Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 4 of 143
Found at i:1206969 original size:9 final size:10
Alignment explanation
Indices: 1206948--1206972 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1206938 ATATATATTA
1206948 TTTTATACTT
1 TTTTATACTT
1206958 TTTTATACTT
1 TTTTATACTT
1206968 TTTTA
1 TTTTA
1206973 ATAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATACTT
Found at i:1219737 original size:16 final size:17
Alignment explanation
Indices: 1219712--1219748 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1219702 AATTAAATAA
1219712 ATAATAATATAAAATTT
1 ATAATAATATAAAATTT
*
1219729 ATAAT-ATATAACATTT
1 ATAATAATATAAAATTT
1219745 ATAA
1 ATAA
1219749 AAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATAATATAAAATTT
Found at i:1220104 original size:22 final size:22
Alignment explanation
Indices: 1220058--1220104 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1220048 ATAAATTATT
** * *
1220058 TTTATAATATATTTTTTTAAGA
1 TTTATAATATAACTTTTAAAAA
1220080 TTTATAATATAACTTTTAAAAA
1 TTTATAATATAACTTTTAAAAA
1220102 TTT
1 TTT
1220105 TGGCTATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTATAATATAACTTTTAAAAA
Found at i:1246576 original size:40 final size:39
Alignment explanation
Indices: 1246507--1246583 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 39
1246497 TCCAAATAAG
* * * *
1246507 CTGAACTTAAAATAATTGAACTCTGAAATGATTCGAAGC
1 CTGAACTAAAAATAACTGAACTCTAAAATGATCCGAAGC
1246546 CTGAACCTAAAAATAGACTGAAC-CTAAAATGATCCGAA
1 CTGAA-CTAAAAATA-ACTGAACTCTAAAATGATCCGAA
1246584 ATTGTAGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 5 0.16
40 21 0.66
41 6 0.19
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.23
Consensus pattern (39 bp):
CTGAACTAAAAATAACTGAACTCTAAAATGATCCGAAGC
Found at i:1247685 original size:31 final size:31
Alignment explanation
Indices: 1247650--1247710 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1247640 TTATATAAAA
* *
1247650 ATAATTAAATTTCA-ATTTTGGTTTTTATACC
1 ATAATAAAATTTCAGA-TTTGATTTTTATACC
*
1247681 ATAATAAAATTTGAGATTTGATTTTTATAC
1 ATAATAAAATTTCAGATTTGATTTTTATAC
1247711 TTAAAGGCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (31 bp):
ATAATAAAATTTCAGATTTGATTTTTATACC
Found at i:1274857 original size:45 final size:45
Alignment explanation
Indices: 1274793--1274884 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
1274783 GGAGAAAAAA
*
1274793 CTGGGTTCTCTTCAAAATGGAACCCGAAGTTCCATGCATATTAAG
1 CTGGGTTCTCTTCAAAATGGAACCCGAAGTTCCATGCATATCAAG
*
1274838 CTGGGTTCTCTTCAAAATGGAACCCGAAGTTCCATGGATATCAAG
1 CTGGGTTCTCTTCAAAATGGAACCCGAAGTTCCATGCATATCAAG
1274883 CT
1 CT
1274885 TAATTGTGCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (45 bp):
CTGGGTTCTCTTCAAAATGGAACCCGAAGTTCCATGCATATCAAG
Found at i:1276874 original size:92 final size:92
Alignment explanation
Indices: 1276753--1276939 Score: 349
Period size: 92 Copynumber: 2.0 Consensus size: 92
1276743 ACCCGACATG
1276753 AAAGCACCCGACCTGAGTATGTTCACTTTTTTCTAAGTTTTTCCATGTACTCAAATGGTTCTTGG
1 AAAGCACCCGACCTGAGTATGTTCACTTTTTTCTAAGTTTTTCCATGTACTCAAATGGTTCTTGG
1276818 AAGATCATATCCCCATATGCATGTCCA
66 AAGATCATATCCCCATATGCATGTCCA
*
1276845 AAAGCGCCCG-CCATGAGTATGTTCACTTTTTTCTAAGTTTTTCCATGTACTCAAATGGTTCTTG
1 AAAGCACCCGACC-TGAGTATGTTCACTTTTTTCTAAGTTTTTCCATGTACTCAAATGGTTCTTG
1276909 GAAGATCATATCCCCATATGCATGTCCA
65 GAAGATCATATCCCCATATGCATGTCCA
1276937 AAA
1 AAA
1276940 ATGTGTTCGA
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
91 2 0.02
92 91 0.98
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.34
Consensus pattern (92 bp):
AAAGCACCCGACCTGAGTATGTTCACTTTTTTCTAAGTTTTTCCATGTACTCAAATGGTTCTTGG
AAGATCATATCCCCATATGCATGTCCA
Found at i:1279610 original size:26 final size:26
Alignment explanation
Indices: 1279573--1279625 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1279563 GAAAATATTA
* *
1279573 AGTTTTTCATTAGCATACAGTAGATT
1 AGTTTTTAATTAGCATACAGTAAATT
1279599 AGTTTTTAATTAGCATACAGTAAATT
1 AGTTTTTAATTAGCATACAGTAAATT
1279625 A
1 A
1279626 TTAAACTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (26 bp):
AGTTTTTAATTAGCATACAGTAAATT
Found at i:1286985 original size:33 final size:33
Alignment explanation
Indices: 1286941--1287003 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1286931 AACACTATCA
*
1286941 TAAATATAATAAATATTTTATTATATTAAAAAC
1 TAAATAAAATAAATATTTTATTATATTAAAAAC
*
1286974 TAAATAAAATAAATATTTTATTGTATTAAA
1 TAAATAAAATAAATATTTTATTATATTAAA
1287004 TATAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (33 bp):
TAAATAAAATAAATATTTTATTATATTAAAAAC
Found at i:1287143 original size:2 final size:2
Alignment explanation
Indices: 1287102--1287126 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1287092 TGGATTAGTG
1287102 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 A
1287127 ATTATTTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1287940 original size:17 final size:17
Alignment explanation
Indices: 1287920--1287969 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
1287910 TAAATCCAAC
*
1287920 TTTTAATTTTAAATTTG
1 TTTTAAATTTAAATTTG
*
1287937 TTTTAAGTTTAAATTTG
1 TTTTAAATTTAAATTTG
1287954 TTTTAAATTTAAATTT
1 TTTTAAATTTAAATTT
1287970 TGAAATGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTTAAATTTAAATTTG
Found at i:1287964 original size:23 final size:23
Alignment explanation
Indices: 1287938--1288004 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
1287928 TTAAATTTGT
*
1287938 TTTAAGTTTAAATTTGTTTTAAA
1 TTTAATTTTAAATTTGTTTTAAA
*
1287961 TTTAAATTTTGAAA-TGGTTTTAAA
1 TTT-AATTTT-AAATTTGTTTTAAA
*
1287985 CTTAATTTTAAATTTAGTTT
1 TTTAATTTTAAATTT-GTTT
1288005 AAAAGTCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
22 3 0.08
23 10 0.28
24 20 0.56
25 3 0.08
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.55
Consensus pattern (23 bp):
TTTAATTTTAAATTTGTTTTAAA
Found at i:1289784 original size:30 final size:29
Alignment explanation
Indices: 1289735--1290073 Score: 189
Period size: 29 Copynumber: 11.6 Consensus size: 29
1289725 GGTCTTTGAA
* * * *
1289735 TTTTCTAAAAATTATATTTTGACCCCAAAAT
1 TTTTC-AAAAA-TACATTTTTACCCCTAAAC
1289766 TTTTCAAAAATCACA-TTTT--CCCTAAAC
1 TTTTCAAAAAT-ACATTTTTACCCCTAAAC
*
1289793 TTTTCAAAAAATACATTTTTACCCTTAAAC
1 TTTTC-AAAAATACATTTTTACCCCTAAAC
* * *
1289823 TCTCCAAAAATACATTTTTACCCCTAAGC
1 TTTTCAAAAATACATTTTTACCCCTAAAC
*
1289852 TTTTCAAAAATTACATTTATAGCCCC-AAAC
1 TTTTCAAAAA-TACATTTTTA-CCCCTAAAC
* * * *
1289882 -TTCCTAAAATTACATTTTAACCCCCAAAC
1 TTTTC-AAAAATACATTTTTACCCCTAAAC
* * * *
1289911 -TTCCAAAATTACATTTTGACCCTTAAAC
1 TTTTCAAAAATACATTTTTACCCCTAAAC
*
1289939 TTTCCAAAAAATACA-TTTTA-CCCTAAAC
1 TTTTC-AAAAATACATTTTTACCCCTAAAC
* * * *
1289967 -TTCCAAAAAATTATATTTTT-GCCCTCGAA-
1 TTTTC-AAAAA-TACATTTTTACCCCT-AAAC
* * * *
1289996 TTTCCAAACATCACGTTTTTACCCC-AAAA
1 TTTTCAAAAAT-ACATTTTTACCCCTAAAC
* *
1290025 TTTCCTAAAATGACATTTTTACCCCTAAAAC
1 TTTTCAAAAAT-ACATTTTTACCCCT-AAAC
* * *
1290056 TTTCCAAAATTGCATTTT
1 TTTTCAAAAATACATTTT
1290074 AACCTTAAAC
Statistics
Matches: 249, Mismatches: 38, Indels: 43
0.75 0.12 0.13
Matches are distributed among these distances:
27 24 0.10
28 48 0.19
29 100 0.40
30 56 0.22
31 21 0.08
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
TTTTCAAAAATACATTTTTACCCCTAAAC
Found at i:1289803 original size:58 final size:57
Alignment explanation
Indices: 1289735--1290084 Score: 234
Period size: 57 Copynumber: 6.0 Consensus size: 57
1289725 GGTCTTTGAA
* * * *
1289735 TTTTCTAAAAATTATATTTTGACCCCAAAATTTTTCAAAAATCACATTTT-CCCTAAAC
1 TTTTC-AAAAATTACATTTTGACCCCTAAACTTTCCAAAAAT-ACATTTTACCCTAAAC
* * * * *
1289793 TTTTCAAAAAATACATTTTTACCCTTAAACTCTCCAAAAATACATTTTTACCCCTAAGC
1 TTTTCAAAAATTACATTTTGACCCCTAAACTTTCCAAAAATACA-TTTTA-CCCTAAAC
* *
1289852 TTTTCAAAAATTACATTTAT-AGCCCC-AAAC-TTCCTAAAATTACATTTTAACCCCCAAAC
1 TTTTCAAAAATTACATTT-TGA-CCCCTAAACTTTCC-AAAAATACATTTT-A-CCCTAAAC
* *
1289911 --TTCCAAAATTACATTTTGACCCTTAAACTTTCCAAAAAATACATTTTACCCTAAAC
1 TTTTCAAAAATTACATTTTGACCCCTAAACTTTCC-AAAAATACATTTTACCCTAAAC
* * * * * * *
1289967 -TTCCAAAAAATTATATTTTTG--CCCTCGAA-TTTCCAAACATCACGTTTTTACCCCAAAA
1 TTTTC-AAAAATTACA-TTTTGACCCCT-AAACTTTCCAAAAAT-AC-ATTTTACCCTAAAC
* * * * * * *
1290025 TTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAATTGCATTTTAACCTTAAAC
1 TTTTCAAAAATTACATTTTGACCCCT-AAACTTTCCAAAAATACATTTT-ACCCTAAAC
1290084 T
1 T
1290085 CTCTGAAACT
Statistics
Matches: 229, Mismatches: 42, Indels: 41
0.73 0.13 0.13
Matches are distributed among these distances:
56 19 0.08
57 69 0.30
58 60 0.26
59 68 0.30
60 13 0.06
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.36
Consensus pattern (57 bp):
TTTTCAAAAATTACATTTTGACCCCTAAACTTTCCAAAAATACATTTTACCCTAAAC
Found at i:1289831 original size:29 final size:29
Alignment explanation
Indices: 1289770--1290084 Score: 213
Period size: 29 Copynumber: 10.9 Consensus size: 29
1289760 CAAAATTTTT
1289770 CAAAAATCACA-TTTT-CCC-TAAACTTTTC
1 CAAAAAT-ACATTTTTACCCTTAAAC-TTTC
* *
1289798 AAAAAATACATTTTTACCCTTAAACTCTC
1 CAAAAATACATTTTTACCCTTAAACTTTC
* * *
1289827 CAAAAATACATTTTTACCCCTAAGCTTTT
1 CAAAAATACATTTTTACCCTTAAACTTTC
* *
1289856 CAAAAATTACATTTATAGCCC-CAAAC-TTC
1 CAAAAA-TACATTTTTA-CCCTTAAACTTTC
* * **
1289885 CTAAAATTACATTTTAACCCCCAAAC-TTC
1 C-AAAAATACATTTTTACCCTTAAACTTTC
* *
1289914 CAAAATTACATTTTGACCCTTAAACTTTC
1 CAAAAATACATTTTTACCCTTAAACTTTC
1289943 CAAAAAATACA-TTTTACCC-TAAAC-TTC
1 C-AAAAATACATTTTTACCCTTAAACTTTC
* * **
1289970 CAAAAAATTATATTTTTGCCCTCGAA-TTTC
1 C-AAAAA-TACATTTTTACCCTTAAACTTTC
* * * *
1290000 CAAACATCACGTTTTTACCC-CAAAATTTC
1 CAAAAAT-ACATTTTTACCCTTAAACTTTC
* *
1290029 CTAAAATGACATTTTTACCCCTAAAACTTTC
1 CAAAAAT-ACATTTTTA-CCCTTAAACTTTC
* * *
1290060 CAAAATTGCA-TTTTAACCTTAAACT
1 CAAAAATACATTTTTACCCTTAAACT
1290085 CTCTGAAACT
Statistics
Matches: 231, Mismatches: 39, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
27 13 0.06
28 54 0.23
29 109 0.47
30 40 0.17
31 15 0.06
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATACATTTTTACCCTTAAACTTTC
Found at i:1290468 original size:96 final size:97
Alignment explanation
Indices: 1290358--1290550 Score: 307
Period size: 96 Copynumber: 2.0 Consensus size: 97
1290348 AAAATATTTA
*
1290358 AAATCGAGGTAATATTCCTTTATTTCGGGTTTTGAAAATTAGTGCCTTAACTTACTAGGCGCGAT
1 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTAGTGCCTTAACTTACTAGGCGCGAT
1290423 TTTT-TTTAAACCGAGATAATCAAATACCCTT
66 TTTTCTTTAAACCGAGATAATCAAATACCCTT
* * *
1290454 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGTCTTAACTTACTAGGCGTGAT
1 AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTAGTGCCTTAACTTACTAGGCGCGAT
* * **
1290519 TTTTCTTTAAATCGGGATAATCGGATACCCTT
66 TTTTCTTTAAACCGAGATAATCAAATACCCTT
1290551 TTTCAAGGTT
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
96 65 0.74
97 23 0.26
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (97 bp):
AAATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAATTAGTGCCTTAACTTACTAGGCGCGAT
TTTTCTTTAAACCGAGATAATCAAATACCCTT
Found at i:1291338 original size:113 final size:113
Alignment explanation
Indices: 1291136--1291365 Score: 388
Period size: 113 Copynumber: 2.0 Consensus size: 113
1291126 ATCTTCTTCC
* * * *
1291136 CTTTTGATTCTAGTATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTGAAACCCATTAAC
1 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATATTTAAAACCCATTAAC
* * *
1291201 CAAAAGATTCAATATCTTTGGTTCCAATATCTTCTTCCCGTTAAGTTT
66 CAAAAGATTCAATATCTTTCGTTCCAATAACTTCTTCCCATTAAGTTT
*
1291249 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATATTTAAAACTCATTAAC
1 CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATATTTAAAACCCATTAAC
1291314 CAAAAGATTCAATATCTTTCGTTCCAATAACTTCTTCCCATTAAGTTT
66 CAAAAGATTCAATATCTTTCGTTCCAATAACTTCTTCCCATTAAGTTT
1291362 CTTT
1 CTTT
1291366 GGGTTAATGG
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 109 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (113 bp):
CTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATATTTAAAACCCATTAAC
CAAAAGATTCAATATCTTTCGTTCCAATAACTTCTTCCCATTAAGTTT
Found at i:1291449 original size:6 final size:6
Alignment explanation
Indices: 1291438--1291465 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1291428 AAAAGGGAAA
1291438 AAGATG AAGATG AAGATG AAGATG AAGA
1 AAGATG AAGATG AAGATG AAGATG AAGA
1291466 AGAGAAGTGA
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:0.54, C:0.00, G:0.32, T:0.14
Consensus pattern (6 bp):
AAGATG
Found at i:1294404 original size:2 final size:2
Alignment explanation
Indices: 1294397--1294439 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1294387 GATAAATGAT
1294397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1294439 T
1 T
1294440 TGTATACCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1295763 original size:15 final size:15
Alignment explanation
Indices: 1295743--1295793 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1295733 TTGTTTCATA
1295743 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* *
1295758 TTATATTTGAAAT-T
1 TTATATTTTAATTAT
*
1295772 TTATATTTTAATCAT
1 TTATATTTTAATTAT
1295787 TTATATT
1 TTATATT
1295794 ATCATTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:1295944 original size:18 final size:18
Alignment explanation
Indices: 1295921--1295963 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1295911 AAATAAGTTT
1295921 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
1295939 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
1295957 TTAATTA
1 TTAATTA
1295964 CATCTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:1297192 original size:16 final size:14
Alignment explanation
Indices: 1297165--1297208 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
1297155 AATGATATTT
1297165 AATTATTTATTTTGAA
1 AATTA-TTATTTT-AA
1297181 AATATATTA-TTTAA
1 AAT-TATTATTTTAA
1297195 AATTATTATTTTAA
1 AATTATTATTTTAA
1297209 GAAGTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.19
14 10 0.38
15 3 0.12
16 6 0.23
17 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
AATTATTATTTTAA
Found at i:1306643 original size:13 final size:13
Alignment explanation
Indices: 1306601--1306646 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
1306591 AGTATACAAT
1306601 AGAATATAGAAAA
1 AGAATATAGAAAA
* *
1306614 AGAAGCATA-AAAT
1 AGAA-TATAGAAAA
1306627 AGAATATAGAAAA
1 AGAATATAGAAAA
1306640 AGAATAT
1 AGAATAT
1306647 TAGGGTGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 3 0.11
13 21 0.78
14 3 0.11
ACGTcount: A:0.65, C:0.02, G:0.15, T:0.17
Consensus pattern (13 bp):
AGAATATAGAAAA
Found at i:1309665 original size:72 final size:72
Alignment explanation
Indices: 1309543--1309681 Score: 251
Period size: 72 Copynumber: 1.9 Consensus size: 72
1309533 TTAGAATTAA
*
1309543 AAACCGTCTTTTGGACTTTCTTATTAGCTTAAACTTTGCTTCTCTATTAAATTAAAATTCCCACT
1 AAACCGTCTTTTAGACTTTCTTATTAGCTTAAACTTTGCTTCTCTATTAAATTAAAATTCCCACT
1309608 CTTTTAG
66 CTTTTAG
* *
1309615 AAACTGTCTTTTAGACTTTCTTATTAGCTTAAACTTTGCTTTTCTATTAAATTAAAATTCCCACT
1 AAACCGTCTTTTAGACTTTCTTATTAGCTTAAACTTTGCTTCTCTATTAAATTAAAATTCCCACT
1309680 CT
66 CT
1309682 AGCTCTTTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.45
Consensus pattern (72 bp):
AAACCGTCTTTTAGACTTTCTTATTAGCTTAAACTTTGCTTCTCTATTAAATTAAAATTCCCACT
CTTTTAG
Found at i:1322640 original size:24 final size:24
Alignment explanation
Indices: 1322596--1322641 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1322586 ATATAATTAA
**
1322596 GAATTATTAATTCTTTCAAAAAAT
1 GAATTATTAATTCAATCAAAAAAT
1322620 GAATTATTAATTACAAT-AAAAA
1 GAATTATTAATT-CAATCAAAAA
1322642 CAATTTGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (24 bp):
GAATTATTAATTCAATCAAAAAAT
Found at i:1323054 original size:21 final size:21
Alignment explanation
Indices: 1323013--1323057 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1323003 CTTTCTTTAC
*
1323013 AATTTAATCATTCTTCGTAAA
1 AATTTAATCATTCTTCCTAAA
*
1323034 AATTT-ATCATTTTTACCTAAA
1 AATTTAATCATTCTT-CCTAAA
1323055 AAT
1 AAT
1323058 AAAAAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTTAATCATTCTTCCTAAA
Found at i:1324829 original size:15 final size:15
Alignment explanation
Indices: 1324809--1324845 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1324799 ATGGGACCCT
1324809 GATAATGTCAGGTTA
1 GATAATGTCAGGTTA
1324824 GATAATGTCAGGTTA
1 GATAATGTCAGGTTA
*
1324839 GCTAATG
1 GATAATG
1324846 AAAGTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.32
Consensus pattern (15 bp):
GATAATGTCAGGTTA
Found at i:1325398 original size:16 final size:16
Alignment explanation
Indices: 1325377--1325444 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
1325367 CAAACATTAT
1325377 TTATTATTATATTTAA
1 TTATTATTATATTTAA
** *
1325393 TTATTAAAATATTTTA
1 TTATTATTATATTTAA
1325409 TATATTATTAATATTATAA
1 T-TATTATT-ATATT-TAA
* *
1325428 ATAAT-TTATA-TTAA
1 TTATTATTATATTTAA
1325442 TTA
1 TTA
1325445 CTTAAAATGT
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
14 5 0.12
15 1 0.03
16 17 0.43
17 7 0.17
18 8 0.20
19 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTATTATATTTAA
Found at i:1325492 original size:24 final size:24
Alignment explanation
Indices: 1325464--1325517 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
1325454 TATTTAAAAT
1325464 TTATTTC-ATGT-ATCATAATATTAA
1 TTATTTCAATGTCAT-ATAA-ATTAA
*
1325488 TTATTTCAATGTCATATAACTTAA
1 TTATTTCAATGTCATATAAATTAA
1325512 TTATTT
1 TTATTT
1325518 TTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 17 0.63
25 8 0.30
26 2 0.07
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (24 bp):
TTATTTCAATGTCATATAAATTAA
Found at i:1327803 original size:28 final size:29
Alignment explanation
Indices: 1327745--1327805 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
1327735 AAAGTTATTG
1327745 TTATTATAAAAATATCTAAGGATCTCATC
1 TTATTATAAAAATATCTAAGGATCTCATC
* *
1327774 TTATTA-AAAAATATTTCATGGATCTC-TC
1 TTATTATAAAAATATCT-AAGGATCTCATC
1327802 TTAT
1 TTAT
1327806 AGTCCCTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.43
Consensus pattern (29 bp):
TTATTATAAAAATATCTAAGGATCTCATC
Found at i:1330747 original size:40 final size:38
Alignment explanation
Indices: 1330692--1330771 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
1330682 TTTAGAGATG
*
1330692 AATTATATTTCAATTTTTTTTTATTAAAAATGAATAAATT
1 AATTATATTTCAA--TTTTTTTATTAAAAATAAATAAATT
* *
1330732 AATTATGTTTTAATTTTTTTATTAAAAATAAATAAATT
1 AATTATATTTCAATTTTTTTATTAAAAATAAATAAATT
1330770 AA
1 AA
1330772 CCTTAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 26 0.70
40 11 0.30
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (38 bp):
AATTATATTTCAATTTTTTTATTAAAAATAAATAAATT
Found at i:1330784 original size:38 final size:37
Alignment explanation
Indices: 1330707--1330792 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 37
1330697 TATTTCAATT
* * *
1330707 TTTTTTTATTAAAAATGAATAAATTAATTATGTTTTAA
1 TTTTTTTATTAAAAATAAATAAATTAATTA-GATATAA
1330745 TTTTTTTATTAAAAATAAATAAATTAACCTTA-ATATAA
1 TTTTTTTATTAAAAATAAATAAATTAA--TTAGATATAA
1330783 TTTTTCTTAT
1 TTTTT-TTAT
1330793 CAATTGACTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 35 0.83
39 4 0.10
40 3 0.07
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (37 bp):
TTTTTTTATTAAAAATAAATAAATTAATTAGATATAA
Found at i:1332354 original size:28 final size:30
Alignment explanation
Indices: 1332300--1332379 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 30
1332290 TTTATATATC
1332300 ATTATATTAAATTATTTGAATACCATT-TATT
1 ATTATATTAAATT-TTTGAATACCATTAT-TT
* *
1332331 ATTATACTAAATTTTTTAA-A-CATTATTT
1 ATTATATTAAATTTTTGAATACCATTATTT
* *
1332359 ATTATATTTAATTTTTAAATA
1 ATTATATTAAATTTTTGAATA
1332380 TGTTATATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
28 22 0.52
29 3 0.07
30 5 0.12
31 12 0.29
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (30 bp):
ATTATATTAAATTTTTGAATACCATTATTT
Found at i:1332388 original size:27 final size:27
Alignment explanation
Indices: 1332358--1332416 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
1332348 AAACATTATT
*
1332358 TATTATATTTAATTTT-TAAAT-ATGTTA
1 TATTATA-TTAATTTTACAAATAAT-TTA
*
1332385 TATTCTATTAATTTTACAAATAATTTA
1 TATTATATTAATTTTACAAATAATTTA
1332412 TATTA
1 TATTA
1332417 ATTGCTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 8 0.30
27 17 0.63
28 2 0.07
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (27 bp):
TATTATATTAATTTTACAAATAATTTA
Found at i:1335744 original size:2 final size:2
Alignment explanation
Indices: 1335739--1335763 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1335729 TTATTGTGTG
1335739 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1335764 TATTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1338068 original size:18 final size:17
Alignment explanation
Indices: 1338032--1338071 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1338022 AACTTCAAAT
1338032 ATAATTTTATTGTTTTA
1 ATAATTTTATTGTTTTA
1338049 ATAA-TTTATAT-TTTT-
1 ATAATTTTAT-TGTTTTA
1338064 ATAATTTT
1 ATAATTTT
1338072 TAAAAGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATAATTTTATTGTTTTA
Found at i:1339701 original size:22 final size:21
Alignment explanation
Indices: 1339661--1339719 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
1339651 AATAATTTTT
*
1339661 AATTATTTATTAGAATTTATTA
1 AATTATTTATAAGAATTTA-TA
* **
1339683 TATTATTTATAAGTTTTTATA
1 AATTATTTATAAGAATTTATA
*
1339704 AATT-TTTATAAAAATT
1 AATTATTTATAAGAATT
1339720 CAAATATATT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 9 0.31
21 5 0.17
22 15 0.52
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
AATTATTTATAAGAATTTATA
Found at i:1339702 original size:19 final size:18
Alignment explanation
Indices: 1339652--1339703 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
1339642 ACAATTTTTA
1339652 ATAATTTTTA-ATTATTT
1 ATAATTTTTATATTATTT
1339669 ATTAGAATTTATTATATTATTT
1 A-T--AATTT-TTATATTATTT
1339691 ATAAGTTTTTATA
1 ATAA-TTTTTATA
1339704 AATTTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
17 1 0.03
18 1 0.03
19 7 0.24
20 8 0.28
21 4 0.14
22 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
ATAATTTTTATATTATTT
Found at i:1339962 original size:10 final size:10
Alignment explanation
Indices: 1339893--1340039 Score: 60
Period size: 10 Copynumber: 15.2 Consensus size: 10
1339883 GTTTTATTTA
1339893 TTTTAT-ATT
1 TTTTATAATT
1339902 TTTTATAATT
1 TTTTATAATT
* *
1339912 TATTA-GATT
1 TTTTATAATT
*
1339921 TTTT-TAA-G
1 TTTTATAATT
*
1339929 TTTTATAATA
1 TTTTATAATT
* *
1339939 TTTAAGTTATT
1 TTTTA-TAATT
1339950 TTTTATAA-T
1 TTTTATAATT
*
1339959 TTTTATAAGT
1 TTTTATAATT
*
1339969 TTCTATTAA-T
1 TTTTA-TAATT
*
1339979 TTTAAT-ATT
1 TTTTATAATT
*
1339988 TTTAAT-ATT
1 TTTTATAATT
*
1339997 TTTCT-TGATT
1 TTT-TATAATT
*
1340007 ATTTATAATT
1 TTTTATAATT
* *
1340017 ATTTATGATT
1 TTTTATAATT
*
1340027 TTTAATAAATT
1 TTTTAT-AATT
1340038 TT
1 TT
1340040 ATGAGAAAAT
Statistics
Matches: 105, Mismatches: 21, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
8 5 0.05
9 41 0.39
10 44 0.42
11 15 0.14
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:1339962 original size:38 final size:37
Alignment explanation
Indices: 1339918--1339999 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 37
1339908 AATTTATTAG
* *
1339918 ATTTTTTTAAGTTT-TA-TAATATTTAAGTTATTTTTTAT
1 ATTTTTATAAGTTTCTATTAAT-TTTAA--TATTTTTAAT
1339956 AATTTTTATAAGTTTCTATTAATTTTAATATTTTTAAT
1 -ATTTTTATAAGTTTCTATTAATTTTAATATTTTTAAT
1339994 ATTTTT
1 ATTTTT
1340000 CTTGATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 6 0.15
38 9 0.23
39 13 0.33
40 7 0.18
41 4 0.10
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (37 bp):
ATTTTTATAAGTTTCTATTAATTTTAATATTTTTAAT
Found at i:1339981 original size:29 final size:27
Alignment explanation
Indices: 1339884--1340028 Score: 98
Period size: 29 Copynumber: 5.1 Consensus size: 27
1339874 TTTAAATATG
* *
1339884 TTTTATTTA-TTTTATATTTTTTATAA
1 TTTTATTAATTTTTATAATTTTTATAA
* *
1339910 -TTTATTAGATTTTTTTAAGTTTTATAA
1 TTTTATTA-ATTTTTATAATTTTTATAA
*
1339937 TATTTAAGTTATTTTTTATAATTTTTATAA
1 T-TTT-A-TTAATTTTTATAATTTTTATAA
* *
1339967 GTTTCTATTAATTTTAAT-ATTTTTAATAT
1 -TTT-TATTAATTTTTATAATTTTT-ATAA
* * *
1339996 TTTTCTTGATTATTTATAATTATTTATGA
1 TTTTATTAATT-TTTATAATT-TTTATAA
1340025 TTTT
1 TTTT
1340029 TAATAAATTT
Statistics
Matches: 92, Mismatches: 15, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
25 6 0.07
26 1 0.01
27 20 0.22
28 13 0.14
29 24 0.26
30 23 0.25
31 5 0.05
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (27 bp):
TTTTATTAATTTTTATAATTTTTATAA
Found at i:1341652 original size:17 final size:16
Alignment explanation
Indices: 1341627--1341662 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1341617 TATTTAAACA
*
1341627 TTATTTATTATTATATT
1 TTATATATTATTA-ATT
1341644 TTATATATTATTAATT
1 TTATATATTATTAATT
1341660 TTA
1 TTA
1341663 CAAATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATATTATTAATT
Found at i:1341721 original size:18 final size:18
Alignment explanation
Indices: 1341673--1341726 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1341663 CAAATAATTT
*
1341673 ATATTAATTACTTAAATA
1 ATATTAATTATTTAAATA
* * *
1341691 GTATTTAA-AATTTATATA
1 ATA-TTAATTATTTAAATA
1341709 ATATTAATTATTTAAATA
1 ATATTAATTATTTAAATA
1341727 TCATATAACA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATTAATTATTTAAATA
Found at i:1342340 original size:24 final size:24
Alignment explanation
Indices: 1342312--1342382 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
1342302 AGAAATAATC
* *
1342312 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
1342336 TTTCAATTAAACCCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
1342360 TTTCAATTAAACTATGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
1342383 ATTTAAGTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:1342854 original size:16 final size:16
Alignment explanation
Indices: 1342833--1342864 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1342823 ACAAATTTCA
1342833 ATCTGTGGCAAGTTCG
1 ATCTGTGGCAAGTTCG
1342849 ATCTGTGGCAAGTTCG
1 ATCTGTGGCAAGTTCG
1342865 GATGATGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (16 bp):
ATCTGTGGCAAGTTCG
Found at i:1344405 original size:24 final size:24
Alignment explanation
Indices: 1344319--1344393 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
1344309 AGAAATAATC
* * *
1344319 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
1344343 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
1344367 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
1344391 TTT
1 TTT
1344394 AAGTCAAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:1345514 original size:85 final size:86
Alignment explanation
Indices: 1345402--1345573 Score: 256
Period size: 85 Copynumber: 2.0 Consensus size: 86
1345392 TTACATGAAG
* * * * * *
1345402 AGATTGTATATGTGAAATTGATATGAAAGCATGAATCCATGCCATTACATGTTAGTATGAA-ACA
1 AGATTGTATATGTGAAACTGACATGAAAACATGAATACATGCCATTAAATGTTAATATGAAGACA
1345466 TTGAATGTGCTTGATAAGCAT
66 TTGAATGTGCTTGATAAGCAT
* *
1345487 AGATTGTATATGTGAAACTGACATGAAAACATGAATACATGCCTTTAAATGTTAATATGAAGATA
1 AGATTGTATATGTGAAACTGACATGAAAACATGAATACATGCCATTAAATGTTAATATGAAGACA
*
1345552 TTGAATGTGTTTGATAAGCAT
66 TTGAATGTGCTTGATAAGCAT
1345573 A
1 A
1345574 ACATCGATTC
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 54 0.70
86 23 0.30
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (86 bp):
AGATTGTATATGTGAAACTGACATGAAAACATGAATACATGCCATTAAATGTTAATATGAAGACA
TTGAATGTGCTTGATAAGCAT
Found at i:1346700 original size:10 final size:10
Alignment explanation
Indices: 1346685--1347073 Score: 68
Period size: 10 Copynumber: 39.2 Consensus size: 10
1346675 TTAAATATGA
1346685 TTTTATAATT
1 TTTTATAATT
1346695 TTTTATAATT
1 TTTTATAATT
** *
1346705 CATTAGAATT
1 TTTTATAATT
*
1346715 TATTAT-ATT
1 TTTTATAATT
* *
1346724 ATTTATAAGT
1 TTTTATAATT
*
1346734 TTTTA-AGAAT
1 TTTTATA-ATT
*
1346744 TTTTATAAGGCT
1 TTTTATAA--TT
**
1346756 TTTTATAAAG
1 TTTTATAATT
* * *
1346766 ATTCATTATT
1 TTTTATAATT
*
1346776 GTTTATTAA--
1 TTTTA-TAATT
1346785 TTTTATAA-T
1 TTTTATAATT
*
1346794 TTTAATAATT
1 TTTTATAATT
*
1346804 TATTATAA--
1 TTTTATAATT
1346812 TTTTATAA-T
1 TTTTATAATT
1346821 TTTTATAA-T
1 TTTTATAATT
*
1346830 ATTTATAAGTT
1 TTTTATAA-TT
1346841 TTTT-T-A-T
1 TTTTATAATT
1346848 TTTTATAA-T
1 TTTTATAATT
* *
1346857 ATTTACAAGTT
1 TTTTATAA-TT
1346868 TATATCTATTTCAATT
1 T-T-T-TA--T-AATT
1346884 TTTT-TAATT
1 TTTTATAATT
* ** *
1346893 GTCAATGATT
1 TTTTATAATT
* **
1346903 TTTTTTCTTAT
1 TTTTATAAT-T
*
1346914 TTTTAGTGA-T
1 TTTTA-TAATT
*
1346924 TTTTATAAGT
1 TTTTATAATT
* *
1346934 TTTTAAAAAT
1 TTTTATAATT
1346944 TTTTAT-ATGT
1 TTTTATAAT-T
**
1346954 TTTTATAAAA
1 TTTTATAATT
1346964 TTTTA-AATAT
1 TTTTATAAT-T
*
1346974 TTTTATTCATT
1 TTTTA-TAATT
** *
1346985 TTACA-AAAT
1 TTTTATAATT
1346994 TTTTATAATT
1 TTTTATAATT
* *
1347004 TATTA-GATT
1 TTTTATAATT
1347013 TTTTA-AATAT
1 TTTTATAAT-T
*
1347023 TTTTATAATA
1 TTTTATAATT
*
1347033 TTTAAGCT-ATT
1 TTTTA--TAATT
1347044 TTTTAT-ATT
1 TTTTATAATT
*
1347053 TTTTATTA-T
1 TTTTATAATT
1347062 TTTTATAATT
1 TTTTATAATT
1347072 TT
1 TT
1347074 CTATCACTTT
Statistics
Matches: 271, Mismatches: 71, Indels: 74
0.65 0.17 0.18
Matches are distributed among these distances:
7 5 0.02
8 11 0.04
9 86 0.32
10 117 0.43
11 27 0.10
12 14 0.05
13 2 0.01
14 3 0.01
15 1 0.00
16 3 0.01
17 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.60
Consensus pattern (10 bp):
TTTTATAATT
Found at i:1346816 original size:27 final size:26
Alignment explanation
Indices: 1346777--1346871 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 26
1346767 TTCATTATTG
* *
1346777 TTTATTAATTTTATAATTTTAATAATT
1 TTTA-TAATTTTATAATTTTTATAATA
1346804 TATTATAATTTTATAATTTTTATAATA
1 T-TTATAATTTTATAATTTTTATAATA
* *
1346831 TTTATAAGTTTTTTTATTTTTATAATA
1 TTTATAA-TTTTATAATTTTTATAATA
* *
1346858 TTTACAAGTTTATA
1 TTTATAATTTTATA
1346872 TCTATTTCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
26 10 0.17
27 45 0.78
28 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTATAATTTTATAATTTTTATAATA
Found at i:1346835 original size:9 final size:8
Alignment explanation
Indices: 1346777--1346871 Score: 73
Period size: 9 Copynumber: 10.8 Consensus size: 8
1346767 TTCATTATTG
1346777 TTTATTAAT
1 TTTA-TAAT
1346786 TTTATAAT
1 TTTATAAT
1346794 TTTAATAATT
1 TTT-ATAA-T
1346804 TATTATAAT
1 T-TTATAAT
1346813 TTTATAATT
1 TTTATAA-T
1346822 TTTATAAT
1 TTTATAAT
1346830 ATTTATAAGTT
1 -TTTATAA--T
* *
1346841 TTTTTATT
1 TTTATAAT
1346849 TTTATAAT
1 TTTATAAT
* *
1346857 ATTTACAAG
1 -TTTATAAT
1346866 TTTATA
1 TTTATA
1346872 TCTATTTCAA
Statistics
Matches: 71, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
8 26 0.37
9 31 0.44
10 11 0.15
11 3 0.04
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (8 bp):
TTTATAAT
Found at i:1346852 original size:36 final size:36
Alignment explanation
Indices: 1346771--1346861 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 36
1346761 TAAAGATTCA
1346771 TTATTGTTTATTAA-TTTTATAATTTTAATAATTTATT
1 TTATT-TTTA-TAATTTTTATAATTTTAATAATTTATT
* *
1346808 ATAATTTTATAATTTTTATAATATTT-ATAAGTTT-TT
1 TTATTTTTATAATTTTTATAAT-TTTAATAA-TTTATT
*
1346844 TTATTTTTATAATATTTA
1 TTATTTTTATAATTTTTA
1346862 CAAGTTTATA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
35 3 0.07
36 34 0.74
37 9 0.20
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (36 bp):
TTATTTTTATAATTTTTATAATTTTAATAATTTATT
Found at i:1346946 original size:30 final size:30
Alignment explanation
Indices: 1346923--1346996 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
1346913 TTTTTAGTGA
**
1346923 TTTTTATAAGTTTTTAAAAATTTTTATATG
1 TTTTTATAAAATTTTAAAAATTTTTATATG
* *
1346953 TTTTTATAAAATTTTAAATATTTTTAT-TC
1 TTTTTATAAAATTTTAAAAATTTTTATATG
* *
1346982 ATTTTACAAAATTTT
1 TTTTTATAAAATTTT
1346997 TATAATTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
29 14 0.37
30 24 0.63
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (30 bp):
TTTTTATAAAATTTTAAAAATTTTTATATG
Found at i:1346968 original size:20 final size:21
Alignment explanation
Indices: 1346922--1346967 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
1346912 ATTTTTAGTG
*
1346922 ATTTTTATAAGTTTTTA-AAA
1 ATTTTTATATGTTTTTATAAA
1346942 ATTTTTATATGTTTTTATAAA
1 ATTTTTATATGTTTTTATAAA
1346963 ATTTT
1 ATTTT
1346968 AAATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (21 bp):
ATTTTTATATGTTTTTATAAA
Found at i:1347036 original size:19 final size:19
Alignment explanation
Indices: 1347014--1347070 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
1347004 TATTAGATTT
1347014 TTTAAATATTTTTATAATA
1 TTTAAATATTTTTATAATA
* *
1347033 TTTAAGCTATTTTT-TATATT
1 TTTAA-ATATTTTTATA-ATA
* *
1347053 TTTTATTATTTTTATAAT
1 TTTAAATATTTTTATAAT
1347071 TTTCTATCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTAAATATTTTTATAATA
Found at i:1347045 original size:29 final size:29
Alignment explanation
Indices: 1346982--1347063 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 29
1346972 ATTTTTATTC
* *
1346982 ATTTTACAAAATTTTTATAAT-TTATTAGAT
1 ATTTTA-AATATTTTTATAATATT-TAAGAT
* *
1347012 TTTTTAAATATTTTTATAATATTTAAGCT
1 ATTTTAAATATTTTTATAATATTTAAGAT
** *
1347041 ATTTTTTATATTTTT-TATTATTT
1 ATTTTAAATATTTTTATAATATTT
1347064 TTATAATTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 7 0.16
29 29 0.67
30 7 0.16
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (29 bp):
ATTTTAAATATTTTTATAATATTTAAGAT
Found at i:1347052 original size:9 final size:9
Alignment explanation
Indices: 1346993--1347093 Score: 51
Period size: 9 Copynumber: 10.4 Consensus size: 9
1346983 TTTTACAAAA
1346993 TTTTTATAAT
1 TTTTTAT-AT
* *
1347003 TTATTAGAT
1 TTTTTATAT
*
1347012 TTTTTAAAT
1 TTTTTATAT
1347021 ATTTTTATAAT
1 -TTTTTAT-AT
* *
1347032 ATTTAAGCTAT
1 TTTTTA--TAT
1347043 TTTTTATAT
1 TTTTTATAT
1347052 TTTTTAT-T
1 TTTTTATAT
1347060 ATTTTTATAAT
1 -TTTTTAT-AT
* *
1347071 TTTCTATCAC
1 TTTTTAT-AT
*
1347081 TTTTAATAT
1 TTTTTATAT
1347090 TTTT
1 TTTT
1347094 ATCATTTAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
8 1 0.01
9 31 0.45
10 27 0.39
11 9 0.13
12 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAT
Found at i:1347458 original size:90 final size:89
Alignment explanation
Indices: 1347342--1347533 Score: 219
Period size: 90 Copynumber: 2.1 Consensus size: 89
1347332 TTAATATAAT
* * * * *
1347342 ATTTGGTACCTGAACTTGATACTTTTTTCCAATTTGGTACATAAGCTTTTT-TGGTTCAATTTGG
1 ATTTGGTACCTAAACTTGATACTTTTTT-CAAGTTGGTACATAAACTTTTTGAGGTCCAATTTGG
*
1347406 TA-CTCAAACTTGACACTTTTTTTCTA
65 TACCT-AAACTTGACAC-TTTTTCCTA
* * * *
1347432 ATTTAGTACCTAAACTTGA-CCTTTTTTTTAAGTTGGTACCTAAACTTTTTGAGGTCCAATTTGG
1 ATTTGGTACCTAAACTTGATAC-TTTTTTCAAGTTGGTACATAAACTTTTTGAGGTCCAATTTGG
* *
1347496 TACCTGAACTTGACTCTTTTTCCTA
65 TACCTAAACTTGACACTTTTTCCTA
1347521 ATTTGGTACCTAA
1 ATTTGGTACCTAA
1347534 TATTTTTTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
89 39 0.45
90 45 0.52
91 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.45
Consensus pattern (89 bp):
ATTTGGTACCTAAACTTGATACTTTTTTCAAGTTGGTACATAAACTTTTTGAGGTCCAATTTGGT
ACCTAAACTTGACACTTTTTCCTA
Found at i:1347471 original size:30 final size:32
Alignment explanation
Indices: 1347402--1347478 Score: 106
Period size: 30 Copynumber: 2.5 Consensus size: 32
1347392 TTGGTTCAAT
*
1347402 TTGGTA-CTCAAACTTGACACTTTTTTTCTAAT
1 TTGGTACCT-AAACTTGACACTTTTTTTCTAAG
*
1347434 TTAGTACCTAAACTTGAC-CTTTTTTT-TAAG
1 TTGGTACCTAAACTTGACACTTTTTTTCTAAG
1347464 TTGGTACCTAAACTT
1 TTGGTACCTAAACTT
1347479 TTTGAGGTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
30 17 0.41
31 8 0.20
32 14 0.34
33 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.45
Consensus pattern (32 bp):
TTGGTACCTAAACTTGACACTTTTTTTCTAAG
Found at i:1347480 original size:89 final size:90
Alignment explanation
Indices: 1347342--1347533 Score: 228
Period size: 89 Copynumber: 2.1 Consensus size: 90
1347332 TTAATATAAT
* * * * *
1347342 ATTTGGTACCTGAACTTGATACTTTTTTCCAATTTGGTACATAAGCTTTTT-TGGTTCAATTTGG
1 ATTTGGTACCTAAACTTGATACTTTTTTCCAAGTTGGTACATAAACTTTTTGAGGTCCAATTTGG
*
1347406 TA-CTCAAACTTGACACTTTTTTTCTA
66 TACCT-AAACTTGACAC-TTTTTCCTA
* * ** *
1347432 ATTTAGTACCTAAACTTGA-CCTTTTTTTTAAGTTGGTACCTAAACTTTTTGAGGTCCAATTTGG
1 ATTTGGTACCTAAACTTGATACTTTTTTCCAAGTTGGTACATAAACTTTTTGAGGTCCAATTTGG
* *
1347496 TACCTGAACTTGACTCTTTTTCCTA
66 TACCTAAACTTGACACTTTTTCCTA
1347521 ATTTGGTACCTAA
1 ATTTGGTACCTAA
1347534 TATTTTTTTA
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
89 45 0.52
90 39 0.45
91 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.45
Consensus pattern (90 bp):
ATTTGGTACCTAAACTTGATACTTTTTTCCAAGTTGGTACATAAACTTTTTGAGGTCCAATTTGG
TACCTAAACTTGACACTTTTTCCTA
Found at i:1348243 original size:132 final size:133
Alignment explanation
Indices: 1347986--1348353 Score: 350
Period size: 132 Copynumber: 2.7 Consensus size: 133
1347976 AACATGCCAG
* * ** ** *
1347986 CTTAAAAAATGTTTTTTTAAAAGAAAAAAAAATTAATTGTGAAAAAGCCCATAAGAAAATGTCAA
1 CTTAAAAAATGATTTTTTAAAAGGAAAAAATTTTAATTGTGAAAAAGCCTTTAAGAAAGTGTCAA
**** * * * * *
1348051 ATTTTTTTTTTTTTTTATTAAATTCACACCTAATTGAACTCCAATTTCAAAGCTTGAGTGTCACA
66 A----AAAATCTTTGTATTAAATTCACACC-AATTGAACTCCAATTCCAAAACTCGAGTGTCACA
*
1348116 GTATTCAA
126 GTATCCAA
* * *
1348124 CTTAAAAAAT-ATTTTTTAAAA-GAAAGAATTTT-ATTGTGAAAAAAATCC-TTACGAAAGTGTC
1 CTTAAAAAATGATTTTTTAAAAGGAAAAAATTTTAATTGTG--AAAAAGCCTTTAAGAAAGTGTC
* * * *
1348185 AAAAAATTCTTTGTATTAAATTCACATCCAATT-AAGTTTCAATTCCAAAACTCGAGTGTCGCAG
64 AAAAAAATCTTTGTATTAAATTCACA-CCAATTGAA-CTCCAATTCCAAAACTCGAGTGTCACAG
1348249 TATCCAA
127 TATCCAA
* * * *
1348256 TTTAAAAAATGTTTTTTTAAAAGGAAAAAATTTTAATTGTGAAAAAGCCTTTAAGAAATTGTTAA
1 CTTAAAAAATGATTTTTTAAAAGGAAAAAATTTTAATTGTGAAAAAGCCTTTAAGAAAGTGTCAA
*
1348321 AAAAATCTTTGTACTAAATTCACACCAAATTGA
66 AAAAATCTTTGTATTAAATTCACACC-AATTGA
1348354 GTTCTTGTCG
Statistics
Matches: 190, Mismatches: 30, Indels: 23
0.78 0.12 0.09
Matches are distributed among these distances:
131 2 0.01
132 59 0.31
133 21 0.11
134 48 0.25
135 13 0.07
136 20 0.11
137 17 0.09
138 10 0.05
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (133 bp):
CTTAAAAAATGATTTTTTAAAAGGAAAAAATTTTAATTGTGAAAAAGCCTTTAAGAAAGTGTCAA
AAAAATCTTTGTATTAAATTCACACCAATTGAACTCCAATTCCAAAACTCGAGTGTCACAGTATC
CAA
Found at i:1348538 original size:28 final size:28
Alignment explanation
Indices: 1348496--1348596 Score: 100
Period size: 28 Copynumber: 3.6 Consensus size: 28
1348486 TATTTTCTCA
*
1348496 TAAAAATTAGAAAAAT-ATAAAAATTAT
1 TAAAAATTATAAAAATAATAAAAATTAT
* * *
1348523 TAAAAATATATTAAAATTGATACAAACTTA-
1 TAAAAAT-TA-TAAAAATAATA-AAAATTAT
1348553 TAAAAATTATAAAAATAATAAAAACTTA-
1 TAAAAATTATAAAAATAATAAAAA-TTAT
*
1348581 TAAATATTATAAAAAT
1 TAAAAATTATAAAAAT
1348597 CAAATTAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 10 0.16
28 29 0.47
29 7 0.11
30 10 0.16
31 6 0.10
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (28 bp):
TAAAAATTATAAAAATAATAAAAATTAT
Found at i:1348674 original size:10 final size:9
Alignment explanation
Indices: 1348495--1348704 Score: 131
Period size: 10 Copynumber: 21.8 Consensus size: 9
1348485 ATATTTTCTC
1348495 ATAAAAATT
1 ATAAAAATT
*
1348504 AGAAAAA-T
1 ATAAAAATT
1348512 ATAAAAATT
1 ATAAAAATT
1348521 ATTAAAAATAT
1 A-TAAAAAT-T
*
1348532 ATTAAAATT
1 ATAAAAATT
*
1348541 GATACAAACTT
1 -ATA-AAAATT
1348552 ATAAAAATT
1 ATAAAAATT
*
1348561 ATAAAAATA
1 ATAAAAATT
1348570 ATAAAAACTT
1 ATAAAAA-TT
*
1348580 ATAAATATT
1 ATAAAAATT
*
1348589 ATAAAAATC
1 ATAAAAATT
*
1348598 A-AATTAATT
1 ATAA-AAATT
*
1348607 CTAATAAATT
1 ATAA-AAATT
1348617 ATAAACAATT
1 ATAAA-AATT
*
1348627 TTATAAAATT
1 ATA-AAAATT
1348637 AATAAAACA-T
1 -ATAAAA-ATT
*
1348647 ATTTAAAATT
1 A-TAAAAATT
*
1348657 CTATAAAATGT
1 ATA-AAAAT-T
1348668 ATAAAAATCCT
1 ATAAAAAT--T
1348679 -TAAAAACTT
1 ATAAAAA-TT
1348688 ATAAAAATT
1 ATAAAAATT
1348697 CATAAAAA
1 -ATAAAAA
1348705 AATCATAAAA
Statistics
Matches: 158, Mismatches: 23, Indels: 39
0.72 0.10 0.18
Matches are distributed among these distances:
8 9 0.06
9 49 0.31
10 83 0.53
11 17 0.11
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:1349649 original size:32 final size:33
Alignment explanation
Indices: 1349613--1349674 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1349603 CTTAATTTGA
*
1349613 AATTC-AATTAATCCTTTTAAAATCCTAACTAG
1 AATTCAAATTAATCATTTTAAAATCCTAACTAG
* **
1349645 AATTCAAATTACTCATTTTTTAATCCTAAC
1 AATTCAAATTAATCATTTTAAAATCCTAAC
1349675 AAGATTTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 5 0.20
33 20 0.80
ACGTcount: A:0.39, C:0.19, G:0.02, T:0.40
Consensus pattern (33 bp):
AATTCAAATTAATCATTTTAAAATCCTAACTAG
Found at i:1350151 original size:29 final size:29
Alignment explanation
Indices: 1350125--1350181 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1350115 TTGGTTTTCT
1350125 AGATTTTATAGTTTGGCCACTATTTTTTA
1 AGATTTTATAGTTTGGCCACTATTTTTTA
* *
1350154 AGATTTTATAGTTTTGCCATTATTTTTT
1 AGATTTTATAGTTTGGCCACTATTTTTT
1350182 TTTTCCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.23, C:0.09, G:0.12, T:0.56
Consensus pattern (29 bp):
AGATTTTATAGTTTGGCCACTATTTTTTA
Found at i:1350250 original size:28 final size:28
Alignment explanation
Indices: 1350181--1350275 Score: 118
Period size: 28 Copynumber: 3.3 Consensus size: 28
1350171 CATTATTTTT
*
1350181 TTTTTCCAAATTTTATAGTTTTGCCACTGG
1 TTTTT-CAAATTTTACAGTTTTGCCACT-G
* * *
1350211 TTTTCCAAATTTTACAATTTTGCTACTG
1 TTTTTCAAATTTTACAGTTTTGCCACTG
* *
1350239 TTTTTCAAATTTTACAGTTTTTCCATTG
1 TTTTTCAAATTTTACAGTTTTGCCACTG
1350267 TTTTTCAAA
1 TTTTTCAAA
1350276 AAAAAATTAC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 33 0.59
29 19 0.34
30 4 0.07
ACGTcount: A:0.23, C:0.16, G:0.08, T:0.53
Consensus pattern (28 bp):
TTTTTCAAATTTTACAGTTTTGCCACTG
Found at i:1352274 original size:11 final size:12
Alignment explanation
Indices: 1352260--1352300 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
1352250 TTCTCATTCA
1352260 TTTCT-TATTTC
1 TTTCTCTATTTC
1352271 TTTCTCT-TTTC
1 TTTCTCTATTTC
1352282 TTT-TCTATTTTC
1 TTTCTCTA-TTTC
1352294 TTTCTCT
1 TTTCTCT
1352301 TTTAATCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.12
11 12 0.46
12 8 0.31
13 3 0.12
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTCTCTATTTC
Found at i:1352303 original size:11 final size:11
Alignment explanation
Indices: 1352267--1352303 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1352257 TCATTTCTTA
1352267 TTTCTTTCTCT
1 TTTCTTTCTCT
*
1352278 TTTCTTTTCTAT
1 TTTC-TTTCTCT
1352290 TTTCTTTCTCT
1 TTTCTTTCTCT
1352301 TTT
1 TTT
1352304 AATCATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTCTCT
Found at i:1352711 original size:21 final size:22
Alignment explanation
Indices: 1352675--1352721 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
1352665 ACCCATTAAG
1352675 CCCAAATTCTATTTAAACCAAA
1 CCCAAATTCTATTTAAACCAAA
1352697 CCCAAATTC-ATTTAAACCAAA
1 CCCAAATTCTATTTAAACCAAA
1352718 CCCA
1 CCCA
1352722 TTTGAACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (22 bp):
CCCAAATTCTATTTAAACCAAA
Found at i:1352723 original size:15 final size:15
Alignment explanation
Indices: 1352705--1352734 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1352695 AACCCAAATT
1352705 CATTTAAACCAAACC
1 CATTTAAACCAAACC
*
1352720 CATTTGAACCAAACC
1 CATTTAAACCAAACC
1352735 AAATGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:1353904 original size:3 final size:3
Alignment explanation
Indices: 1353892--1353945 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
1353882 TATTCTATTC
1353892 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1353939 TAT TAT T
1 TAT TAT T
1353946 TTGGGATGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1362704 original size:3 final size:3
Alignment explanation
Indices: 1362698--1362729 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1362688 TTTTTTTCTT
1362698 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1362730 TGGCATTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1365408 original size:13 final size:13
Alignment explanation
Indices: 1365386--1365420 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1365376 TTGGTTTACA
1365386 AAGGAAGAGGAAG
1 AAGGAAGAGGAAG
*
1365399 AAGGAGGAGGAAG
1 AAGGAAGAGGAAG
1365412 AA-GAAGAGG
1 AAGGAAGAGG
1365421 GTGAATTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (13 bp):
AAGGAAGAGGAAG
Found at i:1376622 original size:15 final size:14
Alignment explanation
Indices: 1376602--1376631 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1376592 AGTAATAGTT
1376602 TAATATATATATATA
1 TAATATATATA-ATA
1376617 TAATATATATAATA
1 TAATATATATAATA
1376631 T
1 T
1376632 TATTTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAATATATATAATA
Found at i:1380101 original size:18 final size:18
Alignment explanation
Indices: 1380078--1380116 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1380068 CAAATTAGTT
* * *
1380078 TATAGTTTAATTTTTTTA
1 TATAGTTCAAATTTTGTA
1380096 TATAGTTCAAATTTTGTA
1 TATAGTTCAAATTTTGTA
1380114 TAT
1 TAT
1380117 TATTTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.59
Consensus pattern (18 bp):
TATAGTTCAAATTTTGTA
Found at i:1380621 original size:20 final size:20
Alignment explanation
Indices: 1380596--1380633 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1380586 CAAAAATATT
*
1380596 AAATAATTTTTATAATTTTA
1 AAATAATTTTAATAATTTTA
1380616 AAATAATTTTAATAATTT
1 AAATAATTTTAATAATTT
1380634 ATTATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATAATTTTAATAATTTTA
Found at i:1380653 original size:29 final size:28
Alignment explanation
Indices: 1380597--1380655 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 28
1380587 AAAAATATTA
1380597 AATAATTTTTATAATTTTAAAATAATTTT
1 AATAATTTTTAT-ATTTTAAAATAATTTT
*
1380626 AATAATTTATTAT-TTTCTAATAATATTTTT
1 AATAATTT-TTATATTT-TAA-AATAATTTT
1380656 TGAATTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 3 0.12
29 11 0.42
30 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
AATAATTTTTATATTTTAAAATAATTTT
Found at i:1395642 original size:12 final size:12
Alignment explanation
Indices: 1395625--1395713 Score: 103
Period size: 12 Copynumber: 7.7 Consensus size: 12
1395615 AGCAGTAAAA
1395625 CAACAAAAATAG
1 CAACAAAAATAG
1395637 CAACAAAAATAG
1 CAACAAAAATAG
* *
1395649 AAACAAAAATAA
1 CAACAAAAATAG
1395661 CAACAAAAATAG
1 CAACAAAAATAG
*
1395673 CAACAAAAACAG
1 CAACAAAAATAG
* *
1395685 CAATAAAAA-AA
1 CAACAAAAATAG
*
1395696 C-ACCAAAATAG
1 CAACAAAAATAG
1395707 CAA-AAAA
1 CAACAAAA
1395714 TAATCAAAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
10 5 0.08
11 7 0.11
12 52 0.81
ACGTcount: A:0.71, C:0.17, G:0.06, T:0.07
Consensus pattern (12 bp):
CAACAAAAATAG
Found at i:1395665 original size:36 final size:35
Alignment explanation
Indices: 1395621--1395713 Score: 127
Period size: 36 Copynumber: 2.7 Consensus size: 35
1395611 AAACAGCAGT
*
1395621 AAAACAACAAAAATAGCAACAAAAATAGAAACAAA
1 AAAACAACAAAAATAGCAACAAAAACAGAAACAAA
* *
1395656 AATAACAACAAAAATAGCAACAAAAACAGCAATAAA
1 AA-AACAACAAAAATAGCAACAAAAACAGAAACAAA
*
1395692 AAAAC-ACCAAAATAGCAA-AAAA
1 AAAACAACAAAAATAGCAACAAAA
1395714 TAATCAAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
33 4 0.08
34 12 0.23
35 5 0.09
36 32 0.60
ACGTcount: A:0.72, C:0.16, G:0.05, T:0.06
Consensus pattern (35 bp):
AAAACAACAAAAATAGCAACAAAAACAGAAACAAA
Found at i:1395748 original size:39 final size:38
Alignment explanation
Indices: 1395678--1395791 Score: 131
Period size: 38 Copynumber: 2.9 Consensus size: 38
1395668 AATAGCAACA
* *
1395678 AAAACAGCAATAAAAAAACACCAAAATAGCAAAAAATAATC
1 AAAACAGC-A-AAAAAAACACCAAAACAGCAAAAAA-AACC
* *
1395719 AAAACAGTAAAAAAAACACTAAAACAGCAAAAAAAACC
1 AAAACAGCAAAAAAAACACCAAAACAGCAAAAAAAACC
* *
1395757 AAAACAGCAAAAAAGTA-ACCAAAACAGTAAAAAAA
1 AAAACAGCAAAAAA-AACACCAAAACAGCAAAAAAA
1395792 TAGCACTAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
38 32 0.50
39 24 0.38
40 1 0.02
41 7 0.11
ACGTcount: A:0.70, C:0.17, G:0.06, T:0.07
Consensus pattern (38 bp):
AAAACAGCAAAAAAAACACCAAAACAGCAAAAAAAACC
Found at i:1395776 original size:20 final size:18
Alignment explanation
Indices: 1395689--1395791 Score: 116
Period size: 20 Copynumber: 5.4 Consensus size: 18
1395679 AAACAGCAAT
*
1395689 AAAAAAACACCAAAATAGC
1 AAAAAAA-ACCAAAACAGC
* *
1395708 AAAAAATAATCAAAACAGT
1 AAAAAA-AACCAAAACAGC
1395727 AAAAAAAACACTAAAACAGC
1 AAAAAAAAC-C-AAAACAGC
1395747 AAAAAAAACCAAAACAGC
1 AAAAAAAACCAAAACAGC
*
1395765 AAAAAAGTAACCAAAACAGT
1 AAAAAA--AACCAAAACAGC
1395785 AAAAAAA
1 AAAAAAA
1395792 TAGCACTAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
18 17 0.23
19 22 0.30
20 34 0.47
ACGTcount: A:0.71, C:0.17, G:0.06, T:0.07
Consensus pattern (18 bp):
AAAAAAAACCAAAACAGC
Found at i:1395781 original size:58 final size:60
Alignment explanation
Indices: 1395665--1395804 Score: 187
Period size: 58 Copynumber: 2.3 Consensus size: 60
1395655 AAATAACAAC
* * *
1395665 AAAAATAGCAACAAAAACAGCAATAAAAAAACACCAAAATAGCAAAAAATAATCAAAACAGTAA
1 AAAAATAGC-ACTAAAACAGC---AAAAAAACACCAAAACAGCAAAAAATAACCAAAACAGTAA
1395729 AAAAA-A-CACTAAAACAGCAAAAAAA-ACCAAAACAGCAAAAAAGTAACCAAAACAGTAA
1 AAAAATAGCACTAAAACAGCAAAAAAACACCAAAACAGCAAAAAA-TAACCAAAACAGTAA
1395787 AAAAATAGCACTAAAACA
1 AAAAATAGCACTAAAACA
1395805 ATAATATAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
57 16 0.23
58 26 0.37
59 1 0.01
60 10 0.14
61 10 0.14
62 1 0.01
63 1 0.01
64 5 0.07
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.08
Consensus pattern (60 bp):
AAAAATAGCACTAAAACAGCAAAAAAACACCAAAACAGCAAAAAATAACCAAAACAGTAA
Found at i:1401651 original size:30 final size:31
Alignment explanation
Indices: 1401594--1401651 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1401584 TTCAAAAATG
* *
1401594 TTTTTGGCACAAAAAATGATTTGGAAAAGCA
1 TTTTTGGCACAAAAAATGATGTAGAAAAGCA
1401625 TTTTTGGC-CAAAAAGA-GATGTAGAAAA
1 TTTTTGGCACAAAAA-ATGATGTAGAAAA
1401652 TTTTAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (31 bp):
TTTTTGGCACAAAAAATGATGTAGAAAAGCA
Found at i:1422678 original size:31 final size:31
Alignment explanation
Indices: 1422631--1422696 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1422621 TAAAAAAATT
1422631 AATAGTCCAATAACTTAAATAAAAACTTTCA
1 AATAGTCCAATAACTTAAATAAAAACTTTCA
* * * *
1422662 AATAGTTCAATGACTTAATTAAAAATTTTCA
1 AATAGTCCAATAACTTAAATAAAAACTTTCA
1422693 AATA
1 AATA
1422697 ATTTATTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (31 bp):
AATAGTCCAATAACTTAAATAAAAACTTTCA
Found at i:1424179 original size:24 final size:22
Alignment explanation
Indices: 1424131--1424179 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
1424121 TTTAAAGTAA
* **
1424131 TTATATTATTATTTTTAATTTT
1 TTATATAATTATTTTTAATAAT
1424153 TTATATAATTAATATTTTAATAAT
1 TTATATAATT-AT-TTTTAATAAT
1424177 TTA
1 TTA
1424180 ATTGATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 2 0.09
24 11 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATATAATTATTTTTAATAAT
Found at i:1424180 original size:16 final size:17
Alignment explanation
Indices: 1424144--1424181 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1424134 TATTATTATT
*
1424144 TTTAATTTTTTATATAA
1 TTTAATATTTTATATAA
1424161 -TTAATATTTTA-ATAA
1 TTTAATATTTTATATAA
1424176 TTTAAT
1 TTTAAT
1424182 TGATAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAATATTTTATATAA
Found at i:1424778 original size:20 final size:20
Alignment explanation
Indices: 1424741--1424780 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1424731 TTCATACTTG
*
1424741 TTTGAAATAATTATAATTTT
1 TTTGAAATAATTAAAATTTT
* *
1424761 TTTGAGATATTTAAAATTTT
1 TTTGAAATAATTAAAATTTT
1424781 AAATATTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTGAAATAATTAAAATTTT
Found at i:1425168 original size:39 final size:39
Alignment explanation
Indices: 1425114--1425200 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1425104 CAGAAGGGTC
* *
1425114 AATTTACATTTTTTCTAATATATATGGGCTAATAAGATT
1 AATTTGCATATTTTCTAATATATATGGGCTAATAAGATT
1425153 AATTTGCATATTTTCTAATATATATGGGCTAATAAGATT
1 AATTTGCATATTTTCTAATATATATGGGCTAATAAGATT
1425192 AATTTGCAT
1 AATTTGCAT
1425201 GTGCAAGCAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (39 bp):
AATTTGCATATTTTCTAATATATATGGGCTAATAAGATT
Found at i:1426538 original size:18 final size:17
Alignment explanation
Indices: 1426515--1426548 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1426505 TGTTGACTCA
*
1426515 TGAATTGATTGAATCGAT
1 TGAATTAATTG-ATCGAT
1426533 TGAATTAATTGATCGA
1 TGAATTAATTGATCGA
1426549 ACCGGTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (17 bp):
TGAATTAATTGATCGAT
Found at i:1426545 original size:22 final size:22
Alignment explanation
Indices: 1426517--1426559 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1426507 TTGACTCATG
* *
1426517 AATTGATTGAATCGATTGAATT
1 AATTGATCGAACCGATTGAATT
*
1426539 AATTGATCGAACCGGTTGAAT
1 AATTGATCGAACCGATTGAAT
1426560 CAACTTTCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (22 bp):
AATTGATCGAACCGATTGAATT
Found at i:1428367 original size:6 final size:6
Alignment explanation
Indices: 1428356--1428393 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
1428346 CTACTTTGAC
1428356 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CA
1 CACCAT CACCAT CACCAT CACCAT CACCAT CACCAT CA
1428394 ACACACTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.50, G:0.00, T:0.16
Consensus pattern (6 bp):
CACCAT
Found at i:1432396 original size:6 final size:6
Alignment explanation
Indices: 1432385--1432409 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1432375 ACCTGCTTTG
1432385 ATCACC ATCACC ATCACC ATCACC A
1 ATCACC ATCACC ATCACC ATCACC A
1432410 AATCCTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (6 bp):
ATCACC
Found at i:1455748 original size:29 final size:30
Alignment explanation
Indices: 1455694--1455755 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
1455684 ATCTCAAAAT
1455694 TATATATGAACTTTGATTTAATGTACAATTA
1 TATATATGAACTTTGATTT-ATGTACAATTA
1455725 TATATATGAACTTT-ATTT-TGGTACAATTA
1 TATATATGAACTTTGATTTAT-GTACAATTA
1455754 TA
1 TA
1455756 CACGTAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 1 0.03
29 11 0.37
30 4 0.13
31 14 0.47
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (30 bp):
TATATATGAACTTTGATTTATGTACAATTA
Found at i:1455967 original size:31 final size:29
Alignment explanation
Indices: 1455932--1456001 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
1455922 GTTAATAATT
* *
1455932 TATAAGAATTGGATCAAATCAAAATTACATA
1 TATAA-AATTAGATAAAATCAAAATT-CATA
* *
1455963 TATAAAATTATATAAAATCAAAATTCATG
1 TATAAAATTAGATAAAATCAAAATTCATA
*
1455992 TATATAATTA
1 TATAAAATTA
1456002 CACATTAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 12 0.35
30 17 0.50
31 5 0.15
ACGTcount: A:0.53, C:0.07, G:0.06, T:0.34
Consensus pattern (29 bp):
TATAAAATTAGATAAAATCAAAATTCATA
Found at i:1456326 original size:10 final size:10
Alignment explanation
Indices: 1456309--1456338 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1456299 TCAATTCAAT
1456309 TAAAAAATTA
1 TAAAAAATTA
*
1456319 TTAAAAATTA
1 TAAAAAATTA
1456329 TAAAAAATTA
1 TAAAAAATTA
1456339 ATTCAATCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:1469850 original size:3 final size:3
Alignment explanation
Indices: 1469842--1469888 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1469832 TTTTGAATAC
1469842 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1469889 GTGATGGCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1475307 original size:13 final size:13
Alignment explanation
Indices: 1475286--1475317 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1475276 TATTATCTTA
1475286 TTTTA-TTTTATT
1 TTTTATTTTTATT
1475298 TTTTATTTTTATT
1 TTTTATTTTTATT
1475311 TTTTATT
1 TTTTATT
1475318 AGACATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:1481298 original size:25 final size:27
Alignment explanation
Indices: 1481270--1481319 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
1481260 GAATATTAGA
*
1481270 GAATTTTGGAAAATA-TATA-AAATAG
1 GAATTTTGAAAAATAGTATAGAAATAG
*
1481295 GAATTTTTAAAAATAGTATAGAAAT
1 GAATTTTGAAAAATAGTATAGAAAT
1481320 TAGAAATACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 4 0.19
27 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (27 bp):
GAATTTTGAAAAATAGTATAGAAATAG
Found at i:1490262 original size:12 final size:13
Alignment explanation
Indices: 1490236--1490272 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1490226 TATCTTTTTC
*
1490236 TTATTATTCTTTA
1 TTATTATTATTTA
1490249 TTATT-TTATTTA
1 TTATTATTATTTA
1490261 TTATTATTATTT
1 TTATTATTATTT
1490273 TAATTACAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:1510626 original size:20 final size:20
Alignment explanation
Indices: 1510603--1510650 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1510593 TATGTATTTA
*
1510603 ATTAAAATAT-TATTTTATAT
1 ATTAAAATATCTATATTAT-T
*
1510623 ATTAGAATATCTATATTATT
1 ATTAAAATATCTATATTATT
*
1510643 AATAAAAT
1 ATTAAAAT
1510651 TTCTGACTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTAAAATATCTATATTATT
Found at i:1519422 original size:6 final size:6
Alignment explanation
Indices: 1519377--1519410 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1519367 TCCCTCATTC
1519377 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTC
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTC
1519411 TTCTTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCCT
Found at i:1527973 original size:27 final size:28
Alignment explanation
Indices: 1527940--1528002 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
1527930 AACACTCAGG
* * *
1527940 GACTAAAATGTTACA-ACAAACTTAAGT
1 GACTAAAATATAACATACAAACATAAGT
*
1527967 GACTAAAATATAACATTTCAAACATAAGT
1 GACTAAAATATAACA-TACAAACATAAGT
1527996 GACTAAA
1 GACTAAA
1528003 GTGTAAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 13 0.43
29 17 0.57
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.25
Consensus pattern (28 bp):
GACTAAAATATAACATACAAACATAAGT
Found at i:1529897 original size:2 final size:2
Alignment explanation
Indices: 1529890--1529918 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1529880 ATGAAGCTAT
1529890 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1529919 TTATATTTAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1537259 original size:23 final size:23
Alignment explanation
Indices: 1537213--1537259 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1537203 GTATAGAGTG
* *
1537213 CTCCAAATTAGTTTATTAAATCC
1 CTCCAAATTAGCTTATCAAATCC
* *
1537236 CTCCAATTTAGCTTATCAAGTCC
1 CTCCAAATTAGCTTATCAAATCC
1537259 C
1 C
1537260 GAGAACCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (23 bp):
CTCCAAATTAGCTTATCAAATCC
Found at i:1543634 original size:18 final size:16
Alignment explanation
Indices: 1543603--1543646 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
1543593 AAGTTTAGGT
*
1543603 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
1543620 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
1543634 TTAAAAATTTATT
1 TTAAAAATTTATT
1543647 CTCATCCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:1544232 original size:121 final size:119
Alignment explanation
Indices: 1544015--1544242 Score: 339
Period size: 121 Copynumber: 1.9 Consensus size: 119
1544005 ACACATTTCG
*
1544015 AAAAGCTACTTTACTCACTTTTCAATAGAAGGCCGAAATACAATTTGCCCCAAAATTCAAAGACT
1 AAAAACTACTTTACTCACTTTTCAATAGAAGGCCGAAATACAATTTGCCCCAAAATTCAAAGACT
* *
1544080 TCCCTGATACTTTTACCTTGATTCCCTCTATTTTATTTGTATTACGAAATGTAT
66 TCCCTGATACTTTTACCTCGATTCCCTCTATTTTAGTTGTATTACGAAATGTAT
** * * *
1544134 AAAAACTACTTTACTCACTTTTCAATAGAAAGGCCGAAATACAATTTGCCCTTTAAGTTCAAGGG
1 AAAAACTACTTTACTCACTTTTCAATAG-AAGGCCGAAATACAATTTGCCC-CAAAATTCAAAGA
* * *
1544199 CTTTCCTGATATTTTTACCTCGGTTCCCTCTATTTTAGTTGTAT
64 CTTCCCTGATACTTTTACCTCGATTCCCTCTATTTTAGTTGTAT
1544243 GATATTGGCC
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
119 27 0.28
120 22 0.23
121 47 0.49
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (119 bp):
AAAAACTACTTTACTCACTTTTCAATAGAAGGCCGAAATACAATTTGCCCCAAAATTCAAAGACT
TCCCTGATACTTTTACCTCGATTCCCTCTATTTTAGTTGTATTACGAAATGTAT
Found at i:1546434 original size:27 final size:27
Alignment explanation
Indices: 1546404--1546456 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1546394 AATAAATTTA
1546404 ATTAGTTAAAAAAATTAAACCCTAAAT
1 ATTAGTTAAAAAAATTAAACCCTAAAT
**
1546431 ATTAGTTAAAAACCTTAAACCCTAAA
1 ATTAGTTAAAAAAATTAAACCCTAAA
1546457 CTCATTTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (27 bp):
ATTAGTTAAAAAAATTAAACCCTAAAT
Found at i:1546656 original size:16 final size:16
Alignment explanation
Indices: 1546616--1546659 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1546606 AGGTTTAGGT
*
1546616 TTAAAAATTCTAATTAA
1 TTAAAAATT-TATTTAA
1546633 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
1546647 TTAAAAATTTATT
1 TTAAAAATTTATT
1546660 CTCATCCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 8 0.33
15 5 0.21
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:1546815 original size:29 final size:29
Alignment explanation
Indices: 1546781--1546851 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
1546771 AAATAATAAT
1546781 ATAAGTGACTAAAATGTAACATT-TCAAAC
1 ATAAGTGACTAAAATGTAAC-TTGTCAAAC
*
1546810 ATAAGTGACTGAAATGTAACTTGAGTCAAAC
1 ATAAGTGACTAAAATGTAACTT--GTCAAAC
*
1546841 AAAAGTGACTA
1 ATAAGTGACTA
1546852 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 2 0.06
29 19 0.53
31 15 0.42
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (29 bp):
ATAAGTGACTAAAATGTAACTTGTCAAAC
Found at i:1547049 original size:22 final size:22
Alignment explanation
Indices: 1547024--1547067 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1547014 ACATTAAAAA
*
1547024 AATA-TACTTATACTAAATATAT
1 AATACTAC-TATACTAAAAATAT
*
1547046 AATACTACTCTACTAAAAATAT
1 AATACTACTATACTAAAAATAT
1547068 TAAAATAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
AATACTACTATACTAAAAATAT
Found at i:1553969 original size:5 final size:5
Alignment explanation
Indices: 1553959--1553988 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1553949 AGTTTGGTCA
1553959 GATGG GATGG GATGG GATGG GATGG GATGG
1 GATGG GATGG GATGG GATGG GATGG GATGG
1553989 AATGAGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (5 bp):
GATGG
Found at i:1565495 original size:20 final size:20
Alignment explanation
Indices: 1565472--1565513 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1565462 GGAATTGGAA
1565472 AAATATCAGCTGAATTTGCT
1 AAATATCAGCTGAATTTGCT
1565492 AAATATCAGCTGAATTTGCT
1 AAATATCAGCTGAATTTGCT
1565512 AA
1 AA
1565514 GAAGGTGGCA
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:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (20 bp):
AAATATCAGCTGAATTTGCT
Found at i:1571536 original size:16 final size:16
Alignment explanation
Indices: 1571503--1571543 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1571493 TGAAATTTAA
* **
1571503 ATATCTTTTTATTTTT
1 ATATATTTTTATAATT
1571519 ATATATTTTTATAATT
1 ATATATTTTTATAATT
1571535 ATATATTTT
1 ATATATTTT
1571544 AGAATTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
ATATATTTTTATAATT
Found at i:1571621 original size:58 final size:58
Alignment explanation
Indices: 1571514--1571629 Score: 135
Period size: 58 Copynumber: 2.0 Consensus size: 58
1571504 TATCTTTTTA
* *
1571514 TTTTTATATATTTTTATAATTATATATTTTAGAATTTTACAAAAAAATATTTATAAAC
1 TTTTTAAATATTTTTATAATTATATATTTTAGAATTTTACAAAAAAATATATATAAAC
* * * * *
1571572 TTTTTAAATTTTTTTATATATTATATTTTTTA-CATTTTAATCAATAATATATATATAA
1 TTTTTAAATATTTTTATA-ATTATATATTTTAGAATTTT-A-CAAAAAAATATATATAA
1571630 TAATAATAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
58 21 0.44
59 13 0.27
60 14 0.29
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (58 bp):
TTTTTAAATATTTTTATAATTATATATTTTAGAATTTTACAAAAAAATATATATAAAC
Found at i:1572422 original size:33 final size:33
Alignment explanation
Indices: 1572380--1572452 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
1572370 TCCTTGACTG
* *
1572380 TCGAAATTTATGGAATTAGTCCCTATTTCATAA
1 TCGAAATTTATGGAAGTAGTCCCTATTTCAAAA
*
1572413 TCGAAATTTATGGAAGTGGTCCCTATTTCAAAA
1 TCGAAATTTATGGAAGTAGTCCCTATTTCAAAA
1572446 TCGAAAT
1 TCGAAAT
1572453 ACACCTACTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (33 bp):
TCGAAATTTATGGAAGTAGTCCCTATTTCAAAA
Found at i:1575774 original size:21 final size:20
Alignment explanation
Indices: 1575742--1575797 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
1575732 CACATCAACA
1575742 TTTAATTAATTTTAAAAATAT
1 TTTAATT-ATTTTAAAAATAT
* * *
1575763 TTTTATATATTTTTAAATTAT
1 TTTAAT-TATTTTAAAAATAT
1575784 TTTAATTATTTTAA
1 TTTAATTATTTTAA
1575798 TTCTTAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 7 0.24
21 21 0.72
22 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAATTATTTTAAAAATAT
Found at i:1575940 original size:23 final size:22
Alignment explanation
Indices: 1575904--1575953 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1575894 GGTAATTTCA
*
1575904 TAAAAAAACGTAAATTTAAA-GAT
1 TAAAAAAAAGTAAA--TAAATGAT
*
1575927 TAAAAAAAATTAAATAAATGAT
1 TAAAAAAAAGTAAATAAATGAT
1575949 TAAAA
1 TAAAA
1575954 TGATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 8 0.33
23 12 0.50
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (22 bp):
TAAAAAAAAGTAAATAAATGAT
Found at i:1576235 original size:22 final size:21
Alignment explanation
Indices: 1576194--1576248 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
1576184 CCTATATTTA
* *
1576194 AATTTTATGTTTTAAATAATTT
1 AATTATATGTTATAAATAA-TT
* *
1576216 TATTATATGTTATAATTAATT
1 AATTATATGTTATAAATAATT
1576237 AATTATAT-TTAT
1 AATTATATGTTAT
1576249 TTTTTATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 9 0.32
22 15 0.54
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
AATTATATGTTATAAATAATT
Found at i:1579893 original size:17 final size:17
Alignment explanation
Indices: 1579871--1579909 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1579861 ACAAAATAAA
*
1579871 AAAAATTATATAAATTC
1 AAAAATTAGATAAATTC
*
1579888 AAAAATTAGCTAAATTC
1 AAAAATTAGATAAATTC
1579905 AAAAA
1 AAAAA
1579910 AAATAAGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAAATTAGATAAATTC
Found at i:1580197 original size:2 final size:2
Alignment explanation
Indices: 1580192--1580216 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1580182 AAAAAAAAAA
1580192 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 A
1580217 ATTGTAGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1581167 original size:14 final size:15
Alignment explanation
Indices: 1581138--1581172 Score: 54
Period size: 14 Copynumber: 2.3 Consensus size: 15
1581128 GACACATTAT
1581138 AATTTTATAAAATTTC
1 AATTTTAT-AAATTTC
1581154 AATTTTAT-AATTTC
1 AATTTTATAAATTTC
1581168 AATTT
1 AATTT
1581173 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
16 8 0.42
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTTATAAATTTC
Done.