Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 4 of 196
Found at i:1014115 original size:18 final size:18
Alignment explanation
Indices: 1014092--1014130 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1014082 GCATCCAAAC
1014092 AAAACAAAACAAAACAAT
1 AAAACAAAACAAAACAAT
* *
1014110 AAAACAAAATAAAATAAT
1 AAAACAAAACAAAACAAT
1014128 AAA
1 AAA
1014131 TAAATTACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (18 bp):
AAAACAAAACAAAACAAT
Found at i:1014541 original size:21 final size:21
Alignment explanation
Indices: 1014515--1014557 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1014505 GGTTCGCTGT
*
1014515 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
1014536 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
1014557 A
1 A
1014558 ATAGAGGTGT
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:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:1014557 original size:16 final size:16
Alignment explanation
Indices: 1014538--1014570 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1014528 TGTATTGGAT
*
1014538 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
1014554 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
1014570 T
1 T
1014571 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:1014615 original size:45 final size:44
Alignment explanation
Indices: 1014549--1014643 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
1014539 GGATTAGAGG
* *
1014549 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
1014594 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
1014638 TGTAAT
1 TGTAAT
1014644 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:1014826 original size:18 final size:17
Alignment explanation
Indices: 1014805--1014839 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1014795 TTATTATTTA
*
1014805 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1014823 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1014840 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1014833 original size:28 final size:27
Alignment explanation
Indices: 1014763--1014835 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
1014753 TTTATTATCA
*
1014763 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
1014791 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
1014818 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
1014836 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:1014952 original size:144 final size:147
Alignment explanation
Indices: 1014724--1014995 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
1014714 ATGATTATTG
1014724 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
1014789 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
1014854 AGAAATTTGCTTTGGTAAA
129 AGAAATTTGCTTTGGTAAA
*
1014873 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
1014935 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
1014996 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGCTTTGGTAAA
Found at i:1014970 original size:18 final size:17
Alignment explanation
Indices: 1014949--1014983 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1014939 TTATTATTAA
*
1014949 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1014967 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1014984 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1015027 original size:54 final size:54
Alignment explanation
Indices: 1014969--1015147 Score: 128
Period size: 55 Copynumber: 3.1 Consensus size: 54
1014959 ATTAAAATAT
*
1014969 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
** * * * * *
1015023 ATAATATATGATACTGTAAAATAT-AAAATAACATAATTATTATTAAATAT-AATATAATTAAAA
1 ATAAT-T-T-A-A---TAAAAT-TCTTAATAA-TTAA-TATTCTT--ATATGAAT-TTACTCAAA
*
1015086 TAT
53 -AC
*
1015089 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
1015143 ATAAT
1 ATAAT
1015148 ATATGATTAT
Statistics
Matches: 91, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
54 10 0.11
55 11 0.12
56 4 0.04
57 7 0.08
58 5 0.05
59 11 0.12
61 11 0.12
62 5 0.05
63 7 0.08
64 4 0.04
65 11 0.12
66 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
Found at i:1015029 original size:61 final size:61
Alignment explanation
Indices: 1014964--1015151 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
1014954 TTTTAATTAA
*
1014964 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * *
1015025 AATATATGATACT-GTAAAA-T-ATAA-AATAACATAATTATTAT-TAAATATAAT-ATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAATAATTA-AT-ATTCTTATATGAATTTACTCA-AATCAT
1015084 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1015145 AATATAT
1 AATATAT
1015152 GATTATAACT
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 29 0.31
60 16 0.17
61 37 0.39
62 6 0.06
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:1015062 original size:120 final size:120
Alignment explanation
Indices: 1014932--1015154 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
1014922 ATCATATTTA
* *
1014932 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1014997 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
1015052 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
1015117 TATTCTTATATGAATTTACTCAAATCATAATATATGAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGAT
1015155 TATAACTAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
Found at i:1015090 original size:18 final size:17
Alignment explanation
Indices: 1015069--1015103 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1015059 TTATTATTAA
1015069 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
1015087 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
1015104 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:1015166 original size:17 final size:16
Alignment explanation
Indices: 1015144--1015190 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1015134 ACTCAAATCA
1015144 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
1015161 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
1015175 TAAATATATGATTTAA
1 T-AATATATGATTTAA
1015191 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:1015191 original size:17 final size:17
Alignment explanation
Indices: 1015163--1015196 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1015153 ATTATAACTA
*
1015163 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
1015180 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
1015197 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:1015339 original size:93 final size:92
Alignment explanation
Indices: 1015229--1015423 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
1015219 GATTATAGTT
* * *
1015229 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
1015292 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
1015322 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
1015387 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
1015414 TATGAATTTA
1 TATGAATTTA
1015424 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:1023124 original size:25 final size:24
Alignment explanation
Indices: 1023057--1023124 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
1023047 ATGAAAATGT
*
1023057 TATTGTATAAATAAAATTA-CAAA
1 TATTGTAAAAATAAAATTATCAAA
* * * *
1023080 TA-TATAAAAATGGAATTTATGAATA
1 TATTGTAAAAAT-AAAATTATCAA-A
1023105 TATTGTAAAAATAAAATTAT
1 TATTGTAAAAATAAAATTAT
1023125 AGAAATGTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 7 0.21
23 7 0.21
24 2 0.06
25 9 0.27
26 8 0.24
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (24 bp):
TATTGTAAAAATAAAATTATCAAA
Found at i:1023283 original size:12 final size:12
Alignment explanation
Indices: 1023267--1023302 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1023257 AATAACATTT
1023267 ATAATAATAGTA
1 ATAATAATAGTA
*
1023279 GTAATAATAGTA
1 ATAATAATAGTA
1023291 ATAATAATAGTA
1 ATAATAATAGTA
1023303 TTATAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:1024762 original size:15 final size:15
Alignment explanation
Indices: 1024742--1024775 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1024732 TTGATTAAAC
1024742 TTAATTAAA-TATTAA
1 TTAATTAAACT-TTAA
1024757 TTAATTAAACTTTAA
1 TTAATTAAACTTTAA
1024772 TTAA
1 TTAA
1024776 CCTAACCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.94
16 1 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATTAAACTTTAA
Found at i:1028272 original size:3 final size:3
Alignment explanation
Indices: 1028264--1028288 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1028254 TCCTTCCTTC
1028264 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1028289 ATTGGGGCAT
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:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1029807 original size:21 final size:21
Alignment explanation
Indices: 1029778--1029835 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1029768 TATTTTTGAA
1029778 AATAA-TTA-TGAACTTTTCTTT
1 AATAATTTATTGAA-TTTT-TTT
1029799 -ATAATTTATTGAATTTTTTT
1 AATAATTTATTGAATTTTTTT
1029819 AATAATTT-TT-AATTTTT
1 AATAATTTATTGAATTTTT
1029836 ATAAAATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
19 7 0.21
20 9 0.26
21 14 0.41
22 4 0.12
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
AATAATTTATTGAATTTTTTT
Found at i:1042238 original size:20 final size:20
Alignment explanation
Indices: 1042215--1042254 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1042205 CTTTGTTTCC
1042215 ATTTACAATGGAGGAATCTG
1 ATTTACAATGGAGGAATCTG
1042235 ATTTACAATGGAGGAATCTG
1 ATTTACAATGGAGGAATCTG
1042255 TTGAAGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
ATTTACAATGGAGGAATCTG
Found at i:1045856 original size:12 final size:12
Alignment explanation
Indices: 1045841--1045870 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1045831 GAAAAGATTA
1045841 CGAATGAGATCG
1 CGAATGAGATCG
1045853 CGAATGAGATCG
1 CGAATGAGATCG
1045865 CGAATG
1 CGAATG
1045871 GTGATGTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (12 bp):
CGAATGAGATCG
Found at i:1052074 original size:32 final size:32
Alignment explanation
Indices: 1052033--1052096 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1052023 AAATTAGGCC
1052033 ACATGCGTATCCATTTAAAAGCATGTACTATG
1 ACATGCGTATCCATTTAAAAGCATGTACTATG
1052065 ACATGCGTATCCATTTAAAAGCATGTACTATG
1 ACATGCGTATCCATTTAAAAGCATGTACTATG
1052097 TTGGAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (32 bp):
ACATGCGTATCCATTTAAAAGCATGTACTATG
Found at i:1053175 original size:10 final size:10
Alignment explanation
Indices: 1053113--1053185 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
1053103 AATACTATAA
1053113 AATATAATTT
1 AATATAATTT
*
1053123 AAAATAA-TT
1 AATATAATTT
*
1053132 -AT-T-ATTA
1 AATATAATTT
1053139 AATATAATTT
1 AATATAATTT
**
1053149 AATA-AAAAT
1 AATATAATTT
1053158 -ATATAATTT
1 AATATAATTT
* *
1053167 AATAAAATTC
1 AATATAATTT
1053177 AATATAATT
1 AATATAATT
1053186 ATTCTTATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 6 0.13
9 9 0.20
10 28 0.61
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATAATTT
Found at i:1053224 original size:117 final size:119
Alignment explanation
Indices: 1053000--1053272 Score: 505
Period size: 117 Copynumber: 2.3 Consensus size: 119
1052990 TTAATCATAT
*
1053000 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TAATATT
1053065 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
1053120 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-AATA-TA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
*
1053183 ATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
1053237 TTTAAAATAATTATTATTAAATATAATTTAATAAAA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAA
1053273 TTCAATATAA
Statistics
Matches: 151, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
117 91 0.60
118 4 0.03
120 56 0.37
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (119 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:1053269 original size:99 final size:98
Alignment explanation
Indices: 1053158--1053345 Score: 367
Period size: 99 Copynumber: 1.9 Consensus size: 98
1053148 TAATAAAAAT
1053158 ATATAATTTAATAAAATTCAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAAT
1 ATATAATTTAATAAAATTCAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAAT
1053223 ACTATAAAATATAATTTAAAATAATTATTATTAA
66 ACTAT-AAATATAATTTAAAATAATTATTATTAA
1053257 ATATAATTTAATAAAATTCAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAAT
1 ATATAATTTAATAAAATTCAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAAT
1053322 ACTATAAATATAATTTAAAATAAT
66 ACTATAAATATAATTTAAAATAAT
1053346 CTACTTTATT
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 19 0.21
99 70 0.79
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (98 bp):
ATATAATTTAATAAAATTCAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAAT
ACTATAAATATAATTTAAAATAATTATTATTAA
Found at i:1053283 original size:36 final size:36
Alignment explanation
Indices: 1053243--1053339 Score: 94
Period size: 36 Copynumber: 2.7 Consensus size: 36
1053233 ATAATTTAAA
1053243 ATAATTATTATTAAATATAATTTAATAAAATTC-AAT
1 ATAATTATTATTAAATATAATTTAATAAAA-TCAAAT
* *
1053279 ATAATTATTCTT--ATATGAATTTACTAAAATCATAAT
1 ATAATTATTATTAAATAT-AATTTAATAAAATCA-AAT
* *
1053315 ATATAATACTA-TAAATATAATTTAA
1 ATA-ATTATTATTAAATATAATTTAA
1053340 AATAATCTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
34 6 0.12
35 11 0.22
36 18 0.37
37 10 0.20
38 4 0.08
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (36 bp):
ATAATTATTATTAAATATAATTTAATAAAATCAAAT
Found at i:1053343 original size:21 final size:21
Alignment explanation
Indices: 1053300--1053343 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1053290 TATATGAATT
*
1053300 TACTAAAATCATAATATATAA
1 TACTAAAATCATAATATAAAA
*
1053321 TACTATAAAT-ATAATTTAAAA
1 TACTA-AAATCATAATATAAAA
1053342 TA
1 TA
1053344 ATCTACTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (21 bp):
TACTAAAATCATAATATAAAA
Found at i:1060634 original size:15 final size:15
Alignment explanation
Indices: 1060593--1060636 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
1060583 TCGCATGCGG
*
1060593 AAATATAATTATACT
1 AAATATAATTATAAT
*
1060608 AAAAATTAAATTATAAT
1 AAATA-T-AATTATAAT
1060625 AAATATAATTAT
1 AAATATAATTAT
1060637 GTGAGACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 12 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATATAATTATAAT
Found at i:1065729 original size:3 final size:3
Alignment explanation
Indices: 1065723--1065769 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1065713 GTAGTAACCC
1065723 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1065770 AATCTTTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1078663 original size:13 final size:13
Alignment explanation
Indices: 1078645--1078699 Score: 76
Period size: 12 Copynumber: 4.2 Consensus size: 13
1078635 TTCAATTTTT
1078645 TATTTTTAATTAA
1 TATTTTTAATTAA
1078658 TATTTTTTCAATTAA
1 TA-TTTTT-AATTAA
*
1078673 TATTTTTAATTTA
1 TATTTTTAATTAA
1078686 T-TTTTTAATTAA
1 TATTTTTAATTAA
1078698 TA
1 TA
1078700 ACTCTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
12 11 0.30
13 8 0.22
14 10 0.27
15 8 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTTAATTAA
Found at i:1078670 original size:15 final size:14
Alignment explanation
Indices: 1078647--1078699 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
1078637 CAATTTTTTA
1078647 TTTTTAATTAATAT
1 TTTTTAATTAATAT
1078661 TTTTTCAATTAATA-
1 TTTTT-AATTAATAT
1078675 TTTTTAATT--TAT
1 TTTTTAATTAATAT
1078687 TTTTTAATTAATA
1 TTTTTAATTAATA
1078700 ACTCTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.06
12 9 0.26
13 4 0.11
14 12 0.34
15 8 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTAATTAATAT
Found at i:1078677 original size:28 final size:27
Alignment explanation
Indices: 1078618--1078699 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 27
1078608 ACATTTGTAT
* * **
1078618 TTTTTATTTCATATTGTTTCAATTTTTTA
1 TTTTTAATT-ATATTTTTTCAA-TTAATA
1078647 TTTTTAATTAATATTTTTTCAATTAATA
1 TTTTTAATT-ATATTTTTTCAATTAATA
1078675 TTTTTAATT-TATTTTTT-AATTAATA
1 TTTTTAATTATATTTTTTCAATTAATA
1078700 ACTCTTTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
25 8 0.17
26 8 0.17
28 13 0.27
29 19 0.40
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (27 bp):
TTTTTAATTATATTTTTTCAATTAATA
Found at i:1078713 original size:27 final size:26
Alignment explanation
Indices: 1078645--1078699 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 26
1078635 TTCAATTTTT
1078645 TATTTTTAATTAATATTTTTTCAATTAA
1 TATTTTTAATT--TATTTTTTCAATTAA
1078673 TATTTTTAATTTATTTTTT-AATTAA
1 TATTTTTAATTTATTTTTTCAATTAA
1078698 TA
1 TA
1078700 ACTCTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 8 0.30
26 8 0.30
28 11 0.41
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
TATTTTTAATTTATTTTTTCAATTAA
Found at i:1079033 original size:105 final size:104
Alignment explanation
Indices: 1078843--1079040 Score: 240
Period size: 105 Copynumber: 1.9 Consensus size: 104
1078833 TGTGTATTTC
* **
1078843 AAATAATTATTTGAAATATTTCACATATAAACGTAATGATATTTGAAATAATTAATTCATATATA
1 AAATAATTACTTGAAATATTTCACATATAAAAATAATGATATTTGAAATAATTAATTCATATATA
* *
1078908 AAAATATTTGAAATATCATA-CCACAATGTAGATGAAAA
66 AAAATATTAGAAATACCATACCCACAATGTAGATGAAAA
* * *
1078946 AAATAA-TACTTGAAATATTTTACATATAAAAATAATAATGATATTTGAAATAATTTATT-TTAT
1 AAATAATTACTTGAAATATTTCACATAT--AAA-AATAATGATATTTGAAATAATTAATTCATAT
* * *
1079009 TTTATAATATTAGAAATCACCATACCCACAAT
63 ATAAAAATATTAGAAAT-ACCATACCCACAAT
1079041 ATAGCTGGAG
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
102 19 0.24
103 6 0.08
104 19 0.24
105 28 0.35
106 7 0.09
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (104 bp):
AAATAATTACTTGAAATATTTCACATATAAAAATAATGATATTTGAAATAATTAATTCATATATA
AAAATATTAGAAATACCATACCCACAATGTAGATGAAAA
Found at i:1081272 original size:20 final size:20
Alignment explanation
Indices: 1081236--1081273 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1081226 ACAAATTTTA
* *
1081236 TATTATTATTGTTATTGCAT
1 TATTATTATTATAATTGCAT
1081256 TATTATTATTATAATTGC
1 TATTATTATTATAATTGC
1081274 TTTTATAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (20 bp):
TATTATTATTATAATTGCAT
Found at i:1081301 original size:22 final size:23
Alignment explanation
Indices: 1081276--1081321 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1081266 ATAATTGCTT
1081276 TTATAGATATATACATATA-TTA
1 TTATAGATATATACATATACTTA
* * *
1081298 TTATATATTTTTACATATACTTA
1 TTATAGATATATACATATACTTA
1081321 T
1 T
1081322 ACACATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATAGATATATACATATACTTA
Found at i:1081329 original size:22 final size:22
Alignment explanation
Indices: 1081287--1081331 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1081277 TATAGATATA
* *
1081287 TACATATATTATTATATATTTT
1 TACATATATTATTACACATTTT
1081309 TACATATACTTA-TACACATTTT
1 TACATATA-TTATTACACATTTT
1081331 T
1 T
1081332 TTTGTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (22 bp):
TACATATATTATTACACATTTT
Found at i:1081450 original size:24 final size:24
Alignment explanation
Indices: 1081423--1081477 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1081413 ATTTCTAACC
1081423 TTTATAAATATATAAATACATATT
1 TTTATAAATATATAAATACATATT
* * **
1081447 TTTACATATATATATGTACATATT
1 TTTATAAATATATAAATACATATT
1081471 TTATATA
1 TT-TATA
1081478 TTTTATAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTATAAATATATAAATACATATT
Found at i:1083201 original size:4 final size:4
Alignment explanation
Indices: 1083194--1083228 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1083184 AAACAATGTA
* *
1083194 ATAC ATAC ATAC ATGC AAAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1083229 GCTACTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:1089842 original size:13 final size:13
Alignment explanation
Indices: 1089809--1089835 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1089799 ACAGAGCTAA
1089809 CCTGATATGATCG
1 CCTGATATGATCG
1089822 CCTGATATGATCG
1 CCTGATATGATCG
1089835 C
1 C
1089836 TTTATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (13 bp):
CCTGATATGATCG
Found at i:1094236 original size:22 final size:21
Alignment explanation
Indices: 1094202--1094248 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
1094192 AAAAAAATTA
1094202 AGAAAAAAAATGGAAGGTTCT
1 AGAAAAAAAATGGAAGGTTCT
*
1094223 AGAAAGAAGAATGGAAGGTTCT
1 AGAAA-AAAAATGGAAGGTTCT
1094245 AGAA
1 AGAA
1094249 TGATCGGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.51, C:0.04, G:0.28, T:0.17
Consensus pattern (21 bp):
AGAAAAAAAATGGAAGGTTCT
Found at i:1100666 original size:43 final size:43
Alignment explanation
Indices: 1100607--1100690 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
1100597 TAGCATAAGG
1100607 AAAAAAACTAAAATGACTAGAATACCCTTAGCATAATTTTTAA
1 AAAAAAACTAAAATGACTAGAATACCCTTAGCATAATTTTTAA
1100650 AAAAAAACTAAAATGACTAGAATACCCTTAGCATAATTTTT
1 AAAAAAACTAAAATGACTAGAATACCCTTAGCATAATTTTT
1100691 TTTAGGTAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (43 bp):
AAAAAAACTAAAATGACTAGAATACCCTTAGCATAATTTTTAA
Found at i:1100873 original size:24 final size:23
Alignment explanation
Indices: 1100803--1100898 Score: 78
Period size: 21 Copynumber: 4.3 Consensus size: 23
1100793 TTATTATTAA
1100803 ATATAATTTAAT-AAA--ATAAT
1 ATATAATTTAATAAAATCATAAT
* **
1100823 ATATAATTTAATAAAATTATTGTT
1 ATATAATTTAATAAAATCA-TAAT
*
1100847 ATATGAATTTACTAAAATCATAAT
1 ATAT-AATTTAATAAAATCATAAT
*
1100871 ATATAATACT-ATAAAA--ATAAT
1 ATATAAT-TTAATAAAATCATAAT
1100892 ATATAAT
1 ATATAAT
1100899 CTACTTTATT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
20 12 0.19
21 15 0.24
23 9 0.15
24 13 0.21
25 13 0.21
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATAATTTAATAAAATCATAAT
Found at i:1102696 original size:13 final size:13
Alignment explanation
Indices: 1102678--1102702 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1102668 GGACATGCAA
1102678 TAATGTAAGGCTG
1 TAATGTAAGGCTG
1102691 TAATGTAAGGCT
1 TAATGTAAGGCT
1102703 CCCTCGACAG
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:0.08, G:0.28, T:0.32
Consensus pattern (13 bp):
TAATGTAAGGCTG
Found at i:1103767 original size:16 final size:16
Alignment explanation
Indices: 1103746--1103800 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
1103736 GCTTGATTCA
*
1103746 CTGTAAT-GAAATAGAG
1 CTGTAATAG-AATAAAG
1103762 CTGTAATAGAATAAAG
1 CTGTAATAGAATAAAG
*
1103778 CTGCAATAGAATAAAG
1 CTGTAATAGAATAAAG
1103794 CTGTAAT
1 CTGTAAT
1103801 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
16 34 0.97
17 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (16 bp):
CTGTAATAGAATAAAG
Found at i:1104090 original size:58 final size:56
Alignment explanation
Indices: 1103960--1104093 Score: 173
Period size: 58 Copynumber: 2.3 Consensus size: 56
1103950 TATTGTTATT
1103960 AAATTTTAATA-AGATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTTA
1 AAATTTTAATATA-ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTTA
* * *
1104016 ACATATTTTAACATAATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTAATA
1 A-A-ATTTTAATATAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTT--TA
1104075 AAATTCTTAATATAATTAT
1 AAATT-TTAATATAATTAT
1104094 AATATGAATT
Statistics
Matches: 68, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
56 1 0.01
57 20 0.29
58 43 0.63
59 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (56 bp):
AAATTTTAATATAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTTA
Found at i:1104103 original size:12 final size:11
Alignment explanation
Indices: 1104037--1104104 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 11
1104027 CATAATTATT
1104037 ATTA-AATATA
1 ATTATAATATA
*
1104047 ATT-TAATAAA
1 ATTATAATATA
*
1104057 ATAAT-ATATA
1 ATTATAATATA
*
1104067 ATT-TAATAAA
1 ATTATAATATA
*
1104077 ATTCTTAATATA
1 ATT-ATAATATA
1104089 ATTATAATATGA
1 ATTATAATAT-A
1104101 ATTA
1 ATTA
1104105 AAAATTCATA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
9 1 0.02
10 23 0.51
11 7 0.16
12 14 0.31
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
ATTATAATATA
Found at i:1107190 original size:70 final size:69
Alignment explanation
Indices: 1107108--1107240 Score: 203
Period size: 70 Copynumber: 1.9 Consensus size: 69
1107098 ATTTAAAAAA
* ** *
1107108 AAAAAAGGTCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCTTAAGATCGTTTAAAATT
1 AAAAAAGGTCATGCCCAATAAGTTAGGACACGATCTCCTCATAATTCTTAAGATCGTTTAAAATT
1107173 TGGG
66 TGGG
* *
1107177 AAAAATGGATCATGCCCAATAAGTTAGGACACGATCTCCTCATAATTCTTGAGATCGTTTAAAA
1 AAAAAAGG-TCATGCCCAATAAGTTAGGACACGATCTCCTCATAATTCTTAAGATCGTTTAAAA
1107241 CTTGAGTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 7 0.12
70 50 0.88
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (69 bp):
AAAAAAGGTCATGCCCAATAAGTTAGGACACGATCTCCTCATAATTCTTAAGATCGTTTAAAATT
TGGG
Found at i:1107680 original size:11 final size:11
Alignment explanation
Indices: 1107666--1107701 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1107656 ATATGTGAAT
1107666 TATAAAATATA
1 TATAAAATATA
*
1107677 TATAAAAAATA
1 TATAAAATATA
*
1107688 TATATAATATA
1 TATAAAATATA
1107699 TAT
1 TAT
1107702 TTTAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TATAAAATATA
Found at i:1107701 original size:13 final size:13
Alignment explanation
Indices: 1107669--1107694 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1107659 TGTGAATTAT
1107669 AAAATATATATAA
1 AAAATATATATAA
1107682 AAAATATATATAA
1 AAAATATATATAA
1107695 TATATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATATATATAA
Found at i:1122680 original size:18 final size:18
Alignment explanation
Indices: 1122653--1122687 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1122643 TGTTTTATCC
*
1122653 TTTTTCTTTTTCTTTTCT
1 TTTTTCTTTTCCTTTTCT
*
1122671 TTTTTTTTTTCCTTTTC
1 TTTTTCTTTTCCTTTTC
1122688 CTTTGCTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTCTTTTCCTTTTCT
Found at i:1126919 original size:21 final size:21
Alignment explanation
Indices: 1126895--1126934 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1126885 TCTATTTAAA
* *
1126895 AAATTAAAAAACACATTTGGT
1 AAATAAAAAAAAACATTTGGT
1126916 AAATAAAAAAAAACATTTG
1 AAATAAAAAAAAACATTTG
1126935 TTTTCAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (21 bp):
AAATAAAAAAAAACATTTGGT
Found at i:1127348 original size:29 final size:29
Alignment explanation
Indices: 1127293--1127349 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1127283 CTCTTTTTAA
* * *
1127293 AATACTAATGGTCAAATTAAACTAAAAAT
1 AATAATAAGGGTCAAATTAAACAAAAAAT
*
1127322 AATAATAAGGGTCAAATTGAA-AAAAAAT
1 AATAATAAGGGTCAAATTAAACAAAAAAT
1127350 GCAAACATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.25
Consensus pattern (29 bp):
AATAATAAGGGTCAAATTAAACAAAAAAT
Found at i:1128179 original size:19 final size:18
Alignment explanation
Indices: 1128136--1128194 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
1128126 TAACATCTCA
1128136 AAAAAT-TATAAAAACAT
1 AAAAATATATAAAAACAT
*
1128153 AAATAATATATAATAAACTT
1 AAA-AATATATAA-AAACAT
*
1128173 AAAAATATA-AACAAAAAT
1 AAAAATATATAA-AAACAT
1128191 AAAA
1 AAAA
1128195 CAAAACCCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.09
18 13 0.37
19 11 0.31
20 8 0.23
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATATATAAAAACAT
Found at i:1132311 original size:12 final size:12
Alignment explanation
Indices: 1132294--1132324 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
1132284 AATGTTTAGG
1132294 CCTGCAATGAAT
1 CCTGCAATGAAT
1132306 CCTGCAATGAAT
1 CCTGCAATGAAT
1132318 CGCTGCA
1 C-CTGCA
1132325 GTGTCGAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (12 bp):
CCTGCAATGAAT
Found at i:1140901 original size:30 final size:31
Alignment explanation
Indices: 1140858--1140919 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
1140848 GAATGGCTTG
*
1140858 GATATGCCTAGATGTTAATAATGTGTTTTGT
1 GATATGCCAAGATGTTAATAATGTGTTTTGT
1140889 GATAT-CCAAGATGTTAATAATGTGTTTTGT
1 GATATGCCAAGATGTTAATAATGTGTTTTGT
1140919 G
1 G
1140920 CCATATTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (31 bp):
GATATGCCAAGATGTTAATAATGTGTTTTGT
Found at i:1148730 original size:30 final size:30
Alignment explanation
Indices: 1148666--1148723 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1148656 GTGTATAATT
*
1148666 ATATCAAATCAAATTTATATATCAAATTAA
1 ATATTAAATCAAATTTATATATCAAATTAA
*
1148696 ATATTAAATCAAAATTTATGTAT-AAATT
1 ATATTAAATC-AAATTTATATATCAAATT
1148724 TGATATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (30 bp):
ATATTAAATCAAATTTATATATCAAATTAA
Found at i:1159172 original size:8 final size:9
Alignment explanation
Indices: 1159154--1159204 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
1159144 AAAATATTTT
1159154 AAAATTAAA
1 AAAATTAAA
1159163 AAAATTAAA
1 AAAATTAAA
**
1159172 AAAGTATT-TT
1 AAA--ATTAAA
1159182 AAAATTAAA
1 AAAATTAAA
1159191 AAAATTTAAA
1 AAAA-TTAAA
1159201 AAAA
1 AAAA
1159205 GTATTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
8 3 0.09
9 16 0.47
10 12 0.35
11 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (9 bp):
AAAATTAAA
Found at i:1159215 original size:11 final size:11
Alignment explanation
Indices: 1159201--1159226 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1159191 AAAATTTAAA
1159201 AAAAGTATTTT
1 AAAAGTATTTT
1159212 AAAAGTATTTT
1 AAAAGTATTTT
1159223 AAAA
1 AAAA
1159227 TTAAAAAATA
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:1159234 original size:30 final size:28
Alignment explanation
Indices: 1159158--1159215 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 28
1159148 TATTTTAAAA
1159158 TTAAAAAAATTAAAAAAGTATTTTAAAA
1 TTAAAAAAATTAAAAAAGTATTTTAAAA
1159186 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
1 TTAAAAAAA-TT-AAAAAAGTATTTTAAAA
1159216 GTATTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 9 0.32
29 2 0.07
30 17 0.61
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (28 bp):
TTAAAAAAATTAAAAAAGTATTTTAAAA
Found at i:1172218 original size:6 final size:6
Alignment explanation
Indices: 1172207--1172253 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
1172197 AGATTTCCAA
* * *
1172207 AAATGG AAATGG AAATGG AAATGG AAATGA AAATGA AAATAG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
1172254 TACAATCCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:1172467 original size:25 final size:25
Alignment explanation
Indices: 1172395--1172468 Score: 103
Period size: 26 Copynumber: 2.9 Consensus size: 25
1172385 AATTTTCTCG
*
1172395 AAATTTTATTGGGGGTAAAATCGTCA
1 AAATTTTATT-GGGGTAAAATTGTCA
* *
1172421 AATTTTTATCGGGGGTAAAATTGTCA
1 AAATTTTAT-TGGGGTAAAATTGTCA
1172447 AAATTTTATTGGGGTAAAATTG
1 AAATTTTATTGGGGTAAAATTG
1172469 GGATGAGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 12 0.29
26 30 0.71
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (25 bp):
AAATTTTATTGGGGTAAAATTGTCA
Found at i:1186440 original size:97 final size:97
Alignment explanation
Indices: 1186266--1186443 Score: 236
Period size: 97 Copynumber: 1.8 Consensus size: 97
1186256 TTGAACATGT
** * *
1186266 GGTTACAAAATTGTGTTTTCATTATAAATTTGAGTAAACAGTTAATGAATTTTGTAGTTGTTGTA
1 GGTTACAAAACCGTGTTTTCATTATAAATTTGAGTAAACAATTAATGAATTTTGTAGTTGTTATA
*
1186331 AAATATTGTTATTTAGAACTTTTAGTGTGTTC
66 AAATATTATTATTTAGAACTTTTAGTGTGTTC
* * *
1186363 GGTTACAAAACCGTGTTTTCATTA-AGAA-TTGAAGTAAATAATTTATGATTTTTGTAGTTGTTA
1 GGTTACAAAACCGTGTTTTCATTATA-AATTTG-AGTAAACAATTAATGAATTTTGTAGTTGTTA
1186426 TAACAA-ATTATTATTTAG
64 TAA-AATATTATTATTTAG
1186444 GGAGATACTT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
96 4 0.06
97 64 0.91
98 2 0.03
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (97 bp):
GGTTACAAAACCGTGTTTTCATTATAAATTTGAGTAAACAATTAATGAATTTTGTAGTTGTTATA
AAATATTATTATTTAGAACTTTTAGTGTGTTC
Found at i:1189702 original size:16 final size:15
Alignment explanation
Indices: 1189681--1189710 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1189671 CACAAAGACG
1189681 GTGGAACCAGTCCCAA
1 GTGGAACCA-TCCCAA
1189697 GTGGAACCATCCCA
1 GTGGAACCATCCCA
1189711 TGGTGTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.13
Consensus pattern (15 bp):
GTGGAACCATCCCAA
Found at i:1190761 original size:18 final size:20
Alignment explanation
Indices: 1190721--1190761 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1190711 TTATTTTAAT
*
1190721 TTTTTTATATAGTATGTAGC
1 TTTTTTATATAGTATATAGC
1190741 TTTTTTAT-TAGTATATA-C
1 TTTTTTATATAGTATATAGC
1190759 TTT
1 TTT
1190762 ATATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (20 bp):
TTTTTTATATAGTATATAGC
Found at i:1194905 original size:91 final size:91
Alignment explanation
Indices: 1194767--1194974 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
1194757 TTGATTTTAG
* *
1194767 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
1194832 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
1194859 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1194924 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
1194950 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
1194975 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:1194943 original size:26 final size:28
Alignment explanation
Indices: 1194889--1194949 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1194879 TATTATCAAG
* *
1194889 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
1194917 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
1194943 AATTATA
1 AATTATA
1194950 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:1194949 original size:44 final size:43
Alignment explanation
Indices: 1194807--1194949 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
1194797 GAATTTTATG
* *
1194807 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
1194851 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
1194898 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
1194942 AAATTATA
1 AAATTATA
1194950 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:1195067 original size:59 final size:57
Alignment explanation
Indices: 1195001--1195189 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
1194991 ATTTTATTAA
1195001 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
1195060 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
1195121 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
1195180 ATCATATATT
1 ATCATATATT
1195190 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:1195098 original size:66 final size:64
Alignment explanation
Indices: 1195028--1195228 Score: 183
Period size: 66 Copynumber: 3.2 Consensus size: 64
1195018 AAATATATTT
1195028 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1195093 G
64 G
* * * * * **
1195094 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
1195148 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1195213 G
64 G
*
1195214 AATATTGATT-TTTAA
1 AATATTAATTATTTAA
1195229 GAATTTTATT
Statistics
Matches: 103, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 9 0.09
65 7 0.07
66 25 0.24
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:1195114 original size:120 final size:120
Alignment explanation
Indices: 1194990--1195287 Score: 508
Period size: 120 Copynumber: 2.5 Consensus size: 120
1194980 AATTATTTTA
* * *
1194990 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
1195054 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
1195110 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
1195175 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTTTTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
1195230 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
1195288 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 160 0.96
121 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:1195150 original size:15 final size:15
Alignment explanation
Indices: 1195115--1195166 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1195105 TTAAGAATTT
*
1195115 TATTAAATTAT-ATA
1 TATTTAATTATAATA
1195129 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
1195143 TATTTAATAATAAT-
1 TATTTAATTATAATA
1195157 TATGTTAATT
1 TAT-TTAATT
1195167 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:1195259 original size:18 final size:17
Alignment explanation
Indices: 1195231--1195265 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1195221 ATTTTTAAGA
*
1195231 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1195248 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1195266 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1195495 original size:44 final size:45
Alignment explanation
Indices: 1195430--1195520 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1195420 ACCTTTATTC
* * *
1195430 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
1195474 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
1195519 CA
1 CA
1195521 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:1195522 original size:16 final size:16
Alignment explanation
Indices: 1195501--1195569 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
1195491 GATTAGCTAT
1195501 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1195517 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
1195534 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1195550 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1195566 TACA
1 TACA
1195570 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1195543 original size:33 final size:32
Alignment explanation
Indices: 1195501--1195569 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
1195491 GATTAGCTAT
1195501 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
1195534 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
1195566 TACA
1 TACA
1195570 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:1197606 original size:6 final size:6
Alignment explanation
Indices: 1197595--1197631 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1197585 TCAGCTTATC
1197595 CTAACA CTAACA CTAACA CTAACA CTAACA CTAACA C
1 CTAACA CTAACA CTAACA CTAACA CTAACA CTAACA C
1197632 CAATTTCCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (6 bp):
CTAACA
Found at i:1201776 original size:18 final size:19
Alignment explanation
Indices: 1201749--1201784 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1201739 AAAATTATTT
*
1201749 AAAAATAAATTTTTTTAAC
1 AAAAATAAATATTTTTAAC
1201768 AAAAA-AAATATTTTTAA
1 AAAAATAAATATTTTTAA
1201785 TTTACACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATAAATATTTTTAAC
Found at i:1203339 original size:18 final size:17
Alignment explanation
Indices: 1203306--1203344 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1203296 TTGTATAAAT
1203306 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
1203324 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
1203341 TGTG
1 TGTG
1203345 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:1203597 original size:23 final size:23
Alignment explanation
Indices: 1203570--1203645 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
1203560 AGTGTTATTG
1203570 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
1203593 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1203616 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1203639 ATCAGTG
1 ATCAGTG
1203646 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1204915 original size:23 final size:25
Alignment explanation
Indices: 1204871--1204922 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
1204861 TGGTTCCTAT
1204871 TTTTTTTCATTTTGAGCAA-TTTAA
1 TTTTTTTCATTTTGAGCAATTTTAA
*
1204895 TTTTTTTC-TTTT-ATGCTATTTTAA
1 TTTTTTTCATTTTGA-GCAATTTTAA
1204919 TTTT
1 TTTT
1204923 AATTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 7 0.28
24 17 0.68
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (25 bp):
TTTTTTTCATTTTGAGCAATTTTAA
Found at i:1207471 original size:15 final size:15
Alignment explanation
Indices: 1207451--1207506 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
1207441 TAAATTTAAA
1207451 AAAAACTAAAATAAT
1 AAAAACTAAAATAAT
1207466 AAAAACT---ATAAT
1 AAAAACTAAAATAAT
*
1207478 AAAAACTAAAAAAAT
1 AAAAACTAAAATAAT
* *
1207493 AATAACTACAATAA
1 AAAAACTAAAATAA
1207507 ACTAAAAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 12 0.35
15 22 0.65
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAACTAAAATAAT
Found at i:1207478 original size:12 final size:12
Alignment explanation
Indices: 1207461--1207485 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1207451 AAAAACTAAA
1207461 ATAATAAAAACT
1 ATAATAAAAACT
1207473 ATAATAAAAACT
1 ATAATAAAAACT
1207485 A
1 A
1207486 AAAAAATAAT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAATAAAAACT
Found at i:1207481 original size:27 final size:27
Alignment explanation
Indices: 1207451--1207537 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 27
1207441 TAAATTTAAA
* *
1207451 AAAAACTAAAATAATAAAAACTATAAT
1 AAAAACTAAAAAAATAAAAACTACAAT
*
1207478 AAAAACTAAAAAAATAATAACTACAAT
1 AAAAACTAAAAAAATAAAAACTACAAT
* *
1207505 --AAACTAAAAAGAAGTTAAAAACTAAAAA
1 AAAAACTAAAAA-AA--TAAAAACTACAAT
1207533 AAAAA
1 AAAAA
1207538 TTGGCACACA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
25 10 0.20
26 2 0.04
27 24 0.49
28 10 0.20
30 3 0.06
ACGTcount: A:0.72, C:0.08, G:0.02, T:0.17
Consensus pattern (27 bp):
AAAAACTAAAAAAATAAAAACTACAAT
Found at i:1211143 original size:16 final size:17
Alignment explanation
Indices: 1211117--1211150 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1211107 AAAATTGGAA
*
1211117 TGAGAAAATTATTTAAT
1 TGAGAAAATTAATTAAT
1211134 TGAG-AAATTAATTAAT
1 TGAGAAAATTAATTAAT
1211150 T
1 T
1211151 TAAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
TGAGAAAATTAATTAAT
Found at i:1212923 original size:10 final size:10
Alignment explanation
Indices: 1212892--1212949 Score: 59
Period size: 10 Copynumber: 5.9 Consensus size: 10
1212882 AAAAAAGGAG
1212892 TAATAAATAAA
1 TAATAAAT-AA
*
1212903 TAAATAGATAA
1 T-AATAAATAA
1212914 TAATAAATAA
1 TAATAAATAA
*
1212924 TAATAAATAG
1 TAATAAATAA
1212934 T-A-AAATAA
1 TAATAAATAA
1212942 -AATAAATA
1 TAATAAATA
1212950 GATGTTCGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 6 0.15
9 6 0.15
10 18 0.45
11 4 0.10
12 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (10 bp):
TAATAAATAA
Found at i:1212932 original size:17 final size:17
Alignment explanation
Indices: 1212897--1212949 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
1212887 AGGAGTAATA
1212897 AATAAATAAATAGAT-AAT
1 AATAAAT-AATA-ATAAAT
1212915 AATAAATAATAATAAAT
1 AATAAATAATAATAAAT
*
1212932 AGTAAAATAA-AATAAAT
1 AAT-AAATAATAATAAAT
1212949 A
1 A
1212950 GATGTTCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 2 0.06
17 17 0.53
18 13 0.41
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (17 bp):
AATAAATAATAATAAAT
Found at i:1217614 original size:31 final size:31
Alignment explanation
Indices: 1217579--1217649 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
1217569 AGTGACCAAA
* *
1217579 ATGAAAATTATTTTTGACG-GTAGTGCCTAAG
1 ATGAAAATTATTTGT-AAGAGTAGTGCCTAAG
* *
1217610 ATGAAAATGATTTGTAAGAGTAGTGCTTAAG
1 ATGAAAATTATTTGTAAGAGTAGTGCCTAAG
1217641 ATGAAAATT
1 ATGAAAATT
1217650 TTTAGTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.34
Consensus pattern (31 bp):
ATGAAAATTATTTGTAAGAGTAGTGCCTAAG
Found at i:1224816 original size:34 final size:34
Alignment explanation
Indices: 1224773--1224838 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
1224763 AGTAAAATAT
* *
1224773 TTTTCGTAAAATGGTTT-CGGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
*
1224806 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACGGGAAAATATTTT
1224839 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 11 0.39
35 12 0.43
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:1226499 original size:3 final size:3
Alignment explanation
Indices: 1226491--1226529 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1226481 AATAAAATAG
1226491 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1226530 AAAATTAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1242699 original size:9 final size:9
Alignment explanation
Indices: 1242685--1242731 Score: 55
Period size: 8 Copynumber: 5.4 Consensus size: 9
1242675 GACAATCTTC
1242685 AAAATTATA
1 AAAATTATA
1242694 AAAATT-TA
1 AAAATTATA
*
1242702 GAAATTAT-
1 AAAATTATA
1242710 AAAA-TATA
1 AAAATTATA
1242718 AAAATTATA
1 AAAATTATA
1242727 TAAAA
1 -AAAA
1242732 ATAAAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
7 3 0.09
8 14 0.44
9 11 0.34
10 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:1242737 original size:17 final size:16
Alignment explanation
Indices: 1242685--1242752 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
1242675 GACAATCTTC
*
1242685 AAAATTATAAAAATTTA
1 AAAATTATAAAAA-ATA
* *
1242702 GAAATTATAAAATATA
1 AAAATTATAAAAAATA
1242718 AAAATTATATAAAAAT-
1 AAAATTATA-AAAAATA
*
1242734 AAAATGA-AAAAAATA
1 AAAATTATAAAAAATA
1242749 AAAA
1 AAAA
1242753 AAAAATATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 6 0.14
15 5 0.12
16 16 0.37
17 16 0.37
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAATTATAAAAAATA
Found at i:1243148 original size:60 final size:58
Alignment explanation
Indices: 1242982--1243164 Score: 176
Period size: 56 Copynumber: 3.2 Consensus size: 58
1242972 GAAATGTTAG
** * *
1242982 GGACTAACTTGGACAAAAAAAAATT-AAACTCGAAG-GTGGGAACAATTGTCAAGTTTAA
1 GGACTAACTT-GACAAAAAAAAATTCAAAC-CCTAGTGTGGGAACAATTATCAAGTTCAA
* ** * ** * * *
1243040 GGACTAATTTG-GGAAAAAAAGTTCAGGCCCTAATGT-GAAATAATTATCAAGTTCAA
1 GGACTAACTTGACAAAAAAAAATTCAAACCCTAGTGTGGGAACAATTATCAAGTTCAA
1243096 GGACTAACTTGAAACAAAAAAAAATTCAAACCCTAGTGTGGGAACAATTATCAAGTTCAA
1 GGACTAACTTG--ACAAAAAAAAATTCAAACCCTAGTGTGGGAACAATTATCAAGTTCAA
*
1243156 AGACTAACT
1 GGACTAACT
1243165 CAAACAACAA
Statistics
Matches: 96, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
56 37 0.39
57 5 0.05
58 9 0.09
59 19 0.20
60 26 0.27
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.23
Consensus pattern (58 bp):
GGACTAACTTGACAAAAAAAAATTCAAACCCTAGTGTGGGAACAATTATCAAGTTCAA
Found at i:1244714 original size:16 final size:17
Alignment explanation
Indices: 1244683--1244715 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1244673 TAAAATTTTA
1244683 AAAATATTAATTTAATAT
1 AAAATATT-ATTTAATAT
1244701 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
1244716 CTATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:1245004 original size:16 final size:16
Alignment explanation
Indices: 1244983--1245013 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1244973 AATATTTATT
*
1244983 ATTTTATTAATATTAA
1 ATTTTATTAAAATTAA
1244999 ATTTTATTAAAATTA
1 ATTTTATTAAAATTA
1245014 TTATTTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTATTAAAATTAA
Found at i:1245564 original size:24 final size:24
Alignment explanation
Indices: 1245519--1245566 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1245509 TTTCGTTTCT
*
1245519 CTTTTTATTTTGCTTTCTTTTTAC
1 CTTTTTATTTTACTTTCTTTTTAC
*
1245543 CTTTTTATTTTATTTTACTTTTTA
1 CTTTTTATTTTACTTT-CTTTTTA
1245567 TTTTATTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (24 bp):
CTTTTTATTTTACTTTCTTTTTAC
Found at i:1245565 original size:17 final size:18
Alignment explanation
Indices: 1245537--1245573 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
1245527 TTTGCTTTCT
1245537 TTTTACCTTTTTATTTTA
1 TTTTACCTTTTTATTTTA
1245555 TTTTA-CTTTTTATTTTA
1 TTTTACCTTTTTATTTTA
1245572 TT
1 TT
1245574 GTTGCAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTACCTTTTTATTTTA
Found at i:1256128 original size:20 final size:20
Alignment explanation
Indices: 1256074--1256129 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 20
1256064 TCCAATTTAA
** *
1256074 AATTTTAAGGTTTTTTTATC
1 AATTTTAATATTTTTATATC
*
1256094 -ATATTT-ATATCTTTATATC
1 AAT-TTTAATATTTTTATATC
1256113 AATTTTAATATTTTTAT
1 AATTTTAATATTTTTAT
1256130 GATTTCTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (20 bp):
AATTTTAATATTTTTATATC
Found at i:1256313 original size:9 final size:9
Alignment explanation
Indices: 1256185--1256320 Score: 57
Period size: 10 Copynumber: 14.7 Consensus size: 9
1256175 TTTAAATATG
1256185 TTTTATTAAT
1 TTTTA-TAAT
*
1256195 TTTTAGAA-
1 TTTTATAAT
1256203 TTTT-TAAT
1 TTTTATAAT
*
1256211 ATTT-T-AT
1 TTTTATAAT
1256218 TTTTATAAT
1 TTTTATAAT
* *
1256227 ATTTAAAAAT
1 -TTTTATAAT
* *
1256237 TACTTATTAT
1 T-TTTATAAT
*
1256247 TTTTATATTT
1 TTTTATA-AT
1256257 TTTTATAAAT
1 TTTTAT-AAT
*
1256267 TTATATCAAT
1 TTTTAT-AAT
*
1256277 TTTAATACAT
1 TTTTATA-AT
*
1256287 ATATT-TAAT
1 -TTTTATAAT
*
1256296 ATTTAATAAT
1 -TTTTATAAT
1256306 TTTTATAAT
1 TTTTATAAT
1256315 TTTTAT
1 TTTTAT
1256321 TTTTCAAAAT
Statistics
Matches: 93, Mismatches: 23, Indels: 21
0.68 0.17 0.15
Matches are distributed among these distances:
7 7 0.08
8 9 0.10
9 29 0.31
10 45 0.48
11 3 0.03
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1264783 original size:23 final size:23
Alignment explanation
Indices: 1264735--1264780 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1264725 AAAATACAAA
* *
1264735 AATTTATTATATATATTATTTTT
1 AATTTATTATAAAAATTATTTTT
1264758 AATTTATTATTAAAAATTATTTT
1 AATTTATTA-TAAAAATTATTTT
1264781 AATAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
AATTTATTATAAAAATTATTTTT
Found at i:1265011 original size:103 final size:95
Alignment explanation
Indices: 1264897--1265141 Score: 339
Period size: 96 Copynumber: 2.5 Consensus size: 95
1264887 AAACCCTAAA
1264897 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTCTTCCTTAAAAA-CACTAAACACTAAACC
1 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTT-TTCCTTAAAAACCA-TAAACACT--A--
1264961 CTAACCCTAATCTAATTTTTTTAAAATTTATAATTAATT
60 --AACCCTAATCTAA-TTTTTTAAAATTTATAATTAATT
*
1265000 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTTCTTAAAAACCATAAACACTAAACCC
1 TACTCAAGTAACCCTAAACCCTAATTTATTTAA-TTTTTCCTTAAAAACCATAAACACTAAACCC
1265065 TAATCTAATTTTTTAAAATTTATAATTAATT
65 TAATCTAATTTTTTAAAATTTATAATTAATT
* * * * *
1265096 TAATTAAGAAACCTTAAACCCTTATTTATTTAATTTTTCCTTAAAA
1 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAA
1265142 CCCTAAAATT
Statistics
Matches: 133, Mismatches: 7, Indels: 12
0.88 0.05 0.08
Matches are distributed among these distances:
95 12 0.09
96 51 0.38
97 13 0.10
101 1 0.01
103 51 0.38
104 5 0.04
ACGTcount: A:0.40, C:0.19, G:0.01, T:0.40
Consensus pattern (95 bp):
TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAAACCATAAACACTAAACCCT
AATCTAATTTTTTAAAATTTATAATTAATT
Found at i:1265096 original size:96 final size:99
Alignment explanation
Indices: 1264897--1265141 Score: 347
Period size: 103 Copynumber: 2.5 Consensus size: 99
1264887 AAACCCTAAA
*
1264897 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTCTTCCTTAAAAACACTAAACACTAAACCC
1 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCTTAAAAACACTAAACACT-AA--C
1264962 TAACCCTAATCTAATTTTTTTAAAATTTATAATTAATT
63 -AACCCTAATCTAATTTTTTTAAAATTTATAATTAATT
*
1265000 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTTCTTAAAAAC-CATAAACACT-A-AA
1 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCTTAAAAACAC-TAAACACTAACAA
1265062 CCCTAATCTAA-TTTTTTAAAATTTATAATTAATT
65 CCCTAATCTAATTTTTTTAAAATTTATAATTAATT
* * * * *
1265096 TAATTAAGAAACCTTAAACCCTTATTTATTTAA-TTTTTCCTTAAAA
1 TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCTTAAAA
1265142 CCCTAAAATT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
95 12 0.09
96 51 0.38
97 13 0.10
101 1 0.01
102 1 0.01
103 55 0.41
ACGTcount: A:0.40, C:0.19, G:0.01, T:0.40
Consensus pattern (99 bp):
TACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCTTAAAAACACTAAACACTAACAAC
CCTAATCTAATTTTTTTAAAATTTATAATTAATT
Found at i:1265300 original size:40 final size:40
Alignment explanation
Indices: 1265256--1265364 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
1265246 CAACGTAGAC
* *
1265256 ACAAAGCGCTCCCTCAAGGAAATGTTTTCTGTCCATGTGG
1 ACAAAGCGCTTCCTCAAGGAAATGTTTTCTGTCCACGTGG
* ** ** *
1265296 ACAAAGTGCTTCCTTGAGGAAGCGTTTTTTGTCCACGTGG
1 ACAAAGCGCTTCCTCAAGGAAATGTTTTCTGTCCACGTGG
1265336 ACAAAGCGCTTCCTCAA-GAAAGTGTTTTC
1 ACAAAGCGCTTCCTCAAGGAAA-TGTTTTC
1265365 CTGCTTTATC
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
39 3 0.06
40 51 0.94
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (40 bp):
ACAAAGCGCTTCCTCAAGGAAATGTTTTCTGTCCACGTGG
Found at i:1273686 original size:19 final size:20
Alignment explanation
Indices: 1273647--1273691 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
1273637 TGTAATTTTC
1273647 TATA-TTTTATTAAATTGTA
1 TATATTTTTATTAAATTGTA
*
1273666 TA-ATTTTTA-TAAATTCTTA
1 TATATTTTTATTAAATT-GTA
1273685 TATATTT
1 TATATTT
1273692 GAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 7 0.32
19 11 0.50
20 4 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TATATTTTTATTAAATTGTA
Found at i:1280265 original size:27 final size:26
Alignment explanation
Indices: 1280215--1280265 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
1280205 TGTACTTAAA
*
1280215 AATAATTATAATTTAATAAAAATTGT
1 AATAATTACAATTTAATAAAAATTGT
1280241 AATAATTACACATTTAA-AAATAATT
1 AATAATTACA-ATTTAATAAA-AATT
1280266 AGAATTTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (26 bp):
AATAATTACAATTTAATAAAAATTGT
Found at i:1281839 original size:19 final size:19
Alignment explanation
Indices: 1281795--1281839 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1281785 TTTAAACCAC
* *
1281795 AATTAACTCAAAATTTAAT
1 AATTAAATCAAAATTTAAA
1281814 AATTAAATCAAAA-TTAAA
1 AATTAAATCAAAATTTAAA
1281832 AATATAAA
1 AAT-TAAA
1281840 ATACAATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTAAATCAAAATTTAAA
Found at i:1282636 original size:20 final size:21
Alignment explanation
Indices: 1282589--1282637 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1282579 GACATTTTAT
1282589 ATTTTTTTAATAAATATTTTG
1 ATTTTTTTAATAAATATTTTG
** *
1282610 AAATTTTTAA-AATTATTTTG
1 ATTTTTTTAATAAATATTTTG
1282630 ATTTTTTT
1 ATTTTTTT
1282638 GATTTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (21 bp):
ATTTTTTTAATAAATATTTTG
Found at i:1282747 original size:18 final size:18
Alignment explanation
Indices: 1282720--1282754 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1282710 CAATCTATCG
*
1282720 TTTGAGTTATTCAAATTA
1 TTTGAATTATTCAAATTA
*
1282738 TTTGAATTATTCGAATT
1 TTTGAATTATTCAAATT
1282755 GTGAAATTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTATTCAAATTA
Found at i:1284298 original size:24 final size:26
Alignment explanation
Indices: 1284265--1284320 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
1284255 CATTTAATCA
* *
1284265 GTAAATATATATTTTTTAA-AAATTT
1 GTAAAAATATATTATTTAATAAATTT
1284290 -TAAAAATATATTATTTAATAAATTT
1 GTAAAAATATATTATTTAATAAATTT
1284315 GTAAAA
1 GTAAAA
1284321 TAAATTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 16 0.59
25 6 0.22
26 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
GTAAAAATATATTATTTAATAAATTT
Found at i:1284320 original size:25 final size:24
Alignment explanation
Indices: 1284265--1284322 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 24
1284255 CATTTAATCA
*
1284265 GTAAATATATATTTTTTAAAAATTT
1 GTAAA-ATATATTATTTAAAAATTT
1284290 -TAAAAATATATTATTTAATAAATTT
1 GT-AAAATATATTATTTAA-AAATTT
1284315 GTAAAATA
1 GTAAAATA
1284323 AATTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 13 0.45
25 15 0.52
26 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (24 bp):
GTAAAATATATTATTTAAAAATTT
Found at i:1284324 original size:13 final size:13
Alignment explanation
Indices: 1284306--1284336 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1284296 TATATTATTT
*
1284306 AATAAATTTGTAA
1 AATAAATTTATAA
1284319 AATAAATTTATAA
1 AATAAATTTATAA
1284332 AATAA
1 AATAA
1284337 GGTGCAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (13 bp):
AATAAATTTATAA
Found at i:1284329 original size:26 final size:25
Alignment explanation
Indices: 1284265--1284329 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
1284255 CATTTAATCA
1284265 GTAAATATATATTT-TTTAAAAATTT
1 GTAAA-ATATATTTATTTAAAAATTT
1284290 -TAAAA-ATATATTATTTAATAAATTT
1 GTAAAATATAT-TTATTTAA-AAATTT
*
1284315 GTAAAATAAATTTAT
1 GTAAAATATATTTAT
1284330 AAAATAAGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 4 0.12
23 3 0.09
24 9 0.26
25 6 0.18
26 9 0.26
27 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
GTAAAATATATTTATTTAAAAATTT
Found at i:1287915 original size:18 final size:19
Alignment explanation
Indices: 1287891--1287933 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1287881 TATTAAAAAT
*
1287891 TAAAAATTACAAAATATTA
1 TAAAAATAACAAAATATTA
*
1287910 -AAAAATAACTAAATATTA
1 TAAAAATAACAAAATATTA
1287928 TAAAAA
1 TAAAAA
1287934 GTTAATTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAATAACAAAATATTA
Found at i:1288646 original size:30 final size:28
Alignment explanation
Indices: 1288589--1288646 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
1288579 CATACATTTG
**
1288589 GAATTTGTCCATATACTTTTATTTTTAA
1 GAATTTGTCCATATACTTTTAGATTTAA
*
1288617 GAATTTAGTCCATCTACTTTTTAGATTTAA
1 GAATTT-GTCCATATAC-TTTTAGATTTAA
1288647 AAATGCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.24
29 9 0.36
30 10 0.40
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (28 bp):
GAATTTGTCCATATACTTTTAGATTTAA
Found at i:1289511 original size:72 final size:73
Alignment explanation
Indices: 1289359--1289622 Score: 304
Period size: 72 Copynumber: 3.6 Consensus size: 73
1289349 ACTGCTCATG
* * * *
1289359 ATTTTAATGTCGAAAATTTGGTCACAAACAAATTGAATAGTTGTGACCATTCATTTTTGTCACAA
1 ATTTTAGTGTCGAAAATTTGGT-ACAAACAAAATGAATAATTGTGACCATTTATTTTTGTCACAA
1289424 TTGCTTACA
65 TTGCTTACA
* * * * * *
1289433 ATTTTAGTGTCGACAATATGGTACAAA-AAAATGAATAATTATGACCATTTATATTTATCAAAAA
1 ATTTTAGTGTCGAAAATTTGGTACAAACAAAATGAATAATTGTGACCATTTATTTTTGTC-ACAA
**
1289497 TTGCTTATG
65 TTGCTTACA
** *
1289506 A-TTTAGTGTAAAAAATTTGGCCACAAACAAAAT-AATAATTGTGACCATTTATTTTTGTCACAA
1 ATTTTAGTGTCGAAAATTTGG-TACAAACAAAATGAATAATTGTGACCATTTATTTTTGTCACAA
1289569 TTGCTTACA
65 TTGCTTACA
* *
1289578 ATTTTAGTGTCGAAAATTTAG-ACAAA-AAAATTTAATAATTGTGAC
1 ATTTTAGTGTCGAAAATTTGGTACAAACAAAA-TGAATAATTGTGAC
1289623 AACTTTGTAA
Statistics
Matches: 158, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
70 4 0.03
71 6 0.04
72 64 0.41
73 60 0.38
74 24 0.15
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (73 bp):
ATTTTAGTGTCGAAAATTTGGTACAAACAAAATGAATAATTGTGACCATTTATTTTTGTCACAAT
TGCTTACA
Found at i:1294000 original size:18 final size:17
Alignment explanation
Indices: 1293978--1294020 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1293968 GAACTTTTAT
1293978 TAAAATAAAAAAAATTA
1 TAAAATAAAAAAAATTA
* *
1293995 TAAAAATACAGAAAA-TA
1 T-AAAATAAAAAAAATTA
1294012 TAAAATAAA
1 TAAAATAAA
1294021 TTGTAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 7 0.32
17 4 0.18
18 11 0.50
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
TAAAATAAAAAAAATTA
Found at i:1294314 original size:16 final size:17
Alignment explanation
Indices: 1294284--1294316 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1294274 TAGTTAATTA
1294284 ATTTTCTTTAAATATTT
1 ATTTTCTTTAAATATTT
*
1294301 ATTTT-TTTATATATTT
1 ATTTTCTTTAAATATTT
1294317 TTTAATATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTCTTTAAATATTT
Found at i:1294664 original size:29 final size:30
Alignment explanation
Indices: 1294621--1294693 Score: 71
Period size: 30 Copynumber: 2.4 Consensus size: 30
1294611 TTTCATTAGG
*
1294621 TTTTTAATATTTTTTTA-ATAAATATTAAAT-A
1 TTTTT-ATATTTTTATATA-AAAT-TTAAATAA
*
1294652 TTTTCTATA-TTTTATATAAAATTTTAATAA
1 TTTT-TATATTTTTATATAAAATTTAAATAA
1294682 TTTTTATATTTT
1 TTTTTATATTTT
1294694 CTCCCTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
29 9 0.25
30 18 0.50
31 8 0.22
32 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTATATTTTTATATAAAATTTAAATAA
Found at i:1307047 original size:44 final size:44
Alignment explanation
Indices: 1306997--1307084 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
1306987 TTTTATAAAC
* * * *
1306997 TACATTTTATAGTTATTTTATTTTAGTTATCTATACTATTATTT
1 TACATTTTATAGCTATTTTATTGTAGTCATCTATACTATGATTT
1307041 TACATTTTATAGCTATTTTATTGTAGTCATCTATACTATGATTT
1 TACATTTTATAGCTATTTTATTGTAGTCATCTATACTATGATTT
1307085 AAGGTTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.57
Consensus pattern (44 bp):
TACATTTTATAGCTATTTTATTGTAGTCATCTATACTATGATTT
Done.