Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006205.1 Hibiscus syriacus cultivar Beakdansim tig00014771_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: 110050
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1465 original size:12 final size:12
Alignment explanation
Indices: 1450--1537 Score: 56
Period size: 12 Copynumber: 7.3 Consensus size: 12
1440 GACCTGGATT
1450 TTGATCGGATAC
1 TTGATCGGATAC
* *
1462 TTGACCTGGAT-T
1 TTGATC-GGATAC
1474 TTGATCGGATAC
1 TTGATCGGATAC
* *
1486 TTGACCTGGATTC
1 TTGATC-GGATAC
*
1499 -TGATCGAATAC
1 TTGATCGGATAC
* *
1510 TTGACCTGGATTC
1 TTGATC-GGATAC
*
1523 -TGATCTGATAC
1 TTGATCGGATAC
1534 TTGA
1 TTGA
1538 CCTGGATTAT
Statistics
Matches: 55, Mismatches: 15, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
11 12 0.22
12 30 0.55
13 13 0.24
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (12 bp):
TTGATCGGATAC
Found at i:1555 original size:24 final size:24
Alignment explanation
Indices: 1434--1545 Score: 188
Period size: 24 Copynumber: 4.7 Consensus size: 24
1424 TTCTATTATA
*
1434 ATACTTGACCTGGATTTTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
*
1458 ATACTTGACCTGGATTTTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
*
1482 ATACTTGACCTGGATTCTGATCGA
1 ATACTTGACCTGGATTCTGATCGG
*
1506 ATACTTGACCTGGATTCTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
1530 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
1546 ATGTTTTGAT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 84 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:7754 original size:7 final size:7
Alignment explanation
Indices: 7742--7783 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
7732 CAATATTATG
7742 TTATATA
1 TTATATA
7749 TTATATA
1 TTATATA
7756 TT-TATA
1 TTATATA
*
7762 TTATAAA
1 TTATATA
*
7769 TTTTATA
1 TTATATA
*
7776 TAATATA
1 TTATATA
7783 T
1 T
7784 ATTCATCCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATATA
Found at i:7765 original size:20 final size:20
Alignment explanation
Indices: 7737--7776 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
7727 TTCCTCAATA
* *
7737 TTATGTTATATATTATATAT
1 TTATATTATAAATTATATAT
*
7757 TTATATTATAAATTTTATAT
1 TTATATTATAAATTATATAT
7777 AATATATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TTATATTATAAATTATATAT
Found at i:8950 original size:2 final size:2
Alignment explanation
Indices: 8943--8982 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
8933 TTATTTTCTA
8943 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
8983 CGTATTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9175 original size:2 final size:2
Alignment explanation
Indices: 9073--9157 Score: 136
Period size: 2 Copynumber: 42.5 Consensus size: 2
9063 TTATTTTTCC
* *
9073 TA TA TGA TA T- TA CA TA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9115 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9157 T
1 T
9158 TATTGTATTT
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.01
2 74 0.96
3 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:9414 original size:4 final size:4
Alignment explanation
Indices: 9400--9499 Score: 55
Period size: 4 Copynumber: 25.0 Consensus size: 4
9390 ATTTTTTTCC
* * *
9400 TTAT CTTAT TTAT TTAG TTAT CTAT TTAT TTAT TT-T TCT-T TT-T TTCT
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT
* * * * **
9447 TTAT CT-T TGAT TTAT TTACT CATAT TTGT TTAT TTAT TTAT CCAT TTAT
1 TTAT TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT TTAT
9496 TTAT
1 TTAT
9500 GTATATTGTC
Statistics
Matches: 73, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
3 7 0.10
4 58 0.79
5 6 0.08
6 2 0.03
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:9473 original size:47 final size:46
Alignment explanation
Indices: 9391--9481 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 46
9381 GTACATATTA
* *
9391 TTTTTTTCCTTATCTTATTTATTTAGTTATCTATTTATTTATTTTTC
1 TTTTTTTCCTTATCTTATTTATTTACTCA-CTATTTATTTATTTTTC
* *
9438 TTTTTTTCTTTATCTTTGATTTATTTACTCA-TATTTGTTTATTT
1 TTTTTTTCCTTATC-TT-ATTTATTTACTCACTATTTATTTATTT
9482 ATTTATCCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 25 0.66
48 2 0.05
49 11 0.29
ACGTcount: A:0.16, C:0.10, G:0.03, T:0.70
Consensus pattern (46 bp):
TTTTTTTCCTTATCTTATTTATTTACTCACTATTTATTTATTTTTC
Found at i:10508 original size:10 final size:10
Alignment explanation
Indices: 10478--10515 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
10468 TTTCTTGCCA
*
10478 TTTATTTTTT
1 TTTATTTATT
10488 TATTA-TTATT
1 T-TTATTTATT
10498 TTTATTTATT
1 TTTATTTATT
10508 TTTATTTA
1 TTTATTTA
10516 ACTGTTTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 19 0.76
11 3 0.12
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTATT
Found at i:20296 original size:105 final size:105
Alignment explanation
Indices: 20110--20880 Score: 1185
Period size: 105 Copynumber: 7.4 Consensus size: 105
20100 AAGTTTTAGC
* * * *
20110 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGATAACGCAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
20175 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTT
* * *
20215 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAATGCAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
20280 ACGAAGGGACCACTGGTTGTCAACAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTT
* *
20320 CAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
20385 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAA-CAACAACTTCCCAATTT
* * *
20426 CAGAGCCAATTTCAACTTCACAGCGAAGTATATTGGTCTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
20491 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCT
66 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTT
* *
20531 CAGAGCCAA--T---C-TCACAGCGAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
20590 ACGAAGGGACCGCTAGTTGTCAACAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTT
*
20630 CAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
20695 ACGAAGGGACCGCTGGTTGTCAACAACAATTTCCCAGTTT
66 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTT
* *
20735 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * * *
20800 ACGAAGGGACCGCTGGTTGTCAATATATAATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAACA-ACAACTTCCCAATTT
* * * *
20841 CAAAACCAATTTCAACTTCACGGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
20881 GGAACAATAC
Statistics
Matches: 613, Mismatches: 45, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
99 90 0.15
100 1 0.00
101 1 0.00
103 1 0.00
104 1 0.00
105 373 0.61
106 146 0.24
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTT
Found at i:20678 original size:310 final size:312
Alignment explanation
Indices: 20110--20822 Score: 1198
Period size: 310 Copynumber: 2.3 Consensus size: 312
20100 AAGTTTTAGC
* *
20110 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGATAACGCAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
*
20175 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCG
66 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAA-TT--ACTTCACAGCG
* *
20240 AAGGATATTGGACTCAAGACAATGCAAGTTCAACTTCACAACGAAGGGACCACTGGTTGTCAACA
128 AAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCACTAGTTGTCAACA
*
20305 ACAACTTCCCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
193 ACAACTTCCCAATTTCAGAACCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGC
20370 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
258 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAACAATTTCCCAATTT
* * *
20426 CAGAGCCAATTTCAACTTCACAGCGAAGTATATTGGTCTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
*
20491 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAA-T-C-TCACAGCGAGG
66 ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTACTTCACAGCGAAG
* *
20553 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTAGTTGTCAACAACA
131 GATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCACTAGTTGTCAACAACA
* *
20618 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAG
196 ACTTCCCAATTTCAGAACCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAG
* *
20683 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAATTTCCCAGTTT
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAATTTCCCAATTT
* * *
20735 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
20800 ACGAAGGGACCGCTGGTTGTCAA
66 ACGAAGGGACCGCTGGTTGTCAA
20823 TATATAATTT
Statistics
Matches: 376, Mismatches: 21, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
309 98 0.26
310 168 0.45
311 1 0.00
314 1 0.00
316 108 0.29
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (312 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTACTTCACAGCGAAG
GATATTGGACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGGACCACTAGTTGTCAACAACA
ACTTCCCAATTTCAGAACCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAG
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAACAATTTCCCAATTT
Found at i:22549 original size:19 final size:20
Alignment explanation
Indices: 22500--22550 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
22490 TACACATATT
22500 TTTATTT-ATTATTATGTTA
1 TTTATTTGATTATTATGTTA
* *
22519 TATATTTG-TTATTAT-TTC
1 TTTATTTGATTATTATGTTA
22537 TTTATTTGATTATT
1 TTTATTTGATTATT
22551 TTTATATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.69
Consensus pattern (20 bp):
TTTATTTGATTATTATGTTA
Found at i:22581 original size:2 final size:2
Alignment explanation
Indices: 22568--22672 Score: 194
Period size: 2 Copynumber: 53.0 Consensus size: 2
22558 GATATACTTG
*
22568 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22651 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
22673 CTTTATTGTA
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 99 0.99
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22928 original size:4 final size:4
Alignment explanation
Indices: 22916--23016 Score: 57
Period size: 4 Copynumber: 25.0 Consensus size: 4
22906 TTTTTTTTCC
* * *
22916 TTAT CTTAT TTAT TTAGT TT-T CTAT TTAT TTAT TT-T TCT-T TTTT TTCT
1 TTAT -TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT
* * * * *
22964 TTAT CT-T TGAT TTAT TTGCT CATAT TTAT TTAT TTAT TTAT TCAT TTAT
1 TTAT TTAT TTAT TTAT TT-AT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT
23013 TTAT
1 TTAT
23017 GTATATTGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
3 6 0.08
4 59 0.79
5 9 0.12
6 1 0.01
ACGTcount: A:0.19, C:0.08, G:0.03, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:28234 original size:16 final size:16
Alignment explanation
Indices: 28210--28243 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28200 TATCGCCGAC
*
28210 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
28226 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
28242 CG
1 CG
28244 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:31446 original size:445 final size:445
Alignment explanation
Indices: 30611--31500 Score: 1735
Period size: 445 Copynumber: 2.0 Consensus size: 445
30601 TAGAGTGAAG
*
30611 AAGCCTATCGAGTAATTTAAGCCCATTGTTAAAAATCTGAATTGTAGTAAAAAATTAACTATACA
1 AAGCCCATCGAGTAATTTAAGCCCATTGTTAAAAATCTGAATTGTAGTAAAAAATTAACTATACA
*
30676 AAGTTCCAGTAGGAAATCCCAGAATAAGATCAACGAAAAAGAAAAAACCTTCATGGTACATCAAT
66 AAGTTCCAGTAGGAAATCACAGAATAAGATCAACGAAAAAGAAAAAACCTTCATGGTACATCAAT
30741 ACAGCAGGGTTGAATTATAAAAATATGGCAGCATCAACATCATGCCTTCGGTTCAAGGACACATC
131 ACAGCAGGGTTGAATTATAAAAATATGGCAGCATCAACATCATGCCTTCGGTTCAAGGACACATC
30806 AACTTTAATGGAGGAGTCAGTTAAGATGATGTCTTTTGAGTTTTCAGCTTTTGGGTGATTATGAG
196 AACTTTAATGGAGGAGTCAGTTAAGATGATGTCTTTTGAGTTTTCAGCTTTTGGGTGATTATGAG
* *
30871 AATTGAACTTTATTCTCACGTGCAATGGTTTTATGAAAATGAGATCTCTCAAATCTCTGTTAGAT
261 AATTGAACTTTATGCTCACGTGCAATGGTTTTATGAAAATGAGATCTCTCAAATCTCAGTTAGAT
30936 TTTAACAAGAACTTGGTGCAAAAATCTTCATTGAACCTTTCATTTCCCTTGGGGTTCAAAATAAT
326 TTTAACAAGAACTTGGTGCAAAAATCTTCATTGAACCTTTCATTTCCCTTGGGGTTCAAAATAAT
31001 TGCTATCCTTGCTGCAAATTTCTCCTGATTGTTGTCATCTTCTACAACATGATTT
391 TGCTATCCTTGCTGCAAATTTCTCCTGATTGTTGTCATCTTCTACAACATGATTT
31056 AAGCCCATCGAGTAATTTAAGCCCATTGTTAAAAATCTGAATTGTAGTAAAAAATTAACTATACA
1 AAGCCCATCGAGTAATTTAAGCCCATTGTTAAAAATCTGAATTGTAGTAAAAAATTAACTATACA
31121 AAGTTCCAGTAGGAAATCACAGAATAAGATCAACGAAAAAGAAAAAACCTTCATGGTACATCAAT
66 AAGTTCCAGTAGGAAATCACAGAATAAGATCAACGAAAAAGAAAAAACCTTCATGGTACATCAAT
*
31186 ACAGCTGGGTTGAATTATAAAAATATGGCAGCATCAACATCATGCCTTCGGTTCAAGGACACATC
131 ACAGCAGGGTTGAATTATAAAAATATGGCAGCATCAACATCATGCCTTCGGTTCAAGGACACATC
31251 AACTTTAATGGAGGAGTCAGTTAAGATGATGTCTTTTGAGTTTTCAGCTTTTGGGTGATTATGAG
196 AACTTTAATGGAGGAGTCAGTTAAGATGATGTCTTTTGAGTTTTCAGCTTTTGGGTGATTATGAG
31316 AATTGAACTTTATGCTCACGTGCAATGGTTTTATGAAAATGAGATCTCTCAAATCTCAGTTAGAT
261 AATTGAACTTTATGCTCACGTGCAATGGTTTTATGAAAATGAGATCTCTCAAATCTCAGTTAGAT
31381 TTTAACAAGAACTTGGTGCAAAAATCTTCATTGAACCTTTCATTTCCCTTGGGGTTCAAAATAAT
326 TTTAACAAGAACTTGGTGCAAAAATCTTCATTGAACCTTTCATTTCCCTTGGGGTTCAAAATAAT
31446 TGCTATCCTTGCTGCAAATTTCTCCTGATTGTTGTCATCTTCTACAACATGATTT
391 TGCTATCCTTGCTGCAAATTTCTCCTGATTGTTGTCATCTTCTACAACATGATTT
31501 CTTCTAAGTT
Statistics
Matches: 440, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
445 440 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (445 bp):
AAGCCCATCGAGTAATTTAAGCCCATTGTTAAAAATCTGAATTGTAGTAAAAAATTAACTATACA
AAGTTCCAGTAGGAAATCACAGAATAAGATCAACGAAAAAGAAAAAACCTTCATGGTACATCAAT
ACAGCAGGGTTGAATTATAAAAATATGGCAGCATCAACATCATGCCTTCGGTTCAAGGACACATC
AACTTTAATGGAGGAGTCAGTTAAGATGATGTCTTTTGAGTTTTCAGCTTTTGGGTGATTATGAG
AATTGAACTTTATGCTCACGTGCAATGGTTTTATGAAAATGAGATCTCTCAAATCTCAGTTAGAT
TTTAACAAGAACTTGGTGCAAAAATCTTCATTGAACCTTTCATTTCCCTTGGGGTTCAAAATAAT
TGCTATCCTTGCTGCAAATTTCTCCTGATTGTTGTCATCTTCTACAACATGATTT
Found at i:37998 original size:3 final size:3
Alignment explanation
Indices: 37990--38034 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
37980 TTTAGTGTGA
37990 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38035 GCATGGATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38514 original size:31 final size:31
Alignment explanation
Indices: 38474--38537 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
38464 CTTATTTGAC
38474 ATATATGAATTAGAAGTTATATCATTTTTGG
1 ATATATGAATTAGAAGTTATATCATTTTTGG
*
38505 ATATCTGAATTAGAAGTTATATCATTTTTGG
1 ATATATGAATTAGAAGTTATATCATTTTTGG
38536 AT
1 AT
38538 TAGATCGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (31 bp):
ATATATGAATTAGAAGTTATATCATTTTTGG
Found at i:43089 original size:59 final size:60
Alignment explanation
Indices: 43011--43150 Score: 176
Period size: 60 Copynumber: 2.4 Consensus size: 60
43001 TTTGGAGATC
* * * **
43011 AATTTAAAAAT-AGGGTCATAGTTTAGGAA-TGAATTAGGATATTTAAAAGTTTAAGGACT
1 AATTT-AAAATGAGAGTCATAGTTTAGGAATTAAATTAGGATATTCAAAAAATTAAGGACT
* * *
43070 AATTTAAAATGAGAGTCATAATTTGGGAATTAAATTAGGATATTCAAAAAATTAAGGATT
1 AATTTAAAATGAGAGTCATAGTTTAGGAATTAAATTAGGATATTCAAAAAATTAAGGACT
*
43130 AATTTAAAATGAGAGTTATAG
1 AATTTAAAATGAGAGTCATAG
43151 GTTATGGACA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 5 0.07
59 20 0.29
60 44 0.64
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.34
Consensus pattern (60 bp):
AATTTAAAATGAGAGTCATAGTTTAGGAATTAAATTAGGATATTCAAAAAATTAAGGACT
Found at i:43624 original size:15 final size:15
Alignment explanation
Indices: 43604--43636 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
43594 GCTATTTTTG
43604 TAATAGTGATAA-TTT
1 TAATAGT-ATAACTTT
43619 TAATAGTATAACTTT
1 TAATAGTATAACTTT
43634 TAA
1 TAA
43637 AAGTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (15 bp):
TAATAGTATAACTTT
Found at i:47616 original size:38 final size:38
Alignment explanation
Indices: 47565--47683 Score: 238
Period size: 38 Copynumber: 3.1 Consensus size: 38
47555 AAAAGCATAT
47565 ACATATTGTATACTTAGAAAAGAAAGTAAAATTCATCA
1 ACATATTGTATACTTAGAAAAGAAAGTAAAATTCATCA
47603 ACATATTGTATACTTAGAAAAGAAAGTAAAATTCATCA
1 ACATATTGTATACTTAGAAAAGAAAGTAAAATTCATCA
47641 ACATATTGTATACTTAGAAAAGAAAGTAAAATTCATCA
1 ACATATTGTATACTTAGAAAAGAAAGTAAAATTCATCA
47679 ACATA
1 ACATA
47684 AAATTAACTA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 81 1.00
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (38 bp):
ACATATTGTATACTTAGAAAAGAAAGTAAAATTCATCA
Found at i:55714 original size:3 final size:3
Alignment explanation
Indices: 55706--55766 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
55696 TAATGAAAGA
55706 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55754 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
55767 GAAGTCTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:57963 original size:16 final size:17
Alignment explanation
Indices: 57934--58012 Score: 85
Period size: 16 Copynumber: 4.7 Consensus size: 17
57924 AAAATATTTT
57934 ATATATAATTAATATAAA
1 ATATATAA-TAATATAAA
*
57952 ATATATAA-AATAT--T
1 ATATATAATAATATAAA
57966 ATATATAATTAATATAAA
1 ATATATAA-TAATATAAA
57984 ATATATAA-AATATAAA
1 ATATATAATAATATAAA
*
58000 AAATATATATAAT
1 ATATATA-ATAAT
58013 CGGGGCGGGG
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
14 8 0.15
16 24 0.46
17 1 0.02
18 19 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATATAATAATATAAA
Found at i:57971 original size:32 final size:32
Alignment explanation
Indices: 57932--57996 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
57922 CGAAAATATT
57932 TTATATATAATTAATATAAAATATATAAAATA
1 TTATATATAATTAATATAAAATATATAAAATA
57964 TTATATATAATTAATATAAAATATATAAAATA
1 TTATATATAATTAATATAAAATATATAAAATA
57996 T
1 T
57997 AAAAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
TTATATATAATTAATATAAAATATATAAAATA
Found at i:57989 original size:9 final size:9
Alignment explanation
Indices: 57945--58008 Score: 74
Period size: 9 Copynumber: 6.6 Consensus size: 9
57935 TATATAATTA
57945 ATATAAAAT
1 ATATAAAAT
57954 ATATAAAAT
1 ATATAAAAT
57963 ATTATATATAATT
1 A-TATA-A-AA-T
57976 AATATAAAAT
1 -ATATAAAAT
57986 ATATAAAAT
1 ATATAAAAT
*
57995 ATAAAAAAT
1 ATATAAAAT
58004 ATATA
1 ATATA
58009 TAATCGGGGC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
9 31 0.65
10 5 0.10
11 3 0.06
12 3 0.06
13 5 0.10
14 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATATAAAAT
Found at i:58525 original size:21 final size:21
Alignment explanation
Indices: 58477--58525 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
58467 AAAGTGAACT
*
58477 TATAAAATTTAAAAAAATAAA
1 TATAAATTTTAAAAAAATAAA
*
58498 AATAAATTTTAAATAAAA-AAA
1 TATAAATTTTAAA-AAAATAAA
58519 TATAAAT
1 TATAAAT
58526 CATTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
TATAAATTTTAAAAAAATAAA
Found at i:58537 original size:25 final size:25
Alignment explanation
Indices: 58486--58534 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
58476 TTATAAAATT
58486 TAAAAAAATAAAAATAAATTTTAAA
1 TAAAAAAATAAAAATAAATTTTAAA
* *
58511 TAAAAAAATATAAAT-CATTTTAAA
1 TAAAAAAATAAAAATAAATTTTAAA
58535 ATATATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
TAAAAAAATAAAAATAAATTTTAAA
Found at i:62964 original size:20 final size:20
Alignment explanation
Indices: 62939--62988 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
62929 AACGGTTCAG
* * *
62939 CATTCAGCGCTGAATTCTTC
1 CATTCAGAGCCGAATTATTC
62959 CATTCAGAGCCGAATTATTC
1 CATTCAGAGCCGAATTATTC
62979 CATTCAGAGC
1 CATTCAGAGC
62989 TAAACAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (20 bp):
CATTCAGAGCCGAATTATTC
Found at i:63136 original size:14 final size:15
Alignment explanation
Indices: 63106--63140 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
63096 GTTTTTTGAA
63106 AATTTTAAATTATTAT
1 AATTTTAAA-TATTAT
63122 AATTTTAAA-ATTAT
1 AATTTTAAATATTAT
63136 AATTT
1 AATTT
63141 CATTGTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
16 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTTAAATATTAT
Found at i:67243 original size:3 final size:3
Alignment explanation
Indices: 67235--67259 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
67225 AACATCAGGT
67235 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
67260 CTAATGAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:72658 original size:23 final size:23
Alignment explanation
Indices: 72615--72683 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 23
72605 ACCAAAATAC
* *
72615 AACTGCTAACAAATCAGCTAACT
1 AACTGATAACAAATCAACTAACT
72638 AACTGATAACAAA-CAAACTAACT
1 AACTGATAACAAATC-AACTAACT
*
72661 ACAAGCTGATAACTAATCAACTA
1 --AA-CTGATAACAAATCAACTA
72684 TAAGCTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.03
23 19 0.50
25 2 0.05
26 15 0.39
27 1 0.03
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.20
Consensus pattern (23 bp):
AACTGATAACAAATCAACTAACT
Found at i:88100 original size:22 final size:24
Alignment explanation
Indices: 88062--88105 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
88052 CCGCCACTAG
88062 TTAGAAGACAAATTTA-TAATATT
1 TTAGAAGACAAATTTATTAATATT
88085 TTAG-AGACGAAA-TTATTAATA
1 TTAGAAGAC-AAATTTATTAATA
88106 AAAAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (24 bp):
TTAGAAGACAAATTTATTAATATT
Found at i:90603 original size:28 final size:27
Alignment explanation
Indices: 90547--90621 Score: 73
Period size: 28 Copynumber: 2.8 Consensus size: 27
90537 GGGATTACAA
90547 TTTA-GAATTTATGGG-TTTTTGAGAAT
1 TTTAGGAATTTA-GGGTTTTTTGAGAAT
* *
90573 TTTAGGAATTTAGGAGTTTTTTGATATT
1 TTTAGGAATTTAGG-GTTTTTTGAGAAT
* * *
90601 TTTTGAAATTTAAGGTTTTTT
1 TTTAGGAATTTAGGGTTTTTT
90622 TTTTTGGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 6 0.15
27 15 0.37
28 20 0.49
ACGTcount: A:0.25, C:0.00, G:0.20, T:0.55
Consensus pattern (27 bp):
TTTAGGAATTTAGGGTTTTTTGAGAAT
Found at i:93585 original size:3 final size:3
Alignment explanation
Indices: 93577--93607 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
93567 TTTATTTTGC
93577 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
93608 AAGTTCACTG
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):
ATA
Found at i:95389 original size:23 final size:23
Alignment explanation
Indices: 95358--95404 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
95348 TATGCACATG
*
95358 AGGATGTCATACAATTTATGTAA
1 AGGACGTCATACAATTTATGTAA
95381 AGGACGTCATACAATTTATGTAA
1 AGGACGTCATACAATTTATGTAA
95404 A
1 A
95405 AAATGTCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (23 bp):
AGGACGTCATACAATTTATGTAA
Found at i:95412 original size:23 final size:23
Alignment explanation
Indices: 95361--95415 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
95351 GCACATGAGG
**
95361 ATGTCATACAATTTATGTAAAGG
1 ATGTCATACAATTTATGTAAAAA
*
95384 ACGTCATACAATTTATGTAAAAA
1 ATGTCATACAATTTATGTAAAAA
95407 ATGTCATAC
1 ATGTCATAC
95416 GATCACATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (23 bp):
ATGTCATACAATTTATGTAAAAA
Found at i:95560 original size:2 final size:2
Alignment explanation
Indices: 95553--95619 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
95543 AGCATATTCA
95553 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
95595 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 A
95620 ATACTTATGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:95962 original size:11 final size:11
Alignment explanation
Indices: 95946--95975 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
95936 ATGTAAAGGT
95946 AAAATTAAAAA
1 AAAATTAAAAA
95957 AAAATT-AAAA
1 AAAATTAAAAA
95967 AAAATTAAA
1 AAAATTAAA
95976 CTGAGGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATTAAAAA
Found at i:97449 original size:3 final size:3
Alignment explanation
Indices: 97441--97491 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
97431 AAATTTGTAT
*
97441 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA T-T TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
97487 TAA TA
1 TAA TA
97492 TATTTTTTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 3 0.07
3 41 0.93
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:98095 original size:136 final size:134
Alignment explanation
Indices: 97858--98199 Score: 480
Period size: 136 Copynumber: 2.6 Consensus size: 134
97848 GACTTGAAAG
* * *
97858 GAACAAGTTCTTCTCATTATGAAC-T-TTCT-CCT-TTAAGATGAGTTATTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTAGGATGAGTTCTTCTCATTATGAACTC
* * * *
97919 T-TTTGGAAATGTCAATCCCTCTAACGAGGCGTCACTGATTCGAAATGCCGTGAATCGAGTGATA
66 TCATTGGAAATATCAATCCCTCTAACGAGACATCACTGATTCGAAATGCCGTGAATCGAGTGATA
97983 GGTC
131 GGTC
* *
97987 GAACAAGCTATTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT-TAGGATGAGTTCTTCTCATTATGAACT
*
98052 CTCAATTGGAAATATCAATCCCTC-AAGCGAGATATCACTGATTCGAAATGCCGTGAATCGAGTG
65 CTC-ATTGGAAATATCAATCCCTCTAA-CGAGACATCACTGATTCGAAATGCCGTGAATCGAGTG
98116 ATAGGTC
128 ATAGGTC
* * *
98123 AAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATTGGATGAATTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT-TAGGATGAGTTCTTCTCATTATGAACT
98188 CTCCATTGGAAA
65 CT-CATTGGAAA
98200 CACTAATGTG
Statistics
Matches: 189, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
129 22 0.12
130 1 0.01
131 4 0.02
132 3 0.02
133 1 0.01
134 26 0.14
135 2 0.01
136 129 0.68
137 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (134 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTAGGATGAGTTCTTCTCATTATGAACTC
TCATTGGAAATATCAATCCCTCTAACGAGACATCACTGATTCGAAATGCCGTGAATCGAGTGATA
GGTC
Found at i:98686 original size:61 final size:60
Alignment explanation
Indices: 98550--98774 Score: 335
Period size: 61 Copynumber: 3.7 Consensus size: 60
98540 AGAGAAGCTC
** * *
98550 TCTCAAGTGAGATAAATTTTGCCTCGAAGGAAAATTGTCTCAA-GGTTTTAAGAAAAACCA
1 TCTCAA-TGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGGGTTTTAAGAAAAACCA
*
98610 TCTCAAATGAGATAAATTTTGTTTCAAAGGAAAACCGTCTCAAGGGTTTTAAGAAAAACCA
1 TCTC-AATGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGGGTTTTAAGAAAAACCA
*
98671 TCTCAATCGAGATAAATTTTGTTTCAAAGGAAAACTATCTCAAGGGTTTTAAGAAAAACCA
1 TCTCAAT-GAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGGGTTTTAAGAAAAACCA
* *
98732 TCTCAATTGAGATAAATTTTGTTTCGAAGGAAAATTGTCTCAA
1 TCTCAA-TGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAA
98775 AAACTTGTTT
Statistics
Matches: 151, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
60 38 0.25
61 112 0.74
62 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (60 bp):
TCTCAATGAGATAAATTTTGTTTCAAAGGAAAACTGTCTCAAGGGTTTTAAGAAAAACCA
Found at i:98783 original size:29 final size:28
Alignment explanation
Indices: 98750--98830 Score: 110
Period size: 27 Copynumber: 2.9 Consensus size: 28
98740 GAGATAAATT
98750 TTGTTTCGAAGGAAAATTGTCTCAAAAAC
1 TTGTTTC-AAGGAAAATTGTCTCAAAAAC
* * *
98779 TTGTTTCAA-GAGAACTATCTCAAAAAC
1 TTGTTTCAAGGAAAATTGTCTCAAAAAC
98806 TTGTTTCAAAGGAAAATTGTCTCAA
1 TTGTTTC-AAGGAAAATTGTCTCAA
98831 GGGATTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
27 22 0.50
28 4 0.09
29 18 0.41
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (28 bp):
TTGTTTCAAGGAAAATTGTCTCAAAAAC
Found at i:98963 original size:36 final size:37
Alignment explanation
Indices: 98890--98964 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 37
98880 AAAACATCTT
98890 AAGGGAGACAAAACTCTGTTTCAAGAGAAACTGTCTC
1 AAGGGAGACAAAACTCTGTTTCAAGAGAAACTGTCTC
* *
98927 AAGGGAGACAAAATTC-GTTTCAAGGGAAA-TGTTCTC
1 AAGGGAGACAAAACTCTGTTTCAAGAGAAACTG-TCTC
98963 AA
1 AA
98965 AATTTTCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
35 2 0.06
36 18 0.51
37 15 0.43
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (37 bp):
AAGGGAGACAAAACTCTGTTTCAAGAGAAACTGTCTC
Found at i:99016 original size:36 final size:36
Alignment explanation
Indices: 98968--99109 Score: 178
Period size: 39 Copynumber: 3.9 Consensus size: 36
98958 TTCTCAAAAT
* * * *
98968 TTTCAAGAGAAACTATTTCAAGGGAGACAAAACTTG
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAACTTA
*
99004 TTTCAAGGGAAACTATCTCAAGTGAGACAAAA-TTA
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAACTTA
*
99039 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTTTA
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAA-C--TTA
* *
99078 TTTCGAGGGAAACTATCTCAAGCGAGATAAAA
1 TTTCAAGGGAAACTATCTCAAGCGAGACAAAA
99110 TCTTTTGTTT
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
35 32 0.34
36 29 0.31
39 34 0.36
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTATCTCAAGCGAGACAAAACTTA
Found at i:99023 original size:60 final size:60
Alignment explanation
Indices: 98908--99024 Score: 175
Period size: 60 Copynumber: 1.9 Consensus size: 60
98898 CAAAACTCTG
* *
98908 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAATGTTCTCAAAAT
1 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCGTTTCAAGGGAAATGATCTCAAAAT
*
98968 TTTCAAGAGAAACTATTTCAAGGGAGACAAAACTT-GTTTCAAGGGAAACT-ATCTCAA
1 TTTCAAGAGAAACTATCTCAAGGGAGACAAAA-TTCGTTTCAAGGGAAA-TGATCTCAA
99025 GTGAGACAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 49 0.94
61 3 0.06
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (60 bp):
TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTCGTTTCAAGGGAAATGATCTCAAAAT
Found at i:99090 original size:39 final size:39
Alignment explanation
Indices: 99039--99581 Score: 576
Period size: 40 Copynumber: 13.8 Consensus size: 39
99029 GACAAAATTA
* ** * *
99039 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTTTA
1 TTTCAAGGGAAACAATCTTGAGCGAGATAAAATCTTCTG
* * ** *
99078 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTTTG
1 TTTCAAGGGAAACAATCTTGAGCGAGATAAAATCTTCTG
* *
99117 TTT-AAGGAAAACAATCTTGAGAGAGATAAAATCTTCTG
1 TTTCAAGGGAAACAATCTTGAGCGAGATAAAATCTTCTG
*
99155 TTTCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTCTG
1 TTTCAAGG-GAAACAATCTTGAGCGAGATAAAATCTTCTG
99195 TTTC-AGGGAAAAACAATCTTGAGCGAGATAAAATCTTCTG
1 TTTCAAGGG--AAACAATCTTGAGCGAGATAAAATCTTCTG
*
99235 TTTCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTCTG
1 TTTCAAGG-GAAACAATCTTGAGCGAGATAAAATCTTCTG
* * *
99275 TTTCAAGGAAAAATAATCTTGAGCGAG--AAAATCTTATG
1 TTTCAAGG-GAAACAATCTTGAGCGAGATAAAATCTTCTG
* *
99313 TTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTG
1 TTTCAAGG-GAAACAATCTTGAGCGAGATAAAATCTTCTG
** *
99353 TTTCAAGAAAAACAATCTTGAGTGAGATAAAATCTTCTG
1 TTTCAAGGGAAACAATCTTGAGCGAGATAAAATCTTCTG
* * *
99392 TTTCAAGGAAAAACAATCTTGAGTGAG--AAAATCTTTTG
1 TTTCAAGG-GAAACAATCTTGAGCGAGATAAAATCTTCTG
* ** *
99430 TTTCAAGGAAAAACAATCTTGAATGAAATAAAATCTTCTG
1 TTTCAAGG-GAAACAATCTTGAGCGAGATAAAATCTTCTG
* * ** * *
99470 TTTCGAGGAAAAACAATCTTGAATGAAATAAAATCTTATG
1 TTTCAAGG-GAAACAATCTTGAGCGAGATAAAATCTTCTG
* **
99510 TTTCAAGGAAAAACAATCTTGAATGAGATAAAATCTTCTG
1 TTTCAAGG-GAAACAATCTTGAGCGAGATAAAATCTTCTG
* * *
99550 TTTCAAGGAAAAACAATCTTCAGTGAGATAAA
1 TTTCAAGG-GAAACAATCTTGAGCGAGATAAA
99582 TCCTCTATAT
Statistics
Matches: 463, Mismatches: 30, Indels: 21
0.90 0.06 0.04
Matches are distributed among these distances:
38 101 0.22
39 85 0.18
40 274 0.59
41 3 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (39 bp):
TTTCAAGGGAAACAATCTTGAGCGAGATAAAATCTTCTG
Found at i:99183 original size:40 final size:40
Alignment explanation
Indices: 99101--99581 Score: 751
Period size: 40 Copynumber: 12.2 Consensus size: 40
99091 TATCTCAAGC
* *
99101 GAGATAAAATCTTTTGTTT-AAGG-AAAACAATCTTGAGA
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
99139 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
99179 GAGATAAAATCTTCTGTTTCAGGGAAAAACAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
99219 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
99259 GAGATAAAATCTTCTGTTTCAAGGAAAAATAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
99299 GAG--AAAATCTTATGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
99337 GAGATAAAATCTTCTGTTTCAA-GAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
99376 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
99416 GAG--AAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
99454 GAAATAAAATCTTCTGTTTCGAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
99494 GAAATAAAATCTTATGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
99534 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTCAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
99574 GAGATAAA
1 GAGATAAA
99582 TCCTCTATAT
Statistics
Matches: 416, Mismatches: 20, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
38 88 0.21
39 43 0.10
40 285 0.69
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:102461 original size:23 final size:23
Alignment explanation
Indices: 102431--102507 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
102421 CAATTTATTT
102431 TTTTTCTTTCTTTCTTTTTTTTC
1 TTTTTCTTTCTTTCTTTTTTTTC
* *
102454 TTTTTCTTTTTTTCTTTTTTTCGC
1 TTTTTCTTTCTTTCTTTTTTT-TC
*
102478 TTTTTCTTTC-TT-TTTTTCTTC
1 TTTTTCTTTCTTTCTTTTTTTTC
102499 TTTTTCTTT
1 TTTTTCTTT
102508 TTTGATGGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 10 0.21
22 6 0.12
23 22 0.46
24 10 0.21
ACGTcount: A:0.00, C:0.17, G:0.01, T:0.82
Consensus pattern (23 bp):
TTTTTCTTTCTTTCTTTTTTTTC
Found at i:102510 original size:8 final size:8
Alignment explanation
Indices: 102429--102510 Score: 94
Period size: 8 Copynumber: 9.8 Consensus size: 8
102419 TTCAATTTAT
102429 TTTTTTTC
1 TTTTTTTC
*
102437 TTTCTTTC
1 TTTTTTTC
102445 TTTTTTT-
1 TTTTTTTC
*
102452 TCTTTTTC
1 TTTTTTTC
102460 TTTTTTTC
1 TTTTTTTC
102468 TTTTTTTCGC
1 TTTTTTT--C
102478 TTTTTCTTTC
1 -TTTT-TTTC
102488 TTTTTTTC
1 TTTTTTTC
102496 TTCTTTTTC
1 TT-TTTTTC
102505 TTTTTT
1 TTTTTT
102511 GATGGATGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
7 6 0.09
8 37 0.58
9 12 0.19
10 2 0.03
11 4 0.06
12 3 0.05
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:104965 original size:26 final size:26
Alignment explanation
Indices: 104898--104965 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
104888 CTATGCAAAT
*
104898 ATGCAAATGCAAAAAAATGAAAATGTAA
1 ATGCAAATGC--AAAAATGAAAATGCAA
* * * **
104926 ATACAAACGTAAAAATGTGAATGCAA
1 ATGCAAATGCAAAAATGAAAATGCAA
104952 ATGCAAATGCAAAA
1 ATGCAAATGCAAAA
104966 GGTATCGATT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
26 24 0.77
28 7 0.23
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (26 bp):
ATGCAAATGCAAAAATGAAAATGCAA
Found at i:105987 original size:14 final size:14
Alignment explanation
Indices: 105968--106003 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
105958 CATAATGATT
105968 ATGCAAATGCGAAG
1 ATGCAAATGCGAAG
105982 ATGCAAATGCGAAG
1 ATGCAAATGCGAAG
*
105996 ATGTAAAT
1 ATGCAAAT
106004 ACAATGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.19
Consensus pattern (14 bp):
ATGCAAATGCGAAG
Done.