Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 95 of 143
Found at i:29444345 original size:17 final size:17
Alignment explanation
Indices: 29444323--29444390 Score: 75
Period size: 17 Copynumber: 4.0 Consensus size: 17
29444313 TAACAAACGA
29444323 AAATGCAATGACAATAC
1 AAATGCAATGACAATAC
*
29444340 AAATGCAGTGACAATTA-
1 AAATGCAATGACAA-TAC
* **
29444357 AAATGTAATGACAATGG
1 AAATGCAATGACAATAC
*
29444374 GAATGCAATGACAATAC
1 AAATGCAATGACAATAC
29444391 GTACTAACAG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 1 0.02
17 38 0.93
18 2 0.05
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAC
Found at i:29444379 original size:34 final size:34
Alignment explanation
Indices: 29444322--29444388 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
29444312 ATAACAAACG
*
29444322 AAAATGCAATGACAATACAAATGCAGTGACAATT
1 AAAATGCAATGACAATACAAATGCAATGACAATT
* ***
29444356 AAAATGTAATGACAATGGGAATGCAATGACAAT
1 AAAATGCAATGACAATACAAATGCAATGACAAT
29444389 ACGTACTAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (34 bp):
AAAATGCAATGACAATACAAATGCAATGACAATT
Found at i:29452926 original size:26 final size:26
Alignment explanation
Indices: 29452833--29452929 Score: 88
Period size: 26 Copynumber: 3.7 Consensus size: 26
29452823 GGTGCCATTT
* * * *
29452833 TGGACATGGTCATACAACGACAACTC
1 TGGACATGTTCATGCAGCGACAATTC
*
29452859 TGGACATGTTCATGCAGCGATAATTC
1 TGGACATGTTCATGCAGCGACAATTC
* * *
29452885 TGGACAAGTTTC-TGTAGCGACAATTT
1 TGGACATG-TTCATGCAGCGACAATTC
* *
29452911 TGGACATGCTCATGTAGCG
1 TGGACATGTTCATGCAGCG
29452930 GCATTAGTAG
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
25 2 0.03
26 53 0.91
27 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (26 bp):
TGGACATGTTCATGCAGCGACAATTC
Found at i:29462301 original size:17 final size:17
Alignment explanation
Indices: 29462266--29462329 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
29462256 TACAAATAAG
29462266 AACGAAAATGCAACTAC
1 AACGAAAATGCAACTAC
*
29462283 AACGCAAATG-AACTAAC
1 AACGAAAATGCAACT-AC
*
29462300 AA-GTAAAATGCAACGAC
1 AACG-AAAATGCAACTAC
* *
29462317 CACTAAAATGCAA
1 AACGAAAATGCAA
29462330 TGACAATCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 5 0.13
17 30 0.79
18 3 0.08
ACGTcount: A:0.53, C:0.22, G:0.12, T:0.12
Consensus pattern (17 bp):
AACGAAAATGCAACTAC
Found at i:29469379 original size:18 final size:18
Alignment explanation
Indices: 29469356--29469393 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29469346 ACTAACACAT
*
29469356 AAAATGCAGTGACAAATA
1 AAAATGCAATGACAAATA
*
29469374 AAAATGCAATGACAACTA
1 AAAATGCAATGACAAATA
29469392 AA
1 AA
29469394 TGCTATGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (18 bp):
AAAATGCAATGACAAATA
Found at i:29480990 original size:18 final size:18
Alignment explanation
Indices: 29480969--29481011 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29480959 TTATATGACT
**
29480969 GCATTTGATTTTGTGATC
1 GCATTTGATCATGTGATC
*
29480987 GCATCTGATCATGTGATC
1 GCATTTGATCATGTGATC
29481005 GCATTTG
1 GCATTTG
29481012 GTCTGGTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (18 bp):
GCATTTGATCATGTGATC
Found at i:29494526 original size:16 final size:16
Alignment explanation
Indices: 29494494--29494540 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
29494484 ATGTTGAATG
29494494 AGAAAAAGAAA-AGAAA
1 AGAAAAA-AAAGAGAAA
* *
29494510 AGGAGAAAAAGAGAAA
1 AGAAAAAAAAGAGAAA
29494526 AGAAAAAAAAG-GAAA
1 AGAAAAAAAAGAGAAA
29494541 TATTACTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.27
16 19 0.73
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAGAGAAA
Found at i:29501129 original size:198 final size:198
Alignment explanation
Indices: 29500791--29501190 Score: 773
Period size: 198 Copynumber: 2.0 Consensus size: 198
29500781 AATCGACTTG
*
29500791 CTATGTCGACAAAAGATCGAGAGATCCAACTGGGGTATTGACTAGTTGATTGAAGGAAAATCCCC
1 CTATGTCGACAAAAGATCGAGAGATCCAACTAGGGTATTGACTAGTTGATTGAAGGAAAATCCCC
*
29500856 AAAACCCAATAATTGAAGAACTCATACGAAAACGACCTAATATCCCCAAAGCCGTTCATAAGAAT
66 AAAACCCAACAATTGAAGAACTCATACGAAAACGACCTAATATCCCCAAAGCCGTTCATAAGAAT
*
29500921 TTCTACATCTCAAATCGCACTTGTATTTTCTATCTTATTTTATTTCATGCTTTCTAAACAAACTC
131 TTCTACATCTCAAATCGCACTTGTATTTTCTATCTTATCTTATTTCATGCTTTCTAAACAAACTC
29500986 TTT
196 TTT
29500989 CTATGTCGACAAAAGATCGAGAGATCCAACTAGGGTATTGACTAGTTGATTGAAGGAAAATCCCC
1 CTATGTCGACAAAAGATCGAGAGATCCAACTAGGGTATTGACTAGTTGATTGAAGGAAAATCCCC
29501054 AAAACCCAACAATTGAAGAACTCATACGAAAACGACCTAATATCCCCAAAGCCGTTCATAAGAAT
66 AAAACCCAACAATTGAAGAACTCATACGAAAACGACCTAATATCCCCAAAGCCGTTCATAAGAAT
29501119 TTCTACATCTCAAATCGCACTTGTATTTTCTATCTTATCTTATTTCATGCTTTCTAAACAAACTC
131 TTCTACATCTCAAATCGCACTTGTATTTTCTATCTTATCTTATTTCATGCTTTCTAAACAAACTC
29501184 TTT
196 TTT
29501187 CTAT
1 CTAT
29501191 TGCTCTTTGT
Statistics
Matches: 199, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
198 199 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (198 bp):
CTATGTCGACAAAAGATCGAGAGATCCAACTAGGGTATTGACTAGTTGATTGAAGGAAAATCCCC
AAAACCCAACAATTGAAGAACTCATACGAAAACGACCTAATATCCCCAAAGCCGTTCATAAGAAT
TTCTACATCTCAAATCGCACTTGTATTTTCTATCTTATCTTATTTCATGCTTTCTAAACAAACTC
TTT
Found at i:29503744 original size:21 final size:20
Alignment explanation
Indices: 29503718--29503771 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
29503708 CAATGCAGAT
29503718 TTCTACTGATACAAGTGTCA-C
1 TTCTACTGATACAA--GTCAGC
*
29503739 TTCTACCGATACAAGTCATGC
1 TTCTACTGATACAAGTCA-GC
29503760 TTCTACTGATAC
1 TTCTACTGATAC
29503772 TAAAAAATCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
21 25 0.86
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
TTCTACTGATACAAGTCAGC
Found at i:29542411 original size:12 final size:12
Alignment explanation
Indices: 29542394--29542428 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
29542384 TCATGCCGAA
29542394 AAGGATGAAGAG
1 AAGGATGAAGAG
*
29542406 AAGGATGAAGCG
1 AAGGATGAAGAG
29542418 AAGGATGAAGA
1 AAGGATGAAGA
29542429 ACACATTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.40, T:0.09
Consensus pattern (12 bp):
AAGGATGAAGAG
Found at i:29555039 original size:15 final size:14
Alignment explanation
Indices: 29555021--29555076 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
29555011 TAATTTCAAA
29555021 AAATATAAAATAAAT
1 AAAT-TAAAATAAAT
**
29555036 AAATTAAAA-AGTT
1 AAATTAAAATAAAT
*
29555049 ATATTAAAATAAAAT
1 AAATTAAAAT-AAAT
*
29555064 AAAATAAAATAAA
1 AAATTAAAATAAA
29555077 AATCCCCCAT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
13 10 0.31
14 8 0.25
15 14 0.44
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
AAATTAAAATAAAT
Found at i:29555061 original size:5 final size:5
Alignment explanation
Indices: 29555053--29555077 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29555043 AAAGTTATAT
29555053 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
29555078 ATCCCCCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:29556141 original size:22 final size:23
Alignment explanation
Indices: 29556110--29556156 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
29556100 TCTATAAAAC
*
29556110 AAGAATGAAAATAACT-AACCTA
1 AAGAAAGAAAATAACTAAACCTA
*
29556132 AAGAAAGAAAATTACTAAACCTA
1 AAGAAAGAAAATAACTAAACCTA
29556155 AA
1 AA
29556157 TTACAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.62, C:0.13, G:0.09, T:0.17
Consensus pattern (23 bp):
AAGAAAGAAAATAACTAAACCTA
Found at i:29557445 original size:29 final size:29
Alignment explanation
Indices: 29557423--29557553 Score: 172
Period size: 29 Copynumber: 4.5 Consensus size: 29
29557413 TATAAAACGA
* * * *
29557423 ATACAGTTCCAGATGCAAATATAGTACAT
1 ATACAGTTACAGATGCAAATATAATATAG
* *
29557452 ATACAGTTATAGATGCAGATATAATATAG
1 ATACAGTTACAGATGCAAATATAATATAG
29557481 ATACAGTTACAGATGCAAATATAATATAG
1 ATACAGTTACAGATGCAAATATAATATAG
* **
29557510 ATACAGTTACATATGCAAATATAATGCAG
1 ATACAGTTACAGATGCAAATATAATATAG
*
29557539 ATATAGTTACAGATG
1 ATACAGTTACAGATG
29557554 GAGGTTCCTA
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 89 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.29
Consensus pattern (29 bp):
ATACAGTTACAGATGCAAATATAATATAG
Found at i:29577130 original size:16 final size:17
Alignment explanation
Indices: 29577097--29577130 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29577087 ATGAGTTAGA
*
29577097 ATAATGTTTAGATATTT
1 ATAATGGTTAGATATTT
29577114 ATAATGGTTAG-TATTT
1 ATAATGGTTAGATATTT
29577130 A
1 A
29577131 GGGTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAGATATTT
Found at i:29580727 original size:29 final size:29
Alignment explanation
Indices: 29580702--29580856 Score: 170
Period size: 29 Copynumber: 5.3 Consensus size: 29
29580692 CAAAAAATAA
* *
29580702 AATTTTTGGAAGTTCGAGGTTAAAAATGG
1 AATTTTTGGAAGTTTGAGGGTAAAAATGG
* * *
29580731 AATTTTTTGAAGTTTGGGGGTAAAAATGT
1 AATTTTTGGAAGTTTGAGGGTAAAAATGG
*
29580760 AATTTTTGGAAGTTTTG-GGGTCAAAATGG
1 AATTTTTGGAAG-TTTGAGGGTAAAAATGG
* * *
29580789 AATTTTTTGAAGTTTAAGGGTAAAAATGT
1 AATTTTTGGAAGTTTGAGGGTAAAAATGG
* **
29580818 AATTTTTGGAAGTTT-AGGGGTCAAAATAT
1 AATTTTTGGAAGTTTGA-GGGTAAAAATGG
29580847 AATTTTTGGA
1 AATTTTTGGA
29580857 CAATTTAGGC
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
28 4 0.04
29 100 0.93
30 4 0.04
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (29 bp):
AATTTTTGGAAGTTTGAGGGTAAAAATGG
Found at i:29580832 original size:58 final size:58
Alignment explanation
Indices: 29580702--29580853 Score: 216
Period size: 58 Copynumber: 2.6 Consensus size: 58
29580692 CAAAAAATAA
* * * **
29580702 AATTTTTGGAAG-TTCGAGGTTAAAAATGGAATTTTTTGAAGTTTGGGGGTAAAAATGT
1 AATTTTTGGAAGTTTAG-GGGTCAAAATGGAATTTTTTGAAGTTTAAGGGTAAAAATGT
*
29580760 AATTTTTGGAAGTTTTGGGGTCAAAATGGAATTTTTTGAAGTTTAAGGGTAAAAATGT
1 AATTTTTGGAAGTTTAGGGGTCAAAATGGAATTTTTTGAAGTTTAAGGGTAAAAATGT
**
29580818 AATTTTTGGAAGTTTAGGGGTCAAAATATAATTTTT
1 AATTTTTGGAAGTTTAGGGGTCAAAATGGAATTTTT
29580854 GGACAATTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
58 82 0.96
59 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.40
Consensus pattern (58 bp):
AATTTTTGGAAGTTTAGGGGTCAAAATGGAATTTTTTGAAGTTTAAGGGTAAAAATGT
Found at i:29587215 original size:18 final size:18
Alignment explanation
Indices: 29587192--29587227 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29587182 AAGCGAGGAC
29587192 GGTATCGCTCTCGTCGAG
1 GGTATCGCTCTCGTCGAG
29587210 GGTATCGCTCTCGTCGAG
1 GGTATCGCTCTCGTCGAG
29587228 TGAATCCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.28, G:0.33, T:0.28
Consensus pattern (18 bp):
GGTATCGCTCTCGTCGAG
Found at i:29593871 original size:58 final size:59
Alignment explanation
Indices: 29593809--29594002 Score: 229
Period size: 58 Copynumber: 3.3 Consensus size: 59
29593799 CAGGGACAAA
* *
29593809 ATGGTAA-TTTTGGAAAAATTTTGGGTTAAAAATGACATTTTAGACATTTAGGGGTAAC
1 ATGGTAATTTTTAGAAAAATTTCGGGTTAAAAATGACATTTTAGACATTTAGGGGTAAC
* * * * *
29593867 ATGGTAATTTTTAGAAAAA--TCGGGATCAAAAATAGGA-TTTTTGGACATCT-GGGGTAAA
1 ATGGTAATTTTTAGAAAAATTTCGGG-TTAAAAAT--GACATTTTAGACATTTAGGGGTAAC
** *
29593925 ATGGTAATTTCGAG-AAAATTTCGGGTTAAAAATGACATTTTAGACATTTAAGGGTAAC
1 ATGGTAATTTTTAGAAAAATTTCGGGTTAAAAATGACATTTTAGACATTTAGGGGTAAC
29593983 ATGGTAATTTTTAGAAAAAT
1 ATGGTAATTTTTAGAAAAAT
29594003 CAGGATAAAA
Statistics
Matches: 110, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
56 2 0.02
57 18 0.16
58 58 0.53
59 30 0.27
60 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (59 bp):
ATGGTAATTTTTAGAAAAATTTCGGGTTAAAAATGACATTTTAGACATTTAGGGGTAAC
Found at i:29593981 original size:116 final size:116
Alignment explanation
Indices: 29593806--29594031 Score: 382
Period size: 116 Copynumber: 1.9 Consensus size: 116
29593796 TTTCAGGGAC
* * *
29593806 AAAATGGTAATTTTGGAAAAATTTTGGGTTAAAAATGACATTTTAGACATTTAGGGGTAACATGG
1 AAAATGGTAATTTCGGAAAAATTTCGGGTTAAAAATGACATTTTAGACATTTAAGGGTAACATGG
* * *
29593871 TAATTTTTAGAAAAATCGGGATCAAAAATAGGATTTTTGGACATCTGGGGT
66 TAATTTTTAGAAAAATCAGGATAAAAAATAGGATTTTTGAACATCTGGGGT
29593922 AAAATGGTAATTTC-GAGAAAATTTCGGGTTAAAAATGACATTTTAGACATTTAAGGGTAACATG
1 AAAATGGTAATTTCGGA-AAAATTTCGGGTTAAAAATGACATTTTAGACATTTAAGGGTAACATG
29593986 GTAATTTTTAGAAAAATCAGGATAAAAAATAGGATTTTTGAACATC
65 GTAATTTTTAGAAAAATCAGGATAAAAAATAGGATTTTTGAACATC
29594032 CGGAGGCAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
115 2 0.02
116 101 0.98
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (116 bp):
AAAATGGTAATTTCGGAAAAATTTCGGGTTAAAAATGACATTTTAGACATTTAAGGGTAACATGG
TAATTTTTAGAAAAATCAGGATAAAAAATAGGATTTTTGAACATCTGGGGT
Found at i:29594023 original size:58 final size:57
Alignment explanation
Indices: 29593845--29594023 Score: 200
Period size: 58 Copynumber: 3.1 Consensus size: 57
29593835 TAAAAATGAC
*
29593845 ATTTTAGACATTTAGGGGTAACATGGTAATTTTTAGAAAAATCGGGATCAAAAATAGG
1 ATTTTAGACATTTAGGGGTAACATGGTAATTTTTAGAAAAATC-GGATAAAAAATAGG
* * * ** * * * *
29593903 ATTTTTGGACATCT-GGGGTAAAATGGTAATTTCGAGAAAATTTCGGGTTAAAAAT-GAC
1 A-TTTTAGACATTTAGGGGTAACATGGTAATTTTTAGAAAA-ATCGGATAAAAAATAG-G
*
29593961 ATTTTAGACATTTAAGGGTAACATGGTAATTTTTAGAAAAATCAGGATAAAAAATAGG
1 ATTTTAGACATTTAGGGGTAACATGGTAATTTTTAGAAAAATC-GGATAAAAAATAGG
29594019 ATTTT
1 ATTTT
29594024 TGAACATCCG
Statistics
Matches: 96, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
57 13 0.14
58 70 0.73
59 13 0.14
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (57 bp):
ATTTTAGACATTTAGGGGTAACATGGTAATTTTTAGAAAAATCGGATAAAAAATAGG
Found at i:29594129 original size:58 final size:59
Alignment explanation
Indices: 29594044--29594232 Score: 174
Period size: 58 Copynumber: 3.2 Consensus size: 59
29594034 GAGGCAAAGT
* * *
29594044 TGTAA-TTTTGGGAGTTTC-GGGGTCAAAAATAG-AATTTTTAGAAGTTCAA-GTTCAAAAA
1 TGTAATTTTTGGAAGTTTCAAGGG-CAAAAAT-GTAATTTTTAGAAGTTCAAGGGT-AAAAA
* * *
29594102 CT-TAATTTTTTGAAGTTT-AAGGGCAAAAATGTAATTTTTGGAAGTTTAAGGGTAAAAA
1 -TGTAATTTTTGGAAGTTTCAAGGGCAAAAATGTAATTTTTAGAAGTTCAAGGGTAAAAA
** * * *
29594160 TGTAATTTTTGGAAGTTTCAAGGTTAAAAATGTAATTTTAGAGAAGTTCAGGGGTCAAAA
1 TGTAATTTTTGGAAGTTTCAAGGGCAAAAATGTAATTTT-TAGAAGTTCAAGGGTAAAAA
* *
29594220 TATAATTTCTGGA
1 TGTAATTTTTGGA
29594233 CAATTTAGAG
Statistics
Matches: 107, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
57 2 0.02
58 45 0.42
59 34 0.32
60 26 0.24
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (59 bp):
TGTAATTTTTGGAAGTTTCAAGGGCAAAAATGTAATTTTTAGAAGTTCAAGGGTAAAAA
Found at i:29594190 original size:30 final size:30
Alignment explanation
Indices: 29594044--29594207 Score: 153
Period size: 29 Copynumber: 5.6 Consensus size: 30
29594034 GAGGCAAAGT
* ** *
29594044 TGTAA-TTTTGGGAGTTTCGGGGTCAAAAA
1 TGTAATTTTTGGAAGTTTCAAGGTTAAAAA
*
29594073 TAG-AATTTTTAGAAG-TTCAA-GTTCAAAAA
1 T-GTAATTTTTGGAAGTTTCAAGGTT-AAAAA
* **
29594102 CT-TAATTTTTTGAAGTTT-AAGGGCAAAAA
1 -TGTAATTTTTGGAAGTTTCAAGGTTAAAAA
*
29594131 TGTAATTTTTGGAAGTTT-AAGGGTAAAAA
1 TGTAATTTTTGGAAGTTTCAAGGTTAAAAA
29594160 TGTAATTTTTGGAAGTTTCAAGGTTAAAAA
1 TGTAATTTTTGGAAGTTTCAAGGTTAAAAA
*
29594190 TGTAATTTTAGAGAAGTT
1 TGTAATTTTTG-GAAGTT
29594208 CAGGGGTCAA
Statistics
Matches: 113, Mismatches: 12, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
28 3 0.03
29 72 0.64
30 32 0.28
31 6 0.05
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (30 bp):
TGTAATTTTTGGAAGTTTCAAGGTTAAAAA
Found at i:29594220 original size:30 final size:29
Alignment explanation
Indices: 29594063--29594232 Score: 157
Period size: 29 Copynumber: 5.8 Consensus size: 29
29594053 GGGAGTTTCG
*
29594063 GGGTCAAAAATAG-AATTTTTAGAAGTTCAA
1 GGGT-AAAAAT-GTAATTTTTGGAAGTTCAA
* * *
29594093 -GTTCAAAAACT-TAATTTTTTGAAGTTTAA
1 GGGT-AAAAA-TGTAATTTTTGGAAGTTCAA
* *
29594122 GGGCAAAAATGTAATTTTTGGAAGTTTAA
1 GGGTAAAAATGTAATTTTTGGAAGTTCAA
29594151 GGGTAAAAATGTAATTTTTGGAAGTTTCAA
1 GGGTAAAAATGTAATTTTTGGAAG-TTCAA
* * *
29594181 GGTTAAAAATGTAATTTTAGAGAAGTTCAG
1 GGGTAAAAATGTAATTTTTG-GAAGTTCAA
* * *
29594211 GGGTCAAAATATAATTTCTGGA
1 GGGTAAAAATGTAATTTTTGGA
29594233 CAATTTAGAG
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.01
29 70 0.59
30 43 0.36
31 4 0.03
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTCAA
Found at i:29594624 original size:5 final size:5
Alignment explanation
Indices: 29594614--29594639 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29594604 GCGGATCTTA
29594614 GGTCG GGTCG GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTCG GGTCG GGTCG G
29594640 ATTCAGGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.62, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:29595421 original size:15 final size:15
Alignment explanation
Indices: 29595385--29595414 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29595375 TTTTTTAACT
*
29595385 TACTATTATTATTAA
1 TACTATTACTATTAA
29595400 TACTATTACTATTAA
1 TACTATTACTATTAA
29595415 ACATATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TACTATTACTATTAA
Found at i:29596300 original size:17 final size:17
Alignment explanation
Indices: 29596278--29596320 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
29596268 AAGTTTAATT
*
29596278 AAATTTAAATTTAAAGC
1 AAATTTAAATTTAAAAC
*
29596295 AAATTTAAATTTAAAAT
1 AAATTTAAATTTAAAAC
29596312 AAATTTAAA
1 AAATTTAAA
29596321 ATAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AAATTTAAATTTAAAAC
Found at i:29596328 original size:10 final size:11
Alignment explanation
Indices: 29596300--29596330 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
29596290 AAAGCAAATT
29596300 TAAATTTAAAA
1 TAAATTTAAAA
29596311 TAAATTTAAAA
1 TAAATTTAAAA
29596322 T-AATTTAAA
1 TAAATTTAAA
29596331 CCTATCTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:29603485 original size:23 final size:23
Alignment explanation
Indices: 29603459--29603506 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
29603449 TCTGTAAAAC
*
29603459 AAGAATGAAAATAACTAAACCTA
1 AAGAAAGAAAATAACTAAACCTA
*
29603482 AAGAAAGAAAATTACTAAACCTA
1 AAGAAAGAAAATAACTAAACCTA
29603505 AA
1 AA
29603507 TTACAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.62, C:0.12, G:0.08, T:0.17
Consensus pattern (23 bp):
AAGAAAGAAAATAACTAAACCTA
Found at i:29604795 original size:29 final size:29
Alignment explanation
Indices: 29604763--29604882 Score: 97
Period size: 29 Copynumber: 4.1 Consensus size: 29
29604753 CATAGACAAT
*
29604763 TATAAAACGAATACAGTTCCAGATGCAAA
1 TATAAAACGAATACAGTTACAGATGCAAA
** * *
29604792 TATAGTAC-ATATACAGTTATAGATGCAGA
1 TATAAAACGA-ATACAGTTACAGATGCAAA
29604821 TATAATATA-G-ATACAGTTACAGATGCAAA
1 TATAA-A-ACGAATACAGTTACAGATGCAAA
* *
29604850 TATAATATA-G-ATATAGTTACATATGCAAA
1 TATAA-A-ACGAATACAGTTACAGATGCAAA
29604879 TATA
1 TATA
29604883 TGCAAATATA
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.01
29 74 0.97
31 1 0.01
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (29 bp):
TATAAAACGAATACAGTTACAGATGCAAA
Found at i:29604868 original size:58 final size:58
Alignment explanation
Indices: 29604773--29604882 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 58
29604763 TATAAAACGA
* * * * *
29604773 ATACAGTTCCAGATGCAAATATAGTACATATACAGTTATAGATGCAGATATAATATAG
1 ATACAGTTACAGATGCAAATATAATACAGATACAGTTACAGATGCAAATATAATATAG
* * *
29604831 ATACAGTTACAGATGCAAATATAATATAGATATAGTTACATATGCAAATATA
1 ATACAGTTACAGATGCAAATATAATACAGATACAGTTACAGATGCAAATATA
29604883 TGCAAATATA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (58 bp):
ATACAGTTACAGATGCAAATATAATACAGATACAGTTACAGATGCAAATATAATATAG
Found at i:29620317 original size:24 final size:23
Alignment explanation
Indices: 29620282--29620334 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
29620272 AGGTCAAGAG
*
29620282 TAAAAATTGTCAGTGCAAATGTAA
1 TAAAAATTGTCAGAGCAAAT-TAA
29620306 TACAAAA-TGTCAGAGCAAATTAA
1 TA-AAAATTGTCAGAGCAAATTAA
29620329 TAAAAA
1 TAAAAA
29620335 GTGAATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.15
23 5 0.19
24 14 0.52
25 4 0.15
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (23 bp):
TAAAAATTGTCAGAGCAAATTAA
Found at i:29622035 original size:24 final size:24
Alignment explanation
Indices: 29621995--29622043 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
29621985 TTATGTCCCA
29621995 CTTCATCTCACCCCCTTATT-TCTC
1 CTTCATCTCACCCCCTT-TTCTCTC
*
29622019 CTTC-TCTCACCATCCTTTTCTCTC
1 CTTCATCTCACC-CCCTTTTCTCTC
29622043 C
1 C
29622044 ATTTTAGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.10, C:0.47, G:0.00, T:0.43
Consensus pattern (24 bp):
CTTCATCTCACCCCCTTTTCTCTC
Found at i:29624339 original size:16 final size:17
Alignment explanation
Indices: 29624306--29624339 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29624296 ATGAGTTAGA
*
29624306 ATAATGTTTAGATATTT
1 ATAATGGTTAGATATTT
29624323 ATAATGGTTAG-TATTT
1 ATAATGGTTAGATATTT
29624339 A
1 A
29624340 AGGTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAGATATTT
Found at i:29624459 original size:21 final size:21
Alignment explanation
Indices: 29624433--29624485 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
29624423 TTGCAGTCGA
*
29624433 TGTCGTGACATAGATAGTGTT
1 TGTCGTGACATAGATAGCGTT
29624454 TGTCGTGACATAGATAGCGTT
1 TGTCGTGACATAGATAGCGTT
*
29624475 TGTCGCGACAT
1 TGTCGTGACAT
29624486 TCCCTTCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (21 bp):
TGTCGTGACATAGATAGCGTT
Found at i:29631064 original size:40 final size:42
Alignment explanation
Indices: 29631020--29631104 Score: 138
Period size: 42 Copynumber: 2.1 Consensus size: 42
29631010 GGAAAAAAGC
*
29631020 CGCTA-TAAA-ACATGGTCTTTAGCGGCGCTTATCCCACAAA
1 CGCTACTAAACACATGGTCTTTAGCAGCGCTTATCCCACAAA
*
29631060 CGCTACTAAACACATGGTCTTTAGCAGCGCTTTTCCCACAAA
1 CGCTACTAAACACATGGTCTTTAGCAGCGCTTATCCCACAAA
29631102 CGC
1 CGC
29631105 CGTTAACATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 5 0.12
41 4 0.10
42 32 0.78
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (42 bp):
CGCTACTAAACACATGGTCTTTAGCAGCGCTTATCCCACAAA
Found at i:29634989 original size:123 final size:123
Alignment explanation
Indices: 29634770--29635021 Score: 319
Period size: 123 Copynumber: 2.0 Consensus size: 123
29634760 AAAATCCACT
** * * * *
29634770 TTTAGCAGCGCTTTTCTATAAGCGCCGCTAATGCTCTGAACTTTAGCGGCGCTTTCCCACAAGCG
1 TTTAGCAGCGCTTGACCATAAGCGCCGCTAATGCTCTGAACTTTAGCGGCGCTTTCCAAAAAGCA
* * * *
29634835 CCGCTAATGCTTTGACCTTTAGCAGTGCTTGCCCGTAAGCGCCATTATTGCTCTGACC
66 CCGCTAATGCTCTAACCTTTAGCAGTGCTTGCCCATAAGCGCCACTATTGCTCTGACC
* * * *
29634893 TTTAGCAGCGCTTGACCGTAAGTGCCGCTATTGCTCT-AACCTTTAGTGGCGCTTTCCAAAAAGC
1 TTTAGCAGCGCTTGACCATAAGCGCCGCTAATGCTCTGAA-CTTTAGCGGCGCTTTCCAAAAAGC
* * *
29634957 ATCGCTATTGCTCTAACCTTTAGC-GATGCTTGCCCATAAGCGCCGCTATTGCTCTGACC
65 ACCGCTAATGCTCTAACCTTTAGCAG-TGCTTGCCCATAAGCGCCACTATTGCTCTGACC
29635016 TTTAGC
1 TTTAGC
29635022 GATGCTTTCC
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
122 3 0.03
123 107 0.97
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (123 bp):
TTTAGCAGCGCTTGACCATAAGCGCCGCTAATGCTCTGAACTTTAGCGGCGCTTTCCAAAAAGCA
CCGCTAATGCTCTAACCTTTAGCAGTGCTTGCCCATAAGCGCCACTATTGCTCTGACC
Found at i:29635022 original size:41 final size:41
Alignment explanation
Indices: 29634787--29635052 Score: 230
Period size: 41 Copynumber: 6.5 Consensus size: 41
29634777 GCGCTTTTCT
* * * *
29634787 ATAAGCGCCGCTAATGCTCTGAACTTTAGCGGCGCTTTCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCC
* * * *
29634828 ACAAGCGCCGCTAATGCTTTGACCTTTAGC-AGTGCTTGCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGA-CGCTTGCCC
* ** *
29634869 GTAAGCGCCATTATTGCTCTGACCTTTAGC-AGCGCTTGACC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGA-CGCTTGCCC
* * * * * * *
29634910 GTAAGTGCCGCTATTGCTCTAACCTTTAGTGGCGCTTTCCA
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCC
* ** * *
29634951 AAAAGCATCGCTATTGCTCTAACCTTTAGCGATGCTTGCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCC
* * *
29634992 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGATGCTTTCCA
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCC
* * *
29635033 AAAAGCACCGTTATTGCTCT
1 ATAAGCGCCGCTATTGCTCT
29635053 ATCTTTTGCA
Statistics
Matches: 181, Mismatches: 42, Indels: 4
0.80 0.19 0.02
Matches are distributed among these distances:
41 181 1.00
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (41 bp):
ATAAGCGCCGCTATTGCTCTGACCTTTAGCGACGCTTGCCC
Found at i:29635048 original size:123 final size:122
Alignment explanation
Indices: 29634770--29635058 Score: 287
Period size: 123 Copynumber: 2.4 Consensus size: 122
29634760 AAAATCCACT
** * * * * * * *
29634770 TTTAGCAGCGCTTTTCTATAAGCGCCGCTAATGCTCTGAACTTTAGCGGCGCTTTCCCACAAGCG
1 TTTAGCAGCGCTTGACCAAAAGCACCGCTATTGCTCT-AACTTTAGCGGCGCTTTCCAAAAAGCA
* * * *
29634835 CCGCTAATGCTTTGACCTTTAGCAGTGCTTGCCCGTAAGCGCCATTATTGCTCTGACC
65 CCGCTAATGCTCTAACCTTTAGCAGTGCTTGCCCATAAGCGCCACTATTGCTCTGACC
** ** *
29634893 TTTAGCAGCGCTTGACCGTAAGTGCCGCTATTGCTCTAACCTTTAGTGGCGCTTTCCAAAAAGCA
1 TTTAGCAGCGCTTGACCAAAAGCACCGCTATTGCTCTAA-CTTTAGCGGCGCTTTCCAAAAAGCA
* * *
29634958 TCGCTATTGCTCTAACCTTTAGC-GATGCTTGCCCATAAGCGCCGCTATTGCTCTGACC
65 CCGCTAATGCTCTAACCTTTAGCAG-TGCTTGCCCATAAGCGCCACTATTGCTCTGACC
* * * *
29635016 TTTAGC-GATGCTT-TCCAAAAAGCACCGTTATTGCTCTATCTTT
1 TTTAGCAG-CGCTTGACC-AAAAGCACCGCTATTGCTCTAACTTT
29635059 TGCAGCGTTT
Statistics
Matches: 137, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
122 10 0.07
123 127 0.93
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (122 bp):
TTTAGCAGCGCTTGACCAAAAGCACCGCTATTGCTCTAACTTTAGCGGCGCTTTCCAAAAAGCAC
CGCTAATGCTCTAACCTTTAGCAGTGCTTGCCCATAAGCGCCACTATTGCTCTGACC
Found at i:29635077 original size:41 final size:40
Alignment explanation
Indices: 29635032--29635108 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
29635022 GATGCTTTCC
*
29635032 AAAAAGCACCGTTATTGCTCTATCTTTTGCAGCGTTTATGT
1 AAAAA-CACCGCTATTGCTCTATCTTTTGCAGCGTTTATGT
* *
29635073 AAAAACGCCGCTATTGCTTTATCTTTTGCAGCGTTT
1 AAAAACACCGCTATTGCTCTATCTTTTGCAGCGTTT
29635109 TCTGTCCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 28 0.85
41 5 0.15
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (40 bp):
AAAAACACCGCTATTGCTCTATCTTTTGCAGCGTTTATGT
Found at i:29638914 original size:16 final size:18
Alignment explanation
Indices: 29638893--29638931 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
29638883 TTTCACTTAA
*
29638893 TTTATTTTA-TTT-TTGT
1 TTTATTTTAGTTTGATGT
29638909 TTTATTTTAGTTTGATGT
1 TTTATTTTAGTTTGATGT
29638927 TTTAT
1 TTTAT
29638932 CTCTAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 3 0.15
18 8 0.40
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.74
Consensus pattern (18 bp):
TTTATTTTAGTTTGATGT
Found at i:29645512 original size:17 final size:16
Alignment explanation
Indices: 29645490--29645523 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29645480 TAATAAAATT
*
29645490 AAATATCGACAATGAAA
1 AAATATCG-CAAAGAAA
29645507 AAATATCGCAAAGAAA
1 AAATATCGCAAAGAAA
29645523 A
1 A
29645524 CAAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.15
Consensus pattern (16 bp):
AAATATCGCAAAGAAA
Found at i:29647989 original size:38 final size:38
Alignment explanation
Indices: 29647905--29647990 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
29647895 AACGACATTC
29647905 TTGGGTGCAA-TTGAAGAATACTTATGCAGCGATAGTT
1 TTGGGTGCAATTTGAAGAATACTTATGCAGCGATAGTT
** * * *
29647942 CAGGATGCAATTTGAAGAATATTTATGCAGTGATAGTT
1 TTGGGTGCAATTTGAAGAATACTTATGCAGCGATAGTT
29647980 TTGGGTGCAAT
1 TTGGGTGCAAT
29647991 CTGGAAGTGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 7 0.17
38 33 0.82
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.34
Consensus pattern (38 bp):
TTGGGTGCAATTTGAAGAATACTTATGCAGCGATAGTT
Found at i:29648017 original size:37 final size:37
Alignment explanation
Indices: 29647973--29648043 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
29647963 TTTATGCAGT
* * *
29647973 GATAGTTTTGGGTGCAATCTGGAAGTGCTCATGCGAC
1 GATAGTTTTAGGCGCAATCTAGAAGTGCTCATGCGAC
29648010 GATAGTTTTAGGCGCAATCTAGAAGTGCTCATGC
1 GATAGTTTTAGGCGCAATCTAGAAGTGCTCATGC
29648044 AGCGACTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (37 bp):
GATAGTTTTAGGCGCAATCTAGAAGTGCTCATGCGAC
Found at i:29650712 original size:16 final size:16
Alignment explanation
Indices: 29650675--29650709 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29650665 AAATAAAGTG
29650675 TTTT-GAGACTTTAAT
1 TTTTGGAGACTTTAAT
29650690 TTTTGGAGACTTGTAAT
1 TTTTGGAGACTT-TAAT
29650707 TTT
1 TTT
29650710 GGATTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 7 0.39
17 7 0.39
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (16 bp):
TTTTGGAGACTTTAAT
Found at i:29664361 original size:8 final size:8
Alignment explanation
Indices: 29664348--29664379 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
29664338 TTATCAGCTC
29664348 TTATTATT
1 TTATTATT
29664356 TTATTATT
1 TTATTATT
29664364 TTATTATT
1 TTATTATT
29664372 TTATTATT
1 TTATTATT
29664380 CTGAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTATT
Found at i:29671295 original size:85 final size:85
Alignment explanation
Indices: 29671150--29671317 Score: 223
Period size: 85 Copynumber: 2.0 Consensus size: 85
29671140 CTATTTCATT
* * *
29671150 GATTTGGTCAACTTCTTTGTATCTCATCAGGAAGATGACTGCCTCATTGTTTTAATCCACTTCTC
1 GATTTGGTCAACTTCTCTGTATCTCATCAGGAAGATGACTGCCTCATTGCTTTAACCCACTTCTC
*
29671215 TGTATCTCATCAGGAAGACG
66 TATATCTCATCAGGAAGACG
* * * * *
29671235 GATTTGGTCTACCTT-TCTGTATCTCATGAGGAAGATGATCT-CTTTATTGCTTTGACCCACTTC
1 GATTTGGTC-AACTTCTCTGTATCTCATCAGGAAGATGA-CTGCCTCATTGCTTTAACCCACTTC
29671298 TCTATATCTCATCAGGAAGA
64 TCTATATCTCATCAGGAAGA
29671318 TGAGGGTTTG
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
85 66 0.92
86 6 0.08
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (85 bp):
GATTTGGTCAACTTCTCTGTATCTCATCAGGAAGATGACTGCCTCATTGCTTTAACCCACTTCTC
TATATCTCATCAGGAAGACG
Found at i:29671507 original size:209 final size:209
Alignment explanation
Indices: 29671144--29671874 Score: 1096
Period size: 209 Copynumber: 3.5 Consensus size: 209
29671134 CTATCTCTAT
* ** *
29671144 TTCATTGATTTGGTCAACTTCTTTGTATCTCATCAGGAAGATGACTGCCTCATTGTTTTAATCCA
1 TTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCA
* *
29671209 CTTCTCTGTATCTCATCAGGAAGACGGATTTGG-TCTACCTT-TCTGTATCTCATGAGGAAGATG
66 CTTCTCTGTATCTCATCAGGAAGACGGATTTGGTTC-A-CTTCTCTGTATCTCATCAGGAAGGTG
* *
29671272 ATCTCTTTATTGCTTTGACCCACTTCTCTATATCTCATCAGGAAGATGAGGGTTTGAAGTTTCAC
129 ATCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGAGGGTTTGAAGTTTCAC
29671337 TCACATTGAGCTTCGC
194 TCACATTGAGCTTCGC
29671353 TTCATTGATTTGG-CTTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCC
1 TTCATTGATTTGGTC-TACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCC
* * ** *
29671417 ATTTTTCTACATCTCATCAGGAAGACGGATTTGGTTTACTTCTCTGTATCTCATCAGGAAGGTGA
65 ACTTCTCTGTATCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGA
* *
29671482 TCGCTTTATTGCTTTGACGCACTTCTCTGTATCTCATCAAGAAGAT-AGGGGTTTGAAGTTTCAC
130 TCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGA-GGGTTTGAAGTTTCAC
29671546 TCACATTGAGCTTCGC
194 TCACATTGAGCTTCGC
* * * *
29671562 TTCATTAATTTGGCCTACTTCTTC-GTATCTCATCAGGAAGATAATCGCCTCATTGTTTTAATCC
1 TTCATTGATTTGGTCTACTTC-TCAGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCC
* *
29671626 ACTTCTCTGTATCTCATCAAGAAGACGGATTTGGTTCACTCCTCTGTATCTCATCAGGAAGGTGA
65 ACTTCTCTGTATCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGA
* * *
29671691 TGGCTTTATTGCTTTAACCCACTTCTTTGTATCTCATCAGGAAGATGAGGGTTTGAAGTTTCACT
130 TCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGAGGGTTTGAAGTTTCACT
* *
29671756 CACATTAAGCTTAGC
195 CACATTGAGCTTCGC
* * *
29671771 TTCATTGATTTGGTCTACTTCTCAATATCTCATCAAGAAGATGACCGCCACATTG-TTTAATCCA
1 TTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCA
* *
29671835 CTTCTCTGTATCTCATTAGGAAGACGGATTTTGTTCACTT
66 CTTCTCTGTATCTCATCAGGAAGACGGATTTGGTTCACTT
29671875 GGGAATGAAA
Statistics
Matches: 471, Mismatches: 43, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
208 52 0.11
209 414 0.88
210 5 0.01
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (209 bp):
TTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCA
CTTCTCTGTATCTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTGAT
CGCTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATGAGGGTTTGAAGTTTCACTC
ACATTGAGCTTCGC
Found at i:29671516 original size:85 final size:85
Alignment explanation
Indices: 29671359--29671526 Score: 203
Period size: 85 Copynumber: 2.0 Consensus size: 85
29671349 TCGCTTCATT
* * *
29671359 GATTTGGCTTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCATTTTTC
1 GATTTGGCTTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGCTTTAATCCACTTCTC
*
29671424 TACATCTCATCAGGAAGACG
66 TACATCTCATCAAGAAGACG
* * * * * * *
29671444 GATTTGGTTTACTTCTCTGTATCTCATCAGGAAGGTGATCGCTTTATTGCTTTGA-CGCACTTCT
1 GATTTGGCTTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGCTTTAATC-CACTTCT
**
29671508 CTGTATCTCATCAAGAAGA
65 CTACATCTCATCAAGAAGA
29671527 TAGGGGTTTG
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
84 1 0.01
85 68 0.99
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (85 bp):
GATTTGGCTTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGCTTTAATCCACTTCTC
TACATCTCATCAAGAAGACG
Found at i:29672321 original size:13 final size:14
Alignment explanation
Indices: 29672297--29672325 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29672287 ATTAAAGACA
29672297 AAAAATTCAAAATG
1 AAAAATTCAAAATG
29672311 AAAAATT-AAAATG
1 AAAAATTCAAAATG
29672324 AA
1 AA
29672326 GAACATTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAAATTCAAAATG
Found at i:29683796 original size:2 final size:2
Alignment explanation
Indices: 29683789--29683814 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29683779 AATTGGCAAT
29683789 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
29683815 AGATAGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29698042 original size:30 final size:30
Alignment explanation
Indices: 29697729--29698034 Score: 249
Period size: 30 Copynumber: 10.3 Consensus size: 30
29697719 AGAGAGTTAA
* *
29697729 GGGTTAAAATGTAATTTT-GGAAAGATTTAG
1 GGGTCAAAATGTAATTTTAGAAAAG-TTTAG
* *
29697759 GGGTAAAAATGTCATTTTAG-AAAGTTCT--
1 GGGTCAAAATGTAATTTTAGAAAAGTT-TAG
* * * * *
29697787 GGGTAAAAATGTGATTTTTTG-GAAGATTAG
1 GGGTCAAAATGT-AATTTTAGAAAAGTTTAG
* * * *
29697817 GGGTAAAAATGTAATTTT-TAAAAGTTCAA
1 GGGTCAAAATGTAATTTTAGAAAAGTTTAG
*
29697846 GGG-CAAAATGTAATTATTGGAAAAGTTTAG
1 GGGTCAAAATGTAATT-TTAGAAAAGTTTAG
* *
29697876 AGGTCAAAATGTAATTTTAGAAAA--TTCG
1 GGGTCAAAATGTAATTTTAGAAAAGTTTAG
29697904 AGGGTCAAAATGTAATTTTAGAAAAGTTT-G
1 -GGGTCAAAATGTAATTTTAGAAAAGTTTAG
* * * * *
29697934 GGAGTTAAAATATGATTTTTGGAAAGTTTAG
1 GG-GTCAAAATGTAATTTTAGAAAAGTTTAG
* *
29697965 GGGTCAACATGTAATTTTGGAAAAGTTTTA-
1 GGGTCAAAATGTAATTTTAGAAAAG-TTTAG
29697995 GGGTCAAAAT-TCAATTTTAGAAAAGTTTAG
1 GGGTCAAAATGT-AATTTTAGAAAAGTTTAG
29698025 GGGTCAAAAT
1 GGGTCAAAAT
29698035 ATTATTTTCG
Statistics
Matches: 225, Mismatches: 34, Indels: 34
0.77 0.12 0.12
Matches are distributed among these distances:
28 27 0.12
29 56 0.25
30 120 0.53
31 22 0.10
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTAGAAAAGTTTAG
Found at i:29699860 original size:17 final size:17
Alignment explanation
Indices: 29699838--29699884 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 17
29699828 GGACATTATT
29699838 AATTTAAATTTAGAATA
1 AATTTAAATTTAGAATA
29699855 AATTTAAATTTTAAGAATA
1 AATTTAAA-TTT-AGAATA
29699874 AA-TTAAATTTA
1 AATTTAAATTTA
29699885 AACTTAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 8 0.29
19 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (17 bp):
AATTTAAATTTAGAATA
Found at i:29699879 original size:18 final size:18
Alignment explanation
Indices: 29699838--29699883 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
29699828 GGACATTATT
29699838 AATTTAAA-TTTAGAATA
1 AATTTAAATTTTAGAATA
29699855 AATTTAAATTTTAAGAATA
1 AATTTAAATTTT-AGAATA
29699874 AA-TTAAATTT
1 AATTTAAATTT
29699884 AAACTTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.30
18 11 0.41
19 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (18 bp):
AATTTAAATTTTAGAATA
Found at i:29700136 original size:101 final size:101
Alignment explanation
Indices: 29699961--29700169 Score: 364
Period size: 101 Copynumber: 2.1 Consensus size: 101
29699951 AGCTGGCCCT
*
29699961 CTTTGCTCGTTACTGTGTAACAGAAACGGAGCAAAGACCAAAAGAAGGCCCAATTTTACCAGGTC
1 CTTTGCTCGTTACTGTGTAACAAAAACGGAGCAAAGACCAAAAGAAGGCCCAATTTTACCAGGTC
*
29700026 TCATCTCTTTGACGTTCCTTCTTCGATTGGCCCACC
66 TCATCTCTTTGACGTTCCTTCTTCGATTGACCCACC
* **
29700062 CTTTGCTCGTTACTGTGTAACAAAAACGGAGCAAAGACCAAAAGGAGGCCCAATTTTGTCAGGTC
1 CTTTGCTCGTTACTGTGTAACAAAAACGGAGCAAAGACCAAAAGAAGGCCCAATTTTACCAGGTC
*
29700127 TCATCTCTTTGACGTTCCTTCTTCGATTGACCCACT
66 TCATCTCTTTGACGTTCCTTCTTCGATTGACCCACC
29700163 CTTTGCT
1 CTTTGCT
29700170 TTCACTGCAT
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (101 bp):
CTTTGCTCGTTACTGTGTAACAAAAACGGAGCAAAGACCAAAAGAAGGCCCAATTTTACCAGGTC
TCATCTCTTTGACGTTCCTTCTTCGATTGACCCACC
Found at i:29700527 original size:39 final size:38
Alignment explanation
Indices: 29700485--29700967 Score: 340
Period size: 39 Copynumber: 12.4 Consensus size: 38
29700475 TCTACCCTAG
*
29700485 GCTCGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAG
1 GCTCGGGGTAAGAGATT-GCTGATGGTGATCTGCCCCAA
* * * * *
29700524 GCTCGAGGAAAAAGATTG--AATGGTTGCACTCTG-CCCAG
1 GCTCGGGGTAAGAGATTGCTGATGG-TG-A-TCTGCCCCAA
* * * *
29700562 GCTCGAGGTAAGAGATTGACTGATGGTGATCTACCCTAG
1 GCTCGGGGTAAGAGATTG-CTGATGGTGATCTGCCCCAA
* * * * * *
29700601 GCTCGGGGTAAAAGATCGAATGGTTGTAATCTGCCCCAA
1 GCTCGGGGTAAGAGATTG-CTGATGGTGATCTGCCCCAA
* * *
29700640 GCTCAGGTTAAGAGATTGCCTGATGGTGATATGCCCCAA
1 GCTCGGGGTAAGAGATTG-CTGATGGTGATCTGCCCCAA
* *
29700679 GCTCGGGGTAAAAGA-T-C-GAATGGCTAAAATCTGCCCCAA
1 GCTCGGGGTAAGAGATTGCTG-ATGG-T--GATCTGCCCCAA
* *
29700718 GCTCGGGGTAAGAGATTGGTTGATAGTGATCTGCCCCAA
1 GCTCGGGGTAAGAGATT-GCTGATGGTGATCTGCCCCAA
29700757 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
1 GCTCGGGGTAAGAGATT-GCTGATGGTGATCTGCCCCAA
* ** * *
29700796 GCTCGGGGTAAAAGA-T-C-GAATGGTTGCAATCTATCCTAG
1 GCTCGGGGTAAGAGATTGCTG-ATGG-TG--ATCTGCCCCAA
*
29700835 GCTTGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAA
1 GCTCGGGGTAAGAGATT-GCTGATGGTGATCTGCCCCAA
* * * *
29700874 GCTCGGGCTAAAAGA-T-CGGATAGTTGTAATCTGCCCCAA
1 GCTCGGGGTAAGAGATTGCTGAT-G--GTGATCTGCCCCAA
* * * *
29700913 GCTTGGGGTAAGAGATTGGCTAATGGTGATCTACCTCAA
1 GCTCGGGGTAAGAGATT-GCTGATGGTGATCTGCCCCAA
* *
29700952 GCTCGAGGTAAAAGAT
1 GCTCGGGGTAAGAGAT
29700968 CGGATGGCTG
Statistics
Matches: 348, Mismatches: 67, Indels: 58
0.74 0.14 0.12
Matches are distributed among these distances:
35 2 0.01
36 18 0.05
37 6 0.02
38 29 0.08
39 267 0.77
40 5 0.01
41 8 0.02
42 11 0.03
43 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (38 bp):
GCTCGGGGTAAGAGATTGCTGATGGTGATCTGCCCCAA
Found at i:29700827 original size:117 final size:117
Alignment explanation
Indices: 29700465--29700928 Score: 454
Period size: 117 Copynumber: 4.0 Consensus size: 117
29700455 TTTTTATTGG
* *
29700465 ATGGTTGCAATCTACCCTAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAGGCTCGA
1 ATGGTTGCAATCTACCCTAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGG
* * * * * *
29700530 GGAAAAAGATT-G--AATGGTTGCACTCTG-CCCAGGCTCGAGGTAAGAGATTGA
66 GGTAAAAGATTGGCTGATGG-TG-A-TCTGCCCCAAGCTCGGGGTAAAAGATCGA
* * * ** * * * * * * *
29700581 CTGATGGTGATCTACCCTAGGCTCGGGGTAAAAGA-TCGAATGGTTGTAATCTGCCCCAAGCTCA
1 ATGGTTGCAATCTACCCTAGGCTCGGGGTAAGAGATTAG-CTGATGGTGATCTGCCCCAAGCTCG
* * * *
29700645 GGTTAAGAGATTGCCTGATGGTGATATGCCCCAAGCTCGGGGTAAAAGATCGA
65 GGGTAAAAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGA
* ** * * * * * *
29700698 ATGGCTAAAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATAGTGATCTGCCCCAAGCTCGG
1 ATGGTTGCAATCTACCCTAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGG
*
29700763 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGA
66 GGTAAAAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGA
* *
29700815 ATGGTTGCAATCTATCCTAGGCTTGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGG
1 ATGGTTGCAATCTACCCTAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGG
* * * * * * *
29700880 GCTAAAAGATCGGAT-AGTTGTAATCTGCCCCAAGCTTGGGGTAAGAGAT
66 GGTAAAAGATTGGCTGA-TGGTGATCTGCCCCAAGCTCGGGGTAAAAGAT
29700929 TGGCTAATGG
Statistics
Matches: 278, Mismatches: 63, Indels: 13
0.79 0.18 0.04
Matches are distributed among these distances:
115 2 0.01
116 60 0.22
117 208 0.75
118 4 0.01
119 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (117 bp):
ATGGTTGCAATCTACCCTAGGCTCGGGGTAAGAGATTAGCTGATGGTGATCTGCCCCAAGCTCGG
GGTAAAAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGA
Found at i:29700999 original size:78 final size:76
Alignment explanation
Indices: 29700707--29701006 Score: 298
Period size: 78 Copynumber: 3.8 Consensus size: 76
29700697 AATGGCTAAA
* * * * * * * *
29700707 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATAGTGATCTGCCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTC-GGGTAAAAGATCGGATGGTTGTAATCTACCTC-AGCTCGGGGTAAGAGA
29700772 TTGGCTGATGGTG
64 TTGGCTGATGGTG
* * *
29700785 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGCAATCTATCCT-AGGCTTGGGGTAAGAG
1 ATCTGCCCCAAGCTC-GGGTAAAAGATCGGATGGTTGTAATCTA-CCTCA-GCTCGGGGTAAGAG
*
29700849 ATTAGCTGATGGTG
63 ATTGGCTGATGGTG
* * * *
29700863 ATCTGCCCCAAGCTCGGGCTAAAAGATCGGATAGTTGTAATCTGCCCCAAGCTTGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGG-TAAAAGATCGGATGGTTGTAATCTACCTC-AGCTCGGGGTAAGAGA
*
29700928 TTGGCTAATGGTG
64 TTGGCTGATGGTG
* * * * *
29700941 ATCTACCTCAAGCTCGAGGTAAAAGATCGGATGGCTGTGATTTACCTCATGAC-CGGGGTAAGAG
1 ATCTGCCCCAAGCTCG-GGTAAAAGATCGGATGGTTGTAATCTACCTCA-G-CTCGGGGTAAGAG
29701005 AT
63 AT
29701007 CGGAATCTTC
Statistics
Matches: 186, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
77 7 0.04
78 173 0.93
79 6 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (76 bp):
ATCTGCCCCAAGCTCGGGTAAAAGATCGGATGGTTGTAATCTACCTCAGCTCGGGGTAAGAGATT
GGCTGATGGTG
Found at i:29701055 original size:41 final size:41
Alignment explanation
Indices: 29701008--29701172 Score: 222
Period size: 41 Copynumber: 4.0 Consensus size: 41
29700998 GTAAGAGATC
*
29701008 GGAATCTTCAATCTGCCCTTCTTGTTTAAGGGTAAAAGACT
1 GGAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACT
** * * *
29701049 AAAATCTTCAATCTGCCCTTCTTAATTAAGGGTAAGAGATT
1 GGAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACT
* * * *
29701090 GGAATATTCAATCTGCCTTTCTTGATTAAGGGTAAGAGATT
1 GGAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACT
* *
29701131 GGAATCTTTAATCTGCCCTTCTTGATTAGGGGTAAAAGACT
1 GGAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACT
29701172 G
1 G
29701173 AATGACGATG
Statistics
Matches: 107, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (41 bp):
GGAATCTTCAATCTGCCCTTCTTGATTAAGGGTAAAAGACT
Found at i:29701641 original size:50 final size:50
Alignment explanation
Indices: 29701456--29702101 Score: 526
Period size: 49 Copynumber: 13.1 Consensus size: 50
29701446 TCCCTTCATC
* * * **
29701456 TCTTC-ATGGTACCGGGTTCACCATTGTGGCCTCAACCTTTCCCTTCATG
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
* * * * *
29701505 TCTTC-ATGGTACTGGATTTACCGTTGCGGCCTCAATCTTTCCCATCACG
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
* * * *
29701554 TCTGC-ATGGTACCAGGTTCATCGTTGCTGCCTCAACCTTTCCCATCACA
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
** * * *
29701603 TCTTCTGA-GGTACCGGGTTCGTCGTTGCGGCCTTAACCTTTCCCTTCATA
1 TCTTCT-ATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
* * * * * * * *
29701653 TTTTC-ATGGTACCGGATTCGCTGTTACGGCCTCAA-TTCTTCCCATAATA
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCT-TTCCCATCACA
* * *
29701702 TCTTCTATGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCTTCAAA
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
* * * * ***
29701752 TTTTC-ATGGTACCGGGTTTACCGTTGTGGCCTCAACCTTTCTCATTGTA
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
* * * * * *
29701801 TC-TCTATGGAACCGGATTCACCATTGCAGCCTCAATCC-TTCCCATAATA
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAA-CCTTTCCCATCACA
* * ** * * * * ** *
29701850 TCTTCTAAGGTACCAGGTTTGCCATTACAGCCTCAGCCTTTCCTGTTACA
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
* * * * * * *
29701900 TCTTCTAAGGTATCGGGTTCGCCGTTGTGGCCTCAACCTTTCACTTCAAA
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
*
29701950 TCTTC-ATGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACA
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
* * * * *
29701999 T-TTC-ATGGTACCGGATTTACCGTTGTGACCTCAATCTTTCCCATCACA
1 TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
* * * *
29702047 TCTTCT-TAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAA
1 TCTTCTAT-GGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
29702097 TCTTC
1 TCTTC
29702102 ATGTTTTTCT
Statistics
Matches: 474, Mismatches: 110, Indels: 25
0.78 0.18 0.04
Matches are distributed among these distances:
48 46 0.10
49 235 0.50
50 191 0.40
51 2 0.00
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.34
Consensus pattern (50 bp):
TCTTCTATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACA
Found at i:29701664 original size:99 final size:99
Alignment explanation
Indices: 29701446--29702101 Score: 520
Period size: 99 Copynumber: 6.6 Consensus size: 99
29701436 TCTTAATCTA
* * **
29701446 TCCCTTCATCTCTTCATGGTACCGGGTTCACCATTG-TGGCCTCAACCTTTCCCTTCATGTCTTC
1 TCCCTTCATATCTTCATGGTACCGGGTTCACCATTGCT-GCCTCAACCTTTCCCATCACATCTTC
* * * *
29701510 -ATGGTACTGGATTTACCGTTGCGGCCTCAATCTT
65 TATGGTACCGGGTTCACCGTTGCGGCCTCAACCTT
* ** * * * *
29701544 TCCCATCACGTCTGCATGGTACCAGGTTCATCGTTGCTGCCTCAACCTTTCCCATCACATCTTCT
1 TCCCTTCATATCTTCATGGTACCGGGTTCACCATTGCTGCCTCAACCTTTCCCATCACATCTTCT
** *
29701609 GA-GGTACCGGGTTCGTCGTTGCGGCCTTAACCTT
66 -ATGGTACCGGGTTCACCGTTGCGGCCTCAACCTT
* * * ** * * * * *
29701643 TCCCTTCATATTTTCATGGTACCGGATTCGCTGTTACGGCCTCAA-TTCTTCCCATAATATCTTC
1 TCCCTTCATATCTTCATGGTACCGGGTTCACCATTGCTGCCTCAACCT-TTCCCATCACATCTTC
*
29701707 TATGGTACCGGGTTCACCATTGCGGCCTCAACCTT
65 TATGGTACCGGGTTCACCGTTGCGGCCTCAACCTT
* * * * * ***
29701742 TCCCTTCAAATTTTCATGGTACCGGGTTTACCGTTG-TGGCCTCAACCTTTCTCATTGTATC-TC
1 TCCCTTCATATCTTCATGGTACCGGGTTCACCATTGCT-GCCTCAACCTTTCCCATCACATCTTC
* * * *
29701805 TATGGAACCGGATTCACCATTGCAGCCTCAATCC-T
65 TATGGTACCGGGTTCACCGTTGCGGCCTCAA-CCTT
* * * * ** * * * ** *
29701840 TCCCATAATATCTTCTAAGGTACCAGGTTTGCCATTACAGCCTCAGCCTTTCCTGTTACATCTTC
1 TCCCTTCATATCTTC-ATGGTACCGGGTTCACCATTGCTGCCTCAACCTTTCCCATCACATCTTC
* * * *
29701905 TAAGGTATCGGGTTCGCCGTTGTGGCCTCAACCTT
65 TATGGTACCGGGTTCACCGTTGCGGCCTCAACCTT
* * *
29701940 TCACTTCAAATCTTCATGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACAT-TTC-
1 TCCCTTCATATCTTCATGGTACCGGGTTCACCATTGCTGCCTCAACCTTTCCCATCACATCTTCT
* * * * *
29702003 ATGGTACCGGATTTACCGTTGTGACCTCAATCTT
66 ATGGTACCGGGTTCACCGTTGCGGCCTCAACCTT
* * * * * * * * *
29702037 TCCCATCACATCTTCTTAGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTC
1 TCCCTTCATATCTTCAT-GGTACCGGGTTCACCATTGCTGCCTCAACCTTTCCCATCACATCTTC
29702102 ATGTTTTTCT
Statistics
Matches: 440, Mismatches: 104, Indels: 27
0.77 0.18 0.05
Matches are distributed among these distances:
97 40 0.09
98 137 0.31
99 224 0.51
100 39 0.09
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.34
Consensus pattern (99 bp):
TCCCTTCATATCTTCATGGTACCGGGTTCACCATTGCTGCCTCAACCTTTCCCATCACATCTTCT
ATGGTACCGGGTTCACCGTTGCGGCCTCAACCTT
Found at i:29701961 original size:247 final size:246
Alignment explanation
Indices: 29701456--29702090 Score: 681
Period size: 247 Copynumber: 2.6 Consensus size: 246
29701446 TCCCTTCATC
* ** * *
29701456 TCTTCATGGTACCGGGTTCACCATTGTGGCCTCAACCTTTCCCTTCATGTCTTCATGGTACTGGA
1 TCTTCATGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCTTCAAATTTTCATGGTACCGGA
* * * * * *
29701521 TTTACCGTTGCGGCCTCAATCTTTCCCATCACGTCTGCATGGTACCAGGTTCATCGTTGCTGCCT
66 TTTACCGTTGTGGCCTCAATCTTTCCCATCACATCTGCATGGAACCAGGTTCACCATTGCAGCCT
* * * * * * * *
29701586 CAACCTTTCCCATCACATCTTCTGAGGTACCGGGTTCGTCGTTGCGGCCTTAACCTTTCCCTTCA
131 CAACCTTTCCCATAACATCTTCTAAGGTACCAGGTTCGCCATTACAGCCTCAACCTTTCCCTTCA
* * * * *
29701651 TATTTTCATGGTACCGGATTCGCTGTTACGGCCTCAATTCTTCCCATAATA
196 TATTCTCAAGGTACCGGATTCGCCGTTACGGCCTCAACTCTTCACATAATA
29701702 TCTTCTATGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCTTCAAATTTTCATGGTACCGG
1 TCTTC-ATGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCTTCAAATTTTCATGGTACCGG
* * * ***
29701767 GTTTACCGTTGTGGCCTCAACCTTTCTCATTGTATCT-CTATGGAACC-GGATTCACCATTGCAG
65 ATTTACCGTTGTGGCCTCAATCTTTCCCATCACATCTGC-ATGGAACCAGG-TTCACCATTGCAG
* * *
29701830 CCTCAATCC-TTCCCATAATATCTTCTAAGGTACCAGGTTTGCCATTACAGCCTCAGCCTTTCCT
128 CCTCAA-CCTTTCCCATAACATCTTCTAAGGTACCAGGTTCGCCATTACAGCCTCAACCTTTCC-
* * * * ** *
29701894 GTTACATCTTCT-AAGGTATCGGGTTCGCCGTTGTGGCCTCAAC-CTTTCACTTCAA-A
191 CTT-CATATTCTCAAGGTACCGGATTCGCCGTTACGGCCTCAACTC-TTCACAT-AATA
* *
29701950 TCTTCATGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACA-TTTCATGGTACCGGA
1 TCTTCATGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCTTCAAATTTTCATGGTACCGGA
* * * * * * * * *
29702014 TTTACCGTTGTGACCTCAATCTTTCCCATCACATCTTCTTAGGTATCGGGTTCGCCGTTGCGGCC
66 TTTACCGTTGTGGCCTCAATCTTTCCCATCACATCTGCAT-GGAACCAGGTTCACCATTGCAGCC
29702079 TCAACCTTTCCC
130 TCAACCTTTCCC
29702091 TTCAAATCTT
Statistics
Matches: 322, Mismatches: 55, Indels: 23
0.81 0.14 0.06
Matches are distributed among these distances:
246 55 0.17
247 218 0.68
248 41 0.13
249 8 0.02
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.34
Consensus pattern (246 bp):
TCTTCATGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCTTCAAATTTTCATGGTACCGGA
TTTACCGTTGTGGCCTCAATCTTTCCCATCACATCTGCATGGAACCAGGTTCACCATTGCAGCCT
CAACCTTTCCCATAACATCTTCTAAGGTACCAGGTTCGCCATTACAGCCTCAACCTTTCCCTTCA
TATTCTCAAGGTACCGGATTCGCCGTTACGGCCTCAACTCTTCACATAATA
Found at i:29703120 original size:7 final size:7
Alignment explanation
Indices: 29703048--29703120 Score: 62
Period size: 7 Copynumber: 10.6 Consensus size: 7
29703038 CGACCTCTCC
29703048 TTTTCTT
1 TTTTCTT
*
29703055 TTTCCTATT
1 TTT--TCTT
*
29703064 TTTTCTA
1 TTTTCTT
*
29703071 TTTTCTA
1 TTTTCTT
29703078 TTTTCTT
1 TTTTCTT
*
29703085 TTTCCTT
1 TTTTCTT
*
29703092 TTTCCTT
1 TTTTCTT
29703099 TTTTC--
1 TTTTCTT
29703104 -TTTCTT
1 TTTTCTT
29703110 TTTTCTT
1 TTTTCTT
29703117 TTTT
1 TTTT
29703121 ATTTATTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
4 4 0.07
7 45 0.82
9 6 0.11
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTCTT
Found at i:29703131 original size:18 final size:18
Alignment explanation
Indices: 29703090--29703134 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
29703080 TTCTTTTTCC
* * *
29703090 TTTTTCCTTTTTTCTTTC
1 TTTTTTCTTTTTTATTTA
29703108 TTTTTTCTTTTTTATTTA
1 TTTTTTCTTTTTTATTTA
29703126 TTTTTTCTT
1 TTTTTTCTT
29703135 CATTGAGTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTCTTTTTTATTTA
Found at i:29703132 original size:25 final size:24
Alignment explanation
Indices: 29703048--29703134 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 24
29703038 CGACCTCTCC
29703048 TTTTCTTTTTCCTATTTTTTCTATTTTCT
1 TTTTCTTTTTCC---TTTTTC-ATTTT-T
*
29703077 ATTTTCTTTTTCCTTTTTCCTTTTT
1 -TTTTCTTTTTCCTTTTTCATTTTT
* *
29703102 TCTTTCTTTTTTCTTTTTTATTTATT
1 T-TTTCTTTTTCCTTTTTCATTT-TT
29703128 TTTTCTT
1 TTTTCTT
29703135 CATTGAGTCC
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
24 1 0.02
25 25 0.49
26 7 0.14
27 6 0.12
30 12 0.24
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTCTTTTTCCTTTTTCATTTTT
Found at i:29703981 original size:15 final size:16
Alignment explanation
Indices: 29703961--29703991 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
29703951 TTGACTTTCC
29703961 TTTCTTTTTTT-CCTT
1 TTTCTTTTTTTGCCTT
29703976 TTTCTTTTTTTGCCTT
1 TTTCTTTTTTTGCCTT
29703992 GGGCTTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTTTGCCTT
Found at i:29704057 original size:9 final size:9
Alignment explanation
Indices: 29704045--29704070 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29704035 TTTATTTGTT
29704045 TTTTTTTTC
1 TTTTTTTTC
29704054 TTTTTTTTC
1 TTTTTTTTC
29704063 TTTTTTTT
1 TTTTTTTT
29704071 AACACGTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:29707999 original size:28 final size:28
Alignment explanation
Indices: 29707958--29708058 Score: 121
Period size: 28 Copynumber: 3.5 Consensus size: 28
29707948 AGTTCGAGTA
*
29707958 AAAATGTGATTTTTTGGAAGTTTAGGGGT
1 AAAATGT-AATTTTTGGAAGTTTAGGGGT
*
29707987 AAAATGTAATTTTTAGAAGTTTAGGGGT
1 AAAATGTAATTTTTGGAAGTTTAGGGGT
* *
29708015 AATATGTAATTTTTGGAAAAGTATAGGGGTT
1 AAAATGTAATTTTTGG--AAGTTTAGGGG-T
*
29708046 AAAATGCAATTTT
1 AAAATGTAATTTT
29708059 GTAAAACTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 33 0.53
29 7 0.11
30 10 0.16
31 12 0.19
ACGTcount: A:0.35, C:0.01, G:0.25, T:0.40
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTAGGGGT
Found at i:29708059 original size:30 final size:30
Alignment explanation
Indices: 29707975--29708140 Score: 158
Period size: 30 Copynumber: 5.6 Consensus size: 30
29707965 GATTTTTTGG
* *
29707975 AAGTTTAGGGG-TAAAATGTAATTTT-TAG
1 AAGTTTAGGGGTTAAAATGTAATTTTGGAA
*
29708003 AAGTTTAGGGG-TAATATGTAATTTTTGGAA
1 AAGTTTAGGGGTTAAAATGTAA-TTTTGGAA
* * *
29708033 AAGTATAGGGGTTAAAATGCAATTTTGTAA
1 AAGTTTAGGGGTTAAAATGTAATTTTGGAA
* * * *
29708063 AACTTTAGGTGTTAAAATATGATTTTGGAA
1 AAGTTTAGGGGTTAAAATGTAATTTTGGAA
* * *
29708093 AAGTTTACGGGTCAAAATATAATTTTGGAA
1 AAGTTTAGGGGTTAAAATGTAATTTTGGAA
* * *
29708123 ATGTTTAGAGGTCAAAAT
1 AAGTTTAGGGGTTAAAAT
29708141 ATGATTTTTG
Statistics
Matches: 113, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
28 20 0.18
29 4 0.04
30 81 0.72
31 8 0.07
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (30 bp):
AAGTTTAGGGGTTAAAATGTAATTTTGGAA
Found at i:29708141 original size:30 final size:30
Alignment explanation
Indices: 29708025--29708157 Score: 117
Period size: 30 Copynumber: 4.4 Consensus size: 30
29708015 AATATGTAAT
* * * ***
29708025 TTTTGGAAAAGTATAGGGGTTAAAATGCAA
1 TTTTGGAAAAGTTTACGGGTCAAAATATGA
* * *
29708055 TTTTGTAAAACTTTA-GGTGTTAAAATATGA
1 TTTTGGAAAAGTTTACGG-GTCAAAATATGA
*
29708085 TTTTGGAAAAGTTTACGGGTCAAAATATAA
1 TTTTGGAAAAGTTTACGGGTCAAAATATGA
*
29708115 TTTTGGAAATGTTTA-GAGGTCAAAATATGA
1 TTTTGGAAAAGTTTACG-GGTCAAAATATGA
* *
29708145 TTTTTGAATAGTT
1 TTTTGGAAAAGTT
29708158 CAGGGACCTT
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
29 3 0.04
30 80 0.94
31 2 0.02
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (30 bp):
TTTTGGAAAAGTTTACGGGTCAAAATATGA
Found at i:29708632 original size:10 final size:10
Alignment explanation
Indices: 29708617--29708645 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
29708607 CCCTTTTTTT
29708617 CATTTTCTTA
1 CATTTTCTTA
29708627 CATTTTCTTA
1 CATTTTCTTA
29708637 CATTTTCTT
1 CATTTTCTT
29708646 TCAAAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (10 bp):
CATTTTCTTA
Found at i:29709967 original size:6 final size:6
Alignment explanation
Indices: 29709958--29709990 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
29709948 ATTTTAAGAA
*
29709958 TAAATT TAAA-T TAAATT TAAATT TAAACT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
29709991 ATAATATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:29709983 original size:12 final size:11
Alignment explanation
Indices: 29709939--29709990 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
29709929 TTGGACATTA
*
29709939 TTAATTTAAATT
1 TTAAATTAAA-T
*
29709951 TTAAGAATAAAT
1 TTAA-ATTAAAT
29709963 TTAAATTAAAT
1 TTAAATTAAAT
*
29709974 TTAAATTTAAAC
1 TTAAA-TTAAAT
29709986 TTAAA
1 TTAAA
29709991 ATAATATCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 11 0.32
12 19 0.56
13 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:29718312 original size:13 final size:13
Alignment explanation
Indices: 29718294--29718327 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
29718284 ATGCATAACA
29718294 GGTTCACAGGTAG
1 GGTTCACAGGTAG
29718307 GGTTCACAGGTAG
1 GGTTCACAGGTAG
29718320 GGTTCACA
1 GGTTCACA
29718328 CATCTAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (13 bp):
GGTTCACAGGTAG
Found at i:29720184 original size:21 final size:19
Alignment explanation
Indices: 29720158--29720196 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
29720148 GAATTTCACA
29720158 TTTCTTTACAAATTTCATAAT
1 TTTC-TTACAAATTT-ATAAT
*
29720179 TTTCTTACAACTTTATAA
1 TTTCTTACAAATTTATAA
29720197 AATTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTCTTACAAATTTATAAT
Found at i:29720323 original size:26 final size:28
Alignment explanation
Indices: 29720278--29720330 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
29720268 TGTTTTCTAA
29720278 TTTTTAATAAAATTTAAAT-ATTTTTAT
1 TTTTTAATAAAATTTAAATAATTTTTAT
*
29720305 TTTTTATTAAAATTT-AATAATTTTTA
1 TTTTTAATAAAATTTAAATAATTTTTA
29720331 GGTTGTGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTAATAAAATTTAAATAATTTTTAT
Found at i:29721532 original size:24 final size:23
Alignment explanation
Indices: 29721495--29721540 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
29721485 TTACTAAAGT
29721495 ATAAATATAATTTTATTATTTTA
1 ATAAATATAATTTTATTATTTTA
*
29721518 ATAATATATATTTTTATTATTTT
1 ATAA-ATATAATTTTATTATTTT
29721541 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATAAATATAATTTTATTATTTTA
Found at i:29721561 original size:30 final size:30
Alignment explanation
Indices: 29721527--29721604 Score: 156
Period size: 30 Copynumber: 2.6 Consensus size: 30
29721517 AATAATATAT
29721527 ATTTTTATTATTTTTAAAAAATTAAATTAA
1 ATTTTTATTATTTTTAAAAAATTAAATTAA
29721557 ATTTTTATTATTTTTAAAAAATTAAATTAA
1 ATTTTTATTATTTTTAAAAAATTAAATTAA
29721587 ATTTTTATTATTTTTAAA
1 ATTTTTATTATTTTTAAA
29721605 GAGTAATTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTTTTATTATTTTTAAAAAATTAAATTAA
Found at i:29721583 original size:25 final size:25
Alignment explanation
Indices: 29721505--29721584 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 25
29721495 ATAAATATAA
* *
29721505 TTTTATTA-TTTT-AATAATATATAT
1 TTTTATTATTTTTAAAAAAT-TAAAT
29721529 TTTTATTATTTTTAAAAAATTAAATTAAAT
1 TTTTATTATTTTT---AAA--AAATTAAAT
29721559 TTTTATTATTTTTAAAAAATTAAAT
1 TTTTATTATTTTTAAAAAATTAAAT
29721584 T
1 T
29721585 AAATTTTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
24 8 0.17
25 14 0.30
27 3 0.06
29 2 0.04
30 17 0.36
31 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTATTATTTTTAAAAAATTAAAT
Found at i:29724575 original size:2 final size:2
Alignment explanation
Indices: 29724563--29724642 Score: 83
Period size: 2 Copynumber: 40.5 Consensus size: 2
29724553 CTTAAAGTCA
* * * * *
29724563 AT AT AT TT AT AT AT AT GT AT AT TT AT AT AT AT GT A- AT -T GAG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
29724604 AT AT TT 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 AT AT A
29724643 AAATATACAT
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
1 2 0.03
2 61 0.97
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:29725173 original size:19 final size:19
Alignment explanation
Indices: 29725146--29725183 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
29725136 TTTTATAAAT
29725146 TTAAAAAAATTATGATTTA
1 TTAAAAAAATTATGATTTA
* *
29725165 TTAATAAAATTATTATTTA
1 TTAAAAAAATTATGATTTA
29725184 GTCAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TTAAAAAAATTATGATTTA
Found at i:29726256 original size:99 final size:99
Alignment explanation
Indices: 29726068--29726249 Score: 337
Period size: 99 Copynumber: 1.8 Consensus size: 99
29726058 CTTTAGAAAA
* *
29726068 ATCTTATTATGTATAAATTATAATTATTAGTTAAATTTATAGTTTCCAAATATAATGTGAGCGAA
1 ATCTTATTATGTATAAATTATAATTATTAGTTAAATTTATAGTTTCCAAATATAATATGAGCAAA
29726133 AGAAAACTATTATGAATACTGTTAATTATTATGT
66 AGAAAACTATTATGAATACTGTTAATTATTATGT
*
29726167 ATCTTATTATGTATAAATTATAATTATTAGTTAAATTTATAGTTTTCAAATATAATATGAGCAAA
1 ATCTTATTATGTATAAATTATAATTATTAGTTAAATTTATAGTTTCCAAATATAATATGAGCAAA
29726232 AGAAAACTATTATGAATA
66 AGAAAACTATTATGAATA
29726250 TCGTTAACTG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (99 bp):
ATCTTATTATGTATAAATTATAATTATTAGTTAAATTTATAGTTTCCAAATATAATATGAGCAAA
AGAAAACTATTATGAATACTGTTAATTATTATGT
Found at i:29726668 original size:28 final size:27
Alignment explanation
Indices: 29726631--29726685 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
29726621 CAAATGCCTA
*
29726631 TTTTCATAATAAATCTGTTTTTCATATT
1 TTTTCATAATAAAT-TATTTTTCATATT
* * *
29726659 TTTTCGTAATTAATTATTTTTTATATT
1 TTTTCATAATAAATTATTTTTCATATT
29726686 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTTCATAATAAATTATTTTTCATATT
Found at i:29732730 original size:29 final size:30
Alignment explanation
Indices: 29732693--29732755 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
29732683 AAAAAAACTT
*
29732693 TTTTTAATTTTGACTTTTC-TC-CCCTCATA
1 TTTTCAATTTTGACTTTTCTTCTCCC-CATA
*
29732722 TTTTCAATTTTTACTTTTCTTCTCCCCATA
1 TTTTCAATTTTGACTTTTCTTCTCCCCATA
29732752 TTTT
1 TTTT
29732756 TTTGTCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 17 0.57
30 10 0.33
31 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.02, T:0.59
Consensus pattern (30 bp):
TTTTCAATTTTGACTTTTCTTCTCCCCATA
Found at i:29733631 original size:3 final size:3
Alignment explanation
Indices: 29733623--29733650 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29733613 AGCTGTATAT
29733623 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
29733651 TGATGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29736486 original size:16 final size:18
Alignment explanation
Indices: 29736448--29736488 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
29736438 GAGCCCAATG
*
29736448 TTATATTTATTAAGTTTTA
1 TTAT-TTTATTAAGTTATA
29736467 TTATTTTATT-AGTTAT-
1 TTATTTTATTAAGTTATA
29736483 TTATTT
1 TTATTT
29736489 CAAATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 6 0.29
17 5 0.24
18 6 0.29
19 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTATTTTATTAAGTTATA
Found at i:29737679 original size:30 final size:30
Alignment explanation
Indices: 29737645--29737701 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
29737635 AAGACATGAG
* * *
29737645 CACTGGTGTTGCAAGCACTCATGTTGCGAA
1 CACTGGAGCTGCAAACACTCATGTTGCGAA
29737675 CACTGGAGCTGCAAACACTCATGTTGC
1 CACTGGAGCTGCAAACACTCATGTTGC
29737702 TAATACACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (30 bp):
CACTGGAGCTGCAAACACTCATGTTGCGAA
Found at i:29745341 original size:22 final size:22
Alignment explanation
Indices: 29745307--29745363 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
29745297 TGAACTAATA
* *
29745307 AAACACTAGGCACCGAAGTGC-
1 AAACACTAAGCACCAAAGTGCG
29745328 AAATCACTAAGCACCAAAGTGCG
1 AAA-CACTAAGCACCAAAGTGCG
*
29745351 AAACAGTAAGCAC
1 AAACACTAAGCAC
29745364 TAAAACGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 25 0.81
23 3 0.10
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (22 bp):
AAACACTAAGCACCAAAGTGCG
Found at i:29746817 original size:11 final size:11
Alignment explanation
Indices: 29746800--29746843 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
29746790 AATAATTTAA
29746800 TAATAAAATAT
1 TAATAAAATAT
*
29746811 TATTAAAA-ACCT
1 TAATAAAATA--T
29746823 TAATAAAATAT
1 TAATAAAATAT
29746834 TAATAAAATA
1 TAATAAAATA
29746844 ACTTTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 18 0.64
12 8 0.29
13 1 0.04
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:29753185 original size:40 final size:40
Alignment explanation
Indices: 29753050--29753446 Score: 420
Period size: 40 Copynumber: 10.1 Consensus size: 40
29753040 AGATCAGATG
* * *
29753050 CTTCAATCTGCCCCATGATTGGGGGTAAAAGATTGGTGTGT
1 CTTCAATCTACCCCATGA-TCGGGGTAAGAGATTGGTGTGT
** *** *
29753091 CTTCAATCTACTTGC-TGATTAAGGTAA-AGATTGG-ATG-
1 CTTCAATCTAC-CCCATGATCGGGGTAAGAGATTGGTGTGT
* *
29753128 CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGTGTGT
1 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
* * *
29753168 TTTCAATCTACCTCATGATCGGGGTAAGGGATTGGTGTGT
1 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
* * ** *
29753208 CTTCAATCTGCCCCCTGATCGGGGT------TTGACGTGC
1 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
* * * * *
29753242 CATT-AATTTTCCTCATGATTGGGGTAAGAGATTGGCGTGT
1 C-TTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
* * *
29753282 CTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGTGTTT
1 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
*
29753322 CTTCAATATACCCCATGATCGGGGTAAGAGATTGGTGTGT
1 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
* *
29753362 CTTCAATTTACCCCATGATCGAGGTAAGAGATTGGTGTGT
1 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
29753402 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
1 CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
29753442 CTTCA
1 CTTCA
29753447 CTGCAACGTC
Statistics
Matches: 294, Mismatches: 49, Indels: 27
0.79 0.13 0.07
Matches are distributed among these distances:
34 23 0.08
35 2 0.01
36 1 0.00
37 18 0.06
38 9 0.03
39 11 0.04
40 216 0.73
41 13 0.04
42 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (40 bp):
CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGT
Found at i:29753397 original size:194 final size:192
Alignment explanation
Indices: 29753063--29753426 Score: 518
Period size: 194 Copynumber: 1.9 Consensus size: 192
29753053 CAATCTGCCC
* ** *
29753063 CATGATTGGGGGTAAAAGATTGGTGTGTCTTCAATCTACTTGCTGATTAAGGTAAAGATTGGATG
1 CATGATTGGGGGTAAAAGATTGGCGTGTCTTCAATCTACTCCCTGATCAAGGTAAAGATTGGATG
* * * * *
29753128 CTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGTGTGTTTTCAATCTACCTCATGATCGGGGT
66 CTTCAATATACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCCATGATCGAGGT
* * *
29753193 AAGGGATTGGTGTGTCTTCAATCTGCCCCCTGATCGGGGTTTGACGTGCCATTAATTTTCCT
131 AAGAGATTGGTGTGTCTTCAATCTACCCCATGATCGGGGTTTGACGTGCCATTAATTTTCCT
* * *
29753255 CATGATT-GGGGTAAGAGATTGGCGTGTCTTCAATCTGC-CCCATGATCAGGGTAAGAGATTGG-
1 CATGATTGGGGGTAAAAGATTGGCGTGTCTTCAATCTACTCCC-TGATCAAGGTAA-AGATTGGA
*
29753317 TGTTTCTTCAATATACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATTTACCCCATGATC
64 TG---CTTCAATATACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCCATGATC
29753382 GAGGTAAGAGATTGGTGTGTCTTCAATCTACCCCATGATCGGGGT
126 GAGGTAAGAGATTGGTGTGTCTTCAATCTACCCCATGATCGGGGT
29753427 AAGAGATTGG
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
190 1 0.01
191 40 0.26
192 14 0.09
194 96 0.64
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (192 bp):
CATGATTGGGGGTAAAAGATTGGCGTGTCTTCAATCTACTCCCTGATCAAGGTAAAGATTGGATG
CTTCAATATACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCCATGATCGAGGT
AAGAGATTGGTGTGTCTTCAATCTACCCCATGATCGGGGTTTGACGTGCCATTAATTTTCCT
Found at i:29758063 original size:20 final size:20
Alignment explanation
Indices: 29758038--29758091 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
29758028 CTCCAGTGAG
* * *
29758038 ACTTCTACCGGTAGAACTCC
1 ACTTCTACCGATACAACTAC
29758058 ACTTCTACCGATACAACTAC
1 ACTTCTACCGATACAACTAC
*
29758078 AGTTCTACCGATAC
1 ACTTCTACCGATAC
29758092 CTTGAAGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.33, G:0.11, T:0.26
Consensus pattern (20 bp):
ACTTCTACCGATACAACTAC
Found at i:29760988 original size:33 final size:33
Alignment explanation
Indices: 29760942--29761007 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
29760932 ATATTTATGC
* *
29760942 CTTAAATTGAAAATGATTTTTA-TATAGGGGGAG
1 CTTAAATTCAAAATGACTTTTATTA-AGGGGGAG
*
29760975 CTTAATTTCAAAATGACTTTTATTAAGGGGGAG
1 CTTAAATTCAAAATGACTTTTATTAAGGGGGAG
29761008 AAATCTATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (33 bp):
CTTAAATTCAAAATGACTTTTATTAAGGGGGAG
Found at i:29761178 original size:20 final size:20
Alignment explanation
Indices: 29761153--29761190 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29761143 CTCCAGTGAA
*
29761153 ACTTCTACCGATAGAACTCC
1 ACTTCTACCGATACAACTCC
29761173 ACTTCTACCGATACAACT
1 ACTTCTACCGATACAACT
29761191 ACAGTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.08, T:0.26
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCC
Found at i:29765542 original size:12 final size:10
Alignment explanation
Indices: 29765509--29765534 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
29765499 TTTTCATGAT
29765509 AAAAAAATAA
1 AAAAAAATAA
29765519 AAAAAAATAA
1 AAAAAAATAA
29765529 AAAAAA
1 AAAAAA
29765535 TTATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:29766533 original size:32 final size:28
Alignment explanation
Indices: 29766473--29766529 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
29766463 GTTCAAATAT
29766473 TCAAAAGTAGACCTTTCTTTCTTTTTTA
1 TCAAAAGTAGACCTTTCTTTCTTTTTTA
29766501 TCAAAAGTAGACCTTTCTTTCTTTTTTA
1 TCAAAAGTAGACCTTTCTTTCTTTTTTA
29766529 T
1 T
29766530 TTATTTGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.51
Consensus pattern (28 bp):
TCAAAAGTAGACCTTTCTTTCTTTTTTA
Found at i:29767863 original size:23 final size:23
Alignment explanation
Indices: 29767833--29767878 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
29767823 TGATACACAT
*
29767833 TTTTTTTAGGTTTAGTAATTTTC
1 TTTTTTTAGGTCTAGTAATTTTC
*
29767856 TTTTTTTAGGTCTAGTTATTTTC
1 TTTTTTTAGGTCTAGTAATTTTC
29767879 ATTCTTGTTT
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:0.15, C:0.07, G:0.13, T:0.65
Consensus pattern (23 bp):
TTTTTTTAGGTCTAGTAATTTTC
Found at i:29769269 original size:20 final size:21
Alignment explanation
Indices: 29769246--29769291 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
29769236 AAGAGAAGAA
* *
29769246 AACAAAGACAA-AAAGCAAAG
1 AACAAACACAAGAAAACAAAG
29769266 AACAAACACAAGAAAACAAAG
1 AACAAACACAAGAAAACAAAG
29769287 AACAA
1 AACAA
29769292 TGATTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.72, C:0.17, G:0.11, T:0.00
Consensus pattern (21 bp):
AACAAACACAAGAAAACAAAG
Found at i:29781915 original size:85 final size:85
Alignment explanation
Indices: 29781772--29781939 Score: 205
Period size: 85 Copynumber: 2.0 Consensus size: 85
29781762 AAACCCCCCA
* * * *
29781772 TCTTCCTGATAAGATACAGAGAAGTGGGTTAAAGCAATAAAGCGGTTACCTTCCTGATGAGATAC
1 TCTTCCTGATAAGATACAGAGAAGTGGGTTAAAACAATAAAGCAGTCAACTTCCTGATGAGATAC
29781837 AGAGAAGT-GAACCAAATCCG
66 AGAGAAGTAG-ACCAAATCCG
* * * * * *
29781857 TCTTCCTGATGAGATACAGAG-AGTTGGTTTAAAATAATGAGGCAGTCAACTTTCTGATGAGATA
1 TCTTCCTGATAAGATACAGAGAAG-TGGGTTAAAACAATAAAGCAGTCAACTTCCTGATGAGATA
*
29781921 CTGAGAAGTAGACCAAATC
65 CAGAGAAGTAGACCAAATC
29781940 AATGAAGCAA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
84 2 0.03
85 67 0.96
86 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (85 bp):
TCTTCCTGATAAGATACAGAGAAGTGGGTTAAAACAATAAAGCAGTCAACTTCCTGATGAGATAC
AGAGAAGTAGACCAAATCCG
Found at i:29782084 original size:211 final size:211
Alignment explanation
Indices: 29781630--29782156 Score: 778
Period size: 211 Copynumber: 2.5 Consensus size: 211
29781620 GCAATGGAGA
29781630 AAAGTGAACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGC-GATC
1 AAAGTGAACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCAG-TC
* *
29781694 ATC-TTCTTGATGAGATATTGAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAA
65 ATCTTTC-TGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCAAAGCCCAATGTGAGTGAAA
* * * *
29781758 CTTCAAACCCCCCATCTTCCTGATAAGATACAGAGAAGTGGGTTAAAGCAATAAAGCGGTTACCT
129 CTTCAAACCCCCCATCTTCCTAATAAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCACCT
29781823 TCCTGATGAGATACAGAG
194 TCCTGATGAGATACAGAG
* * *
29781841 -AAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAG-AGTTGGTTTAAAATAATGAGGCAGTC
1 AAAGTGAACCAAATCTGTCTTCCTGATGAGATACAGAGAAG-TGGATTAAAACAATGAGGCAGTC
*
29781904 AACTTTCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCAAAGCCCAATGTGTGAGTGAA
65 ATCTTTCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCAAAGCCCAA--TGTGAGTGAA
* * *
29781969 ACTTCAAA-CCCCCATCTTCCTAATGAGATACAGAGAAGTGGGTCAAAGCAATAAGGAGGTCATC
128 ACTTCAAACCCCCCATCTTCCTAATAAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCACC
* *
29782033 TTCCTTATGAGATACAGGG
193 TTCCTGATGAGATACAGAG
* * *
29782052 AAAG-GAACCAAATCTATCTTCCTGATGAGATACAAAGAAGTGGATAAAAACAATGAGGCAGTCA
1 AAAGTGAACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCAGTCA
* * *
29782116 TCTTCCTGATGAGATACAGAGAAGTTGACCAAATCAATGAA
66 TCTTTCTGATGAGATACTGAGAAGTAGACCAAATCAATGAA
29782157 ACGGAGATCG
Statistics
Matches: 284, Mismatches: 25, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
209 2 0.01
210 101 0.36
211 158 0.56
212 23 0.08
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (211 bp):
AAAGTGAACCAAATCTGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAGGCAGTCA
TCTTTCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCAAAGCCCAATGTGAGTGAAACT
TCAAACCCCCCATCTTCCTAATAAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCACCTTC
CTGATGAGATACAGAG
Found at i:29782150 original size:85 final size:85
Alignment explanation
Indices: 29781982--29782138 Score: 226
Period size: 85 Copynumber: 1.8 Consensus size: 85
29781972 TCAAACCCCC
* * * * *
29781982 ATCTTCCTAATGAGATACAGAGAAGTGGGTCAAAGCAATAAGGAGGTCATCTTCCTTATGAGATA
1 ATCTTCCTAATGAGATACAAAGAAGTGGATAAAAACAATAAGGAGGTCATCTTCCTGATGAGATA
*
29782047 CAGGGAAAGGAACCAAATCT
66 CAGAGAAAGGAACCAAATCT
* *
29782067 ATCTTCCTGATGAGATACAAAGAAGTGGATAAAAACAATGAGGCA-GTCATCTTCCTGATGAGAT
1 ATCTTCCTAATGAGATACAAAGAAGTGGATAAAAACAATAAGG-AGGTCATCTTCCTGATGAGAT
29782131 ACAGAGAA
65 ACAGAGAA
29782139 GTTGACCAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 62 0.98
86 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (85 bp):
ATCTTCCTAATGAGATACAAAGAAGTGGATAAAAACAATAAGGAGGTCATCTTCCTGATGAGATA
CAGAGAAAGGAACCAAATCT
Found at i:29790651 original size:16 final size:15
Alignment explanation
Indices: 29790595--29790640 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
29790585 GTTTTGATGT
29790595 TATTATTAATAATAA
1 TATTATTAATAATAA
*
29790610 TATTAGTAATAATAAA
1 TATTATTAATAAT-AA
*
29790626 TATCATTAATAATAA
1 TATTATTAATAATAA
29790641 CCATTAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
TATTATTAATAATAA
Found at i:29791868 original size:30 final size:29
Alignment explanation
Indices: 29791791--29792009 Score: 224
Period size: 30 Copynumber: 7.3 Consensus size: 29
29791781 GGAGGTCCTT
* *
29791791 AAACTGTCCAAAAATTATATTTTAACCCCA
1 AAACT-TCCAAAAATTACATTTTTACCCCA
* * *
29791821 CGAACTTCTCCAAAATTACATTTTTGACCTCA
1 -AAACTTC-CAAAAATTACATTTTT-ACCCCA
* * *
29791853 AAACTTCAAAAAATTACATTTTTGCCCCT
1 AAACTTCCAAAAATTACATTTTTACCCCA
* *
29791882 GAACATCCAAAAATTACATTTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTT-ACCCCA
*
29791912 AAACTTCCAAAAATTACATTTTTACCCCT
1 AAACTTCCAAAAATTACATTTTTACCCCA
*
29791941 AAACTTCTCCAAAATTACATTTTTACCCTC-
1 AAACTTC-CAAAAATTACATTTTTACCC-CA
* *
29791971 GAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTT-ACCCCA
*
29792001 AAAATTCCA
1 AAACTTCCA
29792010 TTTTACCCCT
Statistics
Matches: 156, Mismatches: 25, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
29 50 0.32
30 77 0.49
31 24 0.15
32 5 0.03
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCA
Found at i:29791894 original size:29 final size:29
Alignment explanation
Indices: 29791790--29792169 Score: 214
Period size: 29 Copynumber: 13.2 Consensus size: 29
29791780 TGGAGGTCCT
* *
29791790 TAAACTGTCCAAAAATTATATTTTAACCCC
1 TAAACT-TCCAAAAATTACATTTTTACCCC
* *
29791820 -ACGAACTTCTCCAAAATTACATTTTTGACCTC
1 TA--AACTTC-CAAAAATTACATTTTT-ACCCC
* * *
29791852 AAAACTTCAAAAAATTACATTTTTGCCCC
1 TAAACTTCCAAAAATTACATTTTTACCCC
* *
29791881 TGAACATCCAAAAATTACATTTTTAACCCC
1 TAAACTTCCAAAAATTACATTTTT-ACCCC
*
29791911 AAAACTTCCAAAAATTACATTTTTACCCC
1 TAAACTTCCAAAAATTACATTTTTACCCC
*
29791940 TAAACTTCTCCAAAATTACATTTTTA-CCC
1 TAAACTTC-CAAAAATTACATTTTTACCCC
* *
29791969 TCGAACTTCCAAAAATTCCA-TTTT-----
1 T-AAACTTCCAAAAATTACATTTTTACCCC
* * ** *
29791993 T-AAC-CCCAAAAATTCCATTTTACCCCT
1 TAAACTTCCAAAAATTACATTTTTACCCC
* ** * * ** **
29792020 GAACTTCCCAAAATTAT-GTTTTTACCCCC
1 TAAACTTCCAAAAAT-TACATTTTTACCCC
* *
29792049 G-AACTTCCAAAAATTACATTTTTAACCC
1 TAAACTTCCAAAAATTACATTTTTACCCC
* ***
29792077 TAAAATTTTTGAAAATTACA-TTTTA-CCC
1 T-AAACTTCCAAAAATTACATTTTTACCCC
* *
29792105 TAAACTTCTAAAAATTCCATTTTTGACCCC
1 TAAACTTCCAAAAATTACATTTTT-ACCCC
* *
29792135 -GAACTTCCAAAAATTCCATTTTTGACCCC
1 TAAACTTCCAAAAATTACATTTTT-ACCCC
29792164 TAAACT
1 TAAACT
29792170 CTCGAAATTA
Statistics
Matches: 275, Mismatches: 51, Indels: 48
0.74 0.14 0.13
Matches are distributed among these distances:
21 12 0.04
22 6 0.02
24 1 0.00
27 15 0.05
28 29 0.11
29 100 0.36
30 84 0.31
31 23 0.08
32 4 0.01
33 1 0.00
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
TAAACTTCCAAAAATTACATTTTTACCCC
Found at i:29791903 original size:59 final size:59
Alignment explanation
Indices: 29791791--29792186 Score: 249
Period size: 59 Copynumber: 6.9 Consensus size: 59
29791781 GGAGGTCCTT
* * * *
29791791 AAACTGTCCAAAAATTATATTTTAACCCC-ACGAACTTCTCCAAAATTACATTTTTGACCTCA
1 AAACT-TCCAAAAATTACATTTTTACCCCTA--AACATCTCAAAAATTACATTTTT-ACCTCA
* * * *
29791853 AAACTTCAAAAAATTACATTTTTGCCCCTGAACATC-CAAAAATTACATTTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTTACCCCTAAACATCTCAAAAATTACATTTTT-ACCTCA
* *
29791912 AAACTTCCAAAAATTACATTTTTACCCCTAAACTTCTCCAAAATTACATTTTTACCCTC-
1 AAACTTCCAAAAATTACATTTTTACCCCTAAACATCTCAAAAATTACATTTTTA-CCTCA
* * * * * *
29791971 GAACTTCCAAAAATTCCA-TTTT-----T-AAC--CCCAAAAATTCCA-TTTTACCCCT
1 AAACTTCCAAAAATTACATTTTTACCCCTAAACATCTCAAAAATTACATTTTTACCTCA
* * ** ** *
29792020 GAACTTCCCAAAATTATGTTTTTACCCCCGAACTTC-CAAAAATTACATTTTTAACC-CTA
1 AAACTTCCAAAAATTACATTTTTACCCCTAAACATCTCAAAAATTACATTTTT-ACCTC-A
* *** * * *
29792079 AAATTTTTGAAAATTACA-TTTTA-CCCTAAACTTCT-AAAAATTCCATTTTTGACC-CC
1 AAACTTCCAAAAATTACATTTTTACCCCTAAACATCTCAAAAATTACATTTTT-ACCTCA
* * *
29792135 GAACTTCCAAAAATTCCATTTTTGACCCCTAAAC-TCTC-GAAATTACCATTTT
1 AAACTTCCAAAAATTACATTTTT-ACCCCTAAACATCTCAAAAATTA-CATTTT
29792187 ACCCCCGGAT
Statistics
Matches: 264, Mismatches: 48, Indels: 47
0.74 0.13 0.13
Matches are distributed among these distances:
48 3 0.01
49 19 0.07
50 14 0.05
52 3 0.01
53 1 0.00
56 15 0.06
57 41 0.16
58 24 0.09
59 97 0.37
60 23 0.09
61 19 0.07
62 5 0.02
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTACATTTTTACCCCTAAACATCTCAAAAATTACATTTTTACCTCA
Found at i:29792013 original size:20 final size:20
Alignment explanation
Indices: 29791977--29792018 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
29791967 CCTCGAACTT
29791977 CCAAAAATTCCATTTTTAACC
1 CCAAAAATTCCATTTTT-ACC
29791998 CCAAAAATTCCA-TTTTACC
1 CCAAAAATTCCATTTTTACC
29792017 CC
1 CC
29792019 TGAACTTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 12 0.57
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (20 bp):
CCAAAAATTCCATTTTTACC
Found at i:29792052 original size:78 final size:80
Alignment explanation
Indices: 29791918--29792163 Score: 261
Period size: 86 Copynumber: 3.0 Consensus size: 80
29791908 CCCAAAACTT
*
29791918 CCAAAAATTACATTTTTACCCCTAAACTTCTCCAAAATTACATTTTTACCCTCGAACTTCCAAAA
1 CCAAAAATTACATTTTTACCCCTAAACTTCTCCAAAATTACATTTTTACCCCCGAACTTCCAAAA
*
29791983 ATTCCATTTTTAACC
66 ATTACATTTTTAACC
* * **
29791998 CCAAAAATTCCA-TTTTACCCCTGAACTTC-CCAAAATTATGTTTTTACCCCCGAACTTCCAAAA
1 CCAAAAATTACATTTTTACCCCTAAACTTCTCCAAAATTACATTTTTACCCCCGAACTTCCAAAA
29792061 ATTACATTTTTAACC
66 ATTACATTTTTAACC
* * *
29792076 CTAAAATTTTTGAAAATTACA-TTTTA-CCCTAAACTTCT-AAAAATTCCATTTTTGA-CCCCGA
1 C---CA------AAAATTACATTTTTACCCCTAAACTTCTCCAAAATTACATTTTT-ACCCCCGA
* *
29792137 ACTTCCAAAAATTCCATTTTTGACC
56 ACTTCCAAAAATTACATTTTTAACC
29792162 CC
1 CC
29792164 TAAACTCTCG
Statistics
Matches: 139, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
78 46 0.33
79 16 0.12
80 11 0.08
81 1 0.01
86 51 0.37
87 14 0.10
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (80 bp):
CCAAAAATTACATTTTTACCCCTAAACTTCTCCAAAATTACATTTTTACCCCCGAACTTCCAAAA
ATTACATTTTTAACC
Found at i:29792092 original size:108 final size:110
Alignment explanation
Indices: 29791888--29792190 Score: 260
Period size: 108 Copynumber: 2.7 Consensus size: 110
29791878 CCCTGAACAT
* *
29791888 CCAAAAATTACATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCCTAAACTTCTCCAA
1 CCAAAAATTACATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCCCAAACTTCTCAAA
** *
29791953 AATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACC
66 AATTACATTTTTACCCTAAAACTTCCAAAAATTACATTTTTAACC
* ** * ** *
29791998 CCAAAAATTCCA-TTTT-ACCCCTGAACTTCCCAAAATTATGTTTTTACCCCCGAACTTC-CAAA
1 CCAAAAATTACATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCCCAAACTTCTCAAA
* *** *
29792060 AATTACATTTTTAACCCTAAAATTTTTGAAAATTACATTTTACCCTAAACTT
66 AATTACATTTTT-ACCCTAAAACTTCCAAAAATTACATTTT----T-AAC-C
* * * * * * *
29792112 CTAAAAATTCCATTTTTGACCCC-GAACTTCCAAAAATTCCATTTTTGACCCCTAAAC-TCTC-G
1 CCAAAAATTACATTTTTAACCCCAAAACTTCCAAAAATTACATTTTT-ACCCCCAAACTTCTCAA
29792174 AAATTACCA-TTTTACCC
65 AAATTA-CATTTTTACCC
29792191 CCGGATGTCC
Statistics
Matches: 156, Mismatches: 25, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
107 15 0.10
108 56 0.36
109 4 0.03
110 11 0.07
112 1 0.01
113 3 0.02
114 15 0.10
115 35 0.22
116 16 0.10
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (110 bp):
CCAAAAATTACATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCCCAAACTTCTCAAA
AATTACATTTTTACCCTAAAACTTCCAAAAATTACATTTTTAACC
Found at i:29792185 original size:86 final size:87
Alignment explanation
Indices: 29792001--29792190 Score: 221
Period size: 86 Copynumber: 2.2 Consensus size: 87
29791991 TTTAACCCCA
* * *
29792001 AAAATT-CCATTTTACCCCTGAACTTCCCAAAATTATGTTTTTACCCCCGAACTTCCAAAAATTA
1 AAAATTACCATTTTA-CCCTAAACTTCCAAAAATTATGTTTTGACCCCCGAACTTCCAAAAATTA
* * *
29792065 CATTTTTAACCCTAAAATTTTTG
65 CATTTTTAACCCTAAAACTCTCG
*
29792088 AAAATTA-CATTTTACCCTAAACTTCTAAAAATTCCAT-TTTTGA-CCCCGAACTTCCAAAAATT
1 AAAATTACCATTTTACCCTAAACTTCCAAAAATT--ATGTTTTGACCCCCGAACTTCCAAAAATT
* *
29792150 CCATTTTTGACCCCT-AAACTCTCG
64 ACATTTTT-AACCCTAAAACTCTCG
29792174 -AAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
29792191 CCGGATGTCC
Statistics
Matches: 89, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
85 6 0.07
86 58 0.65
87 23 0.26
88 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (87 bp):
AAAATTACCATTTTACCCTAAACTTCCAAAAATTATGTTTTGACCCCCGAACTTCCAAAAATTAC
ATTTTTAACCCTAAAACTCTCG
Found at i:29792186 original size:30 final size:29
Alignment explanation
Indices: 29792102--29792186 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
29792092 TTACATTTTA
*
29792102 CCCTAAACTTCTAAAAATTCCATTTTTGAC
1 CCCTAAAC-TCTCAAAATTCCATTTTTGAC
*
29792132 CCC-GAACT-TCCAAAAATTCCATTTTTGAC
1 CCCTAAACTCT-C-AAAATTCCATTTTTGAC
*
29792161 CCCTAAACTCTCGAAATTACCATTTT
1 CCCTAAACTCTCAAAATT-CCATTTT
29792187 ACCCCCGGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
27 1 0.02
28 1 0.02
29 28 0.61
30 15 0.33
31 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (29 bp):
CCCTAAACTCTCAAAATTCCATTTTTGAC
Found at i:29792483 original size:144 final size:143
Alignment explanation
Indices: 29792234--29792492 Score: 405
Period size: 144 Copynumber: 1.8 Consensus size: 143
29792224 TTTTTTTCTA
** * *
29792234 AAAATTACTGTTTTACCCTCAAGTGTCTAAAATGTCATTCTAACCCTAAATTTTCTAAAATTACC
1 AAAATTACCATTTTACCCTCAAGTGTCTAAAATATCATTCTAACCCTAAATTTTCCAAAATTACC
29792299 ATTTTGCCCCCGAGAGTCCAAAATTACCATTTTGCCCTTGGACATCCAAAAAGTCCCGTTTTGAT
66 ATTTTGCCCCCGAGAGTCCAAAATTACCATTTTGCCCTTGGACATCCAAAAAGTCCCGTTTTGAT
29792364 CCCGATTCGTTTG
131 CCCGATTCGTTTG
* *
29792377 AAAATTACCATTTTACCCTTAAGTGTCTAAAATATCATTTTTTAACCCTAAATTTTTCCAAAATT
1 AAAATTACCATTTTACCCTCAAGTGTCTAAAATATCA--TTCTAACCCTAAA-TTTTCCAAAATT
* *
29792442 ATCA-TTT-CCCCCGAGAGTCCAAAATTACCATTTTGCCCTTGGGCATCCAAA
63 ACCATTTTGCCCCCGAGAGTCCAAAATTACCATTTTGCCCTTGGACATCCAAA
29792493 GTCTCATTTT
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
143 33 0.31
144 43 0.41
145 15 0.14
146 14 0.13
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.35
Consensus pattern (143 bp):
AAAATTACCATTTTACCCTCAAGTGTCTAAAATATCATTCTAACCCTAAATTTTCCAAAATTACC
ATTTTGCCCCCGAGAGTCCAAAATTACCATTTTGCCCTTGGACATCCAAAAAGTCCCGTTTTGAT
CCCGATTCGTTTG
Found at i:29800802 original size:51 final size:52
Alignment explanation
Indices: 29800726--29800849 Score: 175
Period size: 51 Copynumber: 2.5 Consensus size: 52
29800716 GCGTATTTGT
* *
29800726 TACTCACGATGACACAAAGTAATCGGACCT-TTAATTCGTAAAGAATTCATA
1 TACTCACGATGACACAAAGTAATCGGACCTCATAATCCGTAAAGAATTCATA
* * *
29800777 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATA
1 TACTCACGATGACACAAAGTAATCGGACCTCATAATCCGTAAAGAATTCATA
29800829 TACTCACGAT-A-ACAAA-TAATC
1 TACTCACGATGACACAAAGTAATC
29800850 ATTAGACCTA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
49 4 0.06
50 4 0.06
51 29 0.45
52 28 0.43
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (52 bp):
TACTCACGATGACACAAAGTAATCGGACCTCATAATCCGTAAAGAATTCATA
Found at i:29800858 original size:52 final size:52
Alignment explanation
Indices: 29800757--29800858 Score: 141
Period size: 52 Copynumber: 2.0 Consensus size: 52
29800747 ATCGGACCTT
* * * * *
29800757 TAATTCGTAAAGAATTCATATACTCACGATGACACATAGTCATCGGACCTCA
1 TAATCCGTAAAGAATTCATATACTCACGATAACAAATAATCATCAGACCTCA
* *
29800809 TAATCCGTAAAGGATTCATATACTCACGATAACAAATAATCATTAGACCT
1 TAATCCGTAAAGAATTCATATACTCACGATAACAAATAATCATCAGACCT
29800859 ATTTCATTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (52 bp):
TAATCCGTAAAGAATTCATATACTCACGATAACAAATAATCATCAGACCTCA
Found at i:29806112 original size:31 final size:28
Alignment explanation
Indices: 29806070--29806128 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 28
29806060 TATGGTTTAA
29806070 TGTGCATTTATATACATG-AACTTTGATTT
1 TGTGCA-TT-TATACATGAAACTTTGATTT
*
29806099 TGTGCAATATTATACATGAAATTTTGATTT
1 TGTGC-AT-TTATACATGAAACTTTGATTT
29806129 AATCCAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (28 bp):
TGTGCATTTATACATGAAACTTTGATTT
Found at i:29807762 original size:30 final size:30
Alignment explanation
Indices: 29807707--29807764 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29807697 CGAAAAATTA
* * *
29807707 AAAAAAATTACATTAATAGGTCATTTTTTG
1 AAAAAAATTACATGAATAAGCCATTTTTTG
*
29807737 AAAAAAATTACGTGAATAAGCCATTTTT
1 AAAAAAATTACATGAATAAGCCATTTTT
29807765 ACGAAAATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (30 bp):
AAAAAAATTACATGAATAAGCCATTTTTTG
Found at i:29807771 original size:31 final size:30
Alignment explanation
Indices: 29807707--29807771 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
29807697 CGAAAAATTA
* * * *
29807707 AAAAAAATTACATTAATAGGTCATTTTTTG
1 AAAAAAATTACATGAATAAGCCATTTTTCG
*
29807737 AAAAAAATTACGTGAATAAGCCATTTTTACG
1 AAAAAAATTACATGAATAAGCCATTTTT-CG
29807768 AAAA
1 AAAA
29807772 TGCATCCAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (30 bp):
AAAAAAATTACATGAATAAGCCATTTTTCG
Found at i:29810795 original size:34 final size:34
Alignment explanation
Indices: 29810752--29810824 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
29810742 GCATCTTGTC
29810752 AAGTCTCGAGACATACATTTCAGGGACAATTTTT
1 AAGTCTCGAGACATACATTTCAGGGACAATTTTT
29810786 AAGTCTCGAGACATACATTTCAGGGACAATTTTT
1 AAGTCTCGAGACATACATTTCAGGGACAATTTTT
29810820 AAGTC
1 AAGTC
29810825 CCAAATTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (34 bp):
AAGTCTCGAGACATACATTTCAGGGACAATTTTT
Found at i:29811727 original size:22 final size:22
Alignment explanation
Indices: 29811649--29811721 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
29811639 GTTATGCGGC
*
29811649 CCCTTAGAGAATAATACACGAA
1 CCCTTAGAGAATAATAAACGAA
* ** * *
29811671 CCCTTAGTGAATGTTAAGCGAT
1 CCCTTAGAGAATAATAAACGAA
**
29811693 CCCTTAGAGAATAATATTCGAA
1 CCCTTAGAGAATAATAAACGAA
29811715 CCCTTAG
1 CCCTTAG
29811722 TAAATATTAG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (22 bp):
CCCTTAGAGAATAATAAACGAA
Found at i:29811738 original size:44 final size:44
Alignment explanation
Indices: 29811649--29811742 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
29811639 GTTATGCGGC
* * *
29811649 CCCTTAGAGAATAATACACGAACCCTTAGTGAATGTTAAGCGAT
1 CCCTTAGAGAATAATACACGAACCCTTAGTAAATATTAAGAGAT
**
29811693 CCCTTAGAGAATAATATTCGAACCCTTAGTAAATATT-AGAAGAT
1 CCCTTAGAGAATAATACACGAACCCTTAGTAAATATTAAG-AGAT
29811737 CCCTTA
1 CCCTTA
29811743 ATACATAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.05
44 42 0.95
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (44 bp):
CCCTTAGAGAATAATACACGAACCCTTAGTAAATATTAAGAGAT
Found at i:29811759 original size:44 final size:44
Alignment explanation
Indices: 29811649--29811761 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
29811639 GTTATGCGGC
** * * *
29811649 CCCTTAGAGAATAATACACGAACCCTTAGTGAATGTTAAGCGAT
1 CCCTTAGAGAATAATATGCGAACCCTTAGTAAATATTAAGAGAT
*
29811693 CCCTTAGAGAATAATATTCGAACCCTTAGTAAATATT-AGAAGAT
1 CCCTTAGAGAATAATATGCGAACCCTTAGTAAATATTAAG-AGAT
* *
29811737 CCCTTA-ATACATAGTATGCGAACCC
1 CCCTTAGAGA-ATAATATGCGAACCC
29811762 CCCATGTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 4 0.07
44 55 0.93
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (44 bp):
CCCTTAGAGAATAATATGCGAACCCTTAGTAAATATTAAGAGAT
Done.