Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008192.1 Hibiscus syriacus cultivar Beakdansim tig00110809_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1702141
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:993981 original size:24 final size:23
Alignment explanation
Indices: 993931--993982 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
993921 AAATTTTGTC
* *
993931 AAATATTTATTAATATTAAATAA
1 AAATATTTAATAAAATTAAATAA
*
993954 AAATATTTAAATAAAATTTAATAA
1 AAATATTT-AATAAAATTAAATAA
993978 AAATA
1 AAATA
993983 AATGTGGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATATTTAATAAAATTAAATAA
Found at i:995888 original size:107 final size:105
Alignment explanation
Indices: 995519--995896 Score: 452
Period size: 105 Copynumber: 3.6 Consensus size: 105
995509 CTTATTTTTC
* * * * * * *
995519 AAGCTGTAGATACTATTCACACAATGAGAAAGCAAGGCCTTGAGCCTAATGTTGTCACATATACT
1 AAGCTGAAGATATTGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCACGTATAAT
* * *
995584 ACACTGGTTGATGCATATTGCAAGAAGGGAATGGTTTT-TG
66 ATATTGGTTGATGCATATTGCAAGAAAGGAAT-GTTTTCTG
* * * * * * *
995624 AAGCTAAAGATATTGTTGATAAAATGAGAAAGCAAGGCATTCAGCCTGACGTTGTCATGTATAAT
1 AAGCTGAAGATATTGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCACGTATAAT
* * *
995689 ATATTGGTTGATGCTTATTGCAAGAAAGGGATGGTTTCTG
66 ATATTGGTTGATGCATATTGCAAGAAAGGAATGTTTTCTG
* * *
995729 AAGCTGAAGATATTGTTGACACAATGAGAAAACAAAGCATTGAGCCTAATGTTGTCACGTATAGT
1 AAGCTGAAGATATTGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCACGTATAAT
* **
995794 ATATTGGCTGATGCGCATTGCAAGAAAGGAATGATTTCTCTG
66 ATATTGGTTGATGCATATTGCAAGAAAGGAATG-TTT-TCTG
** * *
995836 AAGCTGAAGGCATCGTCGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCACGTA
1 AAGCTGAAGATATTGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCACGTA
995897 CAACACTCTT
Statistics
Matches: 229, Mismatches: 41, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
104 4 0.02
105 164 0.72
106 2 0.01
107 59 0.26
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (105 bp):
AAGCTGAAGATATTGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCACGTATAAT
ATATTGGTTGATGCATATTGCAAGAAAGGAATGTTTTCTG
Found at i:1006037 original size:58 final size:57
Alignment explanation
Indices: 1005929--1006055 Score: 177
Period size: 58 Copynumber: 2.2 Consensus size: 57
1005919 AGTAGCCCTC
* * *
1005929 AGTATCGATATCCTCACCTAGGCTATCAGTATCCCCAATTGTATCGATATTGCCTTG
1 AGTATCGATATCCCCACCTAGGCTATCAGTATCCCCAATGGTATCAATATTGCCTTG
*
1005986 AGTATCGATA-CCCCTCCTAGGCTATC-GATACTCCCCCAATGGTATCAATATTGCCTTG
1 AGTATCGATATCCCCACCTAGGCTATCAG-TA-T-CCCCAATGGTATCAATATTGCCTTG
1006044 AGTATCGATATC
1 AGTATCGATATC
1006056 AAAATTTCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
55 1 0.02
56 16 0.26
57 11 0.18
58 33 0.53
59 1 0.02
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (57 bp):
AGTATCGATATCCCCACCTAGGCTATCAGTATCCCCAATGGTATCAATATTGCCTTG
Found at i:1020002 original size:37 final size:37
Alignment explanation
Indices: 1019948--1020030 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
1019938 TTGCCTTGAG
1019948 ACCACACACCAGAGCCAGAGGCAGTGCAGGACACAAC
1 ACCACACACCAGAGCCAGAGGCAGTGCAGGACACAAC
* *
1019985 ACCACACACCAGTGCCAGAGGCAGTGCAGGACACAGC
1 ACCACACACCAGAGCCAGAGGCAGTGCAGGACACAAC
*
1020022 ACCGCACAC
1 ACCACACAC
1020031 ATCTCAGAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.35, C:0.37, G:0.24, T:0.04
Consensus pattern (37 bp):
ACCACACACCAGAGCCAGAGGCAGTGCAGGACACAAC
Found at i:1023314 original size:21 final size:19
Alignment explanation
Indices: 1023290--1023329 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
1023280 TTCAAGTAAA
1023290 TATAATTGAAGATACTTATTT
1 TATAATTGAA-ATA-TTATTT
*
1023311 TATAATTTAAATATTATTT
1 TATAATTGAAATATTATTT
1023330 AAAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (19 bp):
TATAATTGAAATATTATTT
Found at i:1025447 original size:37 final size:37
Alignment explanation
Indices: 1025374--1025448 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
1025364 GTTGAAAAAT
* *
1025374 ATTTATATATATTTTTTAAAAATTTTAAATTCATAAA
1 ATTTATATATATTTTTTAAAAATTTGAAAATCATAAA
*
1025411 ATTTATATAATTTTTTTTACAAAA-TTGAAAAT-ATAAA
1 ATTTATAT-ATATTTTTTA-AAAATTTGAAAATCATAAA
1025448 A
1 A
1025449 ATGTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 15 0.45
39 4 0.12
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATATTTTTTAAAAATTTGAAAATCATAAA
Found at i:1025767 original size:42 final size:42
Alignment explanation
Indices: 1025720--1025807 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
1025710 ATTCACTATT
1025720 GATAATGTAAGATTACC-GAGAATGACATTCCCGGCCAACCAA
1 GATAATGTAAGATTACCTG-GAATGACATTCCCGGCCAACCAA
1025762 GATAATGTAAGATTACCTGGAATGACATTCCCGGCCAACCAA
1 GATAATGTAAGATTACCTGGAATGACATTCCCGGCCAACCAA
1025804 -ATAA
1 GATAA
1025808 GGGAATGTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
41 4 0.09
42 40 0.89
43 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (42 bp):
GATAATGTAAGATTACCTGGAATGACATTCCCGGCCAACCAA
Found at i:1026128 original size:2 final size:2
Alignment explanation
Indices: 1026086--1026111 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1026076 CCCTCCCTCC
1026086 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1026112 TTCAGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1027109 original size:17 final size:17
Alignment explanation
Indices: 1027087--1027121 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1027077 TTGAACAACA
1027087 CTAATAGCTTCAAAGAT
1 CTAATAGCTTCAAAGAT
1027104 CTAATAGCTTCAAAGAT
1 CTAATAGCTTCAAAGAT
1027121 C
1 C
1027122 AAAGCTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (17 bp):
CTAATAGCTTCAAAGAT
Found at i:1043906 original size:20 final size:21
Alignment explanation
Indices: 1043868--1043906 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1043858 CATCAAAGCC
*
1043868 TTTGTTGAGGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
1043889 TTTGTCGAGGCCAT-AAAT
1 TTTGTCGAGGCCATGAAAT
1043907 TCATGCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (21 bp):
TTTGTCGAGGCCATGAAATCT
Found at i:1058454 original size:25 final size:25
Alignment explanation
Indices: 1058426--1058476 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
1058416 AATATTTTAT
1058426 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
1058451 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
1058476 A
1 A
1058477 AATATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:1058461 original size:34 final size:34
Alignment explanation
Indices: 1058414--1058498 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
1058404 CCCGAACCCG
1058414 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTTTATATATAATTAATATAAAAAATAT
*
1058448 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTTTATATATAATTAATATAAAAAATAT
*
1058482 AAAAAATTTTATATATA
1 AAAATATTTTATATATA
1058499 TATATAATCG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTTTATATATAATTAATATAAAAAATAT
Found at i:1058480 original size:9 final size:9
Alignment explanation
Indices: 1058434--1058488 Score: 51
Period size: 9 Copynumber: 6.3 Consensus size: 9
1058424 ATATATAATT
1058434 AATATAAAA
1 AATATAAAA
1058443 AATAT--AA
1 AATATAAAA
* *
1058450 AATATTATA
1 AATATAAAA
* **
1058459 TATATAATT
1 AATATAAAA
1058468 AATATAAAA
1 AATATAAAA
1058477 AATATAAAA
1 AATATAAAA
1058486 AAT
1 AAT
1058489 TTTATATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
7 7 0.19
9 30 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AATATAAAA
Found at i:1061583 original size:21 final size:22
Alignment explanation
Indices: 1061553--1061600 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
1061543 TTTGTAACCT
1061553 ATATACTATTTTTTTCAATAAA
1 ATATACTATTTTTTTCAATAAA
1061575 ATATA-TATTTTTTTCAATAAA
1 ATATACTATTTTTTTCAATAAA
1061596 ATATA
1 ATATA
1061601 AGTGAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATACTATTTTTTTCAATAAA
Found at i:1065203 original size:48 final size:48
Alignment explanation
Indices: 1065147--1065246 Score: 175
Period size: 48 Copynumber: 2.1 Consensus size: 48
1065137 AATCAACTTT
1065147 CTTTACCCCATTCATATTTTGTGAGTTCATAGATTT-TTTTTAAGTTC
1 CTTTACCCCATTCATATTTTGTGAGTTCATAGATTTCTTTTTAAGTTC
*
1065194 CTTTCACCCCATTCATGTTTTGTGAGTTCATAGATTTCTTTTTAAGTTC
1 CTTT-ACCCCATTCATATTTTGTGAGTTCATAGATTTCTTTTTAAGTTC
1065243 CTTT
1 CTTT
1065247 TTCCTATCTT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 4 0.08
48 31 0.62
49 15 0.30
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (48 bp):
CTTTACCCCATTCATATTTTGTGAGTTCATAGATTTCTTTTTAAGTTC
Found at i:1068648 original size:3 final size:3
Alignment explanation
Indices: 1068640--1068673 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
1068630 ATAAAAATTC
1068640 TAT TAT TAT TAT TAT TAT TAT TAGT TAAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA-T T-AT TAT TA
1068674 GGGTAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.83
4 4 0.14
5 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1068844 original size:3 final size:3
Alignment explanation
Indices: 1068836--1068860 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1068826 CCGTTAACTC
1068836 CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT C
1068861 GGTTGCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:1069269 original size:68 final size:67
Alignment explanation
Indices: 1069143--1069271 Score: 177
Period size: 68 Copynumber: 1.9 Consensus size: 67
1069133 AAGCAGCTTT
* * *
1069143 TTGAACCGGAGCCTTTTCTATAGGCATCGACTTTTCCATCAGATGCACACCCAACATTCAAAAGT
1 TTGAACCAGAGCCTTTTCTATAGGAAACGACTTTTCCATCAGATGCACACCCAACATTCAAAAGT
1069208 GC
66 GC
* ** * *
1069210 TTGAACCAGAGCCTTTTCTATAGATAAACGACTTTTCCATTTGATGCACGCCCAGCATTCAA
1 TTGAACCAGAGCCTTTTCTATAG-GAAACGACTTTTCCATCAGATGCACACCCAACATTCAA
1069272 TGTTTCAGGG
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 22 0.42
68 31 0.58
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (67 bp):
TTGAACCAGAGCCTTTTCTATAGGAAACGACTTTTCCATCAGATGCACACCCAACATTCAAAAGT
GC
Found at i:1070368 original size:38 final size:38
Alignment explanation
Indices: 1070318--1070392 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
1070308 GACAAAAGGA
1070318 GGGGGGGGGGAATCATAATCCAAAACTGTTTTTGAATG
1 GGGGGGGGGGAATCATAATCCAAAACTGTTTTTGAATG
1070356 GGGGGGGGGGAATCATAATCCAAAACTGTTTTTGAAT
1 GGGGGGGGGGAATCATAATCCAAAACTGTTTTTGAAT
1070393 TTGGGTCTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (38 bp):
GGGGGGGGGGAATCATAATCCAAAACTGTTTTTGAATG
Found at i:1083482 original size:2 final size:2
Alignment explanation
Indices: 1083477--1083506 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1083467 CTTGTGTGTG
1083477 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
1083507 ATACCATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1091237 original size:25 final size:25
Alignment explanation
Indices: 1091193--1091249 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1091183 AAATATCGTT
*
1091193 AAAA-ATATATACCTATTGTTTCTA
1 AAAATATATATACCTAATGTTTCTA
*
1091217 AAAATATATATACTTAATGTTTCTA
1 AAAATATATATACCTAATGTTTCTA
*
1091242 AAATTATA
1 AAAATATA
1091250 CGTTTAGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (25 bp):
AAAATATATATACCTAATGTTTCTA
Found at i:1094599 original size:2 final size:2
Alignment explanation
Indices: 1094594--1094622 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1094584 ATTTAATGAT
1094594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1094623 TTGTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1099102 original size:6 final size:6
Alignment explanation
Indices: 1099012--1099101 Score: 135
Period size: 6 Copynumber: 15.0 Consensus size: 6
1099002 CTTTCTTTTC
* *
1099012 ATACAT ATACAT ATACAT ATACAT GTACAT ATACAT GTACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
1099060 ATACAT GTACAT ATACAT ATACAT ATACAT GTACAT GTACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1099102 GGTCCAAGAG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:1101971 original size:25 final size:25
Alignment explanation
Indices: 1101943--1102017 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
1101933 TCATGCTCAC
1101943 AAACATTGGTTCACTCCTACATGAT
1 AAACATTGGTTCACTCCTACATGAT
* ** *
1101968 AAACA--AG-TCACAT--T-CAACAC
1 AAACATTGGTTCAC-TCCTACATGAT
1101988 AAACATTGGTTCACTCCTACATGAT
1 AAACATTGGTTCACTCCTACATGAT
1102013 AAACA
1 AAACA
1102018 AGTCATATTC
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
20 8 0.23
21 1 0.03
22 6 0.17
23 6 0.17
24 1 0.03
25 13 0.37
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.25
Consensus pattern (25 bp):
AAACATTGGTTCACTCCTACATGAT
Found at i:1101990 original size:45 final size:45
Alignment explanation
Indices: 1101940--1102029 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
1101930 CATTCATGCT
1101940 CACAAACATTGGTTCACTCCTACATGATAAACAAGTCACATTCAA
1 CACAAACATTGGTTCACTCCTACATGATAAACAAGTCACATTCAA
*
1101985 CACAAACATTGGTTCACTCCTACATGATAAACAAGTCATATTCAA
1 CACAAACATTGGTTCACTCCTACATGATAAACAAGTCACATTCAA
1102030 GAAGACAATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (45 bp):
CACAAACATTGGTTCACTCCTACATGATAAACAAGTCACATTCAA
Found at i:1108933 original size:20 final size:20
Alignment explanation
Indices: 1108910--1108948 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1108900 GGAATTGAAA
1108910 GTTAGAATATTG-AATTTGAT
1 GTTAGAATA-TGAAATTTGAT
1108930 GTTAGAATATGAAATTTGA
1 GTTAGAATATGAAATTTGA
1108949 CTATTTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (20 bp):
GTTAGAATATGAAATTTGAT
Found at i:1111830 original size:21 final size:22
Alignment explanation
Indices: 1111773--1111832 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
1111763 TAGTTATATG
1111773 ATGATTGTGATTACATGCTAAA
1 ATGATTGTGATTACATGCTAAA
1111795 ATGATTGTGATTACATGCTAAA
1 ATGATTGTGATTACATGCTAAA
*
1111817 ATGATTG-AATTACATG
1 ATGATTGTGATTACATG
1111833 TTCATGACTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 8 0.22
22 29 0.78
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (22 bp):
ATGATTGTGATTACATGCTAAA
Found at i:1113117 original size:84 final size:83
Alignment explanation
Indices: 1113028--1113190 Score: 215
Period size: 84 Copynumber: 2.0 Consensus size: 83
1113018 GAATGCATTT
1113028 CATGCATCGATGCA-CATACCATGCATCAATGCACT-AAGGAT-TTTATGAAAACATCGAATGCA
1 CATGCATCGATGCACCA-ACCATGCATCAATGCACTCAA-GATATTT-TG-AAACATCGAATGCA
*
1113090 TTTGATGCATCGATGCACCAGC
62 CTTGATGCATCGATGCACCAGC
* * * *
1113112 CATGCATCGATGCACCAGCCATGCATCGATGCACTCTAGCTATTTTGAAACATCGAATGCACTTG
1 CATGCATCGATGCACCAACCATGCATCAATGCACTCAAGATATTTTGAAACATCGAATGCACTTG
*
1113177 ATGCATCGGTGCAC
66 ATGCATCGATGCAC
1113191 TCTTAGTGCA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
83 30 0.43
84 34 0.49
85 6 0.09
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (83 bp):
CATGCATCGATGCACCAACCATGCATCAATGCACTCAAGATATTTTGAAACATCGAATGCACTTG
ATGCATCGATGCACCAGC
Found at i:1113118 original size:19 final size:19
Alignment explanation
Indices: 1113094--1113145 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1113084 AATGCATTTG
1113094 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
1113113 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
1113132 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1113146 TCTAGCTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACCAGCC
Found at i:1113207 original size:83 final size:82
Alignment explanation
Indices: 1113076--1113231 Score: 199
Period size: 83 Copynumber: 1.9 Consensus size: 82
1113066 GATTTTATGA
* *
1113076 AAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACCA-GCCATGCATCG
1 AAACATCGAATGCACTTGATGCATCGATGCACCAG-C-TGCACCGATGCACCAGGCCATGCATCG
1113140 ATGCACTCTAGCTATTTTG
64 ATGCACTCTAGCTATTTTG
* **
1113159 AAACATCGAATGCACTTGATGCATCGGTGCACTCTTAG-TGCACCGATGCACCATGGGTATGCAT
1 AAACATCGAATGCACTTGATGCATCGATGCAC-C--AGCTGCACCGATGCACCA-GGCCATGCAT
1113223 CGATGCACT
62 CGATGCACT
1113232 GATGCACCGA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
83 44 0.70
84 1 0.02
85 16 0.25
86 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (82 bp):
AAACATCGAATGCACTTGATGCATCGATGCACCAGCTGCACCGATGCACCAGGCCATGCATCGAT
GCACTCTAGCTATTTTG
Found at i:1113247 original size:37 final size:37
Alignment explanation
Indices: 1113197--1113270 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1113187 GCACTCTTAG
1113197 TGCACCGATGCACCATGGGTATGCATCGATGCACTGA
1 TGCACCGATGCACCATGGGTATGCATCGATGCACTGA
1113234 TGCACCGATGCACCATGGGTATGCATCGATGCACTGA
1 TGCACCGATGCACCATGGGTATGCATCGATGCACTGA
1113271 CACTCCTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (37 bp):
TGCACCGATGCACCATGGGTATGCATCGATGCACTGA
Found at i:1119049 original size:23 final size:23
Alignment explanation
Indices: 1118996--1119060 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1118986 CGATGCATCT
1118996 TTGAATGTGCACCGAT--ACACC
1 TTGAATGTGCACCGATGCACACC
* * *
1119017 ATGAAGGTGCACCGATGCACGCC
1 TTGAATGTGCACCGATGCACACC
*
1119040 TTGAATGTGCATCGATGCACA
1 TTGAATGTGCACCGATGCACA
1119061 AGGCCATGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 14 0.40
23 21 0.60
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.22
Consensus pattern (23 bp):
TTGAATGTGCACCGATGCACACC
Found at i:1120684 original size:21 final size:21
Alignment explanation
Indices: 1120599--1120671 Score: 119
Period size: 21 Copynumber: 3.5 Consensus size: 21
1120589 ACTCCGGGAG
1120599 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTGCTC
1120620 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTGCTC
* * *
1120641 CTAGCTCTTCTCGTGCTACTC
1 CTAGCTCTTCACGAGCTGCTC
1120662 CTAGCTCTTC
1 CTAGCTCTTC
1120672 TCGTGCTCCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.12, C:0.38, G:0.16, T:0.33
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTGCTC
Found at i:1120684 original size:42 final size:42
Alignment explanation
Indices: 1120599--1120684 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
1120589 ACTCCGGGAG
* *
1120599 CTAGCTCTTCACGAGCTGCTCCTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTACTCCTAGCTCTTCACGAGCTCCTC
* * * *
1120641 CTAGCTCTTCTCGTGCTACTCCTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTACTCCTAGCTCTTCACGAGCTCCTC
1120683 CT
1 CT
1120685 CCTCCTCCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.10, C:0.40, G:0.16, T:0.34
Consensus pattern (42 bp):
CTAGCTCTTCACGAGCTACTCCTAGCTCTTCACGAGCTCCTC
Found at i:1121244 original size:2 final size:2
Alignment explanation
Indices: 1121237--1121272 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1121227 CAGCTTAAGC
1121237 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
1121273 ATCAATTGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1121753 original size:147 final size:147
Alignment explanation
Indices: 1121519--1121813 Score: 590
Period size: 147 Copynumber: 2.0 Consensus size: 147
1121509 AGTTTAAATG
1121519 AATTTTAAGATTTTACCAATGATTTTCTAAGTATATTCGATTTAATTAATCGAATATCAAATTAT
1 AATTTTAAGATTTTACCAATGATTTTCTAAGTATATTCGATTTAATTAATCGAATATCAAATTAT
1121584 TACTCCAAGTCTTTCAAGTTCAAATTCAAACCTTACTAAATGTGTAAAATTGTGTTTTATACTTA
66 TACTCCAAGTCTTTCAAGTTCAAATTCAAACCTTACTAAATGTGTAAAATTGTGTTTTATACTTA
1121649 AACTATTTTTGAAACAA
131 AACTATTTTTGAAACAA
1121666 AATTTTAAGATTTTACCAATGATTTTCTAAGTATATTCGATTTAATTAATCGAATATCAAATTAT
1 AATTTTAAGATTTTACCAATGATTTTCTAAGTATATTCGATTTAATTAATCGAATATCAAATTAT
1121731 TACTCCAAGTCTTTCAAGTTCAAATTCAAACCTTACTAAATGTGTAAAATTGTGTTTTATACTTA
66 TACTCCAAGTCTTTCAAGTTCAAATTCAAACCTTACTAAATGTGTAAAATTGTGTTTTATACTTA
1121796 AACTATTTTTGAAACAA
131 AACTATTTTTGAAACAA
1121813 A
1 A
1121814 TTTCATAAAG
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 148 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (147 bp):
AATTTTAAGATTTTACCAATGATTTTCTAAGTATATTCGATTTAATTAATCGAATATCAAATTAT
TACTCCAAGTCTTTCAAGTTCAAATTCAAACCTTACTAAATGTGTAAAATTGTGTTTTATACTTA
AACTATTTTTGAAACAA
Found at i:1121984 original size:65 final size:63
Alignment explanation
Indices: 1121865--1122074 Score: 239
Period size: 65 Copynumber: 3.3 Consensus size: 63
1121855 TTTATCAAAG
*
1121865 TGATGCATCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
1121927 ATT
61 ATT
* *
1121930 TCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
1121994 T
63 T
* * * *
1121995 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
*
1122059 TGATGTATCGATGCAC
1 TGATGCATCGATGCAC
1122075 TCTTAGTTCA
Statistics
Matches: 127, Mismatches: 10, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 47 0.37
65 71 0.56
66 5 0.04
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:1124020 original size:15 final size:15
Alignment explanation
Indices: 1123984--1124037 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
1123974 AGAGCCTCTG
**
1123984 AATCATTCAGCATTT
1 AATCATTCAGCGCTT
1123999 GAATCATTCAGCGCTT
1 -AATCATTCAGCGCTT
*
1124015 AATCATTCAACGCTT
1 AATCATTCAGCGCTT
1124030 AATCATTC
1 AATCATTC
1124038 TAAAGTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
15 22 0.63
16 13 0.37
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.35
Consensus pattern (15 bp):
AATCATTCAGCGCTT
Found at i:1127540 original size:32 final size:33
Alignment explanation
Indices: 1127504--1127565 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1127494 TATTATTTTT
1127504 AGATATTTTAAAT-TTAAGTATT-AATAATTGTA
1 AGATA-TTTAAATGTTAAGTATTAAATAATTGTA
* *
1127536 AGATATTTAAATGTTTATTATTAAATAATT
1 AGATATTTAAATGTTAAGTATTAAATAATT
1127566 AGAGGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 7 0.27
32 12 0.46
33 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (33 bp):
AGATATTTAAATGTTAAGTATTAAATAATTGTA
Found at i:1128408 original size:12 final size:12
Alignment explanation
Indices: 1128371--1128401 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1128361 CAAACGTCTC
1128371 GATAGAGACAGA
1 GATAGAGACAGA
*
1128383 GATAGAGACGGA
1 GATAGAGACAGA
1128395 GATAGAG
1 GATAGAG
1128402 GAAGAGAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.39, T:0.10
Consensus pattern (12 bp):
GATAGAGACAGA
Found at i:1128452 original size:3 final size:3
Alignment explanation
Indices: 1128446--1128471 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1128436 TCATCATCAT
1128446 CAA CAA CAA CAA CAA CAA CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CA
1128472 TCATGTTCAC
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:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:1133095 original size:2 final size:2
Alignment explanation
Indices: 1133082--1133117 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1133072 AACCACTTAA
*
1133082 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1133118 TAGAGCAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1145651 original size:20 final size:20
Alignment explanation
Indices: 1145628--1145679 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1145618 AACGCGATCC
1145628 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
1145648 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
1145668 CCAAAATCGCAA
1 CCAGAATCGCAA
1145680 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:1145696 original size:21 final size:20
Alignment explanation
Indices: 1145669--1145767 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1145659 AATCAGTTTC
1145669 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1145690 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1145711 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1145731 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1145752 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1145768 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1145796 original size:20 final size:20
Alignment explanation
Indices: 1145734--1145927 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1145724 CGATTTTCCA
* ** *
1145734 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1145754 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1145774 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1145794 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1145814 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1145834 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1145854 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1145874 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1145894 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1145915 AAATCGCAACGCG
1 AAATCGCAACGCG
1145928 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1145818 original size:60 final size:60
Alignment explanation
Indices: 1145734--1145927 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1145724 CGATTTTCCA
* ** * *
1145734 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1145794 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1145854 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1145915 AAATCGCAACGCG
1 AAATCGCAACGCG
1145928 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1146347 original size:33 final size:33
Alignment explanation
Indices: 1146308--1146378 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1146298 TTCACTTAGA
*
1146308 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1146341 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1146374 TTTCA
1 TTTCA
1146379 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1146518 original size:14 final size:14
Alignment explanation
Indices: 1146499--1146553 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1146489 AGAATGACTG
1146499 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1146513 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
1146532 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1146546 TCGCAACG
1 TCGCAACG
1146554 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1146566 original size:33 final size:33
Alignment explanation
Indices: 1146499--1146569 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1146489 AGAATGACTG
***
1146499 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1146532 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1146565 TCGCA
1 TCGCA
1146570 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:1146587 original size:19 final size:19
Alignment explanation
Indices: 1146565--1146662 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1146555 GAAACCAAAA
*
1146565 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1146584 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1146598 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1146617 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1146631 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1146650 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1146663 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1146606 original size:14 final size:14
Alignment explanation
Indices: 1146587--1146676 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1146577 TTTCATTTCG
1146587 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1146601 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1146620 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1146634 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1146651 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1146667 CGTTGCGATT
1 CGTTGCGATT
1146677 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1146612 original size:33 final size:33
Alignment explanation
Indices: 1146570--1146684 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1146560 CAAAATCGCA
1146570 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1146603 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1146636 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1146669 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1146685 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1147215 original size:19 final size:19
Alignment explanation
Indices: 1147199--1147300 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1147189 AAAAATGACT
1147199 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1147218 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1147237 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1147251 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1147270 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1147290 ATCGCAATGCG
1 ATCGCAATGCG
1147301 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1147349 original size:33 final size:35
Alignment explanation
Indices: 1147307--1147601 Score: 237
Period size: 33 Copynumber: 8.5 Consensus size: 35
1147297 TGCGTTTATA
1147307 ATTTCGCATTGCGATT-ATCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
*
1147340 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
*
1147376 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
* *
1147411 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTA
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
*
1147449 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
* *
1147485 -TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTCATCTCG-ATTGCGATTTTC
1147520 ATTTCGCATTGCGATTC-TCTCG-TTGCGATTTTC
1 ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
* *
1147553 ATTTCGCATTGCGATT-TTCAT-G-TTGGGATTTTC
1 ATTTCGCATTGCGATTCATC-TCGATTGCGATTTTC
*
1147586 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
1147602 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 10, Indels: 34
0.84 0.04 0.12
Matches are distributed among these distances:
33 119 0.51
34 1 0.00
35 21 0.09
36 22 0.09
38 72 0.31
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (35 bp):
ATTTCGCATTGCGATTCATCTCGATTGCGATTTTC
Found at i:1147353 original size:19 final size:19
Alignment explanation
Indices: 1147329--1147601 Score: 352
Period size: 19 Copynumber: 15.4 Consensus size: 19
1147319 GATTATCTCG
1147329 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1147348 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1147367 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
1147381 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1147400 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1147419 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
1147438 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
1147457 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1147476 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1147490 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1147509 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1147528 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1147542 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1147561 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1147575 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1147594 TTGCGATT
1 TTGCGATT
1147602 GTATTTTCCG
Statistics
Matches: 224, Mismatches: 10, Indels: 40
0.82 0.04 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 24 0.11
19 147 0.66
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1147404 original size:71 final size:73
Alignment explanation
Indices: 1147329--1147573 Score: 316
Period size: 71 Copynumber: 3.4 Consensus size: 73
1147319 GATTATCTCG
1147329 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTCTTTCG-TTGCGATTTTC
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCTTTCGATTGCGATTTTC
1147392 ATTTCGCA
66 ATTTCGCA
* *
1147400 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTT-CTTTCG-ATTGCGATT
1147465 TTCATTTCGCA
63 TTCATTTCGCA
*
1147476 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTC-TTTCG-ATTGCGATT
*
1147534 TTC-TCTCG--
63 TTCATTTCGCA
1147542 TTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCAT
1147574 GTTGGGATTT
Statistics
Matches: 156, Mismatches: 7, Indels: 22
0.84 0.04 0.12
Matches are distributed among these distances:
66 6 0.04
68 7 0.04
69 7 0.04
71 97 0.62
73 6 0.04
74 8 0.05
76 25 0.16
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (73 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCTTTCGATTGCGATTTTC
ATTTCGCA
Found at i:1147601 original size:52 final size:52
Alignment explanation
Indices: 1147307--1147573 Score: 453
Period size: 52 Copynumber: 5.0 Consensus size: 52
1147297 TGCGTTTATA
*
1147307 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1147359 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
1147411 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
1147468 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1147520 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1147572 AT
1 AT
1147574 GTTGGGATTT
Statistics
Matches: 205, Mismatches: 5, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
52 147 0.72
54 7 0.03
55 8 0.04
57 43 0.21
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1149328 original size:12 final size:12
Alignment explanation
Indices: 1149311--1149335 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1149301 TCTTCGGGGA
1149311 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1149323 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1149335 C
1 C
1149336 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1149543 original size:24 final size:24
Alignment explanation
Indices: 1149509--1149555 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1149499 CTGAAACATC
1149509 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1149533 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1149556 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1150256 original size:20 final size:20
Alignment explanation
Indices: 1150228--1150596 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
1150218 AAATTTCAGT
* * * *
1150228 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1150248 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
1150268 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
1150288 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1150308 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1150328 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
1150348 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1150368 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1150388 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1150408 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
1150428 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
1150448 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
1150468 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
1150488 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
1150508 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
1150528 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
1150548 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
1150568 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
1150588 GTTGCGATT
1 GTTGCGATT
1150597 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:1170344 original size:18 final size:18
Alignment explanation
Indices: 1170310--1170355 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1170300 TCTGATAAAA
* *
1170310 CCAAGGTCCAAAGCCAAAT
1 CCAAGG-CCAAACCCAAAC
1170329 CCAAGGCCAAACCCAAAC
1 CCAAGGCCAAACCCAAAC
*
1170347 CCAAAGCCA
1 CCAAGGCCA
1170356 CGAAATCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.43, C:0.39, G:0.13, T:0.04
Consensus pattern (18 bp):
CCAAGGCCAAACCCAAAC
Found at i:1172611 original size:18 final size:18
Alignment explanation
Indices: 1172588--1172638 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
1172578 AATTATATTT
*
1172588 AAAATATTATTTTTACTA
1 AAAATATTATTTTTACCA
1172606 AAAATATTATTTTTACCA
1 AAAATATTATTTTTACCA
*
1172624 AAAATATTAATTTTA
1 AAAATATTATTTTTA
1172639 TTAACTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATATTATTTTTACCA
Found at i:1173645 original size:21 final size:20
Alignment explanation
Indices: 1173619--1173657 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1173609 ATAATTAATT
1173619 ATAAATATGATTTTAGTAAAC
1 ATAAATATGATTTT-GTAAAC
*
1173640 ATAAATATTATTTTGTAA
1 ATAAATATGATTTTGTAA
1173658 TAGTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (20 bp):
ATAAATATGATTTTGTAAAC
Found at i:1174534 original size:3 final size:3
Alignment explanation
Indices: 1174520--1174563 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
1174510 ATTTTAATAT
1174520 TTA TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1174564 ATTTTTATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1175422 original size:2 final size:2
Alignment explanation
Indices: 1175417--1175447 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1175407 TTATAAGGTC
1175417 AT 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 AT A
1175448 GTCCTCATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1175649 original size:29 final size:29
Alignment explanation
Indices: 1175576--1175679 Score: 181
Period size: 29 Copynumber: 3.6 Consensus size: 29
1175566 ATAATATTGA
1175576 TTTTTATGTTTCAAAACATAGAAAATATG
1 TTTTTATGTTTCAAAACATAGAAAATATG
1175605 ATTTTTATGTTTCAAAACATAGAAAATATG
1 -TTTTTATGTTTCAAAACATAGAAAATATG
* *
1175635 TTTTTATATTGCAAAACATAGAAAATATG
1 TTTTTATGTTTCAAAACATAGAAAATATG
1175664 TTTTTATGTTTCAAAA
1 TTTTTATGTTTCAAAA
1175680 AATTAGTATA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
29 41 0.59
30 29 0.41
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (29 bp):
TTTTTATGTTTCAAAACATAGAAAATATG
Found at i:1177449 original size:16 final size:16
Alignment explanation
Indices: 1177428--1177461 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1177418 CCCCCTTACT
*
1177428 TTAACACTTCTCCCCC
1 TTAACACTTCTCACCC
1177444 TTAACACTTCTCACCC
1 TTAACACTTCTCACCC
1177460 TT
1 TT
1177462 TTTGTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAACACTTCTCACCC
Found at i:1181183 original size:11 final size:11
Alignment explanation
Indices: 1181167--1181192 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1181157 AATTAGTGGC
1181167 ATGTAATTATT
1 ATGTAATTATT
1181178 ATGTAATTATT
1 ATGTAATTATT
1181189 ATGT
1 ATGT
1181193 TTTATTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (11 bp):
ATGTAATTATT
Found at i:1182430 original size:21 final size:21
Alignment explanation
Indices: 1182406--1182469 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 21
1182396 TCAGTGCATC
1182406 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* * *
1182427 TTCATAGGGTTGCATCGATGCACC
1 TTCAT---GATGTATCGATGCACA
1182451 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
1182470 TTATGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
21 16 0.47
24 18 0.53
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:1182462 original size:45 final size:44
Alignment explanation
Indices: 1182374--1182469 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 44
1182364 CTCTGTGCAA
*
1182374 CGATGCACATTCAAGGAGTGCATCAGTGCATCTTCATGATGTAT
1 CGATGCACATTCAAGGAGTGCATCAGTGCACCTTCATGATGTAT
1182418 CGATGCACATTCATAGG-GTTGCATC-GATGCACCTTCAT-AGTGTAT
1 CGATGCACATTCA-AGGAG-TGCATCAG-TGCACCTTCATGA-TGTAT
1182463 CGATGCA
1 CGATGCA
1182470 TTATGCACAA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
44 16 0.34
45 31 0.66
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (44 bp):
CGATGCACATTCAAGGAGTGCATCAGTGCACCTTCATGATGTAT
Found at i:1190539 original size:29 final size:29
Alignment explanation
Indices: 1190497--1190553 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1190487 ATATTTCAAA
* *
1190497 GTAATAATCCACAAATGCACCAAACTAAG
1 GTAACAATCCACAAATACACCAAACTAAG
*
1190526 GTAACAATCCACAAATACATCAAACTAA
1 GTAACAATCCACAAATACACCAAACTAA
1190554 CATATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.51, C:0.25, G:0.07, T:0.18
Consensus pattern (29 bp):
GTAACAATCCACAAATACACCAAACTAAG
Found at i:1192875 original size:19 final size:22
Alignment explanation
Indices: 1192851--1192892 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1192841 TGATGCAACT
1192851 AAAATATT-T-AA-AAATAAAA
1 AAAATATTATAAACAAATAAAA
1192870 AAAATATTATAAACAAATAAAA
1 AAAATATTATAAACAAATAAAA
1192892 A
1 A
1192893 TAATTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 2 0.10
22 9 0.45
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATATTATAAACAAATAAAA
Found at i:1192891 original size:18 final size:19
Alignment explanation
Indices: 1192850--1192891 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
1192840 ATGATGCAAC
*
1192850 TAAAATATTTAAAAATAAA
1 TAAAATATTTAAAAACAAA
* *
1192869 AAAAATA-TTATAAACAAA
1 TAAAATATTTAAAAACAAA
1192887 TAAAA
1 TAAAA
1192892 ATAATTAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAATATTTAAAAACAAA
Found at i:1193076 original size:19 final size:18
Alignment explanation
Indices: 1193037--1193085 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1193027 TGATGCAACT
1193037 AAAATATTTAAAATAAAA
1 AAAATATTTAAAATAAAA
*
1193055 AAAATATTATAAACA-AATA
1 AAAATATT-TAAA-ATAAAA
*
1193074 AAAATAATTAAA
1 AAAATATTTAAA
1193086 TTTATGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.44
19 14 0.52
20 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATATTTAAAATAAAA
Found at i:1193083 original size:185 final size:186
Alignment explanation
Indices: 1192826--1193192 Score: 700
Period size: 185 Copynumber: 2.0 Consensus size: 186
1192816 CGCCAACTTC
1192826 ATCTCGGATATTTTATGATGCAACTAAAATATTTAAAAATAAAAAAAATATTATAAACAAATAAA
1 ATCTCGGATATTTTATGATGCAACTAAAATATTTAAAAATAAAAAAAATATTATAAACAAATAAA
1192891 AATAATTAAATTTATGAAATTCAAAAAAAGTTAAATAAAAGAATTTAAACAATTATCGTGCAGCC
66 AATAATTAAATTTATGAAATTCAAAAAAAGTTAAATAAAAGAATTTAAACAATTATCGTGCAGCC
*
1192956 AGATGAAACTTGATCGGTGCTGATGTAATTGACGTAAAAAATGGGAATCGATCTTT
131 AGATGAAACTTGACCGGTGCTGATGTAATTGACGTAAAAAATGGGAATCGATCTTT
1193012 ATCTCGGATATTTTATGATGCAACTAAAATATTT-AAAATAAAAAAAATATTATAAACAAATAAA
1 ATCTCGGATATTTTATGATGCAACTAAAATATTTAAAAATAAAAAAAATATTATAAACAAATAAA
*
1193076 AATAATTAAATTTATGAAATTCAAAAAAAGTTAAATAAAAGAATTTAAACAATTATCTTGCAGCC
66 AATAATTAAATTTATGAAATTCAAAAAAAGTTAAATAAAAGAATTTAAACAATTATCGTGCAGCC
*
1193141 AGATGAAACTTGACCGGTGCTGATGTAATTGGCGTAAAAAATGGGAATCGAT
131 AGATGAAACTTGACCGGTGCTGATGTAATTGACGTAAAAAATGGGAATCGAT
1193193 ACCAAGCCCA
Statistics
Matches: 178, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
185 144 0.81
186 34 0.19
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (186 bp):
ATCTCGGATATTTTATGATGCAACTAAAATATTTAAAAATAAAAAAAATATTATAAACAAATAAA
AATAATTAAATTTATGAAATTCAAAAAAAGTTAAATAAAAGAATTTAAACAATTATCGTGCAGCC
AGATGAAACTTGACCGGTGCTGATGTAATTGACGTAAAAAATGGGAATCGATCTTT
Found at i:1195704 original size:12 final size:11
Alignment explanation
Indices: 1195682--1195715 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1195672 GGTTTTGGCC
1195682 AACCCGACCCG
1 AACCCGACCCG
*
1195693 ATACCTGACCCG
1 A-ACCCGACCCG
1195705 AACCCGACCCG
1 AACCCGACCCG
1195716 TTTTTTGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.26, C:0.50, G:0.18, T:0.06
Consensus pattern (11 bp):
AACCCGACCCG
Found at i:1195961 original size:5 final size:5
Alignment explanation
Indices: 1195951--1195978 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1195941 AAAAAAATAT
1195951 GACCC GACCC GACCC GACCC GACCC GAC
1 GACCC GACCC GACCC GACCC GACCC GAC
1195979 GCAAACTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.57, G:0.21, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:1202470 original size:18 final size:18
Alignment explanation
Indices: 1202427--1202476 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
1202417 TATGGAATTG
* *
1202427 GATTCCAATTCC-TGATA
1 GATTCCAATTCCTTCACA
*
1202444 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1202462 GATTCCAATTCCTTC
1 GATTCCAATTCCTTC
1202477 TTAAACATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1204410 original size:13 final size:13
Alignment explanation
Indices: 1204374--1204410 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1204364 CTCAATGAAC
*
1204374 GTCATAAATGAGA
1 GTCATAAATGTGA
*
1204387 GTCATAAATGTGT
1 GTCATAAATGTGA
1204400 GTCATAAATGT
1 GTCATAAATGT
1204411 ACGTCATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (13 bp):
GTCATAAATGTGA
Found at i:1204416 original size:13 final size:13
Alignment explanation
Indices: 1204367--1204418 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
1204357 AATGACGCTC
*
1204367 AATGAACGTCATA
1 AATGTACGTCATA
*
1204380 AATG-AGAGTCATA
1 AATGTA-CGTCATA
**
1204393 AATGTGTGTCATA
1 AATGTACGTCATA
1204406 AATGTACGTCATA
1 AATGTACGTCATA
1204419 GATTTATGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 1 0.03
13 31 0.97
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (13 bp):
AATGTACGTCATA
Found at i:1204868 original size:19 final size:20
Alignment explanation
Indices: 1204844--1204881 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1204834 TATAAAAAAT
1204844 ATATTCA-AAATTTTTTAAA
1 ATATTCACAAATTTTTTAAA
*
1204863 ATATTCACTAATTTTTTAA
1 ATATTCACAAATTTTTTAA
1204882 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTCACAAATTTTTTAAA
Found at i:1210681 original size:25 final size:26
Alignment explanation
Indices: 1210653--1210703 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1210643 ATTTTGATGA
1210653 ATCATT-ATGCCAACTAATGCACTTT
1 ATCATTGATGCCAACTAATGCACTTT
*
1210678 ATCATTGCTGCCAACTAATGCACTTT
1 ATCATTGATGCCAACTAATGCACTTT
1210704 CGGTGCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.35
Consensus pattern (26 bp):
ATCATTGATGCCAACTAATGCACTTT
Found at i:1229989 original size:20 final size:20
Alignment explanation
Indices: 1229928--1230116 Score: 202
Period size: 20 Copynumber: 9.4 Consensus size: 20
1229918 GATTTTCAAG
* ** *
1229928 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1229948 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1229968 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1229988 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1230008 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1230028 AATCGCAATGCGTATCCATA
1 AATCGCAACGCGTATCCGTA
*
1230048 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1230068 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1230088 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
1230108 AATCGCAAC
1 AATCGCAAC
1230117 ACTGAAATTT
Statistics
Matches: 142, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
19 2 0.01
20 138 0.97
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1231049 original size:13 final size:13
Alignment explanation
Indices: 1231031--1231055 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1231021 ATATAATCCT
1231031 GAAGAAGAAAAAA
1 GAAGAAGAAAAAA
1231044 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1231056 GTCCCCGAAG
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAAAAA
Found at i:1233447 original size:72 final size:72
Alignment explanation
Indices: 1233354--1233587 Score: 295
Period size: 72 Copynumber: 3.3 Consensus size: 72
1233344 GCAACGAGAG
1233354 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1233419 AAATGAA
66 AAATGAA
* * *
1233426 AATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1233491 AAATGAA
66 AAATGAA
* * * * * *
1233498 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
1233558 CG--A-GAG
64 CGAAATGAA
1233564 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
1233588 GCAATGCGAA
Statistics
Matches: 141, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 16 0.11
72 93 0.66
73 8 0.06
74 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:1233475 original size:53 final size:52
Alignment explanation
Indices: 1233340--1233609 Score: 406
Period size: 53 Copynumber: 5.1 Consensus size: 52
1233330 CGGAAATTAC
*
1233340 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1233387 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1233445 AATCACAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1233498 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1233550 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
1233603 AATCGCA
1 AATCGCA
1233610 TTGCGATTCT
Statistics
Matches: 205, Mismatches: 5, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 66 0.32
53 114 0.56
55 2 0.01
56 1 0.00
57 2 0.01
58 10 0.05
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1233559 original size:105 final size:109
Alignment explanation
Indices: 1233340--1233609 Score: 425
Period size: 105 Copynumber: 2.6 Consensus size: 109
1233330 CGGAAATTAC
*
1233340 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG
1233399 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
65 G-AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1233445 AATCACAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGG
*
1233508 -A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
66 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1233550 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1233610 TTGCGATTCT
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 123 0.79
106 16 0.10
108 2 0.01
109 1 0.01
110 2 0.01
111 11 0.07
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (109 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGG
AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1233615 original size:72 final size:68
Alignment explanation
Indices: 1233321--1233614 Score: 267
Period size: 72 Copynumber: 4.2 Consensus size: 68
1233311 GCATTTGACT
** * * *
1233321 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-AAG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
1233385 AAA
66 AAA
* *
1233388 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCACAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
1233453 CG-AGAGA
61 CGAAGAAA
* * * * *
1233460 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
1233522 CGAAATGAAA
61 CG-AA-GAAA
1233532 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
1233596 AAATGAAA
63 -AA-GAAA
*
1233604 ATCGCATTGCG
1 ATCGCAATGCG
1233615 ATTCTCTCGT
Statistics
Matches: 188, Mismatches: 20, Indels: 32
0.78 0.08 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 32 0.17
69 4 0.02
70 1 0.01
71 21 0.11
72 108 0.57
73 3 0.02
74 5 0.03
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (68 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAAG
AAA
Found at i:1233649 original size:53 final size:52
Alignment explanation
Indices: 1233586--1233701 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
1233576 GAAATGAAAA
*
1233586 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** ** *
1233638 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1233691 TCGCATTGCGA
1 TCGCATTGCGA
1233702 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 11 0.20
53 44 0.80
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1233664 original size:19 final size:19
Alignment explanation
Indices: 1233624--1233711 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
1233614 GATTCTCTCG
1233624 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1233644 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1233663 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1233677 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1233696 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1233712 AACATAATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
14 5 0.08
16 7 0.12
17 7 0.12
19 25 0.42
20 15 0.25
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1233821 original size:14 final size:14
Alignment explanation
Indices: 1233802--1233838 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1233792 CATCAATTAC
1233802 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1233816 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1233830 ACAAATCAA
1 ACAAATCAA
1233839 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1235800 original size:19 final size:19
Alignment explanation
Indices: 1235758--1235897 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
1235748 TAGTTTACTT
* *
1235758 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TCAAAA
* *
1235778 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATCAAAA
* *
1235797 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
1235816 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
1235835 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
1235854 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
*
1235868 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
1235887 TCGCAATGCGA
1 TCGCAACGCGA
1235898 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 73 0.73
20 12 0.12
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:1235928 original size:14 final size:14
Alignment explanation
Indices: 1235909--1235967 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1235899 TTTGGTTTCG
1235909 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1235923 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
1235940 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
*
1235956 TGTTGCGATTTT
1 CGTTGCGATTTT
1235968 CATTTCGCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.59
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.30
ACGTcount: A:0.07, C:0.15, G:0.29, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1235935 original size:33 final size:33
Alignment explanation
Indices: 1235893--1236016 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
1235883 AAAATCGCAA
*
1235893 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
*
1235926 TGCGATTTTGGTTTCGCGTTGCGATTCTGTTGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
1235959 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
1235992 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
1236017 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 69 0.85
34 12 0.15
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1235947 original size:19 final size:18
Alignment explanation
Indices: 1235893--1235984 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
1235883 AAAATCGCAA
1235893 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1235912 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
1235926 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
1235945 TGCGATTCTG-TT---GT
1 TGCGATTTTGTTTCGCGT
*
1235959 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1235978 TGCGATT
1 TGCGATT
1235985 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 22 0.37
15 1 0.02
16 3 0.05
17 3 0.05
18 2 0.03
19 29 0.48
ACGTcount: A:0.08, C:0.16, G:0.28, T:0.48
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1236255 original size:93 final size:93
Alignment explanation
Indices: 1236114--1237173 Score: 2093
Period size: 93 Copynumber: 11.4 Consensus size: 93
1236104 TCAGGGTATT
*
1236114 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACAAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1236179 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1236207 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1236272 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1236300 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1236365 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1236393 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1236458 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1236486 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1236551 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1236579 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1236644 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
1236672 AGTTTAGCAGAATTGGCAGCAACCGAAAAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1236737 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1236765 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1236830 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1236858 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1236923 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1236951 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1237016 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
1237044 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1237109 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
1237137 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1237174 AAGCAATCTA
Statistics
Matches: 963, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 963 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:1238920 original size:19 final size:19
Alignment explanation
Indices: 1238855--1238968 Score: 103
Period size: 19 Copynumber: 6.1 Consensus size: 19
1238845 TCTTTTGGTT
*
1238855 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
1238874 GAGAATGACTGTCGCAACAAGA
1 GA-AATGAAAATCGCAAC--GC
1238896 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1238915 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1238932 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1238948 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1238967 GA
1 GA
1238969 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 33 0.43
20 12 0.16
21 12 0.16
22 4 0.05
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1238999 original size:14 final size:14
Alignment explanation
Indices: 1238980--1239036 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1238970 TTTGGTTTCG
1238980 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1238994 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1239013 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1239027 CGTTGCGATT
1 CGTTGCGATT
1239037 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1239012 original size:33 final size:33
Alignment explanation
Indices: 1238964--1239043 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1238954 AAAATCGCAA
**
1238964 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1238997 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1239030 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1239044 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1239049 original size:21 final size:21
Alignment explanation
Indices: 1239024--1239097 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1239014 GTTGCGATTC
1239024 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
1239045 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
1239066 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
1239087 TCTCGTTGCGA
1 TCTCGTTGCGA
1239098 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:1239219 original size:33 final size:33
Alignment explanation
Indices: 1239177--1239247 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1239167 AATACTAACT
1239177 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1239210 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1239243 TGAAA
1 TGAAA
1239248 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1239652 original size:20 final size:20
Alignment explanation
Indices: 1239627--1239758 Score: 176
Period size: 20 Copynumber: 6.6 Consensus size: 20
1239617 CTTTAAAAAT
1239627 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1239647 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
1239667 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1239687 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
1239707 CGAGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1239727 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1239747 CGCGTTGCGATT
1 CGCGTTGCGATT
1239759 CTGGAAAATC
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
20 99 0.99
21 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1244847 original size:23 final size:23
Alignment explanation
Indices: 1244821--1244866 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1244811 CTTTTCTCGA
1244821 AAAATATTTTCTCTCATTCTTAG
1 AAAATATTTTCTCTCATTCTTAG
* *
1244844 AAAATATTTTCTTTCCTTCTTAG
1 AAAATATTTTCTCTCATTCTTAG
1244867 CTTTTCGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.50
Consensus pattern (23 bp):
AAAATATTTTCTCTCATTCTTAG
Found at i:1248036 original size:17 final size:17
Alignment explanation
Indices: 1248014--1248051 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1248004 GATCAAAGGA
1248014 TAACATCGTGGATCCGC
1 TAACATCGTGGATCCGC
1248031 TAACATCGTGGATCCGC
1 TAACATCGTGGATCCGC
1248048 TAAC
1 TAAC
1248052 CAAAGGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (17 bp):
TAACATCGTGGATCCGC
Found at i:1249404 original size:29 final size:28
Alignment explanation
Indices: 1249358--1249429 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
1249348 CTTCCATTTA
**
1249358 TTTTCTTTT-TTTAAAAAGAAATTAATT
1 TTTTCTTTTATTTTTAAAGAAATTAATT
1249385 TCTTTCTTTTATTTTTAAAGAAATTAATT
1 T-TTTCTTTTATTTTTAAAGAAATTAATT
*
1249414 TATTCTTTTTATTTTT
1 TTTTC-TTTTATTTTT
1249430 CTCAGGTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 1 0.03
28 11 0.28
29 27 0.69
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTTCTTTTATTTTTAAAGAAATTAATT
Found at i:1250506 original size:2 final size:2
Alignment explanation
Indices: 1250499--1250538 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1250489 GATACTACAA
1250499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1250539 TACAACGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1251271 original size:2 final size:2
Alignment explanation
Indices: 1251264--1251331 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
1251254 ATTACTTTTA
1251264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1251306 AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1251332 CCTTTATGCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1252295 original size:18 final size:19
Alignment explanation
Indices: 1252274--1252311 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1252264 CCAAAGTTCA
1252274 AAATTTA-ATAAAAATATT
1 AAATTTACATAAAAATATT
1252292 AAATTTACGATAAAAATATT
1 AAATTTAC-ATAAAAATATT
1252312 TAAAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (19 bp):
AAATTTACATAAAAATATT
Found at i:1252744 original size:32 final size:32
Alignment explanation
Indices: 1252702--1252771 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
1252692 CTGATTCAAG
*
1252702 ATTGATCTGAAGCGAAAATCAATAGATTTGAC
1 ATTGACCTGAAGCGAAAATCAATAGATTTGAC
* * * *
1252734 ATTGACCTGAATCGAAAATCGATCGATTTGAT
1 ATTGACCTGAAGCGAAAATCAATAGATTTGAC
1252766 ATTGAC
1 ATTGAC
1252772 ATGATCCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (32 bp):
ATTGACCTGAAGCGAAAATCAATAGATTTGAC
Found at i:1252784 original size:32 final size:32
Alignment explanation
Indices: 1252716--1252793 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
1252706 ATCTGAAGCG
* *
1252716 AAAATCAATAGATTTGACATTGACCTGAATCG
1 AAAATCAATAGATTTGACATTGACATGAATCA
* * *
1252748 AAAATCGATCGATTTGATATTGACATG-ATCCA
1 AAAATCAATAGATTTGACATTGACATGAAT-CA
*
1252780 AAAATCAATTGATT
1 AAAATCAATAGATT
1252794 CAATATTAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 2 0.05
32 36 0.95
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (32 bp):
AAAATCAATAGATTTGACATTGACATGAATCA
Found at i:1255528 original size:23 final size:23
Alignment explanation
Indices: 1255484--1255528 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1255474 AAAACAACCA
* *
1255484 TTCATCTTTATATCATTCTTATT
1 TTCATCTTTATATAATTATTATT
1255507 TTCATTCTTTAT-TAATTATTAT
1 TTCA-TCTTTATATAATTATTAT
1255529 ACTTGAATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.62
Consensus pattern (23 bp):
TTCATCTTTATATAATTATTATT
Found at i:1258331 original size:4 final size:4
Alignment explanation
Indices: 1258296--1258342 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
1258286 TATCTATATA
*
1258296 TATG TATG TATG TATG TATG TATG TATA TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1258343 CGTGTGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1265990 original size:27 final size:27
Alignment explanation
Indices: 1265949--1266009 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
1265939 AACTGTGAAA
* *
1265949 TGGCTTCCCTTATTTTTCCATTTTCAG
1 TGGCCTCCCTCATTTTTCCATTTTCAG
*
1265976 TGGCCTCCCTCATTTTTCCATTTTCGG
1 TGGCCTCCCTCATTTTTCCATTTTCAG
1266003 TGGCCTC
1 TGGCCTC
1266010 TCTTGGCCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.08, C:0.31, G:0.15, T:0.46
Consensus pattern (27 bp):
TGGCCTCCCTCATTTTTCCATTTTCAG
Found at i:1271612 original size:2 final size:2
Alignment explanation
Indices: 1271605--1271633 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1271595 ATATTCAAAC
1271605 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1271634 TAATTTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1272811 original size:70 final size:70
Alignment explanation
Indices: 1272720--1272860 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
1272710 AAAATAAGTA
*
1272720 TTATATATTTAAAATAATGAATATAATTAAAAAGATATTATATCAAAGTTATTAATTATATTTTA
1 TTATATATTTAAAATAATGAATATAATTAAAAAGATATTATATCAAAGTTAATAATTATATTTTA
1272785 TTTAT
66 TTTAT
*
1272790 TTATATATTTAAAATAATGAATATAATTAAAAAGATATTATATCAAAGTTAATAATTATCTTTTA
1 TTATATATTTAAAATAATGAATATAATTAAAAAGATATTATATCAAAGTTAATAATTATATTTTA
1272855 TTTAT
66 TTTAT
1272860 T
1 T
1272861 AAAAAATTTA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (70 bp):
TTATATATTTAAAATAATGAATATAATTAAAAAGATATTATATCAAAGTTAATAATTATATTTTA
TTTAT
Found at i:1274574 original size:16 final size:16
Alignment explanation
Indices: 1274555--1274592 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1274545 GTTGTTATTA
*
1274555 TTTCTAGTTATTACTG
1 TTTCTAGCTATTACTG
*
1274571 TTTCTAGCTATTATTG
1 TTTCTAGCTATTACTG
1274587 TTTCTA
1 TTTCTA
1274593 TTTCTAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (16 bp):
TTTCTAGCTATTACTG
Found at i:1277051 original size:67 final size:67
Alignment explanation
Indices: 1276898--1277055 Score: 165
Period size: 67 Copynumber: 2.4 Consensus size: 67
1276888 TGTTACTCGA
* * *
1276898 CTCGACTCGTTGCTCGTTAA-CTCATTAAAATTTTGCTCGACTCATACTCGTTAAGAAAATTTGC
1 CTCGACTCGTTGCTCGTTAAGCTCGTTAAAATTTTACTCGACTCATACTCATTAAGAAAATTTGC
1276962 TG
66 TG
* * * * * * ** * * *
1276964 CTCAAATCGTTTCTCATTAAGCTCGTTAAAATTTTACTCTATTTGTGCTCATTAAGAAATTTTGG
1 CTCGACTCGTTGCTCGTTAAGCTCGTTAAAATTTTACTCGACTCATACTCATTAAGAAAATTTGC
*
1277029 TT
66 TG
*
1277031 CTCGACTCATTGCTCGTTAAGCTCG
1 CTCGACTCGTTGCTCGTTAAGCTCG
1277056 CTGAATTTCT
Statistics
Matches: 71, Mismatches: 20, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
66 16 0.23
67 55 0.77
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.39
Consensus pattern (67 bp):
CTCGACTCGTTGCTCGTTAAGCTCGTTAAAATTTTACTCGACTCATACTCATTAAGAAAATTTGC
TG
Found at i:1277846 original size:23 final size:21
Alignment explanation
Indices: 1277816--1277859 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1277806 TGAAAATTAT
*
1277816 AAATAAAAAATTAATATAATATA
1 AAAT-AAAAA-TAAAATAATATA
1277839 AAATAAAAATAAAATAATATA
1 AAATAAAAATAAAATAATATA
1277860 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 5 0.25
23 4 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAAAATAAAATAATATA
Found at i:1277862 original size:2 final size:2
Alignment explanation
Indices: 1277855--1277885 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1277845 AAATAAAATA
1277855 AT 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 AT A
1277886 AACCGGGTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1279182 original size:2 final size:2
Alignment explanation
Indices: 1279175--1279207 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1279165 GATCTTAACC
1279175 AT AT 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 AT AT A
1279208 CATTAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.