Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004323.1 Hibiscus syriacus cultivar Beakdansim tig00009479_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: 110216
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3056 original size:13 final size:13
Alignment explanation
Indices: 3038--3063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3028 CAATGTGAGA
3038 TAAAAGTTAAAAG
1 TAAAAGTTAAAAG
3051 TAAAAGTTAAAAG
1 TAAAAGTTAAAAG
3064 GTGTATTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
TAAAAGTTAAAAG
Found at i:8997 original size:26 final size:25
Alignment explanation
Indices: 8966--9015 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
8956 TAAGGGGGTG
*
8966 AACTTATAAAATTTTAAAGGAGAGCA
1 AACTTATAAAAATTTAAA-GAGAGCA
*
8992 AACTTATAAAAATTTAGAGAGAGC
1 AACTTATAAAAATTTAAAGAGAGC
9016 GAAAATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (25 bp):
AACTTATAAAAATTTAAAGAGAGCA
Found at i:10081 original size:19 final size:19
Alignment explanation
Indices: 10059--10099 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
10049 AATAGTACAT
10059 GTCCTCTAAGATAACTCAA
1 GTCCTCTAAGATAACTCAA
10078 GTCCTCTAAGATAACTCAA
1 GTCCTCTAAGATAACTCAA
10097 GTC
1 GTC
10100 GTACTCTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (19 bp):
GTCCTCTAAGATAACTCAA
Found at i:10801 original size:20 final size:19
Alignment explanation
Indices: 10778--10815 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
10768 ATTTAACCTT
10778 TGGTATCGATACCCATCTGC
1 TGGTATCGATACCC-TCTGC
10798 TGGTATCGATACCCTCTG
1 TGGTATCGATACCCTCTG
10816 ACTGATGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.32
Consensus pattern (19 bp):
TGGTATCGATACCCTCTGC
Found at i:27438 original size:60 final size:61
Alignment explanation
Indices: 27310--27439 Score: 149
Period size: 60 Copynumber: 2.1 Consensus size: 61
27300 TTCTGGGCTC
* * *
27310 GAATCGAGTTTCTATTTTTGATTTCAAATCTAGCTTAAAAATTTTAAGCTCGAGAGTTTTC
1 GAATCGAGTTTCGATTTTTGATTTCAAATCTAGCTTAAAAATTTTAAGCTCGAGAGATTTA
* * * * *
27371 GAGTCGAGTTTCGA-TTTTGATTTCGAGT-TAAGCTTAATAATTTTAAGCT-TATGAGATTTA
1 GAATCGAGTTTCGATTTTTGATTTCAAATCT-AGCTTAAAAATTTTAAGCTCGA-GAGATTTA
27431 GAATCGAGT
1 GAATCGAGT
27440 CAAATCAAAC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 2 0.03
60 44 0.76
61 12 0.21
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (61 bp):
GAATCGAGTTTCGATTTTTGATTTCAAATCTAGCTTAAAAATTTTAAGCTCGAGAGATTTA
Found at i:29484 original size:34 final size:37
Alignment explanation
Indices: 29305--29646 Score: 156
Period size: 37 Copynumber: 9.2 Consensus size: 37
29295 TTATATATAT
* *
29305 ACATATTTTGAAACTACGTATATAATATATAGTTTTT-AAT
1 ACAT-TTTTGAAA--ACATATAT-ATATATAGTTTTTGAAA
* * ** **
29345 A-GTTTTTAAAATTATATA-ATATATAGTTTTAAAAAA
1 ACATTTTTGAAAACATATATATATATAGTTTT-TGAAA
* * *
29381 ACATTTTAGAAAATATATATAATATATAATTTTT-AAA
1 ACATTTTTGAAAACATATAT-ATATATAGTTTTTGAAA
*
29418 ATCA-TTTGGAAAACTTATATATATATATATAGTTTTTGAAA
1 A-CATTTTTGAAAAC----ATATATATATATAGTTTTTGAAA
29459 ACATTTTTG-AAACA-ATATAT-TATAG-TTTTGAAA
1 ACATTTTTGAAAACATATATATATATAGTTTTTGAAA
* *
29492 GCA-TTTTGAAAACATTTATATTATATAGTTTTT-AAA
1 ACATTTTTGAAAACATATATA-TATATAGTTTTTGAAA
* * * * **
29528 ACGTTTTGGGAAA-ATTTATATA-ATCTTTTTTGAAA
1 ACATTTTTGAAAACATATATATATATAGTTTTTGAAA
* * * **
29563 ACATGTTGGAAAACATTCGTATATTATATAGTTTTAAAAAAA
1 ACATTTTTGAAAACA-T-ATATA-TATATAGTTTT--TGAAA
** *
29605 ACA-TTTTGAAAATTTATATAT-TGTATGTTTTTGAAA
1 ACATTTTTGAAAACATATATATATATA-GTTTTTGAAA
*
29641 ATATTT
1 ACATTT
29647 ATGTATATAT
Statistics
Matches: 232, Mismatches: 42, Indels: 59
0.70 0.13 0.18
Matches are distributed among these distances:
32 5 0.02
33 15 0.06
34 28 0.12
35 22 0.09
36 30 0.13
37 42 0.18
38 19 0.08
39 18 0.08
40 26 0.11
41 21 0.09
42 6 0.03
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (37 bp):
ACATTTTTGAAAACATATATATATATAGTTTTTGAAA
Found at i:29535 original size:36 final size:36
Alignment explanation
Indices: 29325--29616 Score: 172
Period size: 34 Copynumber: 7.9 Consensus size: 36
29315 AAACTACGTA
* * *
29325 TATAATATATAGTTTTTAATA-GTTTT-TAAA-ATT
1 TATAATATATAGTTTTTAAAACATTTTGAAAACATT
* * *
29358 ATATAATATATAGTTTTAAAAAAACATTTTAGAAAATATA
1 -TATAATATATAGTTTT--TAAAACATTTT-GAAAACATT
* * *
29398 TATAATATATAATTTTTAAAATCATTTGGAAAACTTATA
1 TATAATATATAGTTTTTAAAA-CATTTTGAAAAC--ATT
*
29437 TATATATATATAGTTTTTGAAAACATTTTTG-AAACA-A
1 TATA-ATATATAGTTTTT-AAAACA-TTTTGAAAACATT
* *
29474 TAT-AT-TATAGTTTTGAAAGCATTTTGAAAACATT
1 TATAATATATAGTTTTTAAAACATTTTGAAAACATT
* * *
29508 TATATTATATAGTTTTTAAAACGTTTTGGGAAA-ATT
1 TATAATATATAGTTTTTAAAACATTTT-GAAAACATT
** *
29544 TAT-ATA-ATCTTTTTTGAAAACATGTTGGAAAACATT
1 TATAATATATAGTTTTT-AAAACAT-TTTGAAAACATT
* *
29580 CGTATATTATATAGTTTTAAAAAAAACATTTTGAAAA
1 --TATAATATATAGTTTT---TAAAACATTTTGAAAA
29617 TTTATATATT
Statistics
Matches: 201, Mismatches: 30, Indels: 47
0.72 0.11 0.17
Matches are distributed among these distances:
32 5 0.02
33 10 0.05
34 35 0.17
35 15 0.07
36 31 0.15
37 21 0.10
38 9 0.04
39 27 0.13
40 26 0.13
41 15 0.07
42 7 0.03
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (36 bp):
TATAATATATAGTTTTTAAAACATTTTGAAAACATT
Found at i:29669 original size:3 final size:3
Alignment explanation
Indices: 29656--29691 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
29646 TATGTATATA
29656 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
29692 CATTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30950 original size:6 final size:6
Alignment explanation
Indices: 30939--30965 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30929 GAATCGAGTT
30939 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
30966 TCGCAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:32589 original size:19 final size:19
Alignment explanation
Indices: 32555--32599 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
32545 ATTTAGACAT
32555 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
32573 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
32592 TTTGCATT
1 TTTGCATT
32600 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:36018 original size:84 final size:82
Alignment explanation
Indices: 35922--36850 Score: 964
Period size: 84 Copynumber: 11.2 Consensus size: 82
35912 AGCTCAAGCC
* * * *
35922 AGAAGGGCTATCTGTCCACCAAGACCTTCGAGTTCGACTACGTTCAGCTTTGAAGGCACATCATT
1 AGAAGGGTTATCTG-CCACAAAGACCTTCGAGTTCGACTACGCTCAGC-TTCAAGGCACATCATT
*
35987 TGCAGCATAACTTAAGTCA
64 TGCAGCATAACTTAAGTCG
* * * *
36006 AGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCCCATCATT
1 AGAAGGGTTATCTGC-CAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATT
36071 TGCAGCATAACTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * * *
36090 AGAAGGGTTATCTGCCAACTAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATATCA
1 AGAAGGGTTATCTGCC-AC-AAAGA-CCTTCGAGTTCGACTACGCTCAGCTTCAA-GGCACATCA
* * * *
36154 TTTACAGCATAACTCAAGGCT
62 TTTGCAGCATAACTTAAGTCG
* * *
36175 AGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTGCCA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTT
* *
36240 GCAGAATAGCTTAAGTCG
65 GCAGCATAACTTAAGTCG
* * *
36258 AGAAGGGCTATCTG-C-CAAAGACCCTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
1 AGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTG
* *
36321 CAGAATAGCTTAAGTCG
66 CAGCATAACTTAAGTCG
* * *
36338 AGAAGGGCTATCTG-C-CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATTT
1 AGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTT
* *
36401 GCAGTATAACTTAAGTCA
65 GCAGCATAACTTAAGTCG
* * *
36419 AGAAGGGTTATCTGCCAACTAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCA-ATCA
1 AGAAGGGTTATCTGCC-AC-AAAGA-CCTTCGAGTTCGACTACGCTCAGCTTCAA-GGCACATCA
* * * *
36482 TTTACAGCATAACTCAAGGCT
62 TTTGCAGCATAACTTAAGTCG
** * *
36503 AGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTGCCA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTT
* * *
36568 GCAGAATAGCTTAAGTCA
65 GCAGCATAACTTAAGTCG
* * * * *
36586 AGAAGGGTTATCTG-C-CAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATT
1 AGAAGGGTTATCTGCCACAAAGA-CCTTCGAGTTCGACTACGCTCAGCTTCAA-GGCACATCATT
* * * *
36648 TACAGCATAACTCAAGGCT
64 TGCAGCATAACTTAAGTCG
** * * *
36667 AGAAGGGTTATCTGTTAACAAAAGACCTTTGAGTTTGACTACGCTCAGC-TCAACGGCATATCAT
1 AGAAGGGTTATCTG-CCAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTTCAA-GGCACATCAT
* * * *
36731 TTACAGCATAACTCAAGGCT
63 TTGCAGCATAACTTAAGTCG
* *
36751 AGAAGGGTTATCTGTCATCAAAGACCTTCGAGTGCGACTACGCTCAGC-TCTAAGGCACATCATT
1 AGAAGGGTTATCTGCCA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATT
*
36815 TGCAGCATAGCTTAAGTCG
64 TGCAGCATAACTTAAGTCG
*
36834 AGAAGGGCTATCTGCCA
1 AGAAGGGTTATCTGCCA
36851 AAGACCCCTG
Statistics
Matches: 723, Mismatches: 96, Indels: 53
0.83 0.11 0.06
Matches are distributed among these distances:
80 135 0.19
81 82 0.11
82 10 0.01
83 169 0.23
84 207 0.29
85 117 0.16
86 3 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (82 bp):
AGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTG
CAGCATAACTTAAGTCG
Found at i:36526 original size:248 final size:248
Alignment explanation
Indices: 35914--36937 Score: 1283
Period size: 248 Copynumber: 4.1 Consensus size: 248
35904 TGCAGCTTAG
* * * * * * *
35914 CTCAA-GCCAGAAGGGCTATCTGTCCAC-CAAGACCTTCGAGTTCGACTACGTTCAGCTTTGAAG
1 CTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGACTACGCTCAGC-TTCAAG
* * * * * *
35977 GCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTC
65 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TAACCAAAGACCTTCGAGTTC
* * * *
36042 GACTACGCTCAGCTCCAAGGCCCATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA
129 GACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C-
36107 ACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
192 -C-AAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
* *
36166 CTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGG
* * * * * * * *
36230 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGA
66 CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGA
36292 CTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
131 CTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
** * ** * * *
36357 GACCCTCGAGTTCGACTACGTTCAGCTTCGAA-GGCACATCATTTGCAGTATAA
196 GACCCTTAAGTTCGATTACACTCAGCTTC-AAGGGCATATCATTTACAGCATAA
* * * * * * * * *
36410 CTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAA-G
*
36475 GCA-ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCG
65 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCG
* *
36539 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGTTATCTGCCAA
130 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
*
36604 AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAA
195 AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
* *
36658 CTCAAGGCTAGAAGGGTTATCTGTTAACAAAAGACCTTTGAGTTTGACTACGCTCAGC-TCAACG
1 CTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAA-G
* * * *
36722 GCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTGCG
65 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCG
* *
36787 ACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
130 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
* ** * * * * * *
36852 AGACCCCTGGGTTCGATTACACTCAACTTCGAGGTCATATCAGTTACAACATAG
195 AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
* * * *
36906 CTCAAGGCAAGAAGGGCTATTTGTCAATAAAA
1 CTCAAGGCTAGAAGGGTTATCTGTCAACAAAA
36938 TTGTCGAGTT
Statistics
Matches: 671, Mismatches: 91, Indels: 24
0.85 0.12 0.03
Matches are distributed among these distances:
244 66 0.10
245 66 0.10
246 4 0.01
247 11 0.02
248 431 0.64
252 50 0.07
253 43 0.06
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (248 bp):
CTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGG
CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGA
CTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
GACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAA
Found at i:36854 original size:328 final size:327
Alignment explanation
Indices: 35922--36856 Score: 1202
Period size: 328 Copynumber: 2.8 Consensus size: 327
35912 AGCTCAAGCC
* * ** ** *
35922 AGAAGGGCTATCTGTCCACCAAGACCTTCGAGTTCGACTACGTTCAGCTTTGAAGGCACATCATT
1 AGAAGGGCTATCTG-CCA--AAGACCCTCAAGTTCGACTACACTCAGC-TCCAAGGCACAACATT
35987 TGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTC
62 TGCAGCATAACTTAAGTCAAGAAGGGTTATCTG-TAACAAAAGACCTTTGAGTTCGACTACGCTC
* *
36052 AGCTCCAAGGCCCATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACC
126 AGCT-CAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACC
36117 CTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGG
190 CTTAAGTTCGATTACACTCAGCTTCAAGGGCA-ATCATTTACAGCATAACTCAAGGCTAGAAGGG
36182 TTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAAT
254 TTATCTG--ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAAT
*
36247 AGCTTAAGTCG
317 AGCTTAAGTCA
* * *
36258 AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCA
1 AGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGACTACACTCAGCTCCAAGGCACAACATTTGCA
* * * * * * * *
36323 GAATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGACTACGTTCAGCTT
66 GCATAACTTAAGTCAAGAAGGGTTATCTGTAACAAAAGACCTTTGAGTTCGACTACGCTCAGC-T
*
36385 CGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTA
130 C-AAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTA
36450 AGTTCGATTACACTCAGCTTCAAGGGCAATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC
194 AGTTCGATTACACTCAGCTTCAAGGGCAATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATC
36515 TGTAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTT
259 TG--ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTT
36580 AAGTCA
322 AAGTCA
* * * * * *
36586 AGAAGGGTTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTAC
1 AGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGACTACACTCAGCTCCAA-GGCACAACATTTGC
* * * *
36651 AGCATAACTCAAGGCTAGAAGGGTTATCTGTTAACAAAAGACCTTTGAGTTTGACTACGCTCAGC
65 AGCATAACTTAAGTCAAGAAGGGTTATCTG-TAACAAAAGACCTTTGAGTTCGACTACGCTCAGC
* * * * * * *
36716 TCAACGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCATC-AAAGA-CCTT
129 TCAA-GGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTT
* * * * * * * * * *
36779 CGAGTGCGACTACGCTCAGC-TCTAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
193 -AAGTTCGATTACACTCAGCTTC-AAGGGCA-ATCATTTACAGCATAACTCAAGGCTAGAAGGGT
36842 TATCTG-CCAAAGACC
255 TATCTGACCAAAGACC
36857 CCTGGGTTCG
Statistics
Matches: 533, Mismatches: 55, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
328 187 0.35
329 124 0.23
330 10 0.02
331 57 0.11
332 86 0.16
333 52 0.10
335 3 0.01
336 14 0.03
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (327 bp):
AGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGACTACACTCAGCTCCAAGGCACAACATTTGCA
GCATAACTTAAGTCAAGAAGGGTTATCTGTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTC
AAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAG
TTCGATTACACTCAGCTTCAAGGGCAATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGT
CA
Found at i:37672 original size:33 final size:33
Alignment explanation
Indices: 37552--37761 Score: 170
Period size: 33 Copynumber: 6.0 Consensus size: 33
37542 TTTTTAAAAT
* *
37552 TATATAATATAGTTTTAAAAAACATTTTAGAAATATA
1 TATAT-ATATAGTTTT-GAAAACATTTT-GAAA-ACA
* * *
37589 TATATATATAATTTTTAAAATCATTTGGAAAACTTATA
1 TATATATATAGTTTTGAAAA-CATTTTGAAAAC----A
37627 TATATATATAGTTTTGAAAACATTTTGAAAACA
1 TATATATATAGTTTTGAAAACATTTTGAAAACA
* *
37660 TATATATTTAGTTTTGAAAGCATTTTGAAAACA
1 TATATATATAGTTTTGAAAACATTTTGAAAACA
* * * *
37693 TTTATATATAGTTTTTAAAACGTTTTGGGAAA-A
1 TATATATATAGTTTTGAAAACATTTT-GAAAACA
* ** *
37726 TTTATATAATCTTTTTGAAAACATGTTGGAAAACA
1 TATATAT-ATAGTTTTGAAAACAT-TTTGAAAACA
37761 T
1 T
37762 TCGTATATTA
Statistics
Matches: 143, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
33 61 0.43
34 21 0.15
35 12 0.08
36 14 0.10
37 16 0.11
38 19 0.13
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (33 bp):
TATATATATAGTTTTGAAAACATTTTGAAAACA
Found at i:37758 original size:68 final size:65
Alignment explanation
Indices: 37558--37762 Score: 178
Period size: 68 Copynumber: 3.0 Consensus size: 65
37548 AAATTATATA
* * * *
37558 ATATAGTTTTAAAAAACATTTTAGAAATATATATATATATAATTTTTAAAATCATTTGGAAAACT
1 ATATAGTTTT-GAAAACATTTT-GAAA-ACATATATATCT-ATTTTGAAAA-CATTTGGAAAAC-
37623 TATATATAT
60 -AT-T-TAT
* * *
37632 ATATAGTTTTGAAAACATTTTGAAAACATATATATTTAGTTTTGAAAGCATTTTGAAAACATTTA
1 ATATAGTTTTGAAAACATTTTGAAAACATATATATCTA-TTTTGAAAACATTTGGAAAACATTTA
37697 T
65 T
* * **
37698 ATATAGTTTTTAAAACGTTTTGGGAAAATTTATATAATCT-TTTTGAAAACATGTTGGAAAACAT
1 ATATAGTTTTGAAAACATTTT--GAAAACATATAT-ATCTATTTTGAAAACAT-TTGGAAAACAT
37762 T
62 T
37763 CGTATATTAT
Statistics
Matches: 113, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
66 22 0.19
67 12 0.11
68 23 0.20
69 3 0.03
70 12 0.11
71 17 0.15
72 4 0.04
73 10 0.09
74 10 0.09
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (65 bp):
ATATAGTTTTGAAAACATTTTGAAAACATATATATCTATTTTGAAAACATTTGGAAAACATTTAT
Found at i:37849 original size:3 final size:3
Alignment explanation
Indices: 37841--37878 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
37831 TGTATATATA
37841 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
37879 TTTCATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41049 original size:10 final size:10
Alignment explanation
Indices: 41034--41079 Score: 83
Period size: 10 Copynumber: 4.5 Consensus size: 10
41024 TTGCGGTGAC
41034 TAAATTGAAA
1 TAAATTGAAA
41044 TAAATTGAAA
1 TAAATTGAAA
41054 TAAATTGAAA
1 TAAATTGAAA
41064 TAAATTGAAA
1 TAAATTGAAA
41074 TTAAAT
1 -TAAAT
41080 ATAAAAGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 30 0.86
11 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (10 bp):
TAAATTGAAA
Found at i:42124 original size:14 final size:14
Alignment explanation
Indices: 42099--42134 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
42089 AAGAAGCACA
42099 TTAGAA-TTAGGGT
1 TTAGAATTTAGGGT
42112 TTAGAATTTAGGGT
1 TTAGAATTTAGGGT
*
42126 TTAGGATTT
1 TTAGAATTT
42135 CATGTAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (14 bp):
TTAGAATTTAGGGT
Found at i:42180 original size:3 final size:3
Alignment explanation
Indices: 42172--42223 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
42162 CAAAGTTATA
42172 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42220 AAT A
1 AAT A
42224 CGTTAAAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42275 original size:12 final size:12
Alignment explanation
Indices: 42258--42293 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
42248 GTGACTACAC
42258 ATGTATGAATAA
1 ATGTATGAATAA
42270 ATGTATGAATAA
1 ATGTATGAATAA
42282 ATGTATGAATAA
1 ATGTATGAATAA
42294 GGAGTTAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (12 bp):
ATGTATGAATAA
Found at i:45202 original size:19 final size:21
Alignment explanation
Indices: 45169--45207 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
45159 TGTAAATTAA
*
45169 TGTTAGAGTGATG-AATTTGG
1 TGTTAGAATGATGAAATTTGG
45189 TGTTAGAATG-TGAAATTTG
1 TGTTAGAATGATGAAATTTG
45208 ACTATTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (21 bp):
TGTTAGAATGATGAAATTTGG
Found at i:46702 original size:12 final size:12
Alignment explanation
Indices: 46687--46730 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
46677 TTCTAAAATG
46687 TGAAAGTGAATA
1 TGAAAGTGAATA
*
46699 TGAAAGTGAAAA
1 TGAAAGTGAATA
46711 TGCAAA-TGAGATA
1 TG-AAAGTGA-ATA
46724 TGAAAGT
1 TGAAAGT
46731 TTTGTATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 19 0.70
13 8 0.30
ACGTcount: A:0.50, C:0.02, G:0.25, T:0.23
Consensus pattern (12 bp):
TGAAAGTGAATA
Found at i:46808 original size:39 final size:39
Alignment explanation
Indices: 46760--46842 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
46750 AAAAAGAATA
*
46760 TGATATGACTATTATGTATAATATTGTTTATCATTGCTT
1 TGATATGACTATTATGTATAATATTGTTTATCATGGCTT
* *
46799 TGATATGACTATTATGTATGATATTGTTTATCATGGTTT
1 TGATATGACTATTATGTATAATATTGTTTATCATGGCTT
46838 TGATA
1 TGATA
46843 AAATCATGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.51
Consensus pattern (39 bp):
TGATATGACTATTATGTATAATATTGTTTATCATGGCTT
Found at i:47074 original size:31 final size:32
Alignment explanation
Indices: 47030--47091 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
47020 GATTTTTGAA
47030 AAAATTGAAAGTTTAAGTACTAAA-ACATATC
1 AAAATTGAAAGTTTAAGTACTAAACACATATC
*
47061 AAAATT-AATAGTTTATGTACTAAACACATAT
1 AAAATTGAA-AGTTTAAGTACTAAACACATAT
47092 TTTACCCCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 2 0.07
31 20 0.71
32 6 0.21
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (32 bp):
AAAATTGAAAGTTTAAGTACTAAACACATATC
Found at i:48138 original size:86 final size:85
Alignment explanation
Indices: 47993--48149 Score: 278
Period size: 86 Copynumber: 1.8 Consensus size: 85
47983 ATAGTGGTCG
* * *
47993 AGGGACTCTAATATCTCATGCAATTCAATATTGTTCATACTATTTTTTATTGTTTTAGTTGCATT
1 AGGGACTCTAATATCTCATACAATTCAAAATTGTTCATACAATTTTTTATTGTTTTAGTTGCA-T
48058 TTGAAGTCGTTGAAGTCGTCT
65 TTGAAGTCGTTGAAGTCGTCT
48079 AGGGACTCTAATATCTCATACAATTCAAAATTGTTCATACAATTTTTTATTGTTTTAGTTGCATT
1 AGGGACTCTAATATCTCATACAATTCAAAATTGTTCATACAATTTTTTATTGTTTTAGTTGCATT
48144 TGAAGT
66 TGAAGT
48150 GTTTTTAATA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
85 8 0.12
86 60 0.88
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (85 bp):
AGGGACTCTAATATCTCATACAATTCAAAATTGTTCATACAATTTTTTATTGTTTTAGTTGCATT
TGAAGTCGTTGAAGTCGTCT
Found at i:49032 original size:31 final size:30
Alignment explanation
Indices: 48994--49070 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
48984 AAAAAAAACA
*
48994 TAAGATATGATCACTTTCGTTTTTATTTAAT
1 TAAGATATG-TCACTTTAGTTTTTATTTAAT
*
49025 TAAGATATTGTCACTTTATTTTTTATTTAAT
1 TAAGATA-TGTCACTTTAGTTTTTATTTAAT
*
49056 TAAGATGTGGTCACT
1 TAAGATAT-GTCACT
49071 CCAAGTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
30 1 0.02
31 38 0.93
32 2 0.05
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.51
Consensus pattern (30 bp):
TAAGATATGTCACTTTAGTTTTTATTTAAT
Found at i:50069 original size:31 final size:31
Alignment explanation
Indices: 50025--50097 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
50015 ACTCGGGGTA
* *
50025 ACCAGATCTTAATTAAATAAAAACTAAAGTG
1 ACCATATCTTAATTAAATAAAAACGAAAGTG
* *
50056 ACCATGTCTTAATTAAATAAAAACGAAATTG
1 ACCATATCTTAATTAAATAAAAACGAAAGTG
*
50087 ACTATATCTTA
1 ACCATATCTTA
50098 TGTCTTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (31 bp):
ACCATATCTTAATTAAATAAAAACGAAAGTG
Found at i:50243 original size:6 final size:6
Alignment explanation
Indices: 50234--50269 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
50224 CCGCCGCCGC
50234 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT
1 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT
50270 AATACGTGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
CGTGGT
Found at i:53853 original size:22 final size:22
Alignment explanation
Indices: 53828--53871 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
53818 GAAATCCACA
53828 GTGTTGGTCGTAGGTCGCCATG
1 GTGTTGGTCGTAGGTCGCCATG
53850 GTGTTGGTCGTAGGTCGCCATG
1 GTGTTGGTCGTAGGTCGCCATG
53872 CCTTCCGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.18, G:0.41, T:0.32
Consensus pattern (22 bp):
GTGTTGGTCGTAGGTCGCCATG
Found at i:53892 original size:29 final size:29
Alignment explanation
Indices: 53860--53917 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
53850 GTGTTGGTCG
*
53860 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
53889 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
53918 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:53970 original size:10 final size:9
Alignment explanation
Indices: 53955--53993 Score: 51
Period size: 10 Copynumber: 4.0 Consensus size: 9
53945 CAACACGCTG
53955 GGCATCCGA
1 GGCATCCGA
53964 GGTCATCCGA
1 GG-CATCCGA
53974 GAGCATCCGA
1 G-GCATCCGA
53984 GGCCATCCGA
1 GG-CATCCGA
53994 ACGAGCTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.11
10 23 0.85
11 1 0.04
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.13
Consensus pattern (9 bp):
GGCATCCGA
Found at i:54013 original size:23 final size:20
Alignment explanation
Indices: 53956--53993 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53946 AACACGCTGG
*
53956 GCATCCGAGGTCATCCGAGA
1 GCATCCGAGGCCATCCGAGA
53976 GCATCCGAGGCCATCCGA
1 GCATCCGAGGCCATCCGA
53994 ACGAGCTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.34, G:0.29, T:0.13
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAGA
Found at i:54032 original size:33 final size:33
Alignment explanation
Indices: 53978--54064 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
53968 ATCCGAGAGC
* * * *
53978 ATCCGAGGCCATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
* *
54011 ATCGGAGGGCAATCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
*
54044 ATCCGAGGGCAGCCGAGCGAG
1 ATCCGAGGGCAACCGAGCGAG
54065 GGTAGGTCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.25, C:0.25, G:0.39, T:0.10
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
Found at i:54101 original size:29 final size:29
Alignment explanation
Indices: 54068--54152 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
54058 GAGCGAGGGT
*
54068 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
54097 AGGTCGCCCGGAGGGCATGACGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
54126 AGGTCGCCCTGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
54153 TGTGTTGGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.21, C:0.31, G:0.35, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:54253 original size:29 final size:29
Alignment explanation
Indices: 54211--54267 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
54201 AAGCAAGGGT
*
54211 AGGTAGCCCGGAGTGCATGGCTACCTACA
1 AGGTAGCCCGGAGTGCATGGCGACCTACA
*
54240 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTAGCCCGGAGTGCATGGCGACCTAC
54268 GGCAAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
AGGTAGCCCGGAGTGCATGGCGACCTACA
Found at i:55407 original size:19 final size:19
Alignment explanation
Indices: 55379--55450 Score: 87
Period size: 19 Copynumber: 3.9 Consensus size: 19
55369 TCCTAAATTT
*
55379 TTTAATTTTTTTAATATAA
1 TTTAAGTTTTTTAATATAA
*
55398 TTTAAGTTTTTT-AT-T-T
1 TTTAAGTTTTTTAATATAA
*
55414 TTTAATTTTTTTAATATAA
1 TTTAAGTTTTTTAATATAA
*
55433 TTTAAGTTTTTTTATATA
1 TTTAAGTTTTTTAATATA
55451 TTTTTATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
16 11 0.25
17 3 0.07
18 3 0.07
19 27 0.61
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTAAGTTTTTTAATATAA
Found at i:55416 original size:7 final size:8
Alignment explanation
Indices: 55374--55424 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 8
55364 TCGTTTCCTA
55374 AATTTTTT
1 AATTTTTT
55382 AATTTTTTT
1 AA-TTTTTT
*
55391 AATATAATTT
1 AAT-T-TTTT
55401 AAGTTTTTT
1 AA-TTTTTT
55410 -ATTTTTT
1 AATTTTTT
55417 AATTTTTT
1 AATTTTTT
55425 TAATATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
7 6 0.17
8 11 0.31
9 12 0.33
10 6 0.17
11 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (8 bp):
AATTTTTT
Found at i:55421 original size:35 final size:35
Alignment explanation
Indices: 55375--55444 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
55365 CGTTTCCTAA
55375 ATTTTTTAATTTTTTTAATATAATTTAAGTTTTTT
1 ATTTTTTAATTTTTTTAATATAATTTAAGTTTTTT
55410 ATTTTTTAATTTTTTTAATATAATTTAAGTTTTTT
1 ATTTTTTAATTTTTTTAATATAATTTAAGTTTTTT
55445 TATATATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (35 bp):
ATTTTTTAATTTTTTTAATATAATTTAAGTTTTTT
Found at i:55726 original size:4 final size:4
Alignment explanation
Indices: 55717--55743 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
55707 TCCCTTCGTT
55717 GAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAA
55744 GAGCAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:59957 original size:4 final size:4
Alignment explanation
Indices: 59948--59988 Score: 64
Period size: 4 Copynumber: 9.8 Consensus size: 4
59938 AACAAAATAA
59948 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AATGAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA--AT AAAT AAA
59989 ATTAAGAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 31 0.89
6 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:61126 original size:30 final size:30
Alignment explanation
Indices: 61090--61150 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
61080 GAACCATACT
61090 CGTTAAACGGCAGCTGATGATCACTGGCCC
1 CGTTAAACGGCAGCTGATGATCACTGGCCC
61120 CGTTAAACGGCAGCTGATGATCACTGGCCC
1 CGTTAAACGGCAGCTGATGATCACTGGCCC
61150 C
1 C
61151 CTTCCAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (30 bp):
CGTTAAACGGCAGCTGATGATCACTGGCCC
Found at i:66548 original size:4 final size:4
Alignment explanation
Indices: 66539--66566 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
66529 TATTCTCTTA
66539 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
66567 GTTTCATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:67926 original size:29 final size:29
Alignment explanation
Indices: 67870--67927 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
67860 TAAAACATAC
* *
67870 AAATAGTCCCCTGATTATTAAAAGTTATT
1 AAATAGTCCCCTGACTATTAAAAATTATT
*
67899 AAATAGTCCCTTGACTA-TAGAAAATTATT
1 AAATAGTCCCCTGACTATTA-AAAATTATT
67928 TTGTTGAGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (29 bp):
AAATAGTCCCCTGACTATTAAAAATTATT
Found at i:74969 original size:183 final size:181
Alignment explanation
Indices: 74654--75008 Score: 665
Period size: 183 Copynumber: 2.0 Consensus size: 181
74644 AACAAAATCG
*
74654 TTTTAGGCATTAAACTTTAGTTGTGTATTGATTTTGTCACTAAATTTTTAAATAATTCACTTTTT
1 TTTTAGGCATTAAACTTTAGTGGTGTATTGATTTTGTCACTAAATTTTTAAATAATTCACTTTTT
74719 AGCACTACAAGTTTTCAACCGCCACTGATAGCCAATCATCCCCCGCCCTTGATCGCCTTTCCCGG
66 AGCACTACAAGTTTTCAACCGCCACTGATAGCCAATCATCCCCCGCCCTTGATCGCCTTTCCCGG
74784 TAGAAACGATACCAAAATGTTCTCAAAATCGATAAAAATAAATCTATTTTA
131 TAGAAACGATACCAAAATGTTCTCAAAATCGATAAAAATAAATCTATTTTA
74835 TTTTAGTGTCATTAAACTTTAGTGGTGTATTGATTTTGTCACTAAATTTTTAAATAATTCACTTT
1 TTTTAG-G-CATTAAACTTTAGTGGTGTATTGATTTTGTCACTAAATTTTTAAATAATTCACTTT
* *
74900 TTAGCACTACAATTTTTCAACCGCCACTGATAGCCAATCATCCCCCGTCCTTGATCGCCTTTCCC
64 TTAGCACTACAAGTTTTCAACCGCCACTGATAGCCAATCATCCCCCGCCCTTGATCGCCTTTCCC
74965 GGTAGAAACGATACCAAAATGTTCTCAAAATCGATAAAAATAAA
129 GGTAGAAACGATACCAAAATGTTCTCAAAATCGATAAAAATAAA
75009 CAAAAATTCT
Statistics
Matches: 169, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
181 6 0.04
182 1 0.01
183 162 0.96
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (181 bp):
TTTTAGGCATTAAACTTTAGTGGTGTATTGATTTTGTCACTAAATTTTTAAATAATTCACTTTTT
AGCACTACAAGTTTTCAACCGCCACTGATAGCCAATCATCCCCCGCCCTTGATCGCCTTTCCCGG
TAGAAACGATACCAAAATGTTCTCAAAATCGATAAAAATAAATCTATTTTA
Found at i:78462 original size:14 final size:13
Alignment explanation
Indices: 78424--78463 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
78414 TATAATTGTT
*
78424 CAAACAAAAAATC
1 CAAACAAAAAAAC
*
78437 CAAAAAAAAAAAC
1 CAAACAAAAAAAC
78450 CAAACAAACAAAAC
1 CAAACAAA-AAAAC
78464 AATTTTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 18 0.78
14 5 0.22
ACGTcount: A:0.75, C:0.23, G:0.00, T:0.03
Consensus pattern (13 bp):
CAAACAAAAAAAC
Found at i:82573 original size:60 final size:59
Alignment explanation
Indices: 82480--82610 Score: 244
Period size: 60 Copynumber: 2.2 Consensus size: 59
82470 ATACTAATAC
82480 AAACCAAAACCTACAAGACTACAAATATCACCTAAAACGATGCATTCGTGTATTTTTTAA
1 AAACCAAAACCTACAAGACTACAAATATCACCTAAAACGATGCATTCGTGTATTTTTT-A
82540 AAACCAAAACCTACAAGACTACAAATATCACCTAAAACGATGCATTCGTGTATTTTTTA
1 AAACCAAAACCTACAAGACTACAAATATCACCTAAAACGATGCATTCGTGTATTTTTTA
*
82599 AAACAAAAACCT
1 AAACCAAAACCT
82611 CTATTAAGGA
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
59 12 0.17
60 58 0.83
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (59 bp):
AAACCAAAACCTACAAGACTACAAATATCACCTAAAACGATGCATTCGTGTATTTTTTA
Found at i:84425 original size:30 final size:30
Alignment explanation
Indices: 84364--84425 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
84354 ATAAGATTAC
* * *
84364 TCTATTTATCAATTGTAACAAGCAGGTCAT
1 TCTATTTATCAATTATAACAAGCAAGCCAT
** *
84394 TCTATTTATTGATTATAACAATCAAGCCAT
1 TCTATTTATCAATTATAACAAGCAAGCCAT
84424 TC
1 TC
84426 AATTATAACT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (30 bp):
TCTATTTATCAATTATAACAAGCAAGCCAT
Found at i:86338 original size:3 final size:3
Alignment explanation
Indices: 86316--86363 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
86306 AAAGGAGAAA
*
86316 AAT AA- AAT ATT AAT -AT AAT AAT AAT AAT AAT AAT AAT AA- AAT AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
86362 AA
1 AA
86364 CGAAAAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 6 0.15
3 30 0.77
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:87754 original size:17 final size:17
Alignment explanation
Indices: 87730--87762 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
87720 GGGAGTAGTG
87730 GTTTAGTGGGT-AGGTT
1 GTTTAGTGGGTGAGGTT
87746 GTTTGAGTGGGTGAGGT
1 GTTT-AGTGGGTGAGGT
87763 AATGGTGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.39
Consensus pattern (17 bp):
GTTTAGTGGGTGAGGTT
Found at i:88244 original size:30 final size:30
Alignment explanation
Indices: 88200--88287 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
88190 TTTAGATACA
**
88200 TATTTTGATAAAAAAAATACTTTAGGTATC
1 TATTTTGACCAAAAAAATACTTTAGGTATC
* * * ** *
88230 TATTTTGACCAAAAAGATAAATTCATATATT
1 TATTTTGACCAAAAAAAT-ACTTTAGGTATC
88261 TATTTTGACC-AAAAAATACTTTAGGTA
1 TATTTTGACCAAAAAAATACTTTAGGTA
88288 CTTAAATGAA
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
29 6 0.14
30 21 0.48
31 17 0.39
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (30 bp):
TATTTTGACCAAAAAAATACTTTAGGTATC
Found at i:110001 original size:95 final size:92
Alignment explanation
Indices: 109841--110032 Score: 253
Period size: 95 Copynumber: 2.1 Consensus size: 92
109831 TGCTCTCAAG
*
109841 TATCAAAATGAAGTGATTAGCAGGGATTTAAATAGCGTCCGCTATTGGAATAGCGGCCGTTATAT
1 TATCAAAATGAAGTGATTAGCAGGGATTTAAATAGCATCCGCTATTGGAATAGCGGCCGTTATAT
* *
109906 A-ATGATTTGGTGCCATCTGAAAAACGT
66 AGAGGATTTGGTGCCATCCG-AAAACGT
* *
109933 TATCAAAATGAAGTGATTAGGAGCAGGGATTTAAATAGCTATCCGC-GTTGGAATAGCGGCTGTT
1 TATCAAAATGAAGTGATT---AGCAGGGATTTAAATAGC-ATCCGCTATTGGAATAGCGGCCGTT
* * *
109997 ATATAGCGGTTTTGGTGCCATCCGAAACCGT
62 ATATAGAGGATTTGGTGCCATCCGAAAACGT
110028 TATCA
1 TATCA
110033 CTTGACCGCA
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
92 18 0.21
95 50 0.57
96 19 0.22
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (92 bp):
TATCAAAATGAAGTGATTAGCAGGGATTTAAATAGCATCCGCTATTGGAATAGCGGCCGTTATAT
AGAGGATTTGGTGCCATCCGAAAACGT
Done.