Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 72 of 199
Found at i:21550297 original size:48 final size:48
Alignment explanation
Indices: 21550226--21550319 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
21550216 AGAGGCCAAG
21550226 CAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAATAAA
1 CAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAATAAA
21550274 CAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAATA
1 CAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAATA
21550320 GGCATGGGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.26
Consensus pattern (48 bp):
CAACTAAGAAACAAAAGTATTGCACTTGTGAAAGTATTATGGAATAAA
Found at i:21551745 original size:50 final size:50
Alignment explanation
Indices: 21551699--21551831 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 50
21551689 TTATGAGAGG
*
21551699 TCCCACATAAGACCATATCTAGGACATGGCATTGGTACCGAGATGAGAAC
1 TCCCACATAAGACCATATCTAGGACATGGCATTGGCACCGAGATGAGAAC
* * * *
21551749 TCCC-CTTTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCAC-ATAAGACCATATCTAGGACATGGCATTGGCACCGAGATGAGAAC
* ** * *
21551799 TCTCATGTAAGACCATATCTGGGATATGGCATT
1 TCCCACATAAGACCATATCTAGGACATGGCATT
21551832 TGCAATACAG
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 1 0.01
50 68 0.99
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (50 bp):
TCCCACATAAGACCATATCTAGGACATGGCATTGGCACCGAGATGAGAAC
Found at i:21561850 original size:9 final size:9
Alignment explanation
Indices: 21561836--21561870 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
21561826 ATTCATTAAT
21561836 TTTTAGTTA
1 TTTTAGTTA
21561845 TTTTAGTTA
1 TTTTAGTTA
21561854 TTTTAGTTA
1 TTTTAGTTA
21561863 TTTTAGTT
1 TTTTAGTT
21561871 TGTGTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (9 bp):
TTTTAGTTA
Found at i:21566903 original size:27 final size:27
Alignment explanation
Indices: 21566889--21567092 Score: 257
Period size: 27 Copynumber: 7.6 Consensus size: 27
21566879 GGAATAGCCT
*
21566889 CATAGGGTAAAATGATCGAAATACCCC
1 CATAGGGTAAAATGACCGAAATACCCC
* *
21566916 CATAGGGTAGAATGACCTAAATACCCC
1 CATAGGGTAAAATGACCGAAATACCCC
* *
21566943 CATAGGGTAGAATGACCAAAATA-CCC
1 CATAGGGTAAAATGACCGAAATACCCC
* * *
21566969 CATAAGGTAAAATAACTGAAATACCCC
1 CATAGGGTAAAATGACCGAAATACCCC
* * *
21566996 CATAGGGTAGAATGACAGAAATACCTC
1 CATAGGGTAAAATGACCGAAATACCCC
* *
21567023 CATAAGGTAAAATGACCAAAATACCCC
1 CATAGGGTAAAATGACCGAAATACCCC
* * *
21567050 CATAAGGTAAAATGATCAAAATACCCC
1 CATAGGGTAAAATGACCGAAATACCCC
21567077 CATAGGGTAAAATGAC
1 CATAGGGTAAAATGAC
21567093 TATTCTACCC
Statistics
Matches: 154, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 21 0.14
27 133 0.86
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.18
Consensus pattern (27 bp):
CATAGGGTAAAATGACCGAAATACCCC
Found at i:21567037 original size:80 final size:81
Alignment explanation
Indices: 21566889--21567092 Score: 304
Period size: 80 Copynumber: 2.5 Consensus size: 81
21566879 GGAATAGCCT
* ** * *
21566889 CATAGGGTAAAATGATCGAAATACCCCCATAGGGTAGAATGACCTAAATACCCCCATAGGGTAGA
1 CATAAGGTAAAATGATCGAAATACCCCCATAGGGTAGAATGACAGAAATACCCCCATAAGGTAAA
21566954 ATGACCAAAATA-CCC
66 ATGACCAAAATACCCC
* *
21566969 CATAAGGTAAAAT-AACTGAAATACCCCCATAGGGTAGAATGACAGAAATACCTCCATAAGGTAA
1 CATAAGGTAAAATGATC-GAAATACCCCCATAGGGTAGAATGACAGAAATACCCCCATAAGGTAA
21567033 AATGACCAAAATACCCC
65 AATGACCAAAATACCCC
* *
21567050 CATAAGGTAAAATGATCAAAATACCCCCATAGGGTAAAATGAC
1 CATAAGGTAAAATGATCGAAATACCCCCATAGGGTAGAATGAC
21567093 TATTCTACCC
Statistics
Matches: 111, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
79 2 0.02
80 67 0.60
81 40 0.36
82 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.18
Consensus pattern (81 bp):
CATAAGGTAAAATGATCGAAATACCCCCATAGGGTAGAATGACAGAAATACCCCCATAAGGTAAA
ATGACCAAAATACCCC
Found at i:21569689 original size:27 final size:27
Alignment explanation
Indices: 21569637--21570070 Score: 442
Period size: 27 Copynumber: 16.2 Consensus size: 27
21569627 TTACACAGTT
* * *
21569637 ATGACGGAAATA-CTCCATAGAGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
21569663 ATGACCAAAATACCCCCATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * * * * * *
21569690 ATAATCAAAATCCCCCCACAGGATAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
21569717 ATGACTGAAATATCCCCATACGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * * *
21569744 ATCACCGAAATACCCCCAGAAGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
21569771 ATGACCGAAATA-CCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
21569797 ATGACCGAAATACCCCCATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
** *
21569824 ATGAGTGAAATACCCCCATATGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
21569851 ATGATCGAAATACCCCTATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * **
21569878 ATGATCGAAATACCCTCATAGGGTTGA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
21569905 TTGACCGAAATACCCTCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* **
21569932 ATGATCGAAATACCCCCATAAAGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
21569959 ATGATCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * * * *
21569986 CTAACAGAAATACCCTCATAAGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
21570013 ATGTCTGAAATACCCCCATAGGGTAGA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
21570040 TTGACCGAAATA-CCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
21570066 ATGAC
1 ATGAC
21570071 TGTTATACCC
Statistics
Matches: 333, Mismatches: 73, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
26 51 0.15
27 282 0.85
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAAA
Found at i:21578704 original size:16 final size:15
Alignment explanation
Indices: 21578672--21578710 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
21578662 TGATAATAAC
21578672 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
21578688 TTATTATAATGTATAT
1 TAATTATAAT-TATAT
21578704 TAATTAT
1 TAATTAT
21578711 TATCAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:21580797 original size:22 final size:22
Alignment explanation
Indices: 21580772--21580815 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
21580762 GTTCAGAAAA
*
21580772 TTATTTAATTAAAAAAATTAAT
1 TTATCTAATTAAAAAAATTAAT
**
21580794 TTATCTAATTAAATTAATTAAT
1 TTATCTAATTAAAAAAATTAAT
21580816 AAATAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TTATCTAATTAAAAAAATTAAT
Found at i:21592054 original size:16 final size:16
Alignment explanation
Indices: 21592033--21592066 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
21592023 TAAATAAGCT
*
21592033 TAATAAAATCCCAAAA
1 TAATAAAATACCAAAA
21592049 TAATAAAATACCAAAA
1 TAATAAAATACCAAAA
21592065 TA
1 TA
21592067 TAGTTGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.21
Consensus pattern (16 bp):
TAATAAAATACCAAAA
Found at i:21592596 original size:21 final size:21
Alignment explanation
Indices: 21592570--21592631 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
21592560 TCAGATACAG
*
21592570 ATATTGTGGACAAGCCACCAA
1 ATATTGTGGATAAGCCACCAA
* * *
21592591 ATATTGTAGATAAACTACCAA
1 ATATTGTGGATAAGCCACCAA
* *
21592612 AAATTGTGGTTAAGCCACCA
1 ATATTGTGGATAAGCCACCA
21592632 GAATGTTCAG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.24
Consensus pattern (21 bp):
ATATTGTGGATAAGCCACCAA
Found at i:21593847 original size:24 final size:24
Alignment explanation
Indices: 21593820--21593912 Score: 102
Period size: 24 Copynumber: 3.9 Consensus size: 24
21593810 CTTTTTCCTT
21593820 TTTTAATTTTTATTCTCTCATCTA
1 TTTTAATTTTTATTCTCTCATCTA
* **
21593844 TTTT-ATTTCTT-TTATGAACA-CTA
1 TTTTAATTT-TTATTCT-CTCATCTA
* *
21593867 ATTCAATTTTTATTCTCTCATCTA
1 TTTTAATTTTTATTCTCTCATCTA
21593891 TTTTAATTTTTATTCTCTCATC
1 TTTTAATTTTTATTCTCTCATC
21593913 CATTAAATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
23 16 0.30
24 38 0.70
ACGTcount: A:0.23, C:0.17, G:0.01, T:0.59
Consensus pattern (24 bp):
TTTTAATTTTTATTCTCTCATCTA
Found at i:21593918 original size:22 final size:23
Alignment explanation
Indices: 21593871--21593922 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
21593861 ACACTAATTC
*
21593871 AATTTTTATTCTCTCATCTATTTT
1 AATTTTTATTCTCTCATCCA-TTT
*
21593895 AATTTTTATTCTCTCATCCATTA
1 AATTTTTATTCTCTCATCCATTT
21593918 AATTT
1 AATTT
21593923 AGAAGTGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (23 bp):
AATTTTTATTCTCTCATCCATTT
Found at i:21598486 original size:50 final size:49
Alignment explanation
Indices: 21598393--21598588 Score: 169
Period size: 50 Copynumber: 3.9 Consensus size: 49
21598383 CTTTCTGTAC
* * * * **
21598393 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTTCCAGACATGGTCTTA-ATGGGACCTCTCATATCGG
* * * * *
21598443 TGCCCATGCCATGTTCCAGACATGGTCTTAAGGGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTTCCAGACATGGTCTTAA-TGGGACCTCTCATATCGG
* * * * * * *
21598493 TGCCAACGCCGTG-TCTCAAATATGGTTTTCCATGGGACCTGTCATCTCGG
1 TGCCAACGCCATGTTC-CAGACATGGTCTT-AATGGGACCTCTCATATCGG
*
21598543 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAACGCCATGTTCCAGACATGGTCTTA-ATGGGACCTCTCATA
21598589 ATCTCAATGA
Statistics
Matches: 114, Mismatches: 27, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
49 3 0.03
50 109 0.96
51 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (49 bp):
TGCCAACGCCATGTTCCAGACATGGTCTTAATGGGACCTCTCATATCGG
Found at i:21604110 original size:50 final size:50
Alignment explanation
Indices: 21604052--21604245 Score: 169
Period size: 50 Copynumber: 3.9 Consensus size: 50
21604042 TATTAAGGTT
* * *
21604052 ATGAGAGGTCCCATGTAAGACCATGCCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
* * * * * *
21604102 ATGAGAGGTTCCC-CGCAAGACTATGTCTGGGACATGGCATAGGCACCTAT
1 ATGAGAGG-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
** * * * *
21604152 ATGAGAACTCTCATGTAAGACCATATCTGGGATATGGTATTGGCA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * ** *
21604201 AGGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
21604246 TTTTATTATC
Statistics
Matches: 112, Mismatches: 29, Indels: 7
0.76 0.20 0.05
Matches are distributed among these distances:
49 40 0.36
50 68 0.61
51 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:21609061 original size:40 final size:39
Alignment explanation
Indices: 21609017--21609457 Score: 435
Period size: 40 Copynumber: 11.1 Consensus size: 39
21609007 ATTCTATTTG
* *
21609017 ATTCAGGGTTACC-AGAGTATAAACAGTGGCACGTAAGTGC
1 ATTCAGGGGTACCGA-AGTACAAACAG-GGCACGTAAGTGC
* *
21609057 ATTCAGGGGTACCGAAGTACAAACAAGGGAAC-AAATGTGC
1 ATTCAGGGGTACCGAAGTACAAAC-AGGGCACGTAA-GTGC
* *
21609097 AATCAGGGGTATCGAAGTACAAACAGGCGCACGTAAGTGC
1 ATTCAGGGGTACCGAAGTACAAACAGG-GCACGTAAGTGC
* * *
21609137 ATCCAGGGGTACTGAAGTACAAACAGAGGCACGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACAG-GGCACGTAAGTGC
* * *
21609177 AATCAGGGGTATCGAAGTAC-AACAGGGGCACTTAAGTGC
1 ATTCAGGGGTACCGAAGTACAAACA-GGGCACGTAAGTGC
* * * * *
21609216 ATTCAGGGGTACCAAACTACAAACAAGGGCATGTATGTCC
1 ATTCAGGGGTACCGAAGTACAAAC-AGGGCACGTAAGTGC
* * * *
21609256 AATCAGGGGTATCAAAGTAC-AACTAGGGCATGTAAGTGC
1 ATTCAGGGGTACCGAAGTACAAAC-AGGGCACGTAAGTGC
*
21609295 ATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACA-GGGCACGTAAGTGC
* * *
21609335 AGTCAAGGGTACCGAAGTAC-AACAGGGGCACGTAAGTGT
1 ATTCAGGGGTACCGAAGTACAAACA-GGGCACGTAAGTGC
* *
21609374 AGTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGC
1 ATTCAGGGGTACCGAAGTACAAACA-GGGCACGTAAGTGC
* * * * *
21609414 AATCAAGGGTATCGAAGTA-TAATAGAGGCACGTAAGTGC
1 ATTCAGGGGTACCGAAGTACAAACAG-GGCACGTAAGTGC
21609453 ATTCA
1 ATTCA
21609458 TACAATAATT
Statistics
Matches: 336, Mismatches: 52, Indels: 27
0.81 0.13 0.07
Matches are distributed among these distances:
38 1 0.00
39 125 0.37
40 203 0.60
41 7 0.02
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.18
Consensus pattern (39 bp):
ATTCAGGGGTACCGAAGTACAAACAGGGCACGTAAGTGC
Found at i:21609252 original size:79 final size:79
Alignment explanation
Indices: 21609038--21609457 Score: 574
Period size: 79 Copynumber: 5.3 Consensus size: 79
21609028 CCAGAGTATA
* * **
21609038 AACAGTGGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAACAAGGGAACAAATGTGCAATCAG
1 AACAGGGGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCAATCAG
21609103 GGGTATCGAAGTAC
66 GGGTATCGAAGTAC
* * *
21609117 AAACAGGCGCACGTAAGTGCATCCAGGGGTACTGAAGTACAAAC-AGAGGCACGTATGTGCAATC
1 -AACAGGGGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAACAAG-GGCACGTATGTGCAATC
21609181 AGGGGTATCGAAGTAC
64 AGGGGTATCGAAGTAC
* * * * *
21609197 AACAGGGGCACTTAAGTGCATTCAGGGGTACCAAACTACAAACAAGGGCATGTATGTCCAATCAG
1 AACAGGGGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCAATCAG
*
21609262 GGGTATCAAAGTAC
66 GGGTATCGAAGTAC
* * *
21609276 AACTA-GGGCATGTAAGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAGTCA
1 AAC-AGGGGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCAATCA
* *
21609340 AGGGTACCGAAGTAC
65 GGGGTATCGAAGTAC
* * * *
21609355 AACAGGGGCACGTAAGTGTAGTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATCAA
1 AACAGGGGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCAATCAG
*
21609420 GGGTATCGAAGTAT
66 GGGTATCGAAGTAC
* *
21609434 AATAGAGGCACGTAAGTGCATTCA
1 AACAGGGGCACGTAAGTGCATTCA
21609458 TACAATAATT
Statistics
Matches: 299, Mismatches: 37, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
78 1 0.00
79 226 0.76
80 72 0.24
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.18
Consensus pattern (79 bp):
AACAGGGGCACGTAAGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCAATCAG
GGGTATCGAAGTAC
Found at i:21609321 original size:20 final size:20
Alignment explanation
Indices: 21609298--21609402 Score: 72
Period size: 20 Copynumber: 5.3 Consensus size: 20
21609288 TAAGTGCATT
21609298 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * **
21609318 CAGGGGCA-CGTATGTGCAGT
1 CAGGGGTACCG-AAGTACAAA
*
21609338 CAAGGGTACCGAAGTAC-AA
1 CAGGGGTACCGAAGTACAAA
* ** **
21609357 CAGGGGCA-CGTAAGTGTAGT
1 CAGGGGTACCG-AAGTACAAA
21609377 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
21609397 CAGGGG
1 CAGGGG
21609403 CACGTATGTG
Statistics
Matches: 58, Mismatches: 22, Indels: 10
0.64 0.24 0.11
Matches are distributed among these distances:
18 2 0.03
19 12 0.21
20 40 0.69
21 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.35, T:0.13
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:21612186 original size:33 final size:33
Alignment explanation
Indices: 21612138--21612297 Score: 133
Period size: 33 Copynumber: 4.8 Consensus size: 33
21612128 GCATCTATAG
* *
21612138 AGAGAAAGT-CTATCGGAACAGTAAACACAGAAT
1 AGAGAAAGTAC-ATCGGGACAGTAAACACAGAAC
* **
21612171 AGAGATAGTACATCGGGACAGTAAACATGGAAC
1 AGAGAAAGTACATCGGGACAGTAAACACAGAAC
* * * * * *
21612204 AGAAAAATTTCATCGGGACAATAAACACAAAAT
1 AGAGAAAGTACATCGGGACAGTAAACACAGAAC
* * * * ** *
21612237 AGAGATAGTCCACCGAGAGGGTAAACACGGAAC
1 AGAGAAAGTACATCGGGACAGTAAACACAGAAC
*
21612270 AAAGAAAGTACATCGGGACAGTAAACAC
1 AGAGAAAGTACATCGGGACAGTAAACAC
21612298 GAGGCAAGTC
Statistics
Matches: 93, Mismatches: 33, Indels: 2
0.73 0.26 0.02
Matches are distributed among these distances:
33 92 0.99
34 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.14
Consensus pattern (33 bp):
AGAGAAAGTACATCGGGACAGTAAACACAGAAC
Found at i:21612261 original size:66 final size:66
Alignment explanation
Indices: 21612140--21612297 Score: 185
Period size: 66 Copynumber: 2.4 Consensus size: 66
21612130 ATCTATAGAG
* * * * *
21612140 AGAAAGT-CTATCGGAACAGTAAACACAGAATAGAGATAGTACATCGGGACAGTAAACATGGAAC
1 AGAAAGTAC-ATCGGGACAGTAAACACAAAATAGAGATAGTACACCGAGACAGTAAACACGGAAC
21612204 AGA
65 A-A
* * * * **
21612207 A-AAATTTCATCGGGACAATAAACACAAAATAGAGATAGTCCACCGAGAGGGTAAACACGGAACA
1 AGAAAGTACATCGGGACAGTAAACACAAAATAGAGATAGTACACCGAGACAGTAAACACGGAACA
21612271 A
66 A
21612272 AGAAAGTACATCGGGACAGTAAACAC
1 AGAAAGTACATCGGGACAGTAAACAC
21612298 GAGGCAAGTC
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
65 2 0.03
66 72 0.95
67 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (66 bp):
AGAAAGTACATCGGGACAGTAAACACAAAATAGAGATAGTACACCGAGACAGTAAACACGGAACA
A
Found at i:21616150 original size:13 final size:13
Alignment explanation
Indices: 21616132--21616167 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
21616122 TTAGTTTTCT
*
21616132 AAAAACCTTAGTA
1 AAAAACATTAGTA
21616145 AAAAACATTAGTA
1 AAAAACATTAGTA
21616158 AAAAACATTA
1 AAAAACATTA
21616168 CCGATAAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (13 bp):
AAAAACATTAGTA
Found at i:21619899 original size:30 final size:32
Alignment explanation
Indices: 21619848--21619907 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
21619838 TGGGTCGCAT
*
21619848 CCAAAACAGAATCAATTGGGCCT-AGCCCAAA
1 CCAAAACAGAATCAAGTGGGCCTAAGCCCAAA
*
21619879 CCAATACAGAA-CAAGTGGGCCTAAGCCCA
1 CCAAAACAGAATCAAGTGGGCCTAAGCCCA
21619908 GTATAGTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.40, C:0.30, G:0.18, T:0.12
Consensus pattern (32 bp):
CCAAAACAGAATCAAGTGGGCCTAAGCCCAAA
Found at i:21628238 original size:41 final size:40
Alignment explanation
Indices: 21628181--21628455 Score: 309
Period size: 41 Copynumber: 6.6 Consensus size: 40
21628171 GGACCCCGGT
*
21628181 GGAATCACCACTTAGCAACCACCTTATAATCAATGATACGG
1 GGAATCAGCACTTAGCAACC-CCTTATAATCAATGATACGG
* *
21628222 GGAATCAGCACATAGCAACCCCTT-TCACATTCAAGGATACGG
1 GGAATCAGCACTTAGCAACCCCTTAT-A-A-TCAATGATACGG
*
21628264 TGGAATCAGCACTTAGCAACCACTTTATAATCAATGATACGG
1 -GGAATCAGCACTTAGCAACC-CCTTATAATCAATGATACGG
* * * *
21628306 GGAATCAGCACATAGCAACCCCTTTCACAATCAAGGACACGG
1 GGAATCAGCACTTAGCAACCCC-TT-ATAATCAATGATACGG
* *
21628348 TGGAATCAGCACTTAGCAACCACTTTATAATCAATGATACGA
1 -GGAATCAGCACTTAGCAACC-CCTTATAATCAATGATACGG
* * * *
21628390 GGAATCAGCACATAGCAACCCCTTTTTGATCAATGATTCGG
1 GGAATCAGCACTTAGCAACCCC-TTATAATCAATGATACGG
*
21628431 GGAATCTGCACTTAGCAACCCCTTA
1 GGAATCAGCACTTAGCAACCCCTTA
21628456 CATTCAAAGA
Statistics
Matches: 197, Mismatches: 26, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.01
40 9 0.05
41 93 0.47
42 47 0.24
43 41 0.21
44 5 0.03
45 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
GGAATCAGCACTTAGCAACCCCTTATAATCAATGATACGG
Found at i:21628281 original size:84 final size:83
Alignment explanation
Indices: 21628177--21628455 Score: 427
Period size: 84 Copynumber: 3.4 Consensus size: 83
21628167 CAAAGGACCC
*
21628177 CGGTGGAATCACCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
21628242 CCTTTCACATTCAAGGATA
66 CCTTTCACA-TCAAGGATA
*
21628261 CGGTGGAATCAGCACTTAGCAACCACTTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
*
21628326 CCTTTCACAATCAAGGACA
66 CCTTTCAC-ATCAAGGATA
* *
21628345 CGGTGGAATCAGCACTTAGCAACCACTTTATAATCAATGATACGAGGAATCAGCACATAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
*** * *
21628410 CCTTTTTGATCAATGATT
66 CCTTTCACATCAAGGATA
*
21628428 CGG-GGAATCTGCACTTAGCAACC-CCTTA
1 CGGTGGAATCAGCACTTAGCAACCACCTTA
21628456 CATTCAAAGA
Statistics
Matches: 182, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
81 4 0.02
82 19 0.10
83 10 0.05
84 148 0.81
85 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (83 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACC
CCTTTCACATCAAGGATA
Found at i:21628399 original size:125 final size:125
Alignment explanation
Indices: 21628181--21628462 Score: 347
Period size: 125 Copynumber: 2.3 Consensus size: 125
21628171 GGACCCCGGT
* * * * *
21628181 GGAATCACCACTTAGCAACCACC-TTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
1 GGAATCAGCACTTAGCAACC-CCTTTACAATCAAGGACACGGGGAATCAGCACATAGCAACCACT
* * *
21628245 TTCACATTCAAGGATACGGTGGAATCAGCACTTAGCAACCACTTTATAATCAATGATACGG
65 TTCACAATCAAGGATACGGAGGAATCAGCACATAGCAACCACTTTATAATCAATGATACGG
* *
21628306 GGAATCAGCACATAGCAACCCCTTTCACAATCAAGGACACGGTGGAATCAGCACTTAGCAACCAC
1 GGAATCAGCACTTAGCAACCCCTTT-ACAATCAAGGACACGG-GGAATCAGCACATAGCAACCAC
* * * * * *
21628371 TTT-ATAATCAATGATAC-GAGGAATCAGCACATAGCAACCCCTTTTTGATCAATGATTCGG
64 TTTCACAATCAAGGATACGGAGGAATCAGCACATAGCAACCACTTTATAATCAATGATACGG
* *
21628431 GGAATCTGCACTTAGCAACCCC-TTACATTCAA
1 GGAATCAGCACTTAGCAACCCCTTTACAATCAA
21628463 AGAATCCCAA
Statistics
Matches: 135, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
123 7 0.05
124 4 0.03
125 77 0.57
126 24 0.18
127 23 0.17
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (125 bp):
GGAATCAGCACTTAGCAACCCCTTTACAATCAAGGACACGGGGAATCAGCACATAGCAACCACTT
TCACAATCAAGGATACGGAGGAATCAGCACATAGCAACCACTTTATAATCAATGATACGG
Found at i:21649113 original size:17 final size:18
Alignment explanation
Indices: 21649074--21649114 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
21649064 TTTTATAAAT
21649074 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGATA
21649092 TGTGAATTA-ATATTGA-A
1 TGTGAATTATAT-TTGATA
21649109 TGTGAA
1 TGTGAA
21649115 AAGAAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.44
Consensus pattern (18 bp):
TGTGAATTATATTTGATA
Found at i:21649369 original size:23 final size:23
Alignment explanation
Indices: 21649338--21649413 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
21649328 AGTGTTATTG
*
21649338 ATCAGTGGTAGCTTCGGCCACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
21649361 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
21649384 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
21649407 ATCAGTG
1 ATCAGTG
21649414 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:21650622 original size:50 final size:51
Alignment explanation
Indices: 21650496--21650626 Score: 162
Period size: 51 Copynumber: 2.6 Consensus size: 51
21650486 TGCCTATAAA
* * *
21650496 CACGTGTGTAGTACTAAGTGCAGGCTACT-TCGTGTATCGATAGATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTATCGTGTACCGAAAGAT-ATGGT
*
21650547 CACATGTGTAGTACTATGTGCAGGCTACTAT-GTGTACCGGAAAG-T-TGGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTATCGTGTACC-GAAAGATATGG-T
*
21650597 CACGTGTGTAGTACTATGTGAAGGCTACTA
1 CACGTGTGTAGTACTATGTGCAGGCTACTA
21650627 CGTATTGAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
49 3 0.04
50 29 0.41
51 34 0.48
52 5 0.07
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTATCGTGTACCGAAAGATATGGT
Found at i:21654203 original size:12 final size:12
Alignment explanation
Indices: 21654186--21654212 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21654176 TAGCATTTAT
21654186 TATTGTATGTTG
1 TATTGTATGTTG
21654198 TATTGTATGTTG
1 TATTGTATGTTG
21654210 TAT
1 TAT
21654213 CAAATGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (12 bp):
TATTGTATGTTG
Found at i:21663539 original size:44 final size:44
Alignment explanation
Indices: 21663491--21663585 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
21663481 ATATCTCAAG
*
21663491 GTCCATGTTTATAACATGGCAATTAAGGAAGAATTGACGAAAAA
1 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGAAAAA
*
21663535 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
1 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGAAAAA
*
21663579 GACCATG
1 GTCCATG
21663586 GTTGGACCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (44 bp):
GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGAAAAA
Found at i:21663700 original size:30 final size:30
Alignment explanation
Indices: 21663664--21663723 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
21663654 GAGTGCCTGT
*
21663664 GTAAGACCATGTCTGGGACATGGCTTCGGC
1 GTAAGACCATGTCTGGGACATGGCATCGGC
21663694 GTAAGACCATGTCTGGGACATGGCATCGGC
1 GTAAGACCATGTCTGGGACATGGCATCGGC
21663724 ACAGACTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.23, G:0.33, T:0.22
Consensus pattern (30 bp):
GTAAGACCATGTCTGGGACATGGCATCGGC
Found at i:21663707 original size:80 final size:80
Alignment explanation
Indices: 21663614--21663773 Score: 268
Period size: 80 Copynumber: 2.0 Consensus size: 80
21663604 GTGTGCCAGT
21663614 GTAAGACCATGTCTAGGACATGGCATCGGCACAGACCGAGGAGTGCCT-GTGTAAGACCATGTCT
1 GTAAGACCATGTCTAGGACATGGCATCGGCACAGACCGAGGAGTG-CTAGTGTAAGACCATGTCT
*
21663678 GGGACATGGCTTCGGC
65 GGGACATGGCATCGGC
* * *
21663694 GTAAGACCATGTCTGGGACATGGCATCGGCACAGACTGGGGAGTGCTAGTGTAAGACCATGTCTG
1 GTAAGACCATGTCTAGGACATGGCATCGGCACAGACCGAGGAGTGCTAGTGTAAGACCATGTCTG
21663759 GGACATGGCATCGGC
66 GGACATGGCATCGGC
21663774 ACGGACAAAG
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
79 2 0.03
80 73 0.97
ACGTcount: A:0.24, C:0.23, G:0.34, T:0.20
Consensus pattern (80 bp):
GTAAGACCATGTCTAGGACATGGCATCGGCACAGACCGAGGAGTGCTAGTGTAAGACCATGTCTG
GGACATGGCATCGGC
Found at i:21663748 original size:50 final size:50
Alignment explanation
Indices: 21663694--21663823 Score: 179
Period size: 50 Copynumber: 2.6 Consensus size: 50
21663684 TGGCTTCGGC
*** * *
21663694 GTAAGACCATGTCTGGGACATGGCATCGGCACAGACTGGGGAGTGCTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCACAGACAAAGAAGAGCTAGT
* *
21663744 GTAAGACCATGTCTGGGACATGGCATCGGCACGGACAAAGAAGAGTTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCACAGACAAAGAAGAGCTAGT
* *
21663794 ATAAGACCATGTTTGGGACATGGCATCGGC
1 GTAAGACCATGTCTGGGACATGGCATCGGC
21663824 TAGAGATGTG
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCACAGACAAAGAAGAGCTAGT
Found at i:21673540 original size:26 final size:27
Alignment explanation
Indices: 21673499--21673549 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
21673489 CAAACAGATC
*
21673499 CCAAATACCCACTTAACCTAGCCCAAA
1 CCAAATACCCAATTAACCTAGCCCAAA
21673526 CCAAA-ACCCAATTAACCTAGCCCA
1 CCAAATACCCAATTAACCTAGCCCA
21673550 GCTAATGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.41, C:0.41, G:0.04, T:0.14
Consensus pattern (27 bp):
CCAAATACCCAATTAACCTAGCCCAAA
Found at i:21679511 original size:6 final size:6
Alignment explanation
Indices: 21679500--21679580 Score: 74
Period size: 6 Copynumber: 13.7 Consensus size: 6
21679490 AATTCAAAAA
* * ** **
21679500 AAAATC AAAATC AAAATC AAAATC AAAAAC AAAAT- AGAAGA AAAAGA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
* * *
21679547 AAAATC AAAATC AAAGTC AAAATG AAAATG AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
21679581 AAGAGAGAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
5 3 0.05
6 61 0.95
ACGTcount: A:0.70, C:0.10, G:0.07, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:21679575 original size:41 final size:39
Alignment explanation
Indices: 21679497--21679582 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 39
21679487 TCCAATTCAA
**
21679497 AAAAAAATCAAAATCAAAATCAAAATCAAAAACAAAATAG
1 AAAAAAAGAAAAATCAAAATCAAAATCAAAAACAAAAT-G
* **
21679537 AAGAAAAAGAAAAATCAAAATCAAAGTCAAAATGAAAATG
1 AA-AAAAAGAAAAATCAAAATCAAAATCAAAAACAAAATG
21679577 AAAAAA
1 AAAAAA
21679583 GAGAGAAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 4 0.10
40 5 0.12
41 31 0.77
ACGTcount: A:0.72, C:0.09, G:0.07, T:0.12
Consensus pattern (39 bp):
AAAAAAAGAAAAATCAAAATCAAAATCAAAAACAAAATG
Found at i:21679597 original size:47 final size:46
Alignment explanation
Indices: 21679495--21679589 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 46
21679485 GATCCAATTC
*
21679495 AAAAAAAAATCAAAATCAAAATCAAAATCAAAAACAAAATAGAAGA
1 AAAAAAAAATCAAAATCAAAATCAAAATCAAAAACAAAAAAGAAGA
* * **
21679541 AAAAGAAAAATCAAAATCAAAGTCAAAATGAAAATGAAAAAAGAGAGA
1 AAAA-AAAAATCAAAATCAAAATCAAAATCAAAAACAAAAAAGA-AGA
21679589 A
1 A
21679590 GGAAAAAAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
46 4 0.10
47 34 0.81
48 4 0.10
ACGTcount: A:0.72, C:0.08, G:0.09, T:0.11
Consensus pattern (46 bp):
AAAAAAAAATCAAAATCAAAATCAAAATCAAAAACAAAAAAGAAGA
Found at i:21679613 original size:7 final size:8
Alignment explanation
Indices: 21679588--21679612 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
21679578 AAAAAGAGAG
21679588 AAGGAAAA
1 AAGGAAAA
21679596 AAGGAAAA
1 AAGGAAAA
21679604 AAGGAAAA
1 AAGGAAAA
21679612 A
1 A
21679613 GAAAAGGCGA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AAGGAAAA
Found at i:21680480 original size:8 final size:8
Alignment explanation
Indices: 21680461--21680512 Score: 65
Period size: 9 Copynumber: 6.6 Consensus size: 8
21680451 CTTTGAGTAA
21680461 AAAAAATG
1 AAAAAATG
21680469 -AAAAATG
1 AAAAAATG
21680476 AAAAAAATG
1 -AAAAAATG
21680485 --AAAATG
1 AAAAAATG
21680491 AAAAAATG
1 AAAAAATG
21680499 AAAAAAATG
1 -AAAAAATG
21680508 AAAAA
1 AAAAA
21680513 GTAAAAATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.15
7 7 0.18
8 11 0.28
9 15 0.38
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:21680481 original size:16 final size:16
Alignment explanation
Indices: 21680460--21680503 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 16
21680450 ACTTTGAGTA
21680460 AAAAAAATGAAAAATG
1 AAAAAAATGAAAAATG
21680476 AAAAAAATG-AAAATG
1 AAAAAAATGAAAAATG
21680491 -AAAAAATGAAAAA
1 AAAAAAATGAAAAA
21680504 AATGAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.30
15 10 0.37
16 9 0.33
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAAAATGAAAAATG
Found at i:21680488 original size:23 final size:24
Alignment explanation
Indices: 21680462--21680523 Score: 94
Period size: 23 Copynumber: 2.7 Consensus size: 24
21680452 TTTGAGTAAA
21680462 AAAAATG-AAAAATGAAAAAAATG
1 AAAAATGAAAAAATGAAAAAAATG
21680485 AA-AATGAAAAAATGAAAAAAATG
1 AAAAATGAAAAAATGAAAAAAATG
*
21680508 AAAAA-GTAAAAATGAA
1 AAAAATGAAAAAATGAA
21680524 GAAGAGGCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 4 0.11
23 30 0.83
24 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (24 bp):
AAAAATGAAAAAATGAAAAAAATG
Found at i:21680518 original size:14 final size:15
Alignment explanation
Indices: 21680469--21680523 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
21680459 AAAAAAAATG
*
21680469 AAAAATGAAAAAAAT
1 AAAAATGAAAAAAGT
* *
21680484 GAAAATGAAAAAATGAA
1 AAAAATGAAAAAA-G-T
21680501 AAAAATG-AAAAAGT
1 AAAAATGAAAAAAGT
21680515 AAAAATGAA
1 AAAAATGAA
21680524 GAAGAGGCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 7 0.22
15 14 0.44
16 5 0.16
17 6 0.19
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAATGAAAAAAGT
Found at i:21682899 original size:12 final size:14
Alignment explanation
Indices: 21682876--21682915 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
21682866 GGATATCAAG
21682876 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
*
21682890 AT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
21682903 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
21682916 GAGAGCTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:21689910 original size:129 final size:129
Alignment explanation
Indices: 21689680--21690121 Score: 760
Period size: 129 Copynumber: 3.4 Consensus size: 129
21689670 TCAGTGAAAT
* *
21689680 CACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATATCCCTGGTAAGTAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAA
* * *
21689745 GCAGTAGCGGAGCAGATCAAAGACAGCGAATCTTATCTTCAAGTGTAACGAAGCAGATTTAAGC
66 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
* *
21689809 CACAAGTCCTATATCCCTGGTAAGAAGTGGAATATGTTGGGAAATTACAGATCTTGTCTCCCTAA
1 CACAAGTCCTATATCCCTGGTAAGTAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAA
21689874 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
66 GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
*
21689938 CACAAGTCCTATATCCCTGGTCAA-TAGTAGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTA
1 CACAAGTCCTATATCCCTGGT-AAGTAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTA
*
21690002 AGCAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
65 AGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
* * *
21690067 CACAAGTCCTATATCCCTGGTTAGTAGTGGAATAGGTTGGGAAATTGCAGGTCTT
1 CACAAGTCCTATATCCCTGGTAAGTAGTGGAATAGGTTGGGAAATTACAGATCTT
21690122 ATCCCCCTGA
Statistics
Matches: 297, Mismatches: 14, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
128 1 0.00
129 294 0.99
130 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (129 bp):
CACAAGTCCTATATCCCTGGTAAGTAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAA
GCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
Found at i:21690564 original size:10 final size:10
Alignment explanation
Indices: 21690551--21690607 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
21690541 AGCTCTGACC
21690551 AGCTCAATTG
1 AGCTCAATTG
* *
21690561 AGCTCATTTC
1 AGCTCAATTG
*
21690571 AGCTCAATCG
1 AGCTCAATTG
21690581 AGCTCAATTG
1 AGCTCAATTG
*
21690591 AGCTACAATTC
1 AGCT-CAATTG
21690602 AGCTCA
1 AGCTCA
21690608 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 30 0.77
11 9 0.23
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (10 bp):
AGCTCAATTG
Found at i:21690571 original size:30 final size:30
Alignment explanation
Indices: 21690531--21690607 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
21690521 NNNNNNNNNT
* *
21690531 AGCTCGTTTCAGCTCTGA-CCAGCTCAATTG
1 AGCTCATTTCAGCTC-AATCCAGCTCAATTG
*
21690561 AGCTCATTTCAGCTCAATCGAGCTCAATTG
1 AGCTCATTTCAGCTCAATCCAGCTCAATTG
*
21690591 AGCTACAATTCAGCTCA
1 AGCT-CATTTCAGCTCA
21690608 TTTATTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 1 0.02
30 29 0.71
31 11 0.27
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (30 bp):
AGCTCATTTCAGCTCAATCCAGCTCAATTG
Found at i:21690573 original size:20 final size:20
Alignment explanation
Indices: 21690550--21690610 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
21690540 CAGCTCTGAC
21690550 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
* *
21690570 CAGCTCAATCGAGCTCAATT
1 CAGCTCAATTGAGCTCATTT
* *
21690590 GAGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
21690611 ATTTTATTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:21695240 original size:10 final size:10
Alignment explanation
Indices: 21695227--21695283 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
21695217 AGCTCCGACC
21695227 AGCTCAATTG
1 AGCTCAATTG
* *
21695237 AGCTCATTTC
1 AGCTCAATTG
*
21695247 AGCTCAATCG
1 AGCTCAATTG
21695257 AGCTCAATTG
1 AGCTCAATTG
*
21695267 AGCTACAATTC
1 AGCT-CAATTG
21695278 AGCTCA
1 AGCTCA
21695284 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 30 0.77
11 9 0.23
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (10 bp):
AGCTCAATTG
Found at i:21695241 original size:30 final size:30
Alignment explanation
Indices: 21695207--21695283 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
21695197 TAGCTTTTCT
* *
21695207 AGCTCGTTTCAGCTCCGA-CCAGCTCAATTG
1 AGCTCATTTCAGCT-CAATCCAGCTCAATTG
*
21695237 AGCTCATTTCAGCTCAATCGAGCTCAATTG
1 AGCTCATTTCAGCTCAATCCAGCTCAATTG
*
21695267 AGCTACAATTCAGCTCA
1 AGCT-CATTTCAGCTCA
21695284 TTTATTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 2 0.05
30 28 0.68
31 11 0.27
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (30 bp):
AGCTCATTTCAGCTCAATCCAGCTCAATTG
Found at i:21695249 original size:20 final size:20
Alignment explanation
Indices: 21695226--21695286 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
21695216 CAGCTCCGAC
21695226 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
* *
21695246 CAGCTCAATCGAGCTCAATT
1 CAGCTCAATTGAGCTCATTT
* *
21695266 GAGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
21695287 ATTTTATTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:21702586 original size:21 final size:21
Alignment explanation
Indices: 21702560--21702606 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
21702550 ACTCTAAATT
21702560 GTGTGTCAGATAATTCTTTTC
1 GTGTGTCAGATAATTCTTTTC
*
21702581 GTGTGTCGGATAATTCTTTTC
1 GTGTGTCAGATAATTCTTTTC
21702602 GTGTG
1 GTGTG
21702607 GTTTCAACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.47
Consensus pattern (21 bp):
GTGTGTCAGATAATTCTTTTC
Found at i:21705002 original size:18 final size:19
Alignment explanation
Indices: 21704976--21705012 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
21704966 AATTTTGGAA
*
21704976 TGGATAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
21704994 TGGAAAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
21705013 ATGTGAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.41, T:0.08
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Found at i:21708476 original size:22 final size:22
Alignment explanation
Indices: 21708449--21708491 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
21708439 ATTAGATAGT
21708449 TAAATTAAAATTTACGAGAAAC
1 TAAATTAAAATTTACGAGAAAC
*
21708471 TAAATTAAAATTTAGGAGAAA
1 TAAATTAAAATTTACGAGAAA
21708492 AATTGGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (22 bp):
TAAATTAAAATTTACGAGAAAC
Found at i:21712567 original size:50 final size:51
Alignment explanation
Indices: 21712381--21712571 Score: 158
Period size: 50 Copynumber: 3.8 Consensus size: 51
21712371 GATAATAACA
* * * **
21712381 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTTTCT-GTAC
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCG-AC
* * * * * ** * *
21712430 TGCCAATGTCATATCCCAAATATTGTCTTACATTGGAGTTCTCATATC-AG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGAC
* * * **
21712480 TGCCCATTCTATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGA-
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGAC
*
21712530 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
21712572 TTACCCAAAT
Statistics
Matches: 107, Mismatches: 31, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
49 30 0.28
50 72 0.67
51 5 0.05
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGAC
Found at i:21712939 original size:30 final size:30
Alignment explanation
Indices: 21712904--21712961 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
21712894 TTCTTGACTC
*
21712904 AATTTTGGCAAAATTACAGTTTTGCCCCTA
1 AATTTTGGCAAAATTACACTTTTGCCCCTA
* * *
21712934 AATTTTTGCATATTTACACTTTTGCCCC
1 AATTTTGGCAAAATTACACTTTTGCCCC
21712962 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (30 bp):
AATTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:21720030 original size:50 final size:50
Alignment explanation
Indices: 21719906--21720091 Score: 198
Period size: 50 Copynumber: 3.7 Consensus size: 50
21719896 GATAATAACA
* * * *
21719906 TGCCAAAGCCATGTCCCAGACATGGTCTTATATGGGATGTTTTC-TGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGG
* * *
21719955 TGCCAATGCCATATCCCAGATATGGTCTTACATTGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * ** ** *
21720005 TGCCCATGCTATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
*
21720055 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
21720092 CCTCTTTACC
Statistics
Matches: 112, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
48 6 0.05
49 34 0.30
50 72 0.64
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Found at i:21729732 original size:7 final size:7
Alignment explanation
Indices: 21729701--21729765 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
21729691 ACCAATTAAT
21729701 CTAAACCC
1 CTAAA-CC
21729709 CT-AACC
1 CTAAACC
*
21729715 CTAATCTC
1 CTAAAC-C
21729723 CTAAACC
1 CTAAACC
*
21729730 CTAAATC
1 CTAAACC
* *
21729737 ATAAAAC
1 CTAAACC
*
21729744 ATAAACC
1 CTAAACC
*
21729751 CTAACCC
1 CTAAACC
21729758 CTAAACC
1 CTAAACC
21729765 C
1 C
21729766 ATGACCCCTA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
6 4 0.09
7 34 0.74
8 8 0.17
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:21730178 original size:14 final size:14
Alignment explanation
Indices: 21730161--21730205 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
21730151 TCTTAACCTC
21730161 TAACCCCTAACCCT
1 TAACCCCTAACCCT
*
21730175 TAACCCCTAAACCT
1 TAACCCCTAACCCT
*
21730189 TAAATCCC-AACCCT
1 T-AACCCCTAACCCT
21730203 TAA
1 TAA
21730206 ACCATAATCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 20 0.74
15 5 0.19
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (14 bp):
TAACCCCTAACCCT
Found at i:21730200 original size:21 final size:21
Alignment explanation
Indices: 21730176--21730256 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
21730166 CCTAACCCTT
*
21730176 AACCCCTAAACCTTAAATCCC
1 AACCCTTAAACCTTAAATCCC
*
21730197 AACCCTTAAACCAT-AATCCC
1 AACCCTTAAACCTTAAATCCC
* * * *
21730217 TAATCCATAATCCCTAAAT-CC
1 -AACCCTTAAACCTTAAATCCC
21730238 ATACTCCTTAAACCTTAAA
1 A-AC-CCTTAAACCTTAAA
21730257 ATATGAACTC
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 7 0.15
21 25 0.54
22 14 0.30
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.25
Consensus pattern (21 bp):
AACCCTTAAACCTTAAATCCC
Found at i:21730249 original size:15 final size:15
Alignment explanation
Indices: 21730186--21730249 Score: 62
Period size: 14 Copynumber: 4.5 Consensus size: 15
21730176 AACCCCTAAA
* *
21730186 CCTTAAATCC-CAAC
1 CCTTAAATCCATAAT
21730200 CCTTAAA-CCATAAT
1 CCTTAAATCCATAAT
*
21730214 CCCT-AATCCATAAT
1 CCTTAAATCCATAAT
* *
21730228 CCCTAAATCCATACT
1 CCTTAAATCCATAAT
21730243 CCTTAAA
1 CCTTAAA
21730250 CCTTAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
13 4 0.10
14 23 0.55
15 15 0.36
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.27
Consensus pattern (15 bp):
CCTTAAATCCATAAT
Found at i:21730417 original size:8 final size:7
Alignment explanation
Indices: 21730392--21730510 Score: 57
Period size: 7 Copynumber: 16.7 Consensus size: 7
21730382 AATAATTAAT
21730392 CTAAACC
1 CTAAACC
21730399 CTAAACC
1 CTAAACC
21730406 CTAAATCC
1 CTAAA-CC
21730414 CT-AACTC
1 CTAAAC-C
* *
21730421 TTAACCC
1 CTAAACC
***
21730428 CTAATGT
1 CTAAACC
21730435 CT-AACC
1 CTAAACC
21730441 CTTAAACC
1 C-TAAACC
21730449 TCTAAACC
1 -CTAAACC
21730457 CTAAACC
1 CTAAACC
*
21730464 TTAAATCC
1 CTAAA-CC
21730472 C--AACC
1 CTAAACC
21730477 CTTAAACC
1 C-TAAACC
* *
21730485 ATAATCC
1 CTAAACC
*
21730492 CTAATCC
1 CTAAACC
* *
21730499 ATAATCC
1 CTAAACC
21730506 CTAAA
1 CTAAA
21730511 TCCATACTCC
Statistics
Matches: 85, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
5 3 0.04
6 5 0.06
7 54 0.64
8 22 0.26
9 1 0.01
ACGTcount: A:0.38, C:0.37, G:0.01, T:0.24
Consensus pattern (7 bp):
CTAAACC
Found at i:21730500 original size:14 final size:14
Alignment explanation
Indices: 21730483--21730524 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
21730473 AACCCTTAAA
21730483 CCATAATCCCTAAT
1 CCATAATCCCTAAT
21730497 CCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
21730512 CCATACTCCCTAA
1 CCATAATCCCTAA
21730525 ACCTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:21730514 original size:15 final size:15
Alignment explanation
Indices: 21730479--21730525 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
21730469 TCCCAACCCT
21730479 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
21730493 T-AATCCATAATCCC
1 TAAATCCATAATCCC
*
21730507 TAAATCCATACTCCC
1 TAAATCCATAATCCC
21730522 TAAA
1 TAAA
21730526 CCTTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 2 0.07
14 12 0.40
15 16 0.53
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:21730763 original size:23 final size:25
Alignment explanation
Indices: 21730736--21730790 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
21730726 TAAATGATAG
*
21730736 TATTTTAATT-TTTCCATGTGT-TT
1 TATTTTAATTATTTCCATGTGTCAT
* *
21730759 TATTTCAAATTATTTCTATGTGTCAT
1 TATTT-TAATTATTTCCATGTGTCAT
21730785 TATTTT
1 TATTTT
21730791 GTTCTGAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 5 0.20
24 4 0.16
25 10 0.40
26 6 0.24
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.62
Consensus pattern (25 bp):
TATTTTAATTATTTCCATGTGTCAT
Found at i:21730976 original size:41 final size:40
Alignment explanation
Indices: 21730875--21731109 Score: 238
Period size: 41 Copynumber: 5.8 Consensus size: 40
21730865 TAAAATGTTT
* * * * * *
21730875 TTAGTGGCGCTTTTTCAAAAACGCCACTAAAGCCCCAACA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCGAGCA
** * * *
21730915 TTAGCGGCGCTTTTCCAAAAATGCTGCTAAAGCCCTGAGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCC-GAGCA
* *
21730956 TTAGTGGCGCTTTCTAAAAAACGCCGCTAAAACCCCGAGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAA-CCCGAGCA
* * *
21730997 TTAGTGGTGCTTTCTAAAAAACGCCGCTAAAACCCCGAGCA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAA-CCCGAGCA
*
21731038 TTAGCGGC-ATTTTTAAAAAAACGCCGCTAAAACACCGAGCA
1 TTAGCGGCGCTTTTT-AAAAAACGCCGCTAAAAC-CCGAGCA
* * *
21731079 TTAGCGGCGCTTTTTTAAAAATGCTGCTAAA
1 TTAGCGGCGCTTTTTAAAAAACGCCGCTAAA
21731110 GCCCCTAGCA
Statistics
Matches: 167, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
40 35 0.21
41 124 0.74
42 8 0.05
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (40 bp):
TTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCCGAGCA
Found at i:21731057 original size:82 final size:81
Alignment explanation
Indices: 21730891--21731119 Score: 264
Period size: 82 Copynumber: 2.8 Consensus size: 81
21730881 GCGCTTTTTC
* * * * *
21730891 AAAAACGCCACTAAAGCCCC-AACATTAGCGGCGCTTTTCCAAAAATGCTGCTAAAGCCCTGAGC
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTT-AAAAAATGCTGCTAAAGCCCCGAGC
* *
21730955 ATTAGTGGCGCTTTCTA
65 ATTAGCGGCGATTTCTA
* * * * *
21730972 AAAAACGCCGCTAAAACCCCGAGCATTAGTGGTGCTTTCTAAAAAACGCCGCTAAAACCCCGAGC
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTT-TAAAAAATGCTGCTAAAGCCCCGAGC
*
21731037 ATTAGCGGC-ATTTTTAA
65 ATTAGCGGCGATTTCT-A
* * *
21731054 AAAAACGCCGCTAAAACACCGAGCATTAGCGGCGCTTTTTTAAAAATGCTGCTAAAGCCCCTAGC
1 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGC-TTTTAAAAAATGCTGCTAAAGCCCCGAGC
21731119 A
65 A
21731120 CAAAAACGCC
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
81 22 0.18
82 97 0.79
83 4 0.03
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (81 bp):
AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTAAAAAATGCTGCTAAAGCCCCGAGCA
TTAGCGGCGATTTCTA
Found at i:21731125 original size:26 final size:26
Alignment explanation
Indices: 21731095--21731145 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
21731085 GCGCTTTTTT
* * * *
21731095 AAAAATGCTGCTAAAGCCCCTAGCAC
1 AAAAACGCCGCTAAAACCCCCAGCAC
21731121 AAAAACGCCGCTAAAACCCCCAGCA
1 AAAAACGCCGCTAAAACCCCCAGCA
21731146 TTAGCGACGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.35, G:0.14, T:0.10
Consensus pattern (26 bp):
AAAAACGCCGCTAAAACCCCCAGCAC
Found at i:21731166 original size:41 final size:41
Alignment explanation
Indices: 21731120--21731306 Score: 203
Period size: 41 Copynumber: 4.6 Consensus size: 41
21731110 GCCCCTAGCA
* *
21731120 CAAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTTT
1 CAAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTT
* * * * *
21731161 AAAAAATGCTGCTAAAACACCGAACATTAGCGGCGCTTTTT
1 CAAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTT
* * * * *
21731202 CAAAAACACCGTTAAAACCCCAAGCATTAGAGGCGCATTTT
1 CAAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTT
* * *
21731243 CAAAAACGCAGCTAAAGCCCCGAGCATTAGCTGCGCTTTTT
1 CAAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTT
** * *
21731284 TGAAAACGCCGCCAAAGCCCCGA
1 CAAAAACGCCGCTAAAACCCCGA
21731307 AAGGTAAGAA
Statistics
Matches: 117, Mismatches: 29, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 117 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAAACGCCGCTAAAACCCCGAGCATTAGCGGCGCTTTTT
Found at i:21731207 original size:108 final size:108
Alignment explanation
Indices: 21731013--21731207 Score: 313
Period size: 108 Copynumber: 1.8 Consensus size: 108
21731003 GTGCTTTCTA
* *
21731013 AAAAACGCCGCTAAAACCCCGAGCATTAGCGGCATTTTTAAAAAAACGCCGCTAAAACACCGAGC
1 AAAAACGCCGCTAAAACCCCCAGCATTAGCGGCATTTTTAAAAAAACGCCGCTAAAACACCGAAC
*
21731078 ATTAGCGGCGCTTTTTTAAAAATGCTGCTAAAGCCCCTAGCAC
66 ATTAGCGGCGCTTTTTCAAAAATGCTGCTAAAGCCCCTAGCAC
* *
21731121 AAAAACGCCGCTAAAACCCCCAGCATTAGCGACGC-TTTTT-AAAAAATGCTGCTAAAACACCGA
1 AAAAACGCCGCTAAAACCCCCAGCATTAGCG--GCATTTTTAAAAAAACGCCGCTAAAACACCGA
21731184 ACATTAGCGGCGCTTTTTCAAAAA
64 ACATTAGCGGCGCTTTTTCAAAAA
21731208 CACCGTTAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
108 73 0.91
109 5 0.06
110 2 0.03
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.20
Consensus pattern (108 bp):
AAAAACGCCGCTAAAACCCCCAGCATTAGCGGCATTTTTAAAAAAACGCCGCTAAAACACCGAAC
ATTAGCGGCGCTTTTTCAAAAATGCTGCTAAAGCCCCTAGCAC
Found at i:21731248 original size:149 final size:149
Alignment explanation
Indices: 21730972--21731268 Score: 389
Period size: 149 Copynumber: 2.0 Consensus size: 149
21730962 GCGCTTTCTA
* * ** * *
21730972 AAAAACGCCGCTAAAACCCCGAGCATTAGTGGTGCTTTCTAAAAAACGCCGCTAAAACCCCGAGC
1 AAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAAC
* * * * * *
21731037 ATTAGCGGCATTTTTAAAAAAACGCCGCTAAAACACCGAGCATTAGCGGCGCTTTTTTAAAAATG
66 ATTAGCGGCATTTTTAAAAAAACACCGCTAAAACACCAAGCATTAGAGGCGCATTTTCAAAAACG
* *
21731102 CTGCTAAAGCCCCTAGCAC
131 CAGCTAAAGCCCCGAGCAC
* * *
21731121 AAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTTTAAAAAATGCTGCTAAAACACCGAAC
1 AAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAAC
* * * *
21731186 ATTAGCGGCGCTTTTT-CAAAAACACCGTTAAAACCCCAAGCATTAGAGGCGCATTTTCAAAAAC
66 ATTAGCGGC-ATTTTTAAAAAAACACCGCTAAAACACCAAGCATTAGAGGCGCATTTTCAAAAAC
21731250 GCAGCTAAAGCCCCGAGCA
130 GCAGCTAAAGCCCCGAGCA
21731269 TTAGCTGCGC
Statistics
Matches: 126, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
149 121 0.96
150 5 0.04
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (149 bp):
AAAAACGCCGCTAAAACCCCCAGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAAC
ATTAGCGGCATTTTTAAAAAAACACCGCTAAAACACCAAGCATTAGAGGCGCATTTTCAAAAACG
CAGCTAAAGCCCCGAGCAC
Found at i:21731281 original size:190 final size:190
Alignment explanation
Indices: 21730952--21731304 Score: 458
Period size: 190 Copynumber: 1.9 Consensus size: 190
21730942 TAAAGCCCTG
* * * * * *
21730952 AGCATTAGTGGCGCTTTCTAAAAAACGCCGCTAAAACCCCGAGCATTAGTGGTGCTTTCTAAAAA
1 AGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAACATTAGCGGCGCTTTCTAAAAA
* * *
21731017 ACGCCGCTAAAACCCCGAGCATTAGCGGCATTTTTAAAAAAACGCCGCTAAAACACCGAGCATTA
66 ACACCGCTAAAACCCCAAGCATTAGCGGCATTTTTAAAAAAACGCAGCTAAAACACCGAGCATTA
* * *
21731082 GCGGCGCTTTTTTAAAAATGCTGCTAAAGCCCCTAGCACAAAAACGCCGCTAAAACCCCC
131 GCGGCGCTTTTTTAAAAACGCCGCCAAAGCCCCTAGCACAAAAACGCCGCTAAAACCCCC
* * * * *
21731142 AGCATTAGCGACGCTTTTTAAAAAATGCTGCTAAAACACCGAACATTAGCGGCGCTTTTTCAAAA
1 AGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAACATTAGCGGCGCTTTCTAAAAA
* * * * *
21731207 ACACCGTTAAAACCCCAAGCATTAGAGGCGCA-TTTT-CAAAAACGCAGCTAAAGCCCCGAGCAT
66 ACACCGCTAAAACCCCAAGCATTAG-CG-GCATTTTTAAAAAAACGCAGCTAAAACACCGAGCAT
* *
21731270 TAGCTGCGCTTTTTTGAAAACGCCGCCAAAGCCCC
129 TAGCGGCGCTTTTTTAAAAACGCCGCCAAAGCCCC
21731305 GAAAGGTAAG
Statistics
Matches: 137, Mismatches: 24, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
190 129 0.94
191 5 0.04
192 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (190 bp):
AGCATTAGCGACGCTTTCTAAAAAACGCCGCTAAAACACCGAACATTAGCGGCGCTTTCTAAAAA
ACACCGCTAAAACCCCAAGCATTAGCGGCATTTTTAAAAAAACGCAGCTAAAACACCGAGCATTA
GCGGCGCTTTTTTAAAAACGCCGCCAAAGCCCCTAGCACAAAAACGCCGCTAAAACCCCC
Found at i:21731435 original size:40 final size:40
Alignment explanation
Indices: 21731351--21731463 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 40
21731341 TTTGTGGCAT
** * * *
21731351 TTTTCTAAAAAACACCGCGAATGCTC-ATTTTTAGCGGCGT
1 TTTTC-AAAAAATGCCGCTAATGCTCGATTTTTAGCGCCGA
* *
21731391 TTTTCAAAAAATGCCGCTAATGCTCGATCTTTAGTGCCGA
1 TTTTCAAAAAATGCCGCTAATGCTCGATTTTTAGCGCCGA
* *
21731431 TTTTCATAAAGTGCCGCTAATGCTCGATTTTTA
1 TTTTCAAAAAATGCCGCTAATGCTCGATTTTTA
21731464 TTGGCATTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
39 17 0.27
40 45 0.73
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (40 bp):
TTTTCAAAAAATGCCGCTAATGCTCGATTTTTAGCGCCGA
Found at i:21754646 original size:18 final size:18
Alignment explanation
Indices: 21754623--21754660 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
21754613 TCACTGCCTA
21754623 ACGAATATGCCACATTTG
1 ACGAATATGCCACATTTG
21754641 ACGAATATGCCACATTTG
1 ACGAATATGCCACATTTG
21754659 AC
1 AC
21754661 ACCTCAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (18 bp):
ACGAATATGCCACATTTG
Found at i:21755282 original size:3 final size:3
Alignment explanation
Indices: 21755274--21755313 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
21755264 TTGAAAAAGG
* * *
21755274 TTC TTC TTC ATC TTA TTC TTC TTA TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
21755314 GTAAATGTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:21769916 original size:40 final size:40
Alignment explanation
Indices: 21769872--21770061 Score: 200
Period size: 40 Copynumber: 4.8 Consensus size: 40
21769862 AATTATTGAA
* *
21769872 TGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCC
*
21769912 TGAATGCACATACGTGCCCCTGTTTATACTGCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCC
* ** * *
21769952 TTAATGCACATATATGCCCATGTTTATACTTCAGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCC
* ** * ** * * *
21769992 TAAAAACACATACGTGTCGTTGTTTGTGCTTCGGTACCCT
1 TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCC
* * *
21770032 TGAATGCACTTTCGTGCCCCTATTTATACT
1 TGAATGCACATACGTGCCCCTGTTTATACT
21770062 CTGGTAACTC
Statistics
Matches: 118, Mismatches: 32, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 118 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.34
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCC
Found at i:21769931 original size:20 final size:20
Alignment explanation
Indices: 21769872--21769933 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
21769862 AATTATTGAA
*
21769872 TGAATGCACATATGTGCCCC
1 TGAATGCACATACGTGCCCC
** * * *
21769892 TGTTTGTAC-TTCGGTACCCC
1 TGAATGCACATAC-GTGCCCC
21769912 TGAATGCACATACGTGCCCC
1 TGAATGCACATACGTGCCCC
21769932 TG
1 TG
21769934 TTTATACTGC
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (20 bp):
TGAATGCACATACGTGCCCC
Found at i:21777050 original size:40 final size:40
Alignment explanation
Indices: 21776995--21777104 Score: 150
Period size: 40 Copynumber: 2.8 Consensus size: 40
21776985 TTATAGAATG
21776995 AATGCACATATGTGCCCCTATTTGTACTTCAGTACCCCTA
1 AATGCACATATGTGCCCCTATTTGTACTTCAGTACCCCTA
*
21777035 AATGCACATATGTGCCCCTATTTGTA-TTGCGGTACCCCTA
1 AATGCACATATGTGCCCCTATTTGTACTT-CAGTACCCCTA
* * * * *
21777075 GATGCACTTACGTACCCCTATTTATACTTC
1 AATGCACATATGTGCCCCTATTTGTACTTC
21777105 GATAACTTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
39 2 0.03
40 58 0.94
41 2 0.03
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.34
Consensus pattern (40 bp):
AATGCACATATGTGCCCCTATTTGTACTTCAGTACCCCTA
Found at i:21778714 original size:32 final size:32
Alignment explanation
Indices: 21778673--21778736 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
21778663 TAGCTATTTA
*
21778673 AAAATAATTAGAGAGAT-GAAAGTTTGTTAATT
1 AAAATAATTAGAGAGATAG-AAGTTTGTAAATT
*
21778705 AAAATAATTAGGGAGATAGAAGTTTGTAAATT
1 AAAATAATTAGAGAGATAGAAGTTTGTAAATT
21778737 TTTTGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (32 bp):
AAAATAATTAGAGAGATAGAAGTTTGTAAATT
Found at i:21786852 original size:35 final size:34
Alignment explanation
Indices: 21786773--21786887 Score: 101
Period size: 35 Copynumber: 3.3 Consensus size: 34
21786763 TTTTGCTCTG
* *
21786773 CTTAGTTTTATTCCCAAATC-ATA-TCCTCAAATTCC
1 CTTAATTTT-TTCCCAAA-CAATACTCCCCAAA-TCC
* **
21786808 CTTATTTTTTTCCTCTAAA-AATTTTCCCCAAATCC
1 CTTAATTTTTTCC-C-AAACAATACTCCCCAAATCC
21786843 CTTAATTTTTTCCCAAATCAATACTCCCCAAATCC
1 CTTAATTTTTTCCCAAA-CAATACTCCCCAAATCC
21786878 CTTAGATTTT
1 CTTA-ATTTT
21786888 CCCCAACTGT
Statistics
Matches: 67, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
33 3 0.04
34 5 0.07
35 44 0.66
36 15 0.22
ACGTcount: A:0.28, C:0.29, G:0.02, T:0.42
Consensus pattern (34 bp):
CTTAATTTTTTCCCAAACAATACTCCCCAAATCC
Found at i:21786959 original size:25 final size:25
Alignment explanation
Indices: 21786931--21787005 Score: 105
Period size: 25 Copynumber: 3.0 Consensus size: 25
21786921 ACCTCTATTG
* * *
21786931 CATCGCCGTCAACACTCCTCTGCCC
1 CATCACCGTCGACACTCCTCTACCC
**
21786956 CATCACCGTCGACACTCCTCTACTG
1 CATCACCGTCGACACTCCTCTACCC
21786981 CATCACCGTCGACACTCCTCTACCC
1 CATCACCGTCGACACTCCTCTACCC
21787006 TGAAACAGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.19, C:0.49, G:0.11, T:0.21
Consensus pattern (25 bp):
CATCACCGTCGACACTCCTCTACCC
Found at i:21787179 original size:19 final size:21
Alignment explanation
Indices: 21787141--21787185 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
21787131 ATACATCTAT
* *
21787141 TTTTTGGGTTATTTTTATT-A
1 TTTTTGGGTTATTATCATTAA
21787161 TTTTTGGGTTA-TATCATTAA
1 TTTTTGGGTTATTATCATTAA
21787181 TTTTT
1 TTTTT
21787186 ATTATGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.02, G:0.13, T:0.67
Consensus pattern (21 bp):
TTTTTGGGTTATTATCATTAA
Found at i:21799849 original size:21 final size:22
Alignment explanation
Indices: 21799804--21799849 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
21799794 AGAGAAAAAT
*
21799804 AAAAGTGAAAAAGAAGAAAATG
1 AAAAGTGAAAAAGAAGAAAAGG
**
21799826 AAAA-TGAAAAAGGTGAAAAGG
1 AAAAGTGAAAAAGAAGAAAAGG
21799847 AAA
1 AAA
21799850 GCGAGAGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (22 bp):
AAAAGTGAAAAAGAAGAAAAGG
Found at i:21806481 original size:11 final size:11
Alignment explanation
Indices: 21806465--21806494 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
21806455 CTCGTATCAG
21806465 AAAAAAATAGA
1 AAAAAAATAGA
*
21806476 AAAAAAAGAGA
1 AAAAAAATAGA
21806487 AAAAAAAT
1 AAAAAAAT
21806495 GCATAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (11 bp):
AAAAAAATAGA
Found at i:21812487 original size:22 final size:22
Alignment explanation
Indices: 21812459--21812501 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
21812449 TTTATTGTTC
21812459 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
21812481 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
21812502 TTGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:21820149 original size:20 final size:20
Alignment explanation
Indices: 21820126--21820186 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
21820116 CAGCTCCGAC
*
21820126 CAGCTTAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
21820146 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
21820167 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
21820187 ATTTTATTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:21820181 original size:11 final size:10
Alignment explanation
Indices: 21820126--21820183 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
21820116 CAGCTCCGAC
*
21820126 CAGCTTAATT
1 CAGCTCAATT
* *
21820136 GAGCTCATTT
1 CAGCTCAATT
21820146 CAGCTCAA-T
1 CAGCTCAATT
21820155 CGAGCTCAATT
1 C-AGCTCAATT
*
21820166 TAGCTACAATT
1 CAGCT-CAATT
21820177 CAGCTCA
1 CAGCTCA
21820184 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
9 2 0.05
10 26 0.68
11 10 0.26
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:21823977 original size:806 final size:805
Alignment explanation
Indices: 21822423--21824032 Score: 2015
Period size: 806 Copynumber: 2.0 Consensus size: 805
21822413 TTCAAGCTCT
* *
21822423 TTGATAGAGGGTTGCGAGCGGACCAAGATTGAGTTGCCAAGTCACGAAAAACACCTATGAAAACG
1 TTGATAGAGGGTTGCGAGCGGACCAAGATCGAGTTGCCAAGTCACGAAAAACACCTACGAAAACG
** * * *
21822488 CTAAACGCGTGGATCTGAAACGAAATAGAAAATTAAACTTAGAATCAACAGATCTAAAAACGAAA
66 CTAAACGAATGGATCTGAAACGAAACAGAAAATCAAACTTAGAATCAAAAGATCTAAAAAC-AAA
*** * * **
21822553 CACCCAAATAATAAAGAATCAGCCAAGAATTGAAACACTTATTAATAGGGATTCTTGGATGCCAA
130 CACCCAAATAATAAAGAATCAGCCAAGAACCAAAACACTTATTAATAGAGAATCTTGGAAACCAA
* *
21822618 GAACATGAAATTGAACTTCAAGAAAAGTCTCCAATCATCCAAATCTGACAAGTAAACACAAAACA
195 GAACATGAAATTGAACTTCAAGAAAAGACTCCAATCAGCCAAATCTGACAAGTAAACACAAAACA
* * * *
21822683 GAAAAATTAGACTCAACAGATCACGAAACCCCAAATTGAAGTAGAACTAGGTTTTGTGCGGCAAG
260 GAAAAATCAAACTCAACAGATCACGAAACACCAAATTGAAGTAGAACTAGGGTTTGTGCGGCAAG
* *
21822748 AAAAAAAAGAATTATGAATCAAGAACAATTCTTGATGGCCAAGACTGGTGCCGAATAGATTCTTG
325 AAAAAAAAGAATTATGAATCAAGAACAATTCTTGATGGCCAAGACTGATCCCGAATAGATTCTTG
* *
21822813 AAGATTGAAAGGGCTGGAAATGCAACAAGAGAGATTAAAACAATTTAATCAATGAATCAGCACAA
390 AAGATTGAAAGGGCTGGAAATGCAACAAGAGAGATTAAAACAAGTTAATCAACGAATCAGCACAA
* * *
21822878 GCAGAAAAATTAAAGAGGAATAAACAGTAAGAAAATAAAGAAATGTCCTAAGAAGCCTTGAAATC
455 GCAGAAAAATTAAAGAAGAATAAACAGCAAGAAAATAAAGAAAAGTCCTAAGAAGCCTTGAAATC
* * * *
21822943 GAGAAAGATCTCACAACTCCCTTCAAACGACTCTAATCTCCCCTCCAATGTAGGACAATGGTAAG
520 GAGAAAGATCTCACAACTCCCTTCAAACGACACTAATCTCCCCTCCAATGAAGAACAATGGCAAG
21823008 AAAAAGGCTGAAGATGGCTCCCACAATCAAAAAGATTGTTAAAACTACTTCCAAAGAAAACTCAA
585 AAAAAGGCTGAAGATGGCTCCCACAATCAAAAAGATTGTTAAAACTACTTCCAAAGAAAACTCAA
* * *
21823073 GAAAAAATTCTTGGAGAAAACTCAGAGAATTTTTGACTCAATAAAAAATCTGATTTCAATGTGTT
650 GAAAAAATTCTTGGAG-AAACTCAGAGAATTTTTCACTCAAAAAAAAATCTGATTTCAATGTATT
* * * * *
21823138 GTTCAATGTAATTGTGTATAAGGTGGTCGGCCAAGCC-T-TAT-TATAGGCCTTTTATCTATTTT
714 CTTCAATGTAATTGTGTACAAGATGGCCGGCCAAGCCTTATATATATAGGCC-TCTAT-TATTTT
21823200 CCTAACCCTATTAGGAAAACTAAAAAAACC
777 CCTAACCCTATTA-GAAAACTAAAAAAACC
* * * ** * *
21823230 TTGATAGAGGGTTGCGCGTGGACCAAGATCGAGTTGTCAAGTCACGGGAAACTCCTACGAAAACT
1 TTGATAGAGGGTTGCGAGCGGACCAAGATCGAGTTGCCAAGTCACGAAAAACACCTACGAAAACG
* * * **
21823295 CTAGAC-AATCGGATCTGAAACGAAACAGAAAGATCGAACTTAGAATTAAAAGATCTGAAGTA-A
66 CTAAACGAAT-GGATCTGAAACGAAACAGAAA-ATCAAACTTAGAATCAAAAGATCT-AAAAACA
* * *
21823358 AATACCCAAAATAATAAAGAATCAGCCTAGAGCCAAAACACTTATTAATAGAGAATCTTGGAAAC
128 AACACCC-AAATAATAAAGAATCAGCCAAGAACCAAAACACTTATTAATAGAGAATCTTGGAAAC
* * * *
21823423 TAAGAACATGAAATT-AAGCTTCAAG-AAGGACTCCAATCAGCCGAATCTGTCAAGTAAACACAA
192 CAAGAACATGAAATTGAA-CTTCAAGAAAAGACTCCAATCAGCCAAATCTGACAAGTAAACACAA
** * * *
21823486 AACAGAAACAAATCAAACTCAATGGATCAC-AAA-ATCAAATTGAATTAGATCTAGGGTTTG-GA
256 AACAG-AA-AAATCAAACTCAACAGATCACGAAACACCAAATTGAAGTAGAACTAGGGTTTGTG-
* * * ** ** * * * * **
21823548 TGGTAAG-AAAGAGGGGTTTTTGAAATCAA-AACATTTCTTGTTGTCCAAGGTTGATCCCGAATA
318 CGGCAAGAAAAAAAAGAATTATG-AATCAAGAACAATTCTTGATGGCCAAGACTGATCCCGAATA
* * *
21823611 GATTCTTGAAGGTT-AAACGGGCTGGAGATGCAACAAGAGAG-TTTAAACAAGTTAGAT-AACGA
382 GATTCTTGAAGATTGAAA-GGGCTGGAAATGCAACAAGAGAGATTAAAACAAGTTA-ATCAACG-
* *
21823673 AATC-GACACAAGCA-AAAAATTAAA-AAGATTGAACAGCAAGAACAATAAAGATAAAGTCCTAA
444 AATCAG-CACAAGCAGAAAAATTAAAGAAGAATAAACAGCAAGAA-AATAAAGA-AAAGTCCTAA
* * *
21823735 GAAGCCTTGAAATCGAGAAAGATTTCACAACTCCCTTCAAACGGCACTAATCTCCCCTCTAATGA
506 GAAGCCTTGAAATCGAGAAAGATCTCACAACTCCCTTCAAACGACACTAATCTCCCCTCCAATGA
* *
21823800 AGAACAATGGCAAGAAGAAGGCTGAAGATGGCTCCCACAATCAAAAAGATTGTTAAAACTTCTTC
571 AGAACAATGGCAAGAAAAAGGCTGAAGATGGCTCCCACAATCAAAAAGATTGTTAAAACTACTTC
*
21823865 TAAAGAAAACTCAAGAAAAAATTCTTGGAG-AACTCAAAGAGAA-TTTTCACTCAACAAAACAAA
636 CAAAGAAAACTCAAGAAAAAATTCTTGGAGAAACTC--AGAGAATTTTTCACTCAA-AAAA-AAA
*
21823928 TCTGATTTCCATGTATTCTTCAAGTGT-ATTGT-T-CAAGTATGGCCGGCCAAGCCTTACATATA
697 TCTGATTTCAATGTATTCTTCAA-TGTAATTGTGTACAAG-ATGGCCGGCCAAGCCTT--ATATA
21823990 TATAGGCCTCTATTATTTTCCTAACCCTATTAGAAAACTAAAA
758 TATAGGCCTCTATTATTTTCCTAACCCTATTAGAAAACTAAAA
21824033 CTAAAAAAAC
Statistics
Matches: 689, Mismatches: 88, Indels: 51
0.83 0.11 0.06
Matches are distributed among these distances:
804 19 0.03
805 49 0.07
806 269 0.39
807 190 0.28
808 108 0.16
809 39 0.06
810 7 0.01
811 8 0.01
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (805 bp):
TTGATAGAGGGTTGCGAGCGGACCAAGATCGAGTTGCCAAGTCACGAAAAACACCTACGAAAACG
CTAAACGAATGGATCTGAAACGAAACAGAAAATCAAACTTAGAATCAAAAGATCTAAAAACAAAC
ACCCAAATAATAAAGAATCAGCCAAGAACCAAAACACTTATTAATAGAGAATCTTGGAAACCAAG
AACATGAAATTGAACTTCAAGAAAAGACTCCAATCAGCCAAATCTGACAAGTAAACACAAAACAG
AAAAATCAAACTCAACAGATCACGAAACACCAAATTGAAGTAGAACTAGGGTTTGTGCGGCAAGA
AAAAAAAGAATTATGAATCAAGAACAATTCTTGATGGCCAAGACTGATCCCGAATAGATTCTTGA
AGATTGAAAGGGCTGGAAATGCAACAAGAGAGATTAAAACAAGTTAATCAACGAATCAGCACAAG
CAGAAAAATTAAAGAAGAATAAACAGCAAGAAAATAAAGAAAAGTCCTAAGAAGCCTTGAAATCG
AGAAAGATCTCACAACTCCCTTCAAACGACACTAATCTCCCCTCCAATGAAGAACAATGGCAAGA
AAAAGGCTGAAGATGGCTCCCACAATCAAAAAGATTGTTAAAACTACTTCCAAAGAAAACTCAAG
AAAAAATTCTTGGAGAAACTCAGAGAATTTTTCACTCAAAAAAAAATCTGATTTCAATGTATTCT
TCAATGTAATTGTGTACAAGATGGCCGGCCAAGCCTTATATATATAGGCCTCTATTATTTTCCTA
ACCCTATTAGAAAACTAAAAAAACC
Found at i:21834443 original size:24 final size:23
Alignment explanation
Indices: 21834416--21834466 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
21834406 TTAAAACTAC
21834416 TTCTA-GAGAAAACTCAAGAGAAAA
1 TTCTAGGAG-AAACTCAA-AGAAAA
* *
21834440 TTCTTGGAGAAACTCAAAGAGAA
1 TTCTAGGAGAAACTCAAAGAAAA
21834463 TTCT
1 TTCT
21834467 CAATCAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 12 0.50
25 3 0.12
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (23 bp):
TTCTAGGAGAAACTCAAAGAAAA
Found at i:21837005 original size:29 final size:27
Alignment explanation
Indices: 21836973--21837038 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
21836963 TCAACATCTT
21836973 TTTCTTTTTCAATTTT-TTTTCAATCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
* *
21837002 TTTCCTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
21837029 TTTCTTTTTC
1 TTTCTTTTTC
21837039 TCTCACTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 12 0.36
28 1 0.03
29 15 0.45
30 5 0.15
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:21837073 original size:18 final size:18
Alignment explanation
Indices: 21837052--21837118 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
21837042 CACTTATTCG
*
21837052 ATTTCTTTTTCTTTTGCA
1 ATTTCTTTTTCTTTTTCA
*
21837070 ATTTCTTTTTCTTTTTCG
1 ATTTCTTTTTCTTTTTCA
* *
21837088 TTTTCTTTTGTTTTCTTTCA
1 ATTTCTTTT-TCTT-TTTCA
21837108 ATTTCTTTTTC
1 ATTTCTTTTTC
21837119 AATCTTTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 24 0.60
19 4 0.10
20 12 0.30
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.72
Consensus pattern (18 bp):
ATTTCTTTTTCTTTTTCA
Found at i:21837118 original size:6 final size:6
Alignment explanation
Indices: 21837053--21837096 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
21837043 ACTTATTCGA
* ** *
21837053 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
21837097 GTTTTCTTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:21838211 original size:14 final size:14
Alignment explanation
Indices: 21838183--21838221 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 14
21838173 TTTTTTTTCC
21838183 TTTTTTTTCG-A--
1 TTTTTTTTCGAATT
21838194 TTTTTTTT-GAATT
1 TTTTTTTTCGAATT
21838207 TTTTTTTTCGAATT
1 TTTTTTTTCGAATT
21838221 T
1 T
21838222 CTTCTCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 9 0.38
13 8 0.33
14 6 0.25
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (14 bp):
TTTTTTTTCGAATT
Found at i:21842996 original size:18 final size:16
Alignment explanation
Indices: 21842975--21843009 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
21842965 TTATTTCTCT
21842975 TTTTTTTTATAGTTTTCG
1 TTTTTTTTA-A-TTTTCG
21842993 TTTTTTTTAATTTTCG
1 TTTTTTTTAATTTTCG
21843009 T
1 T
21843010 AACTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 1 0.06
18 9 0.53
ACGTcount: A:0.11, C:0.06, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTTTTTTAATTTTCG
Found at i:21845534 original size:21 final size:21
Alignment explanation
Indices: 21845505--21845545 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21845495 TCTCTCTCGC
*
21845505 TTTCCTTTTCGCCTTTTTCAT
1 TTTCATTTTCGCCTTTTTCAT
**
21845526 TTTCATTTTCTTCTTTTTCA
1 TTTCATTTTCGCCTTTTTCA
21845546 CTTGTATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.24, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTCATTTTCGCCTTTTTCAT
Found at i:21847591 original size:29 final size:27
Alignment explanation
Indices: 21847558--21847612 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
21847548 GTGATTAAAT
21847558 AAAATTGACA-CAAGCAGAATTTAAAAGAA
1 AAAATTGACAGCAAG-A-AA-TTAAAAGAA
21847587 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATTGACAGCAAGAAATTAAAAGA
21847613 TAACTCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.32
28 2 0.08
29 11 0.44
30 4 0.16
ACGTcount: A:0.60, C:0.09, G:0.15, T:0.16
Consensus pattern (27 bp):
AAAATTGACAGCAAGAAATTAAAAGAA
Found at i:21854361 original size:12 final size:12
Alignment explanation
Indices: 21854344--21854400 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
21854334 GTAAAAAAAC
21854344 AAAAAGAAATTG
1 AAAAAGAAATTG
*
21854356 AAAAAGAAAATG
1 AAAAAGAAATTG
* *
21854368 AACATGAAA--G
1 AAAAAGAAATTG
21854378 AAAATAAGAAATTG
1 -AAA-AAGAAATTG
21854392 AAAAAGAAA
1 AAAAAGAAA
21854401 ATGAGAGTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 1 0.03
11 2 0.06
12 29 0.81
13 3 0.08
14 1 0.03
ACGTcount: A:0.70, C:0.02, G:0.16, T:0.12
Consensus pattern (12 bp):
AAAAAGAAATTG
Found at i:21854438 original size:27 final size:26
Alignment explanation
Indices: 21854391--21854447 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
21854381 ATAAGAAATT
* *
21854391 GAAAAAGAAAATGAGAGTGAGAGTGA
1 GAAAAAGAAAAAGAAAGTGAGAGTGA
* *
21854417 GAAAAAGAAAAAAGAAATTGAGATTGA
1 GAAAAAG-AAAAAGAAAGTGAGAGTGA
21854444 -AAAA
1 GAAAA
21854448 GGATGTGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.12
Consensus pattern (26 bp):
GAAAAAGAAAAAGAAAGTGAGAGTGA
Found at i:21868488 original size:15 final size:15
Alignment explanation
Indices: 21868451--21868501 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
21868441 TCGAGCGAGA
*
21868451 AAAAGAAAAAGAGAG
1 AAAAGAAAAAGAGTG
*
21868466 -AAACAAAAAGAGTG
1 AAAAGAAAAAGAGTG
*
21868480 AAAAGAAAAAGAATG
1 AAAAGAAAAAGAGTG
21868495 AAAAGAA
1 AAAAGAA
21868502 TGATGAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.04
Consensus pattern (15 bp):
AAAAGAAAAAGAGTG
Found at i:21868553 original size:7 final size:6
Alignment explanation
Indices: 21868532--21868562 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
21868522 CAAGAGTGAT
*
21868532 AAAAGA AAAAGA AAAAGA AAAAGG AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A
21868563 TGTGAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:21872502 original size:13 final size:12
Alignment explanation
Indices: 21872484--21872518 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
21872474 ACGAGTTTGT
21872484 AAAAAAAATTCG
1 AAAAAAAATTCG
21872496 AAAAAAAATTCG
1 AAAAAAAATTCG
21872508 ACAAAAAAATT
1 A-AAAAAAATT
21872519 TATTTTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:21877896 original size:20 final size:19
Alignment explanation
Indices: 21877860--21877920 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
21877850 TATAAACGCA
*
21877860 ATTGAGCTTAAAATGAGCTG
1 ATTGAGC-TAAAGTGAGCTG
21877880 ATTGAGCTAAGAGTGAGCTCG
1 ATTGAGCTAA-AGTGAGCT-G
21877901 A-TGAGCTAAAGTTGAGCTG
1 ATTGAGCTAAAG-TGAGCTG
21877920 A
1 A
21877921 ATGAACTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 7 0.19
20 28 0.76
21 2 0.05
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (19 bp):
ATTGAGCTAAAGTGAGCTG
Found at i:21884893 original size:20 final size:19
Alignment explanation
Indices: 21884857--21884917 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
21884847 TATAAACGCA
*
21884857 ATTGAGCTTAAAATGAGCTG
1 ATTGAGC-TAAAGTGAGCTG
21884877 ATTGAGCTAAGAGTGAGCTCG
1 ATTGAGCTAA-AGTGAGCT-G
21884898 A-TGAGCTAAAGTTGAGCTG
1 ATTGAGCTAAAG-TGAGCTG
21884917 A
1 A
21884918 ATGAACTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 7 0.19
20 28 0.76
21 2 0.05
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (19 bp):
ATTGAGCTAAAGTGAGCTG
Found at i:21895580 original size:21 final size:21
Alignment explanation
Indices: 21895554--21895595 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
21895544 GAAATTCAAA
21895554 AAAAAAATTTTGAAAAAAAATCG
1 AAAAAAA--TTGAAAAAAAATCG
21895577 AAAAAAATTGAAAAAAAAT
1 AAAAAAATTGAAAAAAAAT
21895596 TGTATACGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (21 bp):
AAAAAAATTGAAAAAAAATCG
Found at i:21895596 original size:11 final size:11
Alignment explanation
Indices: 21895553--21895597 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
21895543 AGAAATTCAA
21895553 AAAAAAAATTTTG
1 AAAAAAAA--TTG
*
21895566 AAAAAAAATCG
1 AAAAAAAATTG
21895577 -AAAAAAATTG
1 AAAAAAAATTG
21895587 AAAAAAAATTG
1 AAAAAAAATTG
21895598 TATACGGTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 9 0.31
11 12 0.41
13 8 0.28
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.20
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:21932336 original size:18 final size:18
Alignment explanation
Indices: 21932303--21932349 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
21932293 TTTTTCAACA
* *
21932303 TCTTTTTCTATATCAATT
1 TCTTTTTCAATCTCAATT
21932321 T-TTTTCTCAATCTCAATT
1 TCTTTT-TCAATCTCAATT
21932339 TCTTTTTCAAT
1 TCTTTTTCAAT
21932350 TTTCTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTTTTCAATCTCAATT
Found at i:21932400 original size:18 final size:18
Alignment explanation
Indices: 21932379--21932437 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
21932369 TTTTCTCTCA
21932379 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
21932397 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
21932415 CTTTTTTGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
21932433 GTTTT
1 CTTTT
21932438 CTTTCAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.75
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:21932426 original size:12 final size:12
Alignment explanation
Indices: 21932411--21932441 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
21932401 TGCAATTTCT
21932411 TTTTCTTTTTTG
1 TTTTCTTTTTTG
21932423 TTTTC-TTTTTG
1 TTTTCTTTTTTG
21932434 TTTTCTTT
1 TTTTCTTT
21932442 CAATTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTTG
Found at i:21932454 original size:6 final size:6
Alignment explanation
Indices: 21932337--21932441 Score: 54
Period size: 6 Copynumber: 17.2 Consensus size: 6
21932327 TCAATCTCAA
* * ** **
21932337 TTTCTT TTTCAAT TTTC-T TTTCTT CATGTTCTT TTTCTC TCACTT TTTCGA
1 TTTCTT TTTC-TT TTTCTT TTTCTT --T-TTCTT TTTCTT TTTCTT TTTCTT
* ** *
21932388 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTT-TGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCT-T TTTCTT TTTCTT
21932435 TTTCTT T
1 TTTCTT T
21932442 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 19, Indels: 16
0.67 0.18 0.15
Matches are distributed among these distances:
5 10 0.14
6 49 0.68
7 7 0.10
8 1 0.01
9 5 0.07
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:21939199 original size:18 final size:18
Alignment explanation
Indices: 21939166--21939212 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
21939156 TTTTTCAACA
* *
21939166 TCTTTTTCTATTTCAATT
1 TCTTTTTCAATCTCAATT
21939184 T-TTTTCTCAATCTCAATT
1 TCTTTT-TCAATCTCAATT
21939202 TCTTTTTCAAT
1 TCTTTTTCAAT
21939213 TTTCTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (18 bp):
TCTTTTTCAATCTCAATT
Found at i:21939263 original size:18 final size:18
Alignment explanation
Indices: 21939242--21939300 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
21939232 TTTTCTCTCA
21939242 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
21939260 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
21939278 CTTTTTTGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
21939296 GTTTT
1 CTTTT
21939301 CTTTCAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.75
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:21939289 original size:12 final size:12
Alignment explanation
Indices: 21939274--21939304 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
21939264 TGCAATTTCT
21939274 TTTTCTTTTTTG
1 TTTTCTTTTTTG
21939286 TTTTC-TTTTTG
1 TTTTCTTTTTTG
21939297 TTTTCTTT
1 TTTTCTTT
21939305 CAATTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTTG
Found at i:21939317 original size:6 final size:6
Alignment explanation
Indices: 21939200--21939304 Score: 61
Period size: 6 Copynumber: 17.2 Consensus size: 6
21939190 TCAATCTCAA
* * * ** **
21939200 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTT TTTCGA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** *
21939251 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTT-TGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCT-T TTTCTT TTTCTT
21939298 TTTCTT T
1 TTTCTT T
21939305 CAATTTCTTT
Statistics
Matches: 71, Mismatches: 23, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
5 5 0.07
6 53 0.75
7 10 0.14
8 3 0.04
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (6 bp):
TTTCTT
Found at i:21940510 original size:11 final size:11
Alignment explanation
Indices: 21940494--21940522 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
21940484 CAACTCAAAA
21940494 TTTTTTTTGA-
1 TTTTTTTTGAC
21940504 TTTTTTTTGAC
1 TTTTTTTTGAC
21940515 TTTTTTTT
1 TTTTTTTT
21940523 ACGTTACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:21942263 original size:13 final size:13
Alignment explanation
Indices: 21942242--21942276 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
21942232 ATAAGTTGCT
* *
21942242 GTTAGTTAAATTA
1 GTTAATTAAATAA
21942255 GTTAATTAAATAA
1 GTTAATTAAATAA
21942268 GTTAATTAA
1 GTTAATTAA
21942277 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:21950900 original size:55 final size:55
Alignment explanation
Indices: 21950816--21950929 Score: 228
Period size: 55 Copynumber: 2.1 Consensus size: 55
21950806 GGCTGATTGG
21950816 AAGTTAATCTTGGGGCTTAATCTCGTGTTATTGGCTTCCAAGAACATCTATTCAT
1 AAGTTAATCTTGGGGCTTAATCTCGTGTTATTGGCTTCCAAGAACATCTATTCAT
21950871 AAGTTAATCTTGGGGCTTAATCTCGTGTTATTGGCTTCCAAGAACATCTATTCAT
1 AAGTTAATCTTGGGGCTTAATCTCGTGTTATTGGCTTCCAAGAACATCTATTCAT
21950926 AAGT
1 AAGT
21950930 GTTTTGATTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (55 bp):
AAGTTAATCTTGGGGCTTAATCTCGTGTTATTGGCTTCCAAGAACATCTATTCAT
Found at i:21956366 original size:52 final size:53
Alignment explanation
Indices: 21956278--21956379 Score: 161
Period size: 52 Copynumber: 1.9 Consensus size: 53
21956268 TAAGGAAACG
* * *
21956278 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAA-GCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTCGAAGGCTCAAACAA
*
21956330 TAATAGACAGCAGCTTAAGACCTCATTTCTATCTCGGTCGAAGGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTCGAAGGCTCAAA
21956380 TATGTGCATG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 38 0.84
53 7 0.16
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (53 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTCGAAGGCTCAAACAA
Found at i:21958258 original size:23 final size:23
Alignment explanation
Indices: 21958232--21958305 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
21958222 GTTACAAAAG
21958232 GGTAATGTGATTTGGTACGAAAT
1 GGTAATGTGATTTGGTACGAAAT
* **
21958255 GGTATTACGATTTGGTACGAAAT
1 GGTAATGTGATTTGGTACGAAAT
21958278 GGTAATGTGATTTGGTACGAAAT
1 GGTAATGTGATTTGGTACGAAAT
21958301 GGTAA
1 GGTAA
21958306 AGATTCAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (23 bp):
GGTAATGTGATTTGGTACGAAAT
Found at i:21962448 original size:19 final size:19
Alignment explanation
Indices: 21962424--21962468 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
21962414 TTTTTCATTC
21962424 TCTTTTTTCAAATTTTC-TT
1 TCTTTTTTC-AATTTTCTTT
*
21962443 TCTTTTTTTCATTTTTCTTT
1 TC-TTTTTTCAATTTTCTTT
21962463 TCTTTT
1 TCTTTT
21962469 GTATTTTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (19 bp):
TCTTTTTTCAATTTTCTTT
Found at i:21962451 original size:20 final size:19
Alignment explanation
Indices: 21962415--21962468 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
21962405 TCTCACTTTT
*
21962415 TTTTCATTCTCTTTTTTCAAA
1 TTTTCTTTCT-TTTTTTC-AA
*
21962436 TTTTCTTTCTTTTTTTCAT
1 TTTTCTTTCTTTTTTTCAA
21962455 TTTTCTTTTCTTTT
1 TTTTC-TTTCTTTT
21962469 GTATTTTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 6 0.20
20 15 0.50
21 9 0.30
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTCTTTCTTTTTTTCAA
Found at i:21964931 original size:23 final size:23
Alignment explanation
Indices: 21964905--21964978 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
21964895 TGTTAAAAAG
21964905 GGTAATGTGATTTGGTACGAAAT
1 GGTAATGTGATTTGGTACGAAAT
* **
21964928 GGTATTACGATTTGGTACGAAAT
1 GGTAATGTGATTTGGTACGAAAT
*
21964951 GGTAATGTGATTTGATACGAAAT
1 GGTAATGTGATTTGGTACGAAAT
21964974 GGTAA
1 GGTAA
21964979 AGATTCAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.34
Consensus pattern (23 bp):
GGTAATGTGATTTGGTACGAAAT
Found at i:21974151 original size:81 final size:81
Alignment explanation
Indices: 21974013--21974176 Score: 283
Period size: 81 Copynumber: 2.0 Consensus size: 81
21974003 AAACGCATTG
*
21974013 GATCTCTGTTACAAGCATCAACAAACCAATTTCGGTAGAAGATGGAATACAAACTGATACGATCC
1 GATCTCCGTTACAAGCATCAACAAACCAATTTCGGTAGAAGATGGAATACAAACTGATACGATCC
*
21974078 GCCTCGGTGTTGAGTC
66 GCCTCGGTGCTGAGTC
* * *
21974094 GATCTCCGTTACGAGCATCAACGAACCAATTTCGGTAGAAGATGGAATACAAGCTGATACGATCC
1 GATCTCCGTTACAAGCATCAACAAACCAATTTCGGTAGAAGATGGAATACAAACTGATACGATCC
21974159 GCCTCGGTGCTGAGTC
66 GCCTCGGTGCTGAGTC
21974175 GA
1 GA
21974177 GTCGTATTTA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (81 bp):
GATCTCCGTTACAAGCATCAACAAACCAATTTCGGTAGAAGATGGAATACAAACTGATACGATCC
GCCTCGGTGCTGAGTC
Done.