Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001434.1 Hibiscus syriacus cultivar Beakdansim tig00002782_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: 120006
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3320 original size:24 final size:23
Alignment explanation
Indices: 3282--3346 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 23
3272 CAGCTTGTAT
*
3282 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACATAG
* * *
3305 AATTTGCACCGTAGTGCCGCATAG
1 AA-ATGCACCGAAGTGCCACATAG
3329 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
3347 TATAAAGTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:3780 original size:20 final size:21
Alignment explanation
Indices: 3733--3783 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
3723 TTTTATGTCT
*
3733 TATCATATAACTTCTCTTTTA
1 TATCATATAACTTCTCTTTCA
3754 TATTCATATAA-TT-TCTTATCA
1 TA-TCATATAACTTCTCTT-TCA
3775 TATCATATA
1 TATCATATA
3784 GTTTATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
22 8 0.30
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (21 bp):
TATCATATAACTTCTCTTTCA
Found at i:4300 original size:64 final size:64
Alignment explanation
Indices: 4187--4327 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 64
4177 TTCCCTTGAA
* * **
4187 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTTAATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCAATGTTCCCATTTTTAA-GGG
* * * * * * *
4251 GTGCACCGATGCACT-CCTTATGCATCGATGCACTAATTACATTCGATGTTCCCATTTTTAATGG
1 GTGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCAATGTTCCCATTTTTAAGGG
4315 GTGCATCGATGCA
1 GTGCATCGATGCA
4328 TTTCCTGTGC
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
63 2 0.03
64 55 0.87
65 6 0.10
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCAATGTTCCCATTTTTAAGGG
Found at i:7658 original size:30 final size:30
Alignment explanation
Indices: 7615--7765 Score: 160
Period size: 30 Copynumber: 5.0 Consensus size: 30
7605 CTTAGTAAAA
* *
7615 TAAAGGACT-AAATAGCAAAAATATAAATT
1 TAAAGGACTAAAATAGCAAAAATAGAAAGT
* * * * *
7644 TATAGGACTAAAATAACCAAAACAGAAACT
1 TAAAGGACTAAAATAGCAAAAATAGAAAGT
* * *
7674 TAAAGGATTAAAATAGTAAAAATAAAAAGT
1 TAAAGGACTAAAATAGCAAAAATAGAAAGT
*
7704 TAAAGGACTAAAATAGAAAAAAAATAGAAAGT
1 TAAAGGACTAAAATAG--CAAAAATAGAAAGT
* *
7736 TAAAGGACTGAAATAACAAAAATAGAAAGT
1 TAAAGGACTAAAATAGCAAAAATAGAAAGT
7766 AAAAAGGCTA
Statistics
Matches: 99, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
29 8 0.08
30 65 0.66
32 26 0.26
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.19
Consensus pattern (30 bp):
TAAAGGACTAAAATAGCAAAAATAGAAAGT
Found at i:7688 original size:60 final size:60
Alignment explanation
Indices: 7615--7765 Score: 169
Period size: 62 Copynumber: 2.5 Consensus size: 60
7605 CTTAGTAAAA
* * * **
7615 TAAAGGACTAAATAGCAAAAATATAAATTTATAGGACTAAAAT-AACCAAAACAGAAACT
1 TAAAGGACTAAATAGCAAAAATAAAAAGTTAAAGGACTAAAATAAAAAAAAACAGAAACT
* * * *
7674 TAAAGGATTAAAATAGTAAAAATAAAAAGTTAAAGGACTAAAATAGAAAAAAAATAGAAAGT
1 TAAAGGACT-AAATAGCAAAAATAAAAAGTTAAAGGACTAAAATA-AAAAAAAACAGAAACT
* *
7736 TAAAGGACTGAAATAACAAAAATAGAAAGT
1 TAAAGGACT-AAATAGCAAAAATAAAAAGT
7766 AAAAAGGCTA
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 8 0.11
60 30 0.40
62 37 0.49
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.19
Consensus pattern (60 bp):
TAAAGGACTAAATAGCAAAAATAAAAAGTTAAAGGACTAAAATAAAAAAAAACAGAAACT
Found at i:9381 original size:3 final size:3
Alignment explanation
Indices: 9373--9406 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
9363 TAAACTTGGT
*
9373 TAA TAA TAA TAA TAA TAA TAT TAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
9407 TTTTTAGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:10993 original size:31 final size:30
Alignment explanation
Indices: 10870--11031 Score: 184
Period size: 30 Copynumber: 5.4 Consensus size: 30
10860 CTTAGTAAAA
*
10870 TAAAGGACT-AAATAGCAAAAATAGAAATT
1 TAAAGGACTAAAATAGCAAAAATAGAAAGT
* * * * *
10899 TACAGGACTAAAATAACCAAAACAGAAACT
1 TAAAGGACTAAAATAGCAAAAATAGAAAGT
* * * *
10929 TAAAGGATTAAAATTGTAAAAATAGAAAAT
1 TAAAGGACTAAAATAGCAAAAATAGAAAGT
* *
10959 TAAAGGACTAAAATAGAAAAAAATAAAAAGT
1 TAAAGGACTAAAATAG-CAAAAATAGAAAGT
10990 TAAAGGACTAAAATAGCAAAAATAGAAAGT
1 TAAAGGACTAAAATAGCAAAAATAGAAAGT
11020 TAAAAGG-CTAAA
1 T-AAAGGACTAAA
11032 CAGTAATTTC
Statistics
Matches: 110, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
29 8 0.07
30 70 0.64
31 32 0.29
ACGTcount: A:0.60, C:0.07, G:0.14, T:0.19
Consensus pattern (30 bp):
TAAAGGACTAAAATAGCAAAAATAGAAAGT
Found at i:11011 original size:61 final size:60
Alignment explanation
Indices: 10870--11031 Score: 193
Period size: 61 Copynumber: 2.7 Consensus size: 60
10860 CTTAGTAAAA
* * ** *
10870 TAAAGGACT-AAATAGCAAAAATAGAAATTTACAGGACTAAAATAACCAAAACAGAAACT
1 TAAAGGACTAAAATAGCAAAAATAGAAAATTAAAGGACTAAAATAAAAAAAACAAAAACT
* * * * *
10929 TAAAGGATTAAAATTGTAAAAATAGAAAATTAAAGGACTAAAATAGAAAAAAATAAAAAGT
1 TAAAGGACTAAAATAGCAAAAATAGAAAATTAAAGGACTAAAATA-AAAAAAACAAAAACT
*
10990 TAAAGGACTAAAATAGCAAAAATAGAAAGTTAAAAGG-CTAAA
1 TAAAGGACTAAAATAGCAAAAATAGAAAATT-AAAGGACTAAA
11032 CAGTAATTTC
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 8 0.09
60 31 0.36
61 42 0.49
62 5 0.06
ACGTcount: A:0.60, C:0.07, G:0.14, T:0.19
Consensus pattern (60 bp):
TAAAGGACTAAAATAGCAAAAATAGAAAATTAAAGGACTAAAATAAAAAAAACAAAAACT
Found at i:12620 original size:3 final size:3
Alignment explanation
Indices: 12612--12637 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12602 TAAACTTGGT
12612 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
12638 TTTTTGGTAG
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:19078 original size:14 final size:14
Alignment explanation
Indices: 19056--19085 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19046 CTATATATAT
*
19056 TAATTTCAATCAAA
1 TAATGTCAATCAAA
19070 TAATGTCAATCAAA
1 TAATGTCAATCAAA
19084 TA
1 TA
19086 TTTTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (14 bp):
TAATGTCAATCAAA
Found at i:19980 original size:28 final size:28
Alignment explanation
Indices: 19940--19996 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
19930 TGAGAAAATG
19940 TACACGCCAATTGGAAATCCAATGGTTT
1 TACACGCCAATTGGAAATCCAATGGTTT
19968 TACACGCCAATTGGAAATCCAATGGTTT
1 TACACGCCAATTGGAAATCCAATGGTTT
19996 T
1 T
19997 CGACCATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (28 bp):
TACACGCCAATTGGAAATCCAATGGTTT
Found at i:21735 original size:14 final size:14
Alignment explanation
Indices: 21716--21764 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
21706 TTTTGGAAAT
21716 TGAATTCTGAAAAA
1 TGAATTCTGAAAAA
* **
21730 TGAATTAATGAAATT
1 TGAATT-CTGAAAAA
*
21745 TGAATTCTGGAAAA
1 TGAATTCTGAAAAA
21759 TGAATT
1 TGAATT
21765 ATATTTCTGG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (14 bp):
TGAATTCTGAAAAA
Found at i:21752 original size:29 final size:28
Alignment explanation
Indices: 21711--21765 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
21701 TGGTTTTTTG
21711 GAAATTGAATTCTGAAAAATGAATTAAT
1 GAAATTGAATTCTGAAAAATGAATTAAT
*
21739 GAAATTTGAATTCTGGAAAATGAATTA
1 GAAA-TTGAATTCTGAAAAATGAATTA
21766 TATTTCTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (28 bp):
GAAATTGAATTCTGAAAAATGAATTAAT
Found at i:22079 original size:26 final size:27
Alignment explanation
Indices: 22028--22079 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
22018 TTATTAATAA
* * *
22028 AAATAAAAATATTGGTATATTTTATTG
1 AAATAAAAATATTGATAAATTATATTG
22055 AAATAAAAATATT-ATAAATTATATT
1 AAATAAAAATATTGATAAATTATATT
22080 AATTATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (27 bp):
AAATAAAAATATTGATAAATTATATTG
Found at i:22331 original size:26 final size:25
Alignment explanation
Indices: 22268--22352 Score: 63
Period size: 26 Copynumber: 3.5 Consensus size: 25
22258 AGTATAAATT
*
22268 TTATTAATAAT-TTATT-ATATATTA
1 TTATT-ATAATATAATTCATATATTA
* * *
22292 TTA-AATAAAAATAATATCTTATATTA
1 TTATTAT-AATATAAT-TCATATATTA
*
22318 TTATTATAATATAATTGAT-TATT-
1 TTATTATAATATAATTCATATATTA
22341 TTATTATAATAT
1 TTATTATAATAT
22353 TAAAAATATA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
22 2 0.04
23 14 0.29
24 10 0.21
25 3 0.06
26 17 0.35
27 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (25 bp):
TTATTATAATATAATTCATATATTA
Found at i:22370 original size:22 final size:23
Alignment explanation
Indices: 22342--22388 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
22332 TTGATTATTT
22342 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
22364 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
22387 TA
1 TA
22389 AATAGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:22375 original size:30 final size:34
Alignment explanation
Indices: 22316--22392 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 34
22306 TATCTTATAT
* * *
22316 TATTATTATAATATAATTGATTATTTTATTA-TAA
1 TATTAATA-AATATAATTGATTATATTATTAGAAA
22350 TATTAA-AAATATAA-T-ATTATATTATTAGAAA
1 TATTAATAAATATAATTGATTATATTATTAGAAA
22381 TATTAATAAATA
1 TATTAATAAATA
22393 GATTTTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 11 0.29
31 9 0.24
32 12 0.32
33 1 0.03
34 5 0.13
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (34 bp):
TATTAATAAATATAATTGATTATATTATTAGAAA
Found at i:22674 original size:41 final size:41
Alignment explanation
Indices: 22619--22710 Score: 157
Period size: 41 Copynumber: 2.2 Consensus size: 41
22609 TTCTTCTAAC
*
22619 CAAACACTGGAAAACATTTTCCGAAAAATGAATTACGTGAAA
1 CAAACAC-GGAAAACATTTTCCGAAAAACGAATTACGTGAAA
*
22661 CAAACACGGAAAACATTTTTCGAAAAACGAATTACGTGAAA
1 CAAACACGGAAAACATTTTCCGAAAAACGAATTACGTGAAA
22702 CAAACACGG
1 CAAACACGG
22711 GATTTCAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 41 0.85
42 7 0.15
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (41 bp):
CAAACACGGAAAACATTTTCCGAAAAACGAATTACGTGAAA
Found at i:22723 original size:37 final size:38
Alignment explanation
Indices: 22641--22730 Score: 92
Period size: 41 Copynumber: 2.3 Consensus size: 38
22631 AACATTTTCC
* ***
22641 GAAAAATGAATTACGTGAAACAAACACGGAAAACATTTTTC
1 GAAAAACGAATTACGTGAAACAAACACGG---ACATTTCAA
*
22682 GAAAAACGAATTACGTGAAACAAACACGG-GATTTCAA
1 GAAAAACGAATTACGTGAAACAAACACGGACATTTCAA
*
22719 GAAAAACCAATT
1 GAAAAACGAATT
22731 CCGTAATTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
37 15 0.35
41 28 0.65
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (38 bp):
GAAAAACGAATTACGTGAAACAAACACGGACATTTCAA
Found at i:30024 original size:21 final size:21
Alignment explanation
Indices: 29998--30042 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29988 GATTTCTGGG
* *
29998 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
30019 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
30040 CAA
1 CAA
30043 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:30886 original size:31 final size:31
Alignment explanation
Indices: 30845--31000 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
30835 AGGGTCGAGG
*
30845 GTTTATCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
30876 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
30907 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
30938 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
30969 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
31000 G
1 G
31001 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:34352 original size:21 final size:21
Alignment explanation
Indices: 34326--34369 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
34316 TTTTCTGGGA
* *
34326 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
34347 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
34368 AA
1 AA
34370 ACGAACAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:35209 original size:31 final size:31
Alignment explanation
Indices: 35171--35312 Score: 232
Period size: 31 Copynumber: 4.6 Consensus size: 31
35161 GGGTCGAGGG
35171 TTTACCTATGTTCTTCGGGACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
35202 TTTACCTATGTTCTTCGGGACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
*
35233 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTA
* *
35264 TTTACCTATGTCCTTCGGGATATATGGACTGA
1 TTTACCTATGTTCTTCGGGACATATGGACT-A
*
35296 -TTACCTAGGTTCTTCGG
1 TTTACCTATGTTCTTCGG
35313 AATCTATGAA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTA
Found at i:45035 original size:18 final size:18
Alignment explanation
Indices: 45009--45043 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44999 ACTGAATATT
*
45009 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
45027 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
45044 GATAATCCCT
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:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:53024 original size:13 final size:13
Alignment explanation
Indices: 53006--53032 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52996 TGATTAGTGT
53006 CGTGAACAGTACC
1 CGTGAACAGTACC
53019 CGTGAACAGTACC
1 CGTGAACAGTACC
53032 C
1 C
53033 ATTGCTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.15
Consensus pattern (13 bp):
CGTGAACAGTACC
Found at i:54089 original size:184 final size:183
Alignment explanation
Indices: 53839--54225 Score: 650
Period size: 184 Copynumber: 2.1 Consensus size: 183
53829 TTTTCTAATT
* * *
53839 TATATAA-AAATTAAATATTTTTTAATTAAAAAAAGTTTATAATTAATTTAAATAATATATAATT
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATT
* * ** *
53903 ATAATATAAAAATTTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTG
66 ATAAGATAAAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
* *
53968 GATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGCCCATATATTA
131 GATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATATTA
54021 TATATAATATATTTAATATTTTTTAATTAAAAAATAGTTTACAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAA-AGTTTACAATTAATTTAAATAATATATAAT
54086 TATAAGATAAAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
65 TATAAGATAAAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
54151 GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCTCATATCTTA
130 GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATATTA
54205 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
54226 AAAATTTAAT
Statistics
Matches: 191, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
182 7 0.04
183 24 0.13
184 160 0.84
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.47
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATT
ATAAGATAAAAAATTTATATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
GATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATATTA
Found at i:55241 original size:23 final size:22
Alignment explanation
Indices: 55197--55241 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
55187 AATCTCATAG
*
55197 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
55219 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
55242 AAATTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:56756 original size:103 final size:103
Alignment explanation
Indices: 56536--56748 Score: 354
Period size: 103 Copynumber: 2.1 Consensus size: 103
56526 GGGTCTACGC
*
56536 GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGATACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
56601 CCTTGGCAAATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCAAATGTATATGATCCTTAAGGAATGATATGT
* *
56639 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATACTTGAT
1 GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
56704 CCCTAGTATATGTATATGATCCTTAAGGAATGATATGT
66 CCCTAGCAAATGTATATGATCCTTAAGGAATGATATGT
56742 GGTCCTT
1 GGTCCTT
56749 ATGGACATTA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCAAATGTATATGATCCTTAAGGAATGATATGT
Found at i:56798 original size:23 final size:23
Alignment explanation
Indices: 56765--56832 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
56755 ATTATTATAT
56765 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
56788 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * *
56811 GGCACTTCAGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
56833 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:63362 original size:7 final size:7
Alignment explanation
Indices: 63352--63386 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
63342 AACTTGAATT
63352 TGGTATA
1 TGGTATA
63359 TGGTATA
1 TGGTATA
*
63366 TGGTCTA
1 TGGTATA
63373 TGGTATA
1 TGGTATA
63380 TGGTATA
1 TGGTATA
63387 GAAGTTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.43
Consensus pattern (7 bp):
TGGTATA
Found at i:65395 original size:21 final size:20
Alignment explanation
Indices: 65368--65466 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
65358 AATCAGTTTC
65368 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
65389 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
65410 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
65430 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
65451 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
65467 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:65482 original size:40 final size:40
Alignment explanation
Indices: 65433--65587 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
65423 CGATTTTCCA
* ** *
65433 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
65473 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
65513 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
65553 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
65588 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:65495 original size:20 final size:20
Alignment explanation
Indices: 65433--65586 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
65423 CGATTTTCCA
* ** *
65433 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
65453 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
65473 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
65493 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
65513 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
65533 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
65553 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
65574 AAATCGCAACGCG
1 AAATCGCAACGCG
65587 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:66007 original size:33 final size:33
Alignment explanation
Indices: 65968--66038 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
65958 TTCACTTAGA
*
65968 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
66001 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
66034 TTTCA
1 TTTCA
66039 AGTTAGTATT
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:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:66161 original size:20 final size:20
Alignment explanation
Indices: 66117--66226 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
66107 TGCAGAAGAG
*
66117 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
66138 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
66158 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
66179 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
66193 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
66212 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
66227 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:66174 original size:41 final size:38
Alignment explanation
Indices: 66110--66226 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
66100 TTCAATTTGC
* *
66110 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
66148 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
66189 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
66222 AGAAT
1 AGAAT
66227 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:66196 original size:14 final size:14
Alignment explanation
Indices: 66177--66233 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
66167 GAGAAATGAA
66177 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
66191 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
66210 AATCGCAACGAGAG
1 AATCGCAACGAGAG
66224 AATCGCAACG
1 AATCGCAACG
66234 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:66209 original size:33 final size:33
Alignment explanation
Indices: 66169--66249 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
66159 CGCAACGAGA
66169 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
66202 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
66235 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
66250 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:66267 original size:19 final size:19
Alignment explanation
Indices: 66245--66328 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
66235 GAAACCAAAA
* *
66245 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
66264 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
66283 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
66297 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
66316 TCGCGTTGCGATT
1 TCGCGTTGCGATT
66329 CTCTCGTTGC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 3 0.05
19 40 0.71
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:66305 original size:14 final size:14
Alignment explanation
Indices: 66286--66342 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
66276 TTTCATTTCG
66286 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
66300 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
66319 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
66333 CGTTGCGATT
1 CGTTGCGATT
66343 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:66309 original size:33 final size:33
Alignment explanation
Indices: 66267--66350 Score: 168
Period size: 33 Copynumber: 2.5 Consensus size: 33
66257 TTTTATTTCG
66267 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
66300 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
66333 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
66351 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:68203 original size:92 final size:92
Alignment explanation
Indices: 68046--68408 Score: 613
Period size: 92 Copynumber: 4.1 Consensus size: 92
68036 TAGATTGCTT
*
68046 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
68111 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
68138 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
68203 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
*
68230 AGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
68295 ----------TTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
68312 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
68377 TTTGTCTTTGTTTTGTCTATTGGTTG-A
66 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
68404 AGTAA
1 AGTAA
68409 TGCAATCCAT
Statistics
Matches: 256, Mismatches: 4, Indels: 22
0.91 0.01 0.08
Matches are distributed among these distances:
82 81 0.32
92 161 0.63
93 14 0.05
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:68350 original size:82 final size:82
Alignment explanation
Indices: 68213--68385 Score: 337
Period size: 82 Copynumber: 2.1 Consensus size: 82
68203 TTGTCTTTGT
68213 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
68278 AACACTGTGAAATAGTA
66 AACACTGTGAAATAGTA
*
68295 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
68360 AACACTGTGAAATAGTA
66 AACACTGTGAAATAGTA
68377 TTTGTCTTT
1 TTTGTCTTT
68386 GTTTTGTCTA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 90 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (82 bp):
TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGATTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
AACACTGTGAAATAGTA
Found at i:68552 original size:52 final size:52
Alignment explanation
Indices: 68474--68573 Score: 182
Period size: 52 Copynumber: 1.9 Consensus size: 52
68464 CGAAACTTAA
**
68474 AATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGACAG
68526 AATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACG
1 AATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACG
68574 CGAAACCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.07
Consensus pattern (52 bp):
AATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGACAG
Found at i:68573 original size:71 final size:72
Alignment explanation
Indices: 68456--68589 Score: 225
Period size: 71 Copynumber: 1.9 Consensus size: 72
68446 TAGTTTACTT
* **
68456 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAAC
1 TCGCAACACGAAACTCAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAAC
68521 GACAGAA
66 GACAGAA
*
68528 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCA
1 TCGCAACACGAAACTCAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCA
68590 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
71 45 0.78
72 13 0.22
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.08
Consensus pattern (72 bp):
TCGCAACACGAAACTCAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAAC
GACAGAA
Found at i:68595 original size:19 final size:19
Alignment explanation
Indices: 68456--68589 Score: 179
Period size: 19 Copynumber: 7.3 Consensus size: 19
68446 TAGTTTACTT
* *
68456 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
68476 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
68495 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
68514 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
68528 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
68547 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
68566 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
68585 TCGCA
1 TCGCA
68590 TTGCGATTTT
Statistics
Matches: 102, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 74 0.73
20 13 0.13
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.08
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:68607 original size:19 final size:19
Alignment explanation
Indices: 68585--68719 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
68575 GAAACCAAAA
*
68585 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
68604 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
68620 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
68637 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
68653 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
68670 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
68689 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
68709 TCGTGTTGCGA
1 TCGCGTTGCGA
68720 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:68626 original size:14 final size:14
Alignment explanation
Indices: 68607--68663 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
68597 TTTCATTTCG
68607 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
68621 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
68638 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
68654 CGTTGCGATT
1 CGTTGCGATT
68664 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:68632 original size:33 final size:33
Alignment explanation
Indices: 68590--68682 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
68580 CAAAATCGCA
*
68590 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
68623 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
68656 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
68683 TTGGTTTCGC
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:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:70667 original size:13 final size:14
Alignment explanation
Indices: 70642--70676 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
70632 ATTGTTTAAT
70642 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
70656 TGATTTGT-AAAGT
1 TGATTTGTAAAAGA
70669 TGATTTGT
1 TGATTTGT
70677 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:70807 original size:19 final size:19
Alignment explanation
Indices: 70783--70880 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
70773 AAAATTGACT
70783 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
70802 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
70821 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
70835 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
70854 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
70874 ATCGCAA
1 ATCGCAA
70881 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:70861 original size:52 final size:53
Alignment explanation
Indices: 70783--70899 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
70773 AAAATTGACT
70783 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
70835 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
70888 ATCGCAATGCGA
1 ATCGCAATGCGA
70900 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:70942 original size:33 final size:35
Alignment explanation
Indices: 70895--71010 Score: 119
Period size: 38 Copynumber: 3.2 Consensus size: 35
70885 AGAATCGCAA
* * *
70895 TGCGATTTTAATTTCACATTGGGATTC-TCTCG-T
1 TGCGATTTTCATTTCGCATTGCGATTCATCTCGAT
*
70928 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTCATCTCG-AT
*
70966 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTCATCTCG-AT
71004 TGCGATT
1 TGCGATT
71011 CTCTCGTTGC
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
33 21 0.28
35 3 0.04
36 4 0.05
38 46 0.62
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (35 bp):
TGCGATTTTCATTTCGCATTGCGATTCATCTCGAT
Found at i:70951 original size:19 final size:19
Alignment explanation
Indices: 70927--71110 Score: 227
Period size: 19 Copynumber: 10.4 Consensus size: 19
70917 GATTCTCTCG
70927 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70946 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70965 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
70984 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
71003 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
71017 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
71036 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
71050 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
71070 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
71084 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
71103 TTGCGATT
1 TTGCGATT
71111 CTCTCGTTGC
Statistics
Matches: 143, Mismatches: 6, Indels: 32
0.79 0.03 0.18
Matches are distributed among these distances:
14 23 0.16
16 16 0.11
17 13 0.09
18 3 0.02
19 76 0.53
20 12 0.08
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:70999 original size:90 final size:85
Alignment explanation
Indices: 70889--71082 Score: 289
Period size: 90 Copynumber: 2.2 Consensus size: 85
70879 AACGGGAGAA
* * *
70889 TCGCAATGCGATTTTAATTTCACATTGGGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCATTTCACATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA--
*
70954 TTCATTTCGCATTGCGATTTTCATT
64 TTC-TCTCG--TTGCGATTTTCATT
*
70979 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTCATTTCACATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
71044 CTCTCGTTGCGATTTTCATT
66 CTCTCGTTGCGATTTTCATT
71064 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
71083 GTTGGGATTT
Statistics
Matches: 98, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
85 15 0.15
86 17 0.17
87 4 0.04
88 3 0.03
90 59 0.60
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.45
Consensus pattern (85 bp):
TCGCATTGCGATTTTCATTTCACATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT
CTCTCGTTGCGATTTTCATT
Found at i:71022 original size:14 final size:14
Alignment explanation
Indices: 71003--71057 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
70993 TCATTTCGCA
71003 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
71017 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
71034 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
71050 TTGCGATT
1 TTGCGATT
71058 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:71102 original size:67 final size:67
Alignment explanation
Indices: 70946--71143 Score: 265
Period size: 67 Copynumber: 2.9 Consensus size: 67
70936 TCATTTCGCA
*
70946 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGAT
71010 TCTCTCG
61 TCTCTCG
*
71017 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTCTC-
71082 T-G
65 TCG
* * * **
71084 TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGTGTTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGAT
71144 AGTCAAATGC
Statistics
Matches: 118, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
66 15 0.13
67 70 0.59
68 5 0.04
69 3 0.03
71 25 0.21
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (67 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTCTCT
CG
Found at i:71132 original size:33 final size:33
Alignment explanation
Indices: 70946--71124 Score: 261
Period size: 33 Copynumber: 5.2 Consensus size: 33
70936 TCATTTCGCA
*
70946 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
70982 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
71017 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
71050 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
71084 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
71117 TTGCGATT
1 TTGCGATT
71125 GTAATTTCCG
Statistics
Matches: 133, Mismatches: 5, Indels: 11
0.89 0.03 0.07
Matches are distributed among these distances:
32 1 0.01
33 70 0.53
34 29 0.22
35 5 0.04
36 3 0.02
38 25 0.19
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:73636 original size:24 final size:24
Alignment explanation
Indices: 73602--73648 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
73592 CTGAAACATC
73602 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
73626 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
73649 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:74358 original size:20 final size:20
Alignment explanation
Indices: 74330--74600 Score: 292
Period size: 20 Copynumber: 13.5 Consensus size: 20
74320 AAATTTCAGT
* *
74330 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
74350 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
74370 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
74390 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
74410 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
74430 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
74450 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
74470 GTTGCGATTTTATGTATTATC
1 GTTGCGA-TTTACGGATTCTC
* *
74491 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
74511 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
74531 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
74551 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
74571 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
74591 GTTGCGATTT
1 GTTGCGATTT
74601 TGGAAAATCG
Statistics
Matches: 214, Mismatches: 34, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
20 198 0.93
21 16 0.07
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:74390 original size:40 final size:40
Alignment explanation
Indices: 74330--74600 Score: 330
Period size: 40 Copynumber: 6.8 Consensus size: 40
74320 AAATTTCAGT
* *
74330 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
74370 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
74410 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* * * *
74450 GTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGA-TTTACGGATTATC
* * * *
74491 GTTGCGATTTACGGATACGCGTTGCGATATACGGA-TACAC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTA-TC
* * * **
74531 GTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACG-GATTATC
* *
74571 GTTGCGATTTTCATATTCGCGTTGCGATTT
1 GTTGCGATTTACAGATTCGCGTTGCGATTT
74601 TGGAAAATCG
Statistics
Matches: 209, Mismatches: 18, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
39 2 0.01
40 167 0.80
41 40 0.19
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
Found at i:74617 original size:21 final size:21
Alignment explanation
Indices: 74587--74669 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
74577 ATTTTCATAT
*
74587 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
74608 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
74629 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
74650 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
74670 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:74660 original size:42 final size:43
Alignment explanation
Indices: 74567--74665 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
74557 ATTTATGTGT
* *
74567 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
74608 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
74650 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
74666 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:79398 original size:14 final size:15
Alignment explanation
Indices: 79379--79435 Score: 66
Period size: 14 Copynumber: 3.9 Consensus size: 15
79369 CGATCTTCAA
79379 TATTT-ATTTTTATT
1 TATTTAATTTTTATT
79393 TATTT-ATTTTTA-T
1 TATTTAATTTTTATT
79406 TATTTAATATCTTTATT
1 TATTTAAT-T-TTTATT
*
79423 TTTTTAATTTTTA
1 TATTTAATTTTTA
79436 ATAATTCTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
13 6 0.16
14 14 0.37
15 5 0.13
16 5 0.13
17 8 0.21
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTAATTTTTATT
Found at i:79447 original size:30 final size:30
Alignment explanation
Indices: 79387--79451 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
79377 AATATTTATT
* *
79387 TTTATTTATTTATTTTTATTATTTAATATC
1 TTTATTTATTTATTTTTAATAATTAATATC
* *
79417 TTTATTTTTTTAATTTTTAATAATT-CTATC
1 TTTATTTATTT-ATTTTTAATAATTAATATC
79447 TTTAT
1 TTTAT
79452 AATACATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (30 bp):
TTTATTTATTTATTTTTAATAATTAATATC
Found at i:79484 original size:23 final size:23
Alignment explanation
Indices: 79443--79486 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
79433 TTAATAATTC
*
79443 TATCTTTATAATACATTTTTCGT
1 TATCTTTATAACACATTTTTCGT
* *
79466 TATCTTTATAGCACGTTTTTC
1 TATCTTTATAACACATTTTTC
79487 AGTCTTTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.55
Consensus pattern (23 bp):
TATCTTTATAACACATTTTTCGT
Found at i:80437 original size:12 final size:12
Alignment explanation
Indices: 80420--80444 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
80410 ACAAAGCACC
80420 ATTTGGTGCCTA
1 ATTTGGTGCCTA
80432 ATTTGGTGCCTA
1 ATTTGGTGCCTA
80444 A
1 A
80445 ATTATTTGAC
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:85894 original size:22 final size:22
Alignment explanation
Indices: 85869--85916 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
85859 AACCGAACAA
85869 TAAACAAACACTA-AATGAACGC
1 TAAACAAACACTACAAT-AACGC
* *
85891 TAAACGAACACTACACTAACGC
1 TAAACAAACACTACAATAACGC
85913 TAAA
1 TAAA
85917 TGAACACGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.52, C:0.25, G:0.08, T:0.15
Consensus pattern (22 bp):
TAAACAAACACTACAATAACGC
Found at i:85957 original size:24 final size:24
Alignment explanation
Indices: 85913--85959 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
85903 ACACTAACGC
* **
85913 TAAATGAACACGTTCGTGAACATA
1 TAAACGAACACGTTCACGAACATA
85937 TAAACGAACACGTTCACGAACAT
1 TAAACGAACACGTTCACGAACAT
85960 GTTCGTAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (24 bp):
TAAACGAACACGTTCACGAACATA
Found at i:87081 original size:52 final size:51
Alignment explanation
Indices: 86965--87128 Score: 160
Period size: 49 Copynumber: 3.3 Consensus size: 51
86955 TGTTAGATTT
* * * * *
86965 TGAATGAGATTGAATCATAAGTTATTGTAGATCAGAAGTTTACAAGTTTTA
1 TGAATGAGATTGAATTATATGTTAATGTAAACCAGAAGTTTACAAGTTTTA
87016 --AATGAGATTGAATTATATGTTAATGTAAACCAGAAGCTTT-CAAGTTTGTA
1 TGAATGAGATTGAATTATATGTTAATGTAAACCAGAAG-TTTACAAGTTT-TA
* * * * * *
87066 TGAATGAAATTGAATTACATGTT-ATAGTAAAGCAAAAGATTACAAG-CTTA
1 TGAATGAGATTGAATTATATGTTAAT-GTAAACCAGAAGTTTACAAGTTTTA
87116 -GAATGAGATTGAA
1 TGAATGAGATTGAA
87129 CCACAAATTA
Statistics
Matches: 95, Mismatches: 12, Indels: 14
0.79 0.10 0.12
Matches are distributed among these distances:
49 50 0.53
50 7 0.07
51 5 0.05
52 33 0.35
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (51 bp):
TGAATGAGATTGAATTATATGTTAATGTAAACCAGAAGTTTACAAGTTTTA
Found at i:107620 original size:13 final size:13
Alignment explanation
Indices: 107602--107626 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
107592 GGACTTCAGC
107602 AGAACATGAAGAT
1 AGAACATGAAGAT
107615 AGAACATGAAGA
1 AGAACATGAAGA
107627 ACATGATCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
AGAACATGAAGAT
Done.