Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006855.1 Hibiscus syriacus cultivar Beakdansim tig00017443_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: 100550
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:8717 original size:2 final size:2
Alignment explanation
Indices: 8712--8802 Score: 55
Period size: 2 Copynumber: 44.5 Consensus size: 2
8702 GCACACACAC
* * *
8712 AT AT AT AT AT -T AT AGT TT AT AGT TT AT AT ACT AT AT AGT TT AT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT A-T AT AT
* *
8755 AT AT TT AT ACT AT AT A- AT -T AT ACT TT AT AT -T AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
8796 AT AT AT A
1 AT AT AT A
8803 AAAGTAGACT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
1 4 0.06
2 57 0.83
3 8 0.12
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:8766 original size:22 final size:21
Alignment explanation
Indices: 8738--8799 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
8728 TTATAGTTTA
8738 TATACTATATAGTTTATATATT
1 TATACTATATA-TTTATATATT
* *
8760 TATACTATATAATTATA-CTT
1 TATACTATATATTTATATATT
* *
8780 TATATTATATATATATATAT
1 TATACTATATATTTATATAT
8800 ATAAAAGTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.48
21 6 0.18
22 11 0.33
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (21 bp):
TATACTATATATTTATATATT
Found at i:8770 original size:13 final size:13
Alignment explanation
Indices: 8752--8802 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
8742 CTATATAGTT
8752 TATATATTTATAC
1 TATATATTTATAC
*
8765 TATATAATTATAC
1 TATATATTTATAC
*
8778 TTTATATTATATA-
1 TATATATT-TATAC
*
8791 TATATATATATA
1 TATATATTTATA
8803 AAAGTAGACT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
12 4 0.12
13 24 0.75
14 4 0.12
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATTTATAC
Found at i:8777 original size:35 final size:32
Alignment explanation
Indices: 8738--8803 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
8728 TTATAGTTTA
*
8738 TATACTATATAGTTTATATATTTATACTATATAAT
1 TATACTATATA--TTATATATATATA-TATATAAT
*
8773 TATACTTTATATTATATATATATATATATAA
1 TATACTATATATTATATATATATATATATAA
8804 AAGTAGACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 7 0.24
33 12 0.41
35 10 0.34
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (32 bp):
TATACTATATATTATATATATATATATATAAT
Found at i:8956 original size:2 final size:2
Alignment explanation
Indices: 8949--9014 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
8939 ATGTATGATA
8949 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
8991 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
9015 TCTTTTAGTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10164 original size:32 final size:32
Alignment explanation
Indices: 10123--10185 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
10113 GTCACATCAC
* *
10123 CCAAGGTGATTATGTGTCTTGTGTAATGTCAT
1 CCAAGGTGATAATGTGTCTTATGTAATGTCAT
*
10155 CCAAGGTGATAATGTGTCTTATGTTATGTCA
1 CCAAGGTGATAATGTGTCTTATGTAATGTCA
10186 GTTAAAGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.40
Consensus pattern (32 bp):
CCAAGGTGATAATGTGTCTTATGTAATGTCAT
Found at i:10196 original size:32 final size:32
Alignment explanation
Indices: 10123--10202 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
10113 GTCACATCAC
* * *
10123 CCAAGGTGATTATGTGTCTTGTGTAATGTCAT
1 CCAAAGTGATAATGTGTCTTATGTAATGTCAT
* *
10155 CCAAGGTGATAATGTGTCTTATGTTATGTCAGT
1 CCAAAGTGATAATGTGTCTTATGTAATGTCA-T
* *
10188 -TAAAGTGATGATGTG
1 CCAAAGTGATAATGTG
10203 ACGTGCAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 40 0.98
33 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.26, T:0.39
Consensus pattern (32 bp):
CCAAAGTGATAATGTGTCTTATGTAATGTCAT
Found at i:11308 original size:24 final size:26
Alignment explanation
Indices: 11264--11324 Score: 108
Period size: 24 Copynumber: 2.4 Consensus size: 26
11254 AATAAAATAA
11264 AAATAAAAATATTTATAATTAAATTT
1 AAATAAAAATATTTATAATTAAATTT
11290 AAATAAAAA-A-TTATAATTAAATTT
1 AAATAAAAATATTTATAATTAAATTT
11314 AAATAAAAATA
1 AAATAAAAATA
11325 ATTGTTGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 23 0.68
25 2 0.06
26 9 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
AAATAAAAATATTTATAATTAAATTT
Found at i:13932 original size:293 final size:293
Alignment explanation
Indices: 13405--13986 Score: 1011
Period size: 293 Copynumber: 2.0 Consensus size: 293
13395 ATCAATTTTC
*
13405 AGTTCCATTAAAATTATTTGGTTAACTTTCTTCTCTTTTTTAAGTCATTTCTGAGTTATATAGGT
1 AGTTCCATTAAAATTACTTGGTTAACTTTCTTCTCTTTTTTAAGTCATTTCTGAGTTATATAGGT
13470 ATATTGAGATGAAGTTGTTGAACCCATGCAAATAGGAAGCTCACTTTTACTCTGGCTTGGTTGGT
66 ATATTGAGATGAAGTTGTTGAACCCATGCAAATAGGAAGCTCACTTTTACTCTGGCTTGGTTGGT
* * * * *
13535 TCATTGTTTTTCTGTTTGAGAATAATTGAGGTGCCTTACGGATTGGTGATCACATACTACCCTCG
131 TCATTGTTTTGCTGTTTGAGAAGAATTGAAGCGCCATACGGATTGGTGATCACATACTACCCTCG
* *
13600 ATTGGATTACCGTCCTCTTGTTCTCAACGGGGTGTAGCTGGGAATCCCCTCTGTCTGTTTCCTGT
196 ATTGGATTACCGTCCTCTTGTTCTCAACAGGGTGTAGCTGGGAATCCCCTATGTCTGTTTCCTGT
13665 TGCTGTTTGAGAAGGTTTGAATTGATTTAGGTA
261 TGCTGTTTGAGAAGGTTTGAATTGATTTAGGTA
* * *
13698 AGTTCCATTGAAATTCCTTGGTTAATTTTCTTCTCTTTTTTAAGTCATTTCTGAGTTATATAGGT
1 AGTTCCATTAAAATTACTTGGTTAACTTTCTTCTCTTTTTTAAGTCATTTCTGAGTTATATAGGT
* **
13763 GTATTGAGATGAAGTTGTTGAACCCATGCAAATAGGAAGCTTGCTTTTACTCTGGCTTGGTTGGT
66 ATATTGAGATGAAGTTGTTGAACCCATGCAAATAGGAAGCTCACTTTTACTCTGGCTTGGTTGGT
13828 TCATTGTTTTGCTGTTTGAGAAGAATTGAAGCGCCATACGGATTGGTGATCACATACTACCCTCG
131 TCATTGTTTTGCTGTTTGAGAAGAATTGAAGCGCCATACGGATTGGTGATCACATACTACCCTCG
* *
13893 ATTGGATTACCTTCCTCTTGTTCTCATCAGGGTGTAGCTGGGAATCCCCTATGTCTGTTTCCTGT
196 ATTGGATTACCGTCCTCTTGTTCTCAACAGGGTGTAGCTGGGAATCCCCTATGTCTGTTTCCTGT
*
13958 TGCTGTTTGAGAAGGTTTGAATTTATTTA
261 TGCTGTTTGAGAAGGTTTGAATTGATTTA
13987 TGGTTGTTCA
Statistics
Matches: 272, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
293 272 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (293 bp):
AGTTCCATTAAAATTACTTGGTTAACTTTCTTCTCTTTTTTAAGTCATTTCTGAGTTATATAGGT
ATATTGAGATGAAGTTGTTGAACCCATGCAAATAGGAAGCTCACTTTTACTCTGGCTTGGTTGGT
TCATTGTTTTGCTGTTTGAGAAGAATTGAAGCGCCATACGGATTGGTGATCACATACTACCCTCG
ATTGGATTACCGTCCTCTTGTTCTCAACAGGGTGTAGCTGGGAATCCCCTATGTCTGTTTCCTGT
TGCTGTTTGAGAAGGTTTGAATTGATTTAGGTA
Found at i:21553 original size:20 final size:20
Alignment explanation
Indices: 21528--21573 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
21518 GATTGGTAAT
21528 GAATCGACTGAAAACCGGTA
1 GAATCGACTGAAAACCGGTA
** *
21548 GAATCGTTTGAAAATCGGTA
1 GAATCGACTGAAAACCGGTA
*
21568 AAATCG
1 GAATCG
21574 TGGTGAACCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (20 bp):
GAATCGACTGAAAACCGGTA
Found at i:21574 original size:20 final size:20
Alignment explanation
Indices: 21536--21574 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21526 ATGAATCGAC
*
21536 TGAAAACCGGTAGAATCGTT
1 TGAAAACCGGTAAAATCGTT
*
21556 TGAAAATCGGTAAAATCGT
1 TGAAAACCGGTAAAATCGT
21575 GGTGAACCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (20 bp):
TGAAAACCGGTAAAATCGTT
Found at i:22649 original size:158 final size:158
Alignment explanation
Indices: 22361--22678 Score: 636
Period size: 158 Copynumber: 2.0 Consensus size: 158
22351 GATCCTCGAT
22361 TTGGGGCTCTTAACTTTGTTGTTGTTTCGTTGTTGTCCCCATGGTTAGTTTAAATTTGTATTTTA
1 TTGGGGCTCTTAACTTTGTTGTTGTTTCGTTGTTGTCCCCATGGTTAGTTTAAATTTGTATTTTA
22426 TAGTTTTATGACCACTGTTTGGTTCATTTTAAATTCATTATATTATGCCCACTTCTTATGTAATG
66 TAGTTTTATGACCACTGTTTGGTTCATTTTAAATTCATTATATTATGCCCACTTCTTATGTAATG
22491 CATACATGTGTTACCATATGCCCTATGC
131 CATACATGTGTTACCATATGCCCTATGC
22519 TTGGGGCTCTTAACTTTGTTGTTGTTTCGTTGTTGTCCCCATGGTTAGTTTAAATTTGTATTTTA
1 TTGGGGCTCTTAACTTTGTTGTTGTTTCGTTGTTGTCCCCATGGTTAGTTTAAATTTGTATTTTA
22584 TAGTTTTATGACCACTGTTTGGTTCATTTTAAATTCATTATATTATGCCCACTTCTTATGTAATG
66 TAGTTTTATGACCACTGTTTGGTTCATTTTAAATTCATTATATTATGCCCACTTCTTATGTAATG
22649 CATACATGTGTTACCATATGCCCTATGC
131 CATACATGTGTTACCATATGCCCTATGC
22677 TT
1 TT
22679 CGTATTGCGT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 160 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (158 bp):
TTGGGGCTCTTAACTTTGTTGTTGTTTCGTTGTTGTCCCCATGGTTAGTTTAAATTTGTATTTTA
TAGTTTTATGACCACTGTTTGGTTCATTTTAAATTCATTATATTATGCCCACTTCTTATGTAATG
CATACATGTGTTACCATATGCCCTATGC
Found at i:24461 original size:14 final size:14
Alignment explanation
Indices: 24442--24479 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
24432 GTCCAGTTAC
24442 TGAGTCAACTCGGT
1 TGAGTCAACTCGGT
**
24456 TGAGTCAACT-TTT
1 TGAGTCAACTCGGT
24469 TGAGTCAACTC
1 TGAGTCAACTC
24480 ATTGACTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (14 bp):
TGAGTCAACTCGGT
Found at i:24484 original size:13 final size:13
Alignment explanation
Indices: 24442--24484 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
24432 GTCCAGTTAC
*
24442 TGAGTCAACTCGGT
1 TGAGTCAACTC-AT
**
24456 TGAGTCAACTTTT
1 TGAGTCAACTCAT
24469 TGAGTCAACTCAT
1 TGAGTCAACTCAT
24482 TGA
1 TGA
24485 CTTTGACAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (13 bp):
TGAGTCAACTCAT
Found at i:26804 original size:13 final size:13
Alignment explanation
Indices: 26759--26808 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
26749 CGCCTGGTCC
*
26759 AGTCAAGTCACTA
1 AGTCAACTCACTA
* * *
26772 AGCCAACTCGGCTT
1 AGTCAACTC-ACTA
26786 AGTCAACTCACTA
1 AGTCAACTCACTA
26799 AGTCAACTCA
1 AGTCAACTCA
26809 TTGAATTTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (13 bp):
AGTCAACTCACTA
Found at i:30097 original size:12 final size:11
Alignment explanation
Indices: 30076--30131 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
30066 AACTTTGAGG
30076 ATGAAGAAGAA
1 ATGAAGAAGAA
*
30087 ATGAGAGAAGAG
1 ATGA-AGAAGAA
30099 ATGAAGAAGAA
1 ATGAAGAAGAA
*
30110 ATGAGAGAAGAG
1 ATGA-AGAAGAA
*
30122 AGGAAGAAGA
1 ATGAAGAAGA
30132 TGACAAGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 20 0.51
12 19 0.49
ACGTcount: A:0.57, C:0.00, G:0.36, T:0.07
Consensus pattern (11 bp):
ATGAAGAAGAA
Found at i:30105 original size:23 final size:23
Alignment explanation
Indices: 30075--30131 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
30065 CAACTTTGAG
30075 GATGAAGAAGAAATGAGAGAAGA
1 GATGAAGAAGAAATGAGAGAAGA
30098 GATGAAGAAGAAATGAGAGAAGA
1 GATGAAGAAGAAATGAGAGAAGA
*
30121 GAGGAAGAAGA
1 GATGAAGAAGA
30132 TGACAAGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (23 bp):
GATGAAGAAGAAATGAGAGAAGA
Found at i:39746 original size:64 final size:64
Alignment explanation
Indices: 39675--39831 Score: 190
Period size: 64 Copynumber: 2.4 Consensus size: 64
39665 AATAGCCTGG
39675 TGCATCGATGCATGGATTGTGCATCGACGCATCAAATGCATTCGATGTTTTAATTAAATCA-GA
1 TGCATCGATGCATGGATTGTGCATCGACGCATCAAATGCATTCGATGTTTTAATTAAATCATGA
* ** ** ** * *
39738 GTGTATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTTTAATTTATTCATTG
1 -TGCATCGATGCATGGATTGTGCATCGACGCATCAAATGCATTCGATGTTTTAATTAAATCA-TG
39803 A
64 A
39804 TGCATCGATGCATGGTATTGATGCATCG
1 TGCATCGATGCATGG-ATTG-TGCATCG
39832 GTGCATGCCT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 52 0.68
65 14 0.18
66 4 0.05
67 7 0.09
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (64 bp):
TGCATCGATGCATGGATTGTGCATCGACGCATCAAATGCATTCGATGTTTTAATTAAATCATGA
Found at i:39759 original size:19 final size:19
Alignment explanation
Indices: 39735--39785 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
39725 TAATTAAATC
*
39735 AGAGTGTATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
39754 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
39773 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
39786 TTTTAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.64
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:39823 original size:21 final size:21
Alignment explanation
Indices: 39799--39838 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39789 TAATTTATTC
39799 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
39820 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
39839 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:41970 original size:16 final size:17
Alignment explanation
Indices: 41949--41990 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
41939 GAAATCCAAT
*
41949 AAAATT-TTTTTTTTGA
1 AAAATTGTTTGTTTTGA
41965 AAAATTGTTTGTTTTGGA
1 AAAATTGTTTGTTTT-GA
41983 AGAAATTG
1 A-AAATTG
41991 GCAGTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 3 0.14
19 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (17 bp):
AAAATTGTTTGTTTTGA
Found at i:41988 original size:19 final size:17
Alignment explanation
Indices: 41949--41990 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
41939 GAAATCCAAT
*
41949 AAAATT-TTTTTTTTGA
1 AAAATTGTTTTTTTGGA
41965 AAAATTGTTTGTTTTGGA
1 AAAATTGTTT-TTTTGGA
41983 AGAAATTG
1 A-AAATTG
41991 GCAGTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 7 0.32
19 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (17 bp):
AAAATTGTTTTTTTGGA
Found at i:48258 original size:64 final size:63
Alignment explanation
Indices: 48152--48330 Score: 184
Period size: 64 Copynumber: 2.8 Consensus size: 63
48142 TTAGACTCCT
* * * * * *
48152 AGTGCATCGGTGCACT-AAGAGTGCAGCGATGCATGAAGTGCATTTGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAATAAATCAG
* ** *
48213 CCTGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAA-TAAATC
48278 AG
62 AG
* *
48280 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATCGAATGCATTCGATGTT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTT
48331 ACAATTTATT
Statistics
Matches: 96, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
63 1 0.01
64 89 0.93
66 4 0.04
67 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAATAAATCAG
Found at i:48366 original size:21 final size:21
Alignment explanation
Indices: 48342--48381 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
48332 CAATTTATTC
48342 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
48363 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
48382 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:52313 original size:22 final size:22
Alignment explanation
Indices: 52288--52337 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
52278 TACTAACACT
*
52288 AAAGTGCGTTCGCACTGATACA
1 AAAGTGCATTCGCACTGATACA
*
52310 AAAGTGCATTTGCACTGATACA
1 AAAGTGCATTCGCACTGATACA
52332 AAAGTG
1 AAAGTG
52338 TCATAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (22 bp):
AAAGTGCATTCGCACTGATACA
Found at i:52347 original size:22 final size:22
Alignment explanation
Indices: 52300--52352 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
52290 AGTGCGTTCG
**
52300 CACTGATACAAAAGTGCATTTG
1 CACTGATACAAAAGTGCATTAA
52322 CACTGATACAAAAGTGTCA-TAA
1 CACTGATACAAAAGTG-CATTAA
52344 CACTTGATA
1 CAC-TGATA
52353 AAAGAATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (22 bp):
CACTGATACAAAAGTGCATTAA
Found at i:52691 original size:12 final size:12
Alignment explanation
Indices: 52674--52699 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52664 GATACCAATT
52674 TTAGCTTCGATG
1 TTAGCTTCGATG
52686 TTAGCTTCGATG
1 TTAGCTTCGATG
52698 TT
1 TT
52700 TGAATTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (12 bp):
TTAGCTTCGATG
Found at i:55136 original size:31 final size:31
Alignment explanation
Indices: 55092--55150 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
55082 CGTCAAACGG
* *
55092 TCGGTTACGTCGGGGACCATATTGTAAATGA
1 TCGGTTACATCGGGGACCATATTATAAATGA
*
55123 TCGGTTATATCGGGGACCATATTATAAA
1 TCGGTTACATCGGGGACCATATTATAAA
55151 CGAATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (31 bp):
TCGGTTACATCGGGGACCATATTATAAATGA
Found at i:58306 original size:29 final size:28
Alignment explanation
Indices: 58274--58397 Score: 144
Period size: 29 Copynumber: 4.3 Consensus size: 28
58264 TCCCGTACAT
58274 AATCAGGACGGCGAATAAAT-TCCATGCAG
1 AATCAGGACGG-GAATAAATCT-CATGCAG
* *
58303 AATCAGGACAAGGAATAAATCTCATGTAG
1 AATCAGGAC-GGGAATAAATCTCATGCAG
*
58332 AATCAGGACGAGG-ATATAATCTCATGCAA
1 AATCAGGACG-GGAATA-AATCTCATGCAG
*
58361 AATCAGGACGGGAAATAAATCCCATGCAG
1 AATCAGGACGGG-AATAAATCTCATGCAG
58390 AATCAGGA
1 AATCAGGA
58398 ATACACCGAT
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
28 5 0.06
29 72 0.88
30 5 0.06
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (28 bp):
AATCAGGACGGGAATAAATCTCATGCAG
Found at i:59288 original size:13 final size:13
Alignment explanation
Indices: 59270--59296 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59260 CGAGTACTAC
59270 AGACTACAGGGGG
1 AGACTACAGGGGG
59283 AGACTACAGGGGG
1 AGACTACAGGGGG
59296 A
1 A
59297 CAAAGACAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.44, T:0.07
Consensus pattern (13 bp):
AGACTACAGGGGG
Found at i:60029 original size:2 final size:2
Alignment explanation
Indices: 60022--60079 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
60012 CATCAAATTA
60022 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
60064 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
60080 TATCTTTCCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61112 original size:27 final size:27
Alignment explanation
Indices: 61057--61226 Score: 174
Period size: 27 Copynumber: 6.4 Consensus size: 27
61047 ACTCCCACTT
*
61057 GGACTCCTGCTAGCA---CATCTTTTA
1 GGACTCCTGCTAGCACTGCGTCTTTTA
61081 GGACTCCTGCTAGCACTGCGTCTTTTA
1 GGACTCCTGCTAGCACTGCGTCTTTTA
* * * *
61108 GGACT-CTGGCTAACACCGCTTCTCTTA
1 GGACTCCT-GCTAGCACTGCGTCTTTTA
* *
61135 GGACTCCGGCTAAG-ACTGCGTCTCTTA
1 GGACTCCTGCT-AGCACTGCGTCTTTTA
*
61162 GGACTCATGCTAGCACTAG-GTCTTTTA
1 GGACTCCTGCTAGCACT-GCGTCTTTTA
*
61189 GGACTCCTGCTAACACTAG-GTCTTTTA
1 GGACTCCTGCTAGCACT-GCGTCTTTTA
61216 GGACTCCTGCT
1 GGACTCCTGCT
61227 CCTTCCTTTT
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.12
26 4 0.03
27 102 0.82
28 3 0.02
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (27 bp):
GGACTCCTGCTAGCACTGCGTCTTTTA
Found at i:66010 original size:135 final size:135
Alignment explanation
Indices: 65768--66048 Score: 427
Period size: 135 Copynumber: 2.1 Consensus size: 135
65758 TGAGATGAAA
* *
65768 AATTATTATTAGTTGAGACCACATATAAAATGATAAATCGGGATCATCTAAAAAAAATTCGTCCG
1 AATTATTATTAGCTGAGACCACATATAAAATGATAAATCGGGATCATCTAAAAAAAATTCGTCCA
* * * * *
65833 TAAGAGGTAGGCACTCATAAGTAGATATCCGTAAACTCCAAATACCCGTATTTTCATGTAACAAT
66 TAAGAGGTAGGCACCCATAAGTAGATATCCATAAACTCCAAATACACATATTCTCATGTAACAAT
65898 TATCC
131 TATCC
* * * * * *
65903 AATTATTATTAGCTGATACTACATATAACATGATGAATCGGGATCATCTAAAAAAATTTCGTTCA
1 AATTATTATTAGCTGAGACCACATATAAAATGATAAATCGGGATCATCTAAAAAAAATTCGTCCA
*
65968 TAAGAGGTAGGCACCCATAAGTAGATATTCATAAACTCCAAATACACATATTCTCATGTAACAAT
66 TAAGAGGTAGGCACCCATAAGTAGATATCCATAAACTCCAAATACACATATTCTCATGTAACAAT
66033 TATCC
131 TATCC
*
66038 AATTAATATTA
1 AATTATTATTA
66049 ATAATTAAAA
Statistics
Matches: 131, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
135 131 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (135 bp):
AATTATTATTAGCTGAGACCACATATAAAATGATAAATCGGGATCATCTAAAAAAAATTCGTCCA
TAAGAGGTAGGCACCCATAAGTAGATATCCATAAACTCCAAATACACATATTCTCATGTAACAAT
TATCC
Found at i:69224 original size:31 final size:31
Alignment explanation
Indices: 69188--69326 Score: 233
Period size: 31 Copynumber: 4.5 Consensus size: 31
69178 ATATTTATAT
* *
69188 ATTTGGTACTTATTACTTACACATTTAATTA
1 ATTTGGTCCTTATTACTTACACATTTAACTA
69219 ATTTGGTCCTTATTACTTACACATTTAACTA
1 ATTTGGTCCTTATTACTTACACATTTAACTA
69250 ATTTGGTCCTTATTACTTACACATTTAACTA
1 ATTTGGTCCTTATTACTTACACATTTAACTA
*
69281 ATTTGGTCCTTATTACTTACACATTTAACCA
1 ATTTGGTCCTTATTACTTACACATTTAACTA
* *
69312 ATTTGATCCTAATTA
1 ATTTGGTCCTTATTA
69327 TAATTTAGTT
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 103 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (31 bp):
ATTTGGTCCTTATTACTTACACATTTAACTA
Found at i:73321 original size:194 final size:195
Alignment explanation
Indices: 72798--73380 Score: 956
Period size: 195 Copynumber: 3.0 Consensus size: 195
72788 AAATCTTACT
* * *
72798 TTCGATATAATCTTATTCTTGTGCTTTTTTTTCCTTGTCTTTAAGCTTACATGTATCTCGATCTC
1 TTCGATATAACCTTATTCTTGTGC-TTTTTTTCCTTGTCCTTAAGCTTGCATGTATCTCGATCTC
* * * *
72863 GTTCACGGTCTATGTAAGCACCAATTCCAATTATATAATTCAAATCATATGTTAGTATCATAATA
65 GTTCACGATCTATGTAAGCGCCATTTCCAATTATATAATTCAAATCATATGTTAGTATCATACTA
*
72928 ACATAGGCGTATGCTAACAAATAAATTTATAAAAATTATTTCAATACTTTTTCGATACTAATTTC
130 ACATAGGCGCATGCTAACAAATAAATTTATAAAAATTATTTCAATACTTTTTCGATACTAATTTC
72993 A
195 A
* * *
72994 TTCGATATAACCTTATTCTTGTGCTTTTTTCCCTTTTCCTTAAGCTTGCATTTATCTCGATCTCG
1 TTCGATATAACCTTATTCTTGTGCTTTTTTTCCTTGTCCTTAAGCTTGCATGTATCTCGATCTCG
73059 TTCACGATCTATGTAAGCGCCATTTCCAATTATATAATTCAAATCATATGTTAGTATCATACTAA
66 TTCACGATCTATGTAAGCGCCATTTCCAATTATATAATTCAAATCATATGTTAGTATCATACTAA
* *
73124 CATAGGCGCATGCTAACAAATAAATTTATAAAAATTCTTTCAATACTTTTTCGATAGTAATTTCA
131 CATAGGCGCATGCTAACAAATAAATTTATAAAAATTATTTCAATACTTTTTCGATACTAATTTCA
*
73189 TTCGTTATAACCTTATTCTTGTG-TTTTTTTCCTTGTCCTTAAGCTTGCATGTATCTCGATCTCG
1 TTCGATATAACCTTATTCTTGTGCTTTTTTTCCTTGTCCTTAAGCTTGCATGTATCTCGATCTCG
* *
73253 TTCACGATCTATGTAAGCGCCTTTTCCAATTATATAATTCAAATCATATGTTAGTATTATACTAA
66 TTCACGATCTATGTAAGCGCCATTTCCAATTATATAATTCAAATCATATGTTAGTATCATACTAA
* * **
73318 CATAGGCACATGCTAGCAAATAAATTTATAAAAA--AAATCAATACTTTTTCGATACTAATTTCA
131 CATAGGCGCATGCTAACAAATAAATTTATAAAAATTATTTCAATACTTTTTCGATACTAATTTCA
73381 CTTTCAAAAC
Statistics
Matches: 362, Mismatches: 25, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
192 25 0.07
194 133 0.37
195 181 0.50
196 23 0.06
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (195 bp):
TTCGATATAACCTTATTCTTGTGCTTTTTTTCCTTGTCCTTAAGCTTGCATGTATCTCGATCTCG
TTCACGATCTATGTAAGCGCCATTTCCAATTATATAATTCAAATCATATGTTAGTATCATACTAA
CATAGGCGCATGCTAACAAATAAATTTATAAAAATTATTTCAATACTTTTTCGATACTAATTTCA
Found at i:80025 original size:6 final size:6
Alignment explanation
Indices: 80014--80040 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
80004 TTCATGGCAA
80014 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
80041 AACTCGATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:82387 original size:11 final size:11
Alignment explanation
Indices: 82348--82396 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
82338 TAATATTACA
82348 ATATTAA-TTT
1 ATATTAATTTT
*
82358 ATATTACTTTT
1 ATATTAATTTT
* *
82369 TTAGTAATTTT
1 ATATTAATTTT
82380 ATATTAATTTT
1 ATATTAATTTT
82391 AATATT
1 -ATATT
82397 TTTCTATAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
10 6 0.19
11 20 0.65
12 5 0.16
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:82414 original size:2 final size:2
Alignment explanation
Indices: 82407--82435 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
82397 TTTCTATAAT
82407 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 T
82436 GTAGAGTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82415 original size:32 final size:32
Alignment explanation
Indices: 82348--82413 Score: 84
Period size: 30 Copynumber: 2.1 Consensus size: 32
82338 TAATATTACA
*
82348 ATATTAATTTATATTACTTTTTTAGTAATTTT
1 ATATTAATTTATAATACTTTTTTAGTAATTTT
*
82380 ATATTAATTT-TAATA-TTTTTCTA-TAATTAT
1 ATATTAATTTATAATACTTTTT-TAGTAATTTT
82410 ATAT
1 ATAT
82414 ATATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 15 0.48
31 6 0.19
32 10 0.32
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (32 bp):
ATATTAATTTATAATACTTTTTTAGTAATTTT
Found at i:82896 original size:8 final size:8
Alignment explanation
Indices: 82885--82981 Score: 76
Period size: 8 Copynumber: 12.0 Consensus size: 8
82875 GGAAAAATAT
82885 TAATAAAA
1 TAATAAAA
82893 TAAT--AA
1 TAATAAAA
82899 TAATAAAA
1 TAATAAAA
82907 TAAATAAAA
1 T-AATAAAA
82916 T-ATAAAGA
1 TAATAAA-A
82924 TAAATAAAA
1 T-AATAAAA
*
82933 GTTAGTAAAA
1 --TAATAAAA
82943 -AATAAAA
1 TAATAAAA
*
82950 AAATAAAA
1 TAATAAAA
*
82958 AAATAAAA
1 TAATAAAA
*
82966 AAATAAAA
1 TAATAAAA
*
82974 AAATAAAA
1 TAATAAAA
82982 AAAATAAAGT
Statistics
Matches: 78, Mismatches: 2, Indels: 18
0.80 0.02 0.18
Matches are distributed among these distances:
6 6 0.08
7 11 0.14
8 40 0.51
9 9 0.12
10 11 0.14
11 1 0.01
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (8 bp):
TAATAAAA
Found at i:82902 original size:14 final size:14
Alignment explanation
Indices: 82880--82909 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
82870 AAAAAGGAAA
*
82880 AATATTAATAAAAT
1 AATAATAATAAAAT
82894 AATAATAATAAAAT
1 AATAATAATAAAAT
82908 AA
1 AA
82910 ATAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:82926 original size:17 final size:16
Alignment explanation
Indices: 82851--83022 Score: 97
Period size: 16 Copynumber: 10.2 Consensus size: 16
82841 ATTAGATTGT
82851 AAAATAAAAATAAATATA
1 AAAAT-AAAA-AAATATA
82869 AAAA-AAGGAAAAATAT-
1 AAAATAA--AAAAATATA
* *
82885 -TAATAAAATAATAATAA
1 AAAATAAAAAAAT-AT-A
82902 TAAAATAAATAAAATATA
1 -AAAATAAA-AAAATATA
*
82920 AAGATAAATAAAAGTTAGTAA
1 AAAATAAA-AAAA--TA-T-A
*
82941 AAAATAAAAAAATAAA
1 AAAATAAAAAAATATA
*
82957 AAAATAAAAAAATAAA
1 AAAATAAAAAAATATA
82973 AAAATAAAAAAA-AT-
1 AAAATAAAAAAATATA
*
82987 AAAGTAAAACAAATA-A
1 AAAATAAAA-AAATATA
83003 ATAAATAAATAAAA-ATA
1 A-AAATAAA-AAAATATA
83020 AAA
1 AAA
83023 GAGACCAAAA
Statistics
Matches: 125, Mismatches: 10, Indels: 40
0.71 0.06 0.23
Matches are distributed among these distances:
14 13 0.10
15 8 0.06
16 38 0.30
17 29 0.23
18 10 0.08
19 10 0.08
20 9 0.07
21 8 0.06
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATAAAAAAATATA
Found at i:82982 original size:8 final size:8
Alignment explanation
Indices: 82897--83017 Score: 107
Period size: 8 Copynumber: 14.0 Consensus size: 8
82887 ATAAAATAAT
*
82897 AATAATAA
1 AATAAAAA
82905 AATAAATAA
1 AATAAA-AA
*
82914 AATATAAA
1 AATAAAAA
*
82922 GATAAATAA
1 AATAAA-AA
82931 AAGTTAGTAAAA
1 AA--TA--AAAA
82943 AATAAAAA
1 AATAAAAA
82951 AATAAAAA
1 AATAAAAA
82959 AATAAAAA
1 AATAAAAA
82967 AATAAAAA
1 AATAAAAA
82975 AATAAAAAA
1 AAT-AAAAA
82984 AATAAAGTAA
1 AATAAA--AA
* *
82994 AACAAATA
1 AATAAAAA
*
83002 AATAAATA
1 AATAAAAA
83010 AATAAAAA
1 AATAAAAA
83018 TAAAAGAGAC
Statistics
Matches: 95, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
8 60 0.63
9 18 0.19
10 9 0.09
11 2 0.02
12 4 0.04
13 2 0.02
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (8 bp):
AATAAAAA
Found at i:83005 original size:51 final size:52
Alignment explanation
Indices: 82897--83017 Score: 129
Period size: 51 Copynumber: 2.3 Consensus size: 52
82887 ATAAAATAAT
* * * * * *
82897 AATAATAAAATAAATAAAATATAAAGATAAATAAAAGTTAGTAAAAAATAAAAA
1 AATAAAAAAATAAA-AAAATAAAAAAATAAATAAAAATAAGT-AAAAACAAAAA
*
82951 AATAAAAAAATAAAAAAATAAAAAAATAAA-AAAAATAAAGT-AAAACAAATA
1 AATAAAAAAATAAAAAAATAAAAAAATAAATAAAAAT-AAGTAAAAACAAAAA
*
83002 AATAAATAAATAAAAA
1 AATAAAAAAATAAAAA
83018 TAAAAGAGAC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
51 23 0.40
52 5 0.09
53 17 0.29
54 13 0.22
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (52 bp):
AATAAAAAAATAAAAAAATAAAAAAATAAATAAAAATAAGTAAAAACAAAAA
Found at i:83545 original size:34 final size:34
Alignment explanation
Indices: 83499--83623 Score: 116
Period size: 34 Copynumber: 3.8 Consensus size: 34
83489 TTCGTCCTAC
*
83499 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTTAAACTCCTAAAAATAGGATAGAATTT
* *
83533 TAGGATTTAAACTCCTAAAGATATGATAGAATTT
1 TAGGATTTAAACTCCTAAAAATAGGATAGAATTT
* * * * *
83567 T--G--CTAGGA-TTCAAAAAATAGGATATAATTT
1 TAGGATTTA-AACTCCTAAAAATAGGATAGAATTT
* *
83597 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTTAAACTCCTAAAAATAGGAT
83624 CCACAAGCAC
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
30 20 0.29
31 1 0.01
32 2 0.03
33 1 0.01
34 46 0.66
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (34 bp):
TAGGATTTAAACTCCTAAAAATAGGATAGAATTT
Found at i:83938 original size:2 final size:2
Alignment explanation
Indices: 83933--83978 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
83923 TTTACTTTAG
* * *
83933 TA TA TA TA TA TA TA TA TA TA TA TA TT TA GA T- TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
83974 TA TA T
1 TA TA T
83979 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:84046 original size:38 final size:39
Alignment explanation
Indices: 83963--84084 Score: 131
Period size: 42 Copynumber: 3.0 Consensus size: 39
83953 TATATTTAGA
* * *
83963 TTATATATAAATATA-TTATTTTTTATTATCAGTTTTATTAAT
1 TTATATATATATATATTTACTTTTTATTAT---TTTT-TTATT
84005 TTATATATATATATATTTACTTTTT-TTATTTTTTTATT
1 TTATATATATATATATTTACTTTTTATTATTTTTTTATT
* *
84043 TTATATATATATTATTTTTACTTTTTTATTATTATTTTATT
1 TTATATATATA-TATATTTAC-TTTTTATTATTTTTTTATT
84084 T
1 T
84085 ATTTGTTTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
38 15 0.21
39 12 0.17
40 5 0.07
41 13 0.18
42 18 0.25
43 8 0.11
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (39 bp):
TTATATATATATATATTTACTTTTTATTATTTTTTTATT
Found at i:84048 original size:36 final size:41
Alignment explanation
Indices: 83964--84086 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 41
83954 ATATTTAGAT
* * * *
83964 TATATATA-AATATATTA-TTTTTTATTATCAGTTTTATTAA
1 TATATATATATTATTTTACTTTTTTATTATTA-TTTTATTTA
* *
84004 TTTATATATATATATATTTAC-TTTTT-TTATTTTTTTATTT-
1 TATATATATAT-TAT-TTTACTTTTTTATTATTATTTTATTTA
84044 TATATATATATTATTTTTACTTTTTTATTATTATTTTATTTA
1 TATATATATATTA-TTTTACTTTTTTATTATTATTTTATTTA
84086 T
1 T
84087 TTGTTTTATT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
39 7 0.10
40 23 0.34
41 21 0.31
42 8 0.12
43 8 0.12
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (41 bp):
TATATATATATTATTTTACTTTTTTATTATTATTTTATTTA
Found at i:84050 original size:30 final size:29
Alignment explanation
Indices: 84014--84139 Score: 110
Period size: 30 Copynumber: 4.1 Consensus size: 29
84004 TTTATATATA
84014 TATATATTTACTTTTTTTATTTTTTTATTT
1 TATATATTTA-TTTTTTTATTTTTTTATTT
* *
84044 TATATATATATTATTTTTACTTTTTTATTAT
1 TATATATTTATT-TTTTTATTTTTTTATT-T
* * *
84075 TATTTTATTTATTTGTTTTATTTCTATATTT
1 TA-TATATTTATTT-TTTTATTTTTTTATTT
* *
84106 TATTTCTTT-TTTTCTTTATTTTTTATATATT
1 TATATATTTATTTT-TTTATTTTTT-TAT-TT
84137 TAT
1 TAT
84140 TTTACTTACT
Statistics
Matches: 79, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.01
29 13 0.16
30 33 0.42
31 12 0.15
32 20 0.25
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (29 bp):
TATATATTTATTTTTTTATTTTTTTATTT
Found at i:84069 original size:25 final size:24
Alignment explanation
Indices: 84041--84117 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
84031 TATTTTTTTA
84041 TTTTATATATATATTATT-TTTACTT
1 TTTTAT-TATATATT-TTATTTACTT
*
84066 TTTTATTAT-TATTTTATTTATTT
1 TTTTATTATATATTTTATTTACTT
*
84089 GTTTTATTTCTATATTTTATTT-CTT
1 -TTTTA-TTATATATTTTATTTACTT
84114 TTTT
1 TTTT
84118 TCTTTATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
22 2 0.04
23 10 0.22
24 12 0.27
25 11 0.24
26 10 0.22
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (24 bp):
TTTTATTATATATTTTATTTACTT
Found at i:84087 original size:4 final size:4
Alignment explanation
Indices: 83996--84141 Score: 57
Period size: 4 Copynumber: 35.8 Consensus size: 4
83986 TATTATCAGT
* * * * * *
83996 TTTA TTAA TTTA TATA TATA TATA TTTA CTTTT TTTA TTTT TTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA -TTTA
* * * *
84046 TATA TATA TTATT TTTA CTTT- TTTA -TTA -TTA TTTTA TTTA TTTGT
1 TTTA TTTA TT-TA TTTA -TTTA TTTA TTTA TTTA -TTTA TTTA TTT-A
* * * * * *
84091 TTTA TTTC TATA TTTTA TTTC TTTT TTTC TTTA TTT- TTTA TATA TTTA
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
84139 TTT
1 TTT
84142 TACTTACTAT
Statistics
Matches: 108, Mismatches: 24, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
3 12 0.11
4 74 0.69
5 22 0.20
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:84095 original size:49 final size:47
Alignment explanation
Indices: 84026--84195 Score: 128
Period size: 49 Copynumber: 3.4 Consensus size: 47
84016 TATATTTACT
*
84026 TTTTTTATTTTTTTATTTTATATATATATTATTTTTACTTTTTTATTA
1 TTTTTTATTTATTTATTTTAT-TATATATTATTTTTACTTTTTTATTA
* * *
84074 TTATTTTATTTATTTGTTTTATTTCTATATT-TTATTT-CTTTTTTTCTTTA
1 TT-TTTTATTTATTTATTTTA-TTATATATTATT-TTTAC-TTTTTT-ATTA
* * * *
84124 TTTTTTATATATTTATTTTACTTACTATTTTATCTTTATTTTCTTTATCTTA
1 TTTTTTATTTATTTATTTTA-TTA-TATATTATTTTTACTTT-TTTA--TTA
* *
84176 TCTTTTATTTAATTTGTTTT
1 TTTTTTATTT-ATTTATTTT
84196 CTCTTTATTT
Statistics
Matches: 95, Mismatches: 15, Indels: 19
0.74 0.12 0.15
Matches are distributed among these distances:
48 5 0.05
49 50 0.53
50 17 0.18
51 4 0.04
52 11 0.12
53 8 0.08
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (47 bp):
TTTTTTATTTATTTATTTTATTATATATTATTTTTACTTTTTTATTA
Found at i:84097 original size:38 final size:39
Alignment explanation
Indices: 84004--84084 Score: 119
Period size: 41 Copynumber: 2.1 Consensus size: 39
83994 GTTTTATTAA
* *
84004 TTTATATATATA-TATATTTACTTTTTTTATTTTTTTAT
1 TTTATATATATATTATTTTTACTTTTTTTATTATTTTAT
84042 TTTATATATATATTATTTTTACTTTTTTATTATTATTTTAT
1 TTTATATATATATTATTTTTAC-TTTTT-TTATTATTTTAT
84083 TT
1 TT
84085 ATTTGTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 12 0.32
39 8 0.21
40 5 0.13
41 13 0.34
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (39 bp):
TTTATATATATATTATTTTTACTTTTTTTATTATTTTAT
Found at i:84104 original size:21 final size:20
Alignment explanation
Indices: 84080--84126 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
84070 ATTATTATTT
*
84080 TATTTATTTGTTTTATTTCTA
1 TATTTATTTCTTTT-TTTCTA
*
84101 TATTTTATTTCTTTTTTTCTT
1 TA-TTTATTTCTTTTTTTCTA
84122 TATTT
1 TATTT
84127 TTTATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.13
21 9 0.39
22 11 0.48
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (20 bp):
TATTTATTTCTTTTTTTCTA
Found at i:84124 original size:38 final size:37
Alignment explanation
Indices: 84072--84185 Score: 81
Period size: 38 Copynumber: 3.0 Consensus size: 37
84062 ACTTTTTTAT
* * *
84072 TATTATTTTATTTATTTGTTTTAT-TTCTATATTTTATTTC
1 TATT-TTTTCTTTATTT-TTTTATATTATAT-TTTA-TTTC
*
84112 T-TTTTTTCTTTATTTTTTATATATT-TATTTTACTTAC
1 TATTTTTTCTTTATTTTTT-TATATTATATTTTA-TTTC
* * *
84149 TATTTTATCTTTATTTTCTTTATCTTATCTTTTATTT
1 TATTTTTTCTTTATTTT-TTTATATTATATTTTATTT
84186 AATTTGTTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
37 10 0.16
38 38 0.62
39 12 0.20
40 1 0.02
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.73
Consensus pattern (37 bp):
TATTTTTTCTTTATTTTTTTATATTATATTTTATTTC
Found at i:84124 original size:53 final size:50
Alignment explanation
Indices: 84025--84142 Score: 118
Period size: 53 Copynumber: 2.3 Consensus size: 50
84015 ATATATTTAC
84025 TTTT-TTTATTTTTTTATTTTATATATATATTATTTTTACTTTTTTATTATT
1 TTTTATTTATTTTTTTATTTTATATATATATTATTTTTA-TTTTTTATT-TT
*
84076 ATTTTATTTATTTGTTTTATTTCTATAT-TTTATT-TCTTTT-TTTCTTTATTTT
1 -TTTTATTTATTT-TTTTATTT-TATATATATATTAT-TTTTATTT-TTTATTTT
84128 TTATATATTTATTTT
1 TT-T-TATTTATTTT
84143 ACTTACTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
51 2 0.03
52 11 0.19
53 23 0.40
54 17 0.29
55 5 0.09
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (50 bp):
TTTTATTTATTTTTTTATTTTATATATATATTATTTTTATTTTTTATTTT
Found at i:84127 original size:21 final size:22
Alignment explanation
Indices: 84078--84127 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
84068 TTATTATTAT
*
84078 TTTA-TTTATTTGTTTTATTTC
1 TTTATTTTATTTCTTTTATTTC
*
84099 TATATTTTATTTCTTTT-TTTC
1 TTTATTTTATTTCTTTTATTTC
84120 TTTATTTT
1 TTTATTTT
84128 TTATATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTATTTTATTTCTTTTATTTC
Found at i:84163 original size:85 final size:85
Alignment explanation
Indices: 84014--84171 Score: 200
Period size: 85 Copynumber: 1.9 Consensus size: 85
84004 TTTATATATA
* *
84014 TATATATTTACTTTTTTTATTTTTTTATTTTATATATATATTATTTTTACTTTTTTATTATTATT
1 TATATATTTACTTTTTTTATTTCTTTATTTTATATATATATTATTTTTACTATTTTATTATTATT
84079 TTATTTATTTGTTTTATTTC
66 TTATTTATTTGTTTTATTTC
*
84099 TATAT-TTTA-TTTCTTTT-TTTCTTTATTTTTTATATAT-TTATTTTACTTACTATTTTATCT-
1 TATATATTTACTTT-TTTTATTTCTTTATTTTATATATATATTA-TTT--TTACTATTTTAT-TA
*
84159 TTATTTTCTTTAT
61 TTATTTTATTTAT
84172 CTTATCTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
82 3 0.05
83 24 0.38
84 8 0.12
85 28 0.44
86 1 0.02
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.73
Consensus pattern (85 bp):
TATATATTTACTTTTTTTATTTCTTTATTTTATATATATATTATTTTTACTATTTTATTATTATT
TTATTTATTTGTTTTATTTC
Found at i:84248 original size:15 final size:15
Alignment explanation
Indices: 84230--84259 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
84220 TATTTATTTC
84230 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
84245 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
84260 ACATGATTTT
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:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:86216 original size:18 final size:18
Alignment explanation
Indices: 86193--86232 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
86183 TTCCTTCAAG
86193 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
86211 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
86229 TCTG
1 TCTG
86233 AAAGACTAAT
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:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
TCTGGATTCACATCCACT
Found at i:86766 original size:8 final size:8
Alignment explanation
Indices: 86746--86791 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
86736 ATGCCTCGAA
86746 CATTTTGTG
1 CATTTT-TG
*
86755 CATTCTTG
1 CATTTTTG
86763 CA-TTTTG
1 CATTTTTG
86770 CATTTTTG
1 CATTTTTG
*
86778 CCTTTTTG
1 CATTTTTG
86786 CATTTT
1 CATTTT
86792 CATCTACATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
7 6 0.19
8 21 0.66
9 5 0.16
ACGTcount: A:0.11, C:0.17, G:0.13, T:0.59
Consensus pattern (8 bp):
CATTTTTG
Found at i:86788 original size:23 final size:24
Alignment explanation
Indices: 86746--86791 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
86736 ATGCCTCGAA
86746 CATTTTGTGCATTCTTGCATTTTG
1 CATTTTGTGCATTCTTGCATTTTG
* *
86770 CATTTT-TGCCTTTTTGCATTTT
1 CATTTTGTGCATTCTTGCATTTT
86792 CATCTACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.11, C:0.17, G:0.13, T:0.59
Consensus pattern (24 bp):
CATTTTGTGCATTCTTGCATTTTG
Found at i:87972 original size:16 final size:16
Alignment explanation
Indices: 87946--87979 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
87936 AGATCCAATC
87946 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
87961 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
87978 AA
1 AA
87980 AAAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:88680 original size:22 final size:22
Alignment explanation
Indices: 88652--88702 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
88642 CCCCATCAAT
88652 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
88674 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
88696 CCTTTGA
1 CCTTTGA
88703 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:89609 original size:36 final size:37
Alignment explanation
Indices: 89562--89666 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 37
89552 GTGCTCACCA
89562 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-CT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
*
89598 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
* * *
89635 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
89667 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 34 0.53
37 30 0.47
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATCT
Found at i:89757 original size:100 final size:100
Alignment explanation
Indices: 89580--89962 Score: 496
Period size: 100 Copynumber: 3.9 Consensus size: 100
89570 CTTGAGACAG
* * * *
89580 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTTTTCTCCCT
1 TTTCCCTTGAAATAAA--TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
89645 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
64 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
89682 TTTCCCTTGAAATAAATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTA
1 TTTCCCTTGAAATAAATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
*
89747 AGACAATTTCTCTTGAAACATAAACATTGAAAACA
66 AGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
89782 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCTT
1 TTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
89846 TGAGACAGTTTCTATTGAAACATAAACTTTGAAAACA
64 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * * * * *
89883 GTTTCCCTTGAAACAAA----ATCT-TTGA-ATATGTTTTACATT-AAAC-AAATTTCGTCTCTC
1 -TTTCCCTTGAAATAAATTGTCTCTCTTGAGATA-G-TTTCCCTTGAAACAAAATTTTGTCTCCC
89940 TTGAGACAGTTTCTCTTGAAACA
63 TTGAGACAGTTTCTCTTGAAACA
89963 AATTTTGTCT
Statistics
Matches: 255, Mismatches: 21, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
94 3 0.01
95 42 0.16
96 9 0.04
100 92 0.36
101 51 0.20
102 58 0.23
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (100 bp):
TTTCCCTTGAAATAAATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
AGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:89829 original size:36 final size:36
Alignment explanation
Indices: 89782--89867 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
89772 ATTGAAAACA
** *
89782 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
89818 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
**
89854 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
89868 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 42 0.95
37 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:89885 original size:30 final size:30
Alignment explanation
Indices: 89850--89908 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
89840 CTCCTTTGAG
*
89850 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
89880 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
89909 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:90036 original size:37 final size:36
Alignment explanation
Indices: 89922--90036 Score: 158
Period size: 36 Copynumber: 3.1 Consensus size: 36
89912 GTTTTACATT
*
89922 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * *
89958 AAACAAATTTTGTCTATCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
*
89995 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
90032 AAACA
1 AAACA
90037 TCAATCCTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
36 24 0.36
37 24 0.36
38 19 0.28
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:90156 original size:34 final size:33
Alignment explanation
Indices: 90078--90193 Score: 155
Period size: 34 Copynumber: 3.5 Consensus size: 33
90068 CCTTGATACA
90078 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC--AAA-AAACCTTTGAAATT
*
90114 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTG-AAATT
*
90148 GTTTCTCTTGAAACAC--AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
90179 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
90194 AATTTTGTCT
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
31 17 0.23
32 10 0.13
33 9 0.12
34 23 0.31
36 16 0.21
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
Found at i:90240 original size:67 final size:67
Alignment explanation
Indices: 90148--90340 Score: 244
Period size: 67 Copynumber: 2.8 Consensus size: 67
90138 TTTGAAAAAT
*
90148 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
90213 CA
66 CA
* * * *
90215 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCTTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAG
* *
90280 GCC
65 ACA
* * * *
90283 GTTTCTCATGAAACAACATATATCTTT-AGTATCGTTTCCCTTGAAACGAATTTTGTCT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAG-ATTGTTTCCCTTGAAACAAATTTTGTCT
90341 TTTTTAAGAC
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
67 40 0.37
68 33 0.31
69 15 0.14
70 19 0.18
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
CA
Found at i:91133 original size:105 final size:105
Alignment explanation
Indices: 90904--91774 Score: 1227
Period size: 105 Copynumber: 8.3 Consensus size: 105
90894 GCCATCTGCG
* * * * * *
90904 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
90969 GGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* *
91013 ATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
91078 ACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
91118 ATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
91183 ACCGCTG-TCTGTCAACAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCT-TGTCAACAACAACTTCTCAATTTCAGAGCCA
91223 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
91288 ACCGCTGCTTGTCAACAACAACTTCTTAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
91328 ATTTCAACTTCACAACAAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
91393 ACCACTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
91433 ATTTCAATTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
91498 ACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
91538 ATTTCAACTTCACAACAAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
91603 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * * * * *
91638 ATTTCAACTTCGCAACGAAGGATACTGGACTCGAGATAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * ** *
91703 A-CGACTGGTTATCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * *
91744 ATTTCAACTTCACGACGGAGGATATTAGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
91775 TGGAACAATG
Statistics
Matches: 697, Mismatches: 55, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
99 2 0.00
100 74 0.11
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 504 0.72
106 78 0.11
107 5 0.01
109 21 0.03
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:92353 original size:34 final size:34
Alignment explanation
Indices: 92310--92434 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
92300 TTCGTCCTAC
92310 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
92344 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
92379 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
92408 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
92435 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:92742 original size:2 final size:2
Alignment explanation
Indices: 92737--92791 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
92727 TTTTACTTTA
* *
92737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AG AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
92778 AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT
92792 TATTTTATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:92840 original size:42 final size:40
Alignment explanation
Indices: 92776--92894 Score: 113
Period size: 42 Copynumber: 3.0 Consensus size: 40
92766 TATATTTAGA
* * *
92776 TTATATATAAATATA-TTATTTTATTATCAGTTTTATTAATTT
1 TTATATATATATTTACTT-TTTTATTAT-A-TTTTATTTATTT
*
92818 TTATATATATATTTACTTTTTTATT-T-TTTT-TTTATAT
1 TTATATATATATTTACTTTTTTATTATATTTTATTTATTT
* *
92855 ATATAT-TATTTTTACTTTTTTATTATTATTTTATTTATTT
1 TTATATATATATTTACTTTTTTATTA-TATTTTATTTATTT
92895 GTTTTATTTC
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
36 17 0.26
37 10 0.15
38 5 0.08
39 4 0.06
40 6 0.09
41 1 0.02
42 20 0.31
43 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.68
Consensus pattern (40 bp):
TTATATATATATTTACTTTTTTATTATATTTTATTTATTT
Found at i:92848 original size:29 final size:28
Alignment explanation
Indices: 92806--92948 Score: 91
Period size: 30 Copynumber: 5.1 Consensus size: 28
92796 TTATTATCAG
*
92806 TTTTATTAATTTTTATATATATATTTACTT
1 TTTTATT-TTTTTTATATATATATTTA-TT
*
92836 TTTTATTTTTTTTTTATATATATATTA-T
1 TTTTATTTTTTTTATATATATAT-TTATT
*
92864 TTTTA-CTTTTTTAT-TAT-TA-TT-TT
1 TTTTATTTTTTTTATATATATATTTATT
* * * *
92887 ATTTATTTGTTTTATTTCTATATTTTATT
1 TTTTATTTTTTTTATATATATA-TTTATT
* * *
92916 TCTTTTTTTTTCTTTATTTTTTATATTTATT
1 T-TTTATTTTT-TTTA-TATATATATTTATT
92947 TT
1 TT
92949 ACTTACTATT
Statistics
Matches: 90, Mismatches: 12, Indels: 22
0.73 0.10 0.18
Matches are distributed among these distances:
23 7 0.08
24 7 0.08
25 4 0.04
26 5 0.06
27 7 0.08
28 8 0.09
29 16 0.18
30 18 0.20
31 11 0.12
32 7 0.08
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (28 bp):
TTTTATTTTTTTTATATATATATTTATT
Found at i:92853 original size:31 final size:30
Alignment explanation
Indices: 92815--92903 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 30
92805 GTTTTATTAA
92815 TTTTTATATATATATTTACTTTTTTATTTTT
1 TTTTTATATATATATTTA-TTTTTTATTTTT
*
92846 TTTTTATATATATA-TTA-TTTTTACTTTT
1 TTTTTATATATATATTTATTTTTTATTTTT
* *
92874 TTATTAT-TATTTTATTTATTTGTTTTATTT
1 TTTTTATATA-TATATTTA-TT-TTTTATTT
92904 CTATATTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
27 2 0.04
28 19 0.39
29 3 0.06
30 3 0.06
31 15 0.31
32 7 0.14
ACGTcount: A:0.22, C:0.02, G:0.01, T:0.74
Consensus pattern (30 bp):
TTTTTATATATATATTTATTTTTTATTTTT
Found at i:92873 original size:36 final size:35
Alignment explanation
Indices: 92819--92888 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
92809 TATTAATTTT
* *
92819 TATATATATATTTACTTTTTTATTTTTTTTTTATA
1 TATATATATATTTACTTTTTTATTATTATTTTATA
*
92854 TATATATTATTTTTACTTTTTTATTATTATTTTAT
1 TATATA-TATATTTACTTTTTTATTATTATTTTAT
92889 TTATTTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (35 bp):
TATATATATATTTACTTTTTTATTATTATTTTATA
Found at i:92899 original size:13 final size:12
Alignment explanation
Indices: 92827--92948 Score: 79
Period size: 13 Copynumber: 9.8 Consensus size: 12
92817 TTTATATATA
*
92827 TATTTACTTTTT
1 TATTTATTTTTT
92839 TATTT-TTTTTT
1 TATTTATTTTTT
* *
92850 TATATATATATTAT
1 TAT-T-TATTTTTT
*
92864 T-TTTACTTTTT
1 TATTTATTTTTT
*
92875 TA-TTATTATTT
1 TATTTATTTTTT
92886 TATTTATTTGTTT
1 TATTTATTT-TTT
* *
92899 TATTTCTATATTT
1 TATTTAT-TTTTT
*
92912 TATTTCTTTTTTTT
1 TA-TT-TATTTTTT
*
92926 TCTTTATTTTTT
1 TATTTATTTTTT
92938 ATATTTATTTT
1 -TATTTATTTT
92949 ACTTACTATT
Statistics
Matches: 84, Mismatches: 16, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
11 23 0.27
12 19 0.23
13 27 0.32
14 13 0.15
15 2 0.02
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (12 bp):
TATTTATTTTTT
Found at i:92900 original size:49 final size:47
Alignment explanation
Indices: 92836--93001 Score: 117
Period size: 49 Copynumber: 3.4 Consensus size: 47
92826 ATATTTACTT
92836 TTTTATTT-TTT-TTTTATATATATATTATTTTTACTTTTTTATTATTA
1 TTTTATTTATTTGTTTTAT-TATATATTATTTTTACTTTTTTATT-TTA
* *
92883 TTTTATTTATTTGTTTTATTTCTATATT-TTATTT-CTTTTTTTTTCTTTA
1 TTTTATTTATTTGTTTTA-TTATATATTATT-TTTAC-TTTTTTAT-TTTA
* * * * *
92932 TTTT-TTATATTTATTTTACTTACTATTTTATCTTTATTTTCTTTATCTTATC
1 TTTTATT-TATTTGTTTTA-TTA-TATATTATTTTTACTTT-TTTAT-TT-TA
92984 TTTTATTTAATTTGTTTT
1 TTTTATTT-ATTTGTTTT
93002 CTCTTTATTT
Statistics
Matches: 94, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
47 8 0.09
48 8 0.09
49 41 0.44
50 13 0.14
51 8 0.09
52 6 0.06
53 10 0.11
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (47 bp):
TTTTATTTATTTGTTTTATTATATATTATTTTTACTTTTTTATTTTA
Found at i:92915 original size:51 final size:53
Alignment explanation
Indices: 92837--92948 Score: 126
Period size: 51 Copynumber: 2.2 Consensus size: 53
92827 TATTTACTTT
92837 TTTATTTTTTTTTTATATATATATTATTT-TTACTTTTTT-ATTATTATTT-TA
1 TTTATTTTTTTTTTATATATATATTATTTCTT-CTTTTTTCATTATTATTTATA
* * * *
92888 TTTATTTGTTTTATTTCTATAT-T-TTATTTCTTTTTTTTTCTTTATTTTTTATA
1 TTTATTT-TTTT-TTTATATATATATTATTTCTTCTTTTTTCATTATTATTTATA
92941 TTTATTTT
1 TTTATTTT
92949 ACTTACTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
51 19 0.37
52 16 0.31
53 17 0.33
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.77
Consensus pattern (53 bp):
TTTATTTTTTTTTTATATATATATTATTTCTTCTTTTTTCATTATTATTTATA
Found at i:92948 original size:23 final size:23
Alignment explanation
Indices: 92922--92977 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
92912 TATTTCTTTT
*
92922 TTTTTCTTTATTTTTTATATTTA
1 TTTTTCTTTATATTTTATATTTA
* *
92945 TTTTAC-TTACTATTTTATCTTTA
1 TTTTTCTTTA-TATTTTATATTTA
92968 -TTTTCTTTAT
1 TTTTTCTTTAT
92978 CTTATCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTCTTTATATTTTATATTTA
Found at i:92971 original size:11 final size:11
Alignment explanation
Indices: 92916--93013 Score: 55
Period size: 11 Copynumber: 9.0 Consensus size: 11
92906 ATATTTTATT
*
92916 TCTTT-TTTTT
1 TCTTTATTTTA
92926 TCTTTATTTTTTA
1 TCTTTA--TTTTA
*
92939 TATTTATTTTA
1 TCTTTATTTTA
92950 -CTTACTATTTTA
1 TCTT--TATTTTA
92962 TCTTTA-TTT-
1 TCTTTATTTTA
*
92971 TCTTTATCTTA
1 TCTTTATTTTA
92982 TCTTT-TATTTA
1 TCTTTAT-TTTA
* * *
92993 -ATTTGTTTTC
1 TCTTTATTTTA
93003 TCTTTATTTTA
1 TCTTTATTTTA
93014 ATTTAATTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 21
0.68 0.10 0.21
Matches are distributed among these distances:
9 6 0.09
10 19 0.28
11 23 0.34
12 7 0.10
13 12 0.18
ACGTcount: A:0.16, C:0.10, G:0.01, T:0.72
Consensus pattern (11 bp):
TCTTTATTTTA
Found at i:93054 original size:15 final size:15
Alignment explanation
Indices: 93036--93065 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
93026 TATTTATTTC
93036 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
93051 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
93066 ACATGGTTTT
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:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:94182 original size:4 final size:4
Alignment explanation
Indices: 94166--94232 Score: 60
Period size: 4 Copynumber: 18.5 Consensus size: 4
94156 GGACCTACAA
94166 AAAT AAA- AAAT AAAT -AAT -AAT -AAT -AAT -AAT -AAT -AAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
94206 AAAT AAAT AAAT AAAT ACAT AATAT AA
1 AAAT AAAT AAAT AAAT AAAT AA-AT AA
94233 TAATTTTTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
3 24 0.41
4 30 0.52
5 4 0.07
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:94186 original size:3 final size:3
Alignment explanation
Indices: 94178--94236 Score: 57
Period size: 3 Copynumber: 18.0 Consensus size: 3
94168 ATAAAAAATA
94178 AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAAT AAAT AAAT AAAT ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT -AAT -AAT -AAT A-AT
94226 AAT -AT AAT AAT
1 AAT AAT AAT AAT
94237 TTTTTTAGAC
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 29 0.55
4 22 0.42
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:94195 original size:12 final size:13
Alignment explanation
Indices: 94166--94229 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 13
94156 GGACCTACAA
94166 AAATAA-AA-AAT
1 AAATAATAATAAT
94177 AAATAATAATAAT
1 AAATAATAATAAT
94190 -AATAATAATAAT
1 AAATAATAATAAT
94202 AAATAAATAAATAAAT
1 AAAT-AAT-AAT-AAT
94218 AAATACATAATA
1 AAATA-ATAATA
94230 TAATAATTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.13
12 14 0.30
13 6 0.13
14 4 0.09
15 7 0.15
16 9 0.20
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:94234 original size:12 final size:10
Alignment explanation
Indices: 94174--94236 Score: 67
Period size: 12 Copynumber: 6.0 Consensus size: 10
94164 AAAAATAAAA
94174 AATAAATAAT
1 AATAAATAAT
94184 AAT-AATAAT
1 AATAAATAAT
94193 AAT-AATAAT
1 AATAAATAAT
94202 AAATAAATAAAT
1 -AATAAAT-AAT
94214 AAATAAATACAT
1 -AATAAATA-AT
94226 AATATAATAAT
1 AATA-AATAAT
94237 TTTTTTAGAC
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
9 15 0.31
10 6 0.12
11 10 0.21
12 17 0.35
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
AATAAATAAT
Found at i:94696 original size:124 final size:124
Alignment explanation
Indices: 94543--94950 Score: 629
Period size: 124 Copynumber: 3.3 Consensus size: 124
94533 ATTCTTTGTC
** * * *
94543 GTGAAGTTGAAATCCAATCTTGAGATGAATGTTGTTGGTGGGCACGATTCCCTTCGCCGTGAAGT
1 GTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGCACAATTCCCTTCGTCGTGAAGT
94608 TGAAACCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTT
66 TGAAACCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTT
* * **
94667 GAGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGAATTATTCCCTTCGTCGTGAAGT
1 GTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGCACAATTCCCTTCGTCGTGAAGT
* * *
94732 TGAAACCGTGGATGGCCCCTTCGTTGTGAAATTGAGCCTTGAATTGGATATCCTTCATCT
66 TGAAACCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGT-T
* * * *
94792 -TGAAGTTGAAATCCAATCTAAAGACGAATGTTACTGGTGAGCACAATTCCCTTCATCGTGAAGT
1 GTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGCACAATTCCCTTCGTCGTGAAGT
* *
94856 TGAAACCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGAATTGGATATCATTCGTC
66 TGAAACCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTT
*
94915 GTGAAGTTGAAATCCAATTTAAAGATGAATGTTGCT
1 GTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCT
94951 TCGAGTCCAA
Statistics
Matches: 255, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
124 254 1.00
125 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (124 bp):
GTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTGGTGGGCACAATTCCCTTCGTCGTGAAGT
TGAAACCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTT
Found at i:95167 original size:110 final size:111
Alignment explanation
Indices: 95007--95418 Score: 366
Period size: 110 Copynumber: 3.6 Consensus size: 111
94997 AAACTGGGAA
** *
95007 GCCCCTTCGCCGTGAAGTTGAG-CTTTGAATTAGATATCCTTCGTCGTGAAGTTGAAATCCAATC
1 GCCCCTTCGTTGTGAAGTTGAGTCTTTGAATTAAATATCCTTCGTCGTGAAGTTGAAATCCAATC
* *
95071 TAGAGTTGGCTTGATATCTTTCGTCGTGAAGTTGAAATCGTGGATG
66 TAGAGTTGGCTCGATATCATTCGTCGTGAAGTTGAAATCGTGGATG
* * * * *
95117 GCCCTTTCCTTGTGAAGTTGAGTC-TTGACTTAAATATCCTTCGTTGTGAAGTTGAAATCCAAGC
1 GCCCCTTCGTTGTGAAGTTGAGTCTTTGAATTAAATATCCTTCGTCGTGAAGTTGAAATCCAATC
* * * * *
95181 TTGTATTGTTTCGAG-TCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAATGAAACTGG
66 TAG-A--G-TT-G-GCT-CGATATCATTCGTCGTGAAGTTGAAA-----TC-G--TG-GA-T-G
** **
95244 GAAACCCCTTCGACGTGAAGTTGA-TCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCA
1 G---CCCCTTCGTTGTGAAGTTGAGTCTTTGAATTAAATATCCTTCGTCGTGAAGTTGAAATCCA
* **
95308 ATCTAGAGTTGGCACGATATCATTCGTTTTGAAGTTGAAATCGTGGATG
63 ATCTAGAGTTGGCTCGATATCATTCGTCGTGAAGTTGAAATCGTGGATG
* * * *
95357 GCCCCTTCGTTGTGAAGTTGAG-CCTTGACTTGAATATCCTTCATCGTGAAGTTGAAATCCAA
1 GCCCCTTCGTTGTGAAGTTGAGTCTTTGAATTAAATATCCTTCGTCGTGAAGTTGAAATCCAA
95419 GTATTATATG
Statistics
Matches: 240, Mismatches: 37, Indels: 50
0.73 0.11 0.15
Matches are distributed among these distances:
110 110 0.46
111 2 0.01
113 3 0.01
114 3 0.01
115 3 0.01
116 25 0.10
118 1 0.00
119 2 0.01
121 2 0.01
122 1 0.00
124 24 0.10
125 2 0.01
126 3 0.01
127 3 0.01
129 3 0.01
130 53 0.22
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (111 bp):
GCCCCTTCGTTGTGAAGTTGAGTCTTTGAATTAAATATCCTTCGTCGTGAAGTTGAAATCCAATC
TAGAGTTGGCTCGATATCATTCGTCGTGAAGTTGAAATCGTGGATG
Found at i:95277 original size:240 final size:244
Alignment explanation
Indices: 94847--95419 Score: 859
Period size: 240 Copynumber: 2.4 Consensus size: 244
94837 ATTCCCTTCA
* * * *
94847 TCGTGAAGTTGAAACCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGAATTGGATATCATTC
1 TCGTGAAGTTGAAATCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGACTTGAATATCCTTC
* *
94912 GTCGTGAAGTTGAAATCCAA-TTTAAAGATGAATGTTGCTTCGAGTCCAATATCCTTCGCCGTTA
66 GTCGTGAAGTTGAAATCCAAGCTT--AGAT-AA-GTTGCTTCGAGTCCAATATCCTTCGCCGTGA
* *
94976 AGTTGAAATTGGCTCTAAATGAAACTGGGAAGCCCCTTCGCCGTGAAGTTGAGCTTTGAATTAGA
127 AGTTGAAATTGGCTCTAAATGAAACTGGGAAACCCCTTCGACGTGAAGTTGAGCTTTGAATTAGA
** *
95041 TATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCTTGATATCTTTCG
192 TATCCTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCATTCG
* * * *
95094 TCGTGAAGTTGAAATCGTGGATGGCCCTTTCCTTGTGAAGTTGAGTCTTGACTTAAATATCCTTC
1 TCGTGAAGTTGAAATCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGACTTGAATATCCTTC
* *
95159 GTTGTGAAGTTGAAATCCAAGCTT-G-T-A-TTGTTTCGAGTCCAATATCCTTCGCCGTGAAGTT
66 GTCGTGAAGTTGAAATCCAAGCTTAGATAAGTTGCTTCGAGTCCAATATCCTTCGCCGTGAAGTT
* * *
95220 GAAATTGGCTCTGAATGAAACTGGGAAACCCCTTCGACGTGAAGTTGATCTTTGAATTGGATATC
131 GAAATTGGCTCTAAATGAAACTGGGAAACCCCTTCGACGTGAAGTTGAGCTTTGAATTAGATATC
95285 CTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCATTCG
196 CTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCATTCG
** *
95334 TTTTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCTTC
1 TCGTGAAGTTGAAATCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGACTTGAATATCCTTC
*
95399 ATCGTGAAGTTGAAATCCAAG
66 GTCGTGAAGTTGAAATCCAAG
95420 TATTATATGT
Statistics
Matches: 297, Mismatches: 28, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
240 216 0.73
242 1 0.00
244 1 0.00
245 1 0.00
247 76 0.26
248 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (244 bp):
TCGTGAAGTTGAAATCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTTGACTTGAATATCCTTC
GTCGTGAAGTTGAAATCCAAGCTTAGATAAGTTGCTTCGAGTCCAATATCCTTCGCCGTGAAGTT
GAAATTGGCTCTAAATGAAACTGGGAAACCCCTTCGACGTGAAGTTGAGCTTTGAATTAGATATC
CTTCGTCGTGAAGTTGAAATCCAATCTAGAGTTGGCACGATATCATTCG
Found at i:96744 original size:96 final size:95
Alignment explanation
Indices: 96522--96778 Score: 336
Period size: 96 Copynumber: 2.7 Consensus size: 95
96512 GGCTAGATGG
* * * * * * *
96522 ATCCATAAAGCCAGTGCGTTTAACCAATTTCTCTAGAGGGACATCTCAATATCATTGTATAG-AT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGATAACTC-A-AGC-TT-TATTGTAT
*
96586 ATTATAATCGCCTTTATCAGGCTAGCTAAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTAAATATT
*
96620 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATATTA
* *
96685 TAATCACCTTTATCAGGCTTAGCTGAATCTT
66 TAATCACCTTTATCAGGC-TAGCTAAATATT
* * *
96716 ATCCATAAAGTCGGGGCGTTTAATCAATTGCTTTAGAGGGATAACTCAAGCTTTATTGTATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATAT
96779 ATGTAATATT
Statistics
Matches: 142, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
94 4 0.03
95 25 0.18
96 71 0.50
97 1 0.01
98 41 0.29
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTAAATATT
Found at i:100166 original size:19 final size:19
Alignment explanation
Indices: 100119--100166 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
100109 GAAAAATAAT
*
100119 AAAATAAAATAAAATAAACC
1 AAAAT-AAATAAAAGAAACC
*
100139 AATAA-AAATAAAAGGAACC
1 AA-AATAAATAAAAGAAACC
100158 AAAATAAAT
1 AAAATAAAT
100167 GATGTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 18 0.75
20 2 0.08
21 2 0.08
ACGTcount: A:0.73, C:0.08, G:0.04, T:0.15
Consensus pattern (19 bp):
AAAATAAATAAAAGAAACC
Done.