Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005854.1 Hibiscus syriacus cultivar Beakdansim tig00013747_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: 67618
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1497 original size:15 final size:15
Alignment explanation
Indices: 1463--1498 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1453 ATCATAAACC
1463 TTACCCACATGAAAT
1 TTACCCACATGAAAT
* *
1478 CTACCCACATGATAT
1 TTACCCACATGAAAT
1493 TTACCC
1 TTACCC
1499 TTGTTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.28
Consensus pattern (15 bp):
TTACCCACATGAAAT
Found at i:4326 original size:3 final size:3
Alignment explanation
Indices: 4320--4350 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4310 AAAAAATATA
4320 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4351 GTATCGGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:7010 original size:14 final size:14
Alignment explanation
Indices: 6991--7040 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
6981 GGTCTAAATC
6991 GAGTCAACTCGT-T
1 GAGTCAACTCGTCT
*
7004 AGAGTCAACTTGTCT
1 -GAGTCAACTCGTCT
*
7019 GAGTCAACTCTTCT
1 GAGTCAACTCGTCT
7033 GAGTCAAC
1 GAGTCAAC
7041 CCATTGACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 31 0.97
15 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (14 bp):
GAGTCAACTCGTCT
Found at i:10006 original size:27 final size:27
Alignment explanation
Indices: 9975--10030 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
9965 TTCCATCAAT
* *
9975 CAGCTTGTTTCATACAAAATAAAAGAC
1 CAGCTTGTTGCATACAAAACAAAAGAC
10002 CAGCTTGTTGCATACAAAACAAAAGAC
1 CAGCTTGTTGCATACAAAACAAAAGAC
10029 CA
1 CA
10031 AAATACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (27 bp):
CAGCTTGTTGCATACAAAACAAAAGAC
Found at i:10712 original size:18 final size:19
Alignment explanation
Indices: 10686--10722 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
10676 AATTGGCTTA
10686 TTTCAAACATTTCCAATAT
1 TTTCAAACATTTCCAATAT
10705 TTTC-AACATTTCCAATAT
1 TTTCAAACATTTCCAATAT
10723 AGGCTGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTCAAACATTTCCAATAT
Found at i:12993 original size:54 final size:54
Alignment explanation
Indices: 12837--13180 Score: 460
Period size: 54 Copynumber: 6.3 Consensus size: 54
12827 TTACCGAAAG
*
12837 GGCACTATGTGTGCAACCTTACA-AAATTCATAATTAGTTTATGAA-TTTCTGTATT
1 GGCACTATGTGTGCAACC-TA-AGAAATTCATAATAAGTTTATGAATTTTC-GTATT
* *
12892 GGAACTATGTGTACAACCTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACC-TAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* *
12947 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCCTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * **
13001 GGAACTGTGTGTGCAACTTAAGAAGCTCATAATAAGTTTATGAATTTTCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * *
13055 GGCACTATGTGTGCAAACTAAGAAATTCATAATAATTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
* * * *
13109 GGCACTGTGTGTGAAACTTAAGAAGTTCATAATAAGTTTATGAA-TTTCTGTATT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATT
*
13163 GGCACTATGGGTGCAACC
1 GGCACTATGTGTGCAACC
13181 CCACGTGATT
Statistics
Matches: 253, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
53 3 0.01
54 185 0.73
55 61 0.24
56 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
Found at i:13058 original size:108 final size:108
Alignment explanation
Indices: 12837--13216 Score: 530
Period size: 108 Copynumber: 3.5 Consensus size: 108
12827 TTACCGAAAG
* * *
12837 GGCACTATGTGTGCAACCTTACA-AAATTCATAATTAGTTTATGAATTTCTGTATTGGAACTATG
1 GGCACTATGTGTGCAACC-TA-AGAAATTCATAATAAGTTTATGAATTTCCGTATTGGAACTGTG
* *
12901 TGTACAACCTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
64 TGTGCAA-CTTAAGAAGTTCATAATAAGTTTATGAATTTTCGTATT
*
12947 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCCTATTGGAACTGTGTG
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGAACTGTGTG
*
13012 TGCAACTTAAGAAGCTCATAATAAGTTTATGAATTTTCGTATT
66 TGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTCGTATT
* * *
13055 GGCACTATGTGTGCAAACTAAGAAATTCATAATAATTTTATGAATTTCCGTATTGGCACTGTGTG
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGAACTGTGTG
*
13120 TGAAACTTAAGAAGTTCATAATAAGTTTATGAA-TTTCTGTATT
66 TGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTC-GTATT
* * * ** * * *
13163 GGCACTATGGGTGCAACCCCACGTGATTCATAATGAGTTTGTGAATTACCGTAT
1 GGCACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
13217 CGGCACAATA
Statistics
Matches: 244, Mismatches: 23, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
107 4 0.02
108 149 0.61
109 73 0.30
110 18 0.07
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (108 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGAACTGTGTG
TGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTCGTATT
Found at i:16846 original size:60 final size:60
Alignment explanation
Indices: 16666--16970 Score: 328
Period size: 60 Copynumber: 5.1 Consensus size: 60
16656 CATTGTTTTT
* * ** * * *
16666 TCATCTAACTAGCATTAGTGGCACCTTAATGCCAAAAATGC-TCATTAGGCATTTAAATTTT
1 TCATCTAACTTGCATTAGTGACACCTTTCTGCC-AAAATGCACCATTAGGCATTT-AACTTA
* * * *
16727 TAATCTAACTTGCATTAGTGGA-ACCTTTCTGTCAAAAATGCACCTTTAGTCATTTAACTTA
1 TCATCTAACTTGCATTAGT-GACACCTTTCTG-CCAAAATGCACCATTAGGCATTTAACTTA
* * * *
16788 TCATCTAACTTGCATTAATGACACTTTTATGCCAAAATGCACCATTAGACATTTAACTTA
1 TCATCTAACTTGCATTAGTGACACCTTTCTGCCAAAATGCACCATTAGGCATTTAACTTA
* *** * *
16848 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCAATGTTAGCCATTTATCTTA
1 TCATCTAACTTGCATTAGTGACACCTTTCTGCCAAAATGCACCATTAGGCATTTAACTTA
* * * *
16908 TCATCTAACTTGCATTAGTGACACATTTCTGCCGAAATGCACCGTCAGGCATTTAACTT-
1 TCATCTAACTTGCATTAGTGACACCTTTCTGCCAAAATGCACCATTAGGCATTTAACTTA
16967 TCAT
1 TCAT
16971 TTTAGAGCAT
Statistics
Matches: 205, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
59 4 0.02
60 130 0.63
61 59 0.29
62 12 0.06
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (60 bp):
TCATCTAACTTGCATTAGTGACACCTTTCTGCCAAAATGCACCATTAGGCATTTAACTTA
Found at i:16930 original size:120 final size:120
Alignment explanation
Indices: 16666--16970 Score: 373
Period size: 120 Copynumber: 2.5 Consensus size: 120
16656 CATTGTTTTT
* * * * * * *
16666 TCATCTAACTAGCATTAGTGGCACCTTAATGCCAAAAATGC-TCATTAGGCATTTAAATTTTTAA
1 TCATCTAACTTGCATTAGTGACACATTTATGCC-AAAATGCACCATTAGGCATTT-AA-CTTTCA
* *
16730 TCTAACTTGCATTAGTGGAACCTTTCTGTCAAAAATGCACCTTTAGTCATTTAACTTA
63 TCTAACTTGCATTAGTGGAACCTTTCTGTCAAAAATGCACATTTAGCCATTTAACTTA
* * *
16788 TCATCTAACTTGCATTAATGACACTTTTATGCCAAAATGCACCATTAGACATTTAACTTATCATC
1 TCATCTAACTTGCATTAGTGACACATTTATGCCAAAATGCACCATTAGGCATTTAACTT-TCATC
* * *
16853 TAACTTGCATTAGTGGCACCTTTCTG-CCAAAATGCA-ATGTTAGCCATTTATCTTA
65 TAACTTGCATTAGTGGAACCTTTCTGTCAAAAATGCACAT-TTAGCCATTTAACTTA
* * * *
16908 TCATCTAACTTGCATTAGTGACACATTTCTGCCGAAATGCACCGTCAGGCATTTAACTTTCAT
1 TCATCTAACTTGCATTAGTGACACATTTATGCCAAAATGCACCATTAGGCATTTAACTTTCAT
16971 TTTAGAGCAT
Statistics
Matches: 159, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
119 5 0.03
120 77 0.48
121 38 0.24
122 39 0.25
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (120 bp):
TCATCTAACTTGCATTAGTGACACATTTATGCCAAAATGCACCATTAGGCATTTAACTTTCATCT
AACTTGCATTAGTGGAACCTTTCTGTCAAAAATGCACATTTAGCCATTTAACTTA
Found at i:17410 original size:22 final size:22
Alignment explanation
Indices: 17380--17441 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
17370 TCGGTACCTC
*
17380 TACTGTGGTATCGATACTTCTA
1 TACTATGGTATCGATACTTCTA
17402 TACTATGGTATCGATACTTCTA
1 TACTATGGTATCGATACTTCTA
* *
17424 TAATATGGTACCGATACT
1 TACTATGGTATCGATACT
17442 CCCTTGCAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (22 bp):
TACTATGGTATCGATACTTCTA
Found at i:17525 original size:18 final size:19
Alignment explanation
Indices: 17483--17530 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
17473 GGAATCCACG
* *
17483 GTATCGATACCTACCTCATA
1 GTATCGATACCCACATCA-A
17503 GTATCGATACCCACATC-A
1 GTATCGATACCCACATCAA
17521 GTATCGATAC
1 GTATCGATAC
17531 TAACTGCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
20 15 0.58
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.27
Consensus pattern (19 bp):
GTATCGATACCCACATCAA
Found at i:22037 original size:54 final size:55
Alignment explanation
Indices: 21972--22406 Score: 589
Period size: 54 Copynumber: 8.0 Consensus size: 55
21962 TCATAATGAG
** * *
21972 TTTCAGTATTGGCGTTATG-GTGCAACCTTAAGAAATTCAAAATAATTTTATGAAT
1 TTTC-GTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
22027 TTTCGTATTGGCACTATGTGTGCAACC-TAAGAAATTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
* *
22081 TTTCGTATTGGCAATGTGTGTGCAA-CTTAAGAAATTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
* * *
22135 TTCCGTATTAGCACTATGTGTGCAACC-TAAGAAATTCATAATAAGGTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
* * * * * *
22189 TTCCCTACTGGAACTGTGTGTGCAA-CTTAAGAAGTTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
22243 TTTCGTATTGGCACTATGTGTGCAACC-TAAGAAATTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
* * *
22297 TTCCGTATTGGCACTGTGTGTGCAA-CTTAAGAAGTTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
* * * * *
22351 TTTTGTATTGGCACTATGTGTGCAACC-CAACGTAATTCATAATGAGTTTTTGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAA-GAAATTCATAATAAGTTTATGAAT
22406 T
1 T
22407 ACCGTATCGG
Statistics
Matches: 337, Mismatches: 35, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
53 3 0.01
54 298 0.88
55 36 0.11
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (55 bp):
TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
Found at i:22124 original size:108 final size:108
Alignment explanation
Indices: 21991--22418 Score: 660
Period size: 108 Copynumber: 3.9 Consensus size: 108
21981 TGGCGTTATG
* *
21991 GTGCAACCTTAAGAAATTCAAAATAATTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTA
1 GTGCAA-CTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTA
*
22056 AGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCAATGTGT
65 AGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATGTGT
* *
22100 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAGCACTATGTGTGCAACCTAA
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAA
* * *
22165 GAAATTCATAATAAGGTTATGAATTTCCCTACTGG-AACTGTGT
66 GAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAA-TGTGT
*
22208 GTGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAA
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAA
*
22273 GAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTGT
66 GAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATGTGT
* * *
22316 GTGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTTGTATTGGCACTATGTGTGCAACCCAA
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAA
* * * * *
22381 CGTAATTCATAATGAGTTTTTGAATTACCGTATCGGCA
66 -GAAATTCATAATAAGTTTATGAATTTCCGTATTGGCA
22419 TTACGTGTAC
Statistics
Matches: 294, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
107 2 0.01
108 253 0.86
109 39 0.13
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Consensus pattern (108 bp):
GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAA
GAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATGTGT
Found at i:24353 original size:18 final size:15
Alignment explanation
Indices: 24314--24354 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
24304 TTCGTTTACT
24314 ACATCTTCTTCCACA
1 ACATCTTCTTCCACA
24329 ACATCTTCTTCCACA
1 ACATCTTCTTCCACA
*
24344 ACATCCTCTTC
1 ACATCTTCTTC
24355 AATATCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.34
Consensus pattern (15 bp):
ACATCTTCTTCCACA
Found at i:25572 original size:47 final size:48
Alignment explanation
Indices: 25511--25621 Score: 147
Period size: 49 Copynumber: 2.3 Consensus size: 48
25501 TCATGATGTA
25511 AAAGACAAAAATAAA-CTTAAAT-AA-AACATGCTAACAAACAAAACTAT
1 AAAGA-AAAAATAAATC-TAAATGAACAACATGCTAACAAACAAAACTAT
* *
25558 AAAGAAAAAGATAAATCTACATGAACCACATGCTAACAAACAAAACTAT
1 AAAGAAAAA-ATAAATCTAAATGAACAACATGCTAACAAACAAAACTAT
*
25607 AAAGAAAATATAAAT
1 AAAGAAAAAATAAAT
25622 ACAAGTACAC
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
46 4 0.07
47 14 0.25
48 9 0.16
49 30 0.53
ACGTcount: A:0.62, C:0.14, G:0.06, T:0.17
Consensus pattern (48 bp):
AAAGAAAAAATAAATCTAAATGAACAACATGCTAACAAACAAAACTAT
Found at i:25639 original size:48 final size:48
Alignment explanation
Indices: 25536--25640 Score: 151
Period size: 49 Copynumber: 2.2 Consensus size: 48
25526 CTTAAATAAA
*
25536 ACATGCTAACAAACAAAACTATAAAGAAAAAGATAAATCTACATGAACC
1 ACATGCTAACAAACAAAACTATAAAGAAAAAGATAAA-CTACAAGAACC
*
25585 ACATGCTAACAAACAAAACTATAAAG-AAAATATAAA-TACAAGTACACC
1 ACATGCTAACAAACAAAACTATAAAGAAAAAGATAAACTACAAG-A-ACC
25633 ACATGCTA
1 ACATGCTA
25641 CCTCAAATCA
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
46 5 0.10
47 1 0.02
48 20 0.38
49 26 0.50
ACGTcount: A:0.56, C:0.19, G:0.08, T:0.17
Consensus pattern (48 bp):
ACATGCTAACAAACAAAACTATAAAGAAAAAGATAAACTACAAGAACC
Found at i:25756 original size:16 final size:16
Alignment explanation
Indices: 25735--25772 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
25725 CTCTTAAACT
*
25735 AAACAATATGTTATAG
1 AAACAATATATTATAG
*
25751 AAACAATATATTATAT
1 AAACAATATATTATAG
25767 AAACAA
1 AAACAA
25773 CTTTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (16 bp):
AAACAATATATTATAG
Found at i:29355 original size:28 final size:28
Alignment explanation
Indices: 29343--29477 Score: 71
Period size: 30 Copynumber: 4.6 Consensus size: 28
29333 AATATTAAAG
29343 AAATATATATATAATAATAATAATAATA
1 AAATATATATATAATAATAATAATAATA
* * *
29371 AAATATAGTAAAAAAATCAAATGAA-AATAATT
1 AAATATA-T-ATATAAT--AAT-AATAATAATA
*
29403 TAATATATATATATATACAT-ATAATAATA
1 AAATATATATATA-ATA-ATAATAATAATA
* * *
29432 ATAACATGA-ATAATAAAAATAA-ATTAATA
1 A-AATAT-ATAT-ATAATAATAATAATAATA
**
29461 AAATATCCATATAATAA
1 AAATATATATATAATAA
29478 ATAAAGGGAC
Statistics
Matches: 80, Mismatches: 14, Indels: 27
0.66 0.12 0.22
Matches are distributed among these distances:
27 6 0.08
28 14 0.17
29 17 0.21
30 19 0.24
31 7 0.09
32 15 0.19
33 2 0.03
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (28 bp):
AAATATATATATAATAATAATAATAATA
Found at i:29446 original size:18 final size:17
Alignment explanation
Indices: 29423--29465 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
29413 ATATATACAT
29423 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
* *
29441 ATAATAAAAATAAATTA
1 ATAATAATAATAAATGA
29458 ATAA-AATA
1 ATAATAATA
29466 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:29921 original size:34 final size:34
Alignment explanation
Indices: 29878--29946 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
29868 GAATCCTAGC
29878 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
29912 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
29946 A
1 A
29947 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:30824 original size:105 final size:105
Alignment explanation
Indices: 30495--31220 Score: 1061
Period size: 105 Copynumber: 7.0 Consensus size: 105
30485 CATTGTTCCA
* * * ** *
30495 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAA-CCAGAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAGTTG-TTGTTGACAA
* * * * *
30559 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * *
30601 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTATTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * *
30661 AGCGGTCCCTTCGTCCTGAAG-TAAACTTGTGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
30700 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
30765 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
30805 ATTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
30870 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
30910 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
30975 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
31015 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
31080 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
31120 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
31185 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
31221 CCTCGAGTGC
Statistics
Matches: 569, Mismatches: 44, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
99 52 0.09
100 29 0.05
101 2 0.00
102 4 0.01
103 4 0.01
104 29 0.05
105 371 0.65
106 78 0.14
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:31997 original size:67 final size:65
Alignment explanation
Indices: 31863--32255 Score: 213
Period size: 65 Copynumber: 5.8 Consensus size: 65
31853 AAGATATCTG
* * * * **
31863 TTGTTTCATGAGAAACGGTCTCAAGGGA-ATAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
31927 TT
64 TT
* * *
31929 TGTGTTTCAAGAGTAACTGTCTCAAGTGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGT
1 T-TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
31994 T
65 T
* * * *
31995 TTGTTTCGAGGGAAACTGTCTCAAGAT-AGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAG-TGAGAC-AAAATTTGTTTTAAGGGAAA-----T--A-A-
** *
32058 AGACAAA-ACT
55 ATTCAAAGATT
* * * * ** * * * * * *
32068 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * *
32133 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGA-T-
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAA-----T-AA-ATTC
* *
32196 AGACGAAAT
59 A-AAG-ATT
* *
32205 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAA
32256 CTGTCTCAAG
Statistics
Matches: 250, Mismatches: 52, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
64 5 0.02
65 80 0.32
66 10 0.04
67 45 0.18
68 7 0.03
70 2 0.01
71 3 0.01
72 55 0.22
73 38 0.15
74 5 0.02
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:32046 original size:36 final size:35
Alignment explanation
Indices: 31995--32275 Score: 263
Period size: 36 Copynumber: 8.0 Consensus size: 35
31985 TTCAAAGGTT
* * *
31995 TTGTTTCGAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
32031 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
32066 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
32104 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
32133 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
32168 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
32205 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
32240 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
32276 CTCTTCTAGT
Statistics
Matches: 203, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 133 0.66
37 33 0.16
38 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:32108 original size:138 final size:137
Alignment explanation
Indices: 31943--32256 Score: 414
Period size: 138 Copynumber: 2.3 Consensus size: 137
31933 TTTCAAGAGT
* * * * * *
31943 AACTGTCTCAAGTGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGGTTTTGTTTCGAGGGA
1 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* *
32008 AACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
32072 TCCAAAAGA
129 TCCAAAAGA
* ** * * * *
32081 AACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
32146 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
32211 CAAGAGA
131 CAAAAGA
32218 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
1 AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
32257 TGTCTCAAGA
Statistics
Matches: 150, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
137 49 0.33
138 101 0.67
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
AACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:32297 original size:35 final size:36
Alignment explanation
Indices: 32137--32309 Score: 172
Period size: 36 Copynumber: 4.8 Consensus size: 36
32127 AATATTTTGT
* * **
32137 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
32173 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
32209 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
32245 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
32279 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
32310 TCTTGTTTTA
Statistics
Matches: 121, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 92 0.76
37 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:33231 original size:22 final size:22
Alignment explanation
Indices: 33205--33253 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
33195 TTGTGTTTGG
* *
33205 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
33227 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
33249 TCAAA
1 TCAAA
33254 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:33260 original size:22 final size:22
Alignment explanation
Indices: 33217--33260 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
33207 AAAGGTTTGG
* * *
33217 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
33239 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
33261 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:33921 original size:8 final size:7
Alignment explanation
Indices: 33909--33978 Score: 61
Period size: 8 Copynumber: 9.1 Consensus size: 7
33899 TGATTTTTGC
33909 TCTTTTT
1 TCTTTTT
33916 TCCTTTTGT
1 T-CTTTT-T
*
33925 TCTTGTT
1 TCTTTTT
33932 TCTCTTTT
1 TCT-TTTT
33940 TCTTTGTT
1 TCTTT-TT
33948 T-TTTTT
1 TCTTTTT
33954 TGCTTTTT
1 T-CTTTTT
33962 TGCTTCTTT
1 T-CTT-TTT
33971 TCTTTTT
1 TCTTTTT
33978 T
1 T
33979 GTTCTTGATT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
6 3 0.06
7 14 0.26
8 31 0.57
9 6 0.11
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:33922 original size:16 final size:17
Alignment explanation
Indices: 33903--33957 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
33893 TTCTTTTGAT
*
33903 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
33919 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* *
33936 TTTTTCT-TTGTTT-TT
1 TTTTGCTCTTGTTTCTC
33951 TTTTGCT
1 TTTTGCT
33958 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 7 0.22
16 19 0.59
17 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:33977 original size:16 final size:16
Alignment explanation
Indices: 33934--33984 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
33924 TTCTTGTTTC
*
33934 TCTTTTTCTTTGTTT-T
1 TCTTTTGCTTT-TTTGT
33950 T-TTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
33966 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
33981 TCTT
1 TCTT
33985 GATTGGATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.10
15 13 0.42
16 11 0.35
17 4 0.13
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:35109 original size:8 final size:8
Alignment explanation
Indices: 35083--35122 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
35073 AATGTAGATG
35083 AAAATGCA
1 AAAATGCA
* *
35091 AAAAGGTA
1 AAAATGCA
35099 AAAATGCA
1 AAAATGCA
35107 AAAATGCA
1 AAAATGCA
*
35115 ATAATGCA
1 AAAATGCA
35123 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.15
Consensus pattern (8 bp):
AAAATGCA
Found at i:37673 original size:2 final size:2
Alignment explanation
Indices: 37660--37697 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
37650 AAAAGGAAAA
*
37660 AT AT AA 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
37698 CAAAGTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38229 original size:18 final size:17
Alignment explanation
Indices: 38206--38248 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
38196 ATATATACAT
38206 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
38224 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
38241 ATAA-AATA
1 ATAATAATA
38249 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:38702 original size:34 final size:34
Alignment explanation
Indices: 38659--38727 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
38649 GAATCCTAGC
38659 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
* *
38693 AAAATTCTATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
38727 A
1 A
38728 GTAGGACGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:41407 original size:3 final size:3
Alignment explanation
Indices: 41395--41457 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
41385 ACCCATTTTT
* *
41395 TTA TTG TTA TTA TAA TTA TTA TT- TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
**
41440 TTA AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
41458 CAAACAAGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:42879 original size:16 final size:16
Alignment explanation
Indices: 42858--42888 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42848 TTTTACTTTC
*
42858 ATATATTTATGATTAT
1 ATATATTTATCATTAT
42874 ATATATTTATCATTA
1 ATATATTTATCATTA
42889 GTATTACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
ATATATTTATCATTAT
Found at i:45366 original size:12 final size:13
Alignment explanation
Indices: 45349--45377 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
45339 ACATTCACAT
45349 ATTTACA-TTTGC
1 ATTTACATTTTGC
45361 ATTTACATTTTGC
1 ATTTACATTTTGC
45374 ATTT
1 ATTT
45378 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:48538 original size:13 final size:14
Alignment explanation
Indices: 48514--48543 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
48504 AAAGCGAAAA
48514 ACACACACACAATC
1 ACACACACACAATC
48528 ACACA-ACACAATC
1 ACACACACACAATC
48541 ACA
1 ACA
48544 TTAGCCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.40, G:0.00, T:0.07
Consensus pattern (14 bp):
ACACACACACAATC
Found at i:53650 original size:21 final size:21
Alignment explanation
Indices: 53604--53644 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
53594 TCACCCGGGT
*
53604 GGGGGAAAACATATATCGGAC
1 GGGGGAAAACATATATCCGAC
53625 GGGGGAAAACATATA-CCGAC
1 GGGGGAAAACATATATCCGAC
53645 TTGGGGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.39, C:0.17, G:0.32, T:0.12
Consensus pattern (21 bp):
GGGGGAAAACATATATCCGAC
Found at i:55063 original size:17 final size:16
Alignment explanation
Indices: 55043--55085 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
55033 TAACTATGTG
55043 AATTAAACAAATGGATA
1 AATTAAACAAATGGA-A
* *
55060 AATTGAAATAAATTGAA
1 AATT-AAACAAATGGAA
55077 AATTAAACA
1 AATTAAACA
55086 TGCAATTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (16 bp):
AATTAAACAAATGGAA
Found at i:60675 original size:18 final size:18
Alignment explanation
Indices: 60652--60687 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
60642 AAGCTATTTG
*
60652 ATACTCAACTTGAAAAGC
1 ATACTCAACTCGAAAAGC
60670 ATACTCAACTCGAAAAGC
1 ATACTCAACTCGAAAAGC
60688 TCGCGAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.19
Consensus pattern (18 bp):
ATACTCAACTCGAAAAGC
Found at i:64070 original size:49 final size:49
Alignment explanation
Indices: 63976--64070 Score: 111
Period size: 50 Copynumber: 1.9 Consensus size: 49
63966 CACTCTCCAA
* * * * * *
63976 TTTGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATTTATCGTG
1 TTTGCCTTTTCATCACGACTAGGAGGGCTCGATAGAGACACTTATCGTG
*
64025 TTTGCCTTTTTCATTACGACTAGGAGGGCTCGATAG-GACACTTATC
1 TTTGCC-TTTTCATCACGACTAGGAGGGCTCGATAGAGACACTTATC
64071 CATCTATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
49 14 0.37
50 24 0.63
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (49 bp):
TTTGCCTTTTCATCACGACTAGGAGGGCTCGATAGAGACACTTATCGTG
Done.