Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003858.1 Hibiscus syriacus cultivar Beakdansim tig00008295_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: 144561
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:6291 original size:19 final size:20
Alignment explanation
Indices: 6255--6292 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6245 GTCCTAAGTC
* *
6255 AAAGAAGAAAAAGGAAATGA
1 AAAGAACAAAAAGAAAATGA
6275 AAAGAACAAAAA-AAAATG
1 AAAGAACAAAAAGAAAATG
6293 GAGAAAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (20 bp):
AAAGAACAAAAAGAAAATGA
Found at i:6360 original size:8 final size:7
Alignment explanation
Indices: 6337--6380 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
6327 GCCCTAAATT
6337 GAAAATAA
1 GAAAA-AA
6345 GAGAAAAA
1 GA-AAAAA
6353 GAACAAAA
1 GAA-AAAA
6361 GAAAAAA
1 GAAAAAA
*
6368 GAGAAAA
1 GAAAAAA
6375 GAAAAA
1 GAAAAA
6381 TAAGGTGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
7 16 0.50
8 13 0.41
9 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.02
Consensus pattern (7 bp):
GAAAAAA
Found at i:7414 original size:43 final size:43
Alignment explanation
Indices: 7304--7423 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 43
7294 ACGAATGGGC
* *
7304 CATCCACGATTTCAACTCCACGACAGAGGATATCATACCTACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCACA
* ** * *
7347 AATCCAATATTTCAACTCCACGACGGAGGATATTATGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCACA
* * *
7390 CATCCACGATTTCAACTTCACGACGAAAGATATC
1 CATCCACGATTTCAACTCCACGACGGAGGATATC
7424 GTGCCAACTC
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCATACCCACA
Found at i:9684 original size:19 final size:18
Alignment explanation
Indices: 9599--9686 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 18
9589 TTGTTATTTA
9599 TTATTATTATATTTTAATT
1 TTATTATTATATTTT-ATT
* * *
9618 TTATTATTCTATTTCTCTA
1 TTATTATTATATTT-TATT
* *
9637 TTATCATTATAACTTTA--
1 TTATTATTAT-ATTTTATT
9654 TTATTAACTTATATTTTATT
1 TTATT-A-TTATATTTTATT
9674 TTATTATT-TATTT
1 TTATTATTATATTT
9687 CATTCATTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
17 9 0.17
18 8 0.15
19 28 0.52
20 9 0.17
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTATTATATTTTATT
Found at i:9714 original size:30 final size:30
Alignment explanation
Indices: 9668--9742 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
9658 TAACTTATAT
9668 TTTATTT-TATTATTTATTTCATTCATTTTC
1 TTTATTTCTATT-TTTATTTCATTCATTTTC
* *
9698 TATT-TTTCTATTTTTATTTCTTTTATTTTC
1 T-TTATTTCTATTTTTATTTCATTCATTTTC
*
9728 TTTATTTCTGTTTTT
1 TTTATTTCTATTTTT
9743 TTCATATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 2 0.05
30 31 0.79
31 6 0.15
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.75
Consensus pattern (30 bp):
TTTATTTCTATTTTTATTTCATTCATTTTC
Found at i:9731 original size:18 final size:18
Alignment explanation
Indices: 9710--9745 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
9700 TTTTTCTATT
9710 TTTATTTCT-TTTATTTTC
1 TTTATTTCTGTTT-TTTTC
9728 TTTATTTCTGTTTTTTTC
1 TTTATTTCTGTTTTTTTC
9746 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.08, C:0.11, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTATTTCTGTTTTTTTC
Found at i:9786 original size:42 final size:40
Alignment explanation
Indices: 9700--9799 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 40
9690 TCATTTTCTA
* ***
9700 TTTTTCTATTTTTATTTCTTTTATTTTCTTTATTTCTGTT
1 TTTTTCTATTTTTATTTTTTTTATTTTCTTTATTTCTACC
9740 TTTTTCATATTTTTATTTTTATTTATTTTCTTTATCTTC-ACC
1 TTTTTC-TATTTTTATTTTT-TTTATTTTCTTTAT-TTCTACC
* *
9782 TTTTTTTATATTTATTTT
1 TTTTTCTATTTTTATTTT
9800 GTTTCTTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
40 6 0.12
41 23 0.45
42 19 0.37
43 3 0.06
ACGTcount: A:0.14, C:0.10, G:0.01, T:0.75
Consensus pattern (40 bp):
TTTTTCTATTTTTATTTTTTTTATTTTCTTTATTTCTACC
Found at i:9809 original size:43 final size:42
Alignment explanation
Indices: 9700--9820 Score: 110
Period size: 43 Copynumber: 2.9 Consensus size: 42
9690 TCATTTTCTA
**
9700 TTTTTC-TATTTTTATTTCTT--TTATTTTCTTTATTTCTGTT
1 TTTTTCATATTTTTATTT-TTACTTATTTTCTTTATTTCCCTT
*
9740 TTTTTCATATTTTTATTTTTATTTATTTTCTTTATCTTCACCTT
1 TTTTTCATATTTTTATTTTTACTTATTTTCTTTAT-TTC-CCTT
*
9784 TTTTT-ATATTTATT-TTGTTT-CTTATTTATTTTTATTT
1 TTTTTCATATTT-TTATT-TTTACTTATTT-TCTTTATTT
9821 TTGTTCTATT
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
40 8 0.12
41 11 0.16
42 13 0.19
43 19 0.28
44 18 0.26
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (42 bp):
TTTTTCATATTTTTATTTTTACTTATTTTCTTTATTTCCCTT
Found at i:9809 original size:47 final size:42
Alignment explanation
Indices: 9700--9794 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
9690 TCATTTTCTA
* **
9700 TTTTTC-TATTTTTATTTCT-TTTATTTTCTTTATTTCTGTT
1 TTTTTCATATTTTTATTTTTATTTATTTTCTTTATTTCCCTT
9740 TTTTTCATATTTTTATTTTTATTTATTTTCTTTATCTTCACCTT
1 TTTTTCATATTTTTATTTTTATTTATTTTCTTTAT-TTC-CCTT
9784 TTTTT-ATATTT
1 TTTTTCATATTT
9795 ATTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
40 6 0.12
41 12 0.25
42 14 0.29
43 9 0.19
44 7 0.15
ACGTcount: A:0.14, C:0.11, G:0.01, T:0.75
Consensus pattern (42 bp):
TTTTTCATATTTTTATTTTTATTTATTTTCTTTATTTCCCTT
Found at i:9811 original size:22 final size:21
Alignment explanation
Indices: 9786--9833 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
9776 TTCACCTTTT
9786 TTTATATTTA-TTTTGTTTCTTA
1 TTTATATTTATTTTTG-TTC-TA
*
9808 TTTATTTTTATTTTTGTTCTA
1 TTTATATTTATTTTTGTTCTA
9829 TTTAT
1 TTTAT
9834 TTAGCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 12 0.50
23 5 0.21
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTATATTTATTTTTGTTCTA
Found at i:9873 original size:11 final size:11
Alignment explanation
Indices: 9857--9891 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
9847 TATTATTAGG
9857 TTTTATTTTAT
1 TTTTATTTTAT
9868 TTTTATTTT-T
1 TTTTATTTTAT
9878 TGTTTATTTTAT
1 T-TTTATTTTAT
9890 TT
1 TT
9892 CTTTTATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.09
11 18 0.82
12 2 0.09
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:9906 original size:22 final size:22
Alignment explanation
Indices: 9859--9909 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
9849 TTATTAGGTT
* **
9859 TTATTTTATTTTTATTTTTTGT
1 TTATTTTATTTTTATTATTTCC
9881 TTATTTTATTTCTT-TTATTTCC
1 TTATTTTATTT-TTATTATTTCC
9903 TTATTTT
1 TTATTTT
9910 TGTATCTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (22 bp):
TTATTTTATTTTTATTATTTCC
Found at i:10400 original size:54 final size:55
Alignment explanation
Indices: 10318--10541 Score: 294
Period size: 55 Copynumber: 4.1 Consensus size: 55
10308 GGTTCCGACA
* *
10318 TGTGCATAAACACAGAATTCATCCTGAGT-GATGAATCACCGTACATGCACTTTG
1 TGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACATGCACTTCG
* *
10372 TGTGCATAATCACAGAATTCATCCTGAGTAGATGAATCACCGTACATGCACTTCA
1 TGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACATGCACTTCG
* * *
10427 TGTGCATAATCAC-GTAATTTATCTTGAGTGGATGAATCACCGTACAGGCACTTCG
1 TGTGCATAATCACAG-AATTCATCCTGAGTGGATGAATCACCGTACATGCACTTCG
* * * * *
10482 TGTGCATATTCACGGAATTCAACATGGGTGGATGAATCACCGTACA-GCACTAT-G
1 TGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACATGCACT-TCG
10536 TGTGCA
1 TGTGCA
10542 ACCCATGGAA
Statistics
Matches: 153, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
54 41 0.27
55 111 0.73
56 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (55 bp):
TGTGCATAATCACAGAATTCATCCTGAGTGGATGAATCACCGTACATGCACTTCG
Found at i:12181 original size:24 final size:24
Alignment explanation
Indices: 12128--12184 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
12118 AGTTTTCATA
*
12128 ATATTAGTATGGTTTTAATATGCT
1 ATATTAATATGGTTTTAATATGCT
* *
12152 AGTATTAATAT-GTTTTACTATGTT
1 A-TATTAATATGGTTTTAATATGCT
12176 GATATTAAT
1 -ATATTAAT
12185 TTTTTTCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.51
Consensus pattern (24 bp):
ATATTAATATGGTTTTAATATGCT
Found at i:13221 original size:15 final size:16
Alignment explanation
Indices: 13183--13222 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
13173 ACAGAACATC
* *
13183 TGAATCATTCAGCATT
1 TGAATCATTCAACACT
13199 TGAATCATTCAACACT
1 TGAATCATTCAACACT
13215 T-AATCATT
1 TGAATCATT
13223 ATGAAGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:21150 original size:17 final size:18
Alignment explanation
Indices: 21125--21171 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
21115 TATGGAATTG
*
21125 GATTTCAATTCC-TAACA
1 GATTCCAATTCCTTAACA
*
21142 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTAACA
*
21160 GATTCTAATTCC
1 GATTCCAATTCC
21172 CTCAAAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTAACA
Found at i:25003 original size:43 final size:43
Alignment explanation
Indices: 24950--25067 Score: 148
Period size: 43 Copynumber: 2.7 Consensus size: 43
24940 TTTTGTTAAA
*
24950 AAAAATGCCGCAATAGGTGTTGATATTTAGCGGCG-TTAATCAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGCTT-ATCAG
* * * * *
24993 AAAAACGCCGCAATAGGTATTGATATTTCGCAGCGCTTGTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGCTTATCAG
* *
25036 AAAAACGCCACAATAGGTGTTGATGTTTAGCG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCG
25068 ACGATTTTCT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 61 0.97
44 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGCTTATCAG
Found at i:25178 original size:43 final size:43
Alignment explanation
Indices: 25090--25203 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 43
25080 AAAATGCCGC
* *
25090 AGTAGGTGTTGATGTTTTGCGGTG-TTTTCCCACAAACGTCGT
1 AGTAGGTGTTGATGTTTTGCGGCGTTTTTCCCACAAACGTCAT
* *
25132 AGTAGGTGTTGATGTTTTGTGGCGTTTTTCTCACAAACG-CTAT
1 AGTAGGTGTTGATGTTTTGCGGCGTTTTTCCCACAAACGTC-AT
** *
25175 AGTAGGCATTGATGTTTTACGGCGTTTTT
1 AGTAGGTGTTGATGTTTTGCGGCGTTTTT
25204 ACTAAAAACG
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
42 23 0.37
43 39 0.63
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (43 bp):
AGTAGGTGTTGATGTTTTGCGGCGTTTTTCCCACAAACGTCAT
Found at i:25213 original size:43 final size:43
Alignment explanation
Indices: 25131--25214 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
25121 ACAAACGTCG
** ** *
25131 TAGTAGGTGTTGATGTTTTGTGGCGTTTTTCTCACAAACGCTA
1 TAGTAGGCATTGATGTTTTACGGCGTTTTTCTCAAAAACGCTA
25174 TAGTAGGCATTGATGTTTTACGGCGTTTTTACT-AAAAACGC
1 TAGTAGGCATTGATGTTTTACGGCGTTTTT-CTCAAAAACGC
25215 CGGTAAAGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 33 0.94
44 2 0.06
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (43 bp):
TAGTAGGCATTGATGTTTTACGGCGTTTTTCTCAAAAACGCTA
Found at i:25641 original size:21 final size:21
Alignment explanation
Indices: 25617--25688 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
25607 GCTGATATGT
25617 TGCTTCTCTCTGTGCTGCCAC
1 TGCTTCTCTCTGTGCTGCCAC
*
25638 TGCTTCTCTCTGTGCTGTCAC
1 TGCTTCTCTCTGTGCTGCCAC
* * *
25659 TGCTTCTTTCTCTGCTTCCAC
1 TGCTTCTCTCTGTGCTGCCAC
*
25680 TGCTGCTCT
1 TGCTTCTCT
25689 GGCTGCTTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.04, C:0.36, G:0.17, T:0.43
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTGCCAC
Found at i:25694 original size:21 final size:21
Alignment explanation
Indices: 25670--25709 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25660 GCTTCTTTCT
25670 CTGCTTCCACTGCTGCTCTGG
1 CTGCTTCCACTGCTGCTCTGG
**
25691 CTGCTTCTGCTGCTGCTCT
1 CTGCTTCCACTGCTGCTCT
25710 CTCTGTTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.38, G:0.23, T:0.38
Consensus pattern (21 bp):
CTGCTTCCACTGCTGCTCTGG
Found at i:38604 original size:147 final size:148
Alignment explanation
Indices: 38314--38610 Score: 526
Period size: 147 Copynumber: 2.0 Consensus size: 148
38304 TTACTGGAAA
38314 ATAAATTCTTTTGTTAATCAGTAATTTTATTAAACTATATCTTTTCGTGAAAACTTTTAAAAACA
1 ATAAATTCTTTTGTTAATCAGTAATTTTATTAAACTATATCTTTTCGTGAAAACTTTTAAAAACA
*
38379 TAATAACGTAATATATTATTTTCATGCATAGATACTGATAAAACTAAGCCAAGTAAAATAAACTA
66 TAATAACGTAATATATTATTTTCATGCATAGATACTGATAAAACTAAACCAAGTAAAATAAACTA
38444 AAATAGTTCTAGTTTACT
131 AAATAGTTCTAGTTTACT
*
38462 ATAAATTCTTTTGTTAATCAGTAATTTTATTAAA-TCATGTCTTTTCGTGAAAACTTTTAAAAAC
1 ATAAATTCTTTTGTTAATCAGTAATTTTATTAAACT-ATATCTTTTCGTGAAAACTTTTAAAAAC
* * *
38526 CTAATAACG-AATATATTCTTTTCATGCATAGATACTGATAAAACTAAACCAAGTAAAATAAATT
65 ATAATAACGTAATATATTATTTTCATGCATAGATACTGATAAAACTAAACCAAGTAAAATAAACT
38590 AAAATAGTTCTAGTTTACT
130 AAAATAGTTCTAGTTTACT
38609 AT
1 AT
38611 TACATATTAT
Statistics
Matches: 143, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
147 74 0.52
148 69 0.48
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (148 bp):
ATAAATTCTTTTGTTAATCAGTAATTTTATTAAACTATATCTTTTCGTGAAAACTTTTAAAAACA
TAATAACGTAATATATTATTTTCATGCATAGATACTGATAAAACTAAACCAAGTAAAATAAACTA
AAATAGTTCTAGTTTACT
Found at i:42362 original size:31 final size:32
Alignment explanation
Indices: 42327--42404 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
42317 CTTTTAAAAC
* * *
42327 TTGTAATATAATCTCC-CAATATTTAGTTTAT
1 TTGTAATATGATCTCCTCAACATTTAGTTCAT
*
42358 TTGTAATATGGTC-CCTCAACATTTAGTTCAT
1 TTGTAATATGATCTCCTCAACATTTAGTTCAT
*
42389 TTGCAATATGATCTCC
1 TTGTAATATGATCTCC
42405 GACGTAACTG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
30 2 0.05
31 35 0.90
32 2 0.05
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (32 bp):
TTGTAATATGATCTCCTCAACATTTAGTTCAT
Found at i:42604 original size:21 final size:21
Alignment explanation
Indices: 42578--42618 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42568 CCAGATAATT
*
42578 TTGTTCAAGCGGGCATGCATC
1 TTGTTCAAGCGGACATGCATC
*
42599 TTGTTCATGCGGACATGCAT
1 TTGTTCAAGCGGACATGCAT
42619 ACTGGAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGTTCAAGCGGACATGCATC
Found at i:44829 original size:31 final size:30
Alignment explanation
Indices: 44790--44854 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 30
44780 TAATATAATC
* *
44790 CCCTAACATTTAGTCTGTTTGCAATATGGT
1 CCCTAACATTTAGTCCGTTTACAATATGGT
44820 CCCTCAACATTTAGTCCGTTTACAATATGGT
1 CCCT-AACATTTAGTCCGTTTACAATATGGT
44851 CCCT
1 CCCT
44855 GACGTAACTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (30 bp):
CCCTAACATTTAGTCCGTTTACAATATGGT
Found at i:45385 original size:15 final size:15
Alignment explanation
Indices: 45365--45400 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
45355 TTCTTCTCTC
45365 TTTTTTTTCAACTGA
1 TTTTTTTTCAACTGA
**
45380 TTTTTTTTCTTCTGA
1 TTTTTTTTCAACTGA
45395 TTTTTT
1 TTTTTT
45401 GTTTTCCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (15 bp):
TTTTTTTTCAACTGA
Found at i:45962 original size:3 final size:3
Alignment explanation
Indices: 45954--45981 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
45944 AACAAAAACA
45954 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45982 GTAGTAGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:48841 original size:15 final size:15
Alignment explanation
Indices: 48818--48857 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
48808 GTAAAAAGAA
48818 AATAGCATGTTAGAG
1 AATAGCATGTTAGAG
* *
48833 AATATCATG-CAGAG
1 AATAGCATGTTAGAG
48847 AATAGCATGTT
1 AATAGCATGTT
48858 GTCTTGCCTC
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (15 bp):
AATAGCATGTTAGAG
Found at i:58534 original size:18 final size:18
Alignment explanation
Indices: 58497--58562 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 18
58487 AAAAATATAA
*
58497 AATTATTTTTATTTAATTAT
1 AATTATTTTTA--AAATTAT
58517 AATTATTTTTAAAATTAT
1 AATTATTTTTAAAATTAT
* *
58535 ATTTATTTATGAAAAGTTAT
1 AATTATTT-TTAAAA-TTAT
58555 -ATTATTTT
1 AATTATTTT
58563 ATATAGAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 14 0.35
19 11 0.28
20 15 0.38
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATTATTTTTAAAATTAT
Found at i:58556 original size:20 final size:17
Alignment explanation
Indices: 58511--58562 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
58501 ATTTTTATTT
*
58511 AATTATAATTATTTTTAA
1 AATTAT-ATTATTTTGAA
58529 AATTATATTTATTTATGAA
1 AATTATA-TTATTT-TGAA
58548 AAGTTATATTATTTT
1 AA-TTATATTATTTT
58563 ATATAGAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.03
18 13 0.43
19 11 0.37
20 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
AATTATATTATTTTGAA
Found at i:58834 original size:21 final size:20
Alignment explanation
Indices: 58799--58875 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 20
58789 AGAAAATTAA
* *
58799 AATTGCTATATACTTAAATT
1 AATTGTTATAAACTTAAATT
58819 AACTTGTTATAAACTTGGGAAATTT
1 AA-TTGTTATAAACTT---AAA-TT
* *
58844 AATTTATTATAAGCTTAAATGT
1 AA-TTGTTATAAACTTAAAT-T
58866 AATTGTTATA
1 AATTGTTATA
58876 CAAAACACTA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
20 2 0.04
21 19 0.42
22 6 0.13
24 3 0.07
25 15 0.33
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.44
Consensus pattern (20 bp):
AATTGTTATAAACTTAAATT
Found at i:59640 original size:5 final size:5
Alignment explanation
Indices: 59630--59660 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
59620 CTTCACAAAG
*
59630 ATAAA ATAAA ATAAA ATAAA ACAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
59661 GTGAAAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:60048 original size:30 final size:29
Alignment explanation
Indices: 59947--60059 Score: 88
Period size: 29 Copynumber: 3.8 Consensus size: 29
59937 AAAAGGACCC
* * *
59947 AAATAGCAAAAAAAAAAAACTTAAGGGAATA
1 AAATAGC--AAAAACAAAATTTAAAGGAATA
59978 AAATAG-AAAAACAACAATTT-AAGGAACTA
1 AAATAGCAAAAACAA-AATTTAAAGGAA-TA
* *
60007 AAACAAC-AAAACAGAAATTTAAAGGAATA
1 AAATAGCAAAAACA-AAATTTAAAGGAATA
* *
60036 AAATGGCAAAAACATAAACTTAAA
1 AAATAGCAAAAACA-AAATTTAAA
60060 AGGCTATAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
28 12 0.18
29 27 0.41
30 21 0.32
31 6 0.09
ACGTcount: A:0.65, C:0.10, G:0.11, T:0.15
Consensus pattern (29 bp):
AAATAGCAAAAACAAAATTTAAAGGAATA
Found at i:61622 original size:3 final size:3
Alignment explanation
Indices: 61595--61650 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
61585 GTAAATTAAA
* * * *
61595 AAT ATT AAT AAA AAT AAG CAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61643 AATT AAT A
1 AA-T AAT A
61651 TTTTTATAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:62081 original size:130 final size:131
Alignment explanation
Indices: 61903--62279 Score: 433
Period size: 130 Copynumber: 2.9 Consensus size: 131
61893 ACTCATACGC
* ** *
61903 GATGAGGACGGCTATTTATCTAGGGGTGACACGGA-TCTTACGTGATGAGGAGGTCTGGTCGAAG
1 GATGAGGACGACTGGTTATCTAGGGGTGACAC-GACTCATACGTGATGAGGAGGTCTGGTCGAAG
* * * *
61967 GATGATATGGTTCCTATGTGATGAGAATGGTAGGCCATCTTTAGGGATGATAACACGATTTCTAC
65 GATGACACGGTTCCTACGTGATGAGAATGGTAGGCCATCTTTAGGGATGATAACACGATTCCTAC
62032 AT
130 AT
*
62034 GATGAGGACGACTGGTTATC-AGGGGTGACACGACTCATACGTGATGAGGAGGTCTAGT--AAGG
1 GATGAGGACGACTGGTTATCTAGGGGTGACACGACTCATACGTGATGAGGAGGTCTGGTCGAA--
* * * *
62096 GGATGACACGGTTCCTACGTGATGA-AGATAGTAGGCCATCTTTAGGAAGGGTTATAACACGGTT
64 GGATGACACGGTTCCTACGTGATGAGA-ATGGTAGGCCATCTTTA-G--GGATGATAACACGATT
*
62160 CCTACGT
125 CCTACAT
* * * * * **
62167 -ATTGAGGATGACTGGTTATCTAGGGGTTGATATGGCTCCTACGTGATGAGGAGGTCTGGTCGGG
1 GA-TGAGGACGACTGGTTATCTAGGGG-TGACACGACTCATACGTGATGAGGAGGTCTGGTCGAA
*
62231 GGATGACACGGTTCCTACGTGATGAGGATGGTAGGCCATCTTTAGGGAT
64 GGATGACACGGTTCCTACGTGATGAGAATGGTAGGCCATCTTTAGGGAT
62280 AATGGTTTCA
Statistics
Matches: 208, Mismatches: 25, Indels: 25
0.81 0.10 0.10
Matches are distributed among these distances:
128 2 0.01
129 3 0.01
130 71 0.34
131 18 0.09
132 4 0.02
133 35 0.17
134 6 0.03
135 69 0.33
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (131 bp):
GATGAGGACGACTGGTTATCTAGGGGTGACACGACTCATACGTGATGAGGAGGTCTGGTCGAAGG
ATGACACGGTTCCTACGTGATGAGAATGGTAGGCCATCTTTAGGGATGATAACACGATTCCTACA
T
Found at i:62115 original size:40 final size:40
Alignment explanation
Indices: 62054--62258 Score: 108
Period size: 40 Copynumber: 4.8 Consensus size: 40
62044 ACTGGTTATC
** *
62054 AGGGG-TGACACGACTCATACGTGATGAGGAGGTCTAGTA
1 AGGGGATGACACGGTTCCTACGTGATGAGGAGGTCTAGTA
*
62093 AGGGGATGACACGGTTCCTACGTGATGAAGATAGTAGGCCATCTTTAGGA
1 AGGGGATGACACGGTTCCTACGTGATG-AG---G-AGG---TC--TAGTA
* * * * *
62143 AGGGTTATAACACGGTTCCTACGT-ATTGAGGATGACTGGTTA
1 AGGG-GATGACACGGTTCCTACGTGA-TGAGGAGGTCTAG-TA
* * * * * *
62185 TCTAGGGGTTGATATGGCTCCTACGTGATGAGGAGGTCTGGTC
1 ---AGGGGATGACACGGTTCCTACGTGATGAGGAGGTCTAGTA
*
62228 GGGGGATGACACGGTTCCTACGTGATGAGGA
1 AGGGGATGACACGGTTCCTACGTGATGAGGA
62259 TGGTAGGCCA
Statistics
Matches: 124, Mismatches: 24, Indels: 35
0.68 0.13 0.19
Matches are distributed among these distances:
39 5 0.04
40 44 0.35
41 4 0.03
42 1 0.01
43 2 0.02
44 25 0.20
45 8 0.06
46 2 0.02
47 1 0.01
48 2 0.02
50 11 0.09
51 19 0.15
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.25
Consensus pattern (40 bp):
AGGGGATGACACGGTTCCTACGTGATGAGGAGGTCTAGTA
Found at i:62241 original size:135 final size:132
Alignment explanation
Indices: 61903--62277 Score: 452
Period size: 135 Copynumber: 2.8 Consensus size: 132
61893 ACTCATACGC
* ** * * **
61903 GATGAGGACGGCTATTTATCTAGGGGTGACACGGATCTTACGTGATGAGGAGGTCTGGTCGAAGG
1 GATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAGGAGGTCTGGTCGGGGG
* * * *
61968 ATGATATGGTTCCTATGTGATG-AGAATGGTAGGCCATCTTTA-GGGATGATAACACGATTTCTA
66 ATGACACGGTTCCTACGTGATGAAG-ATGGTAGGCCATCTTTAGGGGATGATAACACGATTCCTA
62031 CAT
130 CAT
* * **
62034 GATGAGGACGACTGGTTATC-AGGGGTGACACGACTCATACGTGATGAGGAGGTCTAGTAAGGGG
1 GATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAGGAGGTCTGGTCGGGGG
* * * *
62098 ATGACACGGTTCCTACGTGATGAAGATAGTAGGCCATCTTTAGGAAGGGTTATAACACGGTTCCT
66 ATGACACGGTTCCTACGTGATGAAGATGGTAGGCCATCTTTAGG--GGATGATAACACGATTCCT
*
62163 ACGT
129 ACAT
* * * *
62167 -ATTGAGGATGACTGGTTATCTAGGGGTTGATATGGCTCCTACGTGATGAGGAGGTCTGGTCGGG
1 GA-TGAGGACGACTGGTTATCTAGGGG-TGACACGGCTCATACGTGATGAGGAGGTCTGGTCGGG
*
62231 GGATGACACGGTTCCTACGTGATGAGGATGGTAGGCCATCTTTAGGG
64 GGATGACACGGTTCCTACGTGATGAAGATGGTAGGCCATCTTTAGGG
62278 ATAATGGTTT
Statistics
Matches: 207, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
130 71 0.34
131 20 0.10
132 1 0.00
133 36 0.17
134 5 0.02
135 74 0.36
ACGTcount: A:0.25, C:0.15, G:0.34, T:0.27
Consensus pattern (132 bp):
GATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCATACGTGATGAGGAGGTCTGGTCGGGGG
ATGACACGGTTCCTACGTGATGAAGATGGTAGGCCATCTTTAGGGGATGATAACACGATTCCTAC
AT
Found at i:62503 original size:70 final size:70
Alignment explanation
Indices: 62407--62588 Score: 271
Period size: 70 Copynumber: 2.6 Consensus size: 70
62397 AATTTCCACT
* *
62407 TTTGTTT-CAAGAGAAAC-GACTCAAAGATGATTTTT-TCCTCAAAAGAAATTTTCTCAAGAGAG
1 TTTGTTTCCAA-AGAAACAGACTCAAAGATGATTTTTGT-CTCAAAAGAAATTGTCTCAAGAAAG
62469 ATAAAAC
64 ATAAAAC
* *
62476 TTTGTTTCCAAAGAAACAAACTCAAAGATGATTTTTGTTTCAAAAGAAATTGTCTCAAGAAAGAT
1 TTTGTTTCCAAAGAAACAGACTCAAAGATGATTTTTGTCTCAAAAGAAATTGTCTCAAGAAAGAT
62541 AAAAC
66 AAAAC
* *
62546 TTTATTTCCAAAGAAACAGACTCAAAGATGATTTTTGTTTCAA
1 TTTGTTTCCAAAGAAACAGACTCAAAGATGATTTTTGTCTCAA
62589 GTGAAACAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
69 13 0.12
70 90 0.87
71 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (70 bp):
TTTGTTTCCAAAGAAACAGACTCAAAGATGATTTTTGTCTCAAAAGAAATTGTCTCAAGAAAGAT
AAAAC
Found at i:62522 original size:33 final size:33
Alignment explanation
Indices: 62476--62597 Score: 91
Period size: 33 Copynumber: 3.6 Consensus size: 33
62466 GAGATAAAAC
*
62476 TTTGTTTCCAAAGAAACAAACTCAAAGATGATT
1 TTTGTTTCAAAAGAAACAAACTCAAAGATGATT
**** * **
62509 TTTGTTTCAAAAGAAATTGTCTCAAGAAAGATAAAAC
1 TTTGTTTCAAAAGAAACAAACTC---AAAGAT-GATT
* * *
62546 TTTATTTCCAAAGAAACAGACTCAAAGATGATT
1 TTTGTTTCAAAAGAAACAAACTCAAAGATGATT
**
62579 TTTGTTTCAAGTGAAACAA
1 TTTGTTTCAAAAGAAACAA
62598 TTTCAGAATT
Statistics
Matches: 64, Mismatches: 21, Indels: 8
0.69 0.23 0.09
Matches are distributed among these distances:
33 33 0.52
34 6 0.09
36 6 0.09
37 19 0.30
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (33 bp):
TTTGTTTCAAAAGAAACAAACTCAAAGATGATT
Found at i:62570 original size:37 final size:37
Alignment explanation
Indices: 62459--62570 Score: 106
Period size: 37 Copynumber: 3.1 Consensus size: 37
62449 AAGAAATTTT
* *
62459 CTCAAGAGAGATAAAACTTTGTTTCCAAAGAAACAAA
1 CTCAAGAAAGATAAAACTTTGTTTCCAAAGAAACAGA
* ** * ** *
62496 CTC---AAAGAT-GATTTTTGTTTCAAAAGAAATTGT
1 CTCAAGAAAGATAAAACTTTGTTTCCAAAGAAACAGA
*
62529 CTCAAGAAAGATAAAACTTTATTTCCAAAGAAACAGA
1 CTCAAGAAAGATAAAACTTTGTTTCCAAAGAAACAGA
62566 CTCAA
1 CTCAA
62571 AGATGATTTT
Statistics
Matches: 54, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
33 19 0.35
34 5 0.09
36 6 0.11
37 24 0.44
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (37 bp):
CTCAAGAAAGATAAAACTTTGTTTCCAAAGAAACAGA
Found at i:62752 original size:168 final size:166
Alignment explanation
Indices: 62474--62776 Score: 387
Period size: 168 Copynumber: 1.8 Consensus size: 166
62464 GAGAGATAAA
62474 ACTTTGTTTCCAAAGAAACAAACTCAAAGATGATTTTTGTTTCAAAAGAAATTGTCTCAAGAAAG
1 ACTTTGTTTCCAAAGAAACAAACTCAAAGAT-ATTTTTGTTTCAAAAGAAATTGTCTCAAG-AAG
* * * * *
62539 ATAAAACTTTATTTCCAAAGAAACAGACTCAAAGATGATTTTTG-TTTCAAGTGAAACAATTTCA
64 ACAAAACTTTATTTCCAAAGAAACAAAATCAAAGATAAATTTTGTTTTC-AGTGAAACAATTTCA
62603 GAATTTAATGTTTTGAGGAAAACTGTCTCAAGTGAGACG
128 GAATTTAATGTTTTGAGGAAAACTGTCTCAAGTGAGACG
* * * * *
62642 ACTTTGTTTCGAATGAAACAGACTCAAAGAT-TTTTTTTTCTCAAAAGAAATTGTCTCAAG-ATA
1 ACTTTGTTTCCAAAGAAACAAACTCAAAGATATTTTTGTT-TCAAAAGAAATTGTCTCAAGAAGA
* * * *
62705 CAAAACTTTGTTTTCATAGAAATAAAATCAAAGATTACAAATTTTGTTTTCAGTGAAACAATTTC
65 CAAAACTTTATTTCCAAAGAAACAAAATCAAAGA-T--AAATTTTGTTTTCAGTGAAACAATTTC
*
62770 ATAATTT
127 AGAATTT
62777 GCTTTAAAGA
Statistics
Matches: 115, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
165 29 0.25
166 8 0.07
167 20 0.17
168 54 0.47
169 4 0.03
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (166 bp):
ACTTTGTTTCCAAAGAAACAAACTCAAAGATATTTTTGTTTCAAAAGAAATTGTCTCAAGAAGAC
AAAACTTTATTTCCAAAGAAACAAAATCAAAGATAAATTTTGTTTTCAGTGAAACAATTTCAGAA
TTTAATGTTTTGAGGAAAACTGTCTCAAGTGAGACG
Found at i:70506 original size:21 final size:20
Alignment explanation
Indices: 70472--70530 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
70462 ATTTCTTTTC
*
70472 TTTTCTTTTTTTTTTTCTGAT
1 TTTTC-TTTCTTTTTTCTGAT
* **
70493 TTTTCTCTTCTTTTGTCTTTT
1 TTTTCT-TTCTTTTTTCTGAT
70514 TCTTTCTTTCTTTTTTC
1 T-TTTCTTTCTTTTTTC
70531 ACTCCAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 25 0.81
22 5 0.16
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTCTTTCTTTTTTCTGAT
Found at i:70523 original size:26 final size:25
Alignment explanation
Indices: 70463--70524 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
70453 CTCTTTTGAA
* *
70463 TTTCTTTTCTTTTCTTTTTTTTTTTC
1 TTTC-TTTCTCTTCTTTTTCTTTTTC
70489 TGATT-TTTCTCTTCTTTTGTCTTTTTC
1 T--TTCTTTCTCTTCTTTT-TCTTTTTC
70516 TTTCTTTCT
1 TTTCTTTCT
70525 TTTTTCACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
25 2 0.07
26 18 0.60
27 8 0.27
28 2 0.07
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (25 bp):
TTTCTTTCTCTTCTTTTTCTTTTTC
Found at i:74220 original size:5 final size:5
Alignment explanation
Indices: 74210--74240 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
74200 CTTCGCAAAG
*
74210 ATAAA ATAAA ATAAA ATAAA ACAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
74241 GTGGAAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:76195 original size:3 final size:3
Alignment explanation
Indices: 76187--76218 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
76177 GTAAATTAAA
76187 AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
76219 TTTTTGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:77335 original size:22 final size:22
Alignment explanation
Indices: 77288--77335 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
77278 CATATTGTGT
*
77288 AATTTCATTCAAAAATCAAAAT
1 AATTTCATTCAAAAATCAAAAA
* *
77310 AATTTTATT-AAAAATGAATAAA
1 AATTTCATTCAAAAATCAA-AAA
77332 AATT
1 AATT
77336 ATTAAATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (22 bp):
AATTTCATTCAAAAATCAAAAA
Found at i:77607 original size:337 final size:336
Alignment explanation
Indices: 76971--77646 Score: 1106
Period size: 337 Copynumber: 2.0 Consensus size: 336
76961 TATTAAATTT
* * *
76971 TAATTTTATTAAAAATGAGTAAACATTATTAACTGTTATTAAAAAAATAATTAATGAATAATAAT
1 TAATTTTATTAAAAATGAATAAAAATTATTAAATGTTATTAAAAAAATAATTAATGAATAATAAT
* *
77036 TCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTAATATTTTTCATATTTTTAAACATTTAAT
66 TCATTTGAACCCTCAATTGTAATTAAAAGTTTATTTAATATTTTTCATATTTTTAAACAATTAAT
* * *
77101 TTTAAAAGTCAATAAAATTTTCAAAATATATAAAATTTATAATTTTTTAAATTATAAAATATTTA
131 TTTAAAAGTCAATAAAATTTTAAAAATATATAAAATTTATAATTTTTTAAATTATAAAAAAATTA
*
77166 TTATCATCATCATTATCATCATTTTGTAAAAGAAATACTGGTTATAAAACTTTTATAAAATTATT
196 TTATCATCATC--TATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATT
* * *
77231 CATATTTTAAAATACTTACTCTCAAAGTTTTCATATACTAGATTATACATATTGTGTAATTTCAT
259 CATATTTTAAAATACTTACCCTAAAAGTTTTCATATACTAGATTATACATATTGTATAATTTCAT
*
77296 TCAAAAATCAAAA
324 GCAAAAATCAAAA
*
77309 TAATTTTATTAAAAATGAATAAAAATTATTAAATGTTGTTAAAAATAATAATTAATGAATAATAA
1 TAATTTTATTAAAAATGAATAAAAATTATTAAATGTTATTAAAAA-AATAATTAATGAATAATAA
77374 TTCATTTGAACCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTT-ATATTTTTAAACAATTA
65 TTCATTTGAACCCTCAATTGTAATTAAAAGTTTA-TTTAATATTTTTCATATTTTTAAACAATTA
* *
77438 ATTTTAAAAGTCAATAAAGTTTTTAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAAAA
129 ATTTTAAAAGTCAATAAA-ATTTTAAAAATATATAAAATTTATAATTTTTTAAATTATAAAAAAA
77503 TTATTATCATCATC-ATCATCATTTT-TAAAAAGAAATACTAGTTATAAAACTTTTATAAAATTA
193 TTATTATCATCATCTATCATCATTTTGT-AAAAGAAATACTAGTTATAAAACTTTTATAAAATTA
* **
77566 TTCATATTTTAAAATACTTACCCTAAAAGTTTTCCTATACTAGATTATATGTATTGTATAATTTC
257 TTCATATTTTAAAATACTTACCCTAAAAGTTTTCATATACTAGATTATACATATTGTATAATTTC
77631 ATGCAAAAATCAAAA
322 ATGCAAAAATCAAAA
77646 T
1 T
77647 TTATCGAGTT
Statistics
Matches: 315, Mismatches: 19, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
336 1 0.00
337 120 0.38
338 41 0.13
339 86 0.27
340 67 0.21
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (336 bp):
TAATTTTATTAAAAATGAATAAAAATTATTAAATGTTATTAAAAAAATAATTAATGAATAATAAT
TCATTTGAACCCTCAATTGTAATTAAAAGTTTATTTAATATTTTTCATATTTTTAAACAATTAAT
TTTAAAAGTCAATAAAATTTTAAAAATATATAAAATTTATAATTTTTTAAATTATAAAAAAATTA
TTATCATCATCTATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTTTATAAAATTATTCA
TATTTTAAAATACTTACCCTAAAAGTTTTCATATACTAGATTATACATATTGTATAATTTCATGC
AAAAATCAAAA
Found at i:78320 original size:21 final size:21
Alignment explanation
Indices: 78294--78339 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
78284 ACCCCGACCA
78294 CTCGGCTTTAAAGCATCATAT
1 CTCGGCTTTAAAGCATCATAT
*
78315 CTCGGCTTTAAAGCATCATCT
1 CTCGGCTTTAAAGCATCATAT
78336 CTCG
1 CTCG
78340 ACTACTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (21 bp):
CTCGGCTTTAAAGCATCATAT
Found at i:88148 original size:21 final size:22
Alignment explanation
Indices: 88123--88184 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
88113 AGCATATCAT
*
88123 TATATTTTTTAGTATTATAATAA
1 TATATTTATTA-TATTATAATAA
*
88146 TATATTTAATTATATTATAATTA
1 TATATTT-ATTATATTATAATAA
*
88169 TATATGATATTATATT
1 TATAT-TTATTATATT
88185 TTTGTTTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 30 0.88
24 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (22 bp):
TATATTTATTATATTATAATAA
Found at i:88364 original size:23 final size:24
Alignment explanation
Indices: 88302--88371 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
88292 TATTTGAATC
*
88302 AATAACTT-ATATAATTAATAATAT
1 AATAA-TTAATATAATTTATAATAT
* * *
88326 AATAA-TATTATTATTTTTAATA-
1 AATAATTAATATAATTTATAATAT
88348 AATAATTAATATAATTTATAATAT
1 AATAATTAATATAATTTATAATAT
88372 TTATAATATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
22 6 0.17
23 25 0.69
24 5 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
AATAATTAATATAATTTATAATAT
Found at i:88369 original size:46 final size:45
Alignment explanation
Indices: 88278--88414 Score: 131
Period size: 46 Copynumber: 3.0 Consensus size: 45
88268 AGTTTAATAT
* * * *
88278 TATAATAAAATTCTTA-TTTGAATCAATAACTT-ATATAATTAATAA
1 TATAATAATATT-TTATTTTTAATAAATAA-TTAATATAATTTATAA
88323 TATAATAATATTATTATTTTTAATAAATAATTAATATAATTTATAA
1 TATAATAATATT-TTATTTTTAATAAATAATTAATATAATTTATAA
* * *
88369 TATTTATAATATTTT-TATTTACTAAAATAA--AATATAATTTATAA
1 TA-TAATAATATTTTATTTTTAAT-AAATAATTAATATAATTTATAA
88413 TA
1 TA
88415 CAAGTCTTAA
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
44 16 0.20
45 22 0.28
46 33 0.41
47 9 0.11
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (45 bp):
TATAATAATATTTTATTTTTAATAAATAATTAATATAATTTATAA
Found at i:93870 original size:2 final size:2
Alignment explanation
Indices: 93860--94079 Score: 72
Period size: 2 Copynumber: 111.0 Consensus size: 2
93850 AATTGAAAAA
* * *
93860 AT AT A- AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT A- AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
93899 AT AT AT AT AT AT AA ACT AT AT TT AT AT -T AT AA ACT AT AT A- AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
93941 -T AT -T AT A- AGT -T AT AT AT AT AA AT -T AT GT TT AT AT GA- ACT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T
* * * * *
93980 AT AT AT AT AT AA ACT AT AT AT GT AA ACT AT AT AT GT AT AA ACT
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT A-T
* * * *
94023 AT A- AA AA AGT AT AT AGT TT AT AA ACT AT A- AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT
94064 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
94080 TATTCAAAGT
Statistics
Matches: 163, Mismatches: 29, Indels: 52
0.67 0.12 0.21
Matches are distributed among these distances:
1 14 0.09
2 139 0.85
3 10 0.06
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:93892 original size:15 final size:13
Alignment explanation
Indices: 93860--94079 Score: 82
Period size: 13 Copynumber: 17.3 Consensus size: 13
93850 AATTGAAAAA
93860 ATATAATATATAT
1 ATATAATATATAT
93873 ATATAATATA-AGT
1 ATATAATATATA-T
93886 -T-T-ATATATA-
1 ATATAATATATAT
*
93895 A-AAAATATATAT
1 ATATAATATATAT
93907 ATATAA-ACTATAT
1 ATATAATA-TATAT
* * *
93920 TTATATTATAAACT
1 ATATAATATATA-T
93934 ATATAAT-TAT-T
1 ATATAATATATAT
*
93945 ATA-AGT-TATAT
1 ATATAATATATAT
* *
93956 ATATAAATTATGTTT
1 ATAT-AA-TATATAT
93971 ATATGAACTATATAT
1 ATAT-AA-TATATAT
93986 ATATAA-ACTATAT
1 ATATAATA-TATAT
*
93999 ATGTAAACTATATAT
1 ATAT-AA-TATATAT
*
94014 GTATAA-ACTATA-
1 ATATAATA-TATAT
*
94026 A-AAAAGTATATAGT
1 ATATAA-TATATA-T
*
94040 TTATAA-ACTATA-
1 ATATAATA-TATAT
94052 ATAT-ATATATAT
1 ATATAATATATAT
94064 ATAT-ATATATAT
1 ATATAATATATAT
94076 ATAT
1 ATAT
94080 TATTCAAAGT
Statistics
Matches: 155, Mismatches: 24, Indels: 57
0.66 0.10 0.24
Matches are distributed among these distances:
10 10 0.06
11 25 0.16
12 30 0.19
13 43 0.28
14 18 0.12
15 28 0.18
16 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:93907 original size:17 final size:18
Alignment explanation
Indices: 93858--93931 Score: 66
Period size: 17 Copynumber: 4.2 Consensus size: 18
93848 AAAATTGAAA
93858 AAATATAATATATATATAT
1 AAATA-AATATATATATAT
*
93877 AATATAAGT-T-TATATAT
1 AA-ATAAATATATATATAT
93894 AAA-AAATATATATATAT
1 AAATAAATATATATATAT
* *
93911 AAACTATATTTATAT-TAT
1 AAA-TAAATATATATATAT
93929 AAA
1 AAA
93932 CTATATAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
15 3 0.07
16 2 0.04
17 19 0.41
18 7 0.15
19 12 0.26
20 3 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (18 bp):
AAATAAATATATATATAT
Found at i:93907 original size:34 final size:34
Alignment explanation
Indices: 93864--93962 Score: 109
Period size: 34 Copynumber: 3.0 Consensus size: 34
93854 GAAAAAATAT
93864 AATATATATATATAATATAAGTTTATATATAAAA
1 AATATATATATATAATATAAGTTTATATATAAAA
*
93898 AATATATATATATAA-ACTATA-TTTATAT-TATAA
1 AATATATATATATAATA-TA-AGTTTATATATAAAA
* *
93931 ACTATATA-AT-TATTATAAGTTATATATATAAA
1 AATATATATATATAATATAAGTT-TATATATAAA
93963 TTATGTTTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
30 1 0.02
31 6 0.11
32 8 0.15
33 15 0.27
34 24 0.44
35 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (34 bp):
AATATATATATATAATATAAGTTTATATATAAAA
Found at i:94215 original size:19 final size:19
Alignment explanation
Indices: 94180--94265 Score: 88
Period size: 19 Copynumber: 4.6 Consensus size: 19
94170 TTGAGAAATT
*
94180 TTGAGAATATAGA--GAAA
1 TTGAGAATTTAGAGGGAAA
94197 TTGAGAATTTAGAGGGAAA
1 TTGAGAATTTAGAGGGAAA
*
94216 ATGAGAAATTTAGAGGG-AA
1 TTGAG-AATTTAGAGGGAAA
* * *
94235 TAGAAAATTTTGGAGGGAAA
1 TTGAGAA-TTTAGAGGGAAA
94255 TTGAGAATTTA
1 TTGAGAATTTA
94266 TTTGGAAAGA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
17 12 0.22
18 2 0.04
19 23 0.42
20 18 0.33
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.27
Consensus pattern (19 bp):
TTGAGAATTTAGAGGGAAA
Found at i:94238 original size:46 final size:45
Alignment explanation
Indices: 94155--94243 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 45
94145 TTTTATTTGG
* *
94155 GAATTTAGAGGGAAATTGAGAAATTTTGAGAATATAGAGAAATTGA
1 GAATTTAGAGGGAAAATGAGAAATTTAGAGAATATAGA-AAATTGA
*
94201 GAATTTAGAGGGAAAATGAGAAATTTAGAGGGA-ATAGAAAATT
1 GAATTTAGAGGGAAAATGAGAAATTTAGA-GAATATAGAAAATT
94244 TTGGAGGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 5 0.13
46 32 0.82
47 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.26
Consensus pattern (45 bp):
GAATTTAGAGGGAAAATGAGAAATTTAGAGAATATAGAAAATTGA
Found at i:94674 original size:21 final size:21
Alignment explanation
Indices: 94618--94675 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
94608 ATAGTTTATA
* *
94618 AAACCCTAAACCTTAAATCCT
1 AAACCCTAAACCCTAAATCAT
*** * *
94639 AAATTGTGAATCCTAAATCAT
1 AAACCCTAAACCCTAAATCAT
94660 AAACCCTAAACCCTAA
1 AAACCCTAAACCCTAA
94676 CCCCTGAACT
Statistics
Matches: 25, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.24
Consensus pattern (21 bp):
AAACCCTAAACCCTAAATCAT
Found at i:94751 original size:15 final size:14
Alignment explanation
Indices: 94731--94784 Score: 60
Period size: 15 Copynumber: 4.0 Consensus size: 14
94721 ATGTATCGTA
94731 TATATAAACTATAT
1 TATATAAACTATAT
*
94745 GTATATAACCTATA-
1 -TATATAAACTATAT
*
94759 TATATATA-TATA-
1 TATATAAACTATAT
94771 TATATAAACTATAT
1 TATATAAACTATAT
94785 AAAGTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 11 0.33
13 10 0.30
15 12 0.36
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (14 bp):
TATATAAACTATAT
Found at i:95299 original size:11 final size:11
Alignment explanation
Indices: 95285--95328 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
95275 CCATGTATAG
95285 TATATATAAAC
1 TATATATAAAC
95296 TATATATATAACC
1 TATATATA-AA-C
*
95309 TATATATATAC
1 TATATATAAAC
95320 TATACTATA
1 TATA-TATA
95329 CTATACTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 13 0.45
12 7 0.24
13 9 0.31
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (11 bp):
TATATATAAAC
Found at i:95301 original size:13 final size:13
Alignment explanation
Indices: 95285--95340 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
95275 CCATGTATAG
95285 TATATATAAACTA
1 TATATATAAACTA
*
95298 TATATATAACCTA
1 TATATATAAACTA
95311 TATATAT--ACTA
1 TATATATAAACTA
*
95322 TACTATACTATACTA
1 TA-TATA-TAAACTA
95337 TATA
1 TATA
95341 AAGTAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
11 5 0.14
12 4 0.11
13 20 0.54
14 2 0.05
15 6 0.16
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:95303 original size:20 final size:20
Alignment explanation
Indices: 95260--95303 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
95250 TTTTATATTA
95260 ATAT-GTATATATAAACCAT
1 ATATAGTATATATAAACCAT
* *
95279 GTATAGTATATATAAACTAT
1 ATATAGTATATATAAACCAT
95299 ATATA
1 ATATA
95304 TAACCTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATATAAACCAT
Found at i:95481 original size:14 final size:14
Alignment explanation
Indices: 95462--95488 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
95452 GGACTAGCAC
95462 TAAACCATAAACAT
1 TAAACCATAAACAT
95476 TAAACCATAAACA
1 TAAACCATAAACA
95489 ATTGCAAGTT
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:0.59, C:0.22, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACCATAAACAT
Found at i:96191 original size:2 final size:2
Alignment explanation
Indices: 96184--96238 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
96174 AAAAGTAATT
96184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
96226 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
96239 GTAACCAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:96272 original size:22 final size:23
Alignment explanation
Indices: 96247--96289 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
96237 ATGTAACCAA
96247 TATTAAATAATTTTAT-TAATTT
1 TATTAAATAATTTTATATAATTT
96269 TATTAAATAATTTTATATAAT
1 TATTAAATAATTTTATATAAT
96290 ATGTATGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTAAATAATTTTATATAATTT
Found at i:96426 original size:21 final size:21
Alignment explanation
Indices: 96396--96453 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
96386 TAGTTTATAG
* **
96396 AAACCTTAAACCCTAAACTTT
1 AAACCATAAACCCTAAACACT
*
96417 AAACCATAAACACTAAACACT
1 AAACCATAAACCCTAAACACT
*
96438 AAATCATAAACCCTAA
1 AAACCATAAACCCTAA
96454 TATAAATAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACCATAAACCCTAAACACT
Found at i:96630 original size:15 final size:14
Alignment explanation
Indices: 96612--96654 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
96602 TTAATCATGT
*
96612 TTTATATAATTTATA
1 TTTAAATAATTT-TA
96627 TTTAAATAATTTTA
1 TTTAAATAATTTTA
96641 -TTAAATAATTTTA
1 TTTAAATAATTTTA
96654 T
1 T
96655 ATATATGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 13 0.50
14 2 0.08
15 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAAATAATTTTA
Found at i:96711 original size:15 final size:15
Alignment explanation
Indices: 96677--96721 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
96667 ATAAACCATG
96677 TATAGTATATATA-AA
1 TATA-TATATATATAA
*
96692 CTATATATATGTATAA
1 -TATATATATATATAA
96708 TATATATATATATA
1 TATATATATATATA
96722 TAAACTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:96730 original size:17 final size:17
Alignment explanation
Indices: 96677--96732 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 17
96667 ATAAACCATG
96677 TATAGTATATATAAACTA
1 TATA-TATATATAAACTA
*
96695 TATATATGTATAATA-TA
1 TATATATATATAA-ACTA
96712 TATATATATATAAACTA
1 TATATATATATAAACTA
96729 TATA
1 TATA
96733 AAATAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 1 0.03
17 28 0.82
18 5 0.15
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (17 bp):
TATATATATATAAACTA
Found at i:96732 original size:2 final size:2
Alignment explanation
Indices: 96677--96723 Score: 51
Period size: 2 Copynumber: 23.0 Consensus size: 2
96667 ATAAACCATG
* *
96677 TA TA GTA TA TA TA AA CTA TA TA TA TG TA TA -A TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
96720 TA TA
1 TA TA
96724 AACTATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 1 0.03
2 34 0.89
3 3 0.08
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:96817 original size:7 final size:7
Alignment explanation
Indices: 96807--96881 Score: 60
Period size: 7 Copynumber: 10.7 Consensus size: 7
96797 TAGTTTATAG
96807 AAACCCT
1 AAACCCT
96814 AAACCCT
1 AAACCCT
*
96821 AAACTCT
1 AAACCCT
*
96828 AAACTCT
1 AAACCCT
*
96835 AAACTCT
1 AAACCCT
***
96842 AAATTTT
1 AAACCCT
*
96849 AAACCAT
1 AAACCCT
*
96856 AAACACT
1 AAACCCT
*
96863 AAACACT
1 AAACCCT
*
96870 AAACCAT
1 AAACCCT
96877 AAACC
1 AAACC
96882 ATAATGTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 58 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:96824 original size:49 final size:49
Alignment explanation
Indices: 96721--96825 Score: 131
Period size: 48 Copynumber: 2.1 Consensus size: 49
96711 ATATATATAT
* * **
96721 ATAAACTATATAAAATAAATTACTTATATAGTTTATAGAAACACTATGC
1 ATAAACTATATAAAATAAATAAATTATATAGTTTATAGAAACACTAACC
* *
96770 ATAAACTATATAAAGT-AATAAATTATATAGTTTATAGAAACCCTAAACC
1 ATAAACTATATAAAATAAATAAATTATATAGTTTATAGAAACACT-AACC
*
96819 CTAAACT
1 ATAAACT
96826 CTAAACTCTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 25 0.52
49 23 0.48
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (49 bp):
ATAAACTATATAAAATAAATAAATTATATAGTTTATAGAAACACTAACC
Found at i:96836 original size:21 final size:21
Alignment explanation
Indices: 96808--96880 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
96798 AGTTTATAGA
* *
96808 AACCCTAAACCCTAAACTCTA
1 AACCATAAACACTAAACTCTA
* * *
96829 AACTC-TAAACTCTAAATTTTA
1 AAC-CATAAACACTAAACTCTA
*
96850 AACCATAAACACTAAACACTA
1 AACCATAAACACTAAACTCTA
96871 AACCATAAAC
1 AACCATAAAC
96881 CATAATGTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCATAAACACTAAACTCTA
Found at i:97130 original size:13 final size:15
Alignment explanation
Indices: 97102--97139 Score: 62
Period size: 13 Copynumber: 2.7 Consensus size: 15
97092 ATGTTTTATC
97102 TAATTTATATTTAAA
1 TAATTTATATTTAAA
97117 TAATTT-TA-TTAAA
1 TAATTTATATTTAAA
97130 TAATTTATAT
1 TAATTTATAT
97140 AAATCGCCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 11 0.52
14 4 0.19
15 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTATATTTAAA
Found at i:102264 original size:23 final size:23
Alignment explanation
Indices: 102205--102265 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
102195 CTCGTATAAA
* *
102205 TGCACCGAAGTGCAACGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* * *
102228 TACATCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
102251 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
102266 TATAAAATGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:103043 original size:19 final size:20
Alignment explanation
Indices: 102997--103045 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
102987 GGTATGCATT
*
102997 TATATTATATAACATATGTC
1 TATATTATATAACATATATC
103017 -ATATT-TATAAACATATATC
1 TATATTATAT-AACATATATC
103036 TATATTATAT
1 TATATTATAT
103046 GTGTATATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 5 0.20
21 3 0.12
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (20 bp):
TATATTATATAACATATATC
Found at i:103375 original size:21 final size:22
Alignment explanation
Indices: 103332--103376 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
103322 TTCACATAGT
103332 CTTATATTTAATTATCATATAA
1 CTTATATTTAATTATCATATAA
* *
103354 CTTATATTT-ATTCTCTTATAA
1 CTTATATTTAATTATCATATAA
103375 CT
1 CT
103377 CTTCATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (22 bp):
CTTATATTTAATTATCATATAA
Found at i:103594 original size:22 final size:22
Alignment explanation
Indices: 103567--103616 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
103557 CACACATACA
103567 ATAACATATTACTCATACACCC
1 ATAACATATTACTCATACACCC
103589 ATAACATATTACTCATACACCC
1 ATAACATATTACTCATACACCC
103611 ATAACA
1 ATAACA
103617 AACACATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAACATATTACTCATACACCC
Found at i:111921 original size:60 final size:60
Alignment explanation
Indices: 111857--111971 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
111847 TGGTACTTCG
*
111857 ACTATATGA-TACTACTTTATTGAGTCACTCGACTATTAAAAGTTACAAAATGATCCTCTA
1 ACTATA-GAGTACTACTTTATTGAATCACTCGACTATTAAAAGTTACAAAATGATCCTCTA
** * * *
111917 ACTATAGAGTGTTGCTTTGTTGAATCTCTCGACTATTAAAAGTTACAAAATGATC
1 ACTATAGAGTACTACTTTATTGAATCACTCGACTATTAAAAGTTACAAAATGATC
111972 ACCGACTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 2 0.04
60 46 0.96
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.36
Consensus pattern (60 bp):
ACTATAGAGTACTACTTTATTGAATCACTCGACTATTAAAAGTTACAAAATGATCCTCTA
Found at i:113234 original size:26 final size:27
Alignment explanation
Indices: 113165--113223 Score: 102
Period size: 28 Copynumber: 2.2 Consensus size: 27
113155 TGCACATCTC
113165 GTACCACAACATATCATTAAAGCGACTT
1 GTACCACAACATATCATTAAAGCGAC-T
113193 GTACCACAACATATCATTAAAGCGA-T
1 GTACCACAACATATCATTAAAGCGACT
113219 GTACC
1 GTACC
113224 GAAACGTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 6 0.19
28 25 0.81
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.24
Consensus pattern (27 bp):
GTACCACAACATATCATTAAAGCGACT
Found at i:113822 original size:22 final size:24
Alignment explanation
Indices: 113796--113850 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
113786 TTATATATTT
113796 TTATAAAAA-GTATA-TGA-AATAA
1 TTATAAAAAGGTATATTGATAAT-A
*
113818 TTATAAAAAGGTATATTTATAATA
1 TTATAAAAAGGTATATTGATAATA
113842 TTATAAAAA
1 TTATAAAAA
113851 CATTTATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 9 0.31
23 5 0.17
24 12 0.41
25 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.36
Consensus pattern (24 bp):
TTATAAAAAGGTATATTGATAATA
Found at i:113901 original size:19 final size:18
Alignment explanation
Indices: 113879--113933 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
113869 AATTTAATTA
113879 ATTATTTATTTGAAATAAT
1 ATTATTTATTT-AAATAAT
113898 ATTATTT-TTTAAAT--T
1 ATTATTTATTTAAATAAT
113913 ATCTATTTAATTTTAAATAAT
1 AT-TATTT-A-TTTAAATAAT
113934 TTAAATTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
15 3 0.10
16 5 0.17
17 4 0.13
18 3 0.10
19 14 0.47
21 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTATTTATTTAAATAAT
Found at i:114078 original size:15 final size:18
Alignment explanation
Indices: 114039--114078 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
114029 TTATTTCAAA
114039 TAAATAAATAATATGATTT
1 TAAA-AAATAATATGATTT
114058 TAAAAAATAA-AT-ATTT
1 TAAAAAATAATATGATTT
114074 TAAAA
1 TAAAA
114079 TATTTTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
18 6 0.29
19 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAAAATAATATGATTT
Found at i:115203 original size:35 final size:35
Alignment explanation
Indices: 115164--115240 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
115154 AGAACAACAT
* * *
115164 TCTCTTTAACCACTGAAA-TCGTTTGATAAGTTTCA
1 TCTCTTTAACCACT-AAAGTCGCTTGATAAATTCCA
*
115199 TCTCTTTAATCACTAAAGTCGCTTGATAAATTCCA
1 TCTCTTTAACCACTAAAGTCGCTTGATAAATTCCA
115234 TCTCTTT
1 TCTCTTT
115241 TATTATTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 3 0.08
35 34 0.92
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (35 bp):
TCTCTTTAACCACTAAAGTCGCTTGATAAATTCCA
Found at i:130120 original size:20 final size:20
Alignment explanation
Indices: 130095--130139 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
130085 TGGTTCGGTG
130095 CTTTCTTATTGGTGCTGGCA
1 CTTTCTTATTGGTGCTGGCA
*
130115 CTTTCTTGTTGGTGCTGGCA
1 CTTTCTTATTGGTGCTGGCA
130135 CTTTC
1 CTTTC
130140 AGTAGTGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.07, C:0.22, G:0.24, T:0.47
Consensus pattern (20 bp):
CTTTCTTATTGGTGCTGGCA
Found at i:131847 original size:45 final size:46
Alignment explanation
Indices: 131760--131850 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
131750 ACTAGATGAA
*
131760 ACTCTGATTATTTACGTACAGTATTATAGCCTTTGATCATCTAACTG
1 ACTCTGATTATTTACGTACAG-ATGATAGCCTTTGATCATCTAACTG
*
131807 ACTCTGATTATTTACGTAGAG-TGATAGCCTTTGATCATCTAACT
1 ACTCTGATTATTTACGTACAGATGATAGCCTTTGATCATCTAACT
131851 TCGACACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 22 0.52
47 20 0.48
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (46 bp):
ACTCTGATTATTTACGTACAGATGATAGCCTTTGATCATCTAACTG
Found at i:139424 original size:21 final size:21
Alignment explanation
Indices: 139400--139452 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
139390 GGGCAAACCA
139400 GGGTGTCAATTTCTTTCTAAG
1 GGGTGTCAATTTCTTTCTAAG
139421 GGGTGTCAATTTCTTTCTAAG
1 GGGTGTCAATTTCTTTCTAAG
*
139442 GGGTGTTAATT
1 GGGTGTCAATT
139453 ATATATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.43
Consensus pattern (21 bp):
GGGTGTCAATTTCTTTCTAAG
Found at i:141908 original size:9 final size:9
Alignment explanation
Indices: 141894--141923 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
141884 GTAGCGATGC
141894 TGCTGCTGG
1 TGCTGCTGG
141903 TGCTGCTGG
1 TGCTGCTGG
141912 TGCTGCT-G
1 TGCTGCTGG
141920 TGCT
1 TGCT
141924 TCCTTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.00, C:0.23, G:0.40, T:0.37
Consensus pattern (9 bp):
TGCTGCTGG
Found at i:142878 original size:13 final size:13
Alignment explanation
Indices: 142862--142889 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
142852 TAACCGAAGT
142862 TATTAATATTAAA
1 TATTAATATTAAA
142875 TATTAATATTAAA
1 TATTAATATTAAA
142888 TA
1 TA
142890 CGCATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTAATATTAAA
Found at i:143165 original size:23 final size:23
Alignment explanation
Indices: 143110--143167 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
143100 AATATCGTTT
*
143110 CTTTTAAACCTTCACTGTTTCAA
1 CTTTTAAACTTTCACTGTTTCAA
143133 CTTTTAAACTTTCACTGTTTCAA
1 CTTTTAAACTTTCACTGTTTCAA
143156 CTTTTAAACTTT
1 CTTTTAAACTTT
143168 TATCTATTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.22, G:0.03, T:0.48
Consensus pattern (23 bp):
CTTTTAAACTTTCACTGTTTCAA
Found at i:144164 original size:17 final size:17
Alignment explanation
Indices: 144137--144186 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
144127 TAATTTGTAT
144137 TGATAACTGTAAACATA
1 TGATAACTGTAAACATA
* *
144154 TGATATA-TGTAAATATC
1 TGATA-ACTGTAAACATA
144171 TGATAACTGTAAACAT
1 TGATAACTGTAAACAT
144187 TTAGAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 1 0.04
17 26 0.93
18 1 0.04
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (17 bp):
TGATAACTGTAAACATA
Done.