Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005061.1 Hibiscus syriacus cultivar Beakdansim tig00011362_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: 94084
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:140 original size:6 final size:6
Alignment explanation
Indices: 129--164 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
119 GACACGTATT
129 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
165 GACGGCGGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:829 original size:40 final size:39
Alignment explanation
Indices: 773--862 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 39
763 TTAGAAAGAT
*
773 ACTATCGC-ACGCGAAATGGAAATCGCAATGCGATTTTC
1 ACTATCGCAACGCGAAATGAAAATCGCAATGCGATTTTC
**
811 AACTATCGCAACGCGAAATGAAAATCGCGTTGCGATTTTC
1 -ACTATCGCAACGCGAAATGAAAATCGCAATGCGATTTTC
851 ACTATCGCAACG
1 ACTATCGCAACG
863 ACAACTGTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 20 0.43
40 27 0.57
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (39 bp):
ACTATCGCAACGCGAAATGAAAATCGCAATGCGATTTTC
Found at i:916 original size:19 final size:20
Alignment explanation
Indices: 876--927 Score: 97
Period size: 19 Copynumber: 2.6 Consensus size: 20
866 ACTGTAGACT
876 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
896 ATCGCAACGCGAAAT-GAAA
1 ATCGCAACGCGAAATGGAAA
915 ATCGCAACGCGAA
1 ATCGCAACGCGAA
928 TTTGCGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:2213 original size:28 final size:28
Alignment explanation
Indices: 2180--2240 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
2170 AGTTTTTTTT
*
2180 TAAAAAAAAATACGTAAAATATTTTATC
1 TAAAAAAAAATACATAAAATATTTTATC
* * * * *
2208 TAAAAATATATATATAAATTATTTTATG
1 TAAAAAAAAATACATAAAATATTTTATC
2236 TAAAA
1 TAAAA
2241 TAATTATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (28 bp):
TAAAAAAAAATACATAAAATATTTTATC
Found at i:2300 original size:16 final size:17
Alignment explanation
Indices: 2274--2307 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
2264 TTTAAGAAAC
2274 TATTAAATAAATAATAT
1 TATTAAATAAATAATAT
2291 TATT-AATAAATAATAT
1 TATTAAATAAATAATAT
2307 T
1 T
2308 TTTGAGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTAAATAAATAATAT
Found at i:2553 original size:14 final size:14
Alignment explanation
Indices: 2534--2562 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2524 AGGAAAATGA
2534 GAAAAATATTTTTC
1 GAAAAATATTTTTC
2548 GAAAAATATTTTTC
1 GAAAAATATTTTTC
2562 G
1 G
2563 GCTGTCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (14 bp):
GAAAAATATTTTTC
Found at i:19025 original size:7 final size:7
Alignment explanation
Indices: 19013--19053 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
19003 TTTGATCATC
19013 AATTTTT
1 AATTTTT
19020 AA-TTTT
1 AATTTTT
19026 -ATTTATT
1 AATTT-TT
19033 AAATTTTT
1 -AATTTTT
19041 AATTTTT
1 AATTTTT
19048 AATTTT
1 AATTTT
19054 AATAATTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 1 0.03
6 6 0.20
7 17 0.57
8 2 0.07
9 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:19055 original size:21 final size:21
Alignment explanation
Indices: 19013--19055 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
19003 TTTGATCATC
*
19013 AATTTTTAATTTTATTTATTA
1 AATTTTTAATTTTAATTATTA
19034 AATTTTTAATTTTTAATT-TTA
1 AATTTTTAA-TTTTAATTATTA
19055 A
1 A
19056 TAATTGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTTTTAATTTTAATTATTA
Found at i:19565 original size:2 final size:2
Alignment explanation
Indices: 19560--19590 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19550 AGTGTGTGTG
19560 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 T
19591 TAAATTATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27068 original size:18 final size:19
Alignment explanation
Indices: 27045--27080 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
27035 GCAAATAGAC
27045 TAAATAAAT-AAATAATAG
1 TAAATAAATAAAATAATAG
*
27063 TAAATATATAAAATAATA
1 TAAATAAATAAAATAATA
27081 TTAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
TAAATAAATAAAATAATAG
Found at i:27532 original size:16 final size:16
Alignment explanation
Indices: 27508--27571 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
27498 ATCTATTTTA
*
27508 ATTACTATATTTATAT
1 ATTATTATATTTATAT
27524 ATTATTATATTTA-AT
1 ATTATTATATTTATAT
* *
27539 AATTAATATTATTAATAT
1 -ATTATTA-TATTTATAT
27557 ATTTATT-TA-TTATAT
1 A-TTATTATATTTATAT
27572 TCATTTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 7 0.18
16 20 0.51
17 6 0.15
18 6 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:28168 original size:20 final size:20
Alignment explanation
Indices: 28074--28422 Score: 418
Period size: 20 Copynumber: 17.4 Consensus size: 20
28064 GATTTTCCAT
* ** *
28074 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
28094 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
28114 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28134 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
28154 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
28174 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28194 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
28214 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
28234 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28254 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
28274 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28294 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
28314 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28334 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
28354 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
28374 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
28394 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
28414 AATCACAAC
1 AATCGCAAC
28423 ACTGAAATTT
Statistics
Matches: 285, Mismatches: 36, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 279 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:29135 original size:24 final size:24
Alignment explanation
Indices: 29096--29142 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29086 AAATTTGGTC
29096 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
29120 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
29143 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:29334 original size:12 final size:12
Alignment explanation
Indices: 29317--29341 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29307 ATATAATCCT
29317 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29329 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29341 G
1 G
29342 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:31664 original size:19 final size:19
Alignment explanation
Indices: 31642--31966 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
31632 CGGAAAATAC
*
31642 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
31661 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
31675 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
31695 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
31709 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31728 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
31747 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
31761 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31780 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
31799 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
31813 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
31832 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
31851 AATCGCAATACGAAATG-A
1 AATCGCAATGCGAAATGAA
31869 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31888 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31907 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
31921 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31940 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
31959 AATCGCAA
1 AATCGCAA
31967 CGAGATAATC
Statistics
Matches: 267, Mismatches: 12, Indels: 54
0.80 0.04 0.16
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.04
18 21 0.08
19 155 0.58
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:31729 original size:33 final size:34
Alignment explanation
Indices: 31642--31966 Score: 312
Period size: 33 Copynumber: 9.2 Consensus size: 34
31632 CGGAAAATAC
* *
31642 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
31675 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
31709 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
31747 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
31780 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
31813 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
31851 AATCGCAATACGAAATG-AAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
31888 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
31920 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
31959 AATCGCAA
1 AATCGCAA
31967 CGAGATAATC
Statistics
Matches: 255, Mismatches: 12, Indels: 45
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 111 0.44
34 32 0.13
35 9 0.04
36 6 0.02
37 39 0.15
38 54 0.21
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:31903 original size:160 final size:157
Alignment explanation
Indices: 31670--31988 Score: 559
Period size: 160 Copynumber: 2.0 Consensus size: 157
31660 AAATCCCAAC
*
31670 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCA
*
31735 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
31800 ATCGCAACGAGAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
31827 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACGAAA-G-AATCGCAATGCGAAATGAAAAT
31891 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
62 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
*
31956 GAAAATCGCAACGAGATAATCGCAATGCGAA
127 GAAAATCGCAACGAGAGAATCGCAATGCGAA
31987 AT
1 AT
31989 TATAAACGCA
Statistics
Matches: 154, Mismatches: 4, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 5 0.03
159 1 0.01
160 118 0.77
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Found at i:32004 original size:52 final size:52
Alignment explanation
Indices: 31670--31988 Score: 557
Period size: 52 Copynumber: 6.0 Consensus size: 52
31660 AAATCCCAAC
31670 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
31723 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
31775 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
31827 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACGAGA-G-AATCGCAATGCGAA
*
31883 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
31935 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
31987 AT
1 AT
31989 TATAAACGCA
Statistics
Matches: 257, Mismatches: 5, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
52 183 0.71
53 18 0.07
54 11 0.04
55 2 0.01
56 43 0.17
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:32104 original size:19 final size:19
Alignment explanation
Indices: 31995--32096 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
31985 AAATTATAAA
31995 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
32014 CCGCATTGCAATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
32034 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
32050 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
32067 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
32086 CGCATTGCGAT
1 CGCATTGCGAT
32097 AGTCATTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 35 0.48
20 18 0.25
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:32221 original size:14 final size:14
Alignment explanation
Indices: 32202--32238 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
32192 CATCAATTAC
32202 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
32216 ACAAATCATCTTTT
1 ACAAATCAACTTTT
32230 ACAAATCAA
1 ACAAATCAA
32239 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:32250 original size:12 final size:12
Alignment explanation
Indices: 32233--32305 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
32223 ATCTTTTACA
32233 AATCAATTAAAC
1 AATCAATTAAAC
*
32245 AATCAA--AAATTG
1 AATCAATTAAA--C
**
32257 AATCAACTTTTAC
1 AATCAA-TTAAAC
32270 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
32283 AATCAA-AAAAC
1 AATCAATTAAAC
32294 AATCAATTAAAC
1 AATCAATTAAAC
32306 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:32267 original size:38 final size:38
Alignment explanation
Indices: 32219--32291 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
32209 AACTTTTACA
*
32219 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
32257 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
32292 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:34148 original size:19 final size:19
Alignment explanation
Indices: 34108--34223 Score: 117
Period size: 19 Copynumber: 6.6 Consensus size: 19
34098 TAGTTTACTT
* *
34108 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
34128 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34147 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
34161 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
34180 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
34194 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
34213 TCGCAATGCGA
1 TCGCAACGCGA
34224 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 5, Indels: 21
0.76 0.05 0.20
Matches are distributed among these distances:
14 16 0.20
16 11 0.14
17 11 0.14
19 31 0.38
20 12 0.15
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:34164 original size:14 final size:14
Alignment explanation
Indices: 34145--34201 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
34135 GCGAAATGAA
*
34145 AATCGCAACGACAG
1 AATCGCAACGAAAG
34159 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
34176 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
34192 AATCGCAACG
1 AATCGCAACG
34202 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:34168 original size:33 final size:33
Alignment explanation
Indices: 34126--34218 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
34116 CGAAACTTAA
*
34126 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
34159 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
34192 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
34219 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:34241 original size:19 final size:19
Alignment explanation
Indices: 34219--34347 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
34209 AAAATCGCAA
34219 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
34238 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
34252 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
34271 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
34285 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
34304 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
34323 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
34343 TGCGA
1 TGCGA
34348 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:34261 original size:33 final size:33
Alignment explanation
Indices: 34219--34310 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
34209 AAAATCGCAA
34219 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
34252 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
34285 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
34311 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:34680 original size:92 final size:93
Alignment explanation
Indices: 34391--34769 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
34381 TTGAATGGAT
34391 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
34455 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
34483 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
34548 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
34576 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
34640 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
34668 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
34733 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
34761 AAATTTACT
1 AAATTTACT
34770 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 115 0.40
93 169 0.60
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:34703 original size:185 final size:185
Alignment explanation
Indices: 34391--34769 Score: 733
Period size: 185 Copynumber: 2.0 Consensus size: 185
34381 TTGAATGGAT
34391 AAATTTACTTTCAACCAAAAGACAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
34456 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
34521 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
34576 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
34640 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
34705 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
34761 AAATTTACT
1 AAATTTACT
34770 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
185 177 0.92
186 15 0.08
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:36490 original size:14 final size:14
Alignment explanation
Indices: 36471--36560 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
36461 TTGAAATGAA
36471 AATCGCAACGAGAG
1 AATCGCAACGAGAG
36485 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
36502 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
36518 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
36537 AATCGCAACGAGAG
1 AATCGCAACGAGAG
36551 AATCGCAACG
1 AATCGCAACG
36561 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:36508 original size:33 final size:33
Alignment explanation
Indices: 36463--36577 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
36453 TCTTTTGGTT
36463 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
36496 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
36529 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
36562 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
36578 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:36509 original size:19 final size:18
Alignment explanation
Indices: 36470--36582 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
36460 GTTGAAATGA
36470 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
36485 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
36502 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
36518 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
36535 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
36551 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
36568 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
36583 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:36613 original size:14 final size:14
Alignment explanation
Indices: 36594--36648 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
36584 TTTGGTTTCG
36594 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
36608 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
36627 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
36641 CGTTGCGA
1 CGTTGCGA
36649 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:36811 original size:33 final size:33
Alignment explanation
Indices: 36769--36839 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
36759 AATACTAACT
*
36769 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
36802 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
36835 TGAAA
1 TGAAA
36840 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:37072 original size:22 final size:22
Alignment explanation
Indices: 37020--37074 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
37010 TGGTTGTGAG
**
37020 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
37042 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
37064 GGATTTCTTCG
1 GGATTTCTTCG
37075 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:37245 original size:20 final size:20
Alignment explanation
Indices: 37220--37393 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
37210 CTTTAAATAT
37220 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
37240 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
37262 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37281 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
37301 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
37321 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
37341 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
37361 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
37381 CGCGTTGCGATTT
1 CGCGTTGCGATTT
37394 TGGAAAATCG
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 113 0.86
21 15 0.11
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:37385 original size:60 final size:60
Alignment explanation
Indices: 37222--37393 Score: 245
Period size: 60 Copynumber: 2.9 Consensus size: 60
37212 TTAAATATCG
** *
37222 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
37283 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
37343 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
37394 TGGAAAATCG
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:37410 original size:21 final size:20
Alignment explanation
Indices: 37386--37462 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
37376 GTGTTCGCGT
37386 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
37407 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
37427 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
37449 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
37463 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:37473 original size:20 final size:20
Alignment explanation
Indices: 37448--37499 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
37438 AAGAATCGCG
*
37448 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
37468 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
37488 TTGCGATTCTGG
1 TTGCGATTCTGG
37500 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:40729 original size:9 final size:9
Alignment explanation
Indices: 40686--40780 Score: 75
Period size: 9 Copynumber: 10.0 Consensus size: 9
40676 GCTGGAAACT
40686 GGTTTGACC
1 GGTTTGACC
*
40695 GGTTTTTAACC
1 GG--TTTGACC
40706 GGTTCTGACC
1 GGTT-TGACC
40716 GGTTTGACC
1 GGTTTGACC
*
40725 TGTTTCGACC
1 GGTTT-GACC
*
40735 GGTTCGAACC
1 GGTTTG-ACC
40745 -GTTTGACC
1 GGTTTGACC
**
40753 GGTATAAACC
1 GGT-TTGACC
40763 GGTTTGACC
1 GGTTTGACC
*
40772 GGTCTGACC
1 GGTTTGACC
40781 CGACCCGACC
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
8 3 0.04
9 32 0.47
10 25 0.37
11 8 0.12
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (9 bp):
GGTTTGACC
Found at i:40736 original size:19 final size:18
Alignment explanation
Indices: 40687--40774 Score: 63
Period size: 19 Copynumber: 4.6 Consensus size: 18
40677 CTGGAAACTG
**
40687 GTTTGACCGGTTTTTAACC
1 GTTTGACCGG-TTCGAACC
*
40706 GGTTCTGACCGGTTTG-ACC
1 -GTT-TGACCGGTTCGAACC
40725 TGTTTCGACCGGTTCGAACC
1 -GTTT-GACCGGTTCGAACC
*
40745 GTTTGACCGGTAT-AAACC
1 GTTTGACCGGT-TCGAACC
40763 GGTTTGACCGGT
1 -GTTTGACCGGT
40775 CTGACCCGAC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
18 12 0.20
19 31 0.53
20 9 0.15
21 7 0.12
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (18 bp):
GTTTGACCGGTTCGAACC
Found at i:40779 original size:28 final size:28
Alignment explanation
Indices: 40686--40780 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 28
40676 GCTGGAAACT
* *
40686 GGTTTGACCGGTTTTTAACCGGTTCTGACC
1 GGTTTGACCGG-TATAAACCGGTT-TGACC
* * ** *
40716 GGTTTGACCTGTTTCGACCGGTTCGAACC
1 GGTTTGACCGGTATAAACCGGTTTG-ACC
40745 -GTTTGACCGGTATAAACCGGTTTGACC
1 GGTTTGACCGGTATAAACCGGTTTGACC
*
40772 GGTCTGACC
1 GGTTTGACC
40781 CGACCCGACC
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 3 0.06
28 27 0.51
29 13 0.25
30 10 0.19
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (28 bp):
GGTTTGACCGGTATAAACCGGTTTGACC
Found at i:40790 original size:19 final size:19
Alignment explanation
Indices: 40768--40810 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
40758 AAACCGGTTT
* *
40768 GACCGGTCTGACCCGACCC
1 GACCGGACTAACCCGACCC
* *
40787 GACCTGACTAATCCGACCC
1 GACCGGACTAACCCGACCC
40806 GACCG
1 GACCG
40811 TTGACTTCCT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.44, G:0.23, T:0.12
Consensus pattern (19 bp):
GACCGGACTAACCCGACCC
Found at i:49146 original size:20 final size:20
Alignment explanation
Indices: 49123--49162 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
49113 ATCATTATTA
*
49123 ACCTTTTGGTATCGATACCC
1 ACCTGTTGGTATCGATACCC
*
49143 ACCTGTTGGTATTGATACCC
1 ACCTGTTGGTATCGATACCC
49163 CTTGACTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (20 bp):
ACCTGTTGGTATCGATACCC
Found at i:52298 original size:20 final size:20
Alignment explanation
Indices: 52273--52330 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
52263 ATCTTATTCC
52273 CTGGTAATCTTGCATTCCCA
1 CTGGTAATCTTGCATTCCCA
52293 CTGGTAATCTTGCATTCCCA
1 CTGGTAATCTTGCATTCCCA
*
52313 CTGGTAATCTTACATTCC
1 CTGGTAATCTTGCATTCC
52331 GTGAACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (20 bp):
CTGGTAATCTTGCATTCCCA
Found at i:56403 original size:2 final size:2
Alignment explanation
Indices: 56398--56428 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
56388 CAAAAAAAAA
*
56398 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56429 ATTAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:62966 original size:12 final size:12
Alignment explanation
Indices: 62951--62975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62941 CAGCCGAAAC
62951 ATCAGCCTCCAA
1 ATCAGCCTCCAA
62963 ATCAGCCTCCAA
1 ATCAGCCTCCAA
62975 A
1 A
62976 GCAGTGGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.40, G:0.08, T:0.16
Consensus pattern (12 bp):
ATCAGCCTCCAA
Found at i:70570 original size:20 final size:21
Alignment explanation
Indices: 70545--70585 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
70535 ATTTCTTTAG
*
70545 TATAAACTA-CACATTTAATT
1 TATAAACTATCAAATTTAATT
*
70565 TATAAATTATCAAATTTAATT
1 TATAAACTATCAAATTTAATT
70586 CGATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAAACTATCAAATTTAATT
Found at i:72907 original size:2 final size:2
Alignment explanation
Indices: 72900--72924 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
72890 GAGATTCGGA
72900 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
72925 AATATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:73852 original size:25 final size:27
Alignment explanation
Indices: 73809--73872 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
73799 TATTAAATGA
73809 AAATAT-TTTTA-TATCAACTT-A-TT
1 AAATATATTTTATTATCAACTTAATTT
*
73832 AAATATATTTTATTATTAACTTAATTT
1 AAATATATTTTATTATCAACTTAATTT
* *
73859 AAAAACATTTTATT
1 AAATATATTTTATT
73873 TTTATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.18
24 5 0.15
25 8 0.24
26 1 0.03
27 14 0.41
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (27 bp):
AAATATATTTTATTATCAACTTAATTT
Found at i:74848 original size:17 final size:18
Alignment explanation
Indices: 74815--74848 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
74805 CCGCTACTAG
74815 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
74833 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
74849 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:76252 original size:18 final size:17
Alignment explanation
Indices: 76231--76268 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
76221 TTATACATTA
*
76231 TATTATAAATATAATATT
1 TATTATAAAGATAAT-TT
76249 TATTATAAAGATAATTT
1 TATTATAAAGATAATTT
76266 TAT
1 TAT
76269 CTAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TATTATAAAGATAATTT
Found at i:78467 original size:13 final size:12
Alignment explanation
Indices: 78425--78467 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
78415 TTTAATAGTT
78425 TATTATTTTATTA
1 TATTATTTT-TTA
*
78438 TACTATTTTTT-
1 TATTATTTTTTA
78449 TATTATTTTTTA
1 TATTATTTTTTA
78461 TAGTTAT
1 TA-TTAT
78468 AAAATGAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 10 0.38
12 4 0.15
13 12 0.46
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:80936 original size:2 final size:2
Alignment explanation
Indices: 80929--80956 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
80919 ATTGATAATC
80929 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
80957 GCAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82578 original size:2 final size:2
Alignment explanation
Indices: 82571--82599 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
82561 TGTGTATGTG
82571 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 T
82600 CCCTAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82797 original size:21 final size:21
Alignment explanation
Indices: 82771--82823 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
82761 ATTTCCAGAT
82771 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
82792 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
*
82813 TCGCAATGCGA
1 TCGCAACGCGA
82824 TTTATTCCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:82879 original size:21 final size:21
Alignment explanation
Indices: 82837--82879 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
82827 ATTCCAAATT
* **
82837 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAAATCG
82858 CGTTGCGATAGTCCAAAATCG
1 CGTTGCGATAGTCCAAAATCG
82879 C
1 C
82880 AACGACTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAAATCG
Found at i:82975 original size:6 final size:6
Alignment explanation
Indices: 82964--82990 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
82954 GAGATGTATT
82964 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
82991 CGAGACGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:83650 original size:42 final size:42
Alignment explanation
Indices: 83588--83860 Score: 433
Period size: 42 Copynumber: 6.5 Consensus size: 42
83578 TGCGATTTTA
* *
83588 GACTATCGCAACGAATTTGGAATAAATCTCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
83630 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
83672 GACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
83714 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
83756 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
83798 GACTATCGCAACGAA-TTTGAA-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
83838 GACTATCGTAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
83861 CTATCGTAAT
Statistics
Matches: 215, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
40 28 0.13
41 5 0.02
42 178 0.83
43 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:83869 original size:21 final size:21
Alignment explanation
Indices: 83617--83866 Score: 214
Period size: 21 Copynumber: 12.0 Consensus size: 21
83607 GAATAAATCT
*
83617 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTGGACTATCG
*
83638 CAA--CGAACTTGGAATAAATCG
1 CAACGCGAACTTGGACT--ATCG
* *
83659 CAACGCGAACTTCGACTATCA
1 CAACGCGAACTTGGACTATCG
* *
83680 CAA--CGAATTTGGAATAAATCG
1 CAACGCGAACTTGGACT--ATCG
*
83701 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTGGACTATCG
*
83722 CAA--CGAACTTGGAATAAATCG
1 CAACGCGAACTTGGACT--ATCG
*
83743 CAATGCGAACTTGGACTATCG
1 CAACGCGAACTTGGACTATCG
*
83764 CAA--CGAACTTGGAATAAATCG
1 CAACGCGAACTTGGACT--ATCG
83785 CAACGCGAACTTGGACTATCG
1 CAACGCGAACTTGGACTATCG
* * **
83806 CAA--CGAATTTGAAAAATCG
1 CAACGCGAACTTGGACTATCG
*
83825 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTGGACTATCG
*
83846 TAACGCGAACTTGGACTATCG
1 CAACGCGAACTTGGACTATCG
83867 TAATGCTAAT
Statistics
Matches: 183, Mismatches: 28, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
19 55 0.30
21 87 0.48
23 41 0.22
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (21 bp):
CAACGCGAACTTGGACTATCG
Found at i:93191 original size:11 final size:11
Alignment explanation
Indices: 93175--93199 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
93165 ATTTGATGAG
93175 GTTTTATAATA
1 GTTTTATAATA
93186 GTTTTATAATA
1 GTTTTATAATA
93197 GTT
1 GTT
93200 GTTACGATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (11 bp):
GTTTTATAATA
Done.