Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 21
Found at i:3409032 original size:29 final size:29
Alignment explanation
Indices: 3408990--3409095 Score: 176
Period size: 29 Copynumber: 3.7 Consensus size: 29
3408980 CGTAGACCGG
*
3408990 GGTGCTATTTTAGTAATTAATTTGAAATA
1 GGTGCTATTTTAGTAATTAATTCGAAATA
* *
3409019 GGTGCTATTTTAGTAATTAATTCAAAATG
1 GGTGCTATTTTAGTAATTAATTCGAAATA
*
3409048 GGTGTTATTTTAGTAATTAATTCGAAATA
1 GGTGCTATTTTAGTAATTAATTCGAAATA
3409077 GGTGCTATTTTAGTAATTA
1 GGTGCTATTTTAGTAATTA
3409096 TTTTTAAAAG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (29 bp):
GGTGCTATTTTAGTAATTAATTCGAAATA
Found at i:3409110 original size:29 final size:29
Alignment explanation
Indices: 3408990--3409115 Score: 173
Period size: 29 Copynumber: 4.3 Consensus size: 29
3408980 CGTAGACCGG
3408990 GGTGCTATTTTAGTAATTAATTTGAAATA
1 GGTGCTATTTTAGTAATTAATTTGAAATA
** *
3409019 GGTGCTATTTTAGTAATTAATTCAAAATG
1 GGTGCTATTTTAGTAATTAATTTGAAATA
* *
3409048 GGTGTTATTTTAGTAATTAATTCGAAATA
1 GGTGCTATTTTAGTAATTAATTTGAAATA
* *
3409077 GGTGCTATTTTAGTAATTATTTTTAAA-A
1 GGTGCTATTTTAGTAATTAATTTGAAATA
3409105 GTGTGCTATTT
1 G-GTGCTATTT
3409116 CTCTAAAATA
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
28 2 0.02
29 84 0.98
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (29 bp):
GGTGCTATTTTAGTAATTAATTTGAAATA
Found at i:3410387 original size:17 final size:19
Alignment explanation
Indices: 3410362--3410400 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3410352 ATATATGTAT
3410362 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
3410380 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
3410399 TA
1 TA
3410401 AGTTGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:3416157 original size:7 final size:7
Alignment explanation
Indices: 3416138--3416172 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
3416128 CTGGCCCGAT
3416138 CGTTGACC
1 CGTTGA-C
3416146 CGTTGAC
1 CGTTGAC
3416153 CGTTGAC
1 CGTTGAC
3416160 CGTTGAC
1 CGTTGAC
*
3416167 TGTTGA
1 CGTTGA
3416173 TCGGGTGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.14, C:0.26, G:0.29, T:0.31
Consensus pattern (7 bp):
CGTTGAC
Found at i:3416220 original size:29 final size:29
Alignment explanation
Indices: 3416176--3416306 Score: 176
Period size: 29 Copynumber: 4.6 Consensus size: 29
3416166 CTGTTGATCG
*
3416176 GGTGCTATTTTAGTAATTAATTCGAAATA
1 GGTGCTATTTTAGTAATTAATTTGAAATA
* *
3416205 GATGCTATTTTAGTAATTAATTTGAAA-G
1 GGTGCTATTTTAGTAATTAATTTGAAATA
3416233 GGTGCTATTTTAGTAATTAATTTGAAATA
1 GGTGCTATTTTAGTAATTAATTTGAAATA
* *
3416262 GGTGCTATTTTAGTAATT-ATTTTAAAAA
1 GGTGCTATTTTAGTAATTAATTTGAAATA
* *
3416290 GGGTGTTATTTTTGTAA
1 -GGTGCTATTTTAGTAA
3416307 AATGGTTGAT
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
28 34 0.37
29 57 0.63
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (29 bp):
GGTGCTATTTTAGTAATTAATTTGAAATA
Found at i:3416268 original size:57 final size:58
Alignment explanation
Indices: 3416175--3416306 Score: 203
Period size: 57 Copynumber: 2.3 Consensus size: 58
3416165 ACTGTTGATC
*
3416175 GGGTGCTATTTTAGTAATTAATTCGAAATAGATGCTATTTTAGTAATTAATTT-GAAA
1 GGGTGCTATTTTAGTAATTAATTCGAAATAGATGCTATTTTAGTAATTAATTTAAAAA
* * *
3416232 GGGTGCTATTTTAGTAATTAATTTGAAATAGGTGCTATTTTAGTAATTATTTTAAAAA
1 GGGTGCTATTTTAGTAATTAATTCGAAATAGATGCTATTTTAGTAATTAATTTAAAAA
* *
3416290 GGGTGTTATTTTTGTAA
1 GGGTGCTATTTTAGTAA
3416307 AATGGTTGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
57 50 0.74
58 18 0.26
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.45
Consensus pattern (58 bp):
GGGTGCTATTTTAGTAATTAATTCGAAATAGATGCTATTTTAGTAATTAATTTAAAAA
Found at i:3417645 original size:17 final size:19
Alignment explanation
Indices: 3417620--3417658 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3417610 ATATCTGTAT
3417620 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
3417638 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
3417657 TA
1 TA
3417659 AGTTGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:3418548 original size:24 final size:24
Alignment explanation
Indices: 3418521--3418570 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3418511 TGGTGGTTGA
3418521 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
3418545 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
3418569 TT
1 TT
3418571 CGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:3423332 original size:24 final size:24
Alignment explanation
Indices: 3423305--3423354 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3423295 TGGTGGTTGA
3423305 TTTAATGGTTGT-TTGAACTTTATT
1 TTTAATGG-TGTATTGAACTTTATT
* *
3423329 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTGAACTTTATT
3423353 TT
1 TT
3423355 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTGAACTTTATT
Found at i:3428209 original size:24 final size:24
Alignment explanation
Indices: 3428180--3428229 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3428170 TGGTGGTTGA
3428180 TTTAATGGTTGT-TTAAACTTTATT
1 TTTAATGG-TGTATTAAACTTTATT
* *
3428204 TTTAATGGTGTATTTAAGTTTATT
1 TTTAATGGTGTATTAAACTTTATT
3428228 TT
1 TT
3428230 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTGTATTAAACTTTATT
Found at i:3434254 original size:12 final size:12
Alignment explanation
Indices: 3434237--3434261 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3434227 CGCTTGGTAC
3434237 CTCCCACTTTCA
1 CTCCCACTTTCA
3434249 CTCCCACTTTCA
1 CTCCCACTTTCA
3434261 C
1 C
3434262 AATCCCTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (12 bp):
CTCCCACTTTCA
Found at i:3435337 original size:26 final size:25
Alignment explanation
Indices: 3435299--3435375 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 25
3435289 TTTATTTTCG
3435299 CCCT-TAAAATTTTATAATTTTACTC
1 CCCTCTAAAATTTTATAA-TTTACTC
* *
3435324 CCCTCTAAAGTTTTATAAGTTTGCTC
1 CCCTCTAAAATTTTATAA-TTTACTC
* *
3435350 TCCTCTAAAATTTTATAAGTTACTC
1 CCCTCTAAAATTTTATAATTTACTC
3435375 C
1 C
3435376 TAACATAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 9 0.21
26 34 0.79
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (25 bp):
CCCTCTAAAATTTTATAATTTACTC
Found at i:3436803 original size:19 final size:19
Alignment explanation
Indices: 3436781--3436821 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
3436771 GTTCACAAGG
3436781 AACTCAAGCAAAGGATCAA
1 AACTCAAGCAAAGGATCAA
3436800 AACTCAAGCAAAGGATCAA
1 AACTCAAGCAAAGGATCAA
3436819 AAC
1 AAC
3436822 ACTTTACCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.22, G:0.15, T:0.10
Consensus pattern (19 bp):
AACTCAAGCAAAGGATCAA
Found at i:3438531 original size:22 final size:22
Alignment explanation
Indices: 3438503--3438544 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3438493 AATTTTTTGT
3438503 TAGGGTGATA-TTTGTGTAAAAC
1 TAGGGTGATAGTTT-TGTAAAAC
*
3438525 TAGGGTGCTAGTTTTGTAAA
1 TAGGGTGATAGTTTTGTAAA
3438545 TATTGTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.38
Consensus pattern (22 bp):
TAGGGTGATAGTTTTGTAAAAC
Found at i:3440472 original size:2 final size:2
Alignment explanation
Indices: 3440465--3440574 Score: 83
Period size: 2 Copynumber: 59.0 Consensus size: 2
3440455 TCGGGTCGGG
* * * *
3440465 TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
3440505 TA TA TA T- TT TA -A TT TA AA T- TA AA TT TA T- TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3440541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3440575 AAATAATTAT
Statistics
Matches: 83, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
1 8 0.10
2 75 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3440520 original size:38 final size:37
Alignment explanation
Indices: 3440465--3440555 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 37
3440455 TCGGGTCGGG
3440465 TATATATATA-TATATTTAAATTAAATATATAAATAT
1 TATATATATATTATATTTAAATTAAATATATAAATAT
* * *
3440501 TATATATATATTTTAATTTAAATTAAATTTATTAATAT
1 TATATATATATTAT-ATTTAAATTAAATATATAAATAT
3440539 TATATATATATATATAT
1 TATATATATAT-TATAT
3440556 ATATATATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 10 0.21
37 2 0.04
38 34 0.71
39 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TATATATATATTATATTTAAATTAAATATATAAATAT
Found at i:3448389 original size:438 final size:438
Alignment explanation
Indices: 3447574--3448453 Score: 1742
Period size: 438 Copynumber: 2.0 Consensus size: 438
3447564 ATTTTGGGTC
3447574 CACTGAGAAAATTAAGGAGATTTAAGGACTTTAAGGGTAAATTGCCCTTCCTTGGTTTTAGGATG
1 CACTGAGAAAATTAAGGAGATTTAAGGACTTTAAGGGTAAATTGCCCTTCCTTGGTTTTAGGATG
3447639 TTCTAAAGTCCAAATGAGGATTCATATTGTTTTAAGTGAATGTTCATTTTATTCTATTCTATTTT
66 TTCTAAAGTCCAAATGAGGATTCATATTGTTTTAAGTGAATGTTCATTTTATTCTATTCTATTTT
3447704 ATGTTTAATAATCTGGAAAATGAAGAAACATGTTTGAAAGATATTTTTGGGATGACTTTGTTTTA
131 ATGTTTAATAATCTGGAAAATGAAGAAACATGTTTGAAAGATATTTTTGGGATGACTTTGTTTTA
3447769 ACAGAGGAGTTGGAAGCAATCTGATTGACTTAAAAAAATTATTCTTCCCTATCTTGACCCAGAGC
196 ACAGAGGAGTTGGAAGCAATCTGATTGACTTAAAAAAATTATTCTTCCCTATCTTGACCCAGAGC
3447834 ATGAACCACTGTGTTCATCGGGAATAATAGAGAAAACCAACACCGTAAATCAGTTTAATATCAAA
261 ATGAACCACTGTGTTCATCGGGAATAATAGAGAAAACCAACACCGTAAATCAGTTTAATATCAAA
3447899 GTAATAAACTGAAACTTGTAAACTATACCCAACCATCCTATCATCCTTAGATTAACGTTCCAGTG
326 GTAATAAACTGAAACTTGTAAACTATACCCAACCATCCTATCATCCTTAGATTAACGTTCCAGTG
*
3447964 AAACCCCCATTAAGTCTAGCGACCGACGATAAAAGCGATAATCATAGT
391 AAAACCCCATTAAGTCTAGCGACCGACGATAAAAGCGATAATCATAGT
3448012 CACTGAGAAAATTAAGGAGATTTAAGGACTTTAAGGGTAAATTGCCCTTCCTTGGTTTTAGGATG
1 CACTGAGAAAATTAAGGAGATTTAAGGACTTTAAGGGTAAATTGCCCTTCCTTGGTTTTAGGATG
3448077 TTCTAAAGTCCAAATGAGGATTCATATTGTTTTAAGTGAATGTTCATTTTATTCTATTCTATTTT
66 TTCTAAAGTCCAAATGAGGATTCATATTGTTTTAAGTGAATGTTCATTTTATTCTATTCTATTTT
*
3448142 ATGTTTAATAATCTGGAAAATGAAGAAACATGTTTGAAAGCTATTTTTGGGATGACTTTGTTTTA
131 ATGTTTAATAATCTGGAAAATGAAGAAACATGTTTGAAAGATATTTTTGGGATGACTTTGTTTTA
3448207 ACAGAGGAGTTGGAAGCAATCTGATTGACTTAAAAAAATTATTCTTCCCTATCTTGACCCAGAGC
196 ACAGAGGAGTTGGAAGCAATCTGATTGACTTAAAAAAATTATTCTTCCCTATCTTGACCCAGAGC
3448272 ATGAACCACTGTGTTCATCGGGAATAATAGAGAAAACCAACACCGTAAATCAGTTTAATATCAAA
261 ATGAACCACTGTGTTCATCGGGAATAATAGAGAAAACCAACACCGTAAATCAGTTTAATATCAAA
3448337 GTAATAAACTGAAACTTGTAAACTATACCCAACCATCCTATCATCCTTAGATTAACGTTCCAGTG
326 GTAATAAACTGAAACTTGTAAACTATACCCAACCATCCTATCATCCTTAGATTAACGTTCCAGTG
3448402 AAAACCCCATTAAGTCTAGCGACCGACGATAAAAGCGATAATCATAGT
391 AAAACCCCATTAAGTCTAGCGACCGACGATAAAAGCGATAATCATAGT
3448450 CACT
1 CACT
3448454 CATATCCTTC
Statistics
Matches: 440, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
438 440 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (438 bp):
CACTGAGAAAATTAAGGAGATTTAAGGACTTTAAGGGTAAATTGCCCTTCCTTGGTTTTAGGATG
TTCTAAAGTCCAAATGAGGATTCATATTGTTTTAAGTGAATGTTCATTTTATTCTATTCTATTTT
ATGTTTAATAATCTGGAAAATGAAGAAACATGTTTGAAAGATATTTTTGGGATGACTTTGTTTTA
ACAGAGGAGTTGGAAGCAATCTGATTGACTTAAAAAAATTATTCTTCCCTATCTTGACCCAGAGC
ATGAACCACTGTGTTCATCGGGAATAATAGAGAAAACCAACACCGTAAATCAGTTTAATATCAAA
GTAATAAACTGAAACTTGTAAACTATACCCAACCATCCTATCATCCTTAGATTAACGTTCCAGTG
AAAACCCCATTAAGTCTAGCGACCGACGATAAAAGCGATAATCATAGT
Found at i:3450592 original size:33 final size:33
Alignment explanation
Indices: 3450544--3450613 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
3450534 TTTTGTAAAG
* * * *
3450544 GGGAAAGGTTCTAGTTGATCCCGTGAAAAGCTA
1 GGGAAAGGTTATAGTTGAGCCCATGAAAAACTA
* *
3450577 GGGAAATGTTATAGTTTAGCCCATGAAAAACTA
1 GGGAAAGGTTATAGTTGAGCCCATGAAAAACTA
3450610 GGGA
1 GGGA
3450614 GTTTGTAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTATAGTTGAGCCCATGAAAAACTA
Found at i:3453339 original size:18 final size:21
Alignment explanation
Indices: 3453316--3453366 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
3453306 ATATTTTTCC
3453316 AACAATTGGTA-AC-TTT-TT
1 AACAATTGGTATACTTTTGTT
* *
3453334 AACAATTGATATCCTTTTGTT
1 AACAATTGGTATACTTTTGTT
3453355 AACAATTGGTAT
1 AACAATTGGTAT
3453367 CAAAGGGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.37
19 1 0.04
20 3 0.11
21 13 0.48
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (21 bp):
AACAATTGGTATACTTTTGTT
Found at i:3453658 original size:36 final size:36
Alignment explanation
Indices: 3453618--3453686 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
3453608 TCCAAAAAGG
* * *
3453618 GTACCAGTAC-CCCTATGAGTGTATCCATACACTGGT
1 GTACCAATACACCCTA-CAGTGTATCAATACACTGGT
3453654 GTACCAATACACCCTACAGTGTATCAATACACT
1 GTACCAATACACCCTACAGTGTATCAATACACT
3453687 CTGGCTGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 24 0.83
37 5 0.17
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.26
Consensus pattern (36 bp):
GTACCAATACACCCTACAGTGTATCAATACACTGGT
Found at i:3454075 original size:33 final size:33
Alignment explanation
Indices: 3454038--3454108 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
3454028 TCATTGTAAA
* *
3454038 AGGGAAAGGTTATAGTTGATCCCGTGAAAAGCT
1 AGGGAAAGGTTATAGTTGATCCCATGAAAAACT
* * *
3454071 AGGGAAAGGTTCTAGTTTATTCCATGAAAAACT
1 AGGGAAAGGTTATAGTTGATCCCATGAAAAACT
3454104 AGGGA
1 AGGGA
3454109 GTTTGTAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.25
Consensus pattern (33 bp):
AGGGAAAGGTTATAGTTGATCCCATGAAAAACT
Found at i:3462706 original size:103 final size:105
Alignment explanation
Indices: 3462574--3462781 Score: 314
Period size: 103 Copynumber: 2.0 Consensus size: 105
3462564 CATGTATCAA
*
3462574 AACATTTAATGATTATATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
1 AACATTTAATGATTACATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
*
3462639 GCCA-TTTTAACACACA-A-AATTATTATATTACACGTGAT
66 GCCACTTTT-ACACACATATAATTATTATATTACACATGAT
* * * **
3462677 AACATTTAATGATTCCATATTAAAGATATATATAATAAGATTGTATATATAATATTAAATGTAAA
1 AACATTTAATGATTACATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
*
3462742 GCCACTTTTGCACACATATAATTATTATATTACACATGAT
66 GCCACTTTTACACACATATAATTATTATATTACACATGAT
3462782 TAAAAAGCAT
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
103 69 0.73
104 5 0.05
105 20 0.21
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (105 bp):
AACATTTAATGATTACATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
GCCACTTTTACACACATATAATTATTATATTACACATGAT
Found at i:3463899 original size:3 final size:3
Alignment explanation
Indices: 3463891--3463939 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
3463881 TGTAAAATAC
3463891 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3463939 A
1 A
3463940 TTAAAAGACG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3464462 original size:111 final size:111
Alignment explanation
Indices: 3464098--3465107 Score: 1358
Period size: 111 Copynumber: 9.1 Consensus size: 111
3464088 GCTGTCACTC
* * *
3464098 AGGGAATATCAGATCT-GGAGATGTTGATTCATTGAATCAGAGTAGACTTGTTCCACTGTCACTC
1 AGGGAATATCAGATCTGGGAGA-GTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTC
*
3464162 AGGGAATATCAAATCTTGAAAGAGAGAGATCTGTTCCGCTTCCTCTG
65 AGGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
* * * *
3464209 AGGGAATATTAGATATGGGAGAGTTGATCCATTGAATC-GGGCAGATTTGTTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
*
3464273 GGGAATATCAAATCTTGAAAGAAAGAGAGATCTGTTCCGCTTCCTTTG
66 GGGAATATCAAATCTTGAAAG-AA-AGAGATCTGTTCCGCTTCCTCTG
* * * * *
3464321 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCGGGGCAGATTTGTTCTGTTGTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
*
3464386 GGGAATATCAAATCTTGAAAGAAAGAGATTTGTTCCGCTTCCTCTG
66 GGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
* * *
3464432 AGGGAATATCAGATATGGGAGAGTTGATCCATTGAATCGGGGTAGATTTGTTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* * *
3464497 GGGAATATCAAATCTTG-AA-AAAGAGGAATTTGTTTCGCTTCTTCTG
66 GGGAATATCAAATCTTGAAAGAAAGA-G-ATCTGTTCCGCTTCCTCTG
* * *
3464543 ATGGAATATCAGATCTGGGA-ATGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTATCACTT
1 AGGGAATATCAGATCTGGGAGA-GTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTC
* * *
3464607 AAGGAATATCAAATCTTGAAAGAGATG-GATCTATTCCGCTTCCTCTG
65 AGGGAATATCAAATCTTGAAAGA-AAGAGATCTGTTCCGCTTCCTCTG
* * **
3464654 AGGGAATATCAGATCTGGGAAAG-TGATCCATTGAATCAGGGTAGACTTATTCCATTGTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* * * * *
3464718 GGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCTGCTTCCTCTA
66 GGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
* *
3464764 AGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTATCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* * *
3464829 GGGAATATCGAATCTTGAAAGAGATG-GATCTGTTCCGCTTCTTCTG
66 GGGAATATCAAATCTTGAAAGA-AAGAGATCTGTTCCGCTTCCTCTG
* * * * *
3464875 AGGGAATATCAGATCTGGGAAAGTTGATTCATTGAATCATGGTAGACTTGTTCCACTTTCACTCA
1 AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* * *
3464940 GGGAATATCAAATCTTGAAAGAGAGGGATCTGTTCCACTTCCTCTG
66 GGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
* *
3464986 AGGGAATATCAGATCTGGG-GAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTCTCACTC
1 AGGGAATATCAGATCTGGGAG-AGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTC
* * *
3465050 AGGGAATATCAAATCTTGAAA-AAA-ATGATATGTTCCACTTCTTCTG
65 AGGGAATATCAAATCTTGAAAGAAAGA-GATCTGTTCCGCTTCCTCTG
3465096 AAGGGAATATCA
1 -AGGGAATATCA
3465108 TATAGATGGA
Statistics
Matches: 807, Mismatches: 74, Indels: 36
0.88 0.08 0.04
Matches are distributed among these distances:
109 6 0.01
110 164 0.20
111 519 0.64
112 70 0.09
113 46 0.06
114 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (111 bp):
AGGGAATATCAGATCTGGGAGAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
GGGAATATCAAATCTTGAAAGAAAGAGATCTGTTCCGCTTCCTCTG
Found at i:3464791 original size:332 final size:331
Alignment explanation
Indices: 3464098--3465107 Score: 1440
Period size: 332 Copynumber: 3.0 Consensus size: 331
3464088 GCTGTCACTC
* * * *
3464098 AGGGAATATCAGATCT-GGAGATGTTGATTCATTGAATCAGAGTAGACTTGTTCCACTGTCACTC
1 AGGGAATATCAGATCTGGGA-AAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTC
* * *
3464162 AGGGAATATCAAATCTTGAAAGAGA-GAGATCTGTTCCGCTTCCTCTGAGGGAATATTAGATATG
65 AGGGAATATCAAATCTTGAAAGAGAGGA-ATCTGTTCCGCTTCTTCTGAGGGAATATCAGATCTG
* * *
3464226 GGAGAGTTGATCCATTGAATC-GGGCAGATTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTG
129 GGA-AGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTG
* *
3464290 AAAGAAAGAGAGATCTGTTCCGCTTCCTTTGAGGGAATATCAGATCTGGGAGAGTTGATCCATTG
193 AAAG--AGAG-GATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTG
* * * **
3464355 AATCGGGGCAGATTTGTTCTGTTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGAGATTTGTT
255 AATCAGGGTAGACTTGTTCCATTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGAGATTTGTT
*
3464420 CCGCTTCCTCTG
320 CCGCTTCCTCTA
* * * *
3464432 AGGGAATATCAGATATGGGAGAGTTGATCCATTGAATCGGGGTAGATTTGTTCCGCTGTCACTCA
1 AGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
* * * *
3464497 GGGAATATCAAATCTTGAAAAAGAGGAATTTGTTTCGCTTCTTCTGATGGAATATCAGATCTGGG
66 GGGAATATCAAATCTTGAAAGAGAGGAATCTGTTCCGCTTCTTCTGAGGGAATATCAGATCTGGG
* *
3464562 AATGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTATCACTTAAGGAATATCAAATCTTGAA
131 AA-GTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAA
*
3464627 AGAGATGGATCTATTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAG-TGATCCATTGAATC
195 AGAGA-GGATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATC
* * * *
3464691 AGGGTAGACTTATTCCATTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATTTGTTCTGC
259 AGGGTAGACTTGTTCCATTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGAGATTTGTTCCGC
3464756 TTCCTCTA
324 TTCCTCTA
*
3464764 AGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTATCACTCA
1 AGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
*
3464829 GGGAATATCGAATCTTGAAAGAGATGG-ATCTGTTCCGCTTCTTCTGAGGGAATATCAGATCTGG
66 GGGAATATCAAATCTTGAAAGAGA-GGAATCTGTTCCGCTTCTTCTGAGGGAATATCAGATCTGG
* * * *
3464893 GAAAGTTGATTCATTGAATCATGGTAGACTTGTTCCACTTTCACTCAGGGAATATCAAATCTTGA
130 G-AAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGA
* *
3464958 AAGAGAGGGATCTGTTCCACTTCCTCTGAGGGAATATCAGATCTGGGGAAGTTGATCCATTGAAT
194 AAGAGA-GGATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAAT
* * *
3465023 CAGGGTAGACTTGTTCCACTCTCACTCAGGGAATATCAAATCTTGAAA-AAA-ATGATATGTTCC
258 CAGGGTAGACTTGTTCCATTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGA-GATTTGTTCC
* *
3465086 ACTTCTTCTGA
322 GCTTCCTCT-A
3465097 AGGGAATATCA
1 AGGGAATATCA
3465108 TATAGATGGA
Statistics
Matches: 604, Mismatches: 62, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
332 313 0.52
333 118 0.20
334 126 0.21
335 47 0.08
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (331 bp):
AGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCA
GGGAATATCAAATCTTGAAAGAGAGGAATCTGTTCCGCTTCTTCTGAGGGAATATCAGATCTGGG
AAGTTGATCCATTGAATCAGGGTAGACTTGTTCCGCTATCACTCAGGGAATATCAAATCTTGAAA
GAGAGGATCTGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCCATTGAATCAG
GGTAGACTTGTTCCATTGTCACTCAGGGAATATCAAATCTTGAAAGAAAGAGATTTGTTCCGCTT
CCTCTA
Found at i:3465207 original size:79 final size:79
Alignment explanation
Indices: 3465111--3465279 Score: 196
Period size: 79 Copynumber: 2.1 Consensus size: 79
3465101 AATATCATAT
* * * * ** * *
3465111 AGATGGATTTGCTTCACTATTA-TTCCGTGAAGGTTTAAAATGGCCCGGAGGACTTAATCGTCAT
1 AGATGGATTTGCTTCACTA-CACTTCCGTGAAAGATTAAAATGACCCAAAGGACTTAAGCATCAT
* *
3465175 GCTCGGAAGGCTTAC
65 GCTCGAAAGACTTAC
* * * *
3465190 TGATGGATTTGCTTCACTACACTTCGGTGAAAGATTAAGATGACCCAAAGGATTTAAGCATCATG
1 AGATGGATTTGCTTCACTACACTTCCGTGAAAGATTAAAATGACCCAAAGGACTTAAGCATCATG
3465255 CTCGAAAGACTTAC
66 CTCGAAAGACTTAC
3465269 AGATGGATTTG
1 AGATGGATTTG
3465280 ATCATTATGC
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
78 1 0.01
79 73 0.99
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (79 bp):
AGATGGATTTGCTTCACTACACTTCCGTGAAAGATTAAAATGACCCAAAGGACTTAAGCATCATG
CTCGAAAGACTTAC
Found at i:3465290 original size:34 final size:34
Alignment explanation
Indices: 3465239--3465511 Score: 447
Period size: 34 Copynumber: 8.0 Consensus size: 34
3465229 ATGACCCAAA
* * * *
3465239 GGATTTAAGCATCATGCTCGAAAGACTTACAGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
3465273 GGATTTGATCATTATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
3465307 AGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
3465341 TGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
3465375 GGTTTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
*
3465409 GGATTTGATCATCATGCTCGGAAGACTTATTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
* *
3465443 GGATTTGATCATCATGCTCGTAAGACTTAATGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
3465477 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
3465511 G
1 G
3465512 ACCCGAAGGA
Statistics
Matches: 223, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 223 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (34 bp):
GGATTTGATCATCATGCTCGGAAGACTTACTGAT
Found at i:3468116 original size:11 final size:11
Alignment explanation
Indices: 3468100--3468143 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
3468090 TCAATCTTCC
3468100 TTATTCTTTTT
1 TTATTCTTTTT
3468111 TTATTC-TTTT
1 TTATTCTTTTT
3468121 TT-TTCTTTTT
1 TTATTCTTTTT
*
3468131 TTTTTCTTTTT
1 TTATTCTTTTT
3468142 TT
1 TT
3468144 TTGCGAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 3 0.10
10 12 0.39
11 16 0.52
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (11 bp):
TTATTCTTTTT
Found at i:3468126 original size:20 final size:20
Alignment explanation
Indices: 3468103--3468144 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3468093 ATCTTCCTTA
3468103 TTCTTTTTTTATTCTTTTTT
1 TTCTTTTTTTATTCTTTTTT
*
3468123 TTCTTTTTTTTTTCTTTTTT
1 TTCTTTTTTTATTCTTTTTT
3468143 TT
1 TT
3468145 TGCGAAGTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (20 bp):
TTCTTTTTTTATTCTTTTTT
Found at i:3468145 original size:12 final size:12
Alignment explanation
Indices: 3468106--3468145 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3468096 TTCCTTATTC
* *
3468106 TTTTTTTATTCT
1 TTTTTTTCTTTT
3468118 TTTTTTTC-TTT
1 TTTTTTTCTTTT
3468129 TTTTTTTCTTTT
1 TTTTTTTCTTTT
3468141 TTTTT
1 TTTTT
3468146 GCGAAGTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:3476188 original size:15 final size:15
Alignment explanation
Indices: 3476170--3476234 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
3476160 GACATGTATA
*
3476170 ACATATATCATATTC
1 ACATAGATCATATTC
*
3476185 ACATAGATTATA-TC
1 ACATAGATCATATTC
*
3476199 ACATAGA-CATGTACTC
1 ACATAGATCA--TATTC
*
3476215 ACATAGCTCATATTC
1 ACATAGATCATATTC
3476230 ACATA
1 ACATA
3476235 AGATAGCACA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 1 0.02
14 9 0.22
15 21 0.51
16 8 0.20
17 2 0.05
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (15 bp):
ACATAGATCATATTC
Found at i:3477130 original size:20 final size:20
Alignment explanation
Indices: 3477105--3477146 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3477095 AATTTAACCT
3477105 TTAAATCCAATTCCTAAACA
1 TTAAATCCAATTCCTAAACA
3477125 TTAAATCCAATTCCTAAACA
1 TTAAATCCAATTCCTAAACA
3477145 TT
1 TT
3477147 TCTCATACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAATCCAATTCCTAAACA
Found at i:3477672 original size:14 final size:14
Alignment explanation
Indices: 3477653--3477690 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
3477643 TAGATCCTAC
3477653 GAATCAAAATAATT
1 GAATCAAAATAATT
3477667 GAATCAAAATAATT
1 GAATCAAAATAATT
3477681 GAATCAAAAT
1 GAATCAAAAT
3477691 TCTAATAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (14 bp):
GAATCAAAATAATT
Found at i:3479347 original size:21 final size:22
Alignment explanation
Indices: 3479307--3479350 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3479297 CATATGAAAA
3479307 TTCATTGTACGTCAGTTGATAT
1 TTCATTGTACGTCAGTTGATAT
3479329 TTCATTGTACGTC-GTTGATAT
1 TTCATTGTACGTCAGTTGATAT
3479350 T
1 T
3479351 CTAGACTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (22 bp):
TTCATTGTACGTCAGTTGATAT
Found at i:3483816 original size:65 final size:65
Alignment explanation
Indices: 3483712--3483842 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
3483702 CTCGCCGACA
3483712 ACGGTTGTACTTGGGTAATACTCAACAAAGGCTCTCTCTCTCTCTCTCCAAGCATGGGTAAATTT
1 ACGGTTGTACTTGGGTAATACTCAACAAAGGCTCTCTCTCTCTCTCTCCAAGCATGGGTAAATTT
3483777 ACGGTTGTACTTGGGTAATACTCAACAAAGGCTCTCTCTCTCTCTCTCCAAGCATGGGTAAATTT
1 ACGGTTGTACTTGGGTAATACTCAACAAAGGCTCTCTCTCTCTCTCTCCAAGCATGGGTAAATTT
3483842 A
1 A
3483843 TTTCCTGGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (65 bp):
ACGGTTGTACTTGGGTAATACTCAACAAAGGCTCTCTCTCTCTCTCTCCAAGCATGGGTAAATTT
Found at i:3484532 original size:2 final size:2
Alignment explanation
Indices: 3484499--3484555 Score: 68
Period size: 2 Copynumber: 29.5 Consensus size: 2
3484489 TTATTTTTAT
3484499 TA TA T- TA TA TA T- TA TA CTA T- TA CTA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
3484539 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
3484556 GGCTAATATT
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.08
2 41 0.84
3 4 0.08
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3484960 original size:75 final size:75
Alignment explanation
Indices: 3484848--3485039 Score: 260
Period size: 75 Copynumber: 2.5 Consensus size: 75
3484838 GATTACTCAT
* ** *
3484848 AGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGTTTGGCTCCGAGATTTC
1 AGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTC
3484913 CAGAATGCTCGG
64 CAGAATGCTCGG
* *
3484925 AGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGTTCCGAGAATTCCA
1 AGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCA
*
3484990 GTATGCTCGG
66 GAATGCTCGG
* * *
3485000 AGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
3485040 TATACAACGG
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
75 86 0.83
76 6 0.06
77 12 0.12
ACGTcount: A:0.23, C:0.33, G:0.24, T:0.20
Consensus pattern (75 bp):
AGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCA
GAATGCTCGG
Found at i:3490840 original size:23 final size:21
Alignment explanation
Indices: 3490791--3490853 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
3490781 TTTTGGTGCA
* *
3490791 GAGGGAATCGATCCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
3490812 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
3490833 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
3490854 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:3490861 original size:21 final size:21
Alignment explanation
Indices: 3490835--3490874 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3490825 CCCCCTTTGA
*
3490835 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3490856 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3490875 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3493031 original size:16 final size:16
Alignment explanation
Indices: 3493010--3493042 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3493000 GAGTAATTTC
3493010 AAAATTTCAAAACCTG
1 AAAATTTCAAAACCTG
3493026 AAAATTTCAAAACCTG
1 AAAATTTCAAAACCTG
3493042 A
1 A
3493043 TTTCAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAATTTCAAAACCTG
Found at i:3493474 original size:75 final size:75
Alignment explanation
Indices: 3493324--3493530 Score: 263
Period size: 75 Copynumber: 2.7 Consensus size: 75
3493314 CAAAGCCAAA
* ** * **
3493324 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
3493389 TTGGCTCCGAG
65 TTGGCTCCGAG
*
3493400 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
3493465 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
3493475 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGAT--TCCCCCATAGGAGGAACCGATTCCCCC
3493531 TTATACAACG
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
75 67 0.58
76 42 0.37
77 6 0.05
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:3500307 original size:18 final size:18
Alignment explanation
Indices: 3500275--3500313 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3500265 ATTTTTTTTC
*
3500275 AAATAATTATATATA-TA
1 AAATAAATATATATATTA
3500292 AAATAAATATTATATATTA
1 AAATAAATA-TATATATTA
3500311 AAA
1 AAA
3500314 AATTACCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAAATATATATATTA
Found at i:3500314 original size:20 final size:21
Alignment explanation
Indices: 3500275--3500313 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3500265 ATTTTTTTTC
3500275 AAATAATTATATATATAAAAT
1 AAATAATTATATATATAAAAT
3500296 AAAT-ATTATATAT-TAAAA
1 AAATAATTATATATATAAAA
3500314 AATTACCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAATTATATATATAAAAT
Found at i:3500378 original size:13 final size:13
Alignment explanation
Indices: 3500360--3500387 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3500350 AGTAAATATA
3500360 GGAGGAATTGATG
1 GGAGGAATTGATG
3500373 GGAGGAATTGATG
1 GGAGGAATTGATG
3500386 GG
1 GG
3500388 GTGATGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.50, T:0.21
Consensus pattern (13 bp):
GGAGGAATTGATG
Found at i:3500618 original size:2 final size:2
Alignment explanation
Indices: 3500611--3500639 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3500601 CATAGCTAAT
3500611 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3500640 TACGTATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3500853 original size:17 final size:19
Alignment explanation
Indices: 3500821--3500870 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 19
3500811 TCCATATATG
3500821 TATATTATTATTTTAATTT-
1 TATATTATT-TTTTAATTTA
3500840 T-TATTATTTTTTAATTTA
1 TATATTATTTTTTAATTTA
3500858 TATAATTATTTTT
1 TAT-ATTATTTTT
3500871 CATAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 9 0.32
18 8 0.29
19 2 0.07
20 9 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TATATTATTTTTTAATTTA
Found at i:3500914 original size:22 final size:23
Alignment explanation
Indices: 3500830--3500915 Score: 72
Period size: 22 Copynumber: 3.8 Consensus size: 23
3500820 GTATATTATT
*
3500830 ATTTTAATTTTTATTATTTT-TTA
1 ATTTTAATATTTA-TATTTTCTTA
* *
3500853 A-TTTATATAATTAT-TTTTCATA
1 ATTTTA-ATATTTATATTTTCTTA
* *
3500875 ATTTTAATATTTACATTTTCTTT
1 ATTTTAATATTTATATTTTCTTA
*
3500898 ATTTT-ATTTTTATATTTT
1 ATTTTAATATTTATATTTT
3500916 TAGATTCACA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
21 4 0.08
22 25 0.50
23 21 0.42
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTTTAATATTTATATTTTCTTA
Found at i:3508583 original size:21 final size:22
Alignment explanation
Indices: 3508543--3508584 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3508533 ACTTTTTGTA
*
3508543 AAATTTAAATATATTATTAATT
1 AAATTTAAATATAGTATTAATT
*
3508565 AAATTTTAATAT-GTATTAAT
1 AAATTTAAATATAGTATTAAT
3508585 ATCTTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
AAATTTAAATATAGTATTAATT
Found at i:3514098 original size:10 final size:9
Alignment explanation
Indices: 3514050--3514210 Score: 58
Period size: 9 Copynumber: 17.3 Consensus size: 9
3514040 GCTAGTTATC
*
3514050 TTTATTTTG
1 TTTATTTTT
* *
3514059 ATTATTTTA
1 TTTATTTTT
3514068 TTTATTTTT
1 TTTATTTTT
*
3514077 CTTCATTTTT
1 -TTTATTTTT
*
3514087 TTTA-TTTC
1 TTTATTTTT
*
3514095 TTT-TGTTT
1 TTTATTTTT
* *
3514103 TTTATGTTC
1 TTTATTTTT
*
3514112 TTTATTTTA
1 TTTATTTTT
*
3514121 TTTA-GTTT
1 TTTATTTTT
3514129 TTTATCTTTAT
1 TTTAT-TTT-T
3514140 TTTAATTTTT
1 TTT-ATTTTT
* * *
3514150 ATGTCTTTTC
1 -TTTATTTTT
*
3514160 TTTATCTTAT
1 TTTAT-TTTT
**
3514170 TTTCGTTTT
1 TTTATTTTT
*
3514179 TTCATTTATT
1 TTTATTT-TT
**
3514189 TTTATTTCC
1 TTTATTTTT
3514198 TTTATTTTAT
1 TTTATTTT-T
3514208 TTT
1 TTT
3514211 TCTTTAGTTT
Statistics
Matches: 108, Mismatches: 33, Indels: 21
0.67 0.20 0.13
Matches are distributed among these distances:
8 17 0.16
9 49 0.45
10 31 0.29
11 9 0.08
12 2 0.02
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTATTTTT
Found at i:3514215 original size:15 final size:15
Alignment explanation
Indices: 3514176--3514229 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
3514166 TTATTTTCGT
3514176 TTTTTCATTTATTTT-
1 TTTTTC-TTTATTTTA
*
3514191 TATTTCCTTTATTTTA
1 T-TTTTCTTTATTTTA
*
3514207 TTTTTCTTTAGTTTA
1 TTTTTCTTTATTTTA
*
3514222 TTTATCTT
1 TTTTTCTT
3514230 CATTGCCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 28 0.85
16 5 0.15
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTCTTTATTTTA
Found at i:3514221 original size:20 final size:20
Alignment explanation
Indices: 3514049--3514224 Score: 62
Period size: 20 Copynumber: 8.4 Consensus size: 20
3514039 TGCTAGTTAT
3514049 CTTTATTTTGATTATTTTATTTA
1 CTTTATTTT-A-T-TTTTATTTA
3514072 -TTT-TTCTTCATTTTT-TTTA
1 CTTTATT-TT-ATTTTTATTTA
* *
3514091 -TTTCTTTTGTTTTTTATGTT-
1 CTTTATTTT-ATTTTTAT-TTA
*
3514111 CTTTATTTTATTTAGTTTTTTA
1 CTTTATTTTATTT--TTATTTA
*
3514133 TCTTTATTTTAATTTTTATGT-
1 -CTTTATTTT-ATTTTTATTTA
* *
3514154 CTTT-TCTTTA-TCTTATTTT
1 CTTTAT-TTTATTTTTATTTA
* *
3514173 CGTTTTTTCATTTATTTTTATTTC
1 C--TTTAT--TTTATTTTTATTTA
*
3514197 CTTTATTTTATTTTTCTTTA
1 CTTTATTTTATTTTTATTTA
*
3514217 GTTTATTT
1 CTTTATTT
3514225 ATCTTCATTG
Statistics
Matches: 119, Mismatches: 17, Indels: 37
0.69 0.10 0.21
Matches are distributed among these distances:
18 6 0.05
19 17 0.14
20 36 0.30
21 17 0.14
22 18 0.15
23 13 0.11
24 12 0.10
ACGTcount: A:0.14, C:0.08, G:0.04, T:0.74
Consensus pattern (20 bp):
CTTTATTTTATTTTTATTTA
Found at i:3515527 original size:56 final size:55
Alignment explanation
Indices: 3515458--3515584 Score: 193
Period size: 56 Copynumber: 2.3 Consensus size: 55
3515448 CCCTATTTTC
* * *
3515458 TAGATATATTCGA-TTCTGGGACCTTTATTTTTATGCTTCTTAATGGCAACAATTGA
1 TAGATATACTCGATTTC-GGGACCCTTATTTTTATGCTTCTTAAT-GCAACAACTGA
3515514 TAGATATACTCGATTTCGGGACCCTTATTTTTATGCTTCTTAATGCAACAACTGA
1 TAGATATACTCGATTTCGGGACCCTTATTTTTATGCTTCTTAATGCAACAACTGA
*
3515569 TAGATATACTCAATTT
1 TAGATATACTCGATTT
3515585 TGAGGCCCCT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
55 25 0.38
56 38 0.58
57 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (55 bp):
TAGATATACTCGATTTCGGGACCCTTATTTTTATGCTTCTTAATGCAACAACTGA
Found at i:3515625 original size:31 final size:31
Alignment explanation
Indices: 3515564--3515626 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
3515554 TAATGCAACA
** *
3515564 ACTGATAGATATACTCAATTTTGAGGCCCCT
1 ACTGATAGATATACTCAATTTCAAGACCCCT
*
3515595 ACTGATAGATATATTCAATTTCAAGACCCCT
1 ACTGATAGATATACTCAATTTCAAGACCCCT
3515626 A
1 A
3515627 TTTTATGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (31 bp):
ACTGATAGATATACTCAATTTCAAGACCCCT
Found at i:3515915 original size:56 final size:56
Alignment explanation
Indices: 3515808--3516004 Score: 258
Period size: 55 Copynumber: 3.6 Consensus size: 56
3515798 TGATAAATAG
* * *
3515808 AGATATATTCGATTATG-GGACCCCTATTTTATAT--TTCTTAATGGCAACAACTGAT
1 AGATATACTCGATTTTGAGG-CCCCTATTTT-TATGCTTATTAATGGCAACAACTGAT
* * * *
3515863 AGATATACTCGATTTCGAGACTCCTATTTTTATGCTTTTTAATGGCAACAACTGAT
1 AGATATACTCGATTTTGAGGCCCCTATTTTTATGCTTATTAATGGCAACAACTGAT
* *
3515919 ATATATACTCGATTTTG-GGCCCCTATTTTTATGCTTATTAATAGCAACAACTGAT
1 AGATATACTCGATTTTGAGGCCCCTATTTTTATGCTTATTAATGGCAACAACTGAT
*
3515974 AGATATATTCGATTTTGAGGCCCCTATTTTT
1 AGATATACTCGATTTTGAGGCCCCTATTTTT
3516005 TAGGCCCTGC
Statistics
Matches: 124, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
54 3 0.02
55 72 0.58
56 49 0.40
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (56 bp):
AGATATACTCGATTTTGAGGCCCCTATTTTTATGCTTATTAATGGCAACAACTGAT
Found at i:3517582 original size:141 final size:141
Alignment explanation
Indices: 3517288--3517566 Score: 360
Period size: 141 Copynumber: 2.0 Consensus size: 141
3517278 AGATTTCTCA
* * * *
3517288 CACTTTAGTCCTTTAATTTATGGAGTAATTTGAATTGGCTCTCGCATTAACATGCCTAAGGGACC
1 CACTATAGTCTTTTAATTTAGGGAGTAATTTGAATTGGCTCTCGCATTAACATGCCCAAGGGACC
* * * * * *
3517353 ATTTTGATTATTCAATTCAATAATTGGTTAAAATAAATTATGATTAACATTAGAGCCTCAACTTT
66 ATTTCGATTATTCAACTCAATAATTGGTTAAAATAAATTAGGATTAACATAAAAGCATCAACTTT
*
3517418 AGGTTTAATTT
131 AGGTTTAATGT
* * *
3517429 CACTTTAGTCTTTTAATTTAGGGAGTGATTTGAATTGGCTCTCGCATTAACATGCCCGAGGGACC
1 CACTATAGTCTTTTAATTTAGGGAGTAATTTGAATTGGCTCTCGCATTAACATGCCCAAGGGACC
* * * * * * *
3517494 ATTTCGATTATTCGACTCAATCATTGGTTAAAATTAATTAGGGTTAATATAAAAGCATCCATTTT
66 ATTTCGATTATTCAACTCAATAATTGGTTAAAATAAATTAGGATTAACATAAAAGCATCAACTTT
3517559 AAGGTTTA
131 -AGGTTTA
3517567 GTCATCTATG
Statistics
Matches: 119, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
141 112 0.94
142 7 0.06
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (141 bp):
CACTATAGTCTTTTAATTTAGGGAGTAATTTGAATTGGCTCTCGCATTAACATGCCCAAGGGACC
ATTTCGATTATTCAACTCAATAATTGGTTAAAATAAATTAGGATTAACATAAAAGCATCAACTTT
AGGTTTAATGT
Found at i:3519188 original size:68 final size:68
Alignment explanation
Indices: 3519108--3519241 Score: 234
Period size: 68 Copynumber: 2.0 Consensus size: 68
3519098 CATTTATGCA
*
3519108 TTAATCCATCATTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATGCATCCTTTCAT
1 TTAATCCATCATTTTCATGCATTTTCAATTATGGCATCCGCTCATGCCTTAATGCATCCTTTCAT
3519173 GTC
66 GTC
*
3519176 TTAATGCC-TCATTTTCATGTATTTTCAATTATGGCATCCGCTCATGCCTTAATGCATCCTTTCA
1 TTAAT-CCATCATTTTCATGCATTTTCAATTATGGCATCCGCTCATGCCTTAATGCATCCTTTCA
3519240 TG
65 TG
3519242 CATTTTTAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 61 0.97
69 2 0.03
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.43
Consensus pattern (68 bp):
TTAATCCATCATTTTCATGCATTTTCAATTATGGCATCCGCTCATGCCTTAATGCATCCTTTCAT
GTC
Found at i:3519195 original size:21 final size:20
Alignment explanation
Indices: 3519141--3519182 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3519131 TTCAATTATG
* *
3519141 GCATCCGTTCATGCCTTAAT
1 GCATCCTTTCATGTCTTAAT
3519161 GCATCCTTTCATGTCTTAAT
1 GCATCCTTTCATGTCTTAAT
3519181 GC
1 GC
3519183 CTCATTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.29, G:0.14, T:0.38
Consensus pattern (20 bp):
GCATCCTTTCATGTCTTAAT
Found at i:3519255 original size:47 final size:47
Alignment explanation
Indices: 3519161--3519528 Score: 475
Period size: 47 Copynumber: 8.0 Consensus size: 47
3519151 ATGCCTTAAT
* * * * *
3519161 GCATCCTTTCATGTCTTAATGCCTCATTTTCATGTATTTTCAATTATG
1 GCATCCGTTCATGCCTTAATGCATC-CTTTCATGCATTTTCAATTATG
* *
3519209 GCATCCGCTCATGCCTTAATGCATCCTTTCATGCATTTTTAATTATG
1 GCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
* *
3519256 GTATCCGTTGATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
* * * *
3519303 GCATCCATTCATGACTTAATGAATCATTTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
*
3519350 GCATTCGTTCATGCCTTAATGCATCAC-TTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCCTTAATGCATC-CTTTCATGCATTTTCAATTATG
* *
3519397 GCATCCGTTCATGCCTTAATGTATCCTTTCATGC--CTT--A--AT-
1 GCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
* *
3519437 GCATCCTTTCATGCCTTAATGCATACTTTCATGCATTTTCAATTATG
1 GCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
* *
3519484 GCATCCTTTCATGCC-TAATGCATCATTTCATGCATTTTCAATTAT
1 GCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTAT
3519529 TAATTGGATT
Statistics
Matches: 280, Mismatches: 31, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
40 31 0.11
41 2 0.01
42 2 0.01
43 1 0.00
44 1 0.00
45 2 0.01
46 31 0.11
47 189 0.68
48 21 0.08
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (47 bp):
GCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATTATG
Found at i:3519314 original size:27 final size:27
Alignment explanation
Indices: 3519276--3519410 Score: 77
Period size: 27 Copynumber: 5.5 Consensus size: 27
3519266 ATGCCTTAAT
*
3519276 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCATTCATGCATTTTCAATTATG
*
3519303 GCATCCATTCATG-A-CTT--A--AT-
1 GCATCCATTCATGCATTTTCAATTATG
*
3519323 GAAT-CATTTCATGCATTTTCAATTATG
1 GCATCCA-TTCATGCATTTTCAATTATG
* * *
3519350 GCATTCGTTCATGC--CTT--A--AT-
1 GCATCCATTCATGCATTTTCAATTATG
3519370 GCAT-CACTTCATGCATTTTCAATTATG
1 GCATCCA-TTCATGCATTTTCAATTATG
*
3519397 GCATCCGTTCATGC
1 GCATCCATTCATGC
3519411 CTTAATGTAT
Statistics
Matches: 80, Mismatches: 10, Indels: 36
0.63 0.08 0.29
Matches are distributed among these distances:
19 3 0.04
20 20 0.25
21 5 0.06
22 4 0.05
23 2 0.03
24 2 0.03
25 4 0.05
26 5 0.06
27 33 0.41
28 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (27 bp):
GCATCCATTCATGCATTTTCAATTATG
Found at i:3519427 original size:20 final size:20
Alignment explanation
Indices: 3519397--3519516 Score: 125
Period size: 20 Copynumber: 5.7 Consensus size: 20
3519387 TTCAATTATG
*
3519397 GCATCCGTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
3519417 GTATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
3519437 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
3519457 GCATACTTTCATGCATTTTCAATTAT
1 GCATCCTTTCATGC--CTT--A--AT
3519483 GGCATCCTTTCATGCC-TAAT
1 -GCATCCTTTCATGCCTTAAT
*
3519503 GCATCATTTCATGC
1 GCATCCTTTCATGC
3519517 ATTTTCAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
19 13 0.15
20 52 0.61
22 3 0.04
24 2 0.02
26 2 0.02
27 13 0.15
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.40
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:3519506 original size:46 final size:47
Alignment explanation
Indices: 3519437--3519528 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 47
3519427 ATGCCTTAAT
3519437 GCATCCTTTCATGCCTTAATGCAT-ACTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCCTTAATGCATCA-TTTCATGCATTTTCAATTATG
3519484 GCATCCTTTCATGCC-TAATGCATCATTTCATGCATTTTCAATTAT
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTCAATTAT
3519529 TAATTGGATT
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
46 28 0.64
47 16 0.36
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (47 bp):
GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTCAATTATG
Found at i:3519945 original size:20 final size:20
Alignment explanation
Indices: 3519916--3519973 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
3519906 CTAGGCTCTA
*
3519916 TAGTATCGATACTTCTATCC
1 TAGTACCGATACTTCTATCC
*
3519936 TAGTACCGATATTTCTATCC
1 TAGTACCGATACTTCTATCC
3519956 TAGTACCGATACTTCTAT
1 TAGTACCGATACTTCTAT
3519974 AATATGGTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (20 bp):
TAGTACCGATACTTCTATCC
Found at i:3520110 original size:95 final size:96
Alignment explanation
Indices: 3519962--3520157 Score: 288
Period size: 95 Copynumber: 2.1 Consensus size: 96
3519952 ATCCTAGTAC
* * * * *
3519962 CGATACTTCTATAATATGGTACTGATACCCCCTTCTAGTATCGATACCGAAATTAGCTTCGATGT
1 CGATACTACTATAATATGGTACCGATACCCCCTTCAAGTATCGATACCAAAATTAGATTCGATGT
*
3520027 TT-CATGGTATCGATACCCTTACCACGGTAT
66 TTGCATGGTATCGATACCCTTACAACGGTAT
* *
3520057 CGATACTACTATACTATGGTACCGATACCCCCTT-AAGGTATCGATACCAAAATTAGATTTGATG
1 CGATACTACTATAATATGGTACCGATACCCCCTTCAA-GTATCGATACCAAAATTAGATTCGATG
*
3520121 TTTGCATGGTATCGATACCCTTACAATGGTAT
65 TTTGCATGGTATCGATACCCTTACAACGGTAT
3520153 CGATA
1 CGATA
3520158 TTGCATCAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
94 1 0.01
95 58 0.64
96 31 0.34
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (96 bp):
CGATACTACTATAATATGGTACCGATACCCCCTTCAAGTATCGATACCAAAATTAGATTCGATGT
TTGCATGGTATCGATACCCTTACAACGGTAT
Found at i:3526328 original size:47 final size:47
Alignment explanation
Indices: 3526232--3526517 Score: 392
Period size: 47 Copynumber: 6.1 Consensus size: 47
3526222 TTTAATAAAC
* * *
3526232 ATGGCATCCTTTCATGCCTTAATGAATCATTTTCATGCATTTTCAATT
1 ATGGCATCCGTTCATGCCTTAATGCATC-CTTTCATGCATTTTCAATT
* * *
3526280 ATGGCATCCGTTCATGTCGTAATGCTTCCTTTCATGCATTTTCAATT
1 ATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATT
* *
3526327 ATGGAATTCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATT
1 ATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATT
* ** * *
3526374 ATGACATCCGTTCATGCCTTAATGCATTATTTCAGGCATTTTTAATT
1 ATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATT
* *
3526421 ATGGCATCCATTCATGCCTTAATGCATCATTTCATGCATTTTCAATT
1 ATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATT
* * * *
3526468 ATGGCATCCATTCATGCGTTAGTGCATCCTTTCATGTATTTTCAATT
1 ATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATT
3526515 ATG
1 ATG
3526518 AATTTTATTT
Statistics
Matches: 211, Mismatches: 27, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
47 188 0.89
48 23 0.11
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.42
Consensus pattern (47 bp):
ATGGCATCCGTTCATGCCTTAATGCATCCTTTCATGCATTTTCAATT
Found at i:3527042 original size:94 final size:95
Alignment explanation
Indices: 3526924--3527103 Score: 256
Period size: 94 Copynumber: 1.9 Consensus size: 95
3526914 ATCTTAGTAC
* ** * * *
3526924 CGATACTTCTATACTATGGCACCGATACCCCCTTCCGGTAAT-GATACCAAAATTAGCTTTGTTG
1 CGATACTACTATACTATGGCACCGATACCCCCTTAAGGT-ATCGATACCAAAATTAGATTCGATG
* *
3526988 TTT-TATGGTATCGATACCCTTTCCACGTAT
65 TTTGCATGGTATCAATACCCTTTCCACGTAT
*
3527018 CGATACTACTATACTATGGTACCGATACCCCCTTAAGGTATCGATACCAAAATTAGATTCGATGT
1 CGATACTACTATACTATGGCACCGATACCCCCTTAAGGTATCGATACCAAAATTAGATTCGATGT
3527083 TTGCATGGTATCAATACCCTT
66 TTGCATGGTATCAATACCCTT
3527104 ACAATGGTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
93 2 0.03
94 57 0.76
95 16 0.21
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (95 bp):
CGATACTACTATACTATGGCACCGATACCCCCTTAAGGTATCGATACCAAAATTAGATTCGATGT
TTGCATGGTATCAATACCCTTTCCACGTAT
Found at i:3527138 original size:94 final size:94
Alignment explanation
Indices: 3526944--3527139 Score: 209
Period size: 94 Copynumber: 2.1 Consensus size: 94
3526934 ATACTATGGC
** * * * * *
3526944 ACCGATACCCCCTTCCGGTAATGATACCAAAATTAGCTTTGTTGTTTTATGGTATCGATACCCTT
1 ACCGATACCCCCTTAAGGTAATGATACCAAAATTAGATTCGATGTTTCATGGTATCAATACCCTT
* * * * *
3527009 TCCACGTATCGATACTACTATACTATGGT
66 ACAACGTATCGAAACTACTATACAACGGT
3527038 ACCGATACCCCCTTAAGGT-ATCGATACCAAAATTAGATTCGATGTTTGCATGGTATCAATACCC
1 ACCGATACCCCCTTAAGGTAAT-GATACCAAAATTAGATTCGATGTTT-CATGGTATCAATACCC
* *
3527102 TTACAATGGTATCGAAACT-GTAT-CAACGGT
64 TTACAA-CGTATCGAAACTACTATACAACGGT
*
3527132 ATCGATAC
1 ACCGATAC
3527140 TGATTGAATC
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
93 2 0.02
94 51 0.61
95 21 0.25
96 10 0.12
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (94 bp):
ACCGATACCCCCTTAAGGTAATGATACCAAAATTAGATTCGATGTTTCATGGTATCAATACCCTT
ACAACGTATCGAAACTACTATACAACGGT
Found at i:3529764 original size:18 final size:20
Alignment explanation
Indices: 3529728--3529764 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
3529718 TTTCTTTAGA
*
3529728 TTAATATAAGTATTTTCATT
1 TTAATATAAGTATTGTCATT
3529748 TTAATAT-A-TATTGTCAT
1 TTAATATAAGTATTGTCAT
3529765 ATTATGGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 1 0.06
20 7 0.44
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
TTAATATAAGTATTGTCATT
Found at i:3533597 original size:44 final size:44
Alignment explanation
Indices: 3533491--3533602 Score: 118
Period size: 44 Copynumber: 2.5 Consensus size: 44
3533481 AACTGGCTCG
* * **
3533491 TCCATCATATAAGGAGTTGGACCTGCACCTTTCTTTTTACTCGAT
1 TCCATCACATAAGGAGTTGGATCTGCA-CTAACTTTTTACTCGAT
* * * * *
3533536 TCAATCCCATAAAGAGTTGGATCTGCA-TAACTATTTTGCTTGAT
1 TCCATCACATAAGGAGTTGGATCTGCACTAACT-TTTTACTCGAT
3533580 TCCATCACATAAGGAGTTGGATC
1 TCCATCACATAAGGAGTTGGATC
3533603 AACATCATCT
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
43 3 0.06
44 29 0.54
45 22 0.41
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (44 bp):
TCCATCACATAAGGAGTTGGATCTGCACTAACTTTTTACTCGAT
Found at i:3533771 original size:97 final size:97
Alignment explanation
Indices: 3533643--3533868 Score: 312
Period size: 97 Copynumber: 2.3 Consensus size: 97
3533633 AAAACTCATA
* *
3533643 ATCATTTTACTCAAGAT-TTTGTCTCACTTGAGATTGTTTTTCTTAAAACAT-ATTTTGTATCAC
1 ATCATTTCACTC-AGATATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-TGATTTTGTATCAC
3533706 TTGAGAAAGTTTCCATTGAAATCCAAACTTCAAT
64 TTGAGAAAGTTTCCATTGAAATCCAAACTTCAAT
* * * *
3533740 ATCATTTCACTCGGATATTTATCTCACTTGAGATTTTTTTTCTTAAAGCTGATTTTGTCTCACTT
1 ATCATTTCACTCAGATATTTATCTCACTTGAGATTGTTTTTCTTAAAACTGATTTTGTATCACTT
* * * *
3533805 GAGACAGTTTCCCTTGAAGTCTAAACTTCAAT
66 GAGAAAGTTTCCATTGAAATCCAAACTTCAAT
* *
3533837 ATCATTTCACTCAGATTTTTATCTAACTTGAG
1 ATCATTTCACTCAGATATTTATCTCACTTGAG
3533869 TTGGATCAAC
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
96 4 0.04
97 110 0.96
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (97 bp):
ATCATTTCACTCAGATATTTATCTCACTTGAGATTGTTTTTCTTAAAACTGATTTTGTATCACTT
GAGAAAGTTTCCATTGAAATCCAAACTTCAAT
Found at i:3534157 original size:36 final size:36
Alignment explanation
Indices: 3534027--3534174 Score: 145
Period size: 36 Copynumber: 4.1 Consensus size: 36
3534017 TCACTCAGAT
** *
3534027 TTTTATCTCACTTGAGATTGTTTTTATTAAAACTAA
1 TTTTATCTCACTTGAGATTGTTTTCCTTAAAACAAA
* * * ** * *
3534063 TTTCATCTCATTTTAGATCATTTTTCTTAAAACATA
1 TTTTATCTCACTTGAGATTGTTTTCCTTAAAACAAA
*
3534099 TTCTATCTCACTTGAGATTGTTTTCCTTAAAACAAA
1 TTTTATCTCACTTGAGATTGTTTTCCTTAAAACAAA
* * * *
3534135 TTTTATCTCATTTGAAAGTG-TTTCTCTTGAAACAAA
1 TTTTATCTCACTTGAGATTGTTTTC-CTTAAAACAAA
3534171 TTTT
1 TTTT
3534175 CCTTCTCTCA
Statistics
Matches: 90, Mismatches: 21, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
35 4 0.04
36 86 0.96
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (36 bp):
TTTTATCTCACTTGAGATTGTTTTCCTTAAAACAAA
Found at i:3534168 original size:72 final size:72
Alignment explanation
Indices: 3534030--3534168 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 72
3534020 CTCAGATTTT
* * * * *
3534030 TATCTCACTTGAGATTGTTTTTATTAAAACTAATTTCATCTCATTTTAGATCATTTTTCTTAAAA
1 TATCTCACTTGAGATTGTTTTCATTAAAACAAATTTCATCTCATTTGAAATCATTTCTCTTAAAA
3534095 CATATTC
66 CATATTC
* * * *
3534102 TATCTCACTTGAGATTGTTTTCCTTAAAACAAATTTTATCTCATTTGAAAGT-GTTTCTCTTGAA
1 TATCTCACTTGAGATTGTTTTCATTAAAACAAATTTCATCTCATTTGAAA-TCATTTCTCTTAAA
3534166 ACA
65 ACA
3534169 AATTTTCCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 56 0.98
73 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (72 bp):
TATCTCACTTGAGATTGTTTTCATTAAAACAAATTTCATCTCATTTGAAATCATTTCTCTTAAAA
CATATTC
Found at i:3535863 original size:21 final size:21
Alignment explanation
Indices: 3535838--3535903 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
3535828 GAAGAACTTG
3535838 TCTAATAAAGGAGAATAAGTT
1 TCTAATAAAGGAGAATAAGTT
* *
3535859 TCTAAT----GAGAAGAACTT
1 TCTAATAAAGGAGAATAAGTT
3535876 GTCTAATAAAGGAGAATAAGTT
1 -TCTAATAAAGGAGAATAAGTT
3535898 TCTAAT
1 TCTAAT
3535904 GAGAAGAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
17 9 0.25
18 6 0.17
21 12 0.33
22 9 0.25
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (21 bp):
TCTAATAAAGGAGAATAAGTT
Found at i:3535863 original size:39 final size:39
Alignment explanation
Indices: 3535818--3535916 Score: 189
Period size: 39 Copynumber: 2.5 Consensus size: 39
3535808 AATGGAATGA
*
3535818 TTTCTAACGAGAAGAACTTGTCTAATAAAGGAGAATAAG
1 TTTCTAATGAGAAGAACTTGTCTAATAAAGGAGAATAAG
3535857 TTTCTAATGAGAAGAACTTGTCTAATAAAGGAGAATAAG
1 TTTCTAATGAGAAGAACTTGTCTAATAAAGGAGAATAAG
3535896 TTTCTAATGAGAAGAACTTGT
1 TTTCTAATGAGAAGAACTTGT
3535917 TCAACCTGGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.29
Consensus pattern (39 bp):
TTTCTAATGAGAAGAACTTGTCTAATAAAGGAGAATAAG
Found at i:3535890 original size:22 final size:22
Alignment explanation
Indices: 3535826--3535891 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
3535816 GATTTCTAAC
3535826 GAGAAGAACTTGTCTAATAAAG
1 GAGAAGAACTTGTCTAATAAAG
* *
3535848 GAGAATAAGTT-TCTAAT----
1 GAGAAGAACTTGTCTAATAAAG
3535865 GAGAAGAACTTGTCTAATAAAG
1 GAGAAGAACTTGTCTAATAAAG
3535887 GAGAA
1 GAGAA
3535892 TAAGTTTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 9 0.26
18 6 0.17
21 6 0.17
22 14 0.40
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.24
Consensus pattern (22 bp):
GAGAAGAACTTGTCTAATAAAG
Found at i:3536189 original size:36 final size:35
Alignment explanation
Indices: 3536148--3536289 Score: 117
Period size: 36 Copynumber: 3.9 Consensus size: 35
3536138 TCACTTAGAT
3536148 TTTTATCTCACTTGAGATTGTATTTCTTAAAACTGA
1 TTTTATCTCACTTGAGATTGT-TTTCTTAAAACTGA
* * * *
3536184 TTTTATCTCAGTTTAGATAATTTTTTCTTATAACATG-
1 TTTTATCTCACTTGAGAT--TGTTTTCTTAAAAC-TGA
* * **
3536221 TTCTATCTCACTTGACATTGTTTTCCTTAAAACAAA
1 TTTTATCTCACTTGAGATTGTTTT-CTTAAAACTGA
* *
3536257 TTTTATCTCATTTGA-ATGTGTTTCTCTTGAAAC
1 TTTTATCTCACTTGAGAT-TGTTT-TCTTAAAAC
3536290 ACTTTTTCCT
Statistics
Matches: 84, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
35 7 0.08
36 48 0.57
37 25 0.30
38 4 0.05
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (35 bp):
TTTTATCTCACTTGAGATTGTTTTCTTAAAACTGA
Found at i:3537436 original size:2 final size:2
Alignment explanation
Indices: 3537429--3537462 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3537419 TTTGATTCAC
3537429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3537463 CTTTTTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3546845 original size:3 final size:3
Alignment explanation
Indices: 3546837--3546927 Score: 168
Period size: 3 Copynumber: 31.0 Consensus size: 3
3546827 TTATTTTTCA
3546837 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3546885 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3546928 GTGTGTCCTT
Statistics
Matches: 86, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 4 0.05
3 82 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3547519 original size:105 final size:105
Alignment explanation
Indices: 3547337--3547545 Score: 251
Period size: 105 Copynumber: 2.0 Consensus size: 105
3547327 TTATTTATAT
* * * * * *
3547337 GAAAATATAAGAACATAGTTATACCAATATAATTATATGTTTATTTTTAAGCACTAAGATATTGG
1 GAAAATATAAGAACATACTCACACCAATATAATTATATATATATTTTTAAGCACTAAGATATTGA
* * * *
3547402 GAGATGCACATACTTACACCAATATAAGTACATGTTAATA
66 GAGACGCACATACTCAAACCAATATAAGTACATGCTAATA
* * *
3547442 GAAAATAT-AGAAACATACTCACACCAATATAATTATGTATATATTTTTAGGTA-TCAAGATATT
1 GAAAATATAAG-AACATACTCACACCAATATAATTATATATATATTTTTAAGCACT-AAGATATT
* *
3547505 GAGAGACGCACATACTCAAACCAATGTAAGTATATGCTAAT
64 GAGAGACGCACATACTCAAACCAATATAAGTACATGCTAAT
3547546 TCATATATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
104 3 0.03
105 84 0.97
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (105 bp):
GAAAATATAAGAACATACTCACACCAATATAATTATATATATATTTTTAAGCACTAAGATATTGA
GAGACGCACATACTCAAACCAATATAAGTACATGCTAATA
Found at i:3550216 original size:10 final size:10
Alignment explanation
Indices: 3550193--3550282 Score: 77
Period size: 9 Copynumber: 9.7 Consensus size: 10
3550183 GAGGCAAATC
*
3550193 AATAATACAA
1 AATAATACAT
*
3550203 AATAAAACAT
1 AATAATACAT
3550213 AATAATA-AT
1 AATAATACAT
3550222 AATAATA-AT
1 AATAATACAT
*
3550231 GATAATA-AT
1 AATAATACAT
*
3550240 GATAATA-AT
1 AATAATACAT
* *
3550249 GATAAT-GAT
1 AATAATACAT
3550258 AATAATA-AT
1 AATAATACAT
3550267 AATAATA-AT
1 AATAATACAT
3550276 AATAATA
1 AATAATA
3550283 AACAAATCTT
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
9 59 0.81
10 14 0.19
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (10 bp):
AATAATACAT
Found at i:3550217 original size:3 final size:3
Alignment explanation
Indices: 3550211--3550283 Score: 110
Period size: 3 Copynumber: 24.3 Consensus size: 3
3550201 AAAATAAAAC
* * * *
3550211 ATA ATA ATA ATA ATA ATA ATG ATA ATA ATG ATA ATA ATG ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3550259 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3550284 ACAAATCTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3553119 original size:9 final size:9
Alignment explanation
Indices: 3553105--3553131 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3553095 ACCATAAGGG
3553105 CATTTTGGT
1 CATTTTGGT
3553114 CATTTTGGT
1 CATTTTGGT
3553123 CATTTTGGT
1 CATTTTGGT
3553132 GCTCAACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (9 bp):
CATTTTGGT
Found at i:3558175 original size:32 final size:32
Alignment explanation
Indices: 3558130--3558213 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 32
3558120 AAAGTTTTGA
* *
3558130 GGCCACAGGGCCTACCTAAGAACAT-ATCTTAG
1 GGCCGCAGGGCCTACCTAAGAA-ATGATCTCAG
* **
3558162 GGTCGCAGGGCCTACCCGAG-AATGATCTCAG
1 GGCCGCAGGGCCTACCTAAGAAATGATCTCAG
*
3558193 GGCCGCAGAGCCTACCTAAGA
1 GGCCGCAGGGCCTACCTAAGA
3558214 GTCACATTAG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
30 2 0.05
31 23 0.56
32 16 0.39
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.15
Consensus pattern (32 bp):
GGCCGCAGGGCCTACCTAAGAAATGATCTCAG
Found at i:3571613 original size:38 final size:36
Alignment explanation
Indices: 3571537--3571613 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
3571527 TTTTTATATT
*
3571537 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
3571573 TTTAATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAA-AAAATTATATAAATATTAT-CAA
3571611 TTT
1 TTT
3571614 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 5 0.14
37 21 0.60
38 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:3571795 original size:20 final size:20
Alignment explanation
Indices: 3571759--3571796 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3571749 ATCCTATTCC
**
3571759 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
3571779 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3571797 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:3584890 original size:23 final size:23
Alignment explanation
Indices: 3584864--3584912 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3584854 ATAAAGAACC
*
3584864 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
3584887 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
3584910 AAA
1 AAA
3584913 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:3585766 original size:12 final size:12
Alignment explanation
Indices: 3585749--3585787 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
3585739 AATGTGCAAT
3585749 TGATATGGAATG
1 TGATATGGAATG
3585761 TGATATGGAATG
1 TGATATGGAATG
*
3585773 TGATATGAAATG
1 TGATATGGAATG
3585785 TGA
1 TGA
3585788 ATAATGATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (12 bp):
TGATATGGAATG
Found at i:3587277 original size:20 final size:20
Alignment explanation
Indices: 3587252--3587304 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
3587242 CCCTTAATGC
3587252 AAAGGATCGATCCCTCCCCT
1 AAAGGATCGATCCCTCCCCT
3587272 AAAGGATCGATCCCTCCCCT
1 AAAGGATCGATCCCTCCCCT
*
3587292 AATGGATCGATCC
1 AAAGGATCGATCC
3587305 TTATCTCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAGGATCGATCCCTCCCCT
Found at i:3588271 original size:18 final size:17
Alignment explanation
Indices: 3588244--3588277 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3588234 CCCAAGCACA
3588244 TATTCTAAAATTTAAAG
1 TATTCTAAAATTTAAAG
3588261 TATTACTAAAATTTAAA
1 TATT-CTAAAATTTAAA
3588278 TTGATTTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (17 bp):
TATTCTAAAATTTAAAG
Found at i:3590574 original size:10 final size:10
Alignment explanation
Indices: 3590556--3590589 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3590546 TTAGTTAGGC
*
3590556 ATAATTAATA
1 ATAAATAATA
3590566 ATAAATAATA
1 ATAAATAATA
3590576 AT-AATAATA
1 ATAAATAATA
3590585 ATAAA
1 ATAAA
3590590 CATATCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAAATAATA
Found at i:3594230 original size:54 final size:54
Alignment explanation
Indices: 3594161--3594834 Score: 759
Period size: 54 Copynumber: 12.5 Consensus size: 54
3594151 ACCAAATAGG
* * *** *
3594161 CACTAAGTGTGCAAATCATGAAATTCATCATATGTTGATGAATAATTGTTTCTA
1 CACTAAGTGTGCAAATCACGAAATTCATCATATGGTGATGAATAACCATTTCGA
* * * *
3594215 TACTAAGTGTACAAATCAC-ATAATTCATCATATGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAAATCACGA-AATTCATCATATGGTGATGAATAACCATTTCGA
* * * *
3594269 CACTAAGTGTGC-AATCAC-ATAATTCATCATGTGTTGATGAATAACCTTTTCGG
1 CACTAAGTGTGCAAATCACGA-AATTCATCATATGGTGATGAATAACCATTTCGA
* * * * * * *
3594322 TAATAATTGTGTAAATCACGGAATTCATCATATGGTGATGAATAACTATTTCAA
1 CACTAAGTGTGCAAATCACGAAATTCATCATATGGTGATGAATAACCATTTCGA
* * *
3594376 CACTATGTGTGCAAATCACGGAATTAATCATATGGTGATGAATAACCATTTCGA
1 CACTAAGTGTGCAAATCACGAAATTCATCATATGGTGATGAATAACCATTTCGA
* * * *
3594430 CAC-AAGTGTACAAATCATGGAATTCATCATATGGTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAAATCACGAAATTCATCATATGGTGATGAATAACCATTTCGA
* * * * *
3594483 CACTAAATGTGCAAATCATGTAATTCATCATATGTTGATGAATAA-CAGTTTCGG
1 CACTAAGTGTGCAAATCACGAAATTCATCATATGGTGATGAATAACCA-TTTCGA
* * *
3594537 TACTAAGTGTGCAAATCACGGAATTCATCATATGGTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAAATCACGAAATTCATCATATGGTGATGAATAACCATTTCGA
* *
3594591 CACTAATTGTGCAAATCAC-AGAATTCATCATATGGTGATGAATAACCATTTCGG
1 CACTAAGTGTGCAAATCACGA-AATTCATCATATGGTGATGAATAACCATTTCGA
**** * *
3594645 CACTAAGTACATAAATCATGAAATTCATCATATGGTGATGAATAACCATTGCGGA
1 CACTAAGTGTGCAAATCACGAAATTCATCATATGGTGATGAATAACCATTTC-GA
* * * * *
3594700 -ACTAAATGCGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGG
1 CACTAAGTGTGCAAATCACGAAATTCATCATATGGTGATGAATAACCATTTCGA
* *
3594753 CACTAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCATTTCGG
1 CACTAAGTGTGCAAATCACGAAATTCATCATATGGTGATGAATAACCATTTCGA
* * * *
3594807 CACTATGTGTGTAAACCATGAAATTCAT
1 CACTAAGTGTGCAAATCACGAAATTCAT
3594835 AATTTGTTTA
Statistics
Matches: 533, Mismatches: 77, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
53 97 0.18
54 433 0.81
55 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (54 bp):
CACTAAGTGTGCAAATCACGAAATTCATCATATGGTGATGAATAACCATTTCGA
Found at i:3594456 original size:161 final size:162
Alignment explanation
Indices: 3594159--3594834 Score: 844
Period size: 161 Copynumber: 4.2 Consensus size: 162
3594149 TTACCAAATA
* * * * *
3594159 GGCACTAAGTGTGCAAATCATGAAATTCATCATATGTTGATGAATAATTGTTTCTATACTAAGTG
1 GGCACTAAATGTGCAAATCATGAAATTCATCATATGGTGATGAATAACTATTTCGATACTAAGTG
* ** * *
3594224 TACAAATCACATAATTCATCATATGTTGATGAATAACCGTTTCGACACTAAGTGTGC-AATCACA
66 TGCAAATCACGGAATTCATCATATGGTGATGAATAACCATTTCGACACTAAGTGTGCAAATCACA
* * * *
3594288 TAATTCATCATGTGTTGATGAATAACCTTTTC
131 GAATTCATCATATGGTGATGAATAACCATTTC
* * * * * * * * *
3594320 GGTAATAATTGTGTAAATCACGGAATTCATCATATGGTGATGAATAACTATTTCAACACTATGTG
1 GGCACTAAATGTGCAAATCATGAAATTCATCATATGGTGATGAATAACTATTTCGATACTAAGTG
* * **
3594385 TGCAAATCACGGAATTAATCATATGGTGATGAATAACCATTTCGACAC-AAGTGTACAAATCATG
66 TGCAAATCACGGAATTCATCATATGGTGATGAATAACCATTTCGACACTAAGTGTGCAAATCACA
*
3594449 GAATTCATCATATGGTGATGAATAACCGTTTC
131 GAATTCATCATATGGTGATGAATAACCATTTC
* * * *
3594481 GACACTAAATGTGCAAATCATGTAATTCATCATATGTTGATGAATAAC-AGTTTCGGTACTAAGT
1 GGCACTAAATGTGCAAATCATGAAATTCATCATATGGTGATGAATAACTA-TTTCGATACTAAGT
* *
3594545 GTGCAAATCACGGAATTCATCATATGGTGATGAATAACCGTTTCGACACTAATTGTGCAAATCAC
65 GTGCAAATCACGGAATTCATCATATGGTGATGAATAACCATTTCGACACTAAGTGTGCAAATCAC
3594610 AGAATTCATCATATGGTGATGAATAACCATTTC
130 AGAATTCATCATATGGTGATGAATAACCATTTC
* * *
3594643 GGCACT-AA-GTACATAAATCATGAAATTCATCATATGGTGATGAATAACCATTGCGGA-ACTAA
1 GGCACTAAATGTGC--AAATCATGAAATTCATCATATGGTGATGAATAACTATTTC-GATACTAA
* * * *
3594705 ATGCGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGGCACTAAGTGTGCAAATC
63 GTGTGCAAATCACGGAATTCATCATATGGTGATGAATAACCATTTCGACACTAAGTGTGCAAATC
*
3594770 AC-GAAATTCATCATATGTTGATGAATAACCATTTC
128 ACAG-AATTCATCATATGGTGATGAATAACCATTTC
** * *
3594805 GGCACTATGTGTGTAAACCATGAAATTCAT
1 GGCACTAAATGTGCAAATCATGAAATTCAT
3594835 AATTTGTTTA
Statistics
Matches: 443, Mismatches: 62, Indels: 19
0.85 0.12 0.04
Matches are distributed among these distances:
160 11 0.02
161 228 0.51
162 200 0.45
163 2 0.00
164 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (162 bp):
GGCACTAAATGTGCAAATCATGAAATTCATCATATGGTGATGAATAACTATTTCGATACTAAGTG
TGCAAATCACGGAATTCATCATATGGTGATGAATAACCATTTCGACACTAAGTGTGCAAATCACA
GAATTCATCATATGGTGATGAATAACCATTTC
Found at i:3601046 original size:14 final size:14
Alignment explanation
Indices: 3600995--3601047 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
3600985 AAGTTAACGG
*
3600995 GTTGACTCTGACGA
1 GTTGACTCGGACGA
*
3601009 GTTGACTCAGACTGA
1 GTTGACTCGGAC-GA
*
3601024 GATGACTCGGAC-A
1 GTTGACTCGGACGA
3601037 GGTTGACTCGG
1 -GTTGACTCGG
3601048 TGACTGGATC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 1 0.03
14 20 0.61
15 12 0.36
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (14 bp):
GTTGACTCGGACGA
Found at i:3604652 original size:16 final size:15
Alignment explanation
Indices: 3604627--3604656 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3604617 AAAAAAAGTC
3604627 ATTTATAAATTTTAA
1 ATTTATAAATTTTAA
3604642 ATTTGATAAATTTTA
1 ATTT-ATAAATTTTA
3604657 TTACTTCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTATAAATTTTAA
Found at i:3609313 original size:2 final size:2
Alignment explanation
Indices: 3609306--3609354 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3609296 AATGTCATTA
3609306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3609348 AT AT AT A
1 AT AT AT A
3609355 CGCATGTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3611697 original size:21 final size:21
Alignment explanation
Indices: 3611671--3611721 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3611661 GTTGCATATA
*
3611671 TTCCTCGGTCTCCAATGTTGC
1 TTCCTCGGCCTCCAATGTTGC
3611692 TTCCTCGGCCTCCAATGTTGC
1 TTCCTCGGCCTCCAATGTTGC
3611713 TTCCTCGGC
1 TTCCTCGGC
3611722 AACATGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.08, C:0.37, G:0.20, T:0.35
Consensus pattern (21 bp):
TTCCTCGGCCTCCAATGTTGC
Found at i:3617559 original size:22 final size:22
Alignment explanation
Indices: 3617496--3617554 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
3617486 TCACCCTTAG
* * *
3617496 GTATCAATACTCAAAGAA-TAA
1 GTATCGATACTCTAAGAACAAA
3617517 -TATCGATACTCTAAGAACAAA
1 GTATCGATACTCTAAGAACAAA
3617538 GTATCGATACTACTAAG
1 GTATCGATACT-CTAAG
3617555 CCAAAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
22 10 0.31
23 5 0.16
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (22 bp):
GTATCGATACTCTAAGAACAAA
Found at i:3618273 original size:34 final size:34
Alignment explanation
Indices: 3618235--3618303 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
3618225 TTGAAGAGAG
3618235 AGATTGAAATTGAAATGGAGAGTAGAAGATAAGA
1 AGATTGAAATTGAAATGGAGAGTAGAAGATAAGA
3618269 AGATTGAAATTGAAATGGAGAGTAGAAGATAAGA
1 AGATTGAAATTGAAATGGAGAGTAGAAGATAAGA
3618303 A
1 A
3618304 AATATATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.29, T:0.20
Consensus pattern (34 bp):
AGATTGAAATTGAAATGGAGAGTAGAAGATAAGA
Found at i:3618694 original size:24 final size:24
Alignment explanation
Indices: 3618649--3618695 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3618639 TGTGTGGCCA
**
3618649 TGTTATTTATATTTATTTTCTTTT
1 TGTTATTTATATTTATAATCTTTT
3618673 TGTTATTTAT-TTATATAATCTTT
1 TGTTATTTATATT-TATAATCTTT
3618696 GCATCTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (24 bp):
TGTTATTTATATTTATAATCTTTT
Found at i:3618893 original size:18 final size:18
Alignment explanation
Indices: 3618870--3618909 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3618860 AAGGAACACT
3618870 GAGCATGGAAAAGGTCTA
1 GAGCATGGAAAAGGTCTA
*
3618888 GAGCATGGAAAAGTTCTA
1 GAGCATGGAAAAGGTCTA
3618906 GAGC
1 GAGC
3618910 CTGAAACTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.33, T:0.17
Consensus pattern (18 bp):
GAGCATGGAAAAGGTCTA
Found at i:3623770 original size:14 final size:14
Alignment explanation
Indices: 3623753--3623781 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3623743 TAATCCCTGT
3623753 AAATAATTCCCTAC
1 AAATAATTCCCTAC
3623767 AAATAATTCCCTAC
1 AAATAATTCCCTAC
3623781 A
1 A
3623782 TAGAAATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAATTCCCTAC
Found at i:3626509 original size:101 final size:105
Alignment explanation
Indices: 3626379--3626584 Score: 312
Period size: 101 Copynumber: 2.0 Consensus size: 105
3626369 CATGTATCAA
*
3626379 AACATTTAATGATTCTATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
1 AACATTTAATGATTCCATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
*
3626444 GCCA-TTTT-AACACACA-AATTATTATATT-CACGTGAT
66 GCCACTTTTGAACACACATAATTATTATATTACACATGAT
* * **
3626480 AACATTTAATGATTCCATATTAAAGATATATATAATAAGATTGTATATATAATATTAAATGTAAA
1 AACATTTAATGATTCCATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
* *
3626545 GCCACTTTTGCACACATATAATTATTATATTACACATGAT
66 GCCACTTTTGAACACACATAATTATTATATTACACATGAT
3626585 TAAAAAGCAT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
101 64 0.69
102 4 0.04
103 6 0.06
104 12 0.13
105 7 0.08
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (105 bp):
AACATTTAATGATTCCATACTAAACATATATATAATAAGATTGTATATATAATATTAAATACAAA
GCCACTTTTGAACACACATAATTATTATATTACACATGAT
Found at i:3627694 original size:3 final size:3
Alignment explanation
Indices: 3627686--3627727 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
3627676 TATGTAAAAT
3627686 ATA ATA ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3627728 TTAAAAGACG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3631024 original size:17 final size:17
Alignment explanation
Indices: 3630997--3631035 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3630987 AATTTACAAT
3630997 TAATT-TAAATAATAAC
1 TAATTATAAATAATAAC
*
3631013 TAATTATAAATAATATC
1 TAATTATAAATAATAAC
3631030 TAATTA
1 TAATTA
3631036 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTATAAATAATAAC
Found at i:3633263 original size:23 final size:22
Alignment explanation
Indices: 3633211--3633263 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
3633201 ATATTACAAA
*
3633211 AATATTTATTTATTTTTTAAAAT
1 AATA-TTAATTATTTTTTAAAAT
3633234 -ATAATTAATTATTTGTTTAAAAT
1 AAT-ATTAATTATTT-TTTAAAAT
3633257 AATATTA
1 AATATTA
3633264 TTTTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 11 0.42
23 13 0.50
24 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATATTAATTATTTTTTAAAAT
Found at i:3633416 original size:21 final size:20
Alignment explanation
Indices: 3633374--3633431 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
3633364 ATAATTTAAA
*
3633374 AAAT-AATATTTCAAATAAAT
1 AAATAAATATTTTAAA-AAAT
3633394 -AATAATATGATTTTAAAAAAT
1 AAATAA-AT-ATTTTAAAAAAT
3633415 AAATAAATATTTTAAAA
1 AAATAAATATTTTAAAA
3633432 TATTTTCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 3 0.09
20 10 0.30
21 8 0.24
22 12 0.36
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATAAATATTTTAAAAAAT
Found at i:3651945 original size:12 final size:13
Alignment explanation
Indices: 3651927--3651965 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 13
3651917 ATTATCATAA
3651927 ATTATTTTTATTT
1 ATTATTTTTATTT
3651940 -TTATTTTTATTT
1 ATTATTTTTATTT
3651952 ACTTGATTTTTATT
1 A-TT-ATTTTTATT
3651966 AATTTTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 12 0.52
14 2 0.09
15 9 0.39
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (13 bp):
ATTATTTTTATTT
Found at i:3654007 original size:13 final size:14
Alignment explanation
Indices: 3653989--3654018 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3653979 AAGAAAGATA
3653989 TTTTTTAAGAA-AT
1 TTTTTTAAGAACAT
3654002 TTTTTTAAGAACAT
1 TTTTTTAAGAACAT
3654016 TTT
1 TTT
3654019 AGTCCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTTTTAAGAACAT
Found at i:3656737 original size:37 final size:37
Alignment explanation
Indices: 3656681--3657215 Score: 716
Period size: 37 Copynumber: 14.5 Consensus size: 37
3656671 AACTATTTCC
* * *
3656681 AAAACACTATATAATATATATTTTTTCAAAAATATTTT
1 AAAA-ACTATATATTATATATATTTTCAAAAATGTTTT
* *
3656719 AAAATCTATATATTATATA-ATTTTAAAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
*
3656755 CAAAAACTATATATTATATA-AGTTTTC-AAAATAATTTT
1 -AAAAACTATATATTATATATA-TTTTCAAAAAT-GTTTT
*
3656793 AAAAACTATATATTATATATATTTTCTAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
3656830 -AAAACTATATATTATATA-ATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
* *
3656865 AAAAACTATGTAATATATATATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
*
3656902 AAAAACTATATATTATATATATTTTCTAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
3656939 AAAAACTATATATTATATA-ATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
3656975 AAAAACTATATATTATATA-ATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
* * *
3657011 AAAAACTTTGTAATATATATATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
*
3657048 AAAAACTATATATTATATATATTTTCTAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
* *
3657085 AAATACTATATTTTATATA-ATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
* *
3657121 AAAAACTGTATA--ATATATATATTCAAAAATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAATGTTTT
*
3657156 AAAAAAACTATATATTATATACGTATTTTCAAAAACCG-TTT
1 --AAAAACTATATATTATATA--TATTTTCAAAAA-TGTTTT
**
3657197 GCAAACTATATA-TATATAT
1 AAAAACTATATATTATATAT
3657216 GTATAAAATA
Statistics
Matches: 446, Mismatches: 35, Indels: 34
0.87 0.07 0.07
Matches are distributed among these distances:
34 5 0.01
35 32 0.07
36 142 0.32
37 213 0.48
38 24 0.05
39 15 0.03
41 14 0.03
42 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (37 bp):
AAAAACTATATATTATATATATTTTCAAAAATGTTTT
Found at i:3656848 original size:73 final size:73
Alignment explanation
Indices: 3656681--3657190 Score: 708
Period size: 73 Copynumber: 6.9 Consensus size: 73
3656671 AACTATTTCC
* * * * *
3656681 AAAACACTATATAATATATATTTTTTCAAAAATATTTTAAAATCTATATATTATATA-ATTTTAA
1 AAAA-ACTATATATTATATA-ATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCA
3656745 AAAATGTTTT
64 AAAATGTTTT
*
3656755 CAAAAACTATATATTATATAAGTTTTC-AAAATAATTTTAAAAACTATATATTATATATATTTTC
1 -AAAAACTATATATTATATAA-TTTTCAAAAAT-GTTTTAAAAACTATATATTATATATATTTTC
*
3656819 TAAAATGTTTT
63 AAAAATGTTTT
* *
3656830 -AAAACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTATGTAATATATATATTTTCAAA
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAAA
3656894 AATGTTTT
66 AATGTTTT
*
3656902 AAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAACTATATATTATATA-ATTTTCAA
1 AAAAACTATATATTATATA-ATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAA
3656966 AAATGTTTT
65 AAATGTTTT
* * *
3656975 AAAAACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTTTGTAATATATATATTTTCAAA
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAAA
3657040 AATGTTTT
66 AATGTTTT
* * *
3657048 AAAAACTATATATTATATATATTTTCTAAAATGTTTTAAATACTATATTTTATATA-ATTTTCAA
1 AAAAACTATATATTATATA-ATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAA
3657112 AAATGTTTT
65 AAATGTTTT
* * *
3657121 AAAAACTGTATAATATAT-ATATTCAAAAATGTTTTAAAAAAACTATATATTATATACGTATTTT
1 AAAAACTATATATTATATAATTTTCAAAAATGTTTT--AAAAACTATATATTATATA--TATTTT
3657185 CAAAAA
62 CAAAAA
3657191 CCGTTTGCAA
Statistics
Matches: 394, Mismatches: 28, Indels: 25
0.88 0.06 0.06
Matches are distributed among these distances:
71 15 0.04
72 75 0.19
73 169 0.43
74 105 0.27
75 19 0.05
76 11 0.03
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (73 bp):
AAAAACTATATATTATATAATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCAAA
AATGTTTT
Found at i:3657126 original size:110 final size:109
Alignment explanation
Indices: 3656681--3657190 Score: 740
Period size: 110 Copynumber: 4.6 Consensus size: 109
3656671 AACTATTTCC
* * * *
3656681 AAAACACTATATAATATATATTTTTTCAAAAATATTTTAAAATCTATATATTATATAATTTTAAA
1 AAAA-ACTATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATAATTTTCAA
*
3656746 AAATGTTTTCAAAAACTATATATTATATAAGTTTTC-AAAATAATTTT
65 AAATGTTTT-AAAAACTATATATTATATAA-TTTTCAAAAAT-GTTTT
* *
3656793 AAAAACTATATATTATATATATTTTCTAAAATGTTTT-AAAACTATATATTATATAATTTTCAAA
1 AAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATAATTTTCAAA
* *
3656857 AATGTTTTAAAAACTATGTAATATATATATTTTCAAAAATGTTTT
66 AATGTTTTAAAAACTATATATTATATA-ATTTTCAAAAATGTTTT
* *
3656902 AAAAACTATATATTATATATATTTTCTAAAATGTTTTAAAAACTATATATTATATAATTTTCAAA
1 AAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATAATTTTCAAA
3656967 AATGTTTTAAAAACTATATATTATATAATTTTCAAAAATGTTTT
66 AATGTTTTAAAAACTATATATTATATAATTTTCAAAAATGTTTT
* * *
3657011 AAAAACTTTGTAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATATATTTTCTA
1 AAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATA-ATTTTCAA
* *
3657076 AAATGTTTTAAATACTATATTTTATATAATTTTCAAAAATGTTTT
65 AAATGTTTTAAAAACTATATATTATATAATTTTCAAAAATGTTTT
*
3657121 AAAAACTGTATAATATATATA--TTCAAAAATGTTTTAAAAAAACTATATATTATATACGTATTT
1 AAAAACTATATAATATATATATTTTCAAAAATGTTTT--AAAAACTATATATTATATA---ATTT
3657184 TCAAAAA
61 TCAAAAA
3657191 CCGTTTGCAA
Statistics
Matches: 369, Mismatches: 21, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
108 14 0.04
109 132 0.36
110 179 0.49
111 29 0.08
112 15 0.04
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (109 bp):
AAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAACTATATATTATATAATTTTCAAA
AATGTTTTAAAAACTATATATTATATAATTTTCAAAAATGTTTT
Found at i:3658024 original size:84 final size:84
Alignment explanation
Indices: 3657755--3658806 Score: 890
Period size: 84 Copynumber: 12.7 Consensus size: 84
3657745 GCTCTTCTTA
* * * * * *
3657755 CCTTGAGCTATGTTGTAAATTTGATTTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T
1 CCTTGAGCTATGCTGCAAA--TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
* * *
3657817 -TTAGCAGATAGCCCTTCTCG
64 GTTGGCAGATAACCCTTCTAG
* * ** * * * * *
3657837 ACTTAATATATGCTGCAAATAACAGTGCATTGGAGTTGAGCGTAATCGAACTCGAAGG--TTTTG
1 CCTTGAGCTATGCTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
* * *
3657900 TTGACGGATAACCTTTCTAG
65 TTGGCAGATAACCCTTCTAG
** * * * ** *
3657920 CCTTGATTTATGCTGTAAATGATATACCTTAAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTCT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
3657985 TAGCAGATAACCCCTCTAG
66 TGGCAGATAACCCTTCTAG
* * * *
3658004 CCTTGAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
3658069 TGGCAGATAGCCCTTCTCG
66 TGGCAGATAACCCTTCTAG
* * * * ** * *
3658088 ACTTAAGCTATTCTGCAAATAATGGTGCCTCT-GAGCTGAGTATAATCAAACTCGAAGGTC---T
1 CCTTGAGCTATGCTGCAAATGAT-GTGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
3658149 -TTGGCAGATAACCCTTCTAG
64 GTTGGCAGATAACCCTTCTAG
* ** * *
3658169 CCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGATTGTAGTCAAACTCGAAGGTCTTTGGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
3658234 TGGAAGATAACCCTTCTCG
66 TGGCAGATAACCCTTCTAG
* * * * * *
3658253 ACTTAAGCTATGTTACAAATGATGTGCTTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
*
3658318 TGGCAGATAACCCTTCTCG
66 TGGCAGATAACCCTTCTAG
** * * * ** * * *
3658337 ATTTAAGCTATGCTACAAATGATAGTGCCTCT-AAGCTGAGTATAATCGAACTCGAATGTCTTTA
1 CCTTGAGCTATGCTGCAAATGAT-GTGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
3658401 G-T---AGATAACCCTTCTAG
64 GTTGGCAGATAACCCTTCTAG
* * ** *
3658418 CCTTGAGTTATGCTTCAAATGATGTGCCTTTAAGATGAGCGTAGTCGAACTCG-AGGTCTTTTGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * * * *
3658482 TAGCAAATAGCCTTTCTTG
66 TGGCAGATAACCCTTCTAG
* * * * *
3658501 CCTTGAGCTATGTTGCAAATGGTGTGCCTTGGAGCTGAACGTAGTTGAACTCGAAGGTCTTTTGC
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* *
3658566 TGGCAGATAGCCCTTCTCG
66 TGGCAGATAACCCTTCTAG
* * * ** * *
3658585 ACTTAAGCTATGCTTCAAATGATGGTGCCTCT-GAGCTGAGTATAATCGAACTCGAAGGAC---T
1 CCTTGAGCTATGCTGCAAATGAT-GTGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
*
3658646 -TTGGCAGATAACCCTTATAG
64 GTTGGCAGATAACCCTTCTAG
* * * * * * * *
3658666 CCTTAAGTTATGCTACAAATGATGTTCCTTTGAGCCGAGTGTAGTCAAACTCGAAGGTCTTTTGT
1 CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
* * * *
3658731 TGGCAAATAGCCATTCTTG
66 TGGCAGATAACCCTTCTAG
*
3658750 CCTTGAGCTATGTTGCAAAT-AGTGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
1 CCTTGAGCTATGCTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
3658807 CCTTAACTGA
Statistics
Matches: 778, Mismatches: 162, Indels: 58
0.78 0.16 0.06
Matches are distributed among these distances:
79 11 0.01
80 86 0.11
81 133 0.17
82 42 0.05
83 88 0.11
84 325 0.42
85 90 0.12
86 3 0.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (84 bp):
CCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT
TGGCAGATAACCCTTCTAG
Found at i:3658174 original size:165 final size:165
Alignment explanation
Indices: 3657776--3658806 Score: 865
Period size: 165 Copynumber: 6.2 Consensus size: 165
3657766 GTTGTAAATT
* * * * * * * *
3657776 TGATTTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTAGCAGATAGCCCTTCTCGACT
1 TGATGTGCCTCTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGCCT
* * * * * * * *
3657840 T-AATATATGCTGCAAATAACAGTGCATTGGAGTTGAGCGTAATCGAACTCGAAGGT-TTT-GTT
66 TGAGT-TATGCTGCAAATGA-TGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTT
* * * * * * * ** * *
3657902 GACGGATAACCTTTCTAGCCTTGATTTATGCTGTAAA
129 GGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAA
* * * * *
3657939 TGATATACCT-TAAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTCTTAGCAGATAACCCCTCTA
1 TGATGTGCCTCT-GAGCTGAGCGTAGTCGAACTCGAAGGTC--TT-TTGGCAGATAACCCTTCTA
* *
3658003 GCCTTGAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGG
62 GCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGG
3658068 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAA
127 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAA
* ** * *
3658107 TAATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGTC-TTTGGCAGATAACCCTTCTAGCC
1 TGAT-GTGCCTCTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGCC
*
3658171 TTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGATTGTAGTCAAACTCGAAGGTCTTTGGTTG
65 TTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTG
* * *
3658236 GAAGATAACCCTTCTCGACTTAAGCTATGT-TACAAA
130 GCAGATAGCCCTTCTCGACTTAAGCTAT-TCTGCAAA
* * *
3658272 TGATGTG-CTTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTC
1 TGATGTGCCTCT-GAGCTGAGCGTAGTCGAACTCGAAGGTC--TT-TTGGCAGATAACCCTTCTA
** * * * * * * * *
3658336 GATTTAAGCTATGCTACAAATGATAGTGCCTCT-AAGCTGAGTATAATCGAACTCGAATGTCTTT
62 GCCTTGAGTTATGCTGCAAATGAT-GTGCCT-TGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTT
* * * * * * * *
3658400 AG-T---AGATAACCCTTCTAGCCTTGAGTTATGCTTCAAA
125 GGTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAA
* * * * * * *
3658437 TGATGTGCCTTTAAGATGAGCGTAGTCGAACTCG-AGGTCTTTTGTTAGCAAATAGCCTTTCTTG
1 TGATGTGCCTCTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG---GCAGATAACCCTTCTAG
* * * ** ** * *
3658501 CCTTGAGCTATGTTGCAAATGGTGTGCCTTGGAGCTGAACGTAGTTGAACTCGAAGGTCTTTTGC
63 CCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGT
* *
3658566 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAA
128 TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAA
** * * *
3658604 TGATGGTGCCTCTGAGCTGAGTATAATCGAACTCGAAGGAC-TTTGGCAGATAACCCTTATAGCC
1 TGAT-GTGCCTCTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGCC
* * * * * *
3658668 TTAAGTTATGCTACAAATGATGTTCCTTTGAGCCGAGTGTAGTCAAACTCGAAGGTCTTTTGTTG
65 TTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTG
* * * * *
3658733 GCAAATAGCCATTCTTGCCTTGAGCTATGT-TGCAAA
130 GCAGATAGCCCTTCTCGACTTAAGCTAT-TCTGCAAA
3658769 T-AGTGTGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGG
1 TGA-TGTGCCTCT-GAGCTGAGCGTAGTCGAACTCGAAGG
3658807 CCTTAACTGA
Statistics
Matches: 706, Mismatches: 129, Indels: 65
0.78 0.14 0.07
Matches are distributed among these distances:
161 3 0.00
162 4 0.01
163 68 0.10
164 94 0.13
165 265 0.38
166 38 0.05
167 69 0.10
168 100 0.14
169 63 0.09
170 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (165 bp):
TGATGTGCCTCTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGCCT
TGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGG
CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAA
Found at i:3658222 original size:249 final size:249
Alignment explanation
Indices: 3657748--3658806 Score: 1290
Period size: 249 Copynumber: 4.3 Consensus size: 249
3657738 ACATATAGCT
* * * * * *
3657748 CTTCTTACCTTGAGCTATGTTGTAAATTTGATTTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
1 CTTCTTGCCTTGAGCTATGTTGCAAA--TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* ** * * *
3657813 GTC---T-TTAGCAGATAGCCCTTCTCGACTTAATATATGCTGCAAATAACAGTGCAT-TGGAGT
64 GTCTTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATAGTGCCTCT-GAGC
** * * * *
3657873 TGAGCGTAATCGAACTCGAAGGT-TTTGTTGACGGATAACCTTTCTAGCCTTGATTTATGCTGTA
128 TGAGTATAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTAGCCTTGAGTTATGCTGCA
* * * * * *
3657937 AATGATATACCTTAAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTCTTAGCAGATAACC
190 AATGATGTGCCTTTAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTAGCAAATAACC
* * * ** *
3657997 CCTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGT
1 CTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * *
3658062 CTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATAATGGTGCCTCTGAGCTGA
66 CTTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATAGTGCCTCTGAGCTGA
*
3658127 GTATAATCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
131 GTATAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
** ** * *
3658192 GTGCCTTGGAGCTGATTGTAGTCAAACTCGAAGGTCTTTGGTT-GGAAGATAACC
196 GTGCCTTTAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTAGCAA-ATAACC
* * * * * *
3658246 CTTCTCGACTTAAGCTATGTTACAAATGATGTGCTTTGGAGCTGAGCGTAGTCAAACTCGAAGGT
1 CTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * * * *
3658311 CTTTTGTTGGCAGATAACCCTTCTCGATTTAAGCTATGCTACAAATGATAGTGCCTCTAAGCTGA
66 CTTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATAGTGCCTCTGAGCTGA
* * * *
3658376 GTATAATCGAACTCGAATGTCTTTAGTAGATAACCCTTCTAGCCTTGAGTTATGCTTCAAATGAT
131 GTATAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
* * *
3658441 GTGCCTTTAAGATGAGCGTAGTCGAACTCG-AGGTCTTTTGTTAGCAAATAGCC
196 GTGCCTTTAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTAGCAAATAACC
* * * *
3658494 TTTCTTGCCTTGAGCTATGTTGCAAATGGTGTGCCTTGGAGCTGAACGTAGTTGAACTCGAAGGT
1 CTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
* * * *
3658559 CTTTTGCTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGGTGCCTCTGAGCTGA
66 CTTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATAGTGCCTCTGAGCTGA
* * * *
3658624 GTATAATCGAACTCGAAGGACTTTGGCAGATAACCCTTATAGCCTTAAGTTATGCTACAAATGAT
131 GTATAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
* * * * * *
3658689 GTTCCTTTGAGCCGAGTGTAGTCAAACTCGAAGGTCTTTTGTTGGCAAATAGCC
196 GTGCCTTTAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTAGCAAATAACC
*
3658743 ATTCTTGCCTTGAGCTATGTTGCAAAT-AGTGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
1 CTTCTTGCCTTGAGCTATGTTGCAAATGA-TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
3658807 CCTTAACTGA
Statistics
Matches: 696, Mismatches: 104, Indels: 20
0.85 0.13 0.02
Matches are distributed among these distances:
247 35 0.05
248 214 0.31
249 375 0.54
250 1 0.00
251 66 0.09
252 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (249 bp):
CTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
CTTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATAATAGTGCCTCTGAGCTGA
GTATAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
GTGCCTTTAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTAGCAAATAACC
Found at i:3658584 original size:332 final size:330
Alignment explanation
Indices: 3658163--3658803 Score: 774
Period size: 332 Copynumber: 1.9 Consensus size: 330
3658153 CAGATAACCC
* **
3658163 TTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGATTGTAGTCAAACTCGAAGGTC
1 TTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTC
* *
3658228 TTTGGTTGGAAGATAACCCTTCTCGACTTAAGCTATG-TTACAAATGAT-GTG-CTTTGGAGCTG
66 TTTGGCTGGAAGATAACCCTTCTCGACTTAAGCTATGCTT-CAAATGATGGTGCCTCT-GAGCTG
* * * * * *
3658290 AGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGATTTAAGCTATGCTACAA
129 AGCATAATCAAACTCGAAGGAC---T-TTGGCAGATAACCCTTATAGACTTAAGCTATGCTACAA
* * * * *
3658355 ATGATAGTGCCTCTAAGCTGAGTATAATCGAACTCGAATGTCTTTAG-T-AGATAACCCTTCTAG
190 ATGAT-GTGCCTCTAAGCCGAGTATAATCAAACTCGAAGGTCTTTAGTTGAAATAACCATTCTAG
* *
3658418 CCTTGAGTTATGCTT-CAAAT-GATGTGCCTTTAAGATGAGCGTAGTCGAACTCGAGGTCTTTTG
254 CCTTGAGCTATG-TTGCAAATAG-TGTGCCTTGAAGATGAGCGTAGTCGAACTCGAGGTCTTTTG
3658481 TTAGCAAATAGCCT
317 TTAGCAAATAGCCT
* * * **
3658495 TTCTTGCCTTGAGCTATGTTGCAAATGGTGTGCCTTGGAGCTGAACGTAGTTGAACTCGAAGGTC
1 TTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTC
* * *
3658560 TTTTGCTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTTCAAATGATGGTGCCTCTGAGCTGAG
66 TTTGGCTGGAAGATAACCCTTCTCGACTTAAGCTATGCTTCAAATGATGGTGCCTCTGAGCTGAG
* * * *
3658625 TATAATCGAACTCGAAGGACTTTGGCAGATAACCCTTATAGCCTTAAGTTATGCTACAAATGATG
131 CATAATCAAACTCGAAGGACTTTGGCAGATAACCCTTATAGACTTAAGCTATGCTACAAATGATG
* * * * * * * *
3658690 TTCCTTTGAGCCGAGTGTAGTCAAACTCGAAGGTCTTTTGTTGGCAAATAGCCATTCTTGCCTTG
196 TGCCTCTAAGCCGAGTATAATCAAACTCGAAGGTCTTTAGTT-G-AAATAACCATTCTAGCCTTG
* *
3658755 AGCTATGTTGCAAATAGTGTGCCTTGGAGCTGAGCGTAGTCGAACTCGA
259 AGCTATGTTGCAAATAGTGTGCCTTGAAGATGAGCGTAGTCGAACTCGA
3658804 AGGCCTTAAC
Statistics
Matches: 260, Mismatches: 40, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
328 32 0.12
329 39 0.15
330 1 0.00
331 2 0.01
332 154 0.59
333 29 0.11
334 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (330 bp):
TTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTC
TTTGGCTGGAAGATAACCCTTCTCGACTTAAGCTATGCTTCAAATGATGGTGCCTCTGAGCTGAG
CATAATCAAACTCGAAGGACTTTGGCAGATAACCCTTATAGACTTAAGCTATGCTACAAATGATG
TGCCTCTAAGCCGAGTATAATCAAACTCGAAGGTCTTTAGTTGAAATAACCATTCTAGCCTTGAG
CTATGTTGCAAATAGTGTGCCTTGAAGATGAGCGTAGTCGAACTCGAGGTCTTTTGTTAGCAAAT
AGCCT
Found at i:3658625 original size:497 final size:498
Alignment explanation
Indices: 3657906--3658806 Score: 1369
Period size: 497 Copynumber: 1.8 Consensus size: 498
3657896 TTTGTTGACG
* * *
3657906 GATAACCTTTCTAGCCTTGATTTATGCTGTAAATGATATACCTTAAAGCTGAGCGTAGTCGAACT
1 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATACCTTAAAGATGAGCGTAGTCGAACT
* *
3657971 CGAAGGTCTTTTCTTAGCAGATAACCCCTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTGG
66 CGAAGGTCTTTTCTTAGCAAATAACCCCTCTAGCCTTGAGCTATACTGCAAATGATGTGCCTTGG
* * *
3658036 AGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
131 AGCTGAACGTAGTCAAACTCGAAGGTCTTTGGCTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
* *
3658101 TGCAAATAATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGTCTTTGGCAGATAACCCTTC
196 TGCAAATAATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGACTTTGGCAGATAACCCTTA
* * * *
3658166 TAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGATTGTAGTCAAACTCGAAGGTCTTT
261 TAGCCTTAAGTTATGCTACAAATGATGTGCCTTGGAGCCGAGTGTAGTCAAACTCGAAGGTCTTT
* *
3658231 GGTTGG-AAGATAACCCTTCTCGACTTAAGCTATGTTACAAAT-GATGTGCTTTGGAGCTGAGCG
326 GGTTGGCAA-ATAACCATTCTCGACTTAAGCTATGTTACAAATAG-TGTGCCTTGGAGCTGAGCG
3658294 TAGTCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGATTTAAGCTATGCTACAAATGA
389 TAGTCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGATTTAAGCTATGCTACAAATGA
3658359 TAGTGCCTCTAAGCTGAGTATAATCGAACTCGAATGTCTTTAGTA
454 TAGTGCCTCTAAGCTGAGTATAATCGAACTCGAATGTCTTTAGTA
* * *
3658404 GATAACCCTTCTAGCCTTGAGTTATGCT-TCAAATGATGTGCCTTTAAGATGAGCGTAGTCGAAC
1 GATAACCCTTCTAGCCTTGAGTTATGCTGT-AAATGATATACCTTAAAGATGAGCGTAGTCGAAC
* * ** * ** *
3658468 TCG-AGGTCTTTTGTTAGCAAATAGCCTTTCTTGCCTTGAGCTATGTTGCAAATGGTGTGCCTTG
65 TCGAAGGTCTTTTCTTAGCAAATAACCCCTCTAGCCTTGAGCTATACTGCAAATGATGTGCCTTG
** *
3658532 GAGCTGAACGTAGTTGAACTCGAAGGTCTTTTGCTGGCAGATAGCCCTTCTCGACTTAAGCTATG
130 GAGCTGAACGTAGTCAAACTCGAAGGTCTTTGGCTGGCAGATAGCCCTTCTCGACTTAAGCTATG
* * *
3658597 CTTCAAATGATGGTGCCTCTGAGCTGAGTATAATCGAACTCGAAGGACTTTGGCAGATAACCCTT
195 CTGCAAATAATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGACTTTGGCAGATAACCCTT
* *
3658662 ATAGCCTTAAGTTATGCTACAAATGATGTTCCTTTGAGCCGAGTGTAGTCAAACTCGAAGGTCTT
260 ATAGCCTTAAGTTATGCTACAAATGATGTGCCTTGGAGCCGAGTGTAGTCAAACTCGAAGGTCTT
* * * * * *
3658727 TTGTTGGCAAATAGCCATTCTTGCCTTGAGCTATGTTGCAAATAGTGTGCCTTGGAGCTGAGCGT
325 TGGTTGGCAAATAACCATTCTCGACTTAAGCTATGTTACAAATAGTGTGCCTTGGAGCTGAGCGT
*
3658792 AGTCGAACTCGAAGG
390 AGTCAAACTCGAAGG
3658807 CCTTAACTGA
Statistics
Matches: 358, Mismatches: 42, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
497 296 0.83
498 62 0.17
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (498 bp):
GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATACCTTAAAGATGAGCGTAGTCGAACT
CGAAGGTCTTTTCTTAGCAAATAACCCCTCTAGCCTTGAGCTATACTGCAAATGATGTGCCTTGG
AGCTGAACGTAGTCAAACTCGAAGGTCTTTGGCTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
TGCAAATAATGGTGCCTCTGAGCTGAGTATAATCAAACTCGAAGGACTTTGGCAGATAACCCTTA
TAGCCTTAAGTTATGCTACAAATGATGTGCCTTGGAGCCGAGTGTAGTCAAACTCGAAGGTCTTT
GGTTGGCAAATAACCATTCTCGACTTAAGCTATGTTACAAATAGTGTGCCTTGGAGCTGAGCGTA
GTCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGATTTAAGCTATGCTACAAATGATA
GTGCCTCTAAGCTGAGTATAATCGAACTCGAATGTCTTTAGTA
Found at i:3660106 original size:82 final size:87
Alignment explanation
Indices: 3660000--3660221 Score: 233
Period size: 95 Copynumber: 2.5 Consensus size: 87
3659990 AGCTGAATCT
* *
3660000 ATAAAGCCGGGGCATTTAAACAATTGCTCTAGAGGGACAACTCAA-TAT-GTA-AA-CACCTTTA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACCTTTA
* *
3660061 TTAGG-TGAGCTGAATCTTATCC
66 TCAGGCT-AGCTGAATATTATCC
* *
3660083 AT-GAGTCGGGGCGTTTAACCAATTGC-CTTAGAGGGACAACTCAACCTTTATTGTATAGTATAA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTC-A-----A-T-TATAGTATAA
*
3660146 TCGCCTTTATCAGGCTAGCTGAATATTATCC
57 TCACCTTTATCAGGCTAGCTGAATATTATCC
*
3660177 ATAAAGCCGGGGCGTGTAACCAATTGCTCTAGAGGGACAACTCAA
1 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
3660222 GCTTTATTGT
Statistics
Matches: 113, Mismatches: 10, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
81 1 0.01
82 34 0.30
83 3 0.03
88 1 0.01
89 1 0.01
91 3 0.03
92 3 0.03
93 2 0.02
94 28 0.25
95 36 0.32
96 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (87 bp):
ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACCTTTA
TCAGGCTAGCTGAATATTATCC
Found at i:3660217 original size:95 final size:93
Alignment explanation
Indices: 3660055--3660238 Score: 264
Period size: 95 Copynumber: 2.0 Consensus size: 93
3660045 TATGTAAACA
* * * * *
3660055 CCTTTATTAGGTGAGCTGAATCTTATCCATGAGTCGGGGCGTTTAACCAATTGCCTTAGAGGGAC
1 CCTTTATCAGGTGAGCTGAATATTATCCATAAGCCGGGGCGTGTAACCAATTGCCTTAGAGGGAC
3660120 AACTCAACCTTTATTGTATAGTATAATCG
66 AACTCAACCTTTATTGTATA-TATAATCG
3660149 CCTTTATCAGGCT-AGCTGAATATTATCCATAAAGCCGGGGCGTGTAACCAATTG-CTCTAGAGG
1 CCTTTATCAGG-TGAGCTGAATATTATCCAT-AAGCCGGGGCGTGTAACCAATTGCCT-TAGAGG
*
3660212 GACAACTCAAGCTTTATTGTATATATA
63 GACAACTCAACCTTTATTGTATATATA
3660239 TAATTATAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
94 32 0.40
95 49 0.60
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (93 bp):
CCTTTATCAGGTGAGCTGAATATTATCCATAAGCCGGGGCGTGTAACCAATTGCCTTAGAGGGAC
AACTCAACCTTTATTGTATATATAATCG
Found at i:3662986 original size:24 final size:23
Alignment explanation
Indices: 3662959--3663008 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
3662949 CAAAAGAGAA
*
3662959 GAAATGAAATAGAATAAAAAAAAT
1 GAAAT-AAATAGAAGAAAAAAAAT
* *
3662983 GAAAATAAATTGAAGAAATAAAAT
1 G-AAATAAATAGAAGAAAAAAAAT
3663007 GA
1 GA
3663009 GAGAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.05
24 17 0.77
25 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (23 bp):
GAAATAAATAGAAGAAAAAAAAT
Found at i:3663001 original size:19 final size:20
Alignment explanation
Indices: 3662955--3663006 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
3662945 AAATCAAAAG
3662955 AGAAGAAATG-AAATAGAAT
1 AGAAGAAATGAAAATAGAAT
* *
3662974 AAAAAAAATGAAAATA-AAT
1 AGAAGAAATGAAAATAGAAT
*
3662993 TGAAGAAAT-AAAAT
1 AGAAGAAATGAAAAT
3663007 GAGAGAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 5 0.19
19 17 0.63
20 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.17
Consensus pattern (20 bp):
AGAAGAAATGAAAATAGAAT
Found at i:3671771 original size:20 final size:20
Alignment explanation
Indices: 3671729--3671777 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
3671719 TAACTTTTTC
*
3671729 TTTTATCTTTCATTATTCAT
1 TTTTATCTTTCATTATTAAT
* *
3671749 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAT
*
3671768 TTTTACCTTT
1 TTTTATCTTT
3671778 TCTCTTTCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAT
Done.