Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 184 of 208
Found at i:57651903 original size:14 final size:14
Alignment explanation
Indices: 57651874--57651913 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
57651864 CCTTAAGCCT
57651874 TAAACGCATAAACTA
1 TAAAC-CATAAACTA
*
57651889 TAAACCATAATCTA
1 TAAACCATAAACTA
*
57651903 TAAACCTTAAA
1 TAAACCATAAA
57651914 ATAGTAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.25
Consensus pattern (14 bp):
TAAACCATAAACTA
Found at i:57651951 original size:14 final size:14
Alignment explanation
Indices: 57651933--57651975 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
57651923 CCTAAACTTT
57651933 AACCCTAAACCATA
1 AACCCTAAACCATA
* * *
57651947 TACCCTTAACCCTA
1 AACCCTAAACCATA
*
57651961 AACCCTAAACAATA
1 AACCCTAAACCATA
57651975 A
1 A
57651976 TAATAATTAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:57652445 original size:113 final size:112
Alignment explanation
Indices: 57652240--57652491 Score: 380
Period size: 113 Copynumber: 2.2 Consensus size: 112
57652230 CCGAGCATTA
*
57652240 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCATACTCTAGCGACGCTTTTTAAAAAACGCCACT
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCATACTCTAGCGACGCTTTTTAAAAAACGCCACT
* *
57652305 AAAGCCCCTAAAACTCAAAAAATGACGTCGTTGGGCTTAGGTTTTTT
66 AAAGCCCCAAAAACTCAAAAAACGACGTCGTTGGGCTTAGGTTTTTT
* * *
57652352 GCGGCACTTTTTCAAAAACGCCGCTAAAGCCCCATGCAT-TAGCGACGCTTTTTATAAAACGCCA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAG-CCCATAC-TCTAGCGACGCTTTTTAAAAAACGCCA
* *
57652416 CTAAAGCCCCAAAAACTCAGAAAACGACGTCGTTGTGCTTAGGTTTTTT
64 CTAAAGCCCCAAAAACTCAAAAAACGACGTCGTTGGGCTTAGGTTTTTT
* * *
57652465 GTGGCGCTTTTTGAAAAACGCTGCTAA
1 GCGGCGCTTTTTCAAAAACGCCGCTAA
57652492 TGCTCATTTT
Statistics
Matches: 126, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
112 27 0.21
113 98 0.78
114 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (112 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCATACTCTAGCGACGCTTTTTAAAAAACGCCACT
AAAGCCCCAAAAACTCAAAAAACGACGTCGTTGGGCTTAGGTTTTTT
Found at i:57653771 original size:17 final size:17
Alignment explanation
Indices: 57653751--57653810 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
57653741 ATTTTTATTG
*
57653751 TTCATTTTTTTTAAAAT
1 TTCATTTTATTTAAAAT
57653768 TTCAGTTTTATTT--AAT
1 TTCA-TTTTATTTAAAAT
* * *
57653784 TTTAGTTTCTTTAAAATT
1 TTCATTTTATTTAAAA-T
57653802 TTCATTTTA
1 TTCATTTTA
57653811 AAATTAGCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 6 0.19
18 14 0.44
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (17 bp):
TTCATTTTATTTAAAAT
Found at i:57657927 original size:30 final size:30
Alignment explanation
Indices: 57657891--57657957 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
57657881 TTCAATTTTT
57657891 TTTGTTAAATTTTTCCTATTTATTATGGTA
1 TTTGTTAAATTTTTCCTATTTATTATGGTA
*
57657921 TTTGTTAAATTTTTCCTCTTTATTATGGTA
1 TTTGTTAAATTTTTCCTATTTATTATGGTA
57657951 TTATGTT
1 TT-TGTT
57657958 CAACTTGAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.61
Consensus pattern (30 bp):
TTTGTTAAATTTTTCCTATTTATTATGGTA
Found at i:57660222 original size:17 final size:16
Alignment explanation
Indices: 57660200--57660242 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
57660190 AGTTTTAAAA
57660200 AAATAATAAATAATTTT
1 AAATAATAAA-AATTTT
57660217 AAATAATTTAAAAATTTT
1 AAATAA--TAAAAATTTT
57660235 AAA-AATAA
1 AAATAATAA
57660243 GTTATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.12
17 8 0.33
18 9 0.38
19 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAATAAAAATTTT
Found at i:57660240 original size:9 final size:10
Alignment explanation
Indices: 57660206--57660237 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
57660196 AAAAAAATAA
57660206 TAAATAATTT
1 TAAATAATTT
57660216 TAAATAA-TT
1 TAAATAATTT
57660225 TAAA-AATTT
1 TAAATAATTT
57660234 TAAA
1 TAAA
57660238 AATAAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.10
9 12 0.57
10 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAAATAATTT
Found at i:57662547 original size:23 final size:23
Alignment explanation
Indices: 57662520--57662565 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
57662510 TAAATTTTAA
*
57662520 GTGAAGGTATT-TATATATTATAT
1 GTGAAAGTATTATAT-TATTATAT
*
57662543 GTGAAATTATTATATTATTATAT
1 GTGAAAGTATTATATTATTATAT
57662566 TATATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (23 bp):
GTGAAAGTATTATATTATTATAT
Found at i:57663029 original size:21 final size:21
Alignment explanation
Indices: 57663003--57663046 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
57662993 TTTGAGTTTG
57663003 GATGAAATTTGAATAGAAATA
1 GATGAAATTTGAATAGAAATA
57663024 GATGAAATTTGAATAGAAATA
1 GATGAAATTTGAATAGAAATA
57663045 GA
1 GA
57663047 GTGTGAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.27
Consensus pattern (21 bp):
GATGAAATTTGAATAGAAATA
Found at i:57663347 original size:21 final size:21
Alignment explanation
Indices: 57663322--57663363 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
57663312 TGTGTTTGGT
57663322 AAATGAAATGTGAGGTAAGTA
1 AAATGAAATGTGAGGTAAGTA
57663343 AAATGAAATGTGAGGTAAGTA
1 AAATGAAATGTGAGGTAAGTA
57663364 TTATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.24
Consensus pattern (21 bp):
AAATGAAATGTGAGGTAAGTA
Found at i:57663370 original size:3 final size:3
Alignment explanation
Indices: 57663362--57663388 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
57663352 GTGAGGTAAG
57663362 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
57663389 GAGTGAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:57665154 original size:19 final size:20
Alignment explanation
Indices: 57665130--57665172 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
57665120 GTCTAAAAAG
57665130 AAGCAGAAATTTGGCCGT-C
1 AAGCAGAAATTTGGCCGTCC
57665149 AAGCAGAAATTTGGCCGTCC
1 AAGCAGAAATTTGGCCGTCC
57665169 AAGC
1 AAGC
57665173 CATCTTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.19
Consensus pattern (20 bp):
AAGCAGAAATTTGGCCGTCC
Found at i:57666062 original size:11 final size:12
Alignment explanation
Indices: 57666035--57666067 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
57666025 TATTTATAAA
57666035 ATAGAAAAATGT
1 ATAGAAAAATGT
57666047 ATAGAAAAAT-T
1 ATAGAAAAATGT
*
57666058 CTAGAAAAAT
1 ATAGAAAAAT
57666068 AAAATCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (12 bp):
ATAGAAAAATGT
Found at i:57672295 original size:15 final size:14
Alignment explanation
Indices: 57672275--57672304 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
57672265 ATAACCTTCT
57672275 AAATATTTATTATTA
1 AAATATTTA-TATTA
57672290 AAATATTTATATTA
1 AAATATTTATATTA
57672304 A
1 A
57672305 TCAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTTATATTA
Found at i:57673707 original size:57 final size:58
Alignment explanation
Indices: 57673636--57673748 Score: 142
Period size: 57 Copynumber: 2.0 Consensus size: 58
57673626 TAAATTGTTT
* *
57673636 AGGGTTGTCGATTTTGGG-ATTTTGGGTTTTGGGTGGTTTAA-TTTGGGGATTTTGGGTA
1 AGGGTTGTCGATTTTGGGAATTTT-GGTTTAGGGT-GTTTAATTTTGGAGATTTTGGGTA
* * *
57673694 AGGGTT-TTGATTTTGGGAATTTTTGTTTAGGGTTTTTAATTTTGGAGATTTTGGG
1 AGGGTTGTCGATTTTGGGAATTTTGGTTTAGGGTGTTTAATTTTGGAGATTTTGGG
57673749 GATTTCTCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
56 5 0.10
57 32 0.67
58 11 0.23
ACGTcount: A:0.14, C:0.01, G:0.35, T:0.50
Consensus pattern (58 bp):
AGGGTTGTCGATTTTGGGAATTTTGGTTTAGGGTGTTTAATTTTGGAGATTTTGGGTA
Found at i:57673730 original size:29 final size:28
Alignment explanation
Indices: 57673632--57673747 Score: 99
Period size: 29 Copynumber: 4.0 Consensus size: 28
57673622 ACCATAAATT
* *
57673632 GTTTAGGGTTGTCGATTTTGGGATTTTGG
1 GTTTAGGGTTTTTGATTTTGGGATTTT-G
* * * *
57673661 GTTTTGGGTGGTTTAATTTGGGGATTTTG
1 GTTTAGGGT-TTTTGATTTTGGGATTTTG
* * *
57673690 GGTAAGGG-TTTTGATTTTGGGAATTTTT
1 GTTTAGGGTTTTTGATTTTGGG-ATTTTG
*
57673718 GTTTAGGGTTTTTAATTTTGGAGATTTTG
1 GTTTAGGGTTTTTGATTTTGG-GATTTTG
57673747 G
1 G
57673748 GGATTTCTCA
Statistics
Matches: 66, Mismatches: 17, Indels: 8
0.73 0.19 0.09
Matches are distributed among these distances:
27 10 0.15
28 11 0.17
29 31 0.47
30 14 0.21
ACGTcount: A:0.14, C:0.01, G:0.34, T:0.51
Consensus pattern (28 bp):
GTTTAGGGTTTTTGATTTTGGGATTTTG
Found at i:57678010 original size:22 final size:22
Alignment explanation
Indices: 57677982--57678024 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
57677972 GCAACTCGAG
57677982 ATAACTTAATTTGTGGTTTAAT
1 ATAACTTAATTTGTGGTTTAAT
57678004 ATAACTTAATTTGTGGTTTAA
1 ATAACTTAATTTGTGGTTTAA
57678025 CCTCATATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (22 bp):
ATAACTTAATTTGTGGTTTAAT
Found at i:57689788 original size:3 final size:3
Alignment explanation
Indices: 57689780--57689814 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
57689770 TTTAATTGAT
* *
57689780 ATA ATA ATA ATA ATT ATA ATA ATA ATA ATG ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
57689815 TTTAGTTCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:57689797 original size:15 final size:15
Alignment explanation
Indices: 57689779--57689814 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
57689769 TTTTAATTGA
57689779 TATAATAATAATAAT
1 TATAATAATAATAAT
57689794 TATAATAATAATAAT
1 TATAATAATAATAAT
*
57689809 GATAAT
1 TATAAT
57689815 TTTAGTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
TATAATAATAATAAT
Found at i:57691245 original size:26 final size:28
Alignment explanation
Indices: 57691207--57691259 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
57691197 GGTAATTTTG
57691207 TTTCATTTGCTTAATCCATGAC-ATGCT
1 TTTCATTTGCTTAATCCATGACTATGCT
* *
57691234 TTTCA-TTGCTTAGTTCATGACTATGC
1 TTTCATTTGCTTAATCCATGACTATGC
57691260 AATGATTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (28 bp):
TTTCATTTGCTTAATCCATGACTATGCT
Found at i:57697211 original size:15 final size:14
Alignment explanation
Indices: 57697191--57697220 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
57697181 ATTCTTCTCT
57697191 AAATATTTATTATTA
1 AAATATTTA-TATTA
57697206 AAATATTTATATTA
1 AAATATTTATATTA
57697220 A
1 A
57697221 TCAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTTATATTA
Found at i:57700073 original size:16 final size:16
Alignment explanation
Indices: 57700052--57700091 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
57700042 TAATAAATAT
57700052 ATTTTTAATAATTTTA
1 ATTTTTAATAATTTTA
*
57700068 ATTTTTTATAATTTTA
1 ATTTTTAATAATTTTA
57700084 ATTTTTAA
1 ATTTTTAA
57700092 AAAATAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTTAATAATTTTA
Found at i:57704866 original size:3 final size:3
Alignment explanation
Indices: 57704860--57704885 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
57704850 ATTATTATCG
57704860 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
57704886 TTACAATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:57710172 original size:25 final size:25
Alignment explanation
Indices: 57710144--57710199 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
57710134 TTAGGATTTG
* *
57710144 TTAAATTAGTGTCAT-TATACATCTT
1 TTAAATTAATGTCATCT-TACATCTA
*
57710169 TTAAATTAATGTTATCTTACATCTA
1 TTAAATTAATGTCATCTTACATCTA
57710194 TTAAAT
1 TTAAAT
57710200 ATTTAACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.48
Consensus pattern (25 bp):
TTAAATTAATGTCATCTTACATCTA
Found at i:57714942 original size:9 final size:9
Alignment explanation
Indices: 57714928--57714959 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
57714918 GGTTTCGAAT
57714928 TCGAATAAC
1 TCGAATAAC
57714937 TCGAATAAC
1 TCGAATAAC
*
57714946 TCGAATAAT
1 TCGAATAAC
57714955 TCGAA
1 TCGAA
57714960 CATCAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (9 bp):
TCGAATAAC
Found at i:57715144 original size:30 final size:31
Alignment explanation
Indices: 57715110--57715169 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
57715100 AAACCTTTTA
*
57715110 TTTTCCCCCAAAAGTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
57715140 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
57715170 TCACACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.02, T:0.38
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:57718060 original size:14 final size:14
Alignment explanation
Indices: 57718041--57718067 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57718031 TCAACCTTTG
57718041 TTCTTTTTTTAATC
1 TTCTTTTTTTAATC
57718055 TTCTTTTTTTAAT
1 TTCTTTTTTTAAT
57718068 ATATTTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCTTTTTTTAATC
Found at i:57723068 original size:2 final size:2
Alignment explanation
Indices: 57723061--57723102 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
57723051 TTCTTCTCTA
* *
57723061 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57723103 GTACTTCCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57723083 original size:14 final size:14
Alignment explanation
Indices: 57723064--57723102 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
57723054 TTCTCTAATA
57723064 TATATATATATATG
1 TATATATATATATG
57723078 TATATATATATATG
1 TATATATATATATG
57723092 TATATATATAT
1 TATATATATAT
57723103 GTACTTCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
TATATATATATATG
Found at i:57730415 original size:20 final size:21
Alignment explanation
Indices: 57730375--57730416 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
57730365 AAACAGTTTT
57730375 TTAAATATTATAATATACAAA
1 TTAAATATTATAATATACAAA
*
57730396 TTAAATTTTATAAT-TACAAA
1 TTAAATATTATAATATACAAA
57730416 T
1 T
57730417 GCTTTATACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAATATTATAATATACAAA
Found at i:57731815 original size:21 final size:20
Alignment explanation
Indices: 57731789--57731831 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
57731779 CTCCAATCTC
*
57731789 AAACACATAAACAGAGTACTT
1 AAACACAGAAACAGAG-ACTT
*
57731810 AAACACAGATACAGAGACTT
1 AAACACAGAAACAGAGACTT
57731830 AA
1 AA
57731832 TTATTGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.19, G:0.12, T:0.16
Consensus pattern (20 bp):
AAACACAGAAACAGAGACTT
Found at i:57734575 original size:17 final size:17
Alignment explanation
Indices: 57734553--57734589 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
57734543 GGTGTTCTCA
57734553 AAAACATTTGTTTGCGT
1 AAAACATTTGTTTGCGT
*
57734570 AAAACATTTGTTTTCGT
1 AAAACATTTGTTTGCGT
57734587 AAA
1 AAA
57734590 TTGTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.41
Consensus pattern (17 bp):
AAAACATTTGTTTGCGT
Found at i:57736421 original size:15 final size:15
Alignment explanation
Indices: 57736396--57736430 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
57736386 GGCTCTATTT
*
57736396 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
57736410 TAATTAATATTAAGA
1 TAATTAATATTAAGA
57736425 TAATTA
1 TAATTA
57736431 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:57737243 original size:21 final size:20
Alignment explanation
Indices: 57737196--57737243 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
57737186 CTCAACTCTA
57737196 TTTTTAATTTCTCAAATTTT
1 TTTTTAATTTCTCAAATTTT
*
57737216 TTATTTAATATTCT-TAATTTT
1 TT-TTTAAT-TTCTCAAATTTT
57737237 GTTTTTA
1 -TTTTTA
57737244 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 16 0.67
22 6 0.25
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTAATTTCTCAAATTTT
Found at i:57743282 original size:14 final size:13
Alignment explanation
Indices: 57743262--57743294 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
57743252 CCTAAAGCAT
57743262 AAAAAAAACAAAA
1 AAAAAAAACAAAA
57743275 ACAAAAAAACAAAA
1 A-AAAAAAACAAAA
57743289 AAAAAA
1 AAAAAA
57743295 GAAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:57746952 original size:12 final size:12
Alignment explanation
Indices: 57746935--57746966 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
57746925 CGTCTCGCCC
57746935 TATTAATTTTTA
1 TATTAATTTTTA
57746947 TATTAA-TTTTA
1 TATTAATTTTTA
57746958 TA-TAATTTT
1 TATTAATTTT
57746967 AAAAAGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 10 0.53
12 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTAATTTTTA
Found at i:57746965 original size:10 final size:11
Alignment explanation
Indices: 57746935--57746967 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
57746925 CGTCTCGCCC
57746935 TATTAATTTTTA
1 TATTAA-TTTTA
57746947 TATTAATTTTA
1 TATTAATTTTA
57746958 TA-TAATTTTA
1 TATTAATTTTA
57746968 AAAAGATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 7 0.33
12 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTAATTTTA
Found at i:57747123 original size:30 final size:30
Alignment explanation
Indices: 57747089--57747151 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
57747079 ACTTAACAAG
57747089 CAAATGT-TTCTAAAATAATAACAAAATTAA
1 CAAATGTCTT-TAAAATAATAACAAAATTAA
57747119 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTTTAAAATAATAACAAAATTAA
57747149 CAA
1 CAA
57747152 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAACAAAATTAA
Found at i:57749006 original size:31 final size:31
Alignment explanation
Indices: 57748968--57749029 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
57748958 CGTGAGATTG
57748968 AGCTATACTTGATACAGGGGAATTGTAGAGT
1 AGCTATACTTGATACAGGGGAATTGTAGAGT
57748999 AGCTATACTTGATACAGGGGAATTGTAGAGT
1 AGCTATACTTGATACAGGGGAATTGTAGAGT
57749030 CGTTGCTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (31 bp):
AGCTATACTTGATACAGGGGAATTGTAGAGT
Found at i:57758108 original size:21 final size:20
Alignment explanation
Indices: 57758064--57758113 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
57758054 GTTTAAAATT
* **
57758064 TGTTCAAAGTATTTTCTGAG
1 TGTTCAAAGTATTCTCAAAG
57758084 TGTTCAAAGTGATTCTCAAAG
1 TGTTCAAAGT-ATTCTCAAAG
57758105 TGTTTCAAA
1 TG-TTCAAA
57758114 ATTTTGACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.40
21 9 0.36
22 6 0.24
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (20 bp):
TGTTCAAAGTATTCTCAAAG
Found at i:57758166 original size:18 final size:17
Alignment explanation
Indices: 57758134--57758169 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
57758124 TAAACTTCAT
57758134 TAATTTTTATTAAAAAA
1 TAATTTTTATTAAAAAA
*
57758151 TAATTTTTATTCAAAAA
1 TAATTTTTATTAAAAAA
57758168 TA
1 TA
57758170 TTATATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTTTTATTAAAAAA
Found at i:57758178 original size:19 final size:17
Alignment explanation
Indices: 57758134--57758181 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
57758124 TAAACTTCAT
*
57758134 TAATTTTTATTAAAAAA
1 TAATATTTATTAAAAAA
*
57758151 TAATTTTTATTCAAAAATA
1 TAATATTTATT-AAAAA-A
*
57758170 TTATATTTATTA
1 TAATATTTATTA
57758182 TATCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 11 0.41
18 6 0.22
19 10 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATATTTATTAAAAAA
Found at i:57762178 original size:18 final size:18
Alignment explanation
Indices: 57762155--57762209 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
57762145 ACTAAGAAAT
57762155 CATGAAGCACCTTGTCTA
1 CATGAAGCACCTTGTCTA
57762173 CATGAAGCACCTTGTCTA
1 CATGAAGCACCTTGTCTA
57762191 CATGAAGCACCTTGTCTA
1 CATGAAGCACCTTGTCTA
57762209 C
1 C
57762210 CTGTTCCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (18 bp):
CATGAAGCACCTTGTCTA
Found at i:57763405 original size:29 final size:30
Alignment explanation
Indices: 57763373--57763430 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
57763363 TTCTAATATG
*
57763373 CAATATTATACATAAAATTTT-ATTTTATA
1 CAATATTATAAATAAAATTTTGATTTTATA
*
57763402 CAATTTTATAAATAAAATTTTGATTTTAT
1 CAATATTATAAATAAAATTTTGATTTTAT
57763431 TTAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (30 bp):
CAATATTATAAATAAAATTTTGATTTTATA
Found at i:57769835 original size:22 final size:22
Alignment explanation
Indices: 57769791--57769843 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
57769781 AGAACAATAG
*
57769791 GCACCAAAGTGCAAACCACTAA
1 GCACCAAAGTGCAAAACACTAA
* *
57769813 GCACCAAAGTGCAAAATAGTAA
1 GCACCAAAGTGCAAAACACTAA
*
57769835 GCGCCAAAG
1 GCACCAAAG
57769844 CGGGAAACGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.26, G:0.19, T:0.09
Consensus pattern (22 bp):
GCACCAAAGTGCAAAACACTAA
Found at i:57770792 original size:32 final size:32
Alignment explanation
Indices: 57770756--57770820 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
57770746 TTACATTTTA
57770756 CTTAGTCAATTCATCATACCAATATACTCAAC
1 CTTAGTCAATTCATCATACCAATATACTCAAC
57770788 CTTAGTCAATTCATCATACCAATATACTCAAC
1 CTTAGTCAATTCATCATACCAATATACTCAAC
57770820 C
1 C
57770821 ATTATCACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (32 bp):
CTTAGTCAATTCATCATACCAATATACTCAAC
Found at i:57776797 original size:2 final size:2
Alignment explanation
Indices: 57776790--57776818 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57776780 GACACTTATC
57776790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57776819 AAATGACCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57784653 original size:43 final size:43
Alignment explanation
Indices: 57784520--57784659 Score: 131
Period size: 43 Copynumber: 3.3 Consensus size: 43
57784510 ATATAACTAT
57784520 TCAAGTGATATTACTTGAATAGTTATAATTCTTTGTTAAAAAA
1 TCAAGTGATATTACTTGAATAGTTATAATTCTTTGTTAAAAAA
* ** * ** * ** ** *
57784563 TCAAGTGATATAACTCTTCATATTTA-ACAAAC-ATAATAACTAT
1 TCAAGTGATATTACT-TGAATAGTTATA-ATTCTTTGTTAAAAAA
*
57784606 TCAAGTGATATTGCTTGAATAGTTATAATTCTTTGTTAAAAAA
1 TCAAGTGATATTACTTGAATAGTTATAATTCTTTGTTAAAAAA
57784649 TCAAGTGATAT
1 TCAAGTGATAT
57784660 AACTCTTCAT
Statistics
Matches: 68, Mismatches: 25, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
42 9 0.13
43 50 0.74
44 9 0.13
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (43 bp):
TCAAGTGATATTACTTGAATAGTTATAATTCTTTGTTAAAAAA
Found at i:57784657 original size:86 final size:86
Alignment explanation
Indices: 57784512--57784684 Score: 337
Period size: 86 Copynumber: 2.0 Consensus size: 86
57784502 ATAAATAAAT
57784512 ATAACTATTCAAGTGATATTACTTGAATAGTTATAATTCTTTGTTAAAAAATCAAGTGATATAAC
1 ATAACTATTCAAGTGATATTACTTGAATAGTTATAATTCTTTGTTAAAAAATCAAGTGATATAAC
57784577 TCTTCATATTTAACAAACATA
66 TCTTCATATTTAACAAACATA
*
57784598 ATAACTATTCAAGTGATATTGCTTGAATAGTTATAATTCTTTGTTAAAAAATCAAGTGATATAAC
1 ATAACTATTCAAGTGATATTACTTGAATAGTTATAATTCTTTGTTAAAAAATCAAGTGATATAAC
57784663 TCTTCATATTTAACAAACATA
66 TCTTCATATTTAACAAACATA
57784684 A
1 A
57784685 CTCATTATTA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (86 bp):
ATAACTATTCAAGTGATATTACTTGAATAGTTATAATTCTTTGTTAAAAAATCAAGTGATATAAC
TCTTCATATTTAACAAACATA
Found at i:57786117 original size:42 final size:42
Alignment explanation
Indices: 57786058--57786141 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
57786048 ATTACTGAGT
*
57786058 TGAAAACTGTAGTGTCGTTCTGCAGCCCTTTTTGTTTCAGGC
1 TGAAAACTGTAGTGTCGTTCTGCAGCCCTTTTTGTTCCAGGC
*
57786100 TGAAAACTGTAGTGTCGTTCTGCAGCCTTTTTTGTTCCAGGC
1 TGAAAACTGTAGTGTCGTTCTGCAGCCCTTTTTGTTCCAGGC
57786142 AGGGCAGGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (42 bp):
TGAAAACTGTAGTGTCGTTCTGCAGCCCTTTTTGTTCCAGGC
Found at i:57791254 original size:5 final size:5
Alignment explanation
Indices: 57791244--57791325 Score: 110
Period size: 5 Copynumber: 16.0 Consensus size: 5
57791234 CAACTGGGGG
57791244 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA
* * * *
57791294 TATGGGA TATGG TATAA TAAGA TAAGA TATGA
1 TAT--GA TATGA TATGA TATGA TATGA TATGA
57791326 AACATGCTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
5 64 0.93
7 5 0.07
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (5 bp):
TATGA
Found at i:57791763 original size:38 final size:38
Alignment explanation
Indices: 57791688--57791783 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 38
57791678 AATAAACCAT
* **
57791688 AGTTATAAGGTAAATTTGCTATAATGCATTCTGCTGCA
1 AGTTTTAAGGTAAATTTGCTATAATGCATTCCACTGCA
* *
57791726 AGTTTTAAGGTCAATTTGCTATAATG-TTGTCCACTGCA
1 AGTTTTAAGGTAAATTTGCTATAATGCAT-TCCACTGCA
**
57791764 AGTTTTATTG-AAATTTGCTA
1 AGTTTTAAGGTAAATTTGCTA
57791784 AGATGTTTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 10 0.20
38 39 0.80
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (38 bp):
AGTTTTAAGGTAAATTTGCTATAATGCATTCCACTGCA
Found at i:57792300 original size:21 final size:20
Alignment explanation
Indices: 57792271--57792312 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
57792261 ATATATTTTT
57792271 AATAATTATAAATTTTAAAA
1 AATAATTATAAATTTTAAAA
*
57792291 AATAAGTTATATATTTTTAAAA
1 AATAA-TTATA-AATTTTAAAA
57792313 CCTTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AATAATTATAAATTTTAAAA
Found at i:57795381 original size:51 final size:51
Alignment explanation
Indices: 57795280--57795383 Score: 124
Period size: 51 Copynumber: 2.0 Consensus size: 51
57795270 TCATTTTAAT
* *
57795280 TGATTCAATGGGTTTTGTTGATTCAATTAGAATCATTTGATTTTTAATTTGC
1 TGATTCAATGGGTTTTATTGATTCAATTAGAATCACTTGA-TTTTAATTTGC
*
57795332 TGATTCAATGGG-TTTATTGATTCAATGAGTAGTATCACTTGA-TTT-ATTTGC
1 TGATTCAATGGGTTTTATTGATTCAAT---TAGAATCACTTGATTTTAATTTGC
57795383 T
1 T
57795384 TAGTGATTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
51 20 0.43
52 15 0.33
54 11 0.24
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.48
Consensus pattern (51 bp):
TGATTCAATGGGTTTTATTGATTCAATTAGAATCACTTGATTTTAATTTGC
Found at i:57799595 original size:9 final size:9
Alignment explanation
Indices: 57799573--57799615 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
57799563 CATTTCATTA
*
57799573 ATCCAACTT
1 ATCCAAGTT
*
57799582 CTCCAAGTT
1 ATCCAAGTT
57799591 ATCCAAGTT
1 ATCCAAGTT
*
57799600 ATCCAACTT
1 ATCCAAGTT
57799609 ATCCAAG
1 ATCCAAG
57799616 ATGCTGGAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (9 bp):
ATCCAAGTT
Found at i:57800423 original size:14 final size:14
Alignment explanation
Indices: 57800404--57800433 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
57800394 TTTATTATAT
57800404 AATTTAATCAGTTA
1 AATTTAATCAGTTA
*
57800418 AATTTAATCCGTTA
1 AATTTAATCAGTTA
57800432 AA
1 AA
57800434 ATAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (14 bp):
AATTTAATCAGTTA
Found at i:57800566 original size:7 final size:7
Alignment explanation
Indices: 57800521--57800576 Score: 53
Period size: 7 Copynumber: 7.7 Consensus size: 7
57800511 ACGTTGTGTA
57800521 TTTAATT
1 TTTAATT
57800528 TTT-ATAT
1 TTTAAT-T
57800535 TTTAATT
1 TTTAATT
57800542 TGATT-ATT
1 T--TTAATT
57800550 TTTAATT
1 TTTAATT
57800557 TTTAATTT
1 TTTAA-TT
*
57800565 TTTAAAT
1 TTTAATT
57800572 TTTAA
1 TTTAA
57800577 AATTTCATGT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
6 4 0.10
7 23 0.55
8 13 0.31
9 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (7 bp):
TTTAATT
Found at i:57800566 original size:15 final size:14
Alignment explanation
Indices: 57800521--57800575 Score: 58
Period size: 15 Copynumber: 3.8 Consensus size: 14
57800511 ACGTTGTGTA
*
57800521 TTTAATTTTTATAT
1 TTTAATTTTTATTT
57800535 TTTAATTTGATTA-TT
1 TTTAATTT--TTATTT
57800550 TTTAATTTTTAATTT
1 TTTAATTTTT-ATTT
*
57800565 TTTAAATTTTA
1 TTTAATTTTTA
57800576 AAATTTCATG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 2 0.06
14 10 0.29
15 20 0.57
16 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTAATTTTTATTT
Found at i:57801094 original size:18 final size:19
Alignment explanation
Indices: 57801063--57801100 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
57801053 TCTCTTTTTT
*
57801063 AAAAATAAATAAAAATACA
1 AAAAAGAAATAAAAATACA
57801082 AAAAAGAAA-AAAAATACA
1 AAAAAGAAATAAAAATACA
57801100 A
1 A
57801101 GAATTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.11
Consensus pattern (19 bp):
AAAAAGAAATAAAAATACA
Found at i:57806555 original size:21 final size:21
Alignment explanation
Indices: 57806531--57806573 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
57806521 TTCTTGAGAA
*
57806531 AACTTTGATGGCAAGGAAAGC
1 AACTTTGATGGAAAGGAAAGC
57806552 AACTTTGATGGAAAGGAAAGC
1 AACTTTGATGGAAAGGAAAGC
57806573 A
1 A
57806574 TTGTGTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.19
Consensus pattern (21 bp):
AACTTTGATGGAAAGGAAAGC
Found at i:57807718 original size:42 final size:42
Alignment explanation
Indices: 57807659--57807742 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
57807649 ACTGGAAAAA
*
57807659 ATGTTTGTCTGGCATTACAAGAATTTCTTTAAAGTTAATAGT
1 ATGTTTGTCTGCCATTACAAGAATTTCTTTAAAGTTAATAGT
57807701 ATGTTTGTCTGCCATTACAAGAATTTCTTTAAAGTTAATAGT
1 ATGTTTGTCTGCCATTACAAGAATTTCTTTAAAGTTAATAGT
57807743 TTGAGAGATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (42 bp):
ATGTTTGTCTGCCATTACAAGAATTTCTTTAAAGTTAATAGT
Found at i:57808533 original size:33 final size:33
Alignment explanation
Indices: 57808466--57808533 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
57808456 TCGGTCCAAC
*
57808466 TAAAATTTAATTTAAATAATACAAAATTATTTT
1 TAAAATTTAATTTAAATAATACAAAATTACTTT
*
57808499 TAAAATTTAAATTT-AATTATA-AAAATATACTTT
1 TAAAATTT-AATTTAAATAATACAAAAT-TACTTT
57808532 TA
1 TA
57808534 TTTTTTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 5 0.16
33 21 0.68
34 5 0.16
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (33 bp):
TAAAATTTAATTTAAATAATACAAAATTACTTT
Found at i:57812320 original size:34 final size:34
Alignment explanation
Indices: 57812277--57812354 Score: 138
Period size: 34 Copynumber: 2.2 Consensus size: 34
57812267 AACGTCTAGG
57812277 CCAGGTTTGGGGTGTTACAGAGCCTATAAGCTCA
1 CCAGGTTTGGGGTGTTACAGAGCCTATAAGCTCA
57812311 CCAGGTTTGGGGTGTTACAGAGCCTATAAGCTCA
1 CCAGGTTTGGGGTGTTACAGAGCCTATAAGCTCA
57812345 CTCAGTGTTT
1 C-CAG-GTTT
57812355 CTAACTTCTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 35 0.83
35 3 0.07
36 4 0.10
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (34 bp):
CCAGGTTTGGGGTGTTACAGAGCCTATAAGCTCA
Found at i:57814222 original size:16 final size:16
Alignment explanation
Indices: 57814197--57814228 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57814187 ATGTCACACC
*
57814197 CTAATTCAACTCATTG
1 CTAATACAACTCATTG
57814213 CTAATACAACTCATTG
1 CTAATACAACTCATTG
57814229 ACTTGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CTAATACAACTCATTG
Found at i:57814582 original size:16 final size:16
Alignment explanation
Indices: 57814561--57814592 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
57814551 AATTTCACAC
57814561 CCTAATACAACTCATT
1 CCTAATACAACTCATT
57814577 CCTAATACAACTCATT
1 CCTAATACAACTCATT
57814593 GACTTGTATA
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:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (16 bp):
CCTAATACAACTCATT
Found at i:57814964 original size:23 final size:23
Alignment explanation
Indices: 57814920--57814981 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
57814910 TTATATTCTT
**
57814920 GTGAAAAAAAATAATACA-TTAAA
1 GTGAAAAAAAATCTTA-ATTTAAA
57814943 GTGAAAAAAAATCTTAATTTAAA
1 GTGAAAAAAAATCTTAATTTAAA
*
57814966 --GAAAATAAA-CTTAATT
1 GTGAAAAAAAATCTTAATT
57814982 ATTTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 7 0.20
21 8 0.23
22 1 0.03
23 19 0.54
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.27
Consensus pattern (23 bp):
GTGAAAAAAAATCTTAATTTAAA
Found at i:57818274 original size:39 final size:39
Alignment explanation
Indices: 57818220--57818298 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
57818210 TATGACCCAA
57818220 AGACTCACCTTTTTATAAGTCGTCTCCTATCATAATTGC
1 AGACTCACCTTTTTATAAGTCGTCTCCTATCATAATTGC
57818259 AGACTCACCTTTTTATAAGTCGTCTCCTATCATAATTGC
1 AGACTCACCTTTTTATAAGTCGTCTCCTATCATAATTGC
57818298 A
1 A
57818299 TAATAAATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (39 bp):
AGACTCACCTTTTTATAAGTCGTCTCCTATCATAATTGC
Found at i:57823468 original size:18 final size:18
Alignment explanation
Indices: 57823445--57823510 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
57823435 TAACAAATAT
57823445 ATATTTTTTAATTTTAAA
1 ATATTTTTTAATTTTAAA
**
57823463 ATATTTTTTACATACTTTTTTA
1 ATATTTTTT--A-A-TTTTAAA
* *
57823485 ATTTTTTTTAATTTCAAA
1 ATATTTTTTAATTTTAAA
57823503 ATATTTTT
1 ATATTTTT
57823511 AAAATACTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 20 0.54
19 1 0.03
20 2 0.05
21 1 0.03
22 13 0.35
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTTTTTAATTTTAAA
Found at i:57823494 original size:40 final size:40
Alignment explanation
Indices: 57823448--57823629 Score: 267
Period size: 40 Copynumber: 4.5 Consensus size: 40
57823438 CAAATATATA
* *
57823448 TTTTTTAATTTTAAAATATTTTTTACATAC-TTTTTTAATT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA-T
*
57823488 TTTTTTAATTTCAAAATATTTTTAAAATACTTTTTTTTTAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATAC--TTTTTTTAAT
57823530 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
*
57823570 TTTTTTAATTTTAAAATATTTTAAAAATACTTTTTTTAAT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
*
57823610 TTTTTAAAATTATTAAAATA
1 TTTTT-TAATT-TTAAAATA
57823630 AAAATGGGCC
Statistics
Matches: 131, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
40 81 0.62
41 4 0.03
42 38 0.29
43 8 0.06
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (40 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAAT
Found at i:57823536 original size:82 final size:80
Alignment explanation
Indices: 57823448--57823629 Score: 267
Period size: 82 Copynumber: 2.2 Consensus size: 80
57823438 CAAATATATA
* * *
57823448 TTTTTTAATTTTAAAATATTTTTTACATAC-TTTTTTAATTTTTTTTAATTTCAAAATATTTTTA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA-TTTTTTTAATTTCAAAATATTTTAA
57823512 AAATACTTTTTTTTTAAT
65 AAATAC--TTTTTTTAAT
*
57823530 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTAAA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTCAAAATATTTTAAA
57823595 AATACTTTTTTTAAT
66 AATACTTTTTTTAAT
*
57823610 TTTTTAAAATTATTAAAATA
1 TTTTT-TAATT-TTAAAATA
57823630 AAAATGGGCC
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
80 15 0.16
81 4 0.04
82 65 0.71
83 8 0.09
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (80 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTCAAAATATTTTAAA
AATACTTTTTTTAAT
Found at i:57828241 original size:16 final size:16
Alignment explanation
Indices: 57828208--57828241 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57828198 CCAACATGTT
* *
57828208 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
57828224 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
57828240 AA
1 AA
57828242 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:57833015 original size:16 final size:16
Alignment explanation
Indices: 57832982--57833015 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57832972 GGAGATTGTT
* *
57832982 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
57832998 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
57833014 AA
1 AA
57833016 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:57836066 original size:13 final size:13
Alignment explanation
Indices: 57836048--57836072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57836038 ATTATTAAAA
57836048 TTATTAGATTTAG
1 TTATTAGATTTAG
57836061 TTATTAGATTTA
1 TTATTAGATTTA
57836073 ATTTCAAGTT
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:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATTAGATTTAG
Found at i:57841814 original size:9 final size:9
Alignment explanation
Indices: 57841792--57841833 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
57841782 CATTTCATTA
57841792 ATCCAACTT
1 ATCCAACTT
* *
57841801 CTCCAAGTT
1 ATCCAACTT
57841810 ATCCAACTT
1 ATCCAACTT
57841819 ATCCAACTT
1 ATCCAACTT
57841828 ATCCAA
1 ATCCAA
57841834 GATGCTGGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.31
Consensus pattern (9 bp):
ATCCAACTT
Found at i:57842637 original size:59 final size:59
Alignment explanation
Indices: 57842565--57842684 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
57842555 AAATCACACC
57842565 GTTGGTCATTTTAAACTAACATTATTTCTATTTTGGTCACTCTATAATTGCTCGAATTA
1 GTTGGTCATTTTAAACTAACATTATTTCTATTTTGGTCACTCTATAATTGCTCGAATTA
57842624 GTTGGTCATTTTAAACTAACATTATTTCTATTTTGGTCACTCTATAATTGCTCGAATTA
1 GTTGGTCATTTTAAACTAACATTATTTCTATTTTGGTCACTCTATAATTGCTCGAATTA
57842683 GT
1 GT
57842685 CAATGACATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (59 bp):
GTTGGTCATTTTAAACTAACATTATTTCTATTTTGGTCACTCTATAATTGCTCGAATTA
Found at i:57859341 original size:17 final size:18
Alignment explanation
Indices: 57859305--57859344 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
57859295 AATTGTAGGG
57859305 ATTAACATAGTTAATAAT
1 ATTAACATAGTTAATAAT
**
57859323 ATTAACATA-TTTCTAAT
1 ATTAACATAGTTAATAAT
57859340 ATTAA
1 ATTAA
57859345 ATAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAACATAGTTAATAAT
Found at i:57861721 original size:14 final size:14
Alignment explanation
Indices: 57861702--57861731 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
57861692 TTTATTATAT
57861702 AATTTAATCAGTTA
1 AATTTAATCAGTTA
57861716 AATTTAATCAGTTA
1 AATTTAATCAGTTA
57861730 AA
1 AA
57861732 ATAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (14 bp):
AATTTAATCAGTTA
Found at i:57861862 original size:7 final size:7
Alignment explanation
Indices: 57861817--57861872 Score: 53
Period size: 7 Copynumber: 7.7 Consensus size: 7
57861807 ACGTTGTGTA
57861817 TTTAATT
1 TTTAATT
57861824 TTT-ATAT
1 TTTAAT-T
57861831 TTTAATT
1 TTTAATT
57861838 TGATT-ATT
1 T--TTAATT
57861846 TTTAATT
1 TTTAATT
57861853 TTTAATTT
1 TTTAA-TT
*
57861861 TTTAAAT
1 TTTAATT
57861868 TTTAA
1 TTTAA
57861873 AATTTCATGT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
6 4 0.10
7 23 0.55
8 13 0.31
9 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (7 bp):
TTTAATT
Found at i:57861862 original size:15 final size:14
Alignment explanation
Indices: 57861817--57861871 Score: 58
Period size: 15 Copynumber: 3.8 Consensus size: 14
57861807 ACGTTGTGTA
*
57861817 TTTAATTTTTATAT
1 TTTAATTTTTATTT
57861831 TTTAATTTGATTA-TT
1 TTTAATTT--TTATTT
57861846 TTTAATTTTTAATTT
1 TTTAATTTTT-ATTT
*
57861861 TTTAAATTTTA
1 TTTAATTTTTA
57861872 AAATTTCATG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 2 0.06
14 10 0.29
15 20 0.57
16 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (14 bp):
TTTAATTTTTATTT
Found at i:57865948 original size:14 final size:15
Alignment explanation
Indices: 57865920--57865948 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57865910 TAACCTTCTG
57865920 AATATTTATTATTAA
1 AATATTTATTATTAA
57865935 AATATTTA-TATTAA
1 AATATTTATTATTAA
57865949 TCGAAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTTATTATTAA
Found at i:57872124 original size:50 final size:50
Alignment explanation
Indices: 57872070--57872207 Score: 136
Period size: 50 Copynumber: 2.8 Consensus size: 50
57872060 TCTCATAGAG
* *
57872070 GTGCCACTGCCATGTCCTAGACATGGTCTTACGGGGGACATTTCATCTCA
1 GTGCCACTGCCATGTCCTAGACATGGTCTTACAGGGGACATCTCATCTCA
* * * * * **
57872120 GTGCCAATGCCAAGT-CTCAGACATGATCTTACATGGGACCTCTCATCTTG
1 GTGCCACTGCCATGTCCT-AGACATGGTCTTACAGGGGACATCTCATCTCA
* * *
57872170 GTGCCAAC-ACCATGTCCCAGACATGGTCTTACATGGGA
1 GTGCC-ACTGCCATGTCCTAGACATGGTCTTACAGGGGA
57872208 TCTCATTCCC
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
49 2 0.03
50 67 0.94
51 2 0.03
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (50 bp):
GTGCCACTGCCATGTCCTAGACATGGTCTTACAGGGGACATCTCATCTCA
Found at i:57872164 original size:100 final size:100
Alignment explanation
Indices: 57872021--57872201 Score: 231
Period size: 100 Copynumber: 1.8 Consensus size: 100
57872011 TTTCTTGTAT
* * ** *
57872021 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATAGAGGTGCC-ACTGCCATGT
1 TGCCAATGCCATATCCCAGACATGATCTTACATGAGACCTCTCATAGAGGTGCCAAC-ACCATGT
*
57872085 CCTAGACATGGTCTTACGGGGGACATTTCATCTCAG
65 CCCAGACATGGTCTTACGGGGGACATTTCATCTCAG
* * ***
57872121 TGCCAATGCCA-AGTCTCAGACATGATCTTACATGGGACCTCTCATCTTGGTGCCAACACCATGT
1 TGCCAATGCCATA-TCCCAGACATGATCTTACATGAGACCTCTCATAGAGGTGCCAACACCATGT
57872185 CCCAGACATGGTCTTAC
65 CCCAGACATGGTCTTAC
57872202 ATGGGATCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
99 1 0.01
100 65 0.96
101 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (100 bp):
TGCCAATGCCATATCCCAGACATGATCTTACATGAGACCTCTCATAGAGGTGCCAACACCATGTC
CCAGACATGGTCTTACGGGGGACATTTCATCTCAG
Found at i:57873052 original size:12 final size:12
Alignment explanation
Indices: 57873035--57873062 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
57873025 AGATGGACAA
57873035 AATTTGGCTTTT
1 AATTTGGCTTTT
57873047 AATTTGGCTTTT
1 AATTTGGCTTTT
57873059 AATT
1 AATT
57873063 CATTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (12 bp):
AATTTGGCTTTT
Found at i:57873522 original size:18 final size:18
Alignment explanation
Indices: 57873499--57873544 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
57873489 TATTTCTGTG
*
57873499 TCTGTATTTGCATCTGTAT
1 TCTGTATATGCATCTG-AT
57873518 T-TGTATATGCATCTGAT
1 TCTGTATATGCATCTGAT
57873535 TCTGTATATG
1 TCTGTATATG
57873545 AGATTGCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 21 0.84
19 1 0.04
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (18 bp):
TCTGTATATGCATCTGAT
Found at i:57878045 original size:251 final size:250
Alignment explanation
Indices: 57877603--57878092 Score: 953
Period size: 251 Copynumber: 2.0 Consensus size: 250
57877593 TTCCAAAATC
57877603 TATAAAACAAAGAGTAAACATGCACACAGTAAGCTTCCACAGCTAATAAGTCATAAACGAACATT
1 TATAAAACAAAGAGTAAACATGCACACAGTAAGCTTCCACAGCTAATAAGTCATAAACGAACATT
57877668 AATCATATGAACATTAACACTAAATCAAACAGCCAAGTCAATCCAAACCTTAGTTAAATATACAT
66 AATCATATGAACATTAACACTAAATCAAACAGCCAAGTCAATCCAAACCTTAGTTAAATATACAT
57877733 ATATCACACTCACAAGTTTATATGTTACCAAAAATAAATTAGCAGTTATCATCATATAACTAAAT
131 ATATCACACTCACAAGTTTATATGTTACCAAAAATAAATTAGCAGTTATCATCATATAACTAAAT
57877798 GCACAAATACTCATAAACATATATAATTATCACTTTTAAATATTTAACTAAGGTT
196 GCACAAATACTCATAAACATATATAATTATCACTTTTAAATATTTAACTAAGGTT
* *
57877853 TATAAAACAAAGAGTAAACATGCACATAGTAAGCTTCCACAGCTTAGTAAGTCATAAACGAACAT
1 TATAAAACAAAGAGTAAACATGCACACAGTAAGCTTCCACAGC-TAATAAGTCATAAACGAACAT
57877918 TAATCATATGAACATTAACACTAAATCAAACAGCCAAGTCAATCCAAACCTTAGTTAAATATACA
65 TAATCATATGAACATTAACACTAAATCAAACAGCCAAGTCAATCCAAACCTTAGTTAAATATACA
57877983 TATATCACACTCACAAGTTTATATGTTACCAAAAATAAATTAGCAGTTATCATCATATAACTAAA
130 TATATCACACTCACAAGTTTATATGTTACCAAAAATAAATTAGCAGTTATCATCATATAACTAAA
57878048 TGCACAAATACTCATAAACATATATAATTATCACTTTTAAATATT
195 TGCACAAATACTCATAAACATATATAATTATCACTTTTAAATATT
57878093 GCAACGATAT
Statistics
Matches: 237, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
250 42 0.18
251 195 0.82
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (250 bp):
TATAAAACAAAGAGTAAACATGCACACAGTAAGCTTCCACAGCTAATAAGTCATAAACGAACATT
AATCATATGAACATTAACACTAAATCAAACAGCCAAGTCAATCCAAACCTTAGTTAAATATACAT
ATATCACACTCACAAGTTTATATGTTACCAAAAATAAATTAGCAGTTATCATCATATAACTAAAT
GCACAAATACTCATAAACATATATAATTATCACTTTTAAATATTTAACTAAGGTT
Found at i:57878432 original size:43 final size:43
Alignment explanation
Indices: 57878363--57878486 Score: 155
Period size: 43 Copynumber: 2.9 Consensus size: 43
57878353 GGCTCGTACA
* *
57878363 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCA-AA-TATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAGT-T-G
*
57878406 ATG-CAACTGTCCCAGACATCGTCTTACACGTAAACACAAGTTG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAACACAAGTTG
* *
57878449 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACA
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACA
57878487 TATCGAAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
42 4 0.06
43 59 0.83
44 7 0.10
45 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAGTTG
Found at i:57884419 original size:30 final size:31
Alignment explanation
Indices: 57884380--57884439 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
57884370 AGAGGTGGGA
*
57884380 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
57884411 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
57884440 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:57884661 original size:9 final size:9
Alignment explanation
Indices: 57884647--57884683 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
57884637 TATAGTTTGA
57884647 TATTCGAAT
1 TATTCGAAT
57884656 TATTCGAAT
1 TATTCGAAT
* *
57884665 TATTAGAGT
1 TATTCGAAT
57884674 TATTCGAAT
1 TATTCGAAT
57884683 T
1 T
57884684 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:57889713 original size:21 final size:21
Alignment explanation
Indices: 57889687--57889728 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
57889677 AGACACCAAA
57889687 ATATAAAAATAGAAAATCAAT
1 ATATAAAAATAGAAAATCAAT
57889708 ATATAAAAATAGAAAATCAAT
1 ATATAAAAATAGAAAATCAAT
57889729 GGCAAATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
ATATAAAAATAGAAAATCAAT
Found at i:57903145 original size:22 final size:22
Alignment explanation
Indices: 57903115--57903158 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
57903105 AGAGAATGTG
57903115 GGTTCGAGTTCGCTGAAGAGCA
1 GGTTCGAGTTCGCTGAAGAGCA
*
57903137 GGTTTGAGTTCGCTGAAGAGCA
1 GGTTCGAGTTCGCTGAAGAGCA
57903159 TCATCTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.36, T:0.25
Consensus pattern (22 bp):
GGTTCGAGTTCGCTGAAGAGCA
Found at i:57906361 original size:22 final size:21
Alignment explanation
Indices: 57906336--57906388 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
57906326 GAGTTATTAT
57906336 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGTTTATGGATTAT-GG
* *
57906358 TTTAAGGGTTATGGTTTATGG
1 TTTAAGGTTTATGGATTATGG
57906379 TTTAAAGGTT
1 TTT-AAGGTT
57906389 GGGATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (21 bp):
TTTAAGGTTTATGGATTATGG
Found at i:57906451 original size:13 final size:13
Alignment explanation
Indices: 57906430--57906467 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
57906420 GGTCTAGGAT
*
57906430 TTTATGGTTTAGG
1 TTTAAGGTTTAGG
*
57906443 TTTAGGGTTTAGG
1 TTTAAGGTTTAGG
57906456 TTTAAGGTTTAG
1 TTTAAGGTTTAG
57906468 ATTAACTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (13 bp):
TTTAAGGTTTAGG
Found at i:57906505 original size:16 final size:16
Alignment explanation
Indices: 57906484--57906516 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57906474 TAGTGTTTTC
57906484 TAATTTA-TATATTAAT
1 TAATTTATTATA-TAAT
57906500 TAATTTATTATATAAT
1 TAATTTATTATATAAT
57906516 T
1 T
57906517 GTAAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTATTATATAAT
Found at i:57915385 original size:43 final size:43
Alignment explanation
Indices: 57915325--57915415 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
57915315 CTTTGAGTTC
* * *
57915325 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
* *
57915367 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATGTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
57915410 ATTACC
1 ATTACC
57915416 TTGCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:57915877 original size:42 final size:43
Alignment explanation
Indices: 57915816--57915923 Score: 157
Period size: 42 Copynumber: 2.5 Consensus size: 43
57915806 ATAAAAACGT
* *
57915816 CGCTAAAGGTCATGTTCTTTAGTGGCGTTTGTGGT-AAAA-TGC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGTTT-TGGTCAAAAGTCC
* *
57915858 CGCTAAAGGTCATGCTCTTTAGCGGCGTTTTTGTCAAAAGTCC
1 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTTGGTCAAAAGTCC
57915901 CGCTAAAGGTCATGTTCTTTAGC
1 CGCTAAAGGTCATGTTCTTTAGC
57915924 AGCATTTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
41 3 0.05
42 32 0.54
43 24 0.41
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (43 bp):
CGCTAAAGGTCATGTTCTTTAGCGGCGTTTTGGTCAAAAGTCC
Found at i:57916614 original size:18 final size:18
Alignment explanation
Indices: 57916591--57916628 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
57916581 CTCTTTACCA
57916591 CTAGGCCAATTAATCATT
1 CTAGGCCAATTAATCATT
57916609 CTAGGCCAATTAATCATT
1 CTAGGCCAATTAATCATT
57916627 CT
1 CT
57916629 TTTCATAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (18 bp):
CTAGGCCAATTAATCATT
Found at i:57918364 original size:19 final size:17
Alignment explanation
Indices: 57918327--57918360 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
57918317 GCCTTTGGTA
*
57918327 AAAGTAAAGAAAATTTC
1 AAAGTAAAAAAAATTTC
57918344 AAAGTAAAAAATAATTT
1 AAAGTAAAAAA-AATTT
57918361 TCAAGAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAGTAAAAAAAATTTC
Found at i:57929689 original size:23 final size:23
Alignment explanation
Indices: 57929662--57929737 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
57929652 AGTGTTATTG
* *
57929662 ATCAGTGGTAGCTTCAGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
57929685 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
57929708 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
57929731 ATCAGTG
1 ATCAGTG
57929738 TTGCACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:57931220 original size:18 final size:17
Alignment explanation
Indices: 57931187--57931223 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
57931177 ATGGAATGAG
*
57931187 AATAAATTTTTTAATTA
1 AATAAATTTATTAATTA
57931204 AATAAATTTAATTAATTA
1 AATAAATTT-ATTAATTA
57931222 AA
1 AA
57931224 AATTTTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATAAATTTATTAATTA
Found at i:57934813 original size:30 final size:30
Alignment explanation
Indices: 57934779--57934845 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
57934769 GTTCAATTTT
*
57934779 TTTGTTAAATTTGTCTTATTTATTATGGTA
1 TTTGTTAAATTTGTCCTATTTATTATGGTA
*
57934809 TTTGTTAAATTTTTCCTATTTATTATGGTA
1 TTTGTTAAATTTGTCCTATTTATTATGGTA
57934839 TTATGTT
1 TT-TGTT
57934846 CAACTTGAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.61
Consensus pattern (30 bp):
TTTGTTAAATTTGTCCTATTTATTATGGTA
Found at i:57936953 original size:13 final size:13
Alignment explanation
Indices: 57936935--57936959 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57936925 ATTAAAACTA
57936935 AAATTAACTAAAT
1 AAATTAACTAAAT
57936948 AAATTAACTAAA
1 AAATTAACTAAA
57936960 GAACACGGCA
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTAACTAAAT
Found at i:57938085 original size:3 final size:3
Alignment explanation
Indices: 57938077--57938107 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
57938067 ATGTTATTAA
57938077 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
57938108 GAAATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:57939432 original size:3 final size:3
Alignment explanation
Indices: 57939424--57939482 Score: 59
Period size: 3 Copynumber: 19.3 Consensus size: 3
57939414 TAATGTAGGT
* *
57939424 ATA ATA ATA ATT AT- ATA AT- ATA ATA ATA ATAA ATA CTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA
57939468 ATA CAGTA ATA ATA A
1 ATA -A-TA ATA ATA A
57939483 CAATTTAACA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
2 4 0.08
3 37 0.77
4 5 0.10
5 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:57939448 original size:16 final size:15
Alignment explanation
Indices: 57939427--57939470 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
57939417 TGTAGGTATA
*
57939427 ATAATAATTATATAAT
1 ATAATAATAATA-AAT
57939443 ATAATAATAATAAAT
1 ATAATAATAATAAAT
57939458 ACTAATAATAATA
1 A-TAATAATAATA
57939471 CAGTAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:57939463 original size:10 final size:10
Alignment explanation
Indices: 57939424--57939470 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
57939414 TAATGTAGGT
57939424 ATAATAATAA
1 ATAATAATAA
*
57939434 TTATATAATATA
1 ATA-ATAATA-A
57939446 ATAATAATAA
1 ATAATAATAA
*
57939456 ATACTAAT-A
1 ATAATAATAA
57939465 ATAATA
1 ATAATA
57939471 CAGTAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 6 0.19
10 10 0.32
11 12 0.39
12 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAATAATAA
Found at i:57939465 original size:19 final size:19
Alignment explanation
Indices: 57939423--57939470 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
57939413 ATAATGTAGG
*
57939423 TATAATAATAATTATATAA
1 TATAATAATAATTAAATAA
*
57939442 TATAATAATAA-TAAATAC
1 TATAATAATAATTAAATAA
57939460 TAATAATAATA
1 T-ATAATAATA
57939471 CAGTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
TATAATAATAATTAAATAA
Found at i:57939507 original size:20 final size:20
Alignment explanation
Indices: 57939470--57939507 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
57939460 TAATAATAAT
*
57939470 ACAGTAATAATAACAATTTA
1 ACAGTAATAATAAAAATTTA
57939490 ACAGTATATAA-AAAAATT
1 ACAGTA-ATAATAAAAATT
57939508 AAAAATAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (20 bp):
ACAGTAATAATAAAAATTTA
Found at i:57940604 original size:13 final size:14
Alignment explanation
Indices: 57940574--57940606 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
57940564 TTAAATGTTA
*
57940574 AAATAATAAAAAGT
1 AAATAATAAAAAGG
57940588 AAATAAT-AAAAGG
1 AAATAATAAAAAGG
57940601 AAATAA
1 AAATAA
57940607 AAACAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (14 bp):
AAATAATAAAAAGG
Found at i:57941344 original size:3 final size:3
Alignment explanation
Indices: 57941330--57941379 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
57941320 GTGAGGTAAG
* * *
57941330 TAT TAG TAT TAT TAT TGT CAT 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
57941378 TA
1 TA
57941380 AGATGAGTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:57941789 original size:37 final size:39
Alignment explanation
Indices: 57941739--57941830 Score: 109
Period size: 39 Copynumber: 2.4 Consensus size: 39
57941729 CGGATAGATT
* *
57941739 CGATGAGGTACTGGGTAACAACT-TT-CTTCG-ACTTTGC
1 CGATGAGGCACTGGGTAACAACTATTGCTTCGAACTAT-C
* **
57941776 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTAACAACTATTGCTTCGAACTATC
57941815 CGATGAGGCACTGGGT
1 CGATGAGGCACTGGGT
57941831 GCCAATCTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 21 0.46
40 4 0.09
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGGCACTGGGTAACAACTATTGCTTCGAACTATC
Found at i:57941818 original size:39 final size:38
Alignment explanation
Indices: 57941698--57941831 Score: 105
Period size: 39 Copynumber: 3.4 Consensus size: 38
57941688 GACCTCGAGT
* *
57941698 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATA-GATT
1 CGATGAGACACTGGGTGTCAAC--TA-TTCTTC-GA-ACTATC
** ** *
57941739 CGATGAGGTACTGGGTAACAACT-TTCTTCG-ACTTTGC
1 CGATGAGACACTGGGTGTCAACTATTCTTCGAACTAT-C
57941776 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGACACTGGGTGTCAACTATT-CTTCGAACTATC
*
57941815 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
57941832 CCAATCTGGT
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
35 1 0.01
36 1 0.01
37 20 0.27
38 8 0.11
39 22 0.30
40 5 0.07
41 15 0.20
42 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTATTCTTCGAACTATC
Found at i:57945549 original size:29 final size:27
Alignment explanation
Indices: 57945508--57945561 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
57945498 ACCGAAATCA
*
57945508 TATAAAAATAATTAATTATAAAAATGG
1 TATAAAAATAATTAATTACAAAAATGG
57945535 TATAGAAAATAAATTAATTACAAAAAT
1 TATA-AAAAT-AATTAATTACAAAAAT
57945562 AAGGCATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.17
28 5 0.21
29 15 0.62
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (27 bp):
TATAAAAATAATTAATTACAAAAATGG
Found at i:57961592 original size:15 final size:14
Alignment explanation
Indices: 57961572--57961601 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
57961562 ATAACCTTCT
57961572 AAATATTTATTATTA
1 AAATATTTA-TATTA
57961587 AAATATTTATATTA
1 AAATATTTATATTA
57961601 A
1 A
57961602 TCAAAATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTTATATTA
Found at i:57965215 original size:31 final size:33
Alignment explanation
Indices: 57965180--57965243 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
57965170 AGCCCAACTC
57965180 AAATTT-AATTTAAATAATAAAAA-ATA-TTTTA
1 AAATTTAAATTT-AATAATAAAAACATACTTTTA
*
57965211 AAATTTAAATTTAATTATAAAAACATACTTTTA
1 AAATTTAAATTTAATAATAAAAACATACTTTTA
57965244 TTTTTTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 16 0.55
32 8 0.28
33 5 0.17
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (33 bp):
AAATTTAAATTTAATAATAAAAACATACTTTTA
Found at i:57965485 original size:34 final size:34
Alignment explanation
Indices: 57965442--57965513 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
57965432 GGAAACAGCA
*
57965442 TGGGGGTTGCTACGACGTGGGGCGTGCACGGCGC
1 TGGGGGTTGCTACGACGTGGGGCGTGCACGACGC
** *
57965476 TGGGGGTTGCTGTGACGTGGGGTGTGCACGACGC
1 TGGGGGTTGCTACGACGTGGGGCGTGCACGACGC
57965510 TGGG
1 TGGG
57965514 AGAGAAGGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.08, C:0.19, G:0.51, T:0.21
Consensus pattern (34 bp):
TGGGGGTTGCTACGACGTGGGGCGTGCACGACGC
Found at i:57965508 original size:16 final size:18
Alignment explanation
Indices: 57965444--57965513 Score: 53
Period size: 17 Copynumber: 4.2 Consensus size: 18
57965434 AAACAGCATG
57965444 GGGGT-TGCTACGACG-T
1 GGGGTGTGCTACGACGCT
* *
57965460 GGGGCGTGC-ACGGCGCT
1 GGGGTGTGCTACGACGCT
**
57965477 GGGG-GTTGCTGTGACG-T
1 GGGGTG-TGCTACGACGCT
57965494 GGGGTGTGC-ACGACGCT
1 GGGGTGTGCTACGACGCT
57965511 GGG
1 GGG
57965514 AGAGAAGGGG
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
16 14 0.34
17 23 0.56
18 4 0.10
ACGTcount: A:0.09, C:0.20, G:0.51, T:0.20
Consensus pattern (18 bp):
GGGGTGTGCTACGACGCT
Found at i:57968509 original size:3 final size:3
Alignment explanation
Indices: 57968501--57968567 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
57968491 TTTAGCAATT
* *
57968501 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA GTA -TA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * * *
57968546 ATA TTA TTG TCA TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
57968568 GTTTTTTTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:57968629 original size:14 final size:14
Alignment explanation
Indices: 57968612--57968651 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
57968602 GATATATATG
*
57968612 TTTTATTATATTAT
1 TTTTATTATATAAT
57968626 TTTTATTATATAAT
1 TTTTATTATATAAT
57968640 TGTTTA-TATATA
1 T-TTTATTATATA
57968652 TGCGTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TTTTATTATATAAT
Found at i:57969191 original size:18 final size:19
Alignment explanation
Indices: 57969146--57969194 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
57969136 GCTTAGGTGC
* *
57969146 TTTAATTTTTATTTGTTCA
1 TTTACTTTTTATTTATTCA
*
57969165 TTTAC-TTTTATTTATTGA
1 TTTACTTTTTATTTATTCA
57969183 TTT-CTTTTTATT
1 TTTACTTTTTATT
57969195 ATATGTTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 21 0.81
19 4 0.15
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTACTTTTTATTTATTCA
Found at i:57976633 original size:15 final size:14
Alignment explanation
Indices: 57976613--57976642 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
57976603 ATAACCTTCT
57976613 AAATATTTATGATTA
1 AAATATTTAT-ATTA
57976628 AAATATTTATATTA
1 AAATATTTATATTA
57976642 A
1 A
57976643 TCAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
AAATATTTATATTA
Done.