Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006352.1 Hibiscus syriacus cultivar Beakdansim tig00015201_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: 85433
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:1292 original size:17 final size:19
Alignment explanation
Indices: 1264--1312 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1254 TATTTTGAAA
1264 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1282 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1301 CACCGATGCACT
1 CATCGATGCACT
1313 AAGGATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:8243 original size:23 final size:23
Alignment explanation
Indices: 8191--8244 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
8181 TAATAATAAT
*
8191 ATAATAGTACATATATATTTCGAA
1 ATAATA-TACATATATATTTCAAA
*
8215 AT-ATATAC-TATATATTTTTAAA
1 ATAATATACATATATA-TTTCAAA
8237 ATAATATA
1 ATAATATA
8245 TATTTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.23
22 10 0.38
23 8 0.31
24 2 0.08
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (23 bp):
ATAATATACATATATATTTCAAA
Found at i:8268 original size:18 final size:17
Alignment explanation
Indices: 8221--8272 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
8211 CGAAATATAT
8221 ACTATATATTTTT-AAA
1 ACTATATATTTTTCAAA
*
8237 A-TAATATATATTTCAAA
1 ACT-ATATATTTTTCAAA
8254 ACTATATACTTTTTCAAA
1 ACTATATA-TTTTTCAAA
8272 A
1 A
8273 ATAAAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 1 0.03
16 10 0.33
17 9 0.30
18 10 0.33
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (17 bp):
ACTATATATTTTTCAAA
Found at i:8283 original size:23 final size:23
Alignment explanation
Indices: 8251--8297 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
8241 TATATATTTC
* *
8251 AAAACTATATACTTTTTCAAAAAT
1 AAAACTATATA-TATTTAAAAAAT
8275 AAAA-TATATATATTTAAAAAAT
1 AAAACTATATATATTTAAAAAAT
8297 A
1 A
8298 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 6 0.29
24 4 0.19
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAACTATATATATTTAAAAAAT
Found at i:8324 original size:40 final size:39
Alignment explanation
Indices: 8236--8325 Score: 90
Period size: 40 Copynumber: 2.3 Consensus size: 39
8226 ATATTTTTAA
* *
8236 AATAATATATATTTCAAAACTATATACTTTTTCAAAAAT
1 AATAATATATATTTAAAAAATATATACTTTTTCAAAAAT
* * ** * *
8275 AAAATATATATATTTAAAAAATATTTTTTTTTTGAAATAT
1 AATA-ATATATATTTAAAAAATATATACTTTTTCAAAAAT
8315 AATACATATAT
1 AATA-ATATAT
8326 TCATAAATTA
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
39 3 0.08
40 37 0.93
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (39 bp):
AATAATATATATTTAAAAAATATATACTTTTTCAAAAAT
Found at i:8401 original size:2 final size:2
Alignment explanation
Indices: 8394--8487 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
8384 TCAAAACATA
8394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8478 AT AT AT AT AT
1 AT AT AT AT AT
8488 GAACATATAC
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8670 original size:33 final size:33
Alignment explanation
Indices: 8583--8675 Score: 107
Period size: 33 Copynumber: 2.8 Consensus size: 33
8573 AACAAACATG
* * **
8583 ACTTGAAATGACATCAT-TTGATGAAGAGGCACC
1 ACTTGAAATGACA-CCTCTTGGTGAAGAGGCAAA
* *
8616 ACTTGAAATGACACTTTTTGGTGAAGAGGCAAA
1 ACTTGAAATGACACCTCTTGGTGAAGAGGCAAA
*
8649 ACTTGAGATGACACCTCTTGGTGAAGA
1 ACTTGAAATGACACCTCTTGGTGAAGA
8676 TACACATCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
32 2 0.04
33 50 0.96
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (33 bp):
ACTTGAAATGACACCTCTTGGTGAAGAGGCAAA
Found at i:11173 original size:23 final size:22
Alignment explanation
Indices: 11142--11202 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
11132 ATAAGACCAC
*
11142 AAATTATAAACCCTAAACCCCTT
1 AAATCATAAACCCTAAA-CCCTT
*
11165 AAATCATAAACTCTAAACCCTT
1 AAATCATAAACCCTAAACCCTT
* *
11187 -AAGCTTAAACCCTAAA
1 AAATCATAAACCCTAAA
11203 AAGAAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 13 0.39
22 5 0.15
23 15 0.45
ACGTcount: A:0.46, C:0.28, G:0.02, T:0.25
Consensus pattern (22 bp):
AAATCATAAACCCTAAACCCTT
Found at i:14288 original size:2 final size:2
Alignment explanation
Indices: 14281--14313 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14271 GTAATTGAAT
14281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14314 GAGTAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18167 original size:31 final size:31
Alignment explanation
Indices: 18113--18203 Score: 141
Period size: 31 Copynumber: 3.0 Consensus size: 31
18103 TTTTTTCATT
* *
18113 TAAGTACCTAAA-GTAT-TTTTTGGTCAAAA
1 TAAGTATCTAAATTTATCTTTTTGGTCAAAA
18142 TAAGTATCTAAATTTATCTTTTTGGTCAAAA
1 TAAGTATCTAAATTTATCTTTTTGGTCAAAA
*
18173 TAAGTATCTAAATTTATCTTTTTGGTTAAAA
1 TAAGTATCTAAATTTATCTTTTTGGTCAAAA
18204 CAGGTCAGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 11 0.19
30 3 0.05
31 43 0.75
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (31 bp):
TAAGTATCTAAATTTATCTTTTTGGTCAAAA
Found at i:18328 original size:28 final size:28
Alignment explanation
Indices: 18292--18396 Score: 95
Period size: 28 Copynumber: 3.6 Consensus size: 28
18282 GAGAAAATTG
*
18292 AATACTTTAGGTACTTATGTTGACCAAA
1 AATACTTTAGGTACTTATTTTGACCAAA
* * *
18320 AATATTTTATGTACCTATTTTGACCAAAA
1 AATACTTTAGGTACTTATTTTGACC-AAA
*
18349 AGATAAGTTTAGGTACTTATTTTGA-CAAA
1 A-AT-ACTTTAGGTACTTATTTTGACCAAA
* *
18378 ATTCTACTGTAGGTACTTA
1 A--ATACTTTAGGTACTTA
18397 GATGAAAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
28 21 0.34
29 20 0.32
30 4 0.06
31 17 0.27
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (28 bp):
AATACTTTAGGTACTTATTTTGACCAAA
Found at i:18373 original size:31 final size:29
Alignment explanation
Indices: 18292--18378 Score: 97
Period size: 28 Copynumber: 3.0 Consensus size: 29
18282 GAGAAAATTG
* *
18292 AATACTTTAGGTACTTATGTTGACC-AAA
1 AATAGTTTAGGTACTTATTTTGACCAAAA
* * *
18320 AATATTTTATGTACCTATTTTGACCAAAA
1 AATAGTTTAGGTACTTATTTTGACCAAAA
18349 AGATAAGTTTAGGTACTTATTTTGA-CAAAA
1 A-AT-AGTTTAGGTACTTATTTTGACCAAAA
18379 TTCTACTGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
28 21 0.43
29 4 0.08
30 7 0.14
31 17 0.35
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (29 bp):
AATAGTTTAGGTACTTATTTTGACCAAAA
Found at i:19063 original size:24 final size:24
Alignment explanation
Indices: 19031--19083 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
19021 ATATTTCTAG
19031 CCTTAGGAAGCGTTTTAAAACCCT
1 CCTTAGGAAGCGTTTTAAAACCCT
19055 CCTTAGGAAGCGTTTTAAAACCCT
1 CCTTAGGAAGCGTTTTAAAACCCT
19079 CCTTA
1 CCTTA
19084 ATCCCTAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (24 bp):
CCTTAGGAAGCGTTTTAAAACCCT
Found at i:21358 original size:2 final size:2
Alignment explanation
Indices: 21351--21384 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21341 ATGCAGAGAC
21351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21385 GACTTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25650 original size:37 final size:37
Alignment explanation
Indices: 25603--26056 Score: 573
Period size: 37 Copynumber: 12.0 Consensus size: 37
25593 GATTTAATAA
*
25603 TAATTATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
25640 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
25677 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
* * *
25714 TAATGATTTAATTTTAATGATTTAATGATTTAACTTTAATGATT
1 TAATGATTTAACTTTAATGATTTAAT-A-ATAA--TT-A--CTT
25758 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
25795 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
* *
25832 TAATGATTTAATGATTTAATGATTTAATAATAATTATTT
1 TAATGATTTAA--CTTTAATGATTTAATAATAATTACTT
*
25871 TAATGATTTAATGATTTAATGATTTAATAATAATTACTT
1 TAATGATTTAA--CTTTAATGATTTAATAATAATTACTT
*
25910 TAATG-----A-TTT-A-GCTTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
*
25939 TAATGATTTAATGATTTAATGATTTAATAATAATTACTT
1 TAATGATTTAA--CTTTAATGATTTAATAATAATTACTT
* *
25978 TAATGATTTAATTTTAATAATTTAATAATAATTACGTAATTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTAC-----TT
*
26020 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
26057 GACTTTAATG
Statistics
Matches: 378, Mismatches: 15, Indels: 48
0.86 0.03 0.11
Matches are distributed among these distances:
29 23 0.06
30 1 0.00
31 3 0.01
34 2 0.01
37 175 0.46
38 2 0.01
39 100 0.26
40 2 0.01
41 2 0.01
42 40 0.11
43 1 0.00
44 27 0.07
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (37 bp):
TAATGATTTAACTTTAATGATTTAATAATAATTACTT
Found at i:25653 original size:14 final size:14
Alignment explanation
Indices: 25533--26071 Score: 263
Period size: 14 Copynumber: 40.7 Consensus size: 14
25523 TATTTAATAA
* *
25533 TAATTATTTAAATT
1 TAATGATTTAACTT
*
25547 TAATTATTTAACTT
1 TAATGATTTAACTT
*
25561 TAATGATTTAA-TAA
1 TAATGATTTAACT-T
*
25575 TAATTATTTAACTT
1 TAATGATTTAACTT
*
25589 TAATGATTTAA-TAA
1 TAATGATTTAACT-T
*
25603 TAATTATTTAACTT
1 TAATGATTTAACTT
25617 TAATGATTTAA---
1 TAATGATTTAACTT
*
25628 TAAT-AATT-ACTT
1 TAATGATTTAACTT
25640 TAATGATTTAACTT
1 TAATGATTTAACTT
25654 TAATGATTTAA---
1 TAATGATTTAACTT
*
25665 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
25677 TAATGATTTAATTT
1 TAATGATTTAACTT
25691 TAATGATTTAA---
1 TAATGATTTAACTT
*
25702 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
25714 TAATGATTTAATTT
1 TAATGATTTAACTT
*
25728 TAATGATTTAATGATT
1 TAATGATTTAA--CTT
* *
25744 TAA--CTTTAATGATT
1 TAATGATTTAA--CTT
25758 TAATGATTTAACTT
1 TAATGATTTAACTT
25772 TAATGATTTAA---
1 TAATGATTTAACTT
*
25783 TAAT-AATT-ACTT
1 TAATGATTTAACTT
25795 TAATGATTTAACTT
1 TAATGATTTAACTT
25809 TAATGATTTAA---
1 TAATGATTTAACTT
*
25820 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
25832 TAATGATTTAATGATT
1 TAATGATTTAA--CTT
25848 TAATGATTTAA---
1 TAATGATTTAACTT
* *
25859 TAAT-AATT-ATTT
1 TAATGATTTAACTT
*
25871 TAATGATTTAATGATT
1 TAATGATTTAA--CTT
25887 TAATGATTTAA---
1 TAATGATTTAACTT
*
25898 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
25910 TAATGATTTAGCTT
1 TAATGATTTAACTT
*
25924 TAATAATAATT-ACTT
1 TAATGAT--TTAACTT
*
25939 TAATGATTTAATGATT
1 TAATGATTTAA--CTT
25955 TAATGATTTAA---
1 TAATGATTTAACTT
*
25966 TAAT-AATT-ACTT
1 TAATGATTTAACTT
*
25978 TAATGATTTAATTT
1 TAATGATTTAACTT
* *
25992 TAATAATTTAA-TAA
1 TAATGATTTAACT-T
* ** *
26006 TAATTACGTAATTT
1 TAATGATTTAACTT
*
26020 TAATGATTTAATTT
1 TAATGATTTAACTT
*
26034 TAATGATTTAA-TAA
1 TAATGATTTAACT-T
* * *
26048 TAATTACTTGACTT
1 TAATGATTTAACTT
26062 TAATGATTTA
1 TAATGATTTA
26072 TATTTACTGA
Statistics
Matches: 407, Mismatches: 57, Indels: 122
0.69 0.10 0.21
Matches are distributed among these distances:
9 8 0.02
10 24 0.06
11 32 0.08
12 32 0.08
13 30 0.07
14 217 0.53
15 13 0.03
16 51 0.13
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (14 bp):
TAATGATTTAACTT
Found at i:25913 original size:15 final size:15
Alignment explanation
Indices: 25893--25942 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
25883 GATTTAATGA
25893 TTTAATAATAATTAC
1 TTTAATAATAATTAC
*
25908 TTTAATGAT--TTAGC
1 TTTAATAATAATTA-C
25922 TTTAATAATAATTAC
1 TTTAATAATAATTAC
25937 TTTAAT
1 TTTAAT
25943 GATTTAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 9 0.30
15 15 0.50
16 3 0.10
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (15 bp):
TTTAATAATAATTAC
Found at i:25933 original size:29 final size:30
Alignment explanation
Indices: 25877--25958 Score: 130
Period size: 29 Copynumber: 2.7 Consensus size: 30
25867 ATTTTAATGA
25877 TTTAATGATTTAATGATTTAATAATAATTAC
1 TTTAATGATTT-ATGATTTAATAATAATTAC
*
25908 TTTAATGATTTA-GCTTTAATAATAATTAC
1 TTTAATGATTTATGATTTAATAATAATTAC
25937 TTTAATGATTTAATGATTTAAT
1 TTTAATGATTT-ATGATTTAAT
25959 GATTTAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
29 27 0.57
30 2 0.04
31 18 0.38
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (30 bp):
TTTAATGATTTATGATTTAATAATAATTAC
Found at i:25948 original size:68 final size:68
Alignment explanation
Indices: 25776--25998 Score: 299
Period size: 68 Copynumber: 3.2 Consensus size: 68
25766 TAACTTTAAT
*
25776 GATTTAATAATAATTACTTTAATGATTTAA--CTTTAATGATTTAATAATAATTACTTTAATGAT
1 GATTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTTAATAATAATTAC--------T
25839 TTAATGATTTAA
58 TTAATGATTT-A
*
25851 TGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGA
1 -GATTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGA
25916 TTTA
65 TTTA
*
25920 GCTTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGAT
1 GATTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGAT
25985 TTA
66 TTA
25988 -ATTTTAATAAT
1 GA-TTTAATAAT
25999 TTAATAATAA
Statistics
Matches: 139, Mismatches: 5, Indels: 14
0.88 0.03 0.09
Matches are distributed among these distances:
68 75 0.54
69 1 0.01
70 11 0.08
76 29 0.21
78 23 0.17
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (68 bp):
GATTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTTAATGAT
TTA
Found at i:25995 original size:23 final size:22
Alignment explanation
Indices: 25615--25890 Score: 113
Period size: 23 Copynumber: 12.6 Consensus size: 22
25605 ATTATTTAAC
** *
25615 TTTAATGATTTAATAATAATTA
1 TTTAATGATTTAATTTTAATGA
*
25637 CTTTAATGATTTAACTTTAATGA
1 -TTTAATGATTTAATTTTAATGA
* *
25660 TTTAATAATAATT-ACTTTAATGA
1 TTTAATGAT--TTAATTTTAATGA
25683 TTTAAT--TTTAATGATTTAAT-A
1 TTTAATGATTTAAT--TTTAATGA
* *
25704 -ATAATTACTTTAATGATTTAAT--
1 TTTAATGA-TTTAAT--TTTAATGA
*
25726 TTTAATGATTTAATGATTTAA--C
1 TTTAATGATTTAAT--TTTAATGA
*
25748 TTTAATGATTTAATGATTTAA--C
1 TTTAATGATTTAAT--TTTAATGA
** *
25770 TTTAATGATTTAATAATAATTA
1 TTTAATGATTTAATTTTAATGA
*
25792 CTTTAATGATTTAACTTTAATGA
1 -TTTAATGATTTAATTTTAATGA
* *
25815 TTTAATAATAATT-ACTTTAATGA
1 TTTAATGAT--TTAATTTTAATGA
25838 TTTAATGATTTAATGATTT-A--A
1 TTTAATGATTTAAT--TTTAATGA
*
25859 --TAAT-AATT-ATTTTAATGA
1 TTTAATGATTTAATTTTAATGA
25877 TTTAATGATTTAAT
1 TTTAATGATTTAAT
25891 GATTTAATAA
Statistics
Matches: 207, Mismatches: 21, Indels: 51
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 2 0.01
18 4 0.02
19 6 0.03
20 12 0.06
21 8 0.04
22 74 0.36
23 90 0.43
24 7 0.03
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTAATGATTTAATTTTAATGA
Found at i:26004 original size:8 final size:8
Alignment explanation
Indices: 25524--26048 Score: 126
Period size: 8 Copynumber: 68.2 Consensus size: 8
25514 TCGAGTACAT
25524 ATTTAATA
1 ATTTAATA
*
25532 A--TAATT
1 ATTTAATA
25538 ATTT-A-A
1 ATTTAATA
*
25544 ATTTAATT
1 ATTTAATA
25552 ATTT-A-A
1 ATTTAATA
* *
25558 CTTTAATG
1 ATTTAATA
25566 ATTTAATA
1 ATTTAATA
*
25574 ATAATTATTTA
1 AT--TTA-ATA
*
25585 ACTTTAATG
1 A-TTTAATA
25594 ATTTAATA
1 ATTTAATA
*
25602 ATAATTATTTA
1 AT--TTA-ATA
*
25613 ACTTTAATG
1 A-TTTAATA
25622 ATTTAATA
1 ATTTAATA
25630 A--TAATTA
1 ATTTAA-TA
* *
25637 CTTTAATG
1 ATTTAATA
25645 ATTT-A-A
1 ATTTAATA
* *
25651 CTTTAATG
1 ATTTAATA
25659 ATTTAATA
1 ATTTAATA
25667 A--TAATTA
1 ATTTAA-TA
* *
25674 CTTTAATG
1 ATTTAATA
25682 ATTTAAT-
1 ATTTAATA
*
25689 -TTTAATG
1 ATTTAATA
25696 ATTTAATA
1 ATTTAATA
25704 A--TAATTA
1 ATTTAA-TA
* *
25711 CTTTAATG
1 ATTTAATA
25719 ATTTAAT-
1 ATTTAATA
*
25726 -TTTAATG
1 ATTTAATA
*
25733 ATTTAATG
1 ATTTAATA
25741 ATTT-A-A
1 ATTTAATA
* *
25747 CTTTAATG
1 ATTTAATA
*
25755 ATTTAATG
1 ATTTAATA
25763 ATTT-A-A
1 ATTTAATA
* *
25769 CTTTAATG
1 ATTTAATA
25777 ATTTAATA
1 ATTTAATA
25785 A--TAATTA
1 ATTTAA-TA
* *
25792 CTTTAATG
1 ATTTAATA
25800 ATTT-A-A
1 ATTTAATA
* *
25806 CTTTAATG
1 ATTTAATA
25814 ATTTAATA
1 ATTTAATA
25822 A--TAATTA
1 ATTTAA-TA
* *
25829 CTTTAATG
1 ATTTAATA
*
25837 ATTTAATG
1 ATTTAATA
*
25845 ATTTAATG
1 ATTTAATA
25853 ATTTAATA
1 ATTTAATA
25861 A--TAATTA
1 ATTTAA-TA
* *
25868 TTTTAATG
1 ATTTAATA
*
25876 ATTTAATG
1 ATTTAATA
*
25884 ATTTAATG
1 ATTTAATA
25892 ATTTAATA
1 ATTTAATA
25900 A--TAATTA
1 ATTTAA-TA
* *
25907 CTTTAATG
1 ATTTAATA
*
25915 ATTT-A-G
1 ATTTAATA
*
25921 CTTTAATA
1 ATTTAATA
25929 A--TAATTA
1 ATTTAA-TA
* *
25936 CTTTAATG
1 ATTTAATA
*
25944 ATTTAATG
1 ATTTAATA
*
25952 ATTTAATG
1 ATTTAATA
25960 ATTTAATA
1 ATTTAATA
25968 A--TAATTA
1 ATTTAA-TA
* *
25975 CTTTAATG
1 ATTTAATA
25983 ATTTAAT-
1 ATTTAATA
25990 -TTTAATA
1 ATTTAATA
25997 ATTTAATA
1 ATTTAATA
*
26005 ATAATTACGTA
1 AT--TTA-ATA
*
26016 ATTTTAATG
1 A-TTTAATA
26025 ATTTAAT-
1 ATTTAATA
*
26032 -TTTAATG
1 ATTTAATA
26039 ATTTAATA
1 ATTTAATA
26047 AT
1 AT
26049 AATTACTTGA
Statistics
Matches: 381, Mismatches: 73, Indels: 126
0.66 0.13 0.22
Matches are distributed among these distances:
6 79 0.21
7 32 0.08
8 207 0.54
9 33 0.09
10 18 0.05
11 9 0.02
12 3 0.01
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (8 bp):
ATTTAATA
Found at i:26556 original size:6 final size:6
Alignment explanation
Indices: 26545--26569 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
26535 GGTGAGAAGA
26545 ACTCCC ACTCCC ACTCCC ACTCCC A
1 ACTCCC ACTCCC ACTCCC ACTCCC A
26570 GTCCTTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.64, G:0.00, T:0.16
Consensus pattern (6 bp):
ACTCCC
Found at i:28597 original size:171 final size:172
Alignment explanation
Indices: 28307--28663 Score: 565
Period size: 171 Copynumber: 2.1 Consensus size: 172
28297 CATCAAATAT
* *
28307 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
28372 ATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAACT
66 ATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAACT
* *
28437 TTT-ATAATTTACTCTAATTTCTTAAATTCCTCAAATTTTGC
131 TTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* *
28478 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * * *
28542 TTTAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAAC
65 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
* *
28607 TTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
28650 AAAACGGTCCCTAA
1 AAAACGATCCCTAA
28664 AACTTTACAA
Statistics
Matches: 170, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
170 1 0.01
171 122 0.72
172 47 0.28
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.39
Consensus pattern (172 bp):
AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
ATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAACT
TTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:29151 original size:23 final size:23
Alignment explanation
Indices: 29125--29168 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
29115 AGTTGCATGC
29125 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
29148 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
29169 CCTTGCAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:30836 original size:13 final size:14
Alignment explanation
Indices: 30812--30857 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
30802 ATTATAGGTT
* *
30812 ATAATTAAATATTC
1 ATAATTATATATTA
30826 ATAATATATATATT-
1 ATAAT-TATATATTA
30840 ATAATTATATATTA
1 ATAATTATATATTA
30854 ATAA
1 ATAA
30858 AAAAAATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 8 0.28
14 14 0.48
15 7 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
ATAATTATATATTA
Found at i:30848 original size:15 final size:15
Alignment explanation
Indices: 30810--30851 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
30800 ATATTATAGG
30810 TTATAATTA-A-ATA
1 TTATAATTATATATA
30823 TTCATAA-TATATATA
1 TT-ATAATTATATATA
30838 TTATAATTATATAT
1 TTATAATTATATAT
30852 TAATAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.16
14 9 0.36
15 12 0.48
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATAATTATATATA
Found at i:30855 original size:11 final size:14
Alignment explanation
Indices: 30810--30853 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
30800 ATATTATAGG
*
30810 TTATAAT-TAAATA
1 TTATAATATATATA
30823 TTCATAATATATATA
1 TT-ATAATATATATA
30838 TTATAAT-TATATA
1 TTATAATATATATA
30851 TTA
1 TTA
30854 ATAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 11 0.39
14 10 0.36
15 7 0.25
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATAATATATATA
Found at i:30866 original size:28 final size:28
Alignment explanation
Indices: 30810--30866 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
30800 ATATTATAGG
* * * *
30810 TTATAATTAAATATTCATAATATATATA
1 TTATAATTAAATATTAATAAAAAAAATA
*
30838 TTATAATTATATATTAATAAAAAAAATA
1 TTATAATTAAATATTAATAAAAAAAATA
30866 T
1 T
30867 GTCATCCAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TTATAATTAAATATTAATAAAAAAAATA
Found at i:31093 original size:39 final size:40
Alignment explanation
Indices: 31042--31134 Score: 161
Period size: 39 Copynumber: 2.4 Consensus size: 40
31032 TGTTAAACTT
31042 TATTAAGATAATTTCGTACAATATATG-AAAAAACTTTAA
1 TATTAAGATAATTTCGTACAATATATGAAAAAAACTTTAA
* *
31081 TATTCAGATAATTTCGTACAATATATGAAAAAAACTTTAG
1 TATTAAGATAATTTCGTACAATATATGAAAAAAACTTTAA
31121 TATTAAGATAATTT
1 TATTAAGATAATTT
31135 ATACGTTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
39 26 0.52
40 24 0.48
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (40 bp):
TATTAAGATAATTTCGTACAATATATGAAAAAAACTTTAA
Found at i:45239 original size:23 final size:23
Alignment explanation
Indices: 45213--45262 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
45203 TCGTATAAAT
*
45213 GCACCGAAGTGCCACGTAGAATG
1 GCACCGAAATGCCACGTAGAATG
* *
45236 GCACCGAAATGCCGCGTAGAATT
1 GCACCGAAATGCCACGTAGAATG
45259 GCAC
1 GCAC
45263 AGTAGTGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.14
Consensus pattern (23 bp):
GCACCGAAATGCCACGTAGAATG
Found at i:47074 original size:62 final size:61
Alignment explanation
Indices: 46947--47077 Score: 142
Period size: 62 Copynumber: 2.1 Consensus size: 61
46937 CCATAACATT
* **
46947 TGCATCGATGCACTACTTGTGCATCGGTACCCAAATCACCTTCGATGTTTAATCTTAAGGGG
1 TGCATCGATGCACTACTTGTGCATCGGTACCCAAAGCA-CTTCGATGTTTAATCTTAAGAAG
* **
47009 TGCATCGATGCACTAAC-TGTGCATCGGTACACTCAAGGCA-TTCGATGTTTCTTCTTTAA-AAG
1 TGCATCGATGCACT-ACTTGTGCATCGGTAC-C-CAAAGCACTTCGATGTTTAATC-TTAAGAAG
47071 TGCATCG
1 TGCATCG
47078 GTACACATTG
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
62 47 0.80
63 7 0.12
64 5 0.08
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (61 bp):
TGCATCGATGCACTACTTGTGCATCGGTACCCAAAGCACTTCGATGTTTAATCTTAAGAAG
Found at i:50482 original size:23 final size:23
Alignment explanation
Indices: 50456--50522 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
50446 CACCACAGCT
*
50456 CGTATAAATACACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * * *
50479 CGTAGAATTGCATCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
* * *
50502 CGTAGAATTGCACCGTAGTGC
1 CGTAGAAATACACCGAAGTGC
50523 TATATAAGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.24, G:0.25, T:0.21
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:56851 original size:18 final size:18
Alignment explanation
Indices: 56828--56865 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
56818 AAAATACTTT
56828 AATAC-TCAAATCTTATGA
1 AATACTTCAAAT-TTATGA
*
56846 AATACTTGAAATTTATGA
1 AATACTTCAAATTTATGA
56864 AA
1 AA
56866 GATTAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (18 bp):
AATACTTCAAATTTATGA
Found at i:57734 original size:43 final size:42
Alignment explanation
Indices: 57673--57793 Score: 154
Period size: 43 Copynumber: 2.8 Consensus size: 42
57663 TTGATTTGAT
* *
57673 GATAAAAAAAATTATAAATTACTAATTTATTAATTTTCCAATA
1 GATAATAAAAA-TATAAATTATTAATTTATTAATTTTCCAATA
* *
57716 GATAATAAAAATGATAAATTGTTAATCTATTAATTTTCCAATA
1 GATAATAAAAAT-ATAAATTATTAATTTATTAATTTTCCAATA
*
57759 AATAATTAAAAATACTAAATTATTAA-TTATTAATT
1 GATAA-TAAAAATA-TAAATTATTAATTTATTAATT
57794 ATTATTTTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
42 1 0.01
43 50 0.74
44 17 0.25
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (42 bp):
GATAATAAAAATATAAATTATTAATTTATTAATTTTCCAATA
Found at i:63993 original size:22 final size:22
Alignment explanation
Indices: 63966--64012 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
63956 AAATTTAGGA
*
63966 AAACTGAAAGTAACCCGAACCG
1 AAACTGAAAGTAACCCAAACCG
* *
63988 AAACTGAAATTAACCCAAACTG
1 AAACTGAAAGTAACCCAAACCG
64010 AAA
1 AAA
64013 GAAACTCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.23, G:0.13, T:0.13
Consensus pattern (22 bp):
AAACTGAAAGTAACCCAAACCG
Found at i:64887 original size:32 final size:32
Alignment explanation
Indices: 64820--64936 Score: 87
Period size: 32 Copynumber: 3.7 Consensus size: 32
64810 ACTCGACTCA
* * *
64820 ATATTGACCCGACCC-GAAATCTAAC-CAATCAG
1 ATATTGACCCGACCCAAAAATC-AACTGATTC-G
64852 ATATTGACCCGACCCAAAAATCAACTGATTCG
1 ATATTGACCCGACCCAAAAATCAACTGATTCG
* * * *
64884 ATATTGATCTGAATCGAAAAA-CAACTGATTCG
1 ATATTGACCCG-ACCCAAAAATCAACTGATTCG
* * * *
64916 ATAATCACCTGACCCGAAAAT
1 ATATTGACCCGACCCAAAAAT
64937 TGACCTGACC
Statistics
Matches: 68, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
31 6 0.09
32 47 0.69
33 15 0.22
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (32 bp):
ATATTGACCCGACCCAAAAATCAACTGATTCG
Found at i:64927 original size:16 final size:16
Alignment explanation
Indices: 64870--64927 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
64860 CCGACCCAAA
64870 AATCAACTGATTCGAT
1 AATCAACTGATTCGAT
* * * * *
64886 ATTGATCTGAATCGAA
1 AATCAACTGATTCGAT
*
64902 AAACAACTGATTCGAT
1 AATCAACTGATTCGAT
*
64918 AATCACCTGA
1 AATCAACTGA
64928 CCCGAAAATT
Statistics
Matches: 29, Mismatches: 13, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (16 bp):
AATCAACTGATTCGAT
Found at i:67009 original size:2 final size:2
Alignment explanation
Indices: 67002--67078 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
66992 ATCAAAATTA
67002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
67079 ACACAATTAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:68500 original size:103 final size:105
Alignment explanation
Indices: 68311--68519 Score: 289
Period size: 103 Copynumber: 2.0 Consensus size: 105
68301 ACTTTAATTA
* * * * *
68311 TCAATATTTGTTATATTTATCGATTAGTTTAAATTACTTATTGTTAATATATTTTTATAAGGGTG
1 TCAATATTTGTTATATTTATCGATTAATTTAAATTAATTATTGTCAATATATCTTTATAAGAGTG
* *
68376 ATTCTTCGAATTCAATCTACTTCATTCATAATGTCAGAAT
66 ATTCTCCCAATTCAATCTACTTCATTCATAATGTCAGAAT
* *
68416 TCAATATTT-TTTTA-TTAGTCGATTAATTTAAATTAATTGTTGTCAATAT-TCTTTATAAGAGT
1 TCAATATTTGTTATATTTA-TCGATTAATTTAAATTAATTATTGTCAATATATCTTTATAAGAGT
* *
68478 GATTCTCCCAATTTAATTTACTTCATTCATAATGTCAGAAT
65 GATTCTCCCAATTCAATCTACTTCATTCATAATGTCAGAAT
68519 T
1 T
68520 AGAACTCTTA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
103 52 0.57
104 31 0.34
105 9 0.10
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.48
Consensus pattern (105 bp):
TCAATATTTGTTATATTTATCGATTAATTTAAATTAATTATTGTCAATATATCTTTATAAGAGTG
ATTCTCCCAATTCAATCTACTTCATTCATAATGTCAGAAT
Found at i:69219 original size:27 final size:28
Alignment explanation
Indices: 69155--69221 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
69145 CCCGAACCCG
*
69155 AACCCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGAATATCAAACTTAAAAA
*
69183 AACCCAACCCGAATATCAAACTT-AAAA
1 AACCCGACCCGAATATCAAACTTAAAAA
69210 AACCCGACCCGA
1 AACCCGACCCGA
69222 CCCCAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 15 0.42
28 21 0.58
ACGTcount: A:0.46, C:0.34, G:0.07, T:0.12
Consensus pattern (28 bp):
AACCCGACCCGAATATCAAACTTAAAAA
Found at i:69235 original size:28 final size:28
Alignment explanation
Indices: 69204--69340 Score: 85
Period size: 29 Copynumber: 4.6 Consensus size: 28
69194 AATATCAAAC
69204 TTAAAAAACCCGACCCGACCCCAATTTT
1 TTAAAAAACCCGACCCGACCCCAATTTT
* * ** *
69232 TTAAAAAAATCCGACCCTATCCTAAAATTT
1 TT-AAAAAACCCGACCCGA-CCCCAATTTT
* ** * **
69262 TAAAAATAACTTGACCCGACCCGAATATCAAAC
1 TTAAAA-AACCCGACCCGACCCCAAT-T---TT
* *
69295 TTAAAAAACCCGACCCGAACCCGATTTT
1 TTAAAAAACCCGACCCGACCCCAATTTT
*
69323 TTAAAAAATCCGACCCGA
1 TTAAAAAACCCGACCCGA
69341 TTTTTTTTAA
Statistics
Matches: 78, Mismatches: 24, Indels: 14
0.67 0.21 0.12
Matches are distributed among these distances:
28 19 0.24
29 22 0.28
30 17 0.22
31 1 0.01
32 14 0.18
33 5 0.06
ACGTcount: A:0.41, C:0.29, G:0.08, T:0.22
Consensus pattern (28 bp):
TTAAAAAACCCGACCCGACCCCAATTTT
Found at i:69338 original size:22 final size:24
Alignment explanation
Indices: 69313--69365 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 24
69303 CCCGACCCGA
69313 ACCCGA-TTTTTT-AAAAAATCCG
1 ACCCGATTTTTTTAAAAAAATCCG
69335 ACCCGATTTTTTTTAAAAAAATCCG
1 ACCCGA-TTTTTTTAAAAAAATCCG
69360 ACCCGA
1 ACCCGA
69366 ATGCCAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 6 0.21
24 6 0.21
25 16 0.57
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (24 bp):
ACCCGATTTTTTTAAAAAAATCCG
Found at i:69351 original size:24 final size:25
Alignment explanation
Indices: 69319--69365 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
69309 CCGAACCCGA
69319 TTTTTT-AAAAAATCCGACCCGATT
1 TTTTTTAAAAAAATCCGACCCGATT
69343 TTTTTTAAAAAAATCCGACCCGA
1 TTTTTTAAAAAAATCCGACCCGA
69366 ATGCCAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (25 bp):
TTTTTTAAAAAAATCCGACCCGATT
Found at i:69649 original size:57 final size:57
Alignment explanation
Indices: 69581--69688 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
69571 CAAACGTCAC
*
69581 CTTAATTTTATTTAAGGAATTTAATA-TCTTATTTCAGTAAACAAACTATTTTAATAT
1 CTTAATTTTATTTAAGGAATTTAATACT-TTATTTCAGTAAACAAACAATTTTAATAT
* *
69638 CTTAATTTTATTTAAGGAATTTAATACTTTATTTTAGTAAACCAACAATTT
1 CTTAATTTTATTTAAGGAATTTAATACTTTATTTCAGTAAACAAACAATTT
69689 AATCATTGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
57 46 0.98
58 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (57 bp):
CTTAATTTTATTTAAGGAATTTAATACTTTATTTCAGTAAACAAACAATTTTAATAT
Found at i:69880 original size:35 final size:38
Alignment explanation
Indices: 69808--69880 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
69798 AAGGTTTAGT
* * *
69808 TTTTTTTTTCATTTTACTACCCGCTGTTAAAACTTTAA
1 TTTTTGTTTCATTTTAATACCCGCTGTCAAAACTTTAA
69846 TTTTTGTTTCATTTTAATACCCG-T-TCAAAA-TTTAA
1 TTTTTGTTTCATTTTAATACCCGCTGTCAAAACTTTAA
69881 CGTTAAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 5 0.16
36 5 0.16
37 1 0.03
38 21 0.66
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.52
Consensus pattern (38 bp):
TTTTTGTTTCATTTTAATACCCGCTGTCAAAACTTTAA
Found at i:78218 original size:14 final size:14
Alignment explanation
Indices: 78194--78237 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
78184 TCATTCATTT
*
78194 AAATGATAAACAAAC
1 AAAT-ATAAACGAAC
78209 AAATATAAACGAAC
1 AAATATAAACGAAC
*
78223 AGATATAAACGAAC
1 AAATATAAACGAAC
78237 A
1 A
78238 TAAACAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.64, C:0.14, G:0.09, T:0.14
Consensus pattern (14 bp):
AAATATAAACGAAC
Found at i:78232 original size:24 final size:23
Alignment explanation
Indices: 78205--78269 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
78195 AATGATAAAC
* * *
78205 AAACAAATATAAACGAACAGATAT
1 AAACAAACATAAACAAACACA-AT
*
78229 AAACGAACATAAACAAACACAAT
1 AAACAAACATAAACAAACACAAT
* **
78252 AAACGAACACGAACAAAC
1 AAACAAACATAAACAAAC
78270 GAAAGTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
23 18 0.51
24 17 0.49
ACGTcount: A:0.63, C:0.20, G:0.08, T:0.09
Consensus pattern (23 bp):
AAACAAACATAAACAAACACAAT
Found at i:78257 original size:23 final size:24
Alignment explanation
Indices: 78213--78269 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
78203 ACAAACAAAT
* *
78213 ATAAACGAACAGATATAAACGAAC
1 ATAAACAAACACATATAAACGAAC
78237 ATAAACAAACACA-ATAAACGAAC
1 ATAAACAAACACATATAAACGAAC
**
78260 ACGAACAAAC
1 ATAAACAAAC
78270 GAAAGTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.61, C:0.21, G:0.09, T:0.09
Consensus pattern (24 bp):
ATAAACAAACACATATAAACGAAC
Found at i:78260 original size:37 final size:36
Alignment explanation
Indices: 78199--78297 Score: 110
Period size: 37 Copynumber: 2.7 Consensus size: 36
78189 CATTTAAATG
* *
78199 ATAAACAAACAAATATAAACGAACA-GATATAAACGAA
1 ATAAACAAACACA-ATAAACGAACACGA-ACAAACGAA
78236 CATAAACAAACACAATAAACGAACACGAACAAACGAA
1 -ATAAACAAACACAATAAACGAACACGAACAAACGAA
** *
78273 AGTAAATGAACACAATAAATGAACA
1 A-TAAACAAACACAATAAACGAACA
78298 TAAACCAGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.02
37 39 0.72
38 14 0.26
ACGTcount: A:0.63, C:0.17, G:0.09, T:0.11
Consensus pattern (36 bp):
ATAAACAAACACAATAAACGAACACGAACAAACGAA
Found at i:78837 original size:24 final size:24
Alignment explanation
Indices: 78805--78893 Score: 106
Period size: 24 Copynumber: 3.7 Consensus size: 24
78795 GGCTAGACAT
*
78805 AAATGAATGAACATAAACAAACGA
1 AAATAAATGAACATAAACAAACGA
*
78829 AAATGAATGAACATAAACAAACGA
1 AAATAAATGAACATAAACAAACGA
* * * *
78853 AAATAAACGATCGTAAACGAACGA
1 AAATAAATGAACATAAACAAACGA
* *
78877 ACATAAATGAGCATAAA
1 AAATAAATGAACATAAA
78894 TGAATGAACA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.60, C:0.13, G:0.13, T:0.13
Consensus pattern (24 bp):
AAATAAATGAACATAAACAAACGA
Found at i:78915 original size:24 final size:24
Alignment explanation
Indices: 78813--78915 Score: 98
Period size: 24 Copynumber: 4.3 Consensus size: 24
78803 ATAAATGAAT
* * * *
78813 GAACATAAACAAACGAAAATGAAT
1 GAACATAAACGAACGAACATAAAC
* *
78837 GAACATAAACAAACGAAAATAAAC
1 GAACATAAACGAACGAACATAAAC
* * *
78861 GATCGTAAACGAACGAACATAAAT
1 GAACATAAACGAACGAACATAAAC
* * *
78885 GAGCATAAATGAATGAACATAAAC
1 GAACATAAACGAACGAACATAAAC
78909 GAACATA
1 GAACATA
78916 TTACCAAAAG
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.58, C:0.15, G:0.14, T:0.14
Consensus pattern (24 bp):
GAACATAAACGAACGAACATAAAC
Found at i:83772 original size:32 final size:32
Alignment explanation
Indices: 83705--83772 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
83695 AAAGTGACCA
* * **
83705 TTGGGTAGGCTTTGAGGCCCCAAGAAACTTTC
1 TTGGGTAGGCTCTCAGGCCCCAAGAAACTCCC
**
83737 TTGGGTAGGCTCTCAGGCCCCAAGGCACTCCC
1 TTGGGTAGGCTCTCAGGCCCCAAGAAACTCCC
83769 TTGG
1 TTGG
83773 ATAAATCATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.25
Consensus pattern (32 bp):
TTGGGTAGGCTCTCAGGCCCCAAGAAACTCCC
Done.