Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007699.1 Hibiscus syriacus cultivar Beakdansim tig00109909_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: 64151
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:545 original size:25 final size:25
Alignment explanation
Indices: 507--563 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
497 TAAAGGCTAC
*
507 GAGTTTGGCATGTTTTTCAGTTGAT
1 GAGTTCGGCATGTTTTTCAGTTGAT
*
532 GAGTTCGGCTTGTTTTTCAGTTGAT
1 GAGTTCGGCATGTTTTTCAGTTGAT
557 GAGTTCG
1 GAGTTCG
564 TTTATGCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.14, C:0.11, G:0.30, T:0.46
Consensus pattern (25 bp):
GAGTTCGGCATGTTTTTCAGTTGAT
Found at i:4536 original size:18 final size:18
Alignment explanation
Indices: 4513--4552 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
4503 GGAATTACAG
4513 TTTCCTAAAAACTATCAT
1 TTTCCTAAAAACTATCAT
4531 TTTCCTAAAAACTATCAT
1 TTTCCTAAAAACTATCAT
4549 TTTC
1 TTTC
4553 AAATGCAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTCCTAAAAACTATCAT
Found at i:18691 original size:21 final size:21
Alignment explanation
Indices: 18612--18692 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
18602 GCACTGAAAT
18612 TTGTCCCGAAGGACCAC--TA
1 TTGTCCCGAAGGACCACTGTA
* *
18631 -TGTCCC-ATAGGACCATTGCA
1 TTGTCCCGA-AGGACCACTGTA
18651 TTGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
*
18672 TTGTCCCGAATGACCACTGTA
1 TTGTCCCGAAGGACCACTGTA
18693 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.02
18 13 0.25
20 1 0.02
21 36 0.69
22 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTGTA
Found at i:19190 original size:2 final size:2
Alignment explanation
Indices: 19183--19214 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19173 CTTATGTAAG
19183 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
19215 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:19219 original size:2 final size:2
Alignment explanation
Indices: 19214--19241 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19204 ACACACACAC
19214 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
19242 CATACAACGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19613 original size:21 final size:20
Alignment explanation
Indices: 19584--19622 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19574 TTTTATTTAC
19584 GGGGGAATC-GATACCCCCAA
1 GGGGGAATCTG-TACCCCCAA
19604 GGGGAGAATCTGTACCCCC
1 GGGG-GAATCTGTACCCCC
19623 TGTACAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.26, C:0.31, G:0.31, T:0.13
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCAA
Found at i:22058 original size:12 final size:12
Alignment explanation
Indices: 22043--22076 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
22033 TGGAGGGGGA
22043 GGTGGTGGTGCT
1 GGTGGTGGTGCT
*
22055 GGTGCTGGTGCT
1 GGTGGTGGTGCT
22067 GGTGGTGGTG
1 GGTGGTGGTG
22077 GTGGCGGGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.09, G:0.59, T:0.32
Consensus pattern (12 bp):
GGTGGTGGTGCT
Found at i:22080 original size:6 final size:6
Alignment explanation
Indices: 22043--22076 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
22033 TGGAGGGGGA
* *
22043 GGTGGT GGTGCT GGTGCT GGTGCT GGTGGT GGTG
1 GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT GGTG
22077 GTGGCGGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.09, G:0.59, T:0.32
Consensus pattern (6 bp):
GGTGCT
Found at i:22131 original size:6 final size:6
Alignment explanation
Indices: 22121--22186 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
22111 GGGATGGGGT
* * * * *
22121 GGAGGG AGAGGG GGAGGG GGAGGG GGAGGTGG GGATGA GGATGG GGATGG
1 GGAGGG GGAGGG GGAGGG GGAGGG GGA-G-GG GGAGGG GGAGGG GGAGGG
* *
22171 GGAGGA GGAGGA GGAG
1 GGAGGG GGAGGG GGAG
22187 ATTGGTATAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
6 45 0.88
7 1 0.02
8 5 0.10
ACGTcount: A:0.23, C:0.00, G:0.71, T:0.06
Consensus pattern (6 bp):
GGAGGG
Found at i:22147 original size:20 final size:21
Alignment explanation
Indices: 22110--22148 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22100 AATTTTGGTT
* *
22110 GGGGATGGGGTGGAGGGAGAG
1 GGGGAGGGGGAGGAGGGAGAG
22131 GGGGAGGGGGAGG-GGGAG
1 GGGGAGGGGGAGGAGGGAG
22149 GTGGGGATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.18, C:0.00, G:0.77, T:0.05
Consensus pattern (21 bp):
GGGGAGGGGGAGGAGGGAGAG
Found at i:26750 original size:33 final size:30
Alignment explanation
Indices: 26702--26806 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 30
26692 TTAGTATATA
26702 ATTAAAATAAAAATAAATTTAAAAGTTAGAGTG
1 ATTAAAATAAAAAT-AA-TTAAAAGTT-GAGTG
* * *
26735 ATTAAAATCAGAATAATTGAAAGTTGAGTG
1 ATTAAAATAAAAATAATTAAAAGTTGAGTG
* * *
26765 ATTAAATTAAAAA-AATT-AAATTTTAGTG
1 ATTAAAATAAAAATAATTAAAAGTTGAGTG
* *
26793 ATCAAAATAGAAAT
1 ATTAAAATAAAAAT
26807 GAAAAGATAA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 19 0.32
29 4 0.07
30 15 0.25
31 8 0.13
32 2 0.03
33 12 0.20
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (30 bp):
ATTAAAATAAAAATAATTAAAAGTTGAGTG
Found at i:28372 original size:26 final size:26
Alignment explanation
Indices: 28322--28372 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
28312 TAAAATAAGA
* * *
28322 AATAAGTTTATTCATAAAGTGACATT
1 AATAAGTATATTCACAAAGTAACATT
*
28348 AATAAGTATATTCACATAGTAACAT
1 AATAAGTATATTCACAAAGTAACAT
28373 GACTTATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (26 bp):
AATAAGTATATTCACAAAGTAACATT
Found at i:29660 original size:13 final size:13
Alignment explanation
Indices: 29642--29666 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29632 TATTAATATT
29642 AATATAATAATAA
1 AATATAATAATAA
29655 AATATAATAATA
1 AATATAATAATA
29667 CGTTAATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATATAATAATAA
Found at i:30924 original size:14 final size:14
Alignment explanation
Indices: 30905--30939 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
30895 TCACACAAAA
*
30905 CTCCACTAGTAACC
1 CTCCACTAGCAACC
30919 CTCCACTAGCAACC
1 CTCCACTAGCAACC
30933 CTCCACT
1 CTCCACT
30940 TTAGTCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.20
Consensus pattern (14 bp):
CTCCACTAGCAACC
Found at i:31844 original size:20 final size:20
Alignment explanation
Indices: 31819--31870 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
31809 ACGCGATCCC
31819 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
31839 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
31859 CCAAAATCGCAA
1 CCAGAATCGCAA
31871 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:31887 original size:21 final size:20
Alignment explanation
Indices: 31860--31958 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
31850 AATCAGTTTC
31860 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
31881 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
31902 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
31922 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
31943 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
31959 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:31987 original size:20 final size:20
Alignment explanation
Indices: 31925--32119 Score: 205
Period size: 20 Copynumber: 9.7 Consensus size: 20
31915 CGATTTTCCA
* ** *
31925 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
31945 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
31965 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
31985 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
32005 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
32025 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
32045 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
** * *
32065 AAATCGCAAC-AATAATACAT
1 AAATCGCAACGCGT-ATCCGT
32085 AAAATCGCAACGCGTATCCCGT
1 -AAATCGCAACGCGTAT-CCGT
32107 AAATCGCAACGCG
1 AAATCGCAACGCG
32120 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 112 0.78
21 27 0.19
22 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:32009 original size:60 final size:60
Alignment explanation
Indices: 31925--32119 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
31915 CGATTTTCCA
* ** * *
31925 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
31985 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* ***
32045 ATATCGCAACGCGTATCCGTAAATCGCAACAATAATACATAAAATCGCAACGCGTATCCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTAT-CCGT
32107 AAATCGCAACGCG
1 AAATCGCAACGCG
32120 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 22, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 15 0.14
62 16 0.14
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:32540 original size:33 final size:33
Alignment explanation
Indices: 32501--32571 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
32491 TTCACTTAGA
*
32501 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
32534 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
32567 TTTCA
1 TTTCA
32572 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:32711 original size:14 final size:14
Alignment explanation
Indices: 32692--32746 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
32682 AGAATGACTG
32692 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
32706 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
32725 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
32739 TCGCAACG
1 TCGCAACG
32747 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:32759 original size:33 final size:33
Alignment explanation
Indices: 32692--32762 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
32682 AGAATGACTG
***
32692 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
32725 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
32758 TCGCA
1 TCGCA
32763 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:32780 original size:19 final size:19
Alignment explanation
Indices: 32758--32855 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
32748 GAAACCAAAA
*
32758 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
32777 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
32791 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
32810 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
32824 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
32843 TCGCGTTGCGATT
1 TCGCGTTGCGATT
32856 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:32799 original size:14 final size:14
Alignment explanation
Indices: 32780--32869 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
32770 TTTCATTTCG
32780 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
32794 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
32813 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
32827 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
32844 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
32860 CGTTGCGATT
1 CGTTGCGATT
32870 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:32805 original size:33 final size:33
Alignment explanation
Indices: 32763--32877 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
32753 CAAAATCGCA
32763 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
32796 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
32829 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
32862 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
32878 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:34882 original size:184 final size:186
Alignment explanation
Indices: 34573--35044 Score: 921
Period size: 184 Copynumber: 2.5 Consensus size: 186
34563 TAGATTGCTT
34573 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
34638 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
34703 GTGTATTCTTTAACACTGTGAAATA-TA-TTGTCGTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCGTTGTTTTGTCTTTTGGTTGAA
34757 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
34822 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
34887 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCGTTGTTTTGTCTTTTGGTTGAA
34943 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35008 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
35045 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
184 155 0.54
185 2 0.01
186 128 0.45
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCGTTGTTTTGTCTTTTGGTTGAA
Found at i:34889 original size:93 final size:93
Alignment explanation
Indices: 34573--35044 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
34563 TAGATTGCTT
34573 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
34638 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
34666 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
34730 -TTGTCGTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
34757 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
34822 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
34850 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
34915 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
34943 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
35008 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
35036 AGTAAATTT
1 AGTAAATTT
35045 ATCCATTCAA
Statistics
Matches: 375, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 88 0.23
92 4 0.01
93 283 0.75
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:35128 original size:19 final size:19
Alignment explanation
Indices: 35088--35222 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
35078 TAGTTTACTT
* *
35088 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
35108 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
35127 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
35146 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
35160 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
35179 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
**
35193 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
35212 TCGCAATGCGA
1 TCGCAACGCGA
35223 TTTTCATTTC
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 19 0.20
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 50 0.53
20 13 0.14
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:35167 original size:33 final size:32
Alignment explanation
Indices: 35124--35217 Score: 152
Period size: 33 Copynumber: 2.9 Consensus size: 32
35114 CGCGAAACCA
35124 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAATGAAAATCGCAACGAC
**
35156 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAATGAAAATCGCAACGAC
35189 AAGATCGCAACGCGAAATGAAAATCGCAA
1 AA-ATCGCAACGCGAAATGAAAATCGCAA
35218 TGCGATTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:35214 original size:52 final size:51
Alignment explanation
Indices: 35088--35222 Score: 141
Period size: 52 Copynumber: 2.6 Consensus size: 51
35078 TAGTTTACTT
*
35088 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
35140 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAATGA-A-AATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
* *
35193 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAACACGAAATGAAAATCGCAACGCGA
35223 TTTTCATTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
50 4 0.06
51 6 0.09
52 44 0.66
53 4 0.06
54 7 0.10
55 2 0.03
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.10
Consensus pattern (51 bp):
TCGCAACACGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:35234 original size:19 final size:19
Alignment explanation
Indices: 35218--35346 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
35208 AAAATCGCAA
35218 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
35237 TGCGA--TTC-TTT--CGT
1 TGCGATTTTCATTTCGCGT
*
35251 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
*
35270 TGCGA--TTC-TGT--CGT
1 TGCGATTTTCATTTCGCGT
35284 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
35303 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
35322 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
35342 TGCGA
1 TGCGA
35347 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.17
16 11 0.12
17 11 0.12
19 41 0.46
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:35253 original size:14 final size:14
Alignment explanation
Indices: 35234--35290 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35224 TTTCATTTCG
35234 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
35248 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
35265 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
35281 CGTTGCGATT
1 CGTTGCGATT
35291 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:35260 original size:33 final size:33
Alignment explanation
Indices: 35218--35309 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
35208 AAAATCGCAA
*
35218 TGCGATTTTCATTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
35251 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
35284 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
35310 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:37268 original size:14 final size:14
Alignment explanation
Indices: 37249--37284 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
37239 ATTGTTTAAT
37249 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
37263 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
37277 TGATTTGT
1 TGATTTGT
37285 GTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:37407 original size:19 final size:19
Alignment explanation
Indices: 37391--37492 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
37381 AAAAATGACT
37391 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
37410 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37429 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
37443 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
37462 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
37482 ATCGCAATGCG
1 ATCGCAATGCG
37493 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:37541 original size:33 final size:33
Alignment explanation
Indices: 37499--37826 Score: 217
Period size: 33 Copynumber: 9.5 Consensus size: 33
37489 TGCGTTTATA
37499 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
37532 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
37568 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
* *
37603 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTC
*
37641 ATTTCGCATTGCGATTATGTCGGTT-CGATTTTC
1 ATTTCGCATTGCGATTATCTC-GTTGCGATTTTC
*
37674 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
37714 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
37745 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* * *
37778 ATTTCGCGTTGCGATTTTCAT-GTTGGGATTTTC
1 ATTTCGCATTGCGATTATC-TCGTTGCGATTTTC
*
37811 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
37827 GTATTTTCCG
Statistics
Matches: 251, Mismatches: 20, Indels: 48
0.79 0.06 0.15
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 126 0.50
34 3 0.01
35 19 0.08
36 20 0.08
37 4 0.02
38 53 0.21
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:37545 original size:19 final size:19
Alignment explanation
Indices: 37521--37826 Score: 356
Period size: 19 Copynumber: 17.4 Consensus size: 19
37511 GATTATCTCG
37521 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
37540 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
37559 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
37573 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
37592 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
37611 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
37630 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
37649 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
37664 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
37682 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
37701 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
37715 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
37734 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
37753 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
37767 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
37786 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
37800 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
37819 TTGCGATT
1 TTGCGATT
37827 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 13, Indels: 50
0.80 0.04 0.16
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.12
17 31 0.12
18 2 0.01
19 151 0.61
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:37596 original size:71 final size:71
Alignment explanation
Indices: 37521--37760 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
37511 GATTATCTCG
37521 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
37586 TTCGCA
66 TTCGCA
* *
37592 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
* *
37655 TT-ATGTCG-G
61 TTCATTTCGCA
*
37664 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
37728 TTCGCA
66 TTCGCA
37734 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
37761 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 6 0.04
68 6 0.04
69 7 0.05
70 2 0.01
71 107 0.71
72 2 0.01
73 7 0.05
74 7 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:37826 original size:52 final size:52
Alignment explanation
Indices: 37521--37798 Score: 327
Period size: 52 Copynumber: 5.2 Consensus size: 52
37511 GATTATCTCG
*
37521 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC---TCGCGTTGCGATTTTCATTTCGCA
* *
37573 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC---TCGCGTTGCGATTTTCATTTCGCA
* *
37630 TTGCGATTTTAATTTCGCATTGCGATTAT-GTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCG-C-GTTGCGATTTTCATTTCGCA
*
37682 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATTTTCATTTCGCA
* *
37734 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATTTTCATTTCGCA
37786 TTGCGATTTTCAT
1 TTGCGATTTTCAT
37799 GTTGGGATTT
Statistics
Matches: 209, Mismatches: 8, Indels: 18
0.89 0.03 0.08
Matches are distributed among these distances:
51 4 0.02
52 169 0.81
53 2 0.01
54 3 0.01
55 7 0.03
57 24 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCGCGTTGCGATTTTCATTTCGCA
Found at i:40362 original size:24 final size:24
Alignment explanation
Indices: 40328--40374 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40318 CTGAAACATC
40328 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
40352 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
40375 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:41073 original size:20 final size:20
Alignment explanation
Indices: 41045--41413 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
41035 AAATTTCAGT
* * * *
41045 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
41065 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
41085 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
41105 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
41125 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
41145 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
41165 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
41185 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
41205 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
41225 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
41245 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
41265 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
41285 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
41305 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
41325 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
41345 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
41365 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
41385 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
41405 GTTGCGATT
1 GTTGCGATT
41414 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:47212 original size:3 final size:3
Alignment explanation
Indices: 47199--47235 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
47189 TTTTTTATCG
*
47199 TTA TT- TTA TTA TTA TTA TTA TT- TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
47236 CATTTTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:47219 original size:17 final size:17
Alignment explanation
Indices: 47199--47235 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
47189 TTTTTTATCG
*
47199 TTATTTTATTATTATTA
1 TTATTTTATTATTAATA
47216 TTATTTTATTATTAATA
1 TTATTTTATTATTAATA
47233 TTA
1 TTA
47236 CATTTTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTTTATTATTAATA
Found at i:47626 original size:25 final size:25
Alignment explanation
Indices: 47598--47647 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
47588 CATTAAAATA
47598 GTCCTAAATCCCTAAATATTCGGCT
1 GTCCTAAATCCCTAAATATTCGGCT
47623 GTCCTAAATCCCTAAATATTCGGCT
1 GTCCTAAATCCCTAAATATTCGGCT
47648 TTTGGTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (25 bp):
GTCCTAAATCCCTAAATATTCGGCT
Found at i:55141 original size:2 final size:2
Alignment explanation
Indices: 55123--55206 Score: 140
Period size: 2 Copynumber: 44.0 Consensus size: 2
55113 GGAATTCAAA
55123 AT AT -T AT AT AT -T A- 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
55162 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
55203 AT AT
1 AT AT
55207 CTGAAGCTCA
Statistics
Matches: 78, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
1 4 0.05
2 74 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:55388 original size:4 final size:4
Alignment explanation
Indices: 55379--55432 Score: 99
Period size: 4 Copynumber: 13.5 Consensus size: 4
55369 GAGAAAGTAT
*
55379 ATAC ATAC ATAC ACAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
55427 ATAC AT
1 ATAC AT
55433 CCATGATACA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:56508 original size:28 final size:29
Alignment explanation
Indices: 56477--56552 Score: 111
Period size: 28 Copynumber: 2.7 Consensus size: 29
56467 ACAGTTTCTC
56477 TTGAA-AAAAATCTTTGAGTTTATTCCTT
1 TTGAATAAAAATCTTTGAGTTTATTCCTT
* *
56505 TTGAATAAAAATCTTGGAGTTTGTTCC-T
1 TTGAATAAAAATCTTTGAGTTTATTCCTT
*
56533 TTGAATAAATATCTTTGAGT
1 TTGAATAAAAATCTTTGAGT
56553 CGTTCTTTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 24 0.56
29 19 0.44
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (29 bp):
TTGAATAAAAATCTTTGAGTTTATTCCTT
Found at i:56577 original size:24 final size:25
Alignment explanation
Indices: 56481--56577 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 25
56471 TTTCTCTTGA
**
56481 AAAAAATCTTTGAGTTTATTCCTTTTG
1 AAAAAATCTTTGAG-TCGTTCC-TTTG
* *
56508 AATAAAAATCTTGGAGTTTGTTCCTTTG
1 -A-AAAAATCTTTGAG-TCGTTCCTTTG
*
56536 AATAAATATCTTTGAGTCGTTCTTTTG
1 AA-AAA-ATCTTTGAGTCGTTCCTTTG
56563 -AAAAATCTTTGAGTC
1 AAAAAATCTTTGAGTC
56578 TATTTATTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
24 11 0.18
25 3 0.05
26 2 0.03
27 13 0.21
28 13 0.21
29 19 0.31
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.44
Consensus pattern (25 bp):
AAAAAATCTTTGAGTCGTTCCTTTG
Found at i:56677 original size:51 final size:51
Alignment explanation
Indices: 56586--56686 Score: 152
Period size: 49 Copynumber: 2.0 Consensus size: 51
56576 TCTATTTATT
56586 TGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTG-CTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
56637 TGAAACAAAGTTTG-TCTCTTGAGACAATTTTGTGAAAAAAAATCTTTGAG
1 TGAAACAAAGTTTGCTCTCTTGAGACAATTTCGTG--AAAAAATCTTTGAG
56687 ATTGTTTCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
49 19 0.41
51 14 0.30
52 13 0.28
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (51 bp):
TGAAACAAAGTTTGCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:56707 original size:30 final size:30
Alignment explanation
Indices: 56671--56796 Score: 112
Period size: 30 Copynumber: 4.1 Consensus size: 30
56661 CAATTTTGTG
56671 AAAAAAAATCTTTGAGATTGTTTCTTTTGA
1 AAAAAAAATCTTTGAGATTGTTTCTTTTGA
* *
56701 AAAAAAAATCTTTGAGTTTGTTTC-TTGGA
1 AAAAAAAATCTTTGAGATTGTTTCTTTTGA
** * *
56730 AACAAAATTTTTCTCTCTTAAGATAGTTTCTTTTGA
1 AA-AAAA----AATCT-TTGAGATTGTTTCTTTTGA
* *
56766 AACAAAAATCTTTGAGTTTGTTT-TTTTGA
1 AAAAAAAATCTTTGAGATTGTTTCTTTTGA
56795 AA
1 AA
56797 CAGATTTTGT
Statistics
Matches: 75, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
29 14 0.19
30 36 0.48
31 3 0.04
34 3 0.04
35 13 0.17
36 6 0.08
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (30 bp):
AAAAAAAATCTTTGAGATTGTTTCTTTTGA
Found at i:56766 original size:65 final size:64
Alignment explanation
Indices: 56685--56841 Score: 235
Period size: 65 Copynumber: 2.4 Consensus size: 64
56675 AAAATCTTTG
* *
56685 AGATTGTTTCTTTTGAAAAAAAAATCTTTGAGTTTGTTTCTTGGAAACAAAATTTT-TCTCTCTT
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTGGAAAC-AAATTTTGTCTCTC-T
56749 A
64 A
* * *
56750 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTTTTTGAAACAGATTTTGTCTCTCTA
1 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTGGAAACAAATTTTGTCTCTCTA
*
56814 AGATAATTTCTTTTGAAACAAAAATCTT
1 AGATAGTTTCTTTTGAAACAAAAATCTT
56842 GAATATGTTT
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
64 35 0.41
65 50 0.59
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (64 bp):
AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTGGAAACAAATTTTGTCTCTCTA
Found at i:57151 original size:59 final size:59
Alignment explanation
Indices: 57072--57186 Score: 169
Period size: 59 Copynumber: 1.9 Consensus size: 59
57062 GAGATCCATC
* *
57072 TTGAGTCTGTTTCTTTTGAAACAAAATTTATCTCTTAAAGACAATTTCTTTTGAAAAAAT
1 TTGAGTCTGTTTCCTTTGAAACAAAATTTATCTC-TAAAGACAACTTCTTTTGAAAAAAT
* **
57132 TTGAGT-TGTTTCCTTTGAAACAAAATTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 TTGAGTCTGTTTCCTTTGAAACAAAATTTATCTCTAAAGACAACTTCTTTTGAAAA
57187 TACCCACCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 19 0.38
59 25 0.50
60 6 0.12
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (59 bp):
TTGAGTCTGTTTCCTTTGAAACAAAATTTATCTCTAAAGACAACTTCTTTTGAAAAAAT
Found at i:57865 original size:28 final size:28
Alignment explanation
Indices: 57815--57868 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
57805 TCAAAATCCA
* *
57815 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
57843 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
57869 CATTATCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:58450 original size:25 final size:28
Alignment explanation
Indices: 58420--58470 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
58410 CCGGGTTTTT
58420 TTATCG-TATTTTA-TATT-ATATTATA
1 TTATCGTTATTTTATTATTAATATTATA
58445 TTATCGTTATTTTATTATTAATATTA
1 TTATCGTTATTTTATTATTAATATTA
58471 CATTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 7 0.30
27 4 0.17
28 6 0.26
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (28 bp):
TTATCGTTATTTTATTATTAATATTATA
Found at i:58857 original size:24 final size:25
Alignment explanation
Indices: 58825--58873 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
58815 ATTAAAAATA
58825 GTCCTAAAT-CCTAAATATTCGGCT
1 GTCCTAAATCCCTAAATATTCGGCT
58849 GTCCTAAATCCCTAAATATTCGGCT
1 GTCCTAAATCCCTAAATATTCGGCT
58874 TTGGTATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (25 bp):
GTCCTAAATCCCTAAATATTCGGCT
Found at i:61943 original size:30 final size:31
Alignment explanation
Indices: 61909--61970 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
61899 CAAACACATG
61909 AGATACTAATGCTATTG-TACGTAAAAGGTC
1 AGATACTAATGCTATTGATACGTAAAAGGTC
*
61939 AGATACTAATGTTATTGAAATACGTAAAAGGT
1 AGATACTAATGCTATTG--ATACGTAAAAGGT
61971 AATGCTTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 16 0.57
33 12 0.43
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (31 bp):
AGATACTAATGCTATTGATACGTAAAAGGTC
Found at i:62971 original size:18 final size:19
Alignment explanation
Indices: 62944--62979 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
62934 CCTCTTTCAC
*
62944 CATCTTAAA-GTAAATAAG
1 CATCTAAAAGGTAAATAAG
62962 CATCTAAAAGGTAAATAA
1 CATCTAAAAGGTAAATAA
62980 CGGAAAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (19 bp):
CATCTAAAAGGTAAATAAG
Done.