Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008188.1 Hibiscus syriacus cultivar Beakdansim tig00110796_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: 349969
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:217550 original size:23 final size:23
Alignment explanation
Indices: 217494--217582 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
217484 AGTCAAGGGT
* *
217494 TACGCGGTCATTCGAGACAATCC
1 TACGCGGTCCTTCGAGACATTCC
*
217517 TACGCGGTCCTTCGAGACATTTC
1 TACGCGGTCCTTCGAGACATTCC
* *
217540 TACGCGTTCCTTCGGGACA-T-C
1 TACGCGGTCCTTCGAGACATTCC
* * *
217561 TATGTGGTCCTTCGGGACATTC
1 TACGCGGTCCTTCGAGACATTC
217583 TATGTGGCAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
21 17 0.30
22 2 0.04
23 37 0.66
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (23 bp):
TACGCGGTCCTTCGAGACATTCC
Found at i:217587 original size:22 final size:22
Alignment explanation
Indices: 217522--217597 Score: 84
Period size: 21 Copynumber: 3.5 Consensus size: 22
217512 AATCCTACGC
* * *
217522 GGTCCTTCGAGACATTTCTACGC
1 GGTCCTTCGGGACA-TTCTATGT
*
217545 GTTCCTTCGGGACA-TCTATGT
1 GGTCCTTCGGGACATTCTATGT
217566 GGTCCTTCGGGACATTCTATGT
1 GGTCCTTCGGGACATTCTATGT
217588 GG-CACTTCGG
1 GGTC-CTTCGG
217598 TGCACTTCGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
21 19 0.41
22 15 0.33
23 12 0.26
ACGTcount: A:0.14, C:0.26, G:0.26, T:0.33
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTATGT
Found at i:226621 original size:25 final size:26
Alignment explanation
Indices: 226586--226640 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
226576 GGTAATTTTA
* * *
226586 AAATTTTTATTTAAAATCA-AAAAAT
1 AAATTTATATTAAAAAACACAAAAAT
*
226611 AAATTTATATTAAAAAACACAAAATT
1 AAATTTATATTAAAAAACACAAAAAT
226637 AAAT
1 AAAT
226641 ACTTTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATTTATATTAAAAAACACAAAAAT
Found at i:227527 original size:107 final size:106
Alignment explanation
Indices: 227379--227626 Score: 290
Period size: 107 Copynumber: 2.3 Consensus size: 106
227369 AAAAAAATAT
* * ** * *
227379 TTTTTGAAATATATATTATATAGTTTTTTAAAACGT-TTTTTTTAAATTATGTACAATATATAAG
1 TTTTTGAAATATATAATATATAGTTTTTAAAAAAATATTTTTTAAAATT-TATACAATATAT-AG
* *
227443 TTTTAAAACATTTT-GAAAA-TTATATAGTATATAGTTTTGAAATCA
64 TTTAAAAACATTTTGGAAAACTTATATA--ATAT--TTTTAAAATCA
*
227488 -TTTTGAAA-ATATAATATATAGTTTTTAAAAAAATATTTTTTGAAAATTTATATAATATATAGT
1 TTTTTGAAATATATAATATATAGTTTTTAAAAAAATATTTTTT-AAAATTTATACAATATATAGT
227551 TTAAAAACATTTTGGAAAACTTATATAATATTTTTAAAATCA
65 TTAAAAACATTTTGGAAAACTTATATAATATTTTTAAAATCA
*
227593 TTTTTGAAAATTATATAATATATAGTTTTGAAAA
1 TTTTTG-AAA-TATATAATATATAGTTTTTAAAA
227627 CATTTTTAAA
Statistics
Matches: 121, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
105 10 0.08
106 5 0.04
107 44 0.36
108 29 0.24
109 33 0.27
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (106 bp):
TTTTTGAAATATATAATATATAGTTTTTAAAAAAATATTTTTTAAAATTTATACAATATATAGTT
TAAAAACATTTTGGAAAACTTATATAATATTTTTAAAATCA
Found at i:227633 original size:36 final size:36
Alignment explanation
Indices: 227341--227657 Score: 215
Period size: 36 Copynumber: 8.9 Consensus size: 36
227331 TTTGAAAATG
* *
227341 TTTTTGAAAA--ATATAATATAAAGTTTTCAAAAAAATA
1 TTTTTGAAAATTATATAATATATAGTTTT---AAAAACA
* * *
227378 TTTTTTG-AAA-TATATATTATATAGTTTTTTAAAACGT
1 -TTTTTGAAAATTATATAATATATAG-TTTTAAAAAC-A
** *
227415 TTTTTTTAAATTATGTACAATATATAAGTTTT-AAAACA
1 TTTTTGAAAATTA--TATAATATAT-AGTTTTAAAAACA
* * *
227453 -TTTTGAAAATTATATAGTATATAGTTTTGAAATCA
1 TTTTTGAAAATTATATAATATATAGTTTTAAAAACA
*
227488 -TTTTG-AAA--ATATAATATATAGTTTTTAAAAAAATA
1 TTTTTGAAAATTATATAATATATAG-TTTT--AAAAACA
227523 TTTTTTGAAAATTTATATAATATATAG-TTTAAAAACA
1 -TTTTTGAAAA-TTATATAATATATAGTTTTAAAAACA
* *
227560 TTTTGGAAAACTTATAT-A-ATAT--TTTTAAAATCA
1 TTTTTGAAAA-TTATATAATATATAGTTTTAAAAACA
*
227593 TTTTTGAAAATTATATAATATATAGTTTTGAAAACA
1 TTTTTGAAAATTATATAATATATAGTTTTAAAAACA
*
227629 TTTTT---AA--ATATAATATATAGTTTAAAAAA
1 TTTTTGAAAATTATATAATATATAGTTTTAAAAA
227658 TATATATTTT
Statistics
Matches: 229, Mismatches: 27, Indels: 53
0.74 0.09 0.17
Matches are distributed among these distances:
31 20 0.09
32 18 0.08
33 25 0.11
34 17 0.07
35 23 0.10
36 38 0.17
37 27 0.12
38 22 0.10
39 12 0.05
40 12 0.05
41 15 0.07
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
TTTTTGAAAATTATATAATATATAGTTTTAAAAACA
Found at i:239997 original size:14 final size:14
Alignment explanation
Indices: 239974--240020 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
239964 CGCTGGGCAT
*
239974 CCGAGACCATCCGA
1 CCGAGGCCATCCGA
239988 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
240002 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
240016 ACGAG
1 CCGAG
240021 CTATGCGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.26, C:0.40, G:0.28, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:240041 original size:10 final size:10
Alignment explanation
Indices: 240026--240082 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
240016 ACGAGCTATG
240026 CGAGGGCATC
1 CGAGGGCATC
*
240036 CGAGGGCAAC
1 CGAGGGCATC
*
240046 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
240059 CGAGGGAATC
1 CGAGGGCATC
*
240069 CGAGGGCAAC
1 CGAGGGCATC
240079 CGAG
1 CGAG
240083 CGAGGGTAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
10 27 0.73
11 2 0.05
12 3 0.08
13 5 0.14
ACGTcount: A:0.26, C:0.26, G:0.40, T:0.07
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:240054 original size:33 final size:33
Alignment explanation
Indices: 240002--240086 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
239992 GGCCATCCGA
* * * *
240002 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
240035 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
240068 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
240087 GGTAGGTCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.26, C:0.28, G:0.38, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:240159 original size:23 final size:23
Alignment explanation
Indices: 240130--240233 Score: 142
Period size: 23 Copynumber: 4.7 Consensus size: 23
240120 TCGCTCGGTT
*
240130 GCTCGGATTCCCTCGCATAGCTC
1 GCTCGGATGCCCTCGCATAGCTC
240153 GCTCGGATGCCCTCGCATAGCTC
1 GCTCGGATGCCCTCGCATAGCTC
240176 GCTCGGATGCCCTCGCATAGCTC
1 GCTCGGATGCCCTCGCATAGCTC
* * *
240199 GTTCGGATGGCCTCGGAT-GCT-
1 GCTCGGATGCCCTCGCATAGCTC
*
240220 -CTCGGATGGCCTCG
1 GCTCGGATGCCCTCG
240234 GATGCTTTCG
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
20 13 0.17
22 3 0.04
23 60 0.79
ACGTcount: A:0.12, C:0.36, G:0.29, T:0.24
Consensus pattern (23 bp):
GCTCGGATGCCCTCGCATAGCTC
Found at i:240216 original size:10 final size:10
Alignment explanation
Indices: 240201--240254 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
240191 CATAGCTCGT
240201 TCGGATGGCC
1 TCGGATGGCC
240211 TCGGAT-GCTC
1 TCGGATGGC-C
240221 TCGGATGGCC
1 TCGGATGGCC
*
240231 TCGGAT-GCTT
1 TCGGATGGC-C
240241 TCGGATGGCC
1 TCGGATGGCC
240251 TCGG
1 TCGG
240255 TCGAATGGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 4 0.11
10 30 0.79
11 4 0.11
ACGTcount: A:0.09, C:0.28, G:0.37, T:0.26
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:240226 original size:20 final size:21
Alignment explanation
Indices: 240131--240254 Score: 108
Period size: 23 Copynumber: 5.7 Consensus size: 21
240121 CGCTCGGTTG
** *
240131 CTCGGATTCCCTCGCATAGCT
1 CTCGGATGGCCTCGGATAGCT
* *
240152 CGCTCGGATGCCCTCGCATAGCT
1 --CTCGGATGGCCTCGGATAGCT
* *
240175 CGCTCGGATGCCCTCGCATAGCT
1 --CTCGGATGGCCTCGGATAGCT
240198 CGTTCGGATGGCCTCGGAT-GCT
1 C--TCGGATGGCCTCGGATAGCT
240220 CTCGGATGGCCTCGGAT-GCT
1 CTCGGATGGCCTCGGATAGCT
*
240240 TTCGGATGGCCTCGG
1 CTCGGATGGCCTCGG
240255 TCGAATGGTC
Statistics
Matches: 95, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
20 33 0.35
21 1 0.01
22 4 0.04
23 57 0.60
ACGTcount: A:0.11, C:0.34, G:0.30, T:0.25
Consensus pattern (21 bp):
CTCGGATGGCCTCGGATAGCT
Found at i:240377 original size:29 final size:30
Alignment explanation
Indices: 240319--240391 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 30
240309 CTGCATGGAT
240319 TGCATGGCGACCTACCTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
** *
240349 TGCATGGCGACCT-GGTAGGTCGTTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
*
240378 TGCATGGTGACCTA
1 TGCATGGCGACCTA
240392 TATGGGGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 25 0.66
30 13 0.34
ACGTcount: A:0.14, C:0.25, G:0.38, T:0.23
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAGGTCGCTGGGCG
Found at i:241576 original size:22 final size:22
Alignment explanation
Indices: 241548--241599 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
241538 CAACCCCTGA
241548 TTTTCAAAATATGTTTGTTTTC
1 TTTTCAAAATATGTTTGTTTTC
241570 TTTTCAAAATATGTTTGTTTTC
1 TTTTCAAAATATGTTTGTTTTC
241592 TTTTCAAA
1 TTTTCAAA
241600 CATACTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.58
Consensus pattern (22 bp):
TTTTCAAAATATGTTTGTTTTC
Found at i:242816 original size:77 final size:77
Alignment explanation
Indices: 242730--242880 Score: 239
Period size: 77 Copynumber: 2.0 Consensus size: 77
242720 CCATTTCAAC
* *
242730 CCAATATCTAGTCTTATCAAAACTCTTTGGGAAGACAACTCAATAACTAGTCTTGTAAAAAATCC
1 CCAATATCTAGTCTTATCAAAACTCCTTGGGAAGACAACTCAATAACAAGTCTTGTAAAAAATCC
242795 TTAGGAAGACAA
66 TTAGGAAGACAA
* * * *
242807 CCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGACAACTCAATATCAAGTCTTGTCAAAACTCC
1 CCAATATCTAGTCTTATCAAAACTCCTTGGGAAGACAACTCAATAACAAGTCTTGTAAAAAATCC
*
242872 TTGGGAAGA
66 TTAGGAAGA
242881 TCACTTGATA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 67 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (77 bp):
CCAATATCTAGTCTTATCAAAACTCCTTGGGAAGACAACTCAATAACAAGTCTTGTAAAAAATCC
TTAGGAAGACAA
Found at i:242892 original size:39 final size:39
Alignment explanation
Indices: 242726--242880 Score: 231
Period size: 39 Copynumber: 4.0 Consensus size: 39
242716 GAGACCATTT
* * *
242726 CAACCCAATATCTAGTCTTATCAAAACTCTTTGGGAAGA
1 CAACTCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
* * * *
242765 CAACTCAATAACTAGTCTTGTAAAAAATCCTTAGGAAGA
1 CAACTCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
242804 CAAC-CAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
1 CAACTCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
*
242842 CAACTCAATATCAAGTCTTGTCAAAACTCCTTGGGAAGA
1 CAACTCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
242881 TCACTTGATA
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 34 0.33
39 69 0.67
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (39 bp):
CAACTCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
Found at i:249320 original size:21 final size:21
Alignment explanation
Indices: 249270--249320 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
249260 GTTTTGGGTA
*
249270 TTTTAAAATGTTATATTTTTC
1 TTTTAAAATATTATATTTTTC
*
249291 TTTAAAAATATCTA-ATTTTAT-
1 TTTTAAAATAT-TATATTTT-TC
249312 TTTTAAAAT
1 TTTTAAAAT
249321 TTTAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTAAAATATTATATTTTTC
Found at i:251554 original size:21 final size:21
Alignment explanation
Indices: 251528--251568 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
251518 TGCTTTTGAA
251528 AAAATTAAAAGTTTAGGTACT
1 AAAATTAAAAGTTTAGGTACT
* * *
251549 AAAATTGATATTTTAGGTAC
1 AAAATTAAAAGTTTAGGTAC
251569 CAAATGCGTA
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:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (21 bp):
AAAATTAAAAGTTTAGGTACT
Found at i:253325 original size:2 final size:2
Alignment explanation
Indices: 253318--253350 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
253308 TATTTATTTC
253318 TA TA TA 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 TA TA TA T
253351 TGCACAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:253959 original size:44 final size:43
Alignment explanation
Indices: 253872--254130 Score: 203
Period size: 42 Copynumber: 6.1 Consensus size: 43
253862 TGAGAACAAA
* * * *
253872 AAACGCCGCAAAAGGTCG--A--TATAGCGACGTTTTTTGAAC
1 AAACGCAGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
* *
253911 AAACGCAACAAAAGGTCGATATTTATAGCGGCATTTTTTGGAAC
1 AAACGCAGCAAAAGGTCGATATCTATAGCGGCA-TTTTTGGAAC
* *
253955 AAACG-ATGCAAAAGGCCGATATCTATAGAGGCA-TTTTGGAAC
1 AAACGCA-GCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
** * * *
253997 AAACGTC-GCAAAACATCGAGATCGATAGCGGCGTTTTTGGAAC
1 AAACG-CAGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
* * * *
254040 AAATGCCGCAAAAGGTC-ATATCTATAGTGGCATTTTTGAAAC
1 AAACGCAGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
* ** * ** *
254082 AAACGCCGCAAAAAATC-AAATCTATAGCAACATTTTTTGATAC
1 AAACGCAGCAAAAGGTCGATATCTATAGCGGCATTTTTGGA-AC
254125 AAACGC
1 AAACGC
254131 CACTAATTAC
Statistics
Matches: 176, Mismatches: 33, Indels: 18
0.78 0.15 0.08
Matches are distributed among these distances:
39 16 0.09
41 1 0.01
42 85 0.48
43 38 0.22
44 36 0.20
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (43 bp):
AAACGCAGCAAAAGGTCGATATCTATAGCGGCATTTTTGGAAC
Found at i:254083 original size:85 final size:86
Alignment explanation
Indices: 253935--254094 Score: 225
Period size: 85 Copynumber: 1.9 Consensus size: 86
253925 GTCGATATTT
* * *
253935 ATAGCGGCATTTTTTGGAACAAACGATGCAAAAGGCCGATATCTATAGAGGCATTTTGGAACAAA
1 ATAGCGGCAGTTTTTGGAACAAACGACGCAAAAGGCCGATATCTATAGAGGCATTTTGAAACAAA
*
254000 CGTCGCAAAACATCGAGATCG
66 CGCCGCAAAACATCGAGATCG
* * * *
254021 ATAGCGGC-GTTTTTGGAACAAATGCCGCAAAAGGTC-ATATCTATAGTGGCATTTTTGAAACAA
1 ATAGCGGCAGTTTTTGGAACAAACGACGCAAAAGGCCGATATCTATAGAGGCA-TTTTGAAACAA
254084 ACGCCGCAAAA
65 ACGCCGCAAAA
254095 AATCAAATCT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
84 14 0.22
85 43 0.66
86 8 0.12
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (86 bp):
ATAGCGGCAGTTTTTGGAACAAACGACGCAAAAGGCCGATATCTATAGAGGCATTTTGAAACAAA
CGCCGCAAAACATCGAGATCG
Found at i:254119 original size:85 final size:86
Alignment explanation
Indices: 253942--254129 Score: 213
Period size: 85 Copynumber: 2.2 Consensus size: 86
253932 TTTATAGCGG
* * *
253942 CATTTTTTGGAACAAACGATGCAAAAGGCCGATATCTATAGAGGCATTTTGGAACAAACGTCGCA
1 CATTTTTTGGAACAAACGACGCAAAAGGCCGATATCTATAGAGGCATTTTGAAACAAACGCCGCA
* * **
254007 AAACATCGAGATCGATAGCGG
66 AAAAATCGAAATCGATAGCAA
* * * * *
254028 C-GTTTTTGGAACAAATGCCGCAAAAGGTC-ATATCTATAGTGGCATTTTTGAAACAAACGCCGC
1 CATTTTTTGGAACAAACGACGCAAAAGGCCGATATCTATAGAGGCA-TTTTGAAACAAACGCCGC
*
254091 AAAAAATC-AAATCTATAGCAA
65 AAAAAATCGAAATCGATAGCAA
254112 CATTTTTT-GATACAAACG
1 CATTTTTTGGA-ACAAACG
254130 CCACTAATTA
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
84 26 0.31
85 57 0.68
86 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (86 bp):
CATTTTTTGGAACAAACGACGCAAAAGGCCGATATCTATAGAGGCATTTTGAAACAAACGCCGCA
AAAAATCGAAATCGATAGCAA
Found at i:256254 original size:3 final size:3
Alignment explanation
Indices: 256246--256280 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
256236 TATTTATATA
256246 ATG ATG ATG ATG ATG ATG AAT- ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG -ATG ATG ATG ATG ATG AT
256281 TGGTTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 26 0.87
4 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:256697 original size:28 final size:28
Alignment explanation
Indices: 256653--256706 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
256643 TCAATCCAAC
256653 GATCCTAAAAATATGTAAAACTAAAATA
1 GATCCTAAAAATATGTAAAACTAAAATA
*
256681 GATCCTAAAAGA-GTGTAAAACTAAAA
1 GATCCTAAAA-ATATGTAAAACTAAAA
256707 GAGTTTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (28 bp):
GATCCTAAAAATATGTAAAACTAAAATA
Found at i:256742 original size:2 final size:2
Alignment explanation
Indices: 256735--256774 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
256725 GTTGATCATA
256735 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
256775 TGTATGAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:269260 original size:42 final size:43
Alignment explanation
Indices: 269185--269272 Score: 151
Period size: 42 Copynumber: 2.0 Consensus size: 43
269175 TTTTTTTCAT
*
269185 TAGGAATAAATTAGATATATATCACTTATATAAAAACTATTTTA
1 TAGGAATAAATTAGA-ATATATCACTTATATAAAAACTATTATA
269229 TAGGAATAAATTAG-ATATATCACTTATATAAAAACTATTATA
1 TAGGAATAAATTAGAATATATCACTTATATAAAAACTATTATA
269271 TA
1 TA
269273 TTTTTTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
42 29 0.67
44 14 0.33
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (43 bp):
TAGGAATAAATTAGAATATATCACTTATATAAAAACTATTATA
Found at i:281387 original size:93 final size:93
Alignment explanation
Indices: 281228--281413 Score: 320
Period size: 93 Copynumber: 2.0 Consensus size: 93
281218 TCGTCCGAGC
*
281228 CTTTCGTGATTATTGGTGGTCGAGGCATCCATCGGAACGAGGTTGGCCTCTCTTAGCTTGGTCTA
1 CTTTCGTGATTATTGGTGCTCGAGGCATCCATCGGAACGAGGTTGGCCTCTCTTAGCTTGGTCTA
*
281293 CACTATGCACA-GCGGTTCGAGTAGGAGG
66 CACTATGCA-ATCCGGTTCGAGTAGGAGG
* *
281321 CTTTCGTGATTATTGGTGCTCGGGGCATCCATCTGAACGAGGTTGGCCTCTCTTAGCTTGGTCTA
1 CTTTCGTGATTATTGGTGCTCGAGGCATCCATCGGAACGAGGTTGGCCTCTCTTAGCTTGGTCTA
281386 CACTATGCAATCCGGTTCGAGTAGGAGG
66 CACTATGCAATCCGGTTCGAGTAGGAGG
281414 GCGTGGATTC
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 1 0.01
93 87 0.99
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (93 bp):
CTTTCGTGATTATTGGTGCTCGAGGCATCCATCGGAACGAGGTTGGCCTCTCTTAGCTTGGTCTA
CACTATGCAATCCGGTTCGAGTAGGAGG
Found at i:283759 original size:49 final size:49
Alignment explanation
Indices: 283687--283792 Score: 144
Period size: 49 Copynumber: 2.2 Consensus size: 49
283677 CGAAAATATG
* * *
283687 AAAATATATAAGTCACGACAACTTAGTTTAAGGTT-AATGAATGGTAGAT
1 AAAATGTATAAGTCACGACAACTTAATTTAAGGTTAAAT-AATGATAGAT
*
283736 AAAATGTATAAAGT-ACGACAACTTAATTTAAGGTTAAATAATTATAGAT
1 AAAATGTAT-AAGTCACGACAACTTAATTTAAGGTTAAATAATGATAGAT
283785 AAAATGTA
1 AAAATGTA
283793 CAATCGAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 44 0.86
50 7 0.14
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (49 bp):
AAAATGTATAAGTCACGACAACTTAATTTAAGGTTAAATAATGATAGAT
Found at i:284034 original size:14 final size:13
Alignment explanation
Indices: 283993--284034 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
283983 ACATTCAAAT
283993 CATAAATCATAAA
1 CATAAATCATAAA
*
284006 CCCTAAATCAT-AA
1 -CATAAATCATAAA
284019 CATAACATCATAAA
1 CATAA-ATCATAAA
284033 CA
1 CA
284035 ATAGTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 7 0.29
14 13 0.54
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (13 bp):
CATAAATCATAAA
Found at i:285333 original size:38 final size:37
Alignment explanation
Indices: 285291--285362 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
285281 CCTGAATCCG
* *
285291 ACCCGACCCGAACATCACCTTTAAAAAAATTCGACTCA
1 ACCCGACCCAAACATCACATTT-AAAAAATTCGACTCA
* *
285329 ACCCGACCCAAATATTACATTTAAAAAATTCGAC
1 ACCCGACCCAAACATCACATTTAAAAAATTCGAC
285363 CGATCATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 12 0.40
38 18 0.60
ACGTcount: A:0.42, C:0.31, G:0.07, T:0.21
Consensus pattern (37 bp):
ACCCGACCCAAACATCACATTTAAAAAATTCGACTCA
Found at i:294235 original size:2 final size:2
Alignment explanation
Indices: 294228--294259 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
294218 AATGTGGGTC
294228 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
294260 TATTTTTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:295135 original size:34 final size:34
Alignment explanation
Indices: 295066--295138 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
295056 ATGATCGTTT
** *
295066 CCTAACACTTTTACGACCCATCTTTGATTTGAAC
1 CCTAACACTTTTACGACCCATCTTTGACCTAAAC
**
295100 CCTAACACTCTTT-CGGTCCATCTTTGACCTAAAC
1 CCTAACACT-TTTACGACCCATCTTTGACCTAAAC
295134 CCTAA
1 CCTAA
295139 ACCAAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 30 0.91
35 3 0.09
ACGTcount: A:0.26, C:0.33, G:0.08, T:0.33
Consensus pattern (34 bp):
CCTAACACTTTTACGACCCATCTTTGACCTAAAC
Found at i:301718 original size:3 final size:3
Alignment explanation
Indices: 301710--301741 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
301700 TTGATGAATA
301710 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
301742 ATAATAGATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:303000 original size:16 final size:16
Alignment explanation
Indices: 302981--303052 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
302971 TAAATTCGGG
302981 TTACTTTCGGTTCGAA
1 TTACTTTCGGTTCGAA
* *
302997 TTACTTTCGATTCGAG
1 TTACTTTCGGTTCGAA
*
303013 TTGCTTTCGGTTC-AA
1 TTACTTTCGGTTCGAA
* * *
303028 GTTAATTTTGGTTCGGA
1 -TTACTTTCGGTTCGAA
*
303045 TTGCTTTC
1 TTACTTTC
303053 AGTCCAACTA
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
15 1 0.02
16 40 0.95
17 1 0.02
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.47
Consensus pattern (16 bp):
TTACTTTCGGTTCGAA
Found at i:304268 original size:6 final size:6
Alignment explanation
Indices: 304257--304307 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
304247 TAACAGAATA
* * *
304257 TGTGTG TGTGTG TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGTG
1 TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG
304305 TGT
1 TGT
304308 CTGTGTGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.10, G:0.49, T:0.41
Consensus pattern (6 bp):
TGTGCG
Found at i:304277 original size:12 final size:12
Alignment explanation
Indices: 304257--304318 Score: 83
Period size: 12 Copynumber: 5.3 Consensus size: 12
304247 TAACAGAATA
*
304257 TGTGTGTGTGTG
1 TGTGCGTGTGTG
*
304269 TGTGCGTGTGCG
1 TGTGCGTGTGTG
*
304281 TGTGCGTGTGCG
1 TGTGCGTGTGTG
304293 TGTGCGTGTGTG
1 TGTGCGTGTGTG
304305 TGT-C-TGTGTG
1 TGTGCGTGTGTG
304315 TGTG
1 TGTG
304319 TATGTATGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.20
11 1 0.02
12 36 0.78
ACGTcount: A:0.00, C:0.10, G:0.48, T:0.42
Consensus pattern (12 bp):
TGTGCGTGTGTG
Found at i:304283 original size:18 final size:18
Alignment explanation
Indices: 304257--304319 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
304247 TAACAGAATA
*
304257 TGTGTGTGTGTGTGTGCG
1 TGTGCGTGTGTGTGTGCG
*
304275 TGTGCGTGTGCGTGTGCG
1 TGTGCGTGTGTGTGTGCG
304293 TGTGCGTGTGTGTGT-C-
1 TGTGCGTGTGTGTGTGCG
*
304309 TGTGTGTGTGT
1 TGTGCGTGTGT
304320 ATGTATGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.24
17 1 0.02
18 30 0.73
ACGTcount: A:0.00, C:0.10, G:0.48, T:0.43
Consensus pattern (18 bp):
TGTGCGTGTGTGTGTGCG
Found at i:304312 original size:6 final size:6
Alignment explanation
Indices: 304257--304319 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
304247 TAACAGAATA
* * * * *
304257 TGTGTG TGTGTG TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
*
304305 TGTCTG TGTGTG TGT
1 TGTGTG TGTGTG TGT
304320 ATGTATGTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.00, C:0.10, G:0.48, T:0.43
Consensus pattern (6 bp):
TGTGTG
Found at i:304324 original size:4 final size:4
Alignment explanation
Indices: 304317--304341 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
304307 TCTGTGTGTG
304317 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
304342 ATATTTATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:311363 original size:30 final size:30
Alignment explanation
Indices: 311329--311478 Score: 210
Period size: 30 Copynumber: 5.0 Consensus size: 30
311319 TGGGACCTCG
*
311329 TTCCCCGTTCTGACATCTGCATGGGATTAA
1 TTCCCCGTTCTGACATCTGCATGAGATTAA
* *
311359 TTCCCCATTCTAACATCTGCATGAGATTAA
1 TTCCCCGTTCTGACATCTGCATGAGATTAA
* * *
311389 TACCCCCGTTCTGACATCTACATGGGATTAA
1 T-TCCCCGTTCTGACATCTGCATGAGATTAA
* *
311420 TTCCCCATTCTGACATCTGCATGAGATTAG
1 TTCCCCGTTCTGACATCTGCATGAGATTAA
*
311450 TTCCCCGTTCTTACATCTGCATGAGATTA
1 TTCCCCGTTCTGACATCTGCATGAGATTA
311479 TATCTCCGTC
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 79 0.76
31 25 0.24
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (30 bp):
TTCCCCGTTCTGACATCTGCATGAGATTAA
Found at i:311398 original size:61 final size:60
Alignment explanation
Indices: 311331--311478 Score: 233
Period size: 61 Copynumber: 2.5 Consensus size: 60
311321 GGACCTCGTT
311331 CCCCGTTCTGACATCTGCATGGGATTAATTCCCCATTCTAACATCTGCATGAGATTAATAC
1 CCCCGTTCTGACATCTGCATGGGATTAATTCCCCATTCTAACATCTGCATGAGATTAAT-C
* * * *
311392 CCCCGTTCTGACATCTACATGGGATTAATTCCCCATTCTGACATCTGCATGAGATTAGTT
1 CCCCGTTCTGACATCTGCATGGGATTAATTCCCCATTCTAACATCTGCATGAGATTAATC
* *
311452 CCCCGTTCTTACATCTGCATGAGATTA
1 CCCCGTTCTGACATCTGCATGGGATTA
311479 TATCTCCGTC
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
60 24 0.30
61 56 0.70
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (60 bp):
CCCCGTTCTGACATCTGCATGGGATTAATTCCCCATTCTAACATCTGCATGAGATTAATC
Found at i:317650 original size:16 final size:15
Alignment explanation
Indices: 317627--317665 Score: 69
Period size: 16 Copynumber: 2.5 Consensus size: 15
317617 AGAGTCTCTG
317627 AATCATTCAGCACTT
1 AATCATTCAGCACTT
317642 AATTCATTCAGCACTT
1 AA-TCATTCAGCACTT
317658 AATCATTC
1 AATCATTC
317666 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (15 bp):
AATCATTCAGCACTT
Found at i:318107 original size:23 final size:23
Alignment explanation
Indices: 318072--318130 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
318062 GAACAAGTGT
*
318072 AAACGATTATAAACGAACACAAA
1 AAACGAATATAAACGAACACAAA
* *
318095 AAACGAATGTAAACGAACACAAT
1 AAACGAATATAAACGAACACAAA
*
318118 AAATGAA-ATAAAC
1 AAACGAATATAAAC
318131 AAATATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.61, C:0.15, G:0.10, T:0.14
Consensus pattern (23 bp):
AAACGAATATAAACGAACACAAA
Found at i:318199 original size:23 final size:23
Alignment explanation
Indices: 318079--318200 Score: 92
Period size: 23 Copynumber: 5.5 Consensus size: 23
318069 TGTAAACGAT
* *
318079 TATAAACGAACACAAAAAACGAA
1 TATAAACGAACACAATAAATGAA
*
318102 TGTAAACGAACACAATAAATGAA
1 TATAAACGAACACAATAAATGAA
*
318125 -ATAAAC-AA-A-TATAAATGAA
1 TATAAACGAACACAATAAATGAA
** * * *
318144 -ATTGCACAAACATAACAAATGAA
1 TA-TAAACGAACACAATAAATGAA
* *
318167 CATAATCGAACACAATAAATGAA
1 TATAAACGAACACAATAAATGAA
*
318190 TGTAAACGAAC
1 TATAAACGAAC
318201 GTAAGAAACA
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
19 10 0.13
20 4 0.05
21 4 0.05
22 6 0.08
23 51 0.67
24 1 0.01
ACGTcount: A:0.59, C:0.15, G:0.10, T:0.16
Consensus pattern (23 bp):
TATAAACGAACACAATAAATGAA
Found at i:318450 original size:23 final size:23
Alignment explanation
Indices: 318410--318456 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
318400 ACGAACATAA
***
318410 ACGAACATACATGGACATAAATG
1 ACGAACATACACAAACATAAATG
318433 ACGAACATACACAAACATAAATG
1 ACGAACATACACAAACATAAATG
318456 A
1 A
318457 ATGAACGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.15
Consensus pattern (23 bp):
ACGAACATACACAAACATAAATG
Found at i:321596 original size:29 final size:29
Alignment explanation
Indices: 321523--321602 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
321513 CAATTTAACG
321523 GTTCAATGATATAACTTGAAATAAAAATCAAAA
1 GTTCAATGATATAA--TG--ATAAAAATCAAAA
* *
321556 -TTCAGT-ACTATAATGATAAAAATTAAAA
1 GTTCAATGA-TATAATGATAAAAATCAAAA
*
321584 GTTCAATGATATAACGATA
1 GTTCAATGATATAATGATA
321603 CGACGTCTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
28 12 0.30
29 14 0.35
30 3 0.08
31 1 0.03
32 10 0.25
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (29 bp):
GTTCAATGATATAATGATAAAAATCAAAA
Found at i:322912 original size:20 final size:20
Alignment explanation
Indices: 322868--323121 Score: 167
Period size: 20 Copynumber: 12.6 Consensus size: 20
322858 AATGACCAAT
* *
322868 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
322887 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
322907 AAAATCGCAACGTTAAAAAAG
1 AAAATCGCAACG-CGATTTAG
**
322928 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
322948 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
322969 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
322992 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* *
323012 AGAATCGCAACGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* *
323032 AGAATCGCAACGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* *
323052 AGAATCGCAATGCGA-TT-G
1 AAAATCGCAACGCGATTTAG
* * *
323070 AGAGTCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
323090 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
323110 AAAATCGCAACG
1 AAAATCGCAACG
323122 GTCAAAAGAA
Statistics
Matches: 188, Mismatches: 35, Indels: 23
0.76 0.14 0.09
Matches are distributed among these distances:
18 13 0.07
19 20 0.11
20 112 0.60
21 29 0.15
23 14 0.07
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:323094 original size:58 final size:59
Alignment explanation
Indices: 322973--323119 Score: 199
Period size: 58 Copynumber: 2.4 Consensus size: 59
322963 GCTTCCAAGT
* *
322973 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAACGCGATTTATAGAA
1 TCGCAACGCGATTTA-AAG--AATCGCAATGCGATTGA-AGAATCGCAACGCGATTGAGAGAA
* *
323036 TCGCAACGCGATTTATAGAATCGCAATGCGATTG-AGAGTCGCAACGCGATTGAGAGAA
1 TCGCAACGCGATTTAAAGAATCGCAATGCGATTGAAGAATCGCAACGCGATTGAGAGAA
323094 TCGCAACGCGATTTAGAA-AATCGCAA
1 TCGCAACGCGATTTA-AAGAATCGCAA
323120 CGGTCAAAAG
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
58 44 0.56
59 1 0.01
60 16 0.21
62 2 0.03
63 15 0.19
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (59 bp):
TCGCAACGCGATTTAAAGAATCGCAATGCGATTGAAGAATCGCAACGCGATTGAGAGAA
Found at i:323220 original size:6 final size:6
Alignment explanation
Indices: 323209--323265 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
323199 GACACGTATT
323209 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
323257 ACCACG ACC
1 ACCACG ACC
323266 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:323962 original size:6 final size:6
Alignment explanation
Indices: 323951--324037 Score: 174
Period size: 6 Copynumber: 14.5 Consensus size: 6
323941 TCTCGTCTCG
323951 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
323999 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
324038 AATACGTGTC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:324170 original size:20 final size:20
Alignment explanation
Indices: 324147--324357 Score: 307
Period size: 20 Copynumber: 10.4 Consensus size: 20
324137 ATTTTCAACG
*
324147 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTATCAATCGCA
* *
324167 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATCAATCGCA
*
324187 TTGCGATTTTCT-TCTAAATCGCG
1 TTGCGA--TTCTATC--AATCGCA
* *
324210 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTATCAATCGCA
* *
324230 TTGCGATTATATAAATCGCA
1 TTGCGATTCTATCAATCGCA
324250 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
324270 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
324290 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
324310 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
324330 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
324350 TTGCGATT
1 TTGCGATT
324358 TTCTTCTAAA
Statistics
Matches: 173, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
20 151 0.87
21 5 0.03
22 6 0.03
23 11 0.06
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTATCAATCGCA
Found at i:324417 original size:20 final size:20
Alignment explanation
Indices: 324392--324445 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
324382 TGGAAGCTCG
*
324392 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
324412 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
324432 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
324446 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:324472 original size:19 final size:20
Alignment explanation
Indices: 324432--324482 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
324422 TTCTTTTTAA
*
324432 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
324452 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
324471 CGTTGCGATTTT
1 CGTTGCGATTTT
324483 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:327786 original size:13 final size:13
Alignment explanation
Indices: 327768--327819 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
327758 ATAAACCATT
327768 TTTTTAATTTATA
1 TTTTTAATTTATA
*
327781 TTTTTATTTTATA
1 TTTTTAATTTATA
* * *
327794 ATTTAAATTGCATA
1 TTTTTAATT-TATA
327808 TTTTTATATTTA
1 TTTTTA-ATTTA
327820 AAGCAATGAA
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
13 18 0.62
14 8 0.28
15 3 0.10
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (13 bp):
TTTTTAATTTATA
Found at i:328185 original size:12 final size:13
Alignment explanation
Indices: 328163--328195 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
328153 AAAATTTTAA
328163 AATAAATATAATT
1 AATAAATATAATT
328176 AATAAA-ATAATT
1 AATAAATATAATT
*
328188 AATTAATA
1 AATAAATA
328196 CAAAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATAAATATAATT
Found at i:334114 original size:81 final size:81
Alignment explanation
Indices: 333979--334141 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
333969 AGACACATTG
333979 AACCATGAGAAAGAGAAAAATATTCATTATACTAAACTAGTATCTAAAAGTAGTACTCGTGCACC
1 AACCATGAGAAAGAGAAAAATATTCATTATACTAAACTAGTATCTAAAAGTAGTACTCGTGCACC
334044 AGAAAAGTTGATGTTA
66 AGAAAAGTTGATGTTA
334060 AACCATGAGAAAGAGAAAAATATTCATTATACTAAACTAGTATCTAAAAGTAGTACTCGTGCACC
1 AACCATGAGAAAGAGAAAAATATTCATTATACTAAACTAGTATCTAAAAGTAGTACTCGTGCACC
334125 AGAAAAGTTGATGTTA
66 AGAAAAGTTGATGTTA
334141 A
1 A
334142 CCTTCAAGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (81 bp):
AACCATGAGAAAGAGAAAAATATTCATTATACTAAACTAGTATCTAAAAGTAGTACTCGTGCACC
AGAAAAGTTGATGTTA
Found at i:339133 original size:12 final size:12
Alignment explanation
Indices: 339116--339142 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
339106 GAATCGAGTA
339116 AACGAGTTTATG
1 AACGAGTTTATG
339128 AACGAGTTTATG
1 AACGAGTTTATG
339140 AAC
1 AAC
339143 AAATCAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (12 bp):
AACGAGTTTATG
Found at i:341303 original size:15 final size:15
Alignment explanation
Indices: 341283--341312 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
341273 TATCACAATC
341283 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
*
341298 GCGCAGGATTTCGGG
1 GCGCAGGATTCCGGG
341313 AGCACCGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Done.