Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold353
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: 358750
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 3
Found at i:136309 original size:13 final size:13
Alignment explanation
Indices: 136291--136325 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
136281 TTTTCTTTGT
136291 ATCGATACAATGG
1 ATCGATACAATGG
* *
136304 ATCGATACACTGT
1 ATCGATACAATGG
136317 ATCGATACA
1 ATCGATACA
136326 GGGATACAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (13 bp):
ATCGATACAATGG
Found at i:136471 original size:20 final size:20
Alignment explanation
Indices: 136428--136473 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
136418 AAATCTTTTG
136428 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
136449 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
136469 CAAAA
1 CAAAA
136474 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:137969 original size:23 final size:21
Alignment explanation
Indices: 137927--137970 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
137917 GTTTAAAGTT
**
137927 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
137948 TTTGCATTGTACTTTGAATTTTA
1 TTTGC-TTG-ACTTTGAATTTTA
137971 ATCTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:138879 original size:19 final size:20
Alignment explanation
Indices: 138857--138900 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
138847 ACTTGTATCT
*
138857 ATACACAAAATA-TGTAACG
1 ATACACAAAAAATTGTAACG
*
138876 ATACACAAAAAATTGTATCG
1 ATACACAAAAAATTGTAACG
138896 ATACA
1 ATACA
138901 TTAGCTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.23
Consensus pattern (20 bp):
ATACACAAAAAATTGTAACG
Found at i:149570 original size:79 final size:79
Alignment explanation
Indices: 149327--149771 Score: 439
Period size: 79 Copynumber: 5.7 Consensus size: 79
149317 TCATTGATAT
* * * * * * *
149327 TTTTATTTCTAAAATATCGAATTTTCACCATCGGGGATACTCTAACCCCGTTGTTTTTGAGGGGA
1 TTTTATTTCTAAAACATTGATTTTTCACCATCGAGGATACTCTAACCCCATTATTTTTGAAGGGA
* *
149392 TACTCCAACCTTGG
66 TACTCCAACCCTGA
*** * * * * * *
149406 TTTTATTTCTAAAACACCAATTTTCCACCATCGGGGATACTTTAACCTCATTA-TTTTCAAAGGA
1 TTTTATTTCTAAAACATTGATTTTTCACCATCGAGGATACTCTAACCCCATTATTTTTGAAGGGA
*
149470 TACTCCAACCCTAA
66 TACTCCAACCCTGA
* * * * *
149484 TTTTATTTTTAAAACATTGATTTTTCACCATTGGGGATACTCCAACCCCGTTATTTTTGAAGGGA
1 TTTTATTTCTAAAACATTGATTTTTCACCATCGAGGATACTCTAACCCCATTATTTTTGAAGGGA
*
149549 TACTCCAACCCCGA
66 TACTCCAACCCTGA
* * * * * * *
149563 TTTTATTTTTAAAATA-TCAATTTTCTACCATCGAGGATACTCTGACCCTATTATTTTCG-AGGG
1 TTTTATTTCTAAAACATTGATTTTTC-ACCATCGAGGATACTCTAACCCCATTATTTTTGAAGGG
*
149626 ATACTCCAACCTTGA
65 ATACTCCAACCCTGA
* * * * *
149641 TTGTATTTCTAAAACACCT-ATTTTCCACCATCGAGGATACTCCAACCCCATTATTTTTGAGGGG
1 TTTTATTTCTAAAACA-TTGATTTTTCACCATCGAGGATACTCTAACCCCATTATTTTTGAAGGG
**
149705 ATACTCCAACCCCAA
65 ATACTCCAACCCTGA
* * * * *
149720 TTTTGTTTCCAAAATATTGACTTTTCACTATCGAGGATACTCTAACCCCATT
1 TTTTATTTCTAAAACATTGATTTTTCACCATCGAGGATACTCTAACCCCATT
149772 CTTTATTTTC
Statistics
Matches: 297, Mismatches: 63, Indels: 12
0.80 0.17 0.03
Matches are distributed among these distances:
78 129 0.43
79 167 0.56
80 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (79 bp):
TTTTATTTCTAAAACATTGATTTTTCACCATCGAGGATACTCTAACCCCATTATTTTTGAAGGGA
TACTCCAACCCTGA
Found at i:149616 original size:157 final size:157
Alignment explanation
Indices: 149327--149771 Score: 538
Period size: 157 Copynumber: 2.8 Consensus size: 157
149317 TCATTGATAT
* * * * *
149327 TTTTATTTCTAAAATATCGAATTTTCACCATCGGGGATACTCTAACCCCGTTGTTTTTGAGGGGA
1 TTTTATTTCTAAAACATTGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
** * * * * *
149392 TACTCCAACCTTGGTTTTATTTCTAAAACACCAATTTTCCACCATCGGGGATACTTTAA-CCTCA
66 TACTCCAACCCCGATTTTATTTCTAAAATATCAATTTT-CACCATCGAGGATACTCTAACCCTCA
149456 TTATTTTCAAAGGATACTCCAACCCTAA
130 TTATTTTCAAAGGATACTCCAACCCTAA
* * *
149484 TTTTATTTTTAAAACATTGATTTTTCACCATTGGGGATACTCCAACCCCGTTATTTTTGAAGGGA
1 TTTTATTTCTAAAACATTGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
* *
149549 TACTCCAACCCCGATTTTATTTTTAAAATATCAATTTTCTACCATCGAGGATACTCTGACCCT-A
66 TACTCCAACCCCGATTTTATTTCTAAAATATCAATTTTC-ACCATCGAGGATACTCTAACCCTCA
* * * *
149613 TTATTTTCGAGGGATACTCCAACCTTGA
130 TTATTTTCAAAGGATACTCCAACCCTAA
* * * * *
149641 TTGTATTTCTAAAACACCT-ATTTTCCACCATCGAGGATACTCCAACCCCATTATTTTTGAGGGG
1 TTTTATTTCTAAAACA-TTGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGG
* * * * * *
149705 ATACTCCAACCCCAATTTTGTTTCCAAAATATTGACTTTTCACTATCGAGGATACTCTAACCC-C
65 ATACTCCAACCCCGATTTTATTTCTAAAATA-TCAATTTTCACCATCGAGGATACTCTAACCCTC
149769 ATT
129 ATT
149772 CTTTATTTTC
Statistics
Matches: 246, Mismatches: 37, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
156 1 0.00
157 234 0.95
158 11 0.04
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (157 bp):
TTTTATTTCTAAAACATTGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
TACTCCAACCCCGATTTTATTTCTAAAATATCAATTTTCACCATCGAGGATACTCTAACCCTCAT
TATTTTCAAAGGATACTCCAACCCTAA
Found at i:149767 original size:51 final size:52
Alignment explanation
Indices: 149703--149821 Score: 141
Period size: 52 Copynumber: 2.3 Consensus size: 52
149693 ATTTTTGAGG
* ** *
149703 GGATACTCCAACCCCAAT-TTTGTTTCCAAAATATTGACTTTTCACTATCGA
1 GGATACTCCAACCCCAATCTTTATTTCCAAAATATCAACTTTTCACCATCGA
* * * * *
149754 GGATACTCTAACCCCATTCTTTATTTTCGAAATATCAATTTTTCACCATCGA
1 GGATACTCCAACCCCAATCTTTATTTCCAAAATATCAACTTTTCACCATCGA
*
149806 GGATATTCCAACCCCA
1 GGATACTCCAACCCCA
149822 TTATTTTCGA
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
51 16 0.29
52 40 0.71
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.34
Consensus pattern (52 bp):
GGATACTCCAACCCCAATCTTTATTTCCAAAATATCAACTTTTCACCATCGA
Found at i:150602 original size:14 final size:14
Alignment explanation
Indices: 150583--150612 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
150573 GTTTCGTGAC
150583 TCGAGACATTGGTT
1 TCGAGACATTGGTT
150597 TCGAGACATTGGTT
1 TCGAGACATTGGTT
150611 TC
1 TC
150613 AATAGGCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (14 bp):
TCGAGACATTGGTT
Found at i:156871 original size:48 final size:48
Alignment explanation
Indices: 156818--156924 Score: 142
Period size: 48 Copynumber: 2.2 Consensus size: 48
156808 TGTTTGATTG
* *
156818 TATTGGCATTAAAACCTGATCAAACTCAAATCCACTCTCATTTGACTA
1 TATTGGCATTAAAACATGATCAAACTCAAACCCACTCTCATTTGACTA
* ** * * *
156866 TATTGGCGTTAGGATATGGTTAAACTCAAACCCACTCTCATTTGACTA
1 TATTGGCATTAAAACATGATCAAACTCAAACCCACTCTCATTTGACTA
156914 TATTGGCATTA
1 TATTGGCATTA
156925 GGACCTAGTC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (48 bp):
TATTGGCATTAAAACATGATCAAACTCAAACCCACTCTCATTTGACTA
Found at i:156939 original size:48 final size:47
Alignment explanation
Indices: 156849--157128 Score: 255
Period size: 47 Copynumber: 6.0 Consensus size: 47
156839 AAACTCAAAT
* ** * * **
156849 CCACTCTCATTTGACTATATTGGCGTTAGGATATGGTTAAACTCAAAC
1 CCACTCTCATTTGACTATATTGGCATTAGGACCTAGTCAAACTC-TTC
*
156897 CCACTCTCATTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTG
1 CCACTCTCATTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTC
* * * * *
156944 CCA--CTCGTTTGACTACATTGGCGTTATGACCTAGTCAAACTCTTT
1 CCACTCTCATTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTC
* * ** *
156989 CCACTCTCGTTTGACTACATTGGTGTTAGGACCTAGTTAAACTCTTC
1 CCACTCTCATTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTC
* * *
157036 TCA-TCCTCATTTGA-TCGTATTGGCATTAGGACCTAGTCAAACTCTTT
1 CCACT-CTCATTTGACT-ATATTGGCATTAGGACCTAGTCAAACTCTTC
* * ** *
157083 GCACCCTTGTTTGACTATATTGGCATTA-GTCCGTAGTCAAACTCTT
1 CCACTCTCATTTGACTATATTGGCATTAGGACC-TAGTCAAACTCTT
157129 TTCATCCTCA
Statistics
Matches: 194, Mismatches: 31, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
45 40 0.21
46 5 0.03
47 109 0.56
48 40 0.21
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (47 bp):
CCACTCTCATTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTC
Found at i:157081 original size:139 final size:142
Alignment explanation
Indices: 156848--157129 Score: 360
Period size: 140 Copynumber: 2.0 Consensus size: 142
156838 CAAACTCAAA
* * *
156848 TCCACTCTCATTTGACTATATTGGCGTTAGGATATGGTTAAACTCAAACCCACTCTCATTTGACT
1 TCCACTCTCATTTGACTACATTGGCGTTAGGACATAGTTAAACTCAAACCCACTCTCATTTGACT
*
156913 ATATTGGCATTAGGACCTAGTCAAACTC-TTGC-CACTCGTTTGACTACATTGGCGTTATGACC-
66 ATATTGGCATTAGGACCTAGTCAAACTCTTTGCACACTCGTTTGACTACATTGGCATTA-GACCG
156975 TAGTCAAACTCTT
130 TAGTCAAACTCTT
* * * ** *
156988 TCCACTCTCGTTTGACTACATTGGTGTTAGGACCTAGTTAAACTC-TTCTCA-TCCTCATTTGA-
1 TCCACTCTCATTTGACTACATTGGCGTTAGGACATAGTTAAACTCAAACCCACT-CTCATTTGAC
* * * * *
157050 TCGTATTGGCATTAGGACCTAGTCAAACTCTTTGCACCCTTGTTTGACTATATTGGCATTAGTCC
65 T-ATATTGGCATTAGGACCTAGTCAAACTCTTTGCACACTCGTTTGACTACATTGGCATTAGACC
157115 GTAGTCAAACTCTT
129 GTAGTCAAACTCTT
157129 T
1 T
157130 TCATCCTCAT
Statistics
Matches: 122, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
138 2 0.02
139 39 0.32
140 46 0.38
141 35 0.29
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (142 bp):
TCCACTCTCATTTGACTACATTGGCGTTAGGACATAGTTAAACTCAAACCCACTCTCATTTGACT
ATATTGGCATTAGGACCTAGTCAAACTCTTTGCACACTCGTTTGACTACATTGGCATTAGACCGT
AGTCAAACTCTT
Found at i:157095 original size:94 final size:93
Alignment explanation
Indices: 156717--157140 Score: 298
Period size: 94 Copynumber: 4.5 Consensus size: 93
156707 TTCCATCATT
* * * * * *
156717 GTTTGACTATATTGGCATTAGGA-CTTGATCAAACT-ATCT-ACCCTCATTTTACTACGTTGGCG
1 GTTTGACTATATTGGCATTAGGACCTAG-TCAAACTCTTCTCATCCTCATTTGACTA-ATTGGCA
* * *
156779 TTAGGGCCTACTCAAAC-CTTTTCTACCCAT-
64 TTAGGACCTAGTCAAACTC-TTTCCACCC-TC
* * ** *
156809 GTTTGATTGTATTGGCATTAAAACCT-GATCAAACTCAAATC-CA-CTCTCATTTGACTATATTG
1 GTTTGACTATATTGGCATTAGGACCTAG-TCAAACTC--TTCTCATC-CTCATTTGACTA-ATTG
* ** * * *** *
156871 GCGTTAGGATATGGTTAAACTCAAACCCACTCTC
61 GCATTAGGACCTAGTCAAACTC-TTTCCACCCTC
* * *
156905 ATTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTGC-CA--CTCGTTTGACTACATTGGCG
1 GTTTGACTATATTGGCATTAGGACCTAGTCAAACTCTT-CTCATCCTCATTTGACTA-ATTGGCA
* *
156967 TTATGACCTAGTCAAACTCTTTCCACTCTC
64 TTAGGACCTAGTCAAACTCTTTCCACCCTC
* ** *
156997 GTTTGACTACATTGGTGTTAGGACCTAGTTAAACTCTTCTCATCCTCATTTGATCGT-ATTGGCA
1 GTTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTCTCATCCTCATTTGA-C-TAATTGGCA
* *
157061 TTAGGACCTAGTCAAACTCTTTGCACCCTT
64 TTAGGACCTAGTCAAACTCTTTCCACCCTC
* *
157091 GTTTGACTATATTGGCATTA-GTCCGTAGTCAAACTCTTTTCATCCTCATT
1 GTTTGACTATATTGGCATTAGGACC-TAGTCAAACTCTTCTCATCCTCATT
157141 CGATGTGATG
Statistics
Matches: 264, Mismatches: 52, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
91 1 0.00
92 71 0.27
93 37 0.14
94 82 0.31
95 37 0.14
96 35 0.13
97 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (93 bp):
GTTTGACTATATTGGCATTAGGACCTAGTCAAACTCTTCTCATCCTCATTTGACTAATTGGCATT
AGGACCTAGTCAAACTCTTTCCACCCTC
Found at i:157535 original size:85 final size:85
Alignment explanation
Indices: 157201--157580 Score: 362
Period size: 84 Copynumber: 4.5 Consensus size: 85
157191 GGTATCGCTT
* * * *
157201 TTCATC-CCTTGTTTACCCATCAACTTAGTCC-CTAGTAAACCTATTACCTTTATGGTGACCTGT
1 TTCATCTCCTTGTTTACCCATCGACTCAGTCCTC-AGTAAACCCATTACCTCTATGGTGACCTGT
*
157264 CAGCTTAGTCTCTGGTCAACCC
65 CAGCTTAGTCTCCGGTCAA-CC
** * *
157286 TT-ATCTCCTTGTTTACTTATCG-CTCAGT-CTCCGGTAAACCCCTTACACT-TATGGTGACCTG
1 TTCATCTCCTTGTTTACCCATCGACTCAGTCCT-CAGTAAACCCATTAC-CTCTATGGTGACCTG
* *
157347 TTAGCTTAGTCTCCGGTCGACC
64 TCAGCTTAGTCTCCGGTCAACC
* * * * * * * *
157369 TTCATCTCGC-TATTTACCTATGGGCTTAGTCCT-AGTAAACCCCTTACCCCTATAGTGACCTGT
1 TTCATCTC-CTTGTTTACCCATCGACTCAGTCCTCAGTAAACCCATTACCTCTATGGTGACCTGT
157432 CAGCTTAGTCTCCGGTCAACC
65 CAGCTTAGTCTCCGGTCAACC
* * * * *
157453 TTTATTTCCTTGTTTACCCATCGACTCAGTCCTCGGTAAACCTATTACCTCTATGGTGACCTATC
1 TTCATCTCCTTGTTTACCCATCGACTCAGTCCTCAGTAAACCCATTACCTCTATGGTGACCTGTC
* * *
157518 AACTCAGTCTCCAGTCAACC
66 AGCTTAGTCTCCGGTCAACC
* *** * *
157538 TTCATCTTCTTGTTTACTTGTCGCCTCAATCCTCAGTAAACCC
1 TTCATCTCCTTGTTTACCCATCGACTCAGTCCTCAGTAAACCC
157581 TTTATCCCCT
Statistics
Matches: 239, Mismatches: 45, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
83 7 0.03
84 131 0.55
85 99 0.41
86 2 0.01
ACGTcount: A:0.20, C:0.31, G:0.14, T:0.35
Consensus pattern (85 bp):
TTCATCTCCTTGTTTACCCATCGACTCAGTCCTCAGTAAACCCATTACCTCTATGGTGACCTGTC
AGCTTAGTCTCCGGTCAACC
Found at i:157541 original size:169 final size:169
Alignment explanation
Indices: 157224--157544 Score: 432
Period size: 168 Copynumber: 1.9 Consensus size: 169
157214 TACCCATCAA
* ** * *
157224 CTTAGTCCCTAGTAAACCTATTACCTTTATGGTGACCTGTCAGCTTAGTCTCTGGTCAACCCTTA
1 CTTAGTCCCTAGTAAACCCATTACCCCTATAGTGACCTGTCAGCTTAGTCTCCGGTCAACCCTTA
** * * * * *
157289 TCTCCTTGTTTACTTATCGCTCAGTCTCCGGTAAACCCCTTACACTTATGGTGACCTGTTAGCTT
66 TCTCCTTGTTTACCCATCGCTCAGTCTCCGGTAAACCCATTACACTTATGGTGACCTATCAACTC
* *
157354 AGTCTCCGGTCGACCTTCATCTCGCTATTTACCTATGGG
131 AGTCTCCAGTCAACCTTCATCTCGCTATTTACCTATGGG
* *
157393 CTTAGT-CCTAGTAAACCCCTTACCCCTATAGTGACCTGTCAGCTTAGTCTCCGGTCAACCTTTA
1 CTTAGTCCCTAGTAAACCCATTACCCCTATAGTGACCTGTCAGCTTAGTCTCCGGTCAACCCTTA
* *
157457 TTTCCTTGTTTACCCATCGACTCAGTC-CTCGGTAAACCTATTAC-CTCTATGGTGACCTATCAA
66 TCTCCTTGTTTACCCATCG-CTCAGTCTC-CGGTAAACCCATTACACT-TATGGTGACCTATCAA
157520 CTCAGTCTCCAGTCAACCTTCATCT
128 CTCAGTCTCCAGTCAACCTTCATCT
157545 TCTTGTTTAC
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
168 70 0.53
169 61 0.47
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.35
Consensus pattern (169 bp):
CTTAGTCCCTAGTAAACCCATTACCCCTATAGTGACCTGTCAGCTTAGTCTCCGGTCAACCCTTA
TCTCCTTGTTTACCCATCGCTCAGTCTCCGGTAAACCCATTACACTTATGGTGACCTATCAACTC
AGTCTCCAGTCAACCTTCATCTCGCTATTTACCTATGGG
Found at i:165969 original size:9 final size:9
Alignment explanation
Indices: 165952--165985 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
165942 GTCAACCATC
165952 AATGATGAT
1 AATGATGAT
165961 GAA-GATGAT
1 -AATGATGAT
165970 AATGATGAT
1 AATGATGAT
165979 AATGATG
1 AATGATG
165986 GTGACTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (9 bp):
AATGATGAT
Found at i:168411 original size:13 final size:13
Alignment explanation
Indices: 168393--168417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
168383 AAATTGCACA
168393 GTATCGATACATT
1 GTATCGATACATT
168406 GTATCGATACAT
1 GTATCGATACAT
168418 GACCAAATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:168430 original size:20 final size:21
Alignment explanation
Indices: 168405--168457 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
168395 ATCGATACAT
*
168405 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
* *
168425 TGTATCAATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
168446 TGTATCGATACA
1 TGTATCGATACA
168458 GGTCATTGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:168536 original size:13 final size:13
Alignment explanation
Indices: 168518--168543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
168508 ACACCCAATA
168518 TGTATCGATACAT
1 TGTATCGATACAT
168531 TGTATCGATACAT
1 TGTATCGATACAT
168544 CCCAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:168539 original size:32 final size:33
Alignment explanation
Indices: 168498--168565 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
168488 CCTTAACTGT
*
168498 TTGTATCGATACA-CCCAATATGTATCGATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
168530 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
168563 TTG
1 TTG
168566 GCTTGTAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATCCCAAAATGTATCGATACA
Found at i:173403 original size:21 final size:20
Alignment explanation
Indices: 173377--173427 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
173367 AACCCTGAAA
*
173377 GTATCGATACACAGTTTAATT
1 GTATCGATACA-AGTTGAATT
* *
173398 GTATCGATACATGTTGCATT
1 GTATCGATACAAGTTGAATT
173418 GTATCGATAC
1 GTATCGATAC
173428 TTGAAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (20 bp):
GTATCGATACAAGTTGAATT
Found at i:179550 original size:13 final size:13
Alignment explanation
Indices: 179529--179564 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
179519 AAATTCAATT
* *
179529 TATCGATACATTG
1 TATCAATACACTG
179542 TATCAATACACTG
1 TATCAATACACTG
179555 TATCAATACA
1 TATCAATACA
179565 GGGGGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (13 bp):
TATCAATACACTG
Found at i:179730 original size:21 final size:21
Alignment explanation
Indices: 179696--179737 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
179686 CAAAATTCTT
179696 GTTTTTCACTTCAAAATACATCA
1 GTTTTTCAC-TCAAAAT-CATCA
179719 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
179738 TTCAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
23 8 0.42
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (21 bp):
GTTTTTCACTCAAAATCATCA
Found at i:181408 original size:38 final size:38
Alignment explanation
Indices: 181359--181437 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
181349 GTGCAAATAA
181359 ATTTTTGATTAAGGGGGAGAAAGAGATAAGTACTTATG
1 ATTTTTGATTAAGGGGGAGAAAGAGATAAGTACTTATG
*
181397 ATTTTTGATTAAGGGGGAGAAAGAGATAAGTGCTTATG
1 ATTTTTGATTAAGGGGGAGAAAGAGATAAGTACTTATG
181435 ATT
1 ATT
181438 AAGGGGGAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (38 bp):
ATTTTTGATTAAGGGGGAGAAAGAGATAAGTACTTATG
Found at i:182047 original size:20 final size:20
Alignment explanation
Indices: 182022--182071 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
182012 ACCCTGAAAA
*
182022 GTATCGATACACATTTAATT
1 GTATCGATACACATTGAATT
** *
182042 GTATCGATACATGTTGCATT
1 GTATCGATACACATTGAATT
182062 GTATCGATAC
1 GTATCGATAC
182072 TTGAAAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
GTATCGATACACATTGAATT
Found at i:186965 original size:13 final size:13
Alignment explanation
Indices: 186947--186971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
186937 AAATTGCACA
186947 GTATCGATACATT
1 GTATCGATACATT
186960 GTATCGATACAT
1 GTATCGATACAT
186972 GACCAAATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:187090 original size:13 final size:13
Alignment explanation
Indices: 187072--187097 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
187062 ACACCCAATA
187072 TGTATCGATACAT
1 TGTATCGATACAT
187085 TGTATCGATACAT
1 TGTATCGATACAT
187098 CCCAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:187093 original size:32 final size:33
Alignment explanation
Indices: 187052--187119 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
187042 CCTTAACTGT
*
187052 TTGTATCGATACA-CCCAATATGTATCGATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
187084 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACATCCCAAAATGTATCGATACA
187117 TTG
1 TTG
187120 GCTTGTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATCCCAAAATGTATCGATACA
Found at i:190266 original size:20 final size:21
Alignment explanation
Indices: 190233--190274 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
190223 GAAATTTTCT
190233 AGAATGTATCGATACAT-TGA
1 AGAATGTATCGATACATCTGA
* *
190253 AGAATTTATTGATACATCTGA
1 AGAATGTATCGATACATCTGA
190274 A
1 A
190275 AAGCCCAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
AGAATGTATCGATACATCTGA
Found at i:195602 original size:20 final size:20
Alignment explanation
Indices: 195560--195614 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
195550 AAATTCCCAG
**
195560 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
195580 ATGTATCGATACATTGAGT-A
1 ATGTATCGATACATTGA-TCA
*
195600 ATGTATCAATACATT
1 ATGTATCGATACATT
195615 TCCTTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:195652 original size:13 final size:13
Alignment explanation
Indices: 195630--195687 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
195620 GGCAGTAGCT
*
195630 TTGTAGCGATACA
1 TTGTATCGATACA
195643 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
195659 CTTATGTATCGATACA
1 --T-TGTATCGATACA
195675 TTGTATCGATACA
1 TTGTATCGATACA
195688 CACTTATGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:195668 original size:19 final size:18
Alignment explanation
Indices: 195644--195705 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
195634 AGCGATACAT
195644 TGTATCGATACAACACTTA
1 TGTATCGATAC-ACACTTA
195663 TGTATCGAT--ACA--T-
1 TGTATCGATACACACTTA
195676 TGTATCGATACACACTTA
1 TGTATCGATACACACTTA
*
195694 TGTATTGATACA
1 TGTATCGATACA
195706 GTTACTGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
15 3 0.08
16 3 0.08
17 1 0.03
18 11 0.30
19 9 0.24
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACACACTTA
Found at i:195694 original size:31 final size:32
Alignment explanation
Indices: 195631--195705 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
195621 GCAGTAGCTT
*
195631 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
195663 TGTATCGATACATTGTATCGATAC-ACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
195694 TGTATTGATACA
1 TGTATCGATACA
195706 GTTACTGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 18 0.44
32 23 0.56
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:196429 original size:13 final size:13
Alignment explanation
Indices: 196411--196437 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
196401 ACATTATGCT
196411 TTGTATCGATACA
1 TTGTATCGATACA
196424 TTGTATCGATACA
1 TTGTATCGATACA
196437 T
1 T
196438 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:196467 original size:20 final size:19
Alignment explanation
Indices: 196421--196477 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
196411 TTGTATCGAT
*
196421 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
196440 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
196459 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
196478 AAACTAGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:198120 original size:16 final size:15
Alignment explanation
Indices: 198081--198123 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
198071 TCATGATTAA
198081 GAAAAGAAAAAAATC
1 GAAAAGAAAAAAATC
* *
198096 GAAACAGAAATTAAATG
1 GAAA-AGAAA-AAAATC
198113 GAAAAGAAAAA
1 GAAAAGAAAAA
198124 TATTGATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.70, C:0.05, G:0.16, T:0.09
Consensus pattern (15 bp):
GAAAAGAAAAAAATC
Found at i:199232 original size:19 final size:18
Alignment explanation
Indices: 199191--199240 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
199181 TATTTCGTGA
199191 AATGCATGAAAT-AAAGC
1 AATGCATGAAATGAAAGC
*
199208 -ATGCATGAAATGCAATGC
1 AATGCATGAAATG-AAAGC
199226 AATGCATGAAATGAA
1 AATGCATGAAATGAA
199241 CATATGCATG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 11 0.38
18 6 0.21
19 12 0.41
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20
Consensus pattern (18 bp):
AATGCATGAAATGAAAGC
Found at i:200108 original size:166 final size:164
Alignment explanation
Indices: 199695--200108 Score: 455
Period size: 166 Copynumber: 2.5 Consensus size: 164
199685 AGGTATGTAC
* *
199695 ATTCATAAAATAT-TATTATTTAA-TAACTATTAAATCAGTTTTCAAAAATTCATTTATTTGCAT
1 ATTCATCAAATATAT-TTATTTAACTCAC-ATTAAATCAGTTTTCAAAAATTCATTTATTT-CAT
* * * *
199758 GAGTTTTGAATTTTTTTCCTTGAAATTTTTTTATTTCCAAAATACTGAGTTTTCTACTTTGTAAA
63 GAGTTTTAAATTTTTTT-CTTGAAATTTTTCTATTTCCAAAAAACTGAGTTTTCTACTTCGTAAA
* * * *
199823 TGTTTTCGGAAGGATTTTTCTTGGTTCATAATTTTTAAA
127 TATTTTC-GAAGGATTTTTCTTGATTCAAAATTTTAAAA
** * * *
199862 ATTCATCAAATATATTTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCATTTTTATGA
1 ATTCATCAAATATATTTATTTAACTCACATTAAATCAGTTTTCAAAAATTCATTTA-TTTCATGA
* * *
199927 GGTTTT-CATTTTTTTTTTGAAATTTTTCTATTTTCAAAAAA-TCGAGTTTTCTACTTCGTAAAT
65 -GTTTTAAATTTTTTTCTTGAAATTTTTCTATTTCCAAAAAACT-GAGTTTTCTACTTCGTAAAT
*
199990 ATTTTC-AAGGGCATTTTTCTTGATTTAAAATTTTAAAA
128 ATTTTCGAA-GG-ATTTTTCTTGATTCAAAATTTTAAAA
* * *
200028 ATTCATCTAATAT-TTTCATTTAACTCCCATTAAATCAGTTTTGAAAAATTCAATTTATTTCAT-
1 ATTCATCAAATATATTT-ATTTAACTCACATTAAATCAGTTTTCAAAAATTC-ATTTATTTCATG
200091 ATGTTATTAAATTTTTTT
64 A-GTT-TTAAATTTTTTT
200109 GAATATATCA
Statistics
Matches: 209, Mismatches: 27, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
164 2 0.01
165 10 0.05
166 116 0.56
167 70 0.33
168 11 0.05
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.50
Consensus pattern (164 bp):
ATTCATCAAATATATTTATTTAACTCACATTAAATCAGTTTTCAAAAATTCATTTATTTCATGAG
TTTTAAATTTTTTTCTTGAAATTTTTCTATTTCCAAAAAACTGAGTTTTCTACTTCGTAAATATT
TTCGAAGGATTTTTCTTGATTCAAAATTTTAAAA
Found at i:200647 original size:23 final size:22
Alignment explanation
Indices: 200601--200649 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
200591 TTTTGACTAG
*
200601 AAAAAAAAGACAAAAAAAGGAA
1 AAAAAAAAGACAAAAAAAAGAA
* *
200623 AAAAAAAGAGAGAAAAAAAATAA
1 AAAAAAA-AGACAAAAAAAAGAA
200646 AAAA
1 AAAA
200650 TAGGAAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAGACAAAAAAAAGAA
Found at i:208049 original size:199 final size:199
Alignment explanation
Indices: 207709--208107 Score: 701
Period size: 199 Copynumber: 2.0 Consensus size: 199
207699 ATCTTATAAC
207709 TGCCTATTAGGGAGGCCATGGATACACTTAGCCAGGGTCGTCCCATCTTTCTTCCATCAGAAGCT
1 TGCCTATTAGGGAGGCCATGGATACACTTAGCCAGGGTCGTCCCATCTTTCTTCCATCAGAAGCT
* * *
207774 CAAATTTGTACTAGATGACAAAGTAGTCACCATCAGGGCAGAAGAAAAAGTGATTGCCATCGCTT
66 CAAATTTGTACTAGATGACAAAGTAATCACCATCAAGGCAGAAGAAAAAGTGATTGCCACCGCTT
*
207839 TCACTGATGATGTCTACATAGAGCCTACTGAAAATGCAACGGAGCTGTCTTTCCAATCTTTCGAA
131 TCACTGATGATGTCTACATAGAGCCTACTGAAAATGCAACGGAGCTGTCTTTCCAATCTTTCAAA
207904 TTTG
196 TTTG
**
207908 TGCCTATTAGGGAGGCCATGGATACACTTAGCTGGGGTCGTCCCATCTTTCTTCCATCAGAAGCT
1 TGCCTATTAGGGAGGCCATGGATACACTTAGCCAGGGTCGTCCCATCTTTCTTCCATCAGAAGCT
*
207973 CAAATTTGTGCTAGATGACAAAGTAATCACCATCAAGGCAGAAGAAGAAA-TGATTGCCACCGCT
66 CAAATTTGTACTAGATGACAAAGTAATCACCATCAAGGCAGAAGAA-AAAGTGATTGCCACCGCT
* *
208037 TTCACTGATGATGTCTACATAGAGCCTACTGAAAATGCAGCGGAGCTGTCTTTCCAATCTTTTAA
130 TTCACTGATGATGTCTACATAGAGCCTACTGAAAATGCAACGGAGCTGTCTTTCCAATCTTTCAA
208102 ATTTG
195 ATTTG
208107 T
1 T
208108 TAATGCGACC
Statistics
Matches: 190, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
199 187 0.98
200 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (199 bp):
TGCCTATTAGGGAGGCCATGGATACACTTAGCCAGGGTCGTCCCATCTTTCTTCCATCAGAAGCT
CAAATTTGTACTAGATGACAAAGTAATCACCATCAAGGCAGAAGAAAAAGTGATTGCCACCGCTT
TCACTGATGATGTCTACATAGAGCCTACTGAAAATGCAACGGAGCTGTCTTTCCAATCTTTCAAA
TTTG
Found at i:208233 original size:17 final size:17
Alignment explanation
Indices: 208191--208233 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
208181 AAAATGATCG
*
208191 TGGGCAAGAGGTGTTCA
1 TGGGCAAGGGGTGTTCA
*
208208 CGGGCAAGGGGTGTTCA
1 TGGGCAAGGGGTGTTCA
208225 TGGGCAAGG
1 TGGGCAAGG
208234 ACTCAGCAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.21, C:0.14, G:0.47, T:0.19
Consensus pattern (17 bp):
TGGGCAAGGGGTGTTCA
Found at i:214189 original size:28 final size:28
Alignment explanation
Indices: 213602--214181 Score: 650
Period size: 28 Copynumber: 20.3 Consensus size: 28
213592 TTTTTAGAGT
213602 CCACAAGTCAGTGGCATCCTTCTCAAAGC
1 CCACAAGTCAGTGGCATCCTT-TCAAAGC
*
213631 CCACAAGTCAGTGGCATTCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
213659 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
213687 CCACAAGTAAGTGGCATCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
213715 CCACAAGTCAGTCGCATCCTTTCAAAAGC
1 CCACAAGTCAGTGGCATCCTTTC-AAAGC
* *
213744 CCACATGTCAGTGGCATCCTTTCACTAGC
1 CCACAAGTCAGTGGCATCCTTTCA-AAGC
* * *
213773 CCATAAGTCAGTAGTA-CCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
*
213801 CCACGAGTCAGTGGCATCCTTCTCAAAGC
1 CCACAAGTCAGTGGCATCCTT-TCAAAGC
* * *
213830 CCATAAGTCAGTAGCTTCCTTCTCAAAGC
1 CCACAAGTCAGTGGCATCCTT-TCAAAGC
* *
213859 CCACAAGTTAGTGGCACCCCTTT--AAGCC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAG-C
*
213887 CACACAAGTCAGTGGCAACCTCTCTCAAAGC
1 C-CACAAGTCAGTGGCATCCT-T-TCAAAGC
* *
213918 TCACAAGTCAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
213946 CCACAAGTCAGTGGCACCCATTAAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
213974 CCACAAGTCAGTGGCATCCTTCTCAAAGC
1 CCACAAGTCAGTGGCATCCTT-TCAAAGC
* *
214003 CCACAAGTTAGTGGCACCCCTTT--AAGCC
1 CCACAAGTCAGTGGCA-TCCTTTCAAAG-C
* *
214031 CACACAAGTCGGTGGCAACCTCTCTCAAAGC
1 C-CACAAGTCAGTGGCATCCT-T-TCAAAGC
214062 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
* * **
214090 TCACAAGTCAGTGGCACCCTTTTGAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
214118 CCAAAAGTTAGTGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
214146 CCACAAATCAGTGGCATCCTTTTAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
214174 CCACAAGT
1 CCACAAGT
214182 TGATGGCAAC
Statistics
Matches: 471, Mismatches: 58, Indels: 45
0.82 0.10 0.08
Matches are distributed among these distances:
27 6 0.01
28 243 0.52
29 170 0.36
30 43 0.09
31 3 0.01
32 6 0.01
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (28 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGC
Found at i:214211 original size:144 final size:144
Alignment explanation
Indices: 213603--214213 Score: 724
Period size: 144 Copynumber: 4.3 Consensus size: 144
213593 TTTTAGAGTC
* *
213603 CACAAGTCAGTGGCATCCT-TCTCAAAGCCCACAAGTCAGTGGCA-TTCTTTCAAAGCCCACAAG
1 CACAAGTCAGTGGCAACCTCTCTCAAAGCCCACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAG
* * * *
213666 TCAGTGGCATCCTTTCAAAGCCCACAAGTAAGTGGCAT-CTTTTCAAAGCCCACAAGTCAGTCGC
65 TCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGC
*
213730 A-TCCTTTCAAAAG-CC-
130 ACCCCTTT---AAGCCCA
* * * * * * *
213745 CACATGTCAGTGGCATCCT-T-TCACTAGCCCATAAGTCAGTAGTACCTTTTCAAAGCCCACGAG
1 CACAAGTCAGTGGCAACCTCTCTCA-AAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAG
* * * * *
213808 TCAGTGGCATCCTTCTCAAAGCCCATAAGTCAGTAGCTTCCTTCTCAAAGCCCACAAGTTAGTGG
65 TCAGTGGCACCCTT-TCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGG
213873 CACCCCTTTAAGCCCA
129 CACCCCTTTAAGCCCA
* *
213889 CACAAGTCAGTGGCAACCTCTCTCAAAGCTCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGT
1 CACAAGTCAGTGGCAACCTCTCTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGT
* * *
213954 CAGTGGCACCCATTAAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTTAGTGGCA
66 CAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCA
214019 CCCCTTTAAGCCCA
131 CCCCTTTAAGCCCA
* *
214033 CACAAGTCGGTGGCAACCTCTCTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCTCACAAGT
1 CACAAGTCAGTGGCAACCTCTCTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGT
** * * * *
214098 CAGTGGCACCCTTTTGAAGCCCAAAAGTTAGTGGCACCCTT-TCAAAGCCCACAAATCAGTGGCA
66 CAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCA
* *
214162 TCCTTTTAAAG-CC-
131 CCCCTTT-AAGCCCA
* *
214175 CACAAGT-TGATGGCAACCTTCTCTCAAGGCCACACAAGT
1 CACAAGTCAG-TGGCAACC-TCTCTCAAAGCC-CACAAGT
214214 TGGTGGTAGC
Statistics
Matches: 410, Mismatches: 46, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
141 4 0.01
142 82 0.20
143 62 0.15
144 209 0.51
145 50 0.12
146 3 0.01
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (144 bp):
CACAAGTCAGTGGCAACCTCTCTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGT
CAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCA
CCCCTTTAAGCCCA
Found at i:215216 original size:20 final size:20
Alignment explanation
Indices: 215191--215265 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
215181 TTTTACCCAG
*
215191 ATGTATCGATACATTTTTCA
1 ATGTATCAATACATTTTTCA
* * * **
215211 ATGTATCGATACATGTATGT
1 ATGTATCAATACATTTTTCA
* *
215231 ATGTATCAAAACATTCTTCA
1 ATGTATCAATACATTTTTCA
*
215251 ATATATCAATACATT
1 ATGTATCAATACATT
215266 CTGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (20 bp):
ATGTATCAATACATTTTTCA
Found at i:217253 original size:98 final size:98
Alignment explanation
Indices: 217084--217266 Score: 296
Period size: 98 Copynumber: 1.9 Consensus size: 98
217074 AGCGCAATTC
* * *
217084 ATTTGAAACTTATTCTTGCCTAAATTATCATTGTCGGGGACACTCCAACCTCATTCTTCTGAGGG
1 ATTTGAAACTTATTCTTGCCTAAATTATCATTGTCGAGGACACTCCAACCTCATTCCTCTAAGGG
217149 GATACTCCAACCCCATTTTTAAAATTTGTCAAG
66 GATACTCCAACCCCATTTTTAAAATTTGTCAAG
*
217182 ATTTGAAACTTATTCTTGCCTAAATTATCATTGTCGAGGACATTCCAACC-CTATTCCTCTAAGG
1 ATTTGAAACTTATTCTTGCCTAAATTATCATTGTCGAGGACACTCCAACCTC-ATTCCTCTAAGG
* *
217246 GGATACTCTAACCTCATTTTT
65 GGATACTCCAACCCCATTTTT
217267 CAATCAAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 1 0.01
98 77 0.99
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (98 bp):
ATTTGAAACTTATTCTTGCCTAAATTATCATTGTCGAGGACACTCCAACCTCATTCCTCTAAGGG
GATACTCCAACCCCATTTTTAAAATTTGTCAAG
Found at i:224669 original size:29 final size:30
Alignment explanation
Indices: 224623--224680 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 30
224613 TTAAGGCTTT
*
224623 CGTTAAAAATTTTCTCT-CCCTTGATAATC
1 CGTTAAAAAATTTCTCTCCCCTTGATAATC
224652 CGTTAAAAAGATTT-TCTCCCCCTTGATAA
1 CGTTAAAAA-ATTTCTCT-CCCCTTGATAA
224681 AAATTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 12 0.48
30 3 0.12
31 10 0.40
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (30 bp):
CGTTAAAAAATTTCTCTCCCCTTGATAATC
Found at i:224669 original size:31 final size:29
Alignment explanation
Indices: 224623--224680 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
224613 TTAAGGCTTT
*
224623 CGTTAAAAATTTTCTCTCCCTTGATAATC
1 CGTTAAAAATTTTCTCCCCCTTGATAATC
224652 CGTTAAAAAGATTTTCTCCCCCTTGATAA
1 CGTT-AAAA-ATTTTCTCCCCCTTGATAA
224681 AAATTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 4 0.15
31 18 0.69
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (29 bp):
CGTTAAAAATTTTCTCCCCCTTGATAATC
Found at i:237694 original size:33 final size:33
Alignment explanation
Indices: 237652--237721 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
237642 AGTCATTAGG
*
237652 ACAATGTATCAATACTT-T-TCACTATGTATCGAT
1 ACAATGTATCAATA-TTATGT-ACCATGTATCGAT
*
237685 ACAATGTATCGATATTATGTACCATGTATCGAT
1 ACAATGTATCAATATTATGTACCATGTATCGAT
237718 ACAA
1 ACAA
237722 ACGGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 2 0.06
33 30 0.91
34 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (33 bp):
ACAATGTATCAATATTATGTACCATGTATCGAT
Found at i:237704 original size:13 final size:13
Alignment explanation
Indices: 237672--237705 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
237662 AATACTTTTC
237672 ACTATGTATCGAT
1 ACTATGTATCGAT
*
237685 ACAATGTATCGAT
1 ACTATGTATCGAT
*
237698 ATTATGTA
1 ACTATGTA
237706 CCATGTATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (13 bp):
ACTATGTATCGAT
Found at i:237794 original size:19 final size:20
Alignment explanation
Indices: 237750--237800 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
237740 CTGCTAGTTT
237750 CATGTATCGATACAATTGAA
1 CATGTATCGATACAATTGAA
**
237770 TGTGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
237789 CATGTATCGATA
1 CATGTATCGATA
237801 TAGTGTATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:240440 original size:27 final size:27
Alignment explanation
Indices: 240402--240467 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
240392 TAGAACATTG
*
240402 TATCGATACATCTAGGTTTTCTAGATA
1 TATCGATACATCTAGGTTTTCCAGATA
240429 TATCGATACATCTAGGTTTTCCAGATA
1 TATCGATACATCTAGGTTTTCCAGATA
240456 TATCGATACATC
1 TATCGATACATC
240468 ATTCAATGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (27 bp):
TATCGATACATCTAGGTTTTCCAGATA
Found at i:243126 original size:33 final size:33
Alignment explanation
Indices: 243089--243155 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
243079 TTCAACGATC
243089 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
243122 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
243155 T
1 T
243156 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:243127 original size:13 final size:13
Alignment explanation
Indices: 243109--243133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
243099 CATAAAATGT
243109 TGTATCGATACAA
1 TGTATCGATACAA
243122 TGTATCGATACA
1 TGTATCGATACA
243134 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:243217 original size:13 final size:13
Alignment explanation
Indices: 243199--243223 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
243189 ATTACTCACA
243199 TGTATCGATACAT
1 TGTATCGATACAT
243212 TGTATCGATACA
1 TGTATCGATACA
243224 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:243360 original size:52 final size:52
Alignment explanation
Indices: 243232--243352 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
243222 CACTGATCTT
*
243232 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
243284 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
243336 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
243353 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:252983 original size:8 final size:8
Alignment explanation
Indices: 252972--253003 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
252962 AAGTATTTAC
*
252972 TTATTATT
1 TTATTTTT
252980 TTATTTTT
1 TTATTTTT
252988 TTATTTTT
1 TTATTTTT
252996 TTATTTTT
1 TTATTTTT
253004 AAAAATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TTATTTTT
Found at i:260094 original size:19 final size:20
Alignment explanation
Indices: 260044--260099 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
260034 AAAAACCTAG
**
260044 AATGTATCGATACA-AAGCA
1 AATGTATCGATACATTTGCA
*
260063 AATTGTATTGATACATTTG-A
1 AA-TGTATCGATACATTTGCA
260083 AATGTATCGATACATTT
1 AATGTATCGATACATTT
260100 ATATTAAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 16 0.52
20 14 0.45
21 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTTGCA
Found at i:260579 original size:20 final size:20
Alignment explanation
Indices: 260535--260591 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
260525 AACCTTGTGT
*
260535 TTGTATGGATACATGTTTAAA
1 TTGTATCGATACAT-TTTAAA
* *
260556 TTGTATCGATAGATTTTGAA
1 TTGTATCGATACATTTTAAA
260576 TTGTATCGATACATTT
1 TTGTATCGATACATTT
260592 GGCCCAACGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.46
Consensus pattern (20 bp):
TTGTATCGATACATTTTAAA
Found at i:262068 original size:41 final size:38
Alignment explanation
Indices: 261985--262057 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
261975 CAGTTTTGAA
* * **
261985 AAATTCTTTTTATTTTTTGAGTTATTGATTTTCTTTTG
1 AAATTCTTCTTATTTTTTGAATTACAGATTTTCTTTTG
262023 AAATTCTTCTTA-TTTTTGAATTACAGAGTTTTCTT
1 AAATTCTTCTTATTTTTTGAATTACAGA-TTTTCTT
262058 CTTTGTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 12 0.40
38 18 0.60
ACGTcount: A:0.22, C:0.08, G:0.10, T:0.60
Consensus pattern (38 bp):
AAATTCTTCTTATTTTTTGAATTACAGATTTTCTTTTG
Found at i:262285 original size:158 final size:159
Alignment explanation
Indices: 262048--262608 Score: 405
Period size: 166 Copynumber: 3.4 Consensus size: 159
262038 TTGAATTACA
* * * ** * *
262048 GAGTTTTCTTCTTTGTAAATTTTTTCA-AGAGGA-TTTTCATGGGTTTAAAATTCTGAAAATTCA
1 GAGTTTTCTAC-TTGTAAATATTTTCAGAGA-GATTTTTC-TCGGTTTTTAATTTTTAAAATTCA
* ** *
262111 TCAAATATTATTATTTAA-TCACCATTAAACCA-TTTTGAAAAA-ATTCA-CA-T-ATTTTCTAA
63 TCAAATATCACCATTTAATTCA-CAATAAACCATTTTTGAAAAATATTCATCATTCATTTT-T-A
* *
262170 ATGTTTTTCCTTAAAATTTC-CTTATTTCTGAAATAT
125 AT-TTTTTCCTCAAAATTTCTC-TATTTCTAAAATAT
*
262206 GAGTTTTCTACTCTGTAAATCTTTTCAGAGAGATTTTTCTCGGTTTTTAATTTTTAAAATTCATC
1 GAGTTTTCTACT-TGTAAATATTTTCAGAGAGATTTTTCTCGGTTTTTAATTTTTAAAATTCATC
* * * *
262271 ATATATCACCATTTAATTCATAATAAATCATTTTTGAAAAATTCATTCATTTTCATTCATTTTTC
65 AAATATCACCATTTAATTCACAATAAACCATTTTTGAAAAA-T-ATTCA---TCATTCATTTTTA
262336 ATTTTTTCCTCAAAATTTCTCTATTTCTAAAATAT
125 ATTTTTTCCTCAAAATTTCTCTATTTCTAAAATAT
** * **
262371 GAAGTTTTCTACTTCGTAAATATTTTTGGGGAGATTTTTCTTAGTTTTTAATTTTTAAAATTCAT
1 G-AGTTTTCTACTT-GTAAATATTTTCAGAGAGATTTTTCTCGGTTTTTAATTTTTAAAATTCAT
** * * * * * *
262436 CAAATATCATTACTTAATTCATAATAAATCAGTTTTGAGAAATTCATTCACTTTCA-TGAGTTTT
64 CAAATATCACCATTTAATTCACAATAAACCATTTTTGA-AAAAT-ATTCA---TCATTCA--TTT
* ** * ** *
262500 TTTATTTTTTCCTTGAAATTAT-TTTATTTCCGAAATAAG
122 TTAATTTTTTCCTCAAAATT-TCTCTATTTCTAAAAT-AT
*
262539 GAGTTTTCTACTTTGTAAATATTTTC-GAG-GAATTTTTCGT-GGTTTTTAACTTTTAAAATTCA
1 GAGTTTTCTAC-TTGTAAATATTTTCAGAGAG-ATTTTTC-TCGGTTTTTAATTTTTAAAATTCA
262601 -CTAAATAT
63 TC-AAATAT
262609 TATTATTTAA
Statistics
Matches: 335, Mismatches: 42, Indels: 44
0.80 0.10 0.10
Matches are distributed among these distances:
157 1 0.00
158 65 0.19
159 21 0.06
162 5 0.01
165 35 0.10
166 140 0.42
167 58 0.17
168 10 0.03
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (159 bp):
GAGTTTTCTACTTGTAAATATTTTCAGAGAGATTTTTCTCGGTTTTTAATTTTTAAAATTCATCA
AATATCACCATTTAATTCACAATAAACCATTTTTGAAAAATATTCATCATTCATTTTTAATTTTT
TCCTCAAAATTTCTCTATTTCTAAAATAT
Found at i:262429 original size:166 final size:165
Alignment explanation
Indices: 262173--262825 Score: 603
Period size: 166 Copynumber: 4.0 Consensus size: 165
262163 TTTCTAAATG
* * * *
262173 TTTTTCCTTAAAATTTC-CTTATTTCTGAAATATG-AGTTTTCTAC-TCTGTAAATCTTTTCAGA
1 TTTTTCCTTAAAATTTCTC-TATTTCTAAAATATGAAGTTTTCTACTTC-GTAAATATTTTCGGG
* * **
262235 GAGATTTTTCTCGGTTTTTAATTTTTAAAATTCATCATATATCACCATTTAATTCATAATAAATC
64 GAGATTTTTCTCAGTTTTTAATTTTTAAAATTCATCAAATATCATTATTTAATTCATAATAAATC
* *
262300 ATTTTTGAAAAATTCATTCATTTTCATTCATTTTTCAT
129 AGTTTTGAAAAATTCATTCATTTTCA-TGATTTTTCAT
* *
262338 TTTTTCCTCAAAATTTCTCTATTTCTAAAATATGAAGTTTTCTACTTCGTAAATATTTTTGGGGA
1 TTTTTCCTTAAAATTTCTCTATTTCTAAAATATGAAGTTTTCTACTTCGTAAATATTTTCGGGGA
* *
262403 GATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATCATTACTTAATTCATAATAAATCAG
66 GATTTTTCTCAGTTTTTAATTTTTAAAATTCATCAAATATCATTATTTAATTCATAATAAATCAG
* * *
262468 TTTTGAGAAATTCATTCACTTTCATGAGTTTTTTTAT
131 TTTTGAAAAATTCATTCATTTTCATGA--TTTTTCAT
* * ** * * * *
262505 TTTTTCCTTGAAATTAT-TTTATTTCCGAAATAAGGAGTTTTCTACTTTGTAAATATTTTCGAGG
1 TTTTTCCTTAAAATT-TCTCTATTTCTAAAATATGAAGTTTTCTACTTCGTAAATATTTTCGGGG
* * * * *
262569 A-ATTTTTCGT-GGTTTTTAACTTTTAAAATTCA-CTAAATATTATTATTTAATTTATATTAAAT
65 AGATTTTTC-TCAGTTTTTAATTTTTAAAATTCATC-AAATATCATTATTTAATTCATAATAAAT
* * * * * *
262631 TAGTTTTCAAAAATTAATTTATTTTCATGAGTTTTGATT
128 CAGTTTTGAAAAATTCATTCATTTTCATGATTTTTCA-T
* * * * * * *
262670 CTTTTTCTTTGAAATTTTTCTATTTTCGAAAA-ACT-AAGTTTTCTATTTCATAAATATTTTTGG
1 -TTTTTCCTTAAAATTTCTCTA-TTTCTAAAATA-TGAAGTTTTCTACTTCGTAAATATTTTCGG
* * * ** * * *
262733 GG-GATTTTTCTCA-ATTTAAAATTTTAAAATTCATCAAATATTGTTATTAAACTC-CAATAAAA
63 GGAGATTTTTCTCAGTTTTTAATTTTTAAAATTCATCAAATATCATTATTTAATTCATAAT-AAA
* * *
262795 TTAGTTTTGATAAATTCAATT-AATTTCATGA
127 TCAGTTTTGAAAAATTC-ATTCATTTTCATGA
262826 ATTGTGAATT
Statistics
Matches: 404, Mismatches: 66, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
164 7 0.02
165 94 0.23
166 232 0.57
167 70 0.17
168 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.49
Consensus pattern (165 bp):
TTTTTCCTTAAAATTTCTCTATTTCTAAAATATGAAGTTTTCTACTTCGTAAATATTTTCGGGGA
GATTTTTCTCAGTTTTTAATTTTTAAAATTCATCAAATATCATTATTTAATTCATAATAAATCAG
TTTTGAAAAATTCATTCATTTTCATGATTTTTCAT
Found at i:262619 original size:332 final size:331
Alignment explanation
Indices: 262173--262773 Score: 761
Period size: 332 Copynumber: 1.8 Consensus size: 331
262163 TTTCTAAATG
* * *
262173 TTTTTCCTTAAAATTTCCTTATTTCTGAAATATGAGTTTTCTACTCTGTAAATCTTTTCAGAGAG
1 TTTTTCCTTAAAATTTCCTTATTTCCGAAATAGGAGTTTTCTACTCTGTAAATATTTTCAGAGAG
* * *
262238 ATTTTTCTCGGTTTTTAATTTTTAAAATTCATCATATATCACCATTTAATTCATAATAAATCATT
66 ATTTTTCTCGGTTTTTAACTTTTAAAATTCATCAAATATCACCATTTAATTCATAATAAATCAGT
* * * *
262303 TTTGAAAAATTCATTCATTTTCATTCATTTTTCA-T-TTTTTCCTCAAAATTTCTCTA-TTTCTA
131 TTTCAAAAATTAATTCATTTTCA-TCAGTTTTCATTCTTTTTCCTCAAAATTTCTCTATTTTCGA
* * * * *
262365 AAATA-TGAAGTTTTCTACTTCGTAAATATTTTTGGGGAGATTTTTCTTAGTTTTTAATTTTTAA
195 AAA-ACT-AAGTTTTCTACTTCATAAATATTTTTGGGG-GATTTTTCTCA-ATTTAAAATTTTAA
262429 AATTCATCAAATATCATTACTTAATTCATAATAAATCAGTTTTGAGAAATTCATTCACTTTCATG
256 AATTCATCAAATATCATTACTTAATTCATAATAAATCAGTTTTGAGAAATTCATTCACTTTCATG
262494 AGTTTTTTTAT
321 AGTTTTTTTAT
* * *
262505 TTTTTCCTTGAAATTAT-TTTATTTCCGAAATAAGGAGTTTTCTACTTTGTAAATATTTTC-GAG
1 TTTTTCCTTAAAATT-TCCTTATTTCCGAAAT-AGGAGTTTTCTACTCTGTAAATATTTTCAGAG
* ** * *
262568 -GAATTTTTCGT-GGTTTTTAACTTTTAAAATTCA-CTAAATATTATTATTTAATTTATATTAAA
64 AG-ATTTTTC-TCGGTTTTTAACTTTTAAAATTCATC-AAATATCACCATTTAATTCATAATAAA
* * * * * ** *
262630 TTAGTTTTCAAAAATTAATTTATTTTCATGAGTTTTGATTCTTTTTCTTTGAAATTTTTCTATTT
126 TCAGTTTTCAAAAATTAATTCATTTTCATCAGTTTTCATTCTTTTTCCTCAAAATTTCTCTATTT
*
262695 TCGAAAAACTAAGTTTTCTATTTCATAAATATTTTTGGGGGATTTTTCTCAATTTAAAATTTTAA
191 TCGAAAAACTAAGTTTTCTACTTCATAAATATTTTTGGGGGATTTTTCTCAATTTAAAATTTTAA
262760 AATTCATCAAATAT
256 AATTCATCAAATAT
262774 TGTTATTAAA
Statistics
Matches: 228, Mismatches: 32, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
331 34 0.15
332 112 0.49
333 73 0.32
334 9 0.04
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (331 bp):
TTTTTCCTTAAAATTTCCTTATTTCCGAAATAGGAGTTTTCTACTCTGTAAATATTTTCAGAGAG
ATTTTTCTCGGTTTTTAACTTTTAAAATTCATCAAATATCACCATTTAATTCATAATAAATCAGT
TTTCAAAAATTAATTCATTTTCATCAGTTTTCATTCTTTTTCCTCAAAATTTCTCTATTTTCGAA
AAACTAAGTTTTCTACTTCATAAATATTTTTGGGGGATTTTTCTCAATTTAAAATTTTAAAATTC
ATCAAATATCATTACTTAATTCATAATAAATCAGTTTTGAGAAATTCATTCACTTTCATGAGTTT
TTTTAT
Found at i:264226 original size:15 final size:15
Alignment explanation
Indices: 264185--264227 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
264175 AAAATTTTTA
*
264185 AAAATAGAAATAAAT
1 AAAATAAAAATAAAT
*
264200 AAAATAATAATAAA-
1 AAAATAAAAATAAAT
264214 AAAATAACAAATAA
1 AAAATAA-AAATAA
264228 TTTCTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAATAAAAATAAAT
Found at i:266761 original size:20 final size:21
Alignment explanation
Indices: 266718--266764 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
266708 TTCTACAATT
266718 TGTATCGATACAAACAAGTAAA
1 TGTATCGATAC-AACAAGTAAA
* *
266740 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAACAAGTAAA
266760 TGTAT
1 TGTAT
266765 TGATGCATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
22 11 0.48
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAACAAGTAAA
Found at i:266937 original size:20 final size:20
Alignment explanation
Indices: 266912--266966 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
266902 TTTTGACCCA
266912 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
*
266932 AATGTATCGAAACATTCTTC
1 AATGTATCGATACATTCTTC
266952 AATGTATCGATACAT
1 AATGTATCGATACAT
266967 GCAGGCAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:269429 original size:42 final size:42
Alignment explanation
Indices: 269320--269429 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
269310 AAGAGAAAGA
* *
269320 AGAGAGAGGAGGGATGATAGGAGGAAAGACAGGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
269362 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
269404 AGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGAGGAGGGATGATAGGAGGAG
269430 GAGAGAAGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.42, C:0.03, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:278716 original size:143 final size:141
Alignment explanation
Indices: 278459--278831 Score: 536
Period size: 143 Copynumber: 2.6 Consensus size: 141
278449 ATTTTATCAC
* *
278459 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTT-AATATTCTTATAGTTTTTCGTAGGAGTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTTCAATATTCCTATAGTTTTTCGTAGGGGTA
* *
278523 TAGAAATCTTCAAAACTTTTTATATCTTTTCGATTCTCCATCAAAGTACGAAATGAATTTCTTTT
66 TAGAAATCTTCAAAACTTTTCATATCTTTTCGATTCTCCATCAAAATACGAAAT-AATTT-TTTT
278588 GGAAATTAAAAAT
129 GGAAATTAAAAAT
* * * *
278601 TAAATAAAAATTGTTATTTTAATTTTTCAAGATTTTCAATATTCCTATGGTTTTTCATAGGGGTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTTCAATATTCCTATAGTTTTTCGTAGGGGTA
** * *
278666 TAGAAATCTTCAAAACTTTTCATATCTTTTTTATTTTCCATTAAAATACGAAATAATTTTTTTGG
66 TAGAAATCTTCAAAACTTTTCATATCTTTTCGATTCTCCATCAAAATACGAAATAATTTTTTTGG
278731 AAATTAAAAAT
131 AAATTAAAAAT
* * *
278742 TAAAT-AAAATTATTATCTTAATTTTTCAAGA-TTTCTAATATTGCTATAATTTTTCGTAAGGGT
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTTC-AATATTCCTATAGTTTTTCGTAGGGGT
* * *
278805 ATAGAAATTTTTAAAACTTTTCGTATC
65 ATAGAAATCTTCAAAACTTTTCATATC
278832 CCCTGGTTTT
Statistics
Matches: 207, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
139 4 0.02
140 70 0.34
141 22 0.11
142 39 0.19
143 72 0.35
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (141 bp):
TAAATAAAAATTATTATCTTAATTTTTCAAGATTTTCAATATTCCTATAGTTTTTCGTAGGGGTA
TAGAAATCTTCAAAACTTTTCATATCTTTTCGATTCTCCATCAAAATACGAAATAATTTTTTTGG
AAATTAAAAAT
Found at i:278810 original size:140 final size:141
Alignment explanation
Indices: 278459--278831 Score: 529
Period size: 140 Copynumber: 2.6 Consensus size: 141
278449 ATTTTATCAC
278459 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTTAATATTCTTATAGTTTTTCGT-AGGAGTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTTAATATTC-TATAGTTTTTCGTAAGG-GTA
* *
278523 TAGAAATCTTCAAAACTTTTTATATCTTTTCGATTCTCCATCAAAGTACGAAATGAATTTCTTTT
64 TAGAAATCTTCAAAACTTTTCATATCTTTTCGATTCTCCATCAAAATACGAAATGAATTTCTTTT
278588 GGAAATTAAAAAT
129 GGAAATTAAAAAT
* * * * *
278601 TAAATAAAAATTGTTATTTTAATTTTTCAAGATTTTCAATATTCCTATGGTTTTTCATAGGGGTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTTT-AATATT-CTATAGTTTTTCGTAAGGGTA
** * *
278666 TAGAAATCTTCAAAACTTTTCATATCTTTTTTATTTTCCATTAAAATACGAAAT-AATTT-TTTT
64 TAGAAATCTTCAAAACTTTTCATATCTTTTCGATTCTCCATCAAAATACGAAATGAATTTCTTTT
278729 GGAAATTAAAAAT
129 GGAAATTAAAAAT
*
278742 TAAAT-AAAATTATTATCTTAATTTTTCAAGATTTCTAATATTGCTATAATTTTTCGTAAGGGTA
1 TAAATAAAAATTATTATCTTAATTTTTCAAGATTT-TAATATT-CTATAGTTTTTCGTAAGGGTA
* * *
278806 TAGAAATTTTTAAAACTTTTCGTATC
64 TAGAAATCTTCAAAACTTTTCATATC
278832 CCCTGGTTTT
Statistics
Matches: 206, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
140 73 0.35
141 23 0.11
142 39 0.19
143 68 0.33
144 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (141 bp):
TAAATAAAAATTATTATCTTAATTTTTCAAGATTTTAATATTCTATAGTTTTTCGTAAGGGTATA
GAAATCTTCAAAACTTTTCATATCTTTTCGATTCTCCATCAAAATACGAAATGAATTTCTTTTGG
AAATTAAAAAT
Found at i:280659 original size:52 final size:51
Alignment explanation
Indices: 280547--280840 Score: 279
Period size: 52 Copynumber: 5.7 Consensus size: 51
280537 GGTGATAAAG
* * * * * * * * *
280547 GTGCCAATATGCTGATTCAAGGCCAGCGATA-TCGACTAAAAGATGATAAAA
1 GTGCCAATGTGCTGAATCAAGGCTAGTGACATTGGACTTAAAGATG-CAAGA
* * * * *
280598 GTGCCAATGTGCTGAATCAATGCTAGCGACATTAGACTTAAAAATGCGGAGA
1 GTGCCAATGTGCTGAATCAAGGCTAGTGACATTGGACTTAAAGATGC-AAGA
* * *
280650 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATAACAAGA
1 GTGCCAATGTGCTGAATCAAGGCTAGTGACATTGGACTTAAAGAT-GCAAGA
* ** *
280702 GTGCCAATGTGCT-AATTCAAGGCCAGTGATGTTGGACTTAAAGATGAGAAGA
1 GTGCCAATGTGCTGAA-TCAAGGCTAGTGACATTGGACTTAAAGATG-CAAGA
280754 GTGCCAATGTGCT-AATTCAAGGCTAGTGACATTGGACTTAAAGATGACAAGA
1 GTGCCAATGTGCTGAA-TCAAGGCTAGTGACATTGGACTTAAAGATG-CAAGA
* * * *
280806 GTGCTAATGTGTTGATTCAAGGCTAGTAACATTGG
1 GTGCCAATGTGCTGAATCAAGGCTAGTGACATTGG
280841 GCTTTGGAAA
Statistics
Matches: 205, Mismatches: 32, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
51 27 0.13
52 176 0.86
53 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.25
Consensus pattern (51 bp):
GTGCCAATGTGCTGAATCAAGGCTAGTGACATTGGACTTAAAGATGCAAGA
Found at i:280742 original size:104 final size:104
Alignment explanation
Indices: 280547--280828 Score: 343
Period size: 104 Copynumber: 2.7 Consensus size: 104
280537 GGTGATAAAG
* * * * * * *
280547 GTGCCAATATGCTGATTCAAGGCCAGCGATA-TCGACTAAAAGATGATAAAAGTGCCAATGTGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAGAGTGCCAATGTGCT
* * * *
280611 GAA-TCAATGCTAGCGACATTAGACTTAAAAATGCGGAGA
66 -AATTCAAGGCCAGCGACATTAGACTTAAAAATGAGAAGA
*
280650 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATAACAAGAGTGCCAATGTGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAGAGTGCCAATGTGCT
* ** * *
280715 AATTCAAGGCCAGTGATGTTGGACTTAAAGATGAGAAGA
66 AATTCAAGGCCAGCGACATTAGACTTAAAAATGAGAAGA
* * * *
280754 GTGCCAATGTGCTAATTCAAGGCTAGTGACATTGGACTTAAAGATGACAAGAGTGCTAATGTGTT
1 GTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAGAGTGCCAATGTGCT
*
280819 GATTCAAGGC
66 AATTCAAGGC
280829 TAGTAACATT
Statistics
Matches: 154, Mismatches: 23, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
103 30 0.19
104 124 0.81
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (104 bp):
GTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAGAGTGCCAATGTGCT
AATTCAAGGCCAGCGACATTAGACTTAAAAATGAGAAGA
Found at i:280807 original size:156 final size:155
Alignment explanation
Indices: 280547--280840 Score: 394
Period size: 156 Copynumber: 1.9 Consensus size: 155
280537 GGTGATAAAG
* *
280547 GTGCCAATATGCTGATTCAAGGCCAGCGATATCGACTAAAAGATGATAAAAGTGCCAATGTGCTG
1 GTGCCAATATGCTAATTCAAGGCCAGCGATATCGACTAAAAGATGAGAAAAGTGCCAATGTGCTG
* *
280612 AATCAATGCTAGCGACATTAGACTTAAAAATGCGGAGAGTGCCAATGTGCTGATTCAAGGCCAGT
66 AATCAAGGCTAGCGACATTAGACTTAAAAATGCGAAGAGTGCCAATGTGCTGATTCAAGGCCAGT
*
280677 GACATTGGACTTAAAGATAACAAGA
131 AACATTGGACTTAAAGATAACAAGA
* * * * * *
280702 GTGCCAATGTGCTAATTCAAGGCCAGTGATGTTGGACTTAAAGATGAGAAGAGTGCCAATGTGCT
1 GTGCCAATATGCTAATTCAAGGCCAGCGAT-ATCGACTAAAAGATGAGAAAAGTGCCAATGTGCT
* * * * * *
280767 -AATTCAAGGCTAGTGACATTGGACTTAAAGATGAC-AAGAGTGCTAATGTGTTGATTCAAGGCT
65 GAA-TCAAGGCTAGCGACATTAGACTTAAAAATG-CGAAGAGTGCCAATGTGCTGATTCAAGGCC
280830 AGTAACATTGG
128 AGTAACATTGG
280841 GCTTTGGAAA
Statistics
Matches: 119, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
155 29 0.24
156 89 0.75
157 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.25
Consensus pattern (155 bp):
GTGCCAATATGCTAATTCAAGGCCAGCGATATCGACTAAAAGATGAGAAAAGTGCCAATGTGCTG
AATCAAGGCTAGCGACATTAGACTTAAAAATGCGAAGAGTGCCAATGTGCTGATTCAAGGCCAGT
AACATTGGACTTAAAGATAACAAGA
Found at i:281081 original size:60 final size:60
Alignment explanation
Indices: 280954--281087 Score: 214
Period size: 60 Copynumber: 2.2 Consensus size: 60
280944 CAATTTGTAC
* * **
280954 GGACTTTAAAAAAGGATGCCACCAACTTGTGTGGACTTTTGGGGTGCCGCCAGCTCAGAT
1 GGACTTTGAGAAAGGATGCCAAAAACTTGTGTGGACTTTTGGGGTGCCGCCAGCTCAGAT
* *
281014 GGACTTTGAGAAAGGATGCCAAAAACTTGTGTGGGCTTTTGGGGTGCCGCCAGCTCATAT
1 GGACTTTGAGAAAGGATGCCAAAAACTTGTGTGGACTTTTGGGGTGCCGCCAGCTCAGAT
281074 GGACTTTGAGAAAG
1 GGACTTTGAGAAAG
281088 AAAGGTGCCA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (60 bp):
GGACTTTGAGAAAGGATGCCAAAAACTTGTGTGGACTTTTGGGGTGCCGCCAGCTCAGAT
Found at i:281152 original size:29 final size:29
Alignment explanation
Indices: 281091--281548 Score: 245
Period size: 29 Copynumber: 15.8 Consensus size: 29
281081 GAGAAAGAAA
* * * *
281091 GGTGCCATTGAGCCATGGACGTTGAGAAA-
1 GGTGCCACTGAGTCATGGAC-TTTAAAAAG
* **
281120 GGTGCCACT-ATGTCATGGAGTTTAAGGAG
1 GGTGCCACTGA-GTCATGGACTTTAAAAAG
*
281149 GGTGCCACTGAGTTATGGACTTTAAAAAG
1 GGTGCCACTGAGTCATGGACTTTAAAAAG
** *
281178 GGTGCCACTGAGTTGTGGATTTTAAAAAG
1 GGTGCCACTGAGTCATGGACTTTAAAAAG
* * *
281207 GGTGCTACTGAGTCGTAGACTTTAAATAA-
1 GGTGCCACTGAGTCATGGACTTTAAA-AAG
** *
281236 GGTGCCA-TGAAGTTGTGAACTTT-AAAAG
1 GGTGCCACTG-AGTCATGGACTTTAAAAAG
*
281264 GGTGCCAC-GAAGTTATGGACTTTAAAAAG
1 GGTGCCACTG-AGTCATGGACTTTAAAAAG
* *
281293 GGTGCCAC-GTAGTTATAGACTTT-AAAAG
1 GGTGCCACTG-AGTCATGGACTTTAAAAAG
* ** *
281321 GGTGCCACGGAGTTGTGGACTTTCAAAAGG
1 GGTGCCACTGAGTCATGGACTTT-AAAAAG
* ** *
281351 GGTACCA-TAGAGTTGTAGACTTT-AAAAG
1 GGTGCCACT-GAGTCATGGACTTTAAAAAG
* *
281379 GGTGCCACTAAGTCATGGAATTTGAAAAA-
1 GGTGCCACTGAGTCATGGACTTT-AAAAAG
** * * ** * *
281408 ATTACCACTGAATTGTGGACTCTAAGAAG
1 GGTGCCACTGAGTCATGGACTTTAAAAAG
* * * * ** *
281437 GGTACCACTAAGTTATGGAATTTTGTAAAT
1 GGTGCCACTGAGTCATGG-ACTTTAAAAAG
* **
281467 GGTGCCACTAAGTTGTGGACTTTGAAAAAG
1 GGTGCCACTGAGTCATGGACTTT-AAAAAG
** * * *
281497 AATGCCTCAGAGTTATGGACTTTAAAAAG
1 GGTGCCACTGAGTCATGGACTTTAAAAAG
* *
281526 GGTGCCACAGAGTTATGGACTTT
1 GGTGCCACTGAGTCATGGACTTT
281549 GGAAAGAGGT
Statistics
Matches: 337, Mismatches: 74, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
27 2 0.01
28 76 0.23
29 188 0.56
30 71 0.21
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (29 bp):
GGTGCCACTGAGTCATGGACTTTAAAAAG
Found at i:281202 original size:58 final size:57
Alignment explanation
Indices: 281147--281548 Score: 348
Period size: 58 Copynumber: 6.9 Consensus size: 57
281137 GAGTTTAAGG
*
281147 AGGGTGCCACTGAGTTATGGACTTTAAAAAGGGTGCCACTGAGTTGTGGATTTTAAAA
1 AGGGTGCCACTGAGTTATGGACTTTAAAAAGGGTGCCACTGAGTTGTGGACTTT-AAA
* ** * *
281205 AGGGTGCTACTGAGTCGTAGACTTTAAATAA-GGTGCCA-TGAAGTTGTGAACTTTAAA
1 AGGGTGCCACTGAGTTATGGACTTTAAA-AAGGGTGCCACTG-AGTTGTGGACTTTAAA
* *
281262 AGGGTGCCAC-GAAGTTATGGACTTTAAAAAGGGTGCCAC-GTAGTTATAGACTTTAAA
1 AGGGTGCCACTG-AGTTATGGACTTTAAAAAGGGTGCCACTG-AGTTGTGGACTTTAAA
* * * * *
281319 AGGGTGCCACGGAGTTGTGGACTTTCAAAAGGGGTACCA-TAGAGTTGTAGACTTTAAA
1 AGGGTGCCACTGAGTTATGGACTTT-AAAAAGGGTGCCACT-GAGTTGTGGACTTTAAA
* * * ** * * *
281377 AGGGTGCCACTAAGTCATGGAATTTGAAAAA-ATTACCACTGAATTGTGGACTCTAAGA
1 AGGGTGCCACTGAGTTATGGACTTT-AAAAAGGGTGCCACTGAGTTGTGGACTTTAA-A
* * * ** * *
281435 AGGGTACCACTAAGTTATGGAATTTTGTAAATGGTGCCACTAAGTTGTGGACTTTGAAAA
1 AGGGTGCCACTGAGTTATGG-ACTTTAAAAAGGGTGCCACTGAGTTGTGGACTTT--AAA
** * * * *
281495 AGAATGCCTCAGAGTTATGGACTTTAAAAAGGGTGCCACAGAGTTATGGACTTT
1 AGGGTGCCACTGAGTTATGGACTTTAAAAAGGGTGCCACTGAGTTGTGGACTTT
281549 GGAAAGAGGT
Statistics
Matches: 275, Mismatches: 54, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
56 3 0.01
57 88 0.32
58 116 0.42
59 51 0.19
60 15 0.05
61 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (57 bp):
AGGGTGCCACTGAGTTATGGACTTTAAAAAGGGTGCCACTGAGTTGTGGACTTTAAA
Found at i:281278 original size:115 final size:115
Alignment explanation
Indices: 281147--281407 Score: 309
Period size: 115 Copynumber: 2.3 Consensus size: 115
281137 GAGTTTAAGG
* * *
281147 AGGGTGCCACTG-AGTTATGGACTTTAAAAAGGGTGCCAC-TGAGTTGTGGATTTTAAAAAGGGT
1 AGGGTGCCAC-GAAGTTATGGACTTTAAAAAGGGTGCCACGT-AGTTATAGACTTT-AAAAGGGT
* * *
281210 GCTACTGAGTCGTAGACTTT-AAATA-AGGTGCCAT-GAAGTTGT-GAACTTTAAA
63 GCCACGGAGTCGTAGACTTTCAAA-AGAGGTACCATAG-AGTTGTAG-ACTTTAAA
281262 AGGGTGCCACGAAGTTATGGACTTTAAAAAGGGTGCCACGTAGTTATAGACTTTAAAAGGGTGCC
1 AGGGTGCCACGAAGTTATGGACTTTAAAAAGGGTGCCACGTAGTTATAGACTTTAAAAGGGTGCC
* * *
281327 ACGGAGTTGTGGACTTTCAAAAGGGGTACCATAGAGTTGTAGACTTTAAA
66 ACGGAGTCGTAGACTTTCAAAAGAGGTACCATAGAGTTGTAGACTTTAAA
* * *
281377 AGGGTGCCACTAAGTCATGGAATTTGAAAAA
1 AGGGTGCCACGAAGTTATGGACTTT-AAAAA
281408 ATTACCACTG
Statistics
Matches: 127, Mismatches: 12, Indels: 13
0.84 0.08 0.09
Matches are distributed among these distances:
114 26 0.20
115 93 0.73
116 8 0.06
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (115 bp):
AGGGTGCCACGAAGTTATGGACTTTAAAAAGGGTGCCACGTAGTTATAGACTTTAAAAGGGTGCC
ACGGAGTCGTAGACTTTCAAAAGAGGTACCATAGAGTTGTAGACTTTAAA
Found at i:281554 original size:29 final size:28
Alignment explanation
Indices: 281147--281548 Score: 249
Period size: 29 Copynumber: 13.9 Consensus size: 28
281137 GAGTTTAAGG
*
281147 AGGGTGCCACTGAGTTATGGACTTTAAAA
1 AGGGTGCCACAGAGTTATGGACTTT-AAA
* * *
281176 AGGGTGCCACTGAGTTGTGGATTTTAAAA
1 AGGGTGCCACAGAGTTATGGACTTT-AAA
* * ** *
281205 AGGGTGCTACTGAGTCGTAGACTTTAAA
1 AGGGTGCCACAGAGTTATGGACTTTAAA
* * * *
281233 TAAGGTGCCA-TGAAGTTGTGAACTTTAAA
1 -AGGGTGCCACAG-AGTTATGGACTTTAAA
281262 AGGGTGCCAC-GAAGTTATGGACTTTAAAA
1 AGGGTGCCACAG-AGTTATGGACTTT-AAA
*
281291 AGGGTGCCAC-GTAGTTATAGACTTTAAA
1 AGGGTGCCACAG-AGTTATGGACTTTAAA
* *
281319 AGGGTGCCACGGAGTTGTGGACTTTCAAA
1 AGGGTGCCACAGAGTTATGGACTTT-AAA
* * * *
281348 AGGGGTACCATAGAGTTGTAGACTTTAAA
1 A-GGGTGCCACAGAGTTATGGACTTTAAA
* *
281377 AGGGTGCCACTA-AGTCATGGAATTTGAAA
1 AGGGTGCCAC-AGAGTTATGGACTTT-AAA
*** * * * * *
281406 AAATTACCACTGAATTGTGGACTCTAAGA
1 AGGGTGCCACAGAGTTATGGACTTTAA-A
* * *
281435 AGGGTACCACTA-AGTTATGGAATTTTGTAA
1 AGGGTGCCAC-AGAGTTATGG-ACTTT-AAA
* *
281465 ATGGTGCCACTA-AGTTGTGGACTTTGAAAA
1 AGGGTGCCAC-AGAGTTATGGACTTT--AAA
** *
281495 AGAATGCCTCAGAGTTATGGACTTTAAAA
1 AGGGTGCCACAGAGTTATGGACTTT-AAA
281524 AGGGTGCCACAGAGTTATGGACTTT
1 AGGGTGCCACAGAGTTATGGACTTT
281549 GGAAAGAGGT
Statistics
Matches: 296, Mismatches: 61, Indels: 32
0.76 0.16 0.08
Matches are distributed among these distances:
28 68 0.23
29 166 0.56
30 61 0.21
31 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (28 bp):
AGGGTGCCACAGAGTTATGGACTTTAAA
Found at i:284413 original size:15 final size:16
Alignment explanation
Indices: 284395--284426 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
284385 GTTTTCTCCC
284395 AAAATT-TTTCAAAAA
1 AAAATTATTTCAAAAA
284410 AAAATTATTTCAAAAA
1 AAAATTATTTCAAAAA
284426 A
1 A
284427 TCTCTCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTATTTCAAAAA
Found at i:292470 original size:19 final size:20
Alignment explanation
Indices: 292446--292494 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
292436 TTTTAGTGTA
*
292446 TATCGATACAATG-AACATG
1 TATCGATACAAAGCAACATG
*
292465 TATCGATACAAAGCAATATG
1 TATCGATACAAAGCAACATG
*
292485 TATTGATACA
1 TATCGATACA
292495 TTTGTGTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
TATCGATACAAAGCAACATG
Found at i:294024 original size:38 final size:38
Alignment explanation
Indices: 293973--294075 Score: 143
Period size: 38 Copynumber: 2.7 Consensus size: 38
293963 ACAAACTATG
* *
293973 AACAAAAATCACTATTTTAAACTGATGGCATGGTTCGA
1 AACAAAAACCACTATTCTAAACTGATGGCATGGTTCGA
* * *
294011 AACGAAAACCACTATTCTAAACTGGTGGCATGGTTTGA
1 AACAAAAACCACTATTCTAAACTGATGGCATGGTTCGA
* *
294049 AACAAAAACTACTATTCTAAACCGATG
1 AACAAAAACCACTATTCTAAACTGATG
294076 ACACAATTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 56 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (38 bp):
AACAAAAACCACTATTCTAAACTGATGGCATGGTTCGA
Found at i:295076 original size:13 final size:13
Alignment explanation
Indices: 295058--295083 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
295048 CAATTTTTTG
295058 TGTATCGATACAT
1 TGTATCGATACAT
295071 TGTATCGATACAT
1 TGTATCGATACAT
295084 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:295148 original size:21 final size:21
Alignment explanation
Indices: 295122--295197 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
295112 CTGCCAAGAA
295122 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
295143 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
295163 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
295184 ATGTATCGATACAT
1 ATGTATCGATACAT
295198 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:295167 original size:20 final size:20
Alignment explanation
Indices: 295142--295215 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
295132 ACATCTTTTT
295142 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
295162 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
295183 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
295203 CATGTATCGATAC
1 CATGTATCGATAC
295216 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:295179 original size:41 final size:41
Alignment explanation
Indices: 295122--295215 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
295112 CTGCCAAGAA
295122 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
295163 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
295204 ATGTATCGATAC
1 ATGTATCGATAC
295216 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:297146 original size:13 final size:13
Alignment explanation
Indices: 297128--297152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
297118 ACTGAAGCAA
297128 TGTATCGATACAT
1 TGTATCGATACAT
297141 TGTATCGATACA
1 TGTATCGATACA
297153 ATCTGGAAAA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:298744 original size:84 final size:84
Alignment explanation
Indices: 298589--298753 Score: 201
Period size: 84 Copynumber: 2.0 Consensus size: 84
298579 CATTTTCCAC
* * * *
298589 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAGGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAGGAATTATTCTCTAAAC
298654 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
298673 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTTCAA-GAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTCTTTTTAAAGGAAT-T-ATTCTCTA
* * *
298735 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
298754 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
82 4 0.06
83 11 0.16
84 54 0.78
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTCTTTTTAAAGGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:300823 original size:13 final size:13
Alignment explanation
Indices: 300805--300830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
300795 CAATTTTTTG
300805 TGTATCGATACAT
1 TGTATCGATACAT
300818 TGTATCGATACAT
1 TGTATCGATACAT
300831 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:300895 original size:21 final size:21
Alignment explanation
Indices: 300869--300944 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
300859 CTGCCAAGAA
300869 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
300890 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
300910 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
300931 ATGTATCGATACAT
1 ATGTATCGATACAT
300945 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:300914 original size:20 final size:20
Alignment explanation
Indices: 300889--300962 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
300879 ACATCTTTTT
300889 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
300909 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
300930 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
300950 CATGTATCGATAC
1 CATGTATCGATAC
300963 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:300926 original size:41 final size:41
Alignment explanation
Indices: 300869--300962 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
300859 CTGCCAAGAA
300869 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
300910 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
300951 ATGTATCGATAC
1 ATGTATCGATAC
300963 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:301996 original size:21 final size:22
Alignment explanation
Indices: 301967--302008 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
301957 AAATTAATAA
*
301967 AACTAAAATTTATATTATTTTT
1 AACTAAAATATATATTATTTTT
*
301989 AACT-AAATATATTTTATTTT
1 AACTAAAATATATATTATTTT
302009 AGTCAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
AACTAAAATATATATTATTTTT
Found at i:309338 original size:20 final size:21
Alignment explanation
Indices: 309313--309360 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
309303 AAAAACCTAG
309313 AATGTATCGATACAATA-AAT-
1 AATGTATCGATACAA-ACAATA
309333 AATGTATCGATACAAACAATA
1 AATGTATCGATACAAACAATA
309354 AATGTAT
1 AATGTAT
309361 GTATCGATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.69
21 7 0.27
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACAAACAATA
Found at i:309367 original size:25 final size:24
Alignment explanation
Indices: 309324--309371 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
309314 ATGTATCGAT
309324 ACAATAAATAATGTATCGATACAA
1 ACAATAAATAATGTATCGATACAA
*
309348 ACAATAAATGTATGTATCGATACA
1 ACAATAAAT-AATGTATCGATACA
309372 TTTCCTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.27
Consensus pattern (24 bp):
ACAATAAATAATGTATCGATACAA
Found at i:309429 original size:21 final size:21
Alignment explanation
Indices: 309399--309454 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
309389 AGGGTGGTTT
* **
309399 TGTATTGATACATTTCAGGCA
1 TGTATCGATACATTTCACACA
*
309420 TGTATCGATACA-TTCACATA
1 TGTATCGATACATTTCACACA
309440 TGTATCGATACATTT
1 TGTATCGATACATTT
309455 ACTATTTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTCACACA
Found at i:310232 original size:31 final size:31
Alignment explanation
Indices: 310190--310381 Score: 151
Period size: 31 Copynumber: 6.2 Consensus size: 31
310180 TCAAACTTAG
*
310190 GTGCCACCAACTTGTGTGGGCTTTGACTCAA
1 GTGCCACCAACTTATGTGGGCTTTGACTCAA
* * *
310221 GTGCCATCAAC-TATGCGGG-TTTAGACTCAG
1 GTGCCACCAACTTATGTGGGCTTT-GACTCAA
* *
310251 GTGCCACCAGCTTCTGTGGGCTTTGACT-AGA
1 GTGCCACCAACTTATGTGGGCTTTGACTCA-A
* * * *
310282 GTGCCACCAACTCATATGGGCTTAGACTCAG
1 GTGCCACCAACTTATGTGGGCTTTGACTCAA
* * * *
310313 GTGCCGCCAACTTGTGTGAGCTTTAACT-AA
1 GTGCCACCAACTTATGTGGGCTTTGACTCAA
* * **
310343 GGTGCTC-CCAACTTATCTGGGCTTAGACTCGG
1 -GTGC-CACCAACTTATGTGGGCTTTGACTCAA
310375 GTGCCAC
1 GTGCCAC
310382 TAGCTCATGC
Statistics
Matches: 122, Mismatches: 30, Indels: 18
0.72 0.18 0.11
Matches are distributed among these distances:
29 3 0.02
30 24 0.20
31 90 0.74
32 5 0.04
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.27
Consensus pattern (31 bp):
GTGCCACCAACTTATGTGGGCTTTGACTCAA
Found at i:310354 original size:62 final size:61
Alignment explanation
Indices: 310188--310381 Score: 223
Period size: 62 Copynumber: 3.1 Consensus size: 61
310178 ACTCAAACTT
* ** *
310188 AGGTGCCACCAACTTGTGTGGGCTTTGACTCAA-GTGCCATCAACTATGCGGGTTTAGACTC
1 AGGTGCCACCAACTTGTGTGGGCTTTGACT-AAGGTGCCACCAACTATATGGGCTTAGACTC
* *
310249 AGGTGCCACCAGCTTCTGTGGGCTTTGACT-AGAGTGCCACCAACTCATATGGGCTTAGACTC
1 AGGTGCCACCAACTTGTGTGGGCTTTGACTAAG-GTGCCACCAACT-ATATGGGCTTAGACTC
* * * *
310311 AGGTGCCGCCAACTTGTGTGAGCTTTAACTAAGGTGCTC-CCAACTTATCTGGGCTTAGACTC
1 AGGTGCCACCAACTTGTGTGGGCTTTGACTAAGGTGC-CACCAAC-TATATGGGCTTAGACTC
*
310373 GGGTGCCAC
1 AGGTGCCAC
310382 TAGCTCATGC
Statistics
Matches: 113, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
59 1 0.01
61 39 0.35
62 69 0.61
63 4 0.04
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.27
Consensus pattern (61 bp):
AGGTGCCACCAACTTGTGTGGGCTTTGACTAAGGTGCCACCAACTATATGGGCTTAGACTC
Found at i:310403 original size:31 final size:31
Alignment explanation
Indices: 310363--310569 Score: 184
Period size: 31 Copynumber: 6.7 Consensus size: 31
310353 ACTTATCTGG
* * **
310363 GCTTAGACTCGGGTGCCACTAGCTCATGCAA
1 GCTTTGACTCGGGTGCCACCAGCTTGTGCAA
* *
310394 GCTTTGACTCGGGTGTCGCCAGCTTGTGCAA
1 GCTTTGACTCGGGTGCCACCAGCTTGTGCAA
* * *
310425 ACTTTGACTCGGGTGCCTCCAGCTTATGCAA
1 GCTTTGACTCGGGTGCCACCAGCTTGTGCAA
* *
310456 GCTTTGACTAGGGTGCCACCAACTTGTGC-A
1 GCTTTGACTCGGGTGCCACCAGCTTGTGCAA
* * * *
310486 GGTTTAGACTCGGGTGCTA-CAACTTGTGCGA
1 GCTTT-GACTCGGGTGCCACCAGCTTGTGCAA
* * * *
310517 GCTTTGACTCGAGTGCCGCTAGCTTGTGCTTA
1 GCTTTGACTCGGGTGCCACCAGCTTGTGC-AA
* * *
310549 GCTTTAACTTGGATGCCACCA
1 GCTTTGACTCGGGTGCCACCA
310570 ACTCTTACGA
Statistics
Matches: 141, Mismatches: 31, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
30 25 0.18
31 100 0.71
32 16 0.11
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (31 bp):
GCTTTGACTCGGGTGCCACCAGCTTGTGCAA
Found at i:311693 original size:20 final size:20
Alignment explanation
Indices: 311668--311718 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
311658 AAACCCTAGA
311668 AAGTATCGATACAGACCCAG
1 AAGTATCGATACAGACCCAG
*
311688 AAGTATCGATACTGACCCAG
1 AAGTATCGATACAGACCCAG
311708 AAGTATCGATA
1 AAGTATCGATA
311719 GACAGCGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGTATCGATACAGACCCAG
Found at i:313415 original size:3 final size:3
Alignment explanation
Indices: 313407--313471 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
313397 AAGATGATAA
313407 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
313455 GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GA
313472 AGTTAACTTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:319604 original size:30 final size:30
Alignment explanation
Indices: 319549--319865 Score: 208
Period size: 30 Copynumber: 10.6 Consensus size: 30
319539 TCACCCTTCA
*
319549 AAAGCCCACAAGTCAGTGGCATCTTTTTC-
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCT
*
319578 AAAGCCCACAAGTCAGTGGCA-CTCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCT-TTTTCT
319608 AAAGCCCACAAGTCAGTGGCAACC---TTC-
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTTCT
* * *
319635 AAAGCCCACAAATCTGTGGCACCCTTTTCT
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCT
* * * *
319665 GAAGCCCACAAGTCGGTGGCATC-TTTTCC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCT
* * *
319694 AAAGTCCACAACTCCGTGGCACTCTTTTTCTTTT
1 AAAGCCCACAAGTCAGTGGCAC-CTTTTTC---T
* * * * *
319728 GTAAGCTCACAACTCTGTAGCACTCTTTTTCCGTT
1 -AAAGCCCACAAGTCAGTGGCAC-CTTTTT-C--T
* * * *
319763 TAAGCCCACAAGTTAGTGGCACCCTTTTCA
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCT
*
319793 AAAGCCCACAAGTCAGTGGCAACC--TTT-A
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTTCT
* * * *
319821 AAAGCCCACAAGTTAGTAGCA-ATTTTT-A
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCT
319849 AAAGCCCACAAGTCAGT
1 AAAGCCCACAAGTCAGT
319866 AGAAACCTTC
Statistics
Matches: 238, Mismatches: 32, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
26 3 0.01
27 19 0.08
28 44 0.18
29 54 0.23
30 58 0.24
31 9 0.04
32 2 0.01
33 5 0.02
34 17 0.07
35 26 0.11
36 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTTCT
Found at i:319773 original size:34 final size:35
Alignment explanation
Indices: 319699--319773 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
319689 TTTCCAAAGT
* **
319699 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCGTTGTAAGC
* *
319734 TCACAACTCTGTAGCACTCTTTTTCCGTT-TAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCGTTGTAAGC
319768 CCACAA
1 CCACAA
319774 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (35 bp):
CCACAACTCCGTAGCACTCTTTTTCCGTTGTAAGC
Found at i:319832 original size:28 final size:28
Alignment explanation
Indices: 319764--319915 Score: 146
Period size: 28 Copynumber: 5.3 Consensus size: 28
319754 TTTTCCGTTT
* * *
319764 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTAGCAACC-TTT-AA
*
319794 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTAGCAACCTTTAA
* **
319822 AAGCCCACAAGTTAGTAGCAATTTTTAA
1 AAGCCCACAAGTCAGTAGCAACCTTTAA
* *
319850 AAGCCCACAAGTCAGTAGAAACCTTCAA
1 AAGCCCACAAGTCAGTAGCAACCTTTAA
* *
319878 AAGCACACAAGT-TG-ATGCAAACCTTTCAA
1 AAGCCCACAAGTCAGTA-GC-AACCTTT-AA
319907 AAGCCCACA
1 AAGCCCACA
319916 TAAGTTGGTG
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 2 0.02
28 66 0.64
29 13 0.13
30 21 0.20
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTAGCAACCTTTAA
Found at i:319858 original size:56 final size:57
Alignment explanation
Indices: 319764--319915 Score: 175
Period size: 56 Copynumber: 2.7 Consensus size: 57
319754 TTTTCCGTTT
* * * * *
319764 AAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTTAGTAGCA-CATTTTCAAAAGCCCACAAGTCAGTAGAAACCTTCAA
*
319822 AAGCCCACAAGTTAGTAGCA-ATTTTTAAAAGCCCACAAGTCAGTAGAAACCTTCAA
1 AAGCCCACAAGTTAGTAGCACATTTTCAAAAGCCCACAAGTCAGTAGAAACCTTCAA
* * *
319878 AAGCACACAAGTT-G-ATGCAAACCTTTCAAAAGCCCACA
1 AAGCCCACAAGTTAGTA-GCACA-TTTTCAAAAGCCCACA
319916 TAAGTTGGTG
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
54 1 0.01
55 4 0.05
56 44 0.54
57 14 0.17
58 19 0.23
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (57 bp):
AAGCCCACAAGTTAGTAGCACATTTTCAAAAGCCCACAAGTCAGTAGAAACCTTCAA
Found at i:320005 original size:49 final size:49
Alignment explanation
Indices: 319935--320368 Score: 596
Period size: 49 Copynumber: 8.9 Consensus size: 49
319925 GGCGTCTCTT
* *
319935 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * *
319984 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * *
320033 ATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
*
320082 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * *
320131 TTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCACC-TCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* *
320179 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
320227 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----C
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
* * *
320270 TTTAAGTCCAGTATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTATC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-TATC
* * *
320322 TTTAAGTTCAATGTAGTTGGCCTTGAATCAGCACATTGACATCCTTT
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTT
320369 TTCTCATCTT
Statistics
Matches: 346, Mismatches: 29, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
43 39 0.11
44 1 0.00
47 1 0.00
48 91 0.26
49 173 0.50
50 1 0.00
51 2 0.01
52 36 0.10
53 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (49 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATC
Found at i:320271 original size:21 final size:21
Alignment explanation
Indices: 320247--320314 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
320237 ATGTAGCTGG
*
320247 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCATATTGGCA
* * *
320268 CCTTTAAGTCCAGTATAGCTGG--
1 CCTTGAA-T-CAGCATA-TTGGCA
320290 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
320311 CCTT
1 CCTT
320315 TTCTATCTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 10
0.67 0.13 0.19
Matches are distributed among these distances:
19 3 0.09
20 6 0.17
21 11 0.31
22 7 0.20
23 5 0.14
24 3 0.09
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:320347 original size:52 final size:53
Alignment explanation
Indices: 320269--320422 Score: 184
Period size: 52 Copynumber: 2.9 Consensus size: 53
320259 ACATTGGCAC
* *
320269 CTTTAAGTCCAGTATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCT-AT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
320321 CTTTAAGTTCAATGTAGTTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * *
320376 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTT
320423 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
52 36 0.43
53 5 0.06
54 7 0.08
55 36 0.43
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:320480 original size:67 final size:68
Alignment explanation
Indices: 320372--320498 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
320362 ATCCTTTTTC
* * *
320372 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
320436 TCT
66 TCT
* * * *
320439 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
320499 AAAACCCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:321310 original size:20 final size:20
Alignment explanation
Indices: 321266--321323 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
321256 ATTTCAACGA
***
321266 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
321286 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
321306 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
321324 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:321380 original size:13 final size:13
Alignment explanation
Indices: 321362--321386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
321352 ATTACTCAAA
321362 TGTATCGATACAT
1 TGTATCGATACAT
321375 TGTATCGATACA
1 TGTATCGATACA
321387 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:321451 original size:52 final size:52
Alignment explanation
Indices: 321395--321523 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
321385 CACTGATCTT
*
321395 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
321447 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
321499 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
321524 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:325925 original size:9 final size:9
Alignment explanation
Indices: 325913--325973 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 9
325903 CTCTCTCTAT
325913 TATCTCTCC
1 TATCTCTCC
325922 TATCTCTCTTCC
1 TA--TCTC-TCC
*
325934 TATCATCCCTTC
1 TATC-T--CTCC
*
325946 TATCTCTAC
1 TATCTCTCC
325955 TATCTCTCC
1 TATCTCTCC
325964 TATCTCTCC
1 TATCTCTCC
325973 T
1 T
325974 CCTATCATCC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
9 23 0.53
10 2 0.05
11 6 0.14
12 11 0.26
13 1 0.02
ACGTcount: A:0.13, C:0.41, G:0.00, T:0.46
Consensus pattern (9 bp):
TATCTCTCC
Found at i:325943 original size:42 final size:42
Alignment explanation
Indices: 325885--325991 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 42
325875 TTCTTCTCTC
* * * *
325885 CTCCTCCTGTGATCCCTCCTCTCTCTATTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
* *
325927 CTCTTCCTATCATCCCTTCTATCTCTACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
*
325969 CTCCTCCTATCATCCCTTCTATC
1 CTCCTCCTATCATCCCTCCTATC
325992 GTTTCTTTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.12, C:0.43, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
Found at i:330723 original size:17 final size:17
Alignment explanation
Indices: 330675--330725 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
330665 ATTTAAATTA
330675 ATTTG-TCTAAATAAAT
1 ATTTGTTCTAAATAAAT
*
330691 A-TT-TACTAAAATTAAAT
1 ATTTGTTCT-AAA-TAAAT
330708 ATTTGTTCTAAATAAAT
1 ATTTGTTCTAAATAAAT
330725 A
1 A
330726 ACATAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
15 4 0.14
16 4 0.14
17 12 0.43
18 5 0.18
19 3 0.11
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (17 bp):
ATTTGTTCTAAATAAAT
Found at i:334085 original size:158 final size:160
Alignment explanation
Indices: 333752--334085 Score: 352
Period size: 160 Copynumber: 2.1 Consensus size: 160
333742 AATTTTAATT
* * * * * *
333752 ATGGATTCACGTAATAATCTACATTATTTTCATAATTGGGAAACAAAAATAGATTCTCATCATTG
1 ATGGATTCTCGTAATAATCTACATTATTTTCATAACTAGGAAACAAAAACAGACTCTCATCATTA
* * * * * **
333817 GGATACATGATATTGATGCTTTCTTCTCTTAATAAAATGCTTTTCTTCCCATCATTTTACTTATG
66 GGATACATGATATAGAAGCTTGCTTCTCTCAAGAAAATGCTTTTCTTCCCATCATTTTACTTAAA
333882 ATCAAACTTCATCCCTCAAATGAGACAAAC
131 ATCAAACTTCATCCCTCAAATGAGACAAAC
* * * * * * *
333912 AT-AATTTCTCATAATAATCTCCATTATTTTCATGACTAGGCAACAAAAACATG-CTCTCCTTAT
1 ATGGA-TTCTCGTAATAATCTACATTATTTTCATAACTAGGAAACAAAAACA-GACTCTCATCAT
* * *
333975 TAGGATACATGATATAGAAGCTTGGTTTTC-CAAGAAAA-GCTTTTCTTCCCATCATTTTCCTTA
64 TAGGATACATGATATAGAAGCTTGCTTCTCTCAAGAAAATGCTTTTCTTCCCATCATTTTACTTA
* ** * * *
334038 AAATTAATGTTGATCCCTTAAATGAGGCAAAC
129 AAATCAAACTTCATCCCTCAAATGAGACAAAC
*
334070 ATGGATTCTTGTAATA
1 ATGGATTCTCGTAATA
334086 TAGTGATATT
Statistics
Matches: 139, Mismatches: 32, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
158 59 0.42
159 8 0.06
160 71 0.51
161 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.37
Consensus pattern (160 bp):
ATGGATTCTCGTAATAATCTACATTATTTTCATAACTAGGAAACAAAAACAGACTCTCATCATTA
GGATACATGATATAGAAGCTTGCTTCTCTCAAGAAAATGCTTTTCTTCCCATCATTTTACTTAAA
ATCAAACTTCATCCCTCAAATGAGACAAAC
Found at i:336729 original size:13 final size:13
Alignment explanation
Indices: 336711--336736 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
336701 TACAGCAAGT
336711 ATGTATCGATACA
1 ATGTATCGATACA
336724 ATGTATCGATACA
1 ATGTATCGATACA
336737 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:338987 original size:21 final size:21
Alignment explanation
Indices: 338954--338998 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
338944 TTGCAAGTTG
*
338954 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
338976 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
338996 AAA
1 AAA
338999 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:340822 original size:15 final size:15
Alignment explanation
Indices: 340802--340832 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
340792 TAAAAATGTC
*
340802 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
340817 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
340832 C
1 C
340833 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:342929 original size:13 final size:13
Alignment explanation
Indices: 342911--342943 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
342901 ACATTTTTCT
342911 TTGTATCGATACA
1 TTGTATCGATACA
342924 TTGTATCGATACA
1 TTGTATCGATACA
342937 TTGTATC
1 TTGTATC
342944 ATTTGAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:344751 original size:14 final size:14
Alignment explanation
Indices: 344732--344775 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
344722 AAATAAATTT
344732 TTGATATGAATTAC
1 TTGATATGAATTAC
*
344746 TTGATA--AATT-T
1 TTGATATGAATTAC
344757 TTGATATGAATTAC
1 TTGATATGAATTAC
344771 TTGAT
1 TTGAT
344776 TAAGGGGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 4 0.16
14 11 0.44
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (14 bp):
TTGATATGAATTAC
Found at i:344758 original size:25 final size:25
Alignment explanation
Indices: 344724--344775 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
344714 ATATGTGCAA
344724 ATAAATTTTTGATATGAATTACTTG
1 ATAAATTTTTGATATGAATTACTTG
344749 ATAAATTTTTGATATGAATTACTTG
1 ATAAATTTTTGATATGAATTACTTG
344774 AT
1 AT
344776 TAAGGGGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (25 bp):
ATAAATTTTTGATATGAATTACTTG
Found at i:345534 original size:13 final size:13
Alignment explanation
Indices: 345516--345541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
345506 TACAGCAAGT
345516 ATGTATCGATACA
1 ATGTATCGATACA
345529 ATGTATCGATACA
1 ATGTATCGATACA
345542 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:355462 original size:12 final size:12
Alignment explanation
Indices: 355445--355512 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 12
355435 CCCCATATCT
355445 CTTCTATCTCTC
1 CTTCTATCTCTC
355457 CTTCTATCATC-C
1 CTTCTATC-TCTC
355469 CTTCTA--TCT-
1 CTTCTATCTCTC
*
355478 CTACTATCTCTC
1 CTTCTATCTCTC
*
355490 CTCCTATCATC-C
1 CTTCTATC-TCTC
*
355502 CTTCTGTCTCT
1 CTTCTATCTCT
355513 TCTTTCTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
9 7 0.16
11 5 0.11
12 29 0.64
13 4 0.09
ACGTcount: A:0.12, C:0.41, G:0.01, T:0.46
Consensus pattern (12 bp):
CTTCTATCTCTC
Done.