Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_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: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 17
Found at i:2990616 original size:20 final size:22
Alignment explanation
Indices: 2990580--2990619 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2990570 TTAGAAATTT
2990580 AAAATTCATATATTTTATTAAA
1 AAAATTCATATATTTTATTAAA
2990602 AAAATT-ATATA-TTTATTA
1 AAAATTCATATATTTTATTA
2990620 TTTTCATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAATTCATATATTTTATTAAA
Found at i:2990649 original size:20 final size:21
Alignment explanation
Indices: 2990615--2990664 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
2990605 ATTATATATT
2990615 TATTATTTTCATAATATTT-A
1 TATTATTTTCATAATATTTCA
*
2990635 TATTATTTT-ATTAATGTTTCA
1 TATTATTTTCA-TAATATTTCA
*
2990656 TTTTATTTT
1 TATTATTTT
2990665 TCAAGTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 16 0.62
21 9 0.35
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTATTTTCATAATATTTCA
Found at i:2995704 original size:8 final size:8
Alignment explanation
Indices: 2995693--2995731 Score: 51
Period size: 8 Copynumber: 4.5 Consensus size: 8
2995683 TGAAAAAAAC
2995693 AAAAGGAA
1 AAAAGGAA
2995701 AAAAGAAGAAA
1 AAAAG--G-AA
2995712 AAAAGGAA
1 AAAAGGAA
2995720 AAAAGGAA
1 AAAAGGAA
2995728 AAAA
1 AAAA
2995732 TTGAACCAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 19 0.68
9 1 0.04
10 1 0.04
11 7 0.25
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAGGAA
Found at i:2995731 original size:19 final size:18
Alignment explanation
Indices: 2995687--2995731 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
2995677 TATACTTGAA
2995687 AAAAACAAAAGGAAAAAAG
1 AAAAA-AAAAGGAAAAAAG
2995706 AAGAAAAAAAGGAAAAAAG
1 AA-AAAAAAAGGAAAAAAG
*
2995725 GAAAAAA
1 AAAAAAA
2995732 TTGAACCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 16 0.67
20 3 0.12
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGGAAAAAAG
Found at i:3000491 original size:22 final size:22
Alignment explanation
Indices: 3000465--3000522 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
3000455 TACATCTACA
3000465 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
3000487 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
3000509 CTTTTCAAAGATGA
1 CTCTTCAAAGATGA
3000523 AAGCTTTATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:3001365 original size:73 final size:73
Alignment explanation
Indices: 3001190--3001439 Score: 347
Period size: 73 Copynumber: 3.4 Consensus size: 73
3001180 CTATTTCCAA
* * * * *
3001190 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA--TCTT--A
* *
3001255 AACCCTCAAGGT
62 AAGCCTCAGGGT
3001267 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
3001332 CTCAGGGT
66 CTCAGGGT
* ***
3001340 CATCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCATAAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
3001405 CTCAGGGT
66 CTCAGGGT
* *
3001413 CATCTGTAAGCCCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
3001440 ATAAGACCTC
Statistics
Matches: 160, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
73 105 0.66
75 3 0.02
77 52 0.32
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:3001826 original size:123 final size:124
Alignment explanation
Indices: 3001605--3001929 Score: 458
Period size: 123 Copynumber: 2.6 Consensus size: 124
3001595 ATCAACGTTG
* *
3001605 CCAGAGAAAGTTCATAATGAGAAGAATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAG
1 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
* * *
3001670 CTTGTTCAACCTTTTGCATGAATCTATCAC-AAAAGGAGATAGATCAACACCAACT-TTT
66 CTTGTTCAACCTTTTGCATGAATCCATCACAAAAAAGAGATAGAGCAACA-CAACTATTT
*
3001728 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAGGAAGTTCATAATGAGAAGAA
1 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
* * ** * * *
3001793 CTTGTTCAACCTTTTGCTTGACTCCATTTCAAAAAAGAGATAGAGCAGCAGAGCTATTT
66 CTTGTTCAACCTTTTGCATGAATCCATCACAAAAAAGAGATAGAGCAACACAACTATTT
* * * *
3001852 CCAG-GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAAAAGTTCATAATGAGAAGA
1 CCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
3001916 ACTTGTTCAACCTT
65 ACTTGTTCAACCTT
3001930 GCATTGATTT
Statistics
Matches: 181, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
123 91 0.50
124 90 0.50
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (124 bp):
CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACCTTTTGCATGAATCCATCACAAAAAAGAGATAGAGCAACACAACTATTT
Found at i:3001895 original size:124 final size:123
Alignment explanation
Indices: 3001605--3001929 Score: 458
Period size: 124 Copynumber: 2.6 Consensus size: 123
3001595 ATCAACGTTG
* *
3001605 CCAGAGAAAGTTCATAATGAGAAGAATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAG
1 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
* *
3001670 CTTGTTCAACCTTTTGCATGAATCTATCACAAAAGGAGATAGATCAACACCAACTTTT
66 CTTGTTCAACCTTTTGCATGAATCTATCACAAAAAGAGATAGAGCAACACCAACTTTT
*
3001728 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAGGAAGTTCATAATGAGAAGAA
1 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
* * * * * *
3001793 CTTGTTCAACCTTTTGCTTGACTCCATTTCA-AAAAAGAGATAGAGCAGCA-GAGCTATTT
66 CTTGTTCAACCTTTTGCATGAAT-C-TATCACAAAAAGAGATAGAGCAACACCAACT-TTT
* * * *
3001852 CCAG-GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAAAAGTTCATAATGAGAAGA
1 CCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
3001916 ACTTGTTCAACCTT
65 ACTTGTTCAACCTT
3001930 GCATTGATTT
Statistics
Matches: 182, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
123 87 0.48
124 91 0.50
125 4 0.02
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (123 bp):
CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACCTTTTGCATGAATCTATCACAAAAAGAGATAGAGCAACACCAACTTTT
Found at i:3002172 original size:138 final size:139
Alignment explanation
Indices: 3001847--3002203 Score: 445
Period size: 139 Copynumber: 2.6 Consensus size: 139
3001837 GCAGCAGAGC
*
3001847 TATTTCCAG-GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAAAAGTTCATAATGA
1 TATTTCCAGAG-GAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGA
* * * * * *
3001911 GAAGAACTTGTTCAACCTTGCATTGATTTATCTCCGATGGAATTGAATGAAAGAAGAACCTCATT
65 GAAGAATTTGTTCAACCTTACATTAATTCATCTACGATGGAATTGAATCAAAGAAGAACCTCATT
*
3001976 TGAGGATCAA
130 TGAAGATCAA
* * *
3001986 TATTTTCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAG
1 TATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAG
* * ** *
3002051 AAGAATTTGTTCAACCTTACCTTAATTCATC-ACGTATGGAGTTGAATCAACA-AA-TCCCTCTT
66 AAGAATTTGTTCAACCTTACATTAATTCATCTACG-ATGGAATTGAATCAA-AGAAGAACCTCAT
*
3002113 TTGAAGATCAG
129 TTGAAGATCAA
* * *
3002124 TATTTCCAGAAGG-AGTTCATAATAAGAAGAACTCATCTGAAAAAGAAGAAGAAGTTCAAAATGA
1 TATTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGA
* *
3002188 GAAGATTTTTTTCAAC
65 GAAGAATTTGTTCAAC
3002204 TTTTTGCTAG
Statistics
Matches: 189, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
138 84 0.44
139 103 0.54
140 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (139 bp):
TATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAG
AAGAATTTGTTCAACCTTACATTAATTCATCTACGATGGAATTGAATCAAAGAAGAACCTCATTT
GAAGATCAA
Found at i:3002499 original size:39 final size:39
Alignment explanation
Indices: 3002452--3002526 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
3002442 CCCTCCATCC
*
3002452 AGCAGCCCCTCCACACATCATTTCCAGCAGCTTCCAGCG
1 AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGCG
* *
3002491 AGCAGCCCCTCCACGCATCAGTTGCAGCAGCTTCCA
1 AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCA
3002527 ACACTGCCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.23, C:0.43, G:0.17, T:0.17
Consensus pattern (39 bp):
AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGCG
Found at i:3004025 original size:12 final size:12
Alignment explanation
Indices: 3003993--3004035 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3003983 ATCATTACTT
3003993 TTATATTTAATTA
1 TTAT-TTTAATTA
**
3004006 TTGCTTTAATTA
1 TTATTTTAATTA
3004018 TTATTTT-ATTA
1 TTATTTTAATTA
3004029 TTATTTT
1 TTATTTT
3004036 TATCTTATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 11 0.42
12 13 0.50
13 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTATTTTAATTA
Found at i:3004310 original size:18 final size:19
Alignment explanation
Indices: 3004277--3004325 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
3004267 CATTTTCTGA
3004277 TATTTTAA-ATAA-TATAT-
1 TATTTTAATA-AATTATATC
3004294 TACTTTT-ATAAATTATATC
1 TA-TTTTAATAAATTATATC
3004313 TATTTTAATAAAT
1 TATTTTAATAAAT
3004326 GCTTTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 5 0.19
18 14 0.52
19 8 0.30
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTTAATAAATTATATC
Found at i:3007704 original size:35 final size:36
Alignment explanation
Indices: 3007658--3007731 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 36
3007648 TGAACGACTG
3007658 TCCCTGAAACTTCATAGCCGTCTATATTAG-TTGAA
1 TCCCTGAAACTTCATAGCCGTCTATATTAGTTTGAA
3007693 TCCCTGAAACTTCATAGCCGTCTATATTAGTTTGAA
1 TCCCTGAAACTTCATAGCCGTCTATATTAGTTTGAA
3007729 TCC
1 TCC
3007732 ATTCATTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 30 0.79
36 8 0.21
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (36 bp):
TCCCTGAAACTTCATAGCCGTCTATATTAGTTTGAA
Found at i:3013011 original size:12 final size:12
Alignment explanation
Indices: 3012994--3013018 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3012984 AAGAAAAAGC
3012994 ATAAAATATTAA
1 ATAAAATATTAA
3013006 ATAAAATATTAA
1 ATAAAATATTAA
3013018 A
1 A
3013019 AGAGAAAATA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAATATTAA
Found at i:3013031 original size:5 final size:5
Alignment explanation
Indices: 3013023--3013091 Score: 50
Period size: 5 Copynumber: 13.4 Consensus size: 5
3013013 ATTAAAAGAG
* * * *
3013023 AAAAT AAAAAT AAAAT AAAAC AAAAC AAAAC AAAAT AATAAT -AAAT AAAAG
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT
* *
3013074 AGAAAT ATAAT ATAAT AA
1 A-AAAT AAAAT AAAAT AA
3013092 TAAATAATAG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
4 3 0.06
5 39 0.72
6 12 0.22
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:3013162 original size:18 final size:19
Alignment explanation
Indices: 3013141--3013184 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3013131 GTTGTTTTTA
*
3013141 AAATAAAAG-ATAAGAATT
1 AAATAAAAGAAAAAGAATT
*
3013159 AAATAAAAGAAAAATAATT
1 AAATAAAAGAAAAAGAATT
3013178 AAATAAA
1 AAATAAA
3013185 TGATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (19 bp):
AAATAAAAGAAAAAGAATT
Found at i:3014691 original size:42 final size:41
Alignment explanation
Indices: 3014644--3014870 Score: 115
Period size: 42 Copynumber: 5.3 Consensus size: 41
3014634 TTTAGATGAC
3014644 TCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGT
1 TCCCCTTCACGGGAAA-CCATGTGGTATATTCCTCAGGTGGT
* * * ** **
3014686 TCCCCTTCGCGAGTCTAAACCAAGTGAG-ATGA-T-CTTTGGATGAC
1 TCCCCTTCACG-G--GAAACCATGTG-GTAT-ATTCCTCAGG-TGGT
* ** *
3014730 TCCCCTTAATAGGAAAGCCATGTGGTATATACCTCAGGTGGT
1 TCCCCTTCACGGGAAA-CCATGTGGTATATTCCTCAGGTGGT
* * ** **
3014772 TCCCCTTCACGGGTGTTAACCAAGTGAG-ATGA-T-CTTTGGATGAC
1 TCCCCTTCAC-GG-G-AAACCATGTG-GTAT-ATTCCTCAGG-TGGT
3014816 TCCCCTTCACGGGAAACCCATGTGGTATATTCCTCAGGTGGT
1 TCCCCTTCACGGGAAA-CCATGTGGTATATTCCTCAGGTGGT
*
3014858 TCCCCTTCTCGGG
1 TCCCCTTCACGGG
3014871 TCTGAACCAA
Statistics
Matches: 130, Mismatches: 35, Indels: 40
0.63 0.17 0.20
Matches are distributed among these distances:
41 9 0.07
42 52 0.40
43 21 0.16
44 39 0.30
45 9 0.07
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (41 bp):
TCCCCTTCACGGGAAACCATGTGGTATATTCCTCAGGTGGT
Found at i:3014750 original size:86 final size:86
Alignment explanation
Indices: 3014632--3015097 Score: 743
Period size: 86 Copynumber: 5.4 Consensus size: 86
3014622 CGGTCATAAT
*
3014632 TCTTTAGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTCGCG
* *
3014697 AGTCTAAACCAAGTGAGATGA
66 GGTCTGAACCAAGTGAGATGA
* ** * *
3014718 TCTTTGGATGACTCCCCTTAATAGGAAAGCCATGTGGTATATACCTCAGGTGGTTCCCCTTCACG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTCGCG
* *
3014783 GGTGTTAACCAAGTGAGATGA
66 GGTCTGAACCAAGTGAGATGA
* *
3014804 TCTTTGGATGACTCCCCTTCACGGGAAACCCATGTGGTATATTCCTCAGGTGGTTCCCCTTCTCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTCGCG
3014869 GGTCTGAACCAAGTGAGATGA
66 GGTCTGAACCAAGTGAGATGA
* * * *
3014890 TCTTTGGATGACTCCCTTTCACTGGAAAGCCATGTGTTATATTCCTCAGGTGGTTCTCCTTCGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTCGCG
3014955 GGTCTGAACCAAGTGAGATGA
66 GGTCTGAACCAAGTGAGATGA
* * * *
3014976 TCTTTGGATGACTCCCCTTCACGGGAAAACCATGTGGTATATTCCTTAGGTGGTTCTCCTTTGCG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTCGCG
*
3015041 GGTCTGAACCAAGTGATATGA
66 GGTCTGAACCAAGTGAGATGA
3015062 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTG
1 TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTG
3015098 AGGTAGTCTT
Statistics
Matches: 349, Mismatches: 31, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 349 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (86 bp):
TCTTTGGATGACTCCCCTTCACGGGAAAGCCATGTGGTATATTCCTCAGGTGGTTCCCCTTCGCG
GGTCTGAACCAAGTGAGATGA
Found at i:3030752 original size:38 final size:36
Alignment explanation
Indices: 3030705--3030987 Score: 247
Period size: 38 Copynumber: 7.6 Consensus size: 36
3030695 AGAAACTATA
*
3030705 TATATTATATACGTTTTCAAAAACATTTAAAAAAAAC
1 TATATTATATACGTTTTCAAAAACATTT-TAAAAAAC
*
3030742 ATATATTATAT--GTTTTCAAAAATACATTTTCAAAAAC
1 -TATATTATATACGTTTTC-AAAA-ACATTTTAAAAAAC
* **
3030779 TATATTATATATGTTTTCCAAAAACCATTTTTTTTAAAAC
1 TATATTATATACGTTTT-CAAAAA-CA--TTTTAAAAAAC
* * *
3030819 CATA-TAGTATACGTTTTCAAAACCGTTTTAAAAAAC
1 TATATTA-TATACGTTTTCAAAAACATTTTAAAAAAC
*
3030855 TATA-TATTATACGTTTTCAAAACCATTTT-AAAAAC
1 TATATTA-TATACGTTTTCAAAAACATTTTAAAAAAC
* *
3030890 TATATGT-TATATGTTTTCAAAAATACGTTTTAAAAAAC
1 TATAT-TATATACGTTTTC-AAAA-ACATTTTAAAAAAC
* *
3030928 TATATTATATATGTTTTCAAAAATACATTTTCAAAAAC
1 TATATTATATACGTTTTC-AAAA-ACATTTTAAAAAAC
*
3030966 TATA-TATTATACATTTTCAAAA
1 TATATTA-TATACGTTTTCAAAA
3030988 CATATACTAT
Statistics
Matches: 209, Mismatches: 20, Indels: 33
0.80 0.08 0.13
Matches are distributed among these distances:
35 20 0.10
36 55 0.26
37 24 0.11
38 81 0.39
39 8 0.04
40 21 0.10
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.41
Consensus pattern (36 bp):
TATATTATATACGTTTTCAAAAACATTTTAAAAAAC
Found at i:3030957 original size:149 final size:149
Alignment explanation
Indices: 3030703--3030988 Score: 400
Period size: 149 Copynumber: 1.9 Consensus size: 149
3030693 AAAGAAACTA
3030703 TATATATTATATACGTTTTCAAAAACATTTAAAAAAAACATATATTATATGTTTTCAAAAATACA
1 TATATATTATATACGTTTTCAAAAACATTT-AAAAAAACATATATTATATGTTTTCAAAAATACA
* * ** *
3030768 TTTTCAAAAACTATATTATATATGTTTTCCAAAAACCATTTTTTTTAAAACCATATAGTATACGT
65 TTTTAAAAAACTATATTATATATGTTTTCCAAAAAACA--TTTTCAAAAACCATATAGTATACAT
3030833 TTTCAAAACCGTTTTAAAAAAC
128 TTTCAAAACCGTTTTAAAAAAC
* * * *
3030855 TATATA-T-TATACGTTTTCAAAACCATTT-TAAAAACTATATGTTATATGTTTTCAAAAATACG
1 TATATATTATATACGTTTTCAAAAACATTTAAAAAAAC-ATATATTATATGTTTTCAAAAATACA
* *
3030917 TTTTAAAAAACTATATTATATATGTTTT-CAAAAATACATTTTCAAAAACTATATATTATACATT
65 TTTTAAAAAACTATATTATATATGTTTTCCAAAAA-ACATTTTCAAAAACCATATAGTATACATT
3030981 TTCAAAAC
129 TTCAAAAC
3030989 ATATACTATA
Statistics
Matches: 121, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
147 29 0.24
148 12 0.10
149 53 0.44
150 20 0.17
151 1 0.01
152 6 0.05
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.41
Consensus pattern (149 bp):
TATATATTATATACGTTTTCAAAAACATTTAAAAAAACATATATTATATGTTTTCAAAAATACAT
TTTAAAAAACTATATTATATATGTTTTCCAAAAAACATTTTCAAAAACCATATAGTATACATTTT
CAAAACCGTTTTAAAAAAC
Found at i:3030982 original size:24 final size:24
Alignment explanation
Indices: 3030950--3031014 Score: 84
Period size: 22 Copynumber: 2.9 Consensus size: 24
3030940 GTTTTCAAAA
*
3030950 ATACATTTTCAAAAACTATATATT
1 ATACATTTTCAAAAACTATATACT
3030974 ATACATTTTC-AAAAC-ATATACT
1 ATACATTTTCAAAAACTATATACT
*
3030996 AT--ATTTTCAAAAATTATAT
1 ATACATTTTCAAAAACTATAT
3031015 TTGAAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 6 0.16
21 4 0.11
22 12 0.32
23 5 0.14
24 10 0.27
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (24 bp):
ATACATTTTCAAAAACTATATACT
Found at i:3031001 original size:20 final size:22
Alignment explanation
Indices: 3030954--3031007 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
3030944 TCAAAAATAC
*
3030954 ATTTTCAAAAACTATATATTATA
1 ATTTTC-AAAACTATATACTATA
3030977 CATTTTCAAAAC-ATATACTAT-
1 -ATTTTCAAAACTATATACTATA
3030998 ATTTTCAAAA
1 ATTTTCAAAA
3031008 ATTATATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.34
22 8 0.28
23 5 0.17
24 6 0.21
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTTTCAAAACTATATACTATA
Found at i:3036349 original size:21 final size:22
Alignment explanation
Indices: 3036305--3036361 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
3036295 ACATAGAATG
*
3036305 AAGAAAGTAAATAAAATTATAT-
1 AAGAAAG-AAAGAAAATTATATA
3036327 AAGAAAGAAAGAAAA-TATGATA
1 AAGAAAGAAAGAAAATTAT-ATA
3036349 AAGAAA-AAAGAAA
1 AAGAAAGAAAGAAA
3036362 TGTTTGTCGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.09
21 16 0.50
22 13 0.41
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (22 bp):
AAGAAAGAAAGAAAATTATATA
Found at i:3040799 original size:14 final size:13
Alignment explanation
Indices: 3040744--3040803 Score: 52
Period size: 14 Copynumber: 4.6 Consensus size: 13
3040734 TAATATTTGT
*
3040744 TAATAATATATTA
1 TAATAATATATAA
*
3040757 TATATAATAAAT-A
1 TA-ATAATATATAA
* *
3040770 TGATGATA-ATAA
1 TAATAATATATAA
3040782 TAATAATATATAA
1 TAATAATATATAA
3040795 TTAATAATA
1 -TAATAATA
3040804 AAAACAGACA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 2 0.05
12 12 0.32
13 8 0.21
14 16 0.42
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
TAATAATATATAA
Found at i:3041093 original size:42 final size:42
Alignment explanation
Indices: 3041013--3041094 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
3041003 AAGTATTTAT
* *
3041013 CATCTTGCTAGAAAGACTGACAGATGACTCGAAAGATTTAAA
1 CATCATGCTAGAAAGACTGACAGATGACCCGAAAGATTTAAA
* * * *
3041055 CATCATGCTCGAAGGACTTACAGATGACCCGAAGGATTTA
1 CATCATGCTAGAAAGACTGACAGATGACCCGAAAGATTTA
3041095 CAAATTTGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (42 bp):
CATCATGCTAGAAAGACTGACAGATGACCCGAAAGATTTAAA
Found at i:3041406 original size:249 final size:249
Alignment explanation
Indices: 3040966--3041418 Score: 665
Period size: 249 Copynumber: 1.8 Consensus size: 249
3040956 AATTAAAGAG
* * * *
3040966 TGTAAACATCCTACCCAAAGGTCTGATGAACGGCCCTAAGTATTTATCATCTTGCTAGAAAGACT
1 TGTAAACATCCTACCCAAAAGTCTGACGAACGGCCCTAAGTACTTATCATCTGGCTAGAAAGACT
* * *
3041031 GACAGATGACTCGAAAGATTTAAACATCATGCTCGAAGGACTTACAGATGACCCGAAGGATTTAC
66 GACAGATGACCCGAAAGATTTAAACATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTAC
** ** * * *
3041096 AAATTTGTGATTAATAATTTACTAAGTAAGAGACTTTTTACTTTTAAAAAATTTGATTTTCTAGA
131 AAATTCATGAGAAATAATTTACTAAGTAAGAAACTTCTTACTTTTAAAAAATTTCATTTTCTAGA
3041161 ACATTAAATGAGAAACTTTGAAAATCGTAATCTCGTTTTCATGCGAAAATCATA
196 ACATTAAATGAGAAACTTTGAAAATCGTAATCTCGTTTTCATGCGAAAATCATA
* * * *
3041215 TGTAAACATCCTACCCAAAAGTTTGACGGATGGCCCTAGAG-ACTTATCATCTGGCTCGAAAGAC
1 TGTAAACATCCTACCCAAAAGTCTGACGAACGGCCCTA-AGTACTTATCATCTGGCTAGAAAGAC
* * *
3041279 TGACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTGGCAGATGACCCGAAGGATTTA
65 TGACAGATGACCCGAAAGATTTAAACATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTA
* ** *
3041344 CAAATTCATGAGAAATATTTTACTGGGTAAGAAACTTCTTACTTTTCAAAAATTTCATTTTCTAG
130 CAAATTCATGAGAAATAATTTACTAAGTAAGAAACTTCTTACTTTTAAAAAATTTCATTTTCTAG
3041409 AACATTAAAT
195 AACATTAAAT
3041419 TAAATGAGAA
Statistics
Matches: 178, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
249 176 0.99
250 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (249 bp):
TGTAAACATCCTACCCAAAAGTCTGACGAACGGCCCTAAGTACTTATCATCTGGCTAGAAAGACT
GACAGATGACCCGAAAGATTTAAACATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTAC
AAATTCATGAGAAATAATTTACTAAGTAAGAAACTTCTTACTTTTAAAAAATTTCATTTTCTAGA
ACATTAAATGAGAAACTTTGAAAATCGTAATCTCGTTTTCATGCGAAAATCATA
Found at i:3047408 original size:11 final size:11
Alignment explanation
Indices: 3047394--3047418 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3047384 AATAATTAAA
3047394 AAAATCATAAC
1 AAAATCATAAC
3047405 AAAATCATAAC
1 AAAATCATAAC
3047416 AAA
1 AAA
3047419 TTTATTATTT
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:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATCATAAC
Found at i:3049375 original size:3 final size:3
Alignment explanation
Indices: 3049369--3049407 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
3049359 TAAGATGATG
*
3049369 ATA ATA ATA ATA ATA ATG ATA ATA TATA ATTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA ATA A
3049408 AAACAGACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3049954 original size:24 final size:24
Alignment explanation
Indices: 3049916--3049980 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
3049906 GTTAGTTACA
* * *
3049916 GAAGCTTGTGTTTTTGCAGCCGAT
1 GAAGCTTATGCTTTTGCAGCAGAT
* * *
3049940 GAGGCTTATGCTTTTACAGTAGAT
1 GAAGCTTATGCTTTTGCAGCAGAT
*
3049964 GAAGCTTGTGCTTTTGC
1 GAAGCTTATGCTTTTGC
3049981 TACAGGTGAG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.38
Consensus pattern (24 bp):
GAAGCTTATGCTTTTGCAGCAGAT
Found at i:3052690 original size:6 final size:6
Alignment explanation
Indices: 3052679--3052720 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
3052669 ACAAGTTAGT
*
3052679 AAAATA AAAATA ATAATA ATAAA-A AACAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA A-AAATA AA-AATA AAAATA AAAAT
3052721 TCTTACCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 1 0.03
6 25 0.81
7 5 0.16
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:3052709 original size:16 final size:16
Alignment explanation
Indices: 3052679--3052719 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3052669 ACAAGTTAGT
*
3052679 AAAAT-AAAAATAATA
1 AAAATAAAAAACAATA
*
3052694 ATAATAAAAAACAATA
1 AAAATAAAAAACAATA
3052710 AAAATAAAAA
1 AAAATAAAAA
3052720 TTCTTACCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAACAATA
Found at i:3054813 original size:23 final size:23
Alignment explanation
Indices: 3054787--3054837 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
3054777 TAGCACTACA
3054787 GTGCAATTCTACGCT-GCACTTCG
1 GTGCAATTCTACG-TGGCACTTCG
3054810 GTGCAATTCTACGTGGCACTTCG
1 GTGCAATTCTACGTGGCACTTCG
3054833 GTGCA
1 GTGCA
3054838 TTTATACGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.29
Consensus pattern (23 bp):
GTGCAATTCTACGTGGCACTTCG
Found at i:3054845 original size:23 final size:23
Alignment explanation
Indices: 3054787--3054845 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
3054777 TAGCACTACA
*
3054787 GTGCAATTCTACGCT-GCACTTCG
1 GTGCAATTATACG-TGGCACTTCG
*
3054810 GTGCAATTCTACGTGGCACTTCG
1 GTGCAATTATACGTGGCACTTCG
*
3054833 GTGCATTTATACG
1 GTGCAATTATACG
3054846 AGCTGTGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (23 bp):
GTGCAATTATACGTGGCACTTCG
Found at i:3061250 original size:23 final size:23
Alignment explanation
Indices: 3061218--3061284 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
3061208 ATCTTATATA
*
3061218 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* *
3061241 GCACTTCGGTGCAATTCTATGTG
1 GCACTTCGGTGCAATTCTACGCG
* *
3061264 GCACTTCAGTGCAATTATACG
1 GCACTTCGGTGCAATTCTACG
3061285 AGATTGGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.28
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:3067328 original size:20 final size:22
Alignment explanation
Indices: 3067277--3067334 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
3067267 ATGCACAGGT
*
3067277 AGTGCATCGATGCACACATTTAGG
1 AGTGCATCGAT--ACACATATAGG
*
3067301 AGTACATCGATACAC-TATA-G
1 AGTGCATCGATACACATATAGG
3067321 AGTGCATCGATACA
1 AGTGCATCGATACA
3067335 TACCTTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 3 0.10
22 4 0.13
24 10 0.32
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (22 bp):
AGTGCATCGATACACATATAGG
Found at i:3067968 original size:23 final size:23
Alignment explanation
Indices: 3067936--3067994 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
3067926 ATCTTATATA
* *
3067936 GCACTACGGTGCAATTCTATGTG
1 GCACTTCGGTGCAATTCTACGTG
3067959 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGTG
* *
3067982 GTACTTTGGTGCA
1 GCACTTCGGTGCA
3067995 TTTATACGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGTG
Found at i:3068002 original size:23 final size:23
Alignment explanation
Indices: 3067936--3068002 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
3067926 ATCTTATATA
* * *
3067936 GCACTACGGTGCAATTCTATGTG
1 GCACTTCGGTGCAATTATACGTG
*
3067959 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTATACGTG
* * *
3067982 GTACTTTGGTGCATTTATACG
1 GCACTTCGGTGCAATTATACG
3068003 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.34
Consensus pattern (23 bp):
GCACTTCGGTGCAATTATACGTG
Found at i:3070531 original size:36 final size:35
Alignment explanation
Indices: 3070472--3070685 Score: 108
Period size: 36 Copynumber: 5.7 Consensus size: 35
3070462 AAGAAACTAT
3070472 ATATATTATATACGTTTTCAAAAACATTTTAAAAACCC
1 ATATATTATAT--GTTTTCAAAAACATTTTAAAAA-CC
* *
3070510 ATATATTATATGTTTTCAAAAATACGTTTTCAAAAACT
1 ATATATTATATGTTTTC-AAAA-ACATTTT-AAAAACC
* * *
3070548 AAATTATAAATAT-TTTTCAAAATCCATTTTTTTAAAAAAACCC
1 ATA-TAT-TATATGTTTTCAAAA-ACA---TTTT--AAAAA-CC
** * * *
3070591 ATATATTATACATTTTCAAAACCGTTTTAAAAAACT
1 ATATATTATATGTTTTCAAAAACATTTT-AAAAACC
* * * *
3070627 ATATATTATACGTTTTGAAAAATATGTTTTCAAAACC
1 ATATATTATATGTTTTCAAAAACA--TTTTAAAAACC
* *
3070664 -TATACTATATATTTTCAAAAAC
1 ATATATTATATGTTTTCAAAAAC
3070686 TATATTTGAA
Statistics
Matches: 138, Mismatches: 25, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
36 43 0.31
37 15 0.11
38 34 0.25
39 13 0.09
40 4 0.03
41 9 0.07
42 17 0.12
43 3 0.02
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (35 bp):
ATATATTATATGTTTTCAAAAACATTTTAAAAACC
Found at i:3070649 original size:79 final size:80
Alignment explanation
Indices: 3070502--3070649 Score: 176
Period size: 81 Copynumber: 1.9 Consensus size: 80
3070492 AAAACATTTT
** * * **
3070502 AAAAACCCATATATTATATGTTTTCAAAAATACGTTTTCAAAAACTAAATTATAAATATTTTTCA
1 AAAAACCCATATATTATACATTTTCAAAAATACGTTTTAAAAAACTAAATTAT-AACATTTTGAA
3070567 AAATCCATTTTTTTAA
65 AAATCCATTTTTTTAA
* *
3070583 AAAAACCCATATATTATACATTTTC-AAAA-CCGTTTTAAAAAACTATATATTAT-ACGTTTTGA
1 AAAAACCCATATATTATACATTTTCAAAAATACGTTTTAAAAAACTA-A-ATTATAACATTTTGA
3070645 AAAAT
64 AAAAT
3070650 ATGTTTTCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
79 24 0.42
80 5 0.09
81 28 0.49
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (80 bp):
AAAAACCCATATATTATACATTTTCAAAAATACGTTTTAAAAAACTAAATTATAACATTTTGAAA
AATCCATTTTTTTAA
Found at i:3070656 original size:38 final size:38
Alignment explanation
Indices: 3070452--3070684 Score: 124
Period size: 38 Copynumber: 6.0 Consensus size: 38
3070442 ATTAGATTTC
3070452 TATGTTTTCAAAGAAACTATATATATTATATACGTTTTCAAAAA
1 TATGTTTT-AAA-AAAC--TATATA-T-TATACGTTTTCAAAAA
* * * *
3070496 CA--TTTTAAAAACCCATATATTATATGTTTTCAAAAA
1 TATGTTTTAAAAAACTATATATTATACGTTTTCAAAAA
* * * * *
3070532 TACGTTTTCAAAAACTAAATTATAAATA-TTTTTC-AAAA
1 TATGTTTTAAAAAACTATA-TAT-TATACGTTTTCAAAAA
* * *
3070570 TCCATTTTTTTAAAAAAACCCATATATTATACATTTTC-AAAA
1 T--A-TGTTTT-AAAAAA-CTATATATTATACGTTTTCAAAAA
** *
3070612 -CCGTTTTAAAAAACTATATATTATACGTTTTGAAAAA
1 TATGTTTTAAAAAACTATATATTATACGTTTTCAAAAA
* *
3070649 TATGTTTTCAAAACCTATACTA-TATA--TTTTCAAAAA
1 TATGTTTTAAAAAACTATA-TATTATACGTTTTCAAAAA
3070685 CTATATTTGA
Statistics
Matches: 147, Mismatches: 29, Indels: 34
0.70 0.14 0.16
Matches are distributed among these distances:
36 41 0.28
37 11 0.07
38 43 0.29
39 10 0.07
40 7 0.05
41 10 0.07
42 21 0.14
43 3 0.02
44 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (38 bp):
TATGTTTTAAAAAACTATATATTATACGTTTTCAAAAA
Found at i:3070678 original size:22 final size:22
Alignment explanation
Indices: 3070648--3070689 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3070638 GTTTTGAAAA
* *
3070648 ATATGTTTTCAAAACCTATACT
1 ATATATTTTCAAAAACTATACT
3070670 ATATATTTTCAAAAACTATA
1 ATATATTTTCAAAAACTATA
3070690 TTTGAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATATTTTCAAAAACTATACT
Found at i:3070702 original size:2 final size:2
Alignment explanation
Indices: 3070695--3070730 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3070685 CTATATTTGA
3070695 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
3070731 TATGTTATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3076849 original size:54 final size:54
Alignment explanation
Indices: 3076784--3077092 Score: 413
Period size: 54 Copynumber: 5.7 Consensus size: 54
3076774 TTATTCAACT
* *
3076784 AAATTCATAATGAGTTTATGAATTTCCGTATTGGTACTGTGTGTGTAACTTAAG
1 AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTGTGTGCAACTTAAG
* * * *
3076838 AAATTCGTAATGAGTTTGTGAATTTCCCTATTGGCACTGTGTGTGCAACCTAAG
1 AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTGTGTGCAACTTAAG
*
3076892 AAATTCATAATGAGTTTATGAAGTTT-CGTATTGGCACTGCGTGTGCAACTTAAG
1 AAATTCATAATGAGTTTATGAA-TTTCCGTATTGGCACTGTGTGTGCAACTTAAG
*
3076946 AAATTCATAATGAGTTTATTAATTTCCGTATTGGCACTGTGTGTGCAACTTAAG
1 AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTGTGTGCAACTTAAG
* ** * ** *
3077000 AAATTTATAATGAGTTTATGAATTTCCGTATTGGCACTAAGTGTACAACCCCACG
1 AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTGTGTGCAA-CTTAAG
* ** * *
3077055 TAATTCATAATGAGTTGGTGAATTACTGTATTGGCACT
1 AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACT
3077093 ACGTGTACAA
Statistics
Matches: 225, Mismatches: 27, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
53 3 0.01
54 184 0.82
55 38 0.17
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (54 bp):
AAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTGTGTGCAACTTAAG
Found at i:3083727 original size:54 final size:54
Alignment explanation
Indices: 3083575--3083841 Score: 320
Period size: 54 Copynumber: 4.9 Consensus size: 54
3083565 TATGTATTGC
*
3083575 AATTTCCGTATTGGCACTGTGTGTGCAACCTAA-AAATTCATAACGAGTTTATG
1 AATTTCCGTATTGGCACTGTGTGTGCAACCTAAGAAATTCATAATGAGTTTATG
** * * * **
3083628 AATTTTTGTAATTGGAACTGTGTGCGTAATTTAAGAAATTCATAATGAGTTTATG
1 AATTTCCGT-ATTGGCACTGTGTGTGCAACCTAAGAAATTCATAATGAGTTTATG
* * *
3083683 AATTTCCGTATTGACACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTTTG
1 AATTTCCGTATTGGCACTGTGTGTGCAACCTAAGAAATTCATAATGAGTTTATG
* * * *
3083737 ATTTTCCGTATTGGCACTGTATGTGCAACTTAAGAAATTCATAATGTGTTTATG
1 AATTTCCGTATTGGCACTGTGTGTGCAACCTAAGAAATTCATAATGAGTTTATG
* ** * * *
3083791 AATTTCCATATTGGCACTAAGTGTGCAACCCCACGTAATTCATAATGAGTT
1 AATTTCCGTATTGGCACTGTGTGTGCAA-CCTAAGAAATTCATAATGAGTT
3083842 GGGGAATTAC
Statistics
Matches: 176, Mismatches: 35, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
53 7 0.04
54 126 0.72
55 43 0.24
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (54 bp):
AATTTCCGTATTGGCACTGTGTGTGCAACCTAAGAAATTCATAATGAGTTTATG
Found at i:3083891 original size:109 final size:108
Alignment explanation
Indices: 3083659--3083873 Score: 259
Period size: 108 Copynumber: 2.0 Consensus size: 108
3083649 GTGCGTAATT
* * *
3083659 TAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGACACTATGTGTGCAACCTAAGAAATTCA
1 TAAGAAATTCATAATGAGTTTATGAATTTCCATATTGACACTAAGTGTGCAACCCAAGAAATTCA
*** * * ** * *
3083724 TAATGAGTTTTTGATTTTCCGTATTGGCACTGTATGTGCAACT
66 TAATGAGTTGGGGAATTACCGTATTGGCACTACAGGTGCAACA
* * * *
3083767 TAAGAAATTCATAATGTGTTTATGAATTTCCATATTGGCACTAAGTGTGCAACCCCACGTAATTC
1 TAAGAAATTCATAATGAGTTTATGAATTTCCATATTGACACTAAGTGTGCAA-CCCAAGAAATTC
* *
3083832 ATAATGAGTTGGGGAATTACTGTATTGGCACTACGGGTGCAA
65 ATAATGAGTTGGGGAATTACCGTATTGGCACTACAGGTGCAA
3083874 ACCATAGAAT
Statistics
Matches: 89, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
108 48 0.54
109 41 0.46
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (108 bp):
TAAGAAATTCATAATGAGTTTATGAATTTCCATATTGACACTAAGTGTGCAACCCAAGAAATTCA
TAATGAGTTGGGGAATTACCGTATTGGCACTACAGGTGCAACA
Found at i:3083892 original size:163 final size:161
Alignment explanation
Indices: 3083577--3083873 Score: 346
Period size: 163 Copynumber: 1.8 Consensus size: 161
3083567 TGTATTGCAA
* ***
3083577 TTTCCGTATTGGCACTGTGTGTGCAACCTAAAAATTCATAACGAGTTTATGAATTTTTGTAATTG
1 TTTCCGTATTGGCACTGTATGTGCAACCTAAAAATTCATAACGAGTTTATGAATTTCCATAATTG
*** * * * * *
3083642 GAACTGTGTGCGTAATTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGACACTATGTGT
66 GAACTGTGTGCG-AACCCAAGAAATTCATAATGAGTTGAGGAATTACCGTATTGACACTACGGGT
3083707 GCAACCTAAGAAATTCATAATGAGTTTTTGAT
130 GCAACCTAAGAAATTCATAATGAGTTTTTGAT
* * *
3083739 TTTCCGTATTGGCACTGTATGTGCAACTTAAGAAATTCATAATGTGTTTATGAATTTCCAT-ATT
1 TTTCCGTATTGGCACTGTATGTGCAACCTAA-AAATTCATAACGAGTTTATGAATTTCCATAATT
* * * * * *
3083803 GGCACTAAGTGTGC-AACCCCACGTAATTCATAATGAGTTGGGGAATTACTGTATTGGCACTACG
65 GGAACT--GTGTGCGAA-CCCAAGAAATTCATAATGAGTTGAGGAATTACCGTATTGACACTACG
3083867 GGTGCAA
127 GGTGCAA
3083874 ACCATAGAAT
Statistics
Matches: 110, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
162 39 0.35
163 65 0.59
164 6 0.05
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (161 bp):
TTTCCGTATTGGCACTGTATGTGCAACCTAAAAATTCATAACGAGTTTATGAATTTCCATAATTG
GAACTGTGTGCGAACCCAAGAAATTCATAATGAGTTGAGGAATTACCGTATTGACACTACGGGTG
CAACCTAAGAAATTCATAATGAGTTTTTGAT
Found at i:3088595 original size:32 final size:32
Alignment explanation
Indices: 3088491--3088610 Score: 116
Period size: 32 Copynumber: 3.8 Consensus size: 32
3088481 TAGCATAGTT
* *
3088491 AATATTGCGTTCAGATAATGCACAACAGAGTC
1 AATATTGCATTCAAATAATGCACAACAGAGTC
* *
3088523 AATATTGCATTTAGAA-AATGCACAAAAGAGTC
1 AATATTGCATTCA-AATAATGCACAACAGAGTC
* * * *
3088555 AGTATTGCATTCAAATAATGCATAGCAGAGTT
1 AATATTGCATTCAAATAATGCACAACAGAGTC
* * * *
3088587 AGTTTTGCATTTATATAATGCACA
1 AATATTGCATTCAAATAATGCACA
3088611 GGAGTGTTAT
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
31 2 0.03
32 69 0.96
33 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (32 bp):
AATATTGCATTCAAATAATGCACAACAGAGTC
Found at i:3105146 original size:61 final size:61
Alignment explanation
Indices: 3105046--3105203 Score: 226
Period size: 61 Copynumber: 2.6 Consensus size: 61
3105036 ACCGTAGTGC
* * * * *
3105046 TATGACACATAAGGTCGTTCCCACCACCTACACTAAGTTTACACTTTAGTGCTAATCTGGA
1 TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAATGCTAATCCGGA
** * *
3105107 TATGACACATAAGGTCGTGCCCATGACCTGCACTGAGTTTACACTCTAATGCTGATCCGGA
1 TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAATGCTAATCCGGA
*
3105168 TATGACACGTAAGGTCGTGCCCACCACCTGCACTAA
1 TATGACACATAAGGTCGTGCCCACCACCTGCACTAA
3105204 TTGTCCTTAC
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 84 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (61 bp):
TATGACACATAAGGTCGTGCCCACCACCTGCACTAAGTTTACACTCTAATGCTAATCCGGA
Found at i:3106769 original size:29 final size:30
Alignment explanation
Indices: 3106707--3106769 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
3106697 AGTCCATAAT
* * * *
3106707 TTTTCCAAAATTACCAATTGGTCCCCTAAC
1 TTTTCAAAAATTACAAAATGGTCCCCTAAA
*
3106737 TTTTCAAAAATTATAAAATGGTCCCC-AAA
1 TTTTCAAAAATTACAAAATGGTCCCCTAAA
3106766 TTTT
1 TTTT
3106770 GCTAAAGCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (30 bp):
TTTTCAAAAATTACAAAATGGTCCCCTAAA
Found at i:3112581 original size:56 final size:56
Alignment explanation
Indices: 3112425--3112979 Score: 749
Period size: 56 Copynumber: 10.0 Consensus size: 56
3112415 ATTACCAAAT
* * * *
3112425 GGCACTATGCGTGCAAAA-CTAATAAATTCATAATAAGTTTATGAATTCCCGTATG
1 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
3112480 AGCACTTTGTGTG-AAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * *
3112535 AGCACTTTGTGTGCAAAAGCTAAGAAATTTATATTGAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * ** *
3112591 TGCACTTTGTGTGCAAAAGTTAAGAAATTCATAATGAGTTTATGAATTTATGTATT
1 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * * *
3112647 GGCACTTTGTGTGAAAAAGCTAAGAAATTGATAATAAGCTTATGAATTTTCATATG
1 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
** * * * *
3112703 GGCACTTTGTGTGTGAAAGCTAAGAAATTTATAATGAGTTTATGAATTTCCATACG
1 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
*
3112759 GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * * *
3112815 GGCACTTTGTGTGTAAAAGCTAAGAAATTCATAACAAGTTTATGATTTTCTGTATG
1 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* *
3112871 AGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCTGTATG
1 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
* * *
3112926 GGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATAAATTAATGAATTTTCGTAT
1 GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
3112980 TGGTAGTGGG
Statistics
Matches: 444, Mismatches: 54, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
54 4 0.01
55 142 0.32
56 298 0.67
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (56 bp):
GGCACTTTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
Found at i:3112655 original size:112 final size:110
Alignment explanation
Indices: 3112423--3113051 Score: 737
Period size: 112 Copynumber: 5.7 Consensus size: 110
3112413 CGATTACCAA
* * * * *
3112423 ATGGCACTATGCGTGCAAAACTAATAAATTCATAATAAGTTTATGAATTCCCGTATGAGCACTTT
1 ATGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
* *
3112488 GTGTG-AAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGT
66 GTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGT
* * * *
3112532 ATGAGCACTTTGTGTGCAAAAGCTAAGAAATTTATATTGAGTTTATGAATTTCCGTATGTGCACT
1 ATG-GCACTTTGTGTGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT
* * *
3112597 TTGTGTGCAAAAGTTAAGAAATTCATAATGAGTTTATGAATTTATGT
64 TTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGT
* * * * *
3112644 ATTGGCACTTTGTGTGAAAAAGCTAAGAAATTGATAATAAGCTTATGAATTTTCATATGGGCACT
1 A-TGGCACTTTGTGTGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT
** * * **
3112709 TTGTGTGTGAAAGCTAAGAAATTTATAATGAGTTTATGAATTTCCAT
64 TTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGT
*
3112756 ACGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT
1 A-TGGCACTTTGTGTGC-AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT
* * *
3112821 TTGTGTGTAAAAGCTAAGAAATTCATAACAAGTTTATGATTTTCTGT
64 TTGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGT
*
3112868 ATGAGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCTGTATGGGCACTT
1 ATG-GCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT
* *
3112933 TGTGTGCAAAA-CTAAGAAATTCATAATAAATTAATGAATTT-TCGT
65 TGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCT-GT
* * ** * * * * * *
3112978 ATTGGTAGTGGGTGTGC-AACCCATGTAAATT-ATAATAAGTTTGTGAATTACCGTATTGGCACT
1 A-TGGCACTTTGTGTGCAAAACTAAG-AAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT
**
3113041 ACGTGTGCAAA
64 TTGTGTGCAAA
3113052 CTATAGAGTT
Statistics
Matches: 449, Mismatches: 62, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
109 46 0.10
110 58 0.13
111 104 0.23
112 235 0.52
113 6 0.01
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (110 bp):
ATGGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
GTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCTGT
Found at i:3113327 original size:46 final size:46
Alignment explanation
Indices: 3113271--3113358 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 46
3113261 TTAGATGAAG
* * * *
3113271 AACAGTGCATAATTGGCATGAAAGGATGCCATAAATGAAAATGTAT
1 AACAATGCATAATTGGCATGAAAGGATACCACAAATAAAAATGTAT
3113317 AACAATGCATAATTGGCATGAAAGGATACCACAAATAAAAAT
1 AACAATGCATAATTGGCATGAAAGGATACCACAAATAAAAAT
3113359 ACATAACGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (46 bp):
AACAATGCATAATTGGCATGAAAGGATACCACAAATAAAAATGTAT
Found at i:3117494 original size:21 final size:21
Alignment explanation
Indices: 3117465--3117504 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3117455 GAGAAATTAT
*
3117465 TTTCCAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
3117486 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
3117505 AAAATAATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:3121852 original size:13 final size:13
Alignment explanation
Indices: 3121829--3121867 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
3121819 AAAATTACAT
3121829 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAC
3121843 ATTGTTTTCAAAC
1 ATTGTTTTCAAAC
*
3121856 ATAGTTTTCAAA
1 ATTGTTTTCAAA
3121868 ATTTACCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:3131726 original size:22 final size:22
Alignment explanation
Indices: 3131695--3131751 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
3131685 TGCAAGGGAG
*
3131695 TATCGATACCATAGTAGAGAAA
1 TATCGATACCATAGTAAAGAAA
* *
3131717 TATCGGTACCATAGTAAAGAAG
1 TATCGATACCATAGTAAAGAAA
3131739 TATCGATACCATA
1 TATCGATACCATA
3131752 TTAGGGGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (22 bp):
TATCGATACCATAGTAAAGAAA
Found at i:3132428 original size:54 final size:54
Alignment explanation
Indices: 3132086--3132406 Score: 509
Period size: 54 Copynumber: 5.9 Consensus size: 54
3132076 TTATGTGTAC
*
3132086 TATAGGCACTAAGTGTGAAACCCACGAAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
3132140 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
*
3132194 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
* * * *
3132248 TATAGGCACTAAATGTGAAAACCACGAAATTCATCATATGTTGATGAACAACTG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
* * * *
3132302 TATAGGTACTAAGTGTGCAATCCACAAAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
* * *
3132356 TATAGGCACTAAGTGTGCAACCCACTG-AATTCATAATGTGTTTATGAACAA
1 TATAGGCACTAAGTGTGCAACCCAC-GAAATTCATCATATGTTGATGAACAA
3132407 TCATATCAGT
Statistics
Matches: 245, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
54 245 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCG
Found at i:3139276 original size:13 final size:13
Alignment explanation
Indices: 3139258--3139288 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3139248 AAAGTTCCAA
3139258 CTCATGGCTTCAT
1 CTCATGGCTTCAT
*
3139271 CTCATGGTTTCAT
1 CTCATGGCTTCAT
3139284 CTCAT
1 CTCAT
3139289 ATTCAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.29, G:0.13, T:0.42
Consensus pattern (13 bp):
CTCATGGCTTCAT
Found at i:3139439 original size:5 final size:5
Alignment explanation
Indices: 3139429--3139461 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
3139419 TTCTTTCTAT
*
3139429 TTTTC TTTTC TTTTC TTTTC -TTTC TTATC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
3139462 TCCTTTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:3140166 original size:6 final size:6
Alignment explanation
Indices: 3140151--3140246 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
3140141 TGAACCCTCC
* * * * *
3140151 TTTTCA TTTTC- TTTT-T TTCTCTT TTTTCT TCCTT-T TTTTAT TTTTAT
1 TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT T-TTTCT TTTTCT TTTTCT
* *
3140198 TTTTAT TTTTCT TTTTCT TTTT-A TTTTCTT TTTTCT TTTTCT ATTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT -TTTTCT
3140247 AAGCATAATA
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
5 13 0.17
6 44 0.59
7 18 0.24
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:3140177 original size:12 final size:11
Alignment explanation
Indices: 3140162--3140236 Score: 62
Period size: 11 Copynumber: 6.6 Consensus size: 11
3140152 TTTCATTTTC
3140162 TTTTTTTCTCTT
1 TTTTTTTCT-TT
* *
3140174 TTTTCTTCCTT
1 TTTTTTTCTTT
*
3140185 TTTTTAT-TTT
1 TTTTTTTCTTT
* *
3140195 TATTTTTATTT
1 TTTTTTTCTTT
3140206 TTCTTTTTCTTT
1 TT-TTTTTCTTT
*
3140218 TTATTTTCTTT
1 TTTTTTTCTTT
3140229 TTTCTTTT
1 TTT-TTTT
3140237 TCTATTTTCT
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
10 7 0.14
11 21 0.43
12 21 0.43
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:3140206 original size:18 final size:17
Alignment explanation
Indices: 3140157--3140237 Score: 76
Period size: 18 Copynumber: 4.6 Consensus size: 17
3140147 CTCCTTTTCA
*
3140157 TTTTCTTTTT-TTCTCTT
1 TTTTCTTTTTATT-TTTT
*
3140174 TTTTCTTCCTTT-TTTTAT
1 TTTTCTT--TTTATTTTTT
*
3140192 TTTTATTTTTATTTTTCT
1 TTTTCTTTTTATTTTT-T
3140210 TTTTCTTTTTATTTTCTT
1 TTTTCTTTTTATTTT-TT
3140228 TTTTCTTTTT
1 TTTTCTTTTT
3140238 CTATTTTCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
16 3 0.06
17 11 0.20
18 34 0.63
19 6 0.11
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCTTTTTATTTTTT
Found at i:3140230 original size:24 final size:24
Alignment explanation
Indices: 3140185--3140244 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
3140175 TTTCTTCCTT
*
3140185 TTTTTATTTTTATTTTTATTTTTC
1 TTTTTCTTTTTATTTTTATTTTTC
3140209 TTTTTCTTTTTATTTTCT-TTTTTC
1 TTTTTCTTTTTATTTT-TATTTTTC
3140233 TTTTTCTATTTT
1 TTTTTCT-TTTT
3140245 CTAAGCATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTCTTTTTATTTTTATTTTTC
Found at i:3142263 original size:30 final size:30
Alignment explanation
Indices: 3142222--3142283 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
3142212 AAATTTTAAC
*
3142222 TTTATCCCTAAA-TTTTAGAAAAAACACTAA
1 TTTAACCCTAAACTTTTA-AAAAAACACTAA
* *
3142252 TTTAACCCTAAACTTTTAATAAAATACTAA
1 TTTAACCCTAAACTTTTAAAAAAACACTAA
3142282 TT
1 TT
3142284 CAACACTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.37
Consensus pattern (30 bp):
TTTAACCCTAAACTTTTAAAAAAACACTAA
Found at i:3154343 original size:123 final size:123
Alignment explanation
Indices: 3154124--3154369 Score: 492
Period size: 123 Copynumber: 2.0 Consensus size: 123
3154114 TTAGGTATTG
3154124 TTCTAAGCACTGGTTCACCCTCTCTGTTTGTCTATCCGTTTCAGGATGATAAGCAGTGCTAAACA
1 TTCTAAGCACTGGTTCACCCTCTCTGTTTGTCTATCCGTTTCAGGATGATAAGCAGTGCTAAACA
3154189 GGGTCTTAGTTCCTAAGAGCTTCATTAGTTCTCTCCAAAAGACACTAGTGAAGGTCTT
66 GGGTCTTAGTTCCTAAGAGCTTCATTAGTTCTCTCCAAAAGACACTAGTGAAGGTCTT
3154247 TTCTAAGCACTGGTTCACCCTCTCTGTTTGTCTATCCGTTTCAGGATGATAAGCAGTGCTAAACA
1 TTCTAAGCACTGGTTCACCCTCTCTGTTTGTCTATCCGTTTCAGGATGATAAGCAGTGCTAAACA
3154312 GGGTCTTAGTTCCTAAGAGCTTCATTAGTTCTCTCCAAAAGACACTAGTGAAGGTCTT
66 GGGTCTTAGTTCCTAAGAGCTTCATTAGTTCTCTCCAAAAGACACTAGTGAAGGTCTT
3154370 GTCTCTGTCT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (123 bp):
TTCTAAGCACTGGTTCACCCTCTCTGTTTGTCTATCCGTTTCAGGATGATAAGCAGTGCTAAACA
GGGTCTTAGTTCCTAAGAGCTTCATTAGTTCTCTCCAAAAGACACTAGTGAAGGTCTT
Found at i:3171394 original size:3 final size:3
Alignment explanation
Indices: 3171378--3171414 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
3171368 CTAGCAAAAA
*
3171378 TAT TAT TAA T-T TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3171415 ATACAATTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 30 0.97
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3172029 original size:17 final size:16
Alignment explanation
Indices: 3172008--3172053 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
3171998 AGGGGTTTTT
3172008 GAAAAAAAGGAGAGAA
1 GAAAAAAAGGAGAGAA
*
3172024 GAAAAAGAA--ACA-AA
1 GAAAAA-AAGGAGAGAA
3172038 GAAAAAAAGGAGAGAA
1 GAAAAAAAGGAGAGAA
3172054 ATAGAACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
13 2 0.08
14 8 0.33
15 4 0.17
16 8 0.33
17 2 0.08
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (16 bp):
GAAAAAAAGGAGAGAA
Found at i:3172955 original size:30 final size:29
Alignment explanation
Indices: 3172921--3173129 Score: 229
Period size: 30 Copynumber: 7.0 Consensus size: 29
3172911 TTATGATTCG
*
3172921 GTCTTTTAAATTTTTATTTGTTCTATTTTA
1 GTCTTTTAAGTTTTTATTT-TTCTATTTTA
* * *
3172951 GTCTTTTAAGTGTTTATTTGTGCTATTTTG
1 GTCTTTTAAGTTTTTATTT-TTCTATTTTA
* *
3172981 GTCCTTTAAGTTTTTGTTTTTGCTATTTTA
1 GTCTTTTAAGTTTTTATTTTT-CTATTTTA
* * *
3173011 GTCTTTTAATTTTTTGTTTATACTATTTTA
1 GTCTTTTAAGTTTTTATTT-TTCTATTTTA
*
3173041 GTCTTTTAAGTTTATATTTTTCTATTTTA
1 GTCTTTTAAGTTTTTATTTTTCTATTTTA
* *
3173070 GTCCTTTAAGTTTTTGTTTTTTCTATTTTA
1 GTCTTTTAAGTTTTT-ATTTTTCTATTTTA
* *
3173100 GTCCTTTAAGTTTATACTTTTTTCTATTTT
1 GTCTTTTAAGTTTTTA--TTTTTCTATTTT
3173130 GGTCCTCAAG
Statistics
Matches: 153, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
29 23 0.15
30 117 0.76
31 13 0.08
ACGTcount: A:0.17, C:0.09, G:0.10, T:0.65
Consensus pattern (29 bp):
GTCTTTTAAGTTTTTATTTTTCTATTTTA
Found at i:3172995 original size:60 final size:59
Alignment explanation
Indices: 3172925--3173192 Score: 252
Period size: 60 Copynumber: 4.5 Consensus size: 59
3172915 GATTCGGTCT
* * * * * * *
3172925 TTTAAATTTTTATTTGTTCTATTTTAGTCTTTTAAGTGTTTATTTGTGCTATTTTGGTCC
1 TTTAAGTTTATATTT-TTCTATTTTAGTCTTTTAAGTTTTTGTTTATACTATTTTAGTCC
* * * *
3172985 TTTAAGTTTTTGTTTTTGCTATTTTAGTCTTTTAATTTTTTGTTTATACTATTTTAGTCT
1 TTTAAGTTTATATTTTT-CTATTTTAGTCTTTTAAGTTTTTGTTTATACTATTTTAGTCC
* * *
3173045 TTTAAGTTTATATTTTTCTATTTTAGTCCTTTAAGTTTTTGTTTTTTCTATTTTAGTCC
1 TTTAAGTTTATATTTTTCTATTTTAGTCTTTTAAGTTTTTGTTTATACTATTTTAGTCC
* * * * * *
3173104 TTTAAGTTTATACTTTTTTCTATTTTGGTC-CTCAAGTTTCTGTTAATTA-TATTTTGGTCC
1 TTTAAGTTTATA--TTTTTCTATTTTAGTCTTTTAAGTTTTTGTTTA-TACTATTTTAGTCC
* * * *
3173164 TTTAAATTTTTTATTGTTCTTTTTTAGTC
1 TTT-AAGTTTATATTTTTCTATTTTAGTC
3173193 CCTTTTGAAT
Statistics
Matches: 174, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
59 64 0.37
60 87 0.50
61 23 0.13
ACGTcount: A:0.17, C:0.09, G:0.10, T:0.63
Consensus pattern (59 bp):
TTTAAGTTTATATTTTTCTATTTTAGTCTTTTAAGTTTTTGTTTATACTATTTTAGTCC
Found at i:3173088 original size:89 final size:90
Alignment explanation
Indices: 3172921--3173108 Score: 281
Period size: 89 Copynumber: 2.1 Consensus size: 90
3172911 TTATGATTCG
* * *
3172921 GTCTTTTAAATTTTTATTTGTTCTATTTTAGTCTTTTAAGTGTTTATTTGTGCTATTTTGGTCCT
1 GTCTTTTAAATTTTTATTTATACTATTTTAGTCTTTTAAGTGTTTATTTGTGCTATTTTAGTCCT
3172986 TTAAGTTTTTGTTTTTGCTATTTTA
66 TTAAGTTTTTGTTTTTGCTATTTTA
* * *
3173011 GTCTTTTAATTTTTTGTTTATACTATTTTAGTCTTTTAAGT-TTATATTT-TTCTATTTTAGTCC
1 GTCTTTTAAATTTTTATTTATACTATTTTAGTCTTTTAAGTGTT-TATTTGTGCTATTTTAGTCC
*
3173074 TTTAAGTTTTTGTTTTTTCTATTTTA
65 TTTAAGTTTTTGTTTTTGCTATTTTA
*
3173100 GTCCTTTAA
1 GTCTTTTAA
3173109 GTTTATACTT
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
89 47 0.53
90 42 0.47
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.64
Consensus pattern (90 bp):
GTCTTTTAAATTTTTATTTATACTATTTTAGTCTTTTAAGTGTTTATTTGTGCTATTTTAGTCCT
TTAAGTTTTTGTTTTTGCTATTTTA
Found at i:3177913 original size:32 final size:33
Alignment explanation
Indices: 3177871--3177935 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
3177861 AAGAAATGAT
3177871 GAATGATGGGGCATCTTT-GGAGATTCAACATC
1 GAATGATGGGGCATCTTTAGGAGATTCAACATC
* *
3177903 GAATGTTGGGGCATCTTTAGGGGATTCAACATC
1 GAATGATGGGGCATCTTTAGGAGATTCAACATC
3177936 CTGATGTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (33 bp):
GAATGATGGGGCATCTTTAGGAGATTCAACATC
Found at i:3178038 original size:22 final size:22
Alignment explanation
Indices: 3178010--3178052 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3178000 GTATCCTTTG
* *
3178010 ATGTTGTTTCTCTTGAAACAAA
1 ATGTTGTCTCGCTTGAAACAAA
*
3178032 ATGTTGTCTCGCTTGAGACAA
1 ATGTTGTCTCGCTTGAAACAA
3178053 TTTTCTCTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (22 bp):
ATGTTGTCTCGCTTGAAACAAA
Found at i:3178314 original size:63 final size:64
Alignment explanation
Indices: 3178142--3178322 Score: 181
Period size: 63 Copynumber: 2.8 Consensus size: 64
3178132 CATAAATCAT
* * * * *
3178142 CCTTGAGAGAGTTTCTCTTGAAACAAAAATCTTTGAGTCTGTTTCTCTTGAAACCATGTTTTGTT
1 CCTTGAGACAGTTTCTCTTG-AAC-AACATCTTTGAGTCTGTTTCCCTTGAAACCA-GATTTGTC
3178207 TC
63 TC
* * * * *
3178209 TCTTGAGACAGTTTTTCATGAA-AACATATTTGAGAT-TGTTTCCCTTGAAACGA-ATTT-TCTC
1 CCTTGAGACAGTTTCTCTTGAACAACATCTTTGAG-TCTGTTTCCCTTGAAACCAGATTTGTCTC
* *
3178270 CCTTGAGACAGGTTCTCTTGAAGCATCATCTTTGAGTCTGTTTCCCTTGAAAC
1 CCTTGAGACAGTTTCTCTTGAA-CAACATCTTTGAGTCTGTTTCCCTTGAAAC
3178323 TTTATTCCTA
Statistics
Matches: 94, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
61 21 0.22
62 4 0.04
63 25 0.27
64 25 0.27
65 1 0.01
66 2 0.02
67 16 0.17
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (64 bp):
CCTTGAGACAGTTTCTCTTGAACAACATCTTTGAGTCTGTTTCCCTTGAAACCAGATTTGTCTC
Found at i:3178759 original size:3 final size:3
Alignment explanation
Indices: 3178743--3178779 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
3178733 CTACCAAAAA
*
3178743 TAT TAT TAA T-T TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3178780 CAATTGGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 30 0.97
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3180400 original size:30 final size:30
Alignment explanation
Indices: 3180366--3180547 Score: 240
Period size: 30 Copynumber: 6.0 Consensus size: 30
3180356 GATTCATTCT
* *
3180366 TTTAAATTTTTATTTGTT-CTATTTTAGTCC
1 TTTAAGTTTCTATTT-TTGCTATTTTAGTCC
* *
3180396 TTTAAGTTTCTATTTATGCTATTTTGGTCC
1 TTTAAGTTTCTATTTTTGCTATTTTAGTCC
3180426 TTTAAGTTTCTATTTTTGCTATTTTAGTCC
1 TTTAAGTTTCTATTTTTGCTATTTTAGTCC
* * *
3180456 TTTAAGTTTCTGTTTATACTATTTTAGTCC
1 TTTAAGTTTCTATTTTTGCTATTTTAGTCC
* * *
3180486 TTTAAGTTTTTGTTTTTGCTATTTTAGTCT
1 TTTAAGTTTCTATTTTTGCTATTTTAGTCC
*
3180516 TTTAAGTTTCTATTTTTTGCTATTTTGGTCC
1 TTTAAGTTTCTA-TTTTTGCTATTTTAGTCC
3180547 T
1 T
3180548 AATTTTCTGT
Statistics
Matches: 133, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
29 1 0.01
30 115 0.86
31 17 0.13
ACGTcount: A:0.16, C:0.12, G:0.11, T:0.61
Consensus pattern (30 bp):
TTTAAGTTTCTATTTTTGCTATTTTAGTCC
Found at i:3180440 original size:60 final size:60
Alignment explanation
Indices: 3180366--3180547 Score: 267
Period size: 60 Copynumber: 3.0 Consensus size: 60
3180356 GATTCATTCT
*
3180366 TTTAAATTTTTATTTGTT-CTATTTTAGTCCTTTAAGTTTCTATTTATGCTATTTTGGTCC
1 TTTAAGTTTTTATTT-TTGCTATTTTAGTCCTTTAAGTTTCTATTTATGCTATTTTGGTCC
* * * *
3180426 TTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTCTGTTTATACTATTTTAGTCC
1 TTTAAGTTTTTATTTTTGCTATTTTAGTCCTTTAAGTTTCTATTTATGCTATTTTGGTCC
* * *
3180486 TTTAAGTTTTTGTTTTTGCTATTTTAGTCTTTTAAGTTTCTATTTTTTGCTATTTTGGTCC
1 TTTAAGTTTTTATTTTTGCTATTTTAGTCCTTTAAGTTTCTA-TTTATGCTATTTTGGTCC
3180547 T
1 T
3180548 AATTTTCTGT
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
59 2 0.02
60 90 0.83
61 16 0.15
ACGTcount: A:0.16, C:0.12, G:0.11, T:0.61
Consensus pattern (60 bp):
TTTAAGTTTTTATTTTTGCTATTTTAGTCCTTTAAGTTTCTATTTATGCTATTTTGGTCC
Found at i:3180586 original size:90 final size:89
Alignment explanation
Indices: 3180384--3180585 Score: 273
Period size: 90 Copynumber: 2.3 Consensus size: 89
3180374 TTTATTTGTT
* *
3180384 CTATTTTAGTCCTTTAAGTTTCTATTTATGCTATTTTGGTCCTTTAAGTTTCTATTTTTGCTATT
1 CTATTTTAGTCCTTTAAGTTTTTATTTATGCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATT
*
3180449 TTAGTCCTTTAAGTTTCTGTTTATA
66 TTAGTCC-TTAAGTTTCTGTTAATA
* * *
3180474 CTATTTTAGTCCTTTAAGTTTTTGTTTTTGCTATTTTAGTCTTTTAAGTTTCTATTTTTTGCTAT
1 CTATTTTAGTCCTTTAAGTTTTTATTTATGCTATTTTAGTCCTTTAAGTTTCTA-TTTTTGCTAT
* *
3180539 TTTGGTCC-TAATTTTCTGTTAAT-
65 TTTAGTCCTTAAGTTTCTGTTAATA
* *
3180562 CATATTTTGGTCCTTTAAATTTTT
1 C-TATTTTAGTCCTTTAAGTTTTT
3180586 TATTGTTTTG
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
88 1 0.01
89 33 0.33
90 49 0.49
91 17 0.17
ACGTcount: A:0.17, C:0.12, G:0.11, T:0.59
Consensus pattern (89 bp):
CTATTTTAGTCCTTTAAGTTTTTATTTATGCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATT
TTAGTCCTTAAGTTTCTGTTAATA
Found at i:3189615 original size:179 final size:178
Alignment explanation
Indices: 3189430--3189760 Score: 436
Period size: 178 Copynumber: 1.9 Consensus size: 178
3189420 AAAAACAAAA
* * *
3189430 TCATATAGT-AACATGTTTTGTTACTATAAACT-ATAATTACTT-TTACAAAAAAAGTTATCACA
1 TCATATAGTGAA-AAGTTTTGTAACTAT-AACTGATAA-TAATTATTACAAAAAAA-TTATCACA
* * *
3189492 AAAAATAATGAGATGCAAGTTTGTAGTGA-AAATAATGTTTGTAGTTATATATTTTATTTATAGT
62 AAAAATAATGAGATGCAAGTTTGTA-TGATAAATAATATTTGTAGTTATAAATTTTAATTATAGT
*
3189556 GATTAAATATATTGTCATAAATATTTCCCTCCATATTTTAAGTGTAAAAAAGG
126 GATGAAATATATTGTCATAAATATTTCCCTCCATATTTTAAGTGTAAAAAAGG
* * * *
3189609 TCATATAGTGAAAAGTTTTGTAACTATAAGTGTTAATAATTATTATAAAAAAATTATCACAACAA
1 TCATATAGTGAAAAGTTTTGTAACTATAACTGATAATAATTATTACAAAAAAATTATCACAAAAA
* * * * *
3189674 ATGATGATATTCAAGTTTTTATGATAAATTATATTTGTAGTTATAAATTTTAATTATAGTGATGA
66 ATAATGAGATGCAAGTTTGTATGATAAATAATATTTGTAGTTATAAATTTTAATTATAGTGATGA
*
3189739 AATATATTGTCATAACTATTTC
131 AATATATTGTCATAAATATTTC
3189761 ATCCAATTTT
Statistics
Matches: 131, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
177 3 0.02
178 91 0.69
179 35 0.27
180 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (178 bp):
TCATATAGTGAAAAGTTTTGTAACTATAACTGATAATAATTATTACAAAAAAATTATCACAAAAA
ATAATGAGATGCAAGTTTGTATGATAAATAATATTTGTAGTTATAAATTTTAATTATAGTGATGA
AATATATTGTCATAAATATTTCCCTCCATATTTTAAGTGTAAAAAAGG
Found at i:3198757 original size:18 final size:17
Alignment explanation
Indices: 3198727--3198776 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
3198717 ATTGTTAAAC
3198727 TTTTTGATTTGGATGTT
1 TTTTTGATTTGGATGTT
*
3198744 TATGTTTG-TTTGGATATT
1 T-T-TTTGATTTGGATGTT
*
3198762 TTTTTGTTTTGGATG
1 TTTTTGATTTGGATG
3198777 CTTGGACGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
18 11 0.39
19 4 0.14
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (17 bp):
TTTTTGATTTGGATGTT
Found at i:3199501 original size:64 final size:64
Alignment explanation
Indices: 3199385--3199590 Score: 213
Period size: 64 Copynumber: 3.2 Consensus size: 64
3199375 ATTCAAGGGG
* * * *
3199385 ATGCACCGATGCATCAAACCATGCATCGATGCACCTATG-AT-TTAATT-GAACATCGAATGCAT
1 ATGCATCGATGCA-CAAGCCATGCATCGATGCA-CTA-GAATATT-TTTCAAACATCGAATGCAT
3199447 TTC
62 TTC
* *** * *
3199450 ATGCACCGATGCACTCTCCATGCATCGATGCACTCATAATA-TTTTCAAACATCGAATGCATTTG
1 ATGCATCGATGCACAAGCCATGCATCGATGCACT-AGAATATTTTTCAAACATCGAATGCATTTC
** * *
3199514 ATGCATCGATGCACAAGCCATGCATCGATGCACTAGGCTATTTTTTAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTAGAATATTTTTCAAACATCGAATGCATTTC
3199578 ATGCATCGATGCA
1 ATGCATCGATGCA
3199591 TCCTTAGTGC
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
63 7 0.06
64 100 0.83
65 13 0.11
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCCATGCATCGATGCACTAGAATATTTTTCAAACATCGAATGCATTTC
Found at i:3200765 original size:21 final size:23
Alignment explanation
Indices: 3200740--3200787 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
3200730 ACTATTTTTG
*
3200740 TTAAAAT-AAAATCCAAA-AAAA
1 TTAAAATAAAAATCAAAATAAAA
3200761 TTAAAATAAAAATCAAAATAAAA
1 TTAAAATAAAAATCAAAATAAAA
3200784 TTAA
1 TTAA
3200788 TCCAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.29
22 9 0.38
23 8 0.33
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (23 bp):
TTAAAATAAAAATCAAAATAAAA
Found at i:3206375 original size:73 final size:73
Alignment explanation
Indices: 3206255--3206584 Score: 479
Period size: 73 Copynumber: 4.5 Consensus size: 73
3206245 TATGGAAATG
* *
3206255 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAACTTTCTCGAA-CGAGAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAATGAAACTTTCTC-AAGCGAGAA
3206319 ACAATTTGT
65 ACAATTTGT
*
3206328 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCCAATGAAACTTTCTCAAGCGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAATGAAACTTTCTCAAGCGAGAAA
3206393 CAATTTGT
66 CAATTTGT
* **
3206401 TTTAAGAAAAACAATCTCAAGTGAGATGAAATT--TATTT-TAAGTGAAACTTTCTCAATTGAGA
1 TTTAAGAAAAACAATCTCAAGTGAGAT-AAATTGCTATTTCGAA-TGAAACTTTCTCAAGCGAGA
* *
3206463 AATAGTTTGT
64 AACAATTTGT
** * * *
3206473 TTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTATTTCGAGTGAAATTTTGTCAAGCGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAATGAAACTTTCTCAAGCGAGAAA
3206538 CAATTTGT
66 CAATTTGT
*
3206546 TTTAAGAAAAATAATCTCAAGTGAGATAAATTGCTATTT
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
3206585 TAAAACATCT
Statistics
Matches: 232, Mismatches: 19, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
71 7 0.03
72 60 0.26
73 159 0.69
74 6 0.03
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (73 bp):
TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCGAATGAAACTTTCTCAAGCGAGAAA
CAATTTGT
Found at i:3206421 original size:36 final size:35
Alignment explanation
Indices: 3206255--3206577 Score: 188
Period size: 36 Copynumber: 8.9 Consensus size: 35
3206245 TATGGAAATG
*
3206255 TTTAAGAAAAACAATCTCAAGTGAGATAAA-TTGTT
1 TTTAAGAAAAACAATCTCAAGTGAGAAAAATTTG-T
* ** ** *
3206290 ATTTCGAGTGAAACTTTCTCGAA-CGAGAAACAATTTGT
1 -TTT-AAGAAAAACAATCTC-AAGTGAGAAA-AATTTGT
*
3206328 TTTAAGAAAAACAATCTCAAGTGAGATAAA-TTGCT
1 TTTAAGAAAAACAATCTCAAGTGAGAAAAATTTG-T
** *
3206363 ATTTCCAATG--AAACTTTCTCAAGCGAGAAACAATTTGT
1 -TTT--AA-GAAAAACAATCTCAAGTGAGAAA-AATTTGT
* *
3206401 TTTAAGAAAAACAATCTCAAGTGAGATGAAATTTAT
1 TTTAAGAAAAACAATCTCAAGTGAGA-AAAATTTGT
** ** * *
3206437 TTTAAGTGAAACTTTCTCAATTGAGAAATAGTTTGT
1 TTTAAGAAAAACAATCTCAAGTGAGAAA-AATTTGT
* *
3206473 TTTAAGAAAAACAATCTCAAGTGAGATAAATTTTT
1 TTTAAGAAAAACAATCTCAAGTGAGAAAAATTTGT
* ** *** * *
3206508 ATTTCGAGTGAAATTTTGTCAAGCGAGAAACAATTTGT
1 -TTT-AAGAAAAACAATCTCAAGTGAGAAA-AATTTGT
* *
3206546 TTTAAGAAAAATAATCTCAAGTGAGATAAATT
1 TTTAAGAAAAACAATCTCAAGTGAGAAAAATT
3206578 GCTATTTTAA
Statistics
Matches: 211, Mismatches: 57, Indels: 39
0.69 0.19 0.13
Matches are distributed among these distances:
34 4 0.02
35 17 0.08
36 110 0.52
37 57 0.27
38 16 0.08
39 7 0.03
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (35 bp):
TTTAAGAAAAACAATCTCAAGTGAGAAAAATTTGT
Found at i:3206520 original size:145 final size:144
Alignment explanation
Indices: 3206255--3206587 Score: 497
Period size: 145 Copynumber: 2.3 Consensus size: 144
3206245 TATGGAAATG
**
3206255 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCGAGTGAAACTTTCTCGAACGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAA-T-TTATTTTAAGTGAAACTTTCTCGAACGAGAAA
3206320 CAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCCAATGAAACTTTCTCAA
64 CAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCCAATGAAACTTTCTCAA
3206385 GCGAGAAACAATTTGT
129 GCGAGAAACAATTTGT
*
3206401 TTTAAGAAAAACAATCTCAAGTGAGATGAAATTTATTTTAAGTGAAACTTTCTC-AATTGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGAT-AAATTTATTTTAAGTGAAACTTTCTCGAA-CGAGAAA
* * ** * * * *
3206465 TAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTATTTCGAGTGAAATTTTGTCAA
64 CAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCCAATGAAACTTTCTCAA
3206530 GCGAGAAACAATTTGT
129 GCGAGAAACAATTTGT
*
3206546 TTTAAGAAAAATAATCTCAAGTGAGATAAATTGCTATTTTAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATT--TATTTTAA
3206588 AACATCTTGC
Statistics
Matches: 171, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
144 7 0.04
145 125 0.73
146 36 0.21
147 3 0.02
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (144 bp):
TTTAAGAAAAACAATCTCAAGTGAGATAAATTTATTTTAAGTGAAACTTTCTCGAACGAGAAACA
ATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCCAATGAAACTTTCTCAAGC
GAGAAACAATTTGT
Found at i:3207320 original size:22 final size:22
Alignment explanation
Indices: 3207293--3207344 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
3207283 AATAAAGTGT
3207293 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3207315 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3207337 TCATCTTT
1 TCATCTTT
3207345 AAAGAGTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3208802 original size:75 final size:75
Alignment explanation
Indices: 3208708--3208847 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 75
3208698 TGCTGATATG
* * *
3208708 AACGTTCAAAATACATCAATGCTT-CTGATTCTGATTGAAATGGGGCTTTCAGCATGC-CCAGCA
1 AACGTTCAAAATACATCAAT-ATTCCTGATTATGATTAAAAT-GGGCTTTCAGCATGCTCCAGCA
3208771 TTGACTAATACA
64 TTGACTAATACA
*** *
3208783 AACGTTCAAAATGTGTCAATATTCCTGATTATGATTAAAATGGGCTTTCAGCATGCTCCATCATT
1 AACGTTCAAAATACATCAATATTCCTGATTATGATTAAAATGGGCTTTCAGCATGCTCCAGCATT
3208848 TGCTTCTTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
74 17 0.30
75 39 0.70
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (75 bp):
AACGTTCAAAATACATCAATATTCCTGATTATGATTAAAATGGGCTTTCAGCATGCTCCAGCATT
GACTAATACA
Found at i:3211338 original size:32 final size:32
Alignment explanation
Indices: 3211289--3211351 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
3211279 GAAATGGTTA
* * *
3211289 TTATGCTTATCTGGTAGAGATACTTCTTGTTG
1 TTATGCTCATCTCGTAGAAATACTTCTTGTTG
3211321 TTATGCTCATCTCGTAGAAATACTTCTTGTT
1 TTATGCTCATCTCGTAGAAATACTTCTTGTT
3211352 TCCAGACTCT
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:0.21, C:0.16, G:0.17, T:0.46
Consensus pattern (32 bp):
TTATGCTCATCTCGTAGAAATACTTCTTGTTG
Found at i:3214614 original size:14 final size:14
Alignment explanation
Indices: 3214595--3214695 Score: 52
Period size: 14 Copynumber: 7.4 Consensus size: 14
3214585 GCAAAGATGC
3214595 AAATGTAAAAATGA
1 AAATGTAAAAATGA
3214609 AAATGT--AAAT-A
1 AAATGTAAAAATGA
**
3214620 CAAACATAAAAATGAAA
1 -AAATGTAAAAATG--A
*
3214637 AAATG-CAAAATGCA
1 AAATGTAAAAATG-A
*
3214651 AAATGT--AAATGC
1 AAATGTAAAAATGA
* *
3214663 AAATGTAAATATGT
1 AAATGTAAAAATGA
* *
3214677 GAATGTAAAAATAA
1 AAATGTAAAAATGA
3214691 AAATG
1 AAATG
3214696 CAAATTGTGC
Statistics
Matches: 64, Mismatches: 14, Indels: 18
0.67 0.15 0.19
Matches are distributed among these distances:
11 1 0.02
12 14 0.22
13 5 0.08
14 34 0.53
15 6 0.09
16 3 0.05
17 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (14 bp):
AAATGTAAAAATGA
Found at i:3214668 original size:12 final size:13
Alignment explanation
Indices: 3214603--3214672 Score: 54
Period size: 12 Copynumber: 5.3 Consensus size: 13
3214593 GCAAATGTAA
3214603 AAATG-AAAATGT
1 AAATGCAAAATGT
* **
3214615 AAATACAAACATAA
1 AAATGCAAA-ATGT
* *
3214629 AAATGAAAAAATGCA
1 AAATG-CAAAATG-T
3214644 AAATGCAAAATGT
1 AAATGCAAAATGT
3214657 AAATGC-AAATGT
1 AAATGCAAAATGT
3214669 AAAT
1 AAAT
3214673 ATGTGAATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
12 14 0.30
13 9 0.20
14 14 0.30
15 9 0.20
ACGTcount: A:0.61, C:0.07, G:0.11, T:0.20
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:3214681 original size:20 final size:20
Alignment explanation
Indices: 3214583--3214665 Score: 62
Period size: 20 Copynumber: 4.0 Consensus size: 20
3214573 AAATGTAATT
* *
3214583 ATGCAAAGATGCAAATGTAAAA
1 ATGCAAA-ATGTAAATG-CAAA
*
3214605 ATG-AAAATGTAAATACAAA
1 ATGCAAAATGTAAATGCAAA
* *
3214624 CAT-AAAAATGAAAAAATGCAAA
1 -ATGCAAAATG--TAAATGCAAA
3214646 ATGCAAAATGTAAATGCAAA
1 ATGCAAAATGTAAATGCAAA
3214666 TGTAAATATG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
19 3 0.06
20 24 0.49
21 5 0.10
22 17 0.35
ACGTcount: A:0.60, C:0.08, G:0.13, T:0.18
Consensus pattern (20 bp):
ATGCAAAATGTAAATGCAAA
Found at i:3218239 original size:23 final size:23
Alignment explanation
Indices: 3218208--3218253 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3218198 GGGAACATAA
* *
3218208 CGGCGGAGCAGTTGGAGTAGAGG
1 CGGCAGAGCAGTTAGAGTAGAGG
3218231 CGGCAGAGCAGTTAGAGTAGAGG
1 CGGCAGAGCAGTTAGAGTAGAGG
3218254 AACGGCCGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.48, T:0.13
Consensus pattern (23 bp):
CGGCAGAGCAGTTAGAGTAGAGG
Found at i:3218748 original size:15 final size:15
Alignment explanation
Indices: 3218730--3218758 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3218720 TTCCACTATC
3218730 CAAGATTTGTCTGCA
1 CAAGATTTGTCTGCA
3218745 CAAGATTTGTCTGC
1 CAAGATTTGTCTGC
3218759 TAATGATCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (15 bp):
CAAGATTTGTCTGCA
Found at i:3218961 original size:12 final size:12
Alignment explanation
Indices: 3218944--3218979 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3218934 CTTTTTTCCT
3218944 TTGCTACTGGTG
1 TTGCTACTGGTG
3218956 TTGCTACTGGTG
1 TTGCTACTGGTG
*
3218968 TTGCTTCTGGTG
1 TTGCTACTGGTG
3218980 CATATGTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.06, C:0.17, G:0.33, T:0.44
Consensus pattern (12 bp):
TTGCTACTGGTG
Found at i:3220228 original size:16 final size:18
Alignment explanation
Indices: 3220207--3220245 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
3220197 AACGTATTTT
3220207 AAAAAT-AATTTTAAGA-
1 AAAAATCAATTTTAAGAC
3220223 AAAAATCAATTTTAAGAC
1 AAAAATCAATTTTAAGAC
3220241 AAAAA
1 AAAAA
3220246 ACCGATCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.29
17 10 0.48
18 5 0.24
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAATCAATTTTAAGAC
Found at i:3221073 original size:29 final size:30
Alignment explanation
Indices: 3221015--3221093 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 30
3221005 ATATTTAACC
*
3221015 AAACTTGAAGGGCTAAAATAGCTAAAATAG
1 AAACTTGAAGGGCTAAAATAGCAAAAATAG
3221045 AAACTT-AAGGGTCT-AAATAG-AAAATATAG
1 AAACTTGAAGGG-CTAAAATAGCAAAA-ATAG
* * * *
3221074 ACATTTAAAGGACTAAAATA
1 AAACTTGAAGGGCTAAAATA
3221094 AAAAAACAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 3 0.07
29 21 0.51
30 17 0.41
ACGTcount: A:0.52, C:0.09, G:0.16, T:0.23
Consensus pattern (30 bp):
AAACTTGAAGGGCTAAAATAGCAAAAATAG
Found at i:3226386 original size:20 final size:18
Alignment explanation
Indices: 3226362--3226413 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 18
3226352 TGAACTGTTG
3226362 ATTTTTTTTTTGCTGCTAA
1 ATTTTTTTTTTGCTGCT-A
3226381 ATTTTTTTTTTGCTGCTA
1 ATTTTTTTTTTGCTGCTA
3226399 ATTTTAATTTTTTGC
1 ATTTT--TTTTTTGC
3226414 CCATGTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.19
19 17 0.55
20 8 0.26
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (18 bp):
ATTTTTTTTTTGCTGCTA
Found at i:3226409 original size:18 final size:19
Alignment explanation
Indices: 3226369--3226409 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3226359 TTGATTTTTT
**
3226369 TTTTGCTGCTAAATTTTTT
1 TTTTGCTGCTAAATTTTAA
3226388 TTTTGCTGCT-AATTTTAA
1 TTTTGCTGCTAAATTTTAA
3226406 TTTT
1 TTTT
3226410 TTGCCCATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.63
Consensus pattern (19 bp):
TTTTGCTGCTAAATTTTAA
Found at i:3234501 original size:20 final size:20
Alignment explanation
Indices: 3234476--3234534 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
3234466 TTTGGTGCAG
**
3234476 AGGGAATCGATCCCCCCTTT
1 AGGGAATCGATCCCCCCTAC
* *
3234496 AGGGAACCGATTCCCCC-AC
1 AGGGAATCGATCCCCCCTAC
3234515 AGGGGAATCGATACCCCCCT
1 A-GGGAATCGAT-CCCCCCT
3234535 GGGGTTCTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 24 0.80
21 5 0.17
ACGTcount: A:0.24, C:0.37, G:0.22, T:0.17
Consensus pattern (20 bp):
AGGGAATCGATCCCCCCTAC
Found at i:3244215 original size:37 final size:37
Alignment explanation
Indices: 3244174--3244251 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
3244164 TATTTTAATA
*
3244174 TTTTGGATCTGATAAATTTGGGTTGGAAATGTGCATT
1 TTTTGGATCTGATAAATTTGGGTTGGAAATGTGCAAT
3244211 TTTTGGATCTGATAAATTTGGGTTGGAAATGTGCAAT
1 TTTTGGATCTGATAAATTTGGGTTGGAAATGTGCAAT
3244248 TTTT
1 TTTT
3244252 CAGATTTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (37 bp):
TTTTGGATCTGATAAATTTGGGTTGGAAATGTGCAAT
Found at i:3244248 original size:20 final size:20
Alignment explanation
Indices: 3244188--3244249 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
3244178 GGATCTGATA
3244188 AATTTGGGTTGGAAATGTGC
1 AATTTGGGTTGGAAATGTGC
* ** *
3244208 -ATTT--TTTGGATCTGAT-A
1 AATTTGGGTTGGAAATG-TGC
3244225 AATTTGGGTTGGAAATGTGC
1 AATTTGGGTTGGAAATGTGC
3244245 AATTT
1 AATTT
3244250 TTCAGATTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 7 0.24
18 5 0.17
19 5 0.17
20 12 0.41
ACGTcount: A:0.26, C:0.05, G:0.27, T:0.42
Consensus pattern (20 bp):
AATTTGGGTTGGAAATGTGC
Found at i:3251099 original size:3 final size:3
Alignment explanation
Indices: 3251091--3251120 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3251081 TGGACCTGTA
3251091 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3251121 TGGATAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3254114 original size:45 final size:45
Alignment explanation
Indices: 3254051--3254286 Score: 346
Period size: 45 Copynumber: 5.2 Consensus size: 45
3254041 GTTTTCATTA
* *
3254051 CATAAATGAAATGCATAACGGTGCATTAAAGGAATGAAAGGATGA
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* *
3254096 CATAAATGAAATGCATAACAGAGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
3254141 CATGAATGAAATGCATAACGGTGCATTAAAGGTATGAAATGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
3254186 CATAAATGAAATGCATAATGGTGCATGAAAGGCATGAAAGGATTC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * * *
3254231 CATAAATGAAATGCATAATGATACATTAAAGGCATGAAAGGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
3254276 CATAAATGAAA
1 CATAAATGAAA
3254287 ATAATGAATA
Statistics
Matches: 171, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 171 1.00
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:3260402 original size:21 final size:21
Alignment explanation
Indices: 3260377--3260450 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
3260367 TGATGAACAT
3260377 TATCGATACTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
* *
3260398 TATCGATGCTGATGCAATTAA
1 TATCGATACTGATGCAATTAG
*
3260419 TATCGATGCTGATGCAATTAG
1 TATCGATACTGATGCAATTAG
*
3260440 TATCAATACTG
1 TATCGATACTG
3260451 CTTTGGGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (21 bp):
TATCGATACTGATGCAATTAG
Found at i:3261073 original size:45 final size:45
Alignment explanation
Indices: 3261021--3261297 Score: 383
Period size: 45 Copynumber: 6.2 Consensus size: 45
3261011 GTTTTCATTA
* *
3261021 CATAAATGAAATGCATAATGGTGTATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
3261066 CATAAATGAAATGCATAACAGTGCATTAAATGCATGAAAGGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
3261111 CATAAATGAAATGCATAACAGCGCATTAAAGGAATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * * * *
3261156 CATAACTGAAATGCATAATGGTACATTAAAGGCATGAAATGATAC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
3261201 CATAAATGAAATGTATAACGATCCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
* * *
3261246 CATAAATAAAATGCACAACTGTGCATTAAAGGCATGAAAGGATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
3261291 CATAAAT
1 CATAAAT
3261298 TAAAAATAAT
Statistics
Matches: 202, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 202 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGC
Found at i:3261970 original size:139 final size:139
Alignment explanation
Indices: 3261720--3261997 Score: 556
Period size: 139 Copynumber: 2.0 Consensus size: 139
3261710 ATTTATATGA
3261720 ATAATTGGTAAAAGATGAGAAAATGATTTGGACTAGTGAATTAGACTAAATTGTAACAAGGGATG
1 ATAATTGGTAAAAGATGAGAAAATGATTTGGACTAGTGAATTAGACTAAATTGTAACAAGGGATG
3261785 GTTTAGAGGGCATTTTAGTCCTTTAAAGAAAAAATGAATTTAAAATTCTTATTTATAAGATATAA
66 GTTTAGAGGGCATTTTAGTCCTTTAAAGAAAAAATGAATTTAAAATTCTTATTTATAAGATATAA
3261850 AAAGTAAGG
131 AAAGTAAGG
3261859 ATAATTGGTAAAAGATGAGAAAATGATTTGGACTAGTGAATTAGACTAAATTGTAACAAGGGATG
1 ATAATTGGTAAAAGATGAGAAAATGATTTGGACTAGTGAATTAGACTAAATTGTAACAAGGGATG
3261924 GTTTAGAGGGCATTTTAGTCCTTTAAAGAAAAAATGAATTTAAAATTCTTATTTATAAGATATAA
66 GTTTAGAGGGCATTTTAGTCCTTTAAAGAAAAAATGAATTTAAAATTCTTATTTATAAGATATAA
3261989 AAAGTAAGG
131 AAAGTAAGG
3261998 GAAAAGGGAA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 139 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (139 bp):
ATAATTGGTAAAAGATGAGAAAATGATTTGGACTAGTGAATTAGACTAAATTGTAACAAGGGATG
GTTTAGAGGGCATTTTAGTCCTTTAAAGAAAAAATGAATTTAAAATTCTTATTTATAAGATATAA
AAAGTAAGG
Found at i:3263121 original size:45 final size:45
Alignment explanation
Indices: 3263070--3263207 Score: 138
Period size: 45 Copynumber: 3.3 Consensus size: 45
3263060 AGAATAATAC
3263070 ATATGGGTACATTAATGGCATGAAATGATGCCTTAGCTGATATGT
1 ATATGGGTACATTAATGGCATGAAATGATGCCTTAGCTGATATGT
* *
3263115 ATATGGGTACATT-ATCGGCAT-AAA--A-G----A-AT-A-ATGC
1 ATATGGGTACATTAAT-GGCATGAAATGATGCCTTAGCTGATATGT
* * *
3263149 ATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGATATAT
1 ATATGGGTACATTAATGGCATGAAATGATGCCTTAGCTGATATGT
3263194 ATATGGGTACATTA
1 ATATGGGTACATTA
3263208 TCGGCATAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 26
0.68 0.08 0.25
Matches are distributed among these distances:
34 20 0.28
35 5 0.07
36 1 0.01
37 2 0.03
38 1 0.01
41 1 0.01
42 2 0.03
43 1 0.01
44 6 0.08
45 33 0.46
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (45 bp):
ATATGGGTACATTAATGGCATGAAATGATGCCTTAGCTGATATGT
Found at i:3263162 original size:34 final size:34
Alignment explanation
Indices: 3263115--3263242 Score: 103
Period size: 34 Copynumber: 3.4 Consensus size: 34
3263105 GCTGATATGT
3263115 ATATGGGTACATTATCGGCATAAAAGAATAATGC
1 ATATGGGTACATTATCGGCATAAAAGAATAATGC
* * * **
3263149 ATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGATATAT
1 ATATGGGTACATTATCGGCAT-AAA--A-G----A-AT-A-ATGC
3263194 ATATGGGTACATTATCGGCATAAAAGAATAATGC
1 ATATGGGTACATTATCGGCATAAAAGAATAATGC
*
3263228 ATATGGGTGCATTAT
1 ATATGGGTACATTAT
3263243 TGGTTTGAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
34 35 0.49
35 4 0.06
36 1 0.01
37 2 0.03
38 1 0.01
41 1 0.01
42 2 0.03
43 1 0.01
44 4 0.06
45 21 0.29
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (34 bp):
ATATGGGTACATTATCGGCATAAAAGAATAATGC
Found at i:3263186 original size:79 final size:79
Alignment explanation
Indices: 3263055--3263321 Score: 444
Period size: 79 Copynumber: 3.4 Consensus size: 79
3263045 AAACTAATGA
* * *
3263055 ATAAAAGAATAATACATATGGGTACATTAATGGCATGAAATGATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGATATGTATATG
3263120 GGTACATTATCGGC
66 GGTACATTATCGGC
*
3263134 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGATATATATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGATATGTATATG
3263199 GGTACATTATCGGC
66 GGTACATTATCGGC
** **
3263213 ATAAAAGAATAATGCATATGGGTGCATTATTGGTTTGAAAACATGCCTTAGCTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGATATGTATATG
*
3263278 GGTACATTATCAGC
66 GGTACATTATCGGC
*
3263292 ATAACAGAATAATGCATATGGGTGCATTAT
1 ATAAAAGAATAATGCATATGGGTGCATTAT
3263322 CAACATAAAA
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 177 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGATATGTATATG
GGTACATTATCGGC
Found at i:3263426 original size:60 final size:59
Alignment explanation
Indices: 3263333--3263447 Score: 212
Period size: 60 Copynumber: 1.9 Consensus size: 59
3263323 AACATAAAAG
3263333 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATAATA
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCA-TTTGTGTGCTAAAATAATA
*
3263393 AGGAAATCATATTAAGTGTATGAATTTCCAGATAAGGGCATTTGTGTGCTAAAAT
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCATTTGTGTGCTAAAAT
3263448 GATAGGTATT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
59 15 0.28
60 39 0.72
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (59 bp):
AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCATTTGTGTGCTAAAATAATA
Found at i:3265890 original size:2 final size:2
Alignment explanation
Indices: 3265883--3265917 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3265873 TGTTAGAAAG
3265883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3265918 GCTTTTATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3268585 original size:79 final size:79
Alignment explanation
Indices: 3268451--3268734 Score: 430
Period size: 79 Copynumber: 3.6 Consensus size: 79
3268441 AAACTAATGA
*
3268451 ATAAAAGAATAATTG-ATATGGGTGCATTAATGGCATGAAAGGATGCCTTAACTGATATGTATAT
1 ATAAAAGAATAA-TGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAGCTGATATGTATAT
3268515 GGGTACATTATCGAC
65 GGGTACATTATCGAC
*
3268530 ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAGCTGATATGTATATT
1 ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAGCTGATATGTATATG
*
3268595 GGTACATTATCGGC
66 GGTACATTATCGAC
* ** * * *
3268609 ATAAAATAATAATGCATATATGTGAATTAATGTCATGAAAGGATGCCTTAGTTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAGCTGATATGTATATG
3268674 GGTACATTATC-AGC
66 GGTACATTATCGA-C
*
3268688 ATAACAA-AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCC
1 ATAA-AAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCC
3268735 AAAGTTGAAA
Statistics
Matches: 186, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
78 2 0.01
79 182 0.98
80 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.31
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAGCTGATATGTATATG
GGTACATTATCGAC
Found at i:3268741 original size:79 final size:79
Alignment explanation
Indices: 3268451--3268774 Score: 415
Period size: 79 Copynumber: 4.1 Consensus size: 79
3268441 AAACTAATGA
3268451 ATAAAAGAATAATTG-ATATGGGTGCATTAATGGCATGAAAGGATGCCTTAA-CTGATATGTATA
1 ATAAAAGAATAA-TGCATATGGGTGCATTAATGGCATGAAAGGATGCC-TAAGCTGATATGTATA
3268514 TGGGTACATTATC-GAC
64 TGGGTACATTATCAG-C
* *
3268530 ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTTAGCTGATATGTATATT
1 ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTAAGCTGATATGTATATG
*
3268595 GGTACATTATCGGC
66 GGTACATTATCAGC
* ** * * * *
3268609 ATAAAATAATAATGCATATATGTGAATTAATGTCATGAAAGGATGCCTTAGTTGATATGTATATG
1 ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTAAGCTGATATGTATATG
3268674 GGTACATTATCAGC
66 GGTACATTATCAGC
* * * * *
3268688 ATAACAA-AATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGAAATGCATAT
1 ATAA-AAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTAAGCTGATATGTATAT
* *
3268752 GGGTGCATCATCAAG-
65 GGGTACATTATC-AGC
3268767 ATAAAAGA
1 ATAAAAGA
3268775 GGAAATAATA
Statistics
Matches: 218, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
78 6 0.03
79 207 0.95
80 5 0.02
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTAATGGCATGAAAGGATGCCTAAGCTGATATGTATATG
GGTACATTATCAGC
Found at i:3269322 original size:81 final size:81
Alignment explanation
Indices: 3269176--3269324 Score: 181
Period size: 81 Copynumber: 1.8 Consensus size: 81
3269166 CTTTGAGGCC
* * * ** * *
3269176 TAACTGTGAAATTGGAAAAAATGTGTCAAATATGCCAGTTAGATGAATGGTTAAGTACCGTTGAG
1 TAACTGTGAAATTGGAAAAAAGGTGTCAAATATGCCAGTTAGATAAAGGGTTAAACAACGATGAG
3269241 TAAAAGAAAAATAGTT
66 TAAAAGAAAAATAGTT
* * * * * *
3269257 TAACTGTGCAATTGGCATAAAGGTGTCAATTATGCCAGTTCGATAAAGGGTTAAACAATGATGAG
1 TAACTGTGAAATTGGAAAAAAGGTGTCAAATATGCCAGTTAGATAAAGGGTTAAACAACGATGAG
3269322 TAA
66 TAA
3269325 GAGGATAAAG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
81 55 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (81 bp):
TAACTGTGAAATTGGAAAAAAGGTGTCAAATATGCCAGTTAGATAAAGGGTTAAACAACGATGAG
TAAAAGAAAAATAGTT
Found at i:3271377 original size:27 final size:27
Alignment explanation
Indices: 3271320--3271377 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
3271310 ACATTTTGTG
* * **
3271320 CGATCGGCAAGGGTAGAAGAAAGTGTG
1 CGATCAGCAAGGGTAGAAGAAAGGGAC
* *
3271347 CGATCAGCAAGGGTAGAGGAGAGGGAC
1 CGATCAGCAAGGGTAGAAGAAAGGGAC
3271374 CGAT
1 CGAT
3271378 TGCCCAACTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.41, T:0.12
Consensus pattern (27 bp):
CGATCAGCAAGGGTAGAAGAAAGGGAC
Found at i:3281219 original size:21 final size:21
Alignment explanation
Indices: 3281194--3281246 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
3281184 TTTAAGAGTG
3281194 CTTTGTGTACTTAG-AGTAGTA
1 CTTTGTGTACTT-GTAGTAGTA
3281215 CTTTGTGTACTTGTAGTAGTA
1 CTTTGTGTACTTGTAGTAGTA
3281236 CTTTGTGTACT
1 CTTTGTGTACT
3281247 CTGGCACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.19, C:0.11, G:0.23, T:0.47
Consensus pattern (21 bp):
CTTTGTGTACTTGTAGTAGTA
Found at i:3282009 original size:54 final size:54
Alignment explanation
Indices: 3281936--3282373 Score: 401
Period size: 54 Copynumber: 8.1 Consensus size: 54
3281926 TGTAGTGTCG
* * *
3281936 ATACGGTCATTCATAAACATATTATGAATTACGTGGGTTGCACACTTAGTGCCG
1 ATACGGTCGTTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
* * * * * * *
3281990 ATAAGGTCGTTCGTCAACATATGATGAATTTCATGGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
* * * *
3282044 ATACGGTCATTCATAAACACATTATGAATTCCGTGGGTTGCACACTTAGTTCTT
1 ATACGGTCGTTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
* ** * * * **
3282098 ATACGGTCATTCATAAACACATTATGAATTTTGAGGGTTGTATACTTAGTGTAT
1 ATACGGTCGTTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
** * * * * * * *
3282152 ATGGGGGGGTCGTTCATCAACATATGATGAATTATGAGGGTCGCACACTTAGTGCAT
1 AT---ACGGTCGTTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
* * * * *
3282209 ATACGGTTGTTCGTAAACACATTTTAAATTATGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
** * *
3282263 ATACATTCGTTCATAAACACATTATGAATTATGTGGGTTGCACACTTAGTTCCT
1 ATACGGTCGTTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
* * * * * * * *
3282317 ATCCGATCGTTCATCAACATATGATGAATT-CTGTGTGTTGCATACTTAGTTCCT
1 ATACGGTCGTTCATAAACACATTATGAATTAC-GTGGGTTGCACACTTAGTGCCT
3282371 ATA
1 ATA
3282374 GTACACATAG
Statistics
Matches: 314, Mismatches: 66, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
54 271 0.86
57 43 0.14
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (54 bp):
ATACGGTCGTTCATAAACACATTATGAATTACGTGGGTTGCACACTTAGTGCCT
Found at i:3282205 original size:165 final size:165
Alignment explanation
Indices: 3281936--3282312 Score: 456
Period size: 165 Copynumber: 2.3 Consensus size: 165
3281926 TGTAGTGTCG
* * * * *** **
3281936 ATACGGTCATTCATAAACATATTATGAATTACGTGGGTTGCACACTTAGTGCCGAT---AAGGTC
1 ATACAGTCATTCATAAACACATTATGAATTATGAGGGTTGCACACTTAGTGTATATGGGGGGGTC
* * *
3281998 GTTCGTCAACATATGATGAATTTCATGGGTTGCACACTTAGTGCCTATACGGTCATTCATAAACA
66 GTTCATCAACATATGATGAATTTCATGGGTCGCACACTTAGTGCATATACGGTCATTCATAAACA
* * * *
3282063 CATTATGAATTCCGTGGGTTGCACACTTAGTTCTT
131 CATTATAAATTACGTGGGTTGCACACTTAGTGCCT
* * * *
3282098 ATACGGTCATTCATAAACACATTATGAATTTTGAGGGTTGTATACTTAGTGTATATGGGGGGGTC
1 ATACAGTCATTCATAAACACATTATGAATTATGAGGGTTGCACACTTAGTGTATATGGGGGGGTC
* ** *
3282163 GTTCATCAACATATGATGAATTATGA-GGGTCGCACACTTAGTGCATATACGGTTGTTCGTAAAC
66 GTTCATCAACATATGATGAATT-TCATGGGTCGCACACTTAGTGCATATACGGTCATTCATAAAC
* *
3282227 ACATTTTAAATTATGTGGGTTGCACACTTAGTGCCT
130 ACATTATAAATTACGTGGGTTGCACACTTAGTGCCT
* * *
3282263 ATACATTCGTTCATAAACACATTATGAATTATGTGGGTTGCACACTTAGT
1 ATACAGTCATTCATAAACACATTATGAATTATGAGGGTTGCACACTTAGT
3282313 TCCTATCCGA
Statistics
Matches: 180, Mismatches: 31, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
162 47 0.26
165 131 0.73
166 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (165 bp):
ATACAGTCATTCATAAACACATTATGAATTATGAGGGTTGCACACTTAGTGTATATGGGGGGGTC
GTTCATCAACATATGATGAATTTCATGGGTCGCACACTTAGTGCATATACGGTCATTCATAAACA
CATTATAAATTACGTGGGTTGCACACTTAGTGCCT
Found at i:3282346 original size:219 final size:219
Alignment explanation
Indices: 3281940--3282366 Score: 550
Period size: 219 Copynumber: 1.9 Consensus size: 219
3281930 GTGTCGATAC
* * * * *
3281940 GGTCATTCATAAACATATTATGAATTACGTGGGTTGCACACTTAGTGCCGATAAGGTCGTTCGTC
1 GGTCATTCATAAACATATGATGAATTACGAGGGTCGCACACTTAGTGCAGATAAGGTCGTTCGTA
* * *
3282005 AACATATGATGAATTTCATGGGTTGCACACTTAGTGCCTATACGGTCATTCATAAACACATTATG
66 AACACATGATAAATTTCATGGGTTGCACACTTAGTGCCTATACAGTCATTCATAAACACATTATG
* * * * *
3282070 AATTCCGTGGGTTGCACACTTAGTTCTTATACGGTCATTCATAAACACATTATGAATTTTGAGGG
131 AATTACGTGGGTTGCACACTTAGTTCCTATACGATCATTCATAAACACATGATGAATTCTGAGGG
*
3282135 TTGTATACTTAGTGTATATGGGGG
196 TTGCATACTTAGTGTATATGGGGG
* * * * * *
3282159 GGTCGTTCATCAACATATGATGAATTATGAGGGTCGCACACTTAGTGCATATACGGTTGTTCGTA
1 GGTCATTCATAAACATATGATGAATTACGAGGGTCGCACACTTAGTGCAGATAAGGTCGTTCGTA
** * * *
3282224 AACACATTTTAAATTAT-GTGGGTTGCACACTTAGTGCCTATACATTCGTTCATAAACACATTAT
66 AACACATGATAAATT-TCATGGGTTGCACACTTAGTGCCTATACAGTCATTCATAAACACATTAT
* * * * * * *
3282288 GAATTATGTGGGTTGCACACTTAGTTCCTATCCGATCGTTCATCAACATATGATGAATTCTGTGT
130 GAATTACGTGGGTTGCACACTTAGTTCCTATACGATCATTCATAAACACATGATGAATTCTGAGG
3282353 GTTGCATACTTAGT
195 GTTGCATACTTAGT
3282367 TCCTATAGTA
Statistics
Matches: 175, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
219 174 0.99
220 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (219 bp):
GGTCATTCATAAACATATGATGAATTACGAGGGTCGCACACTTAGTGCAGATAAGGTCGTTCGTA
AACACATGATAAATTTCATGGGTTGCACACTTAGTGCCTATACAGTCATTCATAAACACATTATG
AATTACGTGGGTTGCACACTTAGTTCCTATACGATCATTCATAAACACATGATGAATTCTGAGGG
TTGCATACTTAGTGTATATGGGGG
Found at i:3282835 original size:21 final size:21
Alignment explanation
Indices: 3282810--3282865 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
3282800 TCGATACCCA
*
3282810 CATCAATATTGATACTAATTG
1 CATCAATATCGATACTAATTG
3282831 CATCAATATCGATACTAATTG
1 CATCAATATCGATACTAATTG
3282852 CATCAATATCGATA
1 CATCAATATCGATA
3282866 TTATTCATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (21 bp):
CATCAATATCGATACTAATTG
Found at i:3287364 original size:21 final size:21
Alignment explanation
Indices: 3287340--3287392 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
3287330 AGCAACATAT
3287340 TTGACCCAGAAACCGAACAAA
1 TTGACCCAGAAACCGAACAAA
*
3287361 TTGACCCAGAATCCGAACAAA
1 TTGACCCAGAAACCGAACAAA
3287382 TTGACCC-GAAA
1 TTGACCCAGAAA
3287393 GTCCAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 3 0.10
21 27 0.90
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.13
Consensus pattern (21 bp):
TTGACCCAGAAACCGAACAAA
Found at i:3288593 original size:17 final size:16
Alignment explanation
Indices: 3288546--3288593 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
3288536 CCCTATTTTA
*
3288546 ATATCTTTTAATTTATT
1 ATAT-TTTTAATATATT
* *
3288563 ATATTATTACTATATTT
1 ATATTTTTAATATA-TT
3288580 ATATTTTTAATATA
1 ATATTTTTAATATA
3288594 AAGTATGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTTTTAATATATT
Done.