Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 13 of 16
Found at i:2035051 original size:17 final size:18
Alignment explanation
Indices: 2035024--2035058 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2035014 AAATATTCAC
*
2035024 TAATAATATTTTTATTAT
1 TAATAATATTTATATTAT
2035042 TAAT-ATATTTATATTAT
1 TAATAATATTTATATTAT
2035059 ATATAAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TAATAATATTTATATTAT
Found at i:2036546 original size:21 final size:21
Alignment explanation
Indices: 2036520--2036559 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2036510 ATAGGCAGCC
2036520 TCTGGGATGATTATGAAACAA
1 TCTGGGATGATTATGAAACAA
*
2036541 TCTGGGATGATTTTGAAAC
1 TCTGGGATGATTATGAAAC
2036560 CATATATTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (21 bp):
TCTGGGATGATTATGAAACAA
Found at i:2037246 original size:244 final size:243
Alignment explanation
Indices: 2036817--2037446 Score: 931
Period size: 244 Copynumber: 2.6 Consensus size: 243
2036807 AAAAAATTCA
* * * *
2036817 TGTAGGTTTTGCGAAGCTGGCATCGAAATTGGAC-AACTTAGAGATCCTTTACTTAAATTACAAT
1 TGTAGGTTTTACGAAGCTGGCATCGAAATTGGACAAAC-TAGAGATTC-TAACTTAAATTATAAT
* * *
2036881 TATTTTGATGATAGCATTTTGGCATCGTTAAGTGAACTTTCATCACTAAAAATTTTAAATCTAGC
64 TATTTTGATGATAGCATTTTAGCATCGTTAAGTGAACTTTCATCACTCAAAACTTTAAATCTAGC
* * *
2036946 ACGCAATCAATTCGGGCGATCAAATCCTAGTGATGGTAAAGATAATATAGGAATTTGCTGCAGGT
129 AAGCAATCAATTCGGACAATCAAATCCTAGTGATGGTAAAGATAATATAGGAATTTGCTGCAGGT
2037011 TGAAGTAAATAAATTTTGCAACTCATATATATTATGTATAACTTTTTCTT
194 TGAAGTAAATAAATTTTGCAACTCATATATATTATGTATAACTTTTTCTT
* *
2037061 TGTAGGTTTTACGAAGCTGGGATCAAAATTGGACAAACTAGAGATTCTGAACTTAAATTATAATT
1 TGTAGGTTTTACGAAGCTGGCATCGAAATTGGACAAACTAGAGATTCT-AACTTAAATTATAATT
*
2037126 ATTTTGATGATAGCATTTTAGCATCGTTAAGTGAACTTTCATCACTCAAAACTTTAAATCTAGTA
65 ATTTTGATGATAGCATTTTAGCATCGTTAAGTGAACTTTCATCACTCAAAACTTTAAATCTAGCA
* * *
2037191 AGCAATCAATTCGGACAATCAAATCCTAGTGATGGTAAAGTTAATATATGAATTTGCTGTAGGTT
130 AGCAATCAATTCGGACAATCAAATCCTAGTGATGGTAAAGATAATATAGGAATTTGCTGCAGGTT
*
2037256 GAAGTAAATAAATTTTGCAACTCATATATATTATGTATAACTTTTTTTT
195 GAAGTAAATAAATTTTGCAACTCATATATATTATGTATAACTTTTTCTT
* * * * * *
2037305 TGTAGGTTTTGA-GAAGTTGTCATCGAAATTAGACAAATTAGAGATTCTAGACTTAAGTTTTAAT
1 TGTAGGTTTT-ACGAAGCTGGCATCGAAATTGGACAAACTAGAGATTCTA-ACTTAAATTATAAT
* * * ** *
2037369 AATTTTGATGACAGCATTTTAGCATTGTTAAGTGAACTTTCATCACTCAAGTCCTTAAATCTAGC
64 TATTTTGATGATAGCATTTTAGCATCGTTAAGTGAACTTTCATCACTCAAAACTTTAAATCTAGC
*
2037434 AAGCAACCAATTC
129 AAGCAATCAATTC
2037447 ACAGGGTCAA
Statistics
Matches: 349, Mismatches: 33, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
243 2 0.01
244 343 0.98
245 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (243 bp):
TGTAGGTTTTACGAAGCTGGCATCGAAATTGGACAAACTAGAGATTCTAACTTAAATTATAATTA
TTTTGATGATAGCATTTTAGCATCGTTAAGTGAACTTTCATCACTCAAAACTTTAAATCTAGCAA
GCAATCAATTCGGACAATCAAATCCTAGTGATGGTAAAGATAATATAGGAATTTGCTGCAGGTTG
AAGTAAATAAATTTTGCAACTCATATATATTATGTATAACTTTTTCTT
Found at i:2040561 original size:23 final size:26
Alignment explanation
Indices: 2040534--2040581 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 26
2040524 TTTTAAACTA
2040534 TTATTTAACA-GTAAT-GA-AATTAT
1 TTATTTAACAGGTAATAGAGAATTAT
*
2040557 TTATTTTACAGGTAATAGAGAATTA
1 TTATTTAACAGGTAATAGAGAATTA
2040582 AGGTTGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 2 0.10
26 5 0.24
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (26 bp):
TTATTTAACAGGTAATAGAGAATTAT
Found at i:2042243 original size:6 final size:7
Alignment explanation
Indices: 2042227--2042262 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
2042217 ATAAGGAAAT
2042227 AAAATTA
1 AAAATTA
2042234 AAAATTA
1 AAAATTA
2042241 AAAATTA
1 AAAATTA
2042248 AAAATT-
1 AAAATTA
2042254 AAAATTA
1 AAAATTA
2042261 AA
1 AA
2042263 CATATTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATTA
Found at i:2045980 original size:69 final size:69
Alignment explanation
Indices: 2045869--2046014 Score: 256
Period size: 69 Copynumber: 2.1 Consensus size: 69
2045859 CTCCAACCTC
*
2045869 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTTGAGAG
1 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTTAAGAG
2045934 TCTA
66 TCTA
** *
2045938 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATATCTGCTCTTAAGAG
1 ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTTAAGAG
2046003 TCTA
66 TCTA
2046007 ACATCCCT
1 ACATCCCT
2046015 CCAAGTGCTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (69 bp):
ACATCCCTTCAAACATTAGATCTCTCTTCCAATCAATTTTCTGGAAATATAAATGCCCTTAAGAG
TCTA
Found at i:2053192 original size:22 final size:23
Alignment explanation
Indices: 2053144--2053195 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2053134 AATATAATCG
* *
2053144 ATATTT-TTATTTATAAATTAAA
1 ATATTTATTATTAATAAATAAAA
*
2053166 TTATTTATTATTAAT-AATAAAA
1 ATATTTATTATTAATAAATAAAA
2053188 ATATTTAT
1 ATATTTAT
2053196 AATGATAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTTATTATTAATAAATAAAA
Found at i:2056371 original size:10 final size:10
Alignment explanation
Indices: 2056358--2056404 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
2056348 AAAACTGAGA
2056358 AAAAAAAAAG
1 AAAAAAAAAG
*
2056368 AAAATAAAAG
1 AAAAAAAAAG
2056378 AGAAAAAAAAG
1 A-AAAAAAAAG
*
2056389 GAAAAAAAAG
1 AAAAAAAAAG
2056399 AAAAAA
1 AAAAAA
2056405 TACATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 24 0.75
11 8 0.25
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:2056383 original size:21 final size:19
Alignment explanation
Indices: 2056358--2056404 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 19
2056348 AAAACTGAGA
2056358 AAAAAAAAAGAAAATAAAAG
1 AAAAAAAAAGAAAA-AAAAG
2056378 AGAAAAAAAAGGAAAAAAAAG
1 A-AAAAAAAA-GAAAAAAAAG
2056399 AAAAAA
1 AAAAAA
2056405 TACATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.24
21 14 0.56
22 5 0.20
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAGAAAAAAAAG
Found at i:2056447 original size:21 final size:19
Alignment explanation
Indices: 2056410--2056448 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
2056400 AAAAATACAT
*
2056410 ATTTATATTTATGTTTTTC
1 ATTTATATTTATATTTTTC
2056429 ATTTATAATATTATATTTTT
1 ATTTAT-AT-TTATATTTTT
2056449 ATATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
ATTTATATTTATATTTTTC
Found at i:2056472 original size:15 final size:15
Alignment explanation
Indices: 2056430--2056478 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2056420 ATGTTTTTCA
2056430 TTTATAATATT-ATAT
1 TTTAT-ATATTAATAT
*
2056445 TTT-TATATAAATAT
1 TTTATATATTAATAT
*
2056459 TTTATATATTAATAA
1 TTTATATATTAATAT
2056474 TTTAT
1 TTTAT
2056479 TTTATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.14
14 8 0.28
15 17 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTATATATTAATAT
Found at i:2057064 original size:10 final size:10
Alignment explanation
Indices: 2057044--2057085 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
2057034 AACGAGAAAA
2057044 AAAGA-AAAG
1 AAAGACAAAG
2057053 AAAGACAAAG
1 AAAGACAAAG
* *
2057063 AAAAAAAAAG
1 AAAGACAAAG
2057073 AAAGACAAAG
1 AAAGACAAAG
2057083 AAA
1 AAA
2057086 AAATTTTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 5 0.18
10 23 0.82
ACGTcount: A:0.79, C:0.05, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAGACAAAG
Found at i:2057066 original size:20 final size:20
Alignment explanation
Indices: 2057025--2057086 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
2057015 GAAGAGAAGG
* *
2057025 AAGAAAATGAACGAGAAA-AA
1 AAGAAAA-GAAAGACAAAGAA
2057045 AAGAAAAGAAAGACAAAGAA
1 AAGAAAAGAAAGACAAAGAA
*
2057065 AAAAAAAGAAAGACAAAGAA
1 AAGAAAAGAAAGACAAAGAA
2057085 AA
1 AA
2057087 AATTTTGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 8 0.21
20 30 0.79
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.02
Consensus pattern (20 bp):
AAGAAAAGAAAGACAAAGAA
Found at i:2057087 original size:20 final size:20
Alignment explanation
Indices: 2057042--2057088 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
2057032 TGAACGAGAA
2057042 AAAAAGAAAAGAAAGACAAAG
1 AAAAA-AAAAGAAAGACAAAG
2057063 AAAAAAAAAGAAAGACAAAG
1 AAAAAAAAAGAAAGACAAAG
2057083 AAAAAA
1 AAAAAA
2057089 TTTTGTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAAAGACAAAG
Found at i:2057896 original size:22 final size:20
Alignment explanation
Indices: 2057860--2057906 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2057850 TTACAAAACT
*
2057860 GAGAAAAAAAGAAAATAAGA
1 GAGAAAAAAAGAAAAAAAGA
2057880 GAGAAAAAAAGGAAAAAAA-A
1 GAGAAAAAAA-GAAAAAAAGA
2057900 GA-AAAAA
1 GAGAAAAA
2057907 TATATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 5 0.20
20 13 0.52
21 7 0.28
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (20 bp):
GAGAAAAAAAGAAAAAAAGA
Found at i:2057898 original size:10 final size:9
Alignment explanation
Indices: 2057863--2057906 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
2057853 CAAAACTGAG
2057863 AAAAAAAGA
1 AAAAAAAGA
2057872 AAATAAGAGAGA
1 AAA-AA-A-AGA
*
2057884 AAAAAAGGA
1 AAAAAAAGA
2057893 AAAAAAAGA
1 AAAAAAAGA
2057902 AAAAA
1 AAAAA
2057907 TATATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 18 0.60
10 3 0.10
11 3 0.10
12 6 0.20
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:2057949 original size:21 final size:19
Alignment explanation
Indices: 2057912--2057950 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
2057902 AAAAATATAT
*
2057912 ATTTATATTTATGTTTTTC
1 ATTTATATTTATATTTTTC
2057931 ATTTATAATATTATATTTTT
1 ATTTAT-AT-TTATATTTTT
2057951 ACATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
ATTTATATTTATATTTTTC
Found at i:2058407 original size:13 final size:13
Alignment explanation
Indices: 2058391--2058435 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
2058381 CTCCCTCATA
2058391 CCTCTCAAGCATC
1 CCTCTCAAGCATC
*
2058404 CCTCTTAAGCATC
1 CCTCTCAAGCATC
*
2058417 TCTCTCAAGCATC
1 CCTCTCAAGCATC
2058430 CCTCTC
1 CCTCTC
2058436 TTGTATCCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.20, C:0.44, G:0.07, T:0.29
Consensus pattern (13 bp):
CCTCTCAAGCATC
Found at i:2064632 original size:2 final size:2
Alignment explanation
Indices: 2064627--2064651 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2064617 AGCCTTGTTT
2064627 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2064652 TTTCAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2066125 original size:34 final size:34
Alignment explanation
Indices: 2066061--2066243 Score: 269
Period size: 34 Copynumber: 5.4 Consensus size: 34
2066051 TATATATATA
* *
2066061 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
2066094 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
2066128 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
2066162 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
2066196 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
2066230 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2066244 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 11 0.08
34 123 0.92
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:2066236 original size:102 final size:101
Alignment explanation
Indices: 2066061--2066243 Score: 321
Period size: 102 Copynumber: 1.8 Consensus size: 101
2066051 TATATATATA
2066061 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
2066126 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
2066162 TGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTAC
2066227 CATTGTTGATTAAATGG
65 CATTGTTGATTAAATGG
2066244 TGGTTTTTAC
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 12 0.16
102 65 0.84
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:2070720 original size:34 final size:34
Alignment explanation
Indices: 2070654--2070838 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
2070644 AAGTGGGAGA
* *
2070654 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2070687 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2070721 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2070755 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2070789 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2070823 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2070839 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.10
34 123 0.90
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2070829 original size:102 final size:101
Alignment explanation
Indices: 2070654--2070838 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
2070644 AAGTGGGAGA
2070654 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
2070719 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2070755 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
*
2070820 GCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
2070839 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2078270 original size:108 final size:109
Alignment explanation
Indices: 2078067--2078278 Score: 284
Period size: 111 Copynumber: 1.9 Consensus size: 109
2078057 CAGCATTTGT
* *
2078067 TTTAATAATAAAGCGCATATACTTCTCGTGTTTGAATATCTCTTTCTCAAATAATAATAATAATA
1 TTTAATAATAAAGCGCATATAC-TCTCGTGTCTGAATATCTCTTTCTCAAATAACAATAATAATA
*
2078132 ATCGTAAGAAACTTTGAACGATAAATAGACAGTGCATGTAAGACTTGG
65 A---TAAGAAACTTTGAACGACAAATAGACAGTGCATGTAAGACTTGG
* * * * *
2078180 TTTAATGATAAAGTGCATGTAC-CTCGTGTCTGAATCTCTCTTTCTCAAATAACAGTAATAATCA
1 TTTAATAATAAAGCGCATATACTCTCGTGTCTGAATATCTCTTTCTCAAATAACAATAATAAT-A
*
2078244 A-AAGAAACTTTGAATGACAAATAGACAGTGCATGT
65 ATAAGAAACTTTGAACGACAAATAGACAGTGCATGT
2078279 TAGTTGTAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
108 32 0.36
111 36 0.40
112 2 0.02
113 19 0.21
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (109 bp):
TTTAATAATAAAGCGCATATACTCTCGTGTCTGAATATCTCTTTCTCAAATAACAATAATAATAA
TAAGAAACTTTGAACGACAAATAGACAGTGCATGTAAGACTTGG
Found at i:2079275 original size:13 final size:14
Alignment explanation
Indices: 2079230--2079276 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
2079220 AAATAAATAA
2079230 ATAAATTATTATTT
1 ATAAATTATTATTT
*
2079244 -TAAAATATTTATTT
1 ATAAATTA-TTATTT
2079258 AATAAATTATT-TTT
1 -ATAAATTATTATTT
2079272 ATAAA
1 ATAAA
2079277 AAAATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 2 0.07
16 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAAATTATTATTT
Found at i:2085965 original size:2 final size:2
Alignment explanation
Indices: 2085958--2085987 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2085948 GCTCCTTTAG
2085958 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
2085988 TGCTGATTTA
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:2089594 original size:6 final size:6
Alignment explanation
Indices: 2089583--2089611 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2089573 TTCTAAACAA
2089583 ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
2089612 TATTATCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:2094204 original size:2 final size:2
Alignment explanation
Indices: 2094197--2094229 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2094187 GTATACCTGC
2094197 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2094230 CAATTCAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2094999 original size:28 final size:28
Alignment explanation
Indices: 2094959--2095017 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
2094949 CCTAAACCCT
2094959 TAAAATATATAGGATATTGAATCTTAAC
1 TAAAATATATAGGATATTGAATCTTAAC
*
2094987 TAAAATGTATAGGATATTGAATCTTAAC
1 TAAAATATATAGGATATTGAATCTTAAC
2095015 TAA
1 TAA
2095018 TTTGTGCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.36
Consensus pattern (28 bp):
TAAAATATATAGGATATTGAATCTTAAC
Found at i:2105436 original size:20 final size:19
Alignment explanation
Indices: 2105413--2105456 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
2105403 ATTTAAAAAA
2105413 TAATTTATTAATTATATTTT
1 TAATTTATTAATTATA-TTT
* *
2105433 TAATTTTTTAATTTTATTT
1 TAATTTATTAATTATATTT
2105452 TAATT
1 TAATT
2105457 AGTATCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TAATTTATTAATTATATTT
Found at i:2105675 original size:22 final size:20
Alignment explanation
Indices: 2105647--2105690 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
2105637 TATATATTTG
*
2105647 ATTTTATTTTGTTAAGTTTAAA
1 ATTTTATTTTATT-AG-TTAAA
2105669 ATTTTATTTTATTAGTTAAA
1 ATTTTATTTTATTAGTTAAA
2105689 AT
1 AT
2105691 ATATTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 2 0.10
22 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
ATTTTATTTTATTAGTTAAA
Found at i:2106107 original size:19 final size:19
Alignment explanation
Indices: 2106079--2106115 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2106069 GTTATATATG
2106079 TTAATGTTAAAAATAATGA
1 TTAATGTTAAAAATAATGA
* *
2106098 TTAATTTTAATAATAATG
1 TTAATGTTAAAAATAATG
2106116 GAGGTAAGTT
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:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
TTAATGTTAAAAATAATGA
Found at i:2106268 original size:22 final size:22
Alignment explanation
Indices: 2106224--2106266 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2106214 AATATTAAAA
2106224 ATATAATTTTATATTAATATTT
1 ATATAATTTTATATTAATATTT
2106246 ATAT-ATTTTATAATTAA-ATTT
1 ATATAATTTTAT-ATTAATATTT
2106267 TAAAAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATAATTTTATATTAATATTT
Found at i:2119555 original size:14 final size:14
Alignment explanation
Indices: 2119536--2119566 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2119526 CGTCAGTGTC
2119536 TATCTGCGAGAATG
1 TATCTGCGAGAATG
2119550 TATCTGCGAGAATG
1 TATCTGCGAGAATG
2119564 TAT
1 TAT
2119567 ATAACATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (14 bp):
TATCTGCGAGAATG
Found at i:2122007 original size:6 final size:6
Alignment explanation
Indices: 2121996--2122022 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2121986 TGCAAACAAA
2121996 CAAGCT CAAGCT CAAGCT CAAGCT CAA
1 CAAGCT CAAGCT CAAGCT CAAGCT CAA
2122023 TCCTCCCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.33, G:0.15, T:0.15
Consensus pattern (6 bp):
CAAGCT
Found at i:2122189 original size:15 final size:15
Alignment explanation
Indices: 2122162--2122199 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2122152 AGGAACCTCA
2122162 TCATCCTCATCTTCT
1 TCATCCTCATCTTCT
* *
2122177 TCCTCCTCCTCTTCT
1 TCATCCTCATCTTCT
2122192 TCATCCTC
1 TCATCCTC
2122200 TCCATTCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.47, G:0.00, T:0.45
Consensus pattern (15 bp):
TCATCCTCATCTTCT
Found at i:2124992 original size:9 final size:10
Alignment explanation
Indices: 2124962--2125000 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
2124952 ATGAAAAAAT
2124962 ATTTTTTTTAA
1 ATTTTTTTT-A
2124973 ATTTTAATTTTA
1 ATTTT--TTTTA
2124985 ATTTTTTTTA
1 ATTTTTTTTA
2124995 ATTTTT
1 ATTTTT
2125001 CAATCACCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 11 0.42
11 5 0.19
12 6 0.23
13 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:2143979 original size:2 final size:2
Alignment explanation
Indices: 2143972--2144020 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2143962 TTAGTTTCCT
2143972 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2144014 TA TA TA T
1 TA TA TA T
2144021 CCACAGTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2147025 original size:30 final size:28
Alignment explanation
Indices: 2146991--2147063 Score: 71
Period size: 30 Copynumber: 2.6 Consensus size: 28
2146981 ATAAGTGACT
*
2146991 TAATTTATTAATAA-TAGAAATTTAATGATA
1 TAATTTA-TAA-AATTAAAAATTT-ATGATA
2147021 TAATTTGATAAAATTAAAAATTTATGATA
1 TAATTT-ATAAAATTAAAAATTTATGATA
*
2147050 T-ATTTA-AAAGTTAA
1 TAATTTATAAAATTAA
2147064 TGTTAAGTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
26 7 0.18
27 1 0.03
28 4 0.10
29 9 0.23
30 17 0.44
31 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (28 bp):
TAATTTATAAAATTAAAAATTTATGATA
Found at i:2149131 original size:3 final size:3
Alignment explanation
Indices: 2149123--2149152 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2149113 CTATTTTATG
2149123 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2149153 GATTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2156932 original size:2 final size:2
Alignment explanation
Indices: 2156925--2156954 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2156915 TTAGAATGAA
2156925 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
2156955 GGTTTACACA
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:2159189 original size:16 final size:16
Alignment explanation
Indices: 2159150--2159189 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2159140 TTTAGATAAC
*
2159150 TTTAAATTCAAATTAT
1 TTTAGATTCAAATTAT
* *
2159166 GTTGGATTCAAATTAT
1 TTTAGATTCAAATTAT
2159182 TTTAGATT
1 TTTAGATT
2159190 TGTATTATTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (16 bp):
TTTAGATTCAAATTAT
Found at i:2161516 original size:20 final size:20
Alignment explanation
Indices: 2161477--2161516 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2161467 ATATCTTAGC
* *
2161477 GATGAGATAAAAGGATATTA
1 GATGAGATAAAAAGACATTA
2161497 GATGAGATAAAAAGACATTA
1 GATGAGATAAAAAGACATTA
2161517 AAAAAAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.23
Consensus pattern (20 bp):
GATGAGATAAAAAGACATTA
Found at i:2162794 original size:15 final size:14
Alignment explanation
Indices: 2162774--2162817 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
2162764 TTGACATTTC
2162774 AAATTTAATTAATTA
1 AAATTTAATT-ATTA
*
2162789 AAATTTAA-TATTC
1 AAATTTAATTATTA
2162802 AAATTTAATTTATTA
1 AAATTTAA-TTATTA
2162817 A
1 A
2162818 TTTTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 11 0.44
14 1 0.04
15 13 0.52
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTATTA
Found at i:2162807 original size:13 final size:14
Alignment explanation
Indices: 2162771--2162810 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
2162761 AGTTTGACAT
2162771 TTCAAATTTAATTAA
1 TTCAAATTTAA-TAA
*
2162786 TTAAAATTTAAT-A
1 TTCAAATTTAATAA
2162799 TTCAAATTTAAT
1 TTCAAATTTAAT
2162811 TTATTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 1 0.04
15 10 0.43
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (14 bp):
TTCAAATTTAATAA
Found at i:2162833 original size:28 final size:28
Alignment explanation
Indices: 2162772--2162831 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
2162762 GTTTGACATT
*
2162772 TCAAATTTAATTAATTAAAATTTAATAT
1 TCAAATTTAATTAATTAAAATTTAATAA
* **
2162800 TCAAATTTAATTTATTAATTTTTAA-AA
1 TCAAATTTAATTAATTAAAATTTAATAA
2162827 TCAAA
1 TCAAA
2162832 ATAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (28 bp):
TCAAATTTAATTAATTAAAATTTAATAA
Found at i:2164321 original size:16 final size:16
Alignment explanation
Indices: 2164295--2164344 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2164285 AAAAAATTAA
2164295 AATTAATTTTAAATTTG
1 AATT-ATTTTAAATTTG
*
2164312 AATTATTTTATATTT-
1 AATTATTTTAAATTTG
*
2164327 AGATTATTTTGAATTTG
1 A-ATTATTTTAAATTTG
2164344 A
1 A
2164345 TATGTTGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.04
16 22 0.79
17 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (16 bp):
AATTATTTTAAATTTG
Found at i:2164365 original size:30 final size:32
Alignment explanation
Indices: 2164329--2164392 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
2164319 TTATATTTAG
*
2164329 ATTATTTT-GAATTT-GAT-ATGTTGGATTCAA
1 ATTATTTTAG-ATTTGGATCATGTTAGATTCAA
*
2164359 ATTATTTTAGATTTGGATCATTTTAGATTCAA
1 ATTATTTTAGATTTGGATCATGTTAGATTCAA
2164391 AT
1 AT
2164393 AGTTAATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 12 0.41
31 4 0.14
32 13 0.45
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (32 bp):
ATTATTTTAGATTTGGATCATGTTAGATTCAA
Found at i:2170717 original size:17 final size:18
Alignment explanation
Indices: 2170678--2170725 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
2170668 TTAAAATAAA
*
2170678 TTAATAATTTATATTATAT
1 TTAAT-ATTTTTATTATAT
2170697 TTAATATTTTTATTA-AT
1 TTAATATTTTTATTATAT
2170714 TTAATATTTTTA
1 TTAATATTTTTA
2170726 AATAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 14 0.50
18 9 0.32
19 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTAATATTTTTATTATAT
Found at i:2171842 original size:24 final size:24
Alignment explanation
Indices: 2171814--2171859 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2171804 GTAGTTATTT
*
2171814 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATAGTGGCTTG
* *
2171838 TTGTTTGTCAAAATTAGTGGCT
1 TTGTTTGTAAAAAATAGTGGCT
2171860 AATTTTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATAGTGGCTTG
Found at i:2177029 original size:19 final size:19
Alignment explanation
Indices: 2177005--2177041 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2176995 AGGTGGAGAT
2177005 TTATGGTGGATGGCTATCC
1 TTATGGTGGATGGCTATCC
*
2177024 TTATGGTGGGTGGCTATC
1 TTATGGTGGATGGCTATC
2177042 TCTAGTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.14, G:0.35, T:0.38
Consensus pattern (19 bp):
TTATGGTGGATGGCTATCC
Found at i:2177123 original size:28 final size:28
Alignment explanation
Indices: 2177061--2177115 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
2177051 CAAATGTCAC
2177061 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTGTATTTGTCAAATATGGTGGTTT
*
2177089 CCTTTGTATTTTTCAAATATGGTGGTT
1 CCTTTGTATTTGTCAAATATGGTGGTT
2177116 ATTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (28 bp):
CCTTTGTATTTGTCAAATATGGTGGTTT
Found at i:2178135 original size:28 final size:27
Alignment explanation
Indices: 2178076--2178165 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 27
2178066 CACCAATTTG
* *
2178076 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
2178103 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
2178131 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
2178156 TTTGTCAAAA
1 TTTGTCAAAA
2178166 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.06
27 19 0.35
28 21 0.39
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:2178246 original size:20 final size:20
Alignment explanation
Indices: 2178221--2178266 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2178211 AAATAGAGGC
*
2178221 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
2178241 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
2178261 TCCCTC
1 TCCCTC
2178267 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:2180746 original size:21 final size:22
Alignment explanation
Indices: 2180717--2180762 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2180707 TGTTCAGACA
** *
2180717 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2180739 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2180760 AGT
1 AGT
2180763 TTCAACAGAT
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:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2182707 original size:28 final size:27
Alignment explanation
Indices: 2182648--2182737 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 27
2182638 CACCAATTTG
* *
2182648 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
2182675 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
2182703 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
2182728 TTTGTCAAAA
1 TTTGTCAAAA
2182738 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.06
27 19 0.35
28 21 0.39
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:2182818 original size:20 final size:20
Alignment explanation
Indices: 2182793--2182838 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2182783 AAATAGAGGC
*
2182793 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
2182813 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
2182833 TCCCTC
1 TCCCTC
2182839 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:2183835 original size:17 final size:18
Alignment explanation
Indices: 2183807--2183842 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2183797 TTTATGTTAT
*
2183807 ATTAATTATTTTTATTAA
1 ATTAATTATTTTTAATAA
2183825 ATTAA-TATTTTTAATAA
1 ATTAATTATTTTTAATAA
2183842 A
1 A
2183843 ATTACATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTAATTATTTTTAATAA
Found at i:2183844 original size:18 final size:18
Alignment explanation
Indices: 2183807--2183846 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2183797 TTTATGTTAT
*
2183807 ATTAATTATTTTTATTAA
1 ATTAATTATTTTTATAAA
2183825 ATTAA-TATTTTTAATAAA
1 ATTAATTATTTTT-ATAAA
2183843 ATTA
1 ATTA
2183847 CATTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTAATTATTTTTATAAA
Found at i:2183925 original size:23 final size:24
Alignment explanation
Indices: 2183886--2183930 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
2183876 TTCGGGCTTA
2183886 TTTAAATTCAAATAG-TTAATTAG
1 TTTAAATTCAAATAGTTTAATTAG
*
2183909 TTTAAATT-AGATAAGTTTAATT
1 TTTAAATTCAAAT-AGTTTAATT
2183931 TGTGAAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 10 0.53
24 6 0.32
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (24 bp):
TTTAAATTCAAATAGTTTAATTAG
Found at i:2184828 original size:16 final size:16
Alignment explanation
Indices: 2184801--2184899 Score: 105
Period size: 16 Copynumber: 6.2 Consensus size: 16
2184791 TAAAATATTA
2184801 AAATTAATTTTAAATTT
1 AAATT-ATTTTAAATTT
*
2184818 AAATTATTTTATATTT
1 AAATTATTTTAAATTT
*
2184834 GAATTACTTTT-AATTT
1 AAATTA-TTTTAAATTT
* *
2184850 -GA-TATGTTAAATTT
1 AAATTATTTTAAATTT
*
2184864 AAATTATTTTAGATTT
1 AAATTATTTTAAATTT
*
2184880 AAATTATTTTAAATTA
1 AAATTATTTTAAATTT
2184896 AAAT
1 AAAT
2184900 AATTCATATT
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
13 3 0.04
14 7 0.10
15 2 0.03
16 47 0.69
17 9 0.13
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (16 bp):
AAATTATTTTAAATTT
Found at i:2185611 original size:19 final size:19
Alignment explanation
Indices: 2185587--2185624 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2185577 TATAACCAAA
2185587 AAAGTTAAAATTTTAAATT
1 AAAGTTAAAATTTTAAATT
**
2185606 AAAGTTTTAATTTTAAATT
1 AAAGTTAAAATTTTAAATT
2185625 TTGTTTTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
AAAGTTAAAATTTTAAATT
Found at i:2190644 original size:15 final size:17
Alignment explanation
Indices: 2190624--2190660 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2190614 TATATGTTGT
2190624 TTAATG-TTTATTT-TA
1 TTAATGATTTATTTATA
2190639 TTAATGTATTTATTTATA
1 TTAATG-ATTTATTTATA
2190657 TTAA
1 TTAA
2190661 ACAATTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
17 7 0.37
18 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
TTAATGATTTATTTATA
Found at i:2190906 original size:29 final size:29
Alignment explanation
Indices: 2190843--2190912 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
2190833 GAAATTAATA
*
2190843 AAAATAATATAATAAATAAAAAAAAATTTT
1 AAAACAATATAATAAAT-AAAAAAAATTTT
* *
2190873 GAAACAATATCATAAAT-AAAAAAATTTT
1 AAAACAATATAATAAATAAAAAAAATTTT
2190901 CAAAACAATATA
1 -AAAACAATATA
2190913 CTATAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 11 0.32
29 9 0.26
30 14 0.41
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (29 bp):
AAAACAATATAATAAATAAAAAAAATTTT
Found at i:2190921 original size:28 final size:27
Alignment explanation
Indices: 2190860--2190921 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 27
2190850 TATAATAAAT
*
2190860 AAAAAAAAATTTTGAAACAATATCATA
1 AAAAAAAAATTTTAAAACAATATCATA
2190887 AATAAAAAAATTTTCAAAACAATATACTATA
1 AA-AAAAAAATTTT-AAAACAATAT-C-ATA
2190918 AAAA
1 AAAA
2190922 TAATATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.07
28 11 0.37
29 9 0.30
30 3 0.10
31 5 0.17
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.26
Consensus pattern (27 bp):
AAAAAAAAATTTTAAAACAATATCATA
Found at i:2191607 original size:76 final size:82
Alignment explanation
Indices: 2191527--2191675 Score: 229
Period size: 81 Copynumber: 1.9 Consensus size: 82
2191517 GTGAAAATAA
*
2191527 TAAATAGC-A-AAAAAT-AAAGCAAAAAT-A-AAAATAAAGAAAATATTTTTCTTCGTTTCTC-A
1 TAAATAGCAACAAAAATCAAAGCAAAAATAACAAAAAAAAGAAAATATTTTTCTTCGTTTCTCAA
2191586 TTTTTTTTCTTTTTTTT
66 TTTTTTTTCTTTTTTTT
* *
2191603 TAAATAGCAACAAAAATCAAAGCAACAATAACAAAAAAAATAAAATATTTTTCTTCGTTTCTCAA
1 TAAATAGCAACAAAAATCAAAGCAAAAATAACAAAAAAAAGAAAATATTTTTCTTCGTTTCTCAA
2191668 TTTTTTTT
66 TTTTTTTT
2191676 TCTAAATAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
76 8 0.12
77 1 0.02
78 6 0.09
79 10 0.16
80 1 0.02
81 29 0.45
82 9 0.14
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (82 bp):
TAAATAGCAACAAAAATCAAAGCAAAAATAACAAAAAAAAGAAAATATTTTTCTTCGTTTCTCAA
TTTTTTTTCTTTTTTTT
Found at i:2191739 original size:75 final size:73
Alignment explanation
Indices: 2191595--2191740 Score: 170
Period size: 74 Copynumber: 2.0 Consensus size: 73
2191585 ATTTTTTTTC
* * **** *
2191595 TTTTTTTTTAAATAGCAACAAAAATCAAAGCAACAATAACAAAAAAAATAAAATATTTTTCTTCG
1 TTTTTTTTTAAATAGCAAAAAAAATCAAAGCAACAATAACAAAAAAAATAAAAAAAAAATATTC-
2191660 TTTCTCAAT
65 TTTCTCAAT
2191669 TTTTTTTTCTAAATAG-AAAAAAAATCAAAGCAACAATAACAAAAAAAATAAATAAAAGAAAATA
1 TTTTTTTT-TAAATAGCAAAAAAAATCAAAGCAACAATAACAAAAAAAAT-AA-AAAA-AAAATA
2191733 TT-TTTCTC
62 TTCTTTCTC
2191741 CAGTCAGCCT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
74 40 0.66
75 15 0.25
76 3 0.05
77 3 0.05
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (73 bp):
TTTTTTTTTAAATAGCAAAAAAAATCAAAGCAACAATAACAAAAAAAATAAAAAAAAAATATTCT
TTCTCAAT
Found at i:2192182 original size:22 final size:21
Alignment explanation
Indices: 2192151--2192203 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
2192141 AAATAAGTAA
2192151 AATTTATTTAAAT-TTAATTAT
1 AATTTATTTAAATATTAA-TAT
2192172 AATTATATTTAAATATTAATAT
1 AATT-TATTTAAATATTAATAT
2192194 AAATTT-TTTA
1 -AATTTATTTA
2192204 TATTTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.28
22 13 0.45
23 8 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTTATTTAAATATTAATAT
Found at i:2192538 original size:20 final size:19
Alignment explanation
Indices: 2192509--2192568 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 19
2192499 TTAATTTGAT
*
2192509 ATTATATAAACAATTAAAAA
1 ATTATTTAAACAA-TAAAAA
* *
2192529 ATTATTTAAATTAATATAAA
1 ATTATTTAAA-CAATAAAAA
*
2192549 ATTAATTTAATCAATAAAAA
1 ATT-ATTTAAACAATAAAAA
2192569 TTTTAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 24 0.75
21 8 0.25
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTATTTAAACAATAAAAA
Found at i:2193635 original size:20 final size:20
Alignment explanation
Indices: 2193561--2193678 Score: 84
Period size: 20 Copynumber: 5.8 Consensus size: 20
2193551 AGATTATAAA
*
2193561 TTTAATATATTAATATTAATAT
1 TTTAATA-A-TAATAATAATAT
* *
2193583 TTGAAAAATAATAAATAATA-
1 TTTAATAATAAT-AATAATAT
2193603 -TTAAT-AT-A-AATAATAT
1 TTTAATAATAATAATAATAT
*
2193619 TTTAATAATAATGATAATAT
1 TTTAATAATAATAATAATAT
*
2193639 TTTAAATATTAATATAATTAATAT
1 TTT-AATAAT-A-ATAA-TAATAT
2193663 TTTAATAATAAATAAT
1 TTTAATAAT-AATAAT
2193679 TTAGACTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
15 7 0.09
17 6 0.08
18 4 0.05
19 4 0.05
20 14 0.18
21 13 0.17
22 10 0.13
23 10 0.13
24 9 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TTTAATAATAATAATAATAT
Found at i:2193887 original size:10 final size:10
Alignment explanation
Indices: 2193826--2193907 Score: 62
Period size: 10 Copynumber: 8.4 Consensus size: 10
2193816 TTTATTTATA
2193826 TAAATTT-AT
1 TAAATTTAAT
* *
2193835 CAATTTTAAT
1 TAAATTTAAT
*
2193845 TGAAATTTAAA
1 T-AAATTTAAT
* *
2193856 AAAATATAAT
1 TAAATTTAAT
2193866 T-AATTT-AT
1 TAAATTTAAT
2193874 TAAATTTAAT
1 TAAATTTAAT
*
2193884 TAAATTTGAT
1 TAAATTTAAT
* *
2193894 TCAATTTGAT
1 TAAATTTAAT
2193904 TAAA
1 TAAA
2193908 AAAAATTAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
8 3 0.05
9 14 0.25
10 32 0.57
11 7 0.12
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (10 bp):
TAAATTTAAT
Found at i:2194336 original size:16 final size:16
Alignment explanation
Indices: 2194317--2194368 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2194307 TTCAAATTTA
2194317 AAATAACTCAAAACTG
1 AAATAACTCAAAACTG
** *
2194333 AAATAA-TTTAAACTCA
1 AAATAACTCAAAACT-G
*
2194349 AAATAACTCGAAACTG
1 AAATAACTCAAAACTG
2194365 AAAT
1 AAAT
2194369 GATCCAAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 6 0.21
16 16 0.57
17 6 0.21
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.23
Consensus pattern (16 bp):
AAATAACTCAAAACTG
Found at i:2194383 original size:32 final size:32
Alignment explanation
Indices: 2194316--2194376 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
2194306 ATTCAAATTT
**
2194316 AAAATAACTCAAAACTGAAATAATTTAAACTC
1 AAAATAACTCAAAACTGAAATAATCCAAACTC
* *
2194348 AAAATAACTCGAAACTGAAATGATCCAAA
1 AAAATAACTCAAAACTGAAATAATCCAAA
2194377 TCCAAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.21
Consensus pattern (32 bp):
AAAATAACTCAAAACTGAAATAATCCAAACTC
Found at i:2194401 original size:16 final size:17
Alignment explanation
Indices: 2194382--2194414 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2194372 CCAAATCCAA
*
2194382 AAATGATCAAAA-AATT
1 AAATAATCAAAATAATT
2194398 AAATAATCAAAATAATT
1 AAATAATCAAAATAATT
2194415 TATCTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
AAATAATCAAAATAATT
Found at i:2195005 original size:2 final size:2
Alignment explanation
Indices: 2194998--2195029 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2194988 ACAAGGACAA
2194998 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
2195030 GATTTAACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2198272 original size:2 final size:2
Alignment explanation
Indices: 2198265--2198309 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2198255 ACATAAATAC
2198265 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
2198307 AT A
1 AT A
2198310 AACACATTAG
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:2198820 original size:2 final size:2
Alignment explanation
Indices: 2198813--2198847 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
2198803 TCATCTCTTT
*
2198813 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
2198848 ATTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2201339 original size:5 final size:5
Alignment explanation
Indices: 2201282--2201322 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
2201272 ATACAATAAA
2201282 AATA- AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
2201323 CATACAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:2206583 original size:13 final size:13
Alignment explanation
Indices: 2206565--2206592 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2206555 TATTAAAATT
2206565 AAAATAAATAATA
1 AAAATAAATAATA
2206578 AAAATAAATAATA
1 AAAATAAATAATA
2206591 AA
1 AA
2206593 TATTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAATAATA
Found at i:2206601 original size:20 final size:19
Alignment explanation
Indices: 2206556--2206602 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2206546 TATTATTTAT
*
2206556 ATTAAAATTAAAATAAATA
1 ATTAAAATAAAAATAAATA
*
2206575 ATAAAAATAAATAATAAATA
1 ATTAAAATAAA-AATAAATA
*
2206595 TTTAAAAT
1 ATTAAAAT
2206603 TTATATATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTAAAATAAAAATAAATA
Found at i:2207668 original size:3 final size:3
Alignment explanation
Indices: 2207660--2207694 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2207650 AAATACCTCG
2207660 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2207695 CAAATATTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2213444 original size:19 final size:18
Alignment explanation
Indices: 2213420--2213456 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
2213410 TAACAAATTA
2213420 AATTTAAATTTATTATTTT
1 AATTTAAATTTA-TATTTT
2213439 AATTTAAATTTATATTTT
1 AATTTAAATTTATATTTT
2213457 CAATCATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTAAATTTATATTTT
Found at i:2215753 original size:31 final size:29
Alignment explanation
Indices: 2215708--2215768 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 29
2215698 AATATATTTA
2215708 TATATTCATATTAATTAATAATTTTTTATAT
1 TATATTCATATTAA-TAATAA-TTTTTATAT
*
2215739 TATATT-ATATTTAATAATTATTTTTATAT
1 TATATTCATA-TTAATAATAATTTTTATAT
2215768 T
1 T
2215769 TTAATTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 10 0.36
30 8 0.29
31 10 0.36
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
TATATTCATATTAATAATAATTTTTATAT
Found at i:2215756 original size:27 final size:28
Alignment explanation
Indices: 2215695--2215768 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 28
2215685 CTATATAAAT
*
2215695 TTTAAT-ATATTTATATATTCATATTAA
1 TTTAATAATATTTTTATATTCATATTAA
2215722 -TTAATAAT-TTTTTATATT-ATATTATA
1 TTTAATAATATTTTTATATTCATATTA-A
2215748 TTTAATAATTATTTTTATATT
1 TTTAATAA-TATTTTTATATT
2215769 TTAATTTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
25 6 0.15
26 15 0.37
27 9 0.22
28 1 0.02
29 10 0.24
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTAATAATATTTTTATATTCATATTAA
Found at i:2221723 original size:18 final size:18
Alignment explanation
Indices: 2221682--2221733 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
2221672 AATAATGTTT
2221682 ATTTATTATAAATTAA-AA
1 ATTTATTAT-AATTAATAA
2221700 ATTTATTATAATTAATTAA
1 ATTTATTATAATTAA-TAA
*
2221719 A-TTA-TATAAATAATA
1 ATTTATTATAATTAATA
2221734 CTCAATATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 2 0.06
17 14 0.45
18 12 0.39
19 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTATTATAATTAATAA
Found at i:2224863 original size:20 final size:20
Alignment explanation
Indices: 2224819--2224859 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2224809 AAATTTTTAT
2224819 AATTTAAATTATCTAAGTTA
1 AATTTAAATTATCTAAGTTA
2224839 AATTTAAATTAT-TAA-TTA
1 AATTTAAATTATCTAAGTTA
2224857 AAT
1 AAT
2224860 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
19 3 0.14
20 12 0.57
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
AATTTAAATTATCTAAGTTA
Found at i:2224892 original size:22 final size:23
Alignment explanation
Indices: 2224865--2224914 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2224855 TAAATATTTT
* *
2224865 TATTTAAAT-TTAATTTTAAAAA
1 TATTTAAATATTAATATAAAAAA
2224887 TATTTAAATATTAATATAAAAAA
1 TATTTAAATATTAATATAAAAAA
2224910 TATTT
1 TATTT
2224915 TTTAATCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTTAAATATTAATATAAAAAA
Found at i:2228035 original size:34 final size:34
Alignment explanation
Indices: 2227971--2228035 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
2227961 ATTTTTTTTA
* *
2227971 TTTTCAATTTAATTATATTAATAATGAATATCAC
1 TTTTCAATTTAATAATATTAATAATAAATATCAC
2228005 TTTT-AATTTAATAAGTATTAA-AGATAAATAT
1 TTTTCAATTTAATAA-TATTAATA-ATAAATAT
2228036 TATTATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 10 0.37
34 17 0.63
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (34 bp):
TTTTCAATTTAATAATATTAATAATAAATATCAC
Found at i:2228148 original size:22 final size:22
Alignment explanation
Indices: 2228096--2228149 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
2228086 ATTTTTATTC
* * *
2228096 TTAAAATTTTTAAAGATACTTT
1 TTAATATTTTTAAAGATAATTA
*
2228118 TTTATATTTTTAAA-ATAATTA
1 TTAATATTTTTAAAGATAATTA
2228139 TTAATCATTTT
1 TTAAT-ATTTT
2228150 AAATTTTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAATATTTTTAAAGATAATTA
Found at i:2230747 original size:33 final size:33
Alignment explanation
Indices: 2230710--2230775 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2230700 AAATTTGAAA
*
2230710 TATTTATAGATATTTATAAAT-TTAAATTATATT
1 TATTTATAGA-ATTTATAAATATAAAATTATATT
* *
2230743 TATTTATATAATTTTTAAATATAAAATTATATT
1 TATTTATAGAATTTATAAATATAAAATTATATT
2230776 AAATCTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 9 0.31
33 20 0.69
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (33 bp):
TATTTATAGAATTTATAAATATAAAATTATATT
Found at i:2232879 original size:29 final size:29
Alignment explanation
Indices: 2232822--2232879 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2232812 ATTTGAAAGA
* * *
2232822 AAATTTCAAATATTTAAAATTTCTCTTTT
1 AAATTTAAAAAATTTAAAATTTCTATTTT
*
2232851 AAATTTAAAAAATTTAAAATTTTTATTTT
1 AAATTTAAAAAATTTAAAATTTCTATTTT
2232880 TACCAAATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (29 bp):
AAATTTAAAAAATTTAAAATTTCTATTTT
Found at i:2233250 original size:2 final size:2
Alignment explanation
Indices: 2233243--2233301 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2233233 CTCTGATTAC
2233243 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2233285 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
2233302 GTGTGTTCTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2233732 original size:2 final size:2
Alignment explanation
Indices: 2233715--2233747 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2233705 TCAAATCCAA
*
2233715 AT AT -T AT AT GT 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
2233748 TTAAATGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2233831 original size:18 final size:18
Alignment explanation
Indices: 2233790--2233832 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2233780 ATTAAAGAAA
2233790 AAAATATAAAAATATGAT
1 AAAATATAAAAATATGAT
*
2233808 ATAATATAAAAATAAT-AT
1 AAAATATAAAAAT-ATGAT
2233826 AAAATAT
1 AAAATAT
2233833 TTATATGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AAAATATAAAAATATGAT
Found at i:2233853 original size:16 final size:17
Alignment explanation
Indices: 2233825--2233884 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 17
2233815 AAAAATAATA
*
2233825 TAAAATATT-TATATGT
1 TAAAATATTATATATAT
2233841 TAAAAT-TTATATA-A-
1 TAAAATATTATATATAT
*
2233855 CATAAATATTA-ATATAT
1 TA-AAATATTATATATAT
2233872 TAAAAT-TTATATA
1 TAAAATATTATATA
2233885 AATTTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
14 1 0.03
15 12 0.34
16 21 0.60
17 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TAAAATATTATATATAT
Found at i:2233897 original size:33 final size:31
Alignment explanation
Indices: 2233827--2233885 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2233817 AAATAATATA
* *
2233827 AAATATTTATATGTTAAAATTTATATAACAT
1 AAATATTAATATATTAAAATTTATATAACAT
2233858 AAATATTAATATATTAAAATTTATATAA
1 AAATATTAATATATTAAAATTTATATAA
2233886 ATTTATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (31 bp):
AAATATTAATATATTAAAATTTATATAACAT
Found at i:2241402 original size:34 final size:37
Alignment explanation
Indices: 2241334--2241411 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 37
2241324 GTTGTGATAC
2241334 GTGG-AATTTGGCCCACCTGGTCTCTATAATGTTGA-T
1 GTGGCAATTTGGCCCACC-GGTCTCTATAATGTTGATT
2241370 GTGGCAATTTGG-CCACC-GTCT-TATTAATGTTGATT
1 GTGGCAATTTGGCCCACCGGTCTCTA-TAATGTTGATT
2241405 GTGGCAA
1 GTGGCAA
2241412 GATGAAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
33 2 0.05
34 13 0.33
35 8 0.21
36 9 0.23
37 7 0.18
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (37 bp):
GTGGCAATTTGGCCCACCGGTCTCTATAATGTTGATT
Found at i:2241804 original size:6 final size:6
Alignment explanation
Indices: 2241788--2241865 Score: 50
Period size: 6 Copynumber: 12.0 Consensus size: 6
2241778 TTTATCAAAA
** *
2241788 TTAATAT TTAAAT TTAATAT TTTTAT TTAATTTT TTAAAAT ATTAAA-
1 TTAA-AT TTAAAT TTAA-AT TTAAAT TTAA--AT TT-AAAT -TTAAAT
*
2241835 TAAAAT TTTAAAT TTAAAT TTAAAT TTAAAT
1 TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT
2241866 ATATAACTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
5 4 0.07
6 28 0.50
7 17 0.30
8 5 0.09
9 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:2241806 original size:13 final size:13
Alignment explanation
Indices: 2241788--2241863 Score: 56
Period size: 12 Copynumber: 6.3 Consensus size: 13
2241778 TTTATCAAAA
2241788 TTAATATTTAAAT
1 TTAATATTTAAAT
**
2241801 TTAATATTTTTAT
1 TTAATATTTAAAT
* *
2241814 TTAATTTTTTAA-
1 TTAATATTTAAAT
2241826 --AATA-TTAAAT
1 TTAATATTTAAAT
**
2241836 AAAAT-TTTAAAT
1 TTAATATTTAAAT
2241848 TTAA-ATTTAAAT
1 TTAATATTTAAAT
2241860 TTAA
1 TTAA
2241864 ATATATAACT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
9 4 0.08
10 3 0.06
12 22 0.44
13 21 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAATATTTAAAT
Found at i:2250002 original size:21 final size:21
Alignment explanation
Indices: 2249978--2250036 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 21
2249968 TTATTTCTAG
2249978 TGAATGCTTACTTAGTATTGA
1 TGAATGCTTACTTAGTATTGA
* * *
2249999 TGAA-ACTTA-TT--TCTAG-
1 TGAATGCTTACTTAGTATTGA
2250015 TGAATGCTTACTTAGTATTGA
1 TGAATGCTTACTTAGTATTGA
2250036 T
1 T
2250037 AAAACTTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 10
0.63 0.14 0.23
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 2 0.07
19 2 0.07
20 7 0.26
21 5 0.19
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (21 bp):
TGAATGCTTACTTAGTATTGA
Found at i:2250018 original size:37 final size:37
Alignment explanation
Indices: 2249968--2250047 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
2249958 TTTGTTTCAG
*
2249968 TTATTTCTAGTGAATGCTTACTTAGTATTGATGAAAC
1 TTATTTCTAGTGAATGCTTACTTAGTATTGATAAAAC
2250005 TTATTTCTAGTGAATGCTTACTTAGTATTGATAAAAC
1 TTATTTCTAGTGAATGCTTACTTAGTATTGATAAAAC
2250042 TTATTT
1 TTATTT
2250048 TTGTTGTTCC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (37 bp):
TTATTTCTAGTGAATGCTTACTTAGTATTGATAAAAC
Found at i:2251491 original size:21 final size:22
Alignment explanation
Indices: 2251467--2251518 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
2251457 TAAAGGGTTT
2251467 TTATGTTCT-TTATTATTATTA
1 TTATGTTCTGTTATTATTATTA
*
2251488 TTATTGTTGTTGTTATTATTATTA
1 TTA-TGTT-CTGTTATTATTATTA
2251512 -TATGTTC
1 TTATGTTC
2251519 AGCATATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.31
23 3 0.12
24 12 0.46
ACGTcount: A:0.21, C:0.04, G:0.10, T:0.65
Consensus pattern (22 bp):
TTATGTTCTGTTATTATTATTA
Found at i:2257570 original size:17 final size:18
Alignment explanation
Indices: 2257533--2257575 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
2257523 TTGATAATTT
*
2257533 TTATATTTTATATTTATA
1 TTATATTTTATATATATA
2257551 TTA-ATTTTATATGATA-A
1 TTATATTTTATAT-ATATA
2257568 TTATATTT
1 TTATATTT
2257576 AAAATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATATTTTATATATATA
Found at i:2257593 original size:22 final size:24
Alignment explanation
Indices: 2257533--2257593 Score: 56
Period size: 25 Copynumber: 2.5 Consensus size: 24
2257523 TTGATAATTT
*
2257533 TTATAT-TTTATATTTATATTAATT
1 TTATATATTTATATTTATA-TAATA
2257557 TTATATGATAATTATATTTA-A-AATA
1 TTATAT-AT--TTATATTTATATAATA
2257582 TTATATATTTAT
1 TTATATATTTAT
2257594 TTAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
22 4 0.12
24 8 0.25
25 9 0.28
26 1 0.03
27 1 0.03
28 9 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTATATATTTATATTTATATAATA
Found at i:2257684 original size:11 final size:11
Alignment explanation
Indices: 2257659--2257707 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
2257649 TAATATCGAT
*
2257659 TTATATTTTTTA
1 TTATA-TTTTAA
2257671 TTATATTTTAA
1 TTATATTTTAA
2257682 TTAT-TTTTATA
1 TTATATTTTA-A
*
2257693 TTATATTTAAA
1 TTATATTTTAA
2257704 TTAT
1 TTAT
2257708 GTTTAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 5 0.15
11 19 0.58
12 9 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:2257689 original size:22 final size:23
Alignment explanation
Indices: 2257659--2257707 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
2257649 TAATATCGAT
* *
2257659 TTATATTTTTTATTATATTTTAA
1 TTATATTTTATATTATATTTAAA
2257682 TTAT-TTTTATATTATATTTAAA
1 TTATATTTTATATTATATTTAAA
2257704 TTAT
1 TTAT
2257708 GTTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTATATTTTATATTATATTTAAA
Found at i:2257712 original size:11 final size:11
Alignment explanation
Indices: 2257670--2257724 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
2257660 TATATTTTTT
*
2257670 ATTATATTTTA
1 ATTATATTTAA
* *
2257681 ATTATTTTTAT
1 ATTATATTTAA
2257692 ATTATATTTAA
1 ATTATATTTAA
*
2257703 ATTATGTTTAA
1 ATTATATTTAA
2257714 A--ATATTTAA
1 ATTATATTTAA
2257723 AT
1 AT
2257725 AAAAAGATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 8 0.22
11 28 0.78
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (11 bp):
ATTATATTTAA
Found at i:2257712 original size:22 final size:22
Alignment explanation
Indices: 2257669--2257724 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
2257659 TTATATTTTT
* *
2257669 TATTATATTTTAATTATTTTTA
1 TATTATATTTAAATTATGTTTA
2257691 TATTATATTTAAATTATGTTTA
1 TATTATATTTAAATTATGTTTA
*
2257713 -A-AATATTTAAAT
1 TATTATATTTAAAT
2257725 AAAAAGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 10 0.32
21 1 0.03
22 20 0.65
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTATATTTAAATTATGTTTA
Found at i:2261046 original size:21 final size:21
Alignment explanation
Indices: 2261022--2261061 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2261012 TATTTTTATT
2261022 TAAAT-TTAATTATAAAATATA
1 TAAATATTAATTA-AAAATATA
2261043 TAAATATTAATTAAAAATA
1 TAAATATTAATTAAAAATA
2261062 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATTAATTAAAAATATA
Found at i:2263701 original size:13 final size:13
Alignment explanation
Indices: 2263683--2263710 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2263673 AAATTTCTCC
2263683 AAAAAAAAACAAA
1 AAAAAAAAACAAA
2263696 AAAAAAAAACAAA
1 AAAAAAAAACAAA
2263709 AA
1 AA
2263711 GACAAGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:2265092 original size:17 final size:18
Alignment explanation
Indices: 2265070--2265112 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
2265060 ATTAATATTT
2265070 TTATTTTTAT-AAATAAA
1 TTATTTTTATAAAATAAA
*
2265087 TTA-TTTTATAAAATATA
1 TTATTTTTATAAAATAAA
2265104 TT-TTTTTAT
1 TTATTTTTAT
2265113 CGTATACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTTTTATAAAATAAA
Found at i:2266197 original size:80 final size:80
Alignment explanation
Indices: 2266064--2266225 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 80
2266054 ATTGTACATT
2266064 TTGGTAACAACAATGAATAGAAGGAAACCTCATCAACAACCCCAACTACAGGTGTCTGTTCTCTC
1 TTGGTAACAACAATGAATAGAAGGAAACCTCATCAACAACCCCAACTACAGGTGTCTGTTCTCTC
2266129 CAGTTGCCAATAAAC
66 CAGTTGCCAATAAAC
*
2266144 TTGGTAACAACAATGAATGGAAGGAAACCTCATCAACAACCCCAACTACAGGTGTCTGTTCTCTC
1 TTGGTAACAACAATGAATAGAAGGAAACCTCATCAACAACCCCAACTACAGGTGTCTGTTCTCTC
2266209 CAGTTGCCAATAAAC
66 CAGTTGCCAATAAAC
2266224 TT
1 TT
2266226 TGGCGTTTGA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.23
Consensus pattern (80 bp):
TTGGTAACAACAATGAATAGAAGGAAACCTCATCAACAACCCCAACTACAGGTGTCTGTTCTCTC
CAGTTGCCAATAAAC
Found at i:2267365 original size:11 final size:11
Alignment explanation
Indices: 2267349--2267374 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2267339 ACAAATATGC
2267349 AAATCATTATT
1 AAATCATTATT
2267360 AAATCATTATT
1 AAATCATTATT
2267371 AAAT
1 AAAT
2267375 AATAACAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATCATTATT
Found at i:2268071 original size:2 final size:2
Alignment explanation
Indices: 2268064--2268095 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2268054 AGCAAAGAAA
2268064 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2268096 TAGATCTGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2269882 original size:2 final size:2
Alignment explanation
Indices: 2269875--2269909 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2269865 AACATGCATT
2269875 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2269910 TTAAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2270666 original size:30 final size:30
Alignment explanation
Indices: 2270630--2270740 Score: 141
Period size: 30 Copynumber: 3.7 Consensus size: 30
2270620 CCCCACCCGA
* * *
2270630 TGGAGGTCCATGATGACCCGGACCGCCTGC
1 TGGAGGTCCATGCTGACCCGGACCACCTGG
* *
2270660 TGGAGGTCCATGGTGACCTGGACCACCTGG
1 TGGAGGTCCATGCTGACCCGGACCACCTGG
* *
2270690 TGGAGGTCCATGCTGACCAGGACCACCAGG
1 TGGAGGTCCATGCTGACCCGGACCACCTGG
* *
2270720 AGGAGGTCCATGCTGGCCCGG
1 TGGAGGTCCATGCTGACCCGG
2270741 CGGAGGAGGA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.18, C:0.30, G:0.36, T:0.16
Consensus pattern (30 bp):
TGGAGGTCCATGCTGACCCGGACCACCTGG
Found at i:2270798 original size:6 final size:6
Alignment explanation
Indices: 2270787--2270818 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2270777 TGGAGGTCCT
2270787 TGAGGA TGAGGA TGAGGA TGAGGA TGAGGA TG
1 TGAGGA TGAGGA TGAGGA TGAGGA TGAGGA TG
2270819 CATCTTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (6 bp):
TGAGGA
Found at i:2271279 original size:19 final size:20
Alignment explanation
Indices: 2271257--2271306 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
2271247 TATTTTTACC
2271257 TATTATAATTTTTTTA-AAA
1 TATTATAATTTTTTTATAAA
*
2271276 TATTA-AATATTTTTATAAA
1 TATTATAATTTTTTTATAAA
*
2271295 TTTTAATAATTT
1 TATT-ATAATTT
2271307 AATAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 9 0.36
19 11 0.44
20 1 0.04
21 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTATAATTTTTTTATAAA
Found at i:2272526 original size:17 final size:17
Alignment explanation
Indices: 2272490--2272523 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2272480 GGTGGGGGGG
*
2272490 AGGAAATGGAGGAGAGA
1 AGGAAAGGGAGGAGAGA
2272507 AGGAAAGGGAGGA-AGA
1 AGGAAAGGGAGGAGAGA
2272523 A
1 A
2272524 AGGTCGGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (17 bp):
AGGAAAGGGAGGAGAGA
Found at i:2273855 original size:16 final size:17
Alignment explanation
Indices: 2273822--2273855 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2273812 ATATTAACAT
2273822 TTTATTTGAAATAAAAA
1 TTTATTTGAAATAAAAA
*
2273839 TTTATTT-AAATACAAA
1 TTTATTTGAAATAAAAA
2273855 T
1 T
2273856 CAAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTATTTGAAATAAAAA
Done.