Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008067.1 Hibiscus syriacus cultivar Beakdansim tig00110565_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: 68735
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5315 original size:18 final size:18
Alignment explanation
Indices: 5292--5326 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5282 ATCATTAACT
* *
5292 AAATATGAATAATAAAAC
1 AAATATAAAAAATAAAAC
5310 AAATATAAAAAATAAAA
1 AAATATAAAAAATAAAA
5327 ATGAAGTGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (18 bp):
AAATATAAAAAATAAAAC
Found at i:11862 original size:57 final size:59
Alignment explanation
Indices: 11790--11934 Score: 154
Period size: 57 Copynumber: 2.5 Consensus size: 59
11780 CTCTGTTTTA
* * *
11790 TTTGTAATTACTGTTTTAGCCCTTTAAGTTTCTATATTT-GT-TTTAGTCCTTTAAATT
1 TTTGTAATTACTGTTTTAGCCCTTTAAGTTTATATATTTACTGTTTAGTCCTTTAAATG
* ** * * * *
11847 TTTGTTATTGTTGTTTAATCCC-TTAAG-TTATATTTTTACTGTTTAGTCCTTTAAGTG
1 TTTGTAATTACTGTTTTAGCCCTTTAAGTTTATATATTTACTGTTTAGTCCTTTAAATG
* *
11904 TTTGTAATTACTGTTTTAGGCTTTTAAGTTT
1 TTTGTAATTACTGTTTTAGCCCTTTAAGTTT
11935 TCTTTTTGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
55 8 0.12
56 6 0.09
57 46 0.69
58 5 0.07
59 2 0.03
ACGTcount: A:0.20, C:0.10, G:0.13, T:0.57
Consensus pattern (59 bp):
TTTGTAATTACTGTTTTAGCCCTTTAAGTTTATATATTTACTGTTTAGTCCTTTAAATG
Found at i:24530 original size:16 final size:17
Alignment explanation
Indices: 24480--24531 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
24470 ATAAAAAATA
24480 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
24497 TA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
24512 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
24528 AATT
1 AATT
24532 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:26068 original size:35 final size:34
Alignment explanation
Indices: 26029--26140 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
26019 AAAATAGTCC
*
26029 TCAATTTCATTCTAAACCTCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
26064 TCAATTTCACTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
** * *
26099 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTCCAAAATAAT
26134 TCAATTT
1 TCAATTT
26141 AAGGTTTAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.94
36 3 0.04
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:27800 original size:35 final size:34
Alignment explanation
Indices: 27754--27862 Score: 128
Period size: 35 Copynumber: 3.1 Consensus size: 34
27744 AAGAAAGTAT
* **
27754 TTGAAGTATTTTAGAATTTGGGGTTTAGAATTTAA
1 TTGAA-TATTTTGGAATTTGGGGTTTAGAATGAAA
* *
27789 TTGAATTATTTTGGAATTTAGGGTTTAGAGTGAAA
1 TTGAA-TATTTTGGAATTTGGGGTTTAGAATGAAA
* *
27824 TTGACATACTTTGGAATTTGAGGTTTAGAATGAAA
1 TTGA-ATATTTTGGAATTTGGGGTTTAGAATGAAA
27859 TTGA
1 TTGA
27863 GGACTGTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 62 0.98
36 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.42
Consensus pattern (34 bp):
TTGAATATTTTGGAATTTGGGGTTTAGAATGAAA
Found at i:28749 original size:25 final size:27
Alignment explanation
Indices: 28721--28773 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
28711 TAACAATAAC
**
28721 ATATATTTTTTAAATTAAGATAAAAAT
1 ATATATTTAATAAATTAAGATAAAAAT
*
28748 ATATATTTAATAATTTAAGATAAAAA
1 ATATATTTAATAAATTAAGATAAAAA
28774 AAAATATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (27 bp):
ATATATTTAATAAATTAAGATAAAAAT
Found at i:28780 original size:31 final size:31
Alignment explanation
Indices: 28706--28941 Score: 165
Period size: 30 Copynumber: 7.8 Consensus size: 31
28696 ATTAAAAAAG
* * * *
28706 TAAGATAACAATAACATATATTTT-TTAAAT
1 TAAGATAAAAATAAAATATATTTTAATAAGT
*
28736 TAAGATAAAAAT---ATATA-TTTAATAATT
1 TAAGATAAAAATAAAATATATTTTAATAAGT
*
28763 TAAGATAAAAA-AAAATATATTTT-A-AATT
1 TAAGATAAAAATAAAATATATTTTAATAAGT
* * *
28791 TGAGATCTATTAAAATAAAGAATTTTTTTTAA-AAGT
1 TAAGA--TA--AAAAT-AA-AATATATTTTAATAAGT
28827 TAAGATAAAAATAAAATATATTATT--TAAGT
1 TAAGATAAAAATAAAATATATT-TTAATAAGT
* **
28857 TAAGATAAAACTAAAATATATTTTTTTAAGT
1 TAAGATAAAAATAAAATATATTTTAATAAGT
* * *
28888 TAAAATAAAAATAATATATATATT--TAAGT
1 TAAGATAAAAATAAAATATATTTTAATAAGT
*
28917 TAAAGATAAATATAAAATATATTTT
1 T-AAGATAAAAATAAAATATATTTT
28942 TTAAAATTAA
Statistics
Matches: 169, Mismatches: 19, Indels: 36
0.75 0.08 0.16
Matches are distributed among these distances:
26 3 0.02
27 20 0.12
28 8 0.05
29 14 0.08
30 66 0.39
31 29 0.17
32 9 0.05
34 4 0.02
35 8 0.05
36 8 0.05
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (31 bp):
TAAGATAAAAATAAAATATATTTTAATAAGT
Found at i:28888 original size:61 final size:60
Alignment explanation
Indices: 28706--28943 Score: 204
Period size: 61 Copynumber: 3.9 Consensus size: 60
28696 ATTAAAAAAG
* * * * * ** *
28706 TAAGATAACAATAACATATATTTTTTAAATTAAGAT-AAA-AATATATA-TTTAATAATT
1 TAAGATAAAAATAAAATATATTATTTAAGTTAAGATAAAATAAAATATATTTTTTTAAGT
* * *
28763 TAAGATAAAAA-AAAATATATT-TTAAATTTGAGATCTATTAAAATAAAGA-AT-TTTTTTTAAA
1 TAAGATAAAAATAAAATATATTATTTAAGTT-A-A--GA-TAAAATAAA-ATATATTTTTTT--A
28824 AGT
58 AGT
28827 TAAGATAAAAATAAAATATATTATTTAAGTTAAGATAAAACTAAAATATATTTTTTTAAGT
1 TAAGATAAAAATAAAATATATTATTTAAGTTAAGATAAAA-TAAAATATATTTTTTTAAGT
* *
28888 TAAAATAAAAATAATATATA-TATTTAAGTTAAAGATAAATATAAAATATATTTTTT
1 TAAGATAAAAATAAAATATATTATTTAAGTT-AAGATAAA-ATAAAATATATTTTTT
28944 AAAATTAATA
Statistics
Matches: 149, Mismatches: 14, Indels: 32
0.76 0.07 0.16
Matches are distributed among these distances:
55 6 0.04
56 10 0.07
57 11 0.07
59 1 0.01
60 11 0.07
61 54 0.36
62 16 0.11
63 8 0.05
64 15 0.10
65 11 0.07
66 6 0.04
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (60 bp):
TAAGATAAAAATAAAATATATTATTTAAGTTAAGATAAAATAAAATATATTTTTTTAAGT
Found at i:29632 original size:17 final size:16
Alignment explanation
Indices: 29592--29624 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29582 AATATTTTTC
29592 AAAAATTAAATATAAA
1 AAAAATTAAATATAAA
29608 AAAAATTAAA-ATAAA
1 AAAAATTAAATATAAA
29623 AA
1 AA
29625 TTAAATTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATTAAATATAAA
Found at i:29639 original size:16 final size:15
Alignment explanation
Indices: 29592--29645 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
29582 AATATTTTTC
*
29592 AAAAATTAAATATAAA
1 AAAAATTAAAT-TATA
29608 AAAAATTAAA--AT-
1 AAAAATTAAATTATA
29620 AAAAATTAAATTACTA
1 AAAAATTAAATTA-TA
29636 AAAAA-TAAAT
1 AAAAATTAAAT
29646 ATACATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
12 10 0.30
13 1 0.03
14 1 0.03
15 6 0.18
16 15 0.45
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATTAAATTATA
Found at i:29671 original size:22 final size:19
Alignment explanation
Indices: 29631--29686 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
29621 AAAATTAAAT
*
29631 TACTAAAAAATAAATATAC
1 TACTAAAAAATAAAAATAC
*
29650 ATATTAAAAATATTAAAAATAC
1 -TACTAAAAA-A-TAAAAATAC
*
29672 TACTAAAAACTAAAA
1 TACTAAAAAATAAAA
29687 GAAAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.17
20 8 0.27
21 9 0.30
22 8 0.27
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (19 bp):
TACTAAAAAATAAAAATAC
Found at i:33751 original size:17 final size:18
Alignment explanation
Indices: 33721--33759 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
33711 GTGTATCTTT
33721 AAAAGATGGCTTAATATA
1 AAAAGATGGCTTAATATA
* *
33739 AAAAG-TGGTTTAATGTA
1 AAAAGATGGCTTAATATA
33756 AAAA
1 AAAA
33760 CAGGTGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.51, C:0.03, G:0.18, T:0.28
Consensus pattern (18 bp):
AAAAGATGGCTTAATATA
Found at i:35465 original size:19 final size:19
Alignment explanation
Indices: 35441--35478 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
35431 CTAGTCAACG
35441 GGAAGTGTTGAACATTACT
1 GGAAGTGTTGAACATTACT
*
35460 GGAAGTGTTGAGCATTACT
1 GGAAGTGTTGAACATTACT
35479 CAATTAACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (19 bp):
GGAAGTGTTGAACATTACT
Found at i:36037 original size:20 final size:20
Alignment explanation
Indices: 35943--36311 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
35933 GATTTTCCAT
* ** *
35943 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
35963 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
35983 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
36003 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
36023 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
36043 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
36063 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
36083 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
36103 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
36123 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
36143 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
36163 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
36183 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
36203 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
36223 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
36243 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
36263 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
36283 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
36303 AATCACAAC
1 AATCGCAAC
36312 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 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:37023 original size:24 final size:24
Alignment explanation
Indices: 36984--37030 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
36974 AAATTTGGTC
36984 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
37008 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
37031 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:37222 original size:12 final size:12
Alignment explanation
Indices: 37205--37229 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37195 ATATAATCCT
37205 GAAGAAGAAAAA
1 GAAGAAGAAAAA
37217 GAAGAAGAAAAA
1 GAAGAAGAAAAA
37229 G
1 G
37230 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:39555 original size:19 final size:19
Alignment explanation
Indices: 39533--39839 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
39523 CGGAAAATAC
*
39533 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
39552 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
39566 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
39586 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
39600 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
39619 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
39638 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
39652 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
39671 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
39690 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
39704 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
39723 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
39742 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
39761 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
39780 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
39794 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
39813 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
39832 AATCGCAA
1 AATCGCAA
39840 CGAGATAATC
Statistics
Matches: 249, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 16 0.06
17 15 0.06
18 5 0.02
19 151 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:39648 original size:52 final size:53
Alignment explanation
Indices: 39561--39839 Score: 358
Period size: 52 Copynumber: 5.2 Consensus size: 53
39551 AAATCCCAAC
*
39561 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
39614 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
39666 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
39718 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
39775 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
39827 ATGAAAATCGCAA
1 ATGAAAATCGCAA
39840 CGAGATAATC
Statistics
Matches: 212, Mismatches: 8, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
51 2 0.01
52 156 0.74
53 18 0.08
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:39684 original size:71 final size:71
Alignment explanation
Indices: 39600--39839 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
39590 GCAACGAGAG
*
39600 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
39665 AATGAA
66 AATGAA
* * *
39671 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
*
39731 TACGAAATGAA
61 TGCGAAATGAA
39742 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
39807 AATGAA
66 AATGAA
39813 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
39840 CGAGATAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 113 0.75
72 2 0.01
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:39785 original size:142 final size:137
Alignment explanation
Indices: 39533--39871 Score: 497
Period size: 142 Copynumber: 2.4 Consensus size: 137
39523 CGGAAAATAC
* * * *
39533 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAAC-CGAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
39596 AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
63 AGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
39661 GCGAAATGAA
128 GCGAAATGAA
39671 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACCGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
39736 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 -A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
39801 ATGCGAAATGAA
126 ATGCGAAATGAA
39813 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACCGA-ATAATCGCAATGCGAAATTA-AAATCGCA
39872 TTGCGATTTT
Statistics
Matches: 185, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 33 0.18
139 3 0.02
141 1 0.01
142 123 0.66
143 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACCGAATAATCGCAATGCGAAATTAAAATCGCAAACGAGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:39977 original size:19 final size:19
Alignment explanation
Indices: 39868--39969 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
39858 AAATTATAAA
39868 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
39887 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
39907 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
39923 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
39940 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
39959 CGCATTGCGAT
1 CGCATTGCGAT
39970 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:40094 original size:14 final size:14
Alignment explanation
Indices: 40075--40111 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
40065 CATCAATTAC
40075 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
40089 ACAAATCATCTTTT
1 ACAAATCAACTTTT
40103 ACAAATCAA
1 ACAAATCAA
40112 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:42088 original size:14 final size:14
Alignment explanation
Indices: 42069--42125 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
42059 GCGAAATGAA
*
42069 AATCGCAACGACAG
1 AATCGCAACGAAAG
42083 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
42100 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
42116 AATCGCAACG
1 AATCGCAACG
42126 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:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:42096 original size:33 final size:33
Alignment explanation
Indices: 42050--42142 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
42040 GCGAAACCAA
*
42050 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
42083 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
42116 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
42143 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:42107 original size:19 final size:19
Alignment explanation
Indices: 42013--42147 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
42003 TAGTTTACTT
* *
42013 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
42033 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
42052 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
42071 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
42085 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
42104 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
42118 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
42137 TCGCAATGCGA
1 TCGCAACGCGA
42148 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:42165 original size:19 final size:19
Alignment explanation
Indices: 42143--42271 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
42133 AAAATCGCAA
42143 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
42162 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
42176 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
42195 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
42209 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
42228 TGCGATTTTGGTTTCACGT
1 TGCGATTTTGGTTTCGCGT
* *
42247 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
42267 TGCGA
1 TGCGA
42272 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 12 0.14
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:42185 original size:33 final size:33
Alignment explanation
Indices: 42143--42234 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
42133 AAAATCGCAA
42143 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
42176 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
42209 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
42235 TTGGTTTCAC
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:42482 original size:86 final size:88
Alignment explanation
Indices: 42315--42866 Score: 889
Period size: 93 Copynumber: 6.1 Consensus size: 88
42305 TTGAATGGAT
42315 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-----ATACAC
42380 AGTTTAGCAGAATTGGCAGCAACCGAAC
61 AGTTTAGCAGAATTGGCAGCAACCGAAC
42408 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTG-T-TACACAGTTT
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATACACAGTTT
42471 AGCAGAATTGGCAGCAACCGAAC
66 AGCAGAATTGGCAGCAACCGAAC
42494 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTG-T-TACACAGTTT
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATACACAGTTT
42557 AGCAGAATTGGCAGCAACCGAAC
66 AGCAGAATTGGCAGCAACCGAAC
42580 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-----ATACAC
42645 AGTTTAGCAGAATTGGCAGCAACCGAAC
61 AGTTTAGCAGAATTGGCAGCAACCGAAC
42673 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-----ATACAC
42737 AGTTTAGCAGAATTGGCAGCAACCGAAC
61 AGTTTAGCAGAATTGGCAGCAACCGAAC
42765 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-----ATACAC
42830 AGTTTAGCAGAATTGGCAGCAACCGAAC
61 AGTTTAGCAGAATTGGCAGCAACCGAAC
42858 AAATTTACT
1 AAATTTACT
42867 AAGCAATCTA
Statistics
Matches: 451, Mismatches: 0, Indels: 16
0.97 0.00 0.03
Matches are distributed among these distances:
86 171 0.38
87 1 0.00
92 93 0.21
93 186 0.41
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (88 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATACACAGTTT
AGCAGAATTGGCAGCAACCGAAC
Found at i:42803 original size:185 final size:186
Alignment explanation
Indices: 42315--42866 Score: 999
Period size: 185 Copynumber: 3.0 Consensus size: 186
42305 TTGAATGGAT
42315 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
42380 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
42445 TACTATTTCACAGTG-T------TACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
42494 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTG-T------TACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
42552 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
42617 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
42673 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
42737 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
42802 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
42858 AAATTTACT
1 AAATTTACT
42867 AAGCAATCTA
Statistics
Matches: 359, Mismatches: 0, Indels: 22
0.94 0.00 0.06
Matches are distributed among these distances:
172 85 0.24
173 1 0.00
178 13 0.04
179 125 0.35
185 135 0.38
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:44590 original size:14 final size:14
Alignment explanation
Indices: 44571--44660 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
44561 TTGAAATGAA
44571 AATCGCAACGAGAG
1 AATCGCAACGAGAG
44585 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
44602 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
44618 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
44637 AATCGCAACGAGAG
1 AATCGCAACGAGAG
44651 AATCGCAACG
1 AATCGCAACG
44661 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:44608 original size:33 final size:33
Alignment explanation
Indices: 44563--44677 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
44553 TCTTTTGGTT
44563 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
44596 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
44629 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
44662 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
44678 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:44609 original size:19 final size:18
Alignment explanation
Indices: 44570--44682 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
44560 GTTGAAATGA
44570 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
44585 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
44602 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
44618 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
44635 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
44651 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
44668 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
44683 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:44713 original size:14 final size:14
Alignment explanation
Indices: 44694--44748 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
44684 TTTGGTTTCG
44694 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
44708 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
44727 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
44741 CGTTGCGA
1 CGTTGCGA
44749 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:44911 original size:33 final size:33
Alignment explanation
Indices: 44869--44939 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
44859 AATACTAACT
*
44869 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
44902 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
44935 TGAAA
1 TGAAA
44940 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:45173 original size:22 final size:22
Alignment explanation
Indices: 45121--45175 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
45111 TGGTTGTGAG
**
45121 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
45143 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
45165 GGATTTCTTCG
1 GGATTTCTTCG
45176 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:45346 original size:20 final size:20
Alignment explanation
Indices: 45321--45514 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
45311 CTTTAAATAT
45321 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
45341 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
45363 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
45382 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
45402 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
45422 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
45442 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
45462 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
45482 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
45502 CGCGTTGCGATTT
1 CGCGTTGCGATTT
45515 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:45508 original size:60 final size:60
Alignment explanation
Indices: 45321--45514 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
45311 CTTTAAATAT
**
45321 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
45382 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
45442 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
45502 CGCGTTGCGATTT
1 CGCGTTGCGATTT
45515 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:45531 original size:21 final size:20
Alignment explanation
Indices: 45507--45583 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
45497 ATATTCGCGT
45507 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
45528 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
45548 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
45570 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
45584 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:45594 original size:20 final size:20
Alignment explanation
Indices: 45569--45620 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
45559 AAGAATCGCG
*
45569 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
45589 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
45609 TTGCGATTCTGG
1 TTGCGATTCTGG
45621 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:49903 original size:2 final size:2
Alignment explanation
Indices: 49896--49923 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
49886 ACCCTAGATT
49896 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49924 AAAGTTTGAG
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):
TA
Found at i:51408 original size:3 final size:3
Alignment explanation
Indices: 51400--51425 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
51390 ACACTTGATT
51400 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
51426 TTGTATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:52203 original size:22 final size:22
Alignment explanation
Indices: 52191--52249 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
52181 TTTTACTAAC
52191 TTTTATTTATATTTGTTATCTA
1 TTTTATTTATATTTGTTATCTA
*
52213 TTTTATTTAT-TTTATTAT-TA
1 TTTTATTTATATTTGTTATCTA
52233 TTATTATATTAATATTT
1 TT-TTAT-TT-ATATTT
52250 TTTCTTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.12
21 11 0.34
22 12 0.38
23 2 0.06
24 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTATTTATATTTGTTATCTA
Found at i:52281 original size:17 final size:17
Alignment explanation
Indices: 52218--52282 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
52208 ATCTATTTTA
52218 TTTATTTTAT-TATTATT
1 TTTATTTTATAT-TTATT
* *
52235 ATTATATTAATATTT-TT
1 TTTAT-TTTATATTTATT
* *
52252 TCTTGTTTCATATTTATT
1 T-TTATTTTATATTTATT
52270 TTTATTTTATATT
1 TTTATTTTATATT
52283 CTAACATCTT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 24 0.65
18 12 0.32
19 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTATTTTATATTTATT
Found at i:55974 original size:42 final size:43
Alignment explanation
Indices: 55919--56000 Score: 123
Period size: 42 Copynumber: 1.9 Consensus size: 43
55909 AACTCACTGC
* *
55919 TTGTGCTAGTATTGCTCTT-AATTGC-GTAGGTGATATTGTGCT
1 TTGTGCCAGTATTGCTCTTGAATTGCAAT-GGTGATATTGTGCT
55961 TTGTGCCAGTATTGCTCTTGAATTGCAATGGTGATATTGT
1 TTGTGCCAGTATTGCTCTTGAATTGCAATGGTGATATTGT
56001 TGAAAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 18 0.50
43 17 0.47
44 1 0.03
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (43 bp):
TTGTGCCAGTATTGCTCTTGAATTGCAATGGTGATATTGTGCT
Found at i:57418 original size:12 final size:12
Alignment explanation
Indices: 57385--57419 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
57375 CCGTTTCAAG
57385 TCCCCGTATCCA
1 TCCCCGTATCCA
*
57397 TCCCCATATCCA
1 TCCCCGTATCCA
*
57409 TCCCTGTATCC
1 TCCCCGTATCC
57420 GTATCAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.49, G:0.06, T:0.29
Consensus pattern (12 bp):
TCCCCGTATCCA
Found at i:58466 original size:2 final size:2
Alignment explanation
Indices: 58459--58494 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
58449 AAATAACTGA
58459 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
58495 TTCTTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58971 original size:32 final size:32
Alignment explanation
Indices: 58935--58998 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
58925 ACACTTTATC
*
58935 TCAACTATAAATCATTGTCCCGTTTATTCCAA
1 TCAACTATAAATCATTGTCCCATTTATTCCAA
* *
58967 TCAACTATAAATCATTGTTCTATTTATTCCAA
1 TCAACTATAAATCATTGTCCCATTTATTCCAA
58999 ATCGTTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (32 bp):
TCAACTATAAATCATTGTCCCATTTATTCCAA
Found at i:63069 original size:257 final size:255
Alignment explanation
Indices: 62582--63085 Score: 684
Period size: 257 Copynumber: 2.0 Consensus size: 255
62572 TCGGGTCGGG
*
62582 TTTTTAATTCATATATTCGGGTCGGGTCGGGTCCGGTGAAACTTTATTTTGGTCGGGTCAGTTTT
1 TTTTTAATTCATATATTCGGGTCGGGTCGAGTCCGGTGAAACTTTATTTTGGTCGGGTCAGTTTT
** * *
62647 TTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTATGGTGAAAAATACCCGACCCGAAAAT
66 TTTAAGTGTGATATTCAAGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCAAAAAT
* * * *
62712 ATATATTTTACCTTATATATTTAGGAATATTAAATAATATCCCTCTATATATAATTTTTTTCAAT
131 ATATATTTTACCTTATATATTTAGGAATATTAAATAATATCCCTATATATATAATATATTCCAAT
62777 TAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTT-GGGTCGGTCAGGTCAGA
196 TAAGTCACTGTTTTTATTG-A-AAAAATAATTTTTTTATTATTTCGGGTCGGTCAGGTCAGA
* * *
62838 TTTTTAATTCATATATTCGGGTTGGGTCGAGT-CGAGTGAAATTTTATTTTGGTCGGGTCGATTT
1 TTTTTAATTCATATATTCGGGTCGGGTCGAGTCCG-GTGAAACTTTATTTTGGTCGGGTC-AGTT
* *
62902 TTTTTAAGTGTGATATTCAAGTCGGGTCGGGTTCTGGTTTAGGGTGAAAAATACCTGACTCGACC
64 TTTTTAAGTGTGATATTCAAGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATA-C---C-CGACC
* *
62967 CAAAAAATATATAATTTTACC-T-TATATTTAGGATTAATTACATAATAT-CC-ATATATAT-AT
124 C-AAAAATATAT-ATTTTACCTTATATATTTAGGAAT-ATTAAATAATATCCCTATATATATAAT
63027 ATATTCCAATTAAGTCACTGTTTTTTATTG-AAAAAT-ATTTTTTTATTATTTCGGGTCGG
186 ATATTCCAATTAAGTCACTG-TTTTTATTGAAAAAATAATTTTTTTATTATTTCGGGTCGG
63086 GTTTATAATT
Statistics
Matches: 220, Mismatches: 16, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
255 2 0.01
256 53 0.24
257 66 0.30
258 14 0.06
260 19 0.09
261 17 0.08
262 20 0.09
263 21 0.10
264 8 0.04
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (255 bp):
TTTTTAATTCATATATTCGGGTCGGGTCGAGTCCGGTGAAACTTTATTTTGGTCGGGTCAGTTTT
TTTAAGTGTGATATTCAAGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCAAAAAT
ATATATTTTACCTTATATATTTAGGAATATTAAATAATATCCCTATATATATAATATATTCCAAT
TAAGTCACTGTTTTTATTGAAAAAATAATTTTTTTATTATTTCGGGTCGGTCAGGTCAGA
Found at i:63521 original size:17 final size:18
Alignment explanation
Indices: 63499--63546 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
63489 ATATGAAATT
*
63499 GGATTCCAATTCC-TGAC
1 GGATTCCAATTCCTTCAC
63516 GGATTCCAATTCCTTCAC
1 GGATTCCAATTCCTTCAC
*
63534 AGATTCCAATTCC
1 GGATTCCAATTCC
63547 CTCAGAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.31
Consensus pattern (18 bp):
GGATTCCAATTCCTTCAC
Found at i:66646 original size:20 final size:21
Alignment explanation
Indices: 66621--66662 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
66611 AAGCTCATCT
66621 AAAATAA-TGGGTTAGAAAGA
1 AAAATAATTGGGTTAGAAAGA
66641 AAAATAAGTTTGGGTTAGAAAG
1 AAAATAA--TTGGGTTAGAAAG
66663 TAACTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
23 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (21 bp):
AAAATAATTGGGTTAGAAAGA
Found at i:67053 original size:19 final size:19
Alignment explanation
Indices: 67002--67057 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
66992 TATTTTAGCA
* *
67002 TAAATAATTTATTAATAGT
1 TAAATATTTTATTTATAGT
*
67021 CAAATATTTTATTTATAGT
1 TAAATATTTTATTTATAGT
67040 TAAATATTTTATTT-TAGT
1 TAAATATTTTATTTATAGT
67058 GTTTAGTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
18 4 0.12
19 29 0.88
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (19 bp):
TAAATATTTTATTTATAGT
Found at i:68388 original size:35 final size:34
Alignment explanation
Indices: 68319--68428 Score: 150
Period size: 34 Copynumber: 3.2 Consensus size: 34
68309 AAAACATTCC
* *
68319 TCAATTTCATTCTAAACCCCAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
68353 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
68388 TCAATTACATTCTAAAACCCAAATT-CTAAATATT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
68422 TCAATTT
1 TCAATTT
68429 AAGGAGGAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
34 32 0.47
35 30 0.44
36 6 0.09
ACGTcount: A:0.41, C:0.23, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Done.