Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009174.1 Hibiscus syriacus cultivar Beakdansim tig00112737_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1358226
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1206721 original size:73 final size:74
Alignment explanation
Indices: 1206547--1206739 Score: 275
Period size: 73 Copynumber: 2.6 Consensus size: 74
1206537 TTACAGATGA
* * * *
1206547 CCCGAAGGTTTTTGAAAACATCATGTACTGAAGGGCTTACCGATGACCCGAAGGTTTGAAAACAT
1 CCCGAAGGTTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGTTTGAAAACAT
1206612 CAAAAAGCT
66 CAAAAAGCT
* *
1206621 CTCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTACAGATG-CCCTAAGGCTTTGAAAAC
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAAC
1206685 ATC-AAAA-CT
64 ATCAAAAAGCT
*
1206694 CCCGAAGGATTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGTAGGACTTACAGATG
1206740 TGGAAATAGT
Statistics
Matches: 108, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
73 45 0.42
74 18 0.17
75 45 0.42
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (74 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGTTTGAAAACAT
CAAAAAGCT
Found at i:1207468 original size:21 final size:22
Alignment explanation
Indices: 1207404--1207479 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
1207394 AATAAAGCTT
1207404 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1207426 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1207448 TCATCTTTGAAAAGA-AATCTA
1 TCATCTTTGAAAAGAGAATCTA
1207469 TCATCTTTGAA
1 TCATCTTTGAA
1207480 GAGTGTATAG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
21 17 0.33
22 35 0.67
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1213056 original size:6 final size:6
Alignment explanation
Indices: 1213045--1213072 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1213035 AGTGTCAGGA
1213045 TTTGGT TTTGGT TTTGGT TTTGGT TTTG
1 TTTGGT TTTGGT TTTGGT TTTGGT TTTG
1213073 CCAAAGGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (6 bp):
TTTGGT
Found at i:1214750 original size:27 final size:27
Alignment explanation
Indices: 1214720--1214775 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
1214710 GTAATTGTGT
1214720 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGTAAATACAAACGTA
* * *
1214747 AAAAATGCAAATGTAAATGCAAATGTA
1 AAAAATGAAAATGTAAATACAAACGTA
1214774 AA
1 AA
1214776 TATGTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGTAAATACAAACGTA
Found at i:1214764 original size:12 final size:12
Alignment explanation
Indices: 1214749--1214776 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1214739 CAAACGTAAA
1214749 AAATGCAAATGT
1 AAATGCAAATGT
1214761 AAATGCAAATGT
1 AAATGCAAATGT
1214773 AAAT
1 AAAT
1214777 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:1214869 original size:7 final size:7
Alignment explanation
Indices: 1214835--1214876 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1214825 ATAAAAGTAT
1214835 AAATGCA
1 AAATGCA
* *
1214842 TAATGAA
1 AAATGCA
1214849 AAATGCA
1 AAATGCA
1214856 AAGATGCA
1 AA-ATGCA
1214864 AAATGC-
1 AAATGCA
1214870 AAATGCA
1 AAATGCA
1214877 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.17
Consensus pattern (7 bp):
AAATGCA
Found at i:1217023 original size:15 final size:15
Alignment explanation
Indices: 1217005--1217056 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
1216995 ATAAATAAAA
1217005 TATTAATAAAATATT
1 TATTAATAAAATATT
1217020 TATTAA-AAATATAATT
1 TATTAATAAA-AT-ATT
*
1217036 TATAAAAGTAAAATATT
1 TAT-TAA-TAAAATATT
1217053 TATT
1 TATT
1217057 TATTTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.27
16 6 0.20
17 8 0.27
18 2 0.07
19 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TATTAATAAAATATT
Found at i:1218662 original size:16 final size:18
Alignment explanation
Indices: 1218622--1218682 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
1218612 TCTGGGCTTG
1218622 TAATAATTATT-TAATAATA
1 TAATAA-TATTAT-ATAATA
1218641 -AATAATA-TATAT-ATA
1 TAATAATATTATATAATA
*
1218656 TAATAATAATTTTATAATA
1 TAATAAT-ATTATATAATA
1218675 TAATAATA
1 TAATAATA
1218683 ATTTTAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
15 3 0.08
16 9 0.25
17 4 0.11
18 10 0.28
19 10 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATATTATATAATA
Found at i:1218665 original size:19 final size:18
Alignment explanation
Indices: 1218622--1218700 Score: 78
Period size: 19 Copynumber: 4.5 Consensus size: 18
1218612 TCTGGGCTTG
*
1218622 TAATAATTATTTA-ATAA
1 TAATAATTATATATATAA
1218639 TAAATAATATATATATATAA
1 T-AATAAT-TATATATATAA
*
1218659 TAATAATTTTATAATATAA
1 TAATAATTATAT-ATATAA
1218678 TAATAATT-T-TA-ATAA
1 TAATAATTATATATATAA
1218693 TAA-AATTA
1 TAATAATTA
1218701 AGTAAAACGA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 4 0.07
15 7 0.13
16 1 0.02
17 2 0.04
18 11 0.20
19 25 0.45
20 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATTATATATATAA
Found at i:1227002 original size:2 final size:2
Alignment explanation
Indices: 1226997--1227024 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1226987 ACTGGAAACT
1226997 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
1227025 CCTATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1227118 original size:98 final size:93
Alignment explanation
Indices: 1226923--1227104 Score: 287
Period size: 91 Copynumber: 1.9 Consensus size: 93
1226913 CAAAAAGAGT
*
1226923 TATACCTATAATTACGAAGACGATCAACAATACATCATGAATTAAATATTACAATGCATATATCA
1 TATACCTATAATTACGAAGACAATCAACAATACATCATG-----AATATTACAATGCATATATCA
*
1226988 CTGGAAACTTATATATATATATATATATATATA
61 CTGGAAACTTATATATATATATATATAAATATA
1227021 TATACCTATAATTACGAAGACAATCAACAATACATCATG-A-ATTACAATGCATATATCACTGGA
1 TATACCTATAATTACGAAGACAATCAACAATACATCATGAATATTACAATGCATATATCACTGGA
1227084 AACTTATATATATATATATAT
66 AACTTATATATATATATATAT
1227105 GCGAAACAAA
Statistics
Matches: 83, Mismatches: 1, Indels: 7
0.91 0.01 0.08
Matches are distributed among these distances:
91 44 0.53
92 1 0.01
98 38 0.46
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (93 bp):
TATACCTATAATTACGAAGACAATCAACAATACATCATGAATATTACAATGCATATATCACTGGA
AACTTATATATATATATATATAAATATA
Found at i:1227789 original size:42 final size:42
Alignment explanation
Indices: 1227754--1227892 Score: 165
Period size: 42 Copynumber: 3.3 Consensus size: 42
1227744 CGTTTATATT
* *
1227754 AAAAATGCCACTAAGGGACCAAACTAATGTGGCGTTTATTAA
1 AAAAACGCCACTAAGGGACAAAACTAATGTGGCGTTTATTAA
* * *
1227796 AAAAACGCCCCTAAAGGACAAAACTACTGTGGCGTTTATTAA
1 AAAAACGCCACTAAGGGACAAAACTAATGTGGCGTTTATTAA
* * * *
1227838 AAAAACGCCACTAAAGGG-CAAAACTATTGCGGCGTTTCTT-T
1 AAAAACGCCACT-AAGGGACAAAACTAATGTGGCGTTTATTAA
*
1227879 ACAAACGCCACTAA
1 AAAAACGCCACTAA
1227893 AGTACATAGA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 2 0.02
41 11 0.13
42 67 0.80
43 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (42 bp):
AAAAACGCCACTAAGGGACAAAACTAATGTGGCGTTTATTAA
Found at i:1227907 original size:41 final size:39
Alignment explanation
Indices: 1227840--1228019 Score: 171
Period size: 41 Copynumber: 4.4 Consensus size: 39
1227830 TTTATTAAAA
** * * *
1227840 AAACGCCACTAAAGGGCAAAACTATTGCGGCGTTTCTTTAC
1 AAACGCCACTAAAGTACAAGA-TATTGCGGCATTT-TTCAC
*
1227881 AAACGCCACTAAAGTACATAGATATTGCGGCATTTTTTTAC
1 AAACGCCACTAAAGTACA-AGATATTGCGGCA-TTTTTCAC
* * ** *
1227922 AAACGCCGCTAAAGTACATGGATATTGCGGTGTTTGGTCAC
1 AAACGCCACTAAAGTACA-AGATATTGCGGCATTT-TTCAC
* *
1227963 AAACGCCACTAAAGTACAAGGCTATTGCGGCATTTTCTCAG
1 AAACGCCACTAAAGTACAA-GATATTGCGGCATTTT-TCAC
1228004 AAACGCCACTAAAGTA
1 AAACGCCACTAAAGTA
1228020 TATGTCTATT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.03
41 109 0.93
42 5 0.04
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (39 bp):
AAACGCCACTAAAGTACAAGATATTGCGGCATTTTTCAC
Found at i:1227935 original size:82 final size:82
Alignment explanation
Indices: 1227840--1228017 Score: 207
Period size: 82 Copynumber: 2.2 Consensus size: 82
1227830 TTTATTAAAA
* * *
1227840 AAACGCCACTAAAGGGCA-AAACTATTGCGGCGTTTCTTTACAAACGCCACTAAAGTACATA-GA
1 AAACGCCACTAAAGGACATAAA-TATTGCGGCGTTTCGTCACAAACGCCACTAAAGTACA-AGGA
* *
1227903 TATTGCGGCATTTTTTTAC
64 TATTGCGGCATTTTCTCAC
* * ** * * *
1227922 AAACGCCGCTAAAGTACATGGATATTGCGGTGTTTGGTCACAAACGCCACTAAAGTACAAGGCTA
1 AAACGCCACTAAAGGACATAAATATTGCGGCGTTTCGTCACAAACGCCACTAAAGTACAAGGATA
*
1227987 TTGCGGCATTTTCTCAG
66 TTGCGGCATTTTCTCAC
1228004 AAACGCCACTAAAG
1 AAACGCCACTAAAG
1228018 TATATGTCTA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
81 1 0.01
82 78 0.98
83 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (82 bp):
AAACGCCACTAAAGGACATAAATATTGCGGCGTTTCGTCACAAACGCCACTAAAGTACAAGGATA
TTGCGGCATTTTCTCAC
Found at i:1228018 original size:82 final size:82
Alignment explanation
Indices: 1227879--1228056 Score: 225
Period size: 82 Copynumber: 2.2 Consensus size: 82
1227869 GCGTTTCTTT
* * *
1227879 ACAAACGCCACTAAAGTACATAGATATTGCGGCATTTTTTTACAAACGCCGCTAAAGTACATGGA
1 ACAAACGCCACTAAAGTACATAGATATTGCGGCATTTTCTCACAAACGCCACTAAAGTACATGGA
* *
1227944 TATTGCGGTGTTTGGTC
66 TATTGCGGCGTTTGGCC
* * * *
1227961 ACAAACGCCACTAAAGTACA-AGGCTATTGCGGCATTTTCTCAGAAACGCCACTAAAGTATATGT
1 ACAAACGCCACTAAAGTACATA-GATATTGCGGCATTTTCTCACAAACGCCACTAAAGTACATGG
* * *
1228025 CTATTTCGGCGTTTTGCC
65 ATATTGCGGCGTTTGGCC
1228043 ACAAACG-CACTAAA
1 ACAAACGCCACTAAA
1228057 TTAAGAGTAT
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
81 8 0.10
82 75 0.90
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (82 bp):
ACAAACGCCACTAAAGTACATAGATATTGCGGCATTTTCTCACAAACGCCACTAAAGTACATGGA
TATTGCGGCGTTTGGCC
Found at i:1228029 original size:41 final size:41
Alignment explanation
Indices: 1227862--1228056 Score: 189
Period size: 41 Copynumber: 4.8 Consensus size: 41
1227852 AGGGCAAAAC
* * *
1227862 TATTGCGGC-GTTTCTTTACAAACGCCACTAAAGTACATAGA
1 TATTGCGGCATTTTC-TCACAAACGCCACTAAAGTACATGGA
* * *
1227903 TATTGCGGCATTTTTTTACAAACGCCGCTAAAGTACATGGA
1 TATTGCGGCATTTTCTCACAAACGCCACTAAAGTACATGGA
** ** * *
1227944 TATTGCGGTGTTTGGTCACAAACGCCACTAAAGTACAAGGC
1 TATTGCGGCATTTTCTCACAAACGCCACTAAAGTACATGGA
* * **
1227985 TATTGCGGCATTTTCTCAGAAACGCCACTAAAGTATATGTC
1 TATTGCGGCATTTTCTCACAAACGCCACTAAAGTACATGGA
* *
1228026 TATTTCGGCGTTTTGC-CACAAACG-CACTAAA
1 TATTGCGGCATTTT-CTCACAAACGCCACTAAA
1228057 TTAAGAGTAT
Statistics
Matches: 129, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
40 7 0.05
41 118 0.91
42 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (41 bp):
TATTGCGGCATTTTCTCACAAACGCCACTAAAGTACATGGA
Found at i:1229356 original size:22 final size:22
Alignment explanation
Indices: 1229328--1229376 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1229318 CACGGTTTCA
1229328 AAAGCTATTATTTTCCTATTCG
1 AAAGCTATTATTTTCCTATTCG
*
1229350 AAAGCTATTATTTTTCTATTCG
1 AAAGCTATTATTTTCCTATTCG
1229372 AAAGC
1 AAAGC
1229377 AGAAAAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (22 bp):
AAAGCTATTATTTTCCTATTCG
Found at i:1229935 original size:83 final size:83
Alignment explanation
Indices: 1229779--1229969 Score: 201
Period size: 83 Copynumber: 2.3 Consensus size: 83
1229769 TAGTACATGT
* *
1229779 TATTGCGGCATTTTTATAAAAACGCCACTATAAACAAATATATTGCGACATTTTTTTCAAAAAAT
1 TATTGCGGCATTTTTATAAAAACGCCACTATAAACAAATATATTGCGACATTTGTTTCAAAAAAC
** *
1229844 GCCGCTAAATTATTACTC
66 GCCGCTAAATTACCAATC
* * * * * * *
1229862 TATTGCGGCATTTTT-TGCACAAATGCCACTATAAA-GAATCATATTGCGGCGTTTGTTT-GATA
1 TATTGCGGCATTTTTAT--AAAAACGCCACTATAAACAAAT-ATATTGCGACATTTGTTTCAAAA
1229924 AACGCCGCTAAATTACCAATC
63 AACGCCGCTAAATTACCAATC
* *
1229945 TATTGCGGCGTTTGTAT-AAAACGCC
1 TATTGCGGCATTTTTATAAAAACGCC
1229970 GCTAGCATTT
Statistics
Matches: 88, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
81 6 0.07
82 1 0.01
83 50 0.57
84 31 0.35
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (83 bp):
TATTGCGGCATTTTTATAAAAACGCCACTATAAACAAATATATTGCGACATTTGTTTCAAAAAAC
GCCGCTAAATTACCAATC
Found at i:1232688 original size:21 final size:21
Alignment explanation
Indices: 1232664--1232704 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1232654 TAGAGGATAC
1232664 ATGTTATCACTAATTAAAAAA
1 ATGTTATCACTAATTAAAAAA
* *
1232685 ATGTTATCATTGATTAAAAA
1 ATGTTATCACTAATTAAAAA
1232705 GCTATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (21 bp):
ATGTTATCACTAATTAAAAAA
Found at i:1233028 original size:42 final size:43
Alignment explanation
Indices: 1232970--1233163 Score: 180
Period size: 43 Copynumber: 4.5 Consensus size: 43
1232960 TTACCCTAAG
* * *
1232970 TTTTTCAATCTCACTTTGTACTTTTATAATTGA-GCTCATAAT
1 TTTTTCAATATCACTTTTTACTTTTATAATTGAGGCCCATAAT
*
1233012 TTTTTCAATATCACTTTCTAGC-TTTATAATTGAGG-CCATTAAT
1 TTTTTCAATATCACTTTTTA-CTTTTATAATTGAGGCCCA-TAAT
* * * * *
1233055 TTTTTTAATCA-CAATTTTTATTTTTATAATTGAGACCCCTAATTT
1 TTTTTCAAT-ATCACTTTTTACTTTTATAATTGAGGCCCATAA--T
* * * * *
1233100 TTTTTCAATATCACTTTTTGCTTATATAATTTAGGCCCCTAAA
1 TTTTTCAATATCACTTTTTACTTTTATAATTGAGGCCCATAAT
*
1233143 ATTTTCAATATCACTTTTTAC
1 TTTTTCAATATCACTTTTTAC
1233164 CTTTGCAACT
Statistics
Matches: 124, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
42 31 0.25
43 55 0.44
44 4 0.03
45 34 0.27
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.49
Consensus pattern (43 bp):
TTTTTCAATATCACTTTTTACTTTTATAATTGAGGCCCATAAT
Found at i:1233161 original size:88 final size:85
Alignment explanation
Indices: 1232971--1233163 Score: 210
Period size: 88 Copynumber: 2.2 Consensus size: 85
1232961 TACCCTAAGT
* * *
1232971 TTTTCAATCTCACTTTGTACTTTTATAATTGAGCTCATAATTTTTTCAATATCACTTTCTAGCTT
1 TTTTCAATATCACTTTTTACTTTTATAATTGAGCCCATAATTTTTTCAATATCACTTTCTAGCTT
* **
1233036 TATAATTGAGGCCATTAATT
66 TATAATTGAGGCCACTAAAA
* * * * *
1233056 TTTTTAATCA-CAATTTTTATTTTTATAATTGAGACCCCTAATTTTTTTTCAATATCACTTT-TT
1 TTTTCAAT-ATCACTTTTTACTTTTATAATTGAG-CCCATAA--TTTTTTCAATATCACTTTCTA
* *
1233119 GCTTATATAATTTAGGCCCCTAAAA
62 GCTT-TATAATTGAGGCCACTAAAA
1233144 TTTTCAATATCACTTTTTAC
1 TTTTCAATATCACTTTTTAC
1233164 CTTTGCAACT
Statistics
Matches: 86, Mismatches: 16, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
85 27 0.31
86 5 0.06
87 6 0.07
88 48 0.56
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (85 bp):
TTTTCAATATCACTTTTTACTTTTATAATTGAGCCCATAATTTTTTCAATATCACTTTCTAGCTT
TATAATTGAGGCCACTAAAA
Found at i:1233184 original size:43 final size:43
Alignment explanation
Indices: 1233101--1233184 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 43
1233091 CCCTAATTTT
* * * *
1233101 TTTTCAATATCACTTTTTGCTTATATAATTTAGGCCCCTAAAA
1 TTTTCAATATCACTTTTTCCTTATACAACTGAGGCCCCTAAAA
* *
1233144 TTTTCAATATCACTTTTTACCTT-TGCAACTGAGGCTCCTAA
1 TTTTCAATATCACTTTTT-CCTTATACAACTGAGGCCCCTAA
1233185 TCAGGTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 31 0.91
44 3 0.09
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.43
Consensus pattern (43 bp):
TTTTCAATATCACTTTTTCCTTATACAACTGAGGCCCCTAAAA
Found at i:1238008 original size:31 final size:31
Alignment explanation
Indices: 1237969--1238062 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 31
1237959 CCCGAAGGAC
* * *
1237969 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1238000 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1238031 CAGTCCATATGTCCCGAAGAAAATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1238062 C
1 C
1238063 CCTCGACCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 55 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1241802 original size:2 final size:2
Alignment explanation
Indices: 1241795--1241867 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
1241785 ATCATCTATC
*
1241795 AT AT AT AT A- AA 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
1241836 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
1241868 CTCATAACTC
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1242705 original size:31 final size:31
Alignment explanation
Indices: 1242667--1242760 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
1242657 CCCGAAGGAC
* * *
1242667 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1242698 CAGTCCATATGTCCCGAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1242729 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1242760 C
1 C
1242761 CCTCGACCCT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 56 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1245457 original size:45 final size:45
Alignment explanation
Indices: 1245408--1245525 Score: 191
Period size: 45 Copynumber: 2.6 Consensus size: 45
1245398 GCATTAGCAT
*
1245408 CTCCCAAGTATCTCAGGTGAGGTCCGTGTCACATAGCATCGACAC
1 CTCCCAAGTATCTCAGGCGAGGTCCGTGTCACATAGCATCGACAC
* *
1245453 CTCCCAAGTATCTCAGGCGAGGTCTGTGTCATATAGCATCGACAC
1 CTCCCAAGTATCTCAGGCGAGGTCCGTGTCACATAGCATCGACAC
* *
1245498 CTACCAAGTATCTTAGGCGAGGTCCGTG
1 CTCCCAAGTATCTCAGGCGAGGTCCGTG
1245526 CATATAACAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (45 bp):
CTCCCAAGTATCTCAGGCGAGGTCCGTGTCACATAGCATCGACAC
Found at i:1247373 original size:23 final size:23
Alignment explanation
Indices: 1247341--1247401 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1247331 CTCATATAAA
*
1247341 TGCATCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1247364 TGCACTGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1247387 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1247402 TATAAGATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1254312 original size:23 final size:23
Alignment explanation
Indices: 1254294--1254354 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
1254284 CTCGTATAAA
1254294 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1254317 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1254340 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1254355 TATAAGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1255694 original size:14 final size:15
Alignment explanation
Indices: 1255675--1255703 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1255665 TCTTCACGGT
1255675 GAAGAAGAA-AGAAA
1 GAAGAAGAAGAGAAA
1255689 GAAGAAGAAGAGAAA
1 GAAGAAGAAGAGAAA
1255704 TCTGGAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAGAAA
Found at i:1256974 original size:12 final size:12
Alignment explanation
Indices: 1256957--1256986 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1256947 TAGCATAAAC
1256957 GGGTATCGGGCT
1 GGGTATCGGGCT
1256969 GGGTATCGGGCT
1 GGGTATCGGGCT
1256981 GGGTAT
1 GGGTAT
1256987 ATATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.13, G:0.50, T:0.27
Consensus pattern (12 bp):
GGGTATCGGGCT
Found at i:1257049 original size:32 final size:33
Alignment explanation
Indices: 1256984--1257060 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
1256974 TCGGGCTGGG
*
1256984 TATATATA-TATTTAAATTAAATATAAAAATAT
1 TATATATATTTTTTAAATTAAATATAAAAATAT
* **
1257016 TATATATATTTTTTAATTTAAAT-TAAATTTAT
1 TATATATATTTTTTAAATTAAATATAAAAATAT
1257048 TAATATTATATTT
1 T-ATA-TATATTT
1257061 ATATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 16 0.42
33 15 0.39
34 7 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TATATATATTTTTTAAATTAAATATAAAAATAT
Found at i:1265628 original size:24 final size:24
Alignment explanation
Indices: 1265569--1265629 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1265559 AAATAGAGAT
* *
1265569 ATCAAAAATCAAAACAGAATTCAT
1 ATCAAAAATCAGAACAGAATTCAG
* *
1265593 ATCATATATCAGAACAGAATTCAG
1 ATCAAAAATCAGAACAGAATTCAG
*
1265617 ATCAGAAATCAGA
1 ATCAAAAATCAGA
1265630 TCATATTTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.21
Consensus pattern (24 bp):
ATCAAAAATCAGAACAGAATTCAG
Found at i:1265653 original size:36 final size:37
Alignment explanation
Indices: 1265573--1265654 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 37
1265563 AGAGATATCA
* * * *
1265573 AAAATCAAAACAGAATTCATATCATATATCAGAACAG
1 AAAATCAGATCAGAAATCAGATCATATATCAGAACAG
* * *
1265610 -AATTCAGATCAGAAATCAGATCATATTTCA-AACCG
1 AAAATCAGATCAGAAATCAGATCATATATCAGAACAG
1265645 AAAATCAGAT
1 AAAATCAGAT
1265655 AAAACATTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
35 4 0.11
36 32 0.89
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.23
Consensus pattern (37 bp):
AAAATCAGATCAGAAATCAGATCATATATCAGAACAG
Found at i:1265835 original size:16 final size:17
Alignment explanation
Indices: 1265804--1265836 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1265794 TATTAACTGA
1265804 CAGAATCATCAATTATT
1 CAGAATCATCAATTATT
*
1265821 CAGAAT-ATGAATTATT
1 CAGAATCATCAATTATT
1265837 AGGATCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (17 bp):
CAGAATCATCAATTATT
Found at i:1272821 original size:3 final size:3
Alignment explanation
Indices: 1272813--1272846 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1272803 CATTCTTCAT
1272813 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1272847 GCCTTCCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:1276233 original size:27 final size:27
Alignment explanation
Indices: 1276173--1276237 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
1276163 GATATTATCA
*
1276173 AGAGGACCCGACATGAACCCCCTCTCG
1 AGAGGACCCGACATGAACCCCCTCTCC
**
1276200 ATCGGACCCGACATGAACCCCCTCTCC
1 AGAGGACCCGACATGAACCCCCTCTCC
1276227 AGAGGACCCGA
1 AGAGGACCCGA
1276238 ACTCGGAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.26, C:0.42, G:0.22, T:0.11
Consensus pattern (27 bp):
AGAGGACCCGACATGAACCCCCTCTCC
Found at i:1280896 original size:32 final size:32
Alignment explanation
Indices: 1280829--1280938 Score: 103
Period size: 32 Copynumber: 3.4 Consensus size: 32
1280819 TTGTATTCAA
* ** **
1280829 ATAATGCATAACAGAGTCAGTGTGGCATTCGG
1 ATAATGCACAACAGAGTCAGTGTCACATTTAG
1280861 ATAATGCACAACAGAGTCAGTGTCACATTTAG
1 ATAATGCACAACAGAGTCAGTGTCACATTTAG
**** * * * *
1280893 ATAATGCATGGGAGTGTTAATGTTACATTTAG
1 ATAATGCACAACAGAGTCAGTGTCACATTTAG
1280925 ATAATGCACAACAG
1 ATAATGCACAACAG
1280939 TTATAATCAT
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (32 bp):
ATAATGCACAACAGAGTCAGTGTCACATTTAG
Found at i:1284023 original size:19 final size:20
Alignment explanation
Indices: 1283982--1284031 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1283972 AATAATTTTT
* *
1283982 ATTTTG-AAAGCAAAATTAG
1 ATTTTGAAAAACAAAATGAG
1284001 ATTTTGAAAAACAAAATGA-
1 ATTTTGAAAAACAAAATGAG
1284020 ATTTTTGAAAAA
1 A-TTTTGAAAAA
1284032 TGATTTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (20 bp):
ATTTTGAAAAACAAAATGAG
Found at i:1289289 original size:21 final size:22
Alignment explanation
Indices: 1289264--1289312 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1289254 GGTCTGGTGG
* *
1289264 GTTTGTTGTAAAACGGCCTC-A
1 GTTTGGTGAAAAACGGCCTCGA
*
1289285 GTTTGGTGAAAAATGGCCTCGA
1 GTTTGGTGAAAAACGGCCTCGA
1289307 GTTTGG
1 GTTTGG
1289313 GCCTGTAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (22 bp):
GTTTGGTGAAAAACGGCCTCGA
Found at i:1289363 original size:3 final size:3
Alignment explanation
Indices: 1289338--1289421 Score: 93
Period size: 3 Copynumber: 29.0 Consensus size: 3
1289328 AAATATTTAT
* * * * *
1289338 TAA T-A TAA TAC TAA TAA -AA TAA TAA TTA TAA TTA TAA GAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1289384 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1289422 AAAATGAAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
2 6 0.09
3 60 0.91
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1292129 original size:636 final size:628
Alignment explanation
Indices: 1290891--1292154 Score: 2411
Period size: 636 Copynumber: 2.0 Consensus size: 628
1290881 TATTTCAGAT
1290891 TTCGCTAAAGAATTCATGATTGGGATGGTTCATCCATGCAACTATCATACGAATCCACCTCTATC
1 TTCGCTAAAGAATTCATGATTGGGATGGTTCATCCATGCAACTATCATACGAATCCACCTCTATC
1290956 TTTTGATCGAATCCCCATCAATGGAGAACGAGCAGATTGTGATCAGAACCAATTTTGTCCAAATG
66 TTTTGATCGAATCCCCATCAATGGAGAACGAGCAGATTGTGATCAGAACCAATTTTGTCCAAATG
1291021 TAGAATTTTAGAAGTTGGATACAAATTCACCCATTTATCATTCATAAGGCCCCAATCAAGTCTCT
131 TAGAATTTTAGAAGTTGGATACAAATTCACCCATTTATCATTCATAAGGCCCCAATCAAGTCTCT
1291086 TCCAAAGGTTTCACCTTCTCCAAGTAAATTTTACCCCTAGTAGGATAGTCAGTGAGACTATTGTT
196 TCCAAAGGTTTCACCTTCTCCAAGTAAATTTTACCCCTAGTAGGATAGTCAGTGAGACTATTGTT
1291151 AAAAATGAAATCATTAAAGTGCTTCCTGCCTCCATTATTCTGACCATGTCCTCCATGCCTATCCT
261 AAAAATGAAATCATTAAAGTGCTTCCTGCCTCCATTATTCTGACCATGTCCTCCATGCCTATCCT
1291216 CAGTCCTTAAGGTGCCATTAAAGTCGCCTCTCAAAATCCAGGCTCAGCATCACCTGGGTTTAACT
326 CAGTCCTTAAGGTGCCATTAAAGTCGCCTCTCAAAATCCAGGCTCAGCATCACCTGGGTTTAACT
*
1291281 AGATAGAAGAGGCCAAATATGGTTCCTAATAGAAATGTTGGGGCTTGCGTAAACTGCAGTAATAA
391 AGATAAAAGAGGCCAAATATGGTTCCTAATAGAAATGTTGGGGCTTGCGTAAACTGCAGTAATAA
1291346 ATAGCATCTCATACCACTGTTAAGTTTGAATTTCATATGCAAATACTGATTGGAAATCTGGAGGA
456 ATAGCATCTCATACCACTGTTAAGTTTGAATTTCATATGCAAATACTGATTGGAAATCTGGAGGA
1291411 TCTCAACAACGATTGAGTTGTACCAAAGCATCCACTAAACCCTTACGCTTCAATTTGAAATAAGT
521 TCTCAACAACGATTGAGTTGTACCAAAGCATCCACTAAACCCTTACGCTTCAATTTGAAATAAGT
*
1291476 TTTCGAAACCTAGTTTACCAACGATTTTGCCAGCCCTATTTCC
586 TTTCAAAACCTAGTTTACCAACGATTTTGCCAGCCCTATTTCC
1291519 TTCGCTAAAGAATTCATTGATATTGGGATGGTTCATCCATGCAACTATCATACGAATCCACCTCT
1 TTCGCTAAAGAATTCA-TG--ATTGGGATGGTTCATCCATGCAACTATCATACGAATCCACCTCT
1291584 ATCTTTTGATCGAATCCCCATCAATCTGGAGAACGAGCAGATTGTGATCAGAACCAATTTTGTCC
63 ATCTTTTGATCGAATCCCCATCAA--TGGAGAACGAGCAGATTGTGATCAGAACCAATTTTGTCC
*
1291649 AAATGTAGAATTTTAGAAGTTGGATACAAATTCACCCATTTATCATTCATAAGGCCCCATTCAAG
126 AAATGTAGAATTTTAGAAGTTGGATACAAATTCACCCATTTATCATTCATAAGGCCCCAATCAAG
1291714 TCTCTTCCAAAGGTTTCACCTTCTCCAAGTAAAATTTTACCCCTAGTAGGATAGTCAGTGAGACT
191 TCTCTTCCAAAGGTTTCACCTTCTCCAAGT-AAATTTTACCCCTAGTAGGATAGTCAGTGAGACT
1291779 ATTGTTAAAAATGAAATCATTAAAGTGCTTCCTGCCTCCATTATTCTGACCATGTCCTCCATGCC
255 ATTGTTAAAAATGAAATCATTAAAGTGCTTCCTGCCTCCATTATTCTGACCATGTCCTCCATGCC
1291844 TATCCTCAGTCCTTAAGGTGCCATTAAAGTCGCCTCTCAAAATCCAGGCCTCAGCATCACCTGGG
320 TATCCTCAGTCCTTAAGGTGCCATTAAAGTCGCCTCTCAAAATCCAGG-CTCAGCATCACCTGGG
*
1291909 TTTAACTAGATAAAAGAGGCCAAATATGGTTCCTAATAGAAATGTTGGGGCTTGCGTAAAGTGCA
384 TTTAACTAGATAAAAGAGGCCAAATATGGTTCCTAATAGAAATGTTGGGGCTTGCGTAAACTGCA
1291974 GTAATAAAATAGCATCTCATACCACTGTTAAGTTTGAATTTCATATGCAAATACTGATTGGAAAT
449 GTAAT-AAATAGCATCTCATACCACTGTTAAGTTTGAATTTCATATGCAAATACTGATTGGAAAT
*
1292039 CTGGAGGATCTCAACAACGATTGAGTTGTACCAAAGCATCCACTAAACCCTTACGCTTCGATTTG
513 CTGGAGGATCTCAACAACGATTGAGTTGTACCAAAGCATCCACTAAACCCTTACGCTTCAATTTG
1292104 AAATAAGTTTTCAAAACCTAGTTTACCAACGATTTTGCCAGCCCTATTTCC
578 AAATAAGTTTTCAAAACCTAGTTTACCAACGATTTTGCCAGCCCTATTTCC
1292155 ACTAGTTATG
Statistics
Matches: 623, Mismatches: 5, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
628 16 0.03
629 2 0.00
631 68 0.11
633 133 0.21
634 147 0.24
635 84 0.13
636 173 0.28
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (628 bp):
TTCGCTAAAGAATTCATGATTGGGATGGTTCATCCATGCAACTATCATACGAATCCACCTCTATC
TTTTGATCGAATCCCCATCAATGGAGAACGAGCAGATTGTGATCAGAACCAATTTTGTCCAAATG
TAGAATTTTAGAAGTTGGATACAAATTCACCCATTTATCATTCATAAGGCCCCAATCAAGTCTCT
TCCAAAGGTTTCACCTTCTCCAAGTAAATTTTACCCCTAGTAGGATAGTCAGTGAGACTATTGTT
AAAAATGAAATCATTAAAGTGCTTCCTGCCTCCATTATTCTGACCATGTCCTCCATGCCTATCCT
CAGTCCTTAAGGTGCCATTAAAGTCGCCTCTCAAAATCCAGGCTCAGCATCACCTGGGTTTAACT
AGATAAAAGAGGCCAAATATGGTTCCTAATAGAAATGTTGGGGCTTGCGTAAACTGCAGTAATAA
ATAGCATCTCATACCACTGTTAAGTTTGAATTTCATATGCAAATACTGATTGGAAATCTGGAGGA
TCTCAACAACGATTGAGTTGTACCAAAGCATCCACTAAACCCTTACGCTTCAATTTGAAATAAGT
TTTCAAAACCTAGTTTACCAACGATTTTGCCAGCCCTATTTCC
Found at i:1294566 original size:2 final size:2
Alignment explanation
Indices: 1294559--1294584 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1294549 TAATAATTTC
1294559 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
1294585 TAAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1294665 original size:43 final size:46
Alignment explanation
Indices: 1294574--1294681 Score: 150
Period size: 43 Copynumber: 2.3 Consensus size: 46
1294564 TATATATATA
1294574 TATATATATATTAAAAAATAAATTATTTAATAAATTTAACAATATTTT
1 TATATATATATT-AAAAATAAATTA-TTAATAAATTTAACAATATTTT
*
1294622 TTTATATATATTAAAAA-AAATTA-TAATAAA-TTAACAATATTTT
1 TATATATATATTAAAAATAAATTATTAATAAATTTAACAATATTTT
1294665 TATATATAATAGTTAAA
1 TATATAT-ATA-TTAAA
1294682 TTAATTTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
43 19 0.34
44 10 0.18
45 5 0.09
46 6 0.11
47 5 0.09
48 11 0.20
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (46 bp):
TATATATATATTAAAAATAAATTATTAATAAATTTAACAATATTTT
Found at i:1294740 original size:2 final size:2
Alignment explanation
Indices: 1294733--1294759 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1294723 TAATTTCATA
1294733 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1294760 AAGTCACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1296474 original size:196 final size:196
Alignment explanation
Indices: 1296091--1296648 Score: 613
Period size: 196 Copynumber: 2.8 Consensus size: 196
1296081 TACTGTGACA
* * **
1296091 AAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTTTTTGTCACAATTTTTTATTTTTATA
1 AAATAAATTTATTACAATTTGTTATTGTG-AAGAATATTACTTGTCACAA-----T-TTTTTAT-
1296156 ATGAGAAATTAATATTTGTTATAAATTGTTATTTTAATTAAATAAATTTGTCACAATTTTTTATT
58 ATGAGAAATTAATATTTGTTATAAATTGTTATTTTAATTAAATAAATTTGTCACAATTTTTTATT
* * * *
1296221 TTGACAAAATATTATGACGAAATAAATTTGACATAACTTTTTACTTTGACTAAATTTAAC-GTGT
123 TTGACAAAATATTATGACAAAATAAATTTGACATAAATTTTTACTTTGACAAAATTT-ACTATGT
*
1296285 TATTATGACT
187 TATTATAACT
* * * *
1296295 AAATCATTTTATTATAATTTTTTATTGTG-AGAATATTACTTGTCACAATTTTTTATGATGAGAA
1 AAATAAATTTATTACAATTTGTTATTGTGAAGAATATTACTTGTCACAATTTTTTAT-ATGAGAA
* * * * *
1296359 ATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTATTAGAATTTTTTATTTTGACAA
65 ATTAATATTTGTTATAAATTGTTATTTTAATTAAATAAATTTGTCACAATTTTTTATTTTGACAA
* * * * *
1296424 AATATTGTGACAAAATAAATTTGGCATAAATTTTTATTTTGGCAAAATTTACTATGTTATTGTAA
130 AATATTATGACAAAATAAATTTGACATAAATTTTTACTTTGACAAAATTTACTATGTTATTATAA
1296489 CT
195 CT
* * **
1296491 AAATAAATTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCTTAATTTTTTATATTGATG
1 AAATAAATTTATTACAATTTGTTATTGTG-AAGAATATTACTTGTCACAATTTTTTATA-TGA-G
* * * ** * *
1296556 -AATTAATATTTATTA-AAATTTGTTATTATAACTATTTAAATTTGTCATAATTTGTTA-TTTGA
63 AAATTAATATTTGTTATAAA-TTGTTATTTTAATTAAATAAATTTGTCACAATTTTTTATTTTGA
* * *
1296618 GAAAATATTTTGACTAAATAAATTTTGACAT
127 CAAAATATTATGACAAAATAAA-TTTGACAT
1296649 TACAGAATAG
Statistics
Matches: 302, Mismatches: 45, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
195 2 0.01
196 152 0.50
197 29 0.10
198 76 0.25
199 1 0.00
202 17 0.06
204 25 0.08
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (196 bp):
AAATAAATTTATTACAATTTGTTATTGTGAAGAATATTACTTGTCACAATTTTTTATATGAGAAA
TTAATATTTGTTATAAATTGTTATTTTAATTAAATAAATTTGTCACAATTTTTTATTTTGACAAA
ATATTATGACAAAATAAATTTGACATAAATTTTTACTTTGACAAAATTTACTATGTTATTATAAC
T
Found at i:1298489 original size:2 final size:2
Alignment explanation
Indices: 1298482--1298510 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1298472 TGCATATTTT
1298482 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 T
1298511 TAATTATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1298687 original size:14 final size:15
Alignment explanation
Indices: 1298668--1298698 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1298658 TTATATTTCA
1298668 TTTTATCTT-TATTT
1 TTTTATCTTCTATTT
1298682 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
1298697 TT
1 TT
1298699 ATTTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:1298709 original size:14 final size:14
Alignment explanation
Indices: 1298646--1298763 Score: 69
Period size: 15 Copynumber: 7.9 Consensus size: 14
1298636 TATAAATTAA
*
1298646 TATTTTATTATTTT
1 TATTTTTTTATTTT
*
1298660 ATATTTCATTTTATCTT
1 -TATTT--TTTTATTTT
*
1298677 TATTTTTTTATCTTC
1 TATTTTTTTAT-TTT
1298692 TATTTTTATT-TTTT
1 TATTTTT-TTATTTT
* * *
1298706 TATTGTTATTGTTAT
1 TATT-TTTTTATTTT
*
1298721 TATCTTCTTTA-TTT
1 TAT-TTTTTTATTTT
*
1298735 TATGTTTTTTATTTA
1 TAT-TTTTTTATTTT
1298750 TATTTTTTATATTT
1 TATTTTTT-TATTT
1298764 GTTTTTGTGC
Statistics
Matches: 80, Mismatches: 14, Indels: 18
0.71 0.12 0.16
Matches are distributed among these distances:
14 30 0.38
15 35 0.44
16 8 0.10
17 7 0.09
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.74
Consensus pattern (14 bp):
TATTTTTTTATTTT
Found at i:1298762 original size:15 final size:14
Alignment explanation
Indices: 1298668--1298769 Score: 54
Period size: 14 Copynumber: 7.2 Consensus size: 14
1298658 TTATATTTCA
1298668 TTTTATCTTTAT-TT
1 TTTTAT-TTTATGTT
1298682 TTTTATCTTCTAT-TT
1 TTTTAT-TT-TATGTT
*
1298697 TTATTTTTTTATTGTT
1 TT-TTATTTTA-TGTT
*
1298713 ATTGTTA--TTATCTT
1 -TT-TTATTTTATGTT
*
1298727 CTTTATTTTATGTT
1 TTTTATTTTATGTT
*
1298741 TTTTA-TTTATATT
1 TTTTATTTTATGTT
*
1298754 TTTTATATT-TGTT
1 TTTTATTTTATGTT
1298767 TTT
1 TTT
1298770 GTGCCTCTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
12 3 0.04
13 19 0.27
14 26 0.37
15 13 0.19
16 5 0.07
17 4 0.06
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (14 bp):
TTTTATTTTATGTT
Found at i:1298768 original size:13 final size:13
Alignment explanation
Indices: 1298728--1298769 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1298718 TATTATCTTC
1298728 TTTATTTTATGTTT
1 TTTA-TTTATGTTT
*
1298742 TTTATTTATATTT
1 TTTATTTATGTTT
1298755 TTTATATT-TGTTT
1 TTTAT-TTATGTTT
1298768 TT
1 TT
1298770 GTGCCTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTATTTATGTTT
Found at i:1298798 original size:20 final size:20
Alignment explanation
Indices: 1298775--1298839 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
1298765 TTTTTGTGCC
1298775 TCTTTATTTTATTTTCTTTA
1 TCTTTATTTTATTTTCTTTA
** ** *
1298795 TCTTGCTTGCATCTTCTTTA
1 TCTTTATTTTATTTTCTTTA
*
1298815 TC--TATTTTATTTTCTCTA
1 TCTTTATTTTATTTTCTTTA
1298833 -CTTTATT
1 TCTTTATT
1298840 GCATTTATTT
Statistics
Matches: 32, Mismatches: 11, Indels: 5
0.67 0.23 0.10
Matches are distributed among these distances:
17 1 0.03
18 10 0.31
19 4 0.12
20 17 0.53
ACGTcount: A:0.14, C:0.17, G:0.03, T:0.66
Consensus pattern (20 bp):
TCTTTATTTTATTTTCTTTA
Found at i:1309729 original size:110 final size:110
Alignment explanation
Indices: 1309531--1309734 Score: 336
Period size: 110 Copynumber: 1.9 Consensus size: 110
1309521 GCTTTCCAGT
* *
1309531 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* *
1309596 CAATGAAGGGGCGACTGATTGTCAACAAATAACTTTTCAGTTTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCA
* *
1309641 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* *
1309706 CAGCGAAGGGGCGGCTGACTGTCAACAAA
66 CAACGAAGGGGCGACTGACTGTCAACAAA
1309735 CAATTTCCAG
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 86 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAGTTTCA
Found at i:1311134 original size:3 final size:3
Alignment explanation
Indices: 1311128--1311179 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1311118 ACATGCATAT
1311128 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1311176 TTA T
1 TTA T
1311180 ATATATATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1311184 original size:2 final size:2
Alignment explanation
Indices: 1311177--1311203 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1311167 TTATTATTAT
1311177 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 T
1311204 TAATTATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1311270 original size:44 final size:40
Alignment explanation
Indices: 1311222--1311313 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
1311212 TTCATTTGGC
* *
1311222 TATTTATTTCTTTTCTATATTCTATCGTTATATATATATATATA
1 TATTTATTTCTTTT-T-TA-TATATCATTAT-TATATATATATA
* *
1311266 TATTTAATTCTTTTTTATATATCATTATTATTTATATATA
1 TATTTATTTCTTTTTTATATATCATTATTATATATATATA
*
1311306 TTTTTATT
1 TATTTATT
1311314 ACTATAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
40 17 0.40
41 9 0.21
42 2 0.05
43 1 0.02
44 13 0.31
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (40 bp):
TATTTATTTCTTTTTTATATATCATTATTATATATATATA
Found at i:1311319 original size:16 final size:15
Alignment explanation
Indices: 1311249--1311355 Score: 65
Period size: 16 Copynumber: 6.8 Consensus size: 15
1311239 TATTCTATCG
* *
1311249 TTATATATATATATA
1 TTATATATATTTTTA
* *
1311264 -TATATTTAATTCTTTT
1 TTATATAT-ATT-TTTA
*
1311280 TTATATATCATTATTA
1 TTATATAT-ATTTTTA
1311296 TTTATATATATTTTTA
1 -TTATATATATTTTTA
* *
1311312 TTACTATA-ATTATATG
1 TTA-TATATATT-TTTA
1311328 TTATATATATTTATTA
1 TTATATATATTT-TTA
*
1311344 TTTTATATATTT
1 TTATATATATTT
1311356 CATTTTATCT
Statistics
Matches: 70, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
14 6 0.09
15 13 0.19
16 34 0.49
17 17 0.24
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (15 bp):
TTATATATATTTTTA
Found at i:1311332 original size:31 final size:30
Alignment explanation
Indices: 1311277--1311350 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
1311267 ATTTAATTCT
*
1311277 TTTTTA-TATATCATTATTATTTATATATA
1 TTTTTATTATATAATTATTATTTATATATA
1311306 TTTTTATTACTATAATTA-TATGTTATATATA
1 TTTTTATTA-TATAATTATTAT-TTATATATA
*
1311337 TTTATTATTTTATA
1 TTT-TTATTATATA
1311351 TATTTCATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 6 0.15
30 5 0.13
31 23 0.59
32 5 0.13
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTTATTATATAATTATTATTTATATATA
Found at i:1311378 original size:15 final size:15
Alignment explanation
Indices: 1311358--1311389 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1311348 ATATATTTCA
*
1311358 TTTTATCTTTTATTT
1 TTTTATCTTCTATTT
1311373 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
1311388 TT
1 TT
1311390 ATTTTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:1311387 original size:27 final size:26
Alignment explanation
Indices: 1311335--1311397 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 26
1311325 ATGTTATATA
1311335 TATTTATTATTTTATATATTTCA-TTT
1 TATTT-TTATTTTATATATTTCATTTT
*
1311361 TATCTTTTATTTT-TTTATCTTCTATTTT
1 TAT-TTTTATTTTATATAT-TTC-ATTTT
1311389 TATTTTTAT
1 TATTTTTAT
1311398 AATGTTATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 4 0.12
26 13 0.41
27 9 0.28
28 6 0.19
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (26 bp):
TATTTTTATTTTATATATTTCATTTT
Found at i:1311399 original size:79 final size:80
Alignment explanation
Indices: 1311304--1311450 Score: 178
Period size: 79 Copynumber: 1.9 Consensus size: 80
1311294 TATTTATATA
1311304 TATTTTTATTACTATAA--TTATATGTTATATATATT-TATTATTTTATATAT-TTCATTT-TAT
1 TATTTTTATTACTATAATGTTAT-TGTTAT-TATATTCT-TTATTTTATATATCTT-ATTTATAT
1311364 CTTTTATTTTTTTATCTTC
62 CTTTTATTTTTTTATCTTC
** * * *
1311383 TATTTTTATTTTTATAATGTTATTGTTATTATCTTCTTTATTTTATGTATCTTATTTATATTTTT
1 TATTTTTATTACTATAATGTTATTGTTATTATATTCTTTATTTTATATATCTTATTTATATCTTT
1311448 TAT
66 TAT
1311451 ATTTGTTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
79 36 0.62
80 18 0.31
81 4 0.07
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.67
Consensus pattern (80 bp):
TATTTTTATTACTATAATGTTATTGTTATTATATTCTTTATTTTATATATCTTATTTATATCTTT
TATTTTTTTATCTTC
Found at i:1311433 original size:18 final size:18
Alignment explanation
Indices: 1311402--1311441 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1311392 TTTTATAATG
*
1311402 TTATTGTTATTATCTTCT
1 TTATTGTTATTATCTTAT
1311420 TTATT-TTATGTATCTTAT
1 TTATTGTTAT-TATCTTAT
1311438 TTAT
1 TTAT
1311442 ATTTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (18 bp):
TTATTGTTATTATCTTAT
Found at i:1311569 original size:29 final size:29
Alignment explanation
Indices: 1311510--1311572 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1311500 TTTTTATTTG
*
1311510 TTTTATTTTCTCTACTTTATTGCATTTAT
1 TTTTATTTTCTCTACTTTATTGCATTCAT
* **
1311539 TTTTATTTTAC-CTTCTTTATTTTATTCAT
1 TTTTATTTT-CTCTACTTTATTGCATTCAT
1311568 TTTTA
1 TTTTA
1311573 CTACATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.68
Consensus pattern (29 bp):
TTTTATTTTCTCTACTTTATTGCATTCAT
Found at i:1312541 original size:3 final size:3
Alignment explanation
Indices: 1312529--1312569 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1312519 TATATCTTCT
1312529 TAA TAA -AA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1312570 TAAAACATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1312545 original size:11 final size:11
Alignment explanation
Indices: 1312529--1312568 Score: 71
Period size: 11 Copynumber: 3.5 Consensus size: 11
1312519 TATATCTTCT
1312529 TAATAAAATAA
1 TAATAAAATAA
1312540 TAATAAAATAA
1 TAATAAAATAA
1312551 TAATAATAATAA
1 TAATAA-AATAA
1312563 TAATAA
1 TAATAA
1312569 TTAAAACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:1312820 original size:20 final size:20
Alignment explanation
Indices: 1312795--1312845 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1312785 AACAATGAAG
1312795 TAGTACCGATACTGCTAAGT
1 TAGTACCGATACTGCTAAGT
*
1312815 TAGTACCAATACTGCTAAGT
1 TAGTACCGATACTGCTAAGT
* *
1312835 CAGTACTGATA
1 TAGTACCGATA
1312846 TTGTCAAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (20 bp):
TAGTACCGATACTGCTAAGT
Found at i:1314929 original size:8 final size:8
Alignment explanation
Indices: 1314918--1314955 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1314908 AAAGAGAAAG
1314918 AAAGAAGA
1 AAAGAAGA
1314926 AAAGAAGA
1 AAAGAAGA
*
1314934 AAAG-TGA
1 AAAGAAGA
1314941 AGAAGAAGA
1 A-AAGAAGA
1314950 AAAGAA
1 AAAGAA
1314956 TAAGAAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 3 0.12
8 20 0.77
9 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (8 bp):
AAAGAAGA
Found at i:1317034 original size:19 final size:19
Alignment explanation
Indices: 1317010--1317060 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
1317000 TTCCCTATCG
*
1317010 GTGCATCGATGCACTACCT
1 GTGCATCGGTGCACTACCT
1317029 GTGCATCGGTGCACTACCT
1 GTGCATCGGTGCACTACCT
*
1317048 GTTCATCGGTGCA
1 GTGCATCGGTGCA
1317061 TAAATGACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.27
Consensus pattern (19 bp):
GTGCATCGGTGCACTACCT
Found at i:1318897 original size:19 final size:19
Alignment explanation
Indices: 1318864--1318900 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1318854 ACGTGGTCTT
1318864 ATCCGTCATATTCATACAC
1 ATCCGTCATATTCATACAC
1318883 ATCCTGTCATA-TCATACA
1 ATCC-GTCATATTCATACA
1318901 TTTGATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.32
Consensus pattern (19 bp):
ATCCGTCATATTCATACAC
Found at i:1319104 original size:23 final size:23
Alignment explanation
Indices: 1319086--1319220 Score: 261
Period size: 23 Copynumber: 5.9 Consensus size: 23
1319076 CTCGTATAAA
1319086 TGCACCGAAGTGCCACGTAGGAT
1 TGCACCGAAGTGCCACGTAGGAT
*
1319109 TGCACCGAAGTGCCACGTAGTAT
1 TGCACCGAAGTGCCACGTAGGAT
1319132 TGCACCGAAGTGCCACGTAGGAT
1 TGCACCGAAGTGCCACGTAGGAT
1319155 TGCACCGAAGTGCCACGTAGGAT
1 TGCACCGAAGTGCCACGTAGGAT
1319178 TGCACCGAAGTGCCACGTAGGAT
1 TGCACCGAAGTGCCACGTAGGAT
1319201 TGCACCGAAGTGCCACGTAG
1 TGCACCGAAGTGCCACGTAG
1319221 AAAAGTGCCA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 110 1.00
ACGTcount: A:0.26, C:0.27, G:0.30, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGGAT
Found at i:1319870 original size:2 final size:2
Alignment explanation
Indices: 1319797--1319857 Score: 113
Period size: 2 Copynumber: 30.0 Consensus size: 2
1319787 ACACATTTTC
1319797 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1319840 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1319858 CAATAACATA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 56 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1321943 original size:10 final size:10
Alignment explanation
Indices: 1321930--1321964 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
1321920 TTCATATCCA
1321930 TTCATGTTCG
1 TTCATGTTCG
*
1321940 TTCATGTCCG
1 TTCATGTTCG
1321950 TTCATGTTCG
1 TTCATGTTCG
1321960 TTCAT
1 TTCAT
1321965 TTAAATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (10 bp):
TTCATGTTCG
Found at i:1321944 original size:20 final size:20
Alignment explanation
Indices: 1321919--1321964 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1321909 AATATAGTTT
1321919 GTTCATATCCATTCATGTTC
1 GTTCATATCCATTCATGTTC
* *
1321939 GTTCATGTCCGTTCATGTTC
1 GTTCATATCCATTCATGTTC
1321959 GTTCAT
1 GTTCAT
1321965 TTAAATGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.46
Consensus pattern (20 bp):
GTTCATATCCATTCATGTTC
Found at i:1323495 original size:37 final size:37
Alignment explanation
Indices: 1323423--1323495 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
1323413 TTATATTTTT
*
1323423 AATTTTGTAAAAAAATTATATAAATATTATGAATTTA
1 AATTTTGTAAAAAAATTATATAAATATTATCAATTTA
*
1323460 AATTTT-TAAAGAAAA-TATATAAATATTTTACAATTT
1 AATTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
1323496 GTAATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (37 bp):
AATTTTGTAAAAAAATTATATAAATATTATCAATTTA
Found at i:1324610 original size:31 final size:31
Alignment explanation
Indices: 1324547--1324637 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 31
1324537 AATGTTCGAT
* * *
1324547 AATATAATAATTATTTTAT-AGTATTTAGATA
1 AATATAATAAGTATTTTATAAATTTTTA-ATA
* *
1324578 AATTTATTAA-TAATTTTAT-AATCTTTTAATA
1 AATATAATAAGT-ATTTTATAAAT-TTTTAATA
1324609 AATATAATAAGTATTTTATAAATTTTTAA
1 AATATAATAAGTATTTTATAAATTTTTAA
1324638 ATTTTATTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
30 1 0.02
31 41 0.82
32 8 0.16
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (31 bp):
AATATAATAAGTATTTTATAAATTTTTAATA
Found at i:1328565 original size:18 final size:18
Alignment explanation
Indices: 1328542--1328580 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1328532 TCACGTGCCC
1328542 TTTCAAAGTTACTTTA-AT
1 TTTCAAA-TTACTTTATAT
*
1328560 TTTCAAATTATTTTATAT
1 TTTCAAATTACTTTATAT
1328578 TTT
1 TTT
1328581 AATATGTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTCAAATTACTTTATAT
Found at i:1332061 original size:38 final size:38
Alignment explanation
Indices: 1332019--1332100 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
1332009 AAAATTCAGT
*
1332019 AAATAAT-AAACTCATTCGCTTCAATTAAGTAATAAACA
1 AAATAATAAAAC-CATTCGCTTAAATTAAGTAATAAACA
*
1332057 AAATATTAAAACCATTCGCTTAAATTAAGTAATAAACA
1 AAATAATAAAACCATTCGCTTAAATTAAGTAATAAACA
1332095 AAATAA
1 AAATAA
1332101 ACAAAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 36 0.90
39 4 0.10
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (38 bp):
AAATAATAAAACCATTCGCTTAAATTAAGTAATAAACA
Found at i:1335628 original size:21 final size:21
Alignment explanation
Indices: 1335604--1335659 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
1335594 TATGTACTCA
*
1335604 TTTGGAACATATATGCGGTTC
1 TTTGGAACATATATGCGGTCC
* * **
1335625 TTTGGGACAGATATTTGGTCC
1 TTTGGAACATATATGCGGTCC
*
1335646 TTTGGAATATATAT
1 TTTGGAACATATAT
1335660 CTGATCATTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (21 bp):
TTTGGAACATATATGCGGTCC
Found at i:1337168 original size:3 final size:3
Alignment explanation
Indices: 1337162--1337195 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1337152 TTGATGATGA
1337162 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1337196 AGAGATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:1339811 original size:18 final size:18
Alignment explanation
Indices: 1339788--1339876 Score: 169
Period size: 18 Copynumber: 4.9 Consensus size: 18
1339778 AGGGATTAAC
1339788 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1339806 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1339824 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1339842 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1339860 AGTGGTCCTTCGAGACA
1 AGTGGTCCTTCGGGACA
1339877 AATATTCAGT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.18, C:0.22, G:0.33, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1346430 original size:29 final size:29
Alignment explanation
Indices: 1346398--1346460 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1346388 ATCCCTGTCC
*
1346398 TGATTCTACATGAGATCATATCTCTATCA
1 TGATTCTACATGAGATCATATCTCCATCA
* * * *
1346427 TGATTCTACTTGGGATTATATCTCCATCT
1 TGATTCTACATGAGATCATATCTCCATCA
1346456 TGATT
1 TGATT
1346461 TGCATGGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (29 bp):
TGATTCTACATGAGATCATATCTCCATCA
Found at i:1354323 original size:27 final size:27
Alignment explanation
Indices: 1354293--1354358 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
1354283 ATAATGGCTT
* *
1354293 TGAATAATTCAGAATGTACTTCTGTGC
1 TGAATCATTCAGAATGTACTTCTGTAC
*
1354320 TGAATCATTCAGAATGTACTTCTGTAT
1 TGAATCATTCAGAATGTACTTCTGTAC
1354347 TGAATCATTCAG
1 TGAATCATTCAG
1354359 CACTGTTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (27 bp):
TGAATCATTCAGAATGTACTTCTGTAC
Found at i:1356900 original size:20 final size:22
Alignment explanation
Indices: 1356875--1356914 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1356865 TTTAAAAAAA
1356875 TATTAT-TTT-TAAGAATATTT
1 TATTATATTTGTAAGAATATTT
1356895 TATTATATTTGTAAGAATAT
1 TATTATATTTGTAAGAATAT
1356915 AACCAGATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
TATTATATTTGTAAGAATATTT
Done.