Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008252.1 Hibiscus syriacus cultivar Beakdansim tig00110904_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2928487
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 13
Found at i:2443313 original size:17 final size:16
Alignment explanation
Indices: 2443282--2443315 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2443272 CACGTGAGGA
2443282 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
2443298 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
2443315 T
1 T
2443316 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:2444417 original size:73 final size:73
Alignment explanation
Indices: 2444293--2444480 Score: 331
Period size: 73 Copynumber: 2.6 Consensus size: 73
2444283 GGATGTTTTC
* *
2444293 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTATTTCTCTCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTATTTCTCGCTAGAGAAAGT
2444358 TTCACTTG
66 TTCACTTG
* *
2444366 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTATTTCTCGCTAGAGAAAGT
2444431 TTCACTTG
66 TTCACTTG
*
2444439 AAATAGCAATTTATCTCACTTGAGGTTGTTTTTCTTAAAACA
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
2444481 TCTCCAGATA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 110 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (73 bp):
AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTATTTCTCGCTAGAGAAAGT
TTCACTTG
Found at i:2444535 original size:39 final size:39
Alignment explanation
Indices: 2444491--2445185 Score: 466
Period size: 39 Copynumber: 17.5 Consensus size: 39
2444481 TCTCCAGATA
* * *
2444491 GAGTTCATAATCTGAAGAATTCTTCTGAAGAGGAAAAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* * *
2444530 TAGTTCATAATCTGAAGAACTCGTTTGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* * **
2444569 AAGTTCATAATCTAAAGAACTTGTCTGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* * * *
2444608 AAGTTCATAGTCTGAAGAACTCATATGAAAAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* *
2444647 GAGTTCATAGTCTGAAGAACTCATATGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* *
2444686 GAGTTCATAATCTGAAGAACTCGTCGGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* *** * *
2444725 GAGTTCATAATCTGAAGAACT-AGTCTGATTGTTTTTTTTTAAATAAT
1 GAGTTCATAATCTGAAGAACTCA-TCTGA-AG-------AGGAAGAAG
* ** * * * *
2444772 CAGTTTC-TCGT-TGGAGAAAGTTTCA-CTCGAA-A--TAGCA-
1 GAG-TTCATAATCTGAAG-AA--CTCATCT-GAAGAGGAAGAAG
* * ** ** * **
2444809 -A-TTTAT-CTCACTTG-AGATTGTTTTTCTTAA-AACATTTCCAGAAG
1 GAGTTCATAAT--C-TGAAGA--ACTCATCTGAAGAGGA-----AGAAG
* * * * *
2444853 GAGTTCATAGTCTTAACAACTCATATGAAGA-GAAAAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* * * * *
2444891 GAGTTCATAATTTGAGGAACTCGTCTAAAGATGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
2444930 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* *
2444969 G-GTTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAAT
1 GAG-TTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* *
2445008 GAGTTCATACTCTGAAGAACTCATATGAAGAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* * *
2445047 GAGGTCATATTCTGAAGAACTCATCTGAAGAGGAAGAAT
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* * * *
2445086 AAGTTCATAGTCTGAAGAACTCATCTGAAAAGGAAGAAT
1 GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
* *
2445125 GAGTTCATAATCTGAATAACTCATCTGAAAAAGGAAGAAG
1 GAGTTCATAATCTGAAGAACTCATCTG-AAGAGGAAGAAG
* *
2445165 AAGTTCATAGTCTGAAGAACT
1 GAGTTCATAATCTGAAGAACT
2445186 AATTCAACCT
Statistics
Matches: 522, Mismatches: 94, Indels: 79
0.75 0.14 0.11
Matches are distributed among these distances:
34 3 0.01
35 1 0.00
36 7 0.01
37 4 0.01
38 32 0.06
39 401 0.77
40 31 0.06
43 9 0.02
44 2 0.00
45 4 0.01
46 8 0.02
47 11 0.02
48 5 0.01
49 3 0.01
50 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.26
Consensus pattern (39 bp):
GAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGAAG
Found at i:2445063 original size:361 final size:362
Alignment explanation
Indices: 2444412--2445106 Score: 1036
Period size: 361 Copynumber: 1.9 Consensus size: 362
2444402 AAAACAAATT
* *
2444412 GTTTCTCGCTAGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGGTTGTTTTTCTTAA
1 GTTTCTCGCTAGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAA
* * * * *
2444477 AACATCTCCAGATAGAGTTCATAATCTGAAGAATTCTTCTGAAGAGGAAAAAGTAGTTCATAATC
66 AACATCTCCAGATAGAGTTCATAATCTGAACAACTCATATGAAGAGGAAAAAGGAGTTCATAATC
* * **
2444542 TGAAGAACTCGTTTGAAGAGGAAGAAGAAGTTCATAATCTAAAGAACTTGTCTGAAGAGGAAGAA
131 TGAAGAACTCGTCTAAAGAGGAAGAAGAAGTTCATAATCTAAAGAACTCATCTGAAGAGGAAGAA
* * *
2444607 GAAGTTCATAGTCTGAAGAACTCATATGAAAAGGAAGAAGGAGTTCATAGTCTGAAGAACTCATA
196 GAAGTTCATAATCTGAAGAACTCATATGAAAAGGAAAAAGGAGTTCATACTCTGAAGAACTCATA
* * *
2444672 TGAAGAGGAAGAAGGAGTTCATAATCTGAAGAACTCGTCGGAAGAGGAAGAAGGAGTTCATAATC
261 TGAAGAGGAAGAAGGAGGTCATAATCTGAAGAACTCATCGGAAGAGGAAGAAGAAGTTCATAATC
2444737 TGAAGAACTAGTCTGATTGTTTTTTTTTAAATAATCA
326 TGAAGAACTAGTCTGATTGTTTTTTTTTAAATAATCA
* *
2444774 GTTTCTCGTTGGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAA
1 GTTTCTCGCTAGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAA
* * *
2444839 AACATTTCCAGA-AGGAGTTCATAGTCTTAACAACTCATATGAAGA-GAAAAAGGAGTTCATAAT
66 AACATCTCCAGATA-GAGTTCATAATCTGAACAACTCATATGAAGAGGAAAAAGGAGTTCATAAT
* * * * *
2444902 TTGAGGAACTCGTCTAAAGATGAAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAAGA
130 CTGAAGAACTCGTCTAAAGAGGAAGAAGAAGTTCATAATCTAAAGAACTCATCTGAAGAGGAAGA
* * * *
2444967 AG-GGTTTCATAATCTGAAGAACTCATCTGAAGAGGAAAAATGAGTTCATACTCTGAAGAACTCA
195 AGAAG-TTCATAATCTGAAGAACTCATATGAAAAGGAAAAAGGAGTTCATACTCTGAAGAACTCA
* * * *
2445031 TATGAAGAGGAAGAAGGAGGTCATATTCTGAAGAACTCATCTGAAGAGGAAGAATAAGTTCATAG
259 TATGAAGAGGAAGAAGGAGGTCATAATCTGAAGAACTCATCGGAAGAGGAAGAAGAAGTTCATAA
2445096 TCTGAAGAACT
324 TCTGAAGAACT
2445107 CATCTGAAAA
Statistics
Matches: 296, Mismatches: 35, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
360 1 0.00
361 198 0.67
362 97 0.33
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (362 bp):
GTTTCTCGCTAGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAA
AACATCTCCAGATAGAGTTCATAATCTGAACAACTCATATGAAGAGGAAAAAGGAGTTCATAATC
TGAAGAACTCGTCTAAAGAGGAAGAAGAAGTTCATAATCTAAAGAACTCATCTGAAGAGGAAGAA
GAAGTTCATAATCTGAAGAACTCATATGAAAAGGAAAAAGGAGTTCATACTCTGAAGAACTCATA
TGAAGAGGAAGAAGGAGGTCATAATCTGAAGAACTCATCGGAAGAGGAAGAAGAAGTTCATAATC
TGAAGAACTAGTCTGATTGTTTTTTTTTAAATAATCA
Found at i:2446523 original size:34 final size:34
Alignment explanation
Indices: 2446485--2446552 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
2446475 TTATGATATC
* * *
2446485 TTTTATTTTAGTTCTTTACTTTATTTTTTTATTT
1 TTTTATTTTAGTCCTTTACTTTATATTTTAATTT
2446519 TTTTATTTTAGTCCTTTACTTTATATTTTAATTT
1 TTTTATTTTAGTCCTTTACTTTATATTTTAATTT
2446553 ATGTCATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.72
Consensus pattern (34 bp):
TTTTATTTTAGTCCTTTACTTTATATTTTAATTT
Found at i:2446562 original size:26 final size:25
Alignment explanation
Indices: 2446519--2446572 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
2446509 TTTTTTATTT
* * *
2446519 TTTTATTTTAGTCCTTTACTTTATA
1 TTTTAATTTAGTCATTTAATTTATA
*
2446544 TTTTAATTTATGTCATTTAATTTTTA
1 TTTTAATTTA-GTCATTTAATTTATA
2446570 TTT
1 TTT
2446573 ATTTAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTAATTTAGTCATTTAATTTATA
Found at i:2452579 original size:17 final size:17
Alignment explanation
Indices: 2452559--2452591 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2452549 TAGATATTGT
2452559 AATTG-AAATAAATAAAA
1 AATTGCAAAT-AATAAAA
2452576 AATTGCAAATAATAAA
1 AATTGCAAATAATAAA
2452592 GGAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (17 bp):
AATTGCAAATAATAAAA
Found at i:2453769 original size:88 final size:87
Alignment explanation
Indices: 2453661--2453921 Score: 328
Period size: 87 Copynumber: 3.0 Consensus size: 87
2453651 ATGCGAGGGA
* * *
2453661 TGAGTGAAATGAAAACGTCGATCCCCTTTCTTCTGTGATGAAATTGAACGAGATATCGGTGTTGA
1 TGAGTGAAATGAAAATGTCGATCCCC-TCCTTCTGTGATGAAATTGAACGAGATATTGGTGTTGA
*
2453726 TCTACCTCCTTCTGTGATAGATT
65 TCTACCTCATTCTGTGATAGATT
* * *
2453749 TGAGTAAAATGAAAATGTCGATCCCCTCCTTCTGTGA-CATAATTGAACGAGATGTTGGTGTTGA
1 TGAGTGAAATGAAAATGTCGATCCCCTCCTTCTGTGATGA-AATTGAACGAGATATTGGTGTTGA
*
2453813 TCTACCTCATTCTGTGATAGTTT
65 TCTACCTCATTCTGTGATAGATT
* * * * *
2453836 TGAGTGAAATGAAAATGTCGAGCCACCTCCATCTGTGATGGAAA-CGAATGATATATTGGTGTTG
1 TGAGTGAAATGAAAATGTCGATCC-CCTCCTTCTGTGAT-GAAATTGAACGAGATATTGGTGTTG
* * *
2453900 ATCTACCACTTTTTGTGATAGA
64 ATCTACCTCATTCTGTGATAGA
2453922 ATCGAGCAAA
Statistics
Matches: 149, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.01
87 75 0.50
88 70 0.47
89 2 0.01
90 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (87 bp):
TGAGTGAAATGAAAATGTCGATCCCCTCCTTCTGTGATGAAATTGAACGAGATATTGGTGTTGAT
CTACCTCATTCTGTGATAGATT
Found at i:2454221 original size:136 final size:134
Alignment explanation
Indices: 2453975--2454316 Score: 384
Period size: 136 Copynumber: 2.5 Consensus size: 134
2453965 AAACAAGCTA
* * * * * *
2453975 AGGTTGAACAAGTTCGTCTCATTATGAACTT-TTCCTCACTTATCGAATGAGTTATTATCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTT-CTCCCTTGTCG-ATGAGTTCTTCTCATTAT
* ** * * * **
2454039 GAACTCTCCACTGGAAATTTTGATCCTTCGAGTGAGGTCTTGCTGATTCAAAATATTGTGAATCG
64 GAACTCTCCACTGGAAATGTCAATCCCTCAAGCGAGGTCTCACTGATTCAAAATATTGTGAATCG
2454104 AGTGAT
129 AGTGAT
*
2454110 AGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT-TGTC-GATGAGTTCTTCTCATTAT
* * *
2454175 GAACTCTCCATTTGAAATGTCAATCCCTCAAGCGAGG-CGTCACTGATTCAAAATGTTGTGAATC
64 GAACTCTCCACTGGAAATGTCAATCCCTCAAGCGAGGTC-TCACTGATTCAAAATATTGTGAATC
2454239 GAGTGAT
128 GAGTGAT
* ** * * * *
2454246 ACGTCAAACAAGCTCTTCTCATTATGAACCTC-TCTCCCTTGTTGGATGAGTACTTCTCATTATA
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTG-TCGATGAGTTCTTCTCATTATG
2454310 AACTCTC
65 AACTCTC
2454317 TACTATAAAT
Statistics
Matches: 176, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
134 27 0.15
135 42 0.24
136 106 0.60
137 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (134 bp):
AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTGTCGATGAGTTCTTCTCATTATGA
ACTCTCCACTGGAAATGTCAATCCCTCAAGCGAGGTCTCACTGATTCAAAATATTGTGAATCGAG
TGAT
Found at i:2454498 original size:182 final size:181
Alignment explanation
Indices: 2454252--2454588 Score: 480
Period size: 182 Copynumber: 1.9 Consensus size: 181
2454242 TGATACGTCA
* * *
2454252 AACAAGCTCTTCTCATTATGAACCTCTCTCCCTTGTTGGATGAGTACTTCTCATTATAAACTCTC
1 AACAAACTCTTCTCATTATGAACCTCTCTCCCTCGTGGGATGAGTACTTCTCATTATAAACTCTC
* *
2454317 TACTATAAATGTTGA-GTCAAGGTTAAACAAGT-TCTTCTCATTATGAACTACTTCTTCCCCGTC
66 TACTAGAAATGTTGATG-CAAGGCTAAACAA-TCTCTTCTCATTATGAACTACTTCTTCCCCGTC
* *
2454380 GGATGAGTTCTTCTCATTATGCACTCTACACTATAATTGTTGATGCAAGGTTG
129 GGACGAGTTCTTCTCATTATGAACTCTACACTATAATTGTTGATGCAAGGTTG
* * ** * *
2454433 AACAAACTCTTCTCATTATGAACTTTTTCTTTCTCGTGGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAACTCTTCTCATTATGAAC-CTCTCTCCCTCGTGGGATGAGTACTTCTCATTATAAACTCT
* * * *
2454498 CTACTGGAAATGTTGATGCAAGGCTGAACAATCTCTTCTCATTATGAACTTCTTCTTCCTCGTCG
65 CTACTAGAAATGTTGATGCAAGGCTAAACAATCTCTTCTCATTATGAACTACTTCTTCCCCGTCG
2454563 GACGAGTTCTTCTCATTATGAACTCT
130 GACGAGTTCTTCTCATTATGAACTCT
2454589 CCATTGGAAA
Statistics
Matches: 136, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
181 23 0.17
182 112 0.82
183 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (181 bp):
AACAAACTCTTCTCATTATGAACCTCTCTCCCTCGTGGGATGAGTACTTCTCATTATAAACTCTC
TACTAGAAATGTTGATGCAAGGCTAAACAATCTCTTCTCATTATGAACTACTTCTTCCCCGTCGG
ACGAGTTCTTCTCATTATGAACTCTACACTATAATTGTTGATGCAAGGTTG
Found at i:2454599 original size:91 final size:91
Alignment explanation
Indices: 2454252--2454591 Score: 425
Period size: 91 Copynumber: 3.7 Consensus size: 91
2454242 TGATACGTCA
* * * * * * *
2454252 AACAAGCTCTTCTCATTATGAACCTC-TCTCCCTTGTTGGATGAGTACTTCTCATTATAAACTCT
1 AACAATCTCTTCTCATTATGAACTTCTTCTTCCTCGTCGGATGAGTTCTTCTCATTATGAACTCT
* * *
2454316 CTACTATAAATGTTGA-GTCAAGGTTA
66 CCACTAGAAATGTTGATG-CAAGGTTG
* * *
2454342 AACAAGT-TCTTCTCATTATGAACTACTTCTTCCCCGTCGGATGAGTTCTTCTCATTATGCACTC
1 AACAA-TCTCTTCTCATTATGAACTTCTTCTTCCTCGTCGGATGAGTTCTTCTCATTATGAACTC
* * *
2454406 TACACTATAATTGTTGATGCAAGGTTG
65 TCCACTAGAAATGTTGATGCAAGGTTG
* * * *
2454433 AACAAACTCTTCTCATTATGAACTTTTTCTTTCTCGTGGGATGAGTTCTTCTCATTATGAACTCT
1 AACAATCTCTTCTCATTATGAACTTCTTCTTCCTCGTCGGATGAGTTCTTCTCATTATGAACTCT
* * *
2454498 CTACTGGAAATGTTGATGCAAGGCTG
66 CCACTAGAAATGTTGATGCAAGGTTG
*
2454524 AACAATCTCTTCTCATTATGAACTTCTTCTTCCTCGTCGGACGAGTTCTTCTCATTATGAACTCT
1 AACAATCTCTTCTCATTATGAACTTCTTCTTCCTCGTCGGATGAGTTCTTCTCATTATGAACTCT
2454589 CCA
66 CCA
2454592 TTGGAAATAT
Statistics
Matches: 213, Mismatches: 33, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
90 22 0.10
91 190 0.89
92 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (91 bp):
AACAATCTCTTCTCATTATGAACTTCTTCTTCCTCGTCGGATGAGTTCTTCTCATTATGAACTCT
CCACTAGAAATGTTGATGCAAGGTTG
Found at i:2454940 original size:36 final size:36
Alignment explanation
Indices: 2454888--2455227 Score: 221
Period size: 36 Copynumber: 9.7 Consensus size: 36
2454878 GATACATTTC
** * *
2454888 TTGTTTCAACAGAAACTGTCTCAAAAGAGATAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
* *
2454924 TTGTGTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
* * *
2454960 TTGTTTCAAGAGAATCTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
* * **
2454996 TCGTTTTAAGGGAAAC-GTTCTCAA-AG-TTC----T
1 TTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAAT
* * * *
2455026 TTGTTTCAAGAGAAACTATATCACG-GAAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAG-AGACAAAAT
*
2455062 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
* *
2455098 TTGTTTCAAGGGAAAC-GTTTTC-A-A-AG-----TT
1 TTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAAT
* * * * *
2455126 TATGTTTCAAGAGAAACTATCTTATGGGAGACAAAATT
1 T-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
*
2455164 TTGTTTCAAGGGAAACTATCTCAAG-GAAGACAAAACTT
1 TTGTTTCAAGGGAAACTGTCTCAAGAG-AGACAAAA--T
* *
2455202 TCTGTTTCGAGGGAAACTATCTCAAG
1 T-TGTTTCAAGGGAAACTGTCTCAAG
2455228 CGAAATAAAA
Statistics
Matches: 235, Mismatches: 44, Indels: 47
0.72 0.13 0.14
Matches are distributed among these distances:
28 2 0.01
29 16 0.07
30 19 0.08
32 3 0.01
33 2 0.01
34 2 0.01
35 4 0.02
36 129 0.55
37 30 0.13
38 5 0.02
39 23 0.10
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
Found at i:2455073 original size:66 final size:66
Alignment explanation
Indices: 2454960--2455085 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 66
2454950 GAGACAAAAC
* * * * *
2454960 TTGTTTCAAGAGAATCTGTCTCAAGGGAGACAAAATTCGTTTTAAGGGAAAC-GTTCTCAAAGTT
1 TTGTTTCAAGAGAAACTATATCAAGGAAGACAAAATTCGTTTCAAGGGAAACTG-TCTCAAAGTT
2455024 CT
65 CT
* *
2455026 TTGTTTCAAGAGAAACTATATCACGGAAGACAAAATTTGTTTCAAGGGAAACTGTCTCAA
1 TTGTTTCAAGAGAAACTATATCAAGGAAGACAAAATTCGTTTCAAGGGAAACTGTCTCAA
2455086 GAGAGACTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 51 0.98
67 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTATATCAAGGAAGACAAAATTCGTTTCAAGGGAAACTGTCTCAAAGTTC
T
Found at i:2455109 original size:102 final size:101
Alignment explanation
Indices: 2454951--2455226 Score: 340
Period size: 102 Copynumber: 2.7 Consensus size: 101
2454941 GTCTCAAGAG
* * * * *
2454951 AGACAAAACTTGTTTCAAGAGAATCTGTCTCAAGGGAGACAAAATTCGTTTTAAGGGAAACGTTC
1 AGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGTTC
*
2455016 TCAAAGTTCTTTGTTTCAAGAGAAACTATATCACGGA
66 TCAAAGTT-TATGTTTCAAGAGAAACTATATCACGGA
* * *
2455053 AGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGGGAAACGTTT
1 AGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGTTC
* * * *
2455118 TCAAAGTTTATGTTTCAAGAGAAACTATCTTATGGG
66 TCAAAGTTTATGTTTCAAGAGAAACTATATCACGGA
* *
2455154 AGACAAAATTTTGTTTCAAGGGAAACTATCTCAAG-GAAGACAAAACTTTCTGTTTCGAGGGAAA
1 AGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAG-AGACAAAA--TTC-GTTTCAAGGGAAA
2455218 C-TATCTCAA
61 CGT-TCTCAA
2455227 GCGAAATAAA
Statistics
Matches: 150, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
101 32 0.21
102 97 0.65
104 3 0.02
105 18 0.12
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (101 bp):
AGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGTTC
TCAAAGTTTATGTTTCAAGAGAAACTATATCACGGA
Found at i:2455309 original size:39 final size:38
Alignment explanation
Indices: 2455119--2455310 Score: 183
Period size: 39 Copynumber: 5.0 Consensus size: 38
2455109 GAAACGTTTT
* * * * * *
2455119 CAAAGTTTATGTTTCAAGAGAAACTATCTTATGGGAGA
1 CAAAATTTCTGTTTCAAGGGAAACTATCTCAAGCGAGA
2455157 CAAAATTT-TGTTTCAAGGGAAACTATCTCAAG-GAAGA
1 CAAAATTTCTGTTTCAAGGGAAACTATCTCAAGCG-AGA
* *
2455194 CAAAACTTTCTGTTTCGAGGGAAACTATCTCAAGCGAAA
1 CAAAA-TTTCTGTTTCAAGGGAAACTATCTCAAGCGAGA
* * * *
2455233 TAAAATCTTATGTTTCGAA-TGAAACTATCTAAAGCGAGA
1 CAAAAT-TTCTGTTTC-AAGGGAAACTATCTCAAGCGAGA
* * *
2455272 CAAAATGTTCTATTTTAAGGGAAATTATCTCAAGCGAGA
1 CAAAAT-TTCTGTTTCAAGGGAAACTATCTCAAGCGAGA
2455311 TACATCTTCT
Statistics
Matches: 127, Mismatches: 20, Indels: 13
0.79 0.12 0.08
Matches are distributed among these distances:
36 1 0.01
37 29 0.23
38 13 0.10
39 82 0.65
40 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (38 bp):
CAAAATTTCTGTTTCAAGGGAAACTATCTCAAGCGAGA
Found at i:2458055 original size:149 final size:149
Alignment explanation
Indices: 2457785--2458058 Score: 352
Period size: 149 Copynumber: 1.8 Consensus size: 149
2457775 TCAAAACTTC
** * * * * * *
2457785 TACTTCATCTCCTACTTTTAGAAATCTTTCGAGCTGGTTCACGATTTTTAACTGTTGGCTTCGGT
1 TACTTCATCTCCTACTTCCAAAAATCATTCGAGCTGGTTCACGATCTTCAACTGTTGGCTTCAGC
* * * *
2457850 GTTGAATCATCTAGATTCCAACTTGTTACCTCAGCAGGTAAATATCTGGATTGTCTCCTTGGTTG
66 GTCGAATCATCTAGAGTCCAACTTGTTACCTCAGCAGGCAAATACCTGGATTGTCTCCTTGGTTG
2457915 ATAGACTCCTTTTGGCTCA
131 ATAGACTCCTTTTGGCTCA
* **
2457934 TACTTCCTCTCCTACTTCCAAAAATCATTCGAGCTGGTTCGTGATCTTCAACTGTTGGCTTCAGC
1 TACTTCATCTCCTACTTCCAAAAATCATTCGAGCTGGTTCACGATCTTCAACTGTTGGCTTCAGC
* * * * *
2457999 GTCGAATCATCTCGAGTCCAACTTGTTACCGT-AGTAGGCAGATGCCTGGCTTGTCTCCTT
66 GTCGAATCATCTAGAGTCCAACTTGTTACC-TCAGCAGGCAAATACCTGGATTGTCTCCTT
2458059 AGCAGGTAGA
Statistics
Matches: 104, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
149 103 0.99
150 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (149 bp):
TACTTCATCTCCTACTTCCAAAAATCATTCGAGCTGGTTCACGATCTTCAACTGTTGGCTTCAGC
GTCGAATCATCTAGAGTCCAACTTGTTACCTCAGCAGGCAAATACCTGGATTGTCTCCTTGGTTG
ATAGACTCCTTTTGGCTCA
Found at i:2460152 original size:21 final size:21
Alignment explanation
Indices: 2460103--2460152 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2460093 ATTAAAATTC
*
2460103 AAAACCTAAATTAAAACTAAA
1 AAAAACTAAATTAAAACTAAA
**
2460124 AATGACTAAATTAAAA-TAAA
1 AAAAACTAAATTAAAACTAAA
2460144 ATAAAACTA
1 A-AAAACTA
2460153 CATACCAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAAACTAAATTAAAACTAAA
Found at i:2462037 original size:32 final size:32
Alignment explanation
Indices: 2461989--2462074 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
2461979 GTAGTATCAA
* * * **
2461989 TATTACATTGAAATAATGCATTGCATGGTC-T
1 TATTACATTCAGATAATGCATAGCAAAGTCAT
*
2462020 GTATTACATTCAGATAATACATAGCAAAGTCAT
1 -TATTACATTCAGATAATGCATAGCAAAGTCAT
*
2462053 TATTGCATTCAGATAATGCATA
1 TATTACATTCAGATAATGCATA
2462075 TTTTGTAACA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
32 44 0.98
33 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (32 bp):
TATTACATTCAGATAATGCATAGCAAAGTCAT
Found at i:2483341 original size:19 final size:19
Alignment explanation
Indices: 2483319--2483355 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2483309 AAAATTTGCT
*
2483319 ACGCGGTTTCAAATTCGCA
1 ACGCGATTTCAAATTCGCA
*
2483338 ACGCGATTTTAAATTCGC
1 ACGCGATTTCAAATTCGC
2483356 GACATGAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (19 bp):
ACGCGATTTCAAATTCGCA
Found at i:2483427 original size:20 final size:20
Alignment explanation
Indices: 2483404--2483652 Score: 90
Period size: 20 Copynumber: 12.7 Consensus size: 20
2483394 TTTTAAATTT
*
2483404 GCAACTCGAATTTCTTTTTC
1 GCAACACGAATTTCTTTTTC
* * ***
2483424 GCAACGCGATTTTCCAAATTC
1 GCAACACGAATTT-CTTTTTC
* ***
2483445 GCAACACAGAA-GTCAAATTC
1 GCAACAC-GAATTTCTTTTTC
*
2483465 GCAACACAAATTTCTTTTTC
1 GCAACACGAATTTCTTTTTC
*
2483485 ACAACACGAATTTCTTTTTC
1 GCAACACGAATTTCTTTTTC
* * * *
2483505 ACAACACGACTTT-TAATTTA
1 GCAACACGAATTTCT-TTTTC
* *
2483525 GCAACTCG-ATTT-TTGAATTC
1 GCAACACGAATTTCTT--TTTC
* * * *
2483545 ACAATATGAATTTTTTTTTC
1 GCAACACGAATTTCTTTTTC
* *
2483565 GCAACATGAATTTC-TTCTC
1 GCAACACGAATTTCTTTTTC
* *
2483584 TGCAACTA-GATTTTCTTTTTT
1 -GCAAC-ACGAATTTCTTTTTC
2483605 GCAACACGAA-----TTTTC
1 GCAACACGAATTTCTTTTTC
*
2483620 GCAACTA-GATTTTCTTTTTC
1 GCAAC-ACGAATTTCTTTTTC
*
2483640 ACAACACGAATTT
1 GCAACACGAATTT
2483653 TTTGTGTATA
Statistics
Matches: 169, Mismatches: 41, Indels: 38
0.68 0.17 0.15
Matches are distributed among these distances:
15 11 0.07
16 1 0.01
19 13 0.08
20 121 0.72
21 19 0.11
22 4 0.02
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39
Consensus pattern (20 bp):
GCAACACGAATTTCTTTTTC
Found at i:2483624 original size:35 final size:35
Alignment explanation
Indices: 2483585--2483653 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
2483575 TTTCTTCTCT
**
2483585 GCAACTAGATTTTCTTTTTTGCAACACGAATTTTC
1 GCAACTAGATTTTCTTTTTCACAACACGAATTTTC
2483620 GCAACTAGATTTTCTTTTTCACAACACGAATTTT
1 GCAACTAGATTTTCTTTTTCACAACACGAATTTT
2483654 TTGTGTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (35 bp):
GCAACTAGATTTTCTTTTTCACAACACGAATTTTC
Found at i:2484588 original size:24 final size:24
Alignment explanation
Indices: 2484533--2484595 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
2484523 TACTAGTTAG
*
2484533 TATTCGAAATTTGATCTTGGTCAA
1 TATTCGGAATTTGATCTTGGTCAA
** *
2484557 TACCCGGACTTTGATCTTGGTCAA
1 TATTCGGAATTTGATCTTGGTCAA
*
2484581 TATTCGGATTTTGAT
1 TATTCGGAATTTGAT
2484596 GATGTTTTAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
TATTCGGAATTTGATCTTGGTCAA
Found at i:2487122 original size:20 final size:20
Alignment explanation
Indices: 2487085--2487123 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2487075 CTCGAATTCC
*
2487085 AAATTCACAACGCAAAAATA
1 AAATTCACAACACAAAAATA
* *
2487105 AAATTCGCAACACGAAAAT
1 AAATTCACAACACAAAAAT
2487124 CGTGTTTGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.21, G:0.08, T:0.15
Consensus pattern (20 bp):
AAATTCACAACACAAAAATA
Found at i:2487177 original size:20 final size:20
Alignment explanation
Indices: 2487152--2487189 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2487142 ATCACAAGTC
2487152 GATATTAAAATTCGCAACTT
1 GATATTAAAATTCGCAACTT
2487172 GATATTAAAATTCGCAAC
1 GATATTAAAATTCGCAAC
2487190 GCAATTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (20 bp):
GATATTAAAATTCGCAACTT
Found at i:2488888 original size:21 final size:21
Alignment explanation
Indices: 2488864--2488909 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2488854 TCGACATAGT
*
2488864 ATGGAATGTGGATCCTAAACG
1 ATGGAAGGTGGATCCTAAACG
* * *
2488885 ATGGGAGGTGGATCCTGAATG
1 ATGGAAGGTGGATCCTAAACG
2488906 ATGG
1 ATGG
2488910 GATGGGCTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.37, T:0.24
Consensus pattern (21 bp):
ATGGAAGGTGGATCCTAAACG
Found at i:2488910 original size:21 final size:21
Alignment explanation
Indices: 2488871--2489024 Score: 91
Period size: 21 Copynumber: 7.3 Consensus size: 21
2488861 AGTATGGAAT
*
2488871 GTGGATCCTAAACGATGGGAG
1 GTGGATCCTGAACGATGGGAG
*
2488892 GTGGATCCTGAATGATGGGATG
1 GTGGATCCTGAACGATGGGA-G
** * *
2488914 G-GCTTCTTGAATGATGGGAG
1 GTGGATCCTGAACGATGGGAG
* * *
2488934 G-GGCCTCTTGAATGATGGGAG
1 GTGG-ATCCTGAACGATGGGAG
**
2488955 G-GG-TCTCTTGAACGATAAGAG
1 GTGGATC-C-TGAACGATGGGAG
* * *
2488976 GTGAATCTTGAACAATGGGAG
1 GTGGATCCTGAACGATGGGAG
* * *
2488997 GTGGATCCTAAACAATGGTAG
1 GTGGATCCTGAACGATGGGAG
2489018 GTGGATC
1 GTGGATC
2489025 AGGCTTCTTC
Statistics
Matches: 107, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 97 0.91
22 3 0.03
23 2 0.02
ACGTcount: A:0.26, C:0.12, G:0.37, T:0.25
Consensus pattern (21 bp):
GTGGATCCTGAACGATGGGAG
Found at i:2488985 original size:42 final size:42
Alignment explanation
Indices: 2488889--2488997 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 42
2488879 TAAACGATGG
* * * * **
2488889 GAGGTGGATCCTGAATGATGGGATGGGCTTCTTGAATGATGG
1 GAGGTGAATCTTGAATGATGGGAGGGGCTTCTTGAACGATAA
* **
2488931 GAGGGGCCTCTTGAATGATGGGAGGGG-TCTCTTGAACGATAA
1 GAGGTGAATCTTGAATGATGGGAGGGGCT-TCTTGAACGATAA
**
2488973 GAGGTGAATCTTGAACAATGGGAGG
1 GAGGTGAATCTTGAATGATGGGAGG
2488998 TGGATCCTAA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.25, C:0.11, G:0.39, T:0.25
Consensus pattern (42 bp):
GAGGTGAATCTTGAATGATGGGAGGGGCTTCTTGAACGATAA
Found at i:2489413 original size:42 final size:43
Alignment explanation
Indices: 2489322--2489414 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
2489312 TAGAGCACCG
* *
2489322 ACCTCATCACAGAAAGCAACTACTTCACCACGTAAAGAACCAT
1 ACCTCATCACAGAAAACAACTACCTCACCACGTAAAGAACCAT
**
2489365 -TGTCATCAC-GTAAAACAACTACCTCACCACGTAAAG-ACCAT
1 ACCTCATCACAG-AAAACAACTACCTCACCACGTAAAGAACCAT
2489406 ACCTCATCA
1 ACCTCATCA
2489415 TGCCATGCAC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
41 6 0.14
42 36 0.86
ACGTcount: A:0.40, C:0.33, G:0.09, T:0.18
Consensus pattern (43 bp):
ACCTCATCACAGAAAACAACTACCTCACCACGTAAAGAACCAT
Found at i:2489445 original size:21 final size:21
Alignment explanation
Indices: 2489307--2489488 Score: 97
Period size: 21 Copynumber: 8.7 Consensus size: 21
2489297 TAAAACAATC
*
2489307 TCACGTAGAGCACCGA-CCTCA
1 TCACGTAAAGCACC-ATCCTCA
* *
2489328 TCACAG-AAAGCAAC-TACTTCA
1 TCAC-GTAAAGCACCAT-CCTCA
* * **
2489349 CCACGTAAAGAACCATTGTCA
1 TCACGTAAAGCACCATCCTCA
* *
2489370 TCACGTAAAACAAC-TACCTCA
1 TCACGTAAAGCACCAT-CCTCA
*
2489391 CCACGTAAAG-ACCATACCTCA
1 TCACGTAAAGCACCAT-CCTCA
* ** * **
2489412 TCATGCCATGCACCATTGTCA
1 TCACGTAAAGCACCATCCTCA
*
2489433 TCACGTAAAGCACCAACCTCA
1 TCACGTAAAGCACCATCCTCA
* *
2489454 TCACGTAAAGTACTGA-CCTCA
1 TCACGTAAAGCAC-CATCCTCA
2489475 TCACGTAAAGCACC
1 TCACGTAAAGCACC
2489489 TAACTCATCC
Statistics
Matches: 117, Mismatches: 35, Indels: 19
0.68 0.20 0.11
Matches are distributed among these distances:
20 4 0.03
21 105 0.90
22 8 0.07
ACGTcount: A:0.36, C:0.34, G:0.12, T:0.19
Consensus pattern (21 bp):
TCACGTAAAGCACCATCCTCA
Found at i:2489488 original size:63 final size:61
Alignment explanation
Indices: 2489307--2489488 Score: 177
Period size: 63 Copynumber: 2.9 Consensus size: 61
2489297 TAAAACAATC
* * * * *
2489307 TCACGTAGAGCACCGACCTCATCACAG-AAAGCAACTACTTCACCACGTAAAGAACCATTGTCA
1 TCACGTAAAGCACCAACCTCATCAC-GTAAAG--ACTACCTCATCACGTAAAGCACCATTGTCA
* * * * * ** *
2489370 TCACGTAAAACAACTACCTCACCACGTAAAGACCATACCTCATCATGCCATGCACCATTGTCA
1 TCACGTAAAGCACCAACCTCATCACGTAAAGA-C-TACCTCATCACGTAAAGCACCATTGTCA
2489433 TCACGTAAAGCACCAACCTCATCACGTAAAGTACTGACCTCATCACGTAAAGCACC
1 TCACGTAAAGCACCAACCTCATCACGTAAAG-ACT-ACCTCATCACGTAAAGCACC
2489489 TAACTCATCC
Statistics
Matches: 94, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
61 1 0.01
62 3 0.03
63 89 0.95
64 1 0.01
ACGTcount: A:0.36, C:0.34, G:0.12, T:0.19
Consensus pattern (61 bp):
TCACGTAAAGCACCAACCTCATCACGTAAAGACTACCTCATCACGTAAAGCACCATTGTCA
Found at i:2489495 original size:21 final size:21
Alignment explanation
Indices: 2489430--2489497 Score: 86
Period size: 21 Copynumber: 3.2 Consensus size: 21
2489420 TGCACCATTG
2489430 TCATCACGTAAAGCACC-AACC
1 TCATCACGTAAAGCACCTAA-C
* *
2489451 TCATCACGTAAAGTA-CTGACC
1 TCATCACGTAAAGCACCT-AAC
2489472 TCATCACGTAAAGCACCTAAC
1 TCATCACGTAAAGCACCTAAC
2489493 TCATC
1 TCATC
2489498 CCGTGGAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.03
21 36 0.90
22 3 0.08
ACGTcount: A:0.35, C:0.34, G:0.10, T:0.21
Consensus pattern (21 bp):
TCATCACGTAAAGCACCTAAC
Found at i:2489658 original size:42 final size:42
Alignment explanation
Indices: 2489597--2489718 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
2489587 GTGATGGAAT
* * * *
2489597 AAGTGATGGATCTCAGTGTC-ACGGTGTAGAATCGGCTCGATC
1 AAGTGATGGATCTCGGTGTCGA-AGTGGAGAATCGACTCGATC
*
2489639 AAGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATG
1 AAGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATC
* * *
2489681 AGGTGATGGATCTCGGTGTCGAACTGAAGAATCGACTC
1 AAGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTC
2489719 AATGAAAAAG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 70 0.99
43 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (42 bp):
AAGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATC
Found at i:2491274 original size:34 final size:34
Alignment explanation
Indices: 2491231--2491296 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
2491221 CTTGAAACTT
* *
2491231 AAATTCGCAACATGAAAA-TCGCAACTCGAAAATG
1 AAATTCGCAACA-CAAAATTCGCAACGCGAAAATG
2491265 AAATTCGCAACACAAAATTCGCAACGCGAAAA
1 AAATTCGCAACACAAAATTCGCAACGCGAAAA
2491297 CTAAAATCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 4 0.14
34 25 0.86
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.15
Consensus pattern (34 bp):
AAATTCGCAACACAAAATTCGCAACGCGAAAATG
Found at i:2491342 original size:20 final size:20
Alignment explanation
Indices: 2491313--2491351 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2491303 TCACTTTGCG
*
2491313 ATTTTTGTGTTGCAAATTTC
1 ATTTTCGTGTTGCAAATTTC
*
2491333 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCAAATTT
2491352 AAGTTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCAAATTTC
Found at i:2491851 original size:19 final size:20
Alignment explanation
Indices: 2491808--2491877 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
2491798 TTACATTTGT
* *
2491808 GTTGCGAAATTAAAATTCGC
1 GTTGCGAAAATAAAATGCGC
2491828 GTTGCGAAAAT-AAATGCGC
1 GTTGCGAAAATAAAATGCGC
* * **
2491847 TTTGCGAATTATAAAAT-CTT
1 GTTGCGAA-AATAAAATGCGC
2491867 GTTGCGAAAAT
1 GTTGCGAAAAT
2491878 GACTCTTGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
19 16 0.40
20 20 0.50
21 4 0.10
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (20 bp):
GTTGCGAAAATAAAATGCGC
Found at i:2491860 original size:20 final size:20
Alignment explanation
Indices: 2491808--2491861 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
2491798 TTACATTTGT
*
2491808 GTTGCGAAATTA-AAATTCGC
1 GTTGCG-AATTATAAATGCGC
*
2491828 GTTGCGAA-AATAAATGCGC
1 GTTGCGAATTATAAATGCGC
*
2491847 TTTGCGAATTATAAA
1 GTTGCGAATTATAAA
2491862 ATCTTGTTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.04
19 16 0.57
20 11 0.39
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTATAAATGCGC
Found at i:2491942 original size:20 final size:19
Alignment explanation
Indices: 2491886--2492018 Score: 63
Period size: 20 Copynumber: 6.7 Consensus size: 19
2491876 ATGACTCTTG
*
2491886 TGTTGCGAATTTTGAAAATC
1 TGTTGCGAA-TTTGAAATTC
* ***
2491906 GCGTTGCGAAAAAGAAATTC
1 -TGTTGCGAATTTGAAATTC
*
2491926 TAGTTGCGAATTTGAAA-AC
1 T-GTTGCGAATTTGAAATTC
* *
2491945 TGAGTTGCGAATTTGGAAGTTG
1 T--GTTGCGAATTT-GAAATTC
* * *
2491967 TGTTGCGAAATTGGAGTTC
1 TGTTGCGAATTTGAAATTC
*
2491986 GTGTTGCAAATTTGAAA-TC
1 -TGTTGCGAATTTGAAATTC
*
2492005 GCGTTGCGAATTTG
1 -TGTTGCGAATTTG
2492019 TTGGTTATTT
Statistics
Matches: 85, Mismatches: 22, Indels: 12
0.71 0.18 0.10
Matches are distributed among these distances:
19 21 0.25
20 52 0.61
21 11 0.13
22 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.34
Consensus pattern (19 bp):
TGTTGCGAATTTGAAATTC
Found at i:2491952 original size:81 final size:79
Alignment explanation
Indices: 2491804--2491955 Score: 175
Period size: 81 Copynumber: 1.9 Consensus size: 79
2491794 CTATTTACAT
* ** *
2491804 TTGTGTTGCGAAATTAAAATTCGCGTTGCGAAAATAAATGCGCTTTGCGAATTATAAAATCTTGT
1 TTGTGTTGCGAAATTAAAATTCGCGTTGCGAAAAGAAATGCGAGTTGCGAATTATAAAATCTAGT
2491869 TGCGAAAATGACTC
66 TGCGAAAATGACTC
* * *
2491883 TTGTGTTGCGAATTTTGAAAA-TCGCGTTGCGAAAAAGAAATTCTAGTTGCGAATT-TGAAAA-C
1 TTGTGTTGCGAA-ATT-AAAATTCGCGTTGCG-AAAAGAAATGCGAGTTGCGAATTAT-AAAATC
2491945 TGAGTTGCGAA
62 T-AGTTGCGAA
2491956 TTTGGAAGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
79 12 0.20
80 15 0.25
81 34 0.56
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.32
Consensus pattern (79 bp):
TTGTGTTGCGAAATTAAAATTCGCGTTGCGAAAAGAAATGCGAGTTGCGAATTATAAAATCTAGT
TGCGAAAATGACTC
Found at i:2491996 original size:19 final size:20
Alignment explanation
Indices: 2491948--2491997 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2491938 TGAAAACTGA
*
2491948 GTTGCGAATTTGGAAGTTGT
1 GTTGCGAAATTGGAAGTTGT
2491968 GTTGCGAAATTGG-AGTTCGT
1 GTTGCGAAATTGGAAGTT-GT
2491988 GTTGC-AAATT
1 GTTGCGAAATT
2491998 TGAAATCGCG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.22, C:0.08, G:0.32, T:0.38
Consensus pattern (20 bp):
GTTGCGAAATTGGAAGTTGT
Found at i:2493336 original size:2 final size:2
Alignment explanation
Indices: 2493329--2493373 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2493319 CATTTAAAGC
2493329 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
2493371 AT A
1 AT A
2493374 CTATTCATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2497807 original size:19 final size:20
Alignment explanation
Indices: 2497783--2497827 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2497773 CAAATTGACC
2497783 CAATTTT-ACACTCTAACAT
1 CAATTTTGACACTCTAACAT
*
2497802 CAATTTTGACATTCTAACAT
1 CAATTTTGACACTCTAACAT
*
2497822 TAATTT
1 CAATTT
2497828 ATAGAATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (20 bp):
CAATTTTGACACTCTAACAT
Found at i:2499116 original size:29 final size:30
Alignment explanation
Indices: 2499063--2499124 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
2499053 TTTTCATACT
2499063 TAAACTTTCTAAACTTTATACTTTGGCCAC
1 TAAACTTTCTAAACTTTATACTTTGGCCAC
* * *
2499093 TAAACTTTC-AAATTTTATATTTTGGTCAC
1 TAAACTTTCTAAACTTTATACTTTGGCCAC
2499122 TAA
1 TAA
2499125 CCAAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (30 bp):
TAAACTTTCTAAACTTTATACTTTGGCCAC
Found at i:2503281 original size:19 final size:19
Alignment explanation
Indices: 2503232--2503283 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2503222 TCCTATGGGT
*
2503232 AGTATCGATAATCTACCCTAG
1 AGTATCGAT-A-CTCCCCTAG
*
2503253 -GTATCCATACTCCCCTAG
1 AGTATCGATACTCCCCTAG
2503271 AGTATCGATACTC
1 AGTATCGATACTC
2503284 AAATTGTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.30
19 12 0.44
20 7 0.26
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (19 bp):
AGTATCGATACTCCCCTAG
Found at i:2510021 original size:18 final size:20
Alignment explanation
Indices: 2509998--2510043 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2509988 ATTTTGGTAC
2509998 CGATACTCAA-GGG-AGTAT
1 CGATACTCAAGGGGAAGTAT
2510016 CGATAC-CAAGGGGAAAGTAT
1 CGATACTCAAGGGG-AAGTAT
2510036 CGATACTC
1 CGATACTC
2510044 CCCTTAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 9 0.38
20 11 0.46
21 1 0.04
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (20 bp):
CGATACTCAAGGGGAAGTAT
Found at i:2511440 original size:20 final size:20
Alignment explanation
Indices: 2511412--2511452 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2511402 CTTCCACATA
*
2511412 TTTGTTGTC-TTGTTGTATTT
1 TTTGATGTCTTTGTT-TATTT
2511432 TTTGATGTCTTTGTTTATTT
1 TTTGATGTCTTTGTTTATTT
2511452 T
1 T
2511453 CTCGAGCGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.07, C:0.05, G:0.17, T:0.71
Consensus pattern (20 bp):
TTTGATGTCTTTGTTTATTT
Found at i:2514450 original size:2 final size:2
Alignment explanation
Indices: 2514443--2514472 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2514433 TTAAAACATA
2514443 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
2514473 TATTCATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2519900 original size:23 final size:22
Alignment explanation
Indices: 2519869--2519911 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
2519859 ATACGTGAAC
2519869 TTTATAAGGGTAGTATCGATACCT
1 TTTATAA-GG-AGTATCGATACCT
2519893 TTTA-AAGGAGTATCGATAC
1 TTTATAAGGAGTATCGATAC
2519912 TGGGGGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 2 0.11
24 4 0.21
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (22 bp):
TTTATAAGGAGTATCGATACCT
Found at i:2521200 original size:84 final size:84
Alignment explanation
Indices: 2521059--2521223 Score: 258
Period size: 84 Copynumber: 2.0 Consensus size: 84
2521049 TGGTAAGCCA
* *
2521059 CTGGTGGTTCCGTGTAGAACTCTGATCATTCGATTGAGTGTCGTTCTAGTTTAGGGTGTTATATT
1 CTGGTGGTTCCGTGTAGAACTCTGATCAGTCGACTGAGTGTCGTTCTAGTTTAGGGTGTTATATT
2521124 TAAGATGATCGAACCTACC
66 TAAGATGATCGAACCTACC
* * * * *
2521143 CTGGTGGTTCCGTGTAGCACTCTGATCGGTCGACTGGGTGTCGTTTTGGTTTAGGGTGTTATATT
1 CTGGTGGTTCCGTGTAGAACTCTGATCAGTCGACTGAGTGTCGTTCTAGTTTAGGGTGTTATATT
*
2521208 TAAGATGATTGAACCT
66 TAAGATGATCGAACCT
2521224 GGGACCTTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 73 1.00
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.38
Consensus pattern (84 bp):
CTGGTGGTTCCGTGTAGAACTCTGATCAGTCGACTGAGTGTCGTTCTAGTTTAGGGTGTTATATT
TAAGATGATCGAACCTACC
Found at i:2522187 original size:42 final size:42
Alignment explanation
Indices: 2522142--2522241 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
2522132 AACAGTGATA
*
2522142 AAAAAT-ATTTTTGTCACAAATCACCAACTAAGACTAGTAAG
1 AAAAATAATTATTGTCACAAATCACCAACTAAGACTAGTAAG
* * *
2522183 AAAAATAATTATTGTCACAAATGACCAACTAAGACTAGTGAC
1 AAAAATAATTATTGTCACAAATCACCAACTAAGACTAGTAAG
* *
2522225 AAAAACAATCATTGTCA
1 AAAAATAATTATTGTCA
2522242 TCAATAACCA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 6 0.12
42 46 0.88
ACGTcount: A:0.48, C:0.17, G:0.10, T:0.25
Consensus pattern (42 bp):
AAAAATAATTATTGTCACAAATCACCAACTAAGACTAGTAAG
Found at i:2522264 original size:42 final size:42
Alignment explanation
Indices: 2522152--2522266 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
2522142 AAAAATATTT
* * * * * *
2522152 TTGTCACAAATCACCAACTAAGACTAGTAAGAAAAATAATTA
1 TTGTCACAAATAACCAACTAAAACTAGTGACAAAAACAATCA
* *
2522194 TTGTCACAAATGACCAACTAAGACTAGTGACAAAAACAATCA
1 TTGTCACAAATAACCAACTAAAACTAGTGACAAAAACAATCA
* *
2522236 TTGTCATC-AATAACCATCTAAAATTAGTGAC
1 TTGTCA-CAAATAACCAACTAAAACTAGTGAC
2522267 CAACTGTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 62 0.98
43 1 0.02
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.24
Consensus pattern (42 bp):
TTGTCACAAATAACCAACTAAAACTAGTGACAAAAACAATCA
Found at i:2528511 original size:85 final size:84
Alignment explanation
Indices: 2528372--2528567 Score: 249
Period size: 85 Copynumber: 2.3 Consensus size: 84
2528362 AAACTCAAGT
* *
2528372 TTTAGGATAATATTTTAACATTA---TATTTTATCTTTATTTTAAGTATTTTAGTTTAAATAGAT
1 TTTAGGATATTATTTTAAAATTATTTTATTTTATCTTTATTTTAAGTATTTTAGTTTAAATAG-T
*
2528434 TTT-TGTATTTCAATTAGGA
65 TTTAAGTATTTCAATTAGGA
* *
2528453 TTTAGGATATTATTTTAAATATTATTTTATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGT
1 TTTAGGATATTATTTTAAA-ATTATTTTATTTTATCTTTATTTTAAGTATTTTAGTTTAAATAGT
* *
2528518 TTTAAGTGTTTTAATTAGGA
65 TTTAAGTATTTCAATTAGGA
2528538 TTTCA-GATATTATTTTAGAAATTATATTTA
1 TTT-AGGATATTATTTTA-AAATTAT-TTTA
2528568 GCTTGTTTTT
Statistics
Matches: 100, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
81 17 0.17
82 4 0.04
84 4 0.04
85 68 0.68
86 7 0.07
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.56
Consensus pattern (84 bp):
TTTAGGATATTATTTTAAAATTATTTTATTTTATCTTTATTTTAAGTATTTTAGTTTAAATAGTT
TTAAGTATTTCAATTAGGA
Found at i:2529200 original size:17 final size:17
Alignment explanation
Indices: 2529175--2529208 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2529165 CTTTATCCCA
*
2529175 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
2529192 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
2529209 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:2530750 original size:21 final size:21
Alignment explanation
Indices: 2530726--2530775 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2530716 AGAAATTTTA
**
2530726 CAAGAAAAGTTGGTTACATCC
1 CAAGAAAAGTTCATTACATCC
*
2530747 CAAGAAAAGTTCATTGCATCC
1 CAAGAAAAGTTCATTACATCC
*
2530768 CAGGAAAA
1 CAAGAAAA
2530776 ATTCCAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (21 bp):
CAAGAAAAGTTCATTACATCC
Found at i:2534926 original size:19 final size:19
Alignment explanation
Indices: 2534902--2534938 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2534892 TTTTAGCAAA
2534902 ATTTATTTCATTTCATTTC
1 ATTTATTTCATTTCATTTC
* *
2534921 ATTTATTTTATTTTATTT
1 ATTTATTTCATTTCATTT
2534939 TTATTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTATTTCATTTCATTTC
Found at i:2534942 original size:11 final size:11
Alignment explanation
Indices: 2534922--2534950 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2534912 TTTCATTTCA
2534922 TTTA-TTTTAT
1 TTTATTTTTAT
2534932 TTTATTTTTAT
1 TTTATTTTTAT
2534943 TTTATTTT
1 TTTATTTT
2534951 ATCAAATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:2534943 original size:16 final size:16
Alignment explanation
Indices: 2534922--2534952 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2534912 TTTCATTTCA
2534922 TTTATTTTATTTTATT
1 TTTATTTTATTTTATT
2534938 TTTATTTTATTTTAT
1 TTTATTTTATTTTAT
2534953 CAAATGCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTATTTTATTTTATT
Found at i:2534971 original size:5 final size:5
Alignment explanation
Indices: 2534903--2534952 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
2534893 TTTAGCAAAA
* * *
2534903 TTTAT TTCAT TTCAT TTCA- TTTAT TTTAT TTTATT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT
2534953 CAAATGCTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 3 0.07
5 33 0.80
6 5 0.12
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:2537741 original size:18 final size:19
Alignment explanation
Indices: 2537718--2537756 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2537708 AACAAGTACT
*
2537718 AAGTTAT-AACCATTTAAA
1 AAGTTATGAACCAATTAAA
*
2537736 AAGTTATGGACCAATTAAA
1 AAGTTATGAACCAATTAAA
2537755 AA
1 AA
2537757 AATATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (19 bp):
AAGTTATGAACCAATTAAA
Found at i:2537759 original size:217 final size:214
Alignment explanation
Indices: 2537362--2538082 Score: 1007
Period size: 217 Copynumber: 3.3 Consensus size: 214
2537352 ATTTCATGAA
* * * * *
2537362 AAATATAAATTTAAGAACTAAATTGAATAAATATGAAATTACAAATTAAAATTTTAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* * *
2537427 ACAACAGACATTGATGAGGGATCAAATTA-AAATAATTTTAATTTCCGAGGTTGAAATTAATACA
66 ACAACACACATTGATGAGGGATCAAA-TAGAAATAATTTTAATTT-TGAGGTTTAAATTAATAC-
* * * * *
2537491 AAAAAAGTACTAAATTATACCCATTTAAAAAGTTTTGGGCGAATTAAAAAATATAAATATGTAAT
128 -AAAAAGTACTAAATTATAACCATTTAAAAAGTTATGGACCAATTAAAAAATATAAATAAGTAAT
*
2537556 AAGTATGAGCCAATTTCATATGC
192 AAGTATGGGCCAATTTCATATGC
* * * * * * *
2537579 AAGTGTAATTTTAAGGACTAAATTGAACAAATGTTAAATTAAAAATTAAAATTAAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
** * * * *
2537644 ACATTACACATTGATGGGGGATCAAATCGAAATAATTTTATATTTTAAGGTTTAAATGAATACAA
66 ACAACACACATTGATGAGGGATCAAATAGAAATAATTTTA-ATTTTGAGGTTTAAATTAATACAA
*
2537709 ACAAGTACTAAGTTATAACCATTTAAAAAGTTATGGACCAATTAAAAAAATATAAATAAGTAATA
130 A-AAGTACTAAATTATAACCATTTAAAAAGTTATGGACCAATT-AAAAAATATAAATAAGTAATA
*
2537774 AATATGGGCCAATTTCATATGC
193 AGTATGGGCCAATTTCATATGC
*
2537796 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAAATTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* * *
2537861 ACAACACACATTGACGAGGGATTAAATAGAAATAATTTTAAATTATGAGGTTTAAATTAATAC-A
66 ACAACACACATTGATGAGGGATCAAATAGAAATAATTTT-AATTTTGAGGTTTAAATTAATACAA
* * *
2537925 AAAGTACTAATTTATAACCATTTAAAAAGTTAT-GAGCCACTTTAAAAATATAAATAAGTAATAA
130 AAAGTACTAAATTATAACCATTTAAAAAGTTATGGA-CCAATTAAAAAATATAAATAAGTAATAA
*
2537989 GTATGGGACAATTTCATATGC
194 GTATGGGCCAATTTCATATGC
2538010 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
2538075 ACAACACA
66 ACAACACA
2538083 AAGGGATCAA
Statistics
Matches: 448, Mismatches: 50, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
214 114 0.25
215 39 0.09
216 39 0.09
217 251 0.56
218 5 0.01
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (214 bp):
AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACACACATTGATGAGGGATCAAATAGAAATAATTTTAATTTTGAGGTTTAAATTAATACAAA
AAGTACTAAATTATAACCATTTAAAAAGTTATGGACCAATTAAAAAATATAAATAAGTAATAAGT
ATGGGCCAATTTCATATGC
Found at i:2538223 original size:2 final size:2
Alignment explanation
Indices: 2538218--2538309 Score: 50
Period size: 2 Copynumber: 46.5 Consensus size: 2
2538208 CTATATAGTT
* * * *
2538218 TA TA TA TA AA GTA TA TA TA T- TA TA TA TA TA AA CTA TA T- TG TT
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
2538260 TA TA TT TA TA T- TA T- TA TA TA CTC TA TA TA AA CTA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
2538301 TA TA TA TA T
1 TA TA TA TA T
2538310 TATGTATAAA
Statistics
Matches: 69, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
1 5 0.07
2 60 0.87
3 4 0.06
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2538234 original size:22 final size:22
Alignment explanation
Indices: 2538202--2538298 Score: 73
Period size: 22 Copynumber: 4.6 Consensus size: 22
2538192 ATAGAGAGAG
2538202 TATAAAC--TATATAGTTTATA
1 TATAAACTATATATAGTTTATA
*
2538222 TATAAAGTATATATA-TTATATA
1 TATAAACTATATATAGTT-TATA
2538244 TATAAACTATAT-T-GTTTATA
1 TATAAACTATATATAGTTTATA
* * * * *
2538264 TTTATATTAT-TATA-TACTCTA
1 TATAAACTATATATAGT-TTATA
2538285 TATAAACTATATAT
1 TATAAACTATATAT
2538299 TATATATATA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.02
20 19 0.32
21 15 0.25
22 24 0.41
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (22 bp):
TATAAACTATATATAGTTTATA
Found at i:2538241 original size:9 final size:9
Alignment explanation
Indices: 2538229--2538317 Score: 51
Period size: 9 Copynumber: 9.9 Consensus size: 9
2538219 ATATATAAAG
2538229 TATATATAT
1 TATATATAT
2538238 TATATATA-
1 TATATATAT
*
2538246 TAAACTATAT
1 TATA-TATAT
* *
2538256 TGTTTATAT
1 TATATATAT
2538265 T-TATATTAT
1 TATATA-TAT
*
2538274 TATATACT-C
1 TATATA-TAT
* *
2538283 TATATAAAC
1 TATATATAT
2538292 TATATAT-T
1 TATATATAT
2538300 ATATATATAT
1 -TATATATAT
*
2538310 TATGTATA
1 TATATATA
2538318 AACTATAATA
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
8 6 0.10
9 49 0.79
10 7 0.11
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (9 bp):
TATATATAT
Found at i:2538247 original size:11 final size:11
Alignment explanation
Indices: 2538229--2538317 Score: 50
Period size: 11 Copynumber: 8.5 Consensus size: 11
2538219 ATATATAAAG
2538229 TATATATATTA
1 TATATATATTA
2538240 TATATATA--A
1 TATATATATTA
* *
2538249 -A-CTATATTG
1 TATATATATTA
2538258 T-T-TATATT-
1 TATATATATTA
2538266 TATAT-TATTA
1 TATATATATTA
*
2538276 TATACTCTATATA
1 TATA-TATAT-TA
*
2538289 AACTATATATTA
1 TA-TATATATTA
2538301 TATATATATTA
1 TATATATATTA
*
2538312 TGTATA
1 TATATA
2538318 AACTATAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 22
0.69 0.07 0.25
Matches are distributed among these distances:
7 4 0.07
8 2 0.03
9 12 0.20
10 5 0.08
11 23 0.38
12 6 0.10
13 7 0.11
14 2 0.03
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (11 bp):
TATATATATTA
Found at i:2538432 original size:20 final size:20
Alignment explanation
Indices: 2538409--2538467 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
2538399 CTATATATAT
2538409 TATATAGTTTACATATGAAC
1 TATATAGTTTACATATGAAC
2538429 TATAT-G--T--ATA--AAC
1 TATATAGTTTACATATGAAC
*
2538442 TATATAGTTTACATATGACC
1 TATATAGTTTACATATGAAC
2538462 TATATA
1 TATATA
2538468 TATAGTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 14
0.67 0.02 0.30
Matches are distributed among these distances:
13 8 0.26
14 1 0.03
15 3 0.10
16 1 0.03
17 1 0.03
18 3 0.10
19 1 0.03
20 13 0.42
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (20 bp):
TATATAGTTTACATATGAAC
Found at i:2538449 original size:33 final size:33
Alignment explanation
Indices: 2538400--2538471 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
2538390 ATATGTAAAC
* *
2538400 TATATATATTATATAGTTTACATATGAACTATA
1 TATATAAACTATATAGTTTACATATGAACTATA
* *
2538433 TGTATAAACTATATAGTTTACATATGACCTATA
1 TATATAAACTATATAGTTTACATATGAACTATA
2538466 TATATA
1 TATATA
2538472 GTTTATTAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (33 bp):
TATATAAACTATATAGTTTACATATGAACTATA
Found at i:2538514 original size:18 final size:18
Alignment explanation
Indices: 2538488--2538593 Score: 55
Period size: 18 Copynumber: 6.1 Consensus size: 18
2538478 TAGTAAACAA
*
2538488 TATAAACTATTTATATAG
1 TATAAACTATATATATAG
*
2538506 TATATACTATATATATA-
1 TATAAACTATATATATAG
* * *
2538523 AACTATA-TAGTATGTATAG
1 TA-TAAACTA-TATATATAG
* *
2538542 TAT-AA-TTTACAT-TA-
1 TATAAACTATATATATAG
*
2538556 TATAAACTATAGTTTATA-
1 TATAAACTATA-TATATAG
2538574 TATAAACTATATACTATAG
1 TATAAACTATATA-TATAG
2538593 T
1 T
2538594 TGATATTTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 17
0.69 0.14 0.18
Matches are distributed among these distances:
14 3 0.05
15 4 0.06
16 6 0.09
17 7 0.11
18 44 0.67
19 2 0.03
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (18 bp):
TATAAACTATATATATAG
Found at i:2538644 original size:18 final size:18
Alignment explanation
Indices: 2538623--2538662 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2538613 ATAAAAATTA
*
2538623 TATAGTTGGTATATGAAC
1 TATAGTTGATATATGAAC
*
2538641 TATAGTTTATATATGAAC
1 TATAGTTGATATATGAAC
2538659 TATA
1 TATA
2538663 TATAAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (18 bp):
TATAGTTGATATATGAAC
Found at i:2538664 original size:11 final size:11
Alignment explanation
Indices: 2538648--2538686 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2538638 AACTATAGTT
*
2538648 TATATATGAAC
1 TATATATAAAC
2538659 TATATATAAAC
1 TATATATAAAC
2538670 TATAGTA-AAAC
1 TATA-TATAAAC
2538681 TATATA
1 TATATA
2538687 GTTTATATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 2 0.08
11 22 0.85
12 2 0.08
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (11 bp):
TATATATAAAC
Found at i:2538665 original size:60 final size:59
Alignment explanation
Indices: 2538601--2538714 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 59
2538591 AGTTGATATT
* * * *
2538601 TATATATAAACTATA-AAAATTATATAGTTGGTATATGAACTATAGTTTATATATGAAC
1 TATATATAAACTATAGAAAACTATATAGTTGATATACGAACTATAGTTTACATATGAAC
*
2538659 TATATATAAACTATAGTAAAACTATATAGTTTATATACGAACTATAGTTTACATAT
1 TATATATAAACTATAG-AAAACTATATAGTTGATATACGAACTATAGTTTACATAT
2538715 TAACAATAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 15 0.31
60 34 0.69
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (59 bp):
TATATATAAACTATAGAAAACTATATAGTTGATATACGAACTATAGTTTACATATGAAC
Found at i:2538694 original size:31 final size:30
Alignment explanation
Indices: 2538563--2538706 Score: 93
Period size: 31 Copynumber: 4.8 Consensus size: 30
2538553 TTATATAAAC
**
2538563 TATAGTTTATATATAAACTATA-TACTATA
1 TATAGTTTATATATAAACTATAGTAAAATA
2538592 GTTGATA-TTTATATATAAACTATA--AAAATTA
1 --T-ATAGTTTATATATAAACTATAGTAAAA-TA
** * **
2538623 TATAGTTGGTATATGAACTATAGT-TTATA
1 TATAGTTTATATATAAACTATAGTAAAATA
**
2538652 TAT-GAACTATATATAAACTATAGTAAAACTA
1 TATAG-TTTATATATAAACTATAGTAAAA-TA
**
2538683 TATAGTTTATATACGAACTATAGT
1 TATAGTTTATATATAAACTATAGT
2538707 TTACATATTA
Statistics
Matches: 86, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
28 4 0.05
29 34 0.40
30 4 0.05
31 40 0.47
32 4 0.05
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (30 bp):
TATAGTTTATATATAAACTATAGTAAAATA
Found at i:2538753 original size:18 final size:18
Alignment explanation
Indices: 2538633--2538799 Score: 81
Period size: 18 Copynumber: 8.7 Consensus size: 18
2538623 TATAGTTGGT
*
2538633 ATATGAACTATAGTTTAT
1 ATATGAACTATAGTTTAC
*
2538651 ATATGAACTATA-TATAAAC
1 ATATGAACTATAGT-T-TAC
* *
2538670 TATAGTAAAACTATATAGTTTAT
1 -ATA-T-GAAC--TATAGTTTAC
*
2538693 ATACGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
2538711 ATATTAACAATAATTGATATTTAC
1 ATATGAAC--T-A-T-A-GTTTAC
2538735 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
2538753 ATATGAA-T-TA-TATAT
1 ATATGAACTATAGTTTAC
*
2538768 ATATAAACTATATAGTTTAC
1 ATATGAAC--TATAGTTTAC
2538788 ATATGAACTATA
1 ATATGAACTATA
2538800 TATATAGTTT
Statistics
Matches: 111, Mismatches: 19, Indels: 38
0.66 0.11 0.23
Matches are distributed among these distances:
15 9 0.08
16 2 0.02
17 2 0.02
18 45 0.41
19 4 0.04
20 18 0.16
21 3 0.03
22 8 0.07
23 2 0.02
24 17 0.15
25 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:2538861 original size:40 final size:40
Alignment explanation
Indices: 2538817--2538911 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
2538807 TTTATTAAAG
* *
2538817 AACTATATAAACTATTTATATAGTATATACTACATATATA
1 AACTATATATACTATTTATATACTATATACTACATATATA
* * *
2538857 AACTATAGTTTA-TATTTATATACTATATATTATATATATA
1 AACTATA-TATACTATTTATATACTATATACTACATATATA
2538897 AACTATATATACTAT
1 AACTATATATACTAT
2538912 ATAGTATAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 3 0.06
40 42 0.89
41 2 0.04
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (40 bp):
AACTATATATACTATTTATATACTATATACTACATATATA
Found at i:2538863 original size:20 final size:20
Alignment explanation
Indices: 2538840--2538914 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
2538830 ATTTATATAG
*
2538840 TATATACTACATATATAAAC
1 TATATATTACATATATAAAC
* * *
2538860 TATAGT-TTATATTTATATAC
1 TATA-TATTACATATATAAAC
*
2538880 TATATATTATATATATAAAC
1 TATATATTACATATATAAAC
2538900 TATATA-TAC-TATATA
1 TATATATTACATATATA
2538915 GTATAATTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 6 0.13
19 3 0.07
20 36 0.78
21 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.45
Consensus pattern (20 bp):
TATATATTACATATATAAAC
Found at i:2538892 original size:9 final size:9
Alignment explanation
Indices: 2538818--2538914 Score: 54
Period size: 9 Copynumber: 9.9 Consensus size: 9
2538808 TTATTAAAGA
*
2538818 ACTATATAA
1 ACTATATAT
2538827 ACTATTTATAT
1 ACTA--TATAT
*
2538838 AGTATATACT
1 ACTATATA-T
*
2538848 ACATATATAA
1 AC-TATATAT
2538858 ACTATAGTTTAT
1 ACTATA---TAT
*
2538870 A-TTTATAT
1 ACTATATAT
2538878 ACTATATATT
1 ACTATATA-T
2538888 A-TATATAT
1 ACTATATAT
2538896 AAACTATATAT
1 --ACTATATAT
2538907 ACTATATA
1 ACTATATA
2538915 GTATAATTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
8 5 0.07
9 31 0.45
10 7 0.10
11 23 0.33
12 3 0.04
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (9 bp):
ACTATATAT
Found at i:2539112 original size:18 final size:19
Alignment explanation
Indices: 2539091--2539133 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
2539081 TATACTACAA
*
2539091 ATATAGTTTATATAT-ACT
1 ATATAGTTTACATATAACT
2539109 ATATAGTTTACATATGAACT
1 ATATAGTTTACATAT-AACT
2539129 ATATA
1 ATATA
2539134 TAAAAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.64
20 8 0.36
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (19 bp):
ATATAGTTTACATATAACT
Found at i:2539123 original size:20 final size:18
Alignment explanation
Indices: 2539091--2539133 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
2539081 TATACTACAA
2539091 ATATAGTTTATAT-ATACT
1 ATATAGTTTATATGA-ACT
2539109 ATATAGTTTACATATGAACT
1 ATATAGTTT--ATATGAACT
2539129 ATATA
1 ATATA
2539134 TAAAAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.41
20 12 0.55
21 1 0.05
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (18 bp):
ATATAGTTTATATGAACT
Found at i:2539895 original size:20 final size:19
Alignment explanation
Indices: 2539857--2539895 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2539847 ACCATTGTAT
* *
2539857 GGGGGTATTGATACCTCTG
1 GGGGGTATCGATACATCTG
2539876 GGGGGTATCGATACTATCTG
1 GGGGGTATCGATAC-ATCTG
2539896 AGCATTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.18, C:0.15, G:0.36, T:0.31
Consensus pattern (19 bp):
GGGGGTATCGATACATCTG
Found at i:2541858 original size:37 final size:37
Alignment explanation
Indices: 2541782--2541858 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
2541772 TTTTTATATT
* *
2541782 TTTAATTTTGTAAAAAAATTTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATATATATAAATATTATCAA
*
2541819 TTTAATTTTTTAAAGAAAATATATA-AATATATTA-CAA
1 TTTAATTTTGTAAA-AAAATATATATAA-ATATTATCAA
2541856 TTT
1 TTT
2541859 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 20 0.57
38 15 0.43
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAATATATATAAATATTATCAA
Found at i:2542039 original size:20 final size:20
Alignment explanation
Indices: 2542003--2542040 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2541993 ATTCTATTCC
**
2542003 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
2542023 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2542041 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2546627 original size:17 final size:17
Alignment explanation
Indices: 2546605--2546644 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2546595 TCTTCTTCTC
*
2546605 CGTCTCCTTCTTTGGCT
1 CGTCTCCTTCTTTAGCT
2546622 CGTCTCCTTCTTTAGCT
1 CGTCTCCTTCTTTAGCT
2546639 CGTCTC
1 CGTCTC
2546645 TTTTCTCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.03, C:0.38, G:0.15, T:0.45
Consensus pattern (17 bp):
CGTCTCCTTCTTTAGCT
Found at i:2548034 original size:21 final size:21
Alignment explanation
Indices: 2548008--2548085 Score: 92
Period size: 22 Copynumber: 3.8 Consensus size: 21
2547998 ATATGTCTGA
2548008 GGGTATCGGTA-CATCCTGAGG
1 GGGTATCGGTACCAT-CTGAGG
2548029 GGGTATCGGTACCAT-TGCATGG
1 GGGTATCGGTACCATCTG-A-GG
*
2548051 GGGTATCGATACC-TCT-AGG
1 GGGTATCGGTACCATCTGAGG
2548070 GGGTATCGGTACCATC
1 GGGTATCGGTACCATC
2548086 CGAGCATTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
19 14 0.28
20 5 0.10
21 13 0.26
22 18 0.36
ACGTcount: A:0.19, C:0.21, G:0.35, T:0.26
Consensus pattern (21 bp):
GGGTATCGGTACCATCTGAGG
Found at i:2548521 original size:18 final size:18
Alignment explanation
Indices: 2548449--2548521 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 18
2548439 GTTATTAGTG
*
2548449 TATATAAACTATATAATA
1 TATATAAACTATATATTA
2548467 TATATAAACTATATATTA
1 TATATAAACTATATATTA
* *
2548485 TATAGT--TC-AT-TAGTA
1 TATA-TAAACTATATATTA
*
2548500 TATATAAACTATATGTTA
1 TATATAAACTATATATTA
2548518 TATA
1 TATA
2548522 GTACCACATA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 1 0.02
15 8 0.18
16 3 0.07
17 3 0.07
18 28 0.64
19 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (18 bp):
TATATAAACTATATATTA
Found at i:2548572 original size:21 final size:21
Alignment explanation
Indices: 2548524--2548573 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2548514 GTTATATAGT
2548524 ACCACATATATGTTCCAAAGG
1 ACCACATATATGTTCCAAAGG
**
2548545 ATTACATATATG-TCCTAAAGG
1 ACCACATATATGTTCC-AAAGG
2548566 ACCACATA
1 ACCACATA
2548574 GAACCCTCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (21 bp):
ACCACATATATGTTCCAAAGG
Found at i:2548877 original size:11 final size:11
Alignment explanation
Indices: 2548861--2548902 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 11
2548851 GATCATCATC
2548861 ATATAACATAT
1 ATATAACATAT
2548872 ATATAACATAT
1 ATATAACATAT
2548883 ATATATCACATCAT
1 ATATA--ACAT-AT
2548897 ATATAA
1 ATATAA
2548903 TACATATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 16 0.57
12 1 0.04
13 4 0.14
14 7 0.25
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAACATAT
Found at i:2548886 original size:13 final size:14
Alignment explanation
Indices: 2548867--2548901 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2548857 CATCATATAA
2548867 CATATATATAACAT
1 CATATATATAACAT
*
2548881 -ATATATATCACAT
1 CATATATATAACAT
2548894 CATATATA
1 CATATATA
2548902 ATACATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (14 bp):
CATATATATAACAT
Found at i:2551900 original size:16 final size:17
Alignment explanation
Indices: 2551876--2551908 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2551866 CGAGGTGTCA
2551876 CATTGACTTTT-CAAAG
1 CATTGACTTTTACAAAG
*
2551892 CATTTACTTTTACAAAG
1 CATTGACTTTTACAAAG
2551909 TGACAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (17 bp):
CATTGACTTTTACAAAG
Found at i:2554777 original size:18 final size:18
Alignment explanation
Indices: 2554756--2554795 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2554746 TCTAACCTTT
* *
2554756 AACCCTAACCTAAACTCA
1 AACCCAAACCCAAACTCA
2554774 AACCCAAACCCAAACTCA
1 AACCCAAACCCAAACTCA
2554792 AACC
1 AACC
2554796 TAATCACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.42, G:0.00, T:0.10
Consensus pattern (18 bp):
AACCCAAACCCAAACTCA
Found at i:2554805 original size:18 final size:18
Alignment explanation
Indices: 2554767--2554807 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2554757 ACCCTAACCT
*
2554767 AAACTCAAACCCAAACCC
1 AAACTCAAACCCAAACAC
* *
2554785 AAACTCAAACCTAATCAC
1 AAACTCAAACCCAAACAC
2554803 AAACT
1 AAACT
2554808 TGAACCTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (18 bp):
AAACTCAAACCCAAACAC
Found at i:2554870 original size:12 final size:12
Alignment explanation
Indices: 2554852--2554891 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2554842 ACCCATATCC
2554852 AAACTCGAACCT
1 AAACTCGAACCT
* *
2554864 GAACTCGAATCT
1 AAACTCGAACCT
*
2554876 AAACTCGAATCT
1 AAACTCGAACCT
2554888 AAAC
1 AAAC
2554892 CCTAACCCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (12 bp):
AAACTCGAACCT
Found at i:2554927 original size:23 final size:24
Alignment explanation
Indices: 2554876--2554938 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
2554866 ACTCGAATCT
* * *
2554876 AAACTCGAATCTAAACCCTAACCC
1 AAACCCGAATCTAAACCCAAAACC
*
2554900 TAACCC-AATCTAAACCCAAAACC
1 AAACCCGAATCTAAACCCAAAACC
*
2554923 AAACCCGAATCCAAAC
1 AAACCCGAATCTAAAC
2554939 TATTTGAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.46, C:0.38, G:0.03, T:0.13
Consensus pattern (24 bp):
AAACCCGAATCTAAACCCAAAACC
Found at i:2558081 original size:17 final size:18
Alignment explanation
Indices: 2558059--2558099 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2558049 TGGACCTCTC
2558059 TTTTATAATT-TATT-TCA
1 TTTTATAATTCTATTCT-A
*
2558076 TTTTATCATTCTATTCTA
1 TTTTATAATTCTATTCTA
2558094 TTTTAT
1 TTTTAT
2558100 TTTAATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
18 11 0.52
19 1 0.05
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTATAATTCTATTCTA
Found at i:2558251 original size:26 final size:26
Alignment explanation
Indices: 2558222--2558306 Score: 72
Period size: 25 Copynumber: 3.3 Consensus size: 26
2558212 TGATCTGATA
2558222 CTTTTATTTTATGCATTTTAGTCACT
1 CTTTTATTTTATGCATTTTAGTCACT
* * *
2558248 C-TTTA-TTTCTG-A-TTTAGCTATTATT
1 CTTTTATTTTATGCATTTTAG---TCACT
2558273 CTTTTATTTTATGCATTTTAGTCACT
1 CTTTTATTTTATGCATTTTAGTCACT
*
2558299 -GTTTATTT
1 CTTTTATTT
2558307 CTGATTTGGC
Statistics
Matches: 45, Mismatches: 7, Indels: 15
0.67 0.10 0.22
Matches are distributed among these distances:
22 5 0.11
23 1 0.02
24 5 0.11
25 15 0.33
26 8 0.18
27 5 0.11
28 1 0.02
29 5 0.11
ACGTcount: A:0.19, C:0.13, G:0.08, T:0.60
Consensus pattern (26 bp):
CTTTTATTTTATGCATTTTAGTCACT
Found at i:2558277 original size:51 final size:51
Alignment explanation
Indices: 2558222--2558405 Score: 235
Period size: 51 Copynumber: 3.6 Consensus size: 51
2558212 TGATCTGATA
* * *
2558222 CTTTTATTTTATGCATTTTAGTCACTCTTTATTTCTGATTTAGCTATTATT
1 CTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTAATATT
*
2558273 CTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTAATGTT
1 CTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTAATATT
** * *
2558324 CTTCAATTTTATGCATTTTGGTCACTGTTTATTTCTGATATGGCTACA-ATTT
1 CTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTA-ATA-TT
* * *
2558376 TTTTTATTTTATTTCATTTTAGTCATTGTT
1 CTTTTATTTTA-TGCATTTTAGTCACTGTT
2558406 GTTTAAAATA
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
51 89 0.77
52 11 0.10
53 15 0.13
ACGTcount: A:0.19, C:0.12, G:0.11, T:0.58
Consensus pattern (51 bp):
CTTTTATTTTATGCATTTTAGTCACTGTTTATTTCTGATTTGGCTAATATT
Found at i:2571696 original size:55 final size:53
Alignment explanation
Indices: 2571628--2571753 Score: 143
Period size: 54 Copynumber: 2.3 Consensus size: 53
2571618 TACTTGTTGA
2571628 GAGTGTATCGATACCCTTAAAACATCGAATG-T-CATGTGTGTATCGGTACACTGAG
1 GAGTGTATCGATACCCTTAAAA-ATCGAATGCTACA--TGTGTATCGGTACACTG-G
* * *
2571683 GAGTGTATTGATACTCC-TAAAAATTGAGTGCTACATGTGTATCGGTACACTGG
1 GAGTGTATCGATAC-CCTTAAAAATCGAATGCTACATGTGTATCGGTACACTGG
2571736 G-GTAGTATCGATACCCTT
1 GAGT-GTATCGATACCCTT
2571754 GCAATTTCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
52 4 0.06
53 12 0.19
54 23 0.37
55 19 0.31
56 4 0.06
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (53 bp):
GAGTGTATCGATACCCTTAAAAATCGAATGCTACATGTGTATCGGTACACTGG
Found at i:2576178 original size:21 final size:19
Alignment explanation
Indices: 2576150--2576190 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2576140 CATTGCAGGA
2576150 ATTTATGGCCTCAACGAAAG
1 ATTTATGGCCTCAAC-AAAG
*
2576170 ATTTCATGGCCTCCACAAAG
1 ATTT-ATGGCCTCAACAAAG
2576190 A
1 A
2576191 CCTTGATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
ATTTATGGCCTCAACAAAG
Found at i:2582025 original size:30 final size:30
Alignment explanation
Indices: 2581989--2582047 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
2581979 GCGGCAGAAC
* *
2581989 ATTCCATGTCTCGACATCAAATGTCCCTCT
1 ATTCCATGCCTCGAAATCAAATGTCCCTCT
2582019 ATTCCATGCCTCGAAATCAAATGTCCCTC
1 ATTCCATGCCTCGAAATCAAATGTCCCTC
2582048 CAAAGGTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.34, G:0.10, T:0.31
Consensus pattern (30 bp):
ATTCCATGCCTCGAAATCAAATGTCCCTCT
Found at i:2585854 original size:117 final size:118
Alignment explanation
Indices: 2585635--2585854 Score: 313
Period size: 117 Copynumber: 1.9 Consensus size: 118
2585625 ATTCCATCAT
* * *
2585635 AGAAGGAGGTGGATCAACATTTCCGATGAAAGGGTTCATAATGAGAATAACTCGTCCGATGAGGC
1 AGAAGGAGGTGGATCAACATTTCCGATGAAA-GATTCATAATGAGAAGAACTCATCCGATGAGGC
*
2585700 AGAAAAAAGTTCATAATGATAAGAACTTGTTCAACCTTTGTACAATTCGAGCAC
65 AGAAAAAAGTTCATAATGAAAAGAACTTGTTCAACCTTTGTACAATTCGAGCAC
*
2585754 AGAAGGAGGTGGATCAACATTTCCCG-TGGAAA-ATTCATAATGAGAAGAACTCATCTGATGA-G
1 AGAAGGAGGTGGATCAACATTT-CCGAT-GAAAGATTCATAATGAGAAGAACTCATCCGATGAGG
* *
2585816 -AGAGAAGAAGTTTATAATGAAAAGAACTTGTTCAACCTT
64 CAGA-AAAAAGTTCATAATGAAAAGAACTTGTTCAACCTT
2585855 GACTCGTCCA
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
116 3 0.03
117 33 0.36
118 25 0.27
119 23 0.25
120 7 0.08
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (118 bp):
AGAAGGAGGTGGATCAACATTTCCGATGAAAGATTCATAATGAGAAGAACTCATCCGATGAGGCA
GAAAAAAGTTCATAATGAAAAGAACTTGTTCAACCTTTGTACAATTCGAGCAC
Found at i:2585920 original size:42 final size:42
Alignment explanation
Indices: 2585861--2585984 Score: 153
Period size: 42 Copynumber: 3.0 Consensus size: 42
2585851 CCTTGACTCG
* *
2585861 TCCATCACATAAGGAGTTAGATCAACATCATCATTTTGCTCA
1 TCCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCA
* * *
2585903 TCCATCACATAAGGAGTTGGATCAACA-C-TGACCTTGGCTCA
1 TCCATCACATAAGGAGTTGGATCAACATCATCA-TTTCGCTCA
** *
2585944 TCCATCAGGTAAGGAGTTGGATCAGCATCATCATTTCGCTC
1 TCCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTC
2585985 GACCGTCGTA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 2 0.03
41 32 0.46
42 33 0.48
43 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
TCCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCA
Found at i:2587254 original size:51 final size:50
Alignment explanation
Indices: 2587196--2587392 Score: 232
Period size: 51 Copynumber: 3.9 Consensus size: 50
2587186 GATGTATACT
* *
2587196 TTTATTTTATGCATTTTAGTCATTGTTTATTTCTGATTTAGCTATTGTTC
1 TTTATTTTATGCATTTTAGTCACTGATTATTTCTGATTTAGCTATTGTTC
* * *
2587246 ACTTATTTTATGCATTTTAGTCACTGATTATTTTTGATTTAGCTATTGCTC
1 -TTTATTTTATGCATTTTAGTCACTGATTATTTCTGATTTAGCTATTGTTC
* * * *
2587297 TTTTATTTTATGCATTTTAGTCACTGATTATTTTTTATTTGGCTATTTTTC
1 -TTTATTTTATGCATTTTAGTCACTGATTATTTCTGATTTAGCTATTGTTC
* * * * * *
2587348 TTCTATTTTATGCATTTTGGTCGCAGTTTATTTCTGGTTTGGCTA
1 TT-TATTTTATGCATTTTAGTCACTGATTATTTCTGATTTAGCTA
2587393 CAGTTTTTAA
Statistics
Matches: 127, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
50 2 0.02
51 125 0.98
ACGTcount: A:0.18, C:0.12, G:0.13, T:0.57
Consensus pattern (50 bp):
TTTATTTTATGCATTTTAGTCACTGATTATTTCTGATTTAGCTATTGTTC
Found at i:2587379 original size:102 final size:102
Alignment explanation
Indices: 2587194--2587380 Score: 259
Period size: 102 Copynumber: 1.8 Consensus size: 102
2587184 TTGATGTATA
* *
2587194 CTTTTATTTTATGCATTTTAGTCATTGTTTATTTCTGATTTAGCTATTGTTCACTTATTTTATGC
1 CTTTTATTTTATGCATTTTAGTCACTGATTATTTCTGATTTAGCTATTGTTCACTTATTTTATGC
*
2587259 ATTTTAGTCACTGATTATTTTTGATTTAGCTATTGCT
66 ATTTTAGTCACAGATTATTTTTGATTTAGCTATTGCT
* * * * *
2587296 CTTTTATTTTATGCATTTTAGTCACTGATTATTTTTTATTTGGCTATTTTTC-TTCTATTTTATG
1 CTTTTATTTTATGCATTTTAGTCACTGATTATTTCTGATTTAGCTATTGTTCACT-TATTTTATG
* * *
2587360 CATTTTGGTCGCAGTTTATTT
65 CATTTTAGTCACAGATTATTT
2587381 CTGGTTTGGC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 1 0.01
102 72 0.99
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (102 bp):
CTTTTATTTTATGCATTTTAGTCACTGATTATTTCTGATTTAGCTATTGTTCACTTATTTTATGC
ATTTTAGTCACAGATTATTTTTGATTTAGCTATTGCT
Found at i:2589915 original size:112 final size:111
Alignment explanation
Indices: 2589716--2589945 Score: 313
Period size: 112 Copynumber: 2.1 Consensus size: 111
2589706 ACCTAAGTGA
* * *
2589716 CGAAATTGTAATTCACATCATTATGAATACCATGGGTGGCACCTTTTATGCCGAAAATGAACCGT
1 CGAAATGGCAATTCACATCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGAACCGT
* * *
2589781 TATGCATTAAGCAAAATTGATCGATAACTTTCATACACGAAA-TATGT
66 TATACATTAAGCAAAATCGATCGAT-ACTATCATACAC-AAAGTATGT
* * **
2589828 TGAAATGGCAATTCACATCATTATGAATACCATGGGTGGCACCTTTTATGTCAAAAAT-ACATTG
1 CGAAATGGCAATTCACATCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGA-ACCG
2589892 TTATACATGTAA-CAAAATCGATCGATACTATCATACACAAAGTATGT
65 TTATACAT-TAAGCAAAATCGATCGATACTATCATACACAAAGTATGT
2589939 CGAAATG
1 CGAAATG
2589946 CACCTACAAC
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
110 3 0.03
111 23 0.22
112 75 0.72
113 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (111 bp):
CGAAATGGCAATTCACATCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGAACCGT
TATACATTAAGCAAAATCGATCGATACTATCATACACAAAGTATGT
Found at i:2590495 original size:22 final size:22
Alignment explanation
Indices: 2590454--2590509 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
2590444 AGGCTCAACA
*
2590454 GTATCGATAC--CTCTACTATG
1 GTATCGATACTTCTATACTATG
2590474 GTATCGATACTTCTATACTATG
1 GTATCGATACTTCTATACTATG
* *
2590496 GTACCAATACTTCT
1 GTATCGATACTTCT
2590510 TTCAGTATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (22 bp):
GTATCGATACTTCTATACTATG
Found at i:2596181 original size:6 final size:6
Alignment explanation
Indices: 2596170--2596246 Score: 73
Period size: 6 Copynumber: 12.8 Consensus size: 6
2596160 ATAAGATATA
* * ** *
2596170 TATGCG TATGCG TATGCG TATGCG TAGGCA TATATG TAGGCG TATGCG
1 TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG
* * * *
2596218 TAGGCG TATGCG TAGGCA TATGCA TATGC
1 TATGCG TATGCG TATGCG TATGCG TATGC
2596247 ATACATACAT
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (6 bp):
TATGCG
Found at i:2596187 original size:12 final size:12
Alignment explanation
Indices: 2596173--2596240 Score: 91
Period size: 12 Copynumber: 5.7 Consensus size: 12
2596163 AGATATATAT
*
2596173 GCGTATGCGTAT
1 GCGTATGCGTAG
2596185 GCGTATGCGTAG
1 GCGTATGCGTAG
* **
2596197 GCATATATGTAG
1 GCGTATGCGTAG
2596209 GCGTATGCGTAG
1 GCGTATGCGTAG
2596221 GCGTATGCGTAG
1 GCGTATGCGTAG
*
2596233 GCATATGC
1 GCGTATGC
2596241 ATATGCATAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.21, C:0.16, G:0.35, T:0.28
Consensus pattern (12 bp):
GCGTATGCGTAG
Found at i:2597684 original size:22 final size:21
Alignment explanation
Indices: 2597658--2597698 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2597648 GTTACGGAAA
2597658 TGATGGTCTTGATGGATGAAGT
1 TGATGGTCTTGAT-GATGAAGT
*
2597680 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
2597699 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.37, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGT
Found at i:2601920 original size:33 final size:33
Alignment explanation
Indices: 2601883--2601946 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
2601873 GTTCGCTTTC
2601883 TCTTTT-TGAATTTCTT-TTCTTTTAT-TCTTTTAT
1 TCTTTTATG-ATTT-TTCTTCTTTT-TGTCTTTTAT
2601916 TCTTTTATGATTTTTCTTCTTTTTGTCTTTT
1 TCTTTTATGATTTTTCTTCTTTTTGTCTTTT
2601947 TCTTTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
32 3 0.11
33 23 0.82
34 2 0.07
ACGTcount: A:0.09, C:0.12, G:0.05, T:0.73
Consensus pattern (33 bp):
TCTTTTATGATTTTTCTTCTTTTTGTCTTTTAT
Found at i:2601938 original size:8 final size:8
Alignment explanation
Indices: 2601899--2601923 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2601889 TGAATTTCTT
2601899 TTCTTTTA
1 TTCTTTTA
2601907 TTCTTTTA
1 TTCTTTTA
2601915 TTCTTTTA
1 TTCTTTTA
2601923 T
1 T
2601924 GATTTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTA
Found at i:2601946 original size:16 final size:17
Alignment explanation
Indices: 2601899--2601956 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
2601889 TGAATTTCTT
*
2601899 TTCTTTTAT-TCTTTTA
1 TTCTTTTATGTCTTTTC
2601915 TTCTTTTATGAT-TTTTC
1 TTCTTTTATG-TCTTTTC
2601932 TTCTTTT-TGTCTTTTTC
1 TTCTTTTATGTC-TTTTC
2601949 TTTCTTTT
1 -TTCTTTT
2601957 TGCACTCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 1 0.03
16 11 0.31
17 16 0.44
18 8 0.22
ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76
Consensus pattern (17 bp):
TTCTTTTATGTCTTTTC
Found at i:2602237 original size:16 final size:18
Alignment explanation
Indices: 2602206--2602238 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2602196 TTAATAAAAG
2602206 AAAGATTAATGAAATGAT
1 AAAGATTAATGAAATGAT
2602224 AAAGA-TAA-GAAATGA
1 AAAGATTAATGAAATGA
2602239 AATGAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (18 bp):
AAAGATTAATGAAATGAT
Found at i:2602303 original size:22 final size:21
Alignment explanation
Indices: 2602275--2602315 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2602265 GATGTGGAAA
2602275 TGATGGTCTTGATGGATGAATT
1 TGATGGTCTTGAT-GATGAATT
*
2602297 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
2602316 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.34, T:0.39
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAATT
Found at i:2605961 original size:21 final size:22
Alignment explanation
Indices: 2605930--2605970 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2605920 GGATTTTTAT
*
2605930 TTTATATTATTAAAAGATATTC
1 TTTATATTATTAAAAAATATTC
2605952 TTTA-ATTATTAAAAAATAT
1 TTTATATTATTAAAAAATAT
2605971 ACAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTATATTATTAAAAAATATTC
Found at i:2605996 original size:15 final size:15
Alignment explanation
Indices: 2605976--2606053 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
2605966 AATATACAAA
2605976 ATTATTATAAAATAT
1 ATTATTATAAAATAT
*
2605991 ATTATTTTAATAAT-T
1 ATTATTATAA-AATAT
* * *
2606006 -TTA-AATATAATAA
1 ATTATTATAAAATAT
*
2606019 ATAATTAT-AAATAT
1 ATTATTATAAAATAT
2606033 ATTATTATAAAATAT
1 ATTATTATAAAATAT
2606048 ATTATT
1 ATTATT
2606054 TTCGGGTCGG
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 16 0.33
15 24 0.50
16 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATTATAAAATAT
Found at i:2606001 original size:44 final size:43
Alignment explanation
Indices: 2605934--2606038 Score: 108
Period size: 43 Copynumber: 2.4 Consensus size: 43
2605924 TTTTATTTTA
* * *
2605934 TATTATTAAAAGATATT-CTTTAATTATTAAAAAATATACA-AAAT
1 TATTA-TAAAATATATTATTTTAATAATT-AAAAATATA-ATAAAT
**
2605978 TATTATAAAATATATTATTTTAATAATTTTAAATATAATAAAT
1 TATTATAAAATATATTATTTTAATAATTAAAAATATAATAAAT
*
2606021 AATTAT-AAATATATTATT
1 TATTATAAAATATATTATT
2606039 ATAAAATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
42 13 0.25
43 26 0.49
44 14 0.26
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (43 bp):
TATTATAAAATATATTATTTTAATAATTAAAAATATAATAAAT
Found at i:2609265 original size:24 final size:24
Alignment explanation
Indices: 2609238--2609292 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2609228 GTTTCATATT
* * *
2609238 GACCGATTCGATTTTGTTCGGTTG
1 GACCGATTCGATTTGGTTCGGATA
* *
2609262 GACCTATTTGATTTGGTTCGGATA
1 GACCGATTCGATTTGGTTCGGATA
2609286 GACCGAT
1 GACCGAT
2609293 CTGGTTAGGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.38
Consensus pattern (24 bp):
GACCGATTCGATTTGGTTCGGATA
Found at i:2609721 original size:24 final size:24
Alignment explanation
Indices: 2609689--2609736 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2609679 AGTTTTCTCG
2609689 GGGAAAATATACTAAAAAAAACTA
1 GGGAAAATATACTAAAAAAAACTA
2609713 GGGAAAATATACTAAAAAAAACTA
1 GGGAAAATATACTAAAAAAAACTA
2609737 AGAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.17
Consensus pattern (24 bp):
GGGAAAATATACTAAAAAAAACTA
Found at i:2610634 original size:3 final size:3
Alignment explanation
Indices: 2610626--2610672 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
2610616 ATATTTTAAT
* *
2610626 TTA TTA TTA TTA TT- TTCA TTT TTA ATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
2610671 TT
1 TT
2610673 TAAAATGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2610654 original size:18 final size:19
Alignment explanation
Indices: 2610617--2610657 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2610607 GGGTCTTTTA
*
2610617 TATTTTAATTTATTATTAT
1 TATTTTAATTTATTAATAT
*
2610636 TATTTTCATTT-TTAATAT
1 TATTTTAATTTATTAATAT
2610654 TATT
1 TATT
2610658 ATTATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTAATTTATTAATAT
Found at i:2612371 original size:12 final size:12
Alignment explanation
Indices: 2612336--2612374 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2612326 TACTCACATT
2612336 TTTATGTATATA
1 TTTATGTATATA
* * *
2612348 TGTACGTGTATA
1 TTTATGTATATA
2612360 TTTATGTATATA
1 TTTATGTATATA
2612372 TTT
1 TTT
2612375 TAATTATTGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.56
Consensus pattern (12 bp):
TTTATGTATATA
Found at i:2613519 original size:21 final size:20
Alignment explanation
Indices: 2613475--2613519 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2613465 TTTTTCAAAA
* *
2613475 TTAAAATCATAATTATTTTT
1 TTAAAATAATAATTATTATT
*
2613495 TTAAAATAATATTTAATTATT
1 TTAAAATAATAATT-ATTATT
2613516 TTAA
1 TTAA
2613520 CTAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAAATAATAATTATTATT
Found at i:2613936 original size:14 final size:14
Alignment explanation
Indices: 2613892--2613937 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
2613882 TAACATAATG
2613892 AAACGTTAGACACT
1 AAACGTTAGACACT
*
2613906 AAA--TTAGAACAAAT
1 AAACGTTAG-AC-ACT
2613920 AAACGTTAGACACT
1 AAACGTTAGACACT
2613934 AAAC
1 AAAC
2613938 TGGAATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 4 0.15
13 2 0.08
14 14 0.54
15 2 0.08
16 4 0.15
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (14 bp):
AAACGTTAGACACT
Done.