Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001903.1 Hibiscus syriacus cultivar Beakdansim tig00003854_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: 107738
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:792 original size:21 final size:23
Alignment explanation
Indices: 766--813 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
756 TTGTTTCAAG
*
766 TGTTTTAGT-TT-TATTTTTCTC
1 TGTTTTAGTGTTATATTTTTCCC
*
787 TGTTTTGGTGTTATATTTTTCCC
1 TGTTTTAGTGTTATATTTTTCCC
810 TGTT
1 TGTT
814 GTATTAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 2 0.09
23 13 0.57
ACGTcount: A:0.08, C:0.10, G:0.15, T:0.67
Consensus pattern (23 bp):
TGTTTTAGTGTTATATTTTTCCC
Found at i:3960 original size:17 final size:17
Alignment explanation
Indices: 3938--3976 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3928 TAGAATTAGG
3938 ATTTAGATTTTTTAGAA
1 ATTTAGATTTTTTAGAA
*
3955 ATTTAGATTTTTTATAA
1 ATTTAGATTTTTTAGAA
3972 ATTTA
1 ATTTA
3977 ATAATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (17 bp):
ATTTAGATTTTTTAGAA
Found at i:5644 original size:14 final size:14
Alignment explanation
Indices: 5625--5654 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5615 ATGATATGCA
5625 TATATTATATAGAG
1 TATATTATATAGAG
5639 TATATTATATAGAG
1 TATATTATATAGAG
5653 TA
1 TA
5655 AAAAGAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TATATTATATAGAG
Found at i:9877 original size:27 final size:27
Alignment explanation
Indices: 9847--9903 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
9837 AAAAATAATA
9847 CCAGATGCAACTAAGATCCCACTTTCT
1 CCAGATGCAACTAAGATCCCACTTTCT
9874 CCAGATGCAACTAAGATCCCACTTTCT
1 CCAGATGCAACTAAGATCCCACTTTCT
9901 CCA
1 CCA
9904 ACACTGCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.30, C:0.35, G:0.11, T:0.25
Consensus pattern (27 bp):
CCAGATGCAACTAAGATCCCACTTTCT
Found at i:12495 original size:2 final size:2
Alignment explanation
Indices: 12488--12516 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12478 TTTTTAAAAC
12488 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 A
12517 CCCTCATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12730 original size:48 final size:48
Alignment explanation
Indices: 12674--12765 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
12664 AAACGGAGAT
12674 ATCAGAAATCAAAACAAAATCCAGAACAGGTATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAAAATCCAGAACAGGTATCAGAACAGAATCCAG
* * * ** * *
12722 ATCAGAAATCACAACAGAATTCAGGTCATGTATCATAACAGAAT
1 ATCAGAAATCAAAACAAAATCCAGAACAGGTATCAGAACAGAAT
12766 TCAAGTCGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (48 bp):
ATCAGAAATCAAAACAAAATCCAGAACAGGTATCAGAACAGAATCCAG
Found at i:12732 original size:24 final size:24
Alignment explanation
Indices: 12674--12741 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
12664 AAACGGAGAT
*
12674 ATCAGAAATCAAAACAAAATCCAG
1 ATCAGAAATCAAAACAGAATCCAG
* ** *
12698 AACAGGTATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATCCAG
*
12722 ATCAGAAATCACAACAGAAT
1 ATCAGAAATCAAAACAGAAT
12742 TCAGGTCATG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Found at i:12756 original size:24 final size:23
Alignment explanation
Indices: 12703--12768 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
12693 TCCAGAACAG
* *
12703 GTATCAGAACAGAATCCAGATCA
1 GTATCACAACAGAATTCAGATCA
* *
12726 GAAATCACAACAGAATTCAGGTCA
1 G-TATCACAACAGAATTCAGATCA
*
12750 TGTATCATAACAGAATTCA
1 -GTATCACAACAGAATTCA
12769 AGTCGGAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
23 1 0.03
24 33 0.94
25 1 0.03
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (23 bp):
GTATCACAACAGAATTCAGATCA
Found at i:12780 original size:24 final size:25
Alignment explanation
Indices: 12705--12780 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 25
12695 CAGAACAGGT
* *
12705 ATCAGAACAGAA-TCCAGATCA-GAA
1 ATCACAACAGAATTCAAG-TCAGGAA
* * *
12729 ATCACAACAGAATTCAGGTCATG-T
1 ATCACAACAGAATTCAAGTCAGGAA
*
12753 ATCATAACAGAATTCAAGTC-GGAA
1 ATCACAACAGAATTCAAGTCAGGAA
12777 ATCA
1 ATCA
12781 GATAAAATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
23 1 0.02
24 36 0.88
25 4 0.10
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (25 bp):
ATCACAACAGAATTCAAGTCAGGAA
Found at i:21484 original size:24 final size:20
Alignment explanation
Indices: 21427--21504 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
21417 TTTCCCTTGA
*
21427 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
21447 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
*
21470 ATGTGCATCGATGCACTCCT-T
1 A-GTGCATCGATGCA-TCCTAC
21491 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
21505 TAATTGTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 12 0.24
20 14 0.29
21 2 0.04
22 1 0.02
23 4 0.08
24 14 0.29
25 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:22388 original size:23 final size:23
Alignment explanation
Indices: 22357--22425 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
22347 CACCACAGCT
*
22357 CATATAATTGCACCGAAGTGCCA
1 CATAGAATTGCACCGAAGTGCCA
* * **
22380 CGTAGAATTGCACCGGAGTGCTG
1 CATAGAATTGCACCGAAGTGCCA
*
22403 CATAGAATTGCACCGTAGTGCCA
1 CATAGAATTGCACCGAAGTGCCA
22426 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CATAGAATTGCACCGAAGTGCCA
Found at i:22618 original size:103 final size:103
Alignment explanation
Indices: 22436--22658 Score: 410
Period size: 103 Copynumber: 2.2 Consensus size: 103
22426 TATAATAATG
*
22436 TCCCGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCCGAAGGACCACATATCACTCCGTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
22501 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
* * *
22539 TCTCGAAGGACCATATATCACTCCGTAAGAATCATATACATATACTAGGGATCAAGTATGTGTTT
1 TCCCGAAGGACCACATATCACTCCGTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
22604 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
22642 TCCCGAAGGACCACATA
1 TCCCGAAGGACCACATA
22659 GACCCTCGAC
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
TCCCGAAGGACCACATATCACTCCGTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:23498 original size:19 final size:19
Alignment explanation
Indices: 23474--23524 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
23464 TATTACTGGG
23474 ATGCATCGATGCATGCCTT
1 ATGCATCGATGCATGCCTT
23493 ATGCATCGATGCATGCCTT
1 ATGCATCGATGCATGCCTT
23512 ATGCATCGATGCA
1 ATGCATCGATGCA
23525 CTAATTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCATGCCTT
Found at i:23550 original size:83 final size:83
Alignment explanation
Indices: 23409--23589 Score: 226
Period size: 83 Copynumber: 2.2 Consensus size: 83
23399 TTAATGAAGG
* * *
23409 TATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGTATTATTACTGGG
1 TATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAATGGG
*
23474 ATGCATCGATGCA-TGCCT
66 ATGCATCGATGCACT-ACT
* * * *
23492 TATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCCTTATTAAT
1 TATGCATCGATGCACT-ACTGATGCATCGATGCA-TAAAATGCATTCGATGTTGT-ATTATTAAT
23554 GGGATGCATCGATGCACTACT
63 GGGATGCATCGATGCACTACT
23575 TATGCATCGATGCAC
1 TATGCATCGATGCAC
23590 AAATTGCATT
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
82 2 0.02
83 81 0.95
84 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (83 bp):
TATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAATGGG
ATGCATCGATGCACTACT
Found at i:23626 original size:64 final size:64
Alignment explanation
Indices: 23493--23653 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
23483 TGCATGCCTT
* * * * *
23493 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAAAGAG
*
23557 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTCATTATTAAAGAG
* **
23620 AGTGCATCGATACACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
23654 CTTCAAATAA
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 2 0.02
64 78 0.92
65 5 0.06
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:28142 original size:23 final size:23
Alignment explanation
Indices: 28116--28179 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
28106 CAGCTCATAT
28116 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
28139 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
28162 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
28180 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:28372 original size:103 final size:103
Alignment explanation
Indices: 28193--28412 Score: 397
Period size: 103 Copynumber: 2.1 Consensus size: 103
28183 AATAATGTCC
*
28193 CGAAGGACCACATATCACTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCAC
1 CGAAGGACCACATATCACTCCGTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCAC
28258 CAGACTTCACACATGTTCCAAAGAATACATATATATCT
66 CAGACTTCACACATGTTCCAAAGAATACATATATATCT
*
28296 CGAAGGACCATATATCACTCCGTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCAC
1 CGAAGGACCACATATCACTCCGTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCAC
28361 CAGACTTCACACATGTTCCAAAGAATACATATATATC-
66 CAGACTTCACACATGTTCCAAAGAATACATATATATCT
*
28398 CATAAGGACCACATA
1 C-GAAGGACCACATA
28413 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
102 1 0.01
103 111 0.99
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
CGAAGGACCACATATCACTCCGTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCAC
CAGACTTCACACATGTTCCAAAGAATACATATATATCT
Found at i:29267 original size:64 final size:64
Alignment explanation
Indices: 29159--29383 Score: 233
Period size: 64 Copynumber: 3.5 Consensus size: 64
29149 TAATGAAGGT
* ** * * * *
29159 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCAATGCACAAATTGCATTCGATGTT-TCATTATTAATGGG
* * *
29223 ATGCATCGATGCA-TGCCTTATGCATCAATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCAATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
* * **
29287 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCAATGCACAAATTGCATTCGATGT-TTCATTATTAATGGG
** *
29350 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCAATGCAC
29384 CTTCAAACAA
Statistics
Matches: 137, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
63 4 0.03
64 128 0.93
65 5 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCAATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:37007 original size:22 final size:22
Alignment explanation
Indices: 36982--37049 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
36972 TATTGGTAAA
36982 AAATAATTTTATAAATAATATT
1 AAATAATTTTATAAATAATATT
*
37004 AAAT-ATACTTATAAAT-ATATT
1 AAATAAT-TTTATAAATAATATT
* *
37025 TAA-AATTTT-TAAA-AATA-A
1 AAATAATTTTATAAATAATATT
37043 AAATAAT
1 AAATAAT
37050 AATACATTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
18 2 0.05
19 10 0.27
20 2 0.05
21 11 0.30
22 12 0.32
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATAATTTTATAAATAATATT
Found at i:53697 original size:18 final size:19
Alignment explanation
Indices: 53674--53710 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
53664 TTCATAGGGA
53674 TTTTGGT-CCGGAGGGGGG
1 TTTTGGTCCCGGAGGGGGG
53692 TTTTGGTCGCCGGAGGGGG
1 TTTTGGTC-CCGGAGGGGG
53711 ATGAGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.05, C:0.14, G:0.54, T:0.27
Consensus pattern (19 bp):
TTTTGGTCCCGGAGGGGGG
Found at i:64235 original size:33 final size:33
Alignment explanation
Indices: 64193--64315 Score: 210
Period size: 33 Copynumber: 3.7 Consensus size: 33
64183 CAGGCATCAT
* * *
64193 CACAAGCATGTATGAGGAGACATTTCCCATCGC
1 CACAAGCATGTATGAGGAAACATTACCCATCTC
64226 CACAAGCATGTATGAGGAAACATTACCCATCTC
1 CACAAGCATGTATGAGGAAACATTACCCATCTC
64259 CACAAGCATGTATGAGGAAACATTACCCATCTC
1 CACAAGCATGTATGAGGAAACATTACCCATCTC
*
64292 CACAAGCATGTATGAAGAAACATT
1 CACAAGCATGTATGAGGAAACATT
64316 GCCAATTGTT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (33 bp):
CACAAGCATGTATGAGGAAACATTACCCATCTC
Found at i:64744 original size:60 final size:60
Alignment explanation
Indices: 64651--65109 Score: 361
Period size: 60 Copynumber: 7.6 Consensus size: 60
64641 AATCCTGTGA
* ** * *
64651 CCTTGACAGAAGAAATTCCTAGTATTCCGAGAACCTCAGGTGAAGAAACTCCAGCTATTC
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTCAGGTGAAGAAACTCCAGCCATTC
* * * * *
64711 CCTTGGCCGAAGAAACCCCTAGTTTTCCCAGAACCTTAGGTGAAGAAACTCTAGCCA-AC
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTCAGGTGAAGAAACTCCAGCCATTC
* ** * * * * *
64770 CCTGTGGCAGAGGAAACTTCTAGTGTTGTTCCCACAACCTTAGGTGAAGAAACTCCAGCTATTT
1 CCT-TGGCAGAAGAAACCCCTA--G-TATTCCCAGAACCTCAGGTGAAGAAACTCCAGCCATTC
* * * * * * ** * * ****
64834 CCTTGGCGGAGGAAACCACTTGTATTCCCAGAAACT-TGACCGATGAAACGCCAAATGTTC
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTCAG-GTGAAGAAACTCCAGCCATTC
* ** * * * *
64894 CTCTT-GCCGAAGCTACCTCTAGTATTTCAAGAACCTC-GTGTGAAGAAACACCAGCCATTC
1 C-CTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTCAG-GTGAAGAAACTCCAGCCATTC
* * ** **
64954 CCCTGGCAGAAGAACCCCCTAGTATTCCCAGAACCTTGGGTGAAGAAACTCTTGCCATTC
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTCAGGTGAAGAAACTCCAGCCATTC
* * * *
65014 CCTTGGCAGAAGAAACCCCTAATATTCCCAGAACC-CTGAGTGAAGAACCACCAGCCATTC
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTCAG-GTGAAGAAACTCCAGCCATTC
*
65074 TCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCT
1 CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCT
65110 TGAGCGCAGA
Statistics
Matches: 310, Mismatches: 77, Indels: 23
0.76 0.19 0.06
Matches are distributed among these distances:
59 8 0.03
60 248 0.80
61 5 0.02
62 1 0.00
63 45 0.15
64 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (60 bp):
CCTTGGCAGAAGAAACCCCTAGTATTCCCAGAACCTCAGGTGAAGAAACTCCAGCCATTC
Found at i:65119 original size:36 final size:36
Alignment explanation
Indices: 65079--65218 Score: 235
Period size: 36 Copynumber: 3.9 Consensus size: 36
65069 CATTCTCTTG
*
65079 GCAGAAGAAACCCCTAGTATTCCCAGAACCTTGAGC
1 GCAGAAGAAACCCCTAGTATTCCCAGAACCTTGAGT
*
65115 GCAGAAGAAACCCCTAGTGTTCCCAGAACCTTGAGT
1 GCAGAAGAAACCCCTAGTATTCCCAGAACCTTGAGT
* **
65151 GCAGAAGAAACCCCTAGTGTTTGCAGAACCTTGAGT
1 GCAGAAGAAACCCCTAGTATTCCCAGAACCTTGAGT
65187 GCAGAAGAAACCCCTAGTATTCCCAGAACCTT
1 GCAGAAGAAACCCCTAGTATTCCCAGAACCTT
65219 AGGCGAAGAC
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (36 bp):
GCAGAAGAAACCCCTAGTATTCCCAGAACCTTGAGT
Found at i:65602 original size:33 final size:32
Alignment explanation
Indices: 65497--65602 Score: 86
Period size: 33 Copynumber: 3.2 Consensus size: 32
65487 ACTCCAACTA
* * * * *
65497 CCACAATCTTGGGTGATGAAACTGCAACCAGTC
1 CCACAACCTTGGGTGAAGAAGCTTCAACTA-TC
* *
65530 CCACAACCTTTGGTGAAGAATCTTCAACTATC
1 CCACAACCTTGGGTGAAGAAGCTTCAACTATC
* * * *
65562 CTGACAACCTTGGGTGAGGAAGCTTCATCTGTTC
1 C-CACAACCTTGGGTGAAGAAGCTTCAACT-ATC
65596 CCACAAC
1 CCACAAC
65603 TAATGGCGAG
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
32 3 0.05
33 52 0.90
34 3 0.05
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (32 bp):
CCACAACCTTGGGTGAAGAAGCTTCAACTATC
Found at i:67117 original size:6 final size:7
Alignment explanation
Indices: 67092--67116 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
67082 GGTCCTCAAG
67092 TTTTTAT
1 TTTTTAT
67099 TTTTTAT
1 TTTTTAT
67106 TTTTTAT
1 TTTTTAT
67113 TTTT
1 TTTT
67117 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:67351 original size:2 final size:2
Alignment explanation
Indices: 67346--67442 Score: 153
Period size: 2 Copynumber: 49.5 Consensus size: 2
67336 GAGGTTGTTT
67346 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
* * *
67388 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG T- TG T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67428 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
67443 GTTAAAATAT
Statistics
Matches: 91, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 89 0.98
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:68863 original size:30 final size:29
Alignment explanation
Indices: 68819--68880 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
68809 ATGAAAGAAA
*
68819 AATATTAAAAGAAATACCAA-AAAAAATAAT
1 AATAATAAAAGAAATA--AAGAAAAAATAAT
*
68849 AATAATAAATGAAATAAAGTAAAAAATAAT
1 AATAATAAAAGAAATAAAG-AAAAAATAAT
68879 AA
1 AA
68881 CAAAAGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
30 26 0.93
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (29 bp):
AATAATAAAAGAAATAAAGAAAAAATAAT
Found at i:70276 original size:18 final size:18
Alignment explanation
Indices: 70253--70291 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
70243 ACATAAAACA
*
70253 GAATAAA-TGAAATTAAAT
1 GAATAAAGTG-AATAAAAT
70271 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
70289 GAA
1 GAA
70292 AAGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:70302 original size:27 final size:27
Alignment explanation
Indices: 70253--70304 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
70243 ACATAAAACA
**
70253 GAATAAATGAAATTAAATGAATAAAGT
1 GAATAAATGAAAAGAAATGAATAAAGT
70280 GAATAAAATGAAAAGAAAT-AATAAA
1 GAAT-AAATGAAAAGAAATGAATAAA
70305 AATACTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.21
Consensus pattern (27 bp):
GAATAAATGAAAAGAAATGAATAAAGT
Found at i:70445 original size:33 final size:31
Alignment explanation
Indices: 70402--70469 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
70392 ACTATATACC
70402 ATATAGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
70434 ATATGAGTTTTCCAAAATATTTTTAAAACTAT
1 ATAT-AGTTTTCAAAAATATTTTTAAAAATAT
70466 ATAT
1 ATAT
70470 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:70560 original size:35 final size:35
Alignment explanation
Indices: 70516--70598 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 35
70506 TATACATTAT
70516 ATTTTCAAAATGATTTCAAAA-ATATA-TGTTATATA
1 ATTTTCAAAATG-TTTCAAAATATATATTG-TATATA
*
70551 ATTTTCAAAATGTTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAATGTTTCAAAA--TATATATTGTATATA
70588 AGTTTTCAAAA
1 A-TTTTCAAAA
70599 ACGTTTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
34 7 0.17
35 12 0.29
37 12 0.29
38 11 0.26
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (35 bp):
ATTTTCAAAATGTTTCAAAATATATATTGTATATA
Found at i:70605 original size:110 final size:110
Alignment explanation
Indices: 70403--70605 Score: 256
Period size: 110 Copynumber: 1.8 Consensus size: 110
70393 CTATATACCA
* * *
70403 TATAGTTTTCAAAAATGATTTTAAAAATATTATATGAGTTTTCCAAAATATTTTTAAAACTATAT
1 TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATAGTTTTAAAACTATAT
*
70468 ATTATATAAAATTTTCAAAAAATGTTTTTATTTTAAACTATACAT
66 ATTATATAAAATTTTCAAAAAACGTTTTTATTTTAAACTATACAT
70513 TATA-TTTTC-AAAATGATTTCAAAAATATATGTTATAT-AATTTT-CAAAAT-GTTTTAAAACT
1 TATAGTTTTCAAAAATGATTT-AAAAA-ATA--TTATATGAATTTTCCAAAATAGTTTTAAAAC-
* *
70573 TATATATTGTATATAAGTTTTC-AAAAACGTTTT
61 TATATATTATATA-AAATTTTCAAAAAACGTTTT
70606 AAAAGAACTA
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
108 10 0.12
109 18 0.22
110 35 0.43
111 12 0.15
112 6 0.07
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (110 bp):
TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATAGTTTTAAAACTATAT
ATTATATAAAATTTTCAAAAAACGTTTTTATTTTAAACTATACAT
Found at i:70609 original size:39 final size:37
Alignment explanation
Indices: 70537--70609 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
70527 GATTTCAAAA
*
70537 ATATATGTTATATAATTTTCAAAATGTTTTAAAACTT
1 ATATATGTTATATAATTTTCAAAACGTTTTAAAACTT
70574 ATATAT-TGTATATAAGTTTTCAAAAACGTTTTAAAA
1 ATATATGT-TATATAA-TTTTC-AAAACGTTTTAAAA
70610 GAACTACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 1 0.03
37 13 0.41
38 5 0.16
39 13 0.41
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
ATATATGTTATATAATTTTCAAAACGTTTTAAAACTT
Found at i:71457 original size:84 final size:80
Alignment explanation
Indices: 71317--72093 Score: 761
Period size: 84 Copynumber: 9.4 Consensus size: 80
71307 TTGAATATAA
* * *
71317 TCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCA-ACTTAAGCTATGCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCT-AGACTTAAGTTATGCTGCAAATGATGTGCC
*
71381 TTGGAGCTGAGCGGAG
65 TTGGAGCTGAGCGTAG
* * *
71397 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGG---CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
71462 GTCGTT-GAGCTGAGCGTAG
62 G-CCTTGGAGCTGAGCGTAG
* * * * ** *
71481 TCGAACTCAAAGGTCTTTTGTTGGTAGACAACCCTTCTAGACTTAAGTTGTATTGCAAATGATAT
1 TCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
71546 GTCTTGGAGCTGAGCGTAG
62 GCCTTGGAGCTGAGCGTAG
* *
71565 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGT
1 TCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
** * * *
71630 GCCCCCGAAGCTGAGTGTAA
62 G-CCTTGGAGCTGAGCGTAG
* ** * * *
71650 TCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
1 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCT
71715 TGGAGCTGAGCGTAG
66 TGGAGCTGAGCGTAG
* * * * * *
71730 TCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATG
1 TCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* * *
71795 CCCTTGAAGCTGAGTGTAA
63 -CCTTGGAGCTGAGCGTAG
* * * * *
71814 TCGAACT-TAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC
1 TCGAACTCGAA-GGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
*
71878 TAGGAGCTGAGCGTAG
65 TTGGAGCTGAGCGTAG
* * * * *
71894 TCGAACTCGAAGGTCTTTGGCGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATG
1 TCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* * *
71959 CCCTTGAAGCTGAGTGTAA
63 -CCTTGGAGCTGAGCGTAG
* * * *
71978 TCGAACT-TAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 TCGAACTCGAA-GGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
72042 TTGGAGCTGAGCGTAG
65 TTGGAGCTGAGCGTAG
* *
72058 TCGAACTCGAAGGTCTTAGTGGCAGGTAGCCCTTCT
1 TCGAACTCGAAGGTCTT--TGGCAGATAACCCTTCT
72094 GGCCTTGAGC
Statistics
Matches: 569, Mismatches: 103, Indels: 48
0.79 0.14 0.07
Matches are distributed among these distances:
80 98 0.17
81 120 0.21
82 21 0.04
83 76 0.13
84 221 0.39
85 27 0.05
86 2 0.00
87 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (80 bp):
TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCT
TGGAGCTGAGCGTAG
Found at i:71837 original size:164 final size:164
Alignment explanation
Indices: 71314--72102 Score: 1089
Period size: 164 Copynumber: 4.8 Consensus size: 164
71304 AAGTTGAATA
* * *
71314 TAATCGAACTCGAA-GGTCTTTAGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGT
1 TAATCGAACT-TAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* *
71378 GCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGA
65 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGA
* * * *
71443 GTTATGCTGTAAATGATGTGTCGTTG-AGCTGAGCG
129 GTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
* * * * * * * * * **
71478 TAGTCGAACTCAAAGGTCTTTTGTTGGTAGACAACCCTTCTAGACTTAAGTTGTATTGCAAATGA
1 TAATCGAACTTAAGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * * * *
71543 TATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACT
62 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCT
* ** * **
71608 TAAGTTATGCTACAAATGATGTGCCCCCGAAGCTGAGTG
126 TGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
**
71647 TAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
71712 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
*
71777 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
131 TATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
*
71811 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* *
71876 CCTAGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCGACAGATAACCCTTCTAGCCTTGAGT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
*
71941 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
131 TATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
71975 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * * *
72040 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTAGTGGCAGGTAGCCCTTCTGGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
72103 CTAAGCTGCA
Statistics
Matches: 550, Mismatches: 69, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
163 26 0.05
164 322 0.59
165 68 0.12
166 1 0.00
167 1 0.00
168 111 0.20
169 21 0.04
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (164 bp):
TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
TATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
Found at i:75497 original size:19 final size:20
Alignment explanation
Indices: 75470--75516 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
75460 AGTTAATGTG
*
75470 AATGTAAAGAAAATAAC-AA
1 AATGCAAAGAAAATAACGAA
75489 AATGCAAAGAAAATAACGAA
1 AATGCAAAGAAAATAACGAA
75509 AATGCAAA
1 AATGCAAA
75517 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.66, C:0.09, G:0.13, T:0.13
Consensus pattern (20 bp):
AATGCAAAGAAAATAACGAA
Found at i:77339 original size:30 final size:29
Alignment explanation
Indices: 77295--77356 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
77285 ATGAAAGAAA
*
77295 AATATTAAAAGAAATACCAA-AAAAAATAAT
1 AATAATAAAAGAAATA--AAGAAAAAATAAT
*
77325 AATAATAAATGAAATAAAGTAAAAAATAAT
1 AATAATAAAAGAAATAAAG-AAAAAATAAT
77355 AA
1 AA
77357 CAAAAGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
30 26 0.93
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (29 bp):
AATAATAAAAGAAATAAAGAAAAAATAAT
Found at i:78749 original size:18 final size:18
Alignment explanation
Indices: 78726--78764 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
78716 CCATAAAACA
*
78726 GAATAAA-TGAAATTAAAT
1 GAATAAAGTG-AATAAAAT
78744 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
78762 GAA
1 GAA
78765 AAGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:78775 original size:27 final size:27
Alignment explanation
Indices: 78726--78777 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
78716 CCATAAAACA
**
78726 GAATAAATGAAATTAAATGAATAAAGT
1 GAATAAATGAAAAGAAATGAATAAAGT
78753 GAATAAAATGAAAAGAAAT-AATAAA
1 GAAT-AAATGAAAAGAAATGAATAAA
78778 AAATACTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.21
Consensus pattern (27 bp):
GAATAAATGAAAAGAAATGAATAAAGT
Found at i:78801 original size:16 final size:18
Alignment explanation
Indices: 78782--78814 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
78772 AATAAAAAAT
78782 ACTA-ATAATA-ATATAG
1 ACTATATAATATATATAG
78798 ACTATATAATATATATA
1 ACTATATAATATATATA
78815 TCTCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (18 bp):
ACTATATAATATATATAG
Found at i:78943 original size:32 final size:32
Alignment explanation
Indices: 78876--78943 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
78866 ACTATATACC
78876 ATATAGTTTTCAAAAATGATTTTAAAAATATT
1 ATATAGTTTTCAAAAATGATTTTAAAAATATT
* *
78908 ATATGAGTTTTCCAAAAT-ATTTTTAAAACTA-T
1 ATAT-AGTTTTCAAAAATGA-TTTTAAAAATATT
78940 ATAT
1 ATAT
78944 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (32 bp):
ATATAGTTTTCAAAAATGATTTTAAAAATATT
Found at i:79034 original size:35 final size:35
Alignment explanation
Indices: 78990--79072 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 35
78980 TATACATTAT
78990 ATTTTCAAAATGATTTCAAAA-ATATA-TGTTATATA
1 ATTTTCAAAATG-TTTCAAAATATATATTG-TATATA
*
79025 ATTTTCAAAATGTTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAATGTTTCAAAA--TATATATTGTATATA
79062 AGTTTTCAAAA
1 A-TTTTCAAAA
79073 ACGTTTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
34 7 0.17
35 12 0.29
37 12 0.29
38 11 0.26
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (35 bp):
ATTTTCAAAATGTTTCAAAATATATATTGTATATA
Found at i:79079 original size:110 final size:110
Alignment explanation
Indices: 78877--79079 Score: 256
Period size: 110 Copynumber: 1.8 Consensus size: 110
78867 CTATATACCA
* * *
78877 TATAGTTTTCAAAAATGATTTTAAAAATATTATATGAGTTTTCCAAAATATTTTTAAAACTATAT
1 TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATAGTTTTAAAACTATAT
*
78942 ATTATATAAAATTTTCAAAAAATGTTTTTATTTTAAACTATACAT
66 ATTATATAAAATTTTCAAAAAACGTTTTTATTTTAAACTATACAT
78987 TATA-TTTTC-AAAATGATTTCAAAAATATATGTTATAT-AATTTT-CAAAAT-GTTTTAAAACT
1 TATAGTTTTCAAAAATGATTT-AAAAA-ATA--TTATATGAATTTTCCAAAATAGTTTTAAAAC-
* *
79047 TATATATTGTATATAAGTTTTC-AAAAACGTTTT
61 TATATATTATATA-AAATTTTCAAAAAACGTTTT
79080 AAAAGAACTA
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
108 10 0.12
109 18 0.22
110 35 0.43
111 12 0.15
112 6 0.07
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (110 bp):
TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATAGTTTTAAAACTATAT
ATTATATAAAATTTTCAAAAAACGTTTTTATTTTAAACTATACAT
Found at i:79083 original size:39 final size:37
Alignment explanation
Indices: 79011--79083 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
79001 GATTTCAAAA
*
79011 ATATATGTTATATAATTTTCAAAATGTTTTAAAACTT
1 ATATATGTTATATAATTTTCAAAACGTTTTAAAACTT
79048 ATATAT-TGTATATAAGTTTTCAAAAACGTTTTAAAA
1 ATATATGT-TATATAA-TTTTC-AAAACGTTTTAAAA
79084 GAACTACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 1 0.03
37 13 0.41
38 5 0.16
39 13 0.41
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
ATATATGTTATATAATTTTCAAAACGTTTTAAAACTT
Found at i:80661 original size:31 final size:31
Alignment explanation
Indices: 80623--80683 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
80613 CAAACGGTCA
80623 GGGACCATATTACAAACAGACTAAATGTTGG
1 GGGACCATATTACAAACAGACTAAATGTTGG
* *
80654 GGGACCATATTGCAAATAGACTAAATGTTG
1 GGGACCATATTACAAACAGACTAAATGTTG
80684 AGGATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (31 bp):
GGGACCATATTACAAACAGACTAAATGTTGG
Done.