Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008750.1 Hibiscus syriacus cultivar Beakdansim tig00111841_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: 3719443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:1023892 original size:23 final size:22
Alignment explanation
Indices: 1023865--1023928 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
1023855 TCGAGACTAA
1023865 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAA-C
*
1023888 TATGTGGTC-CTTCGG-G-ACAAT
1 TATGTGG-CACTTCGGTGCA-AAC
*
1023909 TATGTGGCACTTTGGTGCAA
1 TATGTGGCACTTCGGTGCAA
1023929 TTTACGAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 5 0.15
23 14 0.41
24 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAAAC
Found at i:1023913 original size:44 final size:44
Alignment explanation
Indices: 1023844--1023928 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
1023834 TTGAGGGTTT
1023844 TATGTGGTCCTTCGAGACTAATATGTGGCACTTCGGTGCAAACC
1 TATGTGGTCCTTCGAGACTAATATGTGGCACTTCGGTGCAAACC
* *
1023888 TATGTGGTCCTTCGGGAC-AATTATGTGGCACTTTGGTGCAA
1 TATGTGGTCCTTCGAGACTAA-TATGTGGCACTTCGGTGCAA
1023929 TTTACGAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 2 0.05
44 36 0.95
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (44 bp):
TATGTGGTCCTTCGAGACTAATATGTGGCACTTCGGTGCAAACC
Found at i:1023914 original size:21 final size:22
Alignment explanation
Indices: 1023843--1023915 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 22
1023833 GTTGAGGGTT
* *
1023843 TTATGTGGTCCTTCGAGACTAA
1 TTATGTGGTCCTTCGGGACAAA
1023865 -TATGTGG-CACTTCGGTG-CAAA
1 TTATGTGGTC-CTTCGG-GACAAA
*
1023886 CCTATGTGGTCCTTCGGGAC-AA
1 -TTATGTGGTCCTTCGGGACAAA
1023908 TTATGTGG
1 TTATGTGG
1023916 CACTTTGGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
20 1 0.02
21 22 0.52
22 4 0.10
23 14 0.33
24 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (22 bp):
TTATGTGGTCCTTCGGGACAAA
Found at i:1023929 original size:21 final size:21
Alignment explanation
Indices: 1023865--1023930 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
1023855 TCGAGACTAA
*
1023865 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGC-AA-T
1023888 TATGTGGTC-CTTCGG-GACAAT
1 TATGTGG-CACTTCGGTG-CAAT
*
1023909 TATGTGGCACTTTGGTGCAAT
1 TATGTGGCACTTCGGTGCAAT
1023930 T
1 T
1023931 TACGAGTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 1 0.03
21 17 0.46
22 4 0.11
23 14 0.38
24 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (21 bp):
TATGTGGCACTTCGGTGCAAT
Found at i:1025774 original size:20 final size:20
Alignment explanation
Indices: 1025749--1025796 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1025739 TGGATATTTA
*
1025749 AAATTTCAAATCGGGTATCC
1 AAATTTCAAATCGGATATCC
**
1025769 AAATTTCCTGATCGGATATCC
1 AAATTT-CAAATCGGATATCC
1025790 AAATTTC
1 AAATTTC
1025797 TGATTGTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
AAATTTCAAATCGGATATCC
Found at i:1025788 original size:21 final size:20
Alignment explanation
Indices: 1025758--1025800 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
1025748 AAAATTTCAA
*
1025758 ATCGGGTATCCAAATTTCCTG
1 ATCGGATATCCAAATTT-CTG
1025779 ATCGGATATCCAAATTTCTG
1 ATCGGATATCCAAATTTCTG
1025799 AT
1 AT
1025801 TGTAACGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (20 bp):
ATCGGATATCCAAATTTCTG
Found at i:1028793 original size:1 final size:1
Alignment explanation
Indices: 1028789--1028815 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1028779 TCTTGTTTAA
1028789 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1028816 GATAGAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1031697 original size:24 final size:24
Alignment explanation
Indices: 1031665--1031721 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
1031655 TTTTTAAAAT
*
1031665 TGTGAGGAATTTGTTTATTTATTA
1 TGTGTGGAATTTGTTTATTTATTA
*
1031689 TGTGTGGAATTTTTTTATTTATTA
1 TGTGTGGAATTTGTTTATTTATTA
1031713 TGTGTGGAA
1 TGTGTGGAA
1031722 GGAGATGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (24 bp):
TGTGTGGAATTTGTTTATTTATTA
Found at i:1034309 original size:15 final size:15
Alignment explanation
Indices: 1034289--1034342 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 15
1034279 TAACCGGTTT
1034289 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
* *
1034304 CGGTTTTTTAAAAAAT
1 CGG-TTTTAAAAAAAC
*
1034320 CGGTTAT-AAAAAAC
1 CGGTTTTAAAAAAAC
*
1034334 CGATTTTAA
1 CGGTTTTAA
1034343 TATTCAGATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
14 11 0.35
15 7 0.23
16 13 0.42
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:1034534 original size:21 final size:21
Alignment explanation
Indices: 1034510--1034562 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1034500 ACACTTAGGG
1034510 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
1034531 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
1034552 TACCGATTCCC
1 AACCGATTCCC
1034563 CCATGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:1034773 original size:13 final size:13
Alignment explanation
Indices: 1034752--1034806 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1034742 AAGTTCGATA
*
1034752 AATTCAAATACTT
1 AATTGAAATACTT
1034765 AATTGAAATACTT
1 AATTGAAATACTT
* *
1034778 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1034792 AATTGAAATACTT
1 AATTGAAATACTT
1034805 AA
1 AA
1034807 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1034833 original size:32 final size:32
Alignment explanation
Indices: 1034790--1034889 Score: 159
Period size: 32 Copynumber: 3.2 Consensus size: 32
1034780 TTAACTCAAC
* * *
1034790 ATAATTGAAATACTTAAATACTTCCAAGTTTG
1 ATAATTCAAATACTTAAAAACTTCCAAGTTCG
1034822 ATAATTCAAATACTTAAAAACTTCCAAGTTCG
1 ATAATTCAAATACTTAAAAACTTCCAAGTTCG
1034854 ATAATTCAAATAC-TAAAAACTT-CAAGTTCG
1 ATAATTCAAATACTTAAAAACTTCCAAGTTCG
1034884 ATAATT
1 ATAATT
1034890 GAAACAAAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 14 0.22
31 9 0.14
32 42 0.65
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (32 bp):
ATAATTCAAATACTTAAAAACTTCCAAGTTCG
Found at i:1034929 original size:21 final size:21
Alignment explanation
Indices: 1034884--1034929 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1034874 TTCAAGTTCG
* **
1034884 ATAATTGAAACAAAGTTTACG
1 ATAATTGAAACAAAGTATAAA
*
1034905 ATAATTGAAATAAAGTATAAA
1 ATAATTGAAACAAAGTATAAA
1034926 ATAA
1 ATAA
1034930 AAGTTCGACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (21 bp):
ATAATTGAAACAAAGTATAAA
Found at i:1041440 original size:21 final size:21
Alignment explanation
Indices: 1041416--1041469 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1041406 CAAAATTGGG
*
1041416 GTGTATTGGTACATCCGAGGA
1 GTGTATCGGTACATCCGAGGA
1041437 GTGTATCGGTACATCCGAGGA
1 GTGTATCGGTACATCCGAGGA
*
1041458 GTGTATCAGTAC
1 GTGTATCGGTAC
1041470 CTCCCTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (21 bp):
GTGTATCGGTACATCCGAGGA
Found at i:1042497 original size:19 final size:19
Alignment explanation
Indices: 1042461--1042498 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1042451 CCTCAAAATC
*
1042461 ATTTTTAAAATTTCATTTT
1 ATTTTTAAAATCTCATTTT
1042480 ATTTTTCAAAATCT-ATTTT
1 ATTTTT-AAAATCTCATTTT
1042499 TGCTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTAAAATCTCATTTT
Found at i:1043699 original size:13 final size:13
Alignment explanation
Indices: 1043681--1043705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1043671 AGGATATTGT
1043681 TATGCCAGCTCAG
1 TATGCCAGCTCAG
1043694 TATGCCAGCTCA
1 TATGCCAGCTCA
1043706 CCTAGGTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (13 bp):
TATGCCAGCTCAG
Found at i:1047419 original size:15 final size:16
Alignment explanation
Indices: 1047391--1047422 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1047381 TTCAAAAAGA
1047391 AAAAAGAAAGAATTTG
1 AAAAAGAAAGAATTTG
1047407 AAAAAGAAA-AATTTG
1 AAAAAGAAAGAATTTG
1047422 A
1 A
1047423 TTTAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (16 bp):
AAAAAGAAAGAATTTG
Found at i:1049376 original size:19 final size:19
Alignment explanation
Indices: 1049352--1049391 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1049342 ATTATCAAAC
1049352 TCAATTTGAGTATATTTTT
1 TCAATTTGAGTATATTTTT
1049371 TCAATTTGAGTATATTTTT
1 TCAATTTGAGTATATTTTT
1049390 TC
1 TC
1049392 TATGTAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.57
Consensus pattern (19 bp):
TCAATTTGAGTATATTTTT
Found at i:1052105 original size:184 final size:185
Alignment explanation
Indices: 1051735--1052106 Score: 430
Period size: 184 Copynumber: 2.0 Consensus size: 185
1051725 TTCAAATTCG
* * * *
1051735 ACTAGACTTCCTCATCAAGTAGGAACAATGTCGTCCACTGACTAGACTTTCTCAACATGAAGGAA
1 ACTAGACGTCCTCATCAAGTAGGAACAATGTCGTCCACTGACTAAACCTACTCAAC---AAGGAA
* * *
1051800 CAATGTCATCATAAGTGACAAGATTCACTTCATCGTAGATGAGCAGTGCCATTACCAACATCAAA
63 CAATGTCATCATAAATGACAAGATTCACTTCATCGTAGATGAGCAGTACCATTACCAACAACAAA
* * * * *
1051865 TTATCTCTAGGCAATCAGATTTCCTCAACAAGAAGGAATAGTGTTGTTTTCAGATGCA
128 TTATCTCTAGGAAATCAGATTTCCTCAACAAGAAGAAAAAGTGTCGTCTTCAGATGCA
* *
1051923 ACTAGACGTCCTCATCAAGTAGGAACAATGTCGTCCGCTGACTAAACCTACTCAAC-AGGAGCAA
1 ACTAGACGTCCTCATCAAGTAGGAACAATGTCGTCCACTGACTAAACCTACTCAACAAGGAACAA
* * * * * * *
1051987 TGTCATCATAAATGGCCAGATTCTCCTT-ATCACGTAG-T-AGCCGTATCGTTTCCAACAACAAA
66 TGTCATCATAAATGACAAGATTC-ACTTCAT--CGTAGATGAGCAGTACCATTACCAACAACAAA
* * *
1052049 TTATCTTTAGGAAATCAGATTTCCTCAATAAGTAGAAACAAG-GTCGTCTTCAGATGCA
128 TTATCTCTAGGAAATCAGATTTCCTCAACAAGAAGAAA-AAGTGTCGTCTTCAGATGCA
1052107 TAGTCATTCA
Statistics
Matches: 156, Mismatches: 24, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
184 94 0.60
185 6 0.04
186 5 0.03
188 51 0.33
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (185 bp):
ACTAGACGTCCTCATCAAGTAGGAACAATGTCGTCCACTGACTAAACCTACTCAACAAGGAACAA
TGTCATCATAAATGACAAGATTCACTTCATCGTAGATGAGCAGTACCATTACCAACAACAAATTA
TCTCTAGGAAATCAGATTTCCTCAACAAGAAGAAAAAGTGTCGTCTTCAGATGCA
Found at i:1053368 original size:21 final size:21
Alignment explanation
Indices: 1053320--1053373 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1053310 GTTTCCAGAT
*
1053320 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1053341 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1053362 TCGCAATACGAA
1 TCGCAATGCGAA
1053374 TATGTAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1053414 original size:21 final size:21
Alignment explanation
Indices: 1053388--1053483 Score: 124
Period size: 21 Copynumber: 4.6 Consensus size: 21
1053378 TAAATCGTAA
1053388 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
* * *
1053409 TGCGAT-TTACATA-TTCACAT
1 TGCGATAGTCCA-AGTTCGCAT
1053429 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
* *
1053450 TGCGATAGTCAAAGCTCGCAT
1 TGCGATAGTCCAAGTTCGCAT
1053471 TGCGATAGTCCAA
1 TGCGATAGTCCAA
1053484 AATCGCAACG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
20 16 0.25
21 47 0.75
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCCAAGTTCGCAT
Found at i:1054102 original size:6 final size:6
Alignment explanation
Indices: 1054076--1054129 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
1054066 CGCCGTCTCG
1054076 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1054121 GGTCGT GGT
1 GGTCGT GGT
1054130 AATACGTGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.31
6 33 0.69
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:1054247 original size:21 final size:21
Alignment explanation
Indices: 1054222--1054412 Score: 233
Period size: 21 Copynumber: 8.8 Consensus size: 21
1054212 ATTTTGGACT
1054222 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
1054243 ATCGCAATGCGAATTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
*
1054266 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
1054287 ATCGCAACGCAAACTTCGACT--
1 ATCGCAACG--AACTTGGAATAA
* *
1054308 ATCGCAACGGATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1054329 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
*
1054352 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1054373 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
1054394 ATCGCAACGCAAACTTGGA
1 ATCGCAACG--AACTTGGA
1054413 CTATCGCAAT
Statistics
Matches: 148, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.04
21 88 0.59
23 54 0.36
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:1054363 original size:86 final size:86
Alignment explanation
Indices: 1054218--1054381 Score: 292
Period size: 86 Copynumber: 1.9 Consensus size: 86
1054208 TGCGATTTTG
* *
1054218 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAATTTGGAATAAATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGA
1054283 ATAAATCGCAACGCAAACTTC
66 ATAAATCGCAACGCAAACTTC
* *
1054304 GACTATCGCAACGGATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGA
1054369 ATAAATCGCAACG
66 ATAAATCGCAACG
1054382 AACTTGGAAT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 74 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (86 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGA
ATAAATCGCAACGCAAACTTC
Found at i:1054398 original size:86 final size:85
Alignment explanation
Indices: 1054221--1054412 Score: 278
Period size: 86 Copynumber: 2.2 Consensus size: 85
1054211 GATTTTGGAC
* *
1054221 TATCGCAACGAACTTGGAATAAATCGCAATGCGAATTTGGAATAAATCGCAACGAATTTGGAATA
1 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATA
*
1054286 AATCGCAACGCAAACTTCGAC
66 AATCGCAACG-AAACTTCGAA
* *
1054307 TATCGCAACGGATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATA
1 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATA
*
1054372 AATCGCAACG-AACTTGGAA
66 AATCGCAACGAAACTTCGAA
1054391 TAAATCGCAACGCAAACTTGGA
1 T--ATCGCAACG--AACTTGGA
1054413 CTATCGCAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
84 8 0.09
86 80 0.85
88 6 0.06
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (85 bp):
TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATA
AATCGCAACGAAACTTCGAA
Found at i:1054408 original size:107 final size:106
Alignment explanation
Indices: 1054222--1054421 Score: 348
Period size: 107 Copynumber: 1.9 Consensus size: 106
1054212 ATTTTGGACT
*
1054222 ATCGCAACGAACTTGGAATAAATCGCAATGCGAATTTGGAATAAATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAA-GCGAATTTGGAATAAATCGCAACGAACTTGGAATAA
1054287 ATCGCAACGCAAACTTCGACTATCGCAACGGATTTGGAATAA
65 ATCGCAACGCAAACTTCGACTATCGCAACGGATTTGGAATAA
1054329 ATCGCAACGCGAACTTGGAATAAATCGCAA-CGAATTTGGAATAAATCGCAACGAACTTGGAATA
1 ATCGCAA--CGAACTTGGAATAAATCGCAAGCGAATTTGGAATAAATCGCAACGAACTTGGAATA
*
1054393 AATCGCAACGCAAACTTGGACTATCGCAA
64 AATCGCAACGCAAACTTCGACTATCGCAA
1054422 TACGAATATG
Statistics
Matches: 89, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
107 68 0.76
109 21 0.24
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (106 bp):
ATCGCAACGAACTTGGAATAAATCGCAAGCGAATTTGGAATAAATCGCAACGAACTTGGAATAAA
TCGCAACGCAAACTTCGACTATCGCAACGGATTTGGAATAA
Found at i:1054419 original size:42 final size:42
Alignment explanation
Indices: 1054222--1054421 Score: 201
Period size: 44 Copynumber: 4.6 Consensus size: 42
1054212 ATTTTGGACT
* *
1054222 ATCGCAACGAACTTGGAATAAATCGCAATGCGAATTTGGAATAA
1 ATCGCAACGAACTTGGAAT-AATCGCAA-CCGAACTTGGAATAA
* * * *
1054266 ATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTCGACT--
1 ATCGCAACGAACTTGGAAT-AATCGCAAC-CGAACTTGGAATAA
* *
1054308 ATCGCAACGGATTTGGAATAAATCGCAACGCGAACTTGGAATAA
1 ATCGCAACGAACTTGGAAT-AATCGCAAC-CGAACTTGGAATAA
*
1054352 ATCGCAACGAATTTGGAATAAATCGCAA-CGAACTTGGAATAA
1 ATCGCAACGAACTTGGAAT-AATCGCAACCGAACTTGGAATAA
*
1054394 ATCGCAACGCAAACTTGGACT-ATCGCAA
1 ATCGCAACG--AACTTGGAATAATCGCAA
1054422 TACGAATATG
Statistics
Matches: 138, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
42 68 0.49
44 70 0.51
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (42 bp):
ATCGCAACGAACTTGGAATAATCGCAACCGAACTTGGAATAA
Found at i:1054428 original size:65 final size:63
Alignment explanation
Indices: 1054222--1054421 Score: 237
Period size: 65 Copynumber: 3.1 Consensus size: 63
1054212 ATTTTGGACT
*
1054222 ATCGCAACGAACTTGGAATAAATCGCAATGCGAATTTGGAATAAATCGCAACG-AATTTGGAATA
1 ATCGCAACGAACTTGGAATAAATCGCAA--CGAATTTGGAATAAATCGCAACGCAACTTGGAAT-
1054286 A
63 A
* * *
1054287 ATCGCAACGCAAACTTCGACT--ATCGCAACGGATTTGGAATAAATCGCAACGCGAACTTGGAAT
1 ATCGCAACG--AACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGC-AACTTGGAAT
1054350 AA
63 -A
* * *
1054352 ATCGCAACGAATTTGGAATAAATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTGGACT-
1 ATCGCAACGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGC-AACTTGGAATA
1054415 ATCGCAA
1 ATCGCAA
1054422 TACGAATATG
Statistics
Matches: 118, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
63 36 0.31
65 74 0.63
67 8 0.07
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (63 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCAACTTGGAATA
Found at i:1057946 original size:19 final size:19
Alignment explanation
Indices: 1057924--1057960 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1057914 CGGGTTGATC
*
1057924 GGTTTAAACCGATTCGACT
1 GGTTCAAACCGATTCGACT
1057943 GGTTCAAACCGATTCGAC
1 GGTTCAAACCGATTCGAC
1057961 CCAACCGTTA
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:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (19 bp):
GGTTCAAACCGATTCGACT
Found at i:1058064 original size:29 final size:29
Alignment explanation
Indices: 1058022--1058168 Score: 206
Period size: 29 Copynumber: 5.1 Consensus size: 29
1058012 ACCGTTGACT
* *
1058022 GGATGTTAGTTTCGTAATTATTTTTAAAA
1 GGATGTTATTTTCGTAAATATTTTTAAAA
1058051 GGATGTTATTTTCGTAAATATTTTTAAAA
1 GGATGTTATTTTCGTAAATATTTTTAAAA
* *
1058080 GGGTGCTATTTTCGTAAATATTTTTAAAA
1 GGATGTTATTTTCGTAAATATTTTTAAAA
1058109 GG-TGTTATTTTCGTAAATATTTTTAAAA
1 GGATGTTATTTTCGTAAATATTTTTAAAA
* * * *
1058137 GGGTGATAGTTTCATAAATATTTCTTAAAA
1 GGATGTTATTTTCGTAAATATTT-TTAAAA
1058167 GG
1 GG
1058169 GTGATAATTG
Statistics
Matches: 108, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
28 27 0.25
29 73 0.68
30 8 0.07
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.46
Consensus pattern (29 bp):
GGATGTTATTTTCGTAAATATTTTTAAAA
Found at i:1058131 original size:57 final size:58
Alignment explanation
Indices: 1058028--1058168 Score: 230
Period size: 57 Copynumber: 2.4 Consensus size: 58
1058018 GACTGGATGT
* *
1058028 TAGTTTCGTAATTATTTTTAAAAGGATGTTATTTTCGTAAATATTTTTAAAAGGGTGC
1 TAGTTTCGTAAATATTTTTAAAAGGATGTTATTTTCGTAAATATTTTTAAAAGGGTGA
*
1058086 TATTTTCGTAAATATTTTTAAAAGG-TGTTATTTTCGTAAATATTTTTAAAAGGGTGA
1 TAGTTTCGTAAATATTTTTAAAAGGATGTTATTTTCGTAAATATTTTTAAAAGGGTGA
*
1058143 TAGTTTCATAAATATTTCTTAAAAGG
1 TAGTTTCGTAAATATTT-TTAAAAGG
1058169 GTGATAATTG
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
57 46 0.60
58 31 0.40
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (58 bp):
TAGTTTCGTAAATATTTTTAAAAGGATGTTATTTTCGTAAATATTTTTAAAAGGGTGA
Found at i:1062663 original size:23 final size:23
Alignment explanation
Indices: 1062637--1062700 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1062627 CAGCTCATAT
**
1062637 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACACAG
* *
1062660 AATTGCACCGGAGTGTCACACAG
1 AATTGCACCGAAGTGCCACACAG
*
1062683 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1062701 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACACAG
Found at i:1062887 original size:103 final size:103
Alignment explanation
Indices: 1062716--1062933 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
1062706 TAATGTCCAT
* *
1062716 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1062781 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1062819 AAGGACCACATATCATTCCTTAAGAATCATATAGATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1062884 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1062922 AAGGACCACATA
1 AAGGACCACATA
1062934 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1063872 original size:64 final size:63
Alignment explanation
Indices: 1063720--1063874 Score: 156
Period size: 64 Copynumber: 2.4 Consensus size: 63
1063710 TTCCCTATCG
* ** *
1063720 GTGCATCGATGCACTACCTGTGCATCGGTGCATAAAATACATTCGATGTTTGTTTATTATTGG
1 GTGCATCGATGCACTACCTGTGCATCGGTGCATAAAATACATTCGATGTTTGTTGATTAAAGA
* * * *
1063783 GATGCATCGATGCA-TGCCTTATGCAT-GGATGCACT-AATTGCATTCGATGTTT-TTAGATTAA
1 G-TGCATCGATGCACTACC-TGTGCATCGG-TGCA-TAAAATACATTCGATGTTTGTT-GATT-A
1063844 AAGA
60 AAGA
1063848 GTGCATCGATGCACTACCTGTGCATCG
1 GTGCATCGATGCACTACCTGTGCATCG
1063875 ATACACCTTC
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
63 8 0.11
64 58 0.78
65 8 0.11
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACCTGTGCATCGGTGCATAAAATACATTCGATGTTTGTTGATTAAAGA
Found at i:1068361 original size:23 final size:23
Alignment explanation
Indices: 1068335--1068398 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1068325 CAGCTCATAT
*
1068335 AATTGCACCGAAGTGTCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1068358 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1068381 AATTGTACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1068399 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1068534 original size:103 final size:103
Alignment explanation
Indices: 1068414--1068631 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
1068404 TAATGTCCAT
* * *
1068414 AAGGACCACATATCATTCCTTAATAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1068479 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1068517 AAGGACCACATATCATTCCTTAAGAATCATATAGATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1068582 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1068620 AAGGACCACATA
1 AAGGACCACATA
1068632 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1069440 original size:19 final size:19
Alignment explanation
Indices: 1069412--1069449 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1069402 GATGCATTCC
1069412 CTATCGGTGCATCGATGCA
1 CTATCGGTGCATCGATGCA
*
1069431 CTATCTGTGCATCGATGCA
1 CTATCGGTGCATCGATGCA
1069450 TAAAATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (19 bp):
CTATCGGTGCATCGATGCA
Found at i:1069494 original size:64 final size:64
Alignment explanation
Indices: 1069418--1069574 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
1069408 TTCCCTATCG
* ** ** *
1069418 GTGCATCGATGCACTATCTGTGCATCGATGCA-TAAAATACATTCGATGTTTTTTTATT-ACTGG
1 GTGCATCGATGCACTACCTGTGCATCGATGCACT-AAATACATTCGATGTTTTTAGATTAAAAGA
* * * *
1069481 GATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTAGATTAAAAG
1 G-TGCATCGATGCACTACC-TGTGCATCGATGCACTAAATACATTCGATGTTTTTAGATTAAAAG
1069545 A
64 A
1069546 GTGCATCGATGCACTACCTGTGCATCGAT
1 GTGCATCGATGCACTACCTGTGCATCGAT
1069575 ACACCTTTAA
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
63 3 0.04
64 67 0.87
65 7 0.09
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTGTGCATCGATGCACTAAATACATTCGATGTTTTTAGATTAAAAGA
Found at i:1074045 original size:70 final size:67
Alignment explanation
Indices: 1073965--1074156 Score: 198
Period size: 63 Copynumber: 2.9 Consensus size: 67
1073955 TTATTCTTTG
*
1073965 AATATGTCAAATTAAAAAGATATTTATTATCTATTTAAATTTGAATATTAAATATAAT-TACATA
1 AATATTTCAAATT-AAAAGATA-TTATTATCTATTTAAATTTGAATATTAAATAT-ATCTACATA
1074029 CTTTTC
63 -TTTTC
* * * *
1074035 AATATTTCAAATT-AAA-ATA--A-TATCTATTTAAGTTTGAATAGTTAAATGTGTCTATATATT
1 AATATTTCAAATTAAAAGATATTATTATCTATTTAAATTTGAATA-TTAAATATATCTACATATT
*
1074095 TTG
65 TTC
* * * *
1074098 AATATTTCAAATTAAAGGATATTATTATATATTTAAATTTAAATATTAAAAGATATCTA
1 AATATTTCAAATTAAAAGATATTATTATCTATTTAAATTTGAATATT-AAATATATCTA
1074157 ATTGGGTTAG
Statistics
Matches: 101, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
63 37 0.37
64 15 0.15
65 3 0.03
67 6 0.06
68 28 0.28
70 12 0.12
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (67 bp):
AATATTTCAAATTAAAAGATATTATTATCTATTTAAATTTGAATATTAAATATATCTACATATTT
TC
Found at i:1074065 original size:131 final size:130
Alignment explanation
Indices: 1073912--1074147 Score: 288
Period size: 131 Copynumber: 1.8 Consensus size: 130
1073902 TTGGCAATTG
*
1073912 CAAATTAAAAAAAATATTTTTAA-TTTGAATA-TT--A-GTAGGATA-ATTATTCTTTGAATATG
1 CAAATTAAAAAAAATATTTTTAAGTTTGAATAGTTAAATGT-GTATATA-TA-T-TTTGAATATG
* *
1073971 TCAAATTAAAAAGATATTTATTATCTATTTAAATTTGAATATTAAATATAATTACATACTTTTCA
62 TCAAATT-AAAAGATA-TTATTATATATTTAAATTTAAATATTAAATATAATTACATACTTTTCA
1074036 ATATTT
125 ATATTT
* * *
1074042 CAAATT-AAAATAATATCTATTTAAGTTTGAATAGTTAAATGTGTCTATATATTTTGAATATTTC
1 CAAATTAAAAAAAATAT-T-TTTAAGTTTGAATAGTTAAATGTGTATATATATTTTGAATATGTC
*
1074106 AAATTAAAGGATATTATTATATATTTAAATTTAAATATTAAA
64 AAATTAAAAGATATTATTATATATTTAAATTTAAATATTAAA
1074148 AGATATCTAA
Statistics
Matches: 91, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
129 9 0.10
130 7 0.08
131 32 0.35
132 15 0.16
133 18 0.20
134 1 0.01
135 6 0.07
136 3 0.03
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (130 bp):
CAAATTAAAAAAAATATTTTTAAGTTTGAATAGTTAAATGTGTATATATATTTTGAATATGTCAA
ATTAAAAGATATTATTATATATTTAAATTTAAATATTAAATATAATTACATACTTTTCAATATTT
Found at i:1074719 original size:25 final size:26
Alignment explanation
Indices: 1074652--1074721 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 26
1074642 TTATTTTAAA
*
1074652 TATT-GAATATAATAAATAATATTATT
1 TATTAGAATATTA-AAATAATATTATT
* * * *
1074678 TATTAGAAAAAT-CAATATTATTATT
1 TATTAGAATATTAAAATAATATTATT
1074703 T-TTAGAATATTAAAATAAT
1 TATTAGAATATTAAAATAAT
1074722 GTATTTAATA
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
24 8 0.24
25 17 0.52
26 4 0.12
27 4 0.12
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (26 bp):
TATTAGAATATTAAAATAATATTATT
Found at i:1074898 original size:11 final size:11
Alignment explanation
Indices: 1074882--1074936 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
1074872 TATTAAAATA
1074882 ATAATATTATT
1 ATAATATTATT
*
1074893 ATAATATAATT
1 ATAATATTATT
* *
1074904 AAAATATAATT
1 ATAATATTATT
*
1074915 AATTATATTATT
1 -ATAATATTATT
1074927 ATAATATTAT
1 ATAATATTAT
1074937 AGTATTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
11 29 0.78
12 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATAATATTATT
Found at i:1074929 original size:8 final size:8
Alignment explanation
Indices: 1074889--1074977 Score: 53
Period size: 8 Copynumber: 11.2 Consensus size: 8
1074879 ATAATAATAT
1074889 TATTATAA
1 TATTATAA
*
1074897 TATAATTAA
1 TATTA-TAA
*
1074906 -AATATAA
1 TATTATAA
*
1074913 TTAATTATAT
1 -T-ATTATAA
1074923 TATTATAA
1 TATTATAA
*
1074931 TATTATAG
1 TATTATAA
1074939 TATTA-AA
1 TATTATAA
*
1074946 -AATATAA
1 TATTATAA
*
1074953 TATTATAT
1 TATTATAA
1074961 TATTA-AA
1 TATTATAA
1074968 -ATTATTAA
1 TATTA-TAA
1074976 TA
1 TA
1074978 AATATATGTT
Statistics
Matches: 60, Mismatches: 12, Indels: 17
0.67 0.13 0.19
Matches are distributed among these distances:
6 7 0.12
7 7 0.12
8 36 0.60
9 5 0.08
10 5 0.08
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (8 bp):
TATTATAA
Found at i:1074952 original size:22 final size:22
Alignment explanation
Indices: 1074926--1074977 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
1074916 ATTATATTAT
1074926 TATAATATTATAGTATTAAAAA
1 TATAATATTATAGTATTAAAAA
* *
1074948 TATAATATTATATTATTAAAAT
1 TATAATATTATAGTATTAAAAA
1074970 TATTAATA
1 TA-TAATA
1074978 AATATATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TATAATATTATAGTATTAAAAA
Found at i:1074982 original size:22 final size:22
Alignment explanation
Indices: 1074926--1075032 Score: 62
Period size: 22 Copynumber: 4.9 Consensus size: 22
1074916 ATTATATTAT
* *
1074926 TATAATATTATAGTATTAAAAA
1 TATAATATAATATTATTAAAAA
* *
1074948 TATAATATTATATTATTAAAAT
1 TATAATATAATATTATTAAAAA
* *
1074970 TATTAATA-AATATATGTTAATAA
1 TA-TAATATAATAT-TATTAAAAA
*
1074993 T-TAATAT--TGTTATTAAAATAA
1 TATAATATAATATTATT-AAA-AA
*
1075014 TACTAAAATAATA-TATTAA
1 TA-TAATATAATATTATTAA
1075033 TATAAATACA
Statistics
Matches: 65, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
19 3 0.05
20 4 0.06
21 8 0.12
22 26 0.40
23 19 0.29
24 4 0.06
25 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (22 bp):
TATAATATAATATTATTAAAAA
Found at i:1075030 original size:24 final size:27
Alignment explanation
Indices: 1075003--1075058 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
1074993 TTAATATTGT
1075003 TATTAAAAT-AATAC-TAAAATAATA-
1 TATTAAAATAAATACATAAAATAATAG
* *
1075027 TATTAATATAAATACATAAAGTAATAG
1 TATTAAAATAAATACATAAAATAATAG
1075054 TATTA
1 TATTA
1075059 TTTTGAGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 8 0.30
25 5 0.19
26 9 0.33
27 5 0.19
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (27 bp):
TATTAAAATAAATACATAAAATAATAG
Found at i:1085591 original size:28 final size:28
Alignment explanation
Indices: 1085559--1085614 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1085549 CCATTTGGCG
1085559 CCTGATATCAA-TAATAAATAATTTGCCA
1 CCTGATATCAAGT-ATAAATAATTTGCCA
1085587 CCTGATATCAAGTATAAATAATTTGCCA
1 CCTGATATCAAGTATAAATAATTTGCCA
1085615 TGTATTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (28 bp):
CCTGATATCAAGTATAAATAATTTGCCA
Found at i:1092338 original size:2 final size:2
Alignment explanation
Indices: 1092331--1092362 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1092321 TACTTAAATC
1092331 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
1092363 TGATTTTTCA
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:1092931 original size:15 final size:14
Alignment explanation
Indices: 1092897--1092930 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1092887 AGGGTTGTTT
*
1092897 GTTTTACGAAAAAC
1 GTTTTTCGAAAAAC
*
1092911 GTTTTTCGAAAAAT
1 GTTTTTCGAAAAAC
1092925 GTTTTT
1 GTTTTT
1092931 TTTATTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (14 bp):
GTTTTTCGAAAAAC
Found at i:1093580 original size:21 final size:20
Alignment explanation
Indices: 1093542--1093580 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1093532 TATTATAAAA
* *
1093542 ATAATAATATTATGTTTTTT
1 ATAATAATAATATCTTTTTT
1093562 ATAATAAATAATATCTTTT
1 ATAAT-AATAATATCTTTT
1093581 ACTATATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
ATAATAATAATATCTTTTTT
Found at i:1094915 original size:31 final size:31
Alignment explanation
Indices: 1094869--1094927 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1094859 CTGGTGAGAT
1094869 TAACGAGCAACAAGTCGAGCAATAATTTTTTC
1 TAACGAGCAACAAGTCGAGCAA-AATTTTTTC
*
1094901 TAACGAG-TACAAGTCGAGCAAAATTTT
1 TAACGAGCAACAAGTCGAGCAAAATTTT
1094928 AACGAGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 6 0.23
31 13 0.50
32 7 0.27
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (31 bp):
TAACGAGCAACAAGTCGAGCAAAATTTTTTC
Found at i:1094934 original size:26 final size:28
Alignment explanation
Indices: 1094868--1094934 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 28
1094858 TCTGGTGAGA
*
1094868 TTAACGAGCAACAAGTCGAGCAATAATTTTT
1 TTAACGAG-TACAAGTCGAGCAATAA--TTT
1094899 TCTAACGAGTACAAGTCGAGCAA-AA-TT
1 T-TAACGAGTACAAGTCGAGCAATAATTT
1094926 TTAACGAGT
1 TTAACGAGT
1094935 TTAATGAGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 8 0.24
27 3 0.09
30 2 0.06
31 14 0.41
32 7 0.21
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (28 bp):
TTAACGAGTACAAGTCGAGCAATAATTT
Found at i:1102820 original size:19 final size:19
Alignment explanation
Indices: 1102796--1102844 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1102786 TGCCATAAGT
1102796 GTATCGGTACCTTAAGGAG
1 GTATCGGTACCTTAAGGAG
* *
1102815 GTATCGGTACCTTGAGGTG
1 GTATCGGTACCTTAAGGAG
*
1102834 GTATCGATACC
1 GTATCGGTACC
1102845 CTGGCAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (19 bp):
GTATCGGTACCTTAAGGAG
Found at i:1102930 original size:20 final size:21
Alignment explanation
Indices: 1102886--1102940 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1102876 TACATGCCTA
1102886 GGTATCGATACCCTTGAAAGGT
1 GGTATCGATACCCTT-AAAGGT
* *
1102908 GGTATCGGTACCCTT-AGGGT
1 GGTATCGATACCCTTAAAGGT
*
1102928 GGTACCGATACCC
1 GGTATCGATACCC
1102941 CCAAGCATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.52
22 14 0.48
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (21 bp):
GGTATCGATACCCTTAAAGGT
Found at i:1103538 original size:22 final size:22
Alignment explanation
Indices: 1103473--1103539 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
1103463 GATGTAACCC
*
1103473 TATGTGGCACTTC-GATGCAAAA
1 TATGTGGCACTTCAG-TGCAAAT
* *
1103495 TATATGGTCA-TTCAG-GAAAAT
1 TATGTGG-CACTTCAGTGCAAAT
1103516 TATGTGGCACTTCAGTGCAAAT
1 TATGTGGCACTTCAGTGCAAAT
1103538 TA
1 TA
1103540 CGAGCTATGG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 2 0.06
21 15 0.42
22 16 0.44
23 3 0.08
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (22 bp):
TATGTGGCACTTCAGTGCAAAT
Found at i:1105145 original size:18 final size:18
Alignment explanation
Indices: 1105076--1105159 Score: 89
Period size: 18 Copynumber: 4.7 Consensus size: 18
1105066 CAACCCGAAT
* * *
1105076 CGACCTGTTTACCCAACC
1 CGACCCGTTGACCCGACC
*
1105094 CGACCAGTTGACCCGACC
1 CGACCCGTTGACCCGACC
* *
1105112 CGAACC-TTGACTCGACC
1 CGACCCGTTGACCCGACC
*
1105129 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACC
*
1105147 CGACCCATTGACC
1 CGACCCGTTGACC
1105160 GTTGACCGCA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 15 0.27
18 40 0.73
ACGTcount: A:0.21, C:0.44, G:0.18, T:0.17
Consensus pattern (18 bp):
CGACCCGTTGACCCGACC
Found at i:1107595 original size:24 final size:24
Alignment explanation
Indices: 1107568--1107655 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 24
1107558 ATTTCAAACT
* *
1107568 TGAATTCTGTTCTGATATATGACC
1 TGAATTCTGTTTTGATATATGATC
* *
1107592 TGAATTCTGTTTTGATTTCTGATC
1 TGAATTCTGTTTTGATATATGATC
* * * *
1107616 TGGATTCTGTTATGATATTTGTTC
1 TGAATTCTGTTTTGATATATGATC
1107640 TGAATTCTGTTTTGAT
1 TGAATTCTGTTTTGAT
1107656 TTTCAGATAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.19, C:0.11, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTTTGATATATGATC
Found at i:1107608 original size:48 final size:48
Alignment explanation
Indices: 1107556--1107657 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
1107546 ATATTTTATC
*
1107556 TGATTTCAAA-CTTGAATTCTGTTCTGATATATGACCTGAATTCTGTTT
1 TGATTTCAAATC-TGAATTCTGTTATGATATATGACCTGAATTCTGTTT
** * * **
1107604 TGATTTCTGATCTGGATTCTGTTATGATATTTGTTCTGAATTCTGTTT
1 TGATTTCAAATCTGAATTCTGTTATGATATATGACCTGAATTCTGTTT
1107652 TGATTT
1 TGATTT
1107658 TCAGATATCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
48 45 0.98
49 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.51
Consensus pattern (48 bp):
TGATTTCAAATCTGAATTCTGTTATGATATATGACCTGAATTCTGTTT
Found at i:1112229 original size:24 final size:24
Alignment explanation
Indices: 1112202--1112265 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
1112192 ATTTTAGACT
*
1112202 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTATGATACATGACC
* ** **
1112226 TGAAATCTGTTATGATATTTGTTC
1 TGAATTCTGTTATGATACATGACC
*
1112250 TGAATTCTGTTTTGAT
1 TGAATTCTGTTATGAT
1112266 TTTCAGATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTATGATACATGACC
Found at i:1116793 original size:24 final size:25
Alignment explanation
Indices: 1116765--1116842 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 25
1116755 AAATATTTTA
* *
1116765 TCTGATTTCCT-ACATGAATTTTGT
1 TCTGATTTCATGACATGAATTCTGT
* *
1116789 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTCATGACATGAATTCTGT
* *
1116813 TCTGATTTC-TGATC-TGGATTATGT
1 TCTGATTTCATGA-CATGAATTCTGT
1116837 TCTGAT
1 TCTGAT
1116843 ATCTGTTCTG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 3 0.07
24 38 0.86
25 3 0.07
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (25 bp):
TCTGATTTCATGACATGAATTCTGT
Found at i:1116817 original size:12 final size:12
Alignment explanation
Indices: 1116802--1116861 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
1116792 GATACATGAC
1116802 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1116814 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
1116826 CTGGATTATGTT
1 CTGAATTCTGTT
1116838 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
*
1116850 CTGAATTATGTT
1 CTGAATTCTGTT
1116862 TTGATTTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1116847 original size:24 final size:24
Alignment explanation
Indices: 1116779--1116866 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
1116769 ATTTCCTACA
* *
1116779 TGAATTTTGTTCTGATA-CATGACC
1 TGAATTATGTTCTGATATC-TGATC
* *
1116803 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTATGTTCTGATATCTGATC
* *
1116827 TGGATTATGTTCTGATATCTGTTC
1 TGAATTATGTTCTGATATCTGATC
*
1116851 TGAATTATGTTTTGAT
1 TGAATTATGTTCTGAT
1116867 TTTATGATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 53 0.98
25 1 0.02
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.49
Consensus pattern (24 bp):
TGAATTATGTTCTGATATCTGATC
Found at i:1121434 original size:24 final size:24
Alignment explanation
Indices: 1121407--1121470 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
1121397 ATTTTAGACT
*
1121407 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTATGATACATGACC
* ** **
1121431 TGAAATCTGTTATGATATTTGTTC
1 TGAATTCTGTTATGATACATGACC
*
1121455 TGAATTCTGTTTTGAT
1 TGAATTCTGTTATGAT
1121471 TTTCAGATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (24 bp):
TGAATTCTGTTATGATACATGACC
Found at i:1125882 original size:24 final size:25
Alignment explanation
Indices: 1125855--1125911 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
1125845 AAATATTTTA
* *
1125855 TCTGATTTCCT-ACTTGAATTATGT
1 TCTGATTTCATGACCTGAATTATGT
* *
1125879 TCTGA-TACATGACCTGAATTTTGT
1 TCTGATTTCATGACCTGAATTATGT
1125903 TCTGATTTC
1 TCTGATTTC
1125912 TTATCTGGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 3 0.12
24 21 0.81
25 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (25 bp):
TCTGATTTCATGACCTGAATTATGT
Found at i:1130502 original size:24 final size:23
Alignment explanation
Indices: 1130475--1130562 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 23
1130465 ATTTTCGACT
*
1130475 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATAC-TGATC
*
1130499 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGA-TACTGATC
* * *
1130523 TGGATTCTGTTATGATATCTGTTC
1 TGAATTCTGTTCTGATA-CTGATC
*
1130547 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
1130563 TTTTTGATAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.02
24 51 0.94
25 2 0.04
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGATC
Found at i:1130513 original size:12 final size:12
Alignment explanation
Indices: 1130475--1130557 Score: 71
Period size: 12 Copynumber: 6.9 Consensus size: 12
1130465 ATTTTCGACT
1130475 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
1130487 TG-ATACATGACC
1 TGAATTC-TGTTC
1130499 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
1130511 TGATTTCTGATC
1 TGAATTCTGTTC
* *
1130523 TGGATTCTGTTA
1 TGAATTCTGTTC
1130535 TG-ATATCTGTTC
1 TGAAT-TCTGTTC
1130547 TGAATTCTGTT
1 TGAATTCTGTT
1130558 TTGATTTTTT
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
11 5 0.09
12 44 0.81
13 5 0.09
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:1137164 original size:16 final size:16
Alignment explanation
Indices: 1137135--1137175 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1137125 AACAGACTTG
1137135 TGTTTTCT--ACAGTC
1 TGTTTTCTACACAGTC
1137149 TGTTTTCTACACAGTC
1 TGTTTTCTACACAGTC
1137165 TGTTTTCTACA
1 TGTTTTCTACA
1137176 TGGTATCAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.32
16 17 0.68
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (16 bp):
TGTTTTCTACACAGTC
Found at i:1141229 original size:14 final size:14
Alignment explanation
Indices: 1141210--1141237 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1141200 TAACATACTT
1141210 GTCTATTTTCTACA
1 GTCTATTTTCTACA
1141224 GTCTATTTTCTACA
1 GTCTATTTTCTACA
1141238 TTACCAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
GTCTATTTTCTACA
Found at i:1142398 original size:81 final size:82
Alignment explanation
Indices: 1142299--1142460 Score: 290
Period size: 81 Copynumber: 2.0 Consensus size: 82
1142289 CGTCGACTCT
*
1142299 TTTTCTTGGTTTCCTTGCAATTCATGAGAGCTTTATTTTAATATAACTTCTTTCTTTTTCGACAG
1 TTTTCTTGGTTTCCTTGCAATTCATGAGAGCTTTATTTTAATATAACTTCTTTCATTTTCGACAG
*
1142364 ATTAACATGATATTTCA
66 ATCAACATGATATTTCA
*
1142381 TTTT-TTGGTTTCCTTGCAATTCATGAGAGCTTTATTTTAATATAACTTCTTTCATTTTCGGCAG
1 TTTTCTTGGTTTCCTTGCAATTCATGAGAGCTTTATTTTAATATAACTTCTTTCATTTTCGACAG
1142445 ATCAACATGATATTTC
66 ATCAACATGATATTTC
1142461 GTCTCGAGTT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 73 0.95
82 4 0.05
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (82 bp):
TTTTCTTGGTTTCCTTGCAATTCATGAGAGCTTTATTTTAATATAACTTCTTTCATTTTCGACAG
ATCAACATGATATTTCA
Found at i:1154207 original size:30 final size:30
Alignment explanation
Indices: 1154171--1154234 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
1154161 TTCGTTTTAA
*
1154171 TTCATTATCATTGACTTCGCTTTGCACACT
1 TTCATTATCATTCACTTCGCTTTGCACACT
*
1154201 TTCATTATCTTTCACTTCGCTTTGCACACT
1 TTCATTATCATTCACTTCGCTTTGCACACT
1154231 TTCA
1 TTCA
1154235 CTCTCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.28, G:0.08, T:0.45
Consensus pattern (30 bp):
TTCATTATCATTCACTTCGCTTTGCACACT
Found at i:1156289 original size:31 final size:31
Alignment explanation
Indices: 1156251--1156313 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1156241 ATTTTATGGT
1156251 TGATAGTTAGAATTTGCTGTAATAGCTACAA
1 TGATAGTTAGAATTTGCTGTAATAGCTACAA
*
1156282 TGATAGTTAGAATTTGCTGTGATAGCTACAA
1 TGATAGTTAGAATTTGCTGTAATAGCTACAA
1156313 T
1 T
1156314 TTAGGCTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.37
Consensus pattern (31 bp):
TGATAGTTAGAATTTGCTGTAATAGCTACAA
Found at i:1163166 original size:54 final size:54
Alignment explanation
Indices: 1163084--1163190 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
1163074 TTGATTACAA
1163084 TATATATATATGTTAGGATCCACTTACACCCAATCTAAAACTATTTTAGAACCC
1 TATATATATATGTTAGGATCCACTTACACCCAATCTAAAACTATTTTAGAACCC
* * *
1163138 TATATATAT-TGGTTAGGATCCACTTACACCCAGTGTAAAATTATTTTAGAACC
1 TATATATATAT-GTTAGGATCCACTTACACCCAATCTAAAACTATTTTAGAACC
1163191 GTTGGATTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
53 1 0.02
54 48 0.98
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.35
Consensus pattern (54 bp):
TATATATATATGTTAGGATCCACTTACACCCAATCTAAAACTATTTTAGAACCC
Found at i:1163367 original size:2 final size:2
Alignment explanation
Indices: 1163360--1163399 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1163350 CCAGCCCTAC
1163360 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
1163400 CAGTGAGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1166076 original size:17 final size:17
Alignment explanation
Indices: 1166039--1166076 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1166029 CAATATAATT
*
1166039 AAAATTAAAAAATATAC
1 AAAATTAAAAAATATAA
1166056 AAAATTAAGAAAA-ATAA
1 AAAATTAA-AAAATATAA
1166073 AAAA
1 AAAA
1166077 ATCTAGTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (17 bp):
AAAATTAAAAAATATAA
Found at i:1167937 original size:20 final size:20
Alignment explanation
Indices: 1167912--1167953 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1167902 TTGACCTGGC
1167912 CCGGCGTTGACCATTGTTGA
1 CCGGCGTTGACCATTGTTGA
1167932 CCGGCGTTGACCATTGTTGA
1 CCGGCGTTGACCATTGTTGA
1167952 CC
1 CC
1167954 AAAACTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (20 bp):
CCGGCGTTGACCATTGTTGA
Found at i:1170505 original size:24 final size:24
Alignment explanation
Indices: 1170402--1170489 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
1170392 TTCTATTATA
* * * **
1170402 ATACCTGACATGGATTCTGATAGG
1 ATACTTGACCTGGATTTTGATCTG
1170426 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTTTGATCTG
1170450 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTTTGATCTG
1170474 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
1170490 ATGTTTTGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTGGATTTTGATCTG
Found at i:1174468 original size:22 final size:22
Alignment explanation
Indices: 1174443--1174492 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1174433 GCTAAAACAC
*
1174443 TTTAGTATCAGTGCTAAGGCAA
1 TTTAGTACCAGTGCTAAGGCAA
* *
1174465 TTTAGTACCAGTGCTTAGGCAC
1 TTTAGTACCAGTGCTAAGGCAA
1174487 TTTAGT
1 TTTAGT
1174493 TATGTGATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (22 bp):
TTTAGTACCAGTGCTAAGGCAA
Found at i:1177170 original size:23 final size:23
Alignment explanation
Indices: 1177140--1177185 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1177130 CTCATAATTG
1177140 AAAGAAAACCAAAGGAAAAACTT
1 AAAGAAAACCAAAGGAAAAACTT
** *
1177163 AAAGAAAACTTAATGAAAAACTT
1 AAAGAAAACCAAAGGAAAAACTT
1177186 GATGTAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.15
Consensus pattern (23 bp):
AAAGAAAACCAAAGGAAAAACTT
Found at i:1181312 original size:14 final size:14
Alignment explanation
Indices: 1181274--1181315 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
1181264 GATTGCATAT
*
1181274 TTTTTATATTT-TA
1 TTTTTCTATTTATA
1181287 TTTTTCTA-TTATA
1 TTTTTCTATTTATA
1181300 TTTTTCTATTTATA
1 TTTTTCTATTTATA
1181314 TT
1 TT
1181316 GTTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 2 0.08
13 17 0.65
14 7 0.27
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTCTATTTATA
Found at i:1191386 original size:39 final size:38
Alignment explanation
Indices: 1191332--1191571 Score: 187
Period size: 39 Copynumber: 5.9 Consensus size: 38
1191322 AGATCCCCAA
*
1191332 AAAATAAAT-TCAACGATTTATTTCCTTTTACAAAACATG
1 AAAATAAATCT-AACGATTTATTTCCTTTTACAAAATA-G
*
1191371 AAAATAAATCTAACGATTTATTTTCTTTTACAAAATAGG
1 AAAATAAATCTAACGATTTATTTCCTTTTACAAAATA-G
* * *
1191410 AAACTAAATCAAACAATTTATTTCCTTTTACAAAATAG
1 AAAATAAATCTAACGATTTATTTCCTTTTACAAAATAG
* *
1191448 AAAAAATAAATCAAACGGGGTTTTTCGATTTATTTCCTTTTACAAAATTCG
1 --AAAATAAATCTAA----------CGATTTATTTCCTTTTACAAAA-TAG
* * * *
1191499 AAACTAAATCCAACAATTTATTTCATTTTACAAAATAG
1 AAAATAAATCTAACGATTTATTTCCTTTTACAAAATAG
* *
1191537 AAAAATAAATTCT-ATGATTTATTTCATTTTACAAA
1 -AAAATAAA-TCTAACGATTTATTTCCTTTTACAAA
1191572 CCAGAATCAT
Statistics
Matches: 166, Mismatches: 19, Indels: 32
0.76 0.09 0.15
Matches are distributed among these distances:
38 3 0.02
39 114 0.69
40 15 0.09
49 11 0.07
50 21 0.13
51 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (38 bp):
AAAATAAATCTAACGATTTATTTCCTTTTACAAAATAG
Found at i:1191535 original size:89 final size:88
Alignment explanation
Indices: 1191384--1191546 Score: 272
Period size: 89 Copynumber: 1.8 Consensus size: 88
1191374 ATAAATCTAA
* * *
1191384 CGATTTATTTTCTTTTACAAAATAGGAAACTAAATCAAACAATTTATTTCCTTTTACAAAATAGA
1 CGATTTATTTCCTTTTACAAAATACGAAACTAAATCAAACAATTTATTTCATTTTACAAAATAG-
1191449 AAAAATAAATCAAACGGGGTTTTT
65 AAAAATAAATCAAACGGGGTTTTT
* *
1191473 CGATTTATTTCCTTTTACAAAATTCGAAACTAAATCCAACAATTTATTTCATTTTACAAAATAGA
1 CGATTTATTTCCTTTTACAAAATACGAAACTAAATCAAACAATTTATTTCATTTTACAAAATAGA
1191538 AAAATAAAT
66 AAAATAAAT
1191547 TCTATGATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 10 0.14
89 59 0.86
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (88 bp):
CGATTTATTTCCTTTTACAAAATACGAAACTAAATCAAACAATTTATTTCATTTTACAAAATAGA
AAAATAAATCAAACGGGGTTTTT
Found at i:1191809 original size:58 final size:56
Alignment explanation
Indices: 1191717--1191901 Score: 225
Period size: 58 Copynumber: 3.3 Consensus size: 56
1191707 TTATTTAATT
*
1191717 TTACAAAATAG-ATCGTTCAAGATTCTCAAGGAAATAAATTCAACAATTTATCTTCC
1 TTACAAAATAGAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTAT-TTCC
*
1191773 TTACAAAGATAGAATCATTCAAGATTATCAAGGAAATAAATTCAACAATTTA--TCC
1 TTACAAA-ATAGAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTCC
** * * *
1191828 TTACAAGGTTAGAATCATTTAAGATTCTCAA-GAAATAAATTCAACTATTTGTTTTCC
1 TTACAA-AATAGAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTT-ATTTCC
*
1191885 TTACGAAATTAGAATCA
1 TTAC-AAAATAGAATCA
1191902 ACGCTAACGA
Statistics
Matches: 113, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
54 18 0.16
55 29 0.26
56 7 0.06
57 20 0.18
58 39 0.35
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (56 bp):
TTACAAAATAGAATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTCC
Found at i:1192085 original size:45 final size:44
Alignment explanation
Indices: 1192035--1192131 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
1192025 GAATTAATTA
1192035 TTTAATTTTAC-CAACAAAATAATCAGAAA-GAACTAATCATTTGAT
1 TTTAATTTT-CGCAAC-AAATAAT-AGAAAGGAACTAATCATTTGAT
* * * *
1192080 TTTAATTTTCGCAACCAATAATTGAAAGGAACTATTCCTTTGAT
1 TTTAATTTTCGCAACAAATAATAGAAAGGAACTAATCATTTGAT
1192124 TTTAATTT
1 TTTAATTT
1192132 ATGCAACCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
43 4 0.09
44 29 0.63
45 13 0.28
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (44 bp):
TTTAATTTTCGCAACAAATAATAGAAAGGAACTAATCATTTGAT
Found at i:1192112 original size:44 final size:44
Alignment explanation
Indices: 1192060--1192146 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
1192050 AAAATAATCA
1192060 GAAAGAACTAATCATTTGATTTTAATTT-TCGCAACCAA-TAATT
1 GAAAGAACTAATCATTTGATTTTAATTTAT-GCAACCAAGTAATT
* *
1192103 GAAAGGAACTATTCCTTTGATTTTAATTTATGCAACCAAGTAAT
1 GAAA-GAACTAATCATTTGATTTTAATTTATGCAACCAAGTAAT
1192147 CAAAAGCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 4 0.10
44 30 0.77
45 5 0.13
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (44 bp):
GAAAGAACTAATCATTTGATTTTAATTTATGCAACCAAGTAATT
Found at i:1192926 original size:23 final size:22
Alignment explanation
Indices: 1192900--1192973 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 22
1192890 TACTTCTATG
1192900 TATTTATAAAATTTATATTAAA
1 TATTTATAAAATTTATATTAAA
1192922 TTATTCTA-AAAATTT-TATTTATAA
1 -TATT-TATAAAATTTATA-TTA-AA
* *
1192946 TA-TTATAAAA-ATATTTTAAAA
1 TATTTATAAAATTTATATT-AAA
1192967 TATTTAT
1 TATTTAT
1192974 TTATTTTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 15
0.71 0.03 0.25
Matches are distributed among these distances:
21 9 0.21
22 13 0.31
23 16 0.38
24 4 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTATAAAATTTATATTAAA
Found at i:1193017 original size:22 final size:20
Alignment explanation
Indices: 1192959--1193019 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 20
1192949 TATAAAAATA
*
1192959 TTTTAAAAT-ATTTATTTAT
1 TTTTGAAATAATTTATTTAT
1192978 TTTTGAAA-ACCATATTATTTATT
1 TTTTGAAATA--AT-TTATTTA-T
1193001 TATTTGAAATAATTTATTT
1 T-TTTGAAATAATTTATTT
1193020 TGAATTATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
19 7 0.21
21 2 0.06
22 13 0.38
23 4 0.12
24 7 0.21
25 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTGAAATAATTTATTTAT
Found at i:1193205 original size:24 final size:24
Alignment explanation
Indices: 1193177--1193243 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
1193167 ATTTTAAAAC
1193177 ATAAATATATATTTTTATAA-TATT
1 ATAAATATA-ATTTTTATAATTATT
*
1193201 ATAAACATAACTTTTTTATAATTATT
1 ATAAATATAA--TTTTTATAATTATT
*
1193227 -T-CATATAATTTTTATAA
1 ATAAATATAATTTTTATAA
1193244 AAATATATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 9 0.24
23 1 0.03
24 13 0.35
25 10 0.27
26 4 0.11
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
ATAAATATAATTTTTATAATTATT
Found at i:1195002 original size:17 final size:17
Alignment explanation
Indices: 1194980--1195018 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1194970 AACGGTCAAC
1194980 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1194997 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
1195014 GGTCA
1 GGTCA
1195019 GACCGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:1195042 original size:19 final size:19
Alignment explanation
Indices: 1195020--1195094 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
1195010 GTCGGGTCAG
*
1195020 ACCGGTCAAACCGGTTCGA
1 ACCGGTCAAACCGGTTCAA
*
1195039 ACCGGTTGAAACCGG-TCAA
1 ACCGG-TCAAACCGGTTCAA
* *
1195058 ACTGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGGTT-CAA
* *
1195079 ATCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
1195095 TCCAGCAGCC
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
18 2 0.05
19 18 0.41
20 17 0.39
21 7 0.16
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:1195054 original size:29 final size:31
Alignment explanation
Indices: 1195020--1195094 Score: 102
Period size: 29 Copynumber: 2.5 Consensus size: 31
1195010 GTCGGGTCAG
1195020 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
1195049 ACCGGTCAAACTGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
* *
1195079 ATCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
1195095 TCCAGCAGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.59
30 13 0.33
31 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:1201385 original size:7 final size:7
Alignment explanation
Indices: 1201361--1201397 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
1201351 ATGCAAAAAA
1201361 GTCAACG
1 GTCAACG
1201368 GTC-ACG
1 GTCAACG
1201374 GTCAACG
1 GTCAACG
*
1201381 ATCAACG
1 GTCAACG
1201388 GTCAACG
1 GTCAACG
1201395 GTC
1 GTC
1201398 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1201433 original size:10 final size:10
Alignment explanation
Indices: 1201418--1201484 Score: 68
Period size: 10 Copynumber: 6.8 Consensus size: 10
1201408 AGACCGGTCA
1201418 AACCGGTTCG
1 AACCGGTTCG
1201428 AACCGGTT-G
1 AACCGGTTCG
*
1201437 AAACCGG-TCA
1 -AACCGGTTCG
1201447 AACCGGTTCG
1 AACCGGTTCG
**
1201457 AACCGGTTTA
1 AACCGGTTCG
1201467 AACCGG-TCAG
1 AACCGGTTC-G
1201477 AACCGGTT
1 AACCGGTT
1201485 GAAAACCGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 9 0.20
10 36 0.78
11 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (10 bp):
AACCGGTTCG
Found at i:1201442 original size:20 final size:19
Alignment explanation
Indices: 1201418--1201504 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 19
1201408 AGACCGGTCA
1201418 AACCGGTTCG-AACCGGTTG
1 AACCGGTT-GAAACCGGTTG
*
1201437 AAACCGG-TCAAACCGGTTCG
1 -AACCGGTTGAAACCGGTT-G
* *
1201457 AACCGGTTTAAACCGGTCAG
1 AACCGGTTGAAACCGGT-TG
*
1201477 AACCGGTTGAAAACCGGTTA
1 AACCGGTTG-AAACCGGTTG
1201497 AACCGGTT
1 AACCGGTT
1201505 TCCAGCAGCC
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.27
20 33 0.59
21 8 0.14
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.20
Consensus pattern (19 bp):
AACCGGTTGAAACCGGTTG
Found at i:1201444 original size:29 final size:28
Alignment explanation
Indices: 1201410--1201503 Score: 136
Period size: 29 Copynumber: 3.2 Consensus size: 28
1201400 GTCGGGTCAG
1201410 ACCGGTCAAACCGGTTCGAACCGGTTGAA
1 ACCGGTCAAACCGGTTCGAACCGGTT-AA
1201439 ACCGGTCAAACCGGTTCGAACCGGTTTAA
1 ACCGGTCAAACCGGTTCGAACCGG-TTAA
1201468 ACCGGTCAGAACCGGTT-GAAAACCGGTTAA
1 ACCGGTCA-AACCGGTTCG--AACCGGTTAA
1201498 ACCGGT
1 ACCGGT
1201504 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
29 35 0.57
30 20 0.33
31 6 0.10
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (28 bp):
ACCGGTCAAACCGGTTCGAACCGGTTAA
Found at i:1202819 original size:14 final size:14
Alignment explanation
Indices: 1202800--1202838 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
1202790 GTTATATGGT
1202800 AATAATATCATAAC
1 AATAATATCATAAC
*
1202814 AATAATATCAT--G
1 AATAATATCATAAC
1202826 AATAATATCATAA
1 AATAATATCATAA
1202839 TTTATTGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 11 0.50
14 11 0.50
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (14 bp):
AATAATATCATAAC
Found at i:1203173 original size:2 final size:2
Alignment explanation
Indices: 1203166--1203198 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1203156 AAATACCATC
1203166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1203199 TTAAGATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1206410 original size:17 final size:18
Alignment explanation
Indices: 1206378--1206417 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1206368 TAGTCTCTTC
1206378 TATTTTAATGATTTTATA
1 TATTTTAATGATTTTATA
* *
1206396 TATTTTGAT-ATTTTATT
1 TATTTTAATGATTTTATA
1206413 TATTT
1 TATTT
1206418 GTTCTCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TATTTTAATGATTTTATA
Found at i:1214928 original size:15 final size:16
Alignment explanation
Indices: 1214901--1214930 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1214891 ATTCGAACCG
1214901 ACCCATGTTCGTCCCA
1 ACCCATGTTCGTCCCA
1214917 ACCCAT-TTCGTCCC
1 ACCCATGTTCGTCCC
1214931 TAATTATCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.47, G:0.10, T:0.27
Consensus pattern (16 bp):
ACCCATGTTCGTCCCA
Found at i:1217215 original size:30 final size:30
Alignment explanation
Indices: 1217179--1217235 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1217169 CTATCACGTT
*
1217179 ATAATTTTTTAACAATTTAAAAAAATAATG
1 ATAATTTTATAACAATTTAAAAAAATAATG
* * *
1217209 ATAATTTTATAATAATTTGATAAAATA
1 ATAATTTTATAACAATTTAAAAAAATA
1217236 TCATTGTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (30 bp):
ATAATTTTATAACAATTTAAAAAAATAATG
Found at i:1225128 original size:25 final size:25
Alignment explanation
Indices: 1225100--1225157 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
1225090 GAAATTAATA
1225100 TAAAAAGTACTAAATTATACATATT
1 TAAAAAGTACTAAATTATACATATT
*
1225125 TAAAAAGTACTAAATTATACCTATT
1 TAAAAAGTACTAAATTATACATATT
1225150 TAAAAAGT
1 TAAAAAGT
1225158 TATGGGCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (25 bp):
TAAAAAGTACTAAATTATACATATT
Found at i:1225440 original size:18 final size:18
Alignment explanation
Indices: 1225400--1225464 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
1225390 ATATACACAC
* *
1225400 TATATATGAACTATATATAT
1 TATATATAAACTATA-GT-T
*
1225420 TATGTATAAACTATAGTT
1 TATATATAAACTATAGTT
* *
1225438 TATATATAAAGTATATTT
1 TATATATAAACTATAGTT
1225456 TACTATATA
1 TA-TATATA
1225465 TATAAACTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 18 0.47
19 7 0.18
20 13 0.34
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATATAAACTATAGTT
Found at i:1225509 original size:43 final size:43
Alignment explanation
Indices: 1225424--1225516 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
1225414 ATATATTATG
* * * *
1225424 TATAAAC--TATAGTTTATATATAAAGTATATTTTACTATATA
1 TATAAACTATATAGTGTATATATAAAGTACATTATAATATATA
1225465 TATAAACTATATAGTGTATATATAAAGTACATATATAATA-ATA
1 TATAAACTATATAGTGTATATATAAAGTACAT-TATAATATATA
1225508 TA-AAA-TATA
1 TATAAACTATA
1225517 ATTATAAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
41 11 0.24
42 3 0.07
43 26 0.58
44 5 0.11
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.41
Consensus pattern (43 bp):
TATAAACTATATAGTGTATATATAAAGTACATTATAATATATA
Found at i:1225547 original size:8 final size:8
Alignment explanation
Indices: 1225530--1225569 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1225520 ATAAAGACTA
1225530 AAGTATAT
1 AAGTATAT
*
1225538 AAGCATAT
1 AAGTATAT
1225546 AA-TATA-
1 AAGTATAT
1225552 AAGTATAT
1 AAGTATAT
1225560 AAGTATAT
1 AAGTATAT
1225568 AA
1 AA
1225570 TTGTCGGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 2 0.07
7 7 0.25
8 19 0.68
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (8 bp):
AAGTATAT
Found at i:1225547 original size:30 final size:30
Alignment explanation
Indices: 1225496--1225569 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
1225486 ATAAAGTACA
*
1225496 TATATAA-TAATATAA-AATATAATTATAAAG
1 TATATAAGT-ATATAAGCATATAA-TATAAAG
1225526 -ACTA-AAGTATATAAGCATATAATATAAAG
1 TA-TATAAGTATATAAGCATATAATATAAAG
1225555 TATATAAGTATATAA
1 TATATAAGTATATAA
1225570 TTGTCGGAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
29 18 0.47
30 20 0.53
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.34
Consensus pattern (30 bp):
TATATAAGTATATAAGCATATAATATAAAG
Found at i:1225553 original size:22 final size:22
Alignment explanation
Indices: 1225528--1225570 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1225518 TTATAAAGAC
1225528 TAAAGTATATAAGCATATAATA
1 TAAAGTATATAAGCATATAATA
*
1225550 TAAAGTATATAAGTATATAAT
1 TAAAGTATATAAGCATATAAT
1225571 TGTCGGAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.35
Consensus pattern (22 bp):
TAAAGTATATAAGCATATAATA
Found at i:1225908 original size:4 final size:4
Alignment explanation
Indices: 1225894--1225932 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
1225884 GAAATGTTAG
*
1225894 ATAA A-AA ATAA ATAA ATAA AT-A TTAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1225933 CATAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 5 0.16
4 26 0.84
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1225920 original size:15 final size:15
Alignment explanation
Indices: 1225902--1225930 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1225892 AGATAAAAAA
1225902 TAAATAAATAAATAT
1 TAAATAAATAAATAT
1225917 TAAATAAATAAATA
1 TAAATAAATAAATA
1225931 AACATAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAATAAATAAATAT
Found at i:1227253 original size:10 final size:10
Alignment explanation
Indices: 1227233--1227265 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
1227223 AAAAAAAAAG
1227233 AAATAAATAAT
1 AAAT-AATAAT
1227244 AAATAATAAT
1 AAATAATAAT
1227254 AAATAATAAT
1 AAATAATAAT
1227264 AA
1 AA
1227266 TATATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAATAATAAT
Found at i:1227420 original size:73 final size:72
Alignment explanation
Indices: 1227314--1227479 Score: 216
Period size: 73 Copynumber: 2.3 Consensus size: 72
1227304 TATATAATAT
*
1227314 ATTTTTAAAAAT-ATTTGAAAACTATATATTATATAGT-TTTCAAAAATGTTTT-AAAACTATAT
1 ATTTTTAAAAATGATTTCAAAACTATATATTATATA-TATTT-AAAAATGTTTTAAAAACTATAT
1227376 ATTATATAA
64 ATTATATAA
*
1227385 ATGTTTTAAAAATGATTTCAAAACTATATATTATATATACTTTTAAAATGTTTTCAAAAACTATA
1 AT-TTTTAAAAATGATTTCAAAACTATATATTATATATA-TTTAAAAATGTTTT-AAAAACTATA
1227450 TATTATAT--
63 TATTATATAA
* *
1227458 ATTTTTTAAAATGTTTTCAAAA
1 ATTTTTAAAAATGATTTCAAAA
1227480 ACCATTTTCA
Statistics
Matches: 85, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
71 2 0.02
72 29 0.34
73 34 0.40
74 3 0.04
75 17 0.20
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (72 bp):
ATTTTTAAAAATGATTTCAAAACTATATATTATATATATTTAAAAATGTTTTAAAAACTATATAT
TATATAA
Found at i:1227433 original size:36 final size:36
Alignment explanation
Indices: 1227310--1227479 Score: 195
Period size: 36 Copynumber: 4.7 Consensus size: 36
1227300 AAATTATATA
*
1227310 ATATATTTTTAAAAAT-ATTTGAAAACTATATATTAT
1 ATATATTTTT-AAAATGATTTCAAAACTATATATTAT
** *
1227346 ATAGT-TTTCAAAAATG-TTTTAAAACTATATATTAT
1 ATA-TATTTTTAAAATGATTTCAAAACTATATATTAT
*
1227381 ATAAATGTTTTAAAAATGATTTCAAAACTATATATTAT
1 ATATAT-TTTT-AAAATGATTTCAAAACTATATATTAT
* *
1227419 ATATACTTTTAAAATGTTTTCAAAAACTATATATTAT
1 ATATATTTTTAAAATGATTTC-AAAACTATATATTAT
*
1227456 ATAT-TTTTTAAAATGTTTTCAAAA
1 ATATATTTTTAAAATGATTTCAAAA
1227480 ACCATTTTCA
Statistics
Matches: 116, Mismatches: 11, Indels: 15
0.82 0.08 0.11
Matches are distributed among these distances:
35 31 0.27
36 33 0.28
37 30 0.26
38 22 0.19
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
ATATATTTTTAAAATGATTTCAAAACTATATATTAT
Found at i:1227480 original size:36 final size:36
Alignment explanation
Indices: 1227285--1227481 Score: 210
Period size: 35 Copynumber: 5.5 Consensus size: 36
1227275 TAATATATAC
* * * *
1227285 AAAAATATATTCAAAAAAT-TATATAATATATTTTT
1 AAAAATGTTTTCAAAAACTATATATTATATATTTTT
* * *
1227320 AAAAAT-ATTT-GAAAACTATATATTATATAGTTTTC
1 AAAAATGTTTTCAAAAACTATATATTATATA-TTTTT
1227355 AAAAATGTTTT--AAAACTATATATTATATAAATGTTTT
1 AAAAATGTTTTCAAAAACTATATATTATAT--AT-TTTT
*
1227392 AAAAATGATTTC-AAAACTATATATTATATATACTTTT
1 AAAAATGTTTTCAAAAACTATATATTATATAT--TTTT
1227429 -AAAATGTTTTCAAAAACTATATATTATATATTTTT
1 AAAAATGTTTTCAAAAACTATATATTATATATTTTT
*
1227464 TAAAATGTTTTCAAAAAC
1 AAAAATGTTTTCAAAAAC
1227482 CATTTTCAAA
Statistics
Matches: 141, Mismatches: 11, Indels: 19
0.82 0.06 0.11
Matches are distributed among these distances:
33 5 0.04
34 12 0.09
35 37 0.26
36 33 0.23
37 37 0.26
38 17 0.12
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
AAAAATGTTTTCAAAAACTATATATTATATATTTTT
Found at i:1227481 original size:73 final size:72
Alignment explanation
Indices: 1227265--1227479 Score: 235
Period size: 72 Copynumber: 3.0 Consensus size: 72
1227255 AATAATAATA
* * * * * *
1227265 ATATATTATATAATATATACAAAAATATATTCAAAAAAT-TATATAATATATTTTTAAAAAT-AT
1 ATATATTATATAGT-T-TTCAAAAATGTTTTCAAAAACTATATATTATATATTTTTAAAAATGAT
*
1227328 TTGAAAACT
64 TTCAAAACT
1227337 ATATATTATATAGTTTTCAAAAATGTTTT--AAAACTATATATTATATAAATGTTTTAAAAATGA
1 ATATATTATATAGTTTTCAAAAATGTTTTCAAAAACTATATATTATAT--AT-TTTTAAAAATGA
1227400 TTTCAAAACT
63 TTTCAAAACT
* * *
1227410 ATATATTATATA-TACTTT-TAAAATGTTTTCAAAAACTATATATTATATATTTTTTAAAATGTT
1 ATATATTATATAGT--TTTCAAAAATGTTTTCAAAAACTATATATTATATATTTTTAAAAATGAT
1227473 TTCAAAA
64 TTCAAAA
1227480 ACCATTTTCA
Statistics
Matches: 124, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
68 5 0.04
69 9 0.07
70 11 0.09
71 3 0.02
72 42 0.34
73 34 0.27
74 3 0.02
75 17 0.14
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (72 bp):
ATATATTATATAGTTTTCAAAAATGTTTTCAAAAACTATATATTATATATTTTTAAAAATGATTT
CAAAACT
Found at i:1227496 original size:39 final size:39
Alignment explanation
Indices: 1227416--1227536 Score: 126
Period size: 39 Copynumber: 3.2 Consensus size: 39
1227406 AACTATATAT
* * *
1227416 TATATATACTTTTAAAATGTTTTCAAAAACTA-TAT--AT
1 TATATATA-TTTTAAAATGTTTTCAAAAACCATTTTCAAA
*
1227453 TATATATTTTTTAAAATGTTTTCAAAAACCATTTTCAAA
1 TATATATATTTTAAAATGTTTTCAAAAACCATTTTCAAA
* *
1227492 TATATATATATT-ATATGTATTTCAAAAA-CATTTTCAAA
1 TATATATATTTTAAAATGT-TTTCAAAAACCATTTTCAAA
1227530 CTATATA
1 -TATATA
1227537 ATATATATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
36 22 0.31
37 9 0.12
38 15 0.21
39 26 0.36
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (39 bp):
TATATATATTTTAAAATGTTTTCAAAAACCATTTTCAAA
Found at i:1227546 original size:39 final size:39
Alignment explanation
Indices: 1227468--1227550 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 39
1227458 ATTTTTTAAA
1227468 ATGT-TTTCAAAAACCATTTTCAAATATATATATATTAT
1 ATGTATTTCAAAAACCATTTTCAAATATATATATATTAT
1227506 ATGTATTTCAAAAA-CATTTTCAAACTATATA-ATATATAT
1 ATGTATTTCAAAAACCATTTTCAAA-TATATATATAT-TAT
1227545 ATGTAT
1 ATGTAT
1227551 ATATAAATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
38 18 0.43
39 24 0.57
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (39 bp):
ATGTATTTCAAAAACCATTTTCAAATATATATATATTAT
Found at i:1228357 original size:167 final size:166
Alignment explanation
Indices: 1228092--1229562 Score: 1743
Period size: 167 Copynumber: 8.8 Consensus size: 166
1228082 AGCTGAATAG
* * * * * * *
1228092 AATCGAACTCAAAGGTATTTGATGACAGATAGCCCTTCTCGCCTTGAGATATGCTGCAAATGATA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
* * *
1228157 TGCCTTTGAGCTTAGTGTAATAGAACTCGAAGGTCTTTTGCTGGAAGATAGCCCTTCTTGCCTTG
66 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-TGGAAGATAACCCTTCTTGCCTTG
* * *
1228222 AGCTATACTGCAAATGATGTGTCTTTGAGCTGAGTGT
130 AGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* ** * * * * * *
1228259 AATCGAACTCAAAACTCTTTGTTGACAAATAACTCTTCTAGCTTTGAGTTATACTGCAAATGATA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
* * * *
1228324 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTATTGGCAGATAGCCCTTCTTGCCTTG
66 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTT-GTGGAAGATAACCCTTCTTGCCTTG
*
1228389 AGTTATGCTGCAAATGATGCGCCTTTGAGCTGAGTGT
130 AGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * * * * * * * *
1228426 AATCGAACTCGAAGCTCTTTGTTGACAAAAAACCCATCTCGCTTTCAGTTATGTTGTAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
* * *
1228491 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC-TTTGTTGGCATATAACCCTTCTTGCCTTG
66 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-TGGAAGATAACCCTTCTTGCCTTG
*
1228555 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
130 AGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * **
1228592 AATTGAACTCGAAGGTCTTTTATTGGA-AGATAACCCTTCTTGCCTTGAGCTATATTGCAAATGA
1 AATCGAACTCGAAGGTC-TTTGTT-GACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGA
* * *
1228656 TGTGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGT-TTTTGTTGACAGATAACCCTTCTAGCCT
64 TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTGGA-AGATAACCCTTCTTGCCT
* * * *
1228720 TGAGTTATGTTGTAAATGATGTGCCCTTGAGCTGAATGT
128 TGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * * * * * *
1228759 AATCAAACTCAAAGGTCTTTGGTTGGCAGATAGCCCTTTTTGCCTTGAGCTATGCTACAAATGGT
1 AATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGAT
* *
1228824 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTT
65 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTGGA-AGATAACCCTTCTTGCCTT
**
1228888 GAGTTATGCTATAAATGATGTGCCTTTGAGCTGAGTGT
129 GAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * * * *
1228926 AATCGAACTCGAAGGT-TTGGTTGGCAGATAACCCTTCTAGACTTGAGTTATGTTGTAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
* * * * *
1228990 TGCCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTTTCCTTG
66 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-TGGAAGATAACCCTTCTTGCCTTG
* *
1229055 AGTTATGCTGCAAATGATGTGTCTTTGAGCTGAGTCT
130 AGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * * **
1229092 AATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTGAGTTATGTTATAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
* *
1229157 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTAT-TGGTAGATAACCCTTCTTGCCTTG
66 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT-TGTGGAAGATAACCCTTCTTGCCTTG
* **
1229221 AGCTACACTGCAAATGATGTGCCTTTGAGCTGAGTGT
130 AGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * * * ** *
1229258 AATCGAACTCGAATGTCTTTTGTTGGCAGATAGCCATTTTTTCTTTGAGCTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGAT
** *
1229323 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTAACAGATAACCCTTCTAGCCTT
65 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTGGA-AGATAACCCTTCTTGCCTT
* * * *
1229387 GAGTTATGTTGTAAATGATGTACCATTGAGCTGAGTGT
129 GAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* ** *
1229425 AATCAAACTCGAAGGTCTTTGGTTGGTAGATAGCCCTTCTTA-CCTTGAGCTATGCTGCAAATGA
1 AATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTC-TAGCCTTGAGCTATGCTGCAAATGA
* * *
1229489 TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCT
64 TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-TGGAAGATAACCCTTCTTGCCT
*
1229554 TGAGCTATG
128 TGAGTTATG
1229563 TTGTAAATAA
Statistics
Matches: 1130, Mismatches: 154, Indels: 39
0.85 0.12 0.03
Matches are distributed among these distances:
165 71 0.06
166 225 0.20
167 802 0.71
168 31 0.03
169 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (166 bp):
AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATG
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTGGAAGATAACCCTTCTTGCCTTGA
GTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
Found at i:1228568 original size:250 final size:249
Alignment explanation
Indices: 1228092--1229562 Score: 1879
Period size: 250 Copynumber: 5.9 Consensus size: 249
1228082 AGCTGAATAG
* * * * *
1228092 AATCGAACTCAAAGGTATTTGA-TGACAGATAGCCCTTCTCGCCTTGAGATATGCTGCAAATGAT
1 AATCGAACTCGAAGGTCTTT-ATTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
* * * * *
1228156 ATGCCTTTGAGCTTAGTGTAATAGAACTCGAAGGTCTTTTGCTGGA-AGATAGCCCTTCTTGCCT
65 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTG-TTGACAGATAACCCTTCTTGCCT
* * * ** *
1228220 TGAGCTATACTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCAAAACTCTTTGTTGAC
128 TGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGC
* * * * * * * *
1228285 AAATAACTCTTCTAGCTTTGAGTTATACTGCAAATGATATGCCTTTGAGCTGAGTGT
193 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * *
1228342 AATCGAACTCGAAGGTATTTTATTGGCAGATAGCCCTTCTTGCCTTGAGTTATGCTGCAAATGAT
1 AATCGAACTCGAAGGT-CTTTATTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
* * * * * * * *
1228407 GCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGCTCTTTGTTGACAAAAAACCCATCTCGCTTTC
65 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTG
* * * * *
1228472 AGTTATGTTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGGCAT
130 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAG
*
1228537 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
195 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * **
1228592 AATTGAACTCGAAGGTCTTTTATTGGA-AGATAACCCTTCTTGCCTTGAGCTATATTGCAAATGA
1 AATCGAACTCGAAGGTC-TTTATT-GACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
* * *
1228656 TGTGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTAGCCTT
64 TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTT
* * * * * * *
1228721 GAGTTATGTTGTAAATGATGTGCCCTTGAGCTGAATGTAATCAAACTCAAAGGTCTTTGGTTGGC
129 GAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGGC
* * *
1228786 AGATAGCCCTTTTTGCCTTGAGCTATGCTACAAATGGTGTGCCTTTGAGCTGAGTGT
193 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* **
1228843 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATG
1 AATCGAACTCGAAGGTCTTTATTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
* * * *
1228908 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-TTGGTTGGCAGATAACCCTTCTAGACTTGA
66 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGA
* * * *
1228972 GTTATGTTGTAAATGATGTGCCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAG
131 GCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGGCAG
* * * *
1229037 ATAGCCCTTCTTTCCTTGAGTTATGCTGCAAATGATGTGTCTTTGAGCTGAGTCT
195 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * * **
1229092 AATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTGAGTTATGTTATAAATGATG
1 AATCGAACTCGAAGGTCTTTATTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
* * **
1229157 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTATTGGTAGATAACCCTTCTTGCCTTGA
66 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGA
** *
1229222 GCTACACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGGCAG
131 GCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCAG
* * * *
1229287 ATAGCCATTTTTTCTTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
195 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
* * * *
1229342 AATCGAACTCGAAGGTCTTTGTTAACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATG
1 AATCGAACTCGAAGGTCTTTATTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
* * * ** * *
1229407 TACCATTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTGGTAGATAGCCCTTCTTACCTTG
66 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTTGCCTTG
1229472 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCA
130 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGGCA
*
1229537 GATAGCCCTTCTCGCCTTGAGCTATG
194 GATAGCCCTTCTTGCCTTGAGCTATG
1229563 TTGTAAATAA
Statistics
Matches: 1090, Mismatches: 121, Indels: 19
0.89 0.10 0.02
Matches are distributed among these distances:
249 237 0.22
250 596 0.55
251 257 0.24
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (249 bp):
AATCGAACTCGAAGGTCTTTATTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTTGCCTTGA
GCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGGCAGA
TAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGT
Found at i:1234848 original size:20 final size:20
Alignment explanation
Indices: 1234805--1234855 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
1234795 TGTTAGATAA
* *
1234805 AAAATAAAAAAATATTAAAT
1 AAAATAAAAAAACATAAAAT
1234825 -AAATAAAAAAACATAAAAT
1 AAAATAAAAAAACATAAAAT
1234844 AAAATAATAAAA
1 AAAATAA-AAAA
1234856 TTAACTAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 17 0.63
20 6 0.22
21 4 0.15
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAATAAAAAAACATAAAAT
Found at i:1234938 original size:36 final size:33
Alignment explanation
Indices: 1234883--1234961 Score: 97
Period size: 36 Copynumber: 2.3 Consensus size: 33
1234873 TCAAAGGAGG
*
1234883 AAAAAATAAAATTAAAAATGAGAATAAATAAGATA
1 AAAAAATAAAATAAAAAATGA-AATAAATAA-ATA
1234918 AAGAAAATAAAA-AAACAAATGAAATAAATAAATA
1 AA-AAAATAAAATAAA-AAATGAAATAAATAAATA
*
1234952 TAAAAATAAA
1 AAAAAATAAA
1234962 GGTATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
33 8 0.20
34 4 0.10
35 13 0.32
36 15 0.38
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (33 bp):
AAAAAATAAAATAAAAAATGAAATAAATAAATA
Found at i:1236322 original size:37 final size:34
Alignment explanation
Indices: 1236212--1236518 Score: 235
Period size: 35 Copynumber: 8.5 Consensus size: 34
1236202 ATTTATATAC
* * *
1236212 AAAAATATTTTCAAAA-AATTATATAATATATTTTT
1 AAAAATGTTTTCAAAACTA-TATATTATATA-TTTT
* **
1236247 AAAAATATTTGAAAAACTATATATTATATATTTT
1 AAAAATGTTTTCAAAACTATATATTATATATTTT
*
1236281 AAAAAATGTTTTCAAAATTATATATTATATAGTTTT
1 -AAAAATGTTTTCAAAACTATATATTATATA-TTTT
* *
1236317 CAAAAATGTTTT-AAAATTATATATTAAATATTTT
1 -AAAAATGTTTTCAAAACTATATATTATATATTTT
** *
1236351 CAAAAAAAATGTTTTTTTAAATTATATATTATATAGTTTT
1 ----AAAAATG-TTTTCAAAACTATATATTATATA-TTTT
*
1236391 CAAAAAAGTTTT-AAAACTATATATTATATAAATGATTT
1 -AAAAATGTTTTCAAAACTATATATTATAT--AT--TTT
*
1236429 AAAAATGATTTCAAAACTATATATTATATTTACTTTT
1 AAAAATGTTTTCAAAACTATATATTATA--TA-TTTT
*
1236466 -AAAATGTTTTGAAAAACTATATATTATATATATTTTT
1 AAAAATGTTTT-CAAAACTATATA-T-TATATA-TTTT
*
1236503 TAAAATGTTTTCAAAA
1 AAAAATGTTTTCAAAA
1236519 ACCATAAATA
Statistics
Matches: 228, Mismatches: 23, Indels: 40
0.78 0.08 0.14
Matches are distributed among these distances:
34 8 0.04
35 82 0.36
36 30 0.13
37 47 0.21
38 35 0.15
39 21 0.09
40 5 0.02
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (34 bp):
AAAAATGTTTTCAAAACTATATATTATATATTTT
Found at i:1236590 original size:15 final size:15
Alignment explanation
Indices: 1236570--1236658 Score: 76
Period size: 15 Copynumber: 5.7 Consensus size: 15
1236560 CAATAATATA
1236570 AAATATATAAGTATT
1 AAATATATAAGTATT
1236585 AAATATA-AAGTATAT
1 AAATATATAAGTAT-T
1236600 ATACATATATAA-TAATAT
1 A-A-ATATATAAGT-AT-T
*
1236618 AAAGTATATAAGAATT
1 AAA-TATATAAGTATT
1236634 AAATATA-AAGTATTT
1 AAATATATAAGTA-TT
*
1236649 AAGTATATAA
1 AAATATATAA
1236659 AGTACATATA
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
14 10 0.16
15 21 0.34
16 8 0.13
17 16 0.26
18 7 0.11
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (15 bp):
AAATATATAAGTATT
Done.