Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 99 of 143
Found at i:30527496 original size:33 final size:32
Alignment explanation
Indices: 30527441--30527503 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
30527431 ATATTAACTG
30527441 ATTAAAAAATAATTAAAAATTATATTTTATTT
1 ATTAAAAAATAATTAAAAATTATATTTTATTT
* *
30527473 ATTAAAATATTAA-TAATAAATTATTTTTTAT
1 ATTAAAA-AATAATTAA-AAATTATATTTTAT
30527504 AATCTTACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 10 0.37
33 17 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
ATTAAAAAATAATTAAAAATTATATTTTATTT
Found at i:30535851 original size:16 final size:17
Alignment explanation
Indices: 30535832--30535876 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
30535822 CGGGATTTCC
30535832 TTCTTTTTCTCTCC-CT
1 TTCTTTTTCTCTCCTCT
*
30535848 TTCTTTCTC-CTTCCTCT
1 TTCTTTTTCTC-TCCTCT
30535865 TTC-TTTTCTCTC
1 TTCTTTTTCTCTC
30535877 TTTTTTGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
TTCTTTTTCTCTCCTCT
Found at i:30545218 original size:42 final size:43
Alignment explanation
Indices: 30545050--30545302 Score: 229
Period size: 42 Copynumber: 5.9 Consensus size: 43
30545040 GAATCACTTG
* * *
30545050 ATGTATAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATT
1 ATGTTTAAATGGAAGACTTATGTCTCGGGATGAGCATAAGATT
* * *
30545093 ATGTTTAAA-GGAAGACTTGTGACTCGGGATGAGCATGAGATT
1 ATGTTTAAATGGAAGACTTATGTCTCGGGATGAGCATAAGATT
** *
30545135 ATGTTTAAA-GGAAGACTCGT-TACTCGGGATGAGCATGAGATT
1 ATGTTTAAATGGAAGACTTATGT-CTCGGGATGAGCATAAGATT
* *
30545177 ATGTTTAAA-GGAAGACTTATGTCTC-GGCTAGAGTATAAGATT
1 ATGTTTAAATGGAAGACTTATGTCTCGGGAT-GAGCATAAGATT
* *
30545219 GT-TTATAAATGGAAGACTTATGTCTC--GACTAGAGCATAAGATC
1 ATGTT-TAAATGGAAGACTTATGTCTCGGGA-T-GAGCATAAGATT
* *
30545262 AT-TTGTAAATAGAAGAACTTATGACTC-GGATAGAGCATAAG
1 ATGTT-TAAATGGAAG-ACTTATGTCTCGGGAT-GAGCATAAG
30545303 GTTAATTCAG
Statistics
Matches: 183, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
41 5 0.03
42 106 0.58
43 49 0.27
44 21 0.11
45 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (43 bp):
ATGTTTAAATGGAAGACTTATGTCTCGGGATGAGCATAAGATT
Found at i:30545218 original size:84 final size:85
Alignment explanation
Indices: 30545050--30545302 Score: 261
Period size: 84 Copynumber: 3.0 Consensus size: 85
30545040 GAATCACTTG
* *
30545050 ATGTATAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTTTAAAGGAAGACTTGTGA
1 ATGTTTAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTTTAAAGGAAGACTTATGA
*
30545115 CTCGGGATGAGCATGAGATT
66 CTCGGGATGAGCATAAGATT
*
30545135 ATGTTTAAA-GGAAGACTCGT-TACTCGGGATGAGCATGAGATTATGTTTAAAGGAAGACTTATG
1 ATGTTTAAATGGAAGACTCATGT-CTCGGGATGAGCATGAGATTATGTTTAAAGGAAGACTTATG
* * *
30545198 TCTC-GGCTAGAGTATAAGATT
65 ACTCGGGAT-GAGCATAAGATT
* * * * *
30545219 GT-TTATAAATGGAAGACTTATGTCTC--GACTAGAGCATAAGATCAT-TTGTAAATAGAAGAAC
1 ATGTT-TAAATGGAAGACTCATGTCTCGGGA-T-GAGCATGAGATTATGTT-TAAA-GGAAG-AC
30545280 TTATGACTC-GGATAGAGCATAAG
60 TTATGACTCGGGAT-GAGCATAAG
30545303 GTTAATTCAG
Statistics
Matches: 142, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
83 8 0.06
84 71 0.50
85 36 0.25
86 5 0.04
87 22 0.15
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (85 bp):
ATGTTTAAATGGAAGACTCATGTCTCGGGATGAGCATGAGATTATGTTTAAAGGAAGACTTATGA
CTCGGGATGAGCATAAGATT
Found at i:30548084 original size:3 final size:3
Alignment explanation
Indices: 30548076--30548100 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30548066 ACAAACACTA
30548076 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
30548101 GTAACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:30550282 original size:2 final size:2
Alignment explanation
Indices: 30550265--30550299 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
30550255 AAACAGAATC
* *
30550265 AT AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30550300 ATTCTGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:30561196 original size:59 final size:59
Alignment explanation
Indices: 30561130--30561391 Score: 336
Period size: 59 Copynumber: 4.4 Consensus size: 59
30561120 ATTTTTGACT
* *
30561130 TTCGGGGGTAAAAAT-GTAATTTTTAGTGAAATCGAGGTCGAAAA-TGGGATTTTAGGAAA-
1 TTCGGGGGT-AAAATGGTAATTTTTGGTGAAATCGAGGT-TAAAAGTGGGATTTT-GGAAAG
* *
30561189 TTTGGGGGTAAAATGGTAA-TTTTGGTGAAATC-AGGGTTAAAAATGGGATTTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGA-GGTTAAAAGTGGGATTTTGGAAAG
* *
30561247 TTCAGGGGTAAAATGGTAATTTTTGGTGAAATAGAGGTTAAAAGTGGGATTTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAGTGGGATTTTGGAAAG
* * * * *
30561306 TTCGAGGGTAAAATGGCAATTTTGGGTGAAATCGGGGTTAAAAGTGGGATTTGGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAGTGGGATTTTGGAAAG
*
30561365 TTTCGAGGGTAAAATGGTAATTTTTGG
1 -TTCGGGGGTAAAATGGTAATTTTTGG
30561392 ATAGTCTAGG
Statistics
Matches: 180, Mismatches: 16, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
57 10 0.06
58 46 0.26
59 99 0.55
60 25 0.14
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (59 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAGTGGGATTTTGGAAAG
Found at i:30561232 original size:30 final size:29
Alignment explanation
Indices: 30561198--30561357 Score: 102
Period size: 29 Copynumber: 5.4 Consensus size: 29
30561188 ATTTGGGGGT
30561198 AAAATGGTAATTTTGGTGAAATCAGGGTTA
1 AAAATGG-AATTTTGGTGAAATCAGGGTTA
* *
30561228 AAAATGGGATTTT-G-GAAAGTTCAGGGGT-
1 AAAATGGAATTTTGGTGAAA--TCAGGGTTA
30561256 AAAATGGTAATTTTTGGTGAAAT-AGAGGTTA
1 AAAATGG-AA-TTTTGGTGAAATCAG-GGTTA
* *
30561287 AAAGTGGGATTTT-G-GAAAGTTCGAGGG-T-
1 AAAATGGAATTTTGGTGAAA--TC-AGGGTTA
*
30561315 AAAATGGCAATTTTGGGTGAAATCGGGGTTA
1 AAAATGG-AATTTT-GGTGAAATCAGGGTTA
* *
30561346 AAAGTGGGATTT
1 AAAATGGAATTT
30561358 GGGAAAGTTT
Statistics
Matches: 101, Mismatches: 11, Indels: 36
0.68 0.07 0.24
Matches are distributed among these distances:
27 8 0.08
28 15 0.15
29 29 0.29
30 25 0.25
31 16 0.16
32 8 0.08
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.31
Consensus pattern (29 bp):
AAAATGGAATTTTGGTGAAATCAGGGTTA
Found at i:30561343 original size:29 final size:27
Alignment explanation
Indices: 30561134--30561388 Score: 101
Period size: 29 Copynumber: 8.7 Consensus size: 27
30561124 TTGACTTTCG
* *
30561134 GGGGTAAAAATGTAATTTTTAGTGAAATC
1 GGGGT-AAAATGGAA-TTTTGGTGAAATC
* * * *
30561163 GAGGTCGAAAATGGGATTTTAG-GAAATTTG
1 GGGGT--AAAATGGAATTTTGGTGAAA--TC
30561193 GGGGTAAAATGGTAATTTTGGTGAAATC
1 GGGGTAAAATGG-AATTTTGGTGAAATC
* *
30561221 AGGGTTAAAAATGGGATTTT-G-GAAAGTTC
1 -GGGGT-AAAATGGAATTTTGGTGAAA--TC
*
30561250 AGGGGTAAAATGGTAATTTTTGGTGAAATA
1 -GGGGTAAAATGG-AA-TTTTGGTGAAATC
* *
30561280 GAGGTTAAAAGTGGGATTTT-G-GAAAGTTC
1 G-GGGTAAAA-TGGAATTTTGGTGAAA--TC
30561309 GAGGGTAAAATGGCAATTTTGGGTGAAATC
1 G-GGGTAAAATGG-AATTTT-GGTGAAATC
*
30561339 GGGGTTAAAAGTGGGA-TTTGG-GAAAGTTTC
1 GGGG-TAAAA-TGGAATTTTGGTGAAA---TC
30561369 GAGGGTAAAATGGTAATTTT
1 G-GGGTAAAATGG-AATTTT
30561389 TGGATAGTCT
Statistics
Matches: 176, Mismatches: 21, Indels: 56
0.70 0.08 0.22
Matches are distributed among these distances:
27 12 0.07
28 26 0.15
29 62 0.35
30 54 0.31
31 14 0.08
32 8 0.05
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.31
Consensus pattern (27 bp):
GGGGTAAAATGGAATTTTGGTGAAATC
Found at i:30562405 original size:15 final size:15
Alignment explanation
Indices: 30562375--30562421 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
30562365 ATTTATTTAT
*
30562375 TTATTAATAATATTA
1 TTATTAATGATATTA
*
30562390 TTAATTACTG-TATTA
1 TT-ATTAATGATATTA
30562405 TTATTAATGATATTA
1 TTATTAATGATATTA
30562420 TT
1 TT
30562422 TAATATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 6 0.22
15 16 0.59
16 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (15 bp):
TTATTAATGATATTA
Found at i:30563133 original size:15 final size:15
Alignment explanation
Indices: 30563109--30563150 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
30563099 GGCCTTATTC
*
30563109 GGGCTATTGTAATTT
1 GGGCTTTTGTAATTT
30563124 GGGCTTTTGTAATTT
1 GGGCTTTTGTAATTT
30563139 GGGCTTTTGTAA
1 GGGCTTTTGTAA
30563151 ATGGACTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.17, C:0.07, G:0.29, T:0.48
Consensus pattern (15 bp):
GGGCTTTTGTAATTT
Found at i:30563229 original size:17 final size:15
Alignment explanation
Indices: 30563179--30563233 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 15
30563169 ATGGACATTT
30563179 AATTT-AATTT-T-A
1 AATTTAAATTTATAA
30563191 AATTTAAATTTATAA
1 AATTTAAATTTATAA
30563206 TAGATTTAAATTGTATACA
1 -A-ATTTAAATT-TATA-A
30563225 AATTTAAAT
1 AATTTAAAT
30563234 CCAAAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.14
13 5 0.14
14 1 0.03
15 1 0.03
16 1 0.03
17 17 0.47
18 5 0.14
19 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (15 bp):
AATTTAAATTTATAA
Found at i:30563714 original size:31 final size:30
Alignment explanation
Indices: 30563661--30563738 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 30
30563651 ATTTAACAGA
*
30563661 GAGTGACCAAATAGAAACGATCTAAAACAT
1 GAGTGACAAAATAGAAACGATCTAAAACAT
* * *
30563691 GAGTGATCAAAATATAAATGATCTAAAGCAT
1 GAGTGA-CAAAATAGAAACGATCTAAAACAT
* * *
30563722 TAGTGACTAAATTGAAA
1 GAGTGACAAAATAGAAA
30563739 ATTTTTATAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 14 0.36
31 25 0.64
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.23
Consensus pattern (30 bp):
GAGTGACAAAATAGAAACGATCTAAAACAT
Found at i:30563994 original size:17 final size:17
Alignment explanation
Indices: 30563974--30564021 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
30563964 TATGTCATTA
30563974 TTTAATATAATTTAATT
1 TTTAATATAATTTAATT
* *
30563991 TTTAATA-AAATAAATT
1 TTTAATATAATTTAATT
*
30564007 TTTATTTATAATTTA
1 TTTA-ATATAATTTA
30564022 GCATAAATGC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAATATAATTTAATT
Found at i:30565818 original size:17 final size:17
Alignment explanation
Indices: 30565791--30565823 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
30565781 TTATTACAAA
30565791 AATATTA-TTTTATTTT
1 AATATTATTTTTATTTT
30565807 AATATGTATTTTTATTT
1 AATAT-TATTTTTATTT
30565824 ATTAAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 2 0.13
18 8 0.53
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
AATATTATTTTTATTTT
Found at i:30565954 original size:25 final size:25
Alignment explanation
Indices: 30565906--30565955 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
30565896 TATATGATAT
* *
30565906 TAATAATATATATAATATATAAAAA
1 TAATAATATACATAATATAGAAAAA
30565931 TAATAATATTACATAAT-TAGAAAAA
1 TAATAATA-TACATAATATAGAAAAA
30565956 ACAAGTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (25 bp):
TAATAATATACATAATATAGAAAAA
Found at i:30568511 original size:19 final size:19
Alignment explanation
Indices: 30568489--30568527 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
30568479 TTATAAAACC
30568489 TGTAAATTTTGATAACTTG
1 TGTAAATTTTGATAACTTG
30568508 TGTAAATTTTGATAACTTG
1 TGTAAATTTTGATAACTTG
30568527 T
1 T
30568528 AATAGTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (19 bp):
TGTAAATTTTGATAACTTG
Found at i:30570853 original size:15 final size:15
Alignment explanation
Indices: 30570816--30570854 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
30570806 CAATTAAAAT
30570816 TATATGTTTTTATTA
1 TATATGTTTTTATTA
*
30570831 TATTTGTTTTT-TTA
1 TATATGTTTTTATTA
30570845 TATAATGTTT
1 TAT-ATGTTT
30570855 ATAAATAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (15 bp):
TATATGTTTTTATTA
Found at i:30571468 original size:14 final size:12
Alignment explanation
Indices: 30571437--30571461 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30571427 TTTTTTATTA
30571437 TCAATATTTTTT
1 TCAATATTTTTT
30571449 TCAATATTTTTT
1 TCAATATTTTTT
30571461 T
1 T
30571462 TCTAATAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TCAATATTTTTT
Found at i:30580329 original size:184 final size:184
Alignment explanation
Indices: 30580020--30580379 Score: 720
Period size: 184 Copynumber: 2.0 Consensus size: 184
30580010 GTTGAATTCA
30580020 TACATGGGGGTCTTGTTGAAATCATCACGAGATCTCAGCCCTATCTGAGTTTTTATTGAATCTTC
1 TACATGGGGGTCTTGTTGAAATCATCACGAGATCTCAGCCCTATCTGAGTTTTTATTGAATCTTC
30580085 AACAGTTTAGCAGTATACTGTTCACAAAAGAGATATTTACATGAGACTATAGAGGTATTATGAAA
66 AACAGTTTAGCAGTATACTGTTCACAAAAGAGATATTTACATGAGACTATAGAGGTATTATGAAA
30580150 TCTTACTTTTTATTTCTAAAAACAAACTTATTTATATAAGTAAACAAACTTATT
131 TCTTACTTTTTATTTCTAAAAACAAACTTATTTATATAAGTAAACAAACTTATT
30580204 TACATGGGGGTCTTGTTGAAATCATCACGAGATCTCAGCCCTATCTGAGTTTTTATTGAATCTTC
1 TACATGGGGGTCTTGTTGAAATCATCACGAGATCTCAGCCCTATCTGAGTTTTTATTGAATCTTC
30580269 AACAGTTTAGCAGTATACTGTTCACAAAAGAGATATTTACATGAGACTATAGAGGTATTATGAAA
66 AACAGTTTAGCAGTATACTGTTCACAAAAGAGATATTTACATGAGACTATAGAGGTATTATGAAA
30580334 TCTTACTTTTTATTTCTAAAAACAAACTTATTTATATAAGTAAACA
131 TCTTACTTTTTATTTCTAAAAACAAACTTATTTATATAAGTAAACA
30580380 TATAAAAAGT
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 176 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (184 bp):
TACATGGGGGTCTTGTTGAAATCATCACGAGATCTCAGCCCTATCTGAGTTTTTATTGAATCTTC
AACAGTTTAGCAGTATACTGTTCACAAAAGAGATATTTACATGAGACTATAGAGGTATTATGAAA
TCTTACTTTTTATTTCTAAAAACAAACTTATTTATATAAGTAAACAAACTTATT
Found at i:30595821 original size:6 final size:6
Alignment explanation
Indices: 30595810--30595844 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
30595800 TGGATTAAGT
30595810 TAGTTC TAGTTC TAGTTC TAGTTC TAGTTC TAGTT
1 TAGTTC TAGTTC TAGTTC TAGTTC TAGTTC TAGTT
30595845 GCTTAGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.51
Consensus pattern (6 bp):
TAGTTC
Found at i:30598838 original size:3 final size:3
Alignment explanation
Indices: 30598830--30598861 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30598820 TGGCTCCCTT
30598830 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30598862 GTAATACTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30599764 original size:7 final size:7
Alignment explanation
Indices: 30599747--30599819 Score: 67
Period size: 7 Copynumber: 10.4 Consensus size: 7
30599737 CCCACTGACC
30599747 GACCTGTT
1 GACC-GTT
30599755 GACCGTT
1 GACCGTT
30599762 GACCGTT
1 GACCGTT
30599769 GACCGTT
1 GACCGTT
* *
30599776 AACTGTT
1 GACCGTT
* **
30599783 AACAATT
1 GACCGTT
30599790 GACCGTT
1 GACCGTT
*
30599797 GATCGTT
1 GACCGTT
*
30599804 GA-CTTT
1 GACCGTT
30599810 GACCGTT
1 GACCGTT
30599817 GAC
1 GAC
30599820 TTTTTTAAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
6 5 0.09
7 45 0.83
8 4 0.07
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (7 bp):
GACCGTT
Found at i:30606920 original size:7 final size:7
Alignment explanation
Indices: 30606910--30606942 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
30606900 CTGTTGATCA
30606910 TTGACAG
1 TTGACAG
30606917 TTGACAG
1 TTGACAG
30606924 TTGACAG
1 TTGACAG
*
30606931 TTGACCG
1 TTGACAG
30606938 TTGAC
1 TTGAC
30606943 TTTGACCGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (7 bp):
TTGACAG
Found at i:30606927 original size:21 final size:21
Alignment explanation
Indices: 30606902--30606942 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30606892 TCACTGACCT
30606902 GTTGATCA-TTGACAGTTGACA
1 GTTGA-CAGTTGACAGTTGACA
*
30606923 GTTGACAGTTGACCGTTGAC
1 GTTGACAGTTGACAGTTGAC
30606943 TTTGACCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (21 bp):
GTTGACAGTTGACAGTTGACA
Found at i:30608184 original size:3 final size:3
Alignment explanation
Indices: 30608178--30608232 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
30608168 ATTATTATTA
*
30608178 TTG TTG TTG TTG TTG TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
30608226 TTTG TTG
1 -TTG TTG
30608233 GACTTCCACT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.02, C:0.00, G:0.31, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:30610773 original size:30 final size:30
Alignment explanation
Indices: 30610706--30610781 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
30610696 AAAATAAATA
30610706 AATTTTTT-AATAAAAAATTAATTTATTCT
1 AATTTTTTAAATAAAAAATTAATTTATTCT
* *
30610735 --TTAATTTAACATAAATAATTAATTTATT-T
1 AATT-TTTTAA-ATAAAAAATTAATTTATTCT
30610764 AATTTTTTAATATAAAAA
1 AATTTTTTAA-ATAAAAA
30610782 CCAAAATACT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
27 2 0.05
28 3 0.08
29 2 0.05
30 28 0.76
31 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
AATTTTTTAAATAAAAAATTAATTTATTCT
Found at i:30617175 original size:26 final size:26
Alignment explanation
Indices: 30617146--30617209 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
30617136 TATATTCTAT
*
30617146 TCGATTCGATTTGAATCTCATCTCAC
1 TCGACTCGATTTGAATCTCATCTCAC
*
30617172 TCGACTCGATTCGAATCTCATCTCAC
1 TCGACTCGATTTGAATCTCATCTCAC
30617198 TCGACTCGATTT
1 TCGACTCGATTT
30617210 AAGAAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (26 bp):
TCGACTCGATTTGAATCTCATCTCAC
Found at i:30617206 original size:21 final size:21
Alignment explanation
Indices: 30617165--30617206 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
30617155 TTTGAATCTC
*
30617165 ATCTCACTCGACTCGATTCGA
1 ATCTCACTCGACTCGACTCGA
30617186 ATCTCATCTC-ACTCGACTCGA
1 ATCTCA-CTCGACTCGACTCGA
30617207 TTTAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.24, C:0.36, G:0.12, T:0.29
Consensus pattern (21 bp):
ATCTCACTCGACTCGACTCGA
Found at i:30618421 original size:16 final size:16
Alignment explanation
Indices: 30618400--30618433 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30618390 ATTTTTTTAA
30618400 AAAAATGTAGCAAATT
1 AAAAATGTAGCAAATT
* *
30618416 AAAAATTTATCAAATT
1 AAAAATGTAGCAAATT
30618432 AA
1 AA
30618434 TTTATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAAATGTAGCAAATT
Found at i:30623447 original size:51 final size:51
Alignment explanation
Indices: 30623392--30623492 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
30623382 TCACTCACGA
30623392 CTTTCAAAAGAAT-GATGATATAAATGCTTAGCAGATACATTCAAATAGTCT
1 CTTTCAAAAGAATAG-TGATATAAATGCTTAGCAGATACATTCAAATAGTCT
*
30623443 CTTTCAAAAGAATAGTGATATAAATGCTTGGCAGATACATTCAAATAGTC
1 CTTTCAAAAGAATAGTGATATAAATGCTTAGCAGATACATTCAAATAGTC
30623493 AATTGAAAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 47 0.98
52 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (51 bp):
CTTTCAAAAGAATAGTGATATAAATGCTTAGCAGATACATTCAAATAGTCT
Found at i:30627034 original size:47 final size:48
Alignment explanation
Indices: 30626977--30627150 Score: 199
Period size: 48 Copynumber: 3.6 Consensus size: 48
30626967 TAGTATGTTG
* * ** * *
30626977 TGGATGAACCACTGGTCGAGTAGAT-GTCTGCCAACTAAAATACGTTG
1 TGGATAAACCACTGGTTGAGTAGATAAACTACCAACTAAAATACGTTA
* ** *
30627024 TGGATAAACCACTAGTTGAGTAGATAAACTACTGACTTAAATACGTTA
1 TGGATAAACCACTGGTTGAGTAGATAAACTACCAACTAAAATACGTTA
* *
30627072 TGGATAAACCACTGGTTGAGCAAATAAACTACCAACTAAAATACGTTA
1 TGGATAAACCACTGGTTGAGTAGATAAACTACCAACTAAAATACGTTA
* *
30627120 TGGATAAACCATTGGTT-AATCAGATAAACTA
1 TGGATAAACCACTGGTTGAGT-AGATAAACTA
30627151 TCGACTACTT
Statistics
Matches: 105, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
47 23 0.22
48 82 0.78
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (48 bp):
TGGATAAACCACTGGTTGAGTAGATAAACTACCAACTAAAATACGTTA
Found at i:30633490 original size:8 final size:8
Alignment explanation
Indices: 30633479--30633505 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
30633469 TAAAAAAATA
30633479 AAATTTAT
1 AAATTTAT
30633487 AAATTTAT
1 AAATTTAT
30633495 AAATTTAT
1 AAATTTAT
30633503 AAA
1 AAA
30633506 AATATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
AAATTTAT
Found at i:30640642 original size:17 final size:18
Alignment explanation
Indices: 30640607--30640647 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
30640597 ATTTTTTAGG
*
30640607 TTTAAATTTATTATTAAA
1 TTTAAATTCATTATTAAA
30640625 TTTAAATTCATT-TTAAA
1 TTTAAATTCATTATTAAA
30640642 TTTAAA
1 TTTAAA
30640648 ATATTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAATTCATTATTAAA
Found at i:30640736 original size:13 final size:13
Alignment explanation
Indices: 30640720--30640767 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
30640710 ATTTACAAAT
30640720 GCCCAAATTAAAG
1 GCCCAAATTAAAG
*
30640733 GCCCAAATTGAAG
1 GCCCAAATTAAAG
30640746 GCCC-AATTACAATG
1 GCCCAAATTA-AA-G
30640760 GCCCAAAT
1 GCCCAAAT
30640768 AGGCCCAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 4 0.13
13 18 0.60
14 5 0.17
15 3 0.10
ACGTcount: A:0.40, C:0.27, G:0.17, T:0.17
Consensus pattern (13 bp):
GCCCAAATTAAAG
Found at i:30641426 original size:58 final size:57
Alignment explanation
Indices: 30641357--30641608 Score: 308
Period size: 59 Copynumber: 4.3 Consensus size: 57
30641347 AAAACTTCAA
* * * * * *
30641357 AAAATTACATTTTGACCCCGAAACTT-CCAAAAATTACCGTTTTACCCTTAAGCTTTCC
1 AAAATTCCATTTTAACCCCG--ATTTACCAAAAATTACCATTTTACCCCTAAACTTTCC
* * *
30641415 AAAATTCCATTTTAACCTCGATTTCACCCAAAATTACCATTTTACCCCTAAACTTTTC
1 AAAATTCCATTTTAACCCCGATTT-ACCAAAAATTACCATTTTACCCCTAAACTTTCC
** * *
30641473 AAAATTCCATTTTTAACCTTGATTTCACCCAAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTCCA-TTTTAACCCCGATTT-ACCAAAAATTACCATTTTACCCCTAAACTTTCC
30641532 AAAATTCCATTTTCAACCCCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCC
1 AAAATTCCATTTT-AACCCCGATTT-ACCAAAAATTACCATTTTACCCCTAAACTTTCC
30641591 AAAATTCCATTTTTAACC
1 AAAATTCCA-TTTTAACC
30641609 TCGAATTTTC
Statistics
Matches: 173, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
56 3 0.02
58 57 0.33
59 109 0.63
60 4 0.02
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (57 bp):
AAAATTCCATTTTAACCCCGATTTACCAAAAATTACCATTTTACCCCTAAACTTTCC
Found at i:30641594 original size:29 final size:29
Alignment explanation
Indices: 30641357--30641603 Score: 160
Period size: 29 Copynumber: 8.5 Consensus size: 29
30641347 AAAACTTCAA
*
30641357 AAAATTA-CATTTTGACCCCGAAAC-TTCC
1 AAAATTACCATTTT-ACCCCTAAACTTTCC
* * *
30641385 AAAAATTACCGTTTTACCCTTAAGCTTTCC
1 -AAAATTACCATTTTACCCCTAAACTTTCC
* **
30641415 AAAATT-CCATTTTA-ACCTCGA-TTTCACCC
1 AAAATTACCATTTTACCCCTAAACTTT---CC
*
30641444 AAAATTACCATTTTACCCCTAAACTTTTC
1 AAAATTACCATTTTACCCCTAAACTTTCC
* **
30641473 AAAATT-CCATTTTTA-ACCTTGA-TTTCACCC
1 AAAATTACCA-TTTTACCCCTAAACTTT---CC
*
30641503 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTACCCCTAAACTTTCC
*
30641532 AAAATT-CCATTTTCAACCCC--GA-TTTCACC
1 AAAATTACCATTTT--ACCCCTAAACTTT--CC
30641561 AAAAATTACCATTTTACCCCTAAACTTTCC
1 -AAAATTACCATTTTACCCCTAAACTTTCC
30641591 AAAATT-CCATTTT
1 AAAATTACCATTTT
30641604 TAACCTCGAA
Statistics
Matches: 170, Mismatches: 24, Indels: 49
0.70 0.10 0.20
Matches are distributed among these distances:
26 3 0.02
27 8 0.05
28 29 0.17
29 61 0.36
30 42 0.25
31 18 0.11
32 9 0.05
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCTAAACTTTCC
Found at i:30641618 original size:29 final size:28
Alignment explanation
Indices: 30641357--30641633 Score: 127
Period size: 29 Copynumber: 9.5 Consensus size: 28
30641347 AAAACTTCAA
* * **
30641357 AAAATTACATTTTGACCCCGAAACTTCC
1 AAAATTCCATTTTAACCCCGAATTTTCC
* ** *
30641385 AAAAATTACCGTTTT-ACCCTTAAGCTTTCC
1 -AAAATT-CCATTTTAACCCCGAA-TTTTCC
* *
30641415 AAAATTCCATTTTAACCTCG-ATTTCACCC
1 AAAATTCCATTTTAACCCCGAATTT--TCC
*
30641444 AAAATTACCATTTT-ACCCCTAAACTTTT-C
1 AAAATT-CCATTTTAACCCC-GAA-TTTTCC
** *
30641473 AAAATTCCATTTTTAACCTTG-ATTTCACCC
1 AAAATTCCA-TTTTAACCCCGAATTT--TCC
* * *
30641503 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATT-CCATTTTAACCCCGAATTTTCC
*
30641532 AAAATTCCATTTTCAACCCCG-ATTTCACC
1 AAAATTCCATTTT-AACCCCGAATTT-TCC
* *
30641561 AAAAATTACCATTTT-ACCCCTAAACTTTCC
1 -AAAATT-CCATTTTAACCCC-GAATTTTCC
*
30641591 AAAATTCCATTTTTAACCTCGAATTTTCTC
1 AAAATTCCA-TTTTAACCCCGAATTTTC-C
* *
30641621 GAAATTACATTTT
1 AAAATTCCATTTT
30641634 TGCCATCGAG
Statistics
Matches: 186, Mismatches: 37, Indels: 50
0.68 0.14 0.18
Matches are distributed among these distances:
27 5 0.03
28 24 0.13
29 84 0.45
30 53 0.28
31 17 0.09
32 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCCGAATTTTCC
Found at i:30641628 original size:59 final size:59
Alignment explanation
Indices: 30641386--30641612 Score: 366
Period size: 59 Copynumber: 3.9 Consensus size: 59
30641376 GAAACTTCCA
* * *
30641386 AAAATTACCGTTTTACCCTTAAGCTTTCCAAAATTCCA-TTTTAACCTCGATTTCACCC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCC
* *
30641444 AAAATTACCATTTTACCCCTAAACTTTTCAAAATTCCATTTTTAACCTTGATTTCACCC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCC
* * * *
30641503 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTCAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCC
30641562 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGA
30641613 ATTTTCTCGA
Statistics
Matches: 154, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
58 34 0.22
59 120 0.78
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCC
Found at i:30648932 original size:21 final size:21
Alignment explanation
Indices: 30648908--30648947 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30648898 ATATATTGTT
*
30648908 TTTTA-AATATATTTAATAATA
1 TTTTAGAAT-TATTAAATAATA
30648929 TTTTAGAATTATTAAATAA
1 TTTTAGAATTATTAAATAA
30648948 AGAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTTAGAATTATTAAATAATA
Found at i:30651395 original size:59 final size:59
Alignment explanation
Indices: 30651123--30651395 Score: 318
Period size: 59 Copynumber: 4.6 Consensus size: 59
30651113 GATTTATTTA
* **
30651123 AAAATTACATTTTAACCCTTAAACTTTTCCAAAATTATGTTTTAA-CCCTCAAACTTCTCC-
1 AAAATCACATTTTAACCCTTAAAC-TTTCCAAAATTACATTTTAACCCCT-AAACTT-TCCT
* * ** * * *
30651183 AAAATTATATTTTAACCCTTAAACTTCTTTAAAATCACATTTTAACCTCTAAACTTTTCT
1 AAAATCACATTTTAACCCTTAAACTT-TCCAAAATTACATTTTAACCCCTAAACTTTCCT
* * * *
30651243 AAAATCACATTTTAACCCCTAAACTTTTCAAAATCACATTTTAACCCCTAAACTTTCCC
1 AAAATCACATTTTAACCCTTAAACTTTCCAAAATTACATTTTAACCCCTAAACTTTCCT
*
30651302 AAAATCACATTTTGA-CCTTAAACTTTCCCAAAATTACATTTTAACCCCTAAACTTTCCT
1 AAAATCACATTTTAACCCTTAAACTTT-CCAAAATTACATTTTAACCCCTAAACTTTCCT
* * *
30651361 AAAATCACATTTTTACCCCTAAACTTTCCCAAATT
1 AAAATCACATTTTAACCCTTAAACTTTCCAAAATT
30651396 TATGTTTTAA
Statistics
Matches: 185, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
58 10 0.05
59 97 0.52
60 75 0.41
61 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.37
Consensus pattern (59 bp):
AAAATCACATTTTAACCCTTAAACTTTCCAAAATTACATTTTAACCCCTAAACTTTCCT
Found at i:30651404 original size:29 final size:30
Alignment explanation
Indices: 30651123--30651393 Score: 300
Period size: 30 Copynumber: 9.1 Consensus size: 30
30651113 GATTTATTTA
* * *
30651123 AAAATTACATTTTAACCCTTAAACTTTTCC
1 AAAATCACATTTTAACCCCTAAACTTTCCC
* **
30651153 AAAATTATGTTTTAA-CCCTCAAAC-TTCTCC
1 AAAATCACATTTTAACCCCT-AAACTTTC-CC
* * * **
30651183 AAAATTATATTTTAACCCTTAAAC-TTCTTT
1 AAAATCACATTTTAACCCCTAAACTTTC-CC
* * *
30651213 AAAATCACATTTTAACCTCTAAACTTTTCT
1 AAAATCACATTTTAACCCCTAAACTTTCCC
*
30651243 AAAATCACATTTTAACCCCTAAACTTT-TC
1 AAAATCACATTTTAACCCCTAAACTTTCCC
30651272 AAAATCACATTTTAACCCCTAAACTTTCCC
1 AAAATCACATTTTAACCCCTAAACTTTCCC
* *
30651302 AAAATCACATTTTGA-CCTTAAACTTTCCC
1 AAAATCACATTTTAACCCCTAAACTTTCCC
* *
30651331 AAAATTACATTTTAACCCCTAAACTTTCCT
1 AAAATCACATTTTAACCCCTAAACTTTCCC
*
30651361 AAAATCACATTTTTACCCCTAAACTTTCCC
1 AAAATCACATTTTAACCCCTAAACTTTCCC
30651391 AAA
1 AAA
30651394 TTTATGTTTT
Statistics
Matches: 208, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
29 58 0.28
30 145 0.70
31 5 0.02
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.37
Consensus pattern (30 bp):
AAAATCACATTTTAACCCCTAAACTTTCCC
Found at i:30656972 original size:22 final size:21
Alignment explanation
Indices: 30656946--30657012 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
30656936 AAAAATAAAT
*
30656946 AAAAAAAAGAAAGAAAAAAGAAG
1 AAAAATAA-AAAGAAAAAAG-AG
* *
30656969 AAAAATTAAAATAAAAAAGAG
1 AAAAATAAAAAGAAAAAAGAG
* *
30656990 AAAAATGGAAAAGAAAAAGGAG
1 AAAAAT-AAAAAGAAAAAAGAG
30657012 A
1 A
30657013 GGTCGTAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 8 0.22
22 23 0.62
23 6 0.16
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAATAAAAAGAAAAAAGAG
Found at i:30657006 original size:21 final size:21
Alignment explanation
Indices: 30656955--30657008 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
30656945 TAAAAAAAAG
*
30656955 AAAGAAAAAAGAAGAAAAATTA
1 AAAG-AAAAAGAAGAAAAATGA
*
30656977 AAATAAAAA-AGAGAAAAATGGA
1 AAAGAAAAAGA-AGAAAAAT-GA
30656999 AAAGAAAAAG
1 AAAGAAAAAG
30657009 GAGAGGTCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 13 0.50
22 12 0.46
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (21 bp):
AAAGAAAAAGAAGAAAAATGA
Found at i:30658222 original size:147 final size:148
Alignment explanation
Indices: 30658024--30658301 Score: 398
Period size: 147 Copynumber: 1.9 Consensus size: 148
30658014 GCGAACCTAA
* * * *
30658024 TACCATGAAGATTTAAAGGGAAAGGTTGAGGTCGCGATGGTGAACCCGATACCTCGGAAGATGTG
1 TACCATGAAGATTTAAAGGGAAAGGTTGAGGCCACGATGGCGAACCCGATACCTCAGAAGATGTG
* * *
30658089 ATAGAAAAGATTGAGGTCGCAATGGCAAATCCGGTACCATGAA-ATGT-AATGGGAAAGGTTGAG
66 ATAGAAAAGATTGAGGCCGCAACGGCAAATCCAGTACCATGAAGATGTGAA-GGGAAAGGTTGAG
30658152 GCTACAACGATGAACATGG
130 GCTACAACGATGAACATGG
* * * *
30658171 TACCATGAAGATTTGAAGGGAAAGGTTGAGGCCATGATGGCGAATCTGATACCTCAGAAGATGTG
1 TACCATGAAGATTTAAAGGGAAAGGTTGAGGCCACGATGGCGAACCCGATACCTCAGAAGATGTG
* * * *
30658236 ATAGGAAAGATTGAGGCCGCAACGGCGAATTCAGTACCATGAAGATTTGAAGGGAAAGGTTGAGG
66 ATAGAAAAGATTGAGGCCGCAACGGCAAATCCAGTACCATGAAGATGTGAAGGGAAAGGTTGAGG
30658301 C
131 C
30658302 CGTGATGGCG
Statistics
Matches: 114, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
147 94 0.82
148 18 0.16
149 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.21
Consensus pattern (148 bp):
TACCATGAAGATTTAAAGGGAAAGGTTGAGGCCACGATGGCGAACCCGATACCTCAGAAGATGTG
ATAGAAAAGATTGAGGCCGCAACGGCAAATCCAGTACCATGAAGATGTGAAGGGAAAGGTTGAGG
CTACAACGATGAACATGG
Found at i:30658259 original size:99 final size:99
Alignment explanation
Indices: 30658168--30658711 Score: 449
Period size: 99 Copynumber: 5.5 Consensus size: 99
30658158 ACGATGAACA
* *
30658168 TGGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCATGATGGCGAATCTGATACCTCAGAAGAT
1 TGGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCATGACGGCGAACCTGATACCTCAGAAGAT
30658233 GTGATAGGAAAGATTGAGGCCGCAACGGCGAAT-
66 GTGATAGGAAAGATTGAGGCCGCAACGGCGAATC
* * * * * *
30658266 TCAGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCGTGATGGCGAATCTGGTACCTCAAAAGA
1 T-GGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCATGACGGCGAACCTGATACCTCAGAAGA
* *
30658331 TGTGAT-GGAAAAGATTAAGACCGCAACGGCGAATC
65 TGTGATAGG-AAAGATTGAGGCCGCAACGGCGAATC
* * * * *
30658366 TGGTACCATGAA-ATGTGATGGGAAAGGTTGAGGCC-TCAACGGCGAACCCGATA-CT-ATGAAT
1 TGGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCAT-GACGGCGAACCTGATACCTCA-GAAG
* * * * * * * *
30658427 ATTTGAAAGGAAAGGTTAAGGCCACAACAGCAAACC
64 ATGTGATAGGAAAGATTGAGGCCGCAACGGCGAATC
** * * * *
30658463 CAGTACCGTGAAGATTTGAAGGGAAAGGTTGAGG-TA-GCAACGGCGAA-CTCGATACTTTAGAA
1 TGGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCATG--ACGGCGAACCT-GATACCTCAGAA
* * *
30658525 GATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACC
63 GATGTGATAGGAAAGATTGAGGCCGCAACGGCGAATC
* * * * * ** * ** * * *
30658562 TAGTACCTTAGAAGATATGATGAGAAAGGTTGAGGCTGTAACGGTAAACCCGATACTTTAGAAGA
1 TGGTACCAT-GAAGATTTGAAGGGAAAGGTTGAGGCCATGACGGCGAACCTGATACCTCAGAAGA
* * * *
30658627 TGTGATGGGAAGGATTGAGGCCGTAACGGTGAATC
65 TGTGATAGGAAAGATTGAGGCCGCAACGGCGAATC
* * * * ***
30658662 CGATACCATGAAGATATGAAAGGAAAGGTTGAGGCCGCAACGGCGAACCT
1 TGGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCATGACGGCGAACCT
30658712 AGCACCTTAG
Statistics
Matches: 361, Mismatches: 68, Indels: 33
0.78 0.15 0.07
Matches are distributed among these distances:
96 1 0.00
97 40 0.11
98 68 0.19
99 171 0.47
100 79 0.22
101 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.20
Consensus pattern (99 bp):
TGGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCATGACGGCGAACCTGATACCTCAGAAGAT
GTGATAGGAAAGATTGAGGCCGCAACGGCGAATC
Found at i:30658373 original size:246 final size:246
Alignment explanation
Indices: 30657929--30658463 Score: 635
Period size: 246 Copynumber: 2.2 Consensus size: 246
30657919 CTGAGAAACT
* * *
30657929 ATGAATATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCTCAAAAGATGTGATGG
1 ATGAATATTTGAAGGGAAAGGTTGAGGCCACAACAGCGAACCCGATACCTCAAAAGATGTGATGG
* * *
30657994 AAAAGGTTGAGGCCATAACAGCGAACCTAATACCATGAAGATTTAAAGGGAAAGGTTGAGGTCGC
66 AAAAGATTGAGGCCACAACAGCGAACCTAATACCATGAAGATTTAAAGGGAAAGGTTGAGGCCGC
* ** * ** *
30658059 GATGGTGAACCCGATACCTCGGAAGATGTGATAGAAAAGATTGAGGTCGCAATGGCAAATCCGGT
131 GATGGCGAACCCGATACCTCAAAAGATGTGATAGAAAAGATTAAGACCGCAACGGCAAATCCGGT
* * *
30658124 ACCATGAAATGTAATGGGAAAGGTTGAGG-CTACAACGATGAACATGGTACC
196 ACCATGAAATGTAATGGGAAAGGTTGAGGCCT-CAACGACGAACACGATACC
* ** ** * * *
30658175 ATGAAGATTTGAAGGGAAAGGTTGAGGCCATGATGGCGAATCTGATACCTCAGAAGATGTGATAG
1 ATGAATATTTGAAGGGAAAGGTTGAGGCCACAACAGCGAACCCGATACCTCAAAAGATGTGAT-G
* * * * *
30658240 G-AAAGATTGAGGCCGCAACGGCGAA-TTCAGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCC
65 GAAAAGATTGAGGCCACAACAGCGAACCT-AATACCATGAAGATTTAAAGGGAAAGGTTGAGGCC
* * * * * * *
30658303 GTGATGGCGAATCTGGTACCTCAAAAGATGTGATGGAAAAGATTAAGACCGCAACGGCGAATCTG
129 GCGATGGCGAACCCGATACCTCAAAAGATGTGATAGAAAAGATTAAGACCGCAACGGCAAATCCG
* * * *
30658368 GTACCATGAAATGTGATGGGAAAGGTTGAGGCCTCAACGGCGAACCCGATACT
194 GTACCATGAAATGTAATGGGAAAGGTTGAGGCCTCAACGACGAACACGATACC
* * *
30658421 ATGAATATTTGAAAGGAAAGGTTAAGGCCACAACAGCAAACCC
1 ATGAATATTTGAAGGGAAAGGTTGAGGCCACAACAGCGAACCC
30658464 AGTACCGTGA
Statistics
Matches: 236, Mismatches: 50, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
245 1 0.00
246 231 0.98
247 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (246 bp):
ATGAATATTTGAAGGGAAAGGTTGAGGCCACAACAGCGAACCCGATACCTCAAAAGATGTGATGG
AAAAGATTGAGGCCACAACAGCGAACCTAATACCATGAAGATTTAAAGGGAAAGGTTGAGGCCGC
GATGGCGAACCCGATACCTCAAAAGATGTGATAGAAAAGATTAAGACCGCAACGGCAAATCCGGT
ACCATGAAATGTAATGGGAAAGGTTGAGGCCTCAACGACGAACACGATACC
Found at i:30658529 original size:196 final size:198
Alignment explanation
Indices: 30658163--30658708 Score: 510
Period size: 196 Copynumber: 2.8 Consensus size: 198
30658153 CTACAACGAT
* * * * * * *
30658163 GAACATGGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCATGATGGCGAATCTGATACCTCAG
1 GAACCTGGTACCATGAAGATATGATGGGAAAGGTTGAGGCCATAACGGCGAACCCGATACCTCAG
* * * * * **
30658228 AAGATGTGATAGGAAAGATTGAGGCCGCAACGGCGAATTCAGTACCATGAAGATTTGAAGGGAAA
66 AAGATGTGAAAGGAAAGATTAAGGCCACAACAGCAAACCCAGTACCATGAAGATTTGAAGGGAAA
* ** * *
30658293 GGTTGAGGCCGTGATGGCGAATCTGGTACCTCAAAAGATGTGATGGAAAAGATTAAGACCGCAAC
131 GGTTGAGGCAGCAACGGCGAATCTGATACCTCAAAAGATGTGATGGAAAAGATTAAGACCGCAAC
30658358 GGC
196 GGC
* *
30658361 GAATCTGGTACCATGAA-ATGTGATGGGAAAGGTTGAGGCC-TCAACGGCGAACCCGATA-CT-A
1 GAACCTGGTACCATGAAGATATGATGGGAAAGGTTGAGGCCAT-AACGGCGAACCCGATACCTCA
* * * *
30658422 TGAATATTTGAAAGGAAAGGTTAAGGCCACAACAGCAAACCCAGTACCGTGAAGATTTGAAGGGA
65 -GAAGATGTGAAAGGAAAGATTAAGGCCACAACAGCAAACCCAGTACCATGAAGATTTGAAGGGA
* * * * * * * *
30658487 AAGGTTGAGGTAGCAACGGCGAA-CTCGATACTTTAGAAGATGTGATGGGAAAGGTTGAGGCCGC
129 AAGGTTGAGGCAGCAACGGCGAATCT-GATACCTCAAAAGATGTGATGGAAAAGATTAAGACCGC
30658551 AACGGC
193 AACGGC
* * * ** ** * *
30658557 GAACCTAGTACCTTAGAAGATATGATGAGAAAGGTTGAGGCTGTAACGGTAAACCCGATACTTTA
1 GAACCTGGTACCAT-GAAGATATGATGGGAAAGGTTGAGGCCATAACGGCGAACCCGATACCTCA
** * * ** * ** * * *
30658622 GAAGATGTGATGGGAAGGATTGAGGCCGTAACGGTGAATCC-GATACCATGAAGATATGAAAGGA
65 GAAGATGTGAAAGGAAAGATTAAGGCCACAACAGCAAACCCAG-TACCATGAAGATTTGAAGGGA
*
30658686 AAGGTTGAGGCCGCAACGGCGAA
129 AAGGTTGAGGCAGCAACGGCGAA
30658709 CCTAGCACCT
Statistics
Matches: 280, Mismatches: 59, Indels: 17
0.79 0.17 0.05
Matches are distributed among these distances:
195 3 0.01
196 121 0.43
197 36 0.13
198 50 0.18
199 69 0.25
200 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (198 bp):
GAACCTGGTACCATGAAGATATGATGGGAAAGGTTGAGGCCATAACGGCGAACCCGATACCTCAG
AAGATGTGAAAGGAAAGATTAAGGCCACAACAGCAAACCCAGTACCATGAAGATTTGAAGGGAAA
GGTTGAGGCAGCAACGGCGAATCTGATACCTCAAAAGATGTGATGGAAAAGATTAAGACCGCAAC
GGC
Found at i:30658537 original size:50 final size:50
Alignment explanation
Indices: 30657935--30658709 Score: 388
Period size: 50 Copynumber: 15.7 Consensus size: 50
30657925 AACTATGAAT
* * * * * *
30657935 ATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCTCAAAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCTTAGAAG
* * ** * * *
30657985 ATGTGATGGAAAAGGTTGAGGCCATAACAGCGAAC-CTAATACCAT-GAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTC-GATACCTTAGAAG
* * * * * * * * **
30658034 ATTTAAAGGGAAAGGTTGAGGTCGCGATGGTGAACCCGATACCTCGGAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCTTAGAAG
* * * * * * * * *
30658084 ATGTGATAGAAAAGATTGAGGTCGCAATGGC-AAATCCGGTACCAT-GAA-
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACT-CGATACCTTAGAAG
* * ** ** * *
30658132 ATGTAATGGGAAAGGTTGAGGCTACAACGATGAACAT-GGTACCAT-GAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAAC-TCGATACCTTAGAAG
* * *** * *
30658181 ATTTGAAGGGAAAGGTTGAGGCCATGATGGCGAA-TCTGATACCTCAGAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTC-GATACCTTAGAAG
* * * * *
30658231 ATGTGATAGGAAAGATTGAGGCCGCAACGGCGAATTC-AGTACCAT-GAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGA-TACCTTAGAAG
* * ** * * * *
30658280 ATTTGAAGGGAAAGGTTGAGGCCGTGATGGCGAA-TCTGGTACCTCAAAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTC-GATACCTTAGAAG
* * * * * * *
30658330 ATGTGATGGAAAAGATTAAGACCGCAACGGCGAA-TCTGGTACCAT-GAA-
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTC-GATACCTTAGAAG
* * * *
30658378 ATGTGATGGGAAAGGTTGAGGCCTCAACGGCGAACCCGATA-C-TATGAAT
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCTTA-GAAG
* ** * * * * * *
30658427 ATTTGAAAGGAAAGGTTAAGGCCACAACAGCAAAC-CCAGTACCGT-GAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGA-TACCTTAGAAG
* * ** *
30658476 ATTTGAAGGGAAAGGTTGAGGTAGCAACGGCGAACTCGATACTTTAGAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCTTAGAAG
* *
30658526 ATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAAC-CTAGTACCTTAGAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGA-TACCTTAGAAG
* * * ** * *
30658576 ATATGATGAGAAAGGTTGAGGCTGTAACGGTAAACCCGATACTTTAGAAG
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCTTAGAAG
* * * *
30658626 ATGTGATGGG-AAGGATTGAGGCCGTAACGGTGAA-TCCGATACCAT-GAAG
1 ATATGATGGGAAAGG-TTGAGGCCGCAACGGCGAACT-CGATACCTTAGAAG
**
30658675 ATATGAAAGGAAAGGTTGAGGCCGCAACGGCGAAC
1 ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAAC
30658710 CTAGCACCTT
Statistics
Matches: 550, Mismatches: 145, Indels: 60
0.73 0.19 0.08
Matches are distributed among these distances:
46 1 0.00
47 2 0.00
48 71 0.13
49 208 0.38
50 263 0.48
51 5 0.01
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.19
Consensus pattern (50 bp):
ATATGATGGGAAAGGTTGAGGCCGCAACGGCGAACTCGATACCTTAGAAG
Found at i:30658539 original size:246 final size:245
Alignment explanation
Indices: 30657929--30658561 Score: 589
Period size: 246 Copynumber: 2.6 Consensus size: 245
30657919 CTGAGAAACT
* * * * * * * * *
30657929 ATGAATATATGAAGGGAAAGGTTGAGGCCGCAACAGCGAACCCGGTACCTCAAAAGATGTGAT-G
1 ATGAAGATTTGAAAGGAAAGGTTAAGGCCACAACAGCAAACCAGATACCT-AGAAGATGTGATAG
* * * * * * *
30657993 GAAAAGGTTGAGGCCA-TAACAGCGAAC-CTAATACCATGAAGATTTAAAGGGAAAGGTTGAGGT
65 G-AAAGATTGAGG-CAGCAACGGCGAACTC-AGTACCATGAAGATGTGAAGGGAAAGGTTGAGGC
* ** * ** *
30658056 CGCGATGGTGAACCCGATACCTCGGAAGATGTGATAGAAAAGATTGAGGTCGCAATGGCAAATCC
127 CGCGATGGCGAACCCGATACCTCAAAAGATGTGATAGAAAAGATTAAGACCGCAACGGCAAATCC
* * *
30658121 GGTACCATGAAATGTAATGGGAAAGGTTGAGGCTACAACGATGAACATGGTACC
192 GGTACCATGAAATGTAATGGGAAAGGTTGAGGCTACAACGACGAACACGATACC
* * ** ** * * *
30658175 ATGAAGATTTGAAGGGAAAGGTTGAGGCCATGATGGCGAATCTGATACCTCAGAAGATGTGATAG
1 ATGAAGATTTGAAAGGAAAGGTTAAGGCCACAACAGCAAACCAGATACCT-AGAAGATGTGATAG
* * * *
30658240 GAAAGATTGAGGCCGCAACGGCGAATTCAGTACCATGAAGATTTGAAGGGAAAGGTTGAGGCCGT
65 GAAAGATTGAGGCAGCAACGGCGAACTCAGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGC
* * * * * *
30658305 GATGGCGAATCTGGTACCTCAAAAGATGTGATGGAAAAGATTAAGACCGCAACGGCGAATCTGGT
130 GATGGCGAACCCGATACCTCAAAAGATGTGATAGAAAAGATTAAGACCGCAACGGCAAATCCGGT
* * * *
30658370 ACCATGAAATGTGATGGGAAAGGTTGAGGCCT-CAACGGCGAACCCGATACT
195 ACCATGAAATGTAATGGGAAAGGTTGAGG-CTACAACGACGAACACGATACC
* *
30658421 ATGAATATTTGAAAGGAAAGGTTAAGGCCACAACAGCAAACCCAG-TACCGT-GAAGATTTGA-A
1 ATGAAGATTTGAAAGGAAAGGTTAAGGCCACAACAGCAAA-CCAGATACC-TAGAAGATGTGATA
* * ** *
30658483 GGGAAAGGTTGAGGTAGCAACGGCGAACTC-GATACTTTAGAAGATGTGATGGGAAAGGTTGAGG
64 -GGAAAGATTGAGGCAGCAACGGCGAACTCAG-TACCAT-GAAGATGTGAAGGGAAAGGTTGAGG
* *
30658547 CCGCAACGGCGAACC
126 CCGCGATGGCGAACC
30658562 TAGTACCTTA
Statistics
Matches: 315, Mismatches: 63, Indels: 18
0.80 0.16 0.05
Matches are distributed among these distances:
244 2 0.01
245 39 0.12
246 266 0.84
247 8 0.03
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (245 bp):
ATGAAGATTTGAAAGGAAAGGTTAAGGCCACAACAGCAAACCAGATACCTAGAAGATGTGATAGG
AAAGATTGAGGCAGCAACGGCGAACTCAGTACCATGAAGATGTGAAGGGAAAGGTTGAGGCCGCG
ATGGCGAACCCGATACCTCAAAAGATGTGATAGAAAAGATTAAGACCGCAACGGCAAATCCGGTA
CCATGAAATGTAATGGGAAAGGTTGAGGCTACAACGACGAACACGATACC
Found at i:30660819 original size:30 final size:30
Alignment explanation
Indices: 30660785--30660976 Score: 172
Period size: 30 Copynumber: 6.4 Consensus size: 30
30660775 ATTTTATTTA
* **
30660785 AAAATTATATTTTAACCCTTAATTTTTTTC
1 AAAATTACATTTTAACCCTTAAACTTTTTC
** *
30660815 AAAATTATGTTTTAACCCTCAAACTTTTTC
1 AAAATTACATTTTAACCCTTAAACTTTTTC
*
30660845 AAAATTACATTTTAACCCTTAAAATTGTTT-
1 AAAATTACATTTTAACCCTTAAACTT-TTTC
** * * *
30660875 AAAATGGCATTTTAACCCCT-AACCTTTCC
1 AAAATTACATTTTAACCCTTAAACTTTTTC
* * * *
30660904 AAGATCATATTTTAACCCTAAAACTTTTTC
1 AAAATTACATTTTAACCCTTAAACTTTTTC
* * **
30660934 AAAATCACATTTTAACCCATAAACTTTCCC
1 AAAATTACATTTTAACCCTTAAACTTTTTC
*
30660964 AAAATAACATTTT
1 AAAATTACATTTT
30660977 GACCTCGAAC
Statistics
Matches: 130, Mismatches: 29, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
28 2 0.02
29 17 0.13
30 108 0.83
31 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAACTTTTTC
Found at i:30660930 original size:29 final size:29
Alignment explanation
Indices: 30660824--30661019 Score: 123
Period size: 30 Copynumber: 6.6 Consensus size: 29
30660814 CAAAATTATG
* * *
30660824 TTTTAACCCTCAAACTTTTTCAAAATTACA
1 TTTTAACCCTAAAAC-TTTCCAAAATCACA
** **
30660854 TTTTAACCCTTAAAA-TTGTTTAAAATGGCA
1 TTTTAACCC-TAAAACTT-TCCAAAATCACA
* * *
30660884 TTTTAACCCCT-AACCTTTCCAAGATCATA
1 TTTTAA-CCCTAAAACTTTCCAAAATCACA
*
30660913 TTTTAACCCTAAAACTTTTTCAAAATCACA
1 TTTTAACCCTAAAAC-TTTCCAAAATCACA
*
30660943 TTTTAACCC-ATAAACTTTCCCAAAATAACA
1 TTTTAACCCTA-AAACTTT-CCAAAATCACA
* ** *
30660973 TTTTGA-CCTCGAACTTTCCTAAAACCACA
1 TTTTAACCCTAAAACTTTCC-AAAATCACA
*
30661002 TTTTTACCCCT-AAACTTT
1 -TTTTAACCCTAAAACTTT
30661020 TCTAAATTTA
Statistics
Matches: 129, Mismatches: 25, Indels: 24
0.72 0.14 0.13
Matches are distributed among these distances:
28 6 0.05
29 38 0.29
30 75 0.58
31 10 0.08
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTTAACCCTAAAACTTTCCAAAATCACA
Found at i:30661005 original size:89 final size:89
Alignment explanation
Indices: 30660824--30661020 Score: 211
Period size: 89 Copynumber: 2.2 Consensus size: 89
30660814 CAAAATTATG
* * ** **
30660824 TTTTAACCCTCAAACTTTTTCAAAATTACATTTTAACCCTTAAAATTGTTTAAAATGGCATTTTA
1 TTTTAACCCT-AAACTTTTTCAAAATCACATTTTAACCCATAAAATTGTCCAAAATAACATTTTA
* * * *
30660889 ACCCCTAACCTTTCCAAGATCATA-
65 ACCCCGAACCTTTCCAAAACCACAT
*
30660913 TTTTAACCCTAAAACTTTTTCAAAATCACATTTTAACCCATAAACTT-TCCCAAAATAACATTTT
1 TTTTAACCCT-AAACTTTTTCAAAATCACATTTTAACCCATAAAATTGT-CCAAAATAACATTTT
* *
30660977 GACCTCGAA-CTTTCCTAAAACCACAT
64 AACCCCGAACCTTTCC-AAAACCACAT
*
30661003 TTTTACCCCTAAACTTTT
1 TTTTAACCCTAAACTTTT
30661021 CTAAATTTAC
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
88 7 0.08
89 74 0.82
90 9 0.10
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (89 bp):
TTTTAACCCTAAACTTTTTCAAAATCACATTTTAACCCATAAAATTGTCCAAAATAACATTTTAA
CCCCGAACCTTTCCAAAACCACAT
Found at i:30661025 original size:30 final size:30
Alignment explanation
Indices: 30660882--30661041 Score: 112
Period size: 30 Copynumber: 5.4 Consensus size: 30
30660872 TTTAAAATGG
* * *
30660882 CATTTTAACCCCTAACCTTTCC-AAGATCA
1 CATTTTTACCCCTAAACTTTCCTAAAATCA
* * *
30660911 TA-TTTTAACCCTAAAACTTT-TTCAAAATCA
1 CATTTTTACCCCT-AAACTTTCCT-AAAATCA
* * * *
30660941 CATTTTAACCCATAAACTTTCCCAAAATAA
1 CATTTTTACCCCTAAACTTTCCTAAAATCA
* * * *
30660971 CATTTTGACCTC-GAACTTTCCTAAAACCA
1 CATTTTTACCCCTAAACTTTCCTAAAATCA
* * *
30661000 CATTTTTACCCCTAAACTTTTCTAAATTTA
1 CATTTTTACCCCTAAACTTTCCTAAAATCA
*
30661030 CATTTTGACCCC
1 CATTTTTACCCC
30661042 AATTTCTCCG
Statistics
Matches: 97, Mismatches: 28, Indels: 11
0.71 0.21 0.08
Matches are distributed among these distances:
28 8 0.08
29 30 0.31
30 52 0.54
31 7 0.07
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (30 bp):
CATTTTTACCCCTAAACTTTCCTAAAATCA
Found at i:30665429 original size:36 final size:34
Alignment explanation
Indices: 30665363--30665523 Score: 160
Period size: 35 Copynumber: 4.6 Consensus size: 34
30665353 CTCAATGATT
* *
30665363 TCTTCAAGTTTCCTAATAATTTAGCTCATACGAGC
1 TCTTCAAGTTTCC-AGTAATTTAACTCATACGAGC
* * *
30665398 CCTTCGAGTTTCTCAGTAATTTTAGCTCATACGAGC
1 TCTTCAAGTTTC-CAGTAA-TTTAACTCATACGAGC
* * *
30665434 TCTTCAAGATTCCTAGTAAATTAACTCATACGAGT
1 TCTTCAAGTTTCC-AGTAATTTAACTCATACGAGC
* *
30665469 TCTTCAAGATTGCCAGTAATTTAACTCATACGAGT
1 TCTTCAAG-TTTCCAGTAATTTAACTCATACGAGC
* *
30665504 TTTTCAAGATTCCCAGTAAT
1 TCTTCAAG-TTTCCAGTAAT
30665524 ATTTTGCTCA
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
35 74 0.69
36 34 0.31
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (34 bp):
TCTTCAAGTTTCCAGTAATTTAACTCATACGAGC
Found at i:30665486 original size:71 final size:70
Alignment explanation
Indices: 30665363--30665522 Score: 187
Period size: 71 Copynumber: 2.3 Consensus size: 70
30665353 CTCAATGATT
* * * * * * *
30665363 TCTTCAAGTTTCCTAATAATTTAGCTCATACGAGCCCTTCGAGTTTCTCAGTAATTTTAGCTCAT
1 TCTTCAAGATTCCTAGTAAATTAACTCATACGAGCCCTTCAAGTTGCTCAGTAA-TTTAACTCAT
30665428 ACGAGC
65 ACGAGC
**
30665434 TCTTCAAGATTCCTAGTAAATTAACTCATACGAGTTCTTCAAGATTGC-CAGTAATTTAACTCAT
1 TCTTCAAGATTCCTAGTAAATTAACTCATACGAGCCCTTCAAG-TTGCTCAGTAATTTAACTCAT
*
30665498 ACGAGT
65 ACGAGC
* *
30665504 TTTTCAAGATTCCCAGTAA
1 TCTTCAAGATTCCTAGTAA
30665523 TATTTTGCTC
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
70 31 0.41
71 42 0.55
72 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (70 bp):
TCTTCAAGATTCCTAGTAAATTAACTCATACGAGCCCTTCAAGTTGCTCAGTAATTTAACTCATA
CGAGC
Found at i:30665583 original size:19 final size:19
Alignment explanation
Indices: 30665556--30665598 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
30665546 CAATAAACGT
*
30665556 TCTTGCGAGCCAGTATTGC
1 TCTTACGAGCCAGTATTGC
30665575 TCTTACGAGCCAGTATTGC
1 TCTTACGAGCCAGTATTGC
30665594 TCTTA
1 TCTTA
30665599 TGAGGTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (19 bp):
TCTTACGAGCCAGTATTGC
Found at i:30671606 original size:42 final size:42
Alignment explanation
Indices: 30671560--30671677 Score: 132
Period size: 42 Copynumber: 2.8 Consensus size: 42
30671550 TATACTTCGG
*
30671560 TTTATCCGGTGATGCACTTACGTGCCAGTATGA-TTACTTCAA
1 TTTATCCAGTGATGCACTTACGTGCCAGTAT-ATTTACTTCAA
* * * **
30671602 TTTATCTAGTGATGCACTTACTTGTCAACATATTTACTTCAA
1 TTTATCCAGTGATGCACTTACGTGCCAGTATATTTACTTCAA
* * *
30671644 -TTATCCAATGATGCACTTATGTGCTAGTATATTT
1 TTTATCCAGTGATGCACTTACGTGCCAGTATATTT
30671678 TGACTTACAT
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 27 0.44
42 34 0.56
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (42 bp):
TTTATCCAGTGATGCACTTACGTGCCAGTATATTTACTTCAA
Found at i:30684603 original size:6 final size:7
Alignment explanation
Indices: 30684586--30684615 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
30684576 GAATGATTTT
30684586 TTTTTAA
1 TTTTTAA
30684593 TTTTTAA
1 TTTTTAA
30684600 TTTTTTAA
1 -TTTTTAA
30684608 TTTTTAA
1 TTTTTAA
30684615 T
1 T
30684616 AATTTATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTAA
Found at i:30684605 original size:15 final size:15
Alignment explanation
Indices: 30684585--30684615 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30684575 TGAATGATTT
30684585 TTTTTTAATTTTTAA
1 TTTTTTAATTTTTAA
30684600 TTTTTTAATTTTTAA
1 TTTTTTAATTTTTAA
30684615 T
1 T
30684616 AATTTATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTAATTTTTAA
Found at i:30684621 original size:15 final size:15
Alignment explanation
Indices: 30684588--30684621 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
30684578 ATGATTTTTT
**
30684588 TTTAATTTTTAATTT
1 TTTAATTTTTAATAA
30684603 TTTAATTTTTAATAA
1 TTTAATTTTTAATAA
30684618 TTTA
1 TTTA
30684622 TTTGCTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTAATTTTTAATAA
Found at i:30687628 original size:30 final size:30
Alignment explanation
Indices: 30687587--30687721 Score: 123
Period size: 30 Copynumber: 4.5 Consensus size: 30
30687577 GAATTTGGGA
* * *
30687587 TCAAAACGTGATTTTGGGAAACTTTAGGGG
1 TCAAAATGTGATTTTGGAAAACTTTAGGAG
*
30687617 TCAAAATGTGATTTTGGAAAAATTTA-GAG
1 TCAAAATGTGATTTTGGAAAACTTTAGGAG
* * * *
30687646 TAAAAAATGTAATTTTTGAAAAGTTTAAGG-G
1 T-CAAAATGTGATTTTGGAAAACTTT-AGGAG
* *
30687677 TTAAAATGTGATTTTTGAAAACTTT-GGAAG
1 TCAAAATGTGATTTTGGAAAACTTTAGG-AG
*
30687707 TCAAAATGTAATTTT
1 TCAAAATGTGATTTT
30687722 TTAATAAAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.02
29 3 0.03
30 78 0.90
31 3 0.03
32 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (30 bp):
TCAAAATGTGATTTTGGAAAACTTTAGGAG
Found at i:30687683 original size:60 final size:60
Alignment explanation
Indices: 30687609--30687722 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
30687599 TTTGGGAAAC
*
30687609 TTTAGGGGTCAAAATGTGATTTTGGAAAAATTTAG-AGTAAAAAATGTAATTTTTGAAAAG
1 TTTAAGGGTCAAAATGTGATTTTGGAAAAATTTAGAAGT-AAAAATGTAATTTTTGAAAAG
* * * * *
30687669 TTTAAGGGTTAAAATGTGATTTTTGAAAACTTTGGAAGTCAAAATGTAATTTTT
1 TTTAAGGGTCAAAATGTGATTTTGGAAAAATTTAGAAGTAAAAATGTAATTTTT
30687723 TAATAAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 44 0.94
61 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.39
Consensus pattern (60 bp):
TTTAAGGGTCAAAATGTGATTTTGGAAAAATTTAGAAGTAAAAATGTAATTTTTGAAAAG
Found at i:30689872 original size:208 final size:207
Alignment explanation
Indices: 30689387--30690562 Score: 1388
Period size: 208 Copynumber: 5.7 Consensus size: 207
30689377 GCTTCATCTC
* * * * * * *
30689387 TTGGTTTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGTTTTAATCCACTTCTCTAT
1 TTGGTCTACTTCTTTGTATCTCATCAGAAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGT
** * * * * * *
30689452 ATCTCATCACCAAGACGGATTCGGTTCACTTCTCTGCATGTCGTCGGGAAA-ATGAACACTTTAT
66 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTTCATCTCATC--AAAAGATGAACACTTTAT
* * * * * *
30689516 TGCTTCAACCCACTCCTCTATATCTTATCAGGAAGATGAGGTTTGAAAGTTTCACTCATATTGAG
129 TGCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGAGGTTTG-AAGTCTCATTCGTATTGAG
* * *
30689581 CTTCACTTCATTTAA
193 CTTCGCTTCATTGAT
* * * * * *
30689596 TTGGTCTACTTCTTTGTATCTCATCAAAAAGATGAACGCTTCATTATTTTAATCCACTTCTTTGT
1 TTGGTCTACTTCTTTGTATCTCATCAGAAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGT
* * *
30689661 ATCTCATCAGGAAGACGAATTTAGTTCATTTCTCTTCATCTCGTCCAAAAGATGAACACTTTATT
66 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTTCATCTCAT-CAAAAGATGAACACTTTATT
* * *
30689726 GCTTCAACCCACTTCTCTATATCTTATTAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCT
130 GCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCT
30689791 TCGCTTCATTGAT
195 TCGCTTCATTGAT
* *
30689804 TTGGTCTATTTCTTTGTATCTCATCAGAAAGATGACTGCCTCATTGTTTCAATCCACTTCTCTGT
1 TTGGTCTACTTCTTTGTATCTCATCAGAAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGT
* * * *
30689869 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATTAGGAAGATGACCAC-TTATT
66 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTTCATCTCATCA-AAAGATGAACACTTTATT
*
30689933 AG-TTCGACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGC
130 -GCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGC
*
30689997 TTCGCTTCTTTGAT
194 TTCGCTTCATTGAT
* *
30690011 TTGGTCTACTTCTTTGTATCTCATCAGAAAGATAACCGCCTTATTGTTTCAATCCACTTCTCTGT
1 TTGGTCTACTTCTTTGTATCTCATCAGAAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGT
** * *
30690076 ATCTCATCAGGAAGACGAATTTGGCCCACTTCTCTAT-ACCTCATCAAGAAGATGACCACTTTAT
66 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCT-TCATCTCATCAA-AAGATGAACACTTTAT
* * *
30690140 TGCTTGGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTT-ACAGTCTCATTCGTATTGAG
129 TGCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGA-AGTCTCATTCGTATTGAG
30690204 CTTCGCTTCATTGAT
193 CTTCGCTTCATTGAT
* * ** *
30690219 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCATCTCATTATTTCAATCCACTTCTCTGT
1 TTGGTCTACTTCTTTGTATCTCATCAGAAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGT
* * * *
30690284 ATCTCATCAGGAAGA-TAGATTT-GATCTACTTCTCTGT-ATCTCATCAGGAAGAT-AACCGCTT
66 ATCTCATCAGGAAGACGA-ATTTGGTTC-ACTTCTCT-TCATCTCATCA-AAAGATGAA-CACTT
* * * *
30690345 TATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTATGAAGTCTCATTCGTATTG
126 TATTGCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTG
*
30690410 AGCTTCGCTTCAATGAT
191 AGCTTCGCTTCATTGAT
* * * *
30690427 TTGGTCTACTTCTTTATATCTCATCA-AGAAGATGACCGCCTCTTTGATTT-AAACCACATCTCT
1 TTGGTCTACTTCTTTGTATCTCATCAGA-AAGATGACCGCCTCATTG-TTTCAATCCACTTCTCT
** * * * * *
30690490 GTATCTCATCAAAAAGATGTATTTGGTTCACTT-T-TTCGTATCTCATCAGGAATATGACCACTT
64 GTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTTC--ATCTCATCA-AAAGATGAACACTT
30690553 TATTGCTTCG
126 TATTGCTTCG
30690563 GATGATTGCA
Statistics
Matches: 848, Mismatches: 97, Indels: 45
0.86 0.10 0.05
Matches are distributed among these distances:
205 1 0.00
206 1 0.00
207 196 0.23
208 493 0.58
209 156 0.18
210 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (207 bp):
TTGGTCTACTTCTTTGTATCTCATCAGAAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGT
ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTTCATCTCATCAAAAGATGAACACTTTATTG
CTTCGACCCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTT
CGCTTCATTGAT
Found at i:30690153 original size:415 final size:413
Alignment explanation
Indices: 30689387--30690561 Score: 1474
Period size: 415 Copynumber: 2.8 Consensus size: 413
30689377 GCTTCATCTC
* * * * *
30689387 TTGGTTTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGTTTTAATCCACTTCTCTAT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGT
** * * * * * * *
30689452 ATCTCATCACCAAGACGGATTCGGTTCACTTCTCTGCATGTCGTCGGGAAAATGAACACTTTATT
66 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGACCACTTTATT
* * * * * *
30689517 GCTTCAACCCACTCCTCTATATCTTATCAGGAAGATGAGGTTTGAAAGTTTCACTCATATTGAGC
131 GCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGAGGTTTG-AAGTCTCATTCGTATTGAGC
* * *
30689582 TTCACTTCATTT-AATTGGTCTACTTCTTTGTATCTCATCAAAAAGATGAA-CG-CTTCATTATT
195 TTCGCTTC-TTTGATTTGGTCTACTTCTTTGTATCTCATC-AAAAGAT-AACCGCCTT-ATT-GT
* * * *
30689644 TTAATCCACTTCTTTGTATCTCATCAGGAAGACGAATTTAGTTCATTTCTCT-TCATCTCGTCCA
255 TTAATCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTAT-A-CTCAT-CA
* * * *
30689708 A-AAGATGAACACTTTATTGCTTCAACCCACTTCTCTATATCTTATTAGGAAGATGAGGTTTGA-
317 AGAAGATGACCACTTTATTGCTTCAACCCACTTCTCTATATCTCATCAAGAAGATGAGGTTT-AC
30689771 AGTCTCATTCGTATTGAGCTTCGCTTCATTGAT
381 AGTCTCATTCGTATTGAGCTTCGCTTCATTGAT
* * * *
30689804 TTGGTCTATTTCTTTGTATCTCATCAGAAAGATGACTGCCTCATTGTTTCAATCCACTTCTCTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGT
*
30689869 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATTAGGAAGATGACCAC-TTATT
66 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGACCACTTTATT
*
30689933 AG-TTCGACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGC
131 -GCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGC
30689997 TTCGCTTCTTTGATTTGGTCTACTTCTTTGTATCTCATCAGAAAGATAACCGCCTTATTGTTTCA
195 TTCGCTTCTTTGATTTGGTCTACTTCTTTGTATCTCATCA-AAAGATAACCGCCTTATTGTTT-A
**
30690062 ATCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGCCCACTTCTCTATACCTCATCAAGAAG
258 ATCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTATA-CTCATCAAGAAG
** *
30690127 ATGACCACTTTATTGCTTGGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTACAGTCTC
322 ATGACCACTTTATTGCTTCAACCCACTTCTCTATATCTCATCAAGAAGATGAGGTTTACAGTCTC
30690192 ATTCGTATTGAGCTTCGCTTCATTGAT
387 ATTCGTATTGAGCTTCGCTTCATTGAT
** *
30690219 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCATCTCATTATTTCAATCCACTTCTCTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGT
* * * * *
30690284 ATCTCATCAGGAAGA-TAGATTT-GATCTACTTCTCTGTATCTCATCAGGAAGATAACCGCTTTA
66 ATCTCATCAGGAAGACGA-ATTTGGTTC-ACTTCTCTGCATCTCATCAGGAAGATGACCACTTTA
* * * *
30690347 TTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGGTATGAAGTCTCATTCGTATTGAG
129 TTGCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAG
** * *
30690412 CTTCGCTTCAATGATTTGGTCTACTTCTTTATATCTCATCAAGAAGATGACCGCCTCT-TTGATT
194 CTTCGCTTCTTTGATTTGGTCTACTTCTTTGTATCTCATCAA-AAGATAACCGCCT-TATTG-TT
* * ** * * * *
30690476 TAAACCACATCTCTGTATCTCATCAAAAAGATGTATTTGGTTCACTTTTTCGTAT-CTCATCAGG
256 TAATCCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCAC-TTCTC-TATACTCATCAAG
*
30690540 AATATGACCACTTTATTGCTTC
319 AAGATGACCACTTTATTGCTTC
30690562 GGATGATTGC
Statistics
Matches: 663, Mismatches: 77, Indels: 37
0.85 0.10 0.05
Matches are distributed among these distances:
414 17 0.03
415 304 0.46
416 225 0.34
417 114 0.17
418 3 0.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (413 bp):
TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTCAATCCACTTCTCTGT
ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTGCATCTCATCAGGAAGATGACCACTTTATT
GCTTCGACCCACTTCTCTATATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCT
TCGCTTCTTTGATTTGGTCTACTTCTTTGTATCTCATCAAAAGATAACCGCCTTATTGTTTAATC
CACTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCTATACTCATCAAGAAGATGA
CCACTTTATTGCTTCAACCCACTTCTCTATATCTCATCAAGAAGATGAGGTTTACAGTCTCATTC
GTATTGAGCTTCGCTTCATTGAT
Found at i:30690361 original size:85 final size:85
Alignment explanation
Indices: 30690216--30690384 Score: 225
Period size: 85 Copynumber: 2.0 Consensus size: 85
30690206 TCGCTTCATT
* * *
30690216 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCATCTCATTATTTCAATCCACTTCTC
1 GATTTGATCTACTTCTCTGTATCTCATCAGGAAGATAACCATCTCATTATTTCAACCCACTTCTC
* *
30690281 TGTATCTCATCAGGAAGATA
66 TATATCTCATCAAGAAGATA
* * * *
30690301 GATTTGATCTACTTCTCTGTATCTCATCAGGAAGATAACC-GCTTTATTGCTTT-GACCCACTTC
1 GATTTGATCTACTTCTCTGTATCTCATCAGGAAGATAACCATC-TCATT-ATTTCAACCCACTTC
30690364 TCTATATCTCATCAAGAAGAT
64 TCTATATCTCATCAAGAAGAT
30690385 GGGGTATGAA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 1 0.01
85 69 0.95
86 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.37
Consensus pattern (85 bp):
GATTTGATCTACTTCTCTGTATCTCATCAGGAAGATAACCATCTCATTATTTCAACCCACTTCTC
TATATCTCATCAAGAAGATA
Found at i:30690647 original size:39 final size:39
Alignment explanation
Indices: 30690564--30690653 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
30690554 ATTGCTTCGG
* *
30690564 ATGATTGCAATCTGCCCCATGATCGGGGTAAAAGATCGA
1 ATGACTGCAATCTGCCCCATGATCGGGGTAAAAGATCAA
* * * * *
30690603 GTGACTGCAATCTGCCTCATGATTGGGGTAAGAGATTAA
1 ATGACTGCAATCTGCCCCATGATCGGGGTAAAAGATCAA
*
30690642 ATGACTGTAATC
1 ATGACTGCAATC
30690654 CACCCCTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (39 bp):
ATGACTGCAATCTGCCCCATGATCGGGGTAAAAGATCAA
Found at i:30690710 original size:41 final size:40
Alignment explanation
Indices: 30690657--30691047 Score: 421
Period size: 41 Copynumber: 9.6 Consensus size: 40
30690647 TGTAATCCAC
* *
30690657 CCCTT-TTAATTAAGGGTAAAAGATCGAAATC-TCTAATCTT
1 CCCTTCTTGATTAAGGGTAAAAGA-CGAAATCTTC-AATCTG
* **
30690697 CCCTTCTTGATTAAGGGTAAAAGACTGGAATCTTCACCCTG
1 CCCTTCTTGATTAAGGGTAAAAGAC-GAAATCTTCAATCTG
* * *
30690738 TCCC-TCTTGATTAAAGGTAAAAGACTAGAATCTTCAATATG
1 -CCCTTCTTGATTAAGGGTAAAAGACGA-AATCTTCAATCTG
* * *
30690779 CCCTTCTTAATTAAGGGTAAAAGATTGAAATCTTCAATTTG
1 CCCTTCTTGATTAAGGGTAAAAGA-CGAAATCTTCAATCTG
* * * * *
30690820 CCTTTTTTGATTAAGGGTAAAATACTGGAATCTTTAATCTG
1 CCCTTCTTGATTAAGGGTAAAAGAC-GAAATCTTCAATCTG
* * *
30690861 CCCCTCTTGATTAGGGGTAAAAGACTAGAATCTTCAATCTG
1 CCCTTCTTGATTAAGGGTAAAAGACGA-AATCTTCAATCTG
* * *
30690902 CCCTTCTTGATTAAGGGTAAAAGATTGGAATCTTCAATTTG
1 CCCTTCTTGATTAAGGGTAAAAGA-CGAAATCTTCAATCTG
30690943 CCCTTCTTGATTAAGGGTAAAAGACCG-AATCTTCAATCTG
1 CCCTTCTTGATTAAGGGTAAAAGA-CGAAATCTTCAATCTG
*
30690983 CCCTTCTTGATTAAGAGTAAAAGACTGAAATCTTCAATCTG
1 CCCTTCTTGATTAAGGGTAAAAGAC-GAAATCTTCAATCTG
* *
30691024 CCCATCTTGACTTAGGGGTAAAAG
1 CCCTTCTTGA-TTAAGGGTAAAAG
30691048 GTTGGAATGA
Statistics
Matches: 293, Mismatches: 45, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.00
40 45 0.15
41 230 0.78
42 17 0.06
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (40 bp):
CCCTTCTTGATTAAGGGTAAAAGACGAAATCTTCAATCTG
Found at i:30690809 original size:123 final size:122
Alignment explanation
Indices: 30690657--30691047 Score: 524
Period size: 123 Copynumber: 3.2 Consensus size: 122
30690647 TGTAATCCAC
*
30690657 CCCTT-TTAATTAAGGGTAAAAGATCGAAATC-TCTAATCTT-CCCTTCTTGATTAAGGGTAAAA
1 CCCTTCTTAATTAAGGGTAAAAGATTGAAATCTTC-AAT-TTGCCCTTCTTGATTAAGGGTAAAA
** *
30690719 GACTGGAATCTTCACCCTGTCCCTCTTGATTAAAGGTAAAAGACTAGAATCTTCAATATG
64 GACTGGAATCTTCAATCTG-CCCTCTTGATTAAAGGTAAAAGACTAGAATCTTCAATCTG
* * *
30690779 CCCTTCTTAATTAAGGGTAAAAGATTGAAATCTTCAATTTGCCTTTTTTGATTAAGGGTAAAATA
1 CCCTTCTTAATTAAGGGTAAAAGATTGAAATCTTCAATTTGCCCTTCTTGATTAAGGGTAAAAGA
* **
30690844 CTGGAATCTTTAATCTGCCCCTCTTGATTAGGGGTAAAAGACTAGAATCTTCAATCTG
66 CTGGAATCTTCAATCTG-CCCTCTTGATTAAAGGTAAAAGACTAGAATCTTCAATCTG
* *
30690902 CCCTTCTTGATTAAGGGTAAAAGATTGGAATCTTCAATTTGCCCTTCTTGATTAAGGGTAAAAGA
1 CCCTTCTTAATTAAGGGTAAAAGATTGAAATCTTCAATTTGCCCTTCTTGATTAAGGGTAAAAGA
*
30690967 C-CGAATCTTCAATCTGCCCTTCTTGATT-AAGAGTAAAAGACT-GAAATCTTCAATCTG
66 CTGGAATCTTCAATCTGCCC-TCTTGATTAAAG-GTAAAAGACTAG-AATCTTCAATCTG
* * *
30691024 CCCATCTTGACTTAGGGGTAAAAG
1 CCCTTCTT-AATTAAGGGTAAAAG
30691048 GTTGGAATGA
Statistics
Matches: 238, Mismatches: 24, Indels: 13
0.87 0.09 0.05
Matches are distributed among these distances:
121 5 0.02
122 58 0.24
123 173 0.73
124 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (122 bp):
CCCTTCTTAATTAAGGGTAAAAGATTGAAATCTTCAATTTGCCCTTCTTGATTAAGGGTAAAAGA
CTGGAATCTTCAATCTGCCCTCTTGATTAAAGGTAAAAGACTAGAATCTTCAATCTG
Found at i:30691446 original size:98 final size:99
Alignment explanation
Indices: 30691329--30691565 Score: 239
Period size: 100 Copynumber: 2.4 Consensus size: 99
30691319 ACTCTTCATG
** * * **
30691329 GTACCGGGTTTGCCATTGCGACCTCAACCTTTCCTATCACATTTCAT-GGAATTGGATTCGCCAT
1 GTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCTATCACATTTCATAGGAACCGGATTCGCCAT
*
30691393 TAC-GACCTCAATC-CTCCCCATCACATCTTCTAAG
66 TACAG-CCTCAA-CACTCCCCATCACATCTTCTAAA
* * * * *
30691427 GTACCGGGTTCACTGTTGCGGTCTCAACCTTTCTCT-TCACATTTTATAGGGTACCGGTTTCGCC
1 GTACCGGGTTCACCGTTGCGGCCTCAACCTTTC-CTATCACATTTCATA-GGAACCGGATTCGCC
* * * *
30691491 GTTGCAGCCTCAACATTTCCCATCACATCTTCTAAA
64 ATTACAGCCTCAACACTCCCCATCACATCTTCTAAA
* * *
30691527 GTACCGGGTTCGCCGTTGCGGCCTCAACTTTTCCCATCA
1 GTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCTATCA
30691566 AATCTTAATG
Statistics
Matches: 112, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
98 37 0.33
99 4 0.04
100 70 0.62
101 1 0.01
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.32
Consensus pattern (99 bp):
GTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCTATCACATTTCATAGGAACCGGATTCGCCAT
TACAGCCTCAACACTCCCCATCACATCTTCTAAA
Found at i:30691480 original size:50 final size:50
Alignment explanation
Indices: 30691409--30691572 Score: 193
Period size: 50 Copynumber: 3.3 Consensus size: 50
30691399 CTCAATCCTC
* * * * *
30691409 CCCATCACATCTTCTAAGGTACCGGGTTCACTGTTGCGGTCTCAACCTTT
1 CCCATCACATCTTATAAGGTACCGGGTTCGCCGTTGCGGCCTCAACATTT
* * * * * *
30691459 CTCTTCACATTTTATAGGGTACCGGTTTCGCCGTTGCAGCCTCAACATTT
1 CCCATCACATCTTATAAGGTACCGGGTTCGCCGTTGCGGCCTCAACATTT
* * *
30691509 CCCATCACATCTTCTAAAGTACCGGGTTCGCCGTTGCGGCCTCAACTTTT
1 CCCATCACATCTTATAAGGTACCGGGTTCGCCGTTGCGGCCTCAACATTT
*
30691559 CCCATCAAATCTTA
1 CCCATCACATCTTA
30691573 ATGGTATCGA
Statistics
Matches: 92, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 92 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (50 bp):
CCCATCACATCTTATAAGGTACCGGGTTCGCCGTTGCGGCCTCAACATTT
Found at i:30692593 original size:7 final size:7
Alignment explanation
Indices: 30692552--30692638 Score: 50
Period size: 7 Copynumber: 11.4 Consensus size: 7
30692542 ATCTCTCCTT
30692552 TTTTTTCC
1 TTTTTT-C
30692560 TATTTTTC
1 T-TTTTTC
*
30692568 TATTTTC
1 TTTTTTC
*
30692575 TTTTTCC
1 TTTTTTC
*
30692582 TTTTTCTT
1 TTTTT-TC
30692590 TTTTTTC
1 TTTTTTC
*
30692597 CTTTTTC
1 TTTTTTC
30692604 ATTTCATTTC
1 -TTT--TTTC
30692614 TTTCTTT-
1 TTT-TTTC
*
30692621 TTTATTTA
1 TTT-TTTC
30692629 TTTTTTC
1 TTTTTTC
30692636 TTT
1 TTT
30692639 ATTAAATTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
7 34 0.55
8 16 0.26
9 8 0.13
10 4 0.06
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:30692595 original size:22 final size:23
Alignment explanation
Indices: 30692553--30692603 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
30692543 TCTCTCCTTT
30692553 TTTTTCCTATTTTTCTATTTT-C
1 TTTTTCCTATTTTTCTATTTTCC
* *
30692575 TTTTTCCT-TTTTCTTTTTTTTCC
1 TTTTTCCTATTTT-TCTATTTTCC
30692598 TTTTTC
1 TTTTTC
30692604 ATTTCATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 14 0.56
23 7 0.28
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTCCTATTTTTCTATTTTCC
Found at i:30698037 original size:30 final size:30
Alignment explanation
Indices: 30697976--30698084 Score: 105
Period size: 29 Copynumber: 3.7 Consensus size: 30
30697966 TTTATGGGTC
* * * *
30697976 AATGTGATTTGGGAAAAGTTTGAGGGTAAA
1 AATGTAATTTTGGAAAAGTTCGAGAGTAAA
30698006 AATGTAATTTT-GAAAAGTTCGAGAGTCAAA
1 AATGTAATTTTGGAAAAGTTCGAGAGT-AAA
* * *
30698036 AATGTGATTTTGGAAAAGTTTG-GGGTAAA
1 AATGTAATTTTGGAAAAGTTCGAGAGTAAA
* * *
30698065 AATATATTTTTTGAAAAGTT
1 AATGTAATTTTGGAAAAGTT
30698085 TAAGGGTCAA
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
29 32 0.48
30 25 0.38
31 9 0.14
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.35
Consensus pattern (30 bp):
AATGTAATTTTGGAAAAGTTCGAGAGTAAA
Found at i:30698055 original size:31 final size:30
Alignment explanation
Indices: 30697976--30698055 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
30697966 TTTATGGGTC
* * *
30697976 AATGTGATTTGGGAAAAGTTTGAGGGTAAA
1 AATGTGATTTTGGAAAAGTTCGAGAGTAAA
*
30698006 AATGTAATTTT-GAAAAGTTCGAGAGTCAAA
1 AATGTGATTTTGGAAAAGTTCGAGAGT-AAA
30698036 AATGTGATTTTGGAAAAGTT
1 AATGTGATTTTGGAAAAGTT
30698056 TGGGGTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.30
30 22 0.51
31 8 0.19
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.33
Consensus pattern (30 bp):
AATGTGATTTTGGAAAAGTTCGAGAGTAAA
Found at i:30698094 original size:60 final size:58
Alignment explanation
Indices: 30697976--30698139 Score: 184
Period size: 60 Copynumber: 2.7 Consensus size: 58
30697966 TTTATGGGTC
* * * *
30697976 AATGTGATTTGGGAAAAGTTTGAGGGTAAAAATGTAATTTTGAAAAGTTCGAGAGTCAAA
1 AATGTGATTTTGGAAAAGTTTG-GGGTAAAAATATATTTTTGAAAAGTTCAAGAGTC-AA
* *
30698036 AATGTGATTTTGGAAAAGTTTGGGGTAAAAATATATTTTTTGAAAAGTTTAAGGGTCAA
1 AATGTGATTTTGGAAAAGTTTGGGGTAAAAATATA-TTTTTGAAAAGTTCAAGAGTCAA
* * ** *
30698095 AATATAATTTTTAAAAAGTTTAGGGGTCAAAATATAATTTTTGAA
1 AATGTGATTTTGGAAAAGTTT-GGGGTAAAAATAT-ATTTTTGAA
30698140 TAAAATAGGG
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
59 31 0.34
60 58 0.64
61 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.35
Consensus pattern (58 bp):
AATGTGATTTTGGAAAAGTTTGGGGTAAAAATATATTTTTGAAAAGTTCAAGAGTCAA
Found at i:30698097 original size:30 final size:30
Alignment explanation
Indices: 30697988--30698139 Score: 155
Period size: 30 Copynumber: 5.1 Consensus size: 30
30697978 TGTGATTTGG
* * *
30697988 GAAAAGTTTGAGGGTAAAAATGTAA-TTTT
1 GAAAAGTTTAAGGGTCAAAATATAATTTTT
** * * * *
30698017 GAAAAGTTCGAGAGTCAAAAATGTGATTTTG
1 GAAAAGTTTAAGGGTC-AAAATATAATTTTT
* * *
30698048 GAAAAGTTT-GGGGTAAAAATATATTTTTT
1 GAAAAGTTTAAGGGTCAAAATATAATTTTT
30698077 GAAAAGTTTAAGGGTCAAAATATAATTTTT
1 GAAAAGTTTAAGGGTCAAAATATAATTTTT
* *
30698107 AAAAAGTTTAGGGGTCAAAATATAATTTTT
1 GAAAAGTTTAAGGGTCAAAATATAATTTTT
30698137 GAA
1 GAA
30698140 TAAAATAGGG
Statistics
Matches: 101, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
29 32 0.32
30 58 0.57
31 11 0.11
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (30 bp):
GAAAAGTTTAAGGGTCAAAATATAATTTTT
Found at i:30706410 original size:33 final size:33
Alignment explanation
Indices: 30706368--30706434 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
30706358 ACCTGTGAAC
30706368 TCACCCTCCCAAAGGGCCTATCCAGGCAACGGA
1 TCACCCTCCCAAAGGGCCTATCCAGGCAACGGA
*
30706401 TCACCCTCCCAAAGGGCCTATCCAGGCAATGGA
1 TCACCCTCCCAAAGGGCCTATCCAGGCAACGGA
30706434 T
1 T
30706435 GGCTTGATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.37, G:0.21, T:0.15
Consensus pattern (33 bp):
TCACCCTCCCAAAGGGCCTATCCAGGCAACGGA
Found at i:30715170 original size:28 final size:28
Alignment explanation
Indices: 30715134--30715193 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
30715124 AAAACACTTT
** *
30715134 TCAAAAGTAATGTTAAACTAGCTTTAAA
1 TCAAAAGTAATACTAAACTAGCCTTAAA
*
30715162 TCAAAAGTAATACTAAACTATCCTTAAA
1 TCAAAAGTAATACTAAACTAGCCTTAAA
30715190 TCAA
1 TCAA
30715194 TTTCCAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (28 bp):
TCAAAAGTAATACTAAACTAGCCTTAAA
Found at i:30716757 original size:16 final size:17
Alignment explanation
Indices: 30716736--30716774 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
30716726 AGATTTGGAT
*
30716736 AAAAATAT-TTTGCTCA
1 AAAAATATGTTTGATCA
*
30716752 AAAAATATGTTTGATCG
1 AAAAATATGTTTGATCA
30716769 AAAAAT
1 AAAAAT
30716775 TACGCCCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (17 bp):
AAAAATATGTTTGATCA
Found at i:30720131 original size:1 final size:1
Alignment explanation
Indices: 30720120--30720155 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
30720110 ATACTCAAAC
*
30720120 AAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
30720156 CCAAGATCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30720747 original size:32 final size:31
Alignment explanation
Indices: 30720632--30720747 Score: 81
Period size: 27 Copynumber: 4.0 Consensus size: 31
30720622 ATTAAGAATG
*
30720632 TTATTAAATTATATTT--T-AT-TTTTATTT
1 TTATTAAATTATATTTAATAATAATTTATTT
*
30720659 TTATTAAGTTATATTTAATAATAA-TTA---
1 TTATTAAATTATATTTAATAATAATTTATTT
* * * *
30720686 -TATTAAAATATGATTAAATTAT-TTATTATTT
1 TTATTAAATTAT-ATTTAATAATAAT-TTATTT
30720717 TTATTAAATTATATTTAATAATAATCTTATT
1 TTATTAAATTATATTTAATAATAAT-TTATT
30720748 AATATTTAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
26 9 0.14
27 23 0.35
28 3 0.05
29 1 0.02
30 5 0.08
31 8 0.12
32 16 0.25
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (31 bp):
TTATTAAATTATATTTAATAATAATTTATTT
Found at i:30721778 original size:27 final size:28
Alignment explanation
Indices: 30721739--30721793 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
30721729 TTGAGCATCT
* *
30721739 CTAATGGATGG-TTGGGCTTCTTCCTCC
1 CTAATGGACGGTTTGGGCTCCTTCCTCC
30721766 CTAATGGACGGTTTGGGCTCCTTCCTCC
1 CTAATGGACGGTTTGGGCTCCTTCCTCC
30721794 TTAGTGGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.11, C:0.29, G:0.25, T:0.35
Consensus pattern (28 bp):
CTAATGGACGGTTTGGGCTCCTTCCTCC
Found at i:30724976 original size:28 final size:29
Alignment explanation
Indices: 30724940--30724995 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
30724930 AATGGAGAAA
*
30724940 AGCACAAAGACAA-AAG-GAAAACAACAAG
1 AGCAAAAAGACAAGAAGAGAAAA-AACAAG
30724968 AGCAAAAAGACAAGAAGAGAAAAAACAA
1 AGCAAAAAGACAAGAAGAGAAAAAACAA
30724996 AATGTATTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 12 0.48
29 8 0.32
30 5 0.20
ACGTcount: A:0.68, C:0.14, G:0.18, T:0.00
Consensus pattern (29 bp):
AGCAAAAAGACAAGAAGAGAAAAAACAAG
Found at i:30724980 original size:17 final size:15
Alignment explanation
Indices: 30724957--30724995 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
30724947 AGACAAAAGG
30724957 AAAACAACAAGAGCAA
1 AAAACAACAAGAG-AA
*
30724973 AAAGACAAGAAGAGAA
1 AAA-ACAACAAGAGAA
30724989 AAAACAA
1 AAAACAA
30724996 AATGTATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 8 0.38
17 9 0.43
ACGTcount: A:0.72, C:0.13, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAACAACAAGAGAA
Found at i:30726082 original size:3 final size:3
Alignment explanation
Indices: 30726074--30726099 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30726064 ATTTTGTTGG
30726074 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
30726100 TTCTTTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30726256 original size:17 final size:17
Alignment explanation
Indices: 30726234--30726269 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30726224 TCTCTTGACT
*
30726234 TTTAACCTTCCATCTTC
1 TTTAACCTTCCATATTC
*
30726251 TTTAACCTTTCATATTC
1 TTTAACCTTCCATATTC
30726268 TT
1 TT
30726270 GTAATTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAACCTTCCATATTC
Found at i:30732490 original size:2 final size:2
Alignment explanation
Indices: 30732483--30732513 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30732473 TGCACTGTTT
30732483 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30732514 TCATTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30737664 original size:3 final size:3
Alignment explanation
Indices: 30737656--30737682 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
30737646 TTAGTATTTG
30737656 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
30737683 TGATCAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:30743349 original size:13 final size:13
Alignment explanation
Indices: 30743326--30743376 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
30743316 TTGAAAAAAA
*
30743326 TCAACGGTCAAAG
1 TCAACGATCAAAG
*
30743339 CCAACGATCAAAG
1 TCAACGATCAAAG
*
30743352 TCAACGATCAACG
1 TCAACGATCAAAG
30743365 ATCAACGATCAA
1 -TCAACGATCAA
30743377 CAATCGGTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
13 22 0.67
14 11 0.33
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (13 bp):
TCAACGATCAAAG
Found at i:30743364 original size:7 final size:7
Alignment explanation
Indices: 30743340--30743377 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
30743330 CGGTCAAAGC
30743340 CAACGAT
1 CAACGAT
*
30743347 CAAAG-T
1 CAACGAT
30743353 CAACGAT
1 CAACGAT
30743360 CAACGAT
1 CAACGAT
30743367 CAACGAT
1 CAACGAT
30743374 CAAC
1 CAAC
30743378 AATCGGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.45, C:0.29, G:0.13, T:0.13
Consensus pattern (7 bp):
CAACGAT
Found at i:30743389 original size:18 final size:18
Alignment explanation
Indices: 30743366--30743409 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
30743356 CGATCAACGA
*
30743366 TCAACGATCAACAATCGG
1 TCAACGATCAACAATCAG
* **
30743384 TCAACGGTCAACGGTCAG
1 TCAACGATCAACAATCAG
30743402 TCAACGAT
1 TCAACGAT
30743410 TGATCAACAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.18
Consensus pattern (18 bp):
TCAACGATCAACAATCAG
Found at i:30743425 original size:11 final size:11
Alignment explanation
Indices: 30743411--30743449 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
30743401 GTCAACGATT
30743411 GATCAACAGTC
1 GATCAACAGTC
30743422 GATCAACAGTC
1 GATCAACAGTC
* *
30743433 GGTCAACTGTC
1 GATCAACAGTC
*
30743444 GGTCAA
1 GATCAA
30743450 TGATCGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (11 bp):
GATCAACAGTC
Found at i:30743460 original size:22 final size:21
Alignment explanation
Indices: 30743370--30743461 Score: 55
Period size: 22 Copynumber: 4.4 Consensus size: 21
30743360 CAACGATCAA
*
30743370 CGATCAACAATCGGTC-A-A-
1 CGATCAACAGTCGGTCAAGAT
* * *
30743388 CGGTCAACGGTCAGTCAACGAT
1 CGATCAACAGTCGGTCAA-GAT
* * *
30743410 TGATCAACAGTCGATCAACAGT
1 CGATCAACAGTCGGTCAAGA-T
* *
30743432 CGGTCAACTGTCGGTCAATGAT
1 CGATCAACAGTCGGTCAA-GAT
30743454 CGATCAAC
1 CGATCAAC
30743462 GATCGGTGAA
Statistics
Matches: 52, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
18 12 0.23
19 1 0.02
21 2 0.04
22 36 0.69
23 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (21 bp):
CGATCAACAGTCGGTCAAGAT
Found at i:30746617 original size:2 final size:2
Alignment explanation
Indices: 30746610--30746657 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
30746600 GATTAATGAA
30746610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30746652 AT -T AT A
1 AT AT AT A
30746658 GCCAAATGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30746841 original size:15 final size:15
Alignment explanation
Indices: 30746800--30746843 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
30746790 ATATATATAT
30746800 AAGAAATAAAAGAATA
1 AAGAAA-AAAAGAATA
*
30746816 AAGAAAGAAAGAA-A
1 AAGAAAAAAAGAATA
30746830 AAGAAACAAAAGAA
1 AAGAAA-AAAAGAA
30746844 GGAAGAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.28
15 12 0.48
16 6 0.24
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (15 bp):
AAGAAAAAAAGAATA
Found at i:30754086 original size:15 final size:15
Alignment explanation
Indices: 30754045--30754088 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
30754035 ATATATATAT
30754045 AAGAAATAAAAGAATA
1 AAGAAA-AAAAGAATA
*
30754061 AAGAAAGAAAGAA-A
1 AAGAAAAAAAGAATA
30754075 AAGAAACAAAAGAA
1 AAGAAA-AAAAGAA
30754089 GGAAGAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.28
15 12 0.48
16 6 0.24
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (15 bp):
AAGAAAAAAAGAATA
Found at i:30756957 original size:24 final size:24
Alignment explanation
Indices: 30756929--30757028 Score: 110
Period size: 24 Copynumber: 4.1 Consensus size: 24
30756919 GTATACTAGT
30756929 TAACCTTTCTGGGCTCGTAAGAGC
1 TAACCTTTCTGGGCTCGTAAGAGC
*
30756953 TAACCTTTCTGGGATCGTAAGAGC
1 TAACCTTTCTGGGCTCGTAAGAGC
* * * *
30756977 TAACCTTTTTGGACTTGTGAGAGC
1 TAACCTTTCTGGGCTCGTAAGAGC
** * *
30757001 TAATTTTATCTGGGCTTGTATGAGC
1 TAACCTT-TCTGGGCTCGTAAGAGC
30757026 TAA
1 TAA
30757029 AATCTGAAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
24 47 0.75
25 16 0.25
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (24 bp):
TAACCTTTCTGGGCTCGTAAGAGC
Found at i:30758350 original size:40 final size:40
Alignment explanation
Indices: 30758306--30758395 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 40
30758296 TACAATTTCA
* * *
30758306 ATTTTTAAAAATAG-CAGAAGATTTTTTCTCAACTGAAAAT
1 ATTTTTAAAAACAGTCAGAAGATTTTCT-TCAACTAAAAAT
**
30758346 ATTTTCT-GCAACAGTCAGAAGATTTTCTTCAACTAAAAAT
1 ATTTT-TAAAAACAGTCAGAAGATTTTCTTCAACTAAAAAT
*
30758386 ATTTTGAAAA
1 ATTTTTAAAA
30758396 TATTATTTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
40 26 0.67
41 13 0.33
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (40 bp):
ATTTTTAAAAACAGTCAGAAGATTTTCTTCAACTAAAAAT
Found at i:30758525 original size:25 final size:24
Alignment explanation
Indices: 30758495--30758548 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
30758485 AATGAAATAA
30758495 AATTTCCACAAACAAACAAAAACCC
1 AATTTCCACAAACAAA-AAAAACCC
** **
30758520 AATTTCTGCAAACAAAAGTAACCC
1 AATTTCCACAAACAAAAAAAACCC
30758544 AATTT
1 AATTT
30758549 TAGTATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.50, C:0.26, G:0.04, T:0.20
Consensus pattern (24 bp):
AATTTCCACAAACAAAAAAAACCC
Found at i:30759289 original size:10 final size:10
Alignment explanation
Indices: 30759262--30759309 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
30759252 TTTTTAATTT
30759262 TTTTAAAAAA
1 TTTTAAAAAA
* *
30759272 ATTCAAAAAA
1 TTTTAAAAAA
* *
30759282 TTGTAAAATTA
1 TTTTAAAA-AA
30759293 TTTTAAAAAA
1 TTTTAAAAAA
30759303 TTTTAAA
1 TTTTAAA
30759310 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:30759300 original size:20 final size:19
Alignment explanation
Indices: 30759276--30759320 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
30759266 AAAAAAATTC
30759276 AAAAAATTGTAAAATTATTTT
1 AAAAAATT-TAAAATTA-TTT
*
30759297 AAAAAATTTTAAATTATTT
1 AAAAAATTTAAAATTATTT
30759316 AAAAA
1 AAAAA
30759321 TATAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAAAATTTAAAATTATTT
Found at i:30759814 original size:18 final size:18
Alignment explanation
Indices: 30759793--30759829 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30759783 TTTATTCCTT
*
30759793 TGTTTCTTTAATTTTTTA
1 TGTTTCTATAATTTTTTA
*
30759811 TGTTTCTATAGTTTTTTA
1 TGTTTCTATAATTTTTTA
30759829 T
1 T
30759830 ATTTAGAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.05, G:0.08, T:0.70
Consensus pattern (18 bp):
TGTTTCTATAATTTTTTA
Found at i:30766944 original size:17 final size:17
Alignment explanation
Indices: 30766918--30766961 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
30766908 CAATCTATAC
30766918 AAATAAATAAATTTTAAT
1 AAATAAATAAA-TTTAAT
*
30766936 ATA-AAAT-AATTTAAT
1 AAATAAATAAATTTAAT
30766951 AAATAAATAAA
1 AAATAAATAAA
30766962 AATTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 6 0.27
18 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATAAATAAATTTAAT
Found at i:30768771 original size:22 final size:23
Alignment explanation
Indices: 30768728--30768772 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
30768718 TTTCAATAAA
30768728 AAAATATATAATTATTAAATATT
1 AAAATATATAATTATTAAATATT
30768751 AAAATAATATAA-TA-TAAATATT
1 AAAAT-ATATAATTATTAAATATT
30768773 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 7 0.33
24 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATATATAATTATTAAATATT
Found at i:30770248 original size:3 final size:3
Alignment explanation
Indices: 30770240--30770279 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
30770230 TTATATAAAG
30770240 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
30770280 AAAAATCAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:30777607 original size:5 final size:5
Alignment explanation
Indices: 30777597--30777629 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
30777587 AGATCAATTT
30777597 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGT
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGT
30777630 ATATAATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.61
Consensus pattern (5 bp):
TGTTA
Found at i:30777761 original size:22 final size:22
Alignment explanation
Indices: 30777733--30777806 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
30777723 CCTATTGTTC
*
30777733 TGCACTACGGTGCTTACTGGTT
1 TGCACTATGGTGCTTACTGGTT
*
30777755 TGCACTATGGTGCCTACT-GTT
1 TGCACTATGGTGCTTACTGGTT
*
30777776 CTGCACTATGGTGCTTACTGATT
1 -TGCACTATGGTGCTTACTGGTT
30777799 TGCACTAT
1 TGCACTAT
30777807 AGTACCTACT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.07
22 41 0.89
23 2 0.04
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (22 bp):
TGCACTATGGTGCTTACTGGTT
Found at i:30777791 original size:44 final size:44
Alignment explanation
Indices: 30777716--30777816 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
30777706 ATAATTGGGT
* * *
30777716 TATAATACCTATTGTTCTGCACTACGGTGCTTACTGGTTTGCAC
1 TATAGTACCTACTGTTCTGCACTACGGTGCTTACTGATTTGCAC
* * *
30777760 TATGGTGCCTACTGTTCTGCACTATGGTGCTTACTGATTTGCAC
1 TATAGTACCTACTGTTCTGCACTACGGTGCTTACTGATTTGCAC
30777804 TATAGTACCTACT
1 TATAGTACCTACT
30777817 TATTTGCACT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (44 bp):
TATAGTACCTACTGTTCTGCACTACGGTGCTTACTGATTTGCAC
Found at i:30777816 original size:22 final size:22
Alignment explanation
Indices: 30777733--30777839 Score: 101
Period size: 22 Copynumber: 4.9 Consensus size: 22
30777723 CCTATTGTTC
** * *
30777733 TGCACTACGGTGCTTACTGGTT
1 TGCACTATAGTGCCTACTGATT
*
30777755 TGCACTATGGTGCCTACTG-TT
1 TGCACTATAGTGCCTACTGATT
* *
30777776 CTGCACTATGGTGCTTACTGATT
1 -TGCACTATAGTGCCTACTGATT
* *
30777799 TGCACTATAGTACCTACTTATT
1 TGCACTATAGTGCCTACTGATT
30777821 TGCACT-TCAGTGCCTACTG
1 TGCACTAT-AGTGCCTACTG
30777840 TTAAAGCACT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.04
22 68 0.93
23 2 0.03
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (22 bp):
TGCACTATAGTGCCTACTGATT
Found at i:30777839 original size:44 final size:43
Alignment explanation
Indices: 30777716--30777839 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 43
30777706 ATAATTGGGT
* * *
30777716 TATAATACCTA-TTGTTCTGCACTACGGTGCTTACTGGTTTGCAC
1 TATAGTACCTACTT-TT-TGCACTTCGGTGCTTACTGATTTGCAC
* * *
30777760 TATGGTGCCTACTGTTCTGCACTAT-GGTGCTTACTGATTTGCAC
1 TATAGTACCTACT-TTTTGCACT-TCGGTGCTTACTGATTTGCAC
* *
30777804 TATAGTACCTACTTATTTGCACTTCAGTGCCTACTG
1 TATAGTACCTACTT-TTTGCACTTCGGTGCTTACTG
30777840 TTAAAGCACT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
43 2 0.03
44 59 0.92
45 2 0.03
46 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (43 bp):
TATAGTACCTACTTTTTGCACTTCGGTGCTTACTGATTTGCAC
Found at i:30779069 original size:13 final size:13
Alignment explanation
Indices: 30779047--30779076 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30779037 GGTTTTCTCC
*
30779047 AAAATGAAAAATA
1 AAAATAAAAAATA
30779060 AAAATAAAAAATA
1 AAAATAAAAAATA
30779073 AAAA
1 AAAA
30779077 ATGATCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:30787157 original size:29 final size:29
Alignment explanation
Indices: 30787103--30787184 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 29
30787093 AGAATTTGAT
*
30787103 AAAATCAAAATTTCATGTATAAAATTGTAC
1 AAAATCAAAA-TTCATGTATAAAATTGCAC
*
30787133 AAAATCAAAATTCATGTATACAATTGCAC
1 AAAATCAAAATTCATGTATAAAATTGCAC
* *
30787162 ATTAAACCATAATTCATGTATAA
1 A--AAATCAAAATTCATGTATAA
30787185 TTTTAAGATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.40
30 10 0.22
31 17 0.38
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAATCAAAATTCATGTATAAAATTGCAC
Found at i:30787666 original size:12 final size:12
Alignment explanation
Indices: 30787649--30787707 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
30787639 AACTAAATTA
30787649 TATAATATTTAT
1 TATAATATTTAT
*
30787661 TATAATTTTTA-
1 TATAATATTTAT
30787672 TACTAA-A-TT-T
1 TA-TAATATTTAT
30787682 TATAATATTTAT
1 TATAATATTTAT
30787694 TATTAATTATTTAT
1 TA-TAA-TATTTAT
30787708 ACTCGGTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
9 3 0.08
10 5 0.13
11 4 0.11
12 16 0.42
13 3 0.08
14 7 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (12 bp):
TATAATATTTAT
Found at i:30787678 original size:33 final size:35
Alignment explanation
Indices: 30787640--30787710 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 35
30787630 TACATAATTA
30787640 ACTAAATTATATAATATTTATTA-TAATT-TTTAT
1 ACTAAATTATATAATATTTATTATTAATTATTTAT
*
30787673 ACTAAATTTTATAATATTTATTATTAATTATTTAT
1 ACTAAATTATATAATATTTATTATTAATTATTTAT
30787708 ACT
1 ACT
30787711 CGGTTAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 22 0.63
34 5 0.14
35 8 0.23
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (35 bp):
ACTAAATTATATAATATTTATTATTAATTATTTAT
Found at i:30800240 original size:18 final size:18
Alignment explanation
Indices: 30800205--30800242 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
30800195 TAAATTTTTG
*
30800205 AATTTGAATAACTTGAAT
1 AATTTGAATAACTCGAAT
30800223 AATTTGAATAAAC-CGAAT
1 AATTTGAAT-AACTCGAAT
30800241 AA
1 AA
30800243 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (18 bp):
AATTTGAATAACTCGAAT
Found at i:30800976 original size:22 final size:22
Alignment explanation
Indices: 30800951--30801001 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
30800941 GTATTTCCAA
30800951 TTTTTTTCATGTAATTTTAAGT
1 TTTTTTTCATGTAATTTTAAGT
** **
30800973 TTTTTTAGATGTTGTTTTAAGT
1 TTTTTTTCATGTAATTTTAAGT
30800995 TTTTTTT
1 TTTTTTT
30801002 AATTTTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.18, C:0.02, G:0.12, T:0.69
Consensus pattern (22 bp):
TTTTTTTCATGTAATTTTAAGT
Found at i:30801049 original size:35 final size:34
Alignment explanation
Indices: 30800985--30801054 Score: 79
Period size: 35 Copynumber: 2.0 Consensus size: 34
30800975 TTTTAGATGT
*
30800985 TGTTTTAAGTTTTTTTTAATTTTAATTAATAAATA
1 TGTTTTAAGTTTTTATTAATTTT-ATTAATAAATA
* *
30801020 TGTTTTCAAGTTTTTAATTCATTTT-TTAATTAATA
1 TGTTTT-AAGTTTTT-ATTAATTTTATTAATAAATA
30801055 AAACTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
35 15 0.50
36 8 0.27
37 7 0.23
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (34 bp):
TGTTTTAAGTTTTTATTAATTTTATTAATAAATA
Found at i:30808522 original size:18 final size:17
Alignment explanation
Indices: 30808499--30808533 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
30808489 CATGTAAAAG
30808499 AAGCGGTGAGGGAGTCAA
1 AAGCGGTG-GGGAGTCAA
*
30808517 AAGCGGTGGGGTGTCAA
1 AAGCGGTGGGGAGTCAA
30808534 TATTTGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.11, G:0.46, T:0.14
Consensus pattern (17 bp):
AAGCGGTGGGGAGTCAA
Found at i:30811337 original size:17 final size:17
Alignment explanation
Indices: 30811323--30811372 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
30811313 TAAAATTTGG
*
30811323 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAA
* *
30811340 TTTGAATTTAAA-TTCA
1 TTTAAATTTAAATTTAA
30811356 TTCTAAATTTAAATTTA
1 TT-TAAATTTAAATTTA
30811373 TTTCTAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 4 0.15
17 20 0.77
18 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Done.