Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 89 of 161
Found at i:28300085 original size:43 final size:44
Alignment explanation
Indices: 28299982--28300217 Score: 219
Period size: 44 Copynumber: 5.4 Consensus size: 44
28299972 GGGTCTCCAA
* * ** *
28299982 TCCC-ATCTTATGTGTATGCGATATGTGAATTTTATCCCGTTCT
1 TCCCTATCTTATGTGTATGCTATGTGTGGGTTTTATCCAGTTCT
* *
28300025 TCCCCATCTTATATGTATGCTATGTGTGGGTTTT-TCCAGTTCT
1 TCCCTATCTTATGTGTATGCTATGTGTGGGTTTTATCCAGTTCT
* * *
28300068 TCCCTATCTTGTGTGTATG-TCATGTATGGGTTTTATCCAATTCT
1 TCCCTATCTTATGTGTATGCT-ATGTGTGGGTTTTATCCAGTTCT
* * * * * *
28300112 TTCCTAT-TTGTGTATATACTATGTGTGGATTTTATCTAGTTCT
1 TCCCTATCTTATGTGTATGCTATGTGTGGGTTTTATCCAGTTCT
* * * * * *
28300155 TCCCTATCTTGTGTGTACGCCATGTATGAGTTTTATCCAATTCT
1 TCCCTATCTTATGTGTATGCTATGTGTGGGTTTTATCCAGTTCT
* *
28300199 TCTCTCTCTTATGTGTATG
1 TCCCTATCTTATGTGTATG
28300218 TCCGTTGTGC
Statistics
Matches: 156, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.01
43 74 0.47
44 81 0.52
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (44 bp):
TCCCTATCTTATGTGTATGCTATGTGTGGGTTTTATCCAGTTCT
Found at i:28300190 original size:44 final size:44
Alignment explanation
Indices: 28300011--28300217 Score: 211
Period size: 43 Copynumber: 4.8 Consensus size: 44
28300001 GATATGTGAA
* * * * * *
28300011 TTTTATCCCGTTCTTCCCCATCTTATATGTATGCTATGTGTGGG
1 TTTTATCCAGTTCTTCCCTATCTTGTGTGTATGCCATGTATGGG
*
28300055 TTTT-TCCAGTTCTTCCCTATCTTGTGTGTATGTCATGTATGGG
1 TTTTATCCAGTTCTTCCCTATCTTGTGTGTATGCCATGTATGGG
* * * * * * *
28300098 TTTTATCCAATTCTTTCCTAT-TTGTGTATATACTATGTGTGGA
1 TTTTATCCAGTTCTTCCCTATCTTGTGTGTATGCCATGTATGGG
* * *
28300141 TTTTATCTAGTTCTTCCCTATCTTGTGTGTACGCCATGTATGAG
1 TTTTATCCAGTTCTTCCCTATCTTGTGTGTATGCCATGTATGGG
* * * *
28300185 TTTTATCCAATTCTTCTCTCTCTTATGTGTATG
1 TTTTATCCAGTTCTTCCCTATCTTGTGTGTATG
28300218 TCCGTTGTGC
Statistics
Matches: 130, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
43 70 0.54
44 60 0.46
ACGTcount: A:0.15, C:0.19, G:0.16, T:0.49
Consensus pattern (44 bp):
TTTTATCCAGTTCTTCCCTATCTTGTGTGTATGCCATGTATGGG
Found at i:28305174 original size:19 final size:18
Alignment explanation
Indices: 28305134--28305174 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
28305124 TTGAGCTTGG
*
28305134 ATTTCACCATATTAAGCC
1 ATTTCACCATATTAAGCA
*
28305152 ATTTCACCATTATTGAGCA
1 ATTTCACCA-TATTAAGCA
28305171 ATTT
1 ATTT
28305175 TTTGTCATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (18 bp):
ATTTCACCATATTAAGCA
Found at i:28305414 original size:79 final size:79
Alignment explanation
Indices: 28305283--28305449 Score: 300
Period size: 79 Copynumber: 2.1 Consensus size: 79
28305273 CAAAACAATT
28305283 TTTTAGGGGCGAATGAAATTTTAACTTTTTATAGTCTATATCTTTATAA-TTTTGAAAGGATTAA
1 TTTTAGGGGCGAATGAAATTTTAACTTTTTATAGTCTATATCTTTATAATTTTTG-AAGGATTAA
*
28305347 ATCGAATTTTTATAA
65 ATAGAATTTTTATAA
*
28305362 TTTTAGGGGCGGATGAAATTTTAACTTTTTATAGTCTATATCTTTATAATTTTTGAAGGATTAAA
1 TTTTAGGGGCGAATGAAATTTTAACTTTTTATAGTCTATATCTTTATAATTTTTGAAGGATTAAA
28305427 TAGAATTTTTATAA
66 TAGAATTTTTATAA
28305441 TTTTAGGGG
1 TTTTAGGGG
28305450 GGCTAAAGTG
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
79 80 0.94
80 5 0.06
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (79 bp):
TTTTAGGGGCGAATGAAATTTTAACTTTTTATAGTCTATATCTTTATAATTTTTGAAGGATTAAA
TAGAATTTTTATAA
Found at i:28307091 original size:26 final size:27
Alignment explanation
Indices: 28307058--28307117 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
28307048 AAAAATAATT
*
28307058 AAAATATTAT-AATTTTTTTATTTATC
1 AAAATATTATAAAATTTTTTATTTATC
28307084 AAAATATTATAAAATTTTTTATTTATC
1 AAAATATTATAAAATTTTTTATTTATC
28307111 AAAATAT
1 AAAATAT
28307118 ACCAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 10 0.31
27 22 0.69
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
AAAATATTATAAAATTTTTTATTTATC
Found at i:28307432 original size:18 final size:18
Alignment explanation
Indices: 28307411--28307445 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28307401 GTAATAACTC
*
28307411 TATTTTAATTTAATAAAT
1 TATTCTAATTTAATAAAT
*
28307429 TATTCTCATTTAATAAA
1 TATTCTAATTTAATAAA
28307446 CTCTAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTCTAATTTAATAAAT
Found at i:28307456 original size:15 final size:15
Alignment explanation
Indices: 28307436--28307465 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28307426 AATTATTCTC
28307436 ATTTAATAAACTCTA
1 ATTTAATAAACTCTA
28307451 ATTTAATAAACTCTA
1 ATTTAATAAACTCTA
28307466 TTTTGGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAATAAACTCTA
Found at i:28307535 original size:45 final size:45
Alignment explanation
Indices: 28307471--28307559 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
28307461 CTCTATTTTG
28307471 GTAATTTGATGAAAATAGTTTATTAAATTAAAATAGAGTTATTAA
1 GTAATTTGATGAAAATAGTTTATTAAATTAAAATAGAGTTATTAA
*
28307516 GTAATTTGATGAGAATAGTTTATTAAATTAAAATAGAGTTATTA
1 GTAATTTGATGAAAATAGTTTATTAAATTAAAATAGAGTTATTA
28307560 CTTATTAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (45 bp):
GTAATTTGATGAAAATAGTTTATTAAATTAAAATAGAGTTATTAA
Found at i:28309257 original size:18 final size:18
Alignment explanation
Indices: 28309234--28309295 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
28309224 TAAAATAGAG
28309234 TTATTAAATAAGAATAGT
1 TTATTAAATAAGAATAGT
* * *
28309252 TTATTAAATTACAATAGA
1 TTATTAAATAAGAATAGT
* * *
28309270 GT-TTAGATGAGAATAGT
1 TTATTAAATAAGAATAGT
28309287 TTATTAAAT
1 TTATTAAAT
28309296 TAAAATAGAG
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.45, C:0.02, G:0.13, T:0.40
Consensus pattern (18 bp):
TTATTAAATAAGAATAGT
Found at i:28309290 original size:35 final size:35
Alignment explanation
Indices: 28309220--28309307 Score: 131
Period size: 35 Copynumber: 2.5 Consensus size: 35
28309210 AATTTTTTTA
28309220 AAATTAAAATAGAGTTATTAAATAAGAATAGTTTATT
1 AAATTAAAATAGAG-T-TTAAATAAGAATAGTTTATT
* * *
28309257 AAATTACAATAGAGTTTAGATGAGAATAGTTTATT
1 AAATTAAAATAGAGTTTAAATAAGAATAGTTTATT
28309292 AAATTAAAATAGAGTT
1 AAATTAAAATAGAGTT
28309308 ATTACTTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
35 33 0.70
36 1 0.02
37 13 0.28
ACGTcount: A:0.49, C:0.01, G:0.14, T:0.36
Consensus pattern (35 bp):
AAATTAAAATAGAGTTTAAATAAGAATAGTTTATT
Found at i:28310018 original size:26 final size:27
Alignment explanation
Indices: 28309967--28310026 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 27
28309957 TGTTTTTGGT
** *
28309967 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTAATAAATAAAAAAAGTTATA
28309994 ATATTTTAATAAAT-AAAAAAGTTATA
1 ATATTTTAATAAATAAAAAAAGTTATA
28310020 ATATTTT
1 ATATTTT
28310027 GTTATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (27 bp):
ATATTTTAATAAATAAAAAAAGTTATA
Found at i:28310469 original size:23 final size:23
Alignment explanation
Indices: 28310443--28310514 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 23
28310433 ATTGTTATTA
*
28310443 ATTTTGAAAAATTTGAAATATAT
1 ATTTTGAAAAATTTTAAATATAT
**
28310466 A-TTTGAAATGTTTTATAATATAT
1 ATTTTGAAAAATTTTA-AATATAT
*
28310489 ATTTT-TAAAATTTTAAATAT-T
1 ATTTTGAAAAATTTTAAATATAT
28310510 ATTTT
1 ATTTT
28310515 TAAATTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
21 6 0.15
22 16 0.39
23 16 0.39
24 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (23 bp):
ATTTTGAAAAATTTTAAATATAT
Found at i:28310499 original size:25 final size:22
Alignment explanation
Indices: 28310450--28310572 Score: 79
Period size: 23 Copynumber: 5.1 Consensus size: 22
28310440 TTAATTTTGA
* *
28310450 AAAATTTGAAATATATA-TTTG
1 AAAATTTTAAATATATATTTTT
*
28310471 AAATGTTTTATAATATATATTTTT
1 AAA-ATTTTA-AATATATATTTTT
28310495 AAAATTTTAAATAT-TATTTTT
1 AAAATTTTAAATATATATTTTT
28310516 AAATTATTTTTTAAATTTTGAATATTATGTTTT
1 AAA--A--TTTTAAA---T--ATA-TAT-TTTT
*
28310549 AAAATATTAAATATATATTTTT
1 AAAATTTTAAATATATATTTTT
28310571 AA
1 AA
28310573 TAATATAAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 29
0.71 0.04 0.25
Matches are distributed among these distances:
21 13 0.16
22 15 0.18
23 17 0.21
24 9 0.11
25 7 0.09
26 1 0.01
28 1 0.01
29 6 0.07
30 2 0.02
31 1 0.01
32 3 0.04
33 7 0.09
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
AAAATTTTAAATATATATTTTT
Found at i:28310524 original size:32 final size:33
Alignment explanation
Indices: 28310487--28310556 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
28310477 TTTATAATAT
28310487 ATATTTTTAAAATTTTAAATATTAT-TTTTAAA
1 ATATTTTTAAAATTTTAAATATTATGTTTTAAA
* * *
28310519 TTATTTTTTAAATTTTGAATATTATGTTTTAAA
1 ATATTTTTAAAATTTTAAATATTATGTTTTAAA
28310552 ATATT
1 ATATT
28310557 AAATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (33 bp):
ATATTTTTAAAATTTTAAATATTATGTTTTAAA
Found at i:28310525 original size:23 final size:23
Alignment explanation
Indices: 28310450--28310518 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 23
28310440 TTAATTTTGA
* *
28310450 AAAATTTGA-AATATATA-TTTG
1 AAAATTTTATAATATATATTTTT
*
28310471 AAATGTTTTATAATATATATTTTT
1 AAA-ATTTTATAATATATATTTTT
28310495 AAAATTTTA-AATAT-TATTTTT
1 AAAATTTTATAATATATATTTTT
28310516 AAA
1 AAA
28310519 TTATTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 13 0.32
22 9 0.22
23 13 0.32
24 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
AAAATTTTATAATATATATTTTT
Found at i:28310529 original size:33 final size:33
Alignment explanation
Indices: 28310473--28310556 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
28310463 TATATTTGAA
28310473 ATGTTTTATAATATATATTTTTAAAATTTTAAATATT
1 ATGTTTTA-AAT-TAT-TTTTT-AAATTTTAAATATT
*
28310510 AT-TTTTAAATTATTTTTTAAATTTTGAATATT
1 ATGTTTTAAATTATTTTTTAAATTTTAAATATT
*
28310542 ATGTTTTAAAATATT
1 ATGTTTTAAATTATT
28310557 AAATATATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 15 0.34
33 16 0.36
34 3 0.07
35 3 0.07
36 5 0.11
37 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (33 bp):
ATGTTTTAAATTATTTTTTAAATTTTAAATATT
Found at i:28310553 original size:22 final size:21
Alignment explanation
Indices: 28310510--28310586 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
28310500 TTTAAATATT
* *
28310510 ATTTTTAA-ATTATTTTTTAA
1 ATTTTAAATATTATTTTTAAA
*
28310530 ATTTTGAATATTATGTTTTAAA
1 ATTTTAAATATTAT-TTTTAAA
*
28310552 ATATTAAATATATATTTTTAATA
1 ATTTTAAATAT-TATTTTTAA-A
* *
28310575 ATATAAAATATT
1 ATTTTAAATATT
28310587 TAAATATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
20 7 0.15
21 5 0.10
22 22 0.46
23 14 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTTAAATATTATTTTTAAA
Found at i:28310583 original size:23 final size:22
Alignment explanation
Indices: 28310536--28310586 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
28310526 TTAAATTTTG
*
28310536 AATATTATGTTTTAAAATATTA
1 AATATTATGTTTTAAAATATAA
28310558 AATATATAT-TTTTAATAATATAA
1 AATAT-TATGTTTTAA-AATATAA
28310581 AATATT
1 AATATT
28310587 TAAATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
AATATTATGTTTTAAAATATAA
Found at i:28310655 original size:19 final size:21
Alignment explanation
Indices: 28310631--28310679 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
28310621 TATTAGTTTT
28310631 TTTAA-TATTTT-TAATATTA
1 TTTAATTATTTTATAATATTA
28310650 TTTAATTTATTTTATAATATT-
1 TTTAA-TTATTTTATAATATTA
*
28310671 TTAAATTAT
1 TTTAATTAT
28310680 GATTTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 4 0.15
21 10 0.38
22 7 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTAATTATTTTATAATATTA
Found at i:28310673 original size:10 final size:9
Alignment explanation
Indices: 28310629--28310672 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 9
28310619 ATTATTAGTT
28310629 TTTTTAATA
1 TTTTTAATA
28310638 TTTTTAATA
1 TTTTTAATA
28310647 TTATTTAATTTA
1 TT-TTTAA--TA
28310659 TTTTATAATA
1 TTTT-TAATA
28310669 TTTT
1 TTTT
28310673 AAATTATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 11 0.35
10 11 0.35
11 2 0.06
12 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTAATA
Found at i:28310673 original size:20 final size:21
Alignment explanation
Indices: 28310636--28310679 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
28310626 GTTTTTTTAA
*
28310636 TATTTTTAATATTATTTAATT
1 TATTTTTAATATTATTTAAAT
28310657 TATTTTATAATA-T-TTTAAAT
1 TATTTT-TAATATTATTTAAAT
28310677 TAT
1 TAT
28310680 GATTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 7 0.33
22 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTTAATATTATTTAAAT
Found at i:28311256 original size:13 final size:13
Alignment explanation
Indices: 28311238--28311263 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28311228 TATAGTGAAA
28311238 ACATTTCAAATAT
1 ACATTTCAAATAT
28311251 ACATTTCAAATAT
1 ACATTTCAAATAT
28311264 GCGCCATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTCAAATAT
Found at i:28312152 original size:7 final size:7
Alignment explanation
Indices: 28312140--28312164 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28312130 TGTTAGAGTT
28312140 TAAAGTA
1 TAAAGTA
28312147 TAAAGTA
1 TAAAGTA
28312154 TAAAGTA
1 TAAAGTA
28312161 TAAA
1 TAAA
28312165 TATTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (7 bp):
TAAAGTA
Found at i:28318826 original size:7 final size:7
Alignment explanation
Indices: 28318810--28318887 Score: 54
Period size: 7 Copynumber: 10.9 Consensus size: 7
28318800 TTAATATCCA
*
28318810 AATAAGT
1 AATAAAT
28318817 AATAAAT
1 AATAAAT
28318824 AAT-AA-
1 AATAAAT
28318829 AATAAAGT
1 AATAAA-T
28318837 AATAAAT
1 AATAAAT
*
28318844 AAAGTAAAGA
1 -AA-TAAA-T
*
28318854 AAAATAAT
1 AATA-AAT
28318862 AATAAAT
1 AATAAAT
*
28318869 AATAAAA
1 AATAAAT
28318876 AATAAA-
1 AATAAAT
28318882 AATAAA
1 AATAAA
28318888 AATTGGGTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
5 3 0.05
6 10 0.17
7 25 0.43
8 12 0.21
9 8 0.14
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (7 bp):
AATAAAT
Found at i:28318838 original size:20 final size:20
Alignment explanation
Indices: 28318809--28318887 Score: 68
Period size: 17 Copynumber: 4.3 Consensus size: 20
28318799 ATTAATATCC
28318809 AAAT-AAGTAATAAATAATA
1 AAATAAAGTAATAAATAATA
28318828 AAATAAAGTAAT--A-AATA
1 AAATAAAGTAATAAATAATA
*
28318845 AAGTAAAG-AA-AAATAAT-
1 AAATAAAGTAATAAATAATA
*
28318862 -AATAAA-TAATAAAAAATAA
1 AAATAAAGTAATAAATAAT-A
28318881 AAATAAA
1 AAATAAA
28318888 AATTGGGTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
16 9 0.19
17 18 0.38
18 4 0.08
19 4 0.08
20 13 0.27
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (20 bp):
AAATAAAGTAATAAATAATA
Found at i:28318885 original size:13 final size:14
Alignment explanation
Indices: 28318821--28318889 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 14
28318811 ATAAGTAATA
28318821 AATAATAAAATAAAG
1 AATAA-AAAATAAAG
28318836 TAATAAATAAAGTAAAG
1 -AATAAA-AAA-TAAAG
* *
28318853 AAAAATAATAATAAAT
1 AATAA-AA-AATAAAG
28318869 AATAAAAAATAAA-
1 AATAAAAAATAAAG
28318882 AATAAAAA
1 AATAAAAA
28318890 TTGGGTTGCC
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
13 8 0.17
14 6 0.13
15 3 0.07
16 21 0.46
17 8 0.17
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.20
Consensus pattern (14 bp):
AATAAAAAATAAAG
Found at i:28319892 original size:39 final size:39
Alignment explanation
Indices: 28319848--28319924 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
28319838 ACATCAAAGA
*
28319848 TTTCGCATACATGAATCGGGGAAAGGGGCATTTGATTTT
1 TTTCGCATACATGAATCGAGGAAAGGGGCATTTGATTTT
28319887 TTTCGCATACATGAATCGAGGAAAGGGGCATTTGATTT
1 TTTCGCATACATGAATCGAGGAAAGGGGCATTTGATTT
28319925 CGTTTAGTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.32
Consensus pattern (39 bp):
TTTCGCATACATGAATCGAGGAAAGGGGCATTTGATTTT
Found at i:28324824 original size:32 final size:32
Alignment explanation
Indices: 28324783--28324855 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
28324773 CTAGCTAACA
*
28324783 ATCGCTTCTGTGGGATCGTCTTATGCTAGATC
1 ATCGCTTCTGTGGGATCATCTTATGCTAGATC
28324815 ATCGCTTCTGTGGGATCATCTTATGCTAGATC
1 ATCGCTTCTGTGGGATCATCTTATGCTAGATC
*
28324847 AACGCTTCT
1 ATCGCTTCT
28324856 CAATGGCGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (32 bp):
ATCGCTTCTGTGGGATCATCTTATGCTAGATC
Found at i:28329835 original size:40 final size:39
Alignment explanation
Indices: 28329737--28329999 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
28329727 TCCTCGTTCA
* * * *
28329737 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
28329776 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
28329815 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
28329855 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
28329895 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
28329935 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
28329976 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28330000 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:28329959 original size:120 final size:119
Alignment explanation
Indices: 28329737--28329999 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
28329727 TCCTCGTTCA
* * *
28329737 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
28329802 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
28329855 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
28329920 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
28329976 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28330000 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:28330008 original size:41 final size:41
Alignment explanation
Indices: 28329931--28330008 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28329921 TTTGTATCTC
* * *
28329931 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28329972 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28330009 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28337775 original size:40 final size:40
Alignment explanation
Indices: 28337723--28337866 Score: 152
Period size: 40 Copynumber: 3.6 Consensus size: 40
28337713 TAACTCATAC
* *
28337723 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
28337763 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
28337803 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
28337844 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28337867 CAGCATTCAA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
39 9 0.10
40 70 0.78
41 11 0.12
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:28341010 original size:21 final size:19
Alignment explanation
Indices: 28340980--28341019 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
28340970 AAAAAATAAA
*
28340980 AAATAATTTTTTATATTTTT
1 AAATAATTTTATA-ATTTTT
28341000 AAATAAATTTTATAATTTTT
1 AAAT-AATTTTATAATTTTT
28341020 TGAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATAATTTTATAATTTTT
Found at i:28341459 original size:17 final size:18
Alignment explanation
Indices: 28341418--28341461 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
28341408 AGTGCTAAAA
28341418 AAGAAAAACACTTTTGGC
1 AAGAAAAACACTTTTGGC
*
28341436 TCA-AAAAACACTTTTGG-
1 -AAGAAAAACACTTTTGGC
28341453 AAGAAAAAC
1 AAGAAAAAC
28341462 TGTGCTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.05
17 6 0.27
18 14 0.64
19 1 0.05
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (18 bp):
AAGAAAAACACTTTTGGC
Found at i:28341916 original size:13 final size:13
Alignment explanation
Indices: 28341900--28341964 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
28341890 TTTAAACCAA
*
28341900 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
28341913 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
28341926 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
*
28341939 AC-TTTCAAAAGT
1 ACTTTTCAAAAGC
*
28341951 ATTTTTCAAAAGC
1 ACTTTTCAAAAGC
28341964 A
1 A
28341965 TTGCTAAACT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
11 4 0.10
12 4 0.10
13 29 0.71
14 4 0.10
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:28343591 original size:25 final size:25
Alignment explanation
Indices: 28343485--28343591 Score: 108
Period size: 25 Copynumber: 4.3 Consensus size: 25
28343475 TATGCTCCTC
* * *
28343485 CGAGCTGTA-AACGGAAAGCTCCTC
1 CGAGCTGTATAACGGGAAGCTCATG
* ** *
28343509 CGAGCTGAATAATAGGAAGTTCATG
1 CGAGCTGTATAACGGGAAGCTCATG
* **
28343534 TGAGCTAAATAACGGGAAGCTCATG
1 CGAGCTGTATAACGGGAAGCTCATG
*
28343559 CGAGCTGTATAACGGGAAGCTCATA
1 CGAGCTGTATAACGGGAAGCTCATG
28343584 CGAGCTGT
1 CGAGCTGT
28343592 GGCGTGTCTG
Statistics
Matches: 66, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
24 8 0.12
25 58 0.88
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.21
Consensus pattern (25 bp):
CGAGCTGTATAACGGGAAGCTCATG
Found at i:28348781 original size:86 final size:86
Alignment explanation
Indices: 28348636--28348804 Score: 302
Period size: 86 Copynumber: 2.0 Consensus size: 86
28348626 ACATGTTTTA
* * *
28348636 TATCGATGGTAGATGTTTCCTATAAAATGGAGATGATATGGAAAGATTTTTTGGAGTTAAGATAA
1 TATCGATGGTAGATGTTTCCTATAAAATGGAAATGATATGGAAAGATCTTTCGGAGTTAAGATAA
28348701 CCTTTGTGGAGAAAATTTACT
66 CCTTTGTGGAGAAAATTTACT
*
28348722 TATCGGTGGTAGATGTTTCCTATAAAATGGAAATGATATGGAAAGATCTTTCGGAGTTAAGATAA
1 TATCGATGGTAGATGTTTCCTATAAAATGGAAATGATATGGAAAGATCTTTCGGAGTTAAGATAA
28348787 CCTTTGTGGAGAAAATTT
66 CCTTTGTGGAGAAAATTT
28348805 TCATGTTGAG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.35
Consensus pattern (86 bp):
TATCGATGGTAGATGTTTCCTATAAAATGGAAATGATATGGAAAGATCTTTCGGAGTTAAGATAA
CCTTTGTGGAGAAAATTTACT
Found at i:28355436 original size:29 final size:29
Alignment explanation
Indices: 28355389--28355464 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
28355379 AATGGTACAT
* * * *
28355389 AGTACTTGATAAATATAACACCGGCATAG
1 AGTACTTGATAACTGTAACAACGGCATAA
* *
28355418 AGT-GTCTGATAACTGTAACAACGGTATAA
1 AGTACT-TGATAACTGTAACAACGGCATAA
28355447 AGTACTTGATAACTGTAA
1 AGTACTTGATAACTGTAA
28355465 TCACTGGCTC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.03
29 36 0.95
30 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (29 bp):
AGTACTTGATAACTGTAACAACGGCATAA
Found at i:28366194 original size:19 final size:19
Alignment explanation
Indices: 28366161--28366205 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
28366151 TGCATTCATT
* *
28366161 TTTCAGTCATCAGCATTACA
1 TTTCA-TCATAAGCATTAAA
28366181 TTTCATCATAAGCATTAAA
1 TTTCATCATAAGCATTAAA
28366200 TTTCAT
1 TTTCAT
28366206 AAAAAATCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (19 bp):
TTTCATCATAAGCATTAAA
Found at i:28368522 original size:9 final size:9
Alignment explanation
Indices: 28368508--28368544 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28368498 GAGGCTAAGG
28368508 AATTCTTGA
1 AATTCTTGA
*
28368517 AATTCTCGA
1 AATTCTTGA
28368526 AATTCTTGA
1 AATTCTTGA
28368535 AATTCTTGA
1 AATTCTTGA
28368544 A
1 A
28368545 GCATAGTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (9 bp):
AATTCTTGA
Found at i:28374412 original size:44 final size:44
Alignment explanation
Indices: 28374343--28374780 Score: 344
Period size: 44 Copynumber: 9.7 Consensus size: 44
28374333 TTTAATATAG
* * *
28374343 CAAATCTTATCTCCCTGAAGATGCAGTGGAGAAAGA-TGAAGCTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAG-CAGATTGAAGCTA
* * * * *
28374387 CAAATCCTATATCCCTAAAGTTGCAGTGGATCGGATTAAAGCTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
*
28374431 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * *
28374475 CAAATCTTATCTCCTTGAAGTTGCAGTAGTGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * *
28374519 CAAATCTTATCTCGCTAAATTTACAGTGGAGCAGATTGAAGCGA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
28374563 CAAATCCTATACT-TCTAAAGTTGCAGTGG-GTCGGATTAAATCTA
1 CAAATCTTAT-CTCCCTAAAGTTGCAGTGGAG-CAGATTGAAGCTA
* * * *
28374607 CCATAGCGAGTCTTATTTCCCTAAAGTTGCAGTGGAACAAATTAAAGCTACAAACTA
1 -CA-A---A-TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATT---G----AAGCTA
* * *
28374664 CAAATCTTATCTCCTTGAAGTTGCAGTAGAGCAGATTGAAGCTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * ** * * *
28374708 CGAATCTTATCTCCCTGAAGTTGCAACGAAGTAGATTGAAACTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * *
28374752 CAATTCCTATAC-CCCTAAAGTTGTAGTGG
1 CAAATCTTAT-CTCCCTAAAGTTGCAGTGG
28374781 GTTAGAATGA
Statistics
Matches: 311, Mismatches: 64, Indels: 38
0.75 0.15 0.09
Matches are distributed among these distances:
43 3 0.01
44 239 0.77
45 5 0.02
46 1 0.00
48 1 0.00
49 2 0.01
50 24 0.08
51 27 0.09
52 1 0.00
55 1 0.00
56 2 0.01
57 5 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
Found at i:28376712 original size:31 final size:31
Alignment explanation
Indices: 28376664--28376730 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
28376654 AATCGTGTTT
28376664 AAATATACTTATCTATTTTTGTACTACGCCC
1 AAATATACTTATCTATTTTTGTACTACGCCC
* * *
28376695 AAATGTACTTATTTATTTTTGTACTATGCCC
1 AAATATACTTATCTATTTTTGTACTACGCCC
28376726 AAATA
1 AAATA
28376731 AGTTAAATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.43
Consensus pattern (31 bp):
AAATATACTTATCTATTTTTGTACTACGCCC
Found at i:28378249 original size:30 final size:31
Alignment explanation
Indices: 28378210--28378269 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
28378200 GGAGGTGGGA
*
28378210 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
28378241 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
28378270 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:28378497 original size:9 final size:9
Alignment explanation
Indices: 28378483--28378519 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28378473 TATAGTTTGA
28378483 TATTCGAAT
1 TATTCGAAT
28378492 TATTCGAAT
1 TATTCGAAT
*
28378501 TATTCGAGT
1 TATTCGAAT
28378510 TATTCGAAT
1 TATTCGAAT
28378519 T
1 T
28378520 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28391334 original size:266 final size:266
Alignment explanation
Indices: 28390821--28391350 Score: 745
Period size: 266 Copynumber: 2.0 Consensus size: 266
28390811 CTTAAAGGAT
* * * * * * * *
28390821 CTTTCCTGAAAGAAAGTATGTATTTATATTTTTAAAGAGGGAATTTGCCATAATAGTCTGTTAGT
1 CTTTCATGAAAGAAAGTATGCATTTATATTTCTAAAGAGGGAATCTGCCATAATAGCCTATCAAT
* * * * *
28390886 TTAGGATATTGGCTTATTCGAAGTTATGAAAAGTATAAGAGTTTATTGGTCTGAGTTGGTCTACG
66 ATAGGATATGGGCATATTCGAAGTTATGAAAAGTATAAGAGTTCATTGGTCTGAGTTGGTCTACA
* * *
28390951 CTATGTAAGGATAAAATCTGAGTTATCTGGCATTCACCATATTTGAATAGTTTTATGTCTAGTTT
131 CTATGTAAGGATAAAACCTGAGTTATCTGGCATCCACCATATTTGAATAGTTTCATGTCTAGTTT
* * * * * * *
28391016 TGAAGTTATCTGAAATTTGAGTCGTTTGTCAATTTAGGCGTTCTTTTGTTATGTAATATAGACGA
196 TGAAGTTATCTAAAATCTAAGCCATTTGTCAATTTAGGCGTTATTGTGTTATGTAATATAGACGA
28391081 TTGGGC
261 TTGGGC
*
28391087 CTTTCATGAAAGAAAGTATGCATTTATATTTCTAAAGAGGGAATCTGCCATAGTAGCCTATCAAT
1 CTTTCATGAAAGAAAGTATGCATTTATATTTCTAAAGAGGGAATCTGCCATAATAGCCTATCAAT
* *
28391152 ATAGGATATGGGCATATTTGAAGTTATGAAAAGTATAAGAGTTCGTTGGTCTGAGTTGGTCTACA
66 ATAGGATATGGGCATATTCGAAGTTATGAAAAGTATAAGAGTTCATTGGTCTGAGTTGGTCTACA
* * * *
28391217 CTATGTAATGATGAAACCTGAGTTATCTGGCATCCGCCATATTTGAATAGTTTCATGTCTCGTTT
131 CTATGTAAGGATAAAACCTGAGTTATCTGGCATCCACCATATTTGAATAGTTTCATGTCTAGTTT
* * * * *
28391282 TGAGGTTATCTAAAATCTAAGCCATTTGTTAATTTGGGTGTTATTGTGTTATGTAATATAGACGC
196 TGAAGTTATCTAAAATCTAAGCCATTTGTCAATTTAGGCGTTATTGTGTTATGTAATATAGACGA
28391347 TTGG
261 TTGG
28391351 AATTCTTCAA
Statistics
Matches: 229, Mismatches: 35, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
266 229 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.39
Consensus pattern (266 bp):
CTTTCATGAAAGAAAGTATGCATTTATATTTCTAAAGAGGGAATCTGCCATAATAGCCTATCAAT
ATAGGATATGGGCATATTCGAAGTTATGAAAAGTATAAGAGTTCATTGGTCTGAGTTGGTCTACA
CTATGTAAGGATAAAACCTGAGTTATCTGGCATCCACCATATTTGAATAGTTTCATGTCTAGTTT
TGAAGTTATCTAAAATCTAAGCCATTTGTCAATTTAGGCGTTATTGTGTTATGTAATATAGACGA
TTGGGC
Found at i:28392712 original size:22 final size:22
Alignment explanation
Indices: 28392658--28392712 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
28392648 TGCCAGTAGT
*
28392658 CAGAATGGCTAAGAGCCGTAAA
1 CAGAATGGCTAAGAGCCATAAA
* * *
28392680 CAGGATAGCTATA-AGCTATAAA
1 CAGAATGGCTA-AGAGCCATAAA
28392702 CAGAATGGCTA
1 CAGAATGGCTA
28392713 CAAGTCATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (22 bp):
CAGAATGGCTAAGAGCCATAAA
Found at i:28392799 original size:32 final size:32
Alignment explanation
Indices: 28392728--28392918 Score: 238
Period size: 32 Copynumber: 6.0 Consensus size: 32
28392718 CATAAGTATA
* * * * *
28392728 GTAATATAATTGGCACAAAGCTATCAGTAGCA
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
* * * *
28392760 GTGATATGATCGGCACACAGCCATCAATAATG
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
**
28392792 GTAATATGATCGGCACAAAGCCATCAGTAATA
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
* *
28392824 GTAATATAATCGGTACAAAGCCATCAGTAACG
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
*
28392856 GTAATATGATCGGTACAAAGCCATCAGTAACG
1 GTAATATGATCGGCACAAAGCCATCAGTAACG
* *
28392888 ATAATATGATCGGCACAAAGCCATTAGTAAC
1 GTAATATGATCGGCACAAAGCCATCAGTAAC
28392919 ATCGCAGCAA
Statistics
Matches: 138, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 138 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (32 bp):
GTAATATGATCGGCACAAAGCCATCAGTAACG
Found at i:28392893 original size:96 final size:96
Alignment explanation
Indices: 28392725--28392917 Score: 278
Period size: 96 Copynumber: 2.0 Consensus size: 96
28392715 AGTCATAAGT
* * * * *
28392725 ATAGTAATATAATTGGCACAAAGCTATCAGTAGCAGTGATATGATCGGCACACAGCCATCAATAA
1 ATAGTAATATAATCGGCACAAAGCCATCAGTAACAGTAATATGATCGGCACAAAGCCATCAATAA
* *
28392790 TGGTAATATGATCGGCACAAAGCCATCAGTA
66 CGATAATATGATCGGCACAAAGCCATCAGTA
* * * *
28392821 ATAGTAATATAATCGGTACAAAGCCATCAGTAACGGTAATATGATCGGTACAAAGCCATCAGTAA
1 ATAGTAATATAATCGGCACAAAGCCATCAGTAACAGTAATATGATCGGCACAAAGCCATCAATAA
*
28392886 CGATAATATGATCGGCACAAAGCCATTAGTA
66 CGATAATATGATCGGCACAAAGCCATCAGTA
28392917 A
1 A
28392918 CATCGCAGCA
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 85 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (96 bp):
ATAGTAATATAATCGGCACAAAGCCATCAGTAACAGTAATATGATCGGCACAAAGCCATCAATAA
CGATAATATGATCGGCACAAAGCCATCAGTA
Found at i:28392981 original size:26 final size:27
Alignment explanation
Indices: 28392919--28392984 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
28392909 CATTAGTAAC
*
28392919 ATCGCAGCAAA-TTTTCCAGCAACAGT
1 ATCGCAGCAAAGCTTTCCAGCAACAGT
* *
28392945 ATCACAACAAAGCTTT-CAGCAACAGT
1 ATCGCAGCAAAGCTTTCCAGCAACAGT
28392971 ATCGCAGCAAAGCT
1 ATCGCAGCAAAGCT
28392985 GCCAGTAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 31 0.91
27 3 0.09
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (27 bp):
ATCGCAGCAAAGCTTTCCAGCAACAGT
Found at i:28393016 original size:27 final size:27
Alignment explanation
Indices: 28392986--28393045 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
28392976 AGCAAAGCTG
28392986 CCAGTAATAGT-ATATGTGACCA-AGCCA
1 CCAGTAATAGTGAT-TGTG-CCAGAGCCA
*
28393013 CCAGTAATAGTGATTGTGGCAGAGCCA
1 CCAGTAATAGTGATTGTGCCAGAGCCA
28393040 CCAGTA
1 CCAGTA
28393046 CAGTACTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 2 0.07
27 26 0.87
28 2 0.07
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (27 bp):
CCAGTAATAGTGATTGTGCCAGAGCCA
Found at i:28393141 original size:24 final size:24
Alignment explanation
Indices: 28393114--28393166 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
28393104 TCATGCTCGG
28393114 AATCAGTCATACAAATCATAGACA
1 AATCAGTCATACAAATCATAGACA
** *
28393138 AATCAGTCATTTACATCATAGACA
1 AATCAGTCATACAAATCATAGACA
28393162 AATCA
1 AATCA
28393167 AACATTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.21, G:0.08, T:0.25
Consensus pattern (24 bp):
AATCAGTCATACAAATCATAGACA
Found at i:28393172 original size:24 final size:24
Alignment explanation
Indices: 28393128--28393176 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
28393118 AGTCATACAA
**
28393128 ATCATAGACAAATCAGTCATTTAC
1 ATCATAGACAAATCAAACATTTAC
28393152 ATCATAGACAAATCAAACATTTAC
1 ATCATAGACAAATCAAACATTTAC
28393176 A
1 A
28393177 CTCGATGGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.27
Consensus pattern (24 bp):
ATCATAGACAAATCAAACATTTAC
Found at i:28393243 original size:27 final size:27
Alignment explanation
Indices: 28393213--28393272 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
28393203 CTCTAAAGGC
*
28393213 ATTACGATCATTTTACCCTA-TGAGGGT
1 ATTACGATCATTTTACCCTACAG-GGGT
* *
28393240 ATTATGGTCATTTTACCCTACAGGGGT
1 ATTACGATCATTTTACCCTACAGGGGT
28393267 ATTACG
1 ATTACG
28393273 GATGTAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (27 bp):
ATTACGATCATTTTACCCTACAGGGGT
Found at i:28394340 original size:3 final size:3
Alignment explanation
Indices: 28394334--28394389 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
28394324 TAATAAATTT
* * *
28394334 TTA TTA TTA TCA TTA TAA TTA TTA -TA TTA TTTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
28394379 CTA TTA TTA TT
1 TTA TTA TTA TT
28394390 TCTATATTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:28394443 original size:21 final size:21
Alignment explanation
Indices: 28394413--28394454 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28394403 ACATACATGG
28394413 TTTTTATATAATATA-TATGCA
1 TTTTTATAT-ATATAGTATGCA
*
28394434 TTTTTTTATATATAGTATGCA
1 TTTTTATATATATAGTATGCA
28394455 CTAGACCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTTATATATATAGTATGCA
Found at i:28394666 original size:22 final size:24
Alignment explanation
Indices: 28394640--28394683 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
28394630 GAAAAATATT
28394640 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
28394662 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
28394684 AAGTTTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:28394782 original size:16 final size:16
Alignment explanation
Indices: 28394743--28394784 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
28394733 AATAATTTGA
*
28394743 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
*
28394759 TAAATTTAATAACAAT
1 TAATTTTAATAACAAT
*
28394775 TAGTTTTAAT
1 TAATTTTAAT
28394785 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:28397396 original size:12 final size:12
Alignment explanation
Indices: 28397381--28397406 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28397371 AAAATTAAGC
28397381 AAAAAATGATGG
1 AAAAAATGATGG
28397393 AAAAAATGATGG
1 AAAAAATGATGG
28397405 AA
1 AA
28397407 CCTCAAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAATGATGG
Found at i:28398768 original size:186 final size:186
Alignment explanation
Indices: 28398454--28399198 Score: 1472
Period size: 186 Copynumber: 4.0 Consensus size: 186
28398444 ATCAAGACAA
28398454 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
1 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
*
28398519 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTTAAGCCTCCACAGCCTC
66 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
28398584 CGTATCCCAAATGGTACGACGTAAGTGCACAATGCGATTATCATGCGGGAATTACG
131 CGTATCCCAAATGGTACGACGTAAGTGCACAATGCGATTATCATGCGGGAATTACG
28398640 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
1 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
28398705 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
66 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
28398770 CGTATCCCAAATGGTACGACGTAAGTGCACAATGCGATTATCATGCGGGAATTACG
131 CGTATCCCAAATGGTACGACGTAAGTGCACAATGCGATTATCATGCGGGAATTACG
28398826 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
1 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
28398891 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
66 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
28398956 CGTATCCCAAATGGTACGACGTAAGTGCACAATGCGATTATCATGCGGGAATTACG
131 CGTATCCCAAATGGTACGACGTAAGTGCACAATGCGATTATCATGCGGGAATTACG
28399012 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
1 GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
28399077 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
66 GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
*
28399142 CGTATCCCAAATGGTACGACGTAAGTACACAATGCGATTATCATGCGGGAATTACG
131 CGTATCCCAAATGGTACGACGTAAGTGCACAATGCGATTATCATGCGGGAATTACG
28399198 G
1 G
28399199 GACACTCAAT
Statistics
Matches: 557, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 557 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (186 bp):
GAATCATGTGTGAGGCAAGGTACTGAAAAACTCCAGTTCACGCCAATTCCAATATCGTACAAGGA
GCTGTATCAAAGTTTATTCGATGCGCATGTTGTTTCTCCTTTACATGTGAAGCCTCCACAGCCTC
CGTATCCCAAATGGTACGACGTAAGTGCACAATGCGATTATCATGCGGGAATTACG
Found at i:28401980 original size:44 final size:44
Alignment explanation
Indices: 28401844--28402075 Score: 125
Period size: 44 Copynumber: 5.3 Consensus size: 44
28401834 GATAGCAGAT
* *
28401844 CTTGCCTTCCTGCACCGATAGCGAAGTAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
* **** * * ** * * *
28401888 CTTGCCTCCCTGGGTTG-CAGC-AGAGCAGGTTAAAAATTA-CAGAT
1 CTTGCCTTCCTGCACCGATAGCGA-AGCAGATCGAAGA-CACCAG-C
28401932 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
** * * ** * * * *
28401976 CTTGCC-TCCTTG-AGTTG-TAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCC-TGCA-CCGATAGCGAAGCAGATCGAAGACACCAG-C
* *
28402020 CTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
*
28402064 CTTGCCTCCCTG
1 CTTGCCTTCCTG
28402076 GGTTGCAGCG
Statistics
Matches: 127, Mismatches: 49, Indels: 24
0.63 0.25 0.12
Matches are distributed among these distances:
42 1 0.01
43 35 0.28
44 55 0.43
45 35 0.28
46 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.22
Consensus pattern (44 bp):
CTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGC
Found at i:28402164 original size:88 final size:88
Alignment explanation
Indices: 28401835--28402141 Score: 472
Period size: 88 Copynumber: 3.5 Consensus size: 88
28401825 ATCAATGAAG
* * *
28401835 ATAGCAGATCTTGCCTTCCTGCACCGATAGCGAAGTAGATCGAAGACACTAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
28401900 GGTTGCAGCAGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* *
28401923 ATTA-CAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCTT
1 A-TAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT
* *
28401987 GAGTTGTAGCGGAGCAGGTTAAAA
65 GGGTTGCAGCGGAGCAGGTTAAAA
*
28402011 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
28402076 GGTTGCAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* * * **
28402099 ATAGTAGATCTTACCTTCCTACACCGACAATGAAGCAGATCGA
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGA
28402142 TGACCCTAGC
Statistics
Matches: 200, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
87 2 0.01
88 196 0.98
89 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGTTAAAA
Found at i:28402182 original size:88 final size:88
Alignment explanation
Indices: 28401835--28402182 Score: 288
Period size: 88 Copynumber: 4.0 Consensus size: 88
28401825 ATCAATGAAG
* * * * * * * *
28401835 ATAGCAGATCTTGCCTTCCTGCACCGATAGCGAAGTAGATCGAAGACACTAGCCTTGCCTCCCTG
1 ATAGCAGATCTTACCTTCCTACACCGACAACGAAGCAGATCGAAGACACCAGCCCTACCTCCCTG
*** * *
28401900 GGTTGCAGCAGAGCAGGTTAAAA
66 GACAGCAGCGGAACAGGTTAAAA
* * * * * *
28401923 ATTA-CAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCT-CCT
1 A-TAGCAGATCTTACCTTCCTACACCGACAACGAAGCAGATCGAAGACACCAGCCCTACCTCCCT
* ** * *
28401986 TGAGTTGTAGCGGAGCAGGTTAAAA
65 GGA-CAGCAGCGGAACAGGTTAAAA
* * * * * *
28402011 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTACCTTCCTACACCGACAACGAAGCAGATCGAAGACACCAGCCCTACCTCCCTG
*** *
28402076 GGTTGCAGCGGAGCAGGTTAAAA
66 GACAGCAGCGGAACAGGTTAAAA
* * * *
28402099 ATAGTAGATCTTACCTTCCTACACCGACAATGAAGCAGATCGATGAC-CCTAGCCCTATCTCCCT
1 ATAGCAGATCTTACCTTCCTACACCGACAACGAAGCAGATCGAAGACACC-AGCCCTACCTCCCT
* *
28402163 GGACAGCAGTGGAATAGGTT
65 GGACAGCAGCGGAACAGGTT
28402183 GAAGATTGTA
Statistics
Matches: 228, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
87 8 0.04
88 214 0.94
89 6 0.03
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (88 bp):
ATAGCAGATCTTACCTTCCTACACCGACAACGAAGCAGATCGAAGACACCAGCCCTACCTCCCTG
GACAGCAGCGGAACAGGTTAAAA
Found at i:28402218 original size:44 final size:43
Alignment explanation
Indices: 28402152--28402273 Score: 174
Period size: 44 Copynumber: 2.8 Consensus size: 43
28402142 TGACCCTAGC
*
28402152 CCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGT-AAGT
1 CCTATCTCCCTGG-CAGTAGTGGAATAGGTTGAAGATTGTGAA-T
28402196 CCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTGAAT
1 CCTATCTCCCTGG-CAGTAGTGGAATAGGTTGAAGATTGTGAAT
* *
28402240 CCTATCTCCCTGAGCAATAGTGGAGTAGGTTGAA
1 CCTATCTCCCTG-GCAGTAGTGGAATAGGTTGAA
28402274 AATAACAGAT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
44 69 0.96
45 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
CCTATCTCCCTGGCAGTAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:28402382 original size:50 final size:51
Alignment explanation
Indices: 28402327--28402439 Score: 124
Period size: 50 Copynumber: 2.3 Consensus size: 51
28402317 AAGACATCAG
* * *
28402327 TCTTATCGT-CTTGACATTGCAATGGAAAAGATTGAAGCCACAACTGCGAA
1 TCTTATCGTCCCTGACATTGCAACGGAAAAGATTGAAGCCACAACGGCGAA
* * * ** *
28402377 TCTTAT-TTCCCTGACATTGTAGCGGAGCAGATTGAAGCCACGACGGCGAA
1 TCTTATCGTCCCTGACATTGCAACGGAAAAGATTGAAGCCACAACGGCGAA
28402427 TCTTATC-TCCCTG
1 TCTTATCGTCCCTG
28402440 GTGTTAAGGC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
49 1 0.02
50 51 0.98
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (51 bp):
TCTTATCGTCCCTGACATTGCAACGGAAAAGATTGAAGCCACAACGGCGAA
Found at i:28402949 original size:133 final size:127
Alignment explanation
Indices: 28402770--28403019 Score: 283
Period size: 133 Copynumber: 1.9 Consensus size: 127
28402760 CATCTAGTCT
* *
28402770 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGCCTTATC-CTCCTGAAGTTGTAGT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGCCTTATCTCT-CTGAAGTTGCAGA
*
28402834 GAGGCAAA-CTGAAGAT-GGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTAA
64 GA-GCAAATC-G--CATCGG-G--TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTAA
28402897 TAATCC
122 TAATCC
** * * *
28402903 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAA-AATCACAGATCTTATCTCTCTGAAGTTGCAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA-AG-CCTTATCTCTCTGAAGTTGCAGA
* *
28402967 GAGCATATCGCATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
64 GAGCAAATCGCATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAA
28403020 ATCACAGATC
Statistics
Matches: 102, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
128 35 0.34
130 3 0.03
131 6 0.06
132 7 0.07
133 49 0.48
134 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (127 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGCCTTATCTCTCTGAAGTTGCAGAGA
GCAAATCGCATCGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTAATAATCC
Found at i:28402998 original size:40 final size:40
Alignment explanation
Indices: 28402944--28403085 Score: 151
Period size: 40 Copynumber: 3.5 Consensus size: 40
28402934 AAATCACAGA
*
28402944 TCTTATCTCTCTGAAGTTGCAGAGAGCATATCGCATCGGG
1 TCTTATCTCCCTGAAGTTGCAGAGAGCATATCGCATCGGG
* * *** * *
28402984 TCTTATCTCCCTGAAGTTGCAGTGGAGTGGAT-TAAAATCACAGA
1 TCTTATCTCCCTGAAGTTGCA---GAGAGCATATCGCAT--CGGG
*
28403028 TCTTATCTCTCTGAAGTTGCAGAGAGCATATCGCATCGGG
1 TCTTATCTCCCTGAAGTTGCAGAGAGCATATCGCATCGGG
28403068 TCTTATCTCCCTGAAGTT
1 TCTTATCTCCCTGAAGTT
28403086 TCAGTGGAGC
Statistics
Matches: 79, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
40 39 0.49
41 6 0.08
42 6 0.08
43 6 0.08
44 22 0.28
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (40 bp):
TCTTATCTCCCTGAAGTTGCAGAGAGCATATCGCATCGGG
Found at i:28403008 original size:84 final size:84
Alignment explanation
Indices: 28402903--28403094 Score: 375
Period size: 84 Copynumber: 2.3 Consensus size: 84
28402893 CTAATAATCC
28402903 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAG
28402968 AGCATATCGCATCGGGTCT
66 AGCATATCGCATCGGGTCT
28402987 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAG
28403052 AGCATATCGCATCGGGTCT
66 AGCATATCGCATCGGGTCT
*
28403071 TATCTCCCTGAAGTTTCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
28403095 CAGACCCAAG
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 107 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAG
AGCATATCGCATCGGGTCT
Found at i:28403118 original size:45 final size:45
Alignment explanation
Indices: 28403067--28403189 Score: 183
Period size: 45 Copynumber: 2.7 Consensus size: 45
28403057 ATCGCATCGG
* *
28403067 GTCTTATCTCCCTGAAGTTTCAGTGGAGCAGACCCAAGAAAGCGA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAA
* *
28403112 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAA
* * *
28403157 GTCTTATCCCCCTGAAATTGCAGTGGGGCAGAC
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
28403190 TAAATAAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (45 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCCAAGAAAGCAA
Found at i:28403190 original size:45 final size:45
Alignment explanation
Indices: 28402765--28403223 Score: 253
Period size: 44 Copynumber: 10.5 Consensus size: 45
28402755 TATCGCATCT
*
28402765 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * * **
28402809 AGCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAAACTGAAGATGGCGA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTCAAGAAAGC-A
* * * * *
28402855 A-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTAA-TA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAAGCA
* ** * *
28402899 A-TCCTATCTCCCTGAAGTTGCAGTGGAGTGGA-T-TA-AAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * * * *
28402940 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCATA-TC--G-CATCG
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* ** * *
28402982 GGTCTTATCTCCCTGAAGTTGCAGTGGAGTGGA-T-TA-AAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * * * *
28403024 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCATA-TC--G-CATCG
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * *
28403066 GGTCTTATCTCCCTGAAGTTTCAGTGGAGCAGACCCAAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
*
28403111 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * * * * *
28403156 AGTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTAAATAAA-AA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
* * *
28403200 AATCCTATCTCCCTAAAGTTGCAG
1 AGTCTTATCTCCCTGAAGTTGCAG
28403224 CAGATCAAGT
Statistics
Matches: 320, Mismatches: 69, Indels: 52
0.73 0.16 0.12
Matches are distributed among these distances:
40 43 0.13
41 14 0.04
42 12 0.04
43 15 0.05
44 120 0.38
45 111 0.35
46 5 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCA
Found at i:28404395 original size:3 final size:3
Alignment explanation
Indices: 28404389--28404444 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
28404379 TAATAAATTG
* * * *
28404389 TTA TTA TTA TCA TTC TAA TTA TTA -TA TTA TTTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
28404434 CTA TTA TTA TT
1 TTA TTA TTA TT
28404445 TCTATATTCA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:28414410 original size:26 final size:26
Alignment explanation
Indices: 28414355--28414412 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
28414345 TTTTATAACT
**
28414355 TTTTAATTTTCTATAATTTTCAAGTT
1 TTTTAATTTTCTATAATTTTCAAGAG
* *
28414381 TTTTAATTTTTTTATAATTTT-ATGAG
1 TTTTAA-TTTTCTATAATTTTCAAGAG
28414407 TTTTAA
1 TTTTAA
28414413 GATTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (26 bp):
TTTTAATTTTCTATAATTTTCAAGAG
Found at i:28414410 original size:27 final size:25
Alignment explanation
Indices: 28414345--28414410 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 25
28414335 AATTTTGTGT
*
28414345 TTTTATAACTTTTTAATTTTCTATAA
1 TTTTAT-AGTTTTTAATTTTCTATAA
*
28414371 TTTTCA-AGTTTTTTAATTTTTTTATAA
1 TTTT-ATAG-TTTTTAA-TTTTCTATAA
28414398 TTTTATGAGTTTT
1 TTTTAT-AGTTTT
28414411 AAGATTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
25 1 0.03
26 12 0.36
27 18 0.55
28 2 0.06
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (25 bp):
TTTTATAGTTTTTAATTTTCTATAA
Found at i:28414748 original size:22 final size:22
Alignment explanation
Indices: 28414720--28414761 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
28414710 ACAAATCCTA
28414720 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
28414742 TCTCAATTTCCTTCCAAAAT
1 TCTCAATTTCCTTCCAAAAT
28414762 TCTCCTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:28414799 original size:22 final size:22
Alignment explanation
Indices: 28414771--28414821 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
28414761 TTCTCCTAAA
* *
28414771 CTCTCAATTTCCTTTC-AAAAT
1 CTCTCAATTTCATTCCAAAAAT
28414792 CCTCTCAATTTCATTCCAAAAAT
1 -CTCTCAATTTCATTCCAAAAAT
28414815 CTCTCAA
1 CTCTCAA
28414822 ATCCATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCTCAATTTCATTCCAAAAAT
Found at i:28414890 original size:31 final size:31
Alignment explanation
Indices: 28414855--28414921 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
28414845 CTTCAATTTC
28414855 ATTTTTT-AAAATAATTTCAAATTTTTTTTAT
1 ATTTTTTAAAAATAATTT-AAATTTTTTTTAT
*
28414886 ATTTTTTAAAAATAATTTTAATTTTTTTTAT
1 ATTTTTTAAAAATAATTTAAATTTTTTTTAT
28414917 ATTTT
1 ATTTT
28414922 CATCAATGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (31 bp):
ATTTTTTAAAAATAATTTAAATTTTTTTTAT
Found at i:28417645 original size:68 final size:68
Alignment explanation
Indices: 28417566--28417843 Score: 515
Period size: 68 Copynumber: 4.1 Consensus size: 68
28417556 TCAAGTTTGT
* *
28417566 TTTACTAATCAAATGTTAGATTTTGTTACAACAAGTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
28417631 AAA
66 AAA
28417634 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
28417699 AAA
66 AAA
28417702 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
28417767 AAA
66 AAA
28417770 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
28417833 AAT
66 AAA
28417836 TTTACTAA
1 TTTACTAA
28417844 CAATTAGTTT
Statistics
Matches: 207, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
66 27 0.13
67 1 0.00
68 179 0.86
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:28417676 original size:9 final size:9
Alignment explanation
Indices: 28417664--28417691 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28417654 TTTTATTACA
28417664 ACAATTAAT
1 ACAATTAAT
28417673 ACAATTAAT
1 ACAATTAAT
28417682 ACAATTAAT
1 ACAATTAAT
28417691 A
1 A
28417692 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:28417744 original size:9 final size:9
Alignment explanation
Indices: 28417732--28417759 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
28417722 TTTTATTACA
28417732 ACAATTAAT
1 ACAATTAAT
28417741 ACAATTAAT
1 ACAATTAAT
28417750 ACAATTAAT
1 ACAATTAAT
28417759 A
1 A
28417760 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:28417857 original size:22 final size:23
Alignment explanation
Indices: 28417822--28417884 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
28417812 ATTAACAATT
*
28417822 AATAATTTGATAATTTTACT-AACA
1 AATAATTT--TAATTTTACTAAAAA
* * *
28417846 ATTAGTTTTAATTTTATTAAAAA
1 AATAATTTTAATTTTACTAAAAA
28417869 AATAATTTTAATTTTA
1 AATAATTTTAATTTTA
28417885 ATTAAAAACG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
22 9 0.28
23 17 0.53
24 6 0.19
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
AATAATTTTAATTTTACTAAAAA
Found at i:28420583 original size:19 final size:19
Alignment explanation
Indices: 28420559--28420603 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
28420549 GATGAGAAGG
*
28420559 GATATAGAACTTTCGATTA
1 GATATAGAACTTTCGAATA
*
28420578 GATATAAAACTTTCGAATA
1 GATATAGAACTTTCGAATA
28420597 G-TATAGA
1 GATATAGA
28420604 TAGTACAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (19 bp):
GATATAGAACTTTCGAATA
Found at i:28420688 original size:21 final size:21
Alignment explanation
Indices: 28420664--28420705 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28420654 TAAATAAAAT
28420664 TTTTA-AATAATTTAATAATTA
1 TTTTATAATAATTTAA-AATTA
*
28420685 TTTTATAATATTTTAAAATTA
1 TTTTATAATAATTTAAAATTA
28420706 ACAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATAATAATTTAAAATTA
Found at i:28424649 original size:9 final size:9
Alignment explanation
Indices: 28424635--28424671 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28424625 TATAGTTTGA
28424635 TATTCGAAT
1 TATTCGAAT
28424644 TATTCGAAT
1 TATTCGAAT
*
28424653 TATTCGAGT
1 TATTCGAAT
28424662 TATTCGAAT
1 TATTCGAAT
28424671 T
1 T
28424672 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28424741 original size:9 final size:9
Alignment explanation
Indices: 28424724--28424754 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28424714 TCGAGTTGAT
28424724 TCGAATAAC
1 TCGAATAAC
*
28424733 TCGATTAAC
1 TCGAATAAC
28424742 TCGAATAAC
1 TCGAATAAC
28424751 TCGA
1 TCGA
28424755 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:28426159 original size:4 final size:4
Alignment explanation
Indices: 28426150--28426187 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
28426140 GAGAAGTTGT
*
28426150 TGTA TGTA TGTA TGTA TGTA TATA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
28426188 GTTGTGTGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:28427862 original size:23 final size:23
Alignment explanation
Indices: 28427827--28427871 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28427817 TGGAGTATAA
* *
28427827 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
28427850 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
28427872 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:28428514 original size:42 final size:42
Alignment explanation
Indices: 28428453--28428625 Score: 267
Period size: 42 Copynumber: 4.1 Consensus size: 42
28428443 CAGTGCCTAT
* * * *
28428453 CAGGTTTATTGCCAGTGAAACAATATCAGACTTTATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* *
28428495 CAGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
28428537 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* *
28428579 CAGGCTTAATGCCGGTGAAACAAT-TCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
28428620 CAGGCT
1 CAGGCT
28428626 AAGTGCCAGT
Statistics
Matches: 121, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
41 21 0.17
42 100 0.83
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
Found at i:28435321 original size:23 final size:23
Alignment explanation
Indices: 28435286--28435330 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28435276 TGGAGTATAA
* *
28435286 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
28435309 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
28435331 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:28435952 original size:42 final size:42
Alignment explanation
Indices: 28435905--28436076 Score: 292
Period size: 42 Copynumber: 4.1 Consensus size: 42
28435895 AGTGCCTATT
28435905 AGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGC
1 AGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGC
* *
28435947 AGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAGC
1 AGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGC
28435989 AGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGC
1 AGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGC
* * *
28436031 AGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAGC
1 AGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGC
28436072 AGGCT
1 AGGCT
28436077 AAGTGCCAGT
Statistics
Matches: 123, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 23 0.19
42 100 0.81
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
AGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAGC
Found at i:28437395 original size:25 final size:25
Alignment explanation
Indices: 28437367--28437578 Score: 180
Period size: 25 Copynumber: 8.5 Consensus size: 25
28437357 TATAAGAAAT
28437367 GCCTTTGTGGCTAGTTATCTGTAAA
1 GCCTTTGTGGCTAGTTATCTGTAAA
* * * *
28437392 GCCTCTATGACAAGTTATCTGTAAA
1 GCCTTTGTGGCTAGTTATCTGTAAA
* * *
28437417 GCCTTTATGACATA-TTATCAT-AAAA
1 GCCTTTGTGGC-TAGTTATC-TGTAAA
* * *
28437442 GCCTTTATGACTAGTTATTTGTAAA
1 GCCTTTGTGGCTAGTTATCTGTAAA
* * * *
28437467 GCATTTGTGGCGAATTATCAT-AAAA
1 GCCTTTGTGGCTAGTTATC-TGTAAA
*
28437492 GCTTTTGTGG-TGAGTTATCTGTAAA
1 GCCTTTGTGGCT-AGTTATCTGTAAA
*
28437517 GCCTTTGTGGCGAGTTATCTGTAAA
1 GCCTTTGTGGCTAGTTATCTGTAAA
* * *
28437542 GCCTTTGTGGCGAATTATCTGAAAA
1 GCCTTTGTGGCTAGTTATCTGTAAA
*
28437567 GTCTTTGTGGCT
1 GCCTTTGTGGCT
28437579 TGTTGTATGG
Statistics
Matches: 153, Mismatches: 26, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
24 4 0.03
25 146 0.95
26 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (25 bp):
GCCTTTGTGGCTAGTTATCTGTAAA
Found at i:28437485 original size:75 final size:75
Alignment explanation
Indices: 28437340--28437572 Score: 217
Period size: 75 Copynumber: 3.1 Consensus size: 75
28437330 GAATCAAACC
* * * * * *
28437340 AAGCCTTTATGGAGA-ATTATAAGAAATGCCTTTGTGGCTAGTTATCTGTAAAGCCTCTATGAC-
1 AAGCCTTTAT-GAGATATTATCATAAAAGCCTTTGTGGCTAGTTATCTGTAAAGCCTTTGTGGCG
*
28437403 AAGTTATCTGTA
65 AA-TTATCTGAA
* * * * *
28437415 AAGCCTTTATGACATATTATCATAAAAGCCTTTATGACTAGTTATTTGTAAAGCATTTGTGGCGA
1 AAGCCTTTATGAGATATTATCATAAAAGCCTTTGTGGCTAGTTATCTGTAAAGCCTTTGTGGCGA
28437480 ATTATCAT-AA
66 ATTATC-TGAA
* * * *
28437490 AAG-CTTT-TGTGGTGAGTTATC-TGTAAAGCCTTTGTGGCGAGTTATCTGTAAAGCCTTTGTGG
1 AAGCCTTTATGAGAT-A-TTATCAT-AAAAGCCTTTGTGGCTAGTTATCTGTAAAGCCTTTGTGG
28437552 CGAATTATCTGAA
63 CGAATTATCTGAA
*
28437565 AAGTCTTT
1 AAGCCTTT
28437573 GTGGCTTGTT
Statistics
Matches: 129, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
73 3 0.02
74 10 0.08
75 109 0.84
76 7 0.05
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (75 bp):
AAGCCTTTATGAGATATTATCATAAAAGCCTTTGTGGCTAGTTATCTGTAAAGCCTTTGTGGCGA
ATTATCTGAA
Found at i:28440027 original size:27 final size:28
Alignment explanation
Indices: 28439981--28440043 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
28439971 AATACTCTTT
* ** *
28439981 TGGCAAACTCCCTAGTTCGTTGAAGCAC
1 TGGCGAACTCCCTAGTTCGTCAAAACAC
28440009 TGGCGAACT-CCTAGTTCGTCAAAACAC
1 TGGCGAACTCCCTAGTTCGTCAAAACAC
28440036 TGGCGAAC
1 TGGCGAAC
28440044 CCTTACTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (28 bp):
TGGCGAACTCCCTAGTTCGTCAAAACAC
Found at i:28441190 original size:268 final size:267
Alignment explanation
Indices: 28440698--28441235 Score: 835
Period size: 268 Copynumber: 2.0 Consensus size: 267
28440688 GTGTTTATTT
* * * * * * *
28440698 GTAATGTAGGTTCTTGAGTTGAACCAGTTCGCCAGAAGGGACCAAGTCAGGAATGCGCAAGGGTG
1 GTAATGCAGCTTCTTGAGTTAAACCAGTTCACCAGAAGGGACCAAGCCAAGAATGCGCAAAGGTG
* *
28440763 GTTGATTATAGTGCGATGTTATGCATAAAGAGGGACACTTTGGGGAATATGTTTTCAAATGATGA
66 GTTGATCATAGTGCGATGTTATGCATAAAAAGGGACACTTTGGGGAATATGTTTTCAAATGATGA
* * ** *
28440828 ATAGTATAATACGCCATGAATATGCCTATCTTATTAAAGATTTAAGTTGTAATGCTTTATACTAC
131 ATAGTATAAGACGCAACAAATATGCCTATCTTATCAAAGATTTAAGTTGTAATGCTTTATACTAC
* * *
28440893 TTTTAAGAGTCTGTTATAAATGATAAACGTTTCATTAAAATTTTTTGACTTAGAAAACATTTTAA
196 TTTTAAGAGTCTGTTATAAATGATAAACGTTTCATTAAAATCTTCTGACTCAGAAAACATTTTAA
28440958 ATAAATAA
261 A-AAATAA
28440966 GTAATGCAGCTTCTTGAGTTAAACCTA-TTCACCAGAAGGGACCAAGCCAAGAATGCGCAAAGGT
1 GTAATGCAGCTTCTTGAGTTAAACC-AGTTCACCAGAAGGGACCAAGCCAAGAATGCGCAAAGGT
28441030 GGTTGATCATAGTGCGATGTTATGCATAAAAAGGGACACTTTGGGGAATATGTTTTCAAATGATG
65 GGTTGATCATAGTGCGATGTTATGCATAAAAAGGGACACTTTGGGGAATATGTTTTCAAATGATG
* * * *
28441095 AATAGTATAAGACGCAACAAATATGCCTATTTTATCAAAGATTTAAGTTTTAATGCTTTATATTG
130 AATAGTATAAGACGCAACAAATATGCCTATCTTATCAAAGATTTAAGTTGTAATGCTTTATACTA
* * *
28441160 CTTTTAAGAGTCTGTTATAAATGCTAAACGTTTCATTCAAATCTTCTGACTCAGAAAAGATTTTA
195 CTTTTAAGAGTCTGTTATAAATGATAAACGTTTCATTAAAATCTTCTGACTCAGAAAACATTTTA
28441225 AAAAATAA
260 AAAAATAA
28441233 GTA
1 GTA
28441236 CATCTTGTAT
Statistics
Matches: 245, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
267 9 0.04
268 235 0.96
269 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (267 bp):
GTAATGCAGCTTCTTGAGTTAAACCAGTTCACCAGAAGGGACCAAGCCAAGAATGCGCAAAGGTG
GTTGATCATAGTGCGATGTTATGCATAAAAAGGGACACTTTGGGGAATATGTTTTCAAATGATGA
ATAGTATAAGACGCAACAAATATGCCTATCTTATCAAAGATTTAAGTTGTAATGCTTTATACTAC
TTTTAAGAGTCTGTTATAAATGATAAACGTTTCATTAAAATCTTCTGACTCAGAAAACATTTTAA
AAAATAA
Found at i:28441823 original size:19 final size:19
Alignment explanation
Indices: 28441800--28441851 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
28441790 AAAAATATTC
28441800 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
* *
28441819 TAAAATTAAAAATATTTAT
1 AAAAATTCAAAATATTTAT
28441838 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
28441852 TTATATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 16 0.59
20 7 0.26
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:28441823 original size:20 final size:20
Alignment explanation
Indices: 28441779--28441851 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
28441769 CTCTCACAAC
* * *
28441779 AAAAATTACAAAAAAATATTC
1 AAAAATT-CAAAATAATTTTT
28441800 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
* *
28441820 -AAAATTAAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTTT
28441838 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
28441852 TTATATTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 5 0.11
19 15 0.34
20 17 0.39
21 7 0.16
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:28441901 original size:19 final size:19
Alignment explanation
Indices: 28441863--28441905 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28441853 TATATTTTAC
*
28441863 AAAAATATAAAAATTCTAA
1 AAAAATATAAAAAGTCTAA
28441882 AAAAATATAAAAAAGT-TAA
1 AAAAATAT-AAAAAGTCTAA
28441901 AAAAA
1 AAAAA
28441906 GTTACAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAATATAAAAAGTCTAA
Found at i:28442760 original size:11 final size:11
Alignment explanation
Indices: 28442746--28442805 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
28442736 AGATAAATAT
28442746 TATTTTATTAA
1 TATTTTATTAA
*
28442757 TATTTTAGTAA
1 TATTTTATTAA
* *
28442768 TATTTAATGAGA
1 TATTTTATTA-A
*
28442780 TATTTTATTAT
1 TATTTTATTAA
*
28442791 TA-TTTATTAT
1 TATTTTATTAA
28442801 TATTT
1 TATTT
28442806 ATTTAGTATA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 10 0.25
11 21 0.52
12 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:28442798 original size:10 final size:10
Alignment explanation
Indices: 28442783--28442808 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28442773 AATGAGATAT
28442783 TTTATTATTA
1 TTTATTATTA
28442793 TTTATTATTA
1 TTTATTATTA
28442803 TTTATT
1 TTTATT
28442809 TAGTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATTATTA
Found at i:28449057 original size:19 final size:20
Alignment explanation
Indices: 28449035--28449072 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28449025 TATATATATT
*
28449035 TAATTTTTGAA-TATTTTTA
1 TAATTTTTAAAGTATTTTTA
28449054 TAATTTTTAAAGTATTTTT
1 TAATTTTTAAAGTATTTTT
28449073 TTGACATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TAATTTTTAAAGTATTTTTA
Found at i:28449436 original size:13 final size:13
Alignment explanation
Indices: 28449420--28449450 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28449410 ATCAAGAAAC
28449420 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
28449433 AAAAGAAAAAAAG
1 AAAAAAAAAAAAG
28449446 AAAAA
1 AAAAA
28449451 GAAATGACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:28450114 original size:22 final size:22
Alignment explanation
Indices: 28450064--28450115 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
28450054 TCAAAACTCA
28450064 AAGTATCAAAACTAGAGGGTTT
1 AAGTATCAAAACTAGAGGGTTT
*
28450086 GAGTATCAAAACTAGAGGGTTT
1 AAGTATCAAAACTAGAGGGTTT
*
28450108 AATTATCA
1 AAGTATCA
28450116 GTACTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (22 bp):
AAGTATCAAAACTAGAGGGTTT
Found at i:28453469 original size:43 final size:43
Alignment explanation
Indices: 28453376--28453462 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
28453366 TCAGAAAACA
28453376 AGATAAATATTTAAAAGAAAACAACGTAAGTGACCAATGAAAT
1 AGATAAATATTTAAAAGAAAACAACGTAAGTGACCAATGAAAT
*
28453419 AGATAAATATTTAAAAGAAAACAAGGTAAGTGACCAATGAAAT
1 AGATAAATATTTAAAAGAAAACAACGTAAGTGACCAATGAAAT
28453462 A
1 A
28453463 AGTAAATTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.21
Consensus pattern (43 bp):
AGATAAATATTTAAAAGAAAACAACGTAAGTGACCAATGAAAT
Found at i:28453637 original size:23 final size:24
Alignment explanation
Indices: 28453593--28453638 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
28453583 GATTGGTTAG
* **
28453593 AATATTTTAGTAATATTTTATTTT
1 AATATTTTAATAATATGATATTTT
28453617 AATATTTTAAT-ATATGATATTT
1 AATATTTTAATAATATGATATTT
28453639 GTATGGAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
AATATTTTAATAATATGATATTTT
Found at i:28454252 original size:34 final size:34
Alignment explanation
Indices: 28454214--28454284 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
28454204 ATAGTAATCA
*
28454214 AAAGTATAATTATTATATACCTCCAATTGAAAGT
1 AAAGTATAATTATTATATACATCCAATTGAAAGT
*
28454248 AAAGTATAATTGTTATATACATCCAATTGAAAGT
1 AAAGTATAATTATTATATACATCCAATTGAAAGT
28454282 AAA
1 AAA
28454285 TACAAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (34 bp):
AAAGTATAATTATTATATACATCCAATTGAAAGT
Found at i:28458697 original size:15 final size:17
Alignment explanation
Indices: 28458666--28458697 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
28458656 AACATATTCT
28458666 ATAATGTTTACATTATA
1 ATAATGTTTACATTATA
28458683 ATAA-GTTTA-ATTATA
1 ATAATGTTTACATTATA
28458698 GTTTTTGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (17 bp):
ATAATGTTTACATTATA
Found at i:28464639 original size:160 final size:159
Alignment explanation
Indices: 28464326--28464642 Score: 393
Period size: 160 Copynumber: 2.0 Consensus size: 159
28464316 CAGGTTAGTA
* * * *
28464326 GGGAAAGCTTTCTACTATTTTTTGCACGATTAGTCAAGGTATAATCATACTACCATACTTCCAAT
1 GGGAAAGCTTTCTACTATTATTTGCACGATTAATCAAGGTATAATCAGACTACCATACTCCCAAT
* * * **
28464391 GACCAAGAGAAGACAACTTTCACGTGTACATATGGTACTTTTGCGGTTAAACGAATGTCGTTCAA
66 GACCAAGAGAAGACAACTTTCACATGCACATATGGTACTTTTGCAGTTAAACGAATACCGTTCAA
* *
28464456 ATAATGGAATGCCTCGGTAACTTTTCAAT
131 ATAATGGAATGCCCCGATAACTTTTCAAT
* * * * * *
28464485 GGGAATGCTTTCTACTATTATTTGGACGATTAATCAGGGTATAATTAGATTGCCATAGCTCCCAA
1 GGGAAAGCTTTCTACTATTATTTGCACGATTAATCAAGGTATAATCAGACTACCATA-CTCCCAA
* * * *
28464550 TGATCAAGAGAAGACAACTTTCACATGCCCATATGGTACTTTTGCATTTAGAC-AGATACCGTTC
65 TGACCAAGAGAAGACAACTTTCACATGCACATATGGTACTTTTGCAGTTAAACGA-ATACCGTTC
* * *
28464614 GAATTATGTAATGCCCCGATAACTTTTCA
129 AAATAATGGAATGCCCCGATAACTTTTCA
28464643 GCGTTGTATG
Statistics
Matches: 132, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
159 49 0.37
160 83 0.63
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (159 bp):
GGGAAAGCTTTCTACTATTATTTGCACGATTAATCAAGGTATAATCAGACTACCATACTCCCAAT
GACCAAGAGAAGACAACTTTCACATGCACATATGGTACTTTTGCAGTTAAACGAATACCGTTCAA
ATAATGGAATGCCCCGATAACTTTTCAAT
Found at i:28471844 original size:17 final size:17
Alignment explanation
Indices: 28471822--28471876 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
28471812 ATTGGGATAA
28471822 AAATAAATAATGAAAAT
1 AAATAAATAATGAAAAT
28471839 AAATAAATAA-GAAAAAT
1 AAATAAATAATG-AAAAT
* *
28471856 AAACAATAGAAT-AAAAT
1 AAATAA-ATAATGAAAAT
28471873 AAAT
1 AAAT
28471877 GAACCAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.03
17 28 0.88
18 3 0.09
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (17 bp):
AAATAAATAATGAAAAT
Found at i:28471856 original size:30 final size:30
Alignment explanation
Indices: 28471820--28471876 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28471810 TAATTGGGAT
*
28471820 AAAAATAAATAATGAAAAT-AAATAAATAAG
1 AAAAATAAACAAT-AAAATAAAATAAATAAG
*
28471850 AAAAATAAACAATAGAATAAAATAAAT
1 AAAAATAAACAATAAAATAAAATAAAT
28471877 GAACCAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (30 bp):
AAAAATAAACAATAAAATAAAATAAATAAG
Found at i:28472002 original size:16 final size:16
Alignment explanation
Indices: 28471981--28472014 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28471971 CTCTCAACCT
28471981 TTAACTAACTAGTCGA
1 TTAACTAACTAGTCGA
28471997 TTAACTAACTAGTCGA
1 TTAACTAACTAGTCGA
28472013 TT
1 TT
28472015 GTTTGATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (16 bp):
TTAACTAACTAGTCGA
Found at i:28472965 original size:8 final size:8
Alignment explanation
Indices: 28472952--28472982 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
28472942 TAATCTTAAG
28472952 ACCTAAAT
1 ACCTAAAT
28472960 ACCTAAAT
1 ACCTAAAT
28472968 ACCTAAAT
1 ACCTAAAT
28472976 ACCTAAA
1 ACCTAAA
28472983 ATGTAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (8 bp):
ACCTAAAT
Found at i:28475208 original size:13 final size:13
Alignment explanation
Indices: 28475190--28475247 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
28475180 TAGTTGGGAT
28475190 AAAAATAAATAAC
1 AAAAATAAATAAC
28475203 AAAAATAAAT-A-
1 AAAAATAAATAAC
* * *
28475214 AATAACAAA-AAT
1 AAAAATAAATAAC
*
28475226 AAATATAAATAAC
1 AAAAATAAATAAC
28475239 AAAAATAAA
1 AAAAATAAA
28475248 ACATGAAGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 8 0.23
12 7 0.20
13 20 0.57
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATAAATAAC
Found at i:28475210 original size:19 final size:19
Alignment explanation
Indices: 28475188--28475248 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
28475178 GATAGTTGGG
28475188 ATAAAAATAAATAACAAAA
1 ATAAAAATAAATAACAAAA
28475207 AT--AAATAAATAACAAAA
1 ATAAAAATAAATAACAAAA
*
28475224 ATAAATATAAATAACAAAA
1 ATAAAAATAAATAACAAAA
28475243 ATAAAA
1 ATAAAA
28475249 CATGAAGGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.45
19 21 0.55
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (19 bp):
ATAAAAATAAATAACAAAA
Found at i:28475214 original size:17 final size:17
Alignment explanation
Indices: 28475192--28475247 Score: 94
Period size: 17 Copynumber: 3.2 Consensus size: 17
28475182 GTTGGGATAA
28475192 AAATAAATAACAAAAAT
1 AAATAAATAACAAAAAT
28475209 AAATAAATAACAAAAAT
1 AAATAAATAACAAAAAT
28475226 AAATATAAATAACAAAAAT
1 -AA-ATAAATAACAAAAAT
28475245 AAA
1 AAA
28475248 ACATGAAGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.49
18 4 0.11
19 15 0.41
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAATAACAAAAAT
Found at i:28477327 original size:30 final size:30
Alignment explanation
Indices: 28477274--28477363 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 30
28477264 GTAAACTCAG
* * **
28477274 GCCACTCGGCATCGCGACATGACTCACTAA
1 GCCACTCGACGTCGCGATGTGACTCACTAA
* * *
28477304 GCCACTCGACGTCGCGATGTGACTTAGTAC
1 GCCACTCGACGTCGCGATGTGACTCACTAA
*
28477334 GACCACTCAACGTCGCGATGTGACTCACTA
1 G-CCACTCGACGTCGCGATGTGACTCACTA
28477364 TTTTGGTCGA
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
30 24 0.49
31 25 0.51
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.20
Consensus pattern (30 bp):
GCCACTCGACGTCGCGATGTGACTCACTAA
Found at i:28478744 original size:46 final size:46
Alignment explanation
Indices: 28478573--28479249 Score: 462
Period size: 46 Copynumber: 14.8 Consensus size: 46
28478563 AAAGTGCTGC
* * * **
28478573 AAATTGAAATGTTTAAA-TGATGTAAATTGAAGTG-TTAAAGTGTTAC
1 AAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAA-TGTTGT
* * **
28478619 AAATTGAAGTGTTTAAA-TGTTGCGAATTGAAGTG-TTAAAGTGTTAC
1 AAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAA-TGTTGT
* * **
28478665 AAATTGCAGTGTTTAAA-TGTTGTGAATTGAAGTGTTTAAATGTTGT
1 AAATTGAAGTG-TTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * * * ** * *
28478711 AAATTGAATTGTTTAAGTACTGCAAATTAAAGTGTTTAGTTGCTGG
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* ** * * *
28478757 AAATTG-AGATATTTTA-T-CATTG-TAATTGAGGTGTATAAATGTTGT
1 AAATTGAAG-TGTTAAAGTGC--TGCAAATTGAAGTGTTTAAATGTTGT
* * * * *
28478802 TAATTAAAATGTTAAAGTGCTGCATATTGAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * *
28478848 AAATTGAAGTGTTAAAGTGTTGCACATTGAAGTGTTTAAAGGTTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * *
28478894 GAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * *
28478940 AAATTAAAGTGTTCAAGTGTTGCAAATTGAAGTGTTTAAATGTTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* *
28478986 AAATTGAAGTGATAAAGTGCTGCAAGTTGAAGTGTTTAAATGTTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * * * ** * *
28479032 AAATTGAGGTGTTCTAAGTACTGCAAATTGAATTGTTTAGTTGCTGA
1 AAATTGAAGTGTT-AAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
** * * * *
28479079 AAATTG-AGATGTTTTAGCGTTG-TAATTGAGGTGTTTAAATGTTGT
1 AAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
** * * * * * * * *
28479124 TTATTG-GGATGTTAAAGTGTTGTAAGTTGAGGTTTTTACATGCTGT
1 AAATTGAAG-TGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * * * * * * *
28479170 AAATTGAAGTGTTTAATTACTACAAATTCAGGTGCTTAAATGATGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
* * *
28479216 AAATTGAAGTATTTAAGTGCTACAAATTG-AGTGT
1 AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGT
28479250 ACAAATGAGT
Statistics
Matches: 498, Mismatches: 120, Indels: 27
0.77 0.19 0.04
Matches are distributed among these distances:
44 1 0.00
45 66 0.13
46 389 0.78
47 42 0.08
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (46 bp):
AAATTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTGT
Found at i:28478969 original size:252 final size:252
Alignment explanation
Indices: 28478509--28478978 Score: 742
Period size: 252 Copynumber: 1.9 Consensus size: 252
28478499 TGTTTCTGTC
* * * *
28478509 TGAGATGTTTTATCACTGTAAATGAGTTGTATAAATGTTGTTAATTGAGATGTTAAAGTGCTGCA
1 TGAGATATTTTATCACTGTAAATGAGGTGTATAAATGTTGTTAATTAAAATGTTAAAGTGCTGCA
*
28478574 AATTGAAATGTTTAAATGATGTAAATTGAAGTGTTAAAGTGTTACAAATTGAAGTGTTTAAATGT
66 AATTGAAATGTTTAAATGATGTAAATTGAAGTGTTAAAGTGTTACAAATTGAAGTGTTTAAAGGT
* * * * * *
28478639 TGCGAATTGAAGTGTTAAAGTGTTACAAATTGCAGTGTTTAAATGTTGTGAATTGAAGTGTTTAA
131 TGCGAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGTAAATTAAAGTGTTCAA
* *
28478704 ATGTTGTAAATTGAATTGTTTAAGTACTGCAAATTAAAGTGTTTAGTTGCTGGAAAT
196 ATGTTGCAAATTGAAGTGTTTAAGTACTGCAAATTAAAGTGTTTAGTTGCTGGAAAT
* *
28478761 TGAGATATTTTATCATTGTAATTGAGGTGTATAAATGTTGTTAATTAAAATGTTAAAGTGCTGCA
1 TGAGATATTTTATCACTGTAAATGAGGTGTATAAATGTTGTTAATTAAAATGTTAAAGTGCTGCA
* * * * *
28478826 TATTGAAGTGTTTAAATGCTGTAAATTGAAGTGTTAAAGTGTTGCACATTGAAGTGTTTAAAGGT
66 AATTGAAATGTTTAAATGATGTAAATTGAAGTGTTAAAGTGTTACAAATTGAAGTGTTTAAAGGT
*
28478891 TGTGAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGTAAATTAAAGTGTTCAA
131 TGCGAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGTAAATTAAAGTGTTCAA
*
28478956 GTGTTGCAAATTGAAGTGTTTAA
196 ATGTTGCAAATTGAAGTGTTTAA
28478979 ATGTTGTAAA
Statistics
Matches: 196, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
252 196 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (252 bp):
TGAGATATTTTATCACTGTAAATGAGGTGTATAAATGTTGTTAATTAAAATGTTAAAGTGCTGCA
AATTGAAATGTTTAAATGATGTAAATTGAAGTGTTAAAGTGTTACAAATTGAAGTGTTTAAAGGT
TGCGAATTGAAGTGTTAAAGTGCTACAAATTGAAGTGTTTAAATGCTGTAAATTAAAGTGTTCAA
ATGTTGCAAATTGAAGTGTTTAAGTACTGCAAATTAAAGTGTTTAGTTGCTGGAAAT
Found at i:28479184 original size:23 final size:23
Alignment explanation
Indices: 28478540--28479231 Score: 406
Period size: 23 Copynumber: 30.1 Consensus size: 23
28478530 ATGAGTTGTA
*
28478540 TAAATGTTGTTAATTG-AGATG-T
1 TAAATGTTGTAAATTGAAG-TGTT
* * *
28478562 TAAAGTGCTGCAAATTGAAATGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
*
28478586 TAAATGATGTAAATTGAAGTG-T
1 TAAATGTTGTAAATTGAAGTGTT
**
28478608 TAAAGTGTTACAAATTGAAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
**
28478632 TAAATGTTGCGAATTGAAGTG-T
1 TAAATGTTGTAAATTGAAGTGTT
** *
28478654 TAAAGTGTTACAAATTGCAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
*
28478678 TAAATGTTGTGAATTGAAGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
*
28478701 TAAATGTTGTAAATTGAATTGTT
1 TAAATGTTGTAAATTGAAGTGTT
* ** * *
28478724 TAAGTACTGCAAATTAAAGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
** * * *
28478747 TAGTTGCTGGAAATTG-AGATATT
1 TAAATGTTGTAAATTGAAG-TGTT
* * * *
28478770 T-TATCATTGT-AATTGAGGTGTA
1 TAAAT-GTTGTAAATTGAAGTGTT
* * *
28478792 TAAATGTTGTTAATTAAAATG-T
1 TAAATGTTGTAAATTGAAGTGTT
* * *
28478814 TAAAGTGCTGCATATTGAAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
*
28478838 TAAATGCTGTAAATTGAAGTG-T
1 TAAATGTTGTAAATTGAAGTGTT
* *
28478860 TAAAGTGTTGCACATTGAAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
* *
28478884 TAAAGGTTGTGAATTGAAGTG-T
1 TAAATGTTGTAAATTGAAGTGTT
* **
28478906 TAAAGTGCTACAAATTGAAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
* *
28478930 TAAATGCTGTAAATTAAAGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
* * *
28478953 CAAGTGTTGCAAATTGAAGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
*
28478976 TAAATGTTGTAAATTGAAGTG-A
1 TAAATGTTGTAAATTGAAGTGTT
* * *
28478998 TAAAGTGCTGCAAGTTGAAGTGTT
1 TAAA-TGTTGTAAATTGAAGTGTT
*
28479022 TAAATGTTGTAAATTGAGGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
* ** * *
28479045 CTAAGTACTGCAAATTGAATTGTT
1 -TAAATGTTGTAAATTGAAGTGTT
** * *
28479069 TAGTTGCTGAAAATTG-AGATGTT
1 TAAATGTTGTAAATTGAAG-TGTT
* ** *
28479092 TTAGCGTTGT-AATTGAGGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
** *
28479114 TAAATGTTGTTTATTG-GGATG-T
1 TAAATGTTGTAAATTGAAG-TGTT
* * *
28479136 TAAAGTGTTGTAAGTTGAGGTTTT
1 TAAA-TGTTGTAAATTGAAGTGTT
* *
28479160 TACATGCTGTAAATTGAAGTGTT
1 TAAATGTTGTAAATTGAAGTGTT
* ** ** * * *
28479183 TAATTACTACAAATTCAGGTGCT
1 TAAATGTTGTAAATTGAAGTGTT
* *
28479206 TAAATGATGTAAATTGAAGTATT
1 TAAATGTTGTAAATTGAAGTGTT
28479229 TAA
1 TAA
28479232 GTGCTACAAA
Statistics
Matches: 507, Mismatches: 135, Indels: 55
0.73 0.19 0.08
Matches are distributed among these distances:
22 71 0.14
23 378 0.75
24 58 0.11
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (23 bp):
TAAATGTTGTAAATTGAAGTGTT
Found at i:28479820 original size:17 final size:17
Alignment explanation
Indices: 28479798--28479830 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28479788 TATCAGATTT
28479798 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
28479815 TGATACCTATATCTTT
1 TGATACCCATATCTTT
28479831 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:28483372 original size:17 final size:17
Alignment explanation
Indices: 28483350--28483382 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28483340 TATCAGATTT
28483350 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
28483367 TGATACTCATATCTTT
1 TGATACCCATATCTTT
28483383 GACTTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:28486030 original size:45 final size:45
Alignment explanation
Indices: 28485974--28486317 Score: 272
Period size: 45 Copynumber: 7.6 Consensus size: 45
28485964 AGGAAATGAT
28485974 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATAAA
* * * *
28486019 TAAGACCATAGTTGAAAGACACTATAGCATTATACAAGAAAAAGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATA-AA
* *
28486065 TAAGACCATAGTTGAAAGACACTATGGCA-TCATACCAGAAATGAG
1 TAAGACCATAGTTGAAAGACACTATGGCACT-ATACCAGAAATAAA
* * * * * * *
28486110 TAAGACCATAGCTGAAAGACATTATGGCA-T-CACGATTCAAACAAG
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCA--GAAATAAA
* *** * ** ** *
28486155 TAAGACCATAGCTGAAAGATGTTATGGTTTCACGAT-TTAGACGT--G
1 TAAGACCATAGTTGAAAGACACTATGG---CACTATACCAGAAATAAA
* *
28486200 TAAGACCATAGTTGAAAGACACTATGGCAAC-ATGACGAGAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGC-ACTAT-ACCAGAAATAAA
* * * *
28486246 TAAGACCATGGTTGAAATACACTATGGCAATATGA-CAGGAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTAT-ACCA-GAAATAAA
28486292 TAAGACCATAGTTGAAAGACACTATG
1 TAAGACCATAGTTGAAAGACACTATG
28486318 ACATTATGTC
Statistics
Matches: 242, Mismatches: 41, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
42 3 0.01
43 5 0.02
44 4 0.02
45 125 0.52
46 101 0.42
47 1 0.00
48 2 0.01
49 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATAAA
Found at i:28486341 original size:91 final size:90
Alignment explanation
Indices: 28485974--28486341 Score: 311
Period size: 91 Copynumber: 4.1 Consensus size: 90
28485964 AGGAAATGAT
* *
28485974 TAAGACCATAGTTGAAAGACACTATGGCACTATACCAGAAATAAATAAGACCATAGTTGAAAGAC
1 TAAGACCATAGTTGAAAGACACTATGGCAATATACCAGAAATGAATAAGACCATAGTTGAAAGAC
*
28486039 ACTAT-AGCATTAT-ACAAGAAAA-AGAA
66 ACTATGA-CATCATGAC--GAAAATA-AA
* *
28486065 TAAGACCATAGTTGAAAGACACTATGGC-ATCATACCAGAAATGAGTAAGACCATAGCTGAAAGA
1 TAAGACCATAGTTGAAAGACACTATGGCAAT-ATACCAGAAATGAATAAGACCATAGTTGAAAGA
* * * *** * *
28486129 CATTATGGCATCACGATTCAAACAAG
65 CACTATGACATCATGACGAAAATAAA
* *** ** ** **
28486155 TAAGACCATAGCTGAAAGATGTTATGGTTTCACGAT-TTAGACGTG--TAAGACCATAGTTGAAA
1 TAAGACCATAGTTGAAAGACACTATGG---CAATATACCAGAAATGAATAAGACCATAGTTGAAA
* * *
28486217 GACACTATGGCAACATGACGAGAAATGAA
63 GACACTATGACATCATGACGA-AAATAAA
* *
28486246 TAAGACCATGGTTGAAATACACTATGGCAATATGA-CAGGAAATGAATAAGACCATAGTTGAAAG
1 TAAGACCATAGTTGAAAGACACTATGGCAATAT-ACCA-GAAATGAATAAGACCATAGTTGAAAG
* *
28486310 ACACTATGACATTATGTCGAAAATAAA
64 ACACTATGACATCATGACGAAAATAAA
28486337 TAAGA
1 TAAGA
28486342 ACATGGATGG
Statistics
Matches: 215, Mismatches: 48, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
88 4 0.02
89 1 0.00
90 63 0.29
91 104 0.48
92 40 0.19
93 3 0.01
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (90 bp):
TAAGACCATAGTTGAAAGACACTATGGCAATATACCAGAAATGAATAAGACCATAGTTGAAAGAC
ACTATGACATCATGACGAAAATAAA
Done.