Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003303.1 Hibiscus syriacus cultivar Beakdansim tig00006949_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: 100828
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1102 original size:16 final size:16
Alignment explanation
Indices: 1081--1113 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1071 TGGTGATGTA
1081 TGTATTC-ATTCACTCT
1 TGTATTCTATTCA-TCT
1097 TGTATTCTATTCATCT
1 TGTATTCTATTCATCT
1113 T
1 T
1114 TAGAGATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.55
Consensus pattern (16 bp):
TGTATTCTATTCATCT
Found at i:6787 original size:31 final size:31
Alignment explanation
Indices: 6632--6773 Score: 257
Period size: 31 Copynumber: 4.6 Consensus size: 31
6622 AGGGTCGAAG
6632 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
6663 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
6694 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
6725 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
6756 GTTTACCTAGGTTCTTCG
1 GTTTACCTATGTTCTTCG
6774 AAATCTATGG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:7508 original size:21 final size:21
Alignment explanation
Indices: 7482--7523 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
7472 TCGAAGTTTC
* *
7482 ATGCATTGGTGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
7503 ATGCATCGATGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
7524 GGTTAATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
ATGCATCGATGCACTGTAGCA
Found at i:7933 original size:13 final size:13
Alignment explanation
Indices: 7915--7941 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7905 ATAAATAGCA
7915 TGTCTCCATTCGG
1 TGTCTCCATTCGG
7928 TGTCTCCATTCGG
1 TGTCTCCATTCGG
7941 T
1 T
7942 TGATTCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.30, G:0.22, T:0.41
Consensus pattern (13 bp):
TGTCTCCATTCGG
Found at i:11316 original size:22 final size:22
Alignment explanation
Indices: 11288--11341 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
11278 TAAAATATGG
*
11288 AATGAACAGTACTGTGAACAAT
1 AATGAACAGTACCGTGAACAAT
*
11310 AATGAACAGTGCCGTGAACAAT
1 AATGAACAGTACCGTGAACAAT
11332 ACCATGAACA
1 A--ATGAACA
11342 ATGAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 21 0.75
24 7 0.25
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (22 bp):
AATGAACAGTACCGTGAACAAT
Found at i:12202 original size:32 final size:31
Alignment explanation
Indices: 12086--12207 Score: 106
Period size: 31 Copynumber: 3.9 Consensus size: 31
12076 CCTCGGAAAC
* * * *
12086 TGTCCATA-GGTCCGAAGAACCTAGGTAAAT
1 TGTCCATATGTTCCGTAGAACATAGGTAATT
* *
12116 TATCCATATGTTCCTTAGAACATAGGT-ATAT
1 TGTCCATATGTTCCGTAGAACATAGGTAAT-T
* * * *
12147 TGTTCATATATACCG-AAAGACATAGGTAATT
1 TGTCCATATGTTCCGTAGA-ACATAGGTAATT
12178 CTGTCCATATGTTCCGTAGAACATAGGTAA
1 -TGTCCATATGTTCCGTAGAACATAGGTAA
12208 ACCCTCGACT
Statistics
Matches: 70, Mismatches: 16, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
30 10 0.14
31 34 0.49
32 24 0.34
33 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (31 bp):
TGTCCATATGTTCCGTAGAACATAGGTAATT
Found at i:15422 original size:27 final size:27
Alignment explanation
Indices: 15381--15473 Score: 168
Period size: 27 Copynumber: 3.4 Consensus size: 27
15371 GATAATAGCT
*
15381 CTGAATCATTCAGAATGTACTTCTGTA
1 CTGAATCATTCAGAATGTACTTCTGTG
*
15408 CTAAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
15435 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
15462 CTGAATCATTCA
1 CTGAATCATTCA
15474 ACACTGTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTG
Found at i:17600 original size:3 final size:3
Alignment explanation
Indices: 17582--17664 Score: 103
Period size: 3 Copynumber: 27.3 Consensus size: 3
17572 TGTAATATTA
* * *
17582 AAT AAT ATAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT TAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
17628 TAT AAT TAT AAT AAT AAT AAT TAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17665 TAAATAACAT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:18116 original size:113 final size:113
Alignment explanation
Indices: 17894--18679 Score: 1260
Period size: 113 Copynumber: 7.0 Consensus size: 113
17884 TAGAGTCATT
* ** * *
17894 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC-T--T-CTTCTCCTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*** ** * *
17955 TTATGAACT-TTTCTGGAAAAATTGACCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
* *
18002 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
18067 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
*
18115 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCATTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
**
18180 TTATGAACTCGATTTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
*
18228 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTATTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
18293 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
18341 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAAGTAATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTC-AG--ATGAGTTCTTC
* *** **
18406 TCATTATGAACTC-TACTTGGAAATTTTAATCCATCAAGTGATAAATTTGAG
63 TCATTATGAACTCGAAC-TGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
18457 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
* *
18522 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
18570 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
18635 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTT
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTT
18680 AAATCTTTGC
Statistics
Matches: 632, Mismatches: 36, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
108 32 0.05
109 1 0.00
111 1 0.00
112 30 0.05
113 459 0.73
114 4 0.01
115 4 0.01
116 101 0.16
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
Found at i:18486 original size:342 final size:339
Alignment explanation
Indices: 17894--18679 Score: 1260
Period size: 342 Copynumber: 2.3 Consensus size: 339
17884 TAGAGTCATT
* ** * *
17894 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTC-T--T-CTTCTCCTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*** ** * *
17955 TTATGAACT-TTTCTGGAAAAATTGACCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
*
18019 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
131 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
**
18084 AAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
196 AAAAGCTAATCCATCAAGTGATAAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
** *
18149 TCTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGATTTGGAAAAGCTAATCCATCAA
261 TCTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAA
*
18214 GTGATGGATTTGAG
326 GTGATAGATTTGAG
*
18228 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTATTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
*
18293 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
*
18358 TCTTCTCATTATGAACTTCTTCATCCTTCTTCAAGTAATGAGTTCTTCTCATTATGAACTC-TAC
131 TCTTCTCATTATGAACTTCTTCATCCTTCTTC-AG--ATGAGTTCTTCTCATTATGAACTCGAAC
***
18422 TTGGAAATTTTAATCCATCAAGTGATAAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATG
193 -TGGAAAAGCTAATCCATCAAGTGATAAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATG
*
18487 AACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCA
257 AACTTCTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCA
18552 TCAAGTGATAGATTTGAG
322 TCAAGTGATAGATTTGAG
18570 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
18635 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTT
66 TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTT
18680 AAATCTTTGC
Statistics
Matches: 416, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
334 33 0.08
335 1 0.00
337 1 0.00
338 29 0.07
339 78 0.19
340 2 0.00
341 2 0.00
342 270 0.65
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (339 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
AAAAGCTAATCCATCAAGTGATAAATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
TCTTCATCATTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAA
GTGATAGATTTGAG
Found at i:19545 original size:83 final size:83
Alignment explanation
Indices: 19403--19783 Score: 683
Period size: 83 Copynumber: 4.6 Consensus size: 83
19393 GGTTCCTACT
* *
19403 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATT-ACTCTTCTAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCA-TCTTCCAAT
19467 TTCAATGATTGGTTCTGCC
65 TTCAATGATTGGTTCTGCC
* *
19486 AAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCTAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
19551 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
* *
19569 AAACCAGATCAGATAACTCAAAGAACACTTACAGAAGATACTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
19634 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
*
19652 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAGCATATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
19717 TCAATGATTGGTTCTGCC
66 TCAATGATTGGTTCTGCC
19735 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCA
19784 CATTGCATTT
Statistics
Matches: 289, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
83 288 1.00
84 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAATT
TCAATGATTGGTTCTGCC
Found at i:20597 original size:16 final size:16
Alignment explanation
Indices: 20576--20612 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
20566 GAATTTTCGA
20576 AAATAAATTGAATCTT-
1 AAATAAATTGAA-CTTG
20592 AAATAAATTGAACTTG
1 AAATAAATTGAACTTG
20608 AAATA
1 AAATA
20613 GATAGAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (16 bp):
AAATAAATTGAACTTG
Found at i:28298 original size:15 final size:15
Alignment explanation
Indices: 28275--28306 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28265 TGAAATGAAT
28275 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
28290 AATGCATGTATGCAA
1 AATGAATGTATGCAA
28305 AA
1 AA
28307 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:33775 original size:3 final size:3
Alignment explanation
Indices: 33757--33845 Score: 133
Period size: 3 Copynumber: 29.3 Consensus size: 3
33747 TGTAATATTA
*
33757 AAT AAT ATAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
33803 AAT TAT AAT TAT AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
33846 TAAATAACAT
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
3 74 0.96
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:35812 original size:27 final size:27
Alignment explanation
Indices: 35764--35815 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
35754 ATGAAAGTAT
*
35764 GAATTAAAAGAAAAATTGAAAAAAAAG
1 GAATTAAAAGAAAAAATGAAAAAAAAG
*
35791 GAATTAAAAATAAAAAAT-AAAAAAA
1 GAATT-AAAAGAAAAAATGAAAAAAA
35816 TAATTGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (27 bp):
GAATTAAAAGAAAAAATGAAAAAAAAG
Found at i:39003 original size:20 final size:20
Alignment explanation
Indices: 38978--39072 Score: 59
Period size: 21 Copynumber: 4.7 Consensus size: 20
38968 GCGAAATAAA
38978 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATCTCCAG
** *
38998 AATCGCAAATC-AGCTCCCAG
1 AATCGCAACGCGATCT-CCAG
* * *
39018 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGAT-CTCCAG
** *
39038 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGA-TCTCCAG
39060 AATCGCAACGCGA
1 AATCGCAACGCGA
39073 ATATGAAAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
19 3 0.05
20 24 0.43
21 25 0.45
22 4 0.07
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGATCTCCAG
Found at i:39085 original size:20 final size:20
Alignment explanation
Indices: 39060--39235 Score: 113
Period size: 20 Copynumber: 8.8 Consensus size: 20
39050 GATTTTCCAG
**
39060 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGAA
* * *
39080 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATCCGAA
* * *
39100 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATCCG-AA
* * *
39121 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
*
39141 AATCGCAACGAC-AAT-AGTAA
1 AATCGCAACG-CGAATCCG-AA
* * *
39161 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGAA
* * *
39181 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGAA
* * *
39201 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGAA
*
39221 AATCGCAACGAGAAT
1 AATCGCAACGCGAAT
39236 ACGTAAATCA
Statistics
Matches: 120, Mismatches: 31, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
19 2 0.02
20 100 0.83
21 18 0.15
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGAA
Found at i:39172 original size:40 final size:40
Alignment explanation
Indices: 39101--39248 Score: 208
Period size: 40 Copynumber: 3.7 Consensus size: 40
39091 GATTCTGACT
* * **
39101 ATCGCAACGAGTATCCGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCACAACGCGTATCCGTAA
*
39142 ATCGCAACGACAATA-GTAAAATCACAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCACAACGCGTATCCGTAA
* *
39182 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAATCACAACGCGTATCCGTAA
39222 ATCGCAACGAGAATACGTAAATCACAA
1 ATCGCAACGAGAATACGTAAATCACAA
39249 TGCGATTTTG
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
40 83 0.86
41 14 0.14
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCACAACGCGTATCCGTAA
Found at i:39241 original size:20 final size:20
Alignment explanation
Indices: 39101--39244 Score: 139
Period size: 20 Copynumber: 7.2 Consensus size: 20
39091 GATTCTGACT
*
39101 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATACGT-AA
* * *
39122 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGTATACGTAA
**
39142 ATCGCAACGACAATA-GTAAA
1 ATCGCAACGAGTATACGT-AA
* * *
39162 ATCACAACGCGTATCCGTAA
1 ATCGCAACGAGTATACGTAA
*
39182 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATACGTAA
*
39202 ATCGCAACGCGTAT-CTGTAA
1 ATCGCAACGAGTATAC-GTAA
*
39222 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATACGTAA
39242 ATC
1 ATC
39245 ACAATGCGAT
Statistics
Matches: 99, Mismatches: 20, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
19 3 0.03
20 77 0.78
21 19 0.19
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGTATACGTAA
Found at i:41096 original size:18 final size:19
Alignment explanation
Indices: 41069--41113 Score: 83
Period size: 18 Copynumber: 2.4 Consensus size: 19
41059 GCAACGAGAG
41069 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41088 AAT-GCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
41106 AATCGCAA
1 AATCGCAA
41114 CGAGTGAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:41201 original size:33 final size:33
Alignment explanation
Indices: 41144--41237 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
41134 ATTAGTTTCA
*
41144 CGTTGCGATTTTTATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
41178 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
41211 CGTTGCGATAGTCATTTCCGCGTTGCG
1 CGTTGCGATTTTCATTT-CGCATTGCG
41238 GTAGTCTGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 33 0.61
34 21 0.39
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:41360 original size:14 final size:14
Alignment explanation
Indices: 41341--41377 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
41331 CATCAATTAA
41341 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
41355 ACAAATCATCTTTT
1 ACAAATCAACATTT
41369 ACAAATCAA
1 ACAAATCAA
41378 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:42838 original size:42 final size:42
Alignment explanation
Indices: 42731--42842 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
42721 TCTAGAATGT
* * *
42731 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
42773 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
*
42815 TAGGG-GATGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
42843 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:43345 original size:20 final size:20
Alignment explanation
Indices: 43322--43404 Score: 121
Period size: 20 Copynumber: 4.2 Consensus size: 20
43312 GAAACTTAAA
*
43322 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
43342 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
43362 ATCGCAATGTGAAAATAACT
1 ATCGCAATGCGAAAATGACT
**
43382 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
43402 ATC
1 ATC
43405 ACAAAGAGAG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:43465 original size:19 final size:19
Alignment explanation
Indices: 43443--43486 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
43433 AAATCGCAAC
*
43443 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCACGTT
* *
43462 GCGATTTTGGTTTCACGTT
1 GCGATTATAGTTTCACGTT
43481 GCGATT
1 GCGATT
43487 TTGTCGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCACGTT
Found at i:43487 original size:19 final size:18
Alignment explanation
Indices: 43452--43521 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 18
43442 CGCGATTATA
43452 GTTTCGCGTTGCGATTTTG
1 GTTTC-CGTTGCGATTTTG
43471 GTTTCACGTTGCGATTTT-
1 GTTTC-CGTTGCGATTTTG
43489 G--T-CGTTGCGATTTTG
1 GTTTCCGTTGCGATTTTG
*
43504 GTTTCTCGTTGTGATTTT
1 GTTTC-CGTTGCGATTTT
43522 CATTCCTCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 28 0.64
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.51
Consensus pattern (18 bp):
GTTTCCGTTGCGATTTTG
Found at i:43496 original size:14 final size:14
Alignment explanation
Indices: 43477--43503 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43467 TTTGGTTTCA
43477 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
43491 CGTTGCGATTTTG
1 CGTTGCGATTTTG
43504 GTTTCTCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:43500 original size:33 final size:33
Alignment explanation
Indices: 43458--43521 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
43448 TATAGTTTCG
43458 CGTTGCGATTTTGGTTTCACGTTGCGATTTTGT
1 CGTTGCGATTTTGGTTTCACGTTGCGATTTTGT
* *
43491 CGTTGCGATTTTGGTTTCTCGTTGTGATTTT
1 CGTTGCGATTTTGGTTTCACGTTGCGATTTT
43522 CATTCCTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.08, C:0.14, G:0.27, T:0.52
Consensus pattern (33 bp):
CGTTGCGATTTTGGTTTCACGTTGCGATTTTGT
Found at i:43555 original size:31 final size:32
Alignment explanation
Indices: 43507--43568 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
43497 GATTTTGGTT
*
43507 TCTCGTTGTGATTTTCATTCCTCGTTGCGATTC
1 TCTCGTTGTGA-TTTCATTCCGCGTTGCGATTC
*
43540 TCTCGTTGTGA-TTCATTTCGCGTTGCGAT
1 TCTCGTTGTGATTTCATTCCGCGTTGCGAT
43569 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 16 0.59
33 11 0.41
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (32 bp):
TCTCGTTGTGATTTCATTCCGCGTTGCGATTC
Found at i:43802 original size:94 final size:94
Alignment explanation
Indices: 43656--44035 Score: 665
Period size: 94 Copynumber: 4.1 Consensus size: 94
43646 ATGGATTGCA
* *
43656 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
43720 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAATAAAT
43749 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
43814 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAATAAAT
* *
43843 TTACTTTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTGAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
43908 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAATAAAT
* *
43937 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAATGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
*
44001 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAATAAAT
44031 TTACT
1 TTACT
44036 AAGCAATCTA
Statistics
Matches: 273, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
93 23 0.08
94 250 0.92
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:45758 original size:20 final size:19
Alignment explanation
Indices: 45735--45805 Score: 97
Period size: 20 Copynumber: 3.6 Consensus size: 19
45725 TGAAATGAAA
45735 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGA-AATGACT
45755 ATCGCAACGTAGAAATGACT
1 ATCGCAACG-AGAAATGACT
* **
45775 ATCGCAACGCGAAATGAAA
1 ATCGCAACGAGAAATGACT
45794 ATCGCAACGAGA
1 ATCGCAACGAGA
45806 GAATCGCAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 18 0.39
20 25 0.54
21 3 0.07
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAACGAGAAATGACT
Found at i:45790 original size:19 final size:19
Alignment explanation
Indices: 45726--45857 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
45716 TCTTTTGGTT
*
45726 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
45745 GAGAATGACTATCGCAACGTA
1 GA-AATGAAAATCGCAACG-C
**
45766 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
45785 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
45802 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
45818 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
45837 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
45856 GA
1 GA
45858 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 47 0.49
20 30 0.31
21 3 0.03
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:45886 original size:19 final size:20
Alignment explanation
Indices: 45864--45974 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
45854 GCGATTTTGG
45864 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
45883 TTTCGCGTTGCGA--TTC--
1 TTTCGCGTTGCGATTTTCAT
*
45899 --TCTCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
* **
45917 TTCTCTCGTTGCGATAGTCAT
1 TT-TCGCGTTGCGATTTTCAT
*
45938 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
**
45958 TTTCATGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
45975 AAGTTTAGAA
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 13 0.17
20 30 0.39
21 18 0.23
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:46536 original size:20 final size:20
Alignment explanation
Indices: 46510--46703 Score: 203
Period size: 20 Copynumber: 9.6 Consensus size: 20
46500 CTTTAAAAAT
46510 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
46530 TGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
46550 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* *
46571 CGCATTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
46591 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
46611 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
46631 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
46651 TGTCGTTGTGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
**
46672 CGCGTTGCGATTTTATAGATA
1 CGCGTTGCGA-TTTACGGATA
*
46693 CTCGTTGCGAT
1 CGCGTTGCGAT
46704 AGTCAGAATC
Statistics
Matches: 144, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
20 94 0.65
21 50 0.35
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:46658 original size:41 final size:40
Alignment explanation
Indices: 46510--46684 Score: 203
Period size: 41 Copynumber: 4.3 Consensus size: 40
46500 CTTTAAAAAT
*
46510 CGCGTTGCGATTTACGGATATGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTACGGATATGCGTTGCGA-TTTACGGATA
* * * *
46550 TGTCGTTGCGATTTACGGATACGCATTGCGATTTACAGATA
1 CG-CGTTGCGATTTACGGATATGCGTTGCGATTTACGGATA
* *
46591 CGCGTTGCGATTTACGTAT-TCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATAT-GCGTTGCGATTTACGGATA
* *
46631 CGCGTTGCGATTTTACGTAT-TGTCGTTGTGATTTACGGATA
1 CGCGTTGCGA-TTTACGGATATG-CGTTGCGATTTACGGATA
46672 CGCGTTGCGATTT
1 CGCGTTGCGATTT
46685 TATAGATACT
Statistics
Matches: 117, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
40 53 0.45
41 64 0.55
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (40 bp):
CGCGTTGCGATTTACGGATATGCGTTGCGATTTACGGATA
Found at i:46735 original size:20 final size:20
Alignment explanation
Indices: 46712--46764 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
46702 ATAGTCAGAA
* *
46712 TCGCGCTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
46732 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
46752 TCGCGTTGCGATT
1 TCGCGTTGCGATT
46765 CTGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.13, C:0.21, G:0.25, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:51195 original size:7 final size:7
Alignment explanation
Indices: 51185--51210 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
51175 CAATTACATT
51185 CAAAACC
1 CAAAACC
51192 CAAAACC
1 CAAAACC
51199 CAAAACC
1 CAAAACC
51206 CAAAA
1 CAAAA
51211 TACTTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAACC
Found at i:52738 original size:31 final size:31
Alignment explanation
Indices: 52713--52824 Score: 179
Period size: 31 Copynumber: 3.6 Consensus size: 31
52703 TCCATAGATT
* * *
52713 CCGAATAACCTAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
*
52744 CCGAAGAACATAGGTAAACAATGCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
*
52775 CCAAAGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
52806 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
52825 CCTCGACCCT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAATCCATATGTC
Found at i:53580 original size:20 final size:20
Alignment explanation
Indices: 53555--53608 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
53545 CGAAATATCC
53555 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
53575 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
53595 ATGCATCGATGCAC
1 ATGCATCGATGCAC
53609 TTACCCATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:54684 original size:35 final size:35
Alignment explanation
Indices: 54645--54724 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
54635 GGGGTTGGGC
*
54645 ATGTAATTGAAGTATTTTGGAA-TTTGATGTTTAGA
1 ATGTAATTGAAGTATTTT-GAATTTTGAGGTTTAGA
*
54680 ATGTAATTGAAGTATTTTGAATTTTGGGGTTTAGA
1 ATGTAATTGAAGTATTTTGAATTTTGAGGTTTAGA
54715 ATGTAATTGA
1 ATGTAATTGA
54725 TGATTGTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 3 0.07
35 39 0.93
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGAATTTTGAGGTTTAGA
Found at i:55082 original size:12 final size:13
Alignment explanation
Indices: 55055--55080 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55045 CTTATTTCAC
55055 TAAAAAATAATTT
1 TAAAAAATAATTT
55068 TAAAAAATAATTT
1 TAAAAAATAATTT
55081 AAGTAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAAAATAATTT
Found at i:58775 original size:63 final size:63
Alignment explanation
Indices: 58702--58955 Score: 413
Period size: 63 Copynumber: 4.0 Consensus size: 63
58692 AGAGTTGAGG
*
58702 AGTATACCTATGTTCTACGGAACATATGGATAGAATTACCTATGTCTTTCGGGACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
*
58765 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGTAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
*
58828 AGTATACCTATGTTCTATGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
* * * * *
58891 AATATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTAGGT-TCTTCGGGACCTATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCT-TTCGGGACATATGGAC
58953 AGT
1 AGT
58956 TACTGAGGTT
Statistics
Matches: 180, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
61 1 0.01
62 26 0.14
63 153 0.85
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (63 bp):
AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
Found at i:58776 original size:31 final size:31
Alignment explanation
Indices: 58702--58955 Score: 264
Period size: 31 Copynumber: 8.1 Consensus size: 31
58692 AGAGTTGAGG
* *
58702 AGTATACCTATGTTCTACGGAACATATGGAT
1 AGTATACCTATGTTCTTCGGAACATATGGAC
* *
58733 AGAATTACCTATG-TCTTTCGGGACATATGGAC
1 AGTA-TACCTATGTTC-TTCGGAACATATGGAC
*
58765 AGTATACCTATGTTCTACGGAACATATGGAC
1 AGTATACCTATGTTCTTCGGAACATATGGAC
* * *
58796 AGAATTACCTATG-TCTTTCGGGACATATGTAC
1 AGTA-TACCTATGTTC-TTCGGAACATATGGAC
58828 AGTATACCTATGTTCTAT-GGAACATATGGAC
1 AGTATACCTATGTTCT-TCGGAACATATGGAC
* *
58859 AGAATTACCTATG-TCTTTCGGGACATATGGAC
1 AGTA-TACCTATGTTC-TTCGGAACATATGGAC
* **
58891 AATATACCTATGTTCTAAGGAACATATGGAC
1 AGTATACCTATGTTCTTCGGAACATATGGAC
* * * *
58922 AGTTTACCTAGGTTCTTCGGGACCTATGGAC
1 AGTATACCTATGTTCTTCGGAACATATGGAC
58953 AGT
1 AGT
58956 TACTGAGGTT
Statistics
Matches: 184, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
31 106 0.58
32 78 0.42
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
AGTATACCTATGTTCTTCGGAACATATGGAC
Found at i:62176 original size:32 final size:31
Alignment explanation
Indices: 62122--62354 Score: 238
Period size: 31 Copynumber: 7.4 Consensus size: 31
62112 GTCGAGGAGT
*
62122 ATACCTATGTTCTACGGAACATATGGATAGA
1 ATACCTATGTTCTACGGAACATATGGACAGA
* * *
62153 ATTACCTATG-TCTTTCGGGACATATGGACAGT
1 A-TACCTATGTTC-TACGGAACATATGGACAGA
*
62185 ATACCTATGTTCTACGGAACATATGGACAAA
1 ATACCTATGTTCTACGGAACATATGGACAGA
* * *
62216 ATTACCTATG-TCTTTCGGGACATATGGACAGT
1 A-TACCTATGTTC-TACGGAACATATGGACAGA
62248 ATACCTATGTTCTACGGAACATATGGACAGA
1 ATACCTATGTTCTACGGAACATATGGACAGA
* * *
62279 ATTACCTATG-TCTTTCGGGACATATGGACAGT
1 A-TACCTATGTTC-TACGGAACATATGGACAGA
* * * *
62311 ATACCTATGTTCCAAGGAATATATGGACAGT
1 ATACCTATGTTCTACGGAACATATGGACAGA
* *
62342 TTACCTAGGTTCT
1 ATACCTATGTTCT
62355 TCGGGACCTA
Statistics
Matches: 167, Mismatches: 26, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
31 88 0.53
32 79 0.47
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
ATACCTATGTTCTACGGAACATATGGACAGA
Found at i:62192 original size:63 final size:63
Alignment explanation
Indices: 62119--62372 Score: 404
Period size: 63 Copynumber: 4.0 Consensus size: 63
62109 AGAGTCGAGG
*
62119 AGTATACCTATGTTCTACGGAACATATGGATAGAATTACCTATGTCTTTCGGGACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
*
62182 AGTATACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGGGACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
62245 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
* * * * * * *
62308 AGTATACCTATGTTCCAAGGAATATATGGACAG-TTTACCTAGGT-TCTTCGGGACCTATAGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCT-TTCGGGACATATGGAC
62370 AGT
1 AGT
62373 TTCTGAGGTT
Statistics
Matches: 180, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
61 1 0.01
62 26 0.14
63 153 0.85
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (63 bp):
AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
Found at i:64515 original size:20 final size:20
Alignment explanation
Indices: 64492--64605 Score: 174
Period size: 20 Copynumber: 5.7 Consensus size: 20
64482 GATTCTGACT
* * *
64492 ATCGCATTGCGATTATGTAA
1 ATCGCAATGCGAATACGTAA
64512 ATCGCAATGCGAATACGTAA
1 ATCGCAATGCGAATACGTAA
64532 ATCGCAATGCGAATACGTAA
1 ATCGCAATGCGAATACGTAA
64552 ATCGCAATGCGAATACGTAA
1 ATCGCAATGCGAATACGTAA
*
64572 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATACGTAA
* *
64592 ATCACAACGCGAAT
1 ATCGCAATGCGAAT
64606 CTGACTATCG
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATACGTAA
Found at i:64537 original size:60 final size:60
Alignment explanation
Indices: 64473--64621 Score: 185
Period size: 60 Copynumber: 2.5 Consensus size: 60
64463 GTTTCCAGAT
* * *
64473 TCGCAACGCGATTCTGACTATCGCATTGCGATTATGTAAATCGCAATGCGAATACGTAAA
1 TCGCAACGCGATTCTGACTATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAA
* * * *
64533 TCGCAATGCGAATAC-GTA-AATCGCAATGCGAATACGTAAATCGCAATGCGAATATGTAAA
1 TCGCAACGCG-ATTCTG-ACTATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAA
* *
64593 TCACAACGCGAATCTGACTATCGCAATGC
1 TCGCAACGCGATTCTGACTATCGCAATGC
64622 AATTTACATA
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
59 3 0.04
60 66 0.90
61 4 0.05
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (60 bp):
TCGCAACGCGATTCTGACTATCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAA
Found at i:64820 original size:22 final size:22
Alignment explanation
Indices: 64802--64857 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
64792 GCGAAATCCA
64802 TCCCCATCTCCGACAAAATCAG
1 TCCCCATCTCCGACAAAATCAG
* * *
64824 TCCCCATCTCCGACGATATTAG
1 TCCCCATCTCCGACAAAATCAG
*
64846 TCTCCATCTCCG
1 TCCCCATCTCCG
64858 GTGAAATCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.23, C:0.41, G:0.11, T:0.25
Consensus pattern (22 bp):
TCCCCATCTCCGACAAAATCAG
Found at i:65253 original size:20 final size:20
Alignment explanation
Indices: 65180--65270 Score: 103
Period size: 20 Copynumber: 4.6 Consensus size: 20
65170 GCGATTCTGT
65180 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
65199 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
65219 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
65239 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
65259 TGTTGCGATTTT
1 CGTTGCGATTTT
65271 AAGTTTCAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
19 12 0.19
20 51 0.81
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:65277 original size:20 final size:20
Alignment explanation
Indices: 65234--65277 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
65224 CGATAGTCAT
* *
65234 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
65254 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
65274 TTTC
1 TTTC
65278 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:67172 original size:20 final size:20
Alignment explanation
Indices: 67147--67303 Score: 126
Period size: 20 Copynumber: 8.5 Consensus size: 20
67137 ATAATAGTTT
*
67147 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
67167 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
67187 ACTATCGTAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
67203 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
67220 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
67236 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
67254 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
67274 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
67294 ACTATCGCAA
1 ACTATCGCAA
67304 CGAAAGAATC
Statistics
Matches: 114, Mismatches: 9, Indels: 28
0.75 0.06 0.19
Matches are distributed among these distances:
14 13 0.11
16 10 0.09
17 8 0.07
18 5 0.04
19 7 0.06
20 71 0.62
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:67216 original size:34 final size:34
Alignment explanation
Indices: 67170--67325 Score: 147
Period size: 34 Copynumber: 4.5 Consensus size: 34
67160 AAAAATGACT
* * *
67170 ATCGCAACGCGAAAATGACTATCGTAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
** *
67204 ATCGCAATGCG-AAATGAAAATCGCAAC-AACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACGAA-AGA
*
67237 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
**
67275 CTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
67311 ATCGCAATGC-AAAAT
1 ATCGCAATGCGAAAAT
67326 AAAAATCGCA
Statistics
Matches: 98, Mismatches: 15, Indels: 19
0.74 0.11 0.14
Matches are distributed among these distances:
32 1 0.01
33 28 0.29
34 33 0.34
36 3 0.03
37 4 0.04
38 5 0.05
40 24 0.24
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:67376 original size:20 final size:20
Alignment explanation
Indices: 67348--67456 Score: 164
Period size: 20 Copynumber: 5.5 Consensus size: 20
67338 GTGATTCTAT
67348 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
67368 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
67388 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
67408 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
**
67428 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
67448 CGTTGCGAT
1 CGTTGCGAT
67457 TTTAAGTTTC
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:68013 original size:21 final size:21
Alignment explanation
Indices: 67989--68047 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
67979 CTATCATCCC
67989 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* * * *
68010 TCAAGAGGCCACTGCCATCGT
1 TCAAGAGTCCCCTCCCACCGT
*
68031 TGAAGAGGT-CCCTCCCA
1 TCAAGA-GTCCCCTCCCA
68048 ACATTCTAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.22, C:0.39, G:0.20, T:0.19
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:69446 original size:14 final size:14
Alignment explanation
Indices: 69427--69462 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
69417 ATTGTTTAAT
69427 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
69441 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
69455 TGATTTGT
1 TGATTTGT
69463 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:69587 original size:14 final size:14
Alignment explanation
Indices: 69568--69621 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
69558 AAAACAGACT
69568 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
69582 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
69601 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
69615 ATCGCAA
1 ATCGCAA
69622 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:69605 original size:33 final size:34
Alignment explanation
Indices: 69568--69642 Score: 143
Period size: 33 Copynumber: 2.2 Consensus size: 34
69558 AAAACAGACT
69568 ATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
69601 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
69635 ATCGCAAC
1 ATCGCAAC
69643 ACGAAACTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 25 0.61
34 16 0.39
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:69683 original size:20 final size:19
Alignment explanation
Indices: 69654--69720 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
69644 CGAAACTAAA
*
69654 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
69674 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
69690 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
69707 TTCGCATTGCGATT
1 TTCGCATTGCGATT
69721 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 3 0.08
18 4 0.10
19 8 0.21
20 11 0.28
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:69715 original size:33 final size:33
Alignment explanation
Indices: 69658--69742 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
69648 ACTAAATTCG
69658 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
69692 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
69725 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
69743 CGTGTTGCGA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.71
34 14 0.29
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:69751 original size:20 final size:20
Alignment explanation
Indices: 69725--69778 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
69715 GCGATTCTCT
69725 CGTTGCGATAGTCAT-TTCCG
1 CGTTGCGATAGTCATATT-CG
*
69745 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATATTCG
69765 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
69779 AATGAATGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATATTCG
Found at i:72222 original size:24 final size:24
Alignment explanation
Indices: 72188--72241 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
72178 CTGAAAAATC
72188 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
72212 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
72236 ATCAAA
1 ATCAAA
72242 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:73108 original size:20 final size:20
Alignment explanation
Indices: 73083--73149 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
73073 AAATTCAGTA
73083 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
73103 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* * *
73123 TTGCGATAGTCATATTCACG
1 TTGCGATAGTCAGAATCTCG
73143 TTGCGAT
1 TTGCGAT
73150 TTACGTATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:73158 original size:20 final size:20
Alignment explanation
Indices: 73143--73285 Score: 187
Period size: 20 Copynumber: 7.1 Consensus size: 20
73133 CATATTCACG
73143 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
73163 TTGCGATTTATGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
73183 TTGAGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
73203 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
73223 TTGCGATTTACATAATCGCA
1 TTGCGATTTACGTATTCGCA
* * ** **
73243 TTGCTATTTTCCAAATTCGTG
1 TTGCGA-TTTACGTATTCGCA
73264 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
73284 TT
1 TT
73286 ACGAATTAGG
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
20 90 0.87
21 14 0.13
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:73167 original size:40 final size:41
Alignment explanation
Indices: 73123--73293 Score: 170
Period size: 40 Copynumber: 4.3 Consensus size: 41
73113 CAGAATCTCG
* * *
73123 TTGCGATAGT-CATATTCACGTTGCGATTTACGTATTCGCA
1 TTGCGATATTACATATTCGCATTGCGATTTACGTATTCGCA
** *
73163 TTGCGAT-TTATGTATTCGCATTGAGATTTACGTATTCGCA
1 TTGCGATATTACATATTCGCATTGCGATTTACGTATTCGCA
* * *
73203 TTGCGAT-TTACGTATTCGCATTGCGATTTACATAATCGCA
1 TTGCGATATTACATATTCGCATTGCGATTTACGTATTCGCA
* * * * **
73243 TTGCTATTTTCCAAATTCGTGTTGCGATTTACGTATTCGCA
1 TTGCGATATTACATATTCGCATTGCGATTTACGTATTCGCA
*
73284 TTACGA-ATTA
1 TTGCGATATTA
73294 GGAAAATCGC
Statistics
Matches: 107, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 76 0.71
41 30 0.28
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (41 bp):
TTGCGATATTACATATTCGCATTGCGATTTACGTATTCGCA
Found at i:73328 original size:61 final size:59
Alignment explanation
Indices: 73136--73330 Score: 187
Period size: 60 Copynumber: 3.2 Consensus size: 59
73126 CGATAGTCAT
* * * *
73136 ATTCACGTTGCGATTTACGTATTCGCATTGCGATTTATG-TATTCGCATTGAGATTTACG
1 ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTA-GATAATCGCATTGCGATTTAAG
* * *
73195 TATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACATAATCGCATTGCTATTTTCCAA-
1 -ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTAGATAATCGCATTGCGA-TTT--AAG
* * * * * *
73257 ATTCGTGTTGCGATTTACGTATTCGCATTACGAATTAGGAAAATCGCAATGCGATAGTAAG
1 ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTA-GATAATCGCATTGCGAT-TTAAG
*
73318 AATCGCGTTGCGA
1 ATTCGCGTTGCGA
73331 ATCTGGAAAC
Statistics
Matches: 110, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
60 48 0.44
61 48 0.44
62 13 0.12
63 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (59 bp):
ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTAGATAATCGCATTGCGATTTAAG
Found at i:74428 original size:2 final size:2
Alignment explanation
Indices: 74421--74460 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
74411 AAAGTGAACC
74421 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
74461 GAATATGAGA
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:74787 original size:32 final size:30
Alignment explanation
Indices: 74733--74951 Score: 206
Period size: 32 Copynumber: 7.0 Consensus size: 30
74723 GTCGAGGAGT
*
74733 ATACCTATGTTCTACGGAACATATGGATAGA
1 ATACCTATG-TCTACGGAACATATGGACAGA
* * * *
74764 ATTACCTATGTCATTCGGGACATATGGATAGT
1 A-TACCTATGTC-TACGGAACATATGGACAGA
*
74796 ATACCTATGTTCTACGGAACATATGGACATA
1 ATACCTATG-TCTACGGAACATATGGACAGA
* * *
74827 ATTACCTATGTCTTTCAGG-ACATATGGATAGT
1 A-TACCTATGTC-TAC-GGAACATATGGACAGA
*
74859 ATACCTATGTTCAACGGAACATATGGACAGA
1 ATACCTATG-TCTACGGAACATATGGACAGA
* * *
74890 ATTACCTATGTCTTTCGGGACATATGGACAGT
1 A-TACCTATGTC-TACGGAACATATGGACAGA
*
74922 ATACCTATGTTCTAAGGAACATATGGACAG
1 ATACCTATG-TCTACGGAACATATGGACAG
74952 TTTACCTAGG
Statistics
Matches: 154, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
30 2 0.01
31 74 0.48
32 76 0.49
33 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (30 bp):
ATACCTATGTCTACGGAACATATGGACAGA
Found at i:74803 original size:63 final size:63
Alignment explanation
Indices: 74730--74979 Score: 387
Period size: 63 Copynumber: 4.0 Consensus size: 63
74720 AGAGTCGAGG
* *
74730 AGTATACCTATGTTCTACGGAACATATGGATAGAATTACCTATGTCATTCGGGACATATGGAT
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAT
* *
74793 AGTATACCTATGTTCTACGGAACATATGGACATAATTACCTATGTCTTTCAGGACATATGGAT
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAT
* *
74856 AGTATACCTATGTTCAACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAT
* * * *
74919 AGTATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTAGGT-TCTTCGGGACCTATGGA
1 AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCT-TTCGGGACATATGGA
74980 CAGTTGTTGA
Statistics
Matches: 173, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
61 1 0.01
62 23 0.13
63 149 0.86
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (63 bp):
AGTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGAT
Found at i:74804 original size:31 final size:31
Alignment explanation
Indices: 74730--74983 Score: 248
Period size: 31 Copynumber: 8.1 Consensus size: 31
74720 AGAGTCGAGG
*
74730 AGTATACCTATGTTCTACGGAACATATGGAT
1 AGTATACCTATGTTCTACGGAACATATGGAC
* * * *
74761 AGAATTACCTATG-TCATTCGGGACATATGGAT
1 AGTA-TACCTATGTTC-TACGGAACATATGGAC
74793 AGTATACCTATGTTCTACGGAACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
* *
74824 A-TAATTACCTATG-TCTTTCAGG-ACATATGGAT
1 AGT-A-TACCTATGTTC-TAC-GGAACATATGGAC
*
74856 AGTATACCTATGTTCAACGGAACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
* * *
74887 AGAATTACCTATG-TCTTTCGGGACATATGGAC
1 AGTA-TACCTATGTTC-TACGGAACATATGGAC
*
74919 AGTATACCTATGTTCTAAGGAACATATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
* * * * *
74950 AGTTTACCTAGGTTCTTCGGGACCTATGGAC
1 AGTATACCTATGTTCTACGGAACATATGGAC
74981 AGT
1 AGT
74984 TGTTGAGGTT
Statistics
Matches: 184, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
30 3 0.02
31 102 0.55
32 76 0.41
33 3 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
AGTATACCTATGTTCTACGGAACATATGGAC
Found at i:75697 original size:12 final size:12
Alignment explanation
Indices: 75680--75732 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
75670 ACTGTAGCAT
*
75680 TGTTCATGGCAC
1 TGTTCATGGTAC
75692 TGTTCAT--TAC
1 TGTTCATGGTAC
*
75702 TGTTCACGGTAC
1 TGTTCATGGTAC
*
75714 TGTTCACGGTAC
1 TGTTCATGGTAC
75726 TGTTCAT
1 TGTTCAT
75733 ATCGTATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 8 0.22
12 28 0.78
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (12 bp):
TGTTCATGGTAC
Found at i:78099 original size:35 final size:33
Alignment explanation
Indices: 78050--78128 Score: 97
Period size: 35 Copynumber: 2.4 Consensus size: 33
78040 TTTAAATTCG
* * *
78050 TAATATTTTTATATTTAATTTTTTAAATATCTTAA
1 TAATTTTTTTATATTTAATATTTTAAAT-T-TAAA
*
78085 TAATTTTTTTATATTTTATATTTTAAATTTAAA
1 TAATTTTTTTATATTTAATATTTTAAATTTAAA
78118 T-ATTTTTTTAT
1 TAATTTTTTTAT
78129 TTTCTAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 10 0.25
33 4 0.10
34 1 0.03
35 25 0.62
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (33 bp):
TAATTTTTTTATATTTAATATTTTAAATTTAAA
Found at i:82605 original size:39 final size:39
Alignment explanation
Indices: 82561--82639 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
82551 ATTGTAACAA
82561 CAACAGAAATTCAAATCTGAGTTTCAAAACGCCGTAGAT
1 CAACAGAAATTCAAATCTGAGTTTCAAAACGCCGTAGAT
82600 CAACAGAAATTCAAATCTGAGTTTCAAAACGCCGTAGAT
1 CAACAGAAATTCAAATCTGAGTTTCAAAACGCCGTAGAT
82639 C
1 C
82640 TAAAATCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.23
Consensus pattern (39 bp):
CAACAGAAATTCAAATCTGAGTTTCAAAACGCCGTAGAT
Found at i:83411 original size:17 final size:18
Alignment explanation
Indices: 83361--83411 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
83351 TATGAATACA
* *
83361 CATAATTAAAATTAGAAT
1 CATAATTAAAATAATAAT
*
83379 CA-AATCAAAA-AATAAT
1 CATAATTAAAATAATAAT
83395 -ATAATTAAAATAATAAT
1 CATAATTAAAATAATAAT
83412 TAAAATATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 1 0.04
16 11 0.41
17 13 0.48
18 2 0.07
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (18 bp):
CATAATTAAAATAATAAT
Found at i:83573 original size:2 final size:2
Alignment explanation
Indices: 83562--83595 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
83552 CTTCTAGAAC
83562 TA TA -A 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 TA T
83596 TGTTGAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83676 original size:29 final size:29
Alignment explanation
Indices: 83642--83700 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
83632 CCTAAATTAA
83642 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
83671 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
83700 T
1 T
83701 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:88348 original size:14 final size:14
Alignment explanation
Indices: 88325--88362 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
88315 TCTGTCTATA
*
88325 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
88338 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
88353 TGCAGGGATT
1 TGCAGGGATT
88363 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:93024 original size:33 final size:33
Alignment explanation
Indices: 92987--93099 Score: 172
Period size: 33 Copynumber: 3.2 Consensus size: 33
92977 CGAGTGACAT
92987 ACGAGCCATACAAGCCATATACTCACCATGCAG
1 ACGAGCCATACAAGCCATATACTCACCATGCAG
93020 ACGAGCCATACAAGCCATATACTCACCATCACCATGCAG
1 ACGAGCCATACAAGCC--ATA-T-A-C-TCACCATGCAG
93059 ACGAGCCATACAAGCCATATACTCACCATGCAG
1 ACGAGCCATACAAGCCATATACTCACCATGCAG
93092 ACGAGCCA
1 ACGAGCCA
93100 GCCAACGGAG
Statistics
Matches: 74, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
33 35 0.47
34 1 0.01
35 4 0.05
36 2 0.03
37 4 0.05
38 1 0.01
39 27 0.36
ACGTcount: A:0.36, C:0.35, G:0.15, T:0.14
Consensus pattern (33 bp):
ACGAGCCATACAAGCCATATACTCACCATGCAG
Found at i:93059 original size:39 final size:39
Alignment explanation
Indices: 92987--93087 Score: 160
Period size: 39 Copynumber: 2.7 Consensus size: 39
92977 CGAGTGACAT
92987 ACGAGCCATACAAGCC--ATA-T-A-C-TCACCATGCAG
1 ACGAGCCATACAAGCCATATACTCACCATCACCATGCAG
93020 ACGAGCCATACAAGCCATATACTCACCATCACCATGCAG
1 ACGAGCCATACAAGCCATATACTCACCATCACCATGCAG
93059 ACGAGCCATACAAGCCATATACTCACCAT
1 ACGAGCCATACAAGCCATATACTCACCAT
93088 GCAGACGAGC
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 16 0.26
35 3 0.05
36 1 0.02
37 1 0.02
38 1 0.02
39 40 0.65
ACGTcount: A:0.37, C:0.35, G:0.13, T:0.16
Consensus pattern (39 bp):
ACGAGCCATACAAGCCATATACTCACCATCACCATGCAG
Found at i:93130 original size:32 final size:32
Alignment explanation
Indices: 93084--93154 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
93074 CATATACTCA
* *
93084 CCATGCAGACGAGCCAGCCAACGGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
* *
93116 CCATGCAAAGGAGCCAGCCAATAGAGAGGTCG
1 CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
93148 CCATGCA
1 CCATGCA
93155 GTCTGGGCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.31, C:0.30, G:0.31, T:0.08
Consensus pattern (32 bp):
CCATGCAAACGAGCCAGCCAACAGAGAGGTCG
Found at i:93246 original size:29 final size:29
Alignment explanation
Indices: 93142--93236 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
93132 GCCAATAGAG
* **
93142 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
93171 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
93200 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
93229 AGGTCGCC
1 AGGTCGCC
93237 CCGGCGTCCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:93305 original size:50 final size:50
Alignment explanation
Indices: 93263--93378 Score: 170
Period size: 50 Copynumber: 2.4 Consensus size: 50
93253 CCCGAGACCA
*
93263 TGCATG-C-ACATGCA-GCCAA-ATAACTTCACGTGCTCCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCAGC
* *
93309 TGCATGCCTGCATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCCGC
1 TGCATGCCTACATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCAGC
93359 TGCATGCCTACA-GCATGCCA
1 TGCATGCCTACATGCATGCCA
93379 TGTGATCCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
46 6 0.09
47 1 0.02
48 6 0.09
49 13 0.20
50 38 0.59
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (50 bp):
TGCATGCCTACATGCATGCCAAGATAACTTCACGTGCTCCTGCTCCCAGC
Found at i:93613 original size:16 final size:18
Alignment explanation
Indices: 93592--93630 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
93582 GGAGATAAGG
*
93592 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
93608 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
93626 TAAAT
1 TAAAT
93631 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:93774 original size:46 final size:47
Alignment explanation
Indices: 93735--93824 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 47
93725 TTATATAGTT
93735 AAAAA-TAATTAATTAGTTTGTT-TT-GTT-AATAGTTAGTTATATAA
1 AAAAATTAATTAATTAGTTT-TTGTTAGTTAAATAGTTAGTTATATAA
*
93779 AAAAATTATTTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTAATTAATTAGTTTTTGTTAGTTAAATAGTT-AGTTATAT
93825 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
44 7 0.17
45 15 0.38
46 3 0.08
47 7 0.17
48 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (47 bp):
AAAAATTAATTAATTAGTTTTTGTTAGTTAAATAGTTAGTTATATAA
Found at i:93899 original size:32 final size:32
Alignment explanation
Indices: 93863--93938 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
93853 TTAGTTAGTA
93863 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAAAT
*
93895 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAT
*
93928 ATTTTATTAGT
1 AGTTTATTAGT
93939 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.28
33 19 0.49
34 5 0.13
35 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (32 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAT
Found at i:94016 original size:16 final size:16
Alignment explanation
Indices: 93984--94030 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
93974 TTTAAAAAGT
*
93984 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
94000 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
94016 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
94031 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:94025 original size:15 final size:14
Alignment explanation
Indices: 94005--94035 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
93995 GTTTATTAGT
94005 TTATTATATTATAAG
1 TTATTATATTA-AAG
94020 TTATTATATTAAAG
1 TTATTATATTAAAG
94034 TT
1 TT
94036 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:96200 original size:17 final size:17
Alignment explanation
Indices: 96178--96210 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
96168 CAATGATGTT
*
96178 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
96195 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
96211 GTATTAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:96229 original size:21 final size:21
Alignment explanation
Indices: 96205--96245 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
96195 TAGTATCAAA
* *
96205 TAATTAGTATTAAATCATTAG
1 TAATAAGTAGTAAATCATTAG
*
96226 TAATAATTAGTAAATCATTA
1 TAATAAGTAGTAAATCATTA
96246 TTATCAAATC
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:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (21 bp):
TAATAAGTAGTAAATCATTAG
Found at i:96382 original size:14 final size:14
Alignment explanation
Indices: 96363--96402 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
96353 TAGTAATAAT
96363 TATTAAATCATTAG
1 TATTAAATCATTAG
*
96377 TATTAAATCATTAT
1 TATTAAATCATTAG
*
96391 TA-TAAATAATTA
1 TATTAAATCATTA
96403 CTAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:96452 original size:12 final size:12
Alignment explanation
Indices: 96345--96578 Score: 77
Period size: 12 Copynumber: 18.9 Consensus size: 12
96335 TTAGTATTCT
96345 ATAATTATTAGTA
1 ATAATTATTA-TA
96358 ATAATTATTA-A
1 ATAATTATTATA
* *
96369 ATCATTAGTATTAA
1 ATAATTATTA-T-A
*
96383 ATCATTATTATAA
1 ATAATTATTAT-A
*
96396 ATAATTACTA-A
1 ATAATTATTATA
**
96407 ATAA-TAACATA
1 ATAATTATTATA
96418 ATAATTATTATAAA
1 ATAATTATTAT--A
*
96432 ATCATTATTATA
1 ATAATTATTATA
* *
96444 ATGATTATTATT
1 ATAATTATTATA
*
96456 A-AATCATTACTAA
1 ATAATTATTA-T-A
* * *
96469 ATCATCA-AATCA
1 ATAATTATTAT-A
* *
96481 TTAAATATT-TAA
1 ATAATTATTAT-A
*
96493 ATCATTATTA-A
1 ATAATTATTATA
* *
96504 ATCATTTTTATA
1 ATAATTATTATA
*
96516 ATGATTATTACTAA
1 ATAATTATTA-T-A
*
96530 ATCATTATTATA
1 ATAATTATTATA
*
96542 ATGATTATTATCAA
1 ATAATTATTAT--A
* *
96556 ATCATTACTATA
1 ATAATTATTATA
*
96568 ATGATTATTAT
1 ATAATTATTAT
96579 CAAATCATTA
Statistics
Matches: 168, Mismatches: 36, Indels: 35
0.70 0.15 0.15
Matches are distributed among these distances:
10 3 0.02
11 35 0.21
12 60 0.36
13 25 0.15
14 45 0.27
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (12 bp):
ATAATTATTATA
Found at i:96459 original size:26 final size:26
Alignment explanation
Indices: 96348--96588 Score: 184
Period size: 26 Copynumber: 9.7 Consensus size: 26
96338 GTATTCTATA
* * *
96348 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATG
*
96372 ATTAGTATTAAATCATTATTATAA--
1 ATTATTATTAAATCATTATTATAATG
* * * ** *
96396 ATAATTACTAAAT-AATAACATAATA
1 ATTATTATTAAATCATTATTATAATG
*
96421 ATTATTATAAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* *
96447 ATTATTATTAAATCATTACTA-AATC
1 ATTATTATTAAATCATTATTATAATG
* *
96472 ATCAAATCATT-AA--A-TATT-TAA--
1 AT--TATTATTAAATCATTATTATAATG
* *
96493 ATCATTATTAAATCATTTTTATAATG
1 ATTATTATTAAATCATTATTATAATG
*
96519 ATTATTACTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* *
96545 ATTATTATCAAATCATTACTATAATG
1 ATTATTATTAAATCATTATTATAATG
*
96571 ATTATTATCAAATCATTA
1 ATTATTATTAAATCATTA
96589 CTAAATCATC
Statistics
Matches: 171, Mismatches: 31, Indels: 28
0.74 0.13 0.12
Matches are distributed among these distances:
19 5 0.03
20 2 0.01
21 2 0.01
22 1 0.01
23 15 0.09
24 21 0.12
25 25 0.15
26 95 0.56
27 5 0.03
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATTATTAAATCATTATTATAATG
Found at i:96585 original size:124 final size:123
Alignment explanation
Indices: 96377--96646 Score: 436
Period size: 124 Copynumber: 2.2 Consensus size: 123
96367 AAATCATTAG
* * *
96377 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACATAATAATTATTATAAAATCATTAT
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACATAATAATTATTATAAAATCATTAC
*
96440 TATAATGATTATTATTAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* ** * *
96498 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAAT-AATAACATAATAATTATTATAAAATCATTA
96563 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
65 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
96622 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
96647 ATAAATACAT
Statistics
Matches: 137, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
121 18 0.13
123 12 0.09
124 107 0.78
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (123 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATAATAACATAATAATTATTATAAAATCATTAC
TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:99408 original size:23 final size:23
Alignment explanation
Indices: 99358--99410 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
99348 AATCATTAAA
*
99358 TATAATATAATATACTATTATAT
1 TATATTATAATATACTATTATAT
99381 TATATTATAATATACTATTATAT
1 TATATTATAATATACTATTATAT
99404 TATATTA
1 TATATTA
99411 ATGATCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TATATTATAATATACTATTATAT
Found at i:99478 original size:24 final size:25
Alignment explanation
Indices: 99442--99502 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
99432 TTTTAACTTG
*
99442 ATTAATTGA-TTAATTACTAATATT-
1 ATTAA-TGATTTAATAACTAATATTA
* *
99466 ATTAATGATTTAATAATTATTATTA
1 ATTAATGATTTAATAACTAATATTA
99491 ATCTAATGATTT
1 AT-TAATGATTT
99503 GATATTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 3 0.10
24 17 0.55
25 2 0.06
26 9 0.29
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (25 bp):
ATTAATGATTTAATAACTAATATTA
Found at i:99769 original size:19 final size:19
Alignment explanation
Indices: 99732--99791 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
99722 AATATAAATA
*
99732 AAACAA-AATAT-TTTTTT
1 AAACAACAATATAATTTTT
*
99749 AAACAACACTA-AATATTTT
1 AAACAACAATATAAT-TTTT
99768 AAAC-ACAATATAATTTTT
1 AAACAACAATATAATTTTT
99786 AAACAA
1 AAACAA
99792 AATTATCTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 6 0.17
18 17 0.49
19 12 0.34
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (19 bp):
AAACAACAATATAATTTTT
Found at i:100245 original size:8 final size:8
Alignment explanation
Indices: 100234--100265 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
100224 TAATAACTTA
100234 AACTAATT
1 AACTAATT
100242 AACTAATT
1 AACTAATT
100250 AACTAATT
1 AACTAATT
100258 AACTAATT
1 AACTAATT
100266 TTTTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
AACTAATT
Found at i:100318 original size:21 final size:21
Alignment explanation
Indices: 100285--100333 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
100275 TAATATATAT
*
100285 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* *
100306 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
100327 ATTAACT
1 A-TAACT
100334 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:100818 original size:33 final size:34
Alignment explanation
Indices: 100762--100827 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
100752 TGGATGCAAC
*
100762 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 GCATGCATGAG-GATACAGTTAAAGCTGGGTCGTT
*
100797 GCATGCATGA-GCTACAGTTAAAGCTGGGTCG
1 GCATGCATGAGGATACAGTTAAAGCTGGGTCG
100828 C
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 19 0.66
35 10 0.34
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (34 bp):
GCATGCATGAGGATACAGTTAAAGCTGGGTCGTT
Done.