ATTTAATATAT
1 ATTTAATAT-T
69421 ATTTAATA
1 ATTTAATA
69429 ATAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:69432 original size:3 final size:3
Alignment explanation
Indices: 69424--69515 Score: 139
Period size: 3 Copynumber: 30.7 Consensus size: 3
69414 AATATATATT
*
69424 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
69472 TGA TAA TAA TAA TAA TAA TTA TTA TAA TAA CAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
69516 TTTATAATAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:70092 original size:114 final size:114
Alignment explanation
Indices: 69841--70390 Score: 924
Period size: 114 Copynumber: 4.8 Consensus size: 114
69831 GATAGAATTA
* *
69841 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * * * * *
69906 GAACTCTAC-CTGGCAATGTTGATCCATCAA-ATGATGAATTCAAGCAAAAGA
63 GAAC-CTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
*
69957 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
70022 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
70071 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
70136 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
70185 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
70250 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
70299 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
70364 CCTTCTCTGGAAAAGATAATCTATCAA
66 CCTTCTCTGGAAAAGATAATCCATCAA
70391 ATGATAGATT
Statistics
Matches: 418, Mismatches: 14, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
112 2 0.00
113 37 0.09
114 334 0.80
116 45 0.11
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (114 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
Found at i:71274 original size:83 final size:83
Alignment explanation
Indices: 71130--71916 Score: 1511
Period size: 83 Copynumber: 9.5 Consensus size: 83
71120 CCTACCGAAT
* * * * *
71130 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATGAACACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
71195 TGATTGGTTCTGCCAAAC
66 TGATTGGTTCTGCTAAAC
71213 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
71278 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCTAAAC
71296 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
71361 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCTAAAC
71379 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
71444 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCTAAAC
71462 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
71527 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCTAAAC
71545 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
71610 TGATTGGTTCTACTAAAC
66 TGATTGGTTCTGCTAAAC
71628 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
71693 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCTAAAC
71711 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
71776 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCTAAAC
71794 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
71859 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCTAAAC
71877 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
71917 GAGCCCTTTG
Statistics
Matches: 696, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 696 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
TGATTGGTTCTGCTAAAC
Found at i:73091 original size:11 final size:10
Alignment explanation
Indices: 73076--73120 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
73066 TGACCCCCCC
73076 TTTTTTCTTT
1 TTTTTTCTTT
73086 TCTTTTTC-TT
1 T-TTTTTCTTT
*
73096 TTTTCTCTTT
1 TTTTTTCTTT
73106 TTTTTTCATTT
1 TTTTTTC-TTT
73117 TTTT
1 TTTT
73121 CTTCAAGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 5 0.17
10 12 0.40
11 13 0.43
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:73098 original size:19 final size:19
Alignment explanation
Indices: 73076--73123 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
73066 TGACCCCCCC
73076 TTTTTTCTTTTCTTTTTC-T
1 TTTTTTCTTTT-TTTTTCAT
73095 TTTTTCTCTTTTTTTTTCAT
1 TTTTT-TCTTTTTTTTTCAT
73115 TTTTTTCTT
1 TTTTTTCTT
73124 CAAGCATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTCTTTTTTTTTCAT
Found at i:85942 original size:11 final size:10
Alignment explanation
Indices: 85912--85952 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
85902 GGGCTTTGTA
85912 ATTTAATATT
1 ATTTAATATT
85922 ATTTATATATGT
1 ATTTA-ATAT-T
85934 ATTTAATATAT
1 ATTTAATAT-T
85945 ATTTAATA
1 ATTTAATA
85953 ATAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:85956 original size:3 final size:3
Alignment explanation
Indices: 85948--86033 Score: 127
Period size: 3 Copynumber: 28.7 Consensus size: 3
85938 AATATATATT
* *
85948 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
85996 TAA TAA TAA TAA TTA TTA TAA TAA CAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
86034 TTTATAATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:96483 original size:30 final size:30
Alignment explanation
Indices: 96448--96504 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
96438 GAAGGACCTA
* *
96448 TCCATATGTTCCGAAGAACATAGGTAACTG
1 TCCATATGTCCCGAAGAACATAAGTAACTG
*
96478 TCCATATGTCCCGAAGGACATAAGTAA
1 TCCATATGTCCCGAAGAACATAAGTAA
96505 ACTATACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (30 bp):
TCCATATGTCCCGAAGAACATAAGTAACTG
Found at i:96633 original size:19 final size:19
Alignment explanation
Indices: 96606--96643 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
96596 ATCACTTATG
*
96606 TCATTTCACATATACACAT
1 TCATATCACATATACACAT
*
96625 TCATATCACATATTCACAT
1 TCATATCACATATACACAT
96644 GTCACATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (19 bp):
TCATATCACATATACACAT
Found at i:96774 original size:32 final size:31
Alignment explanation
Indices: 96705--96774 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
96695 ATAGTTCATT
*
96705 TCATATAACCTCTTATGTTCATATCATATAA
1 TCATATAAACTCTTATGTTCATATCATATAA
*
96736 T-ATATAAACTCTTAAT-TTCTTATCCAGTAT-A
1 TCATATAAACTCTT-ATGTTCATAT-CA-TATAA
96767 TCATATAA
1 TCATATAA
96775 TATGCTGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
30 17 0.52
31 7 0.21
32 9 0.27
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (31 bp):
TCATATAAACTCTTATGTTCATATCATATAA
Found at i:99677 original size:23 final size:23
Alignment explanation
Indices: 99646--99729 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
99636 ACATTTTATA
99646 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
99669 CGGCACTTCGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
* *
99692 TGGCACTTCGGTGCAACTCTACA
1 TGGCACTTCGGTGCAATTCTACG
*
99715 TGGCACTTTGGTGCA
1 TGGCACTTCGGTGCA
99730 TTTATATGAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:105199 original size:24 final size:24
Alignment explanation
Indices: 105167--105219 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
105157 AATCAAATTT
105167 AATTA-AAAATGA-ATAAA-ATCTAA
1 AATTATAAAAT-ATATAAACAT-TAA
105190 AATTATAAAATATATAAACATTAA
1 AATTATAAAATATATAAACATTAA
105214 AATTAT
1 AATTAT
105220 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.22
24 19 0.70
25 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (24 bp):
AATTATAAAATATATAAACATTAA
Found at i:110757 original size:16 final size:16
Alignment explanation
Indices: 110731--110768 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
110721 TCTACTAAAG
110731 CATGATTGGGTAGATAT
1 CATG-TTGGGTAGATAT
110748 CATGTTGGGTAGATAT
1 CATGTTGGGTAGATAT
110764 CATGT
1 CATGT
110769 GAATAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (16 bp):
CATGTTGGGTAGATAT
Found at i:120754 original size:23 final size:23
Alignment explanation
Indices: 120728--120803 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 23
120718 ATTTTGCTTG
120728 AAAAAATAATGAAAAAATGAAATA
1 AAAAAATAATGAAAAAATGAAA-A
*
120752 AAAAAA-AGA-AAAAAAATGAAAA
1 AAAAAATA-ATGAAAAAATGAAAA
*
120774 AGAAAAATGAATGAAAAAAATGGAAA
1 A-AAAAAT-AATG-AAAAAATGAAAA
120800 AAAA
1 AAAA
120804 GAAGGGTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
22 2 0.05
23 17 0.40
24 8 0.19
25 4 0.09
26 12 0.28
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.11
Consensus pattern (23 bp):
AAAAAATAATGAAAAAATGAAAA
Found at i:120755 original size:13 final size:12
Alignment explanation
Indices: 120739--120803 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 12
120729 AAAAATAATG
120739 AAAAAATGAAATA
1 AAAAAATGAAA-A
*
120752 AAAAAA--AGAA
1 AAAAAATGAAAA
120762 AAAAAATGAAAA
1 AAAAAATGAAAA
*
120774 AGAAAAATGAATGA
1 A-AAAAATGAA-AA
120788 AAAAAATGGAAAA
1 AAAAAAT-GAAAA
120801 AAA
1 AAA
120804 GAAGGGTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 7 0.16
11 2 0.05
12 4 0.09
13 25 0.58
14 5 0.12
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (12 bp):
AAAAAATGAAAA
Found at i:120773 original size:16 final size:17
Alignment explanation
Indices: 120729--120791 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 17
120719 TTTTGCTTGA
120729 AAAAAT-AATGAAAAA-
1 AAAAATAAATGAAAAAG
*
120744 ATGAAATAAA--AAAAAG
1 A-AAAATAAATGAAAAAG
120760 AAAAA-AAATGAAAAAG
1 AAAAATAAATGAAAAAG
*
120776 AAAAATGAATGAAAAA
1 AAAAATAAATGAAAAA
120792 AATGGAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 3 0.08
15 9 0.23
16 16 0.41
17 11 0.28
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (17 bp):
AAAAATAAATGAAAAAG
Found at i:121892 original size:55 final size:55
Alignment explanation
Indices: 121807--122625 Score: 1092
Period size: 55 Copynumber: 14.9 Consensus size: 55
121797 AGATTTCCCA
* *
121807 ACGATTATTGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
*
121862 GCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
121917 ACGATTGTTGAAAATTATTCGAGTCTTATACTCTATGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
121972 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT-GAGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAG-GGAGCAGAC
* * * *
122027 ACGATTTTTGAAAATTGTTCGAGTCTTATACTCTATGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
122082 ACGACTGTTGAAGATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
122137 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
122192 ACGATTGATGAAAATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
122247 ACGACTGTTGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
122302 ATGACTGTTGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
122357 ACGATTGATGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
122412 ACGATTGATGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * *
122467 AAGATTTGTTGAAGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAACAGAC
1 ACGA-TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * * *
122523 ACGATTGATGAAGATTCTTCAAGT-TTCTACTCCCT-AAGAAAGAGGGAG-TGAAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG-AC
* ** * *
122576 CCG-TTGACAGAAGATTGTTCGAGT-TATATACTCCCTGAAGAAAGAGGGAG
1 ACGATTG-TTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAG
122626 TGAACTCGTT
Statistics
Matches: 684, Mismatches: 73, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
52 4 0.01
53 28 0.04
54 19 0.03
55 582 0.85
56 51 0.07
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:122626 original size:55 final size:53
Alignment explanation
Indices: 122532--122688 Score: 174
Period size: 55 Copynumber: 2.9 Consensus size: 53
122522 CACGATTGAT
* * *
122532 GAAGATTCTTCAAGTTTCTACTCCCTAAGAAAGAGGGAGTGAACCCGTT-GACA
1 GAAGATTGTTCGAGTTTATACTCCCTAAGAAAGAGGGAGTGAACCCGTTCG-CA
*
122585 GAAGATTGTTCGAGTTATATACTCCCTGAAGAAAGAGGGAGTGAACTCGTTCGCA
1 GAAGATTGTTCGAGTT-TATACTCCCT-AAGAAAGAGGGAGTGAACCCGTTCGCA
* * * * * *
122640 GAAAATTGTTCGAGTCCTATACTCCCCAA-AATGAGGGAGCGAACTCGTT
1 GAAGATTGTTCGAGT-TTATACTCCCTAAGAAAGAGGGAGTGAACCCGTT
122689 TTCCGAATAT
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
53 32 0.35
54 11 0.12
55 47 0.52
56 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (53 bp):
GAAGATTGTTCGAGTTTATACTCCCTAAGAAAGAGGGAGTGAACCCGTTCGCA
Found at i:122930 original size:2 final size:2
Alignment explanation
Indices: 122925--122949 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
122915 ATAATTATTA
122925 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 A
122950 AGCAGTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:126939 original size:17 final size:18
Alignment explanation
Indices: 126906--126939 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
126896 CCGTTATTAG
126906 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
126924 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
126940 GACCGGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:128806 original size:32 final size:33
Alignment explanation
Indices: 128770--128838 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
128760 TCTATTGTGT
*
128770 TAAAATATGTT-CTTTAATTATTAAAAATATAA
1 TAAAATATGTTACTTTAATCATTAAAAATATAA
* * *
128802 TAAAATATTTTATTTTAATCATTTAAAATATAA
1 TAAAATATGTTACTTTAATCATTAAAAATATAA
128835 TAAA
1 TAAA
128839 TGATTATAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (33 bp):
TAAAATATGTTACTTTAATCATTAAAAATATAA
Found at i:128866 original size:13 final size:13
Alignment explanation
Indices: 128850--128908 Score: 70
Period size: 12 Copynumber: 4.8 Consensus size: 13
128840 GATTATAAGT
128850 ATATTATTATAAA
1 ATATTATTATAAA
**
128863 ATA-TATTATTTA
1 ATATTATTATAAA
*
128875 A-ATTATTTTAAA
1 ATATTATTATAAA
128887 ATATTATTATAAA
1 ATATTATTATAAA
128900 ATA-TATTAT
1 ATATTATTAT
128909 TTTAATTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 1 0.03
12 21 0.55
13 16 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATTATTATAAA
Found at i:128871 original size:12 final size:12
Alignment explanation
Indices: 128854--128908 Score: 67
Period size: 13 Copynumber: 4.5 Consensus size: 12
128844 ATAAGTATAT
128854 TATTATAAAATA
1 TATTATAAAATA
*
128866 TATTATTTAAAT-
1 TATTA-TAAAATA
*
128878 TATTTTAAAATA
1 TATTATAAAATA
128890 TTATTATAAAATA
1 -TATTATAAAATA
128903 TATTAT
1 TATTAT
128909 TTTAATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 5 0.14
12 15 0.42
13 16 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATTATAAAATA
Found at i:128900 original size:37 final size:37
Alignment explanation
Indices: 128850--128934 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
128840 GATTATAAGT
128850 ATATTATTATAAAATATATTATTTAAATTATTTTAAA
1 ATATTATTATAAAATATATTATTTAAATTATTTTAAA
*
128887 ATATTATTATAAAATATATTATTTTAATTATTTTAAA
1 ATATTATTATAAAATATATTATTTAAATTATTTTAAA
*
128924 ATATTAATATA
1 ATATTATTATA
128935 TTTGAACCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
ATATTATTATAAAATATATTATTTAAATTATTTTAAA
Found at i:131278 original size:31 final size:31
Alignment explanation
Indices: 131238--131307 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
131228 TTTTTAAATT
*
131238 TTTCAAAAAATAACATATTTTTTAAAAACAAA
1 TTTCAAAAATTAACAT-TTTTTTAAAAACAAA
* *
131270 TTTCAAAAATTGACATTTTTTTAAAAATAAA
1 TTTCAAAAATTAACATTTTTTTAAAAACAAA
*
131301 TCTCAAA
1 TTTCAAA
131308 TTTTATAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.37
Consensus pattern (31 bp):
TTTCAAAAATTAACATTTTTTTAAAAACAAA
Found at i:131515 original size:22 final size:18
Alignment explanation
Indices: 131456--131506 Score: 79
Period size: 16 Copynumber: 2.9 Consensus size: 18
131446 TGAATGAAAA
131456 TTTTTAATTAAAATTTA-
1 TTTTTAATTAAAATTTAT
131473 -TTTTAATTAAAATTTAT
1 TTTTTAATTAAAATTTAT
131490 TTTTTAATTAAATATTT
1 TTTTTAATTAAA-ATTT
131507 TTCATTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.52
18 11 0.35
19 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTAATTAAAATTTAT
Found at i:135092 original size:15 final size:15
Alignment explanation
Indices: 135072--135113 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
135062 AATTAAAAAG
135072 AAATAAAACAAACAA
1 AAATAAAACAAACAA
135087 AAAT-AAACAAACAA
1 AAATAAAACAAACAA
135101 AAACTAAAA-AAAC
1 AAA-TAAAACAAAC
135114 TTCTAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 13 0.52
15 9 0.36
16 3 0.12
ACGTcount: A:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (15 bp):
AAATAAAACAAACAA
Found at i:138330 original size:23 final size:23
Alignment explanation
Indices: 138304--138350 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
138294 AATACCCAAG
*
138304 ATAAA-TATAAATCTACCATTAAA
1 ATAAAGTATAAA-CAACCATTAAA
*
138327 ATAAAGTTTAAACAACCATTAAA
1 ATAAAGTATAAACAACCATTAAA
138350 A
1 A
138351 CAACCCCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
ATAAAGTATAAACAACCATTAAA
Found at i:151815 original size:23 final size:24
Alignment explanation
Indices: 151774--151820 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
151764 GTTCTAGTAA
151774 TTTTAAAAAAATTCTTTAAATTTT
1 TTTTAAAAAAATTCTTTAAATTTT
151798 TTTTAAATAAAA-TC-TTAAATTTT
1 TTTTAAA-AAAATTCTTTAAATTTT
151821 CAAATCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 9 0.41
25 4 0.18
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTAAAAAAATTCTTTAAATTTT
Done.