Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 37
Found at i:3470396 original size:3 final size:3
Alignment explanation
Indices: 3470388--3470419 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3470378 AAGATGAACG
3470388 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3470420 TCAGAGCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3474454 original size:22 final size:22
Alignment explanation
Indices: 3474429--3474477 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
3474419 ACGGCGACAA
3474429 CCGTCCCCATCTCCGACGAAAT
1 CCGTCCCCATCTCCGACGAAAT
* *
3474451 CCGTCCTCATCTCCGGCGAAAT
1 CCGTCCCCATCTCCGACGAAAT
3474473 CCGTC
1 CCGTC
3474478 TATCTCCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
CCGTCCCCATCTCCGACGAAAT
Found at i:3474859 original size:20 final size:20
Alignment explanation
Indices: 3474826--3474954 Score: 110
Period size: 20 Copynumber: 6.8 Consensus size: 20
3474816 AAATCGCAAC
*
3474826 GCGA-TTTTAGTTTCGCGTT
1 GCGATTTTTATTTTCGCGTT
3474845 GCGATTTTTATTTTCGCGTT
1 GCGATTTTTATTTTCGCGTT
*
3474865 GCGA----TA-TTT-GTGTT
1 GCGATTTTTATTTTCGCGTT
*
3474879 GCGATTTTCTAGTTTCGCGTT
1 GCGATTTT-TATTTTCGCGTT
* **
3474900 GCGATTTTAATTTTTTCGTT
1 GCGATTTTTATTTTCGCGTT
* *
3474920 GAGATTTTCATTTTCGCGTT
1 GCGATTTTTATTTTCGCGTT
* *
3474940 ACGATTTTCATTTTC
1 GCGATTTTTATTTTC
3474955 AGAAACTACT
Statistics
Matches: 89, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
14 8 0.09
15 3 0.03
16 2 0.02
19 6 0.07
20 58 0.65
21 12 0.13
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (20 bp):
GCGATTTTTATTTTCGCGTT
Found at i:3477119 original size:21 final size:21
Alignment explanation
Indices: 3477095--3477158 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
3477085 CATTCAATAT
* *
3477095 GCCCCTCTCATCATTGAAGAG
1 GCCCCTCTCATCGTTCAAGAG
* *
3477116 GCCCCTCCCACCGTTCAAGAG
1 GCCCCTCTCATCGTTCAAGAG
* *
3477137 GCCTCTGTCATCGTTCAAGAG
1 GCCCCTCTCATCGTTCAAGAG
3477158 G
1 G
3477159 TCTCGCCCAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.20, C:0.36, G:0.22, T:0.22
Consensus pattern (21 bp):
GCCCCTCTCATCGTTCAAGAG
Found at i:3477133 original size:42 final size:42
Alignment explanation
Indices: 3477095--3477178 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
3477085 CATTCAATAT
* *
3477095 GCCCCTCTCATCATTGAAGAGGCCCCTCCCACCGTTCAAGAG
1 GCCCCTCTCATCATTCAAGAGGCCCCGCCCACCGTTCAAGAG
* * * * *
3477137 GCCTCTGTCATCGTTCAAGAGGTCTCGCCCACCGTTCAAGAG
1 GCCCCTCTCATCATTCAAGAGGCCCCGCCCACCGTTCAAGAG
3477179 CCCGATTCAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.20, C:0.37, G:0.21, T:0.21
Consensus pattern (42 bp):
GCCCCTCTCATCATTCAAGAGGCCCCGCCCACCGTTCAAGAG
Found at i:3477172 original size:21 final size:22
Alignment explanation
Indices: 3477111--3477178 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
3477101 CTCATCATTG
*
3477111 AAGAGGCCCCT-CCCACCGTTC
1 AAGAGGCCTCTGCCCACCGTTC
* *
3477132 AAGAGGCCTCTG-TCATCGTTC
1 AAGAGGCCTCTGCCCACCGTTC
*
3477153 AAGAGGTCTC-GCCCACCGTTC
1 AAGAGGCCTCTGCCCACCGTTC
3477174 AAGAG
1 AAGAG
3477179 CCCGATTCAC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 1 0.03
21 38 0.97
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.19
Consensus pattern (22 bp):
AAGAGGCCTCTGCCCACCGTTC
Found at i:3478758 original size:20 final size:20
Alignment explanation
Indices: 3478733--3478815 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 20
3478723 AAGGTACACT
*
3478733 TTCGCAACACGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
** *
3478753 TTCGCATTGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
* * *
3478773 TTCACAAC-CTTAAAGTTAAA
1 TTCGCAACGC-GAAAGTCAAA
3478793 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
3478813 TTC
1 TTC
3478816 TCGTTGCGAT
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:3481455 original size:24 final size:24
Alignment explanation
Indices: 3481421--3481488 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
3481411 CTGAAACATC
3481421 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
3481445 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
3481469 ATCAAATTTCGAATATTGAC
1 ATCAAAATCCGAGTATTGAC
3481489 TAGTACTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:3482476 original size:21 final size:20
Alignment explanation
Indices: 3482410--3482483 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
3482400 AACTAAAACC
*
3482410 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
* *
3482429 TGTTGCGAATTCGAAAATCG
1 TGTTGCGAATTTGAAATTCG
*
3482449 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTC-G
3482470 TGTTGCGAATTTGA
1 TGTTGCGAATTTGA
3482484 CTTCTTTGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
19 10 0.22
20 22 0.48
21 14 0.30
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:3482528 original size:21 final size:20
Alignment explanation
Indices: 3482491--3482558 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
3482481 TGACTTCTTT
3482491 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
3482511 GTTGCGATTTTCCAAATTCGC
1 GTTGCGA-TTTACAAATTCGC
**
3482532 AATGCGATTTACATAA-TCGC
1 GTTGCGATTTACA-AATTCGC
3482552 GTTGCGA
1 GTTGCGA
3482559 ATTTGGAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 21 0.52
21 19 0.47
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:3485083 original size:2 final size:2
Alignment explanation
Indices: 3485078--3485148 Score: 126
Period size: 2 Copynumber: 36.0 Consensus size: 2
3485068 TTATCTCTTA
3485078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3485120 AT AT AT AT AT AT AT AT A- AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3485149 TACTTTACAT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3485771 original size:20 final size:20
Alignment explanation
Indices: 3485748--3485799 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3485738 AACGCGATCC
3485748 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
3485768 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
3485788 CCAAAATCGCAA
1 CCAGAATCGCAA
3485800 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:3485816 original size:21 final size:20
Alignment explanation
Indices: 3485789--3485888 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
3485779 AATCAGTTTC
3485789 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
3485810 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3485831 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3485851 CCAAAATCGCAACGCGAATATG
1 -CAAAATCGCAACGCG-ATTTT
*
3485873 AAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3485889 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 7
0.71 0.20 0.08
Matches are distributed among these distances:
20 2 0.03
21 54 0.92
22 3 0.05
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3485889 original size:21 final size:20
Alignment explanation
Indices: 3485853--3485907 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
3485843 GCGATTTTCC
* *
3485853 AAAATCGCAACGCGAATATGA
1 AAAATCGCAACGCGAACA-CA
3485874 AAAATCGCAACGCGAACACA
1 AAAATCGCAACGCGAACACA
*
3485894 TAAATCGCAACGCG
1 AAAATCGCAACGCG
3485908 TATCCGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.45, C:0.25, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAACACA
Found at i:3485900 original size:20 final size:20
Alignment explanation
Indices: 3485875--3486048 Score: 127
Period size: 20 Copynumber: 8.7 Consensus size: 20
3485865 CGAATATGAA
3485875 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* *
3485895 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
3485915 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
3485935 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * * *
3485955 AAATCGCAATGCTTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
3485975 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
3485995 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
3486015 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
3486036 AAATCGCAACGCG
1 AAATCGCAACGCG
3486049 ATATTTAAAG
Statistics
Matches: 128, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
19 2 0.02
20 109 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:3485938 original size:40 final size:40
Alignment explanation
Indices: 3485894--3486046 Score: 209
Period size: 40 Copynumber: 3.8 Consensus size: 40
3485884 CGCGAACACA
3485894 TAAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGAT-TATCCG
** * *
3485934 TAAATCGCAACGCGTATGGGTAAATCGCAATGCTTATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGATTATCCG
* * * *
3485974 TATATCGCAACGCGTATCCGTAAATCGCAACGATAATACA
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGATTATCCG
3486014 TAAAATCGCAACGCGTATCCGTAAATCGCAACG
1 T-AAATCGCAACGCGTATCCGTAAATCGCAACG
3486047 CGATATTTAA
Statistics
Matches: 99, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
40 68 0.69
41 31 0.31
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (40 bp):
TAAATCGCAACGCGTATCCGTAAATCGCAACGATTATCCG
Found at i:3485945 original size:60 final size:60
Alignment explanation
Indices: 3485875--3486048 Score: 240
Period size: 60 Copynumber: 2.9 Consensus size: 60
3485865 CGAATATGAA
* *
3485875 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
* *** * * *
3485935 AAATCGCAACGCGTATGGGTAAATCGCAATGCTTATCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
**
3485995 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCG
3486049 ATATTTAAAG
Statistics
Matches: 95, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 65 0.68
61 30 0.32
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:3486469 original size:33 final size:33
Alignment explanation
Indices: 3486430--3486500 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3486420 TTCACTTAGA
*
3486430 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3486463 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3486496 TTTCA
1 TTTCA
3486501 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:3486640 original size:14 final size:14
Alignment explanation
Indices: 3486621--3486675 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3486611 AGAATGACTG
3486621 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
3486635 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
3486654 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
3486668 TCGCAACG
1 TCGCAACG
3486676 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:3486688 original size:33 final size:33
Alignment explanation
Indices: 3486621--3486691 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3486611 AGAATGACTG
***
3486621 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3486654 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
3486687 TCGCA
1 TCGCA
3486692 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:3486709 original size:19 final size:19
Alignment explanation
Indices: 3486687--3486784 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3486677 GAAACCAAAA
*
3486687 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3486706 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3486720 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3486739 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
3486753 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
3486772 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3486785 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:3486728 original size:14 final size:14
Alignment explanation
Indices: 3486709--3486798 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3486699 TTTCATTTCG
3486709 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3486723 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3486742 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3486756 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
3486773 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
3486789 CGTTGCGATT
1 CGTTGCGATT
3486799 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:3486734 original size:33 final size:33
Alignment explanation
Indices: 3486692--3486806 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3486682 CAAAATCGCA
3486692 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3486725 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
3486758 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3486791 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3486807 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:3488818 original size:93 final size:93
Alignment explanation
Indices: 3488505--3488972 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
3488495 TAGATTGCTT
3488505 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATT-TTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3488569 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3488597 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3488661 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3488689 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
3488754 TTTGTCTCTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3488782 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3488847 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3488875 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3488940 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3488968 AGTAA
1 AGTAA
3488973 TTTATCCATT
Statistics
Matches: 372, Mismatches: 2, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
92 136 0.37
93 236 0.63
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3489059 original size:19 final size:19
Alignment explanation
Indices: 3489019--3489147 Score: 98
Period size: 19 Copynumber: 7.3 Consensus size: 19
3489009 TAGTTTACTT
* *
3489019 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3489039 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3489058 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3489077 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
* **
3489091 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3489110 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3489124 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3489143 TCGCA
1 TCGCA
3489148 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3489102 original size:33 final size:32
Alignment explanation
Indices: 3489055--3489147 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
3489045 CGCGAAACCA
3489055 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAATGAAAATCGCAACGAC
*
3489087 AGAATCGCAATGCGAAATGAAAATCGCAACGAC
1 A-AATCGCAACGCGAAATGAAAATCGCAACGAC
**
3489120 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAATGAAAATCGCA
3489148 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (32 bp):
AAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:3489165 original size:19 final size:19
Alignment explanation
Indices: 3489143--3489277 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3489133 GAAACCAAAA
*
3489143 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3489162 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3489178 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3489195 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3489211 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3489228 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3489247 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3489267 TCGTGTTGCGA
1 TCGCGTTGCGA
3489278 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3489184 original size:14 final size:14
Alignment explanation
Indices: 3489165--3489221 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3489155 TTTCATTTCG
3489165 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3489179 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3489196 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
3489212 CGTTGCGATT
1 CGTTGCGATT
3489222 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:3489190 original size:33 final size:33
Alignment explanation
Indices: 3489148--3489240 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3489138 CAAAATCGCA
*
3489148 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
3489181 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3489214 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3489241 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3491129 original size:38 final size:38
Alignment explanation
Indices: 3491086--3491158 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
3491076 AATTGATTGT
*
3491086 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
3491124 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
3491159 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:3491145 original size:19 final size:19
Alignment explanation
Indices: 3491081--3491145 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
3491071 AGTTTAATTG
*
3491081 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
3491100 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
3491118 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
3491138 ATTGATTT
1 ATTGATTT
3491146 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:3491159 original size:14 final size:14
Alignment explanation
Indices: 3491140--3491175 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3491130 ATTGTTTAAT
3491140 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3491154 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3491168 TGATTTGT
1 TGATTTGT
3491176 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:3491304 original size:19 final size:19
Alignment explanation
Indices: 3491288--3491389 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3491278 AAAAATGACT
3491288 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3491307 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3491326 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3491340 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3491359 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3491379 ATCGCAATGCG
1 ATCGCAATGCG
3491390 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:3491442 original size:19 final size:19
Alignment explanation
Indices: 3491418--3491724 Score: 351
Period size: 19 Copynumber: 17.4 Consensus size: 19
3491408 GATTATCTCG
3491418 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3491437 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3491456 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
3491470 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3491489 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3491508 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
3491527 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3491546 TTGCGA--TT-ATGTCTG--
1 TTGCGATTTTCATTTC-GCA
3491561 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3491579 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3491598 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3491612 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3491631 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3491650 TTGCGATTCTCA---CG--
1 TTGCGATTTTCATTTCGCA
3491664 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3491684 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
3491698 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3491717 TTGCGATT
1 TTGCGATT
3491725 GTATTTTCCG
Statistics
Matches: 249, Mismatches: 11, Indels: 56
0.79 0.03 0.18
Matches are distributed among these distances:
14 37 0.15
15 2 0.01
16 26 0.10
17 23 0.09
18 5 0.02
19 144 0.58
20 12 0.05
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3491493 original size:71 final size:71
Alignment explanation
Indices: 3491418--3491657 Score: 348
Period size: 71 Copynumber: 3.4 Consensus size: 71
3491408 GATTATCTCG
3491418 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
3491483 TTCGCA
66 TTCGCA
* *
3491489 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
*
3491552 TT-ATGTCTG--
61 TTCATTTC-GCA
*
3491561 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
3491625 TTCGCA
66 TTCGCA
3491631 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
3491658 CTCACGTTGC
Statistics
Matches: 150, Mismatches: 7, Indels: 24
0.83 0.04 0.13
Matches are distributed among these distances:
66 6 0.04
68 7 0.05
69 6 0.04
70 2 0.01
71 107 0.71
72 2 0.01
73 6 0.04
74 8 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:3491577 original size:142 final size:137
Alignment explanation
Indices: 3491386--3491724 Score: 515
Period size: 142 Copynumber: 2.4 Consensus size: 137
3491376 AAAATCGCAA
3491386 TGCG-TTTATAATTTCGCATTGCGATTA-TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TGCGATTT-TAATTTCGCATTGCGATTATTCT-GTTGCGATTTTCATTTCGCATTGCGATTTTCA
*
3491449 TTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
64 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
*
3491514 TTTTCATTTCGTAT
129 TTCTCA---CG--T
3491528 TGCGATTTTAATTTCGCATTGCGATTATGTCTGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTAT-TCTGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
3491592 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
65 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
3491657 TCTCACGT
130 TCTCACGT
* * *
3491665 TGCGATTTTCATTTCCGCATTGCGATT-TTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATTC-TGTTGCGATTTTCATTTCGCATTGCGATT
3491725 GTATTTTCCG
Statistics
Matches: 186, Mismatches: 5, Indels: 16
0.90 0.02 0.08
Matches are distributed among these distances:
136 2 0.01
137 19 0.10
138 34 0.18
139 2 0.01
142 120 0.65
143 6 0.03
144 3 0.02
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (137 bp):
TGCGATTTTAATTTCGCATTGCGATTATTCTGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
CTCACGT
Found at i:3491658 original size:52 final size:52
Alignment explanation
Indices: 3491418--3491696 Score: 345
Period size: 52 Copynumber: 5.2 Consensus size: 52
3491408 GATTATCTCG
*
3491418 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
3491470 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
3491527 TTGCGATTTTAATTTCGCATTGCGATTATGTCTGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
3491579 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
3491631 TTGCGATTTTCATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
3491684 TTGCGATTTTCAT
1 TTGCGATTTTCAT
3491697 GTTGGGATTT
Statistics
Matches: 211, Mismatches: 8, Indels: 15
0.90 0.03 0.06
Matches are distributed among these distances:
51 3 0.01
52 151 0.72
53 19 0.09
54 6 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:3494046 original size:12 final size:12
Alignment explanation
Indices: 3494029--3494053 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3494019 TCTTCGGGGA
3494029 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3494041 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3494053 C
1 C
3494054 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3494262 original size:24 final size:24
Alignment explanation
Indices: 3494228--3494274 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3494218 CTGAAACATC
3494228 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3494252 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3494275 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:3494976 original size:20 final size:20
Alignment explanation
Indices: 3494948--3495336 Score: 480
Period size: 20 Copynumber: 19.4 Consensus size: 20
3494938 AAATTTCAGT
* * * *
3494948 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3494968 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
3494988 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3495008 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3495028 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3495048 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3495068 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3495088 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3495108 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3495128 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
3495148 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3495168 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3495188 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
3495208 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
**
3495228 GTTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
3495248 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
3495268 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3495288 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
3495308 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
3495328 GTTGCGATT
1 GTTGCGATT
3495337 ATGGAAAATC
Statistics
Matches: 329, Mismatches: 32, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
19 5 0.02
20 319 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:3501273 original size:21 final size:21
Alignment explanation
Indices: 3501240--3501287 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3501230 TCTTTGAAAG
* * *
3501240 AAAACTTGGAAGGCTCCAATC
1 AAAACTTGAAAGGATCAAATC
*
3501261 AAAAGTTGAAAGGATCAAATC
1 AAAACTTGAAAGGATCAAATC
3501282 ATAAAC
1 A-AAAC
3501288 CCAAGGACCA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (21 bp):
AAAACTTGAAAGGATCAAATC
Found at i:3502670 original size:28 final size:26
Alignment explanation
Indices: 3502620--3502677 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
3502610 TCTTTTGTCT
*
3502620 TAAATTATTTTTGTCCTATTTTACCC
1 TAAATTATTTTTGTCCTAATTTACCC
* *
3502646 TAAATTACTTTTTTGTTCTAATTTACTC
1 TAAATTA--TTTTTGTCCTAATTTACCC
3502674 TAAA
1 TAAA
3502678 AATTTTCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 7 0.26
28 20 0.74
ACGTcount: A:0.28, C:0.16, G:0.03, T:0.53
Consensus pattern (26 bp):
TAAATTATTTTTGTCCTAATTTACCC
Found at i:3506992 original size:11 final size:11
Alignment explanation
Indices: 3506976--3507000 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3506966 ATTTCTTTAT
3506976 TGTCTATACAA
1 TGTCTATACAA
3506987 TGTCTATACAA
1 TGTCTATACAA
3506998 TGT
1 TGT
3507001 ATTACAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (11 bp):
TGTCTATACAA
Found at i:3509929 original size:2 final size:2
Alignment explanation
Indices: 3509922--3509976 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
3509912 AGATTTTAAA
3509922 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3509964 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
3509977 GAAATCCAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3518454 original size:23 final size:23
Alignment explanation
Indices: 3518424--3518467 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3518414 TTTCAATAAG
*
3518424 TCTGTCTGTATGACACGTTTTGC
1 TCTGTCTGTATGACACATTTTGC
3518447 TCTGTCTGTATGACACATTTT
1 TCTGTCTGTATGACACATTTT
3518468 CCTATGCCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (23 bp):
TCTGTCTGTATGACACATTTTGC
Found at i:3521338 original size:17 final size:15
Alignment explanation
Indices: 3521310--3521379 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 15
3521300 TTATATTACA
3521310 TTTAAAAATATAATT
1 TTTAAAAATATAATT
3521325 TTTAAAAATTTATAATT
1 TTTAAAAA--TATAATT
* * * *
3521342 ATCAATAATGT-ATT
1 TTTAAAAATATAATT
*
3521356 TTTAATAATATAATT
1 TTTAAAAATATAATT
*
3521371 TTAAAAAAT
1 TTTAAAAAT
3521380 CTAAAATTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
14 11 0.26
15 20 0.47
17 12 0.28
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (15 bp):
TTTAAAAATATAATT
Found at i:3521404 original size:46 final size:46
Alignment explanation
Indices: 3521310--3521405 Score: 111
Period size: 46 Copynumber: 2.1 Consensus size: 46
3521300 TTATATTACA
* * * * **
3521310 TTTAAAAATATAATTTTTAAAAATTTATAATTATCAATAATGTATT
1 TTTAAAAATATAATTTTAAAAAATCTAAAATTATAAATAACATATT
* *
3521356 TTTAATAATATAATTTTAAAAAATCTAAAATTATAATATAACATTTT
1 TTTAAAAATATAATTTTAAAAAATCTAAAATTATAA-ATAACATATT
3521403 TTT
1 TTT
3521406 CAAGTAGTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 31 0.76
47 10 0.24
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (46 bp):
TTTAAAAATATAATTTTAAAAAATCTAAAATTATAAATAACATATT
Found at i:3523378 original size:2 final size:2
Alignment explanation
Indices: 3523371--3523396 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3523361 TGATTATAAA
3523371 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
3523397 TCATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3531455 original size:26 final size:26
Alignment explanation
Indices: 3531399--3531456 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
3531389 TAATGTTAAA
* * *
3531399 TAAATTATTTTTATATTATATTTGTT
1 TAAATTTTTTTTATATTACATTTATT
3531425 T-AATTTTTTTTCATA-TACATTTATT
1 TAAATTTTTTTT-ATATTACATTTATT
3531450 TAAATTT
1 TAAATTT
3531457 ATATGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (26 bp):
TAAATTTTTTTTATATTACATTTATT
Found at i:3550772 original size:18 final size:19
Alignment explanation
Indices: 3550740--3550777 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3550730 AGGTTCAATA
3550740 ATTTAATAATAATAT-TTT
1 ATTTAATAATAATATATTT
3550758 ATTT-ATAATATATATATTT
1 ATTTAATAATA-ATATATTT
3550777 A
1 A
3550778 AAATGTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAATAATAATATATTT
Found at i:3566058 original size:131 final size:132
Alignment explanation
Indices: 3565803--3566073 Score: 370
Period size: 131 Copynumber: 2.1 Consensus size: 132
3565793 CAAAAAAAAA
* *
3565803 AAAAAAAACAATATACTCAACTCCACAACAATCAAGGGGATTAAATTCCCTGCTACAAAAATATA
1 AAAATAAACAATATACTCAACTCCACAACAATCAAGGGGATTAAATTCCCTGCTACAAAAATACA
* * *
3565868 TATATTATAAGAGTTGAGGTAGCCTGGCTAAAATATCAAATGCATTGTAACATACATCAAACT-T
66 TATATCAGAAGAGTTGAGGTAGCCTGGCTAAAATATCAAAGGCATTGTAACATACATCAAA-TGT
3565932 AAG
130 AAG
* * ***
3565935 AAAATAAACAATATAAC-CAACTCCACAATAATCAAGGGGTTTAAATTCCCTGCTAGGGAAA-AC
1 AAAATAAACAATAT-ACTCAACTCCACAACAATCAAGGGGATTAAATTCCCTGCTACAAAAATAC
* * *
3565998 ATATATCAGAAGAGTTGGGGTAGCTTGGCTAAAATATCAAAGGCCA-TGTACCATACATCAAATG
65 ATATATCAGAAGAGTTGAGGTAGCCTGGCTAAAATATCAAAGG-CATTGTAACATACATCAAATG
3566062 TAAG
129 TAAG
3566066 AAAATAAA
1 AAAATAAA
3566074 ATAATTAGAC
Statistics
Matches: 123, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
130 1 0.01
131 66 0.54
132 54 0.44
133 2 0.02
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (132 bp):
AAAATAAACAATATACTCAACTCCACAACAATCAAGGGGATTAAATTCCCTGCTACAAAAATACA
TATATCAGAAGAGTTGAGGTAGCCTGGCTAAAATATCAAAGGCATTGTAACATACATCAAATGTA
AG
Found at i:3569097 original size:21 final size:21
Alignment explanation
Indices: 3569071--3569112 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3569061 TAAATTATAA
3569071 TTATTTAATAAATTTTAAAAG
1 TTATTTAATAAATTTTAAAAG
** *
3569092 TTATTTTGTTAATTTTAAAAG
1 TTATTTAATAAATTTTAAAAG
3569113 ACGAATAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
TTATTTAATAAATTTTAAAAG
Found at i:3582190 original size:25 final size:24
Alignment explanation
Indices: 3582162--3582249 Score: 76
Period size: 25 Copynumber: 3.7 Consensus size: 24
3582152 CACCACAGCT
* *
3582162 CGTATAAATTTGCACCGTAGTGCCA
1 CGTAGAAA-TTGCACCGAAGTGCCA
* *
3582187 CGTAGAATTTTGTC-CCGAAG-GACCG
1 CGTAGAA-ATTG-CACCGAAGTG-CCA
3582212 CGTAGAAA-TGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
3582235 CGTAG-AATTGCACCG
1 CGTAGAAATTGCACCG
3582250 TAGTTCCATA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
22 3 0.06
23 22 0.43
24 2 0.04
25 23 0.45
26 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:3582238 original size:23 final size:23
Alignment explanation
Indices: 3582171--3582249 Score: 81
Period size: 23 Copynumber: 3.3 Consensus size: 23
3582161 TCGTATAAAT
*
3582171 TTGCACCGTAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
3582194 TTTTGTC-CCGAAG-GACCGCGTAGAA
1 --TTG-CACCGAAGTG-CCACGTAGAA
*
3582219 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
3582242 TTGCACCG
1 TTGCACCG
3582250 TAGTTCCATA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
22 1 0.02
23 24 0.53
24 2 0.04
25 17 0.38
26 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:3589206 original size:2 final size:2
Alignment explanation
Indices: 3589199--3589243 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3589189 AATTAAAAAT
3589199 TA TA TA TA TA T- 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
3589240 TA TA
1 TA TA
3589244 CTTTTAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3593291 original size:12 final size:11
Alignment explanation
Indices: 3593273--3593310 Score: 60
Period size: 12 Copynumber: 3.5 Consensus size: 11
3593263 AAGCGTAAAT
3593273 TGCAGTAGCAG
1 TGCAGTAGCAG
3593284 TAGCAGTAGCAG
1 T-GCAGTAGCAG
3593296 TGCAGT-GCAG
1 TGCAGTAGCAG
3593306 TGCAG
1 TGCAG
3593311 AAGGCATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.35
11 6 0.23
12 11 0.42
ACGTcount: A:0.26, C:0.18, G:0.37, T:0.18
Consensus pattern (11 bp):
TGCAGTAGCAG
Found at i:3598832 original size:24 final size:21
Alignment explanation
Indices: 3598790--3598833 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3598780 AAATTAAAAT
*
3598790 ATTTAAAATATAAAAAAATTG
1 ATTTAAAAAATAAAAAAATTG
3598811 ATTTAAAACAATAATAATAAATT
1 ATTTAAAA-AATAA-AA-AAATT
3598834 AAGGACGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 2 0.11
24 5 0.26
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTTAAAAAATAAAAAAATTG
Found at i:3599020 original size:22 final size:20
Alignment explanation
Indices: 3598992--3599031 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
3598982 AATTTCGTCC
3598992 TTATATTATATAATATATATAT
1 TTATATTATA-AAT-TATATAT
3599014 TTATATTATAAATTATAT
1 TTATATTATAAATTATAT
3599032 TATATGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATATTATAAATTATATAT
Found at i:3600174 original size:7 final size:7
Alignment explanation
Indices: 3600134--3600195 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
3600124 TCATTACTTA
3600134 TATATAT
1 TATATAT
*
3600141 T-TTTAT
1 TATATAT
3600147 TATTACTAT
1 TA-TA-TAT
*
3600156 TATAGAT
1 TATATAT
3600163 TATATAT
1 TATATAT
3600170 TATATAT
1 TATATAT
* *
3600177 TTTATTT
1 TATATAT
*
3600184 TATATTT
1 TATATAT
3600191 TATAT
1 TATAT
3600196 TTTTAGGTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
6 5 0.11
7 32 0.71
8 3 0.07
9 5 0.11
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (7 bp):
TATATAT
Found at i:3600210 original size:19 final size:21
Alignment explanation
Indices: 3600153--3600218 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3600143 TTATTATTAC
* * *
3600153 TATTATAGATTATATATTATA
1 TATTTTAGGTTATATTTTATA
**
3600174 TATTTTATTTTATATTTTATA
1 TATTTTAGGTTATATTTTATA
*
3600195 T-TTTTAGGTTAT-TTTTATT
1 TATTTTAGGTTATATTTTATA
3600214 TATTT
1 TATTT
3600219 ATTGGTTTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 7 0.19
20 12 0.32
21 18 0.49
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TATTTTAGGTTATATTTTATA
Found at i:3613747 original size:40 final size:40
Alignment explanation
Indices: 3613681--3613759 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
3613671 AGGAAGTTCG
*
3613681 TTTATGTTCGTTTATTTATTAAATGAACGAACATGAACAAGA
1 TTTATGTTCGTTTA--TATTAAATGAACGAACAAGAACAAGA
*
3613723 TTTAGTGTTCGTTTA-ATTAAATGAATGAACAAGAACA
1 TTTA-TGTTCGTTTATATTAAATGAACGAACAAGAACA
3613760 TATGTCTCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 20 0.59
42 4 0.12
43 10 0.29
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (40 bp):
TTTATGTTCGTTTATATTAAATGAACGAACAAGAACAAGA
Found at i:3613796 original size:20 final size:20
Alignment explanation
Indices: 3613771--3613839 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
3613761 ATGTCTCGTT
3613771 CGTTCATTTACGTTCGTGAA
1 CGTTCATTTACGTTCGTGAA
* * **
3613791 CGTTCAGTTATGTTCGTTCATGTT
1 CGTTCA--T-T-TACGTTCGTGAA
*
3613815 CGTTCCTTTACGTTCGTGAA
1 CGTTCATTTACGTTCGTGAA
3613835 CGTTC
1 CGTTC
3613840 GATTATGTTC
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
20 19 0.53
21 1 0.03
22 2 0.06
23 1 0.03
24 13 0.36
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (20 bp):
CGTTCATTTACGTTCGTGAA
Found at i:3613831 original size:44 final size:44
Alignment explanation
Indices: 3613768--3613868 Score: 159
Period size: 44 Copynumber: 2.3 Consensus size: 44
3613758 CATATGTCTC
3613768 GTTCGTTCATTTACGTTCGTGAACGTTC-AGTTATGTTCGTTCAT
1 GTTCGTTCATTTACGTTCGTGAACGTTCGA-TTATGTTCGTTCAT
* *
3613812 GTTCGTTCCTTTACGTTCGTGAACGTTCGATTATGTTCGTTTAT
1 GTTCGTTCATTTACGTTCGTGAACGTTCGATTATGTTCGTTCAT
*
3613856 GTTCATTCATTTA
1 GTTCGTTCATTTA
3613869 TGTTTAACCC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 51 0.98
45 1 0.02
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.48
Consensus pattern (44 bp):
GTTCGTTCATTTACGTTCGTGAACGTTCGATTATGTTCGTTCAT
Found at i:3613839 original size:24 final size:24
Alignment explanation
Indices: 3613767--3613840 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
3613757 ACATATGTCT
3613767 CGTTCGTTCATTTACGTTCGTGAA
1 CGTTCGTTCATTTACGTTCGTGAA
3613791 CGTTCAGTT-ATGTT-CGTTC----A
1 CGTTC-GTTCAT-TTACGTTCGTGAA
* *
3613811 TGTTCGTTCCTTTACGTTCGTGAA
1 CGTTCGTTCATTTACGTTCGTGAA
3613835 CGTTCG
1 CGTTCG
3613841 ATTATGTTCG
Statistics
Matches: 39, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
19 5 0.13
20 11 0.28
24 18 0.46
25 5 0.13
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.43
Consensus pattern (24 bp):
CGTTCGTTCATTTACGTTCGTGAA
Found at i:3614573 original size:26 final size:26
Alignment explanation
Indices: 3614529--3614585 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3614519 GTCTCCAACG
* * *
3614529 TTTATGTTCGTTTATGTTTGTGTTCT
1 TTTATGTTCGTTTACGTTTATGTTCA
3614555 TTTATGTTCGTGTT-CGTTTATGTTCA
1 TTTATGTTCGT-TTACGTTTATGTTCA
3614581 TTTAT
1 TTTAT
3614586 TTATTAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.63
Consensus pattern (26 bp):
TTTATGTTCGTTTACGTTTATGTTCA
Found at i:3614579 original size:16 final size:16
Alignment explanation
Indices: 3614533--3614579 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
3614523 CCAACGTTTA
*
3614533 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
3614549 TGTTCTTTTATGTTCG
1 TGTTCGTTTATGTTCG
3614565 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
3614580 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.06, C:0.11, G:0.21, T:0.62
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:3617171 original size:13 final size:13
Alignment explanation
Indices: 3617148--3617208 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 13
3617138 TAATTGCAAA
3617148 AAAATAAAATAATT
1 AAAA-AAAATAATT
*
3617162 AAAAAAAAT-ACT
1 AAAAAAAATAATT
*
3617174 AAAAAAAATAAAT
1 AAAAAAAATAATT
* *
3617187 -AATACAATAATT
1 AAAAAAAATAATT
*
3617199 AAATAAAATA
1 AAAAAAAATA
3617209 CTAACAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 20 0.51
13 15 0.38
14 4 0.10
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAAAATAATT
Found at i:3617197 original size:37 final size:39
Alignment explanation
Indices: 3617150--3617236 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 39
3617140 ATTGCAAAAA
3617150 AATAAAATAATTAAAAAAAATACTAA-AAAA-AATAAAT
1 AATAAAATAATTAAAAAAAATACTAACAAAATAATAAAT
* * *
3617187 AATACAATAATTAAATAAAATACTAACAAAATATTAAATAT
1 AATAAAATAATTAAAAAAAATACTAACAAAATAAT-AA-AT
3617228 AATAAAATA
1 AATAAAATA
3617237 CATATTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 24 0.57
38 4 0.10
39 2 0.05
40 2 0.05
41 10 0.24
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (39 bp):
AATAAAATAATTAAAAAAAATACTAACAAAATAATAAAT
Found at i:3617286 original size:10 final size:10
Alignment explanation
Indices: 3617271--3617304 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
3617261 ATGTTTAGTT
3617271 TTTGAGAGGA
1 TTTGAGAGGA
*
3617281 TTTGAGAGAA
1 TTTGAGAGGA
3617291 TTTGAGAGGA
1 TTTGAGAGGA
3617301 TTTG
1 TTTG
3617305 GTGTGGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (10 bp):
TTTGAGAGGA
Found at i:3618728 original size:2 final size:2
Alignment explanation
Indices: 3618721--3618771 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
3618711 CTCCTCAGTG
3618721 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
3618763 TA TA TA TA T
1 TA TA TA TA T
3618772 CGCCATCAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3622848 original size:22 final size:22
Alignment explanation
Indices: 3622820--3622873 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
3622810 ATTAAATCAT
3622820 TATTTTTATTGAATAAAAATAA
1 TATTTTTATTGAATAAAAATAA
3622842 TATTTTTATTGAATAAAAATAA
1 TATTTTTATTGAATAAAAATAA
3622864 TATTTTTATT
1 TATTTTTATT
3622874 ATTTCGAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTTTTATTGAATAAAAATAA
Found at i:3636055 original size:16 final size:15
Alignment explanation
Indices: 3636002--3636053 Score: 86
Period size: 15 Copynumber: 3.4 Consensus size: 15
3635992 AGATAGATTA
3636002 AAAAATGAAATTATT
1 AAAAATGAAATTATT
3636017 AAAAATGAAATTATT
1 AAAAATGAAATTATT
*
3636032 AAAAATTAAATTATT
1 AAAAATGAAATTATT
3636047 AAGAAAT
1 AA-AAAT
3636054 TACTGCATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
15 31 0.89
16 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.33
Consensus pattern (15 bp):
AAAAATGAAATTATT
Found at i:3636444 original size:16 final size:16
Alignment explanation
Indices: 3636423--3636469 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
3636413 AATTTAAGAT
3636423 TATATTTTTATTATCA
1 TATATTTTTATTATCA
* *
3636439 TATATTTTAGTTTTATTA
1 TATATTTT--TATTATCA
3636457 TATATTTTTATTA
1 TATATTTTTATTA
3636470 AAAAATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TATATTTTTATTATCA
Found at i:3636454 original size:21 final size:19
Alignment explanation
Indices: 3636428--3636466 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
3636418 AAGATTATAT
3636428 TTTTATTATCATATATTTTAG
1 TTTTATTAT-ATAT-TTTTAG
3636449 TTTTATTATATATTTTTA
1 TTTTATTATATATTTTTA
3636467 TTAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTATTATATATTTTTAG
Found at i:3646358 original size:14 final size:14
Alignment explanation
Indices: 3646336--3646382 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
3646326 TGAAAAGGAA
*
3646336 AATTAATATAGTTT
1 AATTTATATAGTTT
3646350 AATTTATATA----
1 AATTTATATAGTTT
3646360 AA-TTATATAGTTT
1 AATTTATATAGTTT
3646373 AATTTATATA
1 AATTTATATA
3646383 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:3646369 original size:23 final size:24
Alignment explanation
Indices: 3646335--3646384 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
3646325 ATGAAAAGGA
3646335 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
3646359 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
3646382 AAA
1 AAA
3646385 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:3646577 original size:14 final size:14
Alignment explanation
Indices: 3646560--3646599 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3646550 AGGATTTATG
* *
3646560 GTTTATTGTTTAAT
1 GTTTATGGTTTAAA
3646574 GTTTATGGTTTAAA
1 GTTTATGGTTTAAA
*
3646588 GTTTAGGGTTTA
1 GTTTATGGTTTA
3646600 GGGTTTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTTATGGTTTAAA
Found at i:3646598 original size:21 final size:21
Alignment explanation
Indices: 3646549--3646605 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3646539 CCATTTACAA
* **
3646549 TAGGATTTATGGTTTATTGTT
1 TAGGGTTTATGGTTTAAAGTT
**
3646570 TAATGTTTATGGTTTAAAGTT
1 TAGGGTTTATGGTTTAAAGTT
*
3646591 TAGGGTTTAGGGTTT
1 TAGGGTTTATGGTTT
3646606 CTATAAACTA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (21 bp):
TAGGGTTTATGGTTTAAAGTT
Found at i:3646707 original size:49 final size:48
Alignment explanation
Indices: 3646606--3646707 Score: 116
Period size: 49 Copynumber: 2.1 Consensus size: 48
3646596 TTTAGGGTTT
** * * * *
3646606 CTATAAACTATATACTTTATTACTTTATATAGTTTATGCATACTGTTT
1 CTATAAACTATATAAGTAATTACTTTATATAGTTTATACATACTATTA
*
3646654 CTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATA-TATATA
1 CTATAAACTATATAAGTAA-TTACTTTATATAGTTTATACATACTAT-TA
3646703 CTATA
1 CTATA
3646708 CTATACATGG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
48 18 0.40
49 27 0.60
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (48 bp):
CTATAAACTATATAAGTAATTACTTTATATAGTTTATACATACTATTA
Found at i:3647108 original size:21 final size:21
Alignment explanation
Indices: 3647090--3647129 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3647080 AATATTTAGT
* *
3647090 GTTTAGTGTTTATGGTTTAAA
1 GTTTAGGGTTTAAGGTTTAAA
3647111 GTTTAGGGTTTAAGGTTTA
1 GTTTAGGGTTTAAGGTTTA
3647130 TGATTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (21 bp):
GTTTAGGGTTTAAGGTTTAAA
Found at i:3650930 original size:21 final size:21
Alignment explanation
Indices: 3650904--3650943 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3650894 CAGAACCCCA
*
3650904 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3650925 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3650944 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3650978 original size:20 final size:21
Alignment explanation
Indices: 3650924--3650986 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
3650914 GATTCCCCTG
3650924 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
3650948 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
3650968 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
3650987 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:3657392 original size:2 final size:2
Alignment explanation
Indices: 3657387--3657417 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
3657377 TTATATAGTT
3657387 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
3657418 CATGGTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3657485 original size:21 final size:21
Alignment explanation
Indices: 3657461--3657501 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3657451 TATATAGTTT
*
3657461 ATGGGTTAGGATTTAGGGTTC
1 ATGGGTTAGGATTTAAGGTTC
*
3657482 ATGGGTTAGGGTTTAAGGTT
1 ATGGGTTAGGATTTAAGGTT
3657502 TTTTATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.02, G:0.39, T:0.39
Consensus pattern (21 bp):
ATGGGTTAGGATTTAAGGTTC
Found at i:3657688 original size:21 final size:20
Alignment explanation
Indices: 3657662--3657701 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
3657652 TATATAGTTT
3657662 ATACATATATAGTATACATAC
1 ATACATATATA-TATACATAC
3657683 ATACATATATATATACATA
1 ATACATATATATATACATA
3657702 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (20 bp):
ATACATATATATATACATAC
Found at i:3657925 original size:17 final size:17
Alignment explanation
Indices: 3657903--3657951 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
3657893 CTCAATTTCC
3657903 CTCCAAAATTTTCTATT
1 CTCCAAAATTTTCTATT
*
3657920 CTCCAAATTTTTCTATT
1 CTCCAAAATTTTCTATT
3657937 CTCTCTAAAATTTTC
1 CTC-C-AAAATTTTC
3657952 AATTTCCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 19 0.68
18 1 0.04
19 8 0.29
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (17 bp):
CTCCAAAATTTTCTATT
Found at i:3657950 original size:19 final size:19
Alignment explanation
Indices: 3657907--3657965 Score: 68
Period size: 17 Copynumber: 3.2 Consensus size: 19
3657897 ATTTCCCTCC
3657907 AAAATTTTCTATTCTC-C-
1 AAAATTTTCTATTCTCTCT
*
3657924 AAATTTTTCTATTCTCTCT
1 AAAATTTTCTATTCTCTCT
* *
3657943 AAAATTTTCAATTTCCCTCT
1 AAAATTTTCTA-TTCTCTCT
3657963 AAA
1 AAA
3657966 TTCCTAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.43
18 1 0.03
19 9 0.26
20 10 0.29
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATTTTCTATTCTCTCT
Found at i:3657965 original size:20 final size:19
Alignment explanation
Indices: 3657889--3657961 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 19
3657879 ATAAAATCTC
*
3657889 AATTCTCAATTTCCCTCCAA
1 AATTTTCAA-TTCCCTCCAA
*
3657909 AATTTTCTATT--CTCCAA
1 AATTTTCAATTCCCTCCAA
* * * *
3657926 ATTTTTCTATTCTCTCTAA
1 AATTTTCAATTCCCTCCAA
3657945 AATTTTCAATTTCCCTC
1 AATTTTCAA-TTCCCTC
3657962 TAAATTCCTA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
17 16 0.37
19 14 0.33
20 13 0.30
ACGTcount: A:0.26, C:0.27, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTTCAATTCCCTCCAA
Found at i:3658175 original size:18 final size:17
Alignment explanation
Indices: 3658154--3658193 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
3658144 TATAATAATT
3658154 ATATAGTTTATAATATAA
1 ATATAGTTTAT-ATATAA
*
3658172 ATATAGTTTATATATAT
1 ATATAGTTTATATATAA
3658189 ATATA
1 ATATA
3658194 TTATATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
ATATAGTTTATATATAA
Found at i:3658197 original size:15 final size:16
Alignment explanation
Indices: 3658094--3658199 Score: 62
Period size: 15 Copynumber: 6.7 Consensus size: 16
3658084 ATATACTTTT
*
3658094 TATAGTT-TATACATA
1 TATAGTTATATATATA
* *
3658109 TATAATT-TATATAAA
1 TATAGTTATATATATA
* *
3658124 CATAATT-TATATATA
1 TATAGTTATATATATA
*
3658139 TA-ACTTATA-ATAATTA
1 TATAGTTATATAT-A-TA
*
3658155 TATAGTTTATAATATAAA
1 TATAG-TTAT-ATATATA
3658173 TATAGTTTATATATATA
1 TATAG-TTATATATATA
3658190 TATA-TTATAT
1 TATAGTTATAT
3658200 TTTTTCAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 5 0.07
15 35 0.47
16 4 0.05
17 11 0.15
18 15 0.20
19 2 0.03
20 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
TATAGTTATATATATA
Found at i:3659506 original size:31 final size:32
Alignment explanation
Indices: 3659454--3659523 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
3659444 TTAGTATTCG
*
3659454 GGTCGGATTTTTTTTAAAAAAAAATTGGGATCA
1 GGTCAGATTTTTTTT-AAAAAAAATTGGGATCA
* *
3659487 GGTCAGATTTTTTTT-AAAAAAATTGGGGTCC
1 GGTCAGATTTTTTTTAAAAAAAATTGGGATCA
3659518 GGTCAG
1 GGTCAG
3659524 GTGTTTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 20 0.59
33 14 0.41
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (32 bp):
GGTCAGATTTTTTTTAAAAAAAATTGGGATCA
Found at i:3659623 original size:38 final size:38
Alignment explanation
Indices: 3659527--3659623 Score: 114
Period size: 33 Copynumber: 2.7 Consensus size: 38
3659517 CGGTCAGGTG
* * * *
3659527 TTTTAAGTTTGATATTCGGGTCGAATCGGGTCGGGTTT
1 TTTTAAGTGTGATATTTGGGTCGAGTCGGGTCGAGTTT
*
3659565 TTTTAAGTGTGATA--T---TCGAGTCGGGTTGAGTTT
1 TTTTAAGTGTGATATTTGGGTCGAGTCGGGTCGAGTTT
3659598 TTTTAAGTGTGATATTTGGGTCGAGT
1 TTTTAAGTGTGATATTTGGGTCGAGT
3659624 TTGGGTTTAG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
33 29 0.59
35 1 0.02
38 19 0.39
ACGTcount: A:0.18, C:0.07, G:0.31, T:0.44
Consensus pattern (38 bp):
TTTTAAGTGTGATATTTGGGTCGAGTCGGGTCGAGTTT
Found at i:3669156 original size:29 final size:30
Alignment explanation
Indices: 3669100--3669159 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
3669090 ATTTTTTAAA
* * *
3669100 TTAAATATTTAATGTTTTTTTATTATTATT
1 TTAAATATTAAATATTTTATTATTATTATT
3669130 TTAAAT-TTAAATATTTTATTATTATTATT
1 TTAAATATTAAATATTTTATTATTATTATT
3669159 T
1 T
3669160 GATTTCATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (30 bp):
TTAAATATTAAATATTTTATTATTATTATT
Found at i:3671428 original size:19 final size:19
Alignment explanation
Indices: 3671401--3671437 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3671391 ACAATTTATG
3671401 TAAACATATTATTAAATTT
1 TAAACATATTATTAAATTT
* *
3671420 TAAATATATTTTTAAATT
1 TAAACATATTATTAAATT
3671438 CGTTGCGGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TAAACATATTATTAAATTT
Found at i:3671808 original size:84 final size:82
Alignment explanation
Indices: 3671707--3671862 Score: 192
Period size: 84 Copynumber: 1.9 Consensus size: 82
3671697 ACTTCCAATA
*
3671707 TGTTTGATTTTAATCACCTAACT-ATAA-ATTTTTTCAATT-TCATCAATAAACTTTCAAATTAT
1 TGTTTGATTTTAATCACCTAA-TAATAACA-GTTTTCAATTCT-ATC-A-AAACTTTCAAATTAT
*
3671769 GCTTGTTTAGGTATTTTCAACG
61 GCTTGTTCAGGTATTTTCAACG
** * *
3671791 TGTTTGATTTTGGTCACCTAATAATAACAGTTTTCAATTCTATCACAACTTTTAAATTATGCTTG
1 TGTTTGATTTTAATCACCTAATAATAACAGTTTTCAATTCTATCAAAACTTTCAAATTATGCTTG
3671856 TTCAGGT
66 TTCAGGT
3671863 CATTCAAATG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
82 24 0.38
83 2 0.03
84 35 0.56
85 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (82 bp):
TGTTTGATTTTAATCACCTAATAATAACAGTTTTCAATTCTATCAAAACTTTCAAATTATGCTTG
TTCAGGTATTTTCAACG
Found at i:3672462 original size:2 final size:2
Alignment explanation
Indices: 3672455--3672523 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
3672445 TAGAGTAAAT
3672455 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
3672497 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3672524 TATTAGTGTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3674627 original size:26 final size:26
Alignment explanation
Indices: 3674591--3674646 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
3674581 CCTTCTTACG
*
3674591 TGATCCTTCTTGATTGCCTAACATTC
1 TGATACTTCTTGATTGCCTAACATTC
*
3674617 TGATACTTCTTTATTGCCTAACATTC
1 TGATACTTCTTGATTGCCTAACATTC
3674643 TGAT
1 TGAT
3674647 CCATACAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (26 bp):
TGATACTTCTTGATTGCCTAACATTC
Found at i:3678725 original size:43 final size:43
Alignment explanation
Indices: 3678659--3678741 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
3678649 AACTTCAAAA
* * *
3678659 TAATATTCCATAAATACACCAAACTAATATATTACAACTAAAG
1 TAATAATCCACAAATACACCAAACTAAAATATTACAACTAAAG
* *
3678702 TAATAATCCACAAATACATCAAACTAAAATATTGCAACTA
1 TAATAATCCACAAATACACCAAACTAAAATATTACAACTA
3678742 TTCATAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (43 bp):
TAATAATCCACAAATACACCAAACTAAAATATTACAACTAAAG
Found at i:3681513 original size:60 final size:60
Alignment explanation
Indices: 3681418--3681532 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
3681408 TTTGAGGATC
* * *
3681418 ATAATTTAGGGATGAAATTAAAATATTTAAAAGTTT-AAGCACCAATTTAAAATAAGATTT
1 ATAATTAAGGGATAAAATTAAAATATTCAAAAGTTTAAAG-ACCAATTTAAAATAAGATTT
* * * *
3681478 ATAATTAAGGGATAAAATTAAAATGTTCAAGAGTTTAAAGACTAATTTGAAATAA
1 ATAATTAAGGGATAAAATTAAAATATTCAAAAGTTTAAAGACCAATTTAAAATAA
3681533 ATGCCATTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 44 0.94
61 3 0.06
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.33
Consensus pattern (60 bp):
ATAATTAAGGGATAAAATTAAAATATTCAAAAGTTTAAAGACCAATTTAAAATAAGATTT
Found at i:3687029 original size:2 final size:2
Alignment explanation
Indices: 3687024--3687069 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
3687014 TGAAAAAATA
3687024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT A- AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
3687065 AT AT A
1 AT AT A
3687070 ATTATATTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3687073 original size:10 final size:9
Alignment explanation
Indices: 3687025--3687076 Score: 61
Period size: 10 Copynumber: 5.6 Consensus size: 9
3687015 GAAAAAATAA
3687025 TATATATAT
1 TATATATAT
3687034 ATATATATAT
1 -TATATATAT
3687044 ATATATATAT
1 -TATATATAT
*
3687054 GATA-ATAT
1 TATATATAT
3687062 TATATATAAT
1 TATATAT-AT
3687072 TATAT
1 TATAT
3687077 TTAAAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 7 0.18
9 5 0.13
10 26 0.68
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (9 bp):
TATATATAT
Found at i:3690170 original size:18 final size:20
Alignment explanation
Indices: 3690147--3690189 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3690137 AAAATAAAAA
*
3690147 CATCGAATGC-C-ATTAGTG
1 CATCGAATGCACAAGTAGTG
3690165 CATCG-ATGCACAAGTAGTG
1 CATCGAATGCACAAGTAGTG
3690184 CATCGA
1 CATCGA
3690190 TACACCCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 6 0.29
19 11 0.52
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (20 bp):
CATCGAATGCACAAGTAGTG
Found at i:3690317 original size:63 final size:63
Alignment explanation
Indices: 3690166--3690322 Score: 271
Period size: 63 Copynumber: 2.5 Consensus size: 63
3690156 CCATTAGTGC
* * *
3690166 ATCGATGCACA-AGTAGTGCATCGATACACCCCCTTAAATACAAACATCAAATAGGATTTATGT
1 ATCGATGCATAGA-TAGTGCATCGATGCATCCCCTTAAATACAAACATCAAATAGGATTTATGT
3690229 ATCGATGCATAGATAGTGCATCGATGCATCCCCTTAAATACAAACATCAAATAGGATTTATGT
1 ATCGATGCATAGATAGTGCATCGATGCATCCCCTTAAATACAAACATCAAATAGGATTTATGT
3690292 ATCGATGCATAGATAGTGCATCGATGCATCC
1 ATCGATGCATAGATAGTGCATCGATGCATCC
3690323 GTCAAGGGAT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
63 89 0.99
64 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.27
Consensus pattern (63 bp):
ATCGATGCATAGATAGTGCATCGATGCATCCCCTTAAATACAAACATCAAATAGGATTTATGT
Found at i:3694783 original size:18 final size:17
Alignment explanation
Indices: 3694760--3694793 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3694750 CAGTCTATTT
3694760 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
3694778 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
3694794 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:3702803 original size:18 final size:18
Alignment explanation
Indices: 3702782--3702844 Score: 99
Period size: 18 Copynumber: 3.5 Consensus size: 18
3702772 ATAATGATCT
* *
3702782 TTCGGGACACAGTGGTCC
1 TTCGGGACATAGTGGTCA
3702800 TTCGGGACATAGTGGTCA
1 TTCGGGACATAGTGGTCA
3702818 TTCGGGACATAGTGGTCA
1 TTCGGGACATAGTGGTCA
*
3702836 TACGGGACA
1 TTCGGGACA
3702845 AATTCTACGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (18 bp):
TTCGGGACATAGTGGTCA
Found at i:3702809 original size:36 final size:36
Alignment explanation
Indices: 3702761--3702844 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 36
3702751 GTCTATGCGA
* *
3702761 TCCTTCGAGACATAATGATCTTTCGGGACACAGTGG
1 TCCTTCGGGACATAATGATCATTCGGGACACAGTGG
* * *
3702797 TCCTTCGGGACATAGTGGTCATTCGGGACATAGTGG
1 TCCTTCGGGACATAATGATCATTCGGGACACAGTGG
* *
3702833 TCATACGGGACA
1 TCCTTCGGGACA
3702845 AATTCTACGC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (36 bp):
TCCTTCGGGACATAATGATCATTCGGGACACAGTGG
Found at i:3703773 original size:3 final size:3
Alignment explanation
Indices: 3703767--3703791 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3703757 AAAATTAATA
3703767 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
3703792 TAGATCTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3704885 original size:17 final size:18
Alignment explanation
Indices: 3704849--3704886 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3704839 TAATAATAAT
*
3704849 AATAATTATTATATTTAC
1 AATAATTATTATATTCAC
*
3704867 AATAATT-TTATGTTCAC
1 AATAATTATTATATTCAC
3704884 AAT
1 AAT
3704887 TTTCTTATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (18 bp):
AATAATTATTATATTCAC
Found at i:3705615 original size:25 final size:25
Alignment explanation
Indices: 3705555--3705608 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
3705545 GTAGGGAGGG
3705555 GAGACGGGAGGGAGAAGGGATATAA
1 GAGACGGGAGGGAGAAGGGATATAA
3705580 GAGACGGGAGGGAGAAGGGATATAA
1 GAGACGGGAGGGAGAAGGGATATAA
3705605 GAGA
1 GAGA
3705609 GAGGAGGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.41, C:0.04, G:0.48, T:0.07
Consensus pattern (25 bp):
GAGACGGGAGGGAGAAGGGATATAA
Found at i:3705678 original size:17 final size:19
Alignment explanation
Indices: 3705656--3705698 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 19
3705646 GTTGGGGGAT
3705656 TTTTTTTTAAAA-A-AATA
1 TTTTTTTTAAAATATAATA
3705673 --TTTTTTAAAATATAATA
1 TTTTTTTTAAAATATAATA
3705690 TTTTTTTTA
1 TTTTTTTTA
3705699 TTTTCTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 10 0.45
16 1 0.05
17 4 0.18
19 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTTTTAAAATATAATA
Found at i:3708127 original size:21 final size:21
Alignment explanation
Indices: 3708097--3708145 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3708087 GGACGAAGAC
* *
3708097 CAATGGAGTTGATAGCAGTGA
1 CAATGAAGTTGAAAGCAGTGA
* *
3708118 CAATGAAGTTGAAAGCATTGT
1 CAATGAAGTTGAAAGCAGTGA
3708139 CAATGAA
1 CAATGAA
3708146 AGTGGGAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (21 bp):
CAATGAAGTTGAAAGCAGTGA
Found at i:3711478 original size:13 final size:13
Alignment explanation
Indices: 3711460--3711488 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3711450 ACATGTGTAA
3711460 TTATACTAATTTT
1 TTATACTAATTTT
3711473 TTATACTAATTTT
1 TTATACTAATTTT
3711486 TTA
1 TTA
3711489 AACAATTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATACTAATTTT
Found at i:3713581 original size:13 final size:13
Alignment explanation
Indices: 3713563--3713587 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3713553 GAAAGCATTT
3713563 TATAAAGTCAAAC
1 TATAAAGTCAAAC
3713576 TATAAAGTCAAA
1 TATAAAGTCAAA
3713588 GTTGTGTTTA
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:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (13 bp):
TATAAAGTCAAAC
Found at i:3713784 original size:22 final size:23
Alignment explanation
Indices: 3713753--3713799 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
3713743 TATTCGCGAG
3713753 TTTAGAAGATACGA-TTTTGGGC
1 TTTAGAAGATACGATTTTTGGGC
*
3713775 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTTTGGGC
3713798 TT
1 TT
3713800 GTTTAGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (23 bp):
TTTAGAAGATACGATTTTTGGGC
Found at i:3721390 original size:7 final size:7
Alignment explanation
Indices: 3721378--3721402 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3721368 CATCACTATT
3721378 AAAAATA
1 AAAAATA
3721385 AAAAATA
1 AAAAATA
3721392 AAAAATA
1 AAAAATA
3721399 AAAA
1 AAAA
3721403 GAAAATAAGA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:3721689 original size:15 final size:15
Alignment explanation
Indices: 3721671--3721700 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3721661 ATTAAAGAGA
3721671 TGTAATCAAGCATAT
1 TGTAATCAAGCATAT
3721686 TGTAATCAAGCATAT
1 TGTAATCAAGCATAT
3721701 AGTCATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
TGTAATCAAGCATAT
Found at i:3721979 original size:2 final size:2
Alignment explanation
Indices: 3721972--3722054 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
3721962 ACTAAAAAGT
3721972 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
3722014 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3722055 GGAAGCATGG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3722548 original size:2 final size:2
Alignment explanation
Indices: 3722541--3722587 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
3722531 ATCCCTAAAG
* *
3722541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3722583 TA TA T
1 TA TA T
3722588 TTAGGTATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3726695 original size:8 final size:8
Alignment explanation
Indices: 3726684--3726716 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3726674 AGCCGACAAG
3726684 GCTAGAAA
1 GCTAGAAA
3726692 GCTAGCAAA
1 GCTAG-AAA
3726701 -CTAGAAA
1 GCTAGAAA
3726708 GCTAGAAA
1 GCTAGAAA
3726716 G
1 G
3726717 AATGAACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 3 0.13
8 17 0.74
9 3 0.13
ACGTcount: A:0.48, C:0.15, G:0.24, T:0.12
Consensus pattern (8 bp):
GCTAGAAA
Found at i:3734725 original size:13 final size:14
Alignment explanation
Indices: 3734709--3734741 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
3734699 TTATTGATTA
3734709 TTTAATTTTATAT-
1 TTTAATTTTATATG
3734722 TTTAATTTTATATG
1 TTTAATTTTATATG
3734736 TTTAAT
1 TTTAAT
3734742 GCGGGTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTAATTTTATATG
Done.